TY  - JOUR
AU  - Milovanović, Milan R.
AU  - Stanković, Ivana M.
AU  - Živković, Jelena
AU  - Ninković, Dragan
AU  - Hall, Michael B.
AU  - Zarić, Snežana
PY  - 2022
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5326
AB  - All water–water contacts in the crystal structures from the Cambridge Structural
Database with dOO   4.0 A˚ 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 (dOH   3.0 A˚ and     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 ( 1,  2   160 , 80       140  and
THOHO > 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
PB  - International Union of Crystallography (IUCr)
T2  - IUCrJ
T1  - Water: new aspect of hydrogen bonding in the solid state
VL  - 9
SP  - 639
EP  - 647
DO  - 10.1107/S2052252522006728
ER  - 

@article{
author = "Milovanović, Milan R. and Stanković, Ivana M. and Živković, Jelena and Ninković, Dragan and Hall, Michael B. and Zarić, Snežana",
year = "2022",
abstract = "All water–water contacts in the crystal structures from the Cambridge Structural
Database with dOO   4.0 A˚ 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 (dOH   3.0 A˚ and     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 ( 1,  2   160 , 80       140  and
THOHO > 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",
publisher = "International Union of Crystallography (IUCr)",
journal = "IUCrJ",
title = "Water: new aspect of hydrogen bonding in the solid state",
volume = "9",
pages = "639-647",
doi = "10.1107/S2052252522006728"
}

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

Milovanović MR, Stanković IM, Živković J, Ninković D, Hall MB, Zarić S. Water: new aspect of hydrogen bonding in the solid state. in IUCrJ. 2022;9:639-647.
doi:10.1107/S2052252522006728 .

Milovanović, Milan R., Stanković, Ivana M., Živković, Jelena, Ninković, Dragan, Hall, Michael B., Zarić, Snežana, "Water: new aspect of hydrogen bonding in the solid state" in IUCrJ, 9 (2022):639-647,
https://doi.org/10.1107/S2052252522006728 . .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Blagojević Filipović, Jelena P.
AU  - Vojislavljević-Vasilev, Dubravka Z.
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  - https://cer.ihtm.bg.ac.rs/handle/123456789/5347
AB  - In the recent review it was point out that the crystal structures in the Cambridge Structural Database (CSD), collected, have contributeto various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies ofmolecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage anddelivery [1].In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactionsand 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 quantumchemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for theinteractions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine theinteraction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in thecrystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of thesupramolecular structures in the crystals.Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organicaromatic rings and stacking interactions between two chelate rings. The calculated energies indicate strong stacking interactions ofmetal-chelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules [2]. The data indicateinfluence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strongstacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bondsand stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/Minteractions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongesthydrogen 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 largehorizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; theenergy is 70% of the strongest stacking geometry [7].
PB  - The International Union of Crystallography (IUCr)
C3  - Acta Crystallographica, section A
T1  - Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database
VL  - A77
SP  - C192
DO  - 10.1107/S0108767321094903
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan B. and Blagojević Filipović, Jelena P. and Vojislavljević-Vasilev, Dubravka Z. 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 contributeto various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies ofmolecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage anddelivery [1].In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactionsand 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 quantumchemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for theinteractions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine theinteraction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in thecrystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of thesupramolecular structures in the crystals.Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organicaromatic rings and stacking interactions between two chelate rings. The calculated energies indicate strong stacking interactions ofmetal-chelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules [2]. The data indicateinfluence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strongstacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bondsand stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/Minteractions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongesthydrogen 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 largehorizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; theenergy is 70% of the strongest stacking geometry [7].",
publisher = "The International Union of Crystallography (IUCr)",
journal = "Acta Crystallographica, section A",
title = "Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database",
volume = "A77",
pages = "C192",
doi = "10.1107/S0108767321094903"
}

Milovanović, M. R., Živković, J. M., Ninković, D. B., Blagojević Filipović, J. P., Vojislavljević-Vasilev, D. Z., 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 Acta Crystallographica, section A
The International Union of Crystallography (IUCr)., A77, C192.
https://doi.org/10.1107/S0108767321094903

Milovanović MR, Živković JM, Ninković DB, Blagojević Filipović JP, Vojislavljević-Vasilev DZ, 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 Acta Crystallographica, section A. 2021;A77:C192.
doi:10.1107/S0108767321094903 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan B., Blagojević Filipović, Jelena P., Vojislavljević-Vasilev, Dubravka Z., 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 Acta Crystallographica, section A, A77 (2021):C192,
https://doi.org/10.1107/S0108767321094903 . .

