Lattice dynamics of solid hydrogen chloride

Lattice dynamics of solid hydrogen chloride is studied, assuming a rigid molecule, in the harmonic and pair potential (Lennard-Jones interaction) approximation between atoms with the inclusion of electrostatic interactions between point dipoles placed on atomic centres. The potential parameters for each of the different non-bonded atom pairs were obtained by means of an optimization routine to give a least-squares fit to observed zone centre (k = 0) frequencies, equilibrium conditions and lattice energy of the lattice.     

Seeking for ultrashort “non-bonded” hydrogen–hydrogen contacts in some rigid hydrocarbons and their chlorinated derivatives

In this communication a systematic computational survey on some rigid hydrocarbon skeletons, e.g., half-cage pentacyclododecanes and tetracyclododecanes, and their chlorinated derivatives to seek for the so-called ultrashort “non-bonded” hydrogen–hydrogen contacts is done. It is demonstrated that upon a proper choice and modifications of the main hydrocarbon backbones, and addition of some chlorine atoms instead of the original hydrogen atoms in parts of the employed hydrocarbons, the resulting strain triggers structural changes yielding ultrashort hydrogen–hydrogen contacts with inter-nuclear distances as small as 1.38 Å. Such ultrashort contacts are clearly less than the world record of an ultrashort non-bonded hydrogen–hydrogen contact, 1.56 Å, very recently realized experimentally by Pascal and coworkers in in,in-bis(hydrosilane) (J Am Chem Soc 135:13235, 2013). The resulting computed structures, as well as the developed methodology for structure design open the door for constructing a proper set of molecules for future studies on the nature of the so-called non-bonded hydrogen–hydrogen interactions that is now an active and controversial area of research.     

Allinger's gauche hydrogen hypothesis as tested by an alternative force field model

Allinger's hypothesis that gauche hydrogen, rather than gauche methyl interactions are mainly responsible for conformational equilibria was tested by molecular mechanics calculations using the Engler force field model. For the gauche-anti conformational energy of n-butane, effective cancellation among non-bonded in teractions involving the methyl groups results in the gauche hydrogen interactions across the central C-C bond as the single largest contribution to the energy difference. However, the contribution of this interaction is only one third of the 0.9 kcal difference. For 2,3-dimethylbutane, strain analysis of the gauche-anti conformational energy contributions reveals that geminal and gauche CH₃/CH₃ interactions dominate over the gauche hydrogen interaction Similar analyses for several monosubstituted cyclohexanes confirm that “across-the-ring” interactions. between axial substituents and syn -axial hydrogen atoms are still largely responsible for the instability of the axial relative to the equatorial conformer. In disagreement with Allinger's proposal, the “equatorial hydrogen effect” is found to contribute only a minor amount to the conformational energy difference. Allinger's hypothesis is concluded to be force field dependent, and not to have general validity.     

On the electronic origins of barriers to methyl rotation: CNDO/2 calculations on (CH3)2XHn (X = C,Si, N,P, O,S) molecules

CNDO calculations are performed for the homogeneous series of (CH₃)₂XH_n compounds (X = C, Si, N, P, O, S) in order to determine the molecular equilibrium configuration. In agreement with available experimental data, for all investigated molecules, the theoretical energy minimum is found for the (θ = 60°, ψ = 60°) conformation in which one hydrogen of each methyl group is in the X heavy atoms plane but pointing outside the CXC angle. A partitioning of total energy shows that the variations of this quantity are completely reflected by the variations of the interaction energy between non-bonded terms. A more detailed analysis reveals, only for the third-row compounds, the essential role of the interactions between central atom and methyl hydrogens.     

