Ab-Initio Molecular Dynamics Simulation of Condensed-Phase Reactivity: The Electrolysis of Amino Acids and Peptides

Electrolysis is a potential candidate for a quick method of wastewater cleansing. However, it is necessary to know what compounds might be formed from bioorganic matter. We want to know if there are toxic intermediates and if it is possible to influence the product formation by the variation in initial conditions. In the present study, we use Car–Parrinello molecular dynamics to simulate the fastest reaction steps under such circumstances. We investigate the behavior of amino acids and peptides under anodic conditions. Such highly reactive situations lead to chemical reactions within picoseconds, and we can model the reaction mechanisms in full detail. The role of the electric current is to discharge charged species and, hence, to produce radicals from ions. This leads to ultra-fast radical reactions in a bulk environment, which can also be seen as redox reactions as the oxidation states change. In the case of amino acids, the educts can be zwitterionic, so we also observe complex acid–base chemistry. Hence, we obtain the full spectrum of condensed-phase chemistry.     

Parameterization of a reactive force field using a Monte Carlo algorithm

Parameterization of a molecular dynamics force field is essential in realistically modeling the physicochemical processes involved in a molecular system. This step is often challenging when the equations involved in describing the force field are complicated as well as when the parameters are mostly empirical. ReaxFF is one such reactive force field which uses hundreds of parameters to describe the interactions between atoms. The optimization of the parameters in ReaxFF is done such that the properties predicted by ReaxFF matches with a set of quantum chemical or experimental data. Usually, the optimization of the parameters is done by an inefficient single‐parameter parabolic‐search algorithm. In this study, we use a robust metropolis Monte‐Carlo algorithm with simulated annealing to search for the optimum parameters for the ReaxFF force field in a high‐dimensional parameter space. The optimization is done against a set of quantum chemical data for MgSO₄ hydrates. The optimized force field reproduced the chemical structures, the equations of state, and the water binding curves of MgSO₄ hydrates. The transferability test of the ReaxFF force field shows the extend of transferability for a particular molecular system. This study points out that the ReaxFF force field is not indefinitely transferable. © 2013 Wiley Periodicals, Inc.     

Quantum Control of Gas‐Phase and Liquid‐Phase Femtochemistry

Active control of chemical reactions on a microscopic (molecular) level, that is, the selective breaking or making of chemical bonds, is an old dream. However, conventional control agents used in chemical synthesis are macroscopic variables such as temperature, pressure or concentration, which gives no direct access to the quantum‐mechanical reaction pathway. In quantum control, by contrast, molecular dynamics are guided with specifically designed light fields. Thus it is possible to efficiently and selectively reach user‐defined reaction channels. In the last years, experimental techniques were developed by which many breakthroughs in this field were achieved. Femtosecond laser pulses are manipulated in so‐called pulse shapers to generate electric field profiles which are specifically adapted to a given quantum system and control objective. The search for optimal fields is guided by an automated learning loop, which employs direct feedback from experimental output. Thereby quantum control over gas‐phase as well as liquid‐phase femtochemical processes has become possible. In this review, we first discuss the theoretical and experimental background for many of the recent experiments treated in the literature. Examples from our own research are then used to illustrate several fundamental and practical aspects in gas‐phase as well as liquid‐phase quantum control. Some additional technological applications and developments are also described, such as the automated optimization of the output from commercial femtosecond laser systems, or the control over the polarization state of light on an ultrashort timescale. The increasing number of successful implementations of adaptive learning techniques points at the great versatility of computer‐guided optimization methods. The general approach to active control of light–matter interaction has also applications in many other areas of modern physics and related disciplines.     

Parallel replica dynamics with a heterogeneous distribution of barriers: application to n-hexadecane pyrolysis

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of E(a) = 79.7 kcal/mol and log A/s(-1) = 14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.     

Transition states from empirical force fields

 This is an overview of the use of empirical force fields in the study of reaction mechanisms. Empirical-valence-bond-type methods (including reactive force field and multiconfigurational molecular mechanics) produce full reaction surfaces by mixing, in the simplest case, known force fields describing reactants and products. The SEAM method instead locates approximate transition structures by energy minimization along the intersection of the component force fields. The transition-state force-field approach (including Q2MM) designs a new force field mimicking the transition structure as an energy minimum. The scope and applicability of the various methods are compared. Received: 17 April 2002 / Accepted: 26 July 2002 / Published online: 4 November 2002 Correspondence to: P.-O. Norrby e-mail: pon@kemi.dtu.dk     

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Explicit treatment of electronic polarization in empirical force fields used for molecular dynamics simulations represents an important advancement in simulation methodology. A straightforward means of treating electronic polarization in these simulations is the inclusion of Drude oscillators, which are auxiliary, charge‐carrying particles bonded to the cores of atoms in the system. The additional degrees of freedom make these simulations more computationally expensive relative to simulations using traditional fixed‐charge (additive) force fields. Thus, efficient tools are needed for conducting these simulations. Here, we present the implementation of highly scalable algorithms in the GROMACS simulation package that allow for the simulation of polarizable systems using extended Lagrangian dynamics with a dual Nosé–Hoover thermostat as well as simulations using a full self‐consistent field treatment of polarization. The performance of systems of varying size is evaluated, showing that the present code parallelizes efficiently and is the fastest implementation of the extended Lagrangian methods currently available for simulations using the Drude polarizable force field.     

