Medaković, Vesna

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Authority KeyName Variants
orcid::0000-0001-9022-3168
  • Medaković, Vesna (15)
  • Medaković, Vesna B. (3)
Projects

Author's Bibliography

Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study

Kretić, Danijela S.; Medaković, Vesna B.; Veljković, Ivana S.

(Serbian Crystallographic Society, 2023)

TY  - CONF
AU  - Kretić, Danijela S.
AU  - Medaković, Vesna B.
AU  - Veljković, Ivana S.
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6621
AB  - Noncovalent interactions between S8 molecules have been observed in crystal structures obtained from the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD). Analysis of geometric parameters shows that S8 molecules adopt a parallel-displaced orientation in these crystal structures. This relative position of the S8 rings results in the formation of layers consisting of stacking interactions between the S8 rings.
PB  - Serbian Crystallographic Society
C3  - 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija
T1  - Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study
SP  - 49
EP  - 49
UR  - https://hdl.handle.net/21.15107/rcub_cer_6621
ER  - 
@conference{
author = "Kretić, Danijela S. and Medaković, Vesna B. and Veljković, Ivana S.",
year = "2023",
abstract = "Noncovalent interactions between S8 molecules have been observed in crystal structures obtained from the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD). Analysis of geometric parameters shows that S8 molecules adopt a parallel-displaced orientation in these crystal structures. This relative position of the S8 rings results in the formation of layers consisting of stacking interactions between the S8 rings.",
publisher = "Serbian Crystallographic Society",
journal = "28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija",
title = "Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study",
pages = "49-49",
url = "https://hdl.handle.net/21.15107/rcub_cer_6621"
}
Kretić, D. S., Medaković, V. B.,& Veljković, I. S.. (2023). Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study. in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija
Serbian Crystallographic Society., 49-49.
https://hdl.handle.net/21.15107/rcub_cer_6621
Kretić DS, Medaković VB, Veljković IS. Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study. in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija. 2023;:49-49.
https://hdl.handle.net/21.15107/rcub_cer_6621 .
Kretić, Danijela S., Medaković, Vesna B., Veljković, Ivana S., "Parallel-displaced interactions between S8 rings in crystal structures: comprehensive theoretical study" in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija (2023):49-49,
https://hdl.handle.net/21.15107/rcub_cer_6621 .

Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor

Veljković, Dušan; Malinić, Miroslavka; Veljković, Ivana S.; Medaković, Vesna

(Serbian Crystallographic Society, 2023)

TY  - CONF
AU  - Veljković, Dušan
AU  - Malinić, Miroslavka
AU  - Veljković, Ivana S.
AU  - Medaković, Vesna
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6942
AB  - Here, we analysed crystal stractures and performed interaction energies calculations to evaluate possibility of the apex carbon atom from pyramidane and pyramidane-like molecules to act as hydrogen atom acceptors in hydrogen bonds.
PB  - Serbian Crystallographic Society
C3  - 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija
T1  - Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor
SP  - 15
EP  - 15
UR  - https://hdl.handle.net/21.15107/rcub_cer_6942
ER  - 
@conference{
author = "Veljković, Dušan and Malinić, Miroslavka and Veljković, Ivana S. and Medaković, Vesna",
year = "2023",
abstract = "Here, we analysed crystal stractures and performed interaction energies calculations to evaluate possibility of the apex carbon atom from pyramidane and pyramidane-like molecules to act as hydrogen atom acceptors in hydrogen bonds.",
publisher = "Serbian Crystallographic Society",
journal = "28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija",
title = "Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor",
pages = "15-15",
url = "https://hdl.handle.net/21.15107/rcub_cer_6942"
}
Veljković, D., Malinić, M., Veljković, I. S.,& Medaković, V.. (2023). Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor. in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija
Serbian Crystallographic Society., 15-15.
https://hdl.handle.net/21.15107/rcub_cer_6942
Veljković D, Malinić M, Veljković IS, Medaković V. Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor. in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija. 2023;:15-15.
https://hdl.handle.net/21.15107/rcub_cer_6942 .
Veljković, Dušan, Malinić, Miroslavka, Veljković, Ivana S., Medaković, Vesna, "Strong hydrogen bonds involving carbon atom as hydrogen atom acceptor" in 28th Conference of the Serbian Crystallographic Society, Abstracts, Čačak, Serbia / XXVIII Konferencija Srpskog kristalografskog društva, Izvodi radova, Čačak, Srbija (2023):15-15,
https://hdl.handle.net/21.15107/rcub_cer_6942 .

Relationship between geometry and energy of interactions in S8 dimers

Kretić, Danijela S.; Medaković, Vesna; Veljković, Ivana S.

(Belgrade : Serbian Chemical Society, 2023)

TY  - CONF
AU  - Kretić, Danijela S.
AU  - Medaković, Vesna
AU  - Veljković, Ivana S.
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6827
AB  - Elemental sulfur exists in several allotropes, including α-S8, β-S8, and γ-S8, wherein the arrangement of cyclic S8 molecules varies according to the specific allotrope. Intermolecular interactions among S8 molecules have been detected within crystal structures extracted from the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD). Within these structures, S8 molecules assume a parallel-displaced alignment. Quantum chemical calculations confirm that the parallel-displaced orientation represents the most stable geometry for two S8 molecules. The interaction energy for the most stable geometry is calculated to be ∆ECCSD(T)/CBS= -8.70 kcal/mol. According to the energy decomposition analysis performed using the SAPT 2+(3) method, the dominant attractive force between two S8 molecules arises from dispersion interactions with the significant contribution of electrostatics.
PB  - Belgrade : Serbian Chemical Society
PB  - Belgrade : Serbian Young Chemists’ Club
C3  - 9th Conference of Young Chemists of Serbia, Book of abstracts, 4th November 2023, Novi Sad, Serbia
T1  - Relationship between geometry and energy of interactions in S8 dimers
SP  - 115
EP  - 115
UR  - https://hdl.handle.net/21.15107/rcub_cer_6827
ER  - 
@conference{
author = "Kretić, Danijela S. and Medaković, Vesna and Veljković, Ivana S.",
year = "2023",
abstract = "Elemental sulfur exists in several allotropes, including α-S8, β-S8, and γ-S8, wherein the arrangement of cyclic S8 molecules varies according to the specific allotrope. Intermolecular interactions among S8 molecules have been detected within crystal structures extracted from the Cambridge Structural Database (CSD) and the Inorganic Crystal Structure Database (ICSD). Within these structures, S8 molecules assume a parallel-displaced alignment. Quantum chemical calculations confirm that the parallel-displaced orientation represents the most stable geometry for two S8 molecules. The interaction energy for the most stable geometry is calculated to be ∆ECCSD(T)/CBS= -8.70 kcal/mol. According to the energy decomposition analysis performed using the SAPT 2+(3) method, the dominant attractive force between two S8 molecules arises from dispersion interactions with the significant contribution of electrostatics.",
publisher = "Belgrade : Serbian Chemical Society, Belgrade : Serbian Young Chemists’ Club",
journal = "9th Conference of Young Chemists of Serbia, Book of abstracts, 4th November 2023, Novi Sad, Serbia",
title = "Relationship between geometry and energy of interactions in S8 dimers",
pages = "115-115",
url = "https://hdl.handle.net/21.15107/rcub_cer_6827"
}
Kretić, D. S., Medaković, V.,& Veljković, I. S.. (2023). Relationship between geometry and energy of interactions in S8 dimers. in 9th Conference of Young Chemists of Serbia, Book of abstracts, 4th November 2023, Novi Sad, Serbia
Belgrade : Serbian Chemical Society., 115-115.
https://hdl.handle.net/21.15107/rcub_cer_6827
Kretić DS, Medaković V, Veljković IS. Relationship between geometry and energy of interactions in S8 dimers. in 9th Conference of Young Chemists of Serbia, Book of abstracts, 4th November 2023, Novi Sad, Serbia. 2023;:115-115.
https://hdl.handle.net/21.15107/rcub_cer_6827 .
Kretić, Danijela S., Medaković, Vesna, Veljković, Ivana S., "Relationship between geometry and energy of interactions in S8 dimers" in 9th Conference of Young Chemists of Serbia, Book of abstracts, 4th November 2023, Novi Sad, Serbia (2023):115-115,
https://hdl.handle.net/21.15107/rcub_cer_6827 .

Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures

Kretić, Danijela S.; Medaković, Vesna; Veljković, Ivana S.

(Elsevier, 2023)

TY  - JOUR
AU  - Kretić, Danijela S.
AU  - Medaković, Vesna
AU  - Veljković, Ivana S.
PY  - 2023
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6839
AB  - In this work we conducted a comprehensive study analyzing all crystal structures from the Cambridge Structural Database involving contacts between S8 molecules. Then, we combined those data with high-level quantum chemical calculations. The results revealed that the preferred orientation in the crystal structures is parallel-displaced. Quantum chemical calculations supported this finding, demonstrating that the most stable interaction in the S8 dimer occurs when two molecules adopt a parallel-displaced geometry resembling the one observed in the crystal structures. The interaction in the S8 dimer is very strong, with an energy of −8.70 kcal/mol, calculated at a highly accurate CCSD(T)/CBS level. In this stacking-like geometry, multiple S…S interactions can form, and the NCI analysis indicated an overlap of large surfaces of interacting molecules, significantly contributing to the system's stability. The SAPT2+(3) energy decomposition analysis showed that the predominant attractive force between two S8 molecules is dispersion, although the electrostatic component is also significant.
PB  - Elsevier
T2  - Computational and Theoretical Chemistry
T1  - Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures
VL  - 1230
SP  - 114381
DO  - 10.1016/j.comptc.2023.114381
ER  - 
@article{
author = "Kretić, Danijela S. and Medaković, Vesna and Veljković, Ivana S.",
year = "2023",
abstract = "In this work we conducted a comprehensive study analyzing all crystal structures from the Cambridge Structural Database involving contacts between S8 molecules. Then, we combined those data with high-level quantum chemical calculations. The results revealed that the preferred orientation in the crystal structures is parallel-displaced. Quantum chemical calculations supported this finding, demonstrating that the most stable interaction in the S8 dimer occurs when two molecules adopt a parallel-displaced geometry resembling the one observed in the crystal structures. The interaction in the S8 dimer is very strong, with an energy of −8.70 kcal/mol, calculated at a highly accurate CCSD(T)/CBS level. In this stacking-like geometry, multiple S…S interactions can form, and the NCI analysis indicated an overlap of large surfaces of interacting molecules, significantly contributing to the system's stability. The SAPT2+(3) energy decomposition analysis showed that the predominant attractive force between two S8 molecules is dispersion, although the electrostatic component is also significant.",
publisher = "Elsevier",
journal = "Computational and Theoretical Chemistry",
title = "Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures",
volume = "1230",
pages = "114381",
doi = "10.1016/j.comptc.2023.114381"
}
Kretić, D. S., Medaković, V.,& Veljković, I. S.. (2023). Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures. in Computational and Theoretical Chemistry
Elsevier., 1230, 114381.
https://doi.org/10.1016/j.comptc.2023.114381
Kretić DS, Medaković V, Veljković IS. Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures. in Computational and Theoretical Chemistry. 2023;1230:114381.
doi:10.1016/j.comptc.2023.114381 .
Kretić, Danijela S., Medaković, Vesna, Veljković, Ivana S., "Interplay between energy and geometry of parallel-displaced interactions in S8 dimer structures" in Computational and Theoretical Chemistry, 1230 (2023):114381,
https://doi.org/10.1016/j.comptc.2023.114381 . .

Study of noncovalent interactions using crystal structure data in the Cambridge Structural Database

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.

(The International Union of Crystallography (IUCr), 2021)

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 . .

Noncovalent Interactions оf Metal Complexes аnd Aromatic Molecules

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

(Serbian Crystallographic Society, 2019)

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 .

Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]

Malenov, Dušan P.; Janjić, Goran; Medaković, Vesna; Hall, Michael B.; Zarić, Snežana D.

(Elsevier Science Sa, Lausanne, 2018)

TY  - JOUR
AU  - Malenov, Dušan P.
AU  - Janjić, Goran
AU  - Medaković, Vesna
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2402
PB  - Elsevier Science Sa, Lausanne
T2  - Coordination Chemistry Reviews
T1  - Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]
VL  - 376
SP  - 590
EP  - 590
DO  - 10.1016/j.ccr.2018.06.009
ER  - 
@article{
author = "Malenov, Dušan P. and Janjić, Goran and Medaković, Vesna and Hall, Michael B. and Zarić, Snežana D.",
year = "2018",
publisher = "Elsevier Science Sa, Lausanne",
journal = "Coordination Chemistry Reviews",
title = "Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]",
volume = "376",
pages = "590-590",
doi = "10.1016/j.ccr.2018.06.009"
}
Malenov, D. P., Janjić, G., Medaković, V., Hall, M. B.,& Zarić, S. D.. (2018). Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]. in Coordination Chemistry Reviews
Elsevier Science Sa, Lausanne., 376, 590-590.
https://doi.org/10.1016/j.ccr.2018.06.009
Malenov DP, Janjić G, Medaković V, Hall MB, Zarić SD. Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]. in Coordination Chemistry Reviews. 2018;376:590-590.
doi:10.1016/j.ccr.2018.06.009 .
Malenov, Dušan P., Janjić, Goran, Medaković, Vesna, Hall, Michael B., Zarić, Snežana D., "Corrigendum to “Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes” [Coord. Chem. Rev. 345 (2017) 318–341]" in Coordination Chemistry Reviews, 376 (2018):590-590,
https://doi.org/10.1016/j.ccr.2018.06.009 . .
1
8

Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes

Malenov, Dušan P.; Janjić, Goran; Medaković, Vesna; Hall, Michael B.; Zarić, Snežana D.

