This review provides a comprehensive overview of the structural dynamics in topical gas- and condensed-phase systems on multiple length and time scales. Starting from vibrationally induced dissociation of small molecules in the gas phase, the question of vibrational and internal energy redistribution through conformational dynamics is further developed by considering coupled electron/proton transfer in a model peptide over many orders of magnitude. The influence of the surrounding solvent is probed for electron transfer to the solvent in hydrated I−. Next, the dynamics of a modified PDZ domain over many time scales is analyzed following activation of a photoswitch. The hydration dynamics around halogenated amino acid side chains and their structural dynamics in proteins are relevant for iodinated TyrB26 insulin. Binding of nitric oxide to myoglobin is a process for which experimental and computational analyses have converged to a common view which connects rebinding time scales and the underlying dynamics. Finally, rhodopsin is a paradigmatic system for multiple length- and time-scale processes for which experimental and computational methods provide valuable insights into the functional dynamics. The systems discussed here highlight that for a comprehensive understanding of how structure, flexibility, energetics, and dynamics contribute to functional dynamics, experimental studies in multiple wavelength regions and computational studies including quantum, classical, and more coarse grained levels are required.
Due to their very nature, ultrafast phenomena are often accompanied by the occurrence of nonadiabatic effects. From a theoretical perspective, the treatment of nonadiabatic processes makes it necessary to go beyond the (quasi) static picture provided by the time-independent Schrödinger equation within the Born-Oppenheimer approximation and to find ways to tackle instead the full time-dependent electronic and nuclear quantum problem. In this review, we give an overview of different nonadiabatic processes that manifest themselves in electronic and nuclear dynamics ranging from the nonadiabatic phenomena taking place during tunnel ionization of atoms in strong laser fields to the radiationless relaxation through conical intersections and the nonadiabatic coupling of vibrational modes and discuss the computational approaches that have been developed to describe such phenomena. These methods range from the full solution of the combined nuclear-electronic quantum problem to a hierarchy of semiclassical approaches and even purely classical frameworks. The power of these simulation tools is illustrated by representative applications and the direct confrontation with experimental measurements performed in the National Centre of Competence for Molecular Ultrafast Science and Technology.
Understanding atomistic and molecular aspects of chemical reactions is one of the cornerstones in chemistry and biology. Characterizing reactions in time and space is challenging due to the different length-and time-scales on which the nuclear dynamics takes place [1]. For example, typical reaction times for the Claisen rearrangement [2] in solution are on the order of seconds [3] or milliseconds (in the protein) [4]. However, the chemical step (i.e. C-C bond formation and C-O bond breaking) [5] occurs on the femtosecond time scale. In other words, during 10 9 to 10 15 vibrational periods energy is redistributed in the system until sufficient energy has accumulated along the relevant 'progression coordinate' for the reaction to occur. Because the 'chemical step' is so rapid and the system concentration at the transition state is negligible, direct experimental characterization of the transition state and the dynamics between reactant and product is extremely challenging even with current state-of-the art methods, including NMR, [6] IR, [7] or x-ray [8,9] spectroscopies.Atomistic simulations have shown to provide molecular-level insight into the energetics and dynamics of chemical reactions for systems ranging from small (triatomic) molecules to proteins in the condensed phase [1,[10][11][12][13]]. An essential requirement for a meaningful contribution of computer-based work to characterize chemical reactions is a correct description of the intermolecular interactions along the entire reaction path including the degrees of freedom orthogonal to it. This involves regions around the reactants, products and the transition state(s). Intermolecular interactions in molecular systems are often represented as a Born-Oppenheimer
The Claisen rearrangement is a carbon-carbon bond-forming, pericyclic reaction of fundamental importance due to its relevance in synthetic and mechanistic investigations of organic and biological chemistry. Despite continued efforts, the molecular origins of the rate acceleration in going from the aqueous phase into the protein is still incompletely understood. In the present work the rearrangement reaction for allyl-vinyl-ether (AVE), its dicarboxylated variant (AVE-(CO 2 ) 2 ) and the biologically relevant substrate chorismate is investigated in gas phase, water and in chorismate mutase. Only the rearrangement of chorismate in the enzyme shows a negative differential barrier when compared to the reaction in water, which leads to the experimentally observed catalytic effect for the enzyme. The molecular origin of this effect is the positioning of AVE-(CO 2 ) 2 and chorismate in the protein active site compared to AVE. Furthermore, in going from AVE-(CO 2 ) 2 to chorismate entropic effects due to 1 rigidification and ring formation are operative which lead to changes in the rate. Based on "More O'Ferrall-Jencks" diagrams it is confirmed that C-O bond breaking precedes C-C bond formation in all cases. This effect becomes more pronounced in going from the gas phase to the protein.
The kinetics of MgO + + CH 4 was studied experimentally using the variable ion source, temperature adjustable selected ion flow tube (VISTA-SIFT) apparatus from 300 − 600 K and computationally by running and analyzing reactive atomistic simulations. Rate coefficients and product branching fractions were determined as a function of temperature. The reaction proceeded with a rate of k = 5.9 ± 1.5 × 10 −10 (T /300 K) −0.5±0.2 cm 3 s −1 . MgOH + was the dominant product at all temperatures, but Mg + , the co-product of oxygen-atom transfer to form methanol, was observed with a product branching fraction of 0.08 ± 0.03(T /300 K) −0.8±0.7 . Reactive molecular dynamics simulations using a reactive force field, as well as a neural network trained on thousands of structures yield rate coefficients about one order of magnitude lower.This underestimation of the rates is traced back to the multireference character of the transition state [MgOCH 4 ] + . Statistical modeling of the temperature-dependent kinetics provides further insight into the reactive potential surface. The rate limiting step was found to be consistent with a four-centered activation of the C-H bond, consistent with previous calculations. The product branching was modeled as a competition between dissociation of an insertion intermediate directly after the ratelimiting transition state, and traversing a transition state corresponding to a methyl migration leading to a Mg-CH 3 OH + complex, though only if this transition state is stabilized significantly relative to the dissociated MgOH + + CH 3 product channel.An alternative non-statistical mechanism is discussed, whereby a post-transition state bifurcation in the potential surface could allow the reaction to proceed directly from the four-centered TS to the Mg-CH 3 OH + complex thereby allowing a more robust competition between the product channels. a) rvborgmailbox@us.af.mil b) m.meuwly@unibas.ch
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