The statistical mechanics of ion-dipole-tetrahedral quadrupole mixtures

We examine the solution of the Ornstein-Zernike equations for the correlation functions of a fluid mixture in which the molecular interactions consist of a hard sphere plus a multipolar potential that contains coulombic, dipolar as well as quadrupolar terms. In particular we consider the case in which the molecule has a dipole moment in the z direction of the molecular axis system and a non-linear tetrahedral quadrupole tensor of the form Θ _xx = - Θ _yy , Θ _zz = 0 = Θ_αβ, α ≠ β in the molecular frame. This model is a good representation of the dipolar and quadrupolar properties of water and our analysis will form the basis for constructing a Civilized Model electrolyte in which ions are dissolved in a solvent whose molecules possess water-like multipole moments. One of our main results is that for any theory which retains only the subset of rotational invariants that either appear in the interaction potentials or are generated by angular convolution from those appearing in the interaction potentials, e.g. the linearized hypernetted chain (LHNC) or mean spherical approximations (MSA), the equations for an ion-dipole-tetrahedral quadrupolar mixture only differ from those for an ion-dipole-linear quadrupole mixture (Θ _xx = Θ _yy = - 1/2Θ _zz , Θ_αβ = 0, α ≠ β) in minor details. We have investigated the thermodynamic properties of a fluid of hard spheres with the dipole and tetrahedral moments of water using thermodynamic perturbation theory. We find that contributions to the thermodynamic properties from dipole-quadrupole interaction are very important. For a pure hard sphere tetrahedral quadrupolar fluid there is considerable difference between the results from perturbation theory and from the MSA, for which we have obtained an analytic solution.     

Electronic structure and interactions in well-defined coadsorbate layers

A synopsis of results and models for weakly and strongly interacting, well-defined coadsorbate systems is presented. Some experimental examples are given for various adsorbates on Ni(111) representing weak (different N₂ states, Ar/Xe+N₂) as well as strong (N₂+K) interaction. Models for coadsorbate interaction, in particular between molecules (CO, N₂) and alkali atoms, are discussed.     

Electron scattering from nonlinear molecules using multicentre wavefunction expansions

Summary The scattering of slow electrons by polyatomic molecules is studied within a full quantum formulation of the problem, and the wavefunctions of the target molecular bound electrons are obtained from a multicentre expansion (MCE) of Gaussian-type orbitals (GTOs) within the single-determinant Hartree-Fock (HF)-SCF scheme. It is shown that the scattering calculations require the solution of radial coupled equations where the interaction is obtained as a further multipolar expansion at the target centre of mass (c.o.m.), while the relevant numerical procedures are discussed for systems like SiH₄, GeH₄ and CF₄. The ensuing interaction coefficients are used to carry out convergence studies of the scattering cross-sections, over a broad range of energies, in the case of silane targets. The results are found to be rapidly converging for such a system, while the different behaviour expected for other targets is also analysed and explained.     

Nematic order-disorder state transition in a liquid crystal analogue formed by oriented and migrating amoeboid cells

In cell culture, liquid crystal analogues are formed by elongated, migrating, and interacting amoeboid cells. An apolar nematic liquid crystal analogue is formed by different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (=fat cells), etc. The nematic analogue is quite well described by i) a stochastic machine equation responsible for cell orientation and ii) a self-organized extracellular guiding signal, E₂, which is proportional to the orientational order parameter as well as to the cell density. The investigations were mainly made with melanocytes. The transition to an isotropic state analogue can be accomplished either by changing the strength of interaction (e.g. variation of the cell density) or by influencing the cellular machinery by an externally applied signal: i) An isotropic gaseous state analogue is observed at low cell density (melanocytes/mm^2) and a nematic liquid crystal state analogue at higher cell density. ii) The nematic state analogue disappears if the bipolar shaped melanocytes are forced to become a star-like shape (induced by colchicine or staurosporine). The analogy between nematic liquid crystal state analogue formed by elongated, migrating and interacting cells and the nematic liquid crystal phase formed by interacting elongated molecules is discussed. Received 2 August 1999 and Received in final form 5 January 2000     

