Supplementary information for: "Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures"

Additional graphics and tables; methodology, CSD and PDB searches; results from CSD search; calculations; results from PDB search.The supplementary information for: Živković, J. M., Stanković, I. M., Ninković, D. B.,& Zarić, S. D. (2021). Decisive Influence of Environment on Aromatic/Aromatic Interaction Geometries. Comparison of Aromatic/Aromatic Interactions in Crystal Structures of Small Molecules and in Protein Structures Jelena M. Živković,. Crystal Growth & Design, American Chemical Society., 21(4), 1898-1904. [https://doi.org/10.1021/acs.cgd.0c01514]Published version of the article: [https://cer.ihtm.bg.ac.rs/handle/123456789/4562

Structure of water molecule and water hydrogen bonding: joint Cambridge Structural Database and ab-initio calculations study

In this study we performed analysis of non-coordinated water containing structures archived in Cambridge Structural Database (CSD), as well as ab-initio calculations on a range of bond lengths and bond angles of water molecule and water dimers

New aspects of Hydrogen Bonding: Antiparallel OH/OH Interactions. Cases of Water/Water, Water/Alcohol and Alcohol/Alcohol Dimers.

According to IUPAC definition, the hydrogen bond ‘is an attractive interaction usually presented as X—H Y—Z, where the electropositive hydrogen atom is located between two electronegative species X and Y.[1] The stability of hydrogen bonds varies in the range from -0.2 to -40 kcal/mol depending on the nature of the X and Y species and the geometry of the hydrogen bond. In this presentation, new modes of hydrogen bonding will be discussed. Namely, it was found that nearly 20% of all crystal structures, from Cambridge Structural Database, containing water-water or alcohol dimers, possess, so far, unusual antiparallel OH/OH interactions. The interaction energies of this type of hydrogen bonding (Figure 1.) are systematically calculated at CCSD(T)/CBS level of theory.[2] It was shown that the strength of the antiparallel interactions can be similar as the strength of classical hydrogen bonds, i.e. up to – 4.7 kcal/mol. The geometric parameters describing the antiparallel interactions were suggested, as well

Benzene and water – different or similar?

Considering the properties of water and benzene molecules, one can expect very different benzene/benzene and water/water interactions. Benzene does not have a dipole moment, while water does. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed the most frequent benzene/benzene and water/water geometries. The majority of the benzene/benzene interactions in the crystal structures in the CSD are stacking interactions with large horizontal displacements, and not geometries that are minima on benzene/benzene potential surface. A large number of the water/water contacts in the CSD are hydrogen bonds, 70% of all attractive water/water interactions. In addition, water/water contacts with two water forming antiparallel interactions are 20% of all attractive water/water contacts. In these contacts, the O-H bonds of water molecules are in antiparallel orientation. In benzene/benzene interactions at large horizontal displacements, two C-H bonds also are in the antiparallel orientation. This shows that although the two molecules are different, both of them form antiparallel interactions with a local O-H and C-H dipole moments

Antiparallel Noncovalent Interactions

In spite of being quite different substances, benzene and water can form similar noncovalent interactions. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed similarities in benzene/benzene and water/water interactions, since both benzene/benzene and water/water can form antiparallel interactions. The quantum chemical calculations of potential surface of water/water interactions showed that the minimum is hydrogen bond. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed antiparallel water/water interactions, in addition to classical hydrogen bonds (1). The geometries of all water/water contacts in the CSD were analyzed and for all contacts interaction energies were calculated at accurate CCSD(T)/CBS level. The results showed that the most frequent water/water contacts are hydrogen bonds; hydrogen bonds are 70% of all attractive water/water interactions. In addition, water/water contacts with antiparallel interactions are 20% of all attractive water/water contacts. In these contacts O-H bonds of water molecules are in antiparallel orientation (Figure). The quantum chemical calculations of potential surface of benzene/benzene interactions showed two minima stacking (parallel displaced) geometry and T-shaped geometry. Analysis of all benzene/benzene contacts in the crystal structures in the CSD revealed the most frequent benzene/benzene geometries (2). Majority of the benzene/benzene interactions in the CSD are stacking interactions with large horizontal displacements, and not geometries that are minima on benzene/benzene potential surface. In benzene/benzene interactions at large horizontal displacements two C-H bonds are in the antiparallel orientation (Figure). In these O-H and C-H antiparallel interactions two dipoles are in antiparallel orientation enabling close contact of positive and negative regions of the dipoles. Symmetry Adapted Perturbation Theory (SAPT) analysis showed that electrostatic is the largest attractive force in the antiparallel interactions. Antiparallel interactions are also possible between O-H and C-H bonds; in the crystal structures from the CSD these interactions are observed as one of the types of water benzene interactions (3)

Repulsive water-water contacts from Cambridge Structural Database

Water is one of the most important molecules on the Earth. Since water plays a crucial role in many life processes, it is of great importance to understand every aspect of its behavior and interactions with itself and its surroundings. It is known that water molecules can interact via classical hydrogen bonds and antiparallel interactions, with interaction energies of - 5.02 kcal/mol and -4.22 kcal/mol, respectively. Besides these attractive interactions, repulsive interactions were also noticed. In this work, we analyzed repulsive water-water contacts from the Cambridge Structural Database. All interaction energies were calculated at the so- called gold standard, i.e., CCSD(T)/CBS level of theory. It was found that among all water-water contacts, ca. 20% (2035 contacts) are repulsive with interaction energies mainly up to 2 kcal/mol. Most of these repulsive contacts do not belong to two main groups of water-water contacts. Namely, 12.8% of all repulsive contacts can be classified as classical hydrogen bonds, 2.1% to the antiparallel interactions, and the rest (85.3%) as remaining contacts. This study points out that additional attention should be paid when one deals with contacts including water or, eventually, hydrogen atoms in general

Ultimate pH, colour characteristics and proximate and mineral composition of edible organs, glands and kidney fat from Saanen goat male kids

Ultimate pH value and instrumental colour (CIEL*a*b* values) characteristics, proximate (moisture, protein, total fat and total ash) and mineral composition (K, P, Na, Mg, Ca, Zn, Fe, Cu, Ni and Mn) were determined in 10 (heart, tongue, lungs, spleen, liver, kidney, brain, testicle, thymus and kidney fat) edible by-products of Saanen goat male kids. Many significant or numerical differences were found in the mean values of quality characteristics among the edible by-products. Among edible organs and glands, liver had the lowest surface CIEL* value (darkest colour), and the highest levels of protein, Zn, Cu and Mn. Furthermore, the highest pH(24h), total ash, K, P and Mg levels were determined in the thymus. The testicle had the highest moisture, Ca and Ni levels. The spleen had the lowest fresh cut cross-section CIEL* value (darkest colour), and the highest Fe level. The highest total fat content and Na level were determined in the brain and kidney, respectively. Among all the edible by-products, kidney fat had the highest pH(24h), surface CIEL* value (lightest colour) and total fat content, and the lowest moisture, protein, total ash, K, P, Na, Mg, Ca, Zn, Fe, Cu, Ni and Mn levels

Water: new aspect of hydrogen bonding in the solid state

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 chemistr

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]