Rotational dynamics and conformational kinetics in liquid crystals

Two particular aspects of solute dynamics in ordered media are analysed on the basis of the solution of multivariate diffusion equations: the effects of the solvation dynamics on the rotational motions of dipolar probes in liquid crystal solvents, and the alteration of reaction pathways in isomerization kinetics caused by the solvent order. The introduction of a suitable solvent coordinate allows the interpretation of high frequency contributions in the rotational correlation functions observed by spectroscopic techniques, namely dielectric dispersion, IR and Raman spectroscopy, ESR lineshapes and optical Kerr effect. For molecular systems undergoing conformational changes, a method is offered to evaluate the modification of the torsional barriers resulting from the anisotropic torques modulated by the molecular shape changes along the reaction coordinate.     

A study of molecular dynamics and phase transitions in solid MBBA

Abstract

The solid state polymorphism of liquid crystalline MBBA was investigated by temperature dependent NMR spin-lattice relaxation time measurements. The sensitivity of the method could be utilized because the correlation time of the measurement is in the correlation time region of molecular motion. Motional correlation time and activation energy values were determined and the results show some interesting changes between the different solid phases. Non-trivial variation in the end-chain rotational motion in two crystalline phases has been observed. Conclusions were drawn on the relationship between rotational molecular dynamics, intermolecular order and phase transitions.     

Molecular Dynamics of Excited State Intramolecular Charge Transfer in Solution by Coherent Nuclear Wave Packets

Revealing a proper reaction coordinate in a chemical reaction is the key step towards elucidation of the molecular reaction dynamics. In this report, we investigated the dynamics of intramolecular charge transfer (ICT) of 8-aminopyrene-1,3,6-trisulfonic acid (APTS) occurring in the excited state by time-resolved fluorescence (TF) and TF spectra. Accurate reaction rates and rate-dependent nuclear wave packets in the product state allow detailed investigation of the molecular reaction dynamics. The ICT rate is solvent dependent: (34 fs)⁻¹, (87 fs)⁻¹, and (∞)⁻¹ in water, formamide, and dimethylformamide, respectively. By recording spectra of the nuclear wave packets for different reaction rates, chemical species responsible for the emission spectra can be positively identified. The origin of the wave packets can be deduced from the amplitude change of the wave packets at different reaction rates, and the vibrational modes that are associated with the reaction coordinate could be identified. Theoretical calculations of the vibrational reorganization energies reproduce the experimental spectrum of the nuclear wave packets and corroborate the conclusions.     

Determining symmetry changes during a chemical reaction: the case of diazene isomerization

Analysis of reaction paths in terms of the Continuous Symmetry Measure (CSM) provides an alternative way to analyze the geometrical changes that take place during a reaction. Unique symmetry-profiles, describing the symmetry changes along the internal reaction coordinate were calculated for the cis-trans isomerization reaction of N₂H₂ and for its halogeno derivatives. A “symmetry transition point” is identified at the extremum point along the symmetry-profiles. At this point, the deviation of the molecule from the rotational symmetry of the reactant is the same as its deviation from the rotational symmetry of the product. In a second application we show that the CSM can be used as an alternative reaction coordinate. Calculations at the MP2 and DFT levels result in similar symmetry profiles.     

Dynamics of a supercooled ionic liquid studied by optical and dielectric spectroscopy

We have measured the dynamics of solvation of a triplet state probe, quinoxaline, in the glass-forming ionic liquid dibutylammonium formate near its glass transition temperature Tg=153 K. The Stokes-shift correlation function displays a relaxation time dispersion of considerable magnitude and the optical line width changes systematically along the solvation coordinate. The solvent dynamics in the viscous regime is compared with the rotational behavior of the solute and with the dielectric relaxation of the ionic liquid. Among the different quantities derived from the dielectric experiments, the relaxation of the macroscopic electric field, i.e., the modulus Mt, matches best the solvent response Ct regarding time scale and stretching exponent. Many other properties are reminiscent of the behavior of polar molecular liquids which lack the ionic character.     

