Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures. The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology.

In this thesis, the author introduces two strategies used to construct various types of N-heterocycles, based on the chemistry of zirconacycles and 2,6-diazasemibullvalenes. In the first part, the author presents the development of multi-component cyclization of a zirconacyclobutene-silacyclobutene fused compound, nitriles and unsaturated compounds. These reactions provide synthetically useful methodology for various N-heterocycles such as 3-acyl pyrrole, pyrrolo[3,2-d]pyridazine and dihydropyrroloazepine, which are all difficult to synthesize by other means. The isolation and characterization of the key three-fused-ring Zr/Si-containing intermediates are also described in detail. These results show that the zirconacyclobutene-silacyclobutene fused compound behaves as a "chemical transformer" upon treatment with various substrates via the "coordination-induced skeleton rearrangement" mechanism. In the second part, the author demonstrates the synthesis and isolation of a series of 2,6-diazasemibullvalenes (NSBVs) from the reaction of 1,4-dilithio-1,3-dienes and nitriles, highlighting the significant progress made for the first time in this work: (1) determination of X-ray crystal structure of a substituted 2,6-diazasemibullvalene; (2) measurement of the activation barrier of its rapid intramolecular aza-Cope rearrangement in solution; (3) exploration of several reaction types of NSBV with diverse ring-expansion products and "bowl-shape" or "cage-shape" N-containing polycyclic skeletons; (4) demonstration of the localized structure as the predominant form and the homoaromatic delocalized structure as a minor component in the equilibrium using theoretical analysis. Based on well-founded results, this work sheds new light on this controversial topic.

Synergetics is the quantitative study of multicomponent systems that exhibit nonlinear dynamics and cooperativity. This book specifically considers basic models of the nonlinear dynamics of molecular systems and discusses relevant applications in biological physics and the polymer sciences. Emphasis is placed on specific solutions to the dynamical equations that correspond to the coherent formation of spatial-temporal structures, such as solitons, kinks and breathers, in particular. The emergence of these patterns in molecular structures provides a variety of information on their structural properties and plays a significant part in energy transfer processes, topological defects, dislocations, and related structure transitions. Real media, in which solitons take the form of solitary waves, are also considered. In this context, the formation of nonlinear waves in a continuous medium described by nonlinear equations is associated with spontaneous breaking of the local symmetry of the homogeneous system, which produces a range of interesting phenomena. A particular feature of this text is its combination of analytic and computational strategies to tackle difficult nonlinear problems at the molecular level of matter.

In this thesis, Andrew Logsdail demonstrates that computational chemistry is a powerful tool in contemporary nanoscience, complementing experimental observations and helping guide future experiments. The aim of this particular PhD is to further our understanding of structural and compositional preferences in gold nanoparticles, as well as the compositional and chemical ordering preferences in bimetallic nanoalloys formed with other noble metals, such as palladium and platinum. Highlights include: calculations of the structural preferences and optical-response of gold nanoparticles and gold-containing nanoalloys; the design and implementation of novel numerical algorithms for the structural characterisation of gold nanoparticles from electron microscopy images; and electronic structure calculations investigating the interaction of gold nanoparticles with graphene and graphite substrates.The results presented here have significant implications for future research on the chemical and physical properties of gold-based nanoparticles and are of interest to many researchers working on experimental and theoretical aspects of nanoscience.

This book presents the state-of-the-art in simulation on supercomputers. Leading researchers present results achieved on systems of the High Performance Computing Center Stuttgart (HLRS) for the year 2010. The reports cover all fields of computational science and engineering, ranging from CFD to computational physics and chemistry to computer science, with a special emphasis on industrially relevant applications. Presenting results for both vector systems and microprocessor-based systems, the book makes it possible to compare the performance levels and usability of various architectures. As HLRS operates the largest NEC SX-8 vector system in the world, this book gives an excellent insight into the potential of vector systems, covering the main methods in high performance computing. Its outstanding results in achieving the highest performance for production codes are of particular interest for both scientists and engineers. The book includes a wealth of color illustrations and tables.

In the area of organic chemistry one major challenge we are currently faced with is how to assemble potentially useful molecules in new ways that generate molecular complexity and in sequences that are as efficient as possible. Our efforts in this regard, specifically for the preparation of amino containing compounds incorporating an aromatic ring, are described in this doctoral thesis. We discovered an interesting regioselectivity in an intramolecular Heck reaction, which we studied for a series of substrates that are unbiased in terms of the size of the newly formed ring, where very high levels of selectivity in relation to the new carbon-carbon bond are typically observed. DFT calculations were performed to attempt to shed light on the reaction sequence. This regioselective Heck reaction, combined with the reductive removal of the temporary amino-protecting group, allowed us to synthesize the Sceletium alkaloids: mesembrane, mesembranol and mesembrine.

