Analysis of a carbon dimer bound to a vacancy in iron using density functional theory and a new tight binding model

Recent density functional theory (DFT) calculations by Foerst et al. have predicted that vacancies in both low and high carbon steels have a carbon dimer bound to them. This is likely to change the thinking of metallurgists in the kinetics of the development of microstructures. While the notion of a C2 molecule bound to a vacancy in Fe will potentially assume a central importance in the atomistic modeling of steels, neither a recent tight binding (TB) model nor existing classical interatomic potentials can account for it. Here we present a new TB model for C in Fe, based on our earlier work for H in Fe, which correctly predicts the structure and energetics of the carbon dimer at a vacancy in Fe. Moreover the model is capable of dealing with both concentrated and dilute limits of carbon in both bcc-Fe and fcc-Fe as comparisons with DFT show. We use both DFT and TB to make a detailed analysis of the dimer and to come to an understanding as to what governs the choice of its curious orientation within the vacancy

A parallel multistate framework for atomistic non-equilibrium reaction dynamics of solutes in strongly interacting organic solvents

We describe a parallel linear-scaling computational framework developed to implement arbitrarily large multi-state empirical valence bond (MS-EVB) calculations within CHARMM. Forces are obtained using the Hellman-Feynmann relationship, giving continuous gradients, and excellent energy conservation. Utilizing multi-dimensional Gaussian coupling elements fit to CCSD(T)-F12 electronic structure theory, we built a 64-state MS-EVB model designed to study the F + CD3CN -> DF + CD2CN reaction in CD3CN solvent. This approach allows us to build a reactive potential energy surface (PES) whose balanced accuracy and efficiency considerably surpass what we could achieve otherwise. We use our PES to run MD simulations, and examine a range of transient observables which follow in the wake of reaction, including transient spectra of the DF vibrational band, time dependent profiles of vibrationally excited DF in CD3CN solvent, and relaxation rates for energy flow from DF into the solvent, all of which agree well with experimental observations. Immediately following deuterium abstraction, the nascent DF is in a non-equilibrium regime in two different respects: (1) it is highly excited, with ~23 kcal mol-1 localized in the stretch; and (2) not yet Hydrogen bonded to the CD3CN solvent, its microsolvation environment is intermediate between the non-interacting gas-phase limit and the solution-phase equilibrium limit. Vibrational relaxation of the nascent DF results in a spectral blue shift, while relaxation of its microsolvation environment results in a red shift. These two competing effects result in a post-reaction relaxation profile distinct from that observed when DF vibration excitation occurs within an equilibrium microsolvation environment. The parallel software framework presented in this paper should be more broadly applicable to a range of complex reactive systems.Comment: 58 pages and 29 Figure

Ultrafast structural and vibrational dynamics of the hydration shell around DNA

Two-dimensional infrared spectroscopy in the frequency range of OH- and NH stretch excitations serves for a direct mapping of hydration dynamics around DNA. A moderate slowing down of structural dynamics and resonant OH stretch energy transfer is observed in the DNA water shell compared to bulk water