(Elsevier Science Sa, Lausanne, 2017)

TY  - JOUR
AU  - Malenov, Dušan P.
AU  - Janjić, Goran
AU  - Medaković, Vesna
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2017
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2234
AB  - Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactions, the orientation between chelate and aryl ring is a parallel-displaced orientation, like stacking interactions between aromatic molecules. In fused systems containing chelate and aryl rings, the aryl rings prefer to stack with the chelate rather than with other aryl rings. Quantum chemical calculations show that chelate-aryl stacking is stronger than aryl-aryl stacking. Interaction energies of six-membered chelates of the acetylacetonato type with benzene exceed -6 kcal/mol (CCSD(T)/CBS), more that twice as strong as that for two benzene molecules. Further analysis of the CSD has shown that chelate rings, both isolated and fused stack with other chelate rings. These chelate-chelate stacking interactions can have both face-to-face and parallel-displaced geometries, unlike the stacking interactions between aromatic molecules, for which face-to-face geometry is not typical. Chelate-chelate stacking is stronger than aryl-aryl stacking and stronger even than chelate-aryl stacking. Stacking energies between six-membered chelates of acetylacetonato type exceed -9 kcal/mol, while those between five-membered dithiolene chelates are even stronger. Calculated interaction energies and analysis of supramolecular structures have shown that chelate-chelate and chelate-aryl stacking must be considered in understanding the packing and organization of supramolecular systems and crystal engineering.
PB  - Elsevier Science Sa, Lausanne
T2  - Coordination Chemistry Reviews
T1  - Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes
VL  - 345
SP  - 318
EP  - 341
DO  - 10.1016/j.ccr.2016.12.020
ER  - 
@article{
author = "Malenov, Dušan P. and Janjić, Goran and Medaković, Vesna and Hall, Michael B. and Zarić, Snežana D.",
year = "2017",
abstract = "Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactions, the orientation between chelate and aryl ring is a parallel-displaced orientation, like stacking interactions between aromatic molecules. In fused systems containing chelate and aryl rings, the aryl rings prefer to stack with the chelate rather than with other aryl rings. Quantum chemical calculations show that chelate-aryl stacking is stronger than aryl-aryl stacking. Interaction energies of six-membered chelates of the acetylacetonato type with benzene exceed -6 kcal/mol (CCSD(T)/CBS), more that twice as strong as that for two benzene molecules. Further analysis of the CSD has shown that chelate rings, both isolated and fused stack with other chelate rings. These chelate-chelate stacking interactions can have both face-to-face and parallel-displaced geometries, unlike the stacking interactions between aromatic molecules, for which face-to-face geometry is not typical. Chelate-chelate stacking is stronger than aryl-aryl stacking and stronger even than chelate-aryl stacking. Stacking energies between six-membered chelates of acetylacetonato type exceed -9 kcal/mol, while those between five-membered dithiolene chelates are even stronger. Calculated interaction energies and analysis of supramolecular structures have shown that chelate-chelate and chelate-aryl stacking must be considered in understanding the packing and organization of supramolecular systems and crystal engineering.",
publisher = "Elsevier Science Sa, Lausanne",
journal = "Coordination Chemistry Reviews",
title = "Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes",
volume = "345",
pages = "318-341",
doi = "10.1016/j.ccr.2016.12.020"
}
Malenov, D. P., Janjić, G., Medaković, V., Hall, M. B.,& Zarić, S. D.. (2017). Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes. in Coordination Chemistry Reviews
Elsevier Science Sa, Lausanne., 345, 318-341.
https://doi.org/10.1016/j.ccr.2016.12.020
Malenov DP, Janjić G, Medaković V, Hall MB, Zarić SD. Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes. in Coordination Chemistry Reviews. 2017;345:318-341.
doi:10.1016/j.ccr.2016.12.020 .
Malenov, Dušan P., Janjić, Goran, Medaković, Vesna, Hall, Michael B., Zarić, Snežana D., "Noncovalent bonding: Stacking interactions of chelate rings of transition metal complexes" in Coordination Chemistry Reviews, 345 (2017):318-341,
https://doi.org/10.1016/j.ccr.2016.12.020 . .
1
86
72
82

Crystallographic study on CH/O interactions of aromatic CH donors within proteins

Dragelj, J.Lj.; Stanković, Ivana M.; Božinovski, D.M.; Meyer, T.; Veljković, Dušan; Medaković, Vesna B.; Knapp, Ernst Walter; Zarić, Snežana D.

(Belgrade : The Bioinformatics Research Group, University of Belgrade - Faculty of Mathematics, 2016)

