Ribić, Vesna R.

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  • Ribić, Vesna R. (4)
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Author's Bibliography

New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM

Ribić, Vesna R.; Rečnik, Aleksander; Komelj, Matej; Kokalj, Anton; Branković, Zorica; Zlatović, Mario; Branković, Goran

(Elsevier, 2020)

TY  - JOUR
AU  - Ribić, Vesna R.
AU  - Rečnik, Aleksander
AU  - Komelj, Matej
AU  - Kokalj, Anton
AU  - Branković, Zorica
AU  - Zlatović, Mario
AU  - Branković, Goran
PY  - 2020
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/4755
AB  - Today, ab-initio calculations are becoming a powerful tool to perform virtual experiments that have the capacity to predict and to reproduce experimentally observed non-periodic features, such as interfaces, that are responsible for quantum properties of materials. In our paper we investigate 2D quantum-well structures, known as inversion boundaries (IB). Combining atomistic modeling, DFT calculations and HRTEM analysis we provide a new fundamental insight into the structure and stability of Sb-rich basal-plane IBs in ZnO. DFT screening for potential IB model was based on the known stacking deviations in originating wurtzite structure. The results show that the model with Aβ−Bα−AβC−γB−βC sequence (IB3) is the most stable translation for Sb-doping, as opposed to previously accepted Aβ−Bα−AβC−γA−αC (IB2) model. The key to the stability of IB structures has been found to lie in their cationic stacking. We show that the energies of constituting stacking segments can be used to predict the stability of new IB structures without the need of further ab-initio calculations. DFT optimized models of IBs accurately predict the experimentally observed IB structures with lateral relaxations down to a precision of ~1 pm. The newly determined cation sublattice expansions for experimentally confirmed IB2 and IB3 models, ΔIB(Zn-Zn) are +81 pm and +77 pm, whereas the corresponding O-sublattice contractions ΔIB(O-O) are –53 pm and –57 pm, respectively. The refined structures will help to solve open questions related to their role in electron transport, phonon scattering, p-type conductivity, affinity of dopants to generate IBs and the underlying formation mechanisms, whereas the excellent match between the calculations and experiment demonstrated in our study opens new perspectives for prediction of such properties from first principles.
PB  - Elsevier
T2  - Acta Materialia
T1  - New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM
VL  - 199
SP  - 633
EP  - 648
DO  - 10.1016/j.actamat.2020.08.035
ER  - 
@article{
author = "Ribić, Vesna R. and Rečnik, Aleksander and Komelj, Matej and Kokalj, Anton and Branković, Zorica and Zlatović, Mario and Branković, Goran",
year = "2020",
abstract = "Today, ab-initio calculations are becoming a powerful tool to perform virtual experiments that have the capacity to predict and to reproduce experimentally observed non-periodic features, such as interfaces, that are responsible for quantum properties of materials. In our paper we investigate 2D quantum-well structures, known as inversion boundaries (IB). Combining atomistic modeling, DFT calculations and HRTEM analysis we provide a new fundamental insight into the structure and stability of Sb-rich basal-plane IBs in ZnO. DFT screening for potential IB model was based on the known stacking deviations in originating wurtzite structure. The results show that the model with Aβ−Bα−AβC−γB−βC sequence (IB3) is the most stable translation for Sb-doping, as opposed to previously accepted Aβ−Bα−AβC−γA−αC (IB2) model. The key to the stability of IB structures has been found to lie in their cationic stacking. We show that the energies of constituting stacking segments can be used to predict the stability of new IB structures without the need of further ab-initio calculations. DFT optimized models of IBs accurately predict the experimentally observed IB structures with lateral relaxations down to a precision of ~1 pm. The newly determined cation sublattice expansions for experimentally confirmed IB2 and IB3 models, ΔIB(Zn-Zn) are +81 pm and +77 pm, whereas the corresponding O-sublattice contractions ΔIB(O-O) are –53 pm and –57 pm, respectively. The refined structures will help to solve open questions related to their role in electron transport, phonon scattering, p-type conductivity, affinity of dopants to generate IBs and the underlying formation mechanisms, whereas the excellent match between the calculations and experiment demonstrated in our study opens new perspectives for prediction of such properties from first principles.",
publisher = "Elsevier",
journal = "Acta Materialia",
title = "New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM",
volume = "199",
pages = "633-648",
doi = "10.1016/j.actamat.2020.08.035"
}
Ribić, V. R., Rečnik, A., Komelj, M., Kokalj, A., Branković, Z., Zlatović, M.,& Branković, G.. (2020). New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM. in Acta Materialia
Elsevier., 199, 633-648.
https://doi.org/10.1016/j.actamat.2020.08.035
Ribić VR, Rečnik A, Komelj M, Kokalj A, Branković Z, Zlatović M, Branković G. New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM. in Acta Materialia. 2020;199:633-648.
doi:10.1016/j.actamat.2020.08.035 .
Ribić, Vesna R., Rečnik, Aleksander, Komelj, Matej, Kokalj, Anton, Branković, Zorica, Zlatović, Mario, Branković, Goran, "New inversion boundary structure in Sb-doped ZnO predicted by DFT calculations and confirmed by experimental HRTEM" in Acta Materialia, 199 (2020):633-648,
https://doi.org/10.1016/j.actamat.2020.08.035 . .
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Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050

