The unique characteristics of hydrogen bonding have left our understanding of liquid water far from complete in terms of its structure and properties. In order to better describe the hydrogen bond in water, we seek to understand the electronic states which show sensitivity to hydrogen bonding. We investigate the structure of unoccupied valence states by performing X-ray Absorption calculations on water clusters using Density Functional Theory. For each water cluster, studying how valence electronic structure is perturbed by changes in the local hydrogen bonding environment facilitates our description of the hydrogen bond. Also in this framework, we move toward a depiction of local structures in liquid water by comparison to experimental X-ray absorption spectra. We find consistent localization along internal bonds in the electronic structures of pre- and post-edge states for single-donor species. In addition, we propose a molecular orbital bonding-antibonding picture to explain this directional localization from dimer calculations, and show that the pre- and post-edge spectral regions have a resulting relationship.
The hydrogen bond represents an important interaction between molecules, and the dynamics of hydrogen bonds in water create an ever-present question associated with the process of chemical and biological reactions. In spite of numerous studies, the process remains poorly understood at the microscopic level because hydrogen-bond dynamics, such as bond rearrangements and hydrogen/proton transfer reactions, are extremely difficult to probe. Those studies have been carried out by means of spectroscopic methods where the signal stems from the ensemble of a system and the hydrogen-bond dynamics were inferred indirectly. This book addresses the direct imaging of hydrogen-bond dynamics within water-based model systems assembled on a metal surface, using a scanning tunneling microscope (STM). The dynamics of individual hydrogen bonds in water clusters, hydroxyl clusters, and water-hydroxyl complexes are investigated in conjunction with density functional theory. In these model systems, quantum dynamics of hydrogen bonds, such as tunneling and zero-point nuclear motion, are observed in real space. Most notably, hydrogen atom relay reactions, which are frequently invoked across many fields of chemistry, are visualized and controlled by STM. This work presents a means of studying hydrogen-bond dynamics at the single-molecule level, providing an important contribution to wide fields beyond surface chemistry.
Extensive density functional theory (DFT) studies have been compiled and additional investigation has been performed for several energetically favorable conformers of hydrogen bonded water clusters. The focus here is not to merely reviewing the literature on DFT investigations on water clusters but to understand the basic building blocks, structural patterns and trends in the energetics of the clusters during the cluster growth. The successive addition of water molecules to these clusters alters the hydrogen bonding pattern, that leads to modification in overall cluster geometry which is also reflected in the vibrational frequency shifts in simulated vibrational infra-red (IR) spectra.
Understanding the role of hydrogen bonding in the structure and dynamics of water is an ongoing challenge in physical chemistry. In particular, understanding how the quantum mechanical effects of molecular vibrations govern the structure and dynamics of water is of interest. The cornerstone method used to study this phenomenon in this work is Diffusion Monte Carlo (DMC), which can be used to obtain the ground state vibrational wave function of any arbitrary molecule or molecular cluster. Instead of attempting to model bulk water and its properties outright, small, gas-phase molecular and ionic clusters of water, which provide model systems to study hydrogen bonding and proton transfer, are studied. To begin, DMC will be reviewed, and PyVibDMC, an open source, general purpose Python DMC software package developed as part of this work, will be discussed. As DMC is rigorously a ground state method, extensions to the DMC approach are required to obtain information about excited states. With excited state information, one can then directly compare simulation to experiment through theoretical and experimental spectroscopy. As such, next, the Ground State Probability Amplitude (GSPA) approximation is presented, and it is applied to protonated water clusters. In the GSPA approach, excited state wave functions are approximated based on simple products of polynomials of vibrational displacements with the ground state DMC wave function. The power of this approach is that one can construct a small basis through which to comprehensively examine the vibrational state space of the chemical system of interest. Extensions to the GSPA approach that incorporate excited state mixing and improved descriptions of higher-order excited states states will be presented as well. These improvements lead to good agreement between the GSPA theoretical and gas-phase experimental vibrational spectra of H7O3+ and H9O4+. Using this rich theoretical approach, we are able to draw connections between the molecular vibrations and structures that govern proton transfer and experimental spectroscopy of the clusters. A methodological procedure is presented next, which is the incorporation of machine learning into the DMC workflow. A potential energy surface is required for DMC simulations. Performing on-the-fly, ab initio potential energy calculations of molecular configurations in DMC simulations for systems beyond a few atoms is computationally intractable. As such, fitted potential energy surfaces are often employed for DMC simulations. However, as systems of interest increase in size, even the evaluations of these fitted surfaces become computationally demanding. To this end, a workflow is developed to use the large amount of data obtained from a small-scale DMC simulation to train a neural network to learn the potential energy surface of interest. Neural network structure, choice of descriptor, and hyperparameter optimization are reviewed and discussed in the context of other machine learning methods, and training data collection strategies are discussed, including the need to sample regions of the potential energy surface that are beyond regions accessed by a typical DMC simulation. Once the neural network surface is trained, it is evaluated in an extremely fast and highly-parallel manner, making DMC simulations significantly more efficient for H2O, CH5+, and (H2O)2. In the final section, DMC is set aside, and an exploration of the correlation between the vibrational spectral signature of an individual water molecule with its surrounding chemical environment is discussed. Specifically, the frequency of a hydrogen-bonded OH stretch in a water dimer pair is correlated to the number of solvating water molecules surrounding it. A quantum mechanical model is constructed to quantify this correlation, and applications of the model to a sample water cluster show the causality between the change in quantum mechanical electron density in the hydrogen bonding region of a particular OH bond and its OH stretch frequency. The application of the quantum model formalizes and explains empirical trends and categorization approaches put forth in previous work to characterize hydrogen bonding environments. This model is then applied to the water network found in a Cs+(H2O)20 cluster, where these trends are again quantified and then related to both the first and second solvation shell of a hydrogen-bond donor/acceptor water pair within the larger network.
