Determination of McGowan volumes for ions and correlation with van der Waals volumes

The McGowan volume has been widely used for the analysis of physicochemical and biochemical properties in chemistry and drug industry. Because McGowan volumes are not available for ions, its application is limited to only neutral compounds. Pauling radii of metallic ions have been collected and studied to obtain McGowan volumes for ions. Regression analysis was carried out between Pauling radii (R(p)) and McGowan radii (R(x)) for a wide range of compounds. It was found that Pauling radii and McGowan radii derived from McGowan volumes by using a volume-radius formula are linearly related (R(x) = 1.115R(p) + 0.0623, r(2) = 0.995). This equation is then used to calculate McGowan volumes for various ions and charged groups. McGowan volumes have been calculated for inorganic, organic, and organometallic compounds and correlated with van der Waals volumes. Results show that McGowan volumes (V(x)) are entirely equivalent to computer-calculated van der Waals volumes.     

三元——假二元系的过量体积

提出测量三元——假二元系(1-x)[(1-y)A+yC]+z[(1-y)B+yC]的过量热力学函数的方法, 测量了在298.15 K下两种假二元系: A=环己烷, B=苯, C=甲苯, 甲基环己烷的过量体积V~E, 用van der Waals单流体模型对实验结果进行了讨论。     

Anisotropy of the van der Waals Configuration of Atoms in Complex,Condensed, and Gas-Phase Molecules

Anisotropic van der Waals (vdW) radii of 5b–7bsubgroup elements were determined from structures of gas-phase van der Waals complexes and crystal molecular compounds. The anisotropy of the van der Waals configuration of atoms was shown to decrease when going from isolated molecules to the condensed state. Variations in intermolecular distances, which are usually explained in terms of the formation of hydrogen bonds, are substantially governed by the anisotropic effect.     

Understanding the chiral recognitions between neuraminidases and inhibitors: Studies with DFT,docking, and MD methods

The chiral recognitions between various neuraminidases (NA) and 5‐[(1R,2S)‐1‐(acetylamino)‐2‐ methoxy‐2‐methylpentyl]‐4‐[(1Z)‐1‐propenyl)‐(4S,5R)]‐D‐proline (BL) stereoisomers have been theoretically studied. The zwitterions of BL are responsible for the bioactivities, and electrostatic rather than van der Waals (vdW) contributions play a significant role. With the presence of NA proteins, the orders of relative stabilities of the BL stereoisomers are greatly altered; meanwhile, the ranges are significantly enlarged, ensuring the respective recognitions of the BL9z, BL3z, BL2z, and BL1z stereoisomers by the N1, N2, N9 subtype, and B type NA proteins. It is mainly due to geometric complementarities of the NA active sites with the BL carboxyl and propenyl groups. The recognitions of proteins with chiral ligands are rather targeted, even applicable to N2 and N9 with high structural similarities. Thus, the significance of chirality is addressed for the designs of anti‐influenza drugs, which aids our understanding of chiral recognitions between proteins and ligands. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

晶体中原子的平均范德华半径

根据晶体中原子的平均体积数据提出包括全部金属元素的原子平均范德华半径值.与现有几个重要的范德华半径体系进行了初步的比较,指出范德华半径值在应用中值得注意的问题,简要提出了有关范德华半径今后研究的方向.     

Vibrational and thermodynamic properties of β-HMX: a first-principles investigation

Thermodynamic properties of β-HMX crystal are investigated using the quasi-harmonic approximation and density functional theory within the local density approximation (LDA), generalized gradient approximation (GGA), and GGA + empirical van der Waals (vdW) correction. It is found that GGA well describes the thermal expansion coefficient and heat capacity but fails to produce correct bulk modulus and equilibrium volume. The vdW correction improves the bulk modulus and volume, but worsens the thermal expansion coefficient and heat capacity. In contrast, LDA describes all thermodynamic properties with reasonable accuracy, and overall is a good exchange-correlation functional for β-HMX molecular crystal. The results also demonstrate significant contributions of phonons to the equation of state. The static calculation of equilibrium volume for β-HMX differs from the room-temperature value incorporating lattice vibrations by over 5%. Therefore, for molecular crystals, it is essential to include phonon contributions when calculated equation of state is compared with experimental data at ambient condition.     

Calculation of the van der Waals volumes of organic molecules

A new and more precise method is proposed for calculating van der Waals atomic and molecular volumes of organic compounds. The method provides for intersections of three or more spheres at one point of space. Such a possibility is essential for calculating the volumes of sterically overcrowded molecules and of molecules with intramolecular hydrogen bonds. A computer program for IBM PC/AT(XT) is developed. Depending on the atomic environment in the molecule, the average values of the volume increments for atoms C, N, O, H, F, Cl, and S are obtained using the data from the Cambridge Structural Database.N. S. Kurnakov Institute of General and Inorganic Chemistry, Russian Academy of Sciences, Moscow 117071. Translated from Izvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 922–931, April, 1992.     

