An accurate three-dimensional potential energy surface for the He-Na_2 complex

An accurate three-dimensional potential energy surface(PES) for the He-Na2 van der Waals comple was calculated at the coupled cluster singles-and-doubles with noniterative inclusion of connecte triple(CCSD(T)) level of theory.A mixed basis set,aug-cc-pVQZ for the He atom and cc-pCVQZ for th sodium atom,and an additional(3s3p2d1f) set of midbond functions were used.The computed inte action energies in 819 configurations were fitted to a 96-parameter analytic potential model by leas squares fitting.The PES has two shallow wells corresponding to the T-shaped structure and the linea configuration,which are located at 12.5a0 and 14 a0 with depths of 1.769 and 1.684 cm-1,respectivel The whole potential energy surface exhibits weak anisotropy.Based on the fitted PES,state-to-stat differential cross sections were calculated.     

Theoretical study of potential energy surface and vibrational spectra of ArF2 system

An ab initio potential energy surface (PES) of ArF2 system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm- 1 at R = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm -1 at R = 0.3486 nm. A saddle point is found at R = 0.3486 and θ = 61° with the well depth of -61.53 cm-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.     

Binding neutral guests to concave surfaces of molecular hosts. Rigid structural model for complexation between two lipophilic entities

The 1:2 compound formed between a new cavitand C₄₀H₄₈Si₄O₈ [chemical name: 5,10;12,17;19,24;26,3-tetrakis(dimethylsiladioxa)-1,8,15,22-tetramethyl[1₄]metacyclophane] and CS₂ (M _r =921.42) provided a suitable structural model for a rigid inclusion complex between uncharged lipophilic molecules. The detailed structure of this compound has been determined by single crystal X-ray diffraction at 128 K (Crystal data:a=11.233,b=20.018,c=10.069 Å, =90.84^o,Z=2, space groupP2₁/m). Anisotropic refinement converged atR=0.040 for 3768 reflections above the intensity threshold, leading to positional and thermal parameters of a relatively high precision. The cavitand has an enforced cavity appropriately sized to include only slim linear guests. The crystallographic analysis revealed a 1:1 molecular inclusion complex with CS₂, the guest species being almost entirely encapsulated within the basket-shaped cavity of the host. The complex is stabilized by dispersion forces. All the guest atoms lie within van der Waals distances from the surrounding sections of the host and are well ordered. The second CS₂ molecule is located in the crystal lattice between molecules of the complex and is slightly disordered. Mirror plane symmetry characterizes the entire structure. Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82032 (22 pages).     

A rapid method for molecular shape comparison of medium-sized molecules. Conformational calculations on sandalwood odor,IV

Summary A fast method of a surface comparison of two or more molecules to be matched is presented. The Van der Waals surfaces of molecules are described by points calculated as the intersection of grid lines with the molecular surface. The mean surface of various molecules with the same biological activity can be constructed. It is used for further comparisons with similar molecules lacking this activity. Deviations of any molecular surface from the mean surface can be mapped onto the surface. The method was tested on a distinct group of sandalwood odor molecules and it was shown that such matching and comparison procedures are useful in the investigation of odor structure-activity relationships proposed as CAFD (computer aided fragrance design).Dedicated to Prof. Dr. W. Fleischhacker, on occasion of his 60th anniversary     

Comparison of calorimetric and IR-spectroscopic data for alcohols and alcoholic solutions

The heats of solution of alcohols in hexane can be considered as the energy necessary to break hydrogen bonds (H-bond). The amount of non H-bonded OH groups estimated from caloric data, are in good agreement with IR-spectroscopic data. Comparison of calorimetric and IR-spectroscopically determined H-bond energies permit the separation of intermolecular van der Waals effects from H-bond interactions. This separation shows that van der Waals interactions of alcohols or water should not be underestimated.     

