Intermolecular Interactions of Noble-Gas-Containing Species

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.

Structure of 6-acetoxycoumarin: topochemical photodimerization and analysis of acetoxy...acetoxy interactions in the solid state

C~HaO 4, Mr=204.2, monoclinic, P2Jn,a=3.900(1), =37.530(6), c=6.460(1)A, fl=103.7 (1) °, V= 918.5 (5) A 3, Z = 4, D m = 1.443, D x --- 1.476 Mg m -3, Cu Ks, 2 = 1.5418 ,/k, /t = 0.86 mm -~, F(000) = 424, T= 293 K, R = 0.075 for 1019 significant reflections. Molecules pack in fl-type stacking mode which is characterized by the close packing of parallel and nearly planar reactive double bonds with a separation of 3.900/~ along the a axis.The syn head-head dimer obtained is the direct consequence of this packing arrangement. Molecular packing is stabilized by intermolecular C-H...O hydrogen bonding. Analysis of acetoxy...acetoxy interactions in the acetoxy compounds retrieved from the Cambridge Structural Database reveal that the majority of them are anti-dipolar.

Analysis of Cl center dot center dot center dot Cl and C-H center dot center dot center dot Cl intermolecular interactions involving chlorine in substituted 2-chloroquinoline derivatives

Six crystal structures of substituted 2-chloroquinoline derivatives have been analysed to evaluate the role of Cl atom as a self recognizing unit resulting in the formation of Cl center dot center dot center dot Cl and C-H center dot center dot center dot Cl interactions to generate supramolecular assembly in the solid state. The features of Type I and Type II geometries associated with Cl center dot center dot center dot Cl interactions have been analysed to show directional preferences leading to differences in the packing motifs in these crystal structures. C-H center dot center dot center dot Cl interactions are generated exclusively in structures depicting Type II Cl center dot center dot center dot Cl interaction have been observed in these structures.

Nature of Cl center dot center dot center dot Cl Intermolecular Interactions via Experimental and Theoretical Charge Density Analysis:Correlation of Polar Flattening Effects with Geometry

The experimental charge density distribution in three compounds, 2-chloro-3-quinolinyl methanol, 2-chloro-3-hydroxypyridine, and 2-chloro-3-chloromethyl-8-methylquinoline, has been obtained using high-resolution X-ray diffraction data collected at 100 K based on the aspherical multipole modeling of electron density. These compounds represent type I (cis), type I (trans), and type II geometries, respectively, as defined for short Cl center dot center dot center dot Cl interactions. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from a periodic quantum calculation at the B3LYP/6-31G** level. The topological features derived from the Bader's theory of atoms in molecules (AIM) approach unequivocally suggest that both cis and trans type I geometries show decreased repulsion, whereas type II geometry is attractive based on the nature of polar flattening of the electron density around the Cl atom.

Charge Density Analysis of Heterohalogen (Cl center dot center dot center dot F) and Homohalogen (F center dot center dot center dot F) Intermolecular Interactions

Experimental charge density distribution in 2-chloro-4-fluorobenzoic acid and 4-fluorobenzamide has been carried out using high resolution X-ray diffraction data collected at 100 K using Hansen-Coppens multipolar formalism of electron density. These compounds display short Cl center dot center dot center dot F and F center dot center dot center dot F interactions, respectively. The experimental results are compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculation at the B3LYP/6-31G** level. The topological features were derived from Bader's ``atoms in molecules'' (AIM) approach. Intermolecular Cl center dot center dot center dot F interaction in 2-chloro-4-fluorobenzoic acid is attractive in nature (type II interaction) while the nature of F center dot center dot center dot F interactions in 4-fluorobenzamide shows indication of a minor decrease in repulsion (type I interaction), though the extent of polarization on the fluorine atom is arguably small.

Studies in crystal engineering: Effect of fluorine substitution in crystal packing and topological photodimerization of styryl coumarins in the solid state

Styryl coumarins generally yield centrosymmetric (alpha-mode, anti-HT) photodimers when subjected to irradiation in the solid state, However, the substitution of fluorine dramatically alters the packing mode and steers the molecules 4-(4-fluorostyryl)coumarin 1 and 4-(2-fluorostyryl)coumarin 2 to form a stereospecific photodimer, beta-mode, syn-HH across the styrenic double bond (yield 78-85%). The stereochemistry of the photodimer 2a has been established by X-ray crystallography. There is no evidence for the presence of C-H ... F interactions. The true nature of the weak atom-atom interactions called into play when fluorine is substituted is not clear, It is observed that the fluoro substituted compounds have greater crystal density than the corresponding unsubstituted ones.

