Rahul Shukla

Crystallographic and computational investigation of intermolecular interactions involving organic fluorine with relevance to the hybridization of the carbon atom

The characteristics of the C(sp,sp2,sp3)–H⋯F–C(sp,sp2,sp3) intermolecular interactions present in molecular crystals on the basis of the hybridization of the carbon atom in the interaction have been analyzed. The Cambridge Structure Database has been extensively searched for the existence of such interactions as a function of the different combinations of hybridization possible for C–H⋯F–C interactions. The parameters in the search involve restriction with the following limits: 2.1 A < H⋯F distance < 3.0 A and 110° < C–H⋯F angle < 180°. PIXEL calculations performed on selected molecular pairs showed that C–H⋯F interactions are mainly of a dispersive nature. In molecules involving the presence of a C–H donor atom wherein the carbon exists in sp hybridization, preferential electrostatic contribution was observed. A full topological analysis using the QTAIM approach confirms the presence of a BCP in all the extracted molecular pairs in the crystal geometry, thereby confirming the presence of the C–H⋯F interaction regardless of the hybridization of the participating atoms. Both the electron density (ρ) and the Laplacian (∇2ρ) evaluated at the BCP showed exponential dependence on the bond path length for all the existing interactions.

Experimental and theoretical analysis of lp⋯π intermolecular interactions in derivatives of 1,2,4-triazoles

In the present study, we have synthesized and characterized two biologically active 1,2,4-triazole derivatives, a fluoro derivative, namely (E)-3-(4-fluoro-3-phenoxyphenyl)-4-((4-fluorobenzylidene)amino)-1-(morpholinomethyl)-1H-1,2,4-triazole-5(4H)-thione (TRZ-1), and a chloro derivative, namely (E)-4-((4-chlorobenzylidene)amino)-3-(4-fluoro-3-phenoxyphenyl)-1-(morpholinomethyl)-1H-1,2,4-triazole-5(4H)-thione (TRZ-2), via single crystal and powder X-ray diffraction. The chloro derivative crystallizes in an anhydrous form (TRZ-2A) and a solvated one (TRZ-2B) due to the presence of a toluene molecule in the crystal. This solvatomorphic behavior has been studied in detail using different thermal techniques, namely DSC and TGA, combined with hot stage microscopy (HSM). All of the three crystal structures show the presence of different intermolecular interactions of the type C–H⋯O, C–H⋯SC, C–H⋯π, C–H⋯X (X = –F, –Cl), π⋯π and lp⋯π interactions. The fingerprints for all these interactions were evaluated using Hirshfeld surfaces. The nature and energetics associated with these interactions were characterized using PIXEL and supported by ab initio quantum mechanical calculations using TURBOMOLE. In addition, the calculations performed on the evaluation of the electrostatic potential provide deeper insights into the nature of lp⋯π interactions.

Exploring the Role of Substitution on the Formation of Se···O/N Noncovalent Bonds.

In this article, we have examined the effect of substitution on the formation of neutral XHSe···O/N (X = -H, -F, -CH3, -CF3, -Cl, -OH, -OCH3, -NH2, -NHCH3, -CN) noncovalent bonds with the oxygen atom from H2O molecule and the nitrogen atom from NH3 being the electron donor atoms, respectively. In addition to this, analysis has also been performed on XMeSe···O/N complexes to study the effect of the role of hydrogen bonding with the hydrogen atoms of the methyl group on Se···O/N interactions. Binding energy calculations were performed to determine the strength of these contacts. The obtained results establish the fact that the presence of a methyl group influences the strength of the observed Se···O/N interactions. Also in some cases, the O-H···Se interaction was observed to be more preferable over the Se···O interaction. The major contribution for stabilization of such Se···O/N interactions is from an interplay among the electrostatics and the exchange energy. To obtain deeper insights and understanding of such Se···O/N contacts, a topological analysis, using the QTAIM approach were also performed. This analysis showed that although the presence of a Me group modifies the Se···O/N interaction, it does not necessitate the formation of hydrogen bonds. To obtain insights into the orbital contributions, a natural bond orbital (NBO) analysis were performed which depicts that the strength of such interactions were derived via charge transfer from the oxygen/nitrogen lone pair to the σ* orbital of the Se-X bond.

Understanding the effect of substitution on the formation of S. . .F chalcogen bond

AbstractIn this study, we have investigated the effect of substitution on the formation of S …F non-covalent interactions in XHS …FCH3 complexes (X =-H, -F, -Cl, -OH, -OCH3, -NH2, -NHCH3, -NO2, -CN) at MP2/aug-cc-pVDZ level of theory. The formation of S …F chalcogen bonds was observed in all the cases, except for X = -H. The binding energy of the S …F non-covalent interactions is strongly dependent on the nature of the substituent groups. The energy decomposition analysis revealed that electrostatic and exchange energy component are the dominant contributors towards the stability of these interactions. The topological analysis established the presence of the S …F chalcogen bond due to the presence of a bond critical point exclusively between sulphur and fluorine atoms representing a closed-shell interaction. The natural bond orbital analysis shows that the stability of the interaction comes from a charge transfer from F(lp) to s*(S-X) orbital transition. Graphical AbstractThe aim of this study was to understand the effect of substitution on the nature and characteristics of S…F chalcogen bonds.