Free energy landscapes of electron transfer system in dipolar environment below and above the rotational freezing temperature

Electron transfer reaction in a polar solvent is modeled by a solute dipole surrounded by dipolar molecules with simple rotational dynamics posted on the three-dimensional distorted lattice sites. The interaction energy between the solute and solvent dipoles as a reaction coordinate is adopted and free energy landscapes are calculated by generating all possible states for a 26 dipolar system and by employing Wang-Landau sampling algorithm for a 92 dipolar system. For temperatures higher than the energy scale of dipole-dipole interactions, the free energy landscapes for the small reaction coordinate region have quadratic shape as predicted by Marcus [Rev. Mod. Phys. 65, 599 (1993)] whereas for the large reaction coordinate region, the landscapes exhibit a nonquadratic shape. When the temperature drops, small notched structures appear on the free energy profiles because of the frustrated interactions among dipoles. The formation of notched structure is analyzed with statistical approach and it is shown that the amplitude of notched structure depend upon the segment size of the reaction coordinate and is characterized by the interaction energy among the dipoles. Using simulated free energy landscapes, the authors calculate the reaction rates as a function of the energy gap for various temperatures. At high temperature, the reactions rates follow a bell shaped (inverted parabolic) energy gap law in the small energy gap regions, while it becomes steeper than the parabolic shape in a large energy gap regions due to the nonquadratic shape of the free energy landscape. The peak position of parabola also changes as the function of temperature. At low temperature, the profile of the reaction rates is no longer smooth because of the many local minima of the free energy landscape.     

Direct MP2 molecular dynamics studies of H atom reaction with CD4 and CH4

The mechanism and dynamics of the H + CD₄ → CD₃ + HD (I) and H + CH₄ → CH₃ + H₂ (II) reactions have been investigated by electronic structure methods. The minimum‐energy path and vibrational frequencies along the intrinsic reaction coordinate are calculated at MP2/cc‐pVDZ level. Energy distributions of the products are also obtained by the direct classical trajectory calculations at the MP2/ cc‐pVDZ level. It is found that most of the available energy appears as product translational energy, and very little of the available energy is partitioned into internal excitation of the HD (H₂) product for reaction I (II), which is in agreement with the experimental evidence. The results indicate that the experimental results could be reproduced by the direct MP2 molecular dynamics calculations. The rotational state distributions of the products show the HD (H₂) products are formed with lower rotational quantum numbers than the CD₃ (CH₃) products. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Fast predictions of liquid-phase acid-catalyzed reaction rates using molecular dynamics simulations and convolutional neural networks

The rates of liquid-phase, acid-catalyzed reactions relevant to the upgrading of biomass into high-value chemicals are highly sensitive to solvent composition and identifying suitable solvent mixtures is theoretically and experimentally challenging. We show that the complex atomistic configurations of reactant–solvent environments generated by classical molecular dynamics simulations can be exploited by 3D convolutional neural networks to enable accurate predictions of Brønsted acid-catalyzed reaction rates for model biomass compounds. We develop a 3D convolutional neural network, which we call SolventNet, and train it to predict acid-catalyzed reaction rates using experimental reaction data and corresponding molecular dynamics simulation data for seven biomass-derived oxygenates in water–cosolvent mixtures. We show that SolventNet can predict reaction rates for additional reactants and solvent systems an order of magnitude faster than prior simulation methods. This combination of machine learning with molecular dynamics enables the rapid, high-throughput screening of solvent systems and identification of improved biomass conversion conditions.

Solvent-mediated, acid-catalyzed reaction rates relevant to the upgrading of biomass into high-value chemicals are accurately predicted using a combination of molecular dynamics simulations and 3D convolutional neural networks.     

Quasi-classical Trajectory Study of F+H2O→HF+OH Reaction: Influence of Barrier Height,Reactant Rotational Excitation,and Isotopic Substitution (cited: 4)

The reaction dynamics of the F+H₂O/D₂O→HF/DF+OH/OD are investigated on an ac-curate potential energy surface (PES) using a quasi-classical trajectory method. For bothisotopomers, the hydrogen/deuterium abstraction reaction is dominated by a direct rebound mechanism over a very low “reactant-like” barrier, which leads to a vibrationally hot HF/DF product with an internally cold OH/OD companion. It is shown that the lowered reaction barrier on this PES, as suggested by high-level ab initio calculations, leads to a much better agreement with the experimental reaction cross section, but has little impact on the product state distributions and mode selectivity. Our results further indicate that rotational exci-tation of the H₂O reactant leads to significant enhancement of the reactivity, suggesting a strong coupling with the reaction coordinate.     

