Recent Developments in Kramers’ Theory of Reaction Rates

In this short review, we provide an update of recent developments in Kramers’ theory of reaction rates. After a brief introduction stressing the importance of this theory initially developed for chemical reactions, we briefly present the main theoretical formalism starting from the generalized Langevin equation and continue by showing the main points of the modern Pollak, Grabert and Hänggi theory. Kramers’ theory is then sketched for quantum and classical surface diffusion. As an illustration the surface diffusion of Na atoms on a Cu(110) surface is discussed showing escape rates, jump distributions and diffusion coefficients as a function of reduced friction. Finally, some very recent applications of turnover theory to different fields such as nanoparticle levitation, microcavity polariton dynamics and simulation of reaction in liquids are presented. We end with several open problems and future challenges faced up by Kramers turnover theory.     

E−Z Isomerization in Guanidine: Second-order Saddle Dynamics,Non-statisticality,and Time-frequency Analysis

Our recent work on the E−Z isomerization reaction of guanidine using ab initio chemical dynamics simulations [Rashmi et al., Regul. Chaotic Dyn. 2021 , 26, 119] emphasized the role of second-order saddle ( SOS ) in the isomerization reaction; however, we could not unequivocally establish the non-statistical nature of the dynamics followed in the reaction. In the present study, we performed thousands of on-the-fly trajectories using forces computed at the MNDO level to investigate the influence of second-order saddle in the E−Z isomerization reaction of guanidine and the role of intramolecular vibrational energy redistribution (IVR) on the reaction dynamics. The simulations reveal that while majority of the trajectories follow the traditional transition state pathways, 15 % of the trajectories follow the SOS path. The dynamics was found to be highly non-statistical with the survival probabilities of the reactants showing large deviations from those obtained within the RRKM assumptions. In addition, a detailed analysis of the dynamics using time-dependent frequencies and the frequency ratio spaces reveal the existence of multiple resonance junctions that indicate the existence of regular dynamics and long-lived quasi-periodic trajectories in the phase space associated with non-RRKM behavior.     

Photocatalyzed E→Z Contra-thermodynamic Isomerization of Vinyl Boronates with Binaphthol

The photocatalytic contra-thermodynamic E→Z isomerization of vinyl boronates by using a binaphthol catalyst is disclosed. The reaction, based on the transient formation of a suitable chromophore with a BINOL derivative as the catalyst, allowed geometrical isomerization in good-to-excellent Z/E ratio and excellent-to-quantitative yields. The mechanism of this E→Z contra-thermodynamic isomerization was studied, and the formation of a transient chromophore species is suggested.     

Photocatalytic E→Z Contra-Thermodynamic Isomerization of Vinyl Silanes with Lewis Base

Herein, we disclosed the contra-thermodynamic E→Z isomerization of alkenyl silanes, according to the in situ formation of a chromophoric species, in the presence of rac-BINAP as the catalyst. The reaction carried out in DMSO or CH₃CN under irradiation at 405 nm allowed the interconversion of the E-isomers into the Z-congeners in good to excellent yields and outstanding Z/E selectivities, on 18 examples. Finally, the mechanism of this E→Z isomerization was studied to get insight into the reaction mechanism.     

Understanding the Complex Surface Interplay for Extraction: A Molecular Dynamics Study

By means of classical molecular dynamics simulation the interfacial properties of methanol and n-dodecane, which are two potential candidate solvents for use in non-aqueous liquid–liquid extraction, were assessed. The question of how the interface changes depending on the concentration of extractant (tri-n-butyl phosphate) and salt (LiCl) is addressed. Two different models to represent systems were used to evaluate how LiCl and tri-n-butyl phosphate affect mutual miscibility, and how the last-named behaves depending on the chemical environment. Tri-n-butyl phosphate increases the mutual solubility of the solvents, whereas LiCl counteracts it. The extractant was found to be mostly adsorbed on the interface between the solvents, and therefore the structural features of the adsorption were investigated. Adsorption of tri-n-butyl phosphate changes depending on its concentration and the presence of LiCl. It exhibits a preferential orientation in which the butyl chains point at the n-dodecane phase and the phosphate group points at the methanol phase. For high concentrations of tri-n-butyl phosphate, its molecular orientation is preserved by diffusion of the excess molecules into both the methanol and n-dodecane phases. However, LiCl hinders the diffusion into the methanol phase, and thus increases the concentration of tri-n-butyl phosphate at the interface and forces a rearrangement with subsequent loss of orientation.     

