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  - 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  - 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  - 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  - 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 . .

TY  - JOUR
AU  - Malenov, Dušan P.
AU  - Antonijević, Ivana
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2018
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2423
AB  - Stacking interactions of organometallic sandwich and half-sandwich compounds with cyclopentadienyl (Cp) were studied by searching and observing the crystal structures in the Cambridge Structural Database and performing density functional calculations. The strongest calculated interactions are at an offset of 1.5 angstrom with energies for sandwich and half-sandwich dimers of -3.37 and -2.87 kcal mol(-1), respectively, somewhat stronger than the stacking interaction between two benzene molecules, -2.73 kcal mol(-1). At large offsets of 5.0 angstrom, 74% of the strongest energy is preserved for the sandwich dimer and only 29% for the half-sandwich dimer. In crystal structures, for sandwich compounds, the stacking at large offsets is dominant (73%), since the interaction at large offsets is relatively strong, and the geometries enable additional simultaneous interactions with Cp faces. The stacking at large offsets between half-sandwich compounds is less dominant, since the interaction is weaker. However, Cp half-sandwich compounds stack at large offsets unexpectedly often (almost 60%), since the branching of their other ligands in the compound favors more simultaneous interactions with Cp faces. Strong interaction at large offsets for sandwich compounds is the consequence of favorable electrostatic interaction, which is not the feature of stacking between half-sandwich compounds.
PB  - Royal Soc Chemistry, Cambridge
T2  - Crystengcomm
T1  - Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets
VL  - 20
IS  - 31
SP  - 4506
EP  - 4514
DO  - 10.1039/c8ce00597d
ER  - 

@article{
author = "Malenov, Dušan P. and Antonijević, Ivana and Hall, Michael B. and Zarić, Snežana D.",
year = "2018",
abstract = "Stacking interactions of organometallic sandwich and half-sandwich compounds with cyclopentadienyl (Cp) were studied by searching and observing the crystal structures in the Cambridge Structural Database and performing density functional calculations. The strongest calculated interactions are at an offset of 1.5 angstrom with energies for sandwich and half-sandwich dimers of -3.37 and -2.87 kcal mol(-1), respectively, somewhat stronger than the stacking interaction between two benzene molecules, -2.73 kcal mol(-1). At large offsets of 5.0 angstrom, 74% of the strongest energy is preserved for the sandwich dimer and only 29% for the half-sandwich dimer. In crystal structures, for sandwich compounds, the stacking at large offsets is dominant (73%), since the interaction at large offsets is relatively strong, and the geometries enable additional simultaneous interactions with Cp faces. The stacking at large offsets between half-sandwich compounds is less dominant, since the interaction is weaker. However, Cp half-sandwich compounds stack at large offsets unexpectedly often (almost 60%), since the branching of their other ligands in the compound favors more simultaneous interactions with Cp faces. Strong interaction at large offsets for sandwich compounds is the consequence of favorable electrostatic interaction, which is not the feature of stacking between half-sandwich compounds.",
publisher = "Royal Soc Chemistry, Cambridge",
journal = "Crystengcomm",
title = "Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets",
volume = "20",
number = "31",
pages = "4506-4514",
doi = "10.1039/c8ce00597d"
}

Malenov, D. P., Antonijević, I., Hall, M. B.,& Zarić, S. D.. (2018). Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets. in Crystengcomm
Royal Soc Chemistry, Cambridge., 20(31), 4506-4514.
https://doi.org/10.1039/c8ce00597d

Malenov DP, Antonijević I, Hall MB, Zarić SD. Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets. in Crystengcomm. 2018;20(31):4506-4514.
doi:10.1039/c8ce00597d .

Malenov, Dušan P., Antonijević, Ivana, Hall, Michael B., Zarić, Snežana D., "Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets" in Crystengcomm, 20, no. 31 (2018):4506-4514,
https://doi.org/10.1039/c8ce00597d . .

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 . .

