TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2023
UR  - www.iccbikg2023.kg.ac.rs
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/6346
AB  - Water is one of the most important molecules on the Earth. Since water plays a crucial role in many life processes, it is of great importance to understand every aspect of its behavior and interactions with itself and its surroundings. It is known that water molecules can interact via classical hydrogen bonds and antiparallel interactions, with interaction energies of - 5.02 kcal/mol and -4.22 kcal/mol, respectively. Besides these attractive interactions, repulsive interactions were also noticed. In this work, we analyzed repulsive water-water contacts from the Cambridge Structural Database. All interaction energies were calculated at the so- called gold standard, i.e., CCSD(T)/CBS level of theory. It was found that among all water-water contacts, ca. 20% (2035 contacts) are repulsive with interaction energies mainly up to 2 kcal/mol. Most of these repulsive contacts do not belong to two main groups of water-water contacts. Namely, 12.8% of all repulsive contacts can be classified as classical hydrogen bonds, 2.1% to the antiparallel interactions, and the rest (85.3%) as remaining contacts. This study points out that additional attention should be paid when one deals with contacts including water or, eventually, hydrogen atoms in general.
C3  - 2nd International Conference on Chemo and Bioinformatics (ICCBIKG_2023), Book of Proceedings, 28-29 September 2023, Kragujevac, Serbia, 2023
T1  - Repulsive water-water contacts from Cambridge Structural Database
SP  - 637
EP  - 640
UR  - https://hdl.handle.net/21.15107/rcub_cherry_6346
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan B. and Zarić, Snežana D.",
year = "2023",
abstract = "Water is one of the most important molecules on the Earth. Since water plays a crucial role in many life processes, it is of great importance to understand every aspect of its behavior and interactions with itself and its surroundings. It is known that water molecules can interact via classical hydrogen bonds and antiparallel interactions, with interaction energies of - 5.02 kcal/mol and -4.22 kcal/mol, respectively. Besides these attractive interactions, repulsive interactions were also noticed. In this work, we analyzed repulsive water-water contacts from the Cambridge Structural Database. All interaction energies were calculated at the so- called gold standard, i.e., CCSD(T)/CBS level of theory. It was found that among all water-water contacts, ca. 20% (2035 contacts) are repulsive with interaction energies mainly up to 2 kcal/mol. Most of these repulsive contacts do not belong to two main groups of water-water contacts. Namely, 12.8% of all repulsive contacts can be classified as classical hydrogen bonds, 2.1% to the antiparallel interactions, and the rest (85.3%) as remaining contacts. This study points out that additional attention should be paid when one deals with contacts including water or, eventually, hydrogen atoms in general.",
journal = "2nd International Conference on Chemo and Bioinformatics (ICCBIKG_2023), Book of Proceedings, 28-29 September 2023, Kragujevac, Serbia, 2023",
title = "Repulsive water-water contacts from Cambridge Structural Database",
pages = "637-640",
url = "https://hdl.handle.net/21.15107/rcub_cherry_6346"
}

Milovanović, M. R., Živković, J. M., Stanković, I. M., Ninković, D. B.,& Zarić, S. D.. (2023). Repulsive water-water contacts from Cambridge Structural Database. in 2nd International Conference on Chemo and Bioinformatics (ICCBIKG_2023), Book of Proceedings, 28-29 September 2023, Kragujevac, Serbia, 2023, 637-640.
https://hdl.handle.net/21.15107/rcub_cherry_6346

Milovanović MR, Živković JM, Stanković IM, Ninković DB, Zarić SD. Repulsive water-water contacts from Cambridge Structural Database. in 2nd International Conference on Chemo and Bioinformatics (ICCBIKG_2023), Book of Proceedings, 28-29 September 2023, Kragujevac, Serbia, 2023. 2023;:637-640.
https://hdl.handle.net/21.15107/rcub_cherry_6346 .

Milovanović, Milan R., Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan B., Zarić, Snežana D., "Repulsive water-water contacts from Cambridge Structural Database" in 2nd International Conference on Chemo and Bioinformatics (ICCBIKG_2023), Book of Proceedings, 28-29 September 2023, Kragujevac, Serbia, 2023 (2023):637-640,
https://hdl.handle.net/21.15107/rcub_cherry_6346 .

TY  - CONF
AU  - Zarić, Snežana D.
AU  - Milovanović, Milan R.
AU  - Stanković, Ivana M.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Hall, Michael B.
PY  - 2023
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/6372
AB  - Water is one of the most important molecules; it is clear that life on Earth depends on its anomalous properties derived from its unique structure: small size and high polarity [1] as well as flexibility [2]. A fundamental ability of water is hydrogen bonding.
Hydrogen bonds are generally considered strong when the H···Y distance is 2.2 to 2.5 Å and the X—H···Y angle is 170 to 180⁰, whereas for weak hydrogen-bond interactions, the H···Y distance is larger than 3.2 Å and the bond angle is less than 130⁰. Between strong and weak interactions are those ones of the moderate strength [3].
In this work [4], we analyzed geometries of all water–water interactions in the Cambridge Structural Database (CSD). We found 9928 water-water contacts and for all of them we calculated interaction energies at the accurate CCSD(T)/CBS level. Our results indicate two types of attractive water–water interactions; the first type involves the classical hydrogen bonds (dOH < 3.0 Å and α > 120⁰), whereas the second type involves antiparallel O—H bond interactions (Figure 1). Namely, c.a. 70% of attractive water–water contacts are classical hydrogen bonds with most being stronger than -3.3 kcal/mol, while c.a. 19% of attractive water–water contacts are antiparallel dipolar interactions with interaction energies up to -4.7 kcal/mol.
C3  - 17th International Congress of Quantum Chemistry (17thICQC), Book of abstracts, June 26 – July 1 2023, Bratislava, Slovakia
T1  - Antiparallel interactions as a mode of hydrogen bonding: Case of water in solid state
UR  - https://hdl.handle.net/21.15107/rcub_cherry_6372
ER  - 

@conference{
author = "Zarić, Snežana D. and Milovanović, Milan R. and Stanković, Ivana M. and Živković, Jelena M. and Ninković, Dragan B. and Hall, Michael B.",
year = "2023",
abstract = "Water is one of the most important molecules; it is clear that life on Earth depends on its anomalous properties derived from its unique structure: small size and high polarity [1] as well as flexibility [2]. A fundamental ability of water is hydrogen bonding.
Hydrogen bonds are generally considered strong when the H···Y distance is 2.2 to 2.5 Å and the X—H···Y angle is 170 to 180⁰, whereas for weak hydrogen-bond interactions, the H···Y distance is larger than 3.2 Å and the bond angle is less than 130⁰. Between strong and weak interactions are those ones of the moderate strength [3].
In this work [4], we analyzed geometries of all water–water interactions in the Cambridge Structural Database (CSD). We found 9928 water-water contacts and for all of them we calculated interaction energies at the accurate CCSD(T)/CBS level. Our results indicate two types of attractive water–water interactions; the first type involves the classical hydrogen bonds (dOH < 3.0 Å and α > 120⁰), whereas the second type involves antiparallel O—H bond interactions (Figure 1). Namely, c.a. 70% of attractive water–water contacts are classical hydrogen bonds with most being stronger than -3.3 kcal/mol, while c.a. 19% of attractive water–water contacts are antiparallel dipolar interactions with interaction energies up to -4.7 kcal/mol.",
journal = "17th International Congress of Quantum Chemistry (17thICQC), Book of abstracts, June 26 – July 1 2023, Bratislava, Slovakia",
title = "Antiparallel interactions as a mode of hydrogen bonding: Case of water in solid state",
url = "https://hdl.handle.net/21.15107/rcub_cherry_6372"
}

Zarić, S. D., Milovanović, M. R., Stanković, I. M., Živković, J. M., Ninković, D. B.,& Hall, M. B.. (2023). Antiparallel interactions as a mode of hydrogen bonding: Case of water in solid state. in 17th International Congress of Quantum Chemistry (17thICQC), Book of abstracts, June 26 – July 1 2023, Bratislava, Slovakia.
https://hdl.handle.net/21.15107/rcub_cherry_6372

Zarić SD, Milovanović MR, Stanković IM, Živković JM, Ninković DB, Hall MB. Antiparallel interactions as a mode of hydrogen bonding: Case of water in solid state. in 17th International Congress of Quantum Chemistry (17thICQC), Book of abstracts, June 26 – July 1 2023, Bratislava, Slovakia. 2023;.
https://hdl.handle.net/21.15107/rcub_cherry_6372 .

Zarić, Snežana D., Milovanović, Milan R., Stanković, Ivana M., Živković, Jelena M., Ninković, Dragan B., Hall, Michael B., "Antiparallel interactions as a mode of hydrogen bonding: Case of water in solid state" in 17th International Congress of Quantum Chemistry (17thICQC), Book of abstracts, June 26 – July 1 2023, Bratislava, Slovakia (2023),
https://hdl.handle.net/21.15107/rcub_cherry_6372 .

TY  - JOUR
AU  - Milovanović, Milan R.
AU  - Stanković, Ivana M.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
AU  - Macgillivray, L. R.
PY  - 2022
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5638
AB  - All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O - H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β1, β2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry. © 2022 Milan R. Milovanović et al.
PB  - International Union of Crystallography
T2  - IUCrJ
T1  - Water: new aspect of hydrogen bonding in the solid state
VL  - 9
IS  - 5
SP  - 639
EP  - 647
DO  - 10.1107/S2052252522006728
ER  - 

@article{
author = "Milovanović, Milan R. and Stanković, Ivana M. and Živković, Jelena M. and Ninković, Dragan and Hall, Michael B. and Zarić, Snežana D. and Macgillivray, L. R.",
year = "2022",
abstract = "All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O - H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β1, β2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry. © 2022 Milan R. Milovanović et al.",
publisher = "International Union of Crystallography",
journal = "IUCrJ",
title = "Water: new aspect of hydrogen bonding in the solid state",
volume = "9",
number = "5",
pages = "639-647",
doi = "10.1107/S2052252522006728"
}

Milovanović, M. R., Stanković, I. M., Živković, J. M., Ninković, D., Hall, M. B., Zarić, S. D.,& Macgillivray, L. R.. (2022). Water: new aspect of hydrogen bonding in the solid state. in IUCrJ
International Union of Crystallography., 9(5), 639-647.
https://doi.org/10.1107/S2052252522006728

Milovanović MR, Stanković IM, Živković JM, Ninković D, Hall MB, Zarić SD, Macgillivray LR. Water: new aspect of hydrogen bonding in the solid state. in IUCrJ. 2022;9(5):639-647.
doi:10.1107/S2052252522006728 .

