Science.gov

Sample records for quantum chemistry

  1. Computational quantum chemistry website

    SciTech Connect

    1997-08-22

    This report contains the contents of a web page related to research on the development of quantum chemistry methods for computational thermochemistry and the application of quantum chemistry methods to problems in material chemistry and chemical sciences. Research programs highlighted include: Gaussian-2 theory; Density functional theory; Molecular sieve materials; Diamond thin-film growth from buckyball precursors; Electronic structure calculations on lithium polymer electrolytes; Long-distance electronic coupling in donor/acceptor molecules; and Computational studies of NOx reactions in radioactive waste storage.

  2. Introducing Relativity into Quantum Chemistry

    ERIC Educational Resources Information Center

    Li, Wai-Kee; Blinder, S. M.

    2011-01-01

    It is not often realized by chemists that the special theory of relativity is behind several aspects of quantum chemistry. The Schrdinger equation itself is based on relations between space-time and energy-momentum four vectors. Electron spin is, of course, the most obvious manifestation of relativity. The chemistry of some heavy elements is…

  3. Remedial Mathematics for Quantum Chemistry

    ERIC Educational Resources Information Center

    Koopman, Lodewijk; Brouwer, Natasa; Heck, Andre; Buma, Wybren Jan

    2008-01-01

    Proper mathematical skills are important for every science course and mathematics-intensive chemistry courses rely on a sound mathematical pre-knowledge. In the first-year quantum chemistry course at this university, it was noticed that many students lack basic mathematical knowledge. To tackle the mathematics problem, a remedial mathematics…

  4. Quantum Chemistry via the Periodic Law.

    ERIC Educational Resources Information Center

    Blinder, S. M.

    1981-01-01

    Describes an approach to quantum mechanics exploiting the periodic structure of the elements as a foundation for the quantum theory of matter. Indicates that a quantum chemistry course can be developed using this approach. (SK)

  5. Understanding Quantum Numbers in General Chemistry Textbooks

    ERIC Educational Resources Information Center

    Niaz, Mansoor; Fernandez, Ramon

    2008-01-01

    Quantum numbers and electron configurations form an important part of the general chemistry curriculum and textbooks. The objectives of this study are: (1) Elaboration of a framework based on the following aspects: (a) Origin of the quantum hypothesis, (b) Alternative interpretations of quantum mechanics, (c) Differentiation between an orbital and…

  6. A Quantum Chemistry Concept Inventory for Physical Chemistry Classes

    ERIC Educational Resources Information Center

    Dick-Perez, Marilu; Luxford, Cynthia J.; Windus, Theresa L.; Holme, Thomas

    2016-01-01

    A 14-item, multiple-choice diagnostic assessment tool, the quantum chemistry concept inventory or QCCI, is presented. Items were developed based on published student misconceptions and content coverage and then piloted and used in advanced physical chemistry undergraduate courses. In addition to the instrument itself, data from both a pretest,…

  7. Adiabatic Quantum Simulation of Quantum Chemistry

    PubMed Central

    Babbush, Ryan; Love, Peter J.; Aspuru-Guzik, Alán

    2014-01-01

    We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2-body qubit Hamiltonians with a small set of physically realizable couplings. By combining the Bravyi-Kitaev construction to map fermions to qubits with perturbative gadgets to reduce the Hamiltonian to 2-body, we obtain precision requirements on the coupling strengths and a number of ancilla qubits that scale polynomially in the problem size. Hence our mapping is efficient. The required set of controllable interactions includes only two types of interaction beyond the Ising interactions required to apply the quantum adiabatic algorithm to combinatorial optimization problems. Our mapping may also be of interest to chemists directly as it defines a dictionary from electronic structure to spin Hamiltonians with physical interactions. PMID:25308187

  8. Algorithms Bridging Quantum Computation and Chemistry

    NASA Astrophysics Data System (ADS)

    McClean, Jarrod Ryan

    The design of new materials and chemicals derived entirely from computation has long been a goal of computational chemistry, and the governing equation whose solution would permit this dream is known. Unfortunately, the exact solution to this equation has been far too expensive and clever approximations fail in critical situations. Quantum computers offer a novel solution to this problem. In this work, we develop not only new algorithms to use quantum computers to study hard problems in chemistry, but also explore how such algorithms can help us to better understand and improve our traditional approaches. In particular, we first introduce a new method, the variational quantum eigensolver, which is designed to maximally utilize the quantum resources available in a device to solve chemical problems. We apply this method in a real quantum photonic device in the lab to study the dissociation of the helium hydride (HeH+) molecule. We also enhance this methodology with architecture specific optimizations on ion trap computers and show how linear-scaling techniques from traditional quantum chemistry can be used to improve the outlook of similar algorithms on quantum computers. We then show how studying quantum algorithms such as these can be used to understand and enhance the development of classical algorithms. In particular we use a tool from adiabatic quantum computation, Feynman's Clock, to develop a new discrete time variational principle and further establish a connection between real-time quantum dynamics and ground state eigenvalue problems. We use these tools to develop two novel parallel-in-time quantum algorithms that outperform competitive algorithms as well as offer new insights into the connection between the fermion sign problem of ground states and the dynamical sign problem of quantum dynamics. Finally we use insights gained in the study of quantum circuits to explore a general notion of sparsity in many-body quantum systems. In particular we use

  9. Quantum theory and chemistry: Two propositions

    NASA Technical Reports Server (NTRS)

    Aronowitz, S.

    1980-01-01

    Two propositions concerning quantum chemistry are proposed. First, it is proposed that the nonrelativistic Schroedinger equation, where the Hamiltonian operator is associated with an assemblage of nuclei and electrons, can never be arranged to yield specific molecules in the chemists' sense. It is argued that this result is a necessary condition if the Schroedinger has relevancy to chemistry. Second, once a system is in a particular state with regard to interactions among its components (the assemblage of nuclei and electrons), it cannot spontaneously eliminate any of those interactions. This leads to a subtle form of irreversibility.

  10. Quantum chemistry of macromolecular shape

    NASA Astrophysics Data System (ADS)

    Mezey, Paul G.

    Some of the new developments in the quantum-chemical study of macromolecular shapes are reviewed, with special emphasis on the additive fuzzy electron density fragmentation methods and on the algebraic-topological shape group analysis of global and local shape features of fuzzy three-dimensional bodies of electron densities of macromolecules. Earlier applications of these methods to actual macromolecules are reviewed, including studies on the anticancer drug taxol, the proteins bovine insulin and HIV protease, and other macromolecules. The results of test calculations establishing the accuracy of these methods are also reviewed. The spherically weighted affine transformation technique is described and proposed for the deformation of electron densities approximating the changes occurring in small conformational displacements of atomic nuclei in macromolecules.

  11. Faster quantum chemistry simulation on fault-tolerant quantum computers

    NASA Astrophysics Data System (ADS)

    Cody Jones, N.; Whitfield, James D.; McMahon, Peter L.; Yung, Man-Hong; Van Meter, Rodney; Aspuru-Guzik, Alán; Yamamoto, Yoshihisa

    2012-11-01

    Quantum computers can in principle simulate quantum physics exponentially faster than their classical counterparts, but some technical hurdles remain. We propose methods which substantially improve the performance of a particular form of simulation, ab initio quantum chemistry, on fault-tolerant quantum computers; these methods generalize readily to other quantum simulation problems. Quantum teleportation plays a key role in these improvements and is used extensively as a computing resource. To improve execution time, we examine techniques for constructing arbitrary gates which perform substantially faster than circuits based on the conventional Solovay-Kitaev algorithm (Dawson and Nielsen 2006 Quantum Inform. Comput. 6 81). For a given approximation error ɛ, arbitrary single-qubit gates can be produced fault-tolerantly and using a restricted set of gates in time which is O(log ɛ) or O(log log ɛ) with sufficient parallel preparation of ancillas, constant average depth is possible using a method we call programmable ancilla rotations. Moreover, we construct and analyze efficient implementations of first- and second-quantized simulation algorithms using the fault-tolerant arbitrary gates and other techniques, such as implementing various subroutines in constant time. A specific example we analyze is the ground-state energy calculation for lithium hydride.

  12. Quantum Dots: An Experiment for Physical or Materials Chemistry

    ERIC Educational Resources Information Center

    Winkler, L. D.; Arceo, J. F.; Hughes, W. C.; DeGraff, B. A.; Augustine, B. H.

    2005-01-01

    An experiment is conducted for obtaining quantum dots for physical or materials chemistry. This experiment serves to both reinforce the basic concept of quantum confinement and providing a useful bridge between the molecular and solid-state world.

  13. Quantum Chemistry in Great Britain: Developing a Mathematical Framework for Quantum Chemistry

    NASA Astrophysics Data System (ADS)

    Simões, Ana; Gavroglu, Kostas

    By 1935 quantum chemistry was already delineated as a distinct sub-discipline due to the contributions of Fritz London, Walter Heitler, Friedrich Hund, Erich Hückel, Robert Mulliken, Linus Pauling, John van Vleck and John Slater. These people are credited with showing that the application of quantum mechanics to the solution of chemical problems was, indeed, possible, especially so after the introduction of a number of new concepts and the adoption of certain approximation methods. And though a number of chemists had started talking of the formation of theoretical or, even, mathematical chemistry, a fully developed mathematical framework of quantum chemistry was still wanting. The work of three persons in particular-of John E. Lennard-Jones, Douglas R. Hartree, and Charles Alfred Coulson-has been absolutely crucial in the development of such a framework. In this paper we shall discuss the work of these three researchers who started their careers in the Cambridge tradition of mathematical physics and who at some point of their careers all became professors of applied mathematics. We shall argue that their work consisted of decisive contributions to the development of such a mathematical framework for quantum chemistry.

  14. Experimental study of quantum simulation for quantum chemistry with a nuclear magnetic resonance simulator.

    PubMed

    Lu, Dawei; Xu, Nanyang; Xu, Boruo; Li, Zhaokai; Chen, Hongwei; Peng, Xinhua; Xu, Ruixue; Du, Jiangfeng

    2012-10-13

    Quantum computers have been proved to be able to mimic quantum systems efficiently in polynomial time. Quantum chemistry problems, such as static molecular energy calculations and dynamical chemical reaction simulations, become very intractable on classical computers with scaling up of the system. Therefore, quantum simulation is a feasible and effective approach to tackle quantum chemistry problems. Proof-of-principle experiments have been implemented on the calculation of the hydrogen molecular energies and one-dimensional chemical isomerization reaction dynamics using nuclear magnetic resonance systems. We conclude that quantum simulation will surpass classical computers for quantum chemistry in the near future. PMID:22946038

  15. Alternative algebraic approaches in quantum chemistry

    SciTech Connect

    Mezey, Paul G.

    2015-01-22

    Various algebraic approaches of quantum chemistry all follow a common principle: the fundamental properties and interrelations providing the most essential features of a quantum chemical representation of a molecule or a chemical process, such as a reaction, can always be described by algebraic methods. Whereas such algebraic methods often provide precise, even numerical answers, nevertheless their main role is to give a framework that can be elaborated and converted into computational methods by involving alternative mathematical techniques, subject to the constraints and directions provided by algebra. In general, algebra describes sets of interrelations, often phrased in terms of algebraic operations, without much concern with the actual entities exhibiting these interrelations. However, in many instances, the very realizations of two, seemingly unrelated algebraic structures by actual quantum chemical entities or properties play additional roles, and unexpected connections between different algebraic structures are often giving new insight. Here we shall be concerned with two alternative algebraic structures: the fundamental group of reaction mechanisms, based on the energy-dependent topology of potential energy surfaces, and the interrelations among point symmetry groups for various distorted nuclear arrangements of molecules. These two, distinct algebraic structures provide interesting interrelations, which can be exploited in actual studies of molecular conformational and reaction processes. Two relevant theorems will be discussed.

