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Study Of Hydrogen Bonding In Small Water Clusters With Density Functional Theory Calculations
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Book Synopsis Study of Hydrogen Bonding in Small Water Clusters with Density Functional Theory Calculations by : Johanna Wendlandt
Download or read book Study of Hydrogen Bonding in Small Water Clusters with Density Functional Theory Calculations written by Johanna Wendlandt and published by . This book was released on 2005 with total page 12 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Visualization of Hydrogen-Bond Dynamics by : Takashi Kumagai
Download or read book Visualization of Hydrogen-Bond Dynamics written by Takashi Kumagai and published by Springer Science & Business Media. This book was released on 2012-09-02 with total page 139 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Unraveling Hydrogen Bonded Clustering with Water by : Dr. Anant D. Kulkarni
Download or read book Unraveling Hydrogen Bonded Clustering with Water written by Dr. Anant D. Kulkarni and published by . This book was released on 2020 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Development and Analysis of Computational Methods to Study Hydrogen Bonding in Molecular Clusters by : Ryan J. DiRisio
Download or read book Development and Analysis of Computational Methods to Study Hydrogen Bonding in Molecular Clusters written by Ryan J. DiRisio and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Theoretical Treatments of Hydrogen Bonding by : Dušan Hadži
Download or read book Theoretical Treatments of Hydrogen Bonding written by Dušan Hadži and published by John Wiley & Sons. This book was released on 1997-12-29 with total page 344 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Electronic-Structure Theory by : Trygve Helgaker
Download or read book Molecular Electronic-Structure Theory written by Trygve Helgaker and published by John Wiley & Sons. This book was released on 2014-08-11 with total page 949 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis Molecular Orbital Calculations for Biological Systems by : Anne-Marie Sapse
Download or read book Molecular Orbital Calculations for Biological Systems written by Anne-Marie Sapse and published by Oxford University Press. This book was released on 1998-11-12 with total page 248 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Orbital Calculations for Biological Systems is a hands-on guide to computational quantum chemistry and its applications in organic chemistry, biochemistry, and molecular biology. With improvements in software, molecular modeling techniques are now becoming widely available; they are increasingly used to complement experimental results, saving significant amounts of lab time. Common applications include pharmaceutical research and development; for example, ab initio and semi-empirical methods are playing important roles in peptide investigations and in drug design. The opening chapters provide an introduction for the non-quantum chemist to the basic quantum chemistry methods, ab initio, semi-empirical, and density functionals, as well as to one of the main families of computer programs, the Gaussian series. The second part then describes current research which applies quantum chemistry methods to such biological systems as amino acids, peptides, and anti-cancer drugs. Throughout the authors seek to encourage biochemists to discover aspects of their own research which might benefit from computational work. They also show that the methods are accessible to researchers from a wide range of mathematical backgrounds. Combining concise introductions with practical advice, this volume will be an invaluable tool for research on biological systems.
Book Synopsis Density Functional Theory Studies of Selected Hydrogen Bond Assisted Chemical Reactions by : Zhen Guo
Download or read book Density Functional Theory Studies of Selected Hydrogen Bond Assisted Chemical Reactions written by Zhen Guo and published by . This book was released on 2017-01-27 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: 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
Book Synopsis Importance of Self-Interaction Correction in Hydrogen-Bonded Water Clusters and Water-Ion Clusters by : Kamal Wagle
Download or read book Importance of Self-Interaction Correction in Hydrogen-Bonded Water Clusters and Water-Ion Clusters written by Kamal Wagle and published by . This book was released on 2021 with total page 131 pages. Available in PDF, EPUB and Kindle. Book excerpt: Density functional theory is the most commonly used computational tool to study properties of solids and molecules. Self-interaction error, that arises due to improper cancellation of the self-Hartree and the self exchange correlation energy, has long been identified as a major limitation of practical density functional approximations. We develop and test the performance of different self-interaction corrected functionals in accurately predicting a wide range of properties. This work focuses on use of the Fermi-L\"{o}wdin orbital self-interaction correction (FLOSIC) method to study neutral water complexes and interaction of ions with water clusters. The strongly constrained and appropriately normed (SCAN) density functional approximation (DFA) has been found to give the correct energy ordering of low-lying isomers of water hexamers, resolves the density anomaly between water and ice, and improves the relative lattice energy of ice polymorphs and the infrared spectra of liquid water. However, SCAN is not without its drawbacks. The binding energies of water clusters and lattice energies of ice phases are overestimated by SCAN. We find that by explicitly removing the self-interaction error, the hydrogen-bond binding