Density functional study of carbon vacancies in titanium carbide.

It is well established that TiC contains carbon vacancies not only in carbon-deficient environments but also in carbon-rich environments. We have performed density functional calculations of the vacancy formation energy in TiC for C- as well as Ti-rich conditions using several different approximations to the exchange-correlation functional, and also carefully considering the nature and thermodynamics of the carbon reference state, as well as the effect of varying growth conditions. We find that the formation of carbon vacancies is clearly favorable under Ti-rich conditions, whereas it is slightly energetically unfavorable under C-rich conditions.

Temperature dependence of band gaps and conformational disorder in PEDOT and its selenium and tellurium derivatives: Density functional calculations.

The conducting polymer poly(3,4-ethylenedioxythiophene), or PEDOT, is an attractive material for flexible electronics. We present combined molecular dynamics and quantum chemical calculations, based on density functional theory, of EDOT oligomers and isoelectronic selenium and tellurium derivatives (EDOS and EDOTe) to address the effect of temperature on the geometrical and electronic properties of these systems. With finite size scaling, we also extrapolate our results to the infinite polymers, i.

Conformations, structural transitions and visible near-infrared absorption spectra of four-, five- and six-coordinated Cu(II) aqua complexes.

We have performed Car-Parrinello molecular dynamics simulations at ambient conditions for four-, five- and six-coordinated Cu(II) aqua complexes. The molecular geometry has been investigated in terms of Cu-O, Cu-H bond lengths and O-Cu-O bond angles and compared with earlier experimental measurement results and theoretical calculations. We find that the average Cu-O and Cu-H bond lengths increase with increasing coordination number.

Solvent dependence of conformational distribution, molecular geometry, and electronic structure in adenosine.

Solvation dynamics of adenosine in water and chloroform solvents under ambient conditions has been investigated using both force-field molecular dynamics (MD) and first-principles Car-Parrinello molecular dynamics (CPMD) calculations. First, the solvent dependence of the equilibria between anti-syn forms, C((3'))-endo-C((2'))-endo conformations, and carbinol group rotamers has been discussed from MD calculations. We find that in both the solvents the adenosine molecule can remain either in anti or syn conformations.

Solvent dependence on conformational transition, dipole moment, and molecular geometry of 1,2-dichloroethane: insight from Car-Parrinello molecular dynamics calculations.

We have investigated the molecular geometry and dipole moment distribution for the major conformational states of 1,2-dichloroethane (DCE) in three different solvents under ambient conditions using the Car-Parrinello mixed quantum mechanics/molecular mechanics method. The solvents studied were water, DCE, and chloroform. Within the time scale investigated, we find a conformational equilibrium existing between the gauche and trans forms of DCE in all three solvents.

Investigations into conformational transitions and solvation structure of a 7-piperidino-5,9-methanobenzo[8] annulene in water.

Solvation shell structure of a 7-piperidino-5,9-methanobenzo[8] annulene (PMA) in water has been investigated in ambient conditions using both molecular dynamics (MD) and Car-Parrinello molecular dynamics (CPMD) calculations. From the MD calculations, we find that this molecule exists in three major conformational states out of which two are in twist-boat forms and one in chair form. Due to the limited time scale accessible in CPMD simulations, we have studied all the three conformational states separately using CPMD.

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching.

We introduce a novel procedure to parametrize biomolecular force fields. We perform finite-temperature quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, with the fragment or moiety that has to be parametrized being included in the QM region. By applying a force-matching algorithm, we derive a force field designed in order to reproduce the steric, electrostatic, and dynamic properties of the QM subsystem.

A comparative theoretical study of dipeptide solvation in water.

Molecular dynamics studies have been performed on the zwitterionic form of the dipeptide glycine-alanine in water, with focus on the solvation and electrostatic properties using a range of theoretical methods, from purely classical force fields, through mixed quantum mechanical/molecular mechanical simulations, to fully quantum mechanical Car-Parrinello calculations. The results of these studies show that the solvation pattern is similar for all methods used for most atoms in the dipeptide, but can differ substantially for some groups; namely the carboxy and aminoterminii, and the backbone amid NH group. This might have implications in other theoretical studies of peptides and proteins with charged -NH(3) (+) and -CO(2) (-) side chains solvated in water.