  16. Disciplines, models, and computers: the path to computational quantum chemistry.

    PubMed

    Lenhard, Johannes

    2014-12-01

    Many disciplines and scientific fields have undergone a computational turn in the past several decades. This paper analyzes this sort of turn by investigating the case of computational quantum chemistry. The main claim is that the transformation from quantum to computational quantum chemistry involved changes in three dimensions. First, on the side of instrumentation, small computers and a networked infrastructure took over the lead from centralized mainframe architecture. Second, a new conception of computational modeling became feasible and assumed a crucial role. And third, the field of computa- tional quantum chemistry became organized in a market-like fashion and this market is much bigger than the number of quantum theory experts. These claims will be substantiated by an investigation of the so-called density functional theory (DFT), the arguably pivotal theory in the turn to computational quantum chemistry around 1990. PMID:25571750

  17. Steps toward fault-tolerant quantum chemistry.

    SciTech Connect

    Taube, Andrew Garvin

    2010-05-01

    Developing quantum chemistry programs on the coming generation of exascale computers will be a difficult task. The programs will need to be fault-tolerant and minimize the use of global operations. This work explores the use a task-based model that uses a data-centric approach to allocate work to different processes as it applies to quantum chemistry. After introducing the key problems that appear when trying to parallelize a complicated quantum chemistry method such as coupled-cluster theory, we discuss the implications of that model as it pertains to the computational kernel of a coupled-cluster program - matrix multiplication. Also, we discuss the extensions that would required to build a full coupled-cluster program using the task-based model. Current programming models for high-performance computing are fault-intolerant and use global operations. Those properties are unsustainable as computers scale to millions of CPUs; instead one must recognize that these systems will be hierarchical in structure, prone to constant faults, and global operations will be infeasible. The FAST-OS HARE project is introducing a scale-free computing model to address these issues. This model is hierarchical and fault-tolerant by design, allows for the clean overlap of computation and communication, reducing the network load, does not require checkpointing, and avoids the complexity of many HPC runtimes. Development of an algorithm within this model requires a change in focus from imperative programming to a data-centric approach. Quantum chemistry (QC) algorithms, in particular electronic structure methods, are an ideal test bed for this computing model. These methods describe the distribution of electrons in a molecule, which determine the properties of the molecule. The computational cost of these methods is high, scaling quartically or higher in the size of the molecule, which is why QC applications are major users of HPC resources. The complexity of these algorithms means that

  18. Quantum chemistry-assisted synthesis route development

    NASA Astrophysics Data System (ADS)

    Hori, Kenji; Sumimoto, Michinori; Murafuji, Toshihiro

    2015-12-01

    We have been investigating "quantum chemistry-assisted synthesis route development" using in silico screenings and applied the method to several targets. Another example was conducted to develop synthesis routes for a urea derivative, namely 1-(4-(trifluoromethyl)-2-oxo-2H-chromen-7-yl)urea. While five synthesis routes were examined, only three routes passed the second in silico screening. Among them, the reaction of 7-amino-4-(trifluoromethyl)-2H-chromen-2-one and O-methyl carbamate with BF3 as an additive was ranked as the first choice for synthetic work. We were able to experimentally obtain the target compound even though its yield was as low as 21 %. The theoretical result was thus consistent with that observed. The summary of transition state data base (TSDB) is also provided. TSDB is the key to reducing time of in silico screenings.

  19. Quantum chemistry-assisted synthesis route development

    SciTech Connect

    Hori, Kenji; Sumimoto, Michinori; Murafuji, Toshihiro

    2015-12-31

    We have been investigating “quantum chemistry-assisted synthesis route development” using in silico screenings and applied the method to several targets. Another example was conducted to develop synthesis routes for a urea derivative, namely 1-(4-(trifluoromethyl)-2-oxo-2H-chromen-7-yl)urea. While five synthesis routes were examined, only three routes passed the second in silico screening. Among them, the reaction of 7-amino-4-(trifluoromethyl)-2H-chromen-2-one and O-methyl carbamate with BF{sub 3} as an additive was ranked as the first choice for synthetic work. We were able to experimentally obtain the target compound even though its yield was as low as 21 %. The theoretical result was thus consistent with that observed. The summary of transition state data base (TSDB) is also provided. TSDB is the key to reducing time of in silico screenings.

  20. PyADF--a scripting framework for multiscale quantum chemistry.

    PubMed

    Jacob, Christoph R; Beyhan, S Maya; Bulo, Rosa E; Gomes, André Severo Pereira; Götz, Andreas W; Kiewisch, Karin; Sikkema, Jetze; Visscher, Lucas

    2011-07-30

    Applications of quantum chemistry have evolved from single or a few calculations to more complicated workflows, in which a series of interrelated computational tasks is performed. In particular multiscale simulations, which combine different levels of accuracy, typically require a large number of individual calculations that depend on each other. Consequently, there is a need to automate such workflows. For this purpose we have developed PYADF, a scripting framework for quantum chemistry. PYADF handles all steps necessary in a typical workflow in quantum chemistry and is easily extensible due to its object-oriented implementation in the Python programming language. We give an overview of the capabilities of PYADF and illustrate its usefulness in quantum-chemical multiscale simulations with a number of examples taken from recent applications. PMID:21541961

  1. Quantum chemistry and charge transport in biomolecules with superconducting circuits

    PubMed Central

    García-Álvarez, L.; Las Heras, U.; Mezzacapo, A.; Sanz, M.; Solano, E.; Lamata, L.

    2016-01-01

    We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects. PMID:27324814

  2. Quantum chemistry and charge transport in biomolecules with superconducting circuits

    NASA Astrophysics Data System (ADS)

    García-Álvarez, L.; Las Heras, U.; Mezzacapo, A.; Sanz, M.; Solano, E.; Lamata, L.

    2016-06-01

    We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects.

  3. Quantum chemistry and charge transport in biomolecules with superconducting circuits.

    PubMed

    García-Álvarez, L; Las Heras, U; Mezzacapo, A; Sanz, M; Solano, E; Lamata, L

    2016-01-01

    We propose an efficient protocol for digital quantum simulation of quantum chemistry problems and enhanced digital-analog quantum simulation of transport phenomena in biomolecules with superconducting circuits. Along these lines, we optimally digitize fermionic models of molecular structure with single-qubit and two-qubit gates, by means of Trotter-Suzuki decomposition and Jordan-Wigner transformation. Furthermore, we address the modelling of system-environment interactions of biomolecules involving bosonic degrees of freedom with a digital-analog approach. Finally, we consider gate-truncated quantum algorithms to allow the study of environmental effects. PMID:27324814

  4. Quantum Mechanics in Chemistry (by Jack Simons and Jeff Nichols)

    NASA Astrophysics Data System (ADS)

    McCallum, C. Michael

    1998-12-01

    Topics in Physical Chemistry Series. Oxford University Press: New York, 1997. xxiii + 612 pp. Illustrations. ISBN 0-19-508200-1. $75.00. One of the problems faced by graduate-level quantum mechanics courses in chemistry is that there is often little time for studying chemical problems. Students must learn so much matrix algebra and notation that a first-semester course seems more like a math or physics course than chemistry. Another problem is the focus of most graduate texts. Excellent texts, such as those by Sakurai, and older treatments, such as Messiah and Cohen-Tannoudji, offer a comprehensive amount of mathematical rigor to go along with chemistry problems, but it seems the intended audience is hard-core theoretical or physical chemistry students. Requirements that are more general, such as reaction-path dynamics, structure and term symbols, and symmetry in quantum mechanical problems, are often left behind. Schatz and Ratner's Book Quantum Mechanics in Chemistry (Prentice Hall) is one book that fills this gap (at least for second-semester students); Simons and Nichols' new book is another, but it is a book that requires revision before it can be seriously considered.

  5. Quantum Mechanics and Conceptual Change in High School Chemistry Textbooks.

    ERIC Educational Resources Information Center

    Shiland, Thomas W.

    1997-01-01

    Examines the presentation of quantum mechanics in eight secondary chemistry texts for elements associated with a conceptual change model: (1) dissatisfaction; (2) intelligibility; (3) plausibility; and (4) fruitfulness. Reports that these elements were not present in sufficient quantities to promote conceptual change. Presents recommendations for…

  6. Ab initio quantum chemistry: Methodology and applications

    PubMed Central

    Friesner, Richard A.

    2005-01-01

    This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller–Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly. PMID:15870212

  7. On the Making of Quantum Chemistry in Germany

    NASA Astrophysics Data System (ADS)

    Karachalios, Andreas

    During the 1990s several historians of science have studied the emergence of quantum chemistry as an autonomous discipline in different national contexts (Nye, 1993; Simões, 1993; Simões, forthcoming; Gavroglu and Simões, 1994; Karachalios, 1997a). Beyond these disciplinary studies, a number of contributions to special aspects of this theme have appeared (Schweber, 1990; Gavroglu, 1995; Simões and Gavroglu, 1997, 1999a,b; Schwarz et al., 1999). In this literature the birth of quantum chemistry has generally been associated with two dates: the 1927 paper of Walter Heitler and Fritz London and the year 1931 in which Linus Pauling and John Clarke Slater independently explained the tetrahedral orientation of the four bonds of the carbon atom. To these dates we might also add a third: in 1928 London published a paper, 'Zur Quantentheorie der homöopolaren Valenzzahlen' (London, 1928), in which he gave a quantum mechanical explanation of the classical chemical notion of valency. There he showed a relationship between the valency numbers and the spectroscopical multiplicity, namely that valency=multiplicity-1. This relation established a bridge between physical and chemical facts. Taken together, these developments constitute important events for the international development of quantum chemistry.

  8. Optimizing qubit resources for quantum chemistry simulations in second quantization on a quantum computer

    NASA Astrophysics Data System (ADS)

    Moll, Nikolaj; Fuhrer, Andreas; Staar, Peter; Tavernelli, Ivano

    2016-07-01

    Quantum chemistry simulations on a quantum computer suffer from the overhead needed for encoding the Fermionic problem in a system of qubits. By exploiting the block diagonality of a Fermionic Hamiltonian, we show that the number of required qubits can be reduced while the number of terms in the Hamiltonian will increase. All operations for this reduction can be performed in operator space. The scheme is conceived as a pre-computational step that would be performed prior to the actual quantum simulation. We apply this scheme to reduce the number of qubits necessary to simulate both the Hamiltonian of the two-site Fermi–Hubbard model and the hydrogen molecule. Both quantum systems can then be simulated with a two-qubit quantum computer. Despite the increase in the number of Hamiltonian terms, the scheme still remains a useful tool to reduce the dimensionality of specific quantum systems for quantum simulators with a limited number of resources.

  9. NWChem: Quantum Chemistry Simulations at Scale

    SciTech Connect

    Apra, Edoardo; Kowalski, Karol; Hammond, Jeff R.; Klemm, Michael

    2015-01-17

    Methods based on quantum mechanics equations have been developed since the 1930's with the purpose of accurately studying the electronic structure of molecules. However, it is only during the last two decades that intense development of new computational algorithms has opened the possibility of performing accurate simulations of challenging molecular processes with high-order many-body methods. A wealth of evidence indicates that the proper inclusion of instantaneous interactions between electrons (or the so-called electron correlation effects) is indispensable for the accurate characterization of chemical reactivity, molecular properties, and interactions of light with matter. The availability of reliable methods for benchmarking of medium-size molecular systems provides also a unique chance to propagate high-level accuracy across spatial scales through the multiscale methodologies. Some of these methods have potential to utilize computational resources in an effi*cient way since they are characterized by high numerical complexity and appropriate level of data granularity, which can be effi*ciently distributed over multi-processor architectures. The broad spectrum of coupled cluster (CC) methods falls into this class of methodologies. Several recent CC implementations clearly demonstrated the scalability of CC formalisms on architectures composed of hundreds thousand computational cores. In this context NWChem provides a collection of Tensor Contraction Engine (TCE) generated parallel implementations of various coupled cluster methods capable of taking advantage of many thousand of cores on leadership class parallel architectures.

