Study of C−H⋅⋅⋅π interactions with pyrrole and chelate rings in metal-porphyrin complexes

The Cambridge Structural Database (CSD) was screened in order to find and investigate specific C−H⋅⋅⋅π interactions between C−H groups and two types of rings with delocalized π-bonds that exist in porphyrin: pyrrole and six-membered chelate. Statistical analysis of geometrical parameters for interactions in both types of rings was done. In order to determine preferred positions in porphyrinato ring for C−H⋅⋅⋅π interactions fifteen different points distributed over porphyrin ring have been chosen and each of them have been analyzed. Calculations of these interactions by density functional theory (DFT) have been done on three different model systems.Physical chemistry 2006 : 8th international conference on fundamental and applied aspects of physical chemistry; Belgrade (Serbia); 26-29 September 200

C − H···π interactions in the metal-porphyrin complexes with chelate ring as the h acceptor

Specific C − H···π interactions with the π-system of porphyrinato chelate ring were found in crystal structures of transition metal complexes from the CSD and statistical analysis of geometrical parameters for intramolecular and intermolecular interactions was done. DFT calculations on a model system show that energy of the interaction is 1.58 kcal/mol and that the strongest interaction occurs when the distance between hydrogen atom and the center of the chelate ring is 2.6 Å. This prediction is in good agreement with the distances for intermolecular interactions found in the crystal structures. In many cases the intramolecular interaction distances are much shorter than 2.6 Å, and these short distances appear to be caused by geometrical constrains. The C − H···π interactions with chelate ring of porphyrinato ligand can be important in biomolecules with porphyrin as they can influence the structure, contribute to the stability and play some role in function of biomolecules.Physical chemistry 2004 : 7th international conference on fundamental and applied aspects of physical chemistry; Belgrade (Serbia); 21-23 September 200

How Do Small Differences in Geometries Affect Electrostatic Potentials of High-Energy Molecules? Critical News from Critical Points

The computational design of explosives is becoming very popular since it represents a safe and environmentally friendly way of predicting the properties of these molecules. It is known that positive values of electrostatic potential in the central areas of the molecular surface are a good indicator of the sensitivity of high-energy materials towards detonation. The molecular electrostatic potential is routinely calculated for molecules of explosives using both geometries extracted from crystal structures, and computationally optimized geometries. Here we calculated and compared values of positive electrostatic potential in the centers of five classical high-energy molecules for geometries extracted from different crystal structures and theoretically optimized geometries. Density functional theory calculations performed at M06/cc-PVDZ level showed that there are significant differences in the values of electrostatic potentials in critical points obtained for different geometries of the same high-energy molecules. The study also showed that there was an excellent agreement in the values of electrostatic potentials calculated for optimized geometry of 1,3,5-trinitrobenzene and geometry of this molecule obtained by neutron diffraction experiments. The results of this study could help researchers in the area of the computational development of high-energy molecules to better design their studies and to avoid the production of erroneous results

Supplementary data for the article: Ninković, D. B.; Vojislavljević-Vasilev, D. Z.; Medaković, V. B.; Hall, M. B.; Brothers, E. N.; Zarić, S. D. Aliphatic-Aromatic Stacking Interactions in Cyclohexane-Benzene Are Stronger than Aromatic-Aromatic Interaction in the Benzene Dimer. Physical Chemistry Chemical Physics 2016, 18 (37), 25791–25795. https://doi.org/10.1039/c6cp03734h

Supplementary material for: [https://doi.org/10.1039/c6cp03734h]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2328]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3324

Supplementary data for the article: Ninković, D. B.; Vojislavljević-Vasilev, D. Z.; Medaković, V. B.; Hall, M. B.; Brothers, E. N.; Zarić, S. D. Aliphatic-Aromatic Stacking Interactions in Cyclohexane-Benzene Are Stronger than Aromatic-Aromatic Interaction in the Benzene Dimer. Physical Chemistry Chemical Physics 2016, 18 (37), 25791–25795. https://doi.org/10.1039/c6cp03734h

Supplementary material for: [https://doi.org/10.1039/c6cp03734h]Related to published version: [http://cherry.chem.bg.ac.rs/handle/123456789/2328]Related to accepted version: [http://cherry.chem.bg.ac.rs/handle/123456789/3324

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

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.Belgrade, Serbia, June 20-24, 201

Study of noncovalent interactions using crystal strucutre data and quantum chemical calculations