TY  - CONF
AU  - Dragelj, J.Lj.
AU  - Stanković, Ivana M.
AU  - Božinovski, D.M.
AU  - Meyer, T.
AU  - Veljković, Dušan
AU  - Medaković, Vesna B.
AU  - Knapp, Ernst Walter
AU  - Zarić, Snežana D.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4858
AB  - CH/O interactions represent weak hydrogen bonds that stabilize protein structures
where they contribute up to 25% among the total number of detected
hydrogen bonds. Previously, we showed that CH/O interactions do not show
strong preference for linear contacts and that the energy of CH/O interactions
of aromatic CH donors depends on the type of atom or group in ortho-position to
the interacting CH group [1, 2]. In this work, CH/O interactions of aromatic CH
donors within proteins have been studied by analyzing the data in the Protein
Data Bank (PDB) and by quantum chemical calculations of electrostatic potentials.
The CH/O interactions were studied between three aromatic amino acids;
phenylalanine, tyrosine and tryptophan, with several acceptors.
The analysis of the distribution of the CHO angle in the crystal structures from
the PDB indicates no preference for linear CH/O interactions between aromatic
donors and acceptors in protein structures. Although there is no tendency for
linear CH/O interactions, there is no significant number of bifurcated CH/O
interactions. The analyses also indicate an influence of simultaneous classical
hydrogen bonds. The influence is particularly observed in case of tyrosine. The
hydroxyl group of aromatic ring of tyrosine plays an important role by forming
a simultaneous classical hydrogen bond along with CH/O interaction in orthoposition
to the OH substituent. These investigations could help in future CH/O
interactions studies in proteins or other proteic systems.
PB  - Belgrade : The Bioinformatics Research Group, University of Belgrade - Faculty of Mathematics
C3  - Book of Abstracts - Belgrade BioInformatics Conference 2016, BelBI2016
T1  - Crystallographic study on CH/O interactions of aromatic CH donors within proteins
SP  - 119
EP  - 119
UR  - https://hdl.handle.net/21.15107/rcub_cer_4858
ER  - 
@conference{
author = "Dragelj, J.Lj. and Stanković, Ivana M. and Božinovski, D.M. and Meyer, T. and Veljković, Dušan and Medaković, Vesna B. and Knapp, Ernst Walter and Zarić, Snežana D.",
year = "2016",
abstract = "CH/O interactions represent weak hydrogen bonds that stabilize protein structures
where they contribute up to 25% among the total number of detected
hydrogen bonds. Previously, we showed that CH/O interactions do not show
strong preference for linear contacts and that the energy of CH/O interactions
of aromatic CH donors depends on the type of atom or group in ortho-position to
the interacting CH group [1, 2]. In this work, CH/O interactions of aromatic CH
donors within proteins have been studied by analyzing the data in the Protein
Data Bank (PDB) and by quantum chemical calculations of electrostatic potentials.
The CH/O interactions were studied between three aromatic amino acids;
phenylalanine, tyrosine and tryptophan, with several acceptors.
The analysis of the distribution of the CHO angle in the crystal structures from
the PDB indicates no preference for linear CH/O interactions between aromatic
donors and acceptors in protein structures. Although there is no tendency for
linear CH/O interactions, there is no significant number of bifurcated CH/O
interactions. The analyses also indicate an influence of simultaneous classical
hydrogen bonds. The influence is particularly observed in case of tyrosine. The
hydroxyl group of aromatic ring of tyrosine plays an important role by forming
a simultaneous classical hydrogen bond along with CH/O interaction in orthoposition
to the OH substituent. These investigations could help in future CH/O
interactions studies in proteins or other proteic systems.",
publisher = "Belgrade : The Bioinformatics Research Group, University of Belgrade - Faculty of Mathematics",
journal = "Book of Abstracts - Belgrade BioInformatics Conference 2016, BelBI2016",
title = "Crystallographic study on CH/O interactions of aromatic CH donors within proteins",
pages = "119-119",
url = "https://hdl.handle.net/21.15107/rcub_cer_4858"
}
Dragelj, J.Lj., Stanković, I. M., Božinovski, D.M., Meyer, T., Veljković, D., Medaković, V. B., Knapp, E. W.,& Zarić, S. D.. (2016). Crystallographic study on CH/O interactions of aromatic CH donors within proteins. in Book of Abstracts - Belgrade BioInformatics Conference 2016, BelBI2016
Belgrade : The Bioinformatics Research Group, University of Belgrade - Faculty of Mathematics., 119-119.
https://hdl.handle.net/21.15107/rcub_cer_4858
Dragelj J, Stanković IM, Božinovski D, Meyer T, Veljković D, Medaković VB, Knapp EW, Zarić SD. Crystallographic study on CH/O interactions of aromatic CH donors within proteins. in Book of Abstracts - Belgrade BioInformatics Conference 2016, BelBI2016. 2016;:119-119.
https://hdl.handle.net/21.15107/rcub_cer_4858 .
Dragelj, J.Lj., Stanković, Ivana M., Božinovski, D.M., Meyer, T., Veljković, Dušan, Medaković, Vesna B., Knapp, Ernst Walter, Zarić, Snežana D., "Crystallographic study on CH/O interactions of aromatic CH donors within proteins" in Book of Abstracts - Belgrade BioInformatics Conference 2016, BelBI2016 (2016):119-119,
https://hdl.handle.net/21.15107/rcub_cer_4858 .

C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study

Dragelj, Jovan Lj; Stanković, Ivana; Bozinovski, Dragana M; Meyer, Tim; Veljković, Dušan; Medaković, Vesna; Knapp, Ernst-Walter; Zarić, Snežana D.

(American Chemical Society (ACS), 2016)

TY  - JOUR
AU  - Dragelj, Jovan Lj
AU  - Stanković, Ivana
AU  - Bozinovski, Dragana M
AU  - Meyer, Tim
AU  - Veljković, Dušan
AU  - Medaković, Vesna
AU  - Knapp, Ernst-Walter
AU  - Zarić, Snežana D.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2035
AB  - C-H/O interactions of aromatic C-H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C-H/O interactions were studied between aromatic donors; phenylalanine, tyrosine, and tryptophan and the acceptors; alcohol, backbone amide, and side-chain amide groups. The analysis of the C-H-O angle indicates that protein C-H donors do not show a preference for linear contacts. Although there is no tendency for linear C-H/O interactions, there are only around 3% of bifurcated C-H/O interactions. Furthermore, the analyses of the C-H/O interactions indicate an influence of simultaneous classical hydrogen bonds, especially for the tyrosine systems. The calculated electrostatic potential maps for model systems can explain the results of the crystallographic analysis. These results can be important for recognizing the C-H/O interaction of aromatic rings in the crystal structures of proteic systems.
PB  - American Chemical Society (ACS)
T2  - Crystal Growth & Design
T1  - C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study
VL  - 16
IS  - 4
SP  - 1948
EP  - 1957
DO  - 10.1021/acs.cgd.5b01543
ER  - 
@article{
author = "Dragelj, Jovan Lj and Stanković, Ivana and Bozinovski, Dragana M and Meyer, Tim and Veljković, Dušan and Medaković, Vesna and Knapp, Ernst-Walter and Zarić, Snežana D.",
year = "2016",
abstract = "C-H/O interactions of aromatic C-H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C-H/O interactions were studied between aromatic donors; phenylalanine, tyrosine, and tryptophan and the acceptors; alcohol, backbone amide, and side-chain amide groups. The analysis of the C-H-O angle indicates that protein C-H donors do not show a preference for linear contacts. Although there is no tendency for linear C-H/O interactions, there are only around 3% of bifurcated C-H/O interactions. Furthermore, the analyses of the C-H/O interactions indicate an influence of simultaneous classical hydrogen bonds, especially for the tyrosine systems. The calculated electrostatic potential maps for model systems can explain the results of the crystallographic analysis. These results can be important for recognizing the C-H/O interaction of aromatic rings in the crystal structures of proteic systems.",
publisher = "American Chemical Society (ACS)",
journal = "Crystal Growth & Design",
title = "C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study",
volume = "16",
number = "4",
pages = "1948-1957",
doi = "10.1021/acs.cgd.5b01543"
}
Dragelj, J. L., Stanković, I., Bozinovski, D. M., Meyer, T., Veljković, D., Medaković, V., Knapp, E.,& Zarić, S. D.. (2016). C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study. in Crystal Growth & Design
American Chemical Society (ACS)., 16(4), 1948-1957.
https://doi.org/10.1021/acs.cgd.5b01543
Dragelj JL, Stanković I, Bozinovski DM, Meyer T, Veljković D, Medaković V, Knapp E, Zarić SD. C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study. in Crystal Growth & Design. 2016;16(4):1948-1957.
doi:10.1021/acs.cgd.5b01543 .
Dragelj, Jovan Lj, Stanković, Ivana, Bozinovski, Dragana M, Meyer, Tim, Veljković, Dušan, Medaković, Vesna, Knapp, Ernst-Walter, Zarić, Snežana D., "C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study" in Crystal Growth & Design, 16, no. 4 (2016):1948-1957,
https://doi.org/10.1021/acs.cgd.5b01543 . .
1
20
16
17