  10. The Dalton quantum chemistry program system.

    PubMed

    Aidas, Kestutis; Angeli, Celestino; Bak, Keld L; Bakken, Vebjørn; Bast, Radovan; Boman, Linus; Christiansen, Ove; Cimiraglia, Renzo; Coriani, Sonia; Dahle, Pål; Dalskov, Erik K; Ekström, Ulf; Enevoldsen, Thomas; Eriksen, Janus J; Ettenhuber, Patrick; Fernández, Berta; Ferrighi, Lara; Fliegl, Heike; Frediani, Luca; Hald, Kasper; Halkier, Asger; Hättig, Christof; Heiberg, Hanne; Helgaker, Trygve; Hennum, Alf Christian; Hettema, Hinne; Hjertenæs, Eirik; Høst, Stinne; Høyvik, Ida-Marie; Iozzi, Maria Francesca; Jansík, Branislav; Jensen, Hans Jørgen Aa; Jonsson, Dan; Jørgensen, Poul; Kauczor, Joanna; Kirpekar, Sheela; Kjærgaard, Thomas; Klopper, Wim; Knecht, Stefan; Kobayashi, Rika; Koch, Henrik; Kongsted, Jacob; Krapp, Andreas; Kristensen, Kasper; Ligabue, Andrea; Lutnæs, Ola B; Melo, Juan I; Mikkelsen, Kurt V; Myhre, Rolf H; Neiss, Christian; Nielsen, Christian B; Norman, Patrick; Olsen, Jeppe; Olsen, Jógvan Magnus H; Osted, Anders; Packer, Martin J; Pawlowski, Filip; Pedersen, Thomas B; Provasi, Patricio F; Reine, Simen; Rinkevicius, Zilvinas; Ruden, Torgeir A; Ruud, Kenneth; Rybkin, Vladimir V; Sałek, Pawel; Samson, Claire C M; de Merás, Alfredo Sánchez; Saue, Trond; Sauer, Stephan P A; Schimmelpfennig, Bernd; Sneskov, Kristian; Steindal, Arnfinn H; Sylvester-Hvid, Kristian O; Taylor, Peter R; Teale, Andrew M; Tellgren, Erik I; Tew, David P; Thorvaldsen, Andreas J; Thøgersen, Lea; Vahtras, Olav; Watson, Mark A; Wilson, David J D; Ziolkowski, Marcin; Agren, Hans

    2014-05-01

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree-Fock, Kohn-Sham, multiconfigurational self-consistent-field, Møller-Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms. PMID:25309629

  11. Bond additivity corrections for quantum chemistry methods

    SciTech Connect

    C. F. Melius; M. D. Allendorf

    1999-04-01

    In the 1980's, the authors developed a bond-additivity correction procedure for quantum chemical calculations called BAC-MP4, which has proven reliable in calculating the thermochemical properties of molecular species, including radicals as well as stable closed-shell species. New Bond Additivity Correction (BAC) methods have been developed for the G2 method, BAC-G2, as well as for a hybrid DFT/MP2 method, BAC-Hybrid. These BAC methods use a new form of BAC corrections, involving atomic, molecular, and bond-wise additive terms. These terms enable one to treat positive and negative ions as well as neutrals. The BAC-G2 method reduces errors in the G2 method due to nearest-neighbor bonds. The parameters within the BAC-G2 method only depend on atom types. Thus the BAC-G2 method can be used to determine the parameters needed by BAC methods involving lower levels of theory, such as BAC-Hybrid and BAC-MP4. The BAC-Hybrid method should scale well for large molecules. The BAC-Hybrid method uses the differences between the DFT and MP2 as an indicator of the method's accuracy, while the BAC-G2 method uses its internal methods (G1 and G2MP2) to provide an indicator of its accuracy. Indications of the average error as well as worst cases are provided for each of the BAC methods.

  12. The Dalton quantum chemistry program system

    PubMed Central

    Aidas, Kestutis; Angeli, Celestino; Bak, Keld L; Bakken, Vebjørn; Bast, Radovan; Boman, Linus; Christiansen, Ove; Cimiraglia, Renzo; Coriani, Sonia; Dahle, Pål; Dalskov, Erik K; Ekström, Ulf; Enevoldsen, Thomas; Eriksen, Janus J; Ettenhuber, Patrick; Fernández, Berta; Ferrighi, Lara; Fliegl, Heike; Frediani, Luca; Hald, Kasper; Halkier, Asger; Hättig, Christof; Heiberg, Hanne; Helgaker, Trygve; Hennum, Alf Christian; Hettema, Hinne; Hjertenæs, Eirik; Høst, Stinne; Høyvik, Ida-Marie; Iozzi, Maria Francesca; Jansík, Branislav; Jensen, Hans Jørgen Aa; Jonsson, Dan; Jørgensen, Poul; Kauczor, Joanna; Kirpekar, Sheela; Kjærgaard, Thomas; Klopper, Wim; Knecht, Stefan; Kobayashi, Rika; Koch, Henrik; Kongsted, Jacob; Krapp, Andreas; Kristensen, Kasper; Ligabue, Andrea; Lutnæs, Ola B; Melo, Juan I; Mikkelsen, Kurt V; Myhre, Rolf H; Neiss, Christian; Nielsen, Christian B; Norman, Patrick; Olsen, Jeppe; Olsen, Jógvan Magnus H; Osted, Anders; Packer, Martin J; Pawlowski, Filip; Pedersen, Thomas B; Provasi, Patricio F; Reine, Simen; Rinkevicius, Zilvinas; Ruden, Torgeir A; Ruud, Kenneth; Rybkin, Vladimir V; Sałek, Pawel; Samson, Claire C M; de Merás, Alfredo Sánchez; Saue, Trond; Sauer, Stephan P A; Schimmelpfennig, Bernd; Sneskov, Kristian; Steindal, Arnfinn H; Sylvester-Hvid, Kristian O; Taylor, Peter R; Teale, Andrew M; Tellgren, Erik I; Tew, David P; Thorvaldsen, Andreas J; Thøgersen, Lea; Vahtras, Olav; Watson, Mark A; Wilson, David J D; Ziolkowski, Marcin; Ågren, Hans

    2014-01-01

    Dalton is a powerful general-purpose program system for the study of molecular electronic structure at the Hartree–Fock, Kohn–Sham, multiconfigurational self-consistent-field, Møller–Plesset, configuration-interaction, and coupled-cluster levels of theory. Apart from the total energy, a wide variety of molecular properties may be calculated using these electronic-structure models. Molecular gradients and Hessians are available for geometry optimizations, molecular dynamics, and vibrational studies, whereas magnetic resonance and optical activity can be studied in a gauge-origin-invariant manner. Frequency-dependent molecular properties can be calculated using linear, quadratic, and cubic response theory. A large number of singlet and triplet perturbation operators are available for the study of one-, two-, and three-photon processes. Environmental effects may be included using various dielectric-medium and quantum-mechanics/molecular-mechanics models. Large molecules may be studied using linear-scaling and massively parallel algorithms. Dalton is distributed at no cost from http://www.daltonprogram.org for a number of UNIX platforms. PMID:25309629

  13. Block-adaptive quantum mechanics: an adaptive divide-and-conquer approach to interactive quantum chemistry.

    PubMed

    Bosson, Maël; Grudinin, Sergei; Redon, Stephane

    2013-03-01

    We present a novel Block-Adaptive Quantum Mechanics (BAQM) approach to interactive quantum chemistry. Although quantum chemistry models are known to be computationally demanding, we achieve interactive rates by focusing computational resources on the most active parts of the system. BAQM is based on a divide-and-conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. As a result, each time step may be performed significantly faster, which in turn may accelerate attraction to the neighboring local minima. By applying our approach to the nonself-consistent Atom Superposition and Electron Delocalization Molecular Orbital theory, we demonstrate interactive rates and efficient virtual prototyping for systems containing more than a thousand of atoms on a standard desktop computer. PMID:23108532

  14. The implementation of ab initio quantum chemistry calculations on transporters.

    PubMed

    Cooper, M D; Hillier, I H

    1991-06-01

    The RHF and geometry optimization sections of the ab initio quantum chemistry code, GAMESS, have been optimized for a network of parallel microprocessors, Inmos T800-20 transputers, using both indirect and direct SCF techniques. The results indicate great scope for implementation of such codes on small parallel computer systems, very high efficiencies having been achieved, particularly in the cases of direct SCF and geometry optimization with large basis sets. The work, although performed upon one particular parallel system, the Meiko Computing Surface, is applicable to a wide range of parallel systems with both shared and distributed memory. PMID:1919615

  15. Development of massively parallel quantum chemistry program SMASH

    SciTech Connect

    Ishimura, Kazuya

    2015-12-31

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C{sub 150}H{sub 30}){sub 2} with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

  16. Development of massively parallel quantum chemistry program SMASH

    NASA Astrophysics Data System (ADS)

    Ishimura, Kazuya

    2015-12-01

    A massively parallel program for quantum chemistry calculations SMASH was released under the Apache License 2.0 in September 2014. The SMASH program is written in the Fortran90/95 language with MPI and OpenMP standards for parallelization. Frequently used routines, such as one- and two-electron integral calculations, are modularized to make program developments simple. The speed-up of the B3LYP energy calculation for (C150H30)2 with the cc-pVDZ basis set (4500 basis functions) was 50,499 on 98,304 cores of the K computer.

  17. Investigating Multireference Character and Correlation in Quantum Chemistry.

    PubMed

    Coe, J P; Paterson, M J

    2015-09-01

    We review a range of multireference diagnostics for quantum chemistry and discuss them in terms of choices of the molecular orbitals. We show how an approach1 of P.-O. Löwdin can also be viewed as quantifying the electron correlation via the spatial entanglement relative to a single determinant. We consider three example systems from quantum chemistry that exhibit three different combinations of multireference character and correlation: not strongly multireference and not strongly correlated, strongly multireference but not strongly correlated, and strongly multireference together with strong correlation. We find that a multireference measure (MR) does not change substantially with the cutoff used for a Monte Carlo configuration interaction calculation and investigate the effect of using natural orbitals. We see that a coupled-cluster singles and doubles diagnostic and a density-functional theory diagnostic give a correct general prediction of the multireference character for these systems. We also look at the issue of multireference character for a collection of noninteracting hydrogen molecules and the effect of basis size on the multireference character of a stretched hydrogen molecule. PMID:26575914

  18. Applications of Quantum Chemistry to the Study of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard L.

    2005-01-01

    For several years, scientists at NASA Ames have been studying the properties of carbon nanotubes using various experimental and computational methods. In this talk, I will compare different strategies for using quantum chemistry calculations to describe the electronic structure, deformation and chemical functionalization of single wall carbon nanotubes (SWNT) and the physisorption of small molecules on nanotube surfaces. The SWNT can be treated as an infinite (periodic) or finite length carbon cylinder or as a polycyclic aromatic hydrocarbon (PAH) molecule with an imposed curvature maintained by external constraints (as if it were cut out of the SWNT surface). Calculations are carried out using DFT and MP2 methods and a variety of atomic orbital basis sets from minimal (STO-3G) to valence triple zeta. The optimal approach is based on the particular SWNT property of interest. Examples to be discussed include: nanotube fluorination and other functionalization reactions; coating of nanotubes by water vapor and low-molecular weight organic molecules; and the nature of the interface between SWNT and liquids such as water and amines. In many cases, the quantum chemistry calculations are used to parameterize or validate force fields for molecular dynamics simulations. The results of these calculations have helped explain experimental data and contributed to the design of novel materials and sensors based on carbon nanotubes. Some of this research is described in the following papers:

  19. Fuzzy electron density fragments in macromolecular quantum chemistry, combinatorial quantum chemistry, functional group analysis, and shape-activity relations.