In this festschrift dedicated to Professor Eluvathingal D. Jemmis on the occasion of his 60th birthday, selected researchers in theoretical chemistry present research highlights on major developments in the field. Originally published in the journal Theoretical Chemistry Accounts, these outstanding contributions are now available in a hardcover print format. This volume will be of benefit in particular to those research groups and libraries that have chosen to have only electronic access to the journal. It also provides valuable content for all researchers in theoretical chemistry.

This book presents 25 outstanding papers from leading experts in the field that inspire, provoke, and educate present and future generations of computational chemists and prepares them for the challenges of the 21st century. This special edition of selected papers from the Journal of Molecular Modeling - the first electronic online journal in the history of science - is devoted to the event of Paul von Rague Schleyer's 75th birthday.

The series Topics in Current Chemistry presents critical reviews of the present and future trends in modern chemical research. The scope of coverage is all areas of chemical science including the interfaces with related disciplines such as biology, medicine and materials science. The goal of each thematic volume is to give the non-specialist reader, whether in academia or industry, a comprehensive insight into an area where new research is emerging which is of interest to a larger scientific audience. Each review within the volume critically surveys one aspect of that topic and places it within the context of the volume as a whole. The most significant developments of the last 5 to 10 years are presented using selected examples to illustrate the principles discussed. The coverage is not intended to be an exhaustive summary of the field or include large quantities of data, but should rather be conceptual, concentrating on the methodological thinking that will allow the non-specialist reader to understand the information presented. Contributions also offer an outlook on potential future developments in the field. Review articles for the individual volumes are invited by the volume editors. Readership: research chemists at universities or in industry, graduate students

This work explores the scope and flexibility afforded by integrated quantum photonics, both in terms of practical problem-solving, and for the pursuit of fundamental science. The author demonstrates and fully characterizes a two-qubit quantum photonic chip, capable of arbitrary two-qubit state preparation. Making use of the unprecedented degree of reconfigurability afforded by this device, a novel variation on Wheeler's delayed choice experiment is implemented, and a new technique to obtain nonlocal statistics without a shared reference frame is tested. Also presented is a new algorithm for quantum chemistry, simulating the helium hydride ion. Finally, multiphoton quantum interference in a large Hilbert space is demonstrated, and its implications for computational complexity are examined.

Readers of this volume can take a tour around the research locations in Belgium which are active in theoretical and computational chemistry. Selected researchers from Belgium present research highlights of their work. Originally published in the journal Theoretical Chemistry Accounts, these outstanding contributions are now available in a hardcover print format. This volume will be of benefit in particular to those research groups and libraries that have chosen to have only electronic access to the journal. It also provides valuable content for all researchers in theoretical chemistry.

With contributions by leading quantum physicists, philosophers and historians, this comprehensive A-to-Z of quantum physics provides a lucid understanding of key concepts of quantum theory and experiment. It covers technical and interpretational aspects alike, and includes both traditional and new concepts, making it an indispensable resource for concise, up-to-date information about the many facets of quantum physics.

Since the second half of the 20th century machine computations have played a critical role in science and engineering. Computer-based techniques have become especially important in molecular biology, since they often represent the only viable way to gain insights into the behavior of a biological system as a whole. The complexity of biological systems, which usually needs to be analyzed on different time- and size-scales and with different levels of accuracy, requires the application of different approaches, ranging from comparative analysis of sequences and structural databases, to the analysis of networks of interdependence between cell components and processes, through coarse-grained modeling to atomically detailed simulations, and finally to molecular quantum mechanics. This book provides a comprehensive overview of modern computer-based techniques for computing the structure, properties and dynamics of biomolecules and biomolecular processes. The twenty-two chapters, written by scientists from all over the world, address the theory and practice of computer simulation techniques in the study of biological phenomena. The chapters are grouped into four thematic sections dealing with the following topics: the methodology of molecular simulations; applications of molecular simulations; bioinformatics methods and use of experimental information in molecular simulations; and selected applications of molecular quantum mechanics. The book includes an introductory chapter written by Harold A. Scheraga, one of the true pioneers in simulation studies of biomacromolecules.

