Fluorination of compounds causes an increase in the proton-donating ability and a decrease in the proton-accepting capacity of groups in their vicinity. The formation of F···F interactions is followed by the shift of the electron density in the area of F···F contact, which creates a new region with a larger surface area, a higher negative potential, and, hence, a more pronounced accepting ability. The new region also has a greater ability to form multiple (simultaneous) interactions with species from the environment, thus compensating for the reduction of the accepting capacity of the groups in the vicinity. This phenomenon explains not only the abundance of F···F interactions in crystal structures, but also a large number of structures with F···O interactions. Only C–H···F interactions are more numerous than F···F interactions in crystal structures, which indicates a high affinity of fluorinated compounds for nonpolar groups.

The quantitative assessment of intermolecular interactions and their cooperative effects has been performed in spirohydantoin-based model compounds, 3-benzoyl-1,3-diazaspiro[4.5]decane-2,4-dione (1) and 3-(4-fluorobenzoyl)-1,3-diazaspiro[4.5]decane-2,4-dione (2), through single crystal X-ray crystallography and quantum chemical...

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Statistical analysis of data from crystal structures extracted from the Cambridge Structural Database (CSD) has shown that S and Se atoms display a similar tendency towards specific types of interaction if they are part of a fragment that corresponds to the side chains of cysteine (Cys), methionine (Met) selenocysteine (Sec) and selenomethionine (Mse). The most numerous are structures with C-HÁ Á ÁSe and C-HÁ Á ÁS interactions ($80%), notably less numerous are structures with SeÁ Á ÁSe and SÁ Á ÁS interactions ($5%), and SeÁ Á Á and SÁ Á Á interactions are the least numerous. The results of quantum-chemical calculations have indicated that C-HÁ Á ÁSe ($À0.8 kcal mol À1 ) and C-HÁ Á ÁS interactions are weaker than the most stable parallel interaction ($À3.3 kcal mol À1 ) and electrostatic interactions of / type ($À2.6 kcal mol À1 ). Their significant presence can be explained by the abundance of CH groups compared with the numbers of Se and S atoms in the crystal structures, and also by the influence of substituents bonded to the Se or S atom that further reduce their possibilities for interacting with species from the environment. This can also offer an explanation as to why O-HÁ Á ÁSe ($À4.4 kcal mol À1 ) and N-HÁ Á ÁSe interactions ($À2.2 kcal mol À1 ) are less numerous. Docking studies revealed that S and Se rarely participate in interactions with the amino acid residues of target enzymes, mostly because those residues preferentially interact with the substituents bonded to Se and S. The differences between Se and S ligands in the number and positions of their binding sites are more pronounced if the substituents are polar and if there are more Se/S atoms in the ligand.

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Molecular mechanism by which the electron transfer (ET) is coupled to proton pumping in cytochrome oxidase is one of main unsolved problems in biochemistry. Particularly, the nature and position of the proton-loading site is under dispute. The CuB complex has three ligated histidines, whereas only His290 and His291 are ionizable sites with the equal pKas in aqueous solution, but apparently quite different ones within the enzyme. Earlier, it was proposed a model of proton pumping with the central role of His290. Recent calculations indicate that His291 ligand of CuB center might play the role of the pumping element, since its protonation state depends on the oxidation state of the binuclear complex (BNC). The present electrostatic study is applied to assess the role of the protein environment on acidity of the two histidines. Their pKa values and effects of different energy terms are evaluated to discover the nature of their diverse behavior in the enzyme. Here, a new set of pKas for the non-standard model compounds within the BNC is applied. The enhanced results are compared with results of previous studies in the light of the plausible proton pumping mechanism. The obtained microscopic and apparent pKa values in the oxidized state of BNC are virtually the same, indicating that deprotonated form of His291 accounts for the large pKa increase of His290, since the both titratable sites on CuB center cannot simultaneously be in the charged state. The present results support the underlined His291 pumping model. [Projects of the Serbian Ministry of Education, Science and Technological Development, Grant no. 451-03-68/2020-14/200026 and Grant no. OI 172035]