Non-equilibrium phenomena and molecular reaction dynamics: mode space, energy space and conformer space

status: publishe

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

The Study of Reactive Intermediates in Condensed Phases

Novel experimental techniques and computational methods have provided new insight into the behavior of reactive intermediates in solution. The results of these studies show that some of the earlier ideas about how reactive intermediates ought to behave in solution were incomplete or even incorrect. This Perspective summarizes the new experimental and computational methods and draws attention to the shortcomings that their application has brought to light in previous models. Key areas needing further research are highlighted

Continuous ligand-assisted elution chromatography applied to separation of rare earth elements

Rare earth elements (REEs) are metals used to make many valuable products such as magnets and electronics. Following their extraction from larger materials, REEs are to be separated into their individual components as high purity is required for product manufacture. Purification is very difficult because most (15/17) of the REEs are lanthanides (Ln’s) and Ln ions have the same valence and similar atomic radii. The current industrial process for purifying REEs involves using toxic solvents to perform a series of liquid-liquid extractions. Ling and Wang (2015) proposed a ligand-assisted batch chromatography process to purify Ln’s. The latter approach is a vast improvement over the former in terms of safety, however being a batch process, it is not economical for industrial use. The purpose of this study was to design and test a continuous system based off of Ling and Wang’s ligand-assisted elution chromatography process. A titania sorbent was used with a selective ligand, ethylenediaminetetraacetic acid (EDTA). The continuous system utilizes a stepwise elution process and separates a solution of praseodymium (Pr) and samarium (Sm). A Semba Octave SMB chromatography system was used to perform the experiment. Yields and purities greater than 95% were seen for each of the components in solution and the process can be run indefinitely. This continuous process for Ln separation is of interest because safety is increased in comparison to the aforementioned industrial system, sorbent productivity is increased, and it is more robust and simpler to run than the batch process. This continuous system can be scaled up to produce high purity REEs safely and efficiently

Dynamical Effects and Product Distributions in Simulated CN + Methane Reactions

Dynamics of collisions between structured molecular species quickly become complex as molecules become large. Reactions of methane with halogen and oxygen atoms serve as model systems for polyatomic molecule chemical dynamics, and replacing the atomic reagent with a diatomic radical affords further insights. A new, full-dimensional potential energy surface for collisions between CN + CH4 to form HCN + CH3 is developed and then used to perform quasi-classical simulations of the reaction. Coupled-cluster energies serve as input to an empirical valence bonding (EVB) model, which provides an analytical function for the surface. Efficient sampling permits simulation of velocity-map ion images and exploration of dynamics over a range of collision energies. Reaction populates HCN vibration, and energy partitioning changes with collision energy. The reaction cross-section depends on the orientation of the diatomic CN radical. A two-dimensional extension of the cone of acceptance for an atom in the line-of-centers model appropriately describes its reactivity. The simulation results foster future experiments and diatomic extensions to existing atomic models of chemical collisions and reaction dynamics.status: publishe

Reduced dimensionality spin-orbit dynamics of CH3 + HCl reversible arrow CH4 Cl on ab initio surfaces

A reduced dimensionality quantum scattering method is extended to the study of spin-orbit nonadiabatic transitions in the CH3 + HCl reversible arrow CH4 + Cl(P-2(J)) reaction. Three two-dimensional potential energy surfaces are developed by fitting a 29 parameter double-Morse function to CCSD(T)/IB//MP2/cc-pV(T+d)Z-dk ab initio data; interaction between surfaces is described by geometry-dependent spin-orbit coupling functions fit to MCSCF/cc-pV(T+d)Z-dk ab initio data. Spectator modes are treated adiabatically via inclusion of curvilinear projected frequencies. The total scattering wave function is expanded in a vibronic basis set and close-coupled equations are solved via R-matrix propagation. Ground state thermal rate constants for forward and reverse reactions agree well with experiment. Multi-surface reaction probabilities, integral cross sections, and initial-state selected branching ratios all highlight the importance of vibrational energy in mediating nonadiabatic transition. Electronically excited state dynamics are seen to play a small but significant role as consistent with experimental conclusions. (C) 2011 American Institute of Physics. [doi:10.1063/1.3592732

Expansion of the ligand knowledge base for chelating P,P-donor ligands (LKB-PP)

[Image: see text] We have expanded the ligand knowledge base for bidentate P,P- and P,N-donor ligands (LKB-PP, Organometallics2008, 27, 1372–1383) by 208 ligands and introduced an additional steric descriptor (nHe(8)). This expanded knowledge base now captures information on 334 bidentate ligands and has been processed with principal component analysis (PCA) of the descriptors to produce a detailed map of bidentate ligand space, which better captures ligand variation and has been used for the analysis of ligand properties