An accurate three-dimensional potential energy surface for the He-Na<Subscript>2</Subscript> complex

An accurate three-dimensional potential energy surface (PES) for the He-Na₂ van der Waals complex was calculated at the coupled cluster singles-and-doubles with noniterative inclusion of connected triple (CCSD(T)) level of theory. A mixed basis set, aug-cc-pVQZ for the He atom and cc-pCVQZ for the sodium atom, and an additional (3s3p2d1f) set of midbond functions were used. The computed interaction energies in 819 configurations were fitted to a 96-parameter analytic potential model by least squares fitting. The PES has two shallow wells corresponding to the T-shaped structure and the linear configuration, which are located at 12.5a ₀ and 14 a ₀ with depths of 1.769 and 1.684 cm⁻¹, respectively. The who potential energy surface exhibits weak anisotropy. Based on the fitted PES, state-to-state differential cross sections were calculated. Supported by the Natural Science Foundation of Anhui Educational Committee (Grant No. 2006kj072A) and the Natural Science Foundation of Anhui Province (Grant No. 070416236)     

Determination of van der Waals forces in monolayer films of lipids & biopolymers. Equation of state for two-dimensional films

Amphiphile molecules are characterized by the dual property arising from the interactions between the apolar [alkyl] and the polar part and the surrounding solvent, i.e., water. In assemblies which amphiphiles form in diverse systems, e.g., micelles, soap bubbles, monolayers or bilayers at interfaces, the attractive forces are attributed to the van der Waals forces. It is not easy to estimate the magnitude of van der Waals forces in some of these systems by any direct method.The magnitude of van der Waals forces in spread monolayers of lipids and biopolymers has been reported to be estimated from experimental data. The magnitude of these forces has been estimated by using an equation of state of a very general form, as delineated herein. In the current literature no such attempt has been reported in the analyses of these monolayers spread on aqueous surfaces. These analyses suggest that the predominant surface forces arise from van der Waals interactions, if the magnitude of electrostatic charge repulsions is weak. The equation-of-state as derived indicates that it is useful in providing information about the molecular interaction in monolayers, for both lipids and biopolymers.     

Analytical potential energy function for the Van der Waals molecule He2Ne

A potential energy function has been derived for the two linear isomer structures He₂Ne⁺(X²Σ⁺) using ab initio calculations with the QCISD(T)/6–31++G(d,p) method. Because we use the reasonable dissociation limit (3) instead of the unacceptable one (1), our potential energy function represents considerable topographical features in detail, including the linear [He---Ne⁺---He] structure (R_HeNe = 1.4694 Å, R_He'Ne = 2.0069 Å HeNeHe = 180°) with two symmetric linear saddles (R_HeNe = R_He'Ne = 1.80 Å, HeNeHe = 180° and R_HeNe = 1.5 Å, R_He'Ne = 3.2 A°, HeNeHe = 180°), and the topographical minimum of the [He---He---Ne⁺] structure (R_HeHe = 2.2217 Å, R_HeNe = 1.4426 Å, HeHeNe = 180°), with a linear saddle (R_HeHe' = 3.0 Å, R_HeNe = 1.8 Å, HeHeNe = 180°).     

The crystal and molecular structure of N-(17-methoxy-phenyl)-2-chloropyrrolo (2,3- b ) quinoline

N-(17-methoxy-phenyl)-2-chloropyrrolo (2,3-b) quinoline was solved by direct methods and refined to anR of 0.104 for 950 observed reflections. The intensity data were collected by the multiple film equi-inclination Weissenberg technique and estimated visually. The packing of the molecule is stabilised by van der Waals interaction. The pyrrolo (2,3-b) quinoline ring system is planar and the methoxy phenyl ring is approximately perpendicular to the plane of this ring system with a dihedral angle of 86.5°.     

Potential energy surface and kinetics of the helix–coil transition in a 33-peptide

The CHARMM force field is used to calculate 36 minima along the potential energy surface of the helix–coil conversion of Ac-A₁₄KG₃A₁₄K + 2H⁺ and to interconnect them through 35 transition states. The energy barriers are used to give the rate constants of interconversion between the conformers and the relevant kinetic equations are then solved. Fair to good agreement with the data obtained by drift time spectrometry experiments (D. T. Kaleta, M. F. Jarrold, J. Am. Chem. Soc. 125:7186, 2003) is obtained under a simple hypothesis of the initial conformer distribution. Contribution to the Fernando Bernardi Memorial Issue.     

Volatility and crystal lattice energy of palladium(II) chelates

Temperature dependence of saturated vapor pressure has been measured by gas saturation technique for volatile bis-chelates of palladium(II) with such ligands as acetylacetone, hexafluoroacetylacetone, diethyldithiocarbamate, diisopropyldithiophosphate, and also mixed ligand complex with acetylacetone and cyclooctadiene-2,4. Standard thermodynamic parameters of vaporization ΔH _T ⁰ and ΔS _T ⁰ were calculated. Crystal molecular packings and intermolecular interactions were analyzed basing on structural data. Atomatom potential calculation of van der Waals energy E_cryst in crystal lattice was performed and compared to the experimentally obtained values of sublimation enthalpy for the complexes under study.     