TY  - CONF
AU  - Veljković, Dušan Ž.
AU  - Kretić, Danijela S.
AU  - Malenov, Dušan P.
AU  - Veljković, Ivana S.
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/5348
AB  - У овом раду смо испитивали утицај нековалентних интеракција на електростатичке потенцијале и осетљивост ка детонацији одабраних високоенергетских молекула. Резултати прорачуна рађених на M06/cc-PVDZ нивоу су показали да водоничне везе значајно утичу на вредности електростатичког потенцијала и осетљивост ка детонацији високоенергетских молекула. У случајевима када високоенергетски молекул игра улогу акцептора водоника, вредности електростатичког потенцијала изнад центара високоенергетских молекула се смањују за 20-25%. Ово даје могућност за коришћење водоничног везивања за модификовање осетљивости високоенергетских молекула.
AB  - In this work we studied influence of non-covalent interactions on the electrostatic potentials and  impact sensitivity of selected high energetic molecules (HEM). Study was performed using quantum  chemical calculations on model systems and crystal structures of selected HEMs. Results of M06/cc-PVDZ calculations showed that hydrogen bonding significantly affects electrostatic  potential values and impact sensitivities of HEMs. In cases in which HEM molecules act as  hydrogen atom acceptors, electrostatic potential values in the centers of HEM molecules decreases  by 20-25%. This gives opportunity for modification of impact sensitivities of HEM molecules.
PB  - Belgrade : Serbian Chemical Society
C3  - Book of abstracts / Proceedings 57th Meeting of the Serbian Chemical Society // Kratki izvodi radova / Knjiga radova 57. Savetovanje Srpskog hemijskog društva
T1  - Улога нековалентних интеракција у модификовању особина високоенергетских  материјала
T1  - Role of non-covalent interactions in modification of properties of high energetic materials
SP  - 98
EP  - 98
UR  - https://hdl.handle.net/21.15107/rcub_cer_5348
ER  - 

@conference{
author = "Veljković, Dušan Ž. and Kretić, Danijela S. and Malenov, Dušan P. and Veljković, Ivana S. and Ninković, Dragan B. and Zarić, Snežana D.",
year = "2021",
abstract = "У овом раду смо испитивали утицај нековалентних интеракција на електростатичке потенцијале и осетљивост ка детонацији одабраних високоенергетских молекула. Резултати прорачуна рађених на M06/cc-PVDZ нивоу су показали да водоничне везе значајно утичу на вредности електростатичког потенцијала и осетљивост ка детонацији високоенергетских молекула. У случајевима када високоенергетски молекул игра улогу акцептора водоника, вредности електростатичког потенцијала изнад центара високоенергетских молекула се смањују за 20-25%. Ово даје могућност за коришћење водоничног везивања за модификовање осетљивости високоенергетских молекула., In this work we studied influence of non-covalent interactions on the electrostatic potentials and  impact sensitivity of selected high energetic molecules (HEM). Study was performed using quantum  chemical calculations on model systems and crystal structures of selected HEMs. Results of M06/cc-PVDZ calculations showed that hydrogen bonding significantly affects electrostatic  potential values and impact sensitivities of HEMs. In cases in which HEM molecules act as  hydrogen atom acceptors, electrostatic potential values in the centers of HEM molecules decreases  by 20-25%. This gives opportunity for modification of impact sensitivities of HEM molecules.",
publisher = "Belgrade : Serbian Chemical Society",
journal = "Book of abstracts / Proceedings 57th Meeting of the Serbian Chemical Society // Kratki izvodi radova / Knjiga radova 57. Savetovanje Srpskog hemijskog društva",
title = "Улога нековалентних интеракција у модификовању особина високоенергетских  материјала, Role of non-covalent interactions in modification of properties of high energetic materials",
pages = "98-98",
url = "https://hdl.handle.net/21.15107/rcub_cer_5348"
}

Veljković, D. Ž., Kretić, D. S., Malenov, D. P., Veljković, I. S., Ninković, D. B.,& Zarić, S. D.. (2021). Улога нековалентних интеракција у модификовању особина високоенергетских  материјала. in Book of abstracts / Proceedings 57th Meeting of the Serbian Chemical Society // Kratki izvodi radova / Knjiga radova 57. Savetovanje Srpskog hemijskog društva
Belgrade : Serbian Chemical Society., 98-98.
https://hdl.handle.net/21.15107/rcub_cer_5348

Veljković DŽ, Kretić DS, Malenov DP, Veljković IS, Ninković DB, Zarić SD. Улога нековалентних интеракција у модификовању особина високоенергетских  материјала. in Book of abstracts / Proceedings 57th Meeting of the Serbian Chemical Society // Kratki izvodi radova / Knjiga radova 57. Savetovanje Srpskog hemijskog društva. 2021;:98-98.
https://hdl.handle.net/21.15107/rcub_cer_5348 .

Veljković, Dušan Ž., Kretić, Danijela S., Malenov, Dušan P., Veljković, Ivana S., Ninković, Dragan B., Zarić, Snežana D., "Улога нековалентних интеракција у модификовању особина високоенергетских  материјала" in Book of abstracts / Proceedings 57th Meeting of the Serbian Chemical Society // Kratki izvodi radova / Knjiga radova 57. Savetovanje Srpskog hemijskog društva (2021):98-98,
https://hdl.handle.net/21.15107/rcub_cer_5348 .