Molecular dynamics coupled with a virtual system for effective conformational sampling

An enhanced conformational sampling method is proposed: virtual‐system coupled canonical molecular dynamics (VcMD). Although VcMD enhances sampling along a reaction coordinate, this method is free from estimation of a canonical distribution function along the reaction coordinate. This method introduces a virtual system that does not necessarily obey a physical law. To enhance sampling the virtual system couples with a molecular system to be studied. Resultant snapshots produce a canonical ensemble. This method was applied to a system consisting of two short peptides in an explicit solvent. Conventional molecular dynamics simulation, which is ten times longer than VcMD, was performed along with adaptive umbrella sampling. Free‐energy landscapes computed from the three simulations mutually converged well. The VcMD provided quicker association/dissociation motions of peptides than the conventional molecular dynamics did. The VcMD method is applicable to various complicated systems because of its methodological simplicity. © 2018 Wiley Periodicals, Inc.     

The dynamical role of solvent on the ICN photodissociation reaction: connecting experimental observables directly with molecular dynamics simulations

The ICN photodissociation reaction is the prototype system for understanding energy disposal and curve crossing in small molecule bond-breaking. The wide knowledge base on this reaction in the gas phase makes it an excellent test case to explore and understand the influence of a liquid solvent on the photo-induced reaction dynamics. Molecular dynamics simulations that include surface-hopping have addressed numerous aspects of how the solvent should influence non-adiabatic transitions and energy flow and ultimately determine product branching for this reaction system. In this paper, we report femtosecond transient absorption work directly combined with new molecular dynamics simulations that make direct connection with the spectroscopic observables. The full spectral evolution after initiating ICN photodissociation at 266 nm in water and ethanol is recorded with unprecedented time resolution, fast enough to see the nascent products emerge before interacting with the solvent cage. Use of a 266 nm pump maximizes the probability of subsequent caging on the upper diabat while launching large rotational energy release for trajectories emerging on the lower diabat. The 2D dataset yields a map of the different products and how they interconvert. In particular, information on the branching ratio and spectral evolution of the product bands is revealed as the products relax their electronic and rotational degrees of freedom. An evolution from rotationally hot gas-phase like CN (sharp band, at 390 nm) to equilibrated and solvated CN radicals (broad, at 326 nm in water and 415 nm in ethanol) is clearly observed in both solvents, and signals assignable to I* are also captured. The non-adiabatic molecular dynamics simulations focus on identifying when trajectories curve cross, filtering the trajectory ensemble into spectroscopically distinct sub-populations and analyzing the rotational energy for the CN product population. The experimental results, taken together with the MD simulations, establish the initial surface crossing probability and suggest multiple passes through the curve crossing region determine the final product yields and provide a source of freshly torqued CN radicals that continues to top up the population of rotationally hot photoproduct over the first few picoseconds.     

Dynamics of an enzymatic substitution reaction in haloalkane dehalogenase

Reactive flux molecular dynamics simulations have been carried out using a combined QM/MM potential to study the dynamics of the nucleophilic substitution reaction of dichloroethane by a carboxylate group in haloalkane dehalogenase and in water. We found that protein dynamics accelerates the reaction rate by a factor of 2 over the uncatalyzed reaction. Compared to the thermodynamic effect in barrier reduction, protein dynamic contribution is relatively small. However, analyses of the friction kernel reveal that the origins of the reaction dynamics in water and in the enzyme are different. In aqueous solution, there is significant electrostatic solvation effect, which is reflected by the slow reorganization relaxation of the solvent. On the other hand, there is no strong electrostatic coupling in the enzyme and the major effect on reaction coordinate motion is intramolecular energy relaxation.     

A hydrogen rearrangement of formamidine and the solvent effects thereupon

The nature of the 1,3 hydrogen rearrangement of formamidine (H₂N-CH=NH) and the solvent effects on that reaction are studied with ab initio molecular orbital calculations on the basis of the supermolecule model. The reaction path and the motion of the migrating hydrogen atom are traced by using the concept of the intrinsic reaction coordinate (IRC). Four types of orientation of one water molecule to formamidine at the transition state of reaction are examined and the results are discussed from the standpoint of the orbital interactions.     