Classical trajectory calculations for state-resolved Penning ionisation reactions of polycyclic aromatic hydrocarbon C10H8 in collision with He*(23S)

ABSTRACT

The reaction dynamics of Penning ionisation of a polycyclic aromatic hydrocarbon (PAH), naphthalene C₁₀H₈, in collision with the metastable He*(2³S) atom is studied by classical trajectory calculations using an approximate interaction potential energy surface between He* and the molecule, which is constructed based on ab initio calculations for the isovalent Li?+?C₁₀H₈ system. The ionisation width (rate) around the molecular surface are obtained from overlap integrals of the He 1s orbital and the molecular orbital. The calculated collision energy dependences of partial Penning ionisation cross sections (CEDPICS) in the range 50–500?meV at 300?K have reproduced the experimental results semi-quantitatively. The opacity functions, which represent the reaction probability with respect to the impact parameter b, are discussed in connection with collision energy, interaction with He* and the exterior electron density of molecular orbitals. They indicate that the collisional ionisations of C₁₀H₈ can be classified into three types: π electron ionisations with negative collision energy dependences which are predominantly determined by attractive interaction with He*; σ orbitals ionisations of the hardcore type; σ orbital ionisations which reflect interaction potentials around CH bonds. The critical impact parameters b_c become larger with increasing collision energy due to the centrifugal barrier.     

On the additivity of atomic and molecular dipole properties and dispersion energies using H,N, O,H2, N2, O2, NO,N2O,NH3 and H2O as models

The zeroth-order theory of intermolecular forces is used to derive additivity relations for rotationally averaged molecular dipole properties and dispersion energy constants by assuming that a molecule is comprised of non-interacting atoms or molecules. Some of the additivity rules are new and others, for example the mixture rule for dipole oscillator strength distributions (DOSDs), Bragg's rule for stopping cross sections and Landolt's rule for molecular refractivities, are well known. The additivity rules are tested by using previously constructed DOSDs and reliable values for the dipole oscillator strength sums S_k , L_k and I_k , and dispersion energy constants C ₆, for H, N, O, H₂, N₂, O₂, NO, N₂O, NH₃ and H₂O as models. It is found that additivity is generally unreliable for estimating molecular properties corresponding to k < -2. Generally for k ≥ -2 and for C ₆, and if the hydrogen molecule is used to represent the hydrogen atom in the additivity rules, the additivity relations yield results that are reliable to within ?20 per cent and the estimates improve substantially as k increases. The effects of molecule formation on DOSDs is examined by comparing the various molecular DOSDs with the sum of the DOSDs for the atoms making up the molecules. Molecule formation results in a net decrease in the amount of dipole oscillator strength for low excitation energies and a compensating net increase for higher energies in a region extending from the absorption threshold to about 100 eV. This is shown to imply that estimates of the stopping average energy I ₀, obtained by using bona fide atomic I ₀ values, are lower bounds to the correct molecular I ₀ results.     

Thermodynamic and structural properties of liquids modelled by ‘2-Lennard-Jones centres’ pair potentials

Molecular dynamics calculations have been carried out for model liquid systems of N (=108 or 256) molecules interacting through two Lennard-Jones (12–6) centres coinciding with the positions of the atomic masses (the ‘atom-atom’ pair potential). The objectives were (a) to study the dependence of the properties on the molecular anisotropy defined by the reduced distance l*=l/σ between the centres in the range 0·5–0·8; and (b) to compare the computed quantities with those of real liquids (F₂, Cl₂, Br₂, CO₂). This paper deals with thermodynamic and structural features. Time-dependent correlations will be treated in a future communication.

In the liquid region not too far from the triple point the energy and pressure isochores are well represented by straight lines, the slopes of which increase with density and anisotropy. Thermodynamically consistent expressions for the energy and pressure as functions of density and temperature have been obtained for each system.

With Lennard-Jones parameters adjusted so as to secure the best overall fit, the agreement between experimental and computed thermodynamic properties is very satisfactory for F₂ (l*=0·505), quite good for Cl₂ and Br₂ (l*=0·608–0·63), but rather poor for CO₂ (l*=0·793). The ‘interatomic distances’ are close to the experimental values.