Milovanović, Milan R., Stanković, Ivana M., Živković, Jelena M., Ninković, Dragan, Hall, Michael B., Zarić, Snežana D., Macgillivray, L. R., "Water: new aspect of hydrogen bonding in the solid state" in IUCrJ, 9, no. 5 (2022):639-647,
https://doi.org/10.1107/S2052252522006728 . .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/6355
AB  - Water molecules are omnipresent in nature and are a key part of many life processes. Due its ability of hydrogen binding water molecule plays an important role in the packing of small molecule crystal structures. Over the past years, the structure of a water molecule has been intensively studied. [1] The experimental values for a free water molecule in the gas phase are the bond angle (H–O–H) of 104.52 ± 0.05° and the bond (O–H) length of 0.9572 ± 0.0003 Å. [2] Neutron diffraction experiments of liquid water showed that the bond angle increases to 106.1 ± 1.8° and the bond length increases to 0.970 ± 0.005 Å. [3] Most of the bond angles in structures of ice have values close to a tetrahedral angle. However, in some of the ice structures, the bond angles and bond lengths remarkably deviates. Calculations based on the spectroscopic potential energy surface showed the equilibrium structure of a water molecule with the bond angle of 104.501 ± 0.005° and the bond length of 0.95785 ± 0.00005 Å. [4] In this study, [5] we performed an analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles and bond lengths of water molecule. The results of the analysis of crystal structures solved by neutron as well as by X-ray diffraction analysis showed a large discrepancy of both the bond angle and bond length values. Namely, the ranges of the bond angle and the average bond lengths of neutron solved structures having R factor ≤ 0.05 are from 100.74° to 113.92° and from 0.91 Å to 0.99 Å respectively. The corresponding range of the bond angle of X-ray solved structures is from 13.27° to 180.00°. High level ab initio calculations predicted a possibility for energetically low-cost (±1 kcal mol–1) changes of both the bond angle and bond lengths in a wide range, from 96.4° to 112.8° (Fig. 1) and from 0.930 A to 0.989 A (Fig. 1), respectively. Consequently, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries.
PB  - Wiley
C3  - 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021
T1  - How flexible is the water molecule structure? Cambridge Structural Database and ab initio calculations study.
UR  - https://hdl.handle.net/21.15107/rcub_cherry_6355
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan B. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2021",
abstract = "Water molecules are omnipresent in nature and are a key part of many life processes. Due its ability of hydrogen binding water molecule plays an important role in the packing of small molecule crystal structures. Over the past years, the structure of a water molecule has been intensively studied. [1] The experimental values for a free water molecule in the gas phase are the bond angle (H–O–H) of 104.52 ± 0.05° and the bond (O–H) length of 0.9572 ± 0.0003 Å. [2] Neutron diffraction experiments of liquid water showed that the bond angle increases to 106.1 ± 1.8° and the bond length increases to 0.970 ± 0.005 Å. [3] Most of the bond angles in structures of ice have values close to a tetrahedral angle. However, in some of the ice structures, the bond angles and bond lengths remarkably deviates. Calculations based on the spectroscopic potential energy surface showed the equilibrium structure of a water molecule with the bond angle of 104.501 ± 0.005° and the bond length of 0.95785 ± 0.00005 Å. [4] In this study, [5] we performed an analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles and bond lengths of water molecule. The results of the analysis of crystal structures solved by neutron as well as by X-ray diffraction analysis showed a large discrepancy of both the bond angle and bond length values. Namely, the ranges of the bond angle and the average bond lengths of neutron solved structures having R factor ≤ 0.05 are from 100.74° to 113.92° and from 0.91 Å to 0.99 Å respectively. The corresponding range of the bond angle of X-ray solved structures is from 13.27° to 180.00°. High level ab initio calculations predicted a possibility for energetically low-cost (±1 kcal mol–1) changes of both the bond angle and bond lengths in a wide range, from 96.4° to 112.8° (Fig. 1) and from 0.930 A to 0.989 A (Fig. 1), respectively. Consequently, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries.",
publisher = "Wiley",
journal = "25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021",
title = "How flexible is the water molecule structure? Cambridge Structural Database and ab initio calculations study.",
url = "https://hdl.handle.net/21.15107/rcub_cherry_6355"
}

Milovanović, M. R., Živković, J. M., Ninković, D. B., Stanković, I. M.,& Zarić, S. D.. (2021). How flexible is the water molecule structure? Cambridge Structural Database and ab initio calculations study.. in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021
Wiley..
https://hdl.handle.net/21.15107/rcub_cherry_6355

Milovanović MR, Živković JM, Ninković DB, Stanković IM, Zarić SD. How flexible is the water molecule structure? Cambridge Structural Database and ab initio calculations study.. in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021. 2021;.
https://hdl.handle.net/21.15107/rcub_cherry_6355 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan B., Stanković, Ivana M., Zarić, Snežana D., "How flexible is the water molecule structure? Cambridge Structural Database and ab initio calculations study." in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021 (2021),
https://hdl.handle.net/21.15107/rcub_cherry_6355 .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Blagojević Filipović, Jelena P.
AU  - Vojislavljević-Vasilev, Dubravka
AU  - Veljković, Ivana S.
AU  - Stanković, Ivana M.
AU  - Malenov, Dušan P.
AU  - Medaković, Vesna
AU  - Veljković, Dušan Ž.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5275
UR  - https://iucr25.org/
AB  - In the recent review it was point out that the crystal structures in the Cambridge Structural Database (CSD), collected, have contribute
to various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies of
molecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage and
delivery [1].
In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactions
and to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions,
frequency of the interactions, and preferred geometries of the interactions in the crystal structures. In addition, we perform quantum
chemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for the
interactions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine the
interaction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in the
crystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of the
supramolecular structures in the crystals.
Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic
aromatic rings and stacking interactions between two chelate rings. The calculated energies indicate strong stacking interactions of
metal-chelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules [2]. The data indicate
influence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strong
stacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bonds
and stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/M
interactions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongest
hydrogen bonds in any molecular system [6].
The studies on stacking interactions of benzene molecules in the crystal structures in the CSD show preference for interactions at large
horizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; the
energy is 70% of the strongest stacking geometry [7].
PB  - Wiley
C3  - 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021
T1  - Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database
VL  - A77
SP  - C192
UR  - https://hdl.handle.net/21.15107/rcub_cherry_5275
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan and Blagojević Filipović, Jelena P. and Vojislavljević-Vasilev, Dubravka and Veljković, Ivana S. and Stanković, Ivana M. and Malenov, Dušan P. and Medaković, Vesna and Veljković, Dušan Ž. and Zarić, Snežana D.",
year = "2021",
abstract = "In the recent review it was point out that the crystal structures in the Cambridge Structural Database (CSD), collected, have contribute
to various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies of
molecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage and
delivery [1].
In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactions
and to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions,
frequency of the interactions, and preferred geometries of the interactions in the crystal structures. In addition, we perform quantum
chemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for the
interactions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine the
interaction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in the
crystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of the
supramolecular structures in the crystals.
Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic
aromatic rings and stacking interactions between two chelate rings. The calculated energies indicate strong stacking interactions of
metal-chelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules [2]. The data indicate
influence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strong
stacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bonds
and stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/M
interactions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongest
hydrogen bonds in any molecular system [6].
The studies on stacking interactions of benzene molecules in the crystal structures in the CSD show preference for interactions at large
horizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; the
energy is 70% of the strongest stacking geometry [7].",
publisher = "Wiley",
journal = "25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021",
title = "Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database",
volume = "A77",
pages = "C192",
url = "https://hdl.handle.net/21.15107/rcub_cherry_5275"
}

Milovanović, M. R., Živković, J. M., Ninković, D., Blagojević Filipović, J. P., Vojislavljević-Vasilev, D., Veljković, I. S., Stanković, I. M., Malenov, D. P., Medaković, V., Veljković, D. Ž.,& Zarić, S. D.. (2021). Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database. in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021
Wiley., A77, C192.
https://hdl.handle.net/21.15107/rcub_cherry_5275

Milovanović MR, Živković JM, Ninković D, Blagojević Filipović JP, Vojislavljević-Vasilev D, Veljković IS, Stanković IM, Malenov DP, Medaković V, Veljković DŽ, Zarić SD. Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database. in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021. 2021;A77:C192.
https://hdl.handle.net/21.15107/rcub_cherry_5275 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan, Blagojević Filipović, Jelena P., Vojislavljević-Vasilev, Dubravka, Veljković, Ivana S., Stanković, Ivana M., Malenov, Dušan P., Medaković, Vesna, Veljković, Dušan Ž., Zarić, Snežana D., "Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database" in 25th Congress and General Assembly of the International Union of Crystallography, Prague, Czech Republic, August 2021, A77 (2021):C192,
https://hdl.handle.net/21.15107/rcub_cherry_5275 .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Blagojević Filipović, Jelena P.
AU  - Vojislavljević-Vasilev, Dubravka
AU  - Veljković, Ivana S.
AU  - Stanković, Ivana M.
AU  - Malenov, Dušan P.
AU  - Medaković, Vesna
AU  - Veljković, Dušan Ž.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5274
AB  - The analysis of the crystal structures in the CSD was used to recognize and characterize new types of noncovalent interactions. It was also used to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions, frequency of the interactions, and preferred geometries of the interactions in the crystal structures [1,2].
The quantum chemical calculations were performed to evaluate the energies of the interactions. For the preferred geometries in the crystal structures we can calculate the interaction energies. By calculating potential energy surfaces for the interactions, we can determine the most stable geometries, as well as stability of various geometries [1,2].
Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings. The calculated energies showed that the stacking of metal-chelate rings is stronger than stacking between two benzene molecules. Studies of interactions of coordinated ligands indicate stronger noncovalent interactions that interactions of noncoordinated molecules [2].

