Weak Intermolecular Interactions in a Series of Bioactive Oxazoles

The intermolecular interactions in a series of nine similar 4,5-phenyl-oxazoles were studied on the basis of crystal structures determined by X-ray diffraction. The crystal architectures were analyzed for the importance and hierarchies of different, weak intermolecular interactions using three approaches: the geometrical characteristics, topological analysis (for the model based on the transfer of multipolar parameters), and energetics of the molecule–molecule interactions. The geometries of the molecules were quite similar and close to the typical values. The results of the analysis of the interactions suggest that the number of nonspecific interactions is more important than the apparent strength of the specific interactions. The interactions involving covalently bound bromine and divalent sulfur atoms were classified as secondary, they certainly did not define the crystal packing, and they played a minor role in the overall crystal cohesion energies. Incidentally, another method for confirming the degree of isostructurality, according to the topologies of the interactions, is described.     

Intermolecular interactions in condensed matter

Recent progress in Fourier transform IR and far IR investigation of intermolecular interactions in liquid solutions and cryogenic matrices will be reported. Particular emphasis is given to routine performance checks of the spectrometer and to novel techniques of sample preparation and related equipment. The described examples are the dynamics of H₂O isolated in solid Ar and the aggregational behaviour of HCN and CH₃CN in diverse liquid and solid phases.     

Crystal Structure and Noncovalent Interactions of Heterocyclic Energetic Molecules

Nitrogen-rich heterocyclic compounds are important heterocyclic substances with extensive future applications for energetic materials due to their outstanding density and excellent physicochemical properties. However, the weak intermolecular interactions of these compounds are not clear, which severely limits their widespread application. Three nitrogen-rich heterocyclic compounds were chosen to detect their molecular geometry, stacking mode and intermolecular interactions by crystal structure, Hirshfeld surface, RDG and ESP. The results show that all atoms in each molecule are coplanar and that the stacking mode of the three crystals is a planar layer style. A large amount of inter- and intramolecular interaction exists in the three crystals. All principal types of intermolecular contacts in the three crystals are N···H interactions and they account for 40.9%, 38.9% and 32.9%, respectively. Hydrogen bonding, vdW interactions and steric effects in Crystal c are stronger than in Crystals a and b. The negative ESPs all concentrate on the nitrogen atoms in the three molecules. This work is expected to benefit the crystal engineering of heterocyclic energetic materials.     

Non-covalent intermolecular interactions of colloidal nematic liquid crystals doped with graphene oxide

Graphene oxide (GO) was doped to eutectic uniaxial nematic liquid crystals (NLCs) (E_5CN7) with different percentages to improve the physiochemical properties of NLCs effectively. GO shifts the N-I phase transition temperature to higher values. It has been observed that increasing GO concentration up to 0.75% increases the N-I phase transition temperature substantially while further increase of GO concentration results in an inverse trend. The GO/E_5CN7 non-covalent interactions change the N-I phase transition. The contribution of several terms such as anchoring and polarisation effects on N-I phase transition was quantified as well. The results suggest that the size is an important contributor to GO and liquid crystal interaction. The results show that E_5CN7@GO composites may act as promising candidates to enhance the efficiency of room temperature devices.     

Concerning virial-based estimations of strength of bonding intermolecular interactions in molecular crystals and supramolecular complexes

It is shown that the electronic virial-based correlation should be used to estimate bonding contributions to the rigidity of molecular vibrations in crystals.     

Assessment of hydrophobic interactions and their contributions through the analysis of the methane dimer

Hydrophobic Interactions (HIs) are important in many phenomena of molecular recognition in chemistry and biology. Still, the relevance of HIs is sometimes difficult to evaluate particularly in large systems and intramolecular interactions. We put forward a method to estimate the magnitude and the different contributions of a given HI of the C···C, H? C···H, and H···H type through (i) the analysis of the electron density in the intermolecular region for eleven relative orientations of the methane dimer and (ii) the subsequent decomposition of the corresponding interaction energy in physically significant contributions using Symmetry Adapted Perturbation Theory (SAPT). Strong correlations were found between the topological properties of calculated at intermolecular bond critical points and plus its different contributions with the C···C distance of the considered orientations of (CH₄)₂. These correlations were used to construct Mollier‐like diagrams of and its components as a function of the separation between two carbons and the orientation of the groups bonded to these atoms. The ethane dimer and tert‐butylcyclohexane are used as representative examples of this new approach. Overall, we anticipate that this new method might prove useful in the study of both intramolecular and intermolecular HIs particularly of those within large systems wherein SAPT or electronic structure calculations are computationally expensive or even prohibitive. © 2014 Wiley Periodicals, Inc.     