Design and Applications of Nano materials for Sensors begins with an introductory contribution by the editors that: gives an overview of the present state of computational and theoretical methods for nanotechnology; outlines hot topics in this field and points to expected developments in the near future. This general introduction is followed by 15-30 review chapters by invited experts who have substantially contributed to the recent developments of nano materials for sensors. Guided by molecular and quantum theories, this contributed volume gives a broad picture of the current and past advances that were necessary to develop nano sensors using nano materials. To illustrate the important and relevant applications of nano materials, Design and Applications of Nano materials for Sensors focuses on recent advances that extend the scope of possible applications of the theory, improve the accuracy with respect to experimentation and reduce the cost of these calculations. This volume also features new applications of theoretical chemistry methods to problems of recent general interest in nanotechnology whereby large computational experiments are now necessary.

The present volume is a collection of review articles highlighting the fundamental advances made in this area by the internationally acclaimed research groups , most of them being pioneers themselves and coming together for the first time.

This book extends the development of the thermodynamic theory of specific intermolecular interactions to element-organic and specific organometallic compounds. The fundamentals of an unconventional approach to the theory of H-bonding and specific interactions are formulated, based on a concept of pentacoordinate carbon atoms. Prof. Baev has introduced the theory already in his successful books "Specific Intermolecular Interactions of Organic Compounds" and "Specific Intermolecular Interactions of Nitrogenated and Bioorganic Compounds". In this book he also demonstrates it for element organic and specific organometallic compounds, a class of substances which is of great importance in synthetic chemistry and catalysis. Furthermore, organic compound classes, that have not been treated in the previous books, are included. New types of hydrogen bonds and specific interactions are substantiated and their energies are determined on the basis of the developed methodology. In this way, the influence of the molecular structure on the energy and on intermolecular interactions can be discussed for these particular compound classes.

Amit Agarwal’s thesis reports a substantial contribution to the microscopic simulation of radiation chemical reactions. In his research Agarwal extends existing models to further understand scavenging, spin and relaxation effects. This research has advanced the development of both the Monte Carlo Random Flights and the Independent Reaction Times (IRT) simulation tools. Particular highlights are the extension of these tools to include both the spin-exchange interaction and spin relaxation, both of which are influential in radiolytic systems where many reactions are spin-controlled. In addition, the study has led to the discovery of a novel correlation of the scavenging rate with the recombination time in low permittivity solvents. This finding goes against existing assumptions underlying the theory of diffusion kinetics while still being accommodated in the IRT method which demonstrates the power of this unconventional approach. The work in this thesis can be applied to a wide number of fields including the nuclear industry, medicine, food treatment, polymer curing, the preparation of nano-colloids, power generation and waste disposal.

In this dissertation, Marie-Hélène Larraufie develops original radical and pallado-catalyzed methodologies to enable the synthesis of several classes of bioactive nitrogen-containing heterocycles. New radical cascades employing the N-acylcyanamide moiety offer straightforward routes to quinazolinones and guanidines, as well as new insights into the mechanism of homolytic aromatic substitutions. In parallel, Larraufie expands the scope of visible light photoredox catalysis to the ring opening of epoxides and aziridines, thus providing new sustainable alternatives for the generation of radicals. Furthermore, in a collaborative effort with the Catellani group, the author investigates dual palladium/norbornene catalysis. First, she develops a C-amination coupling variant of the Catellani reaction with unprotected amines which provides an expeditious route to phenanthridines. Then, she examines the influence of the chelating effect on Pd(IV) intermediates reactivity with the help of experimental studies and DFT calculations. The work in this thesis has resulted in numerous publications in high impact journals.The clarity and depth of the experimental section will be useful for students and researchers working in this field. 

The proposed volume provides both fundamental and detailed information about the computational and computational-experimental studies which improve our knowledge of how leaving matter functions, the different properties of drugs (including the calculation and the design of new ones), and the creation of completely new ways of treating numerical diseases. Whenever it is possible, the interplay between theory and experiment is provided. The book features computational techniques such as quantum-chemical and molecular dynamic approaches and quantitative structure-activity relationships. The initial chapters describe the state-of-the art research on the computational investigations in molecular biology, molecular pharmacy, and molecular medicine performed with the use of pure quantum-chemical techniques. The central part of the book illustrates the status of computational techniques that utilize hybrid, so called QM/MM approximations as well as the results of the QSAR studies which now are the most popular in predicting drugs' efficiency. The last chapters describe combined computational and experimental investigations.