REFERENCES
[1] Ninković, D. B., Blagojević Filipović, J. P., Hall, M. B., Brothers, E. N., Zarić, S. D. (2020) ACS Central Science, 6, 420.
[2] Malenov, D. P., Zarić, S. D. (2020) Cood. Chem. Rev. 419, 213338.
PB  - Society of Physical Chemists of Serbia
C3  - 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Book of Abstracts
T1  - Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations
UR  - https://hdl.handle.net/21.15107/rcub_cherry_5274
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan and Blagojević Filipović, Jelena P. and Vojislavljević-Vasilev, Dubravka and Veljković, Ivana S. and Stanković, Ivana M. and Malenov, Dušan P. and Medaković, Vesna and Veljković, Dušan Ž. and Zarić, Snežana D.",
year = "2021",
abstract = "The analysis of the crystal structures in the CSD was used to recognize and characterize new types of noncovalent interactions. It was also used to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions, frequency of the interactions, and preferred geometries of the interactions in the crystal structures [1,2].
The quantum chemical calculations were performed to evaluate the energies of the interactions. For the preferred geometries in the crystal structures we can calculate the interaction energies. By calculating potential energy surfaces for the interactions, we can determine the most stable geometries, as well as stability of various geometries [1,2].
Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings. The calculated energies showed that the stacking of metal-chelate rings is stronger than stacking between two benzene molecules. Studies of interactions of coordinated ligands indicate stronger noncovalent interactions that interactions of noncoordinated molecules [2].

REFERENCES
[1] Ninković, D. B., Blagojević Filipović, J. P., Hall, M. B., Brothers, E. N., Zarić, S. D. (2020) ACS Central Science, 6, 420.
[2] Malenov, D. P., Zarić, S. D. (2020) Cood. Chem. Rev. 419, 213338.",
publisher = "Society of Physical Chemists of Serbia",
journal = "15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Book of Abstracts",
title = "Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations",
url = "https://hdl.handle.net/21.15107/rcub_cherry_5274"
}

Milovanović, M. R., Živković, J. M., Ninković, D., Blagojević Filipović, J. P., Vojislavljević-Vasilev, D., Veljković, I. S., Stanković, I. M., Malenov, D. P., Medaković, V., Veljković, D. Ž.,& Zarić, S. D.. (2021). Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Book of Abstracts
Society of Physical Chemists of Serbia..
https://hdl.handle.net/21.15107/rcub_cherry_5274

Milovanović MR, Živković JM, Ninković D, Blagojević Filipović JP, Vojislavljević-Vasilev D, Veljković IS, Stanković IM, Malenov DP, Medaković V, Veljković DŽ, Zarić SD. Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Book of Abstracts. 2021;.
https://hdl.handle.net/21.15107/rcub_cherry_5274 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan, Blagojević Filipović, Jelena P., Vojislavljević-Vasilev, Dubravka, Veljković, Ivana S., Stanković, Ivana M., Malenov, Dušan P., Medaković, Vesna, Veljković, Dušan Ž., Zarić, Snežana D., "Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations" in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Book of Abstracts (2021),
https://hdl.handle.net/21.15107/rcub_cherry_5274 .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Blagojević Filipović, Jelena P.
AU  - Vojislavljević-Vasilev, Dubravka
AU  - Veljković, Ivana S.
AU  - Stanković, Ivana M.
AU  - Malenov, Dušan P.
AU  - Medaković, Vesna
AU  - Veljković, Dušan Ž.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5354
AB  - The analysis of the crystal structures in the CSD was used to recognize and characterize new types of noncovalent interactions. It was also used to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions, frequency of the interactions, and preferred geometries of the interactions in the crystal structures [1,2].
The quantum chemical calculations were performed to evaluate the energies of the interactions.
For the preferred geometries in the crystal structures we can calculate the interaction energies. By
calculating potential energy surfaces for the interactions, we can determine the most stable
geometries, as well as stability of various geometries [1,2].
Using this methodology our group recognized stacking interactions of planar metal-chelate rings;
stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings.
The calculated energies showed that the stacking of metal-chelate rings is stronger than stacking
between two benzene molecules. Studies of interactions of coordinated ligands indicate stronger
noncovalent interactions that interactions of noncoordinated molecules [2].
PB  - Society of Physical Chemists of Serbia
C3  - 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, PC2021, 22-22
T1  - Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations
SP  - 22
EP  - 22
UR  - https://hdl.handle.net/21.15107/rcub_cherry_5354
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan and Blagojević Filipović, Jelena P. and Vojislavljević-Vasilev, Dubravka and Veljković, Ivana S. and Stanković, Ivana M. and Malenov, Dušan P. and Medaković, Vesna and Veljković, Dušan Ž. and Zarić, Snežana D.",
year = "2021",
abstract = "The analysis of the crystal structures in the CSD was used to recognize and characterize new types of noncovalent interactions. It was also used to study already known noncovalent interactions. Based on the data from the CSD we can determine existence of the interactions, frequency of the interactions, and preferred geometries of the interactions in the crystal structures [1,2].
The quantum chemical calculations were performed to evaluate the energies of the interactions.
For the preferred geometries in the crystal structures we can calculate the interaction energies. By
calculating potential energy surfaces for the interactions, we can determine the most stable
geometries, as well as stability of various geometries [1,2].
Using this methodology our group recognized stacking interactions of planar metal-chelate rings;
stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings.
The calculated energies showed that the stacking of metal-chelate rings is stronger than stacking
between two benzene molecules. Studies of interactions of coordinated ligands indicate stronger
noncovalent interactions that interactions of noncoordinated molecules [2].",
publisher = "Society of Physical Chemists of Serbia",
journal = "15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, PC2021, 22-22",
title = "Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations",
pages = "22-22",
url = "https://hdl.handle.net/21.15107/rcub_cherry_5354"
}

Milovanović, M. R., Živković, J. M., Ninković, D., Blagojević Filipović, J. P., Vojislavljević-Vasilev, D., Veljković, I. S., Stanković, I. M., Malenov, D. P., Medaković, V., Veljković, D. Ž.,& Zarić, S. D.. (2021). Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, PC2021, 22-22
Society of Physical Chemists of Serbia., 22-22.
https://hdl.handle.net/21.15107/rcub_cherry_5354

Milovanović MR, Živković JM, Ninković D, Blagojević Filipović JP, Vojislavljević-Vasilev D, Veljković IS, Stanković IM, Malenov DP, Medaković V, Veljković DŽ, Zarić SD. Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, PC2021, 22-22. 2021;:22-22.
https://hdl.handle.net/21.15107/rcub_cherry_5354 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan, Blagojević Filipović, Jelena P., Vojislavljević-Vasilev, Dubravka, Veljković, Ivana S., Stanković, Ivana M., Malenov, Dušan P., Medaković, Vesna, Veljković, Dušan Ž., Zarić, Snežana D., "Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations" in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, PC2021, 22-22 (2021):22-22,
https://hdl.handle.net/21.15107/rcub_cherry_5354 .

TY  - JOUR
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan
AU  - Zarić, Snežana D.
PY  - 2021
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4532
AB  - Geometries of aromatic/aromatic interactions in crystal structures of small molecules from the Cambridge Structural Database (CSD) (benzene/benzene, toluene/toluene, and p-phenol/p-phenol interactions) and in protein structures from the Protein Data Bank (PDB) (Phe/Phe and Tyr/Tyr interactions) were studied and compared. The data show a larger influence of crystal packing/surrounding, more than the influence of substituents, on geometries of aromatic/aromatic interactions. While the interactions in crystal structures from the CSD show preference for parallel stacking interactions at the large offsets, in proteins from the PDB, they show preference for T-shaped geometries with small offsets.
T2  - Crystal Growth & Design
T1  - Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures
VL  - 21
IS  - 4
SP  - 1898
EP  - 1904
DO  - 10.1021/acs.cgd.0c01514
ER  - 

@article{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan and Zarić, Snežana D.",
year = "2021",
abstract = "Geometries of aromatic/aromatic interactions in crystal structures of small molecules from the Cambridge Structural Database (CSD) (benzene/benzene, toluene/toluene, and p-phenol/p-phenol interactions) and in protein structures from the Protein Data Bank (PDB) (Phe/Phe and Tyr/Tyr interactions) were studied and compared. The data show a larger influence of crystal packing/surrounding, more than the influence of substituents, on geometries of aromatic/aromatic interactions. While the interactions in crystal structures from the CSD show preference for parallel stacking interactions at the large offsets, in proteins from the PDB, they show preference for T-shaped geometries with small offsets.",
journal = "Crystal Growth & Design",
title = "Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures",
volume = "21",
number = "4",
pages = "1898-1904",
doi = "10.1021/acs.cgd.0c01514"
}

Živković, J. M., Stanković, I. M., Ninković, D.,& Zarić, S. D.. (2021). Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. in Crystal Growth & Design, 21(4), 1898-1904.
https://doi.org/10.1021/acs.cgd.0c01514

Živković JM, Stanković IM, Ninković D, Zarić SD. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. in Crystal Growth & Design. 2021;21(4):1898-1904.
doi:10.1021/acs.cgd.0c01514 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan, Zarić, Snežana D., "Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures" in Crystal Growth & Design, 21, no. 4 (2021):1898-1904,
https://doi.org/10.1021/acs.cgd.0c01514 . .

TY  - DATA
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan
AU  - Zarić, Snežana D.
PY  - 2021
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4533
T2  - Crystal Growth & Design
T1  - Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D. B.; Zarić, S. D. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. Crystal Growth & Design 2021, 21 (4), 1898–1904. https://doi.org/10.1021/acs.cgd.0c01514.
UR  - https://hdl.handle.net/21.15107/rcub_cherry_4533
ER  - 

@misc{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan and Zarić, Snežana D.",
year = "2021",
journal = "Crystal Growth & Design",
title = "Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D. B.; Zarić, S. D. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. Crystal Growth & Design 2021, 21 (4), 1898–1904. https://doi.org/10.1021/acs.cgd.0c01514.",
url = "https://hdl.handle.net/21.15107/rcub_cherry_4533"
}

Živković, J. M., Stanković, I. M., Ninković, D.,& Zarić, S. D.. (2021). Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D. B.; Zarić, S. D. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. Crystal Growth & Design 2021, 21 (4), 1898–1904. https://doi.org/10.1021/acs.cgd.0c01514.. in Crystal Growth & Design.
https://hdl.handle.net/21.15107/rcub_cherry_4533

Živković JM, Stanković IM, Ninković D, Zarić SD. Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D. B.; Zarić, S. D. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. Crystal Growth & Design 2021, 21 (4), 1898–1904. https://doi.org/10.1021/acs.cgd.0c01514.. in Crystal Growth & Design. 2021;.
https://hdl.handle.net/21.15107/rcub_cherry_4533 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan, Zarić, Snežana D., "Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D. B.; Zarić, S. D. Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures. Crystal Growth & Design 2021, 21 (4), 1898–1904. https://doi.org/10.1021/acs.cgd.0c01514." in Crystal Growth & Design (2021),
https://hdl.handle.net/21.15107/rcub_cherry_4533 .