Nature and strength of C-H center dot center dot center dot O interactions involving formyl hydrogen atoms: computational and experimental studies of small aldehydes

Structural and electronic properties of C-H center dot center dot center dot O contacts in compounds containing a formyl group are investigated from the perspective of both hydrogen bonding and dipole-dipole interactions, in a systematic and graded approach. The effects of a-substitution and self-association on the nature of the formyl H-atom are studied with the NBO and AIM methodologies. The relative dipole-dipole contributions in formyl C-H center dot center dot center dot O interactions are obtained for aldehyde dimers. The stabilities and energies of aldehyde clusters (dimer through octamer) have been examined computationally. Such studies have an implication in crystallization mechanisms. Experimental X-ray crystal structures of formaldehyde, acrolein and N-methylformamide have been determined in order to ascertain the role of C-H center dot center dot center dot O interactions in the crystal packing of formyl compounds.

Solute solute and solvent solute interactions in solid solutions of Cu+Sn, Au+Sn and Cu+Au+Sn alloys

The chemical potentials of tin in its α-solid solutions with Cu, Au and Cu + Au alloys have been measured using a gas-solid equilibration technique. The variation of the excess chemical potential of tin with its composition in the alloy is related to the solute-solute repulsive interaction, while the excess chemical potential at infinite dilution of the solute is a measure of solvent-solute interaction energies. It is shown that solute-solute interaction is primarily determined by the concentration of (s + p) electrons in the conduction band, although the interaction energies are smaller than those predicted by either the rigid band model or calculation based on Friedel oscillations in the potential function. Finally, the variation of the solvent-solute interaction with solvent composition in the ternary system can be accounted for in terms of a quasi-chemical treatment which takes into account the clustering of the solvent atoms around the solute.

Metal and Alloy Nanoparticles by Amine-Borane Reduction of Metal Salts by Solid-Phase Synthesis: Atom Economy and Green Process

A new solid state synthetic route has been developed toward metal and bimetallic alloy nanoparticles from metal salts employing amine-boranes, as the reducing agent. During the reduction, amine-borane plays a dual role: acts as a reducing agent and reduces the metal salts to their elemental form and simultaneously generates a stabilizing agent in situ which controls the growth of the particles and stabilizes them in the nanosize regime. Employing different amine-boranes with differing reducing ability (ammonia borane (AB), dimethylamine borane (DMAB), and triethylamine borane (TMAB)) was found to have a profound effect on the particle size and the size distribution. Usage of AB as the reducing agent provided the smallest possible size with best size distribution. Employment of TMAB also afforded similar results; however, when DMAB was used as the reducing agent it resulted in larger sized nanoparticles that are polydisperse too. In the AB mediated reduction, BNHx polymer generated in situ acts as a capping agent whereas, the complexing amine of the other amine-boranes (DMAB and TMAB) play the same role. Employing the solid state route described herein, monometallic Au, Ag, Cu, Pd, and Ir and bimetallic CuAg and CuAu alloy nanoparticles of <10 nm were successfully prepared. Nucleation and growth processes that control the size and the size distribution of the resulting nanoparticles have been elucidated in these systems.

Determination of favorable inter-particle interactions for formation of substitutionally ordered solid phases from a binary mixture of oppositely charged colloidal suspensions

The solid phase formed by a binary mixture of oppositely charged colloidal particles can be either substitutionally ordered or substitutionally disordered depending on the nature and strength of interactions among the particles. In this work, we use Monte Carlo molecular simulations along with the Gibbs-Duhem integration technique to map out the favorable inter-particle interactions for the formation of substitutionally ordered crystalline phases from a fluid phase. The inter-particle interactions are modeled using the hard core Yukawa potential but the method can be easily extended to other systems of interest. The study obtains a map of interactions depicting regions indicating the type of the crystalline aggregate that forms upon phase transition.

Dense network of O-H ... O and C-H ... O interactions in the solid state structure of n-pentyl-2-chloro-2-deoxy-alpha-D-manno-sept 3-uloside

Single crystal X-ray structural analysis of a septanoside, namely, n-pentyl-2-chloro-2-deoxy sept-3-uloside (1) provides many finer details of the molecular structure, in addition to its preferred twist-chair conformation, namely, (TC3,4)-T-5,6 conformation. Structural analysis reveals a dense network of O-H...O, C-H...O and van der Waals interactions that stabilize interdigitized, planar bi-layer structure of the crystal lattice. (C) 2014 Elsevier Ltd. All rights reserved.