Jonelle Harvey's book outlines two related experimental techniques, threshold photoelectron spectroscopy and threshold photoelectron photoion coincidence techniques, which are utilised to investigate small halogenated molecules. All the experiments were conducted at the vacuum ultraviolet beamline of the Swiss Light Source, a synchrotron photon source, which has the advantage over popular laser photon-sources of extreme ease of tunability. Three studies are presented which combine experimental and computational ab initio approaches: studying the fast dissociations of halogenated methanes in order to construct a self-consistent thermochemical network; investigating the fragmentations of fluoroethenes from timebombs, which break apart very slowly but explosively, to fast dissociators; and uncovering how vital conical interactions underpin both the results of photoelectron spectra and dissociation patterns. The details included in this thesis are useful for researchers working in the same field and those readers wishing to obtain a solid introduction into the types of systems encountered in threshold photoelectron photoion coincidence spectroscopy.

Yanfei Shen and Takashi Nakanishi Exotic Self-Organized Fullerene Materials Based on Uncommon Hydrophobic–Amphiphilic Approach Yuming Zhao and Guang Chen C60 Fullerene Amphiphiles as Supramolecular Building Blocks for Organized and Well-Defined Nano scale Objects Anna Troeger, Vito Sgobba and Dirk M. Guldi Multilayer Assembly for Solar Energy Conversion Delphine Felder-Flesch Self- or Induced Organization of [60]Fullerene Hexakisadducts Andrés de la Escosura, Olga Trukhina, and Tomás Torres Dual Role of Phthalocyanines in Carbon Nano structure-Based Organic Photovoltaics Riccardo Marega, Davide Giust and Davide Bonifazi Supramolecular Chemistry of Carbon Nano tubes at Interfaces: Toward Applications Stephanie Frankenberger, Johanna A. Januszewski and Rik R. Tykwinski Oligomers from sp-Hybridized Carbon: Cumulenes and Polyynes.

This volume collects research findings presented at the 8th Edition of the Electronic Structure: Principles and Applications (ESPA-2012) International Conference, held in Barcelona, Spain on June 26-29, 2012. The contributions cover research work on methods and fundamentals of theoretical chemistry, chemical reactivity, bimolecular modeling, and materials science. Originally published in the journal Theoretical Chemistry Accounts, these outstanding papers are now available in a hardcover print format, as well as a special electronic edition. This volume provides valuable content for all researchers in theoretical chemistry, and will especially benefit those research groups and libraries with limited access to the journal.

This multi-author contributed volume includes methodological advances and original applications to actual chemical or biochemical phenomena which were not possible before the increased sophistication of modern computers. The chapters contain detailed reviews of the developments of various computational techniques, used to study complex molecular systems such as molecular liquids and solutions (particularly aqueous solutions), liquid-gas, solid-gas interphase and biomacromolecular systems. Quantum modeling of complex molecular systems is a useful resource for graduate students and fledgling researchers and is also an excellent companion for research professionals engaged in computational chemistry, material science, nanotechnology, physics, drug design, and molecular biochemistry.

Find out how theoretical calculations are used to determine, elucidate and propose mechanisms for Pd-catalyzed C-C cross-coupling reactions in Max Garcia Melchor's outstanding thesis. Garcia Melchor investigates one of the most significant and useful types of reactions in modern organic synthesis; the Pd-cross coupling reaction. Due to its versatility, broad scope and selectivity under mild conditions, this type of reaction can now be applied in fields as diverse as the agrochemical and pharmaceutical industry. Garcia Melchor studies the reaction intermediates and transition states involved in the Negishi, the copper-free Sonogashira and the asymmetric version of Suzuki-Miyaura coupling. He also characterizes and provides a detailed picture of the associated reaction mechanisms. The author has won numerous prizes for this work which has led to over eight publications in internationally renowned journals.

After his first book on the topic "Specific Intermolecular Interactions of Organic Compounds", Baev extends in this book the development of the thermodynamic theory of specific intermolecular interactions to a wider spectrum of nitrogenated and bioorganic compounds: amino alcohols, amino acids, peptides and urea derivatives. The fundamentals of an unconventional approach to the theory of H-bonding and specific interactions are formulated based on a concept of penta- coordinated carbon atoms. New types of hydrogen bonds and specific interactions are substantiated and on the basis of the developed methodology their energies are determined. The new concept of the extra stabilizing effect of isomeric methyl groups on the structure and stability of nitrogenated organic molecules and bioorganic compounds is introduced and the destabilization action on specific interactions is outlined.