TY  - JOUR
AU  - Veljković, Ivana S.
AU  - Veljković, Dušan Ž.
AU  - Sarić, Gordana G.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4286
AB  - Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.
PB  - Royal Society of Chemistry
T2  - CrystEngComm
T1  - What is the preferred geometry of sulfur–disulfide interactions?
VL  - 22
SP  - 7262
EP  - 7271
DO  - 10.1039/D0CE00211A
ER  - 

@article{
author = "Veljković, Ivana S. and Veljković, Dušan Ž. and Sarić, Gordana G. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2020",
abstract = "Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.",
publisher = "Royal Society of Chemistry",
journal = "CrystEngComm",
title = "What is the preferred geometry of sulfur–disulfide interactions?",
volume = "22",
pages = "7262-7271",
doi = "10.1039/D0CE00211A"
}

Veljković, I. S., Veljković, D. Ž., Sarić, G. G., Stanković, I. M.,& Zarić, S. D.. (2020). What is the preferred geometry of sulfur–disulfide interactions?. in CrystEngComm
Royal Society of Chemistry., 22, 7262-7271.
https://doi.org/10.1039/D0CE00211A

Veljković IS, Veljković DŽ, Sarić GG, Stanković IM, Zarić SD. What is the preferred geometry of sulfur–disulfide interactions?. in CrystEngComm. 2020;22:7262-7271.
doi:10.1039/D0CE00211A .

Veljković, Ivana S., Veljković, Dušan Ž., Sarić, Gordana G., Stanković, Ivana M., Zarić, Snežana D., "What is the preferred geometry of sulfur–disulfide interactions?" in CrystEngComm, 22 (2020):7262-7271,
https://doi.org/10.1039/D0CE00211A . .

TY  - JOUR
AU  - Veljković, Ivana S.
AU  - Veljković, Dušan Ž.
AU  - Sarić, Gordana G.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4287
AB  - Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.
PB  - Royal Society of Chemistry
T2  - CrystEngComm
T1  - What is the preferred geometry of sulfur–disulfide interactions?
VL  - 22
SP  - 7262
EP  - 7271
DO  - 10.1039/D0CE00211A
ER  - 

@article{
author = "Veljković, Ivana S. and Veljković, Dušan Ž. and Sarić, Gordana G. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2020",
abstract = "Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.Non-covalent interactions between disulfide fragments and sulfur atoms were studied in crystal structures of small molecules and by quantum chemical calculations. Statistical analysis of the geometrical data from the Cambridge Structural Database (CSD) reveals that in most cases, interactions between sulfur and disulfide bonds are bifurcated. Quantum chemical calculations are in agreement with those findings. A strong interaction energy was calculated for bifurcated interactions (ECCSD(T)/CBS = −2.83 kcal mol−1) considering the region along the disulfide bond. Non-bifurcated interactions are weaker except in cases where σ-hole interaction is possible or in cases where S⋯S interaction is accompanied by additional hydrogen bonds (ECCSD(T)/CBS = −3.26 kcal mol−1). SAPT decomposition analysis shows that dispersion is the main attractive force in the studied systems while electrostatics plays a crucial role in defining the geometry of interactions.",
publisher = "Royal Society of Chemistry",
journal = "CrystEngComm",
title = "What is the preferred geometry of sulfur–disulfide interactions?",
volume = "22",
pages = "7262-7271",
doi = "10.1039/D0CE00211A"
}

Veljković, I. S., Veljković, D. Ž., Sarić, G. G., Stanković, I. M.,& Zarić, S. D.. (2020). What is the preferred geometry of sulfur–disulfide interactions?. in CrystEngComm
Royal Society of Chemistry., 22, 7262-7271.
https://doi.org/10.1039/D0CE00211A

Veljković IS, Veljković DŽ, Sarić GG, Stanković IM, Zarić SD. What is the preferred geometry of sulfur–disulfide interactions?. in CrystEngComm. 2020;22:7262-7271.
doi:10.1039/D0CE00211A .

Veljković, Ivana S., Veljković, Dušan Ž., Sarić, Gordana G., Stanković, Ivana M., Zarić, Snežana D., "What is the preferred geometry of sulfur–disulfide interactions?" in CrystEngComm, 22 (2020):7262-7271,
https://doi.org/10.1039/D0CE00211A . .

TY  - JOUR
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3977
AB  - Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level ab initio calculations at the CCSD(T)/CBS level predicted a possibility for energetically low-cost (±1 kcal mol−1) changes of the bond angle and bond lengths in a wide range, from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.
PB  - Royal Society of Chemistry
T2  - Physical Chemistry Chemical Physics
T1  - How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface
VL  - 22
IS  - 7
SP  - 4138
EP  - 4143
DO  - 10.1039/C9CP07042G
ER  - 

@article{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2020",
abstract = "Water molecules from crystal structures archived in the CSD show a relatively large range both in the bond angle and bond lengths. High level ab initio calculations at the CCSD(T)/CBS level predicted a possibility for energetically low-cost (±1 kcal mol−1) changes of the bond angle and bond lengths in a wide range, from 96.4° to 112.8° and from 0.930 Å to 0.989 Å, respectively.",
publisher = "Royal Society of Chemistry",
journal = "Physical Chemistry Chemical Physics",
title = "How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface",
volume = "22",
number = "7",
pages = "4138-4143",
doi = "10.1039/C9CP07042G"
}

Milovanović, M. R., Živković, J. M., Ninković, D., Stanković, I. M.,& Zarić, S. D.. (2020). How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface. in Physical Chemistry Chemical Physics
Royal Society of Chemistry., 22(7), 4138-4143.
https://doi.org/10.1039/C9CP07042G

Milovanović MR, Živković JM, Ninković D, Stanković IM, Zarić SD. How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface. in Physical Chemistry Chemical Physics. 2020;22(7):4138-4143.
doi:10.1039/C9CP07042G .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan, Stanković, Ivana M., Zarić, Snežana D., "How flexible is the water molecule structure? Analysis of crystal structures and the potential energy surface" in Physical Chemistry Chemical Physics, 22, no. 7 (2020):4138-4143,
https://doi.org/10.1039/C9CP07042G . .

TY  - JOUR
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3973
AB  - The study of crystal structures from the Cambridge Structural Database (CSD) shows that most of p-phenol/p-phenol and toluene/toluene stacking interactions are at large horizontal displacements (offsets) as well as benzene/benzene interactions. The interactions at large horizontal displacements are stabilized by the addition of simultaneous interactions in supramolecular structures in crystals. The stacking p-phenol/p-phenol tends to be orientated in a parallel and antiparallel fashion, while stacking toluene/toluene is almost all in an antiparallel orientation. It is in accordance with calculated interaction energies. Namely, the strongest interaction energies for parallel and antiparallel phenol/phenol dimers are −5.12 and −4.40 kcal/mol, at offsets of 1.5 and 3.0 Å, respectively, while for parallel and antiparallel toluene/toluene dimers, energies are −3.98 and −5.39 kcal/mol, at offsets of 3.0 Å. These interactions are stronger than benzene/benzene stacking (−2.85 kcal/mol), as a consequence of the presence of the substituents. Similar to benzene/benzene stacking, interactions for phenol/phenol and toluene/toluene stacking at large offsets (4.0 Å) can be strong, stronger than −2.0 kcal/mol.
PB  - American Chemical Society
T2  - Crystal Growth & Design
T1  - Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces
VL  - 20
IS  - 2
SP  - 1025
EP  - 1034
DO  - 10.1021/acs.cgd.9b01353
ER  - 

@article{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan and Zarić, Snežana D.",
year = "2020",
abstract = "The study of crystal structures from the Cambridge Structural Database (CSD) shows that most of p-phenol/p-phenol and toluene/toluene stacking interactions are at large horizontal displacements (offsets) as well as benzene/benzene interactions. The interactions at large horizontal displacements are stabilized by the addition of simultaneous interactions in supramolecular structures in crystals. The stacking p-phenol/p-phenol tends to be orientated in a parallel and antiparallel fashion, while stacking toluene/toluene is almost all in an antiparallel orientation. It is in accordance with calculated interaction energies. Namely, the strongest interaction energies for parallel and antiparallel phenol/phenol dimers are −5.12 and −4.40 kcal/mol, at offsets of 1.5 and 3.0 Å, respectively, while for parallel and antiparallel toluene/toluene dimers, energies are −3.98 and −5.39 kcal/mol, at offsets of 3.0 Å. These interactions are stronger than benzene/benzene stacking (−2.85 kcal/mol), as a consequence of the presence of the substituents. Similar to benzene/benzene stacking, interactions for phenol/phenol and toluene/toluene stacking at large offsets (4.0 Å) can be strong, stronger than −2.0 kcal/mol.",
publisher = "American Chemical Society",
journal = "Crystal Growth & Design",
title = "Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces",
volume = "20",
number = "2",
pages = "1025-1034",
doi = "10.1021/acs.cgd.9b01353"
}

Živković, J. M., Stanković, I. M., Ninković, D.,& Zarić, S. D.. (2020). Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. in Crystal Growth & Design
American Chemical Society., 20(2), 1025-1034.
https://doi.org/10.1021/acs.cgd.9b01353

Živković JM, Stanković IM, Ninković D, Zarić SD. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. in Crystal Growth & Design. 2020;20(2):1025-1034.
doi:10.1021/acs.cgd.9b01353 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan, Zarić, Snežana D., "Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces" in Crystal Growth & Design, 20, no. 2 (2020):1025-1034,
https://doi.org/10.1021/acs.cgd.9b01353 . .