Clathrate hydrate dissociation conditions of refrigerants R404A,R406A,R408A and R427A: Experimental measurements and thermodynamic modeling

Clathrate hydrate dissociation conditions were measured for four “alternative” refrigerants, viz. R404A, R406A, R408A and R427A. The experimental measurements were performed within the pressure range of (0.079 to 9.995) MPa and temperatures ranging from (272.7 to 288.7) K. An isochoric pressure-search method was used to perform the measurements. A thermodynamic model based on the van der Waals–Platteeuw (vdW–P) model was applied for the prediction of the dissociation conditions which were compared to the experimental measurements. The fluid phase was modeled using the MHV2 G^E-EoS mixing rule along with the UNIFAC (original) activity model. The van der Waals–Platteeuw (vdW–P) model was used for the modeling of the hydrate phase. There was reasonable agreement between the experimental and predicted values.     

Improved evaluation of liquid densities using van der Waals molecular models

A new approach is presented to estimate molar volumes and densities of liquids in ambient conditions from van der Waals models, taking advantage of the correlation between the intermolecular volume and the atomic contributions to the molecular surface area. Using this approach, the role of hydrogen bonds can be quantified. The densities obtained prove remarkably close to the values derived from the ACD group contribution method. However, the present approach requires much less empirical parameters and may be applied to arbitrary H-C-N-O-F-S-Cl-Br compounds. Moreover, it is more reliable than earlier empirical procedures, including quantitative structure property relationships (QSPR). While it does not correct the deficiencies of group contribution methods, it provides a natural approach to introduce temperature effects.     

Approximate scheme for calculating van der Waals interactions between finite cylindrical volume elements

A successful approach to calculating van der Waals (vdW) forces between irregular bodies is to divide the bodies into small cylindrical volume elements and integrate the vdW interactions between opposing elements. In this context it has been common to use Hamaker's expression for parallel plates to approximate the vdW interactions between the opposing elements. This present study shows that Hamaker's vdW expression for parallel plates does not accurately describe the vdW interactions for co-axial cylinders having a ratio of cylinder radius to separation distance (R/D) of 10 or less. This restricts the systems that can be simulated using this technique and explicitly excludes consideration of topographical or compositional variations at the nanoscale for surfaces that are in contact or within a few nm of contact. To address this limitation, approximate analytical expressions for nonretarded vdW forces between finite cylinders in different orientations are derived and are shown to produce a high level of agreement with forces calculated using full numerical solutions of the corresponding Hamaker's equations. The expressions developed here allow accurate calculation of vdW forces in systems where particles are in contact or within a few nm of contact with surfaces and the particles and/or surfaces have heterogeneous nanoscale morphology or composition. These calculations can be performed at comparatively low computational cost compared to the full numerical solution of Hamaker's equations.     

范德华复合物C6H5CH3…N2的共振双光子电离光谱

由复合物C6H5CH3…N2共振双光子电离光谱获得了复合物分子间范德华振动模式和N2的内转动的大量信息.通过对比同位素分子C6D5CD3…N2的光谱，我们合理地归属了所观察到的C6H5CH3…N2复合物的所有谱线.由光解离碎片的机理分析，推得复合物C6H5CH3…N2的激发态和基态的键能大约是494和474 cm－1，与理论计算值非常接近.     

Van der Wals团簇ο-xylene N2的共振双光子电离光谱

The one-color resonant two -photon ionization technique is employed to study jetcooled van der Waals(vdW) complex o-xylene?N2 through the S0-S1 transition around the band. The spectra obtained exhibit rich information about the complex intermolecular vdW vibrational modes. We have tentatively assigned all the observed spectral features. The structure of the complex has been obtained by calculation of the minimum energy structure.     

On the structure and physical origin of the interaction in H(2) ... Cl(-) and H(2) ... Br(-) van der Waals anion complexes

The ab initio three-dimensional potential energy surface (PES) for the weak interaction of hydrogen molecule with bromine anion is presented. The surface was obtained by the supermolecular method at the coupled cluster with single and double excitations and noniterative correction to triple excitations (CCSD(T)) level of theory. Our calculations indicate the van der Waals (vdW) system for the linear orientation at R=3.37 A with a well depth of D(e)=660.1 cm(-1). The presented PES reveals also transition state for the perpendicular orientation at R=4.22 A with a barrier of 607.1 cm(-1). The physical origin of the stability of vdW H(2) ... Br(-) structure with respect to the H(2) ... Cl(-) one was analyzed by the symmetry adapted perturbation theory based on the single determinant Hartree-Fock (HF) wave function. The separation of the interaction energy shows that the dispersion forces play slightly more important role in the stabilization of the vdW system with Br(-) than with Cl(-).     

