THEORETICAL CHEMISTRY: MOLECULAR SPECTROSCOPY and DYNAMICS 263 CHIMIA 2004, 58, No
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References Title: in Search of El Dorado: John Dalton and the Origins of the Atomic Theory. Authors:Rocke, Alan J. Source
References Title: In Search of El Dorado: John Dalton and the Origins of the Atomic Theory. Authors: Rocke, Alan J. Source: Social Research ; Spring2005, Vol. 72 Issue 1, p125-158, 34p Abstract: This article examines how John Dalton formulated his atomic theory of matter. Dalton's work called forth a vigorous international research program that has a continuous history from 1803 t the present-- nanoscience long before the word became vogue. Almost from the start, that research program utterly transformed the science; moreover, it was atomistic theory that enabled chemistry, two generations after Dalton, to become the earliest example of a well-developed science-based theory acquiring the practical power to transform the world of technology and commerce. Dalton knew that water consists of 87.5 oxygen and 12.5 percent hydrogen by weight that is exactly seven times as much as oxygen as hydrogen. If one assumes, with Dalton, that the invisibly small water molecule consists of an atom of hydrogen united to an atom of oxygen, then every oxygen atom must weigh seven times as much as every hydrogen atom, for under these circumstances it is o bvious that the weight ratio of the atoms must match the composition of the compound. In contrast to Dalton, Humphry Davy and Jacob Berzelius assumed (in 1812 and 1814, respectively) that the formula for water was H2O rather than Dalton's HO. ISSN: 0037-783X Accession Number: 16900837 Persistent link to http://proxy.library.upenn.edu:2062/login.aspx?direct=true&db=aph&AN=16900837&site=ehost this record: live Title: Find More Like This J. -
Semiempirical Quantum-Chemical Methods Max-Planck-Institut Für
Max-Planck-Institut für Kohlenforschung This is the peer reviewed version of the following article: WIREs Comput. Mol. Sci. 4, 145-157 (2014), which has been published in final form at https://doi.org/10.1002/wcms.1161. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self- Archived Versions. Semiempirical quantum-chemical methods Walter Thiel Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany [email protected] Abstract The semiempirical methods of quantum chemistry are reviewed, with emphasis on established NDDO-based methods (MNDO, AM1, PM3) and on the more recent orthogonalization-corrected methods (OM1, OM2, OM3). After a brief historical overview, the methodology is presented in non- technical terms, covering the underlying concepts, parameterization strategies, and computational aspects, as well as linear scaling and hybrid approaches. The application section addresses selected recent benchmarks and surveys ground-state and excited-state studies, including recent OM2- based excited-state dynamics investigations. Introduction Quantum mechanics provides the conceptual framework for understanding chemistry and the theoretical foundation for computational methods that model the electronic structure of chemical compounds. There are three types of such approaches: Quantum-chemical ab initio methods provide a convergent path to the exact solution of the Schrödinger equation and can therefore give “the right answer for the right reason”, but they are costly and thus restricted to relatively small molecules (at least in the case of the highly accurate correlated approaches). Density functional theory (DFT) has become the workhorse of computational chemistry because of its favourable price/performance ratio, allowing for fairly accurate calculations on medium-size molecules, but there is no systematic path of improvement in spite of the first-principles character of DFT. -
Theoretical and Computational Chemistry — Theory/Method/Software Developments and Applications
