Supplementary data for the article: Malenov, D. P.; Zarić, S. D. Strong Stacking Interactions of Metal-Chelate Rings Are Caused by Substantial Electrostatic Component. Dalton Transactions 2019, 48 (19), 6328–6332. https://doi.org/10.1039/c9dt00182d

Supplementary material for: [https://pubs.rsc.org/en/content/articlelanding/2019/DT/C9DT00182D#!divAbstract]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/3133]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3134

Supplementary data for the article: Malenov, D. P.; Zarić, S. D. Stacking Interactions of Aromatic Ligands in Transition Metal Complexes. Coordination Chemistry Reviews 2020, 419, 213338. https://doi.org/10.1016/j.ccr.2020.213338

Supplementary material for: [https://doi.org/10.1016/j.ccr.2020.213338]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/4030

Supplementary data for article: Blagojević, J. P.; Zarić, S. D. Stacking Interactions of Hydrogen-Bridged Rings-Stronger than the Stacking of Benzene Molecules. Chemical Communications 2015, 51 (65), 12989–12991. https://doi.org/10.1039/c5cc04139b

Supplementary material for: [https://doi.org/10.1039/c5cc04139b]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/1747]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3424

Identification of Hot spots in Sm protein interfaces

This study aims to characterize the interface hot spot residues of subunits in Sm proteins. We performed an analysis of the X ray structure of 15 Sm motif containing proteins from the Protein Data Bank (PDB) and summarize physicochemical properties in an effort to understand the origin of their stabilizing contributions to protein– protein associations.Our results show that low relCompASA is critical for a residue to be a hot spot. Though many of the hot spot residues have similar relCompASA values with nonhot spot residues, they have different mean values (hot spots: 5.1%, non-hot spots: 29.1%). The P-value for relCompASA is less than 0.05, which indicate that hot spots located near the center of the interface are a general property of the interfaces, and largely protected from bulk solvent (corresponding to low relCompASA). RelDASA indicates the change in the solvent accessibility of a residue, and correlate significantly with relCompASA. Additionally, knowledge-based pair potentials of residues is statistically significant to discriminate hot spots and non-hot spots (P-value = 5.7×10−6). These results indicate that hot spots are mostly buried, tightly packed and form a network of favorable interactions with other residues. Structurally conserved residues and hot spots correlate significantly, and demonstrate that hot spots play an important role in the stability of oligomers

Supplementary information for: "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds"

Figure S1. Distance distribution for hydrogen bonds with coordinated and noncoordinated water, separately for different nucleic bases and positions; Table S1. The calculated interaction energies and distances between five nucleic bases and noncoordinated water molecules, at the B3LYP-D3/def2-TZVP (kcal/mol) and corrected for BSSE), MP2/def2-QZVP (kcal/mol) and noncorrected for BSSE) and CCSD(kcal/mol) and T)/CBS level; Table S2. The calculated interaction energies and distances at the B3LYP-D3/def2-TZVP level between five nucleic bases and water molecules coordinated to Zn2+ ion; Table S3. A number of hydrogen bonds between nucleic bases and coordinated water, and percentage of [M(H2O)n]x+ complexes, with different kinds of metals. Figure S2. Electrostatic potential maps for the nucleic bases. Figure S3. Distribution of the distance between water oxygen and nucleic base oxygen/nitrogen found in PDB structures for noncoordinated and coordinated water;Supplementary information for: Andrić, Jelena M., Stanković, Ivana, Zarić, Snežana D., "Binding of metal ions and water molecules to nucleic acid bases: The influence of water molecule coordination to a metal ion on water–nucleic acid base hydrogen bonds" in Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials, 75 (2019):301-309, [https://doi.org/10.1107/S2052520619001999]Published version of the article: [https://cer.ihtm.bg.ac.rs/handle/123456789/3521

JIMP 2 Software as a teaching tool: Understanding orbitals using fenskee-hall method

Teaching molecular orbital concept to undergraduate students is known to be very challenging; analysis of examination data for undergraduate students reveals that they do not have a clear understanding of the concepts of atomic and molecular orbitals (Tsaparlis, 1997). Understanding of the orbital concept has been subject to considerable debate and research (Barradas-Solas and Sánchez Gómez, 2014). One of teaching strategies to deal with this problem is based on usage of different quantum chemical software to calculate shape, energy and to visualize molecular orbitals. The main downside of this approach is the fact that quantum chemical calculations are often very time-consuming, especially in the case of molecules that contain transition metal atoms. Fenske-Hall method is ab initio method mainly developed for molecular orbitals calculation of transition metal complexes and organometallic compounds (Hall and Fenske, 1972). It was shown that this method is very fast, and very accurate (results are similar to the results obtained by more rigorous and more time-consuming DFT methods). Here we present a series of computational laboratory exercises using Fenske-Hall method incorporated in Jimp2 software to calculate and visualize both atomic and molecular orbitals. Students will learn how to calculate energy and visualize molecular orbitals of simple molecules. Exercises provide deeper insight into relationship between atomic and molecular orbitals with special emphasis on calculation of contribution of atomic orbitals in particular molecular orbital. Using results of Fenske-Hall calculations, students will construct molecular-orbital diagrams for simple molecules