Computational Analysis of Solute–Solvent Coupling Magnitude in the Z/E Isomerization Reaction of Nitroazobenzene and Benzylideneanilines

The dynamic solvent effect often arises in solution reactions, where coupling between chemical reaction and solvent fluctuation plays a decisive role in the reaction kinetics. In this study, the Z/E isomerization reaction of nitoroazobenzene and benzylideneanilines in the ground state was computationally studied by molecular dynamics simulations. The non-equilibrium solvation effect was analyzed using two approaches: (1) metadynamics Gibbs energy surface exploration and (2) solvation Gibbs energy evaluation using a frozen solvation droplet model. The solute–solvent coupling parameter (C_coupled) was estimated by the ratio of the solvent fluctuation Gibbs energy over the corresponding isomerization activation Gibbs energy. The results were discussed in comparison with the ones estimated by means of the analytical models based on a reaction–diffusion equation with a sink term. The second approach using a frozen solvation droplet reached qualitative agreement with the analytical models, while the first metadynamics approach failed. This is because the second approach explicitly considers the non-equilibrium solvation in the droplet, which consists of a solute at the reactant geometry immersed in the pre-organized solvents fitted with the solute at the transition state geometry.     

Molecular Dynamics Study of the Complex Formation of TEM-Type β-Lactamases with Substrates and Inhibitors

The complex formation of TEM-1 β-lactamase and its three mutant forms TEM-32, TEM-37, and TEM-39 with substrates cephalothin and CENTA and serine beta-lactamase inhibitors sulbactam, tazobactam, and clavulanic acid is studied using the methods of molecular dynamics. It is found that the stability of the complexes is caused by the electrostatic attraction between the deprotonated carboxyl group of the β-lactam ring of the substrate (inhibitor) and the positively charged amino groups of the lysine 234 and 73 residues, located in the active site of the enzymes. The formation of a hydrogen bond between this substrate group or its carbonyl oxygen with the hydroxyl group of the catalytic serine 70 residue and also between the negatively charged substituent groups and the positive charge region formed by the arginine 244 guanidine group and the asparagine 276 amino group is observed for some complexes. The binding energy of CENTA with TEM-1 β-lactamase is below the analogous binding energy of cephalothin, which is confirmed by the values of the Michaelis constants, determined experimentally. It is also found that the inhibitors bind to the mutant forms of β-lactamases related to the inhibitor-resistant phenotype, with higher affinity than TEM-1 β-lactamase.     

The Effect of Boron on the Properties of Glucomannan： An Experimental and Molecular Dynamics Simulation Study

1 INTRODUCTION gel using KGM and borax at 60 ℃, which can be used as slow-released reagent of theophylline and Generally, the mixture of Konjac Glucomanan dibucaine. And Hogi Tsuneo utilized KGM and tetra- (KGM) and salts that could be hydrolyzed to form valent boric acid to prepare artificial crystal[1]. This multi-hydroxyl hydrates leads to the generation of kind of crystal has good light transmission property, gelatum. Among the familiar salts, such as borate, elasticity, intensi…     

Dynamics Study of the Influence of Temperature on Konjac Glucomannan Saline Solution’s Viscosity

Molecular dynamics (MD) method is adopted to simulate the conformation variations of konjac glucomannan (KGM) saline solution at different temperatures, and structurally analyze the trends and reasons of viscosity change in KGM saline solution with temperature. The experimental results have been analyzed to find out that the sum of formative hydrogen bonds decreases with the rise of temperature and the amount of intramolecular hydrogen bonds suddenly increases at 323 K. Besides, in terms of molecular orbital data obtained from simulation, we can know that hydrogen bonding energy also decreases with the rise of temperature. Therefore, we can predict the viscosity of KGM saline solution decreases gradually when rising the temperature.     

A Study of the Reaction Dynamics for the H+BrCH_3 System Using Quasi-classical Trajectory Theory

In the present paper, scattering probabilities and rate constants of different channels for the H + BrCH_3 reaction system have been calculated by means of quasiclassical trajectory (QCT) method. Several important kinetic effects such as vibrational enhancement, channel competition, vibrational adiabaticity, mass combination, coupling of angular momenta and the relation between the kinetic effects and the feature of the potential energy surface have been discussed. Based on these analyses, a direct-type rebonded mechanism for this reaction has been inferred and used to explain the nonsymmetric angular distribution of the products crossed-molecular beam experiment. The agreement of calculation with experimental results is satisfactory.     