Lichang Wang Associate Professor Department of Chemistry and Biochemistry Carbondale, IL 62901 Phone: 618-453-6476; FAX: 618-453-6408 E-Mail: [email protected] UT Web: http://www.chem.siu.edu/TUW wang UT Theoretical and Computational Chemistry — Theory/Method/Software Developments and Applications Progress Report No. 2 August 2009 Research Perspective 3 Research Team 5 A. Theory/Method/Software Developments 7 A1. Potential Energy Surface 7 A2. Functional 8 A3. Nuclear Density Functional Theory 8 A4. Advanced Dynamics Simulation 9 B. Transition Metal Clusters and Nanoparticles 11 B1. Structures and Electromagnetic Properties 11 B2. Formation 11 B3. Toxicity 12 C. Fuel Cells 15 C1. Catalysis of Cathode Reaction 15 C2. Catalysis of Hydrogen Production from Natural Gas 16 D. Clean Coal Utilization 17 D1. Catalysis of Hydrogen/Methanol Production from Coal Gasification 17 D2. Catalysis of Petroleum/Liquid-Fuel Production from Direct Coal Liquefaction 17 D3. Solar Cell Materials 17 E. Solar Cells 19 E1. Dye-Sensitized Solar Cells 19 F. Fluorescence Sensors 21 F1. Metal Cation Sensors 21 F2. pH Sensors 21 F3. Organic Molecule Sensors 21 G. MASIS Center 23 G1. Nanoparticle-Enhanced Chiral Recognition of Enantiomers 23 G2. Boron Isotope Separation 23 Publications and Presentations 25 Support 28 Progress Report –August 2009 2 Progress Report –August 2009 Research Perspective Driven by curiosity, passion, and expertise, research in Professor Wang’s group at the Department of Chemistry and Biochemistry, Southern Illinois University Carbondale has been centered on developing theory/method/software and performing Computational Chemistry for studying chemical processes that take place in materials science and biological systems. -
2.5 Department of Theory
Theory 2.5 Department of Theory Director: Walter Thiel (born 1949) Further group leaders: Mario Barbatti (born 1971) Left the Institute in 2015 Elsa Sánchez-García (born 1976) Matthias Heyden (born 1981) Michael Roemelt (born 1982) Joined the Institute in 2015 1 Theory Curriculum Vitae: Walter Thiel 1949 Born in Treysa, Germany 1966-1971 Chemistry studies at Universität Marburg 1971-1973 Doctoral studies at Universität Marburg, with A. Schweig 1973-1975 Postdoctoral fellow at the University of Texas at Austin, with M. J. S. Dewar 1975-1982 Research scientist at Universität Marburg 1981 Habilitation for Theoretical Chemistry 1983-1992 Associate Professor of Theoretical Chemistry at Universität Wuppertal 1987 Guest Professor at the University of California at Berkeley 1992-1999 Full Professor of Chemistry at Universität Zürich 1999 Director at the Max-Planck-Institut für Kohlenforschung in Mülheim/Ruhr 2001 Honorary Professor at Universität Düsseldorf Awards and Honors 1969-1974 Studienstiftung des deutschen Volkes 1975-1977 Liebig Fellowship, Verband der Chemischen Industrie 1982 Heisenberg Fellowship, Deutsche Forschungsgemeinschaft 1988 Förderpreis, Alfried-Krupp Stiftung 1991 Member, European Academy of Sciences and Arts 2002 Schrödinger Medal, World Association of Theoretical Chemists 2007 Member, Deutsche Akademie der Naturforscher Leopoldina 2007 Member, International Academy of Quantum Molecular Sciences 2008 Member, Nordrhein-Westfälische Akademie der Wissenschaften 2009 Festschrift, Journal of Physical Chemistry A 2009, 113 (43), -
Curriculum Vitae
Dr. Pavlo O. Dral Publication List 20.03.2017 List of Publications of Dr. Pavlo O. Dral Peer-Reviewed Articles 18. Bettina D. Gliemann, Ana G. Petrovic, Eva M. Zolnhofer, Pavlo O. Dral, Frank Hampel, Georg Breitenbruch, Schulze Philipp, Vijay Raghavan, Karsten Meyer, Prasad L. Polavarapu, Nina Berova, Milan Kivala, Configurationally Stable Chiral Dithia-Bridged Hetero[4]helicene Radical Cation: Electronic Structure and Absolute Configuration. Chem. Asian J. 2017, 12, 31–35. DOI: 10.1002/asia.201601452. 17. Jakob F. Hitzenberger, Pavlo O. Dral, Ute Meinhardt, Timothy Clark, Walter Thiel, Milan Kivala, Thomas Drewello, Stability of Odd- Versus Even-Electron Gas-Phase (Quasi)Molecular Ions Derived from Pyridine-Substituted N-Heterotriangulenes. ChemPlusChem 2017, 82, 204–211. DOI: 10.1002/cplu.201600416. Appeared as the front cover in ChemPlusChem (p. 161, DOI: 10.1002/cplu.201600597) with the associated cover profile (p. 163, DOI: 10.1002/cplu.201600596). 