Charge-Flow Profiles along Curvilinear Paths: A Flexible Scheme for the Analysis of Charge Displacement upon Intermolecular Interactions

The Charge-Displacement (CD) analysis has proven to be a powerful tool for a quantitative characterization of the electron-density flow occurring upon chemical bonding along a suitably chosen interaction axis. In several classes of interesting intermolecular interactions, however, an interaction axis cannot be straightforwardly defined, and the CD analysis loses consistency and usefulness. In this article, we propose a general, flexible reformulation of the CD analysis capable of providing a quantitative view of the charge displacement along custom curvilinear paths. The new scheme naturally reduces to ordinary CD analysis if the path is chosen to be a straight line. An implementation based on a discrete sampling of the electron densities and a Voronoi space partitioning is described and shown in action on two test cases of a metal-carbonyl and a pyridine-ammonia complex.     

Nature of weak inter- and intramolecular interactions in crystals 3. Intermolecular P=O...C=O contact in crystals of phenyl methylisopropoxyphosphorylformate

Phenyl methylisopropoxyphosphorylformate was studied by high resolution X-ray diffraction. The chemical bonding in the vicinity of the phosphoryl group was studied by analyzing the deformation electron density, the Laplacian of the electron density, and the electron localization function. A P=O...C=O intermolecular contact was revealed and its nature was analyzed.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 3, pp. 553–558, March, 2005.     

Intermolecular hydrogen bonds: Comparison of associates in crystals and liquids

The density and sound velocity were measured within wide ranges of temperature for a number of liquids (water, formamide, diols, aliphatic alcohols, cellosolves, ketones), in which various types of H-associate can exist. The temperature dependences of the adiabatic and molar adiabatic compressibility, density, and molar volume are analyzed. The values of the molar adiabatic compressibility permit one to evaluate the dimensionality of H-associates existing in liquids; the values of adiabatic compressibility do not offer this possibility. The terms responsible for the similarity and difference between H-associates in crystals and liquids are discussed.     

Computational Design of High Energy RDX-Based Derivatives: Property Prediction,Intermolecular Interactions,and Decomposition Mechanisms

A series of new high-energy insensitive compounds were designed based on 1,3,5-trinitro-1,3,5-triazinane (RDX) skeleton through incorporating -N(NO₂)-CH₂-N(NO₂)-, -N(NH₂)-, -N(NO₂)-, and -O- linkages. Then, their electronic structures, heats of formation, detonation properties, and impact sensitivities were analyzed and predicted using DFT. The types of intermolecular interactions between their bimolecular assemble were analyzed. The thermal decomposition of one compound with excellent performance was studied through ab initio molecular dynamics simulations. All the designed compounds exhibit excellent detonation properties superior to 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20), and lower impact sensitivity than CL-20. Thus, they may be viewed as promising candidates for high energy density compounds. Overall, our design strategy that the construction of bicyclic or cage compounds based on the RDX framework through incorporating the intermolecular linkages is very beneficial for developing novel energetic compounds with excellent detonation performance and low sensitivity.     

A comparative study of some lithium and hydrogen‐bonded complexes: Ab initio and QTAIM studies

The nature of the interactions of cyanide with lithium and hydrogen halides was investigated using ab initio calculations and topological analysis of electron density. The computed properties of the lithium‐bonded complexes RCN···LiX (R = H, F, Cl, Br, C?CH, CH?CH₂, CH₃, C₂H₅; X = Cl, Br) were compared with those of corresponding hydrogen‐bonded complexes RCN···HX. The results show that both types of intermolecular interactions are “closed‐shell” noncovalent interactions. The effect of substitution on the interaction energy and electron density at the bond critical points of the lithium and hydrogen bonding interactions is similar. In comparison, the interaction energies of lithium‐bonded complexes are more negative than those of hydrogen‐bonded counterparts. The electrostatic interaction plays a more important role in the lithium bond than in the hydrogen bond. On complex formation, the net charge and energy of the Li atom decrease and the atomic volume increases, while the net charge and energy of the H atom increase and the atomic volume decreases. © 2013 Wiley Periodicals, Inc.     

Multiple Luminescence Responses towards Mechanical Stimulus and Photo-Induction: The Key Role of the Stuck Packing Mode and Tunable Intermolecular Interactions

Organic luminescence with different forms continues to be one of the most active research fields in science and technology. Herein, an ultra-simple organic molecule (TPA-B), which exhibits both mechanoluminescence (ML) and photo-induced room-temperature phosphorescence (RTP) in the crystalline state, provides an opportunity to reveal the internal mechanism of ML and the dynamic process of photo-induced RTP in the same molecule. Through the detailed investigation of photophysical properties together with crystal structures, the key role of molecular packing and intermolecular interactions was highlighted in the luminescence response by mechanical and light stimulus, affording efficient strategies to design potential smart functional materials with multiple luminescence properties.     

Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions

The hydrogen bond (H‐bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O? H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6‐311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G_b and potential V_b densities at the H···O bond critical point and the H‐bond energy E_HB. Comparison of the computed E_HB values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999 , 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V_b?E_HB approach overestimates the energy of moderate H‐bonds (E_HB < 60 kJ/mol) by ～20% and gives unreliably high energies for crystals with strong H‐bonds. On the other hand, the G_b?E_HB approach affords reliable results for the crystals under consideration. The linear relationship between G_b and E_HB is basis set superposition error (BSSE) free and allows to estimate the H‐bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H‐bond energies in molecular crystals, the G_b value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X‐ray diffraction experiments. © 2012 Wiley Periodicals, Inc.     

Comparative analysis of molecular interactions in quaternary fluid system performed by classical and ab initio molecular dynamics

Molecular interactions in the quaternary fluid system acetic acid–n-propanol–n-propyl acetate–water were analyzed by classical and ab initio molecular dynamics methods. It was shown that ab initio molecular dynamics simulation can reproduce the molecular mobility tendency and structural features of a multicomponent system without empirical parameters.     

Central‐Atom Size Effects on the Methyl Torsions of Group XIV Tetratolyls

The Group XIV tetratolyl series X(C₆H₄‐CH₃)₄ (X=C, Si, Ge, Sn, Pb) were studied by using inelastic neutron scattering to measure the low‐energy phonon spectra to directly access the methyl‐group torsional modes. The effect of increased molecular radius as a function of the size of the central atom was shown to have direct influence on the methyl dynamics, reinforced with the findings of molecular dynamics and contact surface calculations, based upon the solid‐state structures. The torsional modes in the lightest analogue were found to be predominantly intramolecular: the Si and Ge analogues have a high degree of intermolecular methyl–methyl group interactions, whilst the heaviest analogues (Sn and Pb) showed pronounced intermolecular methyl interactions with the whole phonon bath of the lattice modes.     

Characteristic features of intra- and intermolecular interactions in crystals of pyrrole-2-carbaldehyde isonicotinoylhydrazone and its hydrate

Pyrrole-2-carbaldehyde isonicotinoylhydrazone (1) and its hydrate [1·H₂O] (2) were studied by single-crystal X-ray diffraction analysis. The introduction of the pyrrole substituent into N"-substituted isonicotinic hydrazide (INH) causes the intramolecular redistribution of the electron density compared to those in INHs studied earlier, which increases the basicity of the hydrazone nitrogen atom (N") involved in intermolecular hydrogen bonding. This effect has not been observed in the structures of N"-substituted INHs and benzhydrazides studied previously. Intermolecular hydrogen bonds play a decisive role in the formation of the crystal structures of 1 and 2.     

Intermolecular interactions on amine‐cured epoxy matrices with different crosslink densities. Influence on the hole and specific volumes and the mechanical behavior

The architecture of an epoxy matrix was modified by curing the resin with mono‐/diamine mixtures having identical chemical structures. Both hole volume and specific volume variations were studied by positron annihilation lifetime spectroscopy and pressure‐volume‐temperature/density measurements, respectively. The average hole volume of the networks at room temperature slightly increased when the monoaminic chain extender content increased. The increment in the intermolecular interactions between functional groups of the networks chains, due to the less hindered nitrogen introduced by the monoamine, appears to be the responsible for the observed behavior. Besides, only small variations on the specific volume were observed on increasing the monoamine content, which points out that for a cured epoxy system, the chemical structure of the curing agent is mainly responsible for chain packing in the networks. On the other hand, intermolecular interactions between chains were considered as the key factor for fixing stiffness and strength. Thus, it was observed that the increase of the intermolecular interactions with the monoamine content produced a decrease in the sub‐T_g small‐range cooperative motions, which increased the low‐deformation mechanical properties at temperatures between β and α relaxations. This conclusion could be applied to previous investigations with epoxy matrices not fully crosslinked (nonstoichiometric or noncompletely cured formulations). Finally, it was found that fracture properties do not significantly depend either on the hole volume or on the intermolecular interactions. Fracture properties are more dependent on the crosslink density and the glass transition temperature. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1240–1252, 2009     

Isostructurality, polymorphism and mechanical properties of some hexahalogenated benzenes: the nature of halogen...halogen interactions