C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study

Dragelj, Jovan Lj; Stanković, Ivana; Bozinovski, Dragana M; Meyer, Tim; Veljković, Dušan; Medaković, Vesna; Knapp, Ernst-Walter; Zarić, Snežana D.

(American Chemical Society (ACS), 2016)

TY  - JOUR
AU  - Dragelj, Jovan Lj
AU  - Stanković, Ivana
AU  - Bozinovski, Dragana M
AU  - Meyer, Tim
AU  - Veljković, Dušan
AU  - Medaković, Vesna
AU  - Knapp, Ernst-Walter
AU  - Zarić, Snežana D.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/4387
AB  - C-H/O interactions of aromatic C-H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C-H/O interactions were studied between aromatic donors; phenylalanine, tyrosine, and tryptophan and the acceptors; alcohol, backbone amide, and side-chain amide groups. The analysis of the C-H-O angle indicates that protein C-H donors do not show a preference for linear contacts. Although there is no tendency for linear C-H/O interactions, there are only around 3% of bifurcated C-H/O interactions. Furthermore, the analyses of the C-H/O interactions indicate an influence of simultaneous classical hydrogen bonds, especially for the tyrosine systems. The calculated electrostatic potential maps for model systems can explain the results of the crystallographic analysis. These results can be important for recognizing the C-H/O interaction of aromatic rings in the crystal structures of proteic systems.
PB  - American Chemical Society (ACS)
T2  - Crystal Growth & Design
T1  - C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study
VL  - 16
IS  - 4
SP  - 1948
EP  - 1957
DO  - 10.1021/acs.cgd.5b01543
ER  - 
@article{
author = "Dragelj, Jovan Lj and Stanković, Ivana and Bozinovski, Dragana M and Meyer, Tim and Veljković, Dušan and Medaković, Vesna and Knapp, Ernst-Walter and Zarić, Snežana D.",
year = "2016",
abstract = "C-H/O interactions of aromatic C-H donors within proteins have been studied by analyzing the data in the Protein Data Bank (PDB). The C-H/O interactions were studied between aromatic donors; phenylalanine, tyrosine, and tryptophan and the acceptors; alcohol, backbone amide, and side-chain amide groups. The analysis of the C-H-O angle indicates that protein C-H donors do not show a preference for linear contacts. Although there is no tendency for linear C-H/O interactions, there are only around 3% of bifurcated C-H/O interactions. Furthermore, the analyses of the C-H/O interactions indicate an influence of simultaneous classical hydrogen bonds, especially for the tyrosine systems. The calculated electrostatic potential maps for model systems can explain the results of the crystallographic analysis. These results can be important for recognizing the C-H/O interaction of aromatic rings in the crystal structures of proteic systems.",
publisher = "American Chemical Society (ACS)",
journal = "Crystal Growth & Design",
title = "C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study",
volume = "16",
number = "4",
pages = "1948-1957",
doi = "10.1021/acs.cgd.5b01543"
}
Dragelj, J. L., Stanković, I., Bozinovski, D. M., Meyer, T., Veljković, D., Medaković, V., Knapp, E.,& Zarić, S. D.. (2016). C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study. in Crystal Growth & Design
American Chemical Society (ACS)., 16(4), 1948-1957.
https://doi.org/10.1021/acs.cgd.5b01543
Dragelj JL, Stanković I, Bozinovski DM, Meyer T, Veljković D, Medaković V, Knapp E, Zarić SD. C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study. in Crystal Growth & Design. 2016;16(4):1948-1957.
doi:10.1021/acs.cgd.5b01543 .
Dragelj, Jovan Lj, Stanković, Ivana, Bozinovski, Dragana M, Meyer, Tim, Veljković, Dušan, Medaković, Vesna, Knapp, Ernst-Walter, Zarić, Snežana D., "C-H/O Interactions of Aromatic CH Donors within Proteins: A Crystallographic Study" in Crystal Growth & Design, 16, no. 4 (2016):1948-1957,
https://doi.org/10.1021/acs.cgd.5b01543 . .
1
20
16
17

Nature of the Water/Aromatic Parallel Alignment Interactions

Mitoraj, Mariusz P; Janjić, Goran; Medaković, Vesna; Veljković, Dušan; Michalak, Artur; Zarić, Snežana D.; Milčić, Miloš

(Wiley, Hoboken, 2015)