Theoretical Study on the Hydration Structure of Divalent Radium Ion Using Fragment Molecular Orbital–Molecular Dynamics (FMO–MD) Simulation

Using fragment molecular orbital–molecular dynamics (FMO–MD) simulation at the FMO3-HF/6-31G(d,p) level, the hydration of a Ra²⁺ ion was theoretically investigated. The first peaks of the radial distribution function (RDF) for Ra–O and Ra–H lengths were predicted to be 2.85 and 3.45 Å with broad envelopes in the ranges of 2.5–3.5 and 2.8–4.3 Å, respectively. The broad peaks shows that the first hydration shell of Ra²⁺ is much more flexible than those in the other hydrated divalent alkaline earth metal ions, i.e., Ra²⁺ is a structure-breaking ion. The hydration number of Ra²⁺ was predicted to be 8.1. From the angular distribution function (ADF), it was clarified that the octa hydrated Ra²⁺ ion has a flexible square antiprism structure at room temperature.     

Solute-Solvent Interactions in Solutions of Solvatochromic Phenoxides: A Dynamics Simulation Study

Solute-solvent interactions in protic (water, methanol and 2-propanol) and aprotic (DMSO) solvents of four solvatochromic phenoxides, the 4- and 2-pyridiniophenoxides, Brooker’s merocyanine and the N-methyloxyquinolinium betaine, were investigated with the aid of molecular dynamics simulations. Although the size of the first solvation shell of the phenoxide oxygen of all betaines remains constant in the three protic solvents, it comprises increasingly fewer solvent molecules as the volume of the hydroxylic solvent increases. In DMSO, the donor phenoxide group of the 4-pyridiniophenoxide betaine is loosely solvated, leading to an internal charge-transfer with smaller transition energies than in protic media.     

A pentiptycene-derived molecular brake: photochemical E→Z and electrochemical Z→E switching of an enone module

The synthesis and brakelike performance of a new molecular system (1) consisting of a pentiptycene rotor and a 2-methyleneindanone brake are reported. The rotation kinetics of the rotor was probed by both variable-temperature (1)H and (13)C NMR spectroscopy and DFT calculations, and the switching between the brake-on and brake-off states was conducted by a combination of photochemical and electrochemical isomerization. Because of the greater steric hindrance between the rotor and the brake units in the Z form ((Z)-1) than in the E form ((E)-1), rotation of the rotor is slowed down 500-fold at room temperature (298 K) on going from (E)-1 to (Z)-1, corresponding to the brake-off and brake-on states, respectively. The (E)-1→(Z)-1 photoisomerization in acetonitrile is efficient and reaches an (E)-1/(Z)-1 ratio of 11:89 in the photostationary state upon excitation at 290 nm, attributable to a much larger isomerization quantum efficiency for (E)-1 versus (Z)-1. An efficient (Z)-1→(E)-1 isomerization (96%) was also achieved by electrochemical treatment through the radical anionic intermediates. Consequently, the reversibility of the E-Z switching of 1 is as high as 85%. The repeated E-Z switching of 1 with alternating photochemical and electrochemical treatments is also demonstrated.     

Molecular Dynamics Simulations of Small Peptides: Can One Derive Conformational Preferences from ROESY Spectra?

Folding properties of beta-peptides were investigated by means of NMR experiments and MD simulations of beta-dipeptides, which serve as small test systems to study the influence of stereocenters and side chains on hydrogen-bond and consequently on secondary-structure formation. Two stereoisomers, SR and SS, of a Val-Phe dipeptide, and of the corresponding Ala-Ala dipeptide, and a Gly-Gly dipeptide were simulated in methanol for 40 ns. In agreement with experiment, the isomers of the Val-Phe dipeptide adopt quite different conformers at 298 K, the differences being reduced at 340 K. Interestingly, the SR isomer shows enhanced hydrogen bonding at the higher temperature. The adopted conformations are primarily determined by the R or S side chain substitution, and less by the type of side chain. Back-calculation of (1)H ROESY spectra and (3)J coupling constants from the MD simulations and comparison with the experimental data for the Val-Phe dipeptides shows good agreement between simulation and experiment, and reveals possible problems and pitfalls, when deriving structural properties of a small and extremely flexible molecule from NMR data only. Inclusion of all aspects of internal dynamics is essential to the correct prediction of the NMR spectra of these small molecules. Cross comparison of calculated with experimental spectra for both isomers shows that only a few out of many ROESY peaks reflect the sizeable conformational differences between the isomers at 298 K.     

A sixfold triplet-sensitized Z/E isomerization of a π-perimeter macrocycle

On irradiation, all-Z [2.2.2.2.2.2]orthoparacyclophene (1) is converted to the all-E isomer (2). The photo-isomerization occurs via the triplet state and proceeds without any groun state intermediates.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Photo-/Electroinduced Irreversible Isomerization of 2,2’-Azobispyridine Ligands in Arene Ruthenium(II) Complexes

Novel arene Ru^II complexes containing 2,2’-azobispyridine ligands were synthesized and characterized by using ¹H and ¹³C NMR spectroscopy, UV/vis spectroscopy, electrochemistry, DFT calculations and single-crystal X-ray diffraction. Z-configured complexes featuring unprecedented seven-membered chelate rings involving the nitrogen atom of both pyridines were isolated and were shown to undergo irreversible isomerization to the corresponding E-configured five-membered chelate complexes in response to light or electrochemical stimulus.     

Insights into the Photoinduced Isomerization Mechanisms of a N,C–Chelate Organoboron Compound: A Theoretical Study

As the first discovered organoboron compound with photochromic property, B(ppy)Mes₂ (ppy=2-phenylpyridine, Mes=mesityl) displays rich photochemistry that constitutes a solid foundation for wide applications in optoelectronic fields. In this work, we investigated the B(ppy)Mes₂ to borirane isomerization mechanisms in the three lowest electronic states (S₀, S₁, and T₁) based on the complete active space self-consistent field (CASSCF) and its second-order perturbation (CASPT2) methods combined with time-dependent density functional theory (TD-DFT) calculations. Our results show that the photoisomerization in the S₁ state is dominant, which is initiated by the cleavage of the B-C_ppy bond. After overcoming a barrier of 0.5 eV, the reaction pathway leads to a conical intersection between the S₁ and S₀ states (S₁/S₀)_x, from which the decay path may go back to the reactant B(ppy)Mes₂ via a closed-shell intermediate (Int1-S₀) or to the product borirane via a biradical intermediate (Int2-S₀). Although triplet states are probably involved in the photoinduced process, the possibility of the photoisomerization in T₁ state is very small owing to the weakly allowed S₁→T₁ intersystem crossing and the high energy barrier (0.77 eV). In addition, we found the photoisomerization is thermally reversible, which is consistent with the experimental observations.     

Insight into the Urea Binding and K166R Mutation Stabilizing Mechanism of TIpB： Molecular Dynamics and Principal Component Analysis Study

Chemoreceptor TlpB（Tlp=transducer-like protein）, which has been demonstrated to respond to pH sensing function, is crucial for the survival ofHelicobacterpylori（H, pylori） in host stomach. Urea was proposed to be essen- tial for TlpB＇s pH sensing function via binding with the Per-ARNT-Sim（PAS） domain of TlpB. Additionally, KI66R mutation of the TlpB protein has also been proven to have a similar effect on TlpB pH sensing as urea binding. Al- though X-ray crystallographic studies have been carried out for urea-bound Tlpl3, the molecular mechanism for the stabilization of TIpB induced by urea binding and K166R mutation remains to be elucidated. In this study, molecular dynamics simulations combined with principal component analysis（PCA） for the simulation results were used to gain an insight into the molecular mechanism of the stabilization of urea on TlpB protein. The formed H-bonds and salt-bridges surrounding Aspll4, which were induced by both urea binding and K166R mutation of TIpB, were im- portant to the stabilization of TlpB by urea. The similarity between the urea binding and K166R mutation as well as their differences in effect has been explicitly demonstrated with computer simulations at atomic-level. The findings may Dave the wav for the further researches of TlpB.     

β-Cyclodextrin and 5-Methoxytryptammonium Ion Host-Guest Association in vacuo: Simulation of Non-Covalent Inclusion by Molecular Dynamics

The structure of gaseous charged host-guest adducts ofcyclodextrins (CDs) generated by mass spectrometry (MS) still requires to be addressed correctly,as these adducts could be true inclusion complexes or non-specific proton bound heterodimers(PBHs). The present theoretical study of inclusion complex vs. PBH of 5-methoxytryptammonium ion(5-MTA⁺) with -CD in vacuo by energy minimisation and moleculardynamics proved that the most stable forms of -CD/5-MTA⁺ non-covalent associationare inclusion complexes. PBHs evolved to genuine inclusion complexes with two differenthost-guest arrangements during MD runs.