16. Gerhard König, Frank C. Pickard IV, Jing Huang, Andrew C. Simmonett, Florentina Tofoleanu, Juyong Lee, Pavlo O. Dral, Samarjeet Prasad, Michael Jones, Yihan Shao, Walter Thiel, Bernard R. Brooks, Calculating Distribution Coefficients Based on Multi- Scale Free Energy Simulations: An Evaluation of MM and QM/MM Explicit Solvent Simulations of Water-Cyclohexane Transfer in the SAMPL5 Challenge. J. Comput. Aided Mol. Des. 2016, 30, 989–1006. DOI: 10.1007/s10822-016-9936-x. 15. Ute Meinhardt, Fabian Lodermeyer, Tobias A. Schaub, Andreas Kunzmann, Pavlo O. Dral, Anna Chiara Sale, Frank Hampel, Dirk M. Guldi, Ruben D. Costa, Milan Kivala, N-Heterotriangulene Chromophores with 4-Pyridyl Anchors for Dye-Sensitized Solar Cells. RSC Adv. -
Chemoinformatics As a Theoretical Chemistry Discipline
10/26/2016 Chemoinformatics as a theoretical chemistry discipline Alexandre Varnek University of Strasbourg BigChem lecture, 26 October 2016 Chemoinformatics: a new discipline … Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization” Frank Brown, 1998 2 1 10/26/2016 Chemoinformatics: definition Chemoinformatics is a generic term that encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization, and use of chemical information G. Paris, 1998 Chemoinformatics is the mixing of those information resources to transform data into information and information into knowledge for the intended purpose of making better decisions faster in the area of drug lead identification and optimization” F.K. Brown, 1998 Chemoinformatics is the application of informatics methods to solve chemical problems J. Gasteiger, 2004 Chemoinformatics is a field based on the representation of molecules as objects (graphs or vectors) in a chemical space A. Varnek & I. Baskin, 2011 Chemoinformatics: new disciline combining several „old“ fields • Chemical databases Michael Lynch Peter Willett • Structure‐Activity modeling (QSAR) Corwin Hansch Johann Gasteiger • Structure‐based drug design Irwin D. Kuntz Hans‐Joachim Böhm • Computer‐aided synthesis design Elias Corey Ivar Ugi 4 2 10/26/2016 Selected books in chemoinformatics Chemoinformatics: -
User:Smallman12q/Articles/Chemistry 1 User:Smallman12q/Articles/Chemistry
User:Smallman12q/articles/Chemistry 1 User:Smallman12q/articles/Chemistry Chemistry (from Egyptian kēme (chem), meaning "earth"[1] ) is the science concerned with the composition, structure, and properties of matter, as well as the changes it undergoes during chemical reactions.[2] It is a physical science for studies of various atoms, molecules, crystals and other aggregates of matter whether in isolation or combination, which incorporates the concepts of energy and entropy in relation to the spontaneity of chemical processes. Modern chemistry evolved out of alchemy following the chemical revolution (1773). Disciplines within chemistry are traditionally grouped by the type of matter being studied or the kind of study. These include inorganic chemistry, the study of inorganic matter; organic chemistry, the study Chemistry is the science concerned with the composition, structure, and properties of matter, of organic matter; biochemistry, the study of substances found in as well as the changes it undergoes during biological organisms; physical chemistry, the energy related studies of chemical reactions. chemical systems at macro, molecular and submolecular scales; analytical chemistry, the analysis of material samples to gain an understanding of their chemical composition and structure. Many more specialized disciplines have emerged in recent years, e.g. neurochemistry the chemical study of the nervous system (see subdisciplines). Summary Chemistry is the scientific study of interaction of chemical [3] substances that are constituted of -
Acronyms Used in Theoretical Chemistry