TY  - CONF
AU  - Veljković, Ivana S.
AU  - Malenov, Dusan P.
AU  - Zarić, Snežana
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7116
AB  - CCSD(T)/CBS energies for stacking interactions between two tetrathiafulvalene molecules were used as benchmark data to evaluate the performance of dispersion-corrected density functionals in calculating the interaction energies. The results showed that the best functional for TTF-TTF stacking is B2PLYP-D3 with 6-311++G** basis set, which successfully reproduces gold standard CCSD(T)/CBS interaction energies. M06L-D3 functional with 6-311++G** basis set consistently underestimates interaction energies, giving potential energy curves of accurate shapes.
PB  - Society of Physical Chemists of Serbia
C3  - 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, "Physical Chemistry 2021," Belgrade, Serbia
T1  - Evaluation of performance of dispersion corrected density functionals for TTF-TTF stacking interactions
SP  - 84
EP  - 84
UR  - https://hdl.handle.net/21.15107/rcub_cer_7116
ER  - 

@conference{
author = "Veljković, Ivana S. and Malenov, Dusan P. and Zarić, Snežana",
year = "2021",
abstract = "CCSD(T)/CBS energies for stacking interactions between two tetrathiafulvalene molecules were used as benchmark data to evaluate the performance of dispersion-corrected density functionals in calculating the interaction energies. The results showed that the best functional for TTF-TTF stacking is B2PLYP-D3 with 6-311++G** basis set, which successfully reproduces gold standard CCSD(T)/CBS interaction energies. M06L-D3 functional with 6-311++G** basis set consistently underestimates interaction energies, giving potential energy curves of accurate shapes.",
publisher = "Society of Physical Chemists of Serbia",
journal = "15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, "Physical Chemistry 2021," Belgrade, Serbia",
title = "Evaluation of performance of dispersion corrected density functionals for TTF-TTF stacking interactions",
pages = "84-84",
url = "https://hdl.handle.net/21.15107/rcub_cer_7116"
}

Veljković, I. S., Malenov, D. P.,& Zarić, S.. (2021). Evaluation of performance of dispersion corrected density functionals for TTF-TTF stacking interactions. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, "Physical Chemistry 2021," Belgrade, Serbia
Society of Physical Chemists of Serbia., 84-84.
https://hdl.handle.net/21.15107/rcub_cer_7116

Veljković IS, Malenov DP, Zarić S. Evaluation of performance of dispersion corrected density functionals for TTF-TTF stacking interactions. in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, "Physical Chemistry 2021," Belgrade, Serbia. 2021;:84-84.
https://hdl.handle.net/21.15107/rcub_cer_7116 .

Veljković, Ivana S., Malenov, Dusan P., Zarić, Snežana, "Evaluation of performance of dispersion corrected density functionals for TTF-TTF stacking interactions" in 15th International Conference on Fundamental and Applied Aspects of Physical Chemistry, "Physical Chemistry 2021," Belgrade, Serbia (2021):84-84,
https://hdl.handle.net/21.15107/rcub_cer_7116 .

TY  - JOUR
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4562
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.
PB  - USA : American Chemical Society
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 B. 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.",
publisher = "USA : American Chemical Society",
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. B.,& 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
USA : American Chemical Society., 21(4), 1898-1904.
https://doi.org/10.1021/acs.cgd.0c01514

Živković JM, Stanković IM, Ninković DB, 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 B., 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 B.
AU  - Zarić, Snežana D.
PY  - 2021
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4562
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4563
AB  - Additional graphics and tables; methodology, CSD and PDB searches; results from CSD search; calculations; results from PDB search.
PB  - USA : American Chemical Society
T2  - Crystal Growth & Design
T1  - Supplementary information for: "Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures"
DO  - 10.1021/acs.cgd.0c01514.s001
ER  - 

@misc{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan B. and Zarić, Snežana D.",
year = "2021",
abstract = "Additional graphics and tables; methodology, CSD and PDB searches; results from CSD search; calculations; results from PDB search.",
publisher = "USA : American Chemical Society",
journal = "Crystal Growth & Design",
title = "Supplementary information for: "Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures"",
doi = "10.1021/acs.cgd.0c01514.s001"
}

Živković, J. M., Stanković, I. M., Ninković, D. B.,& Zarić, S. D.. (2021). Supplementary information for: "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
USA : American Chemical Society..
https://doi.org/10.1021/acs.cgd.0c01514.s001

Živković JM, Stanković IM, Ninković DB, Zarić SD. Supplementary information for: "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;.
doi:10.1021/acs.cgd.0c01514.s001 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan B., Zarić, Snežana D., "Supplementary information for: "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),
https://doi.org/10.1021/acs.cgd.0c01514.s001 . .

TY  - JOUR
AU  - Veljković, Ivana S.
AU  - Veljković, Dušan
AU  - Sarić, Gordana G.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3987
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 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., 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 D, 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, 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
AU  - Sarić, Gordana G.
AU  - Stanković, Ivana M.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3990
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 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., 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 D, 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, 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  - Živković, Jelena M.
AU  - Stanković, Ivana
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3395
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 (ACS)
T2  - Crystal Growth and 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
SP  - 1025
EP  - 1034
DO  - 10.1021/acs.cgd.9b01353
ER  - 

@article{
author = "Živković, Jelena M. and Stanković, Ivana and Ninković, Dragan B. 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 (ACS)",
journal = "Crystal Growth and 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",
pages = "1025-1034",
doi = "10.1021/acs.cgd.9b01353"
}

Živković, J. M., Stanković, I., Ninković, D. B.,& 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 and Design
American Chemical Society (ACS)., 20, 1025-1034.
https://doi.org/10.1021/acs.cgd.9b01353

Živković JM, Stanković I, Ninković DB, 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 and Design. 2020;20:1025-1034.
doi:10.1021/acs.cgd.9b01353 .