    PubMed

    Mezey, Paul G

    2014-09-16

    Conspectus Just as complete molecules have no boundaries and have "fuzzy" electron density clouds approaching zero density exponentially at large distances from the nearest nucleus, a physically justified choice for electron density fragments exhibits similar behavior. Whereas fuzzy electron densities, just as any fuzzy object, such as a thicker cloud on a foggy day, do not lend themselves to easy visualization, one may partially overcome this by using isocontours. Whereas a faithful representation of the complete fuzzy density would need infinitely many such isocontours, nevertheless, by choosing a selected few, one can still obtain a limited pictorial representation. Clearly, such images are of limited value, and one better relies on more complete mathematical representations, using, for example, density matrices of fuzzy fragment densities. A fuzzy density fragmentation can be obtained in an exactly additive way, using the output from any of the common quantum chemical computational techniques, such as Hartree-Fock, MP2, and various density functional approaches. Such "fuzzy" electron density fragments properly represented have proven to be useful in a rather wide range of applications, for example, (a) using them as additive building blocks leading to efficient linear scaling macromolecular quantum chemistry computational techniques, (b) the study of quantum chemical functional groups, (c) using approximate fuzzy fragment information as allowed by the holographic electron density theorem, (d) the study of correlations between local shape and activity, including through-bond and through-space components of interactions between parts of molecules and relations between local molecular shape and substituent effects, (e) using them as tools of density matrix extrapolation in conformational changes, (f) physically valid averaging and statistical distribution of several local electron densities of common stoichiometry, useful in electron density databank mining, for

  20. Quantum-State-Resolved Ion-Molecule Chemistry

    NASA Astrophysics Data System (ADS)

    Chen, Gary; Yang, Tiangang; Campbell, Wesley; Hudson, Eric

    2016-05-01

    We propose a method to achieve quantum-state-resolved ion-molecule chemistry by utilizing cryogenic buffer gas cooling techniques and a combination of ion imaging and mass spectrometry of targets in an RF Paul trap. Cold molecular species produced by a cryogenic buffer gas beam (CBGB) are introduced to target ion species in an linear quadrupole trap (LQT) where ion imaging techniques and time of flight mass spectrometry (ToF) are then used to observe the target ions and the charged reaction products [1,2]. By taking advantage of the large ion-neutral interaction cross sections and characteristically long ion trap lifetimes, we can utilize the precision control over quantum states allowed by an ion trap to resolve state-to-state quantum chemical reactions without high-density molecular sample production, well within proposed capabilities. The combination of these two very general cold species production techniques allows for production and observation of a broad range of ion-neutral reactions. We initially plan to study chemical reactions between sympathetically cooled carbon ions (via laser cooled beryllium ions) with buffer gas cooled water. This work is supported by the US Air Force Office of Scientific Research.

  1. Quantum chemistry structures and properties of 134 kilo molecules.

    PubMed

    Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

    2014-01-01

    Computational de novo design of new drugs and materials requires rigorous and unbiased exploration of chemical compound space. However, large uncharted territories persist due to its size scaling combinatorially with molecular size. We report computed geometric, energetic, electronic, and thermodynamic properties for 134k stable small organic molecules made up of CHONF. These molecules correspond to the subset of all 133,885 species with up to nine heavy atoms (CONF) out of the GDB-17 chemical universe of 166 billion organic molecules. We report geometries minimal in energy, corresponding harmonic frequencies, dipole moments, polarizabilities, along with energies, enthalpies, and free energies of atomization. All properties were calculated at the B3LYP/6-31G(2df,p) level of quantum chemistry. Furthermore, for the predominant stoichiometry, C7H10O2, there are 6,095 constitutional isomers among the 134k molecules. We report energies, enthalpies, and free energies of atomization at the more accurate G4MP2 level of theory for all of them. As such, this data set provides quantum chemical properties for a relevant, consistent, and comprehensive chemical space of small organic molecules. This database may serve the benchmarking of existing methods, development of new methods, such as hybrid quantum mechanics/machine learning, and systematic identification of structure-property relationships. PMID:25977779

  2. Quantum Chemistry for Surface Segregation in Metal Alloys

    SciTech Connect

    Sholl, David

    2006-08-31

    Metal alloys are vital materials for the fabrication of high-flux, high-selectivity hydrogen separation membranes. A phenomenon that occurs in alloys that does not arise in pure metals is surface segregation, where the composition of the surface differs from the bulk composition. Little is known about the strength of surface segregation in the alloys usually considered for hydrogen membranes. Despite this lack of knowledge, surface segregation may play a decisive role in the ability of appropriately chosen alloys to be resistant to chemical poisoning, since membrane poisoning is controlled by surface chemistry. The aim of this Phase I project is to develop quantum chemistry approaches to assess surface segregation in a prototypical hydrogen membrane alloy, fcc Pd{sub 75}Cu{sub 25}. This alloy is known experimentally to have favorable surface properties as a poison resistant H{sub 2} purification membrane (Kamakoti et al., Science 307 (2005) 569-573), but previous efforts at modeling surfaces of this alloy have ignored the possible role of surface segregation (Alfonso et al., Surf. Sci. 546 (2003) 12-26).

  3. Large Scale Electronic Structure Calculations using Quantum Chemistry Methods

    NASA Astrophysics Data System (ADS)

    Scuseria, Gustavo E.

    1998-03-01

    This talk will address our recent efforts in developing fast, linear scaling electronic structure methods for large scale applications. Of special importance is our fast multipole method( M. C. Strain, G. E. Scuseria, and M. J. Frisch, Science 271), 51 (1996). (FMM) for achieving linear scaling for the quantum Coulomb problem (GvFMM), the traditional bottleneck in quantum chemistry calculations based on Gaussian orbitals. Fast quadratures(R. E. Stratmann, G. E. Scuseria, and M. J. Frisch, Chem. Phys. Lett. 257), 213 (1996). combined with methods that avoid the Hamiltonian diagonalization( J. M. Millam and G. E. Scuseria, J. Chem. Phys. 106), 5569 (1997) have resulted in density functional theory (DFT) programs that can be applied to systems containing many hundreds of atoms and ---depending on computational resources or level of theory-- to many thousands of atoms.( A. D. Daniels, J. M. Millam and G. E. Scuseria, J. Chem. Phys. 107), 425 (1997). Three solutions for the diagonalization bottleneck will be analyzed and compared: a conjugate gradient density matrix search (CGDMS), a Hamiltonian polynomial expansion of the density matrix, and a pseudo-diagonalization method. Besides DFT, our near-field exchange method( J. C. Burant, G. E. Scuseria, and M. J. Frisch, J. Chem. Phys. 105), 8969 (1996). for linear scaling Hartree-Fock calculations will be discussed. Based on these improved capabilities, we have also developed programs to obtain vibrational frequencies (via analytic energy second derivatives) and excitation energies (through time-dependent DFT) of large molecules like porphyn or C_70. Our GvFMM has been extended to periodic systems( K. N. Kudin and G. E. Scuseria, Chem. Phys. Lett., in press.) and progress towards a Gaussian-based DFT and HF program for polymers and solids will be reported. Last, we will discuss our progress on a Laplace-transformed \\cal O(N^2) second-order pertubation theory (MP2) method.

  4. Determining the Numerical Stability of Quantum Chemistry Algorithms.

    PubMed

    Knizia, Gerald; Li, Wenbin; Simon, Sven; Werner, Hans-Joachim

    2011-08-01

    We present a simple, broadly applicable method for determining the numerical properties of quantum chemistry algorithms. The method deliberately introduces random numerical noise into computations, which is of the same order of magnitude as the floating point precision. Accordingly, repeated runs of an algorithm give slightly different results, which can be analyzed statistically to obtain precise estimates of its numerical stability. This noise is produced by automatic code injection into regular compiler output, so that no substantial programming effort is required, only a recompilation of the affected program sections. The method is applied to investigate: (i) the numerical stability of the three-center Obara-Saika integral evaluation scheme for high angular momenta, (ii) if coupled cluster perturbative triples can be evaluated with single precision arithmetic, (iii) how to implement the density fitting approximation in Møller-Plesset perturbation theory (MP2) most accurately, and (iv) which parts of density fitted MP2 can be safely evaluated with single precision arithmetic. In the integral case, we find a numerical instability in an equation that is used in almost all integral programs. Due to the results of (ii) and (iv), we conjecture that single precision arithmetic can be applied whenever a calculation is done in an orthogonal basis set and excessively long linear sums are avoided. PMID:26606614

  5. Photoelectron Imaging as a Quantum Chemistry Visualization Tool

    ERIC Educational Resources Information Center

    Grumbling, Emily R.; Pichugin, Kostyantyn; Mabbs, Richard; Sanov, Andrei

    2011-01-01

    An overview and simple example of photoelectron imaging is presented, highlighting its efficacy as a pedagogical tool for visualizing quantum phenomena. Specifically, photoelectron imaging of H[superscript -] (the simplest negative ion) is used to demonstrate several quantum mechanical principles. This example could be incorporated into an…

  6. Linear-scaling and parallelisable algorithms for stochastic quantum chemistry

    NASA Astrophysics Data System (ADS)

    Booth, George H.; Smart, Simon D.; Alavi, Ali

    2014-07-01

    For many decades, quantum chemical method development has been dominated by algorithms which involve increasingly complex series of tensor contractions over one-electron orbital spaces. Procedures for their derivation and implementation have evolved to require the minimum amount of logic and rely heavily on computationally efficient library-based matrix algebra and optimised paging schemes. In this regard, the recent development of exact stochastic quantum chemical algorithms to reduce computational scaling and memory overhead requires a contrasting algorithmic philosophy, but one which when implemented efficiently can achieve higher accuracy/cost ratios with small random errors. Additionally, they can exploit the continuing trend for massive parallelisation which hinders the progress of deterministic high-level quantum chemical algorithms. In the Quantum Monte Carlo community, stochastic algorithms are ubiquitous but the discrete Fock space of quantum chemical methods is often unfamiliar, and the methods introduce new concepts required for algorithmic efficiency. In this paper, we explore these concepts and detail an algorithm used for Full Configuration Interaction Quantum Monte Carlo (FCIQMC), which is implemented and available in MOLPRO and as a standalone code, and is designed for high-level parallelism and linear-scaling with walker number. Many of the algorithms are also in use in, or can be transferred to, other stochastic quantum chemical methods and implementations. We apply these algorithms to the strongly correlated chromium dimer to demonstrate their efficiency and parallelism.

  7. Students' Levels of Explanations, Models, and Misconceptions in Basic Quantum Chemistry: A Phenomenographic Study

    ERIC Educational Resources Information Center

    Stefani, Christina; Tsaparlis, Georgios

    2009-01-01

    We investigated students' knowledge constructions of basic quantum chemistry concepts, namely atomic orbitals, the Schrodinger equation, molecular orbitals, hybridization, and chemical bonding. Ausubel's theory of meaningful learning provided the theoretical framework and phenomenography the method of analysis. The semi-structured interview with…

  8. Molecular Orbitals of NO, NO[superscript+], and NO[superscript-]: A Computational Quantum Chemistry Experiment

    ERIC Educational Resources Information Center

    Orenha, Renato P.; Galembeck, Sérgio E.

    2014-01-01

    This computational experiment presents qualitative molecular orbital (QMO) and computational quantum chemistry exercises of NO, NO[superscript+], and NO[superscript-]. Initially students explore several properties of the target molecules by Lewis diagrams and the QMO theory. Then, they compare qualitative conclusions with EHT and DFT calculations…

  9. The Relationships between PCK Components: The Case of Quantum Chemistry Professors

    ERIC Educational Resources Information Center

    Padilla, Kira; Van Driel, Jan

    2011-01-01

    The purpose of this paper is to capture the pedagogical content knowledge (PCK) of university professors about quantum chemistry. More specifically, we aimed to identify and analyze relationships between specific PCK components, using an adapted version of the model of PCK of Magnusson "et al.". A sample of university professors (n = 6) who teach…

  10. Interval Prediction of Molecular Properties in Parametrized Quantum Chemistry

    NASA Astrophysics Data System (ADS)

    Edwards, David E.; Zubarev, Dmitry Yu.; Packard, Andrew; Lester, William A.; Frenklach, Michael

    2014-06-01

    The accurate evaluation of molecular properties lies at the core of predictive physical models. Most reliable quantum-chemical calculations are limited to smaller molecular systems while purely empirical approaches are limited in accuracy and reliability. A promising approach is to employ a quantum-mechanical formalism with simplifications and to compensate for the latter with parametrization. We propose a strategy of directly predicting the uncertainty interval for a property of interest, based on training-data uncertainties, which sidesteps the need for an optimum set of parameters.