Pure & Appl. Chem., Vol. 68, No. 2, pp. 387-456, 1996. Printed in Great Britain. INTERNATIONAL UNION OF PURE AND APPLIED CHEMISTRY PHYSICAL CHEMISTRY DIVISION WORKING PARTY ON THEORETICAL AND COMPUTATIONAL CHEMISTRY ACRONYMS USED IN THEORETICAL CHEMISTRY Prepared for publication by the Working Party consisting of R. D. BROWN* (Australia, Chiman);J. E. BOWS (USA); R. HILDERBRANDT (USA); K. LIM (Australia); I. M. MILLS (UK); E. NIKITIN (Russia); M. H. PALMER (UK). The focal point to which to send comments and suggestions is the coordinator of the project: RONALD D. BROWN Chemistry Department, Monash University, Clayton, Victoria 3 168, Australia. Responses by e-mail would be particularly appreciated, the number being: rdbrown @ vaxc.cc .monash.edu.au another alternative is fax at: +61 3 9905 4597 Acronyms used in theoretical chemistry synogsis An alphabetic list of acronyms used in theoretical chemistry is presented. Some explanatory references have been added to make acronyms better understandable but still more are needed. Critical comments, additional references, etc. are requested. INTRODUC'IION The IUPAC Working Party on Theoretical Chemistry was persuaded, by discussion with colleagues, that the compilation of a list of acronyms used in theoretical chemistry would be a useful contribution. Initial lists of acronyms drawn up by several members of the working party have been augmented by the provision of a substantial list by Chemical Abstract Service (see footnote below). The working party is particularly grateful to CAS for this generous help. It soon became apparent that many of the acron ms needed more than mere spelling out to make them understandable and so we have added expr anatory references to many of them. -
QM/MM Methods for Biomolecular Systems Hans Martin Senn* and Walter Thiel*
Reviews H. M. Senn and W. Thiel DOI: 10.1002/anie.200802019 Theoretical Chemistry QM/MM Methods for Biomolecular Systems Hans Martin Senn* and Walter Thiel* Keywords: enzyme catalysis · molecular simulations · QM/MM calculations · theoretical chemistry Angewandte Chemie 1198 www.angewandte.org 2009 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Angew. Chem. Int. Ed. 2009, 48, 1198 – 1229 Angewandte QM/MM Methods Chemie Combined quantum-mechanics/molecular-mechanics (QM/MM) From the Contents approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are 1. Introduction 1199 required for describing chemical reactions and other electronic pro- 2. The QM/MM Method 1199 cesses, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. 3. Optimization and Simulation However, the size and conformational complexity of biopolymers calls Techniques for QM/MM 1206 for methods capable of treating up to several 100000 atoms and 4. Survey of QM/MM Applications 1208 allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics 5. Recent Biomolecular QM/MM (MM) methods. Thus to model large biomolecules the logical Studies 1214 approach is to combine the two techniques and to use a QM method 6. Summary and Outlook 1214 for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. -
A Series Reporting Advances in Theoretical Molecular and Material
A series reporting advances in theoretical molecular and material sciences, including theoretical, mathematical and computational chemistry, physical chemistry and chemical physics Aim and Scope Science progresses by a symbiotic interaction between theory and experiment: theory is used to interpret experimental results and may suggest new experiments; experiment helps to test theoretical predictions and may lead to improved theories. Theoretical Chemistry (including Physical Chemistry and Chemical Physics) provides the conceptual and technical background and apparatus for the rationalisation of phenomena in the chemical sciences. It is, therefore, a wide ranging subject, reflecting the diversity of molecular and related species and processes arising in chemical systems. The book series Progress in Theoretical Chemistry and Physics aims to report advances in methods and applications in this extended domain. It will comprise monographs as well as collections of papers on particular themes, which may arise from proceedings of symposia or invited papers on specific topics as well as from initiatives from authors or translations. The basic theories of physics – classical mechanics and electromagnetism, relativity theory, quantum mechanics, statistical mechanics, quantum electrodynamics – support the theoretical apparatus which is used in molecular sciences. Quantum mechanics plays a particular role in theoretical chemistry, providing the basis for the spectroscopic models employed in the determination of structural information from spectral -