TY  - DATA
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3979
PB  - American Chemical Society
T2  - Crystal Growth & Design
T1  - Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D.; Zarić, S. D. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. Crystal Growth & Design 2020, 20 (2), 1025–1034. https://doi.org/10.1021/acs.cgd.9b01353
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3979
ER  - 

@misc{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan and Zarić, Snežana D.",
year = "2020",
publisher = "American Chemical Society",
journal = "Crystal Growth & Design",
title = "Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D.; Zarić, S. D. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. Crystal Growth & Design 2020, 20 (2), 1025–1034. https://doi.org/10.1021/acs.cgd.9b01353",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3979"
}

Živković, J. M., Stanković, I. M., Ninković, D.,& Zarić, S. D.. (2020). Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D.; Zarić, S. D. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. Crystal Growth & Design 2020, 20 (2), 1025–1034. https://doi.org/10.1021/acs.cgd.9b01353. in Crystal Growth & Design
American Chemical Society..
https://hdl.handle.net/21.15107/rcub_cherry_3979

Živković JM, Stanković IM, Ninković D, Zarić SD. Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D.; Zarić, S. D. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. Crystal Growth & Design 2020, 20 (2), 1025–1034. https://doi.org/10.1021/acs.cgd.9b01353. in Crystal Growth & Design. 2020;.
https://hdl.handle.net/21.15107/rcub_cherry_3979 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan, Zarić, Snežana D., "Supplementary data for the article: Živković, J. M.; Stanković, I. M.; Ninković, D.; Zarić, S. D. Phenol and Toluene Stacking Interactions, Including Interactions at Large Horizontal Displacements. Study of Crystal Structures and Calculation of Potential Energy Surfaces. Crystal Growth & Design 2020, 20 (2), 1025–1034. https://doi.org/10.1021/acs.cgd.9b01353" in Crystal Growth & Design (2020),
https://hdl.handle.net/21.15107/rcub_cherry_3979 .

TY  - JOUR
AU  - Stanković, Ivana M.
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3983
AB  - The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations
VL  - 157
SP  - 1
EP  - 9
DO  - 10.1016/j.ijbiomac.2020.03.251
ER  - 

@article{
author = "Stanković, Ivana M. and Blagojević Filipović, Jelena P. and Zarić, Snežana D.",
year = "2020",
abstract = "The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations",
volume = "157",
pages = "1-9",
doi = "10.1016/j.ijbiomac.2020.03.251"
}

Stanković, I. M., Blagojević Filipović, J. P.,& Zarić, S. D.. (2020). Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules
Elsevier., 157, 1-9.
https://doi.org/10.1016/j.ijbiomac.2020.03.251

Stanković IM, Blagojević Filipović JP, Zarić SD. Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules. 2020;157:1-9.
doi:10.1016/j.ijbiomac.2020.03.251 .

Stanković, Ivana M., Blagojević Filipović, Jelena P., Zarić, Snežana D., "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations" in International Journal of Biological Macromolecules, 157 (2020):1-9,
https://doi.org/10.1016/j.ijbiomac.2020.03.251 . .

TY  - JOUR
AU  - Stanković, Ivana M.
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3984
AB  - The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations
VL  - 157
SP  - 1
EP  - 9
DO  - 10.1016/j.ijbiomac.2020.03.251
ER  - 

@article{
author = "Stanković, Ivana M. and Blagojević Filipović, Jelena P. and Zarić, Snežana D.",
year = "2020",
abstract = "The geometries of the contacts between monosaccharides and aromatic rings of amino acids found in X-ray crystallography structures, in the Protein Data Bank (PDB), were analyzed, while the energies of the interactions were calculated using quantum chemical method. We found 1913 sugar/aromatic ring contacts, 1054 of them (55%) with CH/π interactions and 859 of them (45%) without CH/π interactions. We showed that only the carbohydrate/aromatic contacts with CH/π interactions are preferentially parallel and enable sliding in the plane parallel to aromatic ring. The calculated interaction energies in systems with CH/π interactions are in the range from −1.7 kcal/mol to −6.8 kcal/mol, while in the systems without CH/π interactions are in the range −0.2 to −3.2 kcal/mol. Hence, the binding that does not include CH/π interactions, can also be important for aromatic amino acid and carbohydrate binding processes, since some of these interactions can be as strong as the CH/π interactions. At the same time, these interactions can be weak enough to enable releasing of small carbohydrate fragments after the enzymatic reaction. The analysis of the protein-substrate patterns showed that every second or third carbohydrate unit in long substrates stacks with protein aromatic amino acids.",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations",
volume = "157",
pages = "1-9",
doi = "10.1016/j.ijbiomac.2020.03.251"
}

Stanković, I. M., Blagojević Filipović, J. P.,& Zarić, S. D.. (2020). Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules
Elsevier., 157, 1-9.
https://doi.org/10.1016/j.ijbiomac.2020.03.251

Stanković IM, Blagojević Filipović JP, Zarić SD. Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations. in International Journal of Biological Macromolecules. 2020;157:1-9.
doi:10.1016/j.ijbiomac.2020.03.251 .

Stanković, Ivana M., Blagojević Filipović, Jelena P., Zarić, Snežana D., "Carbohydrate – Protein aromatic ring interactions beyond CH/π interactions: A Protein Data Bank survey and quantum chemical calculations" in International Journal of Biological Macromolecules, 157 (2020):1-9,
https://doi.org/10.1016/j.ijbiomac.2020.03.251 . .

TY  - DATA
AU  - Stanković, Ivana M.
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3987
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Supplementary material for the article: Stanković, I. M.; Blagojević Filipović, J. P.; Zarić, S. D. Carbohydrate – Protein Aromatic Ring Interactions beyond CH/π Interactions: A Protein Data Bank Survey and Quantum Chemical Calculations. Int. J. Biol. Macromol. 2020, 157, 1–9. https://doi.org/10.1016/j.ijbiomac.2020.03.251
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3987
ER  - 

@misc{
author = "Stanković, Ivana M. and Blagojević Filipović, Jelena P. and Zarić, Snežana D.",
year = "2020",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Supplementary material for the article: Stanković, I. M.; Blagojević Filipović, J. P.; Zarić, S. D. Carbohydrate – Protein Aromatic Ring Interactions beyond CH/π Interactions: A Protein Data Bank Survey and Quantum Chemical Calculations. Int. J. Biol. Macromol. 2020, 157, 1–9. https://doi.org/10.1016/j.ijbiomac.2020.03.251",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3987"
}

Stanković, I. M., Blagojević Filipović, J. P.,& Zarić, S. D.. (2020). Supplementary material for the article: Stanković, I. M.; Blagojević Filipović, J. P.; Zarić, S. D. Carbohydrate – Protein Aromatic Ring Interactions beyond CH/π Interactions: A Protein Data Bank Survey and Quantum Chemical Calculations. Int. J. Biol. Macromol. 2020, 157, 1–9. https://doi.org/10.1016/j.ijbiomac.2020.03.251. in International Journal of Biological Macromolecules
Elsevier..
https://hdl.handle.net/21.15107/rcub_cherry_3987

Stanković IM, Blagojević Filipović JP, Zarić SD. Supplementary material for the article: Stanković, I. M.; Blagojević Filipović, J. P.; Zarić, S. D. Carbohydrate – Protein Aromatic Ring Interactions beyond CH/π Interactions: A Protein Data Bank Survey and Quantum Chemical Calculations. Int. J. Biol. Macromol. 2020, 157, 1–9. https://doi.org/10.1016/j.ijbiomac.2020.03.251. in International Journal of Biological Macromolecules. 2020;.
https://hdl.handle.net/21.15107/rcub_cherry_3987 .

Stanković, Ivana M., Blagojević Filipović, Jelena P., Zarić, Snežana D., "Supplementary material for the article: Stanković, I. M.; Blagojević Filipović, J. P.; Zarić, S. D. Carbohydrate – Protein Aromatic Ring Interactions beyond CH/π Interactions: A Protein Data Bank Survey and Quantum Chemical Calculations. Int. J. Biol. Macromol. 2020, 157, 1–9. https://doi.org/10.1016/j.ijbiomac.2020.03.251" in International Journal of Biological Macromolecules (2020),
https://hdl.handle.net/21.15107/rcub_cherry_3987 .

TY  - JOUR
AU  - Stanković, Ivana M.
AU  - Niu, Shuqiang
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4176
AB  - Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.
PB  - Elsevier
T2  - International Journal of Biological Macromolecules
T1  - Role of aromatic amino acids in amyloid self-assembly
VL  - 156
SP  - 949
EP  - 959
DO  - 10.1016/j.ijbiomac.2020.03.064
ER  - 

@article{
author = "Stanković, Ivana M. and Niu, Shuqiang and Hall, Michael B. and Zarić, Snežana D.",
year = "2020",
abstract = "Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.",
publisher = "Elsevier",
journal = "International Journal of Biological Macromolecules",
title = "Role of aromatic amino acids in amyloid self-assembly",
volume = "156",
pages = "949-959",
doi = "10.1016/j.ijbiomac.2020.03.064"
}

Stanković, I. M., Niu, S., Hall, M. B.,& Zarić, S. D.. (2020). Role of aromatic amino acids in amyloid self-assembly. in International Journal of Biological Macromolecules
Elsevier., 156, 949-959.
https://doi.org/10.1016/j.ijbiomac.2020.03.064

Stanković IM, Niu S, Hall MB, Zarić SD. Role of aromatic amino acids in amyloid self-assembly. in International Journal of Biological Macromolecules. 2020;156:949-959.
doi:10.1016/j.ijbiomac.2020.03.064 .