  11. FORTRAN interface for code interoperability in quantum chemistry: the Q5Cost library.

    PubMed

    Borini, S; Monari, A; Rossi, E; Tajti, A; Angeli, C; Bendazzoli, G L; Cimiraglia, R; Emerson, A; Evangelisti, S; Maynau, D; Sanchez-Marin, J; Szalay, P G

    2007-01-01

    Ab initio quantum-chemistry programs produce and use large amounts of data, which are usually stored on disk in the form of binary files. A FORTRAN library, named Q5Cost, has been designed and implemented in order to allow the storage of these data sets in a special data format built with the HDF5 technology. This data format allows the data to be represented as tree structures and is portable between different platforms and operating systems, making code interoperability and communication much easier. The libraries have been used to build many interfaces among different quantum chemistry codes, and the first scientific applications have been realized. This activity was carried out within the COST in Chemistry D23 project "MetaChem", in the Working Group "A meta-laboratory for code integration in ab initio methods". PMID:17492830

  12. Communication: Test of quantum chemistry in vibrationally hot hydrogen molecules

    NASA Astrophysics Data System (ADS)

    Niu, M. L.; Salumbides, E. J.; Ubachs, W.

    2015-08-01

    Precision measurements are performed on highly excited vibrational quantum states of molecular hydrogen. The v = 12, J = 0 - 3 rovibrational levels of H2 ( X 1 Σg + ), lying only 2000 cm-1 below the first dissociation limit, were populated by photodissociation of H2S and their level energies were accurately determined by two-photon Doppler-free spectroscopy. A comparison between the experimental results on v = 12 level energies with the best ab initio calculations shows a good agreement, where the present experimental accuracy of 3.5 × 10-3 cm-1 is more precise than theory, hence providing a gateway to further test theoretical advances in this benchmark quantum system.

  13. Implementation of replica-exchange umbrella sampling in the DFTB + semiempirical quantum chemistry package

    NASA Astrophysics Data System (ADS)

    Ito, Shingo; Irle, Stephan; Okamoto, Yuko

    2016-07-01

    The replica-exchange umbrella sampling (REUS) method combines replica-exchange and umbrella sampling methods and allows larger conformational sampling than conventional simulation methods. This method has been used in many studies to understand docking mechanisms and the functions of molecules. However, REUS has not been combined with quantum chemical codes. Therefore, we implemented the REUS simulation technique in the DFTB + quantum chemistry code utilizing approximate density functional theory. We performed REUS simulations of an intra-molecular proton transfer reaction of malonaldehyde and a formation of a phthalocyanine from four phthalonitriles and one iron atom to validate the reliability of our implemented REUS-DFTB + combination.

  14. Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

  15. Low frequency internal vibrations of norbornane and its derivatives studied by IINS and quantum chemistry calculations

    SciTech Connect

    Holderna-Natkaniec, K.; Natkaniec, I.; Khavryutchenko, V. D.

    1999-06-15

    The observed and calculated INS vibrational densities of states for globular molecules of norbornane, norborneole and borneole are compared in the frequency range up to 600 cm{sup -1}. Inelastic incoherent neutron scattering (IINS) spectra were measured at ca. 20 K on the high resolution NERA spectrometer at the IBR-2 pulsed reactor. The IINS intensities were calculated by semi-empirical quantum chemistry method and the assignments of the low-frequency internal modes were proposed.

  16. Generating Efficient Quantum Chemistry Codes for Novel Architectures.

    PubMed

    Titov, Alexey V; Ufimtsev, Ivan S; Luehr, Nathan; Martinez, Todd J

    2013-01-01

    We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures. PMID:26589024

  17. Quantum chemistry of the minimal CdSe clusters

    NASA Astrophysics Data System (ADS)

    Yang, Ping; Tretiak, Sergei; Masunov, Artëm E.; Ivanov, Sergei

    2008-08-01

    Colloidal quantum dots are semiconductor nanocrystals (NCs) which have stimulated a great deal of research and have attracted technical interest in recent years due to their chemical stability and the tunability of photophysical properties. While internal structure of large quantum dots is similar to bulk, their surface structure and passivating role of capping ligands (surfactants) are not fully understood to date. We apply ab initio wavefunction methods, density functional theory, and semiempirical approaches to study the passivation effects of substituted phosphine and amine ligands on the minimal cluster Cd2Se2, which is also used to benchmark different computational methods versus high level ab initio techniques. Full geometry optimization of Cd2Se2 at different theory levels and ligand coverage is used to understand the affinities of various ligands and the impact of ligands on cluster structure. Most possible bonding patterns between ligands and surface Cd/Se atoms are considered, including a ligand coordinated to Se atoms. The degree of passivation of Cd and Se atoms (one or two ligands attached to one atom) is also studied. The results suggest that B3LYP/LANL2DZ level of theory is appropriate for the system modeling, whereas frequently used semiempirical methods (such as AM1 and PM3) produce unphysical results. The use of hydrogen atom for modeling of the cluster passivating ligands is found to yield unphysical results as well. Hence, the surface termination of II-VI semiconductor NCs with hydrogen atoms often used in computational models should probably be avoided. Basis set superposition error, zero-point energy, and thermal corrections, as well as solvent effects simulated with polarized continuum model are found to produce minor variations on the ligand binding energies. The effects of Cd-Se complex structure on both the electronic band gap (highest occupied molecular orbital-lowest unoccupied molecular orbital energy difference) and ligand binding

  18. Photodissociation of quantum state-selected diatomic molecules yields new insight into ultracold chemistry

    NASA Astrophysics Data System (ADS)

    McDonald, Mickey; McGuyer, Bart H.; Lee, Chih-Hsi; Apfelbeck, Florian; Zelevinsky, Tanya

    2016-05-01

    When a molecule is subjected to a sufficiently energetic photon it can break apart into fragments through a process called ``photodissociation''. For over 70 years this simple chemical reaction has served as a vital experimental tool for acquiring information about molecular structure, since the character of the photodissociative transition can be inferred by measuring the 3D photofragment angular distribution (PAD). While theoretical understanding of this process has gradually evolved from classical considerations to a fully quantum approach, experiments to date have not yet revealed the full quantum nature of this process. In my talk I will describe recent experiments involving the photodissociation of ultracold, optical lattice-trapped, and fully quantum state-resolved 88Sr2 molecules. Optical absorption images of the PADs produced in these experiments reveal features which are inherently quantum mechanical in nature, such as matter-wave interference between output channels, and are sensitive to the quantum statistics of the molecular wavefunctions. The results of these experiments cannot be predicted using quasiclassical methods. Instead, we describe our results with a fully quantum mechanical model yielding new intuition about ultracold chemistry.

  19. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters.

    PubMed

    Turi, László

    2016-04-21

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory(DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavitystructure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model. PMID:27389224

  20. On the applicability of one- and many-electron quantum chemistry models for hydrated electron clusters

    NASA Astrophysics Data System (ADS)

    Turi, László

    2016-04-01

    We evaluate the applicability of a hierarchy of quantum models in characterizing the binding energy of excess electrons to water clusters. In particular, we calculate the vertical detachment energy of an excess electron from water cluster anions with methods that include one-electron pseudopotential calculations, density functional theory (DFT) based calculations, and ab initio quantum chemistry using MP2 and eom-EA-CCSD levels of theory. The examined clusters range from the smallest cluster size (n = 2) up to nearly nanosize clusters with n = 1000 molecules. The examined cluster configurations are extracted from mixed quantum-classical molecular dynamics trajectories of cluster anions with n = 1000 water molecules using two different one-electron pseudopotenial models. We find that while MP2 calculations with large diffuse basis set provide a reasonable description for the hydrated electron system, DFT methods should be used with precaution and only after careful benchmarking. Strictly tested one-electron psudopotentials can still be considered as reasonable alternatives to DFT methods, especially in large systems. The results of quantum chemistry calculations performed on configurations, that represent possible excess electron binding motifs in the clusters, appear to be consistent with the results using a cavity structure preferring one-electron pseudopotential for the hydrated electron, while they are in sharp disagreement with the structural predictions of a non-cavity model.

  1. Comparing intracellular stability and targeting of sulfobetaine quantum dots with other surface chemistries in live cells.

    PubMed

    Muro, Eleonora; Fragola, Alexandra; Pons, Thomas; Lequeux, Nicolas; Ioannou, Andriani; Skourides, Paris; Dubertret, Benoit

    2012-04-10

    The in vivo labeling of intracellular components with quantum dots (QDs) is very limited because of QD aggregation in the cell cytoplasm and/or QD confinement into lysosomal compartments. In order to improve intracellular targeting with QDs, various surface chemistries and delivery methods have been explored, but they have not yet been compared systematically with respect to the QD intracellular stability. In this work, the intracellular aggregation kinetics of QDs for three different surface chemistries based on ligand exchange or encapsulation with amphiphilic polymers are compared. For each surface chemistry, three delivery methods for bringing the nanoparticles into the cells are compared: electroporation, microinjection, and pinocytosis. It is concluded that the QD intracellular aggregation behavior is strongly dependent on the surface chemistry. QDs coated with dihydrolipoic acid-sulfobetaine (DHLA-SB) ligands diffuse freely in cells for longer periods of time than for QDs in the other chemistries tested, and they can access all cytoplasmic compartments. Even when conjugated to streptavidin, these DHLA-SB QDs remain freely diffusing inside the cytoplasm and unaggregated, and they are able to reach a biotinylated target inside HeLa cells. Such labeling was more efficient when compared to commercial streptavidin-conjugated QDs, which may be due to the smaller size of DHLA-SB QDs and/or to their superior intracellular stability. PMID:22378567

  2. Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

    PubMed

    Ramakrishnan, Raghunathan; Dral, Pavlo O; Rupp, Matthias; von Lilienfeld, O Anatole

    2015-05-12

    Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy. PMID:26574412

  3. Quantum Chemistry, and Eclectic Mix: From Silicon Carbide to Size Consistency

    SciTech Connect

    Jamie Marie Rintelman

    2004-12-19

    Chemistry is a field of great breadth and variety. It is this diversity that makes for both an interesting and challenging field. My interests have spanned three major areas of theoretical chemistry: applications, method development, and method evaluation. The topics presented in this thesis are as follows: (1) a multi-reference study of the geometries and relative energies of four atom silicon carbide clusters in the gas phase; (2) the reaction of acetylene on the Si(100)-(2x1) surface; (3) an improvement to the Effective Fragment Potential (EFP) solvent model to enable the study of reactions in both aqueous and nonaqueous solution; and (4) an evaluation of the size consistency of Multireference Perturbation Theory (MRPT). In the following section, the author briefly discusses two topics central to, and present throughout, this thesis: Multi-reference methods and Quantum Mechanics/Molecular Mechanics (QM/MM) methods.

  4. On the Chemical Basis of Trotter-Suzuki Errors in Quantum Chemistry Simulation

    NASA Astrophysics Data System (ADS)

    Babbush, Ryan; McClean, Jarrod; Wecker, Dave; Aspuru-Guzik, Alán; Wiebe, Nathan

    2015-03-01

    Although the simulation of quantum chemistry is one of the most anticipated applications of quantum computing, the scaling of known upper bounds on the complexity of these algorithms is daunting. Prior work has bounded errors due to Trotterization in terms of the norm of the error operator and analyzed scaling with respect to the number of spin-orbitals. However, we find that these error bounds can be loose by up to sixteen orders of magnitude for some molecules. Furthermore, numerical results for small systems fail to reveal any clear correlation between ground state error and number of spin-orbitals. We instead argue that chemical properties, such as the maximum nuclear charge in a molecule and the filling fraction of orbitals, can be decisive for determining the cost of a quantum simulation. Our analysis motivates several strategies to use classical processing to further reduce the required Trotter step size and to estimate the necessary number of steps, without requiring additional quantum resources. Finally, we demonstrate improved methods for state preparation techniques which are asymptotically superior to proposals in the simulation literature.