Živković, Jelena M., Stanković, Ivana, Ninković, Dragan B., 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 and Design, 20 (2020):1025-1034,
https://doi.org/10.1021/acs.cgd.9b01353 . .

TY  - JOUR
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan
AU  - Stanković, Ivana
AU  - Zarić, Snežana D.
PY  - 2020
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/3977
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3586
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 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.,& 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 I, 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, 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  - Stanković, Ivana
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3519
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 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., 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 I, 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, 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
AU  - Blagojević Filipović, Jelena P.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3520
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 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., 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 I, 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, 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
AU  - Niu, Shuqiang
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3606
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 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., 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 I, 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, 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  - JOUR
AU  - Stanković, Ivana
AU  - Niu, Shuqiang
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2020
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3609
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 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., 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 I, 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, 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  - Ninković, Dragan
AU  - Malenov, Dušan
AU  - Veljković, Dušan
AU  - Andrić, Jelena M.
AU  - Vojislavljević-Vasilev, Dubravka
AU  - Veljković, Ivana
AU  - Zarić, Snežana
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/7502
AB  - We studied noncovalent interactions of metal complexes and described several new types of these interactions. Our studies are 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.Our study of planar metal-chelate rings interactions, based on data in the CSD, showed possibility of chelate ring stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings in crystal structures. The quantum chemical calculations indicate strong stacking interactions of metal-chelate 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. Namely in the crystal structures the interaction distances are shorter, while the calculations show larger interactions energies.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.
C3  - XVII International Conference on Coordination and Bioinorganic Chemistry, Progressive Trends in Coordination, Bioinorganic, and Applied Inorganic Chemistry, Smolenice, Slovakia, June 2-7, 2019
T1  - Noncovalent interactions of metal complexes
SP  - 122
EP  - 122
UR  - https://hdl.handle.net/21.15107/rcub_cer_7502
ER  - 

@conference{
author = "Ninković, Dragan and Malenov, Dušan and Veljković, Dušan and Andrić, Jelena M. and Vojislavljević-Vasilev, Dubravka and Veljković, Ivana and Zarić, Snežana",
year = "2019",
abstract = "We studied noncovalent interactions of metal complexes and described several new types of these interactions. Our studies are 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.Our study of planar metal-chelate rings interactions, based on data in the CSD, showed possibility of chelate ring stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings in crystal structures. The quantum chemical calculations indicate strong stacking interactions of metal-chelate 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. Namely in the crystal structures the interaction distances are shorter, while the calculations show larger interactions energies.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.",
journal = "XVII International Conference on Coordination and Bioinorganic Chemistry, Progressive Trends in Coordination, Bioinorganic, and Applied Inorganic Chemistry, Smolenice, Slovakia, June 2-7, 2019",
title = "Noncovalent interactions of metal complexes",
pages = "122-122",
url = "https://hdl.handle.net/21.15107/rcub_cer_7502"
}

Ninković, D., Malenov, D., Veljković, D., Andrić, J. M., Vojislavljević-Vasilev, D., Veljković, I.,& Zarić, S.. (2019). Noncovalent interactions of metal complexes. in XVII International Conference on Coordination and Bioinorganic Chemistry, Progressive Trends in Coordination, Bioinorganic, and Applied Inorganic Chemistry, Smolenice, Slovakia, June 2-7, 2019, 122-122.
https://hdl.handle.net/21.15107/rcub_cer_7502

Ninković D, Malenov D, Veljković D, Andrić JM, Vojislavljević-Vasilev D, Veljković I, Zarić S. Noncovalent interactions of metal complexes. in XVII International Conference on Coordination and Bioinorganic Chemistry, Progressive Trends in Coordination, Bioinorganic, and Applied Inorganic Chemistry, Smolenice, Slovakia, June 2-7, 2019. 2019;:122-122.
https://hdl.handle.net/21.15107/rcub_cer_7502 .

Ninković, Dragan, Malenov, Dušan, Veljković, Dušan, Andrić, Jelena M., Vojislavljević-Vasilev, Dubravka, Veljković, Ivana, Zarić, Snežana, "Noncovalent interactions of metal complexes" in XVII International Conference on Coordination and Bioinorganic Chemistry, Progressive Trends in Coordination, Bioinorganic, and Applied Inorganic Chemistry, Smolenice, Slovakia, June 2-7, 2019 (2019):122-122,
https://hdl.handle.net/21.15107/rcub_cer_7502 .