The analysis of the crystal structures in the CSD was used to recognize and characterize new types of noncovalent interactions. It was also used 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 [1,2]. The quantum chemical calculations were performed to evaluate the energies of the interactions. For the preferred geometries in the crystal structures we can calculate the interaction energies. By calculating potential energy surfaces for the interactions, we can determine the most stable geometries, as well as stability of various geometries [1,2]. Using this methodology our group recognized stacking interactions of planar metal-chelate rings; stacking interactions with organic aromatic rings, and stacking interactions between two chelate rings. The calculated energies showed that the stacking of metal-chelate rings is stronger than stacking between two benzene molecules. Studies of interactions of coordinated ligands indicate stronger noncovalent interactions that interactions of noncoordinated molecules [2]. REFERENCES [1] Ninković, D. B., Blagojević Filipović, J. P., Hall, M. B., Brothers, E. N., Zarić, S. D. (2020) ACS Central Science, 6, 420. [2] Malenov, D. P., Zarić, S. D. (2020) Cood. Chem. Rev. 419, 213338

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

In the recent review it was point out that the crystal structures in the Cambridge Structural Database (CSD), collected, have contribute to various fields of chemical research such as geometries of molecules, noncovalent interactions of molecules, and large assemblies of molecules. The CSD also contributed to the study and the design of biologically active molecules and the study of gas storage and delivery [1]. In our group we use analysis of the crystal structures in the CSD to recognize and characterize new types of noncovalent interactions and 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 quantum chemical calculations to evaluate the energies of the interactions. Based on the calculated potential energy surfaces for the interactions, we can determine the most stable geometries, as well as stability of various geometries. We also can determine the interaction energies for the preferred geometries in the crystal structures. In the cases where the most preferred geometries in the crystal structures are not the most stable geometries at the potential energy surface, one can find significant influence of the supramolecular structures in the crystals. Using this methodology our group recognized stacking interactions of planar metal-chelate rings; 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 [2]. The data indicate influence of the metal and ligand type in the metal chelate ring on the strength of the interactions. Our results also indicate strong stacking interactions of coordinated aromatic rings [3]. Studies of interactions of coordinated water indicate stronger hydrogen bonds and stronger OH/π interactions of coordinated in comparison to noncoordianted water molecule [4,5]. The calculations on OH/M interactions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongest hydrogen bonds in any molecular system [6]. The studies on stacking interactions of benzene molecules in the crystal structures in the CSD show preference for interactions at large horizontal displacements, while high level quantum chemical calculations indicate significantly strong interactions at large offsets; the energy is 70% of the strongest stacking geometry [7]

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

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]

Noncovalent interactions of metal complexes and aromatic molecules

Наше истраживање се заснива на анализи података у кристалним структурама из Кембичке базе структурних података (CSD) и на квантнo хемијским прорачунима. Анализа података из CSD-а омогућава да се препознају интеракције у кристалним структурама и да се опишу геометрије ових интеракција, док помоћу квантно-хемијских прорачуна можемо проценити интеракционе енергије и пронаћи најстабилније геометрије интеракција. Користећи ову методологију успели смо да препознамо и опишемо неколико нових типова интеракција. Наше проучавање интеракција планарних метал-хелатних прстенова показало је могућност стекинг интеракција са органским ароматичним прстеновима и интеракције између два хелатна прстена. Израчунате енергије указују на јаке стекинг интеракције метал-хелатних прстенова; стекинг метал-хелатних прстенова је јачи од стекинга између два молекула бензена. Испитивања интеракција координираних молекула воде и амонијака указују на јаче водоничне везе и јаче ОH/π и NH/π интеракције координираних у односу на некоординоване молекуле воде и амонијака. Прорачуни ОH/М интеракција између металног јона у квадратнo планарним комплексима и молекулa воде указују да су ове интеракције међу најјачим водоничним везама у било ком молекулском систему. Студије о ароматичним молекулима указују на стекинг интеракције са великим хоризонталним померањима између два ароматична молекула са значајно јаким интеракцијама, енергија је 70% најјаче стекинг интеракције. Наши подаци такође указују на то да су интеракције алифатичних прстенова са ароматичним прстеном јаче од интеракција између два ароматична молекула, док су алифатично/ароматичне интеракције веома честе у протеинским структурама.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 metalchelate rings; the stacking of metal-chelate rings is stronger than stacking between two benzene molecules. Studies of interactions of coordinated water and ammonia indicate stronger hydrogen bonds and stronger OH/π and NH/π interactions of coordinated in comparison to noncoordianted water and ammonia. The calculations on OH/M interactions between metal ion in square-planar complexes and water molecule indicate that these interactions are among the strongest hydrogen bonds in any molecular system. 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