Calculation of conformations of organic molecules

The most stable conformation of the molecule has a minimum of potential energy that arises due to the competition between the tendency of the valency angles to take ideal values and that of non-bonded atoms to be situated at an equilibrium distance. The equilibrium distance is equal to the sum of intermolecular radii determined by measuring the distances between atoms of adjacent molecules in the crystal. This idea is suggested as underlying a method of computation that enables to solve two problems. Firstly, the structure of the molecule being known, it becomes possible to ascertain the points of the interaction curve of the non-bonded atoms and secondly, with the interaction curve known, one can calculate the optimal configuration of the molecule.

To illustrate the suggested theory the conformation of molecules of some cyclic hydrocarbons has been calculated. It is to be stressed that the investigation of the conformation of strained molecules affords the main means of studying the interaction of non-bonded atoms.     

The interaction curve of non-bonded carbon and hydrogen atoms and its application

A universal interaction curve of non-bonded carbon and hydrogen atoms has been proposed. This curve has been successfully applied to determine numerous properties of various saturated and unsaturated hydrocarbons such as the equilibrium of molecular conformation, the strain energy of molecules, the sublimation heat of organic crystals and so on.     

1,1-二氟乙烷和1,2-二氟乙烷分子内原子间非键相互作用

用从头算势诱导极小二乘拟合(PD/LSF)和(exp-6-1)函数研究了1,1-二氟乙烷和1,2-二氟乙烷分子内非键原子间的相互作用。计算结果表明, 同分异构体的能量稳定性差, 在于分子内非键原子间的相互作用。该模式提供了一种简单、实用的研究分子内非键相互作用的方法。     

Aromatic Rings as Molecular Determinants for the Molecular Recognition of Protein Kinase Inhibitors

Protein kinases are key enzymes in many signal transduction pathways, and play a crucial role in cellular proliferation, differentiation, and various cell regulatory processes. However, aberrant function of kinases has been associated with cancers and many other diseases. Consequently, competitive inhibition of the ATP binding site of protein kinases has emerged as an effective means of curing these diseases. Over the past three decades, thousands of protein kinase inhibitors (PKIs) with varying molecular frames have been developed. Large-scale data mining of the Protein Data Bank resulted in a database of 2139 non-redundant high-resolution X-ray crystal structures of PKIs bound to protein kinases. This provided us with a unique opportunity to study molecular determinants for the molecular recognition of PKIs. A chemoinformatic analysis of 2139 PKIs resulted in findings that PKIs are “flat” molecules with high aromatic ring counts and low fractions of sp³ carbon. All but one PKI possessed one or more aromatic rings. More importantly, it was found that the average weighted hydrogen bond count is inversely proportional to the number of aromatic rings. Based on this linear relationship, we put forward the exchange rule of hydrogen bonding interactions and non-bonded π-interactions. Specifically, a loss of binding affinity caused by a decrease in hydrogen bonding interactions is compensated by a gain in binding affinity acquired by an increase in aromatic ring-originated non-bonded interactions (i.e., π–π stacking interactions, CH–π interactions, cation–π interactions, etc.), and vice versa. The very existence of this inverse relationship strongly suggests that both hydrogen bonding and aromatic ring-originated non-bonded interactions are responsible for the molecular recognition of PKIs. As an illustration, two representative PKI–kinase complexes were employed to examine the relative importance of different modes of non-bonded interactions for the molecular recognition of PKIs. For this purpose, two FDA-approved PKI drugs, ibrutinib and lenvatinib, were chosen. The binding pockets of both PKIs were thoroughly examined to identify all non-bonded intermolecular interactions. Subsequently, the strengths of interaction energies between ibrutinib and its interacting residues in tyrosine kinase BTK were quantified by means of the double hybrid DFT method B2PLYP. The resulting energetics for the binding of ibrutinib in tyrosine kinase BTK showed that CH–π interactions and π–π stacking interactions between aromatic rings of the drug and hydrophobic residues in its binding pocket dominate the binding interactions. Thus, this work establishes that, in addition to hydrogen bonding, aromatic rings function as important molecular determinants for the molecular recognition of PKIs. In conclusion, our findings support the following pharmacophore model for ATP-competitive kinase inhibitors: a small molecule features a scaffold of one or more aromatic rings which is linked with one or more hydrophilic functional groups. The former has the structural role of acting as a scaffold and the functional role of participating in aromatic ring-originated non-bonded interactions with multiple hydrophobic regions in the ATP binding pocket of kinases. The latter ensure water solubility and form hydrogen bonds with the hinge region and other hydrophilic residues of the ATP binding pocket.     

