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

Ab initio atomistic thermodynamics and statistical mechanics of surface properties and functions

Previous and present "academic" research aiming at atomic scale understanding is mainly concerned with the study of individual molecular processes possibly underlying materials science applications. Appealing properties of an individual process are then frequently discussed in terms of their direct importance for the envisioned material function, or reciprocally, the function of materials is somehow believed to be understandable by essentially one prominent elementary process only. What is often overlooked in this approach is that in macroscopic systems of technological relevance typically a large number of distinct atomic scale processes take place. Which of them are decisive for observable system properties and functions is then not only determined by the detailed individual properties of each process alone, but in many, if not most cases also the interplay of all processes, i.e. how they act together, plays a crucial role. For a "predictive materials science modeling with microscopic understanding", a description that treats the statistical interplay of a large number of microscopically well-described elementary processes must therefore be applied. Modern electronic structure theory methods such as DFT have become a standard tool for the accurate description of individual molecular processes. Here, we discuss the present status of emerging methodologies which attempt to achieve a (hopefully seamless) match of DFT with concepts from statistical mechanics or thermodynamics, in order to also address the interplay of the various molecular processes. The new quality of, and the novel insights that can be gained by, such techniques is illustrated by how they allow the description of crystal surfaces in contact with realistic gas-phase environments.Comment: 24 pages including 17 figures, related publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm

Heuristics-Guided Exploration of Reaction Mechanisms

For the investigation of chemical reaction networks, the efficient and accurate determination of all relevant intermediates and elementary reactions is mandatory. The complexity of such a network may grow rapidly, in particular if reactive species are involved that might cause a myriad of side reactions. Without automation, a complete investigation of complex reaction mechanisms is tedious and possibly unfeasible. Therefore, only the expected dominant reaction paths of a chemical reaction network (e.g., a catalytic cycle or an enzymatic cascade) are usually explored in practice. Here, we present a computational protocol that constructs such networks in a parallelized and automated manner. Molecular structures of reactive complexes are generated based on heuristic rules derived from conceptual electronic-structure theory and subsequently optimized by quantum chemical methods to produce stable intermediates of an emerging reaction network. Pairs of intermediates in this network that might be related by an elementary reaction according to some structural similarity measure are then automatically detected and subjected to an automated search for the connecting transition state. The results are visualized as an automatically generated network graph, from which a comprehensive picture of the mechanism of a complex chemical process can be obtained that greatly facilitates the analysis of the whole network. We apply our protocol to the Schrock dinitrogen-fixation catalyst to study alternative pathways of catalytic ammonia production.Comment: 27 pages, 9 figure

Quantitative wave function analysis for excited states of transition metal complexes

The character of an electronically excited state is one of the most important descriptors employed to discuss the photophysics and photochemistry of transition metal complexes. In transition metal complexes, the interaction between the metal and the different ligands gives rise to a rich variety of excited states, including metal-centered, intra-ligand, metal-to-ligand charge transfer, ligand-to-metal charge transfer, and ligand-to-ligand charge transfer states. Most often, these excited states are identified by considering the most important wave function excitation coefficients and inspecting visually the involved orbitals. This procedure is tedious, subjective, and imprecise. Instead, automatic and quantitative techniques for excited-state characterization are desirable. In this contribution we review the concept of charge transfer numbers---as implemented in the TheoDORE package---and show its wide applicability to characterize the excited states of transition metal complexes. Charge transfer numbers are a formal way to analyze an excited state in terms of electron transitions between groups of atoms based only on the well-defined transition density matrix. Its advantages are many: it can be fully automatized for many excited states, is objective and reproducible, and provides quantitative data useful for the discussion of trends or patterns. We also introduce a formalism for spin-orbit-mixed states and a method for statistical analysis of charge transfer numbers. The potential of this technique is demonstrated for a number of prototypical transition metal complexes containing Ir, Ru, and Re. Topics discussed include orbital delocalization between metal and carbonyl ligands, nonradiative decay through metal-centered states, effect of spin-orbit couplings on state character, and comparison among results obtained from different electronic structure methods.Comment: 47 pages, 19 figures, including supporting information (7 pages, 1 figure

Insights into enzymatic halogenation from computational studies

The halogenases are a group of enzymes that have only come to the fore over the last 10 years thanks to the discovery and characterization of several novel representatives. They have revealed the fascinating variety of distinct chemical mechanisms that nature utilizes to activate halogens and introduce them into organic substrates. Computational studies using a range of approaches have already elucidated many details of the mechanisms of these enzymes, often in synergistic combination with experiment. This Review summarizes the main insights gained from these studies. It also seeks to identify open questions that are amenable to computational investigations. The studies discussed herein serve to illustrate some of the limitations of the current computational approaches and the challenges encountered in computational mechanistic enzymology

Exploration of Reaction Pathways and Chemical Transformation Networks

For the investigation of chemical reaction networks, the identification of all relevant intermediates and elementary reactions is mandatory. Many algorithmic approaches exist that perform explorations efficiently and automatedly. These approaches differ in their application range, the level of completeness of the exploration, as well as the amount of heuristics and human intervention required. Here, we describe and compare the different approaches based on these criteria. Future directions leveraging the strengths of chemical heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure

From quantum mechanics to the physical metallurgy of steels

In the last decade there has been a breakthrough in the construction of theories leading to models for the simulation of atomic scale processes in steel. In this paper the theory is described and developed and used to demonstrate calculations of the diffusivity and trapping of hydrogen in iron and the structures of carbon vacancy complexes in steel.Comment: Paper presented at "Adventures in the Physical Metallurgy of Steels," Cambridge, August 2013. See http://www.msm.cam.ac.uk/apms where the slides and video of the talk can also be seen. Paper is submitted to a special issue of Materials Science and Technolog