2,148 research outputs found
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
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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
Vibronic excitations of large molecules in solution studied by two-color pumpâprobe experiments on the 20 fs time scale
The ultrafast vibronic response of organic dye molecules in solution is studied in pumpâprobe experiments with 30 fs excitation pulses resonant to S0âSn transitions. The molecular dynamics is probed either by pulses at the same spectral position or by 20 fs pulses overlapping with both the S0âS1 absorption and emission bands. Three contributions on distinctly different time scales are observed in the temporally and spectrally resolved two-color measurements. In the regime below 50 fs, a strong coherent coupling of the S0âSn and the S0âS1 transitions occurs that is due to coherent vibrational motions in the electronic ground state. This signal is superimposed on the fast bleaching of the electronic ground state, resulting in a steplike increase of transmission. In the range of the S0âS1 emission band, one finds a subsequent picosecond rise of transmission that is due to stimulated emission from vibronic S1 states. The data demonstrate that the relaxation of Sn states directly populated by the pump pulses is much faster than the buildup of stimulated emission. This gives insight into different steps of intramolecular vibronic redistribution and is compared to the SnâS1 relaxation in other molecules
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