Stanković, Ivana M., Niu, Shuqiang, Hall, Michael B., Zarić, Snežana D., "Role of aromatic amino acids in amyloid self-assembly" in International Journal of Biological Macromolecules, 156 (2020):949-959,
https://doi.org/10.1016/j.ijbiomac.2020.03.064 . .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://icni2019.eventos.chemistry.pt/
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/6358
AB  - Water molecule is ubiquitous in nature. Due to polar structure and ability for hydrogen bonding water molecule plays important role in many life processes as well as in packing of small molecules crystal structures. Over the past decades, the structure of water molecule [1] and water dimers [2] has been intensively studied. The experimental values for a free water molecule in the gas phase are the bond (O-H) length of 0.9572 ± 0.0003 Å and the bond angle (H-O-H) of 104.52 ± 0.05⁰. [3] Calculations have showed that equilibrium structure of water molecule has the bond length of 0.95785 ± 0.00005 Å and the bond angle of 104.501± 0.005⁰. [4] Energy of hydrogen bonded water dimer predicted by theory is -4.77 kcal/mol. [5] In this study, we performed an analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles and bond lengths of water molecule and water dimers. We analyzed different geometrical parameters. The results of analysis of crystal structures showed that there is a large discrepancy of both the bond length and the bond angle values form the ideal ones. For example, the range of the bond angles of X-ray solved structures having R factor ≤ 0.05 is 22.43⁰-180.00⁰, while reliable bond angles predicted by calculations are in the range of ca. 93.2⁰-116.4⁰. Consequently, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries. Calculations on hydrogen bond potential energy surface were compared with the analysis of the all hydrogen bonds of non-coordinated water molecules in the CSD. We were able to correlate the calculated data with two regions of hydrogen bonded water dimers found in the CSD.
C3  - 1st International Conferences on Noncovalent Interactions (ICNI-2019), Lisbon, Portugal, 2-6 September, 2019
T1  - Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study.
UR  - https://hdl.handle.net/21.15107/rcub_cherry_6358
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan B. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2019",
abstract = "Water molecule is ubiquitous in nature. Due to polar structure and ability for hydrogen bonding water molecule plays important role in many life processes as well as in packing of small molecules crystal structures. Over the past decades, the structure of water molecule [1] and water dimers [2] has been intensively studied. The experimental values for a free water molecule in the gas phase are the bond (O-H) length of 0.9572 ± 0.0003 Å and the bond angle (H-O-H) of 104.52 ± 0.05⁰. [3] Calculations have showed that equilibrium structure of water molecule has the bond length of 0.95785 ± 0.00005 Å and the bond angle of 104.501± 0.005⁰. [4] Energy of hydrogen bonded water dimer predicted by theory is -4.77 kcal/mol. [5] In this study, we performed an analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles and bond lengths of water molecule and water dimers. We analyzed different geometrical parameters. The results of analysis of crystal structures showed that there is a large discrepancy of both the bond length and the bond angle values form the ideal ones. For example, the range of the bond angles of X-ray solved structures having R factor ≤ 0.05 is 22.43⁰-180.00⁰, while reliable bond angles predicted by calculations are in the range of ca. 93.2⁰-116.4⁰. Consequently, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries. Calculations on hydrogen bond potential energy surface were compared with the analysis of the all hydrogen bonds of non-coordinated water molecules in the CSD. We were able to correlate the calculated data with two regions of hydrogen bonded water dimers found in the CSD.",
journal = "1st International Conferences on Noncovalent Interactions (ICNI-2019), Lisbon, Portugal, 2-6 September, 2019",
title = "Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study.",
url = "https://hdl.handle.net/21.15107/rcub_cherry_6358"
}

Milovanović, M. R., Živković, J. M., Ninković, D. B., Stanković, I. M.,& Zarić, S. D.. (2019). Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study.. in 1st International Conferences on Noncovalent Interactions (ICNI-2019), Lisbon, Portugal, 2-6 September, 2019.
https://hdl.handle.net/21.15107/rcub_cherry_6358

Milovanović MR, Živković JM, Ninković DB, Stanković IM, Zarić SD. Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study.. in 1st International Conferences on Noncovalent Interactions (ICNI-2019), Lisbon, Portugal, 2-6 September, 2019. 2019;.
https://hdl.handle.net/21.15107/rcub_cherry_6358 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan B., Stanković, Ivana M., Zarić, Snežana D., "Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study." in 1st International Conferences on Noncovalent Interactions (ICNI-2019), Lisbon, Portugal, 2-6 September, 2019 (2019),
https://hdl.handle.net/21.15107/rcub_cherry_6358 .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/6359
AB  - Water molecule is omnipresent in nature. Due to polar structure and ability for hydrogen bonding water molecule plays important role in many life processes as well as in packing of small molecules crystal structures. Over the past decades, the structure of water molecule has been intensively studied [1,2]. It has been found that a free water molecule in gas phase has the bond angle (H–O–H) of 104.52 ± 0.05° [3], while the bond angle of crystalline hydrates from over 40 structures solved by neutron diffraction analysis is in range from 102.50° to 115.25° [4]. Spectroscopic potential energy surface based calculations showed that equilibrium structure of water molecule has the bond angle of 104.501°± 0.005 [5].
In this study, we performed an analysis of water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles of water molecule. 
Results of analysis of structures solved by neutron as well as by X-ray diffraction analysis with R factor ≤ 0.1 showed that there is a large discrepancy of the bond angle values from the ideal one(s). Namely, the range of the bond angle in neutron solved structures is 79.76–141.64° while in X-ray solved structures is 17.03–180.00°. By calculating the energy protentional curve of the bond angle change it is shown the bond angles beyond the range of ca. 93.0–116.0° are rather doubtful. Accordingly, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries.
PB  - Belgrade : Serbian Crystallographic Society
C3  - 26th Conference of the Serbian Crystallographic Society, June 27–28rd, 2019 Silver lake, Serbia
T1  - Are the bond angles of water molecules in crystal structures reliable? Joint cambridge structural database and ab-initio calculation analysis
SP  - 34
EP  - 35
UR  - https://hdl.handle.net/21.15107/rcub_cherry_6359
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan B. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2019",
abstract = "Water molecule is omnipresent in nature. Due to polar structure and ability for hydrogen bonding water molecule plays important role in many life processes as well as in packing of small molecules crystal structures. Over the past decades, the structure of water molecule has been intensively studied [1,2]. It has been found that a free water molecule in gas phase has the bond angle (H–O–H) of 104.52 ± 0.05° [3], while the bond angle of crystalline hydrates from over 40 structures solved by neutron diffraction analysis is in range from 102.50° to 115.25° [4]. Spectroscopic potential energy surface based calculations showed that equilibrium structure of water molecule has the bond angle of 104.501°± 0.005 [5].
In this study, we performed an analysis of water containing structures archived in Cambridge Structural Database (CSD) as well as ab-initio calculations on a range of bond angles of water molecule. 
Results of analysis of structures solved by neutron as well as by X-ray diffraction analysis with R factor ≤ 0.1 showed that there is a large discrepancy of the bond angle values from the ideal one(s). Namely, the range of the bond angle in neutron solved structures is 79.76–141.64° while in X-ray solved structures is 17.03–180.00°. By calculating the energy protentional curve of the bond angle change it is shown the bond angles beyond the range of ca. 93.0–116.0° are rather doubtful. Accordingly, it would lead to at least 15% of X-ray solved structures that contain questionable water molecule geometries.",
publisher = "Belgrade : Serbian Crystallographic Society",
journal = "26th Conference of the Serbian Crystallographic Society, June 27–28rd, 2019 Silver lake, Serbia",
title = "Are the bond angles of water molecules in crystal structures reliable? Joint cambridge structural database and ab-initio calculation analysis",
pages = "34-35",
url = "https://hdl.handle.net/21.15107/rcub_cherry_6359"
}

Milovanović, M. R., Živković, J. M., Ninković, D. B., Stanković, I. M.,& Zarić, S. D.. (2019). Are the bond angles of water molecules in crystal structures reliable? Joint cambridge structural database and ab-initio calculation analysis. in 26th Conference of the Serbian Crystallographic Society, June 27–28rd, 2019 Silver lake, Serbia
Belgrade : Serbian Crystallographic Society., 34-35.
https://hdl.handle.net/21.15107/rcub_cherry_6359

Milovanović MR, Živković JM, Ninković DB, Stanković IM, Zarić SD. Are the bond angles of water molecules in crystal structures reliable? Joint cambridge structural database and ab-initio calculation analysis. in 26th Conference of the Serbian Crystallographic Society, June 27–28rd, 2019 Silver lake, Serbia. 2019;:34-35.
https://hdl.handle.net/21.15107/rcub_cherry_6359 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan B., Stanković, Ivana M., Zarić, Snežana D., "Are the bond angles of water molecules in crystal structures reliable? Joint cambridge structural database and ab-initio calculation analysis" in 26th Conference of the Serbian Crystallographic Society, June 27–28rd, 2019 Silver lake, Serbia (2019):34-35,
https://hdl.handle.net/21.15107/rcub_cherry_6359 .

TY  - CONF
AU  - Ninković, Dragan
AU  - Veljković, Dušan Ž.
AU  - Malenov, Dušan P.
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Veljković, Ivana S.
AU  - Medaković, Vesna
AU  - Blagojević Filipović, Jelena P.
AU  - Vojislavljević-Vasilev, Dubravka
AU  - Zarić, Snežana D.
PY  - 2019
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5266
AB  - Наше истраживање се заснива на анализи података у кристалним структурама
из Кембичке базе структурних података (CSD) и на квантнo хемијским
прорачунима. Анализа података из CSD-а омогућава да се препознају интеракције у
кристалним структурама и да се опишу геометрије ових интеракција, док помоћу
квантно-хемијских прорачуна можемо проценити интеракционе енергије и пронаћи
најстабилније геометрије интеракција. Користећи ову методологију успели смо да
препознамо и опишемо неколико нових типова интеракција.
Наше проучавање интеракција планарних метал-хелатних прстенова показало је
могућност стекинг интеракција са органским ароматичним прстеновима и
интеракције између два хелатна прстена. Израчунате енергије указују на јаке
стекинг интеракције метал-хелатних прстенова; стекинг метал-хелатних прстенова
је јачи од стекинга између два молекула бензена. Испитивања интеракција
координираних молекула воде и амонијака указују на јаче водоничне везе и јаче
ОH/π и NH/π интеракције координираних у односу на некоординоване молекуле
воде и амонијака. Прорачуни ОH/М интеракција између металног јона у квадратнo
планарним комплексима и молекулa воде указују да су ове интеракције међу
најјачим водоничним везама у било ком молекулском систему.
Студије о ароматичним молекулима указују на стекинг интеракције са великим
хоризонталним померањима између два ароматична молекула са значајно јаким
интеракцијама, енергија је 70% најјаче стекинг интеракције. Наши подаци такође
указују на то да су интеракције алифатичних прстенова са ароматичним прстеном
јаче од интеракција између два ароматична молекула, док су
алифатично/ароматичне интеракције веома честе у протеинским структурама.
AB  - Our research is based on analyzing data in crystal structures from the Cambridge
Structural Database (CSD) and on quantum chemical calculations. The analysis of the
data from the CSD enable to recognize interactions in crystal structures and to describe
the geometries of these interactions, while by quantum chemical calculations we can
evaluate interaction energies and find the most stable interaction geometries. Using this
methodology we were able to recognize and describe several new types of noncovalent
interactions.
Our study of planar metal-chelate rings interactions showed possibility of chelate ring
stacking interactions with organic aromatic rings, and stacking interactions between two
chelate rings. The calculated energies indicate strong stacking interactions of metalchelate rings; the stacking of metal-chelate rings is stronger than stacking between two
benzene molecules. Studies of interactions of coordinated water and ammonia indicate
stronger hydrogen bonds and stronger OH/π and NH/π interactions of coordinated in
comparison to noncoordianted water and ammonia. The calculations on OH/M interactions between metal ion in square-planar complexes and water molecule indicate that
these interactions are among the strongest hydrogen bonds in any molecular system.
The studies on aromatic molecules indicate stacking interactions at large horizontal
dispacements between two aromatic molecules with significantly strong interacitons, the
energy is 70% of the strongest stacking geometry. Our data also indicate that stacking
interactions of an aliphatic rings with an aromatic ring are stonger than interactions between two aromatic molecules, while aliphatic/aromatic interactions are very frequent in
protein structures.
PB  - Српско кристалографско друштво
C3  - XXVI Конференција Српског кристалографског друштва, Књига апстраката
T1  - Нековалентне интеракције комплекса метала и ароматичних молекула
T1  - Noncovalent interactions of metal complexes and aromatic molecules
UR  - https://hdl.handle.net/21.15107/rcub_cherry_5266
ER  - 