energy of water clusters can be significantly improved. In particular, self-interaction correction to the SCAN functional (FLOSIC-SCAN) improves binding energies without altering the correct energetic ordering of the low-lying water hexamers. So, orbital-by-orbital removal of self-interaction error applied on top of a proper DFA can lead to an improved description of water complexes. To gain further insight into the performance of different functionals on the relative stability of water clusters, we decompose the total interaction energy into many-body components. We see that the major portion of error in SCAN comes from the two-body interaction, and the FLOSIC-SCAN improves two-body interactions over SCAN and predicts higher-order many-body interactions with about the same accuracy as SCAN. The SCAN functional gives good account of monomer deformation energy (one-body energy), PBE estimated it too low and self-interaction corrected methods FLOSIC-PBE and FLOSIC-SCAN estimated too high monomer deformation energies. Improvement in the total interaction energy by FLOSIC-PBE and FLOSIC-SCAN is happening because of error cancellation by one-body interaction energy. Aqueous solutions of ions are of particular interest due to their profound applications in environmental chemistry, solvation mechanics, the desalination process, etc. This motivated us to study ion-water systems, which include hydronium ion-water clusters, hydroxyl ion-water clusters, halide ion-water clusters, and alkali ion-water clusters. The erroneous delocalization of the extra-electron in anions obtained with DFAs is basis-set dependent. DFAs like LSDA, PBE, or SCAN can bind only a fraction of the excess electron in the complete basis set limit, implying that a moderate-sized localized basis would be a good choice for them. But, accurate description of hydrogen bonds often requires a large basis with some extra diffuse functions. So, in negatively charged hydrogen-bonded systems like deprotonated water clusters, the suitable choice of basis-set is both difficult and ambiguous. We explore this issue systematically in this work. Further, we have found that the better performance by application of FLOSIC is seen in all systems that are connected at least with one hydrogen bond and the error in the binding energy decreases with increase in the size of an ion or equivalently decreases with the length of the hydrogen bond. Moreover, within the same ion-water system, error in the binding energy decreases with increase in the size of the cluster. Non-hydrogen-bonded water-alkali clusters are not affected by the self-interaction errors.
Book Synopsis Hydrogen Bonding - New Insights by : Slawomir Grabowski
Download or read book Hydrogen Bonding - New Insights written by Slawomir Grabowski and published by Springer Science & Business Media. This book was released on 2006-10-07 with total page 536 pages. Available in PDF, EPUB and Kindle. Book excerpt: 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.
Book Synopsis A Comparative Study of Hydrogen Bonding Using Density Functional Theory by : Ching-Han Hu
Download or read book A Comparative Study of Hydrogen Bonding Using Density Functional Theory written by Ching-Han Hu and published by . This book was released on with total page 8 pages. Available in PDF, EPUB and Kindle. Book excerpt:
Book Synopsis The Science of Victorian Brown Coal by : R.A. Durie
Download or read book The Science of Victorian Brown Coal written by R.A. Durie and published by Butterworth-Heinemann. This book was released on 2013-10-22 with total page 767 pages. Available in PDF, EPUB and Kindle. Book excerpt: The Science of Victorian Brown Coal provides extensive information on Victorian brown coal, which is a major fossil fuel resource by any standard and constitutes about 97% of Victoria's recoverable energy reserves. Energy from brown coal has been the mainstay of the Victorian economy, providing low-cost electricity to the state grid, briquettes as a fuel for industry and town gas prior to the discovery of natural gas. Because of the unique properties of the coal, it has been necessary to develop an in-depth scientific knowledge of the coal and its behavior, as well as innovative technologies for its effective utilization. The economic benefit brown coal has provided to Victoria is demonstrated throughout the chapters. This book aims to provide the springboard for further research and lead to a new era in the development of value-added products and the more efficient utilization of this major resource. This text is a useful reference for students or individuals conducting research on fossil fuel energy, specifically on brown coals.
Book Synopsis Spectroscopic Investigations of Hydrogen Bond Network Structures in Water Clusters by : Kenta Mizuse
Download or read book Spectroscopic Investigations of Hydrogen Bond Network Structures in Water Clusters written by Kenta Mizuse and published by Springer Science & Business Media. This book was released on 2013-01-22 with total page 187 pages. Available in PDF, EPUB and Kindle. Book excerpt: The properties and nature of water clusters studied with novel spectroscopic approaches are presented in this thesis. Following a general introduction on the chemistry of water and water clusters, detailed descriptions of the experiments and analyses are given. All the experimental results, including first size-selective spectra of large clusters consisting of 200 water molecules, are presented with corresponding analyses. Hitherto unidentified hydrogen bond network structures, dynamics, and reactivity of various water clusters have been characterized at the molecular level. The main targets of this book are physical chemists and chemical physicists who are interested in water chemistry or cluster chemistry.
Book Synopsis Intermolecular Interactions by : Ilya G. Kaplan
Download or read book Intermolecular Interactions written by Ilya G. Kaplan and published by John Wiley & Sons. This book was released on 2006-05-01 with total page 380 pages. Available in PDF, EPUB and Kindle. Book excerpt: The subject of this book — intermolecular interactions — is as important in physics as in chemistry and molecular biology. Intermolecular interactions are responsible for the existence of liquids and solids in nature. They determine the physical and chemical properties of gases, liquids, and crystals, the stability of chemical complexes and biological compounds. In the first two chapters of this book, the detailed qualitative description of different types of intermolecular forces at large, intermediate and short-range distances is presented. For the first time in the monographic literature, the temperature dependence of the dispersion forces is discussed, and it is shown that at finite temperatures the famous Casimir-Polder asymptotic formula is correct only at narrow distance range. The author has aimed to make the presentation understandable to a broad scope of readers without oversimplification. In Chapter 3, the methods of quantitative calculation of the intermolecular interactions are discussed and modern achievements are presented. This chapter should be helpful for scientists performing computer calculations of many-electron systems. The last two chapters are devoted to the many-body effects and model potentials. More than 50 model potentials exploited for processing experimental data and computer simulation in different fields of physics, chemistry and molecular biology are represented. The widely used global optimisation methods: simulated annealing, diffusion equation method, basin-hopping algorithm, and genetic algorithm are described in detail. Significant efforts have been made to present the book in a self-sufficient way for readers. All the necessary mathematical apparatus, including vector and tensor calculus and the elements of the group theory, as well as the main methods used for quantal calculation of many-electron systems are presented in the appendices.
Book Synopsis Molecular Theory of Solvation by : F. Hirata
Download or read book Molecular Theory of Solvation written by F. Hirata and published by Springer Science & Business Media. This book was released on 2006-04-11 with total page 366 pages. Available in PDF, EPUB and Kindle. Book excerpt: Molecular Theory of Solvation presents the recent progress in the statistical mechanics of molecular liquids applied to the most intriguing problems in chemistry today, including chemical reactions, conformational stability of biomolecules, ion hydration, and electrode-solution interface. The continuum model of "solvation" has played a dominant role in describing chemical processes in solution during the last century. This book discards and replaces it completely with molecular theory taking proper account of chemical specificity of solvent. The main machinery employed here is the reference-interaction-site-model (RISM) theory, which is combined with other tools in theoretical chemistry and physics: the ab initio and density functional theories in quantum chemistry, the generalized Langevin theory, and the molecular simulation techniques. This book will be of benefit to graduate students and industrial scientists who are struggling to find a better way of accounting and/or predicting "solvation" properties.
Book Synopsis Hydrogen Bonding by : Steve Scheiner
Download or read book Hydrogen Bonding written by Steve Scheiner and published by Oxford University Press. This book was released on 1997-09-04 with total page 396 pages. Available in PDF, EPUB and Kindle. Book excerpt: Because of the importance of the hydrogen bond, there have been scores of insights gained about its fundamental nature by quantum chemical computations over the years. Such methods can probe subtle characteristics of the electronic structure and examine regions of the potential energy surface that are simply not accessible by experimental means. The maturation of the techniques, codes, and computer hardware have permitted calculations of unprecedented reliability and rivaling the accuracy of experimental data. This book strives first toward an appreciation of the power of quantum chemistry to analyze the deepest roots of the hydrogen bond phenomenon. It offers a systematic and understandable account of decades of such calculations, focusing on the most important findings. This book provides readers with the tools to understand the original literature, and to perhaps carry out some calculations of their very own on systems of interest.
Book Synopsis The Structure and Properties of Water by : D Eisenberg
Download or read book The Structure and Properties of Water written by D Eisenberg and published by Oxford University Press, USA. This book was released on 2005-10-20 with total page 315 pages. Available in PDF, EPUB and Kindle. Book excerpt: The authors have correlated many experimental observations and theoretical discussions from the scientific literature on water. Topics covered include the water molecule and forces between water molecules; the thermodynamic properties of steam; the structures of the ices; the thermodynamic, electrical, spectroscopic, and transport properties of the ices and of liquid water; hydrogen bonding in ice and water; and models for liquid water. The main emphasis of the book is on relatingthe properties of ice and water to their structures. Some background material in physical chemistry has been included in order to ensure that the material is accessible to readers in fields such as biology, biochemistry, and geology, as well as to chemists and physicists.
