Computational study on the ring distortions of 1,4-dicyanobenzene in the gas phase and in the crystal

A molecular mechanics software enhanced to perform empirical energy calculations on crystals (KESSHOU) was further developed to handle intermolecular electrostatic interactions as well. The packing of the molecules of 1,4-dicyanobenzene and 1,4-diisocyanobenzene in the crystal was studied. The role of the van der Waals and the electrostatic interactions in the balance of nonbonded atom-atom interactions is analyzed. The packing forces are dominated by van der Waals forces. The electrostatic interactions have higher stabilizing contribution for the dicyano isomer than for the diisocyano form. The dependence of the results on the size of the crystal, the molecular mechanics force field (MM2 vs MM3), and the dielectric constant are also assessed. Ab initio MP2/6–311G** geometries of the isolated molecules are in accordance with the observed benzene ring distortions determined by electron diffraction.     

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.     

One-dimensional molecular zippers

We synthesized an azobenzene derivative to demonstrate a one-dimensional molecular zipper. The formation and underlying mechanism of the molecular zipper formed by combined hydrogen-bonding and van der Waals interactions between adjacent molecules were investigated on a Au(111) surface using scanning tunneling microscopy and density functional theory calculations.     

Polarization-corrected molecular electrostatic potential for the cation binding problem

The molecular electrostatic potential (MESP) and polarization-corrected MESP (PMESP) minima for some small molecules are calculated on the surface generated by rolling cations (Li⁺ and Na⁺) on their van der Waals surfaces. The cation binding energies of these molecules are obtained with HF/6-31G^** level ab initio calculations. A noteworthy outcome of the present study is that the plot of these binding energies and the corresponding PMESP surface minimum values turns out to be remarkably linear with a slope close to unity. The PMESP is thus found to work as a powerful tool for unearthing the patterns of cation binding sites and energetics for molecular systems.     

On the angular shape of van der Waals dimers of small polar molecules

Ab initio calculations on twenty van der Waals dimers of small polar molecules at the experimentally observed intermolecular separation R, using Hartree-Fock molecular moments, show that the minima in the electrostatic interaction expanded up to R⁻⁶ converges to angular structures which are close to those observed experimentally for such complexes.     

The interaction of C6H6 and C6H12 with noble metal surfaces: electronic level alignment and the origin of the interface dipole

The electronic interaction of two molecules, the aromatic benzene (C6H6) and the saturated hydrocarbon cyclohexane (C6H12) with a Cu(111) surface, have been determined using precise, ab initio electronic structure calculations. For the interaction of these adsorbates with the substrate, we present a detailed analysis and decomposition of various individual chemical mechanisms that contribute. A novel aspect of this analysis is the use of charge-density difference contour plots to graphically display the chemistry. A wave-function-based approach was used in order to avoid problems when the presently most commonly employed approach, density-functional theory, is applied to weakly chemisorbed molecules, where the interaction is dominated by van der Waals forces. The present information are not only relevant with regard to understanding the chemistry going on when molecules are adsorbed on a Cu surface but also have important consequences with regard to charge injection in molecular electronic devices, e.g., organic field-effect transistors and organic light-emitting diodes.     

Van der Waals interactions: evaluations by use of a statistical mechanical method

In this work the induced van der Waals interaction between a pair of neutral atoms or molecules is considered by use of a statistical mechanical method. With use of the Schro?dinger equation this interaction can be obtained by standard quantum mechanical perturbation theory to second order. However, the latter is restricted to electrostatic interactions between dipole moments. So with radiating dipole-dipole interaction where retardation effects are important for large separations of the particles, other methods are needed, and the resulting induced interaction is the Casimir-Polder interaction usually obtained by field theory. It can also be evaluated, however, by a statistical mechanical method that utilizes the path integral representation. We here show explicitly by use of this method the equivalence of the Casimir-Polder interaction and the van der Waals interaction based upon the Schro?dinger equation. The equivalence is to leading order for short separations where retardation effects can be neglected. In recent works [J. S. H?ye, Physica A 389, 1380 (2010); Phys. Rev. E 81, 061114 (2010)], the Casimir-Polder or Casimir energy was added as a correction to calculations of systems like the electron clouds of molecules. The equivalence to van der Waals interactions indicates that the added Casimir energy will improve the accuracy of calculated molecular energies. Thus, we give numerical estimates of this energy including analysis and estimates for the uniform electron gas.     