Fine-tuning solid-state luminescence in NPIs (1,8-naphthalimides): impact of the molecular environment and cumulative interactions

An investigation of a series of seven angular ``V'' shaped NPIs (1-7) is presented. The effect of substitution of these structurally similar NPIs on their photophysical properties in the solution-state and the solid-state is presented and discussed in light of experimental and computational findings. Compounds 1-7 show negligible to intensely strong emission yields in their solid-state depending on the nature of substituents appended to the oxoaryl moiety. The solution and solid-state properties of the compounds can be directly correlated with their structural rigidity, nature of substituents and intermolecular interactions. The versatile solid-state structures of the NPI siblings are deeply affected by the pendant substituents. All of the NPIs (1-7) show antiparallel dimeric pi-pi stacking interactions in their solid-state which can further extend in a parallel, alternate, orthogonal or lateral fashion depending on the steric and electronic nature of the C-4' substituents. Structural investigations including Hirshfeld surface analysis methods reveal that where strongly interacting systems show weak to moderate emission in their condensed states, weakly interacting systems show strong emission yields under the same conditions. The nature of packing and extended structures also affects the emission colors of the NPIs in their solid-states. Furthermore, DFT computational studies were utilized to understand the molecular and cumulative electronic behaviors of the NPIs. The comprehensive studies provide insight into the condensed-state luminescence of aggregationprone small molecules like NPIs and help to correlate the structure-property relationships.

Computational Study of the Formation of Short Centrosymmetric N-center dot center dot center dot S Supramolecular Synthon and Related Weak Interactions in Crystalline 1,2,4-Triazoles

A comprehensive analysis of the crystal packing and the energetic features of a series of four biologically active molecules belonging to the family of substituted 4-(benzylideneamino)-3-(4-fluoro-3-phenoxyphenyl)-1H-1,2,4-triazole-5-(4 H)-thione derivatives have been performed based on the molecular conformation and the supramolecular packing. This involves the formation of a short centrosymmetric R-2(2)(8) NH...S supramolecular synthon in the solid state, including the presence of CH...S, CH...O, CH...N, CH...F, CH...Cl, CF...FC, CCl...ClC, and CH...pi intermolecular interactions along with pp stacking to evaluate the role of noncovalent interactions in the crystal. The presence of such synthons has a substantial contribution toward the interaction energy (-18 to -20 kcal/mol) as obtained from the PIXEL calculation, wherein the Coulombic and polarization contribution are more significant than the dispersion contribution. The geometrical characteristics of such synthons favor short distance, and the population of related molecules having these geometries is rare as has been obtained from the Cambridge Structural Database (CSD). Furthermore, their interaction energies have been compared with those present in our molecules in the solid state. The topological characteristics of the NH...S supramolecular synthon, in addition to related weak interactions, CH...N, CH...Cl, CF...FC, and CCl...ClC, have been estimated using the quantum theory of atoms in molecules (QTAIM). In addition, an analysis of the Hirshfeld surface and associated fingerprint plots of these four molecules also have provided a platform for the evaluation of the contribution of different atom...atom contacts, which contribute toward the packing of the molecules in solids.

Charge density distribution and electrostatic interactions of ethionamide: an inhibitor of the enoyl acyl carrier protein reductase (inhA) enzyme of Mycobacterium tuberculosis

An experimental charge density analysis of an anti-TB drug ethionamide was carried out from high resolution X-ray diffraction at 100 K to understand its charge density distribution and electrostatic properties. The experimental results were validated from periodic theoretical charge density calculations performed using CRYSTAL09 at the B3LYP/6-31G** level of theory. The electron density rho(bcp)(r) and the Laplacian of electron density del(2)(rho bcp)(r) of the molecule calculated from both the methods display the charge density distribution of the ethionamide molecule in the crystal field. The electrostatic potential map shows a large electropositive region around the pyridine ring and a large electronegative region at the vicinity of the thiol atom. The calculated experimental dipole moment is 10.6D, which is higher than the value calculated from theory (8.2D). The topological properties of C-H center dot center dot center dot S, N-H center dot center dot center dot N and N-H center dot center dot center dot S hydrogen bonds were calculated, revealing their strength. The charge density analysis of the ethionamide molecule determined from both the experiment and theory gives the topological and electrostatic properties of the molecule, which allows to precisely understand the nature of intra and intermolecular interactions.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.