Lattice Dynamics of Solid Cubane within the Quasi-Harmonic Approximation

Solid cubane, which is composed of weakly interacting cubic molecules, exhibits many unusual and interesting properties, such as a very large thermal expansion and a first-order phase transition at T$_{p}$=394 K from an orientationally-ordered phase of R$\bar{3}$ symmetry to a {\it non-cubic} disordered phase of the same symmetry with a volume expansion of 5.4%, among the largest ever observed. We study the lattice dynamics of solid cubane within the quasi-harmonic and rigid-molecule approximation to explain some of these unusual dynamical properties. The calculated phonon density of states, dispersion curves and thermal expansion agree surprisingly well with available experimental data. We find that the amplitude of thermally excited orientational excitations (i.e. librons) increases rapidly with increasing temperature and reaches about 35$^{\rm o}$ just before the orientational phase transition. Hence, the transition is driven by large-amplitude collective motions of the cubane molecules. Similarly the amplitude of the translational excitations shows a strong temperature dependence and reaches one tenth of the lattice constant at T=440 K. This temperature is in fair agreement with the experimental melting temperature of 405 K, indicating that the Lindemann criterion works well even for this unusual molecular solid.Comment: 15 pages, 6 figures (devoted to Prof. Ciraci in honor of his sixtieth birthday

From dimers to the solid-state: Distributed intermolecular force-fields for pyridine

A.A. thanks A.W.E. financial support through the EngDoc studentship from M3S Centre for Doctoral Training (EPSRC Grant No. EP/G036675/1). General computational infrastructure used is developed under No. EPSRC EP/K039229/1

Quantum mechanical calculation of the effects of stiff and rigid constraints in the conformational equilibrium of the Alanine dipeptide

If constraints are imposed on a macromolecule, two inequivalent classical models may be used: the stiff and the rigid one. This work studies the effects of such constraints on the Conformational Equilibrium Distribution (CED) of the model dipeptide HCO-L-Ala-NH2 without any simplifying assumption. We use ab initio Quantum Mechanics calculations including electron correlation at the MP2 level to describe the system, and we measure the conformational dependence of all the correcting terms to the naive CED based in the Potential Energy Surface (PES) that appear when the constraints are considered. These terms are related to mass-metric tensors determinants and also occur in the Fixman's compensating potential. We show that some of the corrections are non-negligible if one is interested in the whole Ramachandran space. On the other hand, if only the energetically lower region, containing the principal secondary structure elements, is assumed to be relevant, then, all correcting terms may be neglected up to peptides of considerable length. This is the first time, as far as we know, that the analysis of the conformational dependence of these correcting terms is performed in a relevant biomolecule with a realistic potential energy function.Comment: 37 pages, 4 figures, LaTeX, BibTeX, AMSTe

Quasi Harmonic Lattice Dynamics and Molecular Dynamics calculations for the Lennard-Jones solids

We present Molecular Dynamics (MD), Quasi Harmonic Lattice Dynamics (QHLD) and Energy Minimization (EM) calculations for the crystal structure of Ne, Ar, Kr and Xe as a function of pressure and temperature. New Lennard-Jones (LJ) parameters are obtained for Ne, Kr and Xe to reproduce the experimental pressure dependence of the density. We employ a simple method which combines results of QHLD and MD calculations to achieve densities in good agreement with experiment from 0 K to melting. Melting is discussed in connection with intrinsic instability of the solid as given by the QHLD approximation. (See http://www.fci.unibo.it/~valle for related papers)Comment: 7 pages, 5 figures, REVte

To wet or not to wet: that is the question

Wetting transitions have been predicted and observed to occur for various combinations of fluids and surfaces. This paper describes the origin of such transitions, for liquid films on solid surfaces, in terms of the gas-surface interaction potentials V(r), which depend on the specific adsorption system. The transitions of light inert gases and H2 molecules on alkali metal surfaces have been explored extensively and are relatively well understood in terms of the least attractive adsorption interactions in nature. Much less thoroughly investigated are wetting transitions of Hg, water, heavy inert gases and other molecular films. The basic idea is that nonwetting occurs, for energetic reasons, if the adsorption potential's well-depth D is smaller than, or comparable to, the well-depth of the adsorbate-adsorbate mutual interaction. At the wetting temperature, Tw, the transition to wetting occurs, for entropic reasons, when the liquid's surface tension is sufficiently small that the free energy cost in forming a thick film is sufficiently compensated by the fluid- surface interaction energy. Guidelines useful for exploring wetting transitions of other systems are analyzed, in terms of generic criteria involving the "simple model", which yields results in terms of gas-surface interaction parameters and thermodynamic properties of the bulk adsorbate.Comment: Article accepted for publication in J. Low Temp. Phy

When a proton attacks cellobiose in the gas phase: ab initio molecular dynamics simulations

Investigations of reaction pathways between a proton and cellobiose (CB), a glucose disaccharide of importance, were carried out in cis and trans CB using Ab Initio Molecular Dynamics (AIMD) simulations starting from optimized configurations where the proton is initially placed near groups with affinity for it. Near and above 300 K, protonated CB (H(+)CB) undergoes several transient reactions including charge transfer to the sugar backbone, water formation and dehydration, ring breaking and glycosidic bond breaking events as well as mutarotation and ring puckering events, all on a 10 ps timescale. cis H(+)CB is energetically favoured over trans H(+)CB in vacuo, with an energy gap larger than for the neutral CB

Computational chemistry for graphene-based energy applications: progress and challenges

YesResearch in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.vesk