非手性的酞菁铜分子在Bi(111)表面上的手性特征

利用低温扫描隧道显微镜（LT-STM）研究了酞菁铜（CuPc）分子在Bi（111）表面上的吸附和手性自组装结构。由于较弱的分子-衬底相互作用,我们发现在液氮温度（78 K）下吸附在Bi（111）表面上的单个CuPc分子围绕着分子中心发生旋转,直到遇到其他分子形成团簇为止。随着分子覆盖度的增加,CuPc分子形成了自组装分子单层。高分辨STM图表明,非手性的CuPc分子出现了手性特征：两个相对的酞菁基团发生了弯曲。当覆盖度超过一个分子层,酞菁铜分子的吸附取向由“平躺”转变到“站立”姿态。我们认为,酞菁铜分子的手性起源是由两种因素共同导致的结果：一种是分子-衬底之间的非对称电荷转移,另一种是相邻分子间的非对称性的范德华力作用。     

Distribution patterns and controllable transport of water inside and outside charged single-walled carbon nanotubes

The density distribution patterns of water inside and outside neutral and charged single-walled carbon nanotubes (SWNTs) soaked in water have been studied using molecular dynamics simulations based on TIP3P potential and Lennard-Jones parameters of CHARMM force field, in conjunction with ab initio calculations to provide the electron density distributions of the systems. Water molecules show different electropism near positively and negatively charged SWNTs. Different density distribution patterns of water, depending on the diameter and chirality of the SWNTs, are observed inside and outside the tube wall. These special distribution patterns formed can be explained in terms of the van der Waals and electrostatic interactions between the water molecules and the carbon atoms on the hexagonal network of carbon nanotubes. The electric field produced by the highly charged SWNTs leads to high filling speed of water molecules, while it prevents them from flowing out of the nanotube. Water molecules enter the neutral SWNTs slowly and can flow out of the nanotube in a fluctuating manner. It indicates that by adjusting the electric charge on the SWNTs, one can control the adsorption and transport behavior of polar molecules in SWNTs to be used as stable storage medium with template effect or transport channels. The transport rate can be tailored by changing the charge on the SWNTs.     

Adsorption of benzene on coinage metals: a theoretical analysis using wavefunction-based methods

The interaction of benzene with a Ag(111) surface has been determined using reliable ab initio electronic structure calculations. The results are compared to a recent detailed analysis of the interaction of benzene with copper and gold surfaces, thus making it possible to derive a consistent picture for the electronic structure changes encountered when benzene is brought into contact with the densely packed coinage metal surfaces. To avoid the problems encountered when the presently most frequently employed computational approach, density functional theory (DFT), is applied to adsorbate systems where dispersion (or van der Waals) forces contribute substantially, we use a wavefunction-based approach. In this approach, the weak van der Waals interactions, which are dominated by correlation effects, are described using second-order perturbation theory. The surface dipole moment and the work function changes induced upon adsorption are also discussed.     

Effect of electronic polarization on charge-transport parameters in molecular organic semiconductors

Theoretical investigations of charge transport in organic materials are generally based on the "energy splitting in dimer" method and routinely assume that the transport parameters (site energies and transfer integrals) determined from monomer and dimer calculations can be reliably used to describe extended systems. Here, we demonstrate that this transferability can fail even in molecular crystals with weak van der Waals intermolecular interactions, due to the substantial (but often ignored) impact of polarization effects, particularly on the site energies. We show that the neglect of electronic polarization leads to qualitatively incorrect values and trends for the transfer integrals computed with the energy splitting method, even in simple prototypes such as ethylene or pentacene dimers. The polarization effect in these systems is largely electrostatic in nature and can change dramatically upon transition from a dimer to an extended system. For example, the difference in site energy for a prototypical "face-to-edge" one-dimensional stack of pentacene molecules is calculated to be 30% greater than that in the "face-to-edge" dimer, whereas the site energy difference in the pentacene crystal is vanishingly small. Importantly, when computed directly in the framework of localized monomer orbitals, the transfer integral values for dimer and extended systems are very similar.     

Ab initio intermolecular energies between Li+ and H2 near the van der waals minimum: comparison between a perturbative procedure and an SCF supermolecule treatment

The electrostatic, exchange, polarization, and dispersion energies are computed without using the multipole expansion. It is seen that the overlap between the orbitals of the interacting molecules must be taken into account to describe qualitatively the first order term. The neglect of overlap in the polarization term overestimates the attractive energy around the van der Waals minimum. An interpretation of the polarization phenomena in terms of molecular orbitals is proposed. The results are compared with SCF calculations and the use of small basis sets is considered.     

