An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.Comment: 15 pages, 9 figures. To appear in J. Chem. Phy

Influence of Protein Electromagnetic Field on Hydrogen Bonding

The quantum-mechanical mechanisms by which the enzymes catalyze the hydrogen transfer in biochemical reactions are considered. Up to date it was established both experimentally and theoretically that in many cases the proton tunnelling through the intermolecular potential barrier is essential. We argue that in this case the enzyme excitation and internal motion facilitate proton transfer between reactants by squeezing the potential barrier which otherwise is practically impenetrable. In the similar fashion, the enzymes can facilitate the formation of hydrogen (H) bonds between the molecules. By means of barrier squeezing, the enzymes not only facilitate such reactions but also can control their rate and their final outcome, depending of enzyme excitation. In particular, such effects can play the major role in DNA polymerization reactions where preliminary DNTP selection is quite important.Comment: 13 pages, 1 figur

Chemical dynamics

CHEMICAL EDUCATION is changing rapidly, not only because of the explosive growth of knowledge but also because the new knowledge has stimulated reformulation of working principles in the science. Undergraduate curricula and individual courses are in constant flux. Nowhere is the change and challenge greater than in freshman chemistry. Teachers of freshmen must meet the intellectual needs of students who have had more sophisticated and stimulating high school courses than those given a decade ago. At the same time, the freshman teacher must be aware of the constant modification of the more advanced courses in chemistry and other fields that his students will study later. Continuous reformulation of courses sometimes results in the inclusion of valuable new material at the expense of other equally valuable material. We believe that this has happened in some of the sophisticated courses in freshman chemistry. Structural chemistry often receives far greater emphasis than chemical dynamics. In 1965, the Westheimer Report (Chemistry: Opportunities and Needs, National Academy of Sciences, 1965) identified the three major fields of chemistry as structure, dynamics, and synthesis. We firmly believe that a balanced course in general chemistry should reflect the outlook of this report. The study of modern chemical synthesis is too demanding to be covered in depth in an introductory course. However, chemical dynamics -- the systematic study of reactions and reactivity -- can and should be studied at the freshman level. The study of changing chemical systems is the most fascinating part of the field for many students, and its early introduction forms a solid foundation for later study. This small volume is our attempt to answer the need. The book is intended for students who have had introductory stoichiometry, energetics, and structure at the level of a modern freshman textbook (for example, Basic Principles of Chemistry, by H. B. Gray and G. P. Haight, Jr., W. A. Benjamin, Inc., New York, 1961). Chemical Dynamics is designed to accompany approximately 20-25 lectures to be given as the concluding section of a freshman chemistry course. We have chosen topics for their fundamental importance in dynamics and then tried to develop a presentation suitable for freshman classes. Discussion of each topic is limited, because chemistry majors will inevitably return to all the subject matter in more advanced courses. We hope that the following ideas have been introduced with a firm conceptual basis and in enough detail for the student to apply them to chemical reality. 1. Thermodynamics and kinetics are two useful measures of reactivity. 2. Characteristic patterns of reactivity are systematically related to molecular geometry and electronic structure. 3. Reaction mechanisms are fascinating in their own right and indispensable for identification of significant problems in reaction rate theory. 4. The concepts underlying experiments with elementary reaction processes (molecular beams) are simple, even though the engineering of the experiments is complicated. 5. Application of theories of elementary reaction rates to most reactions (slow reactions, condensed media, etc.) provides enough challenge to satisfy the most ambitious young scientist. The book includes exercises at the end of each chapter except the last. Their purpose is didactic, inasmuch as most have been written with the aim of strengthening a particular point emphasized in the chapter, or of introducing an important topic which was not developed in the text for reasons of space and which would normally be taken up in greater detail in later courses. The material in this volume has been adapted primarily from a portion of the lectures given by H.B.G. and G.S.H. to the Chemistry 2 students at the California Institute of Technology during the academic years 1966-1967 and 1967-1968. These lectures were taped, written up by J.B.D., and distributed to the students in the form of class notes. The final manuscript was written after class-testing of the notes. Our decision to revise the Chemistry 2 notes in the form of an introductory text was made after H.B.G. and G.S.H. participated in the San Clemente Chemical Dynamics Conference, held in December 1966 under the sponsorship of the Advisory Council of College Chemistry. At San Clemente we found we were not the only group concerned over the exclusion of significant reference to chemical reactions and reactivity relationships in freshman courses. In addition to their general encouragement, which provided the necessary additional impetus, these colleagues prepared a series of papers for publication in an issue of the Journal of Chemical Education. It is a pleasure to acknowledge here the direct contribution these papers made in shaping the final form of our volume; specifically, in preparing Chapter 6, we have drawn examples from the San Clemente papers of Professors R. Marcus, A. Kuppermann and E. F. Greene, and J. Halpern. The concluding chapter of this book was developed from the lectures given by Professors E. F. Greene (dynamics in simple systems), Richard Wolfgang (atomic carbon), John D. Roberts (nuclear magnetic resonance), and F. C. Anson (electrochemical dynamics) to the students of Chemistry 2 in May 1967. These colleagues have kindly given us permission to use their material. We are grateful to Professors Ralph G. Pearson and Paul Haake, who read the entire manuscript and offered valuable criticism. It is a special pleasure to acknowledge the enormous contribution our students in Chemistry 2 made to the project. Their enthusiastic, critical attitude helped us make many improvements in the manuscript. Thanks are also due to four very special members of the staff of W. A. Benjamin, Inc., for seeing this project through with infectious vigor. Finally, and not the least, we acknowledge the role Susan Brittenham and Eileen McKoy played in preparing the final manuscript. JOSEPH B. DENCE HARRY B. GRAY GEORGE S. HAMMOND Pasadena, California January 196