The static structural correlations are discussed in terms of the pair-correlation functions (pcf) g _A(r*) for the separation between ‘atoms’, the first few functions g_ll'm (R*) which arise from the expansion of the g(R*, θ₁, θ₂, φ₁₂) in spherical harmonics, and the pcf's for certain special near-neighbour configurations. The computed atom-atom structure factor is compared with the experimental data for liquid Br₂.

Mean square forces and torques have been evaluated and are related to some experimental results.     

Terthiophene as a model sensor for some atmospheric gases: theoretical study

ABSTRACT

We use density functional theory (DFT) to assess the ability of terthiophene (as a simplest model of polythiophene, denoted as TTP) for detecting of atmospheric gases. Specifically, at the ωB97XD/6-31G(d,p) level of theory, the sensitivity of TTP towards CO, CO₂, SO₂ and CH₃OH is investigated. To better understand the electronic properties of interacting TTP, natural-bond-orbital (NBO) and density-of-states (DOSs) analyses are performed for TPP in free mode and interacted form with the above molecules. The types of interactions between these species with TTP were studied in terms of the HOMO and LUMO energies. UV-Vis spectra are calculated for all systems and the data shows that the λ_max values are red or blue shifted depending on the analyte, which are proving for successfully interaction. The calculated interaction energies are ?16.7, ?14.3, ?8.2 and ?5.3 kJ/mol for TTP-CH₃OH, TTP-SO₂, TTP-CO₂ and TTP-CO, respectively.     

Theoretical studies on the single proton transfer process in adenine base

The effect of metal ions (Mⁿ⁺ = Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺ and hydrated Mg²⁺ ions) and water molecules on the tautomerism of adenine induced by single intramolecular proton transfer (SPT) have been investigated theoretically. Calculated results show that the single proton transfer process in adenine base is favored and even becomes thermodynamically spontaneous because of the presence of Mⁿ⁺ interacting at the N₃ position of adenine. On the contrary, if Mⁿ⁺ coordinated to N₇ site, the single proton transfer process will become unfavorable than that in the neutral system. The effects of metal ions on the SPT of adenine base are more pronounced if Lewis acidity of metal ion is increased. Water plays a more important role than metal ions during the SPT process. It is found that water can act not only as a solvent but also as a mediator which gives and accepts protons to promote SPT, playing a bridge role. As a result, inclusion of a water molecule drastically reduces the energy barrier for the SPT. Moreover, two water molecules can yield larger assisting effect on the SPTs compared with one water molecule. We can conclude that the tautomerism of DNA adenine base can be modulated by the metal ions and water molecules. Copyright © 2015 John Wiley & Sons, Ltd.     

The Structure of Water Clusters Interacting with Gaseous Acetylene

The interaction of water clusters with acetylene molecules at T = 230 K was studied by the molecular dynamics method. The structure of clusters was analyzed by constructing Voronoi polyhedra. Water clusters interacting with C₂H₂ molecules are characterized by a diversity of H-bond orientations, a more uniform distribution of H-bonds over the cluster volume, a larger number of bonds per atom, and smaller bond lengths. The spectrum of bond lengths broadens as the number of acetylene molecules interacting with the water cluster increases. C₂H₂ molecules have a pressing action on water clusters.     

Accurate equilibrium structures of fluoro- and chloroderivatives of methane

This work is a systematic study of molecular structure of fluoro-, chloro-, and fluorochloromethanes. For the first time, the accurate ab initio structure is computed for 10 molecules (CF₄, CClF₃, CCl₂F₂, CCl₃F, CHClF₂, CHCl₂F, CH₂F₂, CH₂ClF, CH₂Cl₂, and CCl₄) at the coupled cluster level of electronic structure theory including single and double excitations augmented by a perturbational estimate of the effects of connected triple excitations [CCSD(T)] with all electrons being correlated and Gaussian basis sets of at least quadruple-ζ quality. Furthermore, when possible, namely for the molecules CH₂F₂, CH₂Cl₂, CH₂ClF, CHClF₂, and CCl₂F₂, accurate semi-experimental equilibrium (r^SE_e) structure has also been determined. This is achieved through a least-squares structural refinement procedure based on the equilibrium rotational constants of all available isotopomers, determined by correcting the experimental ground-state rotational constants with computed ab initio vibration–rotation interaction constants and electronic g-factors. The computed and semi-experimental equilibrium structures are in excellent agreement with each other, but the r^SE_e structure is generally more accurate, in particular for the CF and CCl bond lengths. The carbon–halogen bond length is discussed within the framework of the ligand close-packing model as a function of the atomic charges. For this purpose, the accurate equilibrium structures of some other molecules with alternative ligands, such as CH₃Li, CF₃CCH, and CF₃CN, are also computed.     