TY  - JOUR
AU  - Mitoraj, Mariusz P
AU  - Janjić, Goran
AU  - Medaković, Vesna
AU  - Veljković, Dušan
AU  - Michalak, Artur
AU  - Zarić, Snežana D.
AU  - Milčić, Miloš
PY  - 2015
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1784
AB  - The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its OH bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to E-CCSD(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CHO water/benzene interactions, but weaker than OH interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type sigma*(OH) between the monomers also exists.
PB  - Wiley, Hoboken
T2  - Journal of Computational Chemistry
T1  - Nature of the Water/Aromatic Parallel Alignment Interactions
VL  - 36
IS  - 3
SP  - 171
EP  - 180
DO  - 10.1002/jcc.23783
ER  - 
@article{
author = "Mitoraj, Mariusz P and Janjić, Goran and Medaković, Vesna and Veljković, Dušan and Michalak, Artur and Zarić, Snežana D. and Milčić, Miloš",
year = "2015",
abstract = "The water/aromatic parallel alignment interactions are interactions where the water molecule or one of its OH bonds is parallel to the aromatic ring plane. The calculated energies of the interactions are significant, up to E-CCSD(T)(limit) = -2.45 kcal mol(-1) at large horizontal displacement, out of benzene ring and CH bond region. These interactions are stronger than CHO water/benzene interactions, but weaker than OH interactions. To investigate the nature of water/aromatic parallel alignment interactions, energy decomposition methods, symmetry-adapted perturbation theory, and extended transition state-natural orbitals for chemical valence (NOCV), were used. The calculations have shown that, for the complexes at large horizontal displacements, major contribution to interaction energy comes from electrostatic interactions between monomers, and for the complexes at small horizontal displacements, dispersion interactions are dominant binding force. The NOCV-based analysis has shown that in structures with strong interaction energies charge transfer of the type sigma*(OH) between the monomers also exists.",
publisher = "Wiley, Hoboken",
journal = "Journal of Computational Chemistry",
title = "Nature of the Water/Aromatic Parallel Alignment Interactions",
volume = "36",
number = "3",
pages = "171-180",
doi = "10.1002/jcc.23783"
}
Mitoraj, M. P., Janjić, G., Medaković, V., Veljković, D., Michalak, A., Zarić, S. D.,& Milčić, M.. (2015). Nature of the Water/Aromatic Parallel Alignment Interactions. in Journal of Computational Chemistry
Wiley, Hoboken., 36(3), 171-180.
https://doi.org/10.1002/jcc.23783
Mitoraj MP, Janjić G, Medaković V, Veljković D, Michalak A, Zarić SD, Milčić M. Nature of the Water/Aromatic Parallel Alignment Interactions. in Journal of Computational Chemistry. 2015;36(3):171-180.
doi:10.1002/jcc.23783 .
Mitoraj, Mariusz P, Janjić, Goran, Medaković, Vesna, Veljković, Dušan, Michalak, Artur, Zarić, Snežana D., Milčić, Miloš, "Nature of the Water/Aromatic Parallel Alignment Interactions" in Journal of Computational Chemistry, 36, no. 3 (2015):171-180,
https://doi.org/10.1002/jcc.23783 . .
9
9
10

Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water

Vojislavljevic-Vasilev, Dubravka Z; Janjić, Goran; Medaković, Vesna; Blagojevic, Jelena P; Zarić, Snežana D.

(Wiley-V C H Verlag Gmbh, Weinheim, 2014)

TY  - JOUR
AU  - Vojislavljevic-Vasilev, Dubravka Z
AU  - Janjić, Goran
AU  - Medaković, Vesna
AU  - Blagojevic, Jelena P
AU  - Zarić, Snežana D.
PY  - 2014
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1570
AB  - The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/pi interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one O-H bond is parallel to the aromatic ring, whereas the other O-H bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/pi orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1). The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.
PB  - Wiley-V C H Verlag Gmbh, Weinheim
T2  - Chemphyschem
T1  - Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water
VL  - 15
IS  - 11
SP  - 2386
EP  - 2396
DO  - 10.1002/cphc.201402004
ER  - 
@article{
author = "Vojislavljevic-Vasilev, Dubravka Z and Janjić, Goran and Medaković, Vesna and Blagojevic, Jelena P and Zarić, Snežana D.",
year = "2014",
abstract = "The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/pi interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one O-H bond is parallel to the aromatic ring, whereas the other O-H bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/pi orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1). The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.",
publisher = "Wiley-V C H Verlag Gmbh, Weinheim",
journal = "Chemphyschem",
title = "Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water",
volume = "15",
number = "11",
pages = "2386-2396",
doi = "10.1002/cphc.201402004"
}
Vojislavljevic-Vasilev, D. Z., Janjić, G., Medaković, V., Blagojevic, J. P.,& Zarić, S. D.. (2014). Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water. in Chemphyschem
Wiley-V C H Verlag Gmbh, Weinheim., 15(11), 2386-2396.
https://doi.org/10.1002/cphc.201402004
Vojislavljevic-Vasilev DZ, Janjić G, Medaković V, Blagojevic JP, Zarić SD. Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water. in Chemphyschem. 2014;15(11):2386-2396.
doi:10.1002/cphc.201402004 .
Vojislavljevic-Vasilev, Dubravka Z, Janjić, Goran, Medaković, Vesna, Blagojevic, Jelena P, Zarić, Snežana D., "Parallel Water/Aromatic Interactions of Non-Coordinated and Coordinated Water" in Chemphyschem, 15, no. 11 (2014):2386-2396,
https://doi.org/10.1002/cphc.201402004 . .
5
4
5

Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions

Janjić, Goran; Milčić, Miloš; Medaković, Vesna

(Univ Babes-Bolyai, Cluj-Napoca, 2013)

TY  - JOUR
AU  - Janjić, Goran
AU  - Milčić, Miloš
AU  - Medaković, Vesna
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1246
AB  - The parallel alignment interactions between water molecules and C-6-aryl groups in crystal structures and influence of supramolecular structures in crystals were studied by analyzing data in the Cambridge Structural Database (CSD). Analyses of crystal structures from the CSD reveal that the water/aromatic parallel alignment interactions, where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane, are very frequent at large horizontal displacements. These orientations, observed in crystal structures, were compared with the results of ab initio calculations and explained by influence of supramolecular structures in crystals.
PB  - Univ Babes-Bolyai, Cluj-Napoca
T2  - Studia Universitatis Babes-Bolyai Chemia
T1  - Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions
VL  - 58
IS  - 3
SP  - 143
EP  - 154
UR  - https://hdl.handle.net/21.15107/rcub_cherry_1856
ER  - 
@article{
author = "Janjić, Goran and Milčić, Miloš and Medaković, Vesna",
year = "2013",
abstract = "The parallel alignment interactions between water molecules and C-6-aryl groups in crystal structures and influence of supramolecular structures in crystals were studied by analyzing data in the Cambridge Structural Database (CSD). Analyses of crystal structures from the CSD reveal that the water/aromatic parallel alignment interactions, where the water molecule or one of its O-H bonds is parallel to the aromatic ring plane, are very frequent at large horizontal displacements. These orientations, observed in crystal structures, were compared with the results of ab initio calculations and explained by influence of supramolecular structures in crystals.",
publisher = "Univ Babes-Bolyai, Cluj-Napoca",
journal = "Studia Universitatis Babes-Bolyai Chemia",
title = "Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions",
volume = "58",
number = "3",
pages = "143-154",
url = "https://hdl.handle.net/21.15107/rcub_cherry_1856"
}
Janjić, G., Milčić, M.,& Medaković, V.. (2013). Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions. in Studia Universitatis Babes-Bolyai Chemia
Univ Babes-Bolyai, Cluj-Napoca., 58(3), 143-154.
https://hdl.handle.net/21.15107/rcub_cherry_1856
Janjić G, Milčić M, Medaković V. Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions. in Studia Universitatis Babes-Bolyai Chemia. 2013;58(3):143-154.
https://hdl.handle.net/21.15107/rcub_cherry_1856 .
Janjić, Goran, Milčić, Miloš, Medaković, Vesna, "Influence of supramolecular structure in the crystals on water/aromatic parallel alignment interactions" in Studia Universitatis Babes-Bolyai Chemia, 58, no. 3 (2013):143-154,
https://hdl.handle.net/21.15107/rcub_cherry_1856 .
2

CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors

Medaković, Vesna; Bogdanović, Goran A.; Milčić, Miloš; Janjić, Goran; Zarić, Snežana D.