TY  - CONF
AU  - Ninković, Dragan B.
AU  - Veljković, Dušan
AU  - Malenov, Dusan P.
AU  - Milovanović, Milan R.
AU  - Stanković, Ivana
AU  - Veljković, Ivana S.
AU  - Medaković, Vesna B.
AU  - Blagojević Filipović, Jelena
AU  - Vojislavljević-Vasilev, Dubravka Z.
AU  - Zarić, Snežana
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6620
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 metal-chelate 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/pi and NH/pi interactions of coordinated in comparison to noncoordianted water and ammonia. The calculations on OH/M interac-tions 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  - Serbian Crystallographic Society
C3  - 26th Conference of the Serbian Crystallographic Society, Abstracts, Silver Lake, Serbia / XXVI Konferencija Srpskog kristalografskog društva, Izvodi radova, Srebrno jezero, Srbija
T1  - Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules
SP  - 9
EP  - 9
UR  - https://hdl.handle.net/21.15107/rcub_cer_6620
ER  - 

@conference{
author = "Ninković, Dragan B. and Veljković, Dušan and Malenov, Dusan P. and Milovanović, Milan R. and Stanković, Ivana and Veljković, Ivana S. and Medaković, Vesna B. and Blagojević Filipović, Jelena and Vojislavljević-Vasilev, Dubravka Z. and Zarić, Snežana",
year = "2019",
abstract = "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 metal-chelate 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/pi and NH/pi interactions of coordinated in comparison to noncoordianted water and ammonia. The calculations on OH/M interac-tions 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 = "Serbian Crystallographic Society",
journal = "26th Conference of the Serbian Crystallographic Society, Abstracts, Silver Lake, Serbia / XXVI Konferencija Srpskog kristalografskog društva, Izvodi radova, Srebrno jezero, Srbija",
title = "Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules",
pages = "9-9",
url = "https://hdl.handle.net/21.15107/rcub_cer_6620"
}

Ninković, D. B., Veljković, D., Malenov, D. P., Milovanović, M. R., Stanković, I., Veljković, I. S., Medaković, V. B., Blagojević Filipović, J., Vojislavljević-Vasilev, D. Z.,& Zarić, S.. (2019). Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules. in 26th Conference of the Serbian Crystallographic Society, Abstracts, Silver Lake, Serbia / XXVI Konferencija Srpskog kristalografskog društva, Izvodi radova, Srebrno jezero, Srbija
Serbian Crystallographic Society., 9-9.
https://hdl.handle.net/21.15107/rcub_cer_6620

Ninković DB, Veljković D, Malenov DP, Milovanović MR, Stanković I, Veljković IS, Medaković VB, Blagojević Filipović J, Vojislavljević-Vasilev DZ, Zarić S. Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules. in 26th Conference of the Serbian Crystallographic Society, Abstracts, Silver Lake, Serbia / XXVI Konferencija Srpskog kristalografskog društva, Izvodi radova, Srebrno jezero, Srbija. 2019;:9-9.
https://hdl.handle.net/21.15107/rcub_cer_6620 .

Ninković, Dragan B., Veljković, Dušan, Malenov, Dusan P., Milovanović, Milan R., Stanković, Ivana, Veljković, Ivana S., Medaković, Vesna B., Blagojević Filipović, Jelena, Vojislavljević-Vasilev, Dubravka Z., Zarić, Snežana, "Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules" in 26th Conference of the Serbian Crystallographic Society, Abstracts, Silver Lake, Serbia / XXVI Konferencija Srpskog kristalografskog društva, Izvodi radova, Srebrno jezero, Srbija (2019):9-9,
https://hdl.handle.net/21.15107/rcub_cer_6620 .

TY  - JOUR
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana
AU  - Zarić, Snežana D.
PY  - 2019
UR  - http://cherry.chem.bg.ac.rs/handle/123456789/3675
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/3521
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 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.,& 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 I, 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, 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
AU  - Zarić, Snežana
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4863
AB  - Figure S1. Distance distribution for hydrogen bonds with coordinated and noncoordinated water, separately for different nucleic bases and positions; Table S1. The calculated interaction energies and distances between five nucleic bases and noncoordinated water molecules, at the B3LYP-D3/def2-TZVP (kcal/mol) and corrected for BSSE), MP2/def2-QZVP (kcal/mol) and noncorrected for BSSE) and CCSD(kcal/mol) and T)/CBS level; Table S2. The calculated interaction energies and distances at the B3LYP-D3/def2-TZVP
level between five nucleic bases and water molecules coordinated to Zn2+ ion; Table S3. A number of hydrogen bonds between nucleic bases and coordinated water, and percentage of [M(H2O)n]x+ complexes, with different kinds of metals. Figure S2. Electrostatic potential maps for the nucleic bases. Figure S3. Distribution of the distance between water oxygen and nucleic base oxygen/nitrogen found in
PDB structures for noncoordinated and coordinated water;
PB  - International Union of Crystallography
T2  - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
T1  - Supplementary information for: "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"
DO  - 10.1107/S2052520619001999/px5010sup1.pdf
ER  - 