Water-silica interaction in clusters

The interaction of water with SiO ₂ is an important problem in geophysics, materials physics, and environmental science. In this paper, we present recent results on studies of H ₂ O-silica clusters from first-principles Born-Oppenheimer molecular dynamics calculations. Bond strength and chemical stability are investigated as a function of cluster size and chemical composition. Both physisorption and chemisorption of water molecules on the clusters are discussed via analysis of energetics. Calculations of clusters are compared with the results from extended surfaces. The validity of clusters as models of surfaces is discussed.     

A quasi analytical method for the calculation of virial coefficients for realistic intermolecular potentials

The difficulties of accurately representing the Ursell function, f, for molecules interacting with a Lennard-Jones potential by a hard sphere core and a truncated exponential series are discussed. The range of R for which a hard sphere approximates f with negligible error is established and the range of arguments in f is determined. The accuracy with which the exponential series, S_k , truncated after k terms, represents the function is established for several ranges of arguments. It is shown that it is possible to represent f accurately by a hard sphere core and S ₄ or S ₆ for all values of R except over a short range of R.

Values of B and C, accurate to within a few per cent, can be obtained analytically through approximating f by S ₄ or S ₆ and a hard core whose diameter is determined by the range of arguments for which the series is valid. More accurate values of B and C required additional approximations for f. Two of these, the repulsive square well and the Barker-Henderson radius, give accurate values of B and C at all temperatures that were examined.     

Temperature Dependence of the Vibrational Relaxation Rate Constants of CO2 (0001) in Binary Mixtures

The rate constants of intramolecular intermode relaxation of the CO₂ molecule (00⁰1) in pure CO₂ and in binary mixtures with He, Ar, H₂, O₂, N₂, CO, NO, N₂O, and H₂O were measured in the temperature range 300–1000 K by means of a laser-induced luminescence method. It is shown that these relaxation rate constants K for all the gas mixtures investigated increase with increase in the gas temperature in this range; the most efficient in deactivation of the 00⁰1 level are the collisions of CO₂ molecules with H₂O molecules; the mechanisms of relaxation of the 00⁰1 level of CO₂ and their channels depend not only on the temperature but also on the parameters of colliding particles; for each of the colliding partners of the CO₂ molecules there is a certain temperature T _c above which the temperature dependence of K is coordinated with the Landau–Teller dependence, and, moreover, the simpler the structure of the colliding partner of the CO₂ molecule, the higher the temperature T _c. Deviations from these dependences at temperatures T < T _c are attributed to the influence of intermolecular forces of attraction, change of relaxation channels, and formation of molecular clusters. For all the colliding partners of the CO₂ molecules, the interaction radii are determined from the intermolecular potentials of interaction used in the theoretical model.     

Electron scattering with open-shell molecules: R-matrix method

Many molecules with an even number of electrons belong to open-shell systems due to π ² ground state electronic configuration. This configuration gives rise to three low-lying states X ³ Σ ⁻, a Δ ¹ and b ¹ Σ ⁺. The inclusion of these target states in a trial wave function of the entire scattering system have important implications in the resonances that may be detected in these open-shell molecules. Various molecules like O₂, PX (X = H and halogens), SO, Si₂, BF have π ² ground state configuration. The R-matrix method is a well established ab initio formalism to calculate differential, integral and momentum-transfer cross sections for the elastic scattering of electrons by molecules. We have calculated these cross sections for PH and SO molecules in the incident electron energy range 0–10 eV. The results are obtained by using the R-matrix method in which the closecoupling expansion of the wave function of the scattering system includes only the ground state. This target state is described by configuration interaction wave function that includes correlation effects. The cross section for electron impact on PH and SO are presented.     