(Elsevier Science Inc, New York, 2012)

TY  - JOUR
AU  - Medaković, Vesna
AU  - Bogdanović, Goran A.
AU  - Milčić, Miloš
AU  - Janjić, Goran
AU  - Zarić, Snežana D.
PY  - 2012
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1121
AB  - CH/pi interactions in metal porphyrinato complexes were studied by analyzing data in crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The analysis of the data in the CSD shows that both five-membered pyrrole and six-membered chelate rings form CH/pi interactions. The interactions occur more frequently with five-membered rings. The analysis of distances in crystal structures and calculated energies show stronger interactions with six-membered chelate rings, indicating that a larger number of interactions with five-membered rings are not the consequence of stronger interactions, but better accessibility of five-membered pyrrole rings. The calculated energies of the interactions with positions in six-membered rings are -2.09 to -2.83 kcal/mol, while the energies with five-membered rings are -2.05 to -2.26 kcal/mol. The results reveal that stronger interactions of six-membered rings are the consequence of stronger electrostatic interactions. Substituents on the porphyrin ring significantly strengthen the interactions. Substituents on the six-membered ring strengthen the interaction energy by about 20%. The results show that CH/pi interactions play an important role in molecular recognition of metalloporphyrins. The significant influence of the substituents on interaction energies can be very important for the design of model systems in bioinorganic chemistry.
PB  - Elsevier Science Inc, New York
T2  - Journal of Inorganic Biochemistry
T1  - CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors
VL  - 117
SP  - 157
EP  - 163
DO  - 10.1016/j.jinorgbio.2012.09.002
ER  - 
@article{
author = "Medaković, Vesna and Bogdanović, Goran A. and Milčić, Miloš and Janjić, Goran and Zarić, Snežana D.",
year = "2012",
abstract = "CH/pi interactions in metal porphyrinato complexes were studied by analyzing data in crystal structures from the Cambridge Structural Database (CSD) and by quantum chemical calculations. The analysis of the data in the CSD shows that both five-membered pyrrole and six-membered chelate rings form CH/pi interactions. The interactions occur more frequently with five-membered rings. The analysis of distances in crystal structures and calculated energies show stronger interactions with six-membered chelate rings, indicating that a larger number of interactions with five-membered rings are not the consequence of stronger interactions, but better accessibility of five-membered pyrrole rings. The calculated energies of the interactions with positions in six-membered rings are -2.09 to -2.83 kcal/mol, while the energies with five-membered rings are -2.05 to -2.26 kcal/mol. The results reveal that stronger interactions of six-membered rings are the consequence of stronger electrostatic interactions. Substituents on the porphyrin ring significantly strengthen the interactions. Substituents on the six-membered ring strengthen the interaction energy by about 20%. The results show that CH/pi interactions play an important role in molecular recognition of metalloporphyrins. The significant influence of the substituents on interaction energies can be very important for the design of model systems in bioinorganic chemistry.",
publisher = "Elsevier Science Inc, New York",
journal = "Journal of Inorganic Biochemistry",
title = "CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors",
volume = "117",
pages = "157-163",
doi = "10.1016/j.jinorgbio.2012.09.002"
}
Medaković, V., Bogdanović, G. A., Milčić, M., Janjić, G.,& Zarić, S. D.. (2012). CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors. in Journal of Inorganic Biochemistry
Elsevier Science Inc, New York., 117, 157-163.
https://doi.org/10.1016/j.jinorgbio.2012.09.002
Medaković V, Bogdanović GA, Milčić M, Janjić G, Zarić SD. CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors. in Journal of Inorganic Biochemistry. 2012;117:157-163.
doi:10.1016/j.jinorgbio.2012.09.002 .
Medaković, Vesna, Bogdanović, Goran A., Milčić, Miloš, Janjić, Goran, Zarić, Snežana D., "CH/pi interactions in metal-porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors" in Journal of Inorganic Biochemistry, 117 (2012):157-163,
https://doi.org/10.1016/j.jinorgbio.2012.09.002 . .
11
12
12

XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins

Stojanović, Srđan; Medaković, Vesna; Predović, Goran; Beljanski, Miloš; Zarić, Snežana

(Springer, 2007)

TY  - JOUR
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Beljanski, Miloš
AU  - Zarić, Snežana
PY  - 2007
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6507
AB  - Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.
PB  - Springer
T2  - Journal of Biological Inorganic Chemistry
T1  - XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins
VL  - 12
SP  - 1063
EP  - 1071
DO  - 10.1007/s00775-007-0276-0
ER  - 
@article{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Beljanski, Miloš and Zarić, Snežana",
year = "2007",
abstract = "Searching structures of porphyrin-containing
proteins from the Protein Data Bank revealed that the
p system of every porphyrin ring is involved in XH/p
interactions, with most of the porphyrins having several
interactions. Both five-membered pyrrole rings and sixmembered
chelate rings are involved in XH/p interactions;
the number of interactions with five-membered rings is
larger than the number of interactions with six-membered
rings. We found interactions with C–H and N–H groups as
hydrogen-atom donors; however, the number of CH/p
interactions is much larger than the number of NH/p
interactions. The amino acids involved in the interactions
show a high conservation score. Our results that every
porphyrin is involved in XH/p interactions and that amino
acids involved in these interactions are highly conserved 
demonstrate that XH/p interactions play an important role
in porphyrin–protein stability.",
publisher = "Springer",
journal = "Journal of Biological Inorganic Chemistry",
title = "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins",
volume = "12",
pages = "1063-1071",
doi = "10.1007/s00775-007-0276-0"
}
Stojanović, S., Medaković, V., Predović, G., Beljanski, M.,& Zarić, S.. (2007). XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry
Springer., 12, 1063-1071.
https://doi.org/10.1007/s00775-007-0276-0
Stojanović S, Medaković V, Predović G, Beljanski M, Zarić S. XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins. in Journal of Biological Inorganic Chemistry. 2007;12:1063-1071.
doi:10.1007/s00775-007-0276-0 .
Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Beljanski, Miloš, Zarić, Snežana, "XH/pi interactions with the pi system of porphyrin ring in porphyrin-containing proteins" in Journal of Biological Inorganic Chemistry, 12 (2007):1063-1071,
https://doi.org/10.1007/s00775-007-0276-0 . .
27
26
29