Proton transfer in a polar solvent from ring polymer reaction rate theory

We have used the ring polymer molecular dynamics method to study the Azzouz-Borgis model for proton transfer between phenol (AH) and trimethylamine (B) in liquid methyl chloride. When the A-H distance is used as the reaction coordinate, the ring polymer trajectories are found to exhibit multiple recrossings of the transition state dividing surface and to give a rate coefficient that is smaller than the quantum transition state theory value by an order of magnitude. This is to be expected on kinematic grounds for a heavy-light-heavy reaction when the light atom transfer coordinate is used as the reaction coordinate, and it clearly precludes the use of transition state theory with this reaction coordinate. As has been shown previously for this problem, a solvent polarization coordinate defined in terms of the expectation value of the proton transfer distance in the ground adiabatic quantum state provides a better reaction coordinate with less recrossing. These results are discussed in light of the wide body of earlier theoretical work on the Azzouz-Borgis model and the considerable range of previously reported values for its proton and deuteron transfer rate coefficients.     

Implementation of the IMOMM methodology for performing combined QM/MM molecular dynamics simulations and frequency calculations

A technique for implementing the integrated molecular orbital and molecular mechanics (IMOMM) methodology developed by Maseras and Morokuma that is used to perform combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, frequency calculations and simulations of macromolecules including explicit solvent is presented. Although the IMOMM methodology is generalized to any coordinate system, the implementation first described by Maseras and Morokuma requires that the QM and MM gradients be transformed into internal coordinates before they are added together. This coordinate transformation can be cumbersome for macromolecular systems and can become ill-defined during the course of a molecular dynamics simulation. We describe an implementation of the IMOMM method in which the QM and MM gradients are combined in the cartesian coordinate system, thereby avoiding potential problems associated with using the internal coordinate system. The implementation can be used to perform combined QM/MM molecular dynamics simulations and frequency calculations within the IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM framework. Finally, we have examined the applicability of thermochemical data derived from IMOMM frequency calculations. Received: 11 May 1998 / Accepted: 14 August 1998 / Published online: 16 November 1998     

Reaction Coordinates by Nonlinear Dimensionality Reduction

Deriving reaction coordinates for the characterization of chemical reactions has long been a demanding task. In our previous work [ACS Cent. Sci. 3 , 407 (2017)], the reaction coordinate of a (retro-) Claisen rearrangement in aqueous solution optimized through a Bayesian measure, a linear combination of bond lengths formation and breakage, was judged to be optimal among all trails. Here, considering the nonlinearity of the transition state, we use isometric mapping and locally linear embedding to obtain one reaction coordinate which is composed of a few collective variables. With these methods, we find a more reasonable and powerful one-dimensional reaction coordinate, which can well describe the reaction progression. To explore the reaction mechanism, we analyze the contribution of intrinsic molecular properties and the solvent-solute interactions to the nonlinear reaction coordinate. Furthermore, another coordinate is identified to characterize the heterogeneity of reaction mechanisms.     

Metadynamics simulations of R–NHC reductive elimination in intermediate palladium complexes of cross-coupling and Mizoroki–Heck reactions

Exploring the free energy surface of the R–NHC coupling reaction in the key intermediates of the Mizoroki–Heck and cross-coupling catalytic cycles has been conducted by the methods of biased and unbiased molecular dynamics. Molecular dynamics simulations were carried out both in vacuum and in a polar solvent, with the following main observations on the influence of the media: (1) the solvent prevents the dissociation of the solvate ligand, so the R–NHC coupling proceeds in a four-coordination complex (rather than in a three-coordination one, as in the case of a gas-phase reaction); (2) in the condensed phase, the potential barrier of the reaction is significantly higher compared to the same process in vacuum (17.7 vs. 21.8 kcal mol^-1); (3) polar solvent stabilizes the R–NHC coupling product. The reaction in a polar medium is exergonic (ΔG = −3.9 kcal mol^-1), in contrast to the in vacuum modeling, where the process is endergonic (ΔG = 0.4 kcal mol^-1).     

Effect of Cation Size on Solvation and Association with Superoxide Anion in Aprotic Solvents

Influence of cation size on solvation strength, diffusion, and kinetics of the association reaction with anions O₂⁻ in aprotic solvents, such as acetonitrile and dimethyl sulfoxide, has been investigated by means of molecular dynamics simulations. The work is motivated by the need to understand the molecular nature of the solvent-induced changes in capacity of Li-air batteries. We have shown that the dependence of the solvation shell stability on the cation size has a maximum at a particular ion radius that corresponds to a solvent coordination number of 4. The shell stability maximum coincides with the diffusion coefficient minimum. The variation of the cation shell stability has a crucial impact on the kinetics of the cation-O₂⁻ association. We have demonstrated that profound inhibition of the association reaction for Li⁺ in dimethyl sulfoxide is a result of the lock-and-key effect that cannot be described in the framework of Hard Soft Acid Base theory.