@conference{
author = "Ninković, Dragan and Veljković, Dušan Ž. and Malenov, Dušan P. and Milovanović, Milan R. and Živković, Jelena M. and Stanković, Ivana M. and Veljković, Ivana S. and Medaković, Vesna and Blagojević Filipović, Jelena P. and Vojislavljević-Vasilev, Dubravka and Zarić, Snežana D.",
year = "2019",
abstract = "Наше истраживање се заснива на анализи података у кристалним структурама
из Кембичке базе структурних података (CSD) и на квантнo хемијским
прорачунима. Анализа података из CSD-а омогућава да се препознају интеракције у
кристалним структурама и да се опишу геометрије ових интеракција, док помоћу
квантно-хемијских прорачуна можемо проценити интеракционе енергије и пронаћи
најстабилније геометрије интеракција. Користећи ову методологију успели смо да
препознамо и опишемо неколико нових типова интеракција.
Наше проучавање интеракција планарних метал-хелатних прстенова показало је
могућност стекинг интеракција са органским ароматичним прстеновима и
интеракције између два хелатна прстена. Израчунате енергије указују на јаке
стекинг интеракције метал-хелатних прстенова; стекинг метал-хелатних прстенова
је јачи од стекинга између два молекула бензена. Испитивања интеракција
координираних молекула воде и амонијака указују на јаче водоничне везе и јаче
ОH/π и NH/π интеракције координираних у односу на некоординоване молекуле
воде и амонијака. Прорачуни ОH/М интеракција између металног јона у квадратнo
планарним комплексима и молекулa воде указују да су ове интеракције међу
најјачим водоничним везама у било ком молекулском систему.
Студије о ароматичним молекулима указују на стекинг интеракције са великим
хоризонталним померањима између два ароматична молекула са значајно јаким
интеракцијама, енергија је 70% најјаче стекинг интеракције. Наши подаци такође
указују на то да су интеракције алифатичних прстенова са ароматичним прстеном
јаче од интеракција између два ароматична молекула, док су
алифатично/ароматичне интеракције веома честе у протеинским структурама., Our research is based on analyzing data in crystal structures from the Cambridge
Structural Database (CSD) and on quantum chemical calculations. The analysis of the
data from the CSD enable to recognize interactions in crystal structures and to describe
the geometries of these interactions, while by quantum chemical calculations we can
evaluate interaction energies and find the most stable interaction geometries. Using this
methodology we were able to recognize and describe several new types of noncovalent
interactions.
Our study of planar metal-chelate rings interactions showed possibility of chelate ring
stacking interactions with organic aromatic rings, and stacking interactions between two
chelate rings. The calculated energies indicate strong stacking interactions of metalchelate rings; the stacking of metal-chelate rings is stronger than stacking between two
benzene molecules. Studies of interactions of coordinated water and ammonia indicate
stronger hydrogen bonds and stronger OH/π and NH/π interactions of coordinated in
comparison to noncoordianted water and ammonia. The calculations on OH/M interactions between metal ion in square-planar complexes and water molecule indicate that
these interactions are among the strongest hydrogen bonds in any molecular system.
The studies on aromatic molecules indicate stacking interactions at large horizontal
dispacements between two aromatic molecules with significantly strong interacitons, the
energy is 70% of the strongest stacking geometry. Our data also indicate that stacking
interactions of an aliphatic rings with an aromatic ring are stonger than interactions between two aromatic molecules, while aliphatic/aromatic interactions are very frequent in
protein structures.",
publisher = "Српско кристалографско друштво",
journal = "XXVI Конференција Српског кристалографског друштва, Књига апстраката",
title = "Нековалентне интеракције комплекса метала и ароматичних молекула, Noncovalent interactions of metal complexes and aromatic molecules",
url = "https://hdl.handle.net/21.15107/rcub_cherry_5266"
}

Ninković, D., Veljković, D. Ž., Malenov, D. P., Milovanović, M. R., Živković, J. M., Stanković, I. M., Veljković, I. S., Medaković, V., Blagojević Filipović, J. P., Vojislavljević-Vasilev, D.,& Zarić, S. D.. (2019). Нековалентне интеракције комплекса метала и ароматичних молекула. in XXVI Конференција Српског кристалографског друштва, Књига апстраката
Српско кристалографско друштво..
https://hdl.handle.net/21.15107/rcub_cherry_5266

Ninković D, Veljković DŽ, Malenov DP, Milovanović MR, Živković JM, Stanković IM, Veljković IS, Medaković V, Blagojević Filipović JP, Vojislavljević-Vasilev D, Zarić SD. Нековалентне интеракције комплекса метала и ароматичних молекула. in XXVI Конференција Српског кристалографског друштва, Књига апстраката. 2019;.
https://hdl.handle.net/21.15107/rcub_cherry_5266 .

Ninković, Dragan, Veljković, Dušan Ž., Malenov, Dušan P., Milovanović, Milan R., Živković, Jelena M., Stanković, Ivana M., Veljković, Ivana S., Medaković, Vesna, Blagojević Filipović, Jelena P., Vojislavljević-Vasilev, Dubravka, Zarić, Snežana D., "Нековалентне интеракције комплекса метала и ароматичних молекула" in XXVI Конференција Српског кристалографског друштва, Књига апстраката (2019),
https://hdl.handle.net/21.15107/rcub_cherry_5266 .

TY  - JOUR
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3675
AB  - The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.
PB  - International Union of Crystallography
T2  - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
T1  - Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds
VL  - 75
SP  - 301
EP  - 309
DO  - 10.1107/S2052520619001999
ER  - 

@article{
author = "Andrić, Jelena M. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2019",
abstract = "The interactions of nucleic acid bases with non-coordinated and coordinated water molecules were studied by analyzing data in the Protein Data Bank (PDB) and by quantum chemical calculations. The analysis of the data in the crystal structures from the PDB indicates that hydrogen bonds involving oxygen or nitrogen atoms of nucleic acid bases and water molecules are shorter when water is bonded to a metal ion. These results are in agreement with the quantum chemical calculations on geometries and interaction energies of hydrogen bonds; the calculations on model systems show that hydrogen bonds of nucleic acid bases with water bonded to a metal ion are stronger than hydrogen bonds with non-coordinated water. These calculated values are similar to the strength of hydrogen bonds between nucleic acid bases. The results presented in this paper may be relevant to understand the role of water molecules and metal ions in the process of replication and stabilization of nucleic acids and also to understand the possible toxicity of metal ion interactions with nucleic acids.",
publisher = "International Union of Crystallography",
journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials",
title = "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds",
volume = "75",
pages = "301-309",
doi = "10.1107/S2052520619001999"
}

Andrić, J. M., Stanković, I. M.,& Zarić, S. D.. (2019). Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
International Union of Crystallography., 75, 301-309.
https://doi.org/10.1107/S2052520619001999

Andrić JM, Stanković IM, Zarić SD. Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials. 2019;75:301-309.
doi:10.1107/S2052520619001999 .

Andrić, Jelena M., Stanković, Ivana M., Zarić, Snežana D., "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75 (2019):301-309,
https://doi.org/10.1107/S2052520619001999 . .

TY  - DATA
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3676
PB  - International Union of Crystallography
T2  - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
T1  - Supplementary material for the article: Andrić, J. M.; Stanković, I. M.; Zarić, S. D. Binding of Metal Ions and Water Molecules to Nucleic Acid Bases: The Influence of Water Molecule Coordination to a Metal Ion on Water–Nucleic Acid Base Hydrogen Bonds. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials 2019, 75, 301–309. https://doi.org/10.1107/S2052520619001999
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3676
ER  - 

@misc{
author = "Andrić, Jelena M. and Stanković, Ivana M. and Zarić, Snežana D.",
year = "2019",
publisher = "International Union of Crystallography",
journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials",
title = "Supplementary material for the article: Andrić, J. M.; Stanković, I. M.; Zarić, S. D. Binding of Metal Ions and Water Molecules to Nucleic Acid Bases: The Influence of Water Molecule Coordination to a Metal Ion on Water–Nucleic Acid Base Hydrogen Bonds. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials 2019, 75, 301–309. https://doi.org/10.1107/S2052520619001999",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3676"
}

Andrić, J. M., Stanković, I. M.,& Zarić, S. D.. (2019). Supplementary material for the article: Andrić, J. M.; Stanković, I. M.; Zarić, S. D. Binding of Metal Ions and Water Molecules to Nucleic Acid Bases: The Influence of Water Molecule Coordination to a Metal Ion on Water–Nucleic Acid Base Hydrogen Bonds. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials 2019, 75, 301–309. https://doi.org/10.1107/S2052520619001999. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
International Union of Crystallography..
https://hdl.handle.net/21.15107/rcub_cherry_3676

Andrić JM, Stanković IM, Zarić SD. Supplementary material for the article: Andrić, J. M.; Stanković, I. M.; Zarić, S. D. Binding of Metal Ions and Water Molecules to Nucleic Acid Bases: The Influence of Water Molecule Coordination to a Metal Ion on Water–Nucleic Acid Base Hydrogen Bonds. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials 2019, 75, 301–309. https://doi.org/10.1107/S2052520619001999. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials. 2019;.
https://hdl.handle.net/21.15107/rcub_cherry_3676 .

Andrić, Jelena M., Stanković, Ivana M., Zarić, Snežana D., "Supplementary material for the article: Andrić, J. M.; Stanković, I. M.; Zarić, S. D. Binding of Metal Ions and Water Molecules to Nucleic Acid Bases: The Influence of Water Molecule Coordination to a Metal Ion on Water–Nucleic Acid Base Hydrogen Bonds. Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials 2019, 75, 301–309. https://doi.org/10.1107/S2052520619001999" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials (2019),
https://hdl.handle.net/21.15107/rcub_cherry_3676 .