Hydrogen bonding is crucial in many chemical and biochemical reactions, as well as in determining material properties. A good insight into the theoretical methods of treating hydrogen bonding is essential for those wishing to model its effects computationally in a wide range of fields involving hydrogen bonding, as well as those wishing to extract the maximal amount of information from experimental data. Theoretical Treatments of Hydrogen Bonding presents the reader with the state of the art of the key theoretical approaches to hydrogen bonding and considers the hydrogen bond from the various aspects. The first five chapters are devoted to the methods used for treating the electronic basis of hydrogen bonding, including a consideration of the electrostatic model, density functional theory and molecular orbital methods. Later chapters consider the dynamics of hydrogen bonds with particular attention to the treatment of proton transfer; manifestations of dynamics as reflected in infrared spectra and nuclear magnetic relaxation are also considered. Hydrogen bonding in liquids and solids such as ferroelectrics are included. The book concludes with an epilogue which discusses the likely development of hydrogen bond computations in very large chemical systems. Theoretical Treatments of Hydrogen Bonding offers the reader a comprehensive view of the current theoretical approaches to hydrogen bonding. It is a valuable presentation of theoretical tools useful to those looking for the most appropriate approach for treating a particular problem involving hydrogen bonding.
Nanodroplets, the basis of complex and advanced nanostructures such as quantum rings, quantum dots and quantum dot clusters for future electronic and optoelectronic materials and devices, have attracted the interdisciplinary interest of chemists, physicists and engineers. This book combines experimental and theoretical analyses of nanosized droplets which reveal many attractive properties. Coverage includes nanodroplet synthesis, structure, unique behaviors and their nanofabrication, including chapters on focused ion beam, atomic force microscopy, molecular beam epitaxy and the "vapor-liquid- solid" route. Particular emphasis is given to the behavior of metallic nanodroplets, water nanodroplets and nanodroplets in polymer and metamaterial nanocomposites. The contributions of leading scientists and their research groups will provide readers with deeper insight into the chemical and physical mechanisms, properties, and potential applications of various nanodroplets.
Ab initio quantum chemistry has emerged as an important tool in chemical research and is appliced to a wide variety of problems in chemistry and molecular physics. Recent developments of computational methods have enabled previously intractable chemical problems to be solved using rigorous quantum-mechanical methods. This is the first comprehensive, up-to-date and technical work to cover all the important aspects of modern molecular electronic-structure theory. Topics covered in the book include: * Second quantization with spin adaptation * Gaussian basis sets and molecular-integral evaluation * Hartree-Fock theory * Configuration-interaction and multi-configurational self-consistent theory * Coupled-cluster theory for ground and excited states * Perturbation theory for single- and multi-configurational states * Linear-scaling techniques and the fast multipole method * Explicity correlated wave functions * Basis-set convergence and extrapolation * Calibration and benchmarking of computational methods, with applications to moelcular equilibrium structure, atomization energies and reaction enthalpies. Molecular Electronic-Structure Theory makes extensive use of numerical examples, designed to illustrate the strengths and weaknesses of each method treated. In addition, statements about the usefulness and deficiencies of the various methods are supported by actual examples, not just model calculations. Problems and exercises are provided at the end of each chapter, complete with hints and solutions. This book is a must for researchers in the field of quantum chemistry as well as for nonspecialists who wish to acquire a thorough understanding of ab initio molecular electronic-structure theory and its applications to problems in chemistry and physics. It is also highly recommended for the teaching of graduates and advanced undergraduates.
Ab initio molecular dynamics revolutionized the field of realistic computer simulation of complex molecular systems and processes, including chemical reactions, by unifying molecular dynamics and electronic structure theory. This book provides the first coherent presentation of this rapidly growing field, covering a vast range of methods and their applications, from basic theory to advanced methods. This fascinating text for graduate students and researchers contains systematic derivations of various ab initio molecular dynamics techniques to enable readers to understand and assess the merits and drawbacks of commonly used methods. It also discusses the special features of the widely used Car–Parrinello approach, correcting various misconceptions currently found in research literature. The book contains pseudo-code and program layout for typical plane wave electronic structure codes, allowing newcomers to the field to understand commonly used program packages and enabling developers to improve and add new features in their code.
This dissertation, "Density Functional Theory Studies of Selected Hydrogen Bond Assisted Chemical Reactions" by Zhen, Guo, 郭臻, was obtained from The University of Hong Kong (Pokfulam, Hong Kong) and is being sold pursuant to Creative Commons: Attribution 3.0 Hong Kong License. The content of this dissertation has not been altered in any way. We have altered the formatting in order to facilitate the ease of printing and reading of the dissertation. All rights not granted by the above license are retained by the author. DOI: 10.5353/th_b4218233 Subjects: Hydrogen bonding Molecular structure Water Chemical reactions - Mathematical models Density functionals
This book uses examples from experimental studies to illustrate theoretical investigations, allowing greater understanding of hydrogen bonding phenomena. The most important topics in recent studies are covered. This volume is an invaluable resource that will be of particular interest to physical and theoretical chemists, spectroscopists, crystallographers and those involved with chemical physics.