The nature of intermolecular interactions between halogen atoms, X...X (X = Cl, Br, I), continues to be of topical interest because these interactions may be used as design elements in crystal engineering. Hexahalogenated benzenes (C6Cl(6-n)Br(n), C6Cl(6-n)I(n), C6Br(6-n)I(n)) crystallise in two main packing modes, which take the monoclinic space group P2(1)/n and the triclinic space group P1. The former, which is isostructural to C6Cl6, is more common. For molecules that lack inversion symmetry, adoption of this monoclinic structure would necessarily lead to crystallographic disorder. In C6Cl6, the planar molecules form Cl...Cl contacts and also pi...pi stacking interactions. When crystals of C6Cl6 are compressed mechanically along their needle length, that is, [010], a bending deformation takes place, because of the stronger interactions in the stacking direction. Further compression propagates consecutively in a snakelike motion through the crystal, similar to what has been suggested for the motion of dislocations. The bending of C6Cl6 crystals is related to the weakness of the Cl...Cl interactions compared with the stronger pi...pi stacking interactions. The triclinic packing is less common and is restricted to molecules that have a symmetrical (1,3,5- and 2,4,6-) halogen substitution pattern. This packing type is characterised by specific, polarisation-induced X...X interactions that result in threefold-symmetrical X3 synthons, especially when X = I; this leads to a layered pseudohexagonal structure in which successive planar layers are inversion related and stacked so that bumps in one layer fit into the hollows of the next in a space-filling manner. The triclinic crystals shear on application of a mechanical stress only along the plane of deformation. This shearing arises from the sliding of layers against one another. Nonspecificity of the weak interlayer interactions here is demonstrated by the structure of twinned crystals of these compounds. One of the compounds studied (1,3,5-tribromo-2,4,6-triiodobenzene) is dimorphic, adopting both the monoclinic and triclinic structures, and the reasons for polymorphism are suggested. To summarise, both chemical and geometrical models need to be considered for X...X interactions in hexahalogenated benzenes. The X...X interactions in the monoclinic group are nonspecific, whereas in the triclinic group some X...X interactions are anisotropic, chemically specific and crystal-structure directing.     

The nature of intermolecular CuI...CuI interactions: a combined theoretical and structural database analysis

The nature of intermolecular interactions between dicoordinate Cu(I) ions is analyzed by means of combined theoretical and structural database studies. Energetically stable Cu(I).Cu(I) interactions are only found when the two monomers involved in the interaction are neutral or carry opposite charges, thus allowing us to speak of bonding between the components of the bimolecular aggregate. A perturbative evaluation of the components of the intermolecular interaction energies, by means the IMPT scheme of Stone, indicates that both the Coulombic and dispersion forces are important in determining the Cu(I).Cu(I) bonding interactions, because only a small part of that energy is attributable to Cu.Cu interactions, while a large component results from Cu.ligand interactions. The electrostatic component is the dominant one by far in the interaction between charged monomers, while in the interaction between neutral complexes, the electrostatic component is found to be of the same order of magnitude as the dispersion term. Bimolecular aggregates that have like charges are repulsive by themselves, and their presence in the solid state results from anion.cation interactions with ions external to this aggregate. In these cases, the short-contact Cu.Cu interactions here should be more properly called counterion-mediated Cu.Cu bonds.     

Qualitative and quantitative analysis of intermolecular interactions in xanthenedione derivatives

The existence of intermolecular interactions and the conformational geometry adopted by molecules are related to biological activity. Xanthenedione molecules are promising and emerging antioxidants and acetylcholinesterase inhibitors. To examine the role of different functional groups involved in the intermolecular interactions and conformational geometries adopted in xanthenediones, a series of three substituted xanthenediones have been crystallized [9‐(3‐hydroxyphenyl)‐3,3,6,6‐tetramethyl‐3,4,5,6,7,9‐hexahydro‐1H‐xanthene‐1,8(2H)‐dione, C₂₃H₂₆O₄, 9‐(5‐bromo‐2‐methoxyphenyl)‐3,3,6,6‐tetramethyl‐3,4,6,7‐tetrahydro‐2H‐xanthene‐1,8(5H,9H)‐dione, C₂₄H₂₇BrO₄, and 3,3,6,6‐tetramethyl‐9‐(pyridin‐2‐yl)‐3,4,6,7‐tetrahydro‐2H‐xanthene‐1,8(5H,9H)‐dione, C₂₂H₂₅NO₃] and their intermolecular interactions analyzed via Hirshfeld analysis. The results show that all the derivatives adopt the same structural conformation, where the central ring has a shallow boat conformation and the outer rings have a twisted boat conformation. The intermolecular interactions in the molecules are predominantly O—H…O, C—H…O and π–π interactions. The optimized structures of the derivatives from theoretical B3LYP/6‐311G** calculations show a good correlation with the experimental structures. The lattice energy involved in the intermolecular interactions has been explored using PIXELC.