Non-conventional interactions in proteins containing porphyrine

Stojanović, Srđan; Medaković, Vesna; Predović, Goran

(Society of Physical Chemists of Serbia, 2006)

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6528
AB  - The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.
PB  - Society of Physical Chemists of Serbia
C3  - Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
T1  - Non-conventional interactions in proteins containing porphyrine
VL  - I
SP  - 368
EP  - 370
UR  - https://hdl.handle.net/21.15107/rcub_cer_6528
ER  - 
@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran",
year = "2006",
abstract = "The significant number of XH/TI interactions with Ti-system of five-membered pyrrole rings and six-membered chelate rings from porphyrin was found in crystal structures of proteins. There is a larger number of the interactions with five-membered than with six-membered rings. Hydrogen-atom donors can be C-H and N-H groups. The num­ ber of CH/TI interactions is much larger than number of NH/TI interactions. The list of amino acids involved in CH/TI interactions contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Besides, amino acids involving in these interactions shows significant conservation score.",
publisher = "Society of Physical Chemists of Serbia",
journal = "Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia",
title = "Non-conventional interactions in proteins containing porphyrine",
volume = "I",
pages = "368-370",
url = "https://hdl.handle.net/21.15107/rcub_cer_6528"
}
Stojanović, S., Medaković, V.,& Predović, G.. (2006). Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia
Society of Physical Chemists of Serbia., I, 368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528
Stojanović S, Medaković V, Predović G. Non-conventional interactions in proteins containing porphyrine. in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia. 2006;I:368-370.
https://hdl.handle.net/21.15107/rcub_cer_6528 .
Stojanović, Srđan, Medaković, Vesna, Predović, Goran, "Non-conventional interactions in proteins containing porphyrine" in Proceedings - 8th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Physical Chemistry 2006, September 26-29, 2006,  Belgrade, Serbia, I (2006):368-370,
https://hdl.handle.net/21.15107/rcub_cer_6528 .

Nekonvencionalne interakcije u proteinima koji sadrže hem

Stojanović, Srđan; Medaković, Vesna; Predović, Goran; Zarić, Snežana

(Belgrade : Serbian Crystallographic Society, 2006)

TY  - CONF
AU  - Stojanović, Srđan
AU  - Medaković, Vesna
AU  - Predović, Goran
AU  - Zarić, Snežana
PY  - 2006
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6577
AB  - For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability.
AB  - Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.
PB  - Belgrade : Serbian Crystallographic Society
C3  - XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
T1  - Nekonvencionalne interakcije u proteinima koji sadrže hem
T1  - Non-conventional interactions in proteins with the heme group
SP  - 38
EP  - 39
UR  - https://hdl.handle.net/21.15107/rcub_cer_6577
ER  - 
@conference{
author = "Stojanović, Srđan and Medaković, Vesna and Predović, Goran and Zarić, Snežana",
year = "2006",
abstract = "For this study, the Protein Data Bank (PDB) Select October 2004 list of non-redundant protein chains (25% threshold version, 2485 protein chains and 388067 amino acid residues) was used to examine systematically the occurrence and the role of X-H⋅⋅⋅π-interactions in heme-protein structures. The following criteria were employed to assemble the set: (1) no theoretical model structures and no NMR structures were accepted, (2) only crystal structures with a resolution of 3.0 Å or better and a crystallographic R-factor of 25.0% or lower were accepted, (3) crystal structures containing porphyrin were accepted.
The significant number of interactions with π system of five-membered pyrrole rings and with π system of six-membered chelate rings were founded to satisfy selection criteria. H-atom donors can be Cα-H, Cali-H, Caro-H and N-H. The number of C-H⋅⋅⋅π-interactions is much larger than the number of N-H⋅⋅⋅π-interactions. The list of Cali-H with five-membered rings contains more hydrophobic residues, which is probably due to the fact that these interactions are, on average, closer to the interior of the protein. Analysis of average distances for Cali and Caro of C-H⋅⋅⋅π interactions indicate that Cali makes interactions with shorter distances. Another interesting observation is the possibility of C-H(porphyrin) donor groups to exhibit an interaction between five-membered rings from another porphyrine group in proteins and its own side-chain groups (involving hydrogen atoms from methyl and propionyl groups). Amino acids involving in X-H⋅⋅⋅π-interactions shows significant conservation score. The number of these interactions as well as conservation of amino acids indicates importance of X-H⋅⋅⋅π-interactions in heme-protein stability., Za ispitivanje pojave i uloge X-H⋅⋅⋅π-interakcija u hem-proteinskim strukturama korišćena 
je proteinska baza podataka (PDB Select) iz oktobra 2004. godine, ne-redundantna lista
(verzija 25%) koja sadrži 2485 proteinskih lanaca i 388067 aminokiselinskih ostataka.
Primenjeni su sledeći kriterijumi za sastavljanje skupa: (1) nisu prihvaćeni teorijski modeli 
i NMR strukture, (2) samo su prihvaćene kristalne strukture sa rezolucijom 3.0 Å ili boljom
i kristalografskim R-faktorom 25.0% ili nižim, (3) obuhvaćene su kristalne strukture koje 
sadrže porfirinski prsten.",
publisher = "Belgrade : Serbian Crystallographic Society",
journal = "XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia",
title = "Nekonvencionalne interakcije u proteinima koji sadrže hem, Non-conventional interactions in proteins with the heme group",
pages = "38-39",
url = "https://hdl.handle.net/21.15107/rcub_cer_6577"
}
Stojanović, S., Medaković, V., Predović, G.,& Zarić, S.. (2006). Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia
Belgrade : Serbian Crystallographic Society., 38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577
Stojanović S, Medaković V, Predović G, Zarić S. Nekonvencionalne interakcije u proteinima koji sadrže hem. in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia. 2006;:38-39.
https://hdl.handle.net/21.15107/rcub_cer_6577 .
Stojanović, Srđan, Medaković, Vesna, Predović, Goran, Zarić, Snežana, "Nekonvencionalne interakcije u proteinima koji sadrže hem" in XIII konferencija Srpskog kristalografskog društva, Izvodi radova, Novi Sad / XIII Conference Of The Serbian Crystallographic Society, Novi Sad, Serbia (2006):38-39,
https://hdl.handle.net/21.15107/rcub_cer_6577 .