TY  - CONF
AU  - Stanković, Ivana M.
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2018
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/5277
AB  - Код различитих ензима активних на угљеним хидратима, клизајући, паралелни
стекинг између моносахаридне јединице и аминокиселине протеина је важан за
препознавање супстрата и феномен процесивности [1]. Поред хидрофобног
ефекта, они интерагују путем неконвенционалних водоничних веза: C-H/π
интеракција [2]. Ниједна од ових интеракција није посебно усмерена,
омогућавајући клизајући карактер. Овде смо систематски анализирали геометрије
ароматично/сахаридних контаката нађених у кристалографским структурама у
Протеинској Банци Података. Критеријум за C-H/π интеракције је био исти као у
[3]. Скрипте и програми за претрагу су написани у језику Python са коришћењем
библиотеке MDAnalysis [4] за читање PDB датотека. Показали смо да само
ароматично/сахаридни контакти са C-H/π
интеракцијама имају претежно паралелни
и клизајући карактер у равни паралелној са
ароматичним прстеном (Слика 1).
Геометрије нису специфичне у равни
паралелној са ароматичним прстеном, само
показују тежњу ка нормалним растојањима
између прстенова око 4 Å, док су
хоризонтална померања у опсегу 0-2 Å.
Анализа образаца ензим/супстрат показала
је да свака друга или трећа јединица
супстрата код дугих сахарида интерагује са
ароматичном аминокиселином ензима
(Слика 1).
AB  - In different carbohydrate active enzymes, the sliding, parallel stacking between a
monosaccharide unit and a protein aromatic ring is important for substrate recognition
and processivity [1]. Along with the hydrophobic effect, they interact by
nonconventional hydrogen bonds: the C-H/π interactions [2]. Neither of these
interactions is highly directional, therefore enable sliding.
Here, we systematically analyze geometry of monosaccharide/aromatic amino acid
contacts found in X-ray crystallography structures, in the Protein Data Bank. The criteria
for the C-H/π interaction are the same as in [3]. Homemade scripts for the search were
written in Python with the MDAnalysis [4] python library for protein file parsing.
We showed that only the carbohydrate/aromatic contacts with C-H/π interactions are
preferentially parallel and of sliding character in the plane parallel to aromatic ring
(Figure 1).
The geometries are not specific in the
plane parallel to the aromatic ring, they
only show tendency for the normal
distance between rings of around 4 Å,
while horizontal displacement are in the
range of 0-2 Å.
The analysis of enzyme-substrate
patterns showed that every second or
third carbohydrate unit in long
substrates stacks with enzyme aromatic
amino acids (Figure 1).
C3  - 25th Conference of the Serbian Crystallographic Society
T1  - Interactions between Carbohydrates and Aromatic Amino Acids: A Crystallographic Survey
T1  - Интеракције између угљених хидрата и ароматичних аминокиселина: кристалографска претрага
UR  - https://hdl.handle.net/21.15107/rcub_cherry_5277
ER  - 

@conference{
author = "Stanković, Ivana M. and Blagojević Filipović, Jelena P. and Zarić, Snežana D.",
year = "2018",
abstract = "Код различитих ензима активних на угљеним хидратима, клизајући, паралелни
стекинг између моносахаридне јединице и аминокиселине протеина је важан за
препознавање супстрата и феномен процесивности [1]. Поред хидрофобног
ефекта, они интерагују путем неконвенционалних водоничних веза: C-H/π
интеракција [2]. Ниједна од ових интеракција није посебно усмерена,
омогућавајући клизајући карактер. Овде смо систематски анализирали геометрије
ароматично/сахаридних контаката нађених у кристалографским структурама у
Протеинској Банци Података. Критеријум за C-H/π интеракције је био исти као у
[3]. Скрипте и програми за претрагу су написани у језику Python са коришћењем
библиотеке MDAnalysis [4] за читање PDB датотека. Показали смо да само
ароматично/сахаридни контакти са C-H/π
интеракцијама имају претежно паралелни
и клизајући карактер у равни паралелној са
ароматичним прстеном (Слика 1).
Геометрије нису специфичне у равни
паралелној са ароматичним прстеном, само
показују тежњу ка нормалним растојањима
између прстенова око 4 Å, док су
хоризонтална померања у опсегу 0-2 Å.
Анализа образаца ензим/супстрат показала
је да свака друга или трећа јединица
супстрата код дугих сахарида интерагује са
ароматичном аминокиселином ензима
(Слика 1)., In different carbohydrate active enzymes, the sliding, parallel stacking between a
monosaccharide unit and a protein aromatic ring is important for substrate recognition
and processivity [1]. Along with the hydrophobic effect, they interact by
nonconventional hydrogen bonds: the C-H/π interactions [2]. Neither of these
interactions is highly directional, therefore enable sliding.
Here, we systematically analyze geometry of monosaccharide/aromatic amino acid
contacts found in X-ray crystallography structures, in the Protein Data Bank. The criteria
for the C-H/π interaction are the same as in [3]. Homemade scripts for the search were
written in Python with the MDAnalysis [4] python library for protein file parsing.
We showed that only the carbohydrate/aromatic contacts with C-H/π interactions are
preferentially parallel and of sliding character in the plane parallel to aromatic ring
(Figure 1).
The geometries are not specific in the
plane parallel to the aromatic ring, they
only show tendency for the normal
distance between rings of around 4 Å,
while horizontal displacement are in the
range of 0-2 Å.
The analysis of enzyme-substrate
patterns showed that every second or
third carbohydrate unit in long
substrates stacks with enzyme aromatic
amino acids (Figure 1).",
journal = "25th Conference of the Serbian Crystallographic Society",
title = "Interactions between Carbohydrates and Aromatic Amino Acids: A Crystallographic Survey, Интеракције између угљених хидрата и ароматичних аминокиселина: кристалографска претрага",
url = "https://hdl.handle.net/21.15107/rcub_cherry_5277"
}

Stanković, I. M., Blagojević Filipović, J. P.,& Zarić, S. D.. (2018). Interactions between Carbohydrates and Aromatic Amino Acids: A Crystallographic Survey. in 25th Conference of the Serbian Crystallographic Society.
https://hdl.handle.net/21.15107/rcub_cherry_5277

Stanković IM, Blagojević Filipović JP, Zarić SD. Interactions between Carbohydrates and Aromatic Amino Acids: A Crystallographic Survey. in 25th Conference of the Serbian Crystallographic Society. 2018;.
https://hdl.handle.net/21.15107/rcub_cherry_5277 .

Stanković, Ivana M., Blagojević Filipović, Jelena P., Zarić, Snežana D., "Interactions between Carbohydrates and Aromatic Amino Acids: A Crystallographic Survey" in 25th Conference of the Serbian Crystallographic Society (2018),
https://hdl.handle.net/21.15107/rcub_cherry_5277 .

TY  - JOUR
AU  - Stanković, Ivana M.
AU  - Božinovski, Dragana M.
AU  - Brothers, Edward N.
AU  - Belić, Milivoj R.
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2017
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/2566
AB  - Aromatic-aromatic interactions have long been considered important in the self assembly of amyloids. In spite of their importance, aromatic amino acids are not detected in every amyloid. In the present study, the occurrence and geometry of these interactions were analyzed for the amyloid structures found in the Protein Data Bank. The data confirm that aromatic amino acids are not crucial for amyloid fibril formation. In fact, aromatic-aliphatic interactions are more frequent than the aromatic-aromatic interactions. Aromatic-aliphatic interactions are present in higher numbers of structures and in certain amyloid sequences they are more frequent than aromatic-aromatic interactions. An analysis of aromatic/aromatic interactions shows different interaction geometries in intrasheet and intersheet contacts; the intrasheet aromatic-aromatic interactions are mostly parallel and displaced, while intersheet interactions are not parallel. Thus, among the aromatic-aromatic interactions there are important edge-to-face attractions in addition to parallel stacking ones.
PB  - Amer Chemical Soc, Washington
T2  - Crystal Growth and Design
T1  - Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data
VL  - 17
IS  - 12
SP  - 6353
EP  - 6362
DO  - 10.1021/acs.cgd.7b01035
ER  - 

@article{
author = "Stanković, Ivana M. and Božinovski, Dragana M. and Brothers, Edward N. and Belić, Milivoj R. and Hall, Michael B. and Zarić, Snežana D.",
year = "2017",
abstract = "Aromatic-aromatic interactions have long been considered important in the self assembly of amyloids. In spite of their importance, aromatic amino acids are not detected in every amyloid. In the present study, the occurrence and geometry of these interactions were analyzed for the amyloid structures found in the Protein Data Bank. The data confirm that aromatic amino acids are not crucial for amyloid fibril formation. In fact, aromatic-aliphatic interactions are more frequent than the aromatic-aromatic interactions. Aromatic-aliphatic interactions are present in higher numbers of structures and in certain amyloid sequences they are more frequent than aromatic-aromatic interactions. An analysis of aromatic/aromatic interactions shows different interaction geometries in intrasheet and intersheet contacts; the intrasheet aromatic-aromatic interactions are mostly parallel and displaced, while intersheet interactions are not parallel. Thus, among the aromatic-aromatic interactions there are important edge-to-face attractions in addition to parallel stacking ones.",
publisher = "Amer Chemical Soc, Washington",
journal = "Crystal Growth and Design",
title = "Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data",
volume = "17",
number = "12",
pages = "6353-6362",
doi = "10.1021/acs.cgd.7b01035"
}

Stanković, I. M., Božinovski, D. M., Brothers, E. N., Belić, M. R., Hall, M. B.,& Zarić, S. D.. (2017). Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data. in Crystal Growth and Design
Amer Chemical Soc, Washington., 17(12), 6353-6362.
https://doi.org/10.1021/acs.cgd.7b01035

Stanković IM, Božinovski DM, Brothers EN, Belić MR, Hall MB, Zarić SD. Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data. in Crystal Growth and Design. 2017;17(12):6353-6362.
doi:10.1021/acs.cgd.7b01035 .

Stanković, Ivana M., Božinovski, Dragana M., Brothers, Edward N., Belić, Milivoj R., Hall, Michael B., Zarić, Snežana D., "Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data" in Crystal Growth and Design, 17, no. 12 (2017):6353-6362,
https://doi.org/10.1021/acs.cgd.7b01035 . .