@misc{
author = "Andrić, Jelena M. and Stanković, Ivana and Zarić, Snežana",
year = "2019",
abstract = "Figure S1. Distance distribution for hydrogen bonds with coordinated and noncoordinated water, separately for different nucleic bases and positions; Table S1. The calculated interaction energies and distances between five nucleic bases and noncoordinated water molecules, at the B3LYP-D3/def2-TZVP (kcal/mol) and corrected for BSSE), MP2/def2-QZVP (kcal/mol) and noncorrected for BSSE) and CCSD(kcal/mol) and T)/CBS level; Table S2. The calculated interaction energies and distances at the B3LYP-D3/def2-TZVP
level between five nucleic bases and water molecules coordinated to Zn2+ ion; Table S3. A number of hydrogen bonds between nucleic bases and coordinated water, and percentage of [M(H2O)n]x+ complexes, with different kinds of metals. Figure S2. Electrostatic potential maps for the nucleic bases. Figure S3. Distribution of the distance between water oxygen and nucleic base oxygen/nitrogen found in
PDB structures for noncoordinated and coordinated water;",
publisher = "International Union of Crystallography",
journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials",
title = "Supplementary information for: "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"",
doi = "10.1107/S2052520619001999/px5010sup1.pdf"
}

Andrić, J. M., Stanković, I.,& Zarić, S.. (2019). Supplementary information for: "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..
https://doi.org/10.1107/S2052520619001999/px5010sup1.pdf

Andrić JM, Stanković I, Zarić S. Supplementary information for: "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;.
doi:10.1107/S2052520619001999/px5010sup1.pdf .

Andrić, Jelena M., Stanković, Ivana, Zarić, Snežana, "Supplementary information for: "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),
https://doi.org/10.1107/S2052520619001999/px5010sup1.pdf . .

TY  - JOUR
AU  - Antonijević, Ivana
AU  - Malenov, Dušan P.
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2962
AB  - Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol −1 . All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.
PB  - Wiley
T2  - Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
T1  - Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations
VL  - 75
IS  - 1
SP  - 1
EP  - 7
DO  - 10.1107/S2052520618015494
ER  - 

@article{
author = "Antonijević, Ivana and Malenov, Dušan P. and Hall, Michael B. and Zarić, Snežana D.",
year = "2019",
abstract = "Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol −1 . All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.",
publisher = "Wiley",
journal = "Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials",
title = "Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations",
volume = "75",
number = "1",
pages = "1-7",
doi = "10.1107/S2052520618015494"
}

Antonijević, I., Malenov, D. P., Hall, M. B.,& Zarić, S. D.. (2019). Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
Wiley., 75(1), 1-7.
https://doi.org/10.1107/S2052520618015494

Antonijević I, Malenov DP, Hall MB, Zarić SD. Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations. in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials. 2019;75(1):1-7.
doi:10.1107/S2052520618015494 .

Antonijević, Ivana, Malenov, Dušan P., Hall, Michael B., Zarić, Snežana D., "Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75, no. 1 (2019):1-7,
https://doi.org/10.1107/S2052520618015494 . .

TY  - CONF
AU  - Milovanović, Milan R.
AU  - Živković, Jelena M.
AU  - Ninković, Dragan B.
AU  - Stanković, Ivana
AU  - Zarić, Snežana
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6149
AB  - In this study we performed analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD), as well as ab-initio calculations on a range of bond lengths and bond angles of water molecule and water dimers.
PB  - Sociedade Portuguesa de Química
C3  - Book of abstracts - 1st Interantional Conference on Noncovalent Interactions (ICNI 2019),2-6 September, Lisbon, Portugal
T1  - Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study
SP  - P101
UR  - https://hdl.handle.net/21.15107/rcub_cer_6149
ER  - 

@conference{
author = "Milovanović, Milan R. and Živković, Jelena M. and Ninković, Dragan B. and Stanković, Ivana and Zarić, Snežana",
year = "2019",
abstract = "In this study we performed analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD), as well as ab-initio calculations on a range of bond lengths and bond angles of water molecule and water dimers.",
publisher = "Sociedade Portuguesa de Química",
journal = "Book of abstracts - 1st Interantional Conference on Noncovalent Interactions (ICNI 2019),2-6 September, Lisbon, Portugal",
title = "Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study",
pages = "P101",
url = "https://hdl.handle.net/21.15107/rcub_cer_6149"
}

Milovanović, M. R., Živković, J. M., Ninković, D. B., Stanković, I.,& Zarić, S.. (2019). Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study. in Book of abstracts - 1st Interantional Conference on Noncovalent Interactions (ICNI 2019),2-6 September, Lisbon, Portugal
Sociedade Portuguesa de Química., P101.
https://hdl.handle.net/21.15107/rcub_cer_6149

Milovanović MR, Živković JM, Ninković DB, Stanković I, Zarić S. Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study. in Book of abstracts - 1st Interantional Conference on Noncovalent Interactions (ICNI 2019),2-6 September, Lisbon, Portugal. 2019;:P101.
https://hdl.handle.net/21.15107/rcub_cer_6149 .

Milovanović, Milan R., Živković, Jelena M., Ninković, Dragan B., Stanković, Ivana, Zarić, Snežana, "Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study" in Book of abstracts - 1st Interantional Conference on Noncovalent Interactions (ICNI 2019),2-6 September, Lisbon, Portugal (2019):P101,
https://hdl.handle.net/21.15107/rcub_cer_6149 .