Assessment of atomic charge models for gas-phase computations on polypeptides

The concept of the atomic charge is extensively used to model the electrostatic properties of proteins. Atomic charges are not only the basis for the electrostatic energy term in biomolecular force fields but are also derived from quantum mechanical computations on protein fragments to get more insight into their electronic structure. Unfortunately there are many atomic charge schemes which lead to significantly different results, and it is not trivial to determine which scheme is most suitable for biomolecular studies. Therefore, we present an extensive methodological benchmark using a selection of atomic charge schemes [Mulliken, natural, restrained electrostatic potential, Hirshfeld-I, electronegativity equalization method (EEM), and split-charge equilibration (SQE)] applied to two sets of penta-alanine conformers. Our analysis clearly shows that Hirshfeld-I charges offer the best compromise between transferability (robustness with respect to conformational changes) and the ability to reproduce electrostatic properties of the penta-alanine. The benchmark also considers two charge equilibration models (EEM and SQE), which both clearly fail to describe the locally charged moieties in the zwitterionic form of penta-alanine. This issue is analyzed in detail because charge equilibration models are computationally much more attractive than the Hirshfeld-I scheme. Based on the latter analysis, a straightforward extension of the SQE model is proposed, SQE+Q0, that is suitable to describe biological systems bearing many locally charged functional groups

Cobalt-Porphyrin Catalyzed Electrochemical Reduction of Carbon Dioxide in Water II: Mechanism from First Principles

We apply first principles computational techniques to analyze the two-electron, multi-step, electrochemical reduction of CO2 to CO in water using cobalt porphyrin as a catalyst. Density Functional Theory calculations with hybrid functionals and dielectric continuum solvation are used to determine the steps at which electrons are added. This information is corroborated with ab initio molecular dynamics simulations in an explicit aqueous environment which reveal the critical role of water in stabilizing a key intermediate formed by CO2 bound to cobalt. Using potential of mean force calculations, the intermediate is found to spontaneously accept a proton to form a carboxylate acid group at pH<9.0, and the subsequent cleavage of a C-OH bond to form CO is exothermic and associated with a small free energy barrier. These predictions suggest that the proposed reaction mechanism is viable if electron transfer to the catalyst is sufficiently fast. The variation in cobalt ion charge and spin states during bond breaking, DFT+U treatment of cobalt 3d orbitals, and the need for computing electrochemical potentials are emphasized.Comment: 33 pages, 7 figure