Theoretical study of potential energy surface and vibrational spectra of ArF2 system

Anab initio potential energy surface (PES) of ArF₂ system has been obtained by using MP4 calculation with a large basis set including bond functions. There are two local minimums on the PES: one is T-shaped and the other is L-shaped. The L-shaped minimum is the global minimum with a well depth of -119.62 cm^-1 atR = 0.3883nm. The T-shaped minimum has a well depth of -85.93cm^-1 atR = 0.3486 nm. A saddle point is found atR = 0.3486 and τ = 61° with the well depth of -61.53 cm^-1. The vibrational energy levels have been calculated by using VSCF-CI method. The results show that this PES supports 27 vibrational bound states, and the ground states are two degenerate states assigned to the L-type vibration.     

The topology of catchment regions of potential energy hypersurfaces

A simple proof is presented for a fundamental topological property of catchment regions of potential energy hypersurfaces: each catchment region C(λ,i), representing a chemical species and its conformational range on the potential energy hypersurface, is simply k-connected for each dimension k=1,2,…3N−6−λ, where λ is the index of the catchment region. The consequences of this property on the structure of the fundamental group of reaction mechanisms (the one-dimensional homotopy group of reaction paths) is discussed. Received: 8 July 1998 / Accepted: 6 October 1998 / Published online: 23 February 1999     

DFT study of the NMR properties of xenon in covalent compounds and van der waals complexes-implications for the use of 129Xe as a molecular probe

The NMR properties (chemical shift and spin-spin coupling constants) of (129)Xe in covalent compounds and weakly bound complexes have been investigated by DFT methods including relativistic effects. For covalent species, a good agreement between experimental and calculated results is achieved without scalar relativistic effects, but their inclusion (with a triple-zeta, double-polarization basis set) leads to some improvement in the quality of the correlation. The spin-orbit coupling term has a significant effect on the shielding constant, but makes a small contribution to the chemical shift. Coupling constants contain substantial contributions from the Fermi contact and paramagnetic spin-orbit terms; unlike light nuclei the spin-dipole term is also large, whereas the diamagnetic spin-orbit term is negligible. For van der Waals dimers, the dependence of the xenon chemical shift and anisotropy is calculated as a function of the distance. Small (<1 Hz) but non-negligible through-space coupling constants between (129)Xe and (13)C or (1)H are predicted. Much larger couplings, of the order of few Hz, are calculated between xenon and (17)O in a model silicate residue.     

T-hull relations for shape envelopes of molecular contours

Electron density T-hulls have been proposed earlier for the analysis of various molecular shape constraints in solvent-solute interactions and in biomolecular complementarity. Some relations between T-hulls have been applied to relative shape analysis of molecular electron density contour surfaces (MIDCOs). In this contribution, theorems on several additional properties of T-hulls are proven. The results are suitable for comparisons between shape analysis results obtained using different reference molecules, for example, if shape comparisons are carried out using different solvent molecules as shape reference.     

The comparison of geometric and electronic properties of molecular surfaces by neural networks: Application to the analysis of corticosteroid-binding globulin activity of steroids

Summary It is shown how a self-organizing neural network such as the one introduced by Kohonen can be used to analyze features of molecular surfaces, such as shape and the molecular electrostatic potential. On the one hand, two-dimensional maps of molecular surface properties can be generated and used for the comparison of a set of molecules. On the other hand, the surface geometry of one molecule can be stored in a network and this network can be used as a template for the analysis of the shape of various other molecules. The application of these techniques to a series of steroids exhibiting a range of binding activities to the corticosteroid-binding globulin receptor allows one to pinpoint the essential features necessary for biological activity.     

Finite extensibility and orientational effects in rubbers. A physical interpretation of the ‘van der Waals equation’ for the elastic force

We propose a physical interpretation of the so-called van der Waals equation of state for rubbers, which gives a relation between the force and the deformation. On a phenomenological basis this equation takes the finite extensibility and a non-defined interaction into account. Here the fininte extensibility is discussed for the dilute case (no entanglements) and the highly entangled limit. The intramolecular interactions are described by orientational effects. The resulting equation of state for the force shows the same features as the van der Waals equation.Dedicated to Prof. H.-G. Kilian on the occasion of his 60th birthday.