Ribić, Vesna R.; Stojanović, Srđan Đ.; Zlatović, Mario

(Elsevier Science Bv, Amsterdam, 2018)

TY  - DATA
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3152
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050
UR  - https://hdl.handle.net/21.15107/rcub_cherry_3152
ER  - 
@misc{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050",
url = "https://hdl.handle.net/21.15107/rcub_cherry_3152"
}
Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam..
https://hdl.handle.net/21.15107/rcub_cherry_3152
Ribić VR, Stojanović SĐ, Zlatović M. Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050. in International Journal of Biological Macromolecules. 2018;.
https://hdl.handle.net/21.15107/rcub_cherry_3152 .
Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Supplementary material for the article: Ribić, V. R.; Stojanović, S. Đ.; Zlatović, M. V. Anion–π Interactions in Active Centers of Superoxide Dismutases. International Journal of Biological Macromolecules 2018, 106, 559–568. https://doi.org/10.1016/j.ijbiomac.2017.08.050" in International Journal of Biological Macromolecules (2018),
https://hdl.handle.net/21.15107/rcub_cherry_3152 .

Anion-pi interactions in active centers of superoxide dismutases

Ribić, Vesna R.; Stojanović, Srđan Đ.; Zlatović, Mario

(Elsevier Science Bv, Amsterdam, 2018)

TY  - JOUR
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/3151
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 
@article{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}
Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050
Ribić VR, Stojanović SĐ, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .
Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .
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Anion-pi interactions in active centers of superoxide dismutases

Ribić, Vesna R.; Stojanović, Srđan Đ.; Zlatović, Mario

(Elsevier Science Bv, Amsterdam, 2018)

TY  - JOUR
AU  - Ribić, Vesna R.
AU  - Stojanović, Srđan Đ.
AU  - Zlatović, Mario
PY  - 2018
UR  - https://cherry.chem.bg.ac.rs/handle/123456789/2564
AB  - We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.
PB  - Elsevier Science Bv, Amsterdam
T2  - International Journal of Biological Macromolecules
T1  - Anion-pi interactions in active centers of superoxide dismutases
VL  - 106
SP  - 559
EP  - 568
DO  - 10.1016/j.ijbiomac.2017.08.050
ER  - 
@article{
author = "Ribić, Vesna R. and Stojanović, Srđan Đ. and Zlatović, Mario",
year = "2018",
abstract = "We investigated 1060 possible anion-pi interactions in a data set of 41 superoxide dismutase active centers. Our observations indicate that majority of the aromatic residues are capable to form anion-pi interactions, mainly by long-range contacts, and that there is preference of Trp over other aromatic residues in these interactions. Furthermore, 68% of total predicted interactions in the dataset are multiple anion-pi interactions. Anion-pi interactions are distance and orientation dependent. We analyzed the energy contribution resulting from anion-pi interactions using ab initio calculations. The results showed that, while most of their interaction energies lay in the range from -0 to -4 kcal mol(-1), those energies can be up to -9 kcal mol(-1) and about 34% of interactions were found to be repulsive. Majority of the suggested anion-pi interacting residues in ternary complexes are metal-assisted. Stabilization centers for these proteins showed that all the six residues found in predicted anion-pi interactions are important in locating one or more of such centers. The anion-pi interacting residues in these proteins were found to be highly conserved. We hope that these studies might contribute useful information regarding structural stability and its interaction in future designs of novel metalloproteins. (C) 2017 Elsevier B.V. All rights reserved.",
publisher = "Elsevier Science Bv, Amsterdam",
journal = "International Journal of Biological Macromolecules",
title = "Anion-pi interactions in active centers of superoxide dismutases",
volume = "106",
pages = "559-568",
doi = "10.1016/j.ijbiomac.2017.08.050"
}
Ribić, V. R., Stojanović, S. Đ.,& Zlatović, M.. (2018). Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules
Elsevier Science Bv, Amsterdam., 106, 559-568.
https://doi.org/10.1016/j.ijbiomac.2017.08.050
Ribić VR, Stojanović SĐ, Zlatović M. Anion-pi interactions in active centers of superoxide dismutases. in International Journal of Biological Macromolecules. 2018;106:559-568.
doi:10.1016/j.ijbiomac.2017.08.050 .
Ribić, Vesna R., Stojanović, Srđan Đ., Zlatović, Mario, "Anion-pi interactions in active centers of superoxide dismutases" in International Journal of Biological Macromolecules, 106 (2018):559-568,
https://doi.org/10.1016/j.ijbiomac.2017.08.050 . .
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