TY  - CONF
AU  - Živković, Jelena M.
AU  - Stanković, Ivana M.
AU  - Ninković, Dragan B.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6261
AB  - Here, we searched the Cambridge Structural Database to find interactions of stacking benzene, p-phenol and toluene dimers. Beside this, we calculated interaction energies of phenol and toluene dimers and compared with benzene dimers previously calculated.
PB  - Serbian Chemical Society
C3  - Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade
T1  - Study of phenol and toluene stacking interactions, including interactions at large horizontal displacements, in crystal structures and calculated potential energy surfaces
SP  - 154
EP  - 154
UR  - https://hdl.handle.net/21.15107/rcub_cer_6261
ER  - 

@conference{
author = "Živković, Jelena M. and Stanković, Ivana M. and Ninković, Dragan B. and Zarić, Snežana D.",
year = "2019",
abstract = "Here, we searched the Cambridge Structural Database to find interactions of stacking benzene, p-phenol and toluene dimers. Beside this, we calculated interaction energies of phenol and toluene dimers and compared with benzene dimers previously calculated.",
publisher = "Serbian Chemical Society",
journal = "Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade",
title = "Study of phenol and toluene stacking interactions, including interactions at large horizontal displacements, in crystal structures and calculated potential energy surfaces",
pages = "154-154",
url = "https://hdl.handle.net/21.15107/rcub_cer_6261"
}

Živković, J. M., Stanković, I. M., Ninković, D. B.,& Zarić, S. D.. (2019). Study of phenol and toluene stacking interactions, including interactions at large horizontal displacements, in crystal structures and calculated potential energy surfaces. in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade
Serbian Chemical Society., 154-154.
https://hdl.handle.net/21.15107/rcub_cer_6261

Živković JM, Stanković IM, Ninković DB, Zarić SD. Study of phenol and toluene stacking interactions, including interactions at large horizontal displacements, in crystal structures and calculated potential energy surfaces. in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade. 2019;:154-154.
https://hdl.handle.net/21.15107/rcub_cer_6261 .

Živković, Jelena M., Stanković, Ivana M., Ninković, Dragan B., Zarić, Snežana D., "Study of phenol and toluene stacking interactions, including interactions at large horizontal displacements, in crystal structures and calculated potential energy surfaces" in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade (2019):154-154,
https://hdl.handle.net/21.15107/rcub_cer_6261 .

TY  - CONF
AU  - Stanković, Ivana M.
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2019
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6260
AB  - Amyloids are insoluble proteins of a cross-β structure found as deposits in many diseases. They are largely examined structurally, but there is a lack of a unique structural database for amyloid proteins resolved with atomic resolution. Here, we present a constructed set of amyloid structures found in the Protein Data Bank based on keyword criterion as well as structural features of amyloids described in literature. An amyloid consists of parallel self-assembled β-sheets or coils. The searching filter was performed by python programming. The total number of structures is 109 and it keeps increasing. This database can help further structural general and statistical analysis 
of amyloids.
PB  - Serbian Chemical Society
C3  - Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade
T1  - Amyloid PDB structure set
SP  - 152
EP  - 152
UR  - https://hdl.handle.net/21.15107/rcub_cer_6260
ER  - 

@conference{
author = "Stanković, Ivana M. and Hall, Michael B. and Zarić, Snežana D.",
year = "2019",
abstract = "Amyloids are insoluble proteins of a cross-β structure found as deposits in many diseases. They are largely examined structurally, but there is a lack of a unique structural database for amyloid proteins resolved with atomic resolution. Here, we present a constructed set of amyloid structures found in the Protein Data Bank based on keyword criterion as well as structural features of amyloids described in literature. An amyloid consists of parallel self-assembled β-sheets or coils. The searching filter was performed by python programming. The total number of structures is 109 and it keeps increasing. This database can help further structural general and statistical analysis 
of amyloids.",
publisher = "Serbian Chemical Society",
journal = "Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade",
title = "Amyloid PDB structure set",
pages = "152-152",
url = "https://hdl.handle.net/21.15107/rcub_cer_6260"
}

Stanković, I. M., Hall, M. B.,& Zarić, S. D.. (2019). Amyloid PDB structure set. in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade
Serbian Chemical Society., 152-152.
https://hdl.handle.net/21.15107/rcub_cer_6260

Stanković IM, Hall MB, Zarić SD. Amyloid PDB structure set. in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade. 2019;:152-152.
https://hdl.handle.net/21.15107/rcub_cer_6260 .

Stanković, Ivana M., Hall, Michael B., Zarić, Snežana D., "Amyloid PDB structure set" in Book of Abstracts - 7th Conference of the Young Chemists of Serbia, 2.11.2019, Belgrade (2019):152-152,
https://hdl.handle.net/21.15107/rcub_cer_6260 .