投影解析法求直链烷烃内旋转时非键原子对间距离

用旋转投影解析几何的方法,计算了链烃分子链上相邻原子上的非键原子对间的距离r(φ_i),及相间原子上的非键原子对间的距离r(φ_i,φ₁₊₁.所得公式适用于链上不含双键的链状分子.     

Structural evidence for the radical scavenging mechanism of some aminothiol group of radioprotectants

Aminothiols constitute an important group of radioprotectants. The structures of a few well-known compounds belonging to the family of radioprotectants have been determined by single crystal x-ray diffraction methods. The sulphur and the amino nitrogen atoms are separated by two tetrahedral carbon atoms in these compounds. Thegauche conformation of the sulphur and the nitrogen atoms and the consequent non-bonded intramolecular S … N interaction observed in some of the crystal structures appear to favour the hypothesis that the protective mechanism of these compounds is by free radical scavenging.     

Long-range interaction in the D and D′ states of H2

The interaction energy between two hydrogen atoms in the D and D′ ¹Π_u states of the hydrogen molecule has been calculated for large internuclear distances (12 ? R ? 25 bohr). The variational method and a very flexible trial wave-function were used. The results indicate that for the states under consideration the Rayleigh-Schrödinger perturbation theory with the multipole expansion of the interaction hamiltonian gives reliable results only for R > 25 bohr i.e. in the region where the interaction energies are practically negligible.     

Combining rules for interatomic potential functions of Buckingham form

The geometric mean combining rule for the total interaction energy of two non-bonded atoms, the energy being described by the Buckingham type potential, is suggested. Some numerical examples are given to compare this rule with the combining rules for the exp-six potentials proposed by Mason and Rice.     

The Role of Aromatic Residues in Stabilizing the Secondary and Tertiary Structure of Avian Pancreatic Polypeptide

Avian Pancreatic Polypeptide is a 36 residue protein that exhibits a tertiary fold. Results of previous experimental and computational studies indicate that the structure of aPP is stabilized more by non-bonded interactions than by the hydrophobic effect. Aromatic residues are known to participate in a variety of long range non-bonded interactions, with both backbone atoms and the atoms of other side-chains, which could be responsible, in part, for the stability of both the local secondary structure and the tertiary fold. The effect of these aromatic interactions on the stability of aPP was calculated using BHandHLYP/cc-pVTZ. Aromatic residues were shown to participate in multiple hydrogen bonded and weakly polar interactions in the secondary structure. The energies of the weakly polar interactions are comparable with those of hydrogen bonds. Aromatic residues were also shown to participate in multiple weakly polar interactions across the tertiary fold, again with energies similar to those of hydrogen bonds.     

An investigation into the role of chloro-substituents in hydrogen-bonded crystals: The crystal structures of the dichlorophenols

A graphical analysis has been made of hydrogen-bonding patterns and non-bonded interactions in the crystal structures of the six dichlorophenols. This shows that hydrogen bonding is the primary interaction in stabilising all the isomers, and that C?C and Cl?Cl non-bonded interactions are also important in stabilising structures characterised by a short (≈ 4 Ã) axis.     

Experimental and computational studies of molecules with close,non-bonded hydrogen–hydrogen contacts: common computational methods grossly overestimate some ‘through-space’ NMR scalar coupling constants

The NMR spin–spin scalar coupling constants (J_HH's) of closely contacting, but non-bonded hydrogen atoms in a series of highly strained molecules (including a new in,in-cyclophane made specifically for this study) have been examined both experimentally and computationally. The experimental J_HH's are invariably quite small (0.1–0.6 Hz), but common DFT methods with modest basis sets nearly always overestimate these values, by factors of 10–30, and even with quite large basis sets (up to cc-pVQZ) the J_HH's of two of the molecules are overestimated by a factor of 10 or more. Possible reasons for these discrepancies are discussed.     