TY  - JOUR
AU  - Stanković, Ivana
AU  - Bozinovski, Dragana M.
AU  - Brothers, Edward N.
AU  - Belić, Milivoj
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2017
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/2115
AB  - Aromatic-aromatic interactions have long been considered important in the self assembly of amyloids. In spite of their importance, aromatic amino acids are not detected in every amyloid. In the present study, the occurrence and geometry of these interactions were analyzed for the amyloid structures found in the Protein Data Bank. The data confirm that aromatic amino acids are not crucial for amyloid fibril formation. In fact, aromatic-aliphatic interactions are more frequent than the aromatic-aromatic interactions. Aromatic-aliphatic interactions are present in higher numbers of structures and in certain amyloid sequences they are more frequent than aromatic-aromatic interactions. An analysis of aromatic/aromatic interactions shows different interaction geometries in intrasheet and intersheet contacts; the intrasheet aromatic-aromatic interactions are mostly parallel and displaced, while intersheet interactions are not parallel. Thus, among the aromatic-aromatic interactions there are important edge-to-face attractions in addition to parallel stacking ones.
PB  - American Chemical Society (ACS)
T2  - Crystal Growth & Design
T1  - Interactions of Aromatic Residues in Amyloids: A Survey of Protein Data Bank Crystallographic Data
VL  - 17
IS  - 12
SP  - 6353
EP  - 6362
DO  - 10.1021/acs.cgd.7b01035
ER  - 

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

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

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

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

TY  - JOUR
AU  - Stanković, Ivana
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2017
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/6084
UR  - http://ipsitransactions.org/journals/papers/tir/2017jan/p6.pdf
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. We present a constructed amyloid
database made on keyword criterion as well as
structural features of amyloids described in
literature. The searching filter performed by python
programming, gave the total number of 109
structures. This database can help further
structural general and statistical analysis of
amyloids, that can lead to understanding of
disease mechanisms related to amyloid proteins.
PB  - Belgrade : IPSI
T2  - IPSI Transactions on Internet Research
T1  - Construction of Amyloid PDB Files Database
VL  - 13
IS  - 1
SP  - 49-8
UR  - https://hdl.handle.net/21.15107/rcub_cer_6084
ER  - 

@article{
author = "Stanković, Ivana and Hall, Michael B. and Zarić, Snežana D.",
year = "2017",
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. We present a constructed amyloid
database made on keyword criterion as well as
structural features of amyloids described in
literature. The searching filter performed by python
programming, gave the total number of 109
structures. This database can help further
structural general and statistical analysis of
amyloids, that can lead to understanding of
disease mechanisms related to amyloid proteins.",
publisher = "Belgrade : IPSI",
journal = "IPSI Transactions on Internet Research",
title = "Construction of Amyloid PDB Files Database",
volume = "13",
number = "1",
pages = "49-8",
url = "https://hdl.handle.net/21.15107/rcub_cer_6084"
}

Stanković, I., Hall, M. B.,& Zarić, S. D.. (2017). Construction of Amyloid PDB Files Database. in IPSI Transactions on Internet Research
Belgrade : IPSI., 13(1), 49-8.
https://hdl.handle.net/21.15107/rcub_cer_6084

Stanković I, Hall MB, Zarić SD. Construction of Amyloid PDB Files Database. in IPSI Transactions on Internet Research. 2017;13(1):49-8.
https://hdl.handle.net/21.15107/rcub_cer_6084 .

Stanković, Ivana, Hall, Michael B., Zarić, Snežana D., "Construction of Amyloid PDB Files Database" in IPSI Transactions on Internet Research, 13, no. 1 (2017):49-8,
https://hdl.handle.net/21.15107/rcub_cer_6084 .

TY  - JOUR
AU  - Sredojević, Dušan
AU  - Petrović, Predrag V.
AU  - Janjić, Goran
AU  - Brothers, Edward N
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2016
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1998
AB  - The strength of the stacking interactions in the bipy complexes of nickel, palladium, and platinum, [M(CN)(2)bipy](2) (M=Ni, Pd, Pt), was calculated using the omega B97xD/def2-TZVP method. The results show that for all considered geometries, interactions are the strongest for platinum, and weakest for nickel complexes, as a result of higher dispersion contributions of platinum over the palladium and nickel complexes. It was also shown that strength of interactions considerably rises with an increase of the stacking overlap area. As a consequence of the favorable electrostatic term, the strength of interactions also rises when metal atom and cyano ligands are involved in the overlap with bipy ligand. The strongest interaction was calculated in the platinum complex, for the geometry that has overlap of metal and cyano ligands with bipy ligand with an energy of -39.80 kcal mol(-1). The energies for similar geometries of palladiumand nickel complexes are -34.60 and -32.45 kcal mol(-1). These energies, remarkably, exceed the strength of the stacking interactions between organic aromatic molecules. These results can be of importance in all systems with stacking interactions, from materials to biomolecules.
PB  - Springer, New York
T2  - Journal of Molecular Modeling
T1  - The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions
VL  - 22
IS  - 1
DO  - 10.1007/s00894-015-2888-6
ER  - 