Prediction of physicochemical properties of organic molecules using van der Waals surface electrostatic potentials

The generalized interaction properties function (GIPF) methodology developed by Politzer and coworkers, which calculated molecular surface electrostatic potential (MSESP) on a density envelope surface, was modified by calculating the MSESP on a much simpler van der Waals (vdW) surface of a molecule. In this work, vdW molecular surfaces were obtained from the fully optimized structures confirmed by frequency calculations at B3LYP/6-31G(d) level of theory. Multiple linear regressions for normal boiling point, heats of vaporization, heats of sublimation, heats of fusion, liquid density, and solid density were performed using GIPF variables from vdW model surface. Results from our model are compared with those from Politzer and coworkers. The surface-dependent beta (and gamma) values are dependent on the surface models but the surface-independent alpha and regression coefficients (r) are constant when vdW surface and density surface with 0.001 a.u. contour value are compared. This interesting phenomenon is explained by linear dependencies of GIPF variables.     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学(MD)模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物(分别记为M1、M2和M3)与ACh E的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用(vd W)。用MM-PBSA方法计算的3种抑制剂与ACh E之间的结合自由能与抑制剂的实验生物活性数据(IC50值)相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与ACh E之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与ACh E之间的结合自由能有较大的贡献,在区分抑制剂M1(或M2)和M3的生物活性上发挥着重要的作用。     

乙酰胆碱酯酶AChE与1,7-二氮杂咔唑抑制剂的作用机理的分子动力学模拟

通过分子对接、分子动力学（MD）模拟以及成键自由能分析方法,从原子水平上模拟研究了3种1,7-二氮杂咔唑衍生物（分别记为M1、M2和M3）与AChE的结合模式及相互作用机理,分析和讨论了研究体系的静电相互作用和范德华相互作用（vdW）。用MM-PBSA方法计算的3种抑制剂与AChE之间的结合自由能与抑制剂的实验生物活性数据（IC₅₀值）相对应。分析结果表明,残基S286与抑制剂之间形成的氢键作用有利于抑制剂与AChE之间的结合。范德华相互作用,尤其是抑制剂与关键残基W279和Y334的作用,对抑制剂与AChE之间的结合自由能有较大的贡献,在区分抑制剂M1（或M2）和M3的生物活性上发挥着重要的作用。     

Partial molar volumes of organic compounds in water. III. Carbohydrates

Partial molar volumes in water at 25°C have been determined for a number of carbohydrates, including mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, and polysaccharides and their derivatives. The experimental values can be calculated from the van der Waals volumes of the molecules if account is taken of the shrinkage in volume caused by hydrogen-bonding of solvent molecules to the hydroxyl groups of the sugars.     

Correlation and prediction of liquid-liquid distribution coefficients in aqueous systems using a modified Wilson model

A modified Wilson model is tested for its ability to correlate and predict distribution coefficients in two representative systems: 1-butanol-water and cyclohexanewater. The model is fitted to ternary equilibrium data for various solutes in these systems using a procedure involving minimization of the least-squares distance between calculated and experimental logarithmic distribution ratios. In addition, benzene-water, hexane-water, and cyclohexane-water distribution coefficients for infinitely diluted liquid solutes are predicted using only binary system information. All computations involve using both van der Waals and molar volumes as structural parameters to account for the geometry of the molecules studied. Satisfactory representations of experimental distribution ratios and fairly accurate distribution coefficients at infinite dilution are obtained for both systems. However, in a number of cyclohexane-water systems, miscibilities of constituent binary mixtures are poorly predicted from ternary system information when van der Waals volumes are used. Replacement of van der Waals volumes by molar volumes has little influence on the fit, but significant improvement is observed for the prediction of both binary miscibility properties and for distribution coefficients at infinite dilution in all the solvent-water systems considered.Presentation to First International Symposium on Solubility Phenomena, University of Western Ontario, London, Ontario, August 21–23, 1984.     

An ab initio study of the CO–N2 complex

The interaction energy and van der Waals intermolecule bond length of several structures of the CO–N₂ complex are calculated by the supermolecule CCSD(T) and MP4 methods using aug-cc-pVXZ (X=D,T,Q) basis sets extended by a set of midbond functions centered in the middle of the vdW bond. The most stable structures are found to be two distorted T-shaped configurations with the N atom pointing towards the C–O bond. This conclusion is compatible with the results of high-resolution infrared, microwave and millimeter studies.