Hydrogen–hydrogen bonding in biphenyl revisited

The evidence for the stabilizing nature of the H–H bonding in planar biphenyl is succinctly reviewed. The stabilizing nature of the H–H bonding is revealed through a comparison of the atomic energy of every atom in planar biphenyl with the same atom in the twisted equilibrium structure. It is shown that the barrier to rotation via the planar transition state is the net resultant of a stabilisation of the four ortho-hydrogen atoms (by 8 kcal/mol each), a stabilisation of the two para-carbon atoms (by 3 kcal/mol each) and by the dominant destabilisation of the two carbon atoms joining the two rings—the two junction carbon atoms—(by 22 kcal/mol each). The energetic stabilisation of the four ortho-hydrogen atoms is further shown to be in large proportion due to the formation of the hydrogen–hydrogen interatomic surface. Furthermore, neither the “bond order” between the two junction carbon atoms nor the total electron delocalisation between the two rings exhibit a significant change in going from the planar to the twisted equilibrium geometry. These findings are in contrast with the classical view of a balance between “steric non-bonded repulsion” and better electron delocalisation as a function of the twist dihedral angle. Similar conclusions have been recently reached by Pacios and Gómez through a study of the electrostatic potential at the position of the hydrogen nuclei. We dedicate this article to Professor TM Krygowski on the occasion of his 70th birthday wishing him a long and productive life.     

Unusually high electron density in an intermolecular non-bonding region: Role of metal substrate

It has been demonstrated that intermolecular interaction,crucial in a plenty of chemical and physical processes,may vary in the presence of metal surface.However,such modification is yet to be quantitatively revealed.Here,we present a systematical density functional theory study on adsorbed bis(para-pyridyl)acetylene(BPPA)tetramer on Au(111)surface.We observed unusually high electron density between two head-to-head N atoms,an intermolecular "non-bonded" region,in adsorbed BPPA tetramer.This exceptional electron density originates from the wavefunction hybridization of the two compressed N lone-electron-pair states of two BPPA,as squeezed by a newly revealed N-Au-N three-center bonding.This bond,together with the minor contribution from N H-C intermolecular hydrogen bonding,shortens the N-N distance from over 4 Å to 3.30 Å and offers an attractive lateral interacting energy of 0.60 eV,effectively to a surface-confined in-plane pressure.The overlapped non-bonding wavefunction hybridization arising from the effective pressure induced by the N-Au-N three-center bonding,as not been fully recognized in earlier studies,was manifested in non-contact Atomic Force Microscopy.     

Weak intermolecular interaction

The SCF interaction energy (ΔE ^SCF) between two hydrogen molecules was separated into (Coulomb + exchange) and (induction + charge-transfer) components. The effect of the basis set and orientation of the two molecules on the ΔE ^SCF energy and its components are discussed.     

Inorganic Chemistry in Liquid Ammonia : by David Nicholls,Elsevier Scientific Publ. Co., Amsterdam/Oxford/New York, 1979, x + 238 pp., Dfl. 110.00, $ 49.00.

Substitution of the hydrogen atoms of the cyclopentadienyl ring of (N, N-dimethylaminomethyl)cymantrene by deuterium changes the direction of orientation of metalation of this amine.     

Bonding in small ring paddlanes

The geometries of [1.1.1.1]paddlane and [2.2.2.2]paddlane have been calculated via ab initio mo theory. In both cases, a short bridgehead-bridgehead distance and a relatively large bond order was found, indicating a bonding interaction between these formally non-bonded atoms. The energies of conversion to more stable compounds were estimated.