Generating intense beams of low-energy molecules

A method for obtaining intense pulsed beams of molecules possessing low kinetic energies is proposed. The method is based on the formation of a cold pressure shock (shock wave) in an intense pulsed molecular beam interacting with a solid surface, which serves as a source of the secondary beam of low-energy molecules. The proposed method was successfully used to obtain intense beams of H₂, He, CH₄, and Kr molecules with kinetic energies not exceeding 10 meV, and H₂/Kr and He/Kr beams with kinetic energies of H₂ and He molecules below 1 meV.     

Ultrasonic and DFT study of intermolecular association through hydrogen bonding in aqueous solutions of glycerol

The experimental measurements of density, viscosity and ultrasonic velocity of aqueous glycerol solutions were carried out as functions of concentration (0.1 ≤ m [mol kg^− 1] ≤ 1.0) and temperature (303.15 ≤ T [K] ≤323.15). The isentropic compressibility (β_s), acoustic impedance (Z), hydration number (H_n), intermolecular free length (L_f), classical sound absorption (α/f²)_class and shear relaxation time (τ) were calculated by using the measured data. These parameters have been interpreted in terms of solute–solvent interactions. The quantum chemical calculations were performed to study the hydrogen bonding in interacting complex formed between glycerol and water molecules. Computations have been done by using Density Functional Theory (DFT) method at B3LYP/6–31 + g(d) level of theory to study the equilibrium structure of glycerol, glycerol–water interacting complex and vibrational frequencies. The solution phase study was carried out using Onsager's reaction field model in water solvent. The computed vibrational frequencies are in good agreement with the main features of the experimental spectrum when four water molecules are considered explicitly with glycerol. The interaction energy (E_total), hydrogen bond lengths and dipole moment (µ_m) of the interacting complex are also presented and discussed with in the light of solute–solvent interactions.     

Interacting entropy-corrected holographic dark energy with apparent horizon as an infrared cutoff

In this work we consider the entropy-corrected version of interacting holographic dark energy (HDE), in the non-flat universe enclosed by apparent horizon. Two corrections of entropy so-called logarithmic ‘LEC’ and power-law ‘PLEC’ in HDE model with apparent horizon as an IR-cutoff are studied. The ratio of dark matter to dark energy densities u, equation of state parameter w _D and deceleration parameter q are obtained. We show that the cosmic coincidence problem is solved for interacting models. By studying the effect of interaction in EoS parameter of both models, we see that the phantom divide may be crossed and also understand that the interacting models can drive an acceleration expansion at the present and future, while in non-interacting case, this expansion can happen only at the early time. The graphs of deceleration parameter for interacting models, show that the present acceleration expansion is preceded by a sufficiently long period deceleration at past. Moreover, the thermodynamical interpretation of interaction between LECHDE and dark matter is described. We obtain a relation between the interaction term of dark components and thermal fluctuation in a non-flat universe, bounded by the apparent horizon. In limiting case, for ordinary HDE, the relation of interaction term versus thermal fluctuation is also calculated.     

Symmetries of electrostatic interaction between DNA molecules

A model for pair interaction U of DNA molecules generated by the discrete dipole moments of base-pairs and the charges of phosphate groups is studied. A noncommutative group of eighth order ℒ of symmetries that leave U invariant is found. The minima are classified with the use of group ℒ and numerical methods are employed for finding them. The minima may correspond to several cholesteric phases, as well as to phases formed by crosslike conformations of molecules at an angle close to 90°—the “snowflake phase.” The results depend on the effective charge Q of the phosphate group, which can be modified by the polycations or the ions of metals. The snowflake phase could exist for Q above the threshold Q _C. Below Q _C, there could be several cholesteric phases. Close to Q _C, the snowflake phase could change into the cholesteric one at constant distance between adjacent molecules. The text was submitted by the authors in English.