Asymmetric charge patterning on surfaces and interfaces: formation of hexagonal domains

The structure of soft matter systems at interfaces is of utmost importance in the fields of nanopatterning and self-assembly. It has been shown that lamellar and hexagonal patterns can form on interfaces, for a wide variety of systems. The asphericity of charged domains is considered here for different strengths of the electrostatics, determined by the interface media, relative to the short range van der Waals interactions between the molecular components. The phase behavior of the surface structure is explored by using molecular dynamics simulations, including some dynamical aspects of the interaction between neighboring domains, using the Lindemann criterion [F. Lindemann, Z. Phys. 11, 609 (1910)]. The charge ratio of the electrostatic components influences the shape of the domains, as well as the degree of local order in the interdomain structure.     

The Structure of Cellulose by Conformational Analysis. 1. Cellobiose and Methyl-β-cellobioside

Conformational analysis studies on the tertiary structure of cellobiose and methyl-β-cellobioside were carried out by using calculations of van der Waals, H-bond, electrostatic, and torsional energy interactions between the atoms and groups of the molecules. Energy maps as functions of the rotational anglesΨo and Φ° of the glucosidic bond were obtained in increments of 20° and refined in increments of 1°. Two “primary” and one “secondary” conformations of minimum energy were obtained for both cellobiose and methyl-β-cellobioside, some of which are equivalent to results obtained by x-ray diffraction. The H-bond forces are shown to be, together with the van der Waals forces, the predominant factors in the fixation of the conformations of minimum energy. The position and energy contributions of the H-bonds patterns for the favored conformations are identified.     

Two-dimensional self-assembly of a two-component molecular system: formation of an ordered and homogeneous molecular mesh

The formation of nanoscaled objects often relies on the two-dimensional self-assembly of organic molecules on solid substrates, leading to a number of interesting structures with nanometer dimensions. Assembly of single-component systems driven by chain-chain van der Waals interactions, hydrogen bonding, and dipolar interactions governs the structures typically formed. The two-dimensional self-assembly of a two-component molecular system is described here, where the structure involves mixing of the components at the molecular level. A mixture of 5-octadecyloxyisophthalic acid and octanoic acid forms an ordered stoichiometric array of homogeneous nanometer-sized openings of dimension 8.5 A x 13.5 A x1.8 A, verified by atomic resolution scanning tunneling microscopy. Assembly in the structure is driven by van der Waals and hydrogen bonding interactions between the molecular components.     

Diffusional Dynamics of Cytochrome cMolecules in the Presence of a Charged Surface

A new Brownian dynamics code was developed that is capable of computing trajectories of several spherical particles in the presence of a charged planar surface. The code takes into account electrostatic, van der Waals, and hydrodynamic interactions. In this work we describe the methods used in the program and show results from calculations for cytochrome cmolecules interacting with a negatively charged lipid bilayer. This system is of particular biological interest since these molecules play a major role as electron carriers, e.g., in photosynthesis. The shape and charge distribution of cytochrome cmolecules can be well approximated as spherical particles with an embedded monopole and dipole and can therefore easily be handled by the program. That level of approximation makes it possible to study large systems with many (up to 100) particles over time scales up to milliseconds, which would be computationally too expensive using detailed atomistic models.     

BC3 Sheet Functionalized with Lithium‐Rich Species Emerging as a Reversible Hydrogen Storage Material

The decoration of a BC₃ monolayer with the polylithiated molecules CLi₄ and OLi₂ has been extensively investigated to study the hydrogen‐storage efficiency of the materials by first principles electronic structure calculations. The binding energies of both lithiated species with the BC₃ substrate are much higher than their respective cohesive energies, which confirms the stability of the doped systems. A significant positive charge on the Li atom in each of the dopants facilitates the adsorption of multiple H₂ molecules under the influence of electrostatic and van der Waals interactions. We observe a high H₂‐storage capacity of 11.88 and 8.70 wt % for the BC₃‐CLi₄ and BC₃‐OLi₂ systems, respectively, making them promising candidates as efficient energy‐storage systems.     

Van der Waals Radii of Hydrogen in Gas-Phase and Condensed Molecules

Van der Waalsa radii of hydrogen in the different gas-phase and condensed molecules are determined and shown that a value of the van der Waals radius depends on the effective charge of the H atom. Is described also the van der Waals anisotropy of H in some molecules.