Стекинг интеракције прстенова формираних водоничним везивањем потпомогнутим резонанцијом

Resonance-assisted hydrogen-bridged rings are often found in crystal structures in parallel alignment; 44% of all crystal structuresfound in Cambridge structural database, that contain this ring type, form parallel contacts. Distances betw een ring planes are typical for stacking (3.0-4.0 Å) and rings are in anti orientation. Quantum chemical calculations of th e stacking interaction energies are performed using different methods that are in good agreement with CCSD(T)/CBS methods, on model systems composed on dimers of molecules whose derivatives are the most common in crystal structures. The stro ngest calculated interactions (up to -5.1 kcal/mol) are comparable with stacking interactions of saturated hydrogen-bridged rings (-4.9 kcal/mol [1]) and stacking interactions between saturated hydrogen-bridged rings and C6-aromatic rings (-4.4 kcal/mol [2]), as well as with hydrogen bonds between water molecules (-4.8 kcal/mol [3]). Results indicate that energies of stack ing interactions of resonance-assisted hydrogen-bridged rings are not substantially different than energies of stacking interactions between saturated hydrogen-bridged rings

Construction of Amyloid PDB Files Database

Amyloids are insoluble proteins of a cross-_ 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 amyloid database made based on keyword criterion as well as structural features of amyloids described in literature. The searching filter was performed by python programming. The total number of structures is 109. This database can help further structural general and statistical analysis of amyloids, as we know the molecular basis can lead to understanding of disease mechanisms related to amyloid proteins.Belgrade, Serbia, June 20-24, 201

Hydrogen bonds of porphyrins in porphyrin containing proteins

This study aims to systematically characterize all hydrogen bonds of porphyrins in porphyrin containing proteins. Structures of porphyrin containing proteins from the Protein Data Bank (PDB) Select January 2007, the list of non-redundant protein chains (25% threshold), were searched in order to find out hydrogen bonds of porphyrins in proteins. The study has revealed that hydrogen bonds are commonly found in porphyrin containing proteins and are widely present in different regions of the protein chain, such as the backbone, or side chain, and in different secondary structural regions such as helices, strands and turns. The results revealed that the significant number of hydrogen bonds with acetyl and propionate groups of porphyrins exists. The most frequently observed donors are charged amino acid residues from porphyrin surrounding. Sidechains hydrogen bonds are more frequent than those with peptide donors; they involve water molecules sometimes that are classified as bridged hydrogen bonds. The average conservation score for the amino acids making hydrogen bonds with the porphyrin is statistically significantly higher than for the amino acids that do not make hydrogen bonds. The significance of hydrogen bonds as stabilizers of porphyrin rings in proteins has been illustrated on several examples.Cilj ovih istraživanja je sistematska karakterizacija svih vodoničnih veza porfirina u proteinima koji sadrže porfirin. Za ispitivanje pojave vodoničnih veza smo koristili proteinsku bazu podataka (PDB Select, januar 2007), ne-redundantna lista (verzija 25%). Istraživanja pokazuju da su vodonične veze u proteinima koji sadrže porfirin prisutne u različitim regionima proteinskog lanca, kao što su polipeptidna kičma ili bočni ostaci, i u različitim sekundarnim strukturnim regionima (heliks, nabrana pločica i zavijutak). Rezultati pokazuju značajan broj vodoničnih veza sa acetil i propionat grupama porfirina. Najučestaliji donori su naelektrisane aminokiseline iz okruženja porfirinskog prstena. Vodonične veze aminokiselinskih ostataka su učestalije od vodoničnih veza peptidnih donora; one ponekad uključuju molekul vode pri čemu se klasifikuju kao premošćene vodonične veze. Konzervacioni skor aminokiselina koje grade vodonične veze sa porfirinima je statistički značajno veći u odnosu na aminokiseline koje ne grade vodonične veze. Značaj vodoničnih veza kao stabilizatora strukture porfirinskog prstena u proteinima je prikazana na nekoliko primera

Hydrogen bonds and hydrophobic interactions of porphyrins in porphyrin-containing proteins

Structures of porphyrin-containing proteins from the Protein Data Bank (PDB) Select January 2007, were searched in order to find and systematically characterize hydrogen bonds and hydrophobic interactions of porphyrins in proteins. The results revealed that every porphyrin is involved in at least one hydrogen bond, most of the porphyrins form several, while some of them form up to thirteen hydrogen bonds. In most of the hydrogen bonds propionate groups of porphyrins interact with side-chains of residues. The most frequently observed donor is side chain of arginine. Histidine, lysine, threonine, serine and tyrozine form substantial number of hydrogen bonds too. The study has revealed that hydrophobic interactions are common between porphyrin and protein. Side-chains hydrophobic interactions are more frequent than those with backbone. The average conservation score for the amino acids making hydrogen bonds (7.2) and hydrophobic interactions (7.3) is statistically significantly higher than for the amino acids that are not involved in noncovalent interactions (5.7) with the porphyrin, indicating importance of hydrogen bonds and hydrophobic interactions with the porphyrin