  5. Chemical basis of Trotter-Suzuki errors in quantum chemistry simulation

    NASA Astrophysics Data System (ADS)

    Babbush, Ryan; McClean, Jarrod; Wecker, Dave; Aspuru-Guzik, Alán; Wiebe, Nathan

    2015-02-01

    Although the simulation of quantum chemistry is one of the most anticipated applications of quantum computing, the scaling of known upper bounds on the complexity of these algorithms is daunting. Prior work has bounded errors due to discretization of the time evolution (known as "Trotterization") in terms of the norm of the error operator and analyzed scaling with respect to the number of spin orbitals. However, we find that these error bounds can be loose by up to 16 orders of magnitude for some molecules. Furthermore, numerical results for small systems fail to reveal any clear correlation between ground-state error and number of spin orbitals. We instead argue that chemical properties, such as the maximum nuclear charge in a molecule and the filling fraction of orbitals, can be decisive for determining the cost of a quantum simulation. Our analysis motivates several strategies to use classical processing to further reduce the required Trotter step size and estimate the necessary number of steps, without requiring additional quantum resources. Finally, we demonstrate improved methods for state preparation techniques which are asymptotically superior to proposals in the simulation literature.

  6. A Green's-Function Approach to Exchange Spin Coupling As a New Tool for Quantum Chemistry.

    PubMed

    Steenbock, Torben; Tasche, Jos; Lichtenstein, Alexander I; Herrmann, Carmen

    2015-12-01

    Exchange spin coupling is usually evaluated in quantum chemistry from the energy difference between a high-spin determinant and a Broken-Symmetry (BS) determinant in combination with Kohn-Sham density functional theory (KS-DFT), based on the work of Noodleman. As an alternative, an efficient approximate approach relying on Green's functions has been developed by one of the authors. This approach stems from solid-state physics and has never been systematically tested for molecular systems. We rederive a version of the Green's-function approach originally suggested by Han, Ozaki, and Yu. This new derivation employs local projection operators as common in quantum chemistry for defining local properties such as partial charges, rather than using a dual basis as in the Han-Ozaki-Yu approach. The result is a simple postprocessing procedure for KS-DFT calculations, which in contrast to the BS energy-difference approach requires the electronic structure of only one spin state. We show for several representative small molecules, diradicals, and dinuclear transition metal complexes that this method gives qualitatively consistent results with the BS energy-difference approach as long as it is applied to high-spin determinants and as long as structural relaxation effects in different spin states do not play an important role. PMID:26579585

  7. How many-body perturbation theory (MBPT) has changed quantum chemistry

    NASA Astrophysics Data System (ADS)

    Kutzelnigg, Werner

    The history of many-body perturbation theory (MBPT) and its impact on Quantum Chemistry is reviewed, starting with Brueckner's conjecture of a linked-cluster expansion and the time-dependent derivation by Goldstone of such an expansion. A central part of this article is the time-independent formulation of quantum chemistry in Fock space and its diagrammatic representation including the particle-hole picture and the inversion of a commutator. The results of the time-independent derivation of MBPT are compared with those of Goldstone. It is analyzed which ingredients of Goldstone's approach are decisive. The connected diagram theorem is derived both in a constructive way based on a Lie-algebraic formulation and a nonconstructive way making use of the separation theorem. It is discussed why the Goldstone derivation starting from a unitary time-evolution operator, ends up with a wave operator in intermediate normalization. The Møller-Plesset perturbation expansions of Bartlett and Pople are compared. Examples of complete summations of certain classes of diagrams are discussed, for example, that which leads to the Bethe-Goldstone expansion. MBPT for energy differences is analyzed. The paper ends with recent developments and challenges, such as the generalization of normal ordering to arbitrary reference states, contracted Schrödinger k-particle equations and Brillouin conditions, and finally the Nakatsuji theorem and the Nooijen conjecture. Content:text/plain; charset="UTF-8"

  8. Analysis of temporal evolution of quantum dot surface chemistry by surface-enhanced Raman scattering

    PubMed Central

    Doğan, İlker; Gresback, Ryan; Nozaki, Tomohiro; van de Sanden, Mauritius C. M.

    2016-01-01

    Temporal evolution of surface chemistry during oxidation of silicon quantum dot (Si-QD) surfaces were probed using surface-enhanced Raman scattering (SERS). A monolayer of hydrogen and chlorine terminated plasma-synthesized Si-QDs were spin-coated on silver oxide thin films. A clearly enhanced signal of surface modes, including Si-Clx and Si-Hx modes were observed from as-synthesized Si-QDs as a result of the plasmonic enhancement of the Raman signal at Si-QD/silver oxide interface. Upon oxidation, a gradual decrease of Si-Clx and Si-Hx modes, and an emergence of Si-Ox and Si-O-Hx modes have been observed. In addition, first, second and third transverse optical modes of Si-QDs were also observed in the SERS spectra, revealing information on the crystalline morphology of Si-QDs. An absence of any of the abovementioned spectral features, but only the first transverse optical mode of Si-QDs from thick Si-QD films validated that the spectral features observed from Si-QDs on silver oxide thin films are originated from the SERS effect. These results indicate that real-time SERS is a powerful diagnostic tool and a novel approach to probe the dynamic surface/interface chemistry of quantum dots, especially when they involve in oxidative, catalytic, and electrochemical surface/interface reactions. PMID:27389331

  9. Analysis of temporal evolution of quantum dot surface chemistry by surface-enhanced Raman scattering

    NASA Astrophysics Data System (ADS)

    Doğan, Ilker; Gresback, Ryan; Nozaki, Tomohiro; van de Sanden, Mauritius C. M.

    2016-07-01

    Temporal evolution of surface chemistry during oxidation of silicon quantum dot (Si-QD) surfaces were probed using surface-enhanced Raman scattering (SERS). A monolayer of hydrogen and chlorine terminated plasma-synthesized Si-QDs were spin-coated on silver oxide thin films. A clearly enhanced signal of surface modes, including Si-Clx and Si-Hx modes were observed from as-synthesized Si-QDs as a result of the plasmonic enhancement of the Raman signal at Si-QD/silver oxide interface. Upon oxidation, a gradual decrease of Si-Clx and Si-Hx modes, and an emergence of Si-Ox and Si-O-Hx modes have been observed. In addition, first, second and third transverse optical modes of Si-QDs were also observed in the SERS spectra, revealing information on the crystalline morphology of Si-QDs. An absence of any of the abovementioned spectral features, but only the first transverse optical mode of Si-QDs from thick Si-QD films validated that the spectral features observed from Si-QDs on silver oxide thin films are originated from the SERS effect. These results indicate that real-time SERS is a powerful diagnostic tool and a novel approach to probe the dynamic surface/interface chemistry of quantum dots, especially when they involve in oxidative, catalytic, and electrochemical surface/interface reactions.

  10. Accurate prediction of lattice energies and structures of molecular crystals with molecular quantum chemistry methods.

    PubMed

    Fang, Tao; Li, Wei; Gu, Fangwei; Li, Shuhua

    2015-01-13

    We extend the generalized energy-based fragmentation (GEBF) approach to molecular crystals under periodic boundary conditions (PBC), and we demonstrate the performance of the method for a variety of molecular crystals. With this approach, the lattice energy of a molecular crystal can be obtained from the energies of a series of embedded subsystems, which can be computed with existing advanced molecular quantum chemistry methods. The use of the field compensation method allows the method to take long-range electrostatic interaction of the infinite crystal environment into account and make the method almost translationally invariant. The computational cost of the present method scales linearly with the number of molecules in the unit cell. Illustrative applications demonstrate that the PBC-GEBF method with explicitly correlated quantum chemistry methods is capable of providing accurate descriptions on the lattice energies and structures for various types of molecular crystals. In addition, this approach can be employed to quantify the contributions of various intermolecular interactions to the theoretical lattice energy. Such qualitative understanding is very useful for rational design of molecular crystals. PMID:26574207

  11. A Synthesis of Fluid Dynamics and Quantum Chemistry for the Design of Nanoelectronics

    NASA Technical Reports Server (NTRS)

    MacDougall, Preston J.

    1998-01-01

    In 1959, during a famous lecture entitled "There's Plenty of Room at the Bottom", Richard Feynman focused on the startling technical possibilities that would exist at the limit of miniaturization, that being atomically precise devices with dimensions in the nanometer range. A nanometer is both a convenient unit of length for medium to large sized molecules, and the root of the name of the new interdisciplinary field of "nanotechnology". Essentially, "nanoelectronics" denotes the goal of shrinking electronic devices, such as diodes and transistors, as well as integrated circuits of such devices that can perform logical operations, down to dimensions in the range of 100 nanometers. The thirty-year hiatus in the development of nanotechnology can figuratively be seen as a period of waiting for the bottom-up and atomically precise construction skills of synthetic chemistry to meet the top-down reductionist aspirations of device physics. The sub-nanometer domain of nineteenth-century classical chemistry has steadily grown, and state-of-the-art supramolecular chemistry can achieve atomic precision in non-repeating molecular assemblies of the size desired for nanotechnology. For nanoelectronics in particular, a basic understanding of the electron transport properties of molecules must also be developed. Quantum chemistry provides powerful computational methods that can accurately predict the properties of small to medium sized molecules on a desktop workstation, and those of large molecules if one has access to a supercomputer. Of the many properties of a molecule that quantum chemistry routinely predicts, the ability to carry a current is one that had not even been considered until recently. "Currently", there is a controversy over just how to define this key property. Reminiscent of the situation in high-Tc superconductivity, much of the difficulty arises from the different models that are used to simplify the complex electronic structure of real materials. A model

  12. Genotoxic capacity of Cd/Se semiconductor quantum dots with differing surface chemistries

    PubMed Central

    Manshian, Bella B.; Soenen, Stefaan J.; Brown, Andy; Hondow, Nicole; Wills, John; Jenkins, Gareth J. S.; Doak, Shareen H.

    2016-01-01

    Quantum dots (QD) have unique electronic and optical properties promoting biotechnological advances. However, our understanding of the toxicological structure–activity relationships remains limited. This study aimed to determine the biological impact of varying nanomaterial surface chemistry by assessing the interaction of QD with either a negative (carboxyl), neutral (hexadecylamine; HDA) or positive (amine) polymer coating with human lymphoblastoid TK6 cells. Following QD physico-chemical characterisation, cellular uptake was quantified by optical and electron microscopy. Cytotoxicity was evaluated and genotoxicity was characterised using the micronucleus assay (gross chromosomal damage) and the HPRT forward mutation assay (point mutagenicity). Cellular damage mechanisms were also explored, focusing on oxidative stress and mitochondrial damage. Cell uptake, cytotoxicity and genotoxicity were found to be dependent on QD surface chemistry. Carboxyl-QD demonstrated the smallest agglomerate size and greatest cellular uptake, which correlated with a dose dependent increase in cytotoxicity and genotoxicity. Amine-QD induced minimal cellular damage, while HDA-QD promoted substantial induction of cell death and genotoxicity. However, HDA-QD were not internalised by the cells and the damage they caused was most likely due to free cadmium release caused by QD dissolution. Oxidative stress and induced mitochondrial reactive oxygen species were only partially associated with cytotoxicity and genotoxicity induced by the QD, hence were not the only mechanisms of importance. Colloidal stability, nanoparticle (NP) surface chemistry, cellular uptake levels and the intrinsic characteristics of the NPs are therefore critical parameters impacting genotoxicity induced by QD. PMID:26275419

  13. Conformations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane: are ab initio quantum chemistry predictions accurate?