@article{
author = "Sredojević, Dušan and Petrović, Predrag V. and Janjić, Goran and Brothers, Edward N and Hall, Michael B. and Zarić, Snežana D.",
year = "2016",
abstract = "The strength of the stacking interactions in the bipy complexes of nickel, palladium, and platinum, [M(CN)(2)bipy](2) (M=Ni, Pd, Pt), was calculated using the omega B97xD/def2-TZVP method. The results show that for all considered geometries, interactions are the strongest for platinum, and weakest for nickel complexes, as a result of higher dispersion contributions of platinum over the palladium and nickel complexes. It was also shown that strength of interactions considerably rises with an increase of the stacking overlap area. As a consequence of the favorable electrostatic term, the strength of interactions also rises when metal atom and cyano ligands are involved in the overlap with bipy ligand. The strongest interaction was calculated in the platinum complex, for the geometry that has overlap of metal and cyano ligands with bipy ligand with an energy of -39.80 kcal mol(-1). The energies for similar geometries of palladiumand nickel complexes are -34.60 and -32.45 kcal mol(-1). These energies, remarkably, exceed the strength of the stacking interactions between organic aromatic molecules. These results can be of importance in all systems with stacking interactions, from materials to biomolecules.",
publisher = "Springer, New York",
journal = "Journal of Molecular Modeling",
title = "The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions",
volume = "22",
number = "1",
doi = "10.1007/s00894-015-2888-6"
}

Sredojević, D., Petrović, P. V., Janjić, G., Brothers, E. N., Hall, M. B.,& Zarić, S. D.. (2016). The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions. in Journal of Molecular Modeling
Springer, New York., 22(1).
https://doi.org/10.1007/s00894-015-2888-6

Sredojević D, Petrović PV, Janjić G, Brothers EN, Hall MB, Zarić SD. The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions. in Journal of Molecular Modeling. 2016;22(1).
doi:10.1007/s00894-015-2888-6 .

Sredojević, Dušan, Petrović, Predrag V., Janjić, Goran, Brothers, Edward N, Hall, Michael B., Zarić, Snežana D., "The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions" in Journal of Molecular Modeling, 22, no. 1 (2016),
https://doi.org/10.1007/s00894-015-2888-6 . .

TY  - JOUR
AU  - Sredojević, Dušan
AU  - Ninković, Dragan B.
AU  - Janjić, Goran
AU  - Zhou, Jia
AU  - Hall, Michael B.
AU  - Zarić, Snežana D.
PY  - 2013
UR  - https://cer.ihtm.bg.ac.rs/handle/123456789/1339
PB  - Wiley-V C H Verlag Gmbh, Weinheim
T2  - Chemphyschem
T1  - Stacking Interactions of Ni(acac) Chelates with Benzene: Calculated Interaction Energies
VL  - 14
IS  - 9
SP  - 1797
EP  - 1800
DO  - 10.1002/cphc.201201062
ER  - 

@article{
author = "Sredojević, Dušan and Ninković, Dragan B. and Janjić, Goran and Zhou, Jia and Hall, Michael B. and Zarić, Snežana D.",
year = "2013",
publisher = "Wiley-V C H Verlag Gmbh, Weinheim",
journal = "Chemphyschem",
title = "Stacking Interactions of Ni(acac) Chelates with Benzene: Calculated Interaction Energies",
volume = "14",
number = "9",
pages = "1797-1800",
doi = "10.1002/cphc.201201062"
}

Sredojević, D., Ninković, D. B., Janjić, G., Zhou, J., Hall, M. B.,& Zarić, S. D.. (2013). Stacking Interactions of Ni(acac) Chelates with Benzene: Calculated Interaction Energies. in Chemphyschem
Wiley-V C H Verlag Gmbh, Weinheim., 14(9), 1797-1800.
https://doi.org/10.1002/cphc.201201062

Sredojević D, Ninković DB, Janjić G, Zhou J, Hall MB, Zarić SD. Stacking Interactions of Ni(acac) Chelates with Benzene: Calculated Interaction Energies. in Chemphyschem. 2013;14(9):1797-1800.
doi:10.1002/cphc.201201062 .

Sredojević, Dušan, Ninković, Dragan B., Janjić, Goran, Zhou, Jia, Hall, Michael B., Zarić, Snežana D., "Stacking Interactions of Ni(acac) Chelates with Benzene: Calculated Interaction Energies" in Chemphyschem, 14, no. 9 (2013):1797-1800,
https://doi.org/10.1002/cphc.201201062 . .