Theoretical and Computational Chemistry — Method Development and Computation of Phenomena at Nanoscales
Lichang Wang Assistant Professor Department of Chemistry & Biochemistry Carbondale, IL 62901-4409 Phone: 618-453-6476; FAX: 618-453-6408 E-Mail: [email protected] http://www.science.siu.edu/chemistry/lwang Theoretical and Computational Chemistry — Method Development and Computation of Phenomena at Nanoscales Research Progress August 2006 Page No. Research Perspective .………………………………………........ 2 Research Team …………………………………………………... 3 A. Method Development …….………………………………....... 4 B. Transition Metal Nanoparticles ……………………………….. 8 C. Hydrogen Bonding Network in SAMs ………………..……….. 17 D. Fluorescence Sensors …..………………………………............ 19 Publications and Presentations …...…………………………......... 20 Support ..…….…………………….…………………………........ 24 Progress Report August 2006 Research Perspective Research in Professor Wang’s group at the Department of Chemistry and Biochemistry, Southern Illinois University Carbondale has been centered on the development of theoretical methods and computation of thermodynamics, dynamics, and kinetics of chemical processes that take place in materials science and biological systems. On the research of method development, our interests focus on developing advanced theories for dynamics simulations that are used to deal with large and complex systems. Particular efforts include finding methods to better describe dynamics of large systems with significant quantum effects and constructing potential energy surfaces (PESs) to describe accurately the interactions among atoms. During the past five years, we have been developing methods to provide a measurement on the accuracy of the mixed quantum/classical dynamics theory in the calculation of critical properties, such as reaction probabilities, for large systems that have a strong quantum character but a full quantum treatment is not feasible. We are also in the process of developing and implementing a Nuclear Density Functional Theory (NDFT) to treat the dynamics of large systems full quantum mechanically. -
Deniz Tuna January 7, 2019
Deniz Tuna January 7, 2019 Stanford University Department of Chemistry Stanford, California 94305 +1 650 926 4057 [email protected] www: Stanford Profiles, Google Scholar Postdoctoral Research Experience 05/2017–present Stanford University, Stanford, USA and SLAC National Accelerator Laboratory, Menlo Park, USA Advisor: Todd J. Martínez. Research focus: Ab initio multiple spawning nonadiabatic dynamics simulations of biochromophores in solution and in protein environments with QM/MM. 05/2014–04/2017 Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany Advisor: Walter Thiel. Research focus: Application of semiempirical methods to electronically excited states of organic and biomolecules. Benchmarks of linear-response and semiempirical methods for excited states and conical intersections. Trajectory-surface-hopping nonadiabatic dynamics simulations of biomolecules. Education 04/2014 Technische Universität München, Garching, Germany: conferment of Dr. rer. nat. degree. Grade: summa cum laude (“with highest distinction”). 01/2010–04/2014 Technische Universität München, Garching, Germany: doctoral student. Advisor: Wolfgang Domcke. Title of thesis: “Quantum-Chemical Deniz Tuna – page 1 Investigations into the Photophysics and Photochemistry of Bioorganic Molecules”. 12/2009 Philipps-Universität Marburg, Marburg, Germany: conferment of “Diplom-Chemiker” degree. Grade: 1.1 (on a scale from 1.0 to 5.0 with 1.0 being the best possible grade). 03/2009–12/2009 Technische Universität München, Garching, Germany: research for diploma thesis. Advisor: Wolfgang Domcke. First examiner at Philipps- Universität Marburg: Gernot Frenking. 10/2007–03/2008 Heriot-Watt University, Edinburgh, Scotland, UK: study-abroad semester. Research project (six months) in computational chemistry. Supervisor: Stuart A. Macgregor. Resulted in publication no. 1. 04/2006–02/2009 Philipps-Universität Marburg, Marburg, Germany: main-study period in Chemistry.