    NASA Astrophysics Data System (ADS)

    Smith, Grant D.; Jaffe, Richard L.; Yoon, Do. Y.

    1998-06-01

    High-level ab initio quantum chemistry calculations are shown to predict conformer populations of 1,2-dimethoxypropane and 5-methoxy-1,3-dioxane that are consistent with gas-phase NMR vicinal coupling constant measurements. The conformational energies of the cyclic ether 5-methoxy-1,3-dioxane are found to be consistent with those predicted by a rotational isomeric state (RIS) model based upon the acyclic analog 1,2-dimethoxypropane. The quantum chemistry and RIS calculations indicate the presence of strong attractive 1,5 C(H 3)⋯O electrostatic interactions in these molecules, similar to those found in 1,2-dimethoxyethane.

  14. Quantum Diffusion-Controlled Chemistry: Reactions of Atomic Hydrogen with Nitric Oxide in Solid Parahydrogen.

    PubMed

    Ruzi, Mahmut; Anderson, David T

    2015-12-17

    Our group has been working to develop parahydrogen (pH2) matrix isolation spectroscopy as a method to study low-temperature condensed-phase reactions of atomic hydrogen with various reaction partners. Guided by the well-defined studies of cold atom chemistry in rare-gas solids, the special properties of quantum hosts such as solid pH2 afford new opportunities to study the analogous chemical reactions under quantum diffusion conditions in hopes of discovering new types of chemical reaction mechanisms. In this study, we present Fourier transform infrared spectroscopic studies of the 193 nm photoinduced chemistry of nitric oxide (NO) isolated in solid pH2 over the 1.8 to 4.3 K temperature range. Upon short-term in situ irradiation the NO readily undergoes photolysis to yield HNO, NOH, NH, NH3, H2O, and H atoms. We map the postphotolysis reactions of mobile H atoms with NO and document first-order growth in HNO and NOH reaction products for up to 5 h after photolysis. We perform three experiments at 4.3 K and one at 1.8 K to permit the temperature dependence of the reaction kinetics to be quantified. We observe Arrhenius-type behavior with a pre-exponential factor of A = 0.036(2) min(-1) and Ea = 2.39(1) cm(-1). This is in sharp contrast to previous H atom reactions we have studied in solid pH2 that display definitively non-Arrhenius behavior. The contrasting temperature dependence measured for the H + NO reaction is likely related to the details of H atom quantum diffusion in solid pH2 and deserves further study. PMID:26317154

  15. Quantum Chemistry in Nanoscale Environments: Insights on Surface-Enhanced Raman Scattering and Organic Photovoltaics

    NASA Astrophysics Data System (ADS)

    Olivares-Amaya, Roberto

    The understanding of molecular effects in nanoscale environments is becoming increasingly relevant for various emerging fields. These include spectroscopy for molecular identification as well as in finding molecules for energy harvesting. Theoretical quantum chemistry has been increasingly useful to address these phenomena to yield an understanding of these effects. In the first part of this dissertation, we study the chemical effect of surface-enhanced Raman scattering (SERS). We use quantum chemistry simulations to study the metal-molecule interactions present in these systems. We find that the excitations that provide a chemical enhancement contain a mixed contribution from the metal and the molecule. Moreover, using atomistic studies we propose an additional source of enhancement, where a transition metal dopant surface could provide an additional enhancement. We also develop methods to study the electrostatic effects of molecules in metallic environments. We study the importance of image-charge effects, as well as field-bias to molecules interacting with perfect conductors. The atomistic modeling and the electrostatic approximation enable us to study the effects of the metal interacting with the molecule in a complementary fashion, which provides a better understanding of the complex effects present in SERS. In the second part of this dissertation, we present the Harvard Clean Energy Project, a high-throughput approach for a large-scale computational screening and design of organic photovoltaic materials. We create molecular libraries to search for candidates structures and use quantum chemistry, machine learning and cheminformatics methods to characterize these systems and find structure-property relations. The scale of this study requires an equally large computational resource. We rely on distributed volunteer computing to obtain these properties. In the third part of this dissertation we present our work related to the acceleration of electronic structure

  16. The successful merger of theoretical thermochemistry with fragment-based methods in quantum chemistry.

    PubMed

    Ramabhadran, Raghunath O; Raghavachari, Krishnan

    2014-12-16

    CONSPECTUS: Quantum chemistry and electronic structure theory have proven to be essential tools to the experimental chemist, in terms of both a priori predictions that pave the way for designing new experiments and rationalizing experimental observations a posteriori. Translating the well-established success of electronic structure theory in obtaining the structures and energies of small chemical systems to increasingly larger molecules is an exciting and ongoing central theme of research in quantum chemistry. However, the prohibitive computational scaling of highly accurate ab initio electronic structure methods poses a fundamental challenge to this research endeavor. This scenario necessitates an indirect fragment-based approach wherein a large molecule is divided into small fragments and is subsequently reassembled to compute its energy accurately. In our quest to further reduce the computational expense associated with the fragment-based methods and overall enhance the applicability of electronic structure methods to large molecules, we realized that the broad ideas involved in a different area, theoretical thermochemistry, are transferable to the area of fragment-based methods. This Account focuses on the effective merger of these two disparate frontiers in quantum chemistry and how new concepts inspired by theoretical thermochemistry significantly reduce the total number of electronic structure calculations needed to be performed as part of a fragment-based method without any appreciable loss of accuracy. Throughout, the generalized connectivity based hierarchy (CBH), which we developed to solve a long-standing problem in theoretical thermochemistry, serves as the linchpin in this merger. The accuracy of our method is based on two strong foundations: (a) the apt utilization of systematic and sophisticated error-canceling schemes via CBH that result in an optimal cutting scheme at any given level of fragmentation and (b) the use of a less expensive second

  17. Coupled effects of solution chemistry and hydrodynamics on the mobility and transport of quantum dot nanomaterials in the Vadose Zone

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To investigate the coupled effects of solution chemistry and vadose zone processes on the mobility of quantum dot (QD) nanoparticles, laboratory scale transport experiments were performed. The complex coupled effects of ionic strength, size of QD aggregates, surface tension, contact angle, infiltrat...

  18. Bridging the Gap Between Quantum Chemistry and Classical Simulations for CO2 Capture

    SciTech Connect

    Gagliardi, Laura

    2015-09-17

    We have developed a systematic procedure to generate transferable force fields to simulate the behavior of CO2 and other gases in open-metal-site metal organic frameworks using high-level quantum chemical calculations. Monte Carlo simulations based on an ab initio force field for CO2 in the Mg2(dobpdc) material have been employed to describe the interactions of CO2 with open metals. Our study has shed some light on the interpretation of thermodynamic data of flue gas in Mg2(dobpdc). This force field accurately describes the chemistry of the open metal sites, and is transferable to other structures.

  19. Advances in methods and algorithms in a modern quantum chemistry program package.

    PubMed

    Shao, Yihan; Molnar, Laszlo Fusti; Jung, Yousung; Kussmann, Jörg; Ochsenfeld, Christian; Brown, Shawn T; Gilbert, Andrew T B; Slipchenko, Lyudmila V; Levchenko, Sergey V; O'Neill, Darragh P; DiStasio, Robert A; Lochan, Rohini C; Wang, Tao; Beran, Gregory J O; Besley, Nicholas A; Herbert, John M; Lin, Ching Yeh; Van Voorhis, Troy; Chien, Siu Hung; Sodt, Alex; Steele, Ryan P; Rassolov, Vitaly A; Maslen, Paul E; Korambath, Prakashan P; Adamson, Ross D; Austin, Brian; Baker, Jon; Byrd, Edward F C; Dachsel, Holger; Doerksen, Robert J; Dreuw, Andreas; Dunietz, Barry D; Dutoi, Anthony D; Furlani, Thomas R; Gwaltney, Steven R; Heyden, Andreas; Hirata, So; Hsu, Chao-Ping; Kedziora, Gary; Khalliulin, Rustam Z; Klunzinger, Phil; Lee, Aaron M; Lee, Michael S; Liang, Wanzhen; Lotan, Itay; Nair, Nikhil; Peters, Baron; Proynov, Emil I; Pieniazek, Piotr A; Rhee, Young Min; Ritchie, Jim; Rosta, Edina; Sherrill, C David; Simmonett, Andrew C; Subotnik, Joseph E; Woodcock, H Lee; Zhang, Weimin; Bell, Alexis T; Chakraborty, Arup K; Chipman, Daniel M; Keil, Frerich J; Warshel, Arieh; Hehre, Warren J; Schaefer, Henry F; Kong, Jing; Krylov, Anna I; Gill, Peter M W; Head-Gordon, Martin

    2006-07-21

    Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces. PMID:16902710

  20. A quantum chemistry study of curvature effects on boron nitride nanotubes/nanosheets for gas adsorption.

    PubMed

    Sha, Haoyan; Faller, Roland

    2016-07-20

    Quantum chemistry calculations were performed to investigate the effect of the surface curvature of a Boron Nitride (BN) nanotube/nanosheet on gas adsorption. Curved boron nitride layers with different curvatures interacting with a number of different gases including noble gases, oxygen, and water on both their convex and concave sides of the surface were studied using density functional theory (DFT) with a high level dispersion corrected functional. Potential energy surfaces of the gas molecules interacting with the selected BN surfaces were investigated. In addition, the charge distribution and electrostatic potential contour of the selected BN surfaces are discussed. The results reveal how the curvature of the BN surfaces affects gas adsorption. In particular, small curvatures lead to a slight difference in the physisorption energy, while large curvatures present distinct potential energy surfaces, especially for the short-range repulsion. PMID:27399852

  1. Progesterone and testosterone studies by neutron scattering and nuclear magnetic resonance methods and quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Szyczewski, A.; Hołderna-Natkaniec, K.; Natkaniec, I.

    2004-05-01

    Inelastic incoherent neutron scattering spectra of progesterone and testosterone measured at 20 and 290 K were compared with the IR spectra measured at 290 K. The Phonon Density of States spectra display well resolved peaks of low frequency internal vibration modes up to 1200 cm -1. The quantum chemistry calculations were performed by semiempirical PM3 method and by the density functional theory method with different basic sets for isolated molecule, as well as for the dimer system of testosterone. The proposed assignment of internal vibrations of normal modes enable us to conclude about the sequence of the onset of the torsion movements of the CH 3 groups. These conclusions were correlated with the results of proton molecular dynamics studies performed by NMR method. The GAUSSIAN program had been used for calculations.

  2. Internal rotation and equilibrium structure of 2-nitropropane from gas electron diffraction and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Tarasov, Yu. I.; Kochikov, I. V.; Kovtun, D. M.; Ivanov, A. A.

    2009-03-01

    In this paper, the equilibrium structural parameters of the 2-nitropropane molecule and the barrier of internal rotation of the nitrogroup are determined from the gas electron diffraction data, with the use of quantum chemistry calculations and experimental vibrational frequencies, in the framework of the large-amplitude motion model for internal rotation. Quantum chemistry calculations at the MP2 and B3LYP levels of theory with various Pople and Dunning basis sets unambiguously predict the same minimum energy molecular conformation, with relatively close values of internal rotation barrier (375-525 cm -1). The results of present analysis show that the minimum of the potential function of the nitrogroup internal rotation is located in syn-H position when one of the oxygen atoms eclipses hydrogen atom that does not belong to any of CH 3 groups (dihedral angle H-C-N-O is zero). It has also been found that internal rotation is hindered, with the barrier height in the range of 220-560 cm -1 (0.6-1.6 kcal/mol) with the most probable value near 380 cm -1 (1.1 kcal/mol). The main equilibrium structure parameters in syn-H configuration are as follows (values in parentheses correspond to 3 times standard deviations): re(C-C) = 1.516(5) Å, re(C-N) = 1.501(5) Å, re (N dbnd O) = 1.225(4) Å, ∠C-C-N=108.7(1.0)°,∠O dbnd N dbnd O =124.8(0.4)°. We also provide thermally averaged parameters for comparison with the results of previous studies.