Impact of the complementary electronic nature of C–X and M–X halogens and intramolecular X⋯O interaction on supramolecular assemblies of Zn(II) complexes of o-halophenyl substituted hydrazides

The disparity in the electronic nature of organic (C–X) and inorganic (M–X) halogens in a supramolecular context has been demonstrated herein. Metal complexes [Zn(hyd-X)Cl2]·nDMF of three o-halophenyl substituted hydrazide based ligands hyd-X (hyd = hydrazide, X = F, Cl and Br) have been synthesized and characterized by single crystal XRD. The C–X halogen atom in these complexes is involved in either intramolecular X⋯O interaction (when X = Cl/Br) or intramolecular N–H⋯X (when X = F) hydrogen bonding. Supramolecular networks propagated via intermolecular C–X⋯N halogen bonds and N–H⋯X(M) hydrogen bonds are observed in crystal structures of the complexes. Intramolecular X⋯O interaction and intramolecular N–H⋯F hydrogen bonds exert decisive roles in locking the molecular conformation of these compounds. DFT, AIM and NBO studies have been employed to acquire quantitative accounts of the halogen mediated non-covalent interactions.

Characterization of N⋯O non-covalent interactions involving σ-holes: “electrostatics” or “dispersion”

In this article, the existence of NO noncovalent interactions was explored in per-halo substituted ammonia-water complexes. Optimized geometry at the MP2/aug-cc-pVTZ level shows that the NO distance in all complexes is less than the sum of the vdW radii of N and O. The strength of these contacts was directly dependent on the extent of chlorine substitution on N or O atoms. Also, the level of theory and the basis set employed for the binding energy calculations have a direct effect on the strength of the NO contacts. Energy decomposition analysis reveals that dispersion was the major contributor towards the stability of these contacts followed by electrostatic energy. The topological analysis further confirmed the existence of NO contacts due to the presence of a bond critical point between the N and the O atom in all the complexes. These contacts have characteristics of a σ-hole interaction with the NBO analysis revealing that the primary charge transfer in all the complexes is occurring from O(lp) to σ*(N-X) orbitals, confirming these interactions to be predominantly in the category of pnicogen bonds.

Analysis of intermolecular interactions in 3-(4-fluoro-3-phenoxyphenyl)-1-((4-methylpiperazin-1-yl)methyl)-1H-1,2,4-triazole-5-thiol

AbstractIn the present study, we have prepared and structurally characterized a derivative of 1,2,4 triazoles, namely 3-(4-fluoro-3-phenoxyphenyl)-1-((4-methylpiperazin-1-yl)methyl)-1H-1,2,4-triazole-5-thiol (T-1) via single crystal X-ray diffraction. The crystal structure was observed to be stabilized by the presence of various intermolecular interactions in the crystalline solid such as O-H ⋯S, C-H ⋯F, C-H ⋯S, C-H ⋯N, C-H ⋯O, C-H ⋯π, lp⋯π and π⋯π intermolecular interactions. The interaction energy of these interactions was evaluated through PIXEL method with decomposition of the total energy into the coulombic, polarization, dispersion and repulsion contribution. The study of the nature of H-bonds with sulfur reveals that stabilization due to contribution from polarization plays a significant role. It is noteworthy that the presence of the solvent molecules in the crystal structure were observed to provide stabilization to an otherwise destabilized molecular pair (comprising of two molecules of 1,2,4 triazoles in the asymmetric unit). Graphical AbstractThis study highlights the significant role of intermolecular H-bonds of an organic molecule with the solvent in the formation of the crystalline solid.

Characterization of the short OC⋯OC π-hole tetrel bond in the solid state

The nature and characteristics of the intermolecular OC⋯OC π-hole tetrel bond in the solid state have been explored and the driving force for tetrel bond formation is the electrostatically driven π-hole interaction between the most electropositive carbon atom of the carbonyl group and the most electronegative oxygen atom in the crystal. NBO calculations establish the n → π* orbital interaction present and CSD analysis quantitatively establishes the Burgi–Dunitz angle to be ∼97.7° driven via tetrel bond formation.

Quantitative investigation of intermolecular interactions in dimorphs of 3-Chloro-N-(2-fluorophenyl)benzamide and 2-Iodo-N-(4- bromophenyl)benzamide

In this study, we have analyzed the role of different intermolecular interactions in the polymorphic modifications of 3-chloro-N-(2-fluorophenyl)benzamide (I) and 2-iodo-N-(4- bromophenyl)benzamide (II). The crystals were obtained via slow evaporation method with the alteration of solvents for crystallization. The already reported form [Cryst. Growth Des. (2011) 11:1578] crystallizes in P2