TY  - JOUR
AU  - Andrić, Jelena M.
AU  - Antonijević, Ivana
AU  - Janjić, Goran
AU  - Zarić, Snežana D.
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2333
AB  - Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules
VL  - 24
IS  - 3
SP  - 60
DO  - 10.1007/s00894-017-3570-y
ER  - 

@article{
author = "Andrić, Jelena M. and Antonijević, Ivana and Janjić, Goran and Zarić, Snežana D.",
year = "2018",
abstract = "Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules",
volume = "24",
number = "3",
pages = "60",
doi = "10.1007/s00894-017-3570-y"
}

Andrić, J. M., Antonijević, I., Janjić, G.,& Zarić, S. D.. (2018). Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. in Journal of Molecular Modeling
Springer, New York., 24(3), 60.
https://doi.org/10.1007/s00894-017-3570-y

Andrić JM, Antonijević I, Janjić G, Zarić SD. Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules. in Journal of Molecular Modeling. 2018;24(3):60.
doi:10.1007/s00894-017-3570-y .

Andrić, Jelena M., Antonijević, Ivana, Janjić, Goran, Zarić, Snežana D., "Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules" in Journal of Molecular Modeling, 24, no. 3 (2018):60,
https://doi.org/10.1007/s00894-017-3570-y . .

TY  - CONF
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana
AU  - Zarić, Snežana
PY  - 2018
UR  - https://ojs.pmf.uns.ac.rs/index.php/dbe_serbica/issue/view/25/showToc
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4861
AB  - Hydrogen bond interactions between nucleic bases and water have been analyzed by surveying Protein Data Bank (PDB) and quantum chemical calculations, for the noncoordinated and coordinated water molecule. Python homemade script was used for the PDB search and Gaussian09 program was used for the calculations of interaction energy at MP2/def2-QZVP level on model systems. The results from PDB survey and from the calculations are in agreement:
hydrogen bonds are shorter and stronger when water is bonded to a metal ion.
PB  - Novi sad : Faculty of Sciences. Department of Biology and Ecology
C3  - Biologia Serbica
T1  - Binding of metal ions and water molecules to nucleic bases
VL  - 40
IS  - 1
SP  - 98
EP  - 98
UR  - https://hdl.handle.net/21.15107/rcub_cer_4861
ER  - 

@conference{
author = "Andrić, Jelena M. and Stanković, Ivana and Zarić, Snežana",
year = "2018",
abstract = "Hydrogen bond interactions between nucleic bases and water have been analyzed by surveying Protein Data Bank (PDB) and quantum chemical calculations, for the noncoordinated and coordinated water molecule. Python homemade script was used for the PDB search and Gaussian09 program was used for the calculations of interaction energy at MP2/def2-QZVP level on model systems. The results from PDB survey and from the calculations are in agreement:
hydrogen bonds are shorter and stronger when water is bonded to a metal ion.",
publisher = "Novi sad : Faculty of Sciences. Department of Biology and Ecology",
journal = "Biologia Serbica",
title = "Binding of metal ions and water molecules to nucleic bases",
volume = "40",
number = "1",
pages = "98-98",
url = "https://hdl.handle.net/21.15107/rcub_cer_4861"
}

Andrić, J. M., Stanković, I.,& Zarić, S.. (2018). Binding of metal ions and water molecules to nucleic bases. in Biologia Serbica
Novi sad : Faculty of Sciences. Department of Biology and Ecology., 40(1), 98-98.
https://hdl.handle.net/21.15107/rcub_cer_4861

Andrić JM, Stanković I, Zarić S. Binding of metal ions and water molecules to nucleic bases. in Biologia Serbica. 2018;40(1):98-98.
https://hdl.handle.net/21.15107/rcub_cer_4861 .

Andrić, Jelena M., Stanković, Ivana, Zarić, Snežana, "Binding of metal ions and water molecules to nucleic bases" in Biologia Serbica, 40, no. 1 (2018):98-98,
https://hdl.handle.net/21.15107/rcub_cer_4861 .

TY  - CONF
AU  - Andrić, Jelena M.
AU  - Stanković, Ivana
AU  - Zarić, Snežana
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4862
AB  - Poster presented at Belgrade BioInformatics Conference 2018 - BelBi 2018, Belgrade, Serbia, June 18-22, 2018
T1  - Binding of metal ions and water molecules to nucleic bases
UR  - https://hdl.handle.net/21.15107/rcub_cer_4862
ER  - 

@conference{
author = "Andrić, Jelena M. and Stanković, Ivana and Zarić, Snežana",
year = "2018",
abstract = "Poster presented at Belgrade BioInformatics Conference 2018 - BelBi 2018, Belgrade, Serbia, June 18-22, 2018",
title = "Binding of metal ions and water molecules to nucleic bases",
url = "https://hdl.handle.net/21.15107/rcub_cer_4862"
}

Andrić, J. M., Stanković, I.,& Zarić, S.. (2018). Binding of metal ions and water molecules to nucleic bases. .
https://hdl.handle.net/21.15107/rcub_cer_4862

Andrić JM, Stanković I, Zarić S. Binding of metal ions and water molecules to nucleic bases. 2018;.
https://hdl.handle.net/21.15107/rcub_cer_4862 .

Andrić, Jelena M., Stanković, Ivana, Zarić, Snežana, "Binding of metal ions and water molecules to nucleic bases" (2018),
https://hdl.handle.net/21.15107/rcub_cer_4862 .