Generation of initial trajectories for transition path sampling of chemical reactions with ab initio molecular dynamics

Transition path sampling is an innovative method for focusing a molecular dynamics simulation on a reactive event. Although transition path sampling methods can generate an ensemble of reactive trajectories, an initial reactive trajectory must be generated by some other means. In this paper, the authors have evaluated three methods for generating initial reactive trajectories for transition path sampling with ab initio molecular dynamics. The authors have tested each of these methods on a set of chemical reactions involving the breaking and making of covalent bonds: the 1,2-hydrogen elimination in the borane-ammonia adduct, a tautomerization, and the Claisen rearrangement. The first method is to initiate trajectories from the potential energy transition state, which was effective for all reactions in the test set. Assigning atomic velocities found using normal mode analysis greatly improved the success of this method. The second method uses a high temperature molecular dynamics simulation and then iteratively reduces the total energy of the simulation until a low temperature reactive trajectory is found. This was effective in generating a low temperature trajectory from an initial trajectory run at 3000 K of the tautomerization reaction, although it failed for the other two. The third uses an orbital based bias potential to find a reactive trajectory and uses this trajectory to initiate an unbiased trajectory. The authors found that a highest occupied molecular orbital-lowest unoccupied molecular orbital bias could be used to find a reactive trajectory for the Claisen rearrangement, although it failed for the other two reactions. These techniques will help make it practical to use transition path sampling to study chemical reaction mechanisms that involve bond breaking and forming.     

Cyclobutanes in catalysis

The exploitation of ring strain as a driving force to facilitate chemical reactions is a well‐appreciated principle in organic chemistry. The most prominent and most frequently used compound classes in this respect are oxiranes and cyclopropanes. For rather a long time, cyclobutanes lagged behind these three‐membered‐ring compounds in their development as reactive substrates, but during the past decade an increasing number of useful reactions of four‐membered‐ring substrates have emerged. This Minireview examines corresponding catalytic reactions ranging from Lewis or Brønsted acid catalyzed processes to enzymatic reactions. The main focus is placed on transition‐metal‐catalyzed C C bond‐insertion and β‐carbon‐elimination processes, which enable exciting downstream reactions that deliver versatile building blocks.     

Since 1995 the new chemistry of multicomponent reactions and their libraries,including their heterocyclic chemistry

A growing number of products, including many heterocycles, can be prepared by the one‐pot MultiComponent Reactions (MCRs) just by mixing three or more educts, and in many cases practically quantitative yields of pure products can be obtained. The 3CR by α‐aminoalkylations of nucleophiles began in the middle of the last century, and the syntheses of heterocycles by MCRs of three and four components were introduced by Hantzsch in the 1880s. The MCRs of the isocyanides with four and more educts began in 1959, and their compound libraries were mentioned since 1961. However, only since 1995 the often automated one‐pot chemistry of the MCR of the isocyanides is used extensively. If a chemical compound can be prepared by a sequence of two component reactions or a suitable MCR, the latter is always a superior procedure. The U‐4CR can be combined with other chemical reactions and MCRs as one‐pot reactions of n > 4 components, and such unions even have a much greater variety of structurally and stereochemically different products. The educts and products of Ugi‐type MCRs are more variable than those of all previous chemical reactions and other MCRs. Due to the progress in screening and automation processes in the last few years, many new compounds have been formed and investigated more rapidly than ever before. The search for new desirable products can be accomplished more than 10,000 times faster than by the older conventional methods. The now popular chemistry of the MCRs of the isocyanides fills the since long empty part of organic chemistry.     

Silver Tarnishing Mechanism Revealed by Molecular Dynamics Simulations

The mechanism of silver–oxygen and silver–sulfur reactions is revealed by means of molecular dynamics simulations, performed with reactive force fields purposely built and extensively tested against quantum‐chemical results. Different reaction mechanisms and rates for Ag–O and Ag–S emerge. This study solves the long‐lasting question why silver exposed to the environment is strongly vulnerable to sulfur corrosion (tarnishing) but hardly reacts with O₂, despite the thermodynamic prediction that both oxide and sulfide should form. The reliability of the simulation results is confirmed by the agreement with a multitude of experimental results from the literature.     

Rate Coefficients of Roaming Reaction H+MgH Using Ring Polymer Molecular Dynamics

The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients of the multi-channel roaming reaction H+MgH→Mg+H₂. Two reaction channels, tight and roaming, are explicitly considered. This is a pioneering attempt of exerting RPMD method to multi-channel reactions. With the help of a newly developed optimization-interpolation protocol for preparing the initial structures and adaptive protocol for choosing the force constants, we have successfully obtained the thermal rate coefficients. The results are consistent with those from other theoretical methods, such as variational transition state theory and quantum dynamics. Especially, RPMD results exhibit negative temperature dependence, which is similar to the results from variational transition state theory but different from the ones from ground state quantum dynamics calculations.     

Robust Atomistic Modeling of Materials,Organometallic, and Biochemical Systems

Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal‐organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000‐atom size regime semi‐quantitatively is not self‐evident. For this purpose, a generic force field named GFN‐FF is presented, which is completely newly developed to enable fast structure optimizations and molecular‐dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential‐energy terms are constructed. GFN‐FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum‐mechanical methods in many cases.     

化学反应过渡态的结构和动力学

化学反应过渡态决定了包括反应速率和微观反应动力学在内的化学反应的基本特性,而无论是从理论还是实验上研究和观测化学反应过渡态都是极具挑战性的课题.近年来,我国科学家们利用交叉分子束-里德堡氢原子飞行时间谱仪,结合高精度的量子动力学计算,对H＋H2和F＋H2这两个教科书式的典型反应体系进行了全量子态分辨的反应动力学研究,从中得出了关于这两个反应体系的过渡态的结构和动力学性质的结论性的研究成果.     

Invoking Pairwise Interactions in Water‐Promoted Diels–Alder Reactions by using Ionic Liquids as Cosolvents

Rate constants and derived activation parameters of organic reactions in aqueous media, in particular Diels–Alder reactions, are sensitive to the presence of cosolvents in water. To enhance the solubility window of water, we introduced ionic liquids as cosolvents in the aqueous Diels–Alder reaction between anthracene‐9‐carbinol and N‐ethylmaleimide. The reactive potentials of the organic compounds are parameterized by using semi‐empirical quantum chemical methods. The principle of Savage–Wood additivity of group interactions is used to quantify the pairwise group interactions among chemically inert ionic liquids and organic reactants, both at initial and transition states of the reaction. The present approach shows promise, as the use of simple calculations from easily available kinetic data can help researchers to understand the versatility of green ionic‐liquid alternatives to volatile organic solvents.     

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.     

Reaction Dynamics with Molecular Beams and Oriented Molecular Beams: A Tool for Looking Closer to Chemical Reactions and Photodissociations

Experimental studies on reaction dynamics by use of molecular beams and oriented molecular beams are reviewed in order for looking closer to chemical reactions as well as photodissociations at the molecular level. We discuss about versatility and usefulness of the electrostatic hexapole sate‐selector as a non‐destructive selector for molecular structure analysis. Some experimental evidences on novel reaction dynamics in photodissociation and stereodynamics are presented followed by concluding remarks and future perspectives for controlling chemical reactions from the point of view of green chemistry, by manipulating molecular orientation without any catalyst nor by applying any external forces like intense electromagnetic field.     

基元化学反应态态动力学研究*

化学反应动力学是化学领域最基础的学科之一,量子态分辨的基元化学反应动力学在最为基本的原子与分子的层次上对化学反应的机制提供深刻的理解。该领域的科学家们通过精心设计的实验和高精度的理论计算,使得态态反应动力学在过去的半个多世纪中取得了长足的进步,实验和理论的相互结合极大地促进了我们对化学反应本质的认识。本文从实验研究的角度,通过对实验技术的发展和对H₂O光解离、H+H₂、F+H₂、Cl+H₂、OH+H₂、F+CH₄等具体实例的态态动力学研究的简介,概况介绍了过去二十年里态态化学反应动力学研究所取得的进展,希望借此为读者提供对化学反应动力学领域的一个概略认识。     

化学反应散射共振态的实验检测与理论模拟

化学反应中的散射共振态（或称反应性共振）控制着化学反应的分支比、产物的态分布及空间分布等。反应性共振的实验检测分为间接法和直接法。从理论上,一是构造反应体系的势能面,从势能面过渡态的结构来研究散射共振态;二是计算态-态反应动力学,尤其是用寿命矩阵来研究散射共振态。本文介绍反应性散射共振态的实验检测及理论模拟方法,并对今后的发展动向作出展望。     

Transition‐state spectroscopy using ultrashort laser pulses

To gain a complete understanding of a chemical reaction, it is necessary to determine the structural changes that occur to the reacting molecules during the reaction. Chemists have long dreamed of being able to determine the molecular structure changes that occur during a chemical reaction, including the structures of transition states (TSs). The use of ultrafast spectroscopy to gain a detailed knowledge of chemical reactions (including their TSs) promises to be a revolutionary way to increase reaction efficiencies and enhance the reaction products, which is difficult to do using conventional methods that are based on trial and error. To confirm the molecular structures of TSs predicted by theoretical analysis, chemists have long desired to directly observe the TSs of chemical reactions. Direct observations have been realized by ultrafast spectroscopy using ultrashort laser pulses. Our group has been able to stably generate visible to near‐infrared sub‐5‐fs laser pulses using a noncollinear optical parametric amplifier (NOPA). We used these sub‐5‐fs pulses to study reaction processes (including their TSs) by detecting structural changes. We determine reaction mechanisms by observing the TSs in a chemical reaction and by performing density‐functional theory calculations. DOI 10.1002/tcr.201000018