  3. Strong electron correlation in UO2(-): a photoelectron spectroscopy and relativistic quantum chemistry study.

    PubMed

    Li, Wei-Li; Su, Jing; Jian, Tian; Lopez, Gary V; Hu, Han-Shi; Cao, Guo-Jin; Li, Jun; Wang, Lai-Sheng

    2014-03-01

    The electronic structures of actinide systems are extremely complicated and pose considerable challenges both experimentally and theoretically because of significant electron correlation and relativistic effects. Here we report an investigation of the electronic structure and chemical bonding of uranium dioxides, UO2(-) and UO2, using photoelectron spectroscopy and relativistic quantum chemistry. The electron affinity of UO2 is measured to be 1.159(20) eV. Intense detachment bands are observed from the UO2(-) low-lying (7sσg)(2)(5fϕu)(1) orbitals and the more deeply bound O2p-based molecular orbitals which are separated by a large energy gap from the U-based orbitals. Surprisingly, numerous weak photodetachment transitions are observed in the gap region due to extensive two-electron transitions, suggesting strong electron correlations among the (7sσg)(2)(5fϕu)(1) electrons in UO2(-) and the (7sσg)(1)(5fϕu)(1) electrons in UO2. These observations are interpreted using multi-reference ab initio calculations with inclusion of spin-orbit coupling. The strong electron correlations and spin-orbit couplings generate orders-of-magnitude more detachment transitions from UO2(-) than expected on the basis of the Koopmans' theorem. The current experimental data on UO2(-) provide a long-sought opportunity to arbitrating various relativistic quantum chemistry methods aimed at handling systems with strong electron correlations. PMID:24606360

  4. The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age.

    PubMed

    Adams, Sam; de Castro, Pablo; Echenique, Pablo; Estrada, Jorge; Hanwell, Marcus D; Murray-Rust, Peter; Sherwood, Paul; Thomas, Jens; Townsend, Joe

    2011-01-01

    Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication.In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today.Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other

  5. The Quixote project: Collaborative and Open Quantum Chemistry data management in the Internet age

    PubMed Central

    2011-01-01

    Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication. In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today. Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other

  6. The structural chemistry of metallocorroles: combined X-ray crystallography and quantum chemistry studies afford unique insights.

    PubMed

    Thomas, Kolle E; Alemayehu, Abraham B; Conradie, Jeanet; Beavers, Christine M; Ghosh, Abhik

    2012-08-21

    Although they share some superficial structural similarities with porphyrins, corroles, trianionic ligands with contracted cores, give rise to fundamentally different transition metal complexes in comparison with the dianionic porphyrins. Many metallocorroles are formally high-valent, although a good fraction of them are also noninnocent, with significant corrole radical character. These electronic-structural characteristics result in a variety of fascinating spectroscopic behavior, including highly characteristic, paramagnetically shifted NMR spectra and textbook cases of charge-transfer spectra. Although our early research on corroles focused on spectroscopy, we soon learned that the geometric structures of metallocorroles provide a fascinating window into their electronic-structural characteristics. Thus, we used X-ray structure determinations and quantum chemical studies, chiefly using DFT, to obtain a comprehensive understanding of metallocorrole geometric and electronic structures. This Account describes our studies of the structural chemistry of metallocorroles. At first blush, the planar or mildly domed structure of metallocorroles might appear somewhat uninteresting particularly when compared to metalloporphyrins. Metalloporphyrins, especially sterically hindered ones, are routinely ruffled or saddled, but the missing meso carbon apparently makes the corrole skeleton much more resistant to nonplanar distortions. Ruffling, where the pyrrole rings are alternately twisted about the M-N bonds, is energetically impossible for metallocorroles. Saddling is also uncommon; thus, a number of sterically hindered, fully substituted metallocorroles exhibit almost perfectly planar macrocycle cores. Against this backdrop, copper corroles stand out as an important exception. As a result of an energetically favorable Cu(d(x2-y2))-corrole(π) orbital interaction, copper corroles, even sterically unhindered ones, are inherently saddled. Sterically hindered substituents

  7. GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations.

    PubMed

    Maia, Julio Daniel Carvalho; Urquiza Carvalho, Gabriel Aires; Mangueira, Carlos Peixoto; Santana, Sidney Ramos; Cabral, Lucidio Anjos Formiga; Rocha, Gerd B

    2012-09-11

    In this study, we present some modifications in the semiempirical quantum chemistry MOPAC2009 code that accelerate single-point energy calculations (1SCF) of medium-size (up to 2500 atoms) molecular systems using GPU coprocessors and multithreaded shared-memory CPUs. Our modifications consisted of using a combination of highly optimized linear algebra libraries for both CPU (LAPACK and BLAS from Intel MKL) and GPU (MAGMA and CUBLAS) to hasten time-consuming parts of MOPAC such as the pseudodiagonalization, full diagonalization, and density matrix assembling. We have shown that it is possible to obtain large speedups just by using CPU serial linear algebra libraries in the MOPAC code. As a special case, we show a speedup of up to 14 times for a methanol simulation box containing 2400 atoms and 4800 basis functions, with even greater gains in performance when using multithreaded CPUs (2.1 times in relation to the single-threaded CPU code using linear algebra libraries) and GPUs (3.8 times). This degree of acceleration opens new perspectives for modeling larger structures which appear in inorganic chemistry (such as zeolites and MOFs), biochemistry (such as polysaccharides, small proteins, and DNA fragments), and materials science (such as nanotubes and fullerenes). In addition, we believe that this parallel (GPU-GPU) MOPAC code will make it feasible to use semiempirical methods in lengthy molecular simulations using both hybrid QM/MM and QM/QM potentials. PMID:26605718

  8. A unified view on heterogeneous and homogeneous catalysts through a combination of spectroscopy and quantum chemistry.

    PubMed

    Maganas, Dimitrios; Trunschke, Annette; Schlögl, Robert; Neese, Frank

    2016-07-01

    Identifying catalytically active structures or intermediates in homogeneous and heterogeneous catalysis is a formidable challenge. However, obtaining experimentally verified insight into the active species in heterogeneous catalysis is a tremendously challenging problem. Many highly advanced spectroscopic and microscopic methods have been developed to probe surfaces. In this discussion we employ a combination of spectroscopic methods to study two closely related systems from the heterogeneous (the silica-supported vanadium oxide VOx/SBA-15) and homogeneous (the complex K[VO(O2)Hheida]) domains. Spectroscopic measurements were conducted strictly in parallel for both systems and consisted of oxygen K-edge and vanadium L-edge X-ray absorption measurements in conjunction with resonance Raman spectroscopy. It is shown that the full information content of the spectra can be developed through advanced quantum chemical calculations that directly address the sought after structure-spectra relationships. To this end we employ the recently developed restricted open shell configuration interaction theory together with the time-dependent theory of electronic spectroscopy to calculate XAS and rR spectra respectively. The results of the study demonstrate that: (a) a combination of several spectroscopic techniques is of paramount importance in identifying signature structural motifs and (b) quantum chemistry is an extremely powerful guide in cross connecting theory and experiment as well as the homogeneous and heterogeneous catalysis fields. It is emphasized that the calculation of spectroscopic observables provides an excellent way for the critical experimental validation of theoretical results. PMID:27062973

  9. Excitons in a photosynthetic light-harvesting system: A combined molecular dynamics, quantum chemistry, and polaron model study

    NASA Astrophysics Data System (ADS)

    Damjanović, Ana; Kosztin, Ioan; Kleinekathöfer, Ulrich; Schulten, Klaus

    2002-03-01

    The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. For each of the 16 B850 bacteriochlorophylls (BChls), we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function, are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 BChl ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption and circular dichroism spectra of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained results are found to be in good agreement with the experimentally measured absorption and circular dichroism spectra.

  10. Quantum Chemistry Meets Spectroscopy for Astrochemistry: Increasing Complexity toward Prebiotic Molecules.

    PubMed

    Barone, Vincenzo; Biczysko, Malgorzata; Puzzarini, Cristina

    2015-05-19

    For many years, scientists suspected that the interstellar medium was too hostile for organic species and that only a few simple molecules could be formed under such extreme conditions. However, the detection of approximately 180 molecules in interstellar or circumstellar environments in recent decades has changed this view dramatically. A rich chemistry has emerged, and relatively complex molecules such as C60 and C70 are formed. Recently, researchers have also detected complex organic and potentially prebiotic molecules, such as amino acids, in meteorites and in other space environments. Those discoveries have further stimulated the debate on the origin of the building blocks of life in the universe. Many efforts continue to focus on the physical, chemical, and astrophysical processes by which prebiotic molecules can be formed in the interstellar dust and dispersed to Earth or to other planets.Spectroscopic techniques, which are widely used to infer information about molecular structure and dynamics, play a crucial role in the investigation of planetary atmosphere and the interstellar medium. Increasingly these astrochemical investigations are assisted by quantum-mechanical calculations of structures as well as spectroscopic and thermodynamic properties, such as transition frequencies and reaction enthalpies, to guide and support observations, line assignments, and data analysis in these new and chemically complicated situations. However, it has proved challenging to extend accurate quantum-chemical computational approaches to larger systems because of the unfavorable scaling with the number of degrees of freedom (both electronic and nuclear).In this Account, we show that it is now possible to compute physicochemical properties of building blocks of biomolecules with an accuracy rivaling that of the most sophisticated experimental techniques, and we summarize specific contributions from our groups. As a test case, we present the underlying computational machinery

  11. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect

    Krishnamoorthy, Sriram; Bernholdt, David E; Pitzer, R. M.; Sadayappan, Ponnuswamy

    2009-01-01

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness.

  12. Performance Optimization of Tensor Contraction Expressions for Many Body Methods in Quantum Chemistry

    SciTech Connect

    Hartono, Albert; Lu, Qingda; henretty, thomas; Krishnamoorthy, Sriram; zhang, huaijian; Baumgartner, Gerald; Bernholdt, David E.; Nooijen, Marcel; Pitzer, Russell M.; Ramanujam, J.; Sadayappan, Ponnuswamy

    2009-11-12

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations such as minimization of cache misses and utilization of multimedia vector instructions are discussed. A library for efficient index permutation of multi-dimensional tensors is described and experimental performance data is provided that demonstrates its effectiveness.

  13. Quantum chemistry investigation on the reaction mechanism of the elemental mercury, chlorine, bromine and ozone system.

    PubMed

    Gao, Zhengyang; Lv, Shaokun; Yang, Weijie; Yang, Pengfei; Ji, Shuo; Meng, Xinxin

    2015-06-01

    Ab initio calculations were performed to study the quantum chemistry reactions mechanisms among Hg(0), elemental halogen and O3. The geometry of reactions, transition states (TS), intermediates (M) and products were optimized using the MP2 method at the SDD basis function level for Hg, and using 6-311++G (3df, 3pd) for other species. Molecular energies were calculated at QCISD (T) level with zero point energy. Activation energies were calculated along with pre-exponential factors . The reaction rate constants within 298-1800 K were calculated according to transition state theory (TST). The influences of O3 on the reaction of Hg(0) with halogen are discussed. Hg(0) can be oxidized to Hg(1+) by halogen and O3, and halogen and O3 can be arranged in decreasing order as: Br2 > BrO > O3 > Br > Cl, BrCl > HBr > HCl, Br2 > Cl2 according to reaction rate constants. When O3 is presented, Br2, HBr, BrCl, Cl2 and HCl react with O3 and are initially converted to BrO and ClO. O3 is unfavorable for oxidation of Hg(0) by Br2. The mixture of HBr and O3 has better oxidizing Hg(0) performance than HBr and O3. Cl is less effective than Br for oxidation of Hg(0). