Intermolecular interactions between halothane and dimethyl ether: a cryosolution infrared and Ab initio study.

The complex of halothane (CHClBrCF(3)) and dimethyl ether has been investigated experimentally in solutions of liquid krypton using infrared spectroscopy and theoretically using ab initio calculations at the MP2/6-311++G(d,p) level. The formation of a 1:1 complex was experimentally detected. The most stable ab initio geometry found is the one in which the C--H bond of halothane interacts with the oxygen atom of dimethyl ether. The complexes in which the chlorine or the bromine atom of halothane interacts with the oxygen atom of the ether were found to be local energy minima and were less stable by 14.5 and 9.3 kJ mol(-1), respectively, than the global minimum. The formation of a single complex species was observed in the infrared spectra; the standard complexation enthalpy of this complex was determined to be -12.3(8) kJ mol(-1). Analysis of the observed complexation shifts supports the identification of the complex as the hydrogen-bonded species. The C--H stretching vibration of halothane was found to show a redshift upon complexation of 19(2) cm(-1). The infrared intensity ratios epsilon(complex)/epsilon(monomer) for the fundamental and its first overtone were measured to be 6.5(1) and 0.31(1). The frequency shift was analyzed using Morokuma-type analysis, and the infrared intensity ratios were rationalized using a model including the mechanical and electric anharmonicity of the C--H stretching fundamental.     

Molecular mechanics studies of the conformations of metal complexes of 1,4,7,10,13,16-hexaazacyclooctadecane: Calculations of macrocyclic cavity size

Molecular mechanics calculations are reported on metal complexes of 18-azacrown-6. Four possible conformations are considered which encapsulate the metal in different geometric environments, namely, chiral octahedral, meso octahedral, trigonal prismatic, and hexagonal bipyramidal. Crystal structures are available for all but the last geometry, and molecular mechanics calculations show an excellent fit to the experimental data. The strain energy of the macrocycle has been calculated for a range of M-N distances, and thus the hole size of the macrocycle has been obtained for various conformations. Two different methods were used to calculate the strain energy of the metal environment. We either used the conventional molecular mechanics term for angle bending,k _b — ₀)², and chose the ideal angles to fit the particular metal geometry, or we set the angle force constants to zero and introduced 1,3 van der Waals interactions between the ligand donor nitrogen atoms. Results from the two methods are compared.     

从对接结构中挑选近天然构象的新方法

分析了包含静电能(ΔEele)、去水化自由能(ΔGACE)以及范德华能(ΔEvdw)的打分函数在蛋白质－蛋白质对接中评价近天然构象的能力.对17种蛋白质复合物对接体系进行打分的结果表明，包含范德华能的打分函数（ΔEele＋ΔGACE＋ΔEvdw）比通常的打分函数（ΔEele、ΔGACE、ΔEele＋ΔGACE、ΔEele＋ΔEvdw、ΔGACE＋ΔEvdw）具有更好的区分近天然构象的能力.进一步的研究表明，优化（EM）对接体系后再进行打分，上面几种打分函数对对接结构的评价效果都有不同程度的改善，其中打分函数（ΔEele＋ΔGACE＋ΔEvdw）有更明显的改善.为了进一步确定候选结构中的近天然构象，以一种蛋白质复合物为例，对候选结构进行分子动力学（MD）模拟，根据MD轨迹中构象相对于初始构象的平方平均偏差（MSD）随时间的变化来辅助打分函数排除错误构象，得到了较好的结果.     

Van der Waals interactions in aromatic systems: structure and energetics of dimers and trimers of pyridine.

Full geometry optimizations at the dispersion-corrected DFT-BLYP level of theory were carried out for dimers and trimers of pyridine. The DFT-D interaction energies were checked against results from single-point SCS-MP2/aug-cc-pVTZ calculations. Three stacked structures and a planar H-bonded dimer were found to be very close in energy (interaction energies in the range from -3.4 to -4.0 kcal mol(-1)). Two T-shaped geometries are higher lying, by about 1 kcal mol(-1), which is explained by the more favorable electrostatic interactions in the stacked and H-bonded arrangements. The DFT-D approach has proved to be a reliable and efficient tool to explore the conformational space of aromatic van der Waals complexes and furthermore provides interaction energies with errors of less than 10-20 % of DeltaE. Comparisons with previous results obtained by using only partially optimized model geometries strongly indicate that unconstrained optimizations are mandatory in such weakly bonded low-symmetry systems.     

Synthesis and Structure of a One-Dimensional Coordination Polymer Based Upon Tetracyanocalix[4]arene in the Cone Conformation

Abstract

Tetracyanocalix[4]arene has been synthesized in a cone conformation and crystallized from solution in an orthorhombic system, space group P2₁2₁2₁, with a = 13.7999(9) Å, b = 16.820(1) Å, c = 21.754(1) Å, D_c = 1.218 g/cm³, Z = 4 (C₆₂H₄₇N₅O₄). Refinement based on 11008 observed reflections yielded R1 = 0.042. Further crystallographic studies have revealed that this compound self-assembles into a one-dimensional coordination polymer in the presence of Ag⁺ cation. This extended structure also crystallizes in an orthorhombic system, space group Cmca, with a = 17.770(1) Å, b = 31.498(2) Å, c = 23.107(2) Å, D_c = 1.319 g/cm³, Z = 8 (C₆₃H₅₂AgCl₂F₆N₄O₆P). Refinement based on 7391 observed reflections yielded R1 = 0.109.     

Dependence of the Interaction Potentials of Ar-HF and N2-HF on HF Bond Length

We explore in detail the nature of the intermolecular interactions in two HF containing complexes, ArHF and N₂ HF, at vibrationally excited HF stretching states using both high overtone spectroscopic and ab initio computational methods. By using an infrared intracavity laser-induced fluorescence technique, second overtone spectra of the two HF complexes have been obtained for the HF stretches and their combination modes with low-frequency van der Waals vibrations. The two complexes show the same trend that both van der Waals bond strength and rotational constant increase smoothly with v of the HF stretch. The investigation of the intermolecular potential above minimum provides a rigorous test of ab initio calculations. In particular for the ab initio calculations using an efficient basis set incorporating bond functions, the technique reproduces reasonably well the anisotropy of the interaction potential of Ar and HF. It is found that the intermolecular potential depends strongly upon the HF bond length only at the linear Ar-H-F geometry.     

Anisotropy of Atomic Van der Waals Radii in the Gas-Phase and Condensed Molecules\sp{1}

The anisotropic components of van der Waals radii for 5b, 6b and 7b Group elements were determined from the structures of gaseous van der Waals complexes and of crystalline molecular solids. The transition from the gaseous to the solid state reduces the anisotropy of a van der Waals atomic shape. This anisotropy is largely responsible for the changes of intermolecular distances, which are often misinterpreted as an effect of hydrogen bonds.     

Effect of the damping function in dispersion corrected density functional theory

It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.     

Behavior of Halogen Bonds of the Y−X⋅⋅⋅π Type (X,Y=F,Cl, Br,I) in the Benzene π System,Elucidated by Using a Quantum Theory of Atoms in Molecules Dual‐Functional Analysis

The nature of halogen bonds of the Y?X‐?‐π(C₆H₆) type (X, Y=F, Cl, Br, and I) have been elucidated by using the quantum theory of atoms in molecules (QTAIM) dual‐functional analysis (QTAIM‐DFA), which we proposed recently. Asterisks (?) emphasize the presence of bond‐critical points (BCPs) in the interactions in question. Total electron energy densities, H_b( r _c), are plotted versus H_b( r _c)?V_b( r _c)/2 [=(?²/8m)?²ρ_b( r _c)] for the interactions in QTAIM‐DFA, in which V_b( r _c) are potential energy densities at the BCPs. Data for perturbed structures around fully optimized structures were used for the plots, in addition to those of the fully optimized ones. The plots were analyzed by using the polar (R, θ) coordinate for the data of fully optimized structures with (θ_p, κ_p) for those that contained the perturbed structures; θ_p corresponds to the tangent line of the plot and κ_p is the curvature. Whereas (R, θ) corresponds to the static nature, (θ_p, κ_p) represents the dynamic nature of the interactions. All interactions in Y?X‐?‐π(C₆H₆) are classified by pure closed‐shell interactions and characterized to have vdW nature, except for Y?I‐?‐π(C₆H₆) (Y=F, Cl, Br) and F?Br‐?‐π(C₆H₆), which have typical hydrogen‐bond nature without covalency. I?I‐?‐π(C₆H₆) has a borderline nature between the two. Y?F‐?‐π(C₆H₆) (Y=Br, I) were optimized as bent forms, in which Y‐?‐π interactions were detected. The Y‐?‐π interactions in the bent forms are predicted to be substantially weaker than those in the linear F?Y‐?‐π(C₆H₆) forms.     

Synthesis of thermoplastic curdlan alkyl carbamates having hydrogen bonding ability

Rigid and little moldable curdlan, a linear β-1,3-glucan having intra- and interchain hydrogen bonds, was reacted with several alkyl isocyanates, which gave thermoplastic curdlan alkyl carbamates (CrdC) with degree of substitution about 2. The alkyl carbamation at hydroxy groups in the glucan skeleton effectively broke the interchain hydrogen bonds of curdlan and increased flexibility of CrdC, while the newly formed carbamate moieties could moderately keep the hydrogen bonding ability in CrdC. Elongating the alkyl groups in the carbamate side chains increased solubility in organic solvents and thermoplasticity of CrdC, which enabled to make homogeneous and free-standing films by both methods of solution-casting and hot-pressing.     

Optimized Liquid-Phase Exfoliation of Magnetic van der Waals Heterostructures: Towards the Single Layer and Deterministic Fabrication of Devices

Van der Waals magnetic materials are promising candidates for spintronics and testbeds for exotic magnetic phenomena in low dimensions. The two-dimensional (2D) limit in these materials is typically reached by mechanically breaking the van der Waals interactions between layers. Alternative approaches to producing large amounts of flakes rely on wet methods such as liquid-phase exfoliation (LPE). Here, we report an optimized route for obtaining monolayers of magnetic cylindrite by LPE. We show that the selection of exfoliation times is the determining factor in producing a statistically significant amount of monolayers while keeping relatively big flake areas (~1 µm²). We show that the cylindrite lattice is preserved in the flakes after LPE. To study the electron transport properties, we have fabricated field-effect transistors based on LPE cylindrite. Flakes are deterministically positioned between nanoscale electrodes by dielectrophoresis. We show that dielectrophoresis can selectively move the larger flakes into the devices. Cylindrite nanoscale flakes present a p-doped semiconducting behaviour, in agreement with the mechanically exfoliated counterparts. Alternating current (AC) admittance spectroscopy sheds light on the role played by potential barriers between different flakes in terms of electron transport properties. The present large-scale exfoliation and device fabrication strategy can be extrapolated to other families of magnetic materials.     

On the van der Waals interactions and the stability of polypeptide chains in helical conformations

In this work, we aim to investigate the contribution of van der Waals (vdW) interactions to the stability of polypeptides in helical conformations studying infinitely long chains of alanine and glycine with density functional theory. To account for vdW interactions, we have used the interatomic pairwise dispersion approach proposed by Tkatchenko–Scheffler (TS), the TS approach with self‐consistent screening (SCS) that self‐consistently includes long‐range electrostatic effects (TS + SCS), the D2 and D3 methods of Grimme et al., and the Langreth–Lundqvist procedure that treats nonlocally the correlation part of the approximation to the exchange‐correlation (xc) functional (called DF). First, we have tested the performance of these strategies studying a set of representative hydrogen bonded dimers. Next, we have studied polyalanine and polyglicine in π‐helix, α‐helix, ‐helix, 2₇, and polyproline‐II conformations and in a fully extended structure. We have found that the DF methodology in combination with a modified version for the Becke approximation to the exchange (optB86b), the D2, D3, TS, and TS + SCS strategies in combination with the Perdew–Burke–Ernzerhof approximation to the xc functional, describe fairly well dimer association energies. Furthermore, the DF method and the D2, D3, TS, and TS + SCS strategies predict very similar helical stabilities even though the approximation used in DF for describing the long‐range dispersion interactions is different that the one used in D2/D3 and TS/TS + SCS. We found that the stability doubles for π and α helices if vdW interactions are taken into account. © 2015 Wiley Periodicals, Inc.     

Steric crowding can stabilize a labile molecule: solving the hexaphenylethane riddle

12 not so angry men: Hexaphenylethane is unstable, a phenomenon traditionally attributed to steric repulsion between the six phenyl rings. However, adding 12 bulky tert-butyl groups, one to each of the 12 meta positions, gives a stabile ethane derivative (see space-filling model and potential energy curve for the dissociation of the central C-C bond). This unexpected stabilization is shown to result from attractive dispersion interactions between the substituents.     

基于二维材料WX_2构建的范德华异质结的结构和性质及应变效应的理论研究

二维材料过渡金属硫属化物(TMDs),因其优越的物理化学特性及其在光电子器件、光催化等领域的潜在应用价值,得到了人们的广泛关注。基于TMDs材料可以构建具有不同性能的范德华(vdW)异质结,但构建的异质结由于其固有的能带带隙大小限制了其在全光谱上的响应,因而对其能带带隙调控变得十分重要。本文基于第一性原理方法系统地研究了WX_2 (X=S, Se, Te)从单层到体相的结构和性质,以及由此组装的vdW异质结构WS_2/WSe_2、WS_2/WTe_2和WSe_2/WTe_2的结构和性质以及应力应变对异质结构的能带带隙的影响。结果表明:结合HSE06泛函和自旋轨道耦合(SOC)效应的计算方案可以精确描述WX_2体系;异质结构WS_2/WSe_2,WS_2/WTe_2和WSe_2/WTe_2呈现type-II能带分类;在施加单轴或双轴的应力应变后,能带带隙大小发生相应改变,当晶格形变大于4%后,异质结构由半导体特性变成具有金属性。这些研究为光电子器件的设计提供了重要的指导意义。     

Van der Waals radii of elements from the data of structural inorganic chemistry

Van der Waals radii of elements were determined from the data of the structural inorganic chemistry: from intersitial distances in CdX₂- and graphite-type structures, bond lengths in van der Waals molecules, molar volumes of A₂-type substances, refractometry data, and from quantum chemical and correlation ratios. The recommended values of van der Waals radii of elements are tabulated.Translated fromIzyestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 24–29, January, 1995.The author is grateful to the administration of the Department of Chemistry at the University of Durham (Great Britain) for the opportunity to perform this work and to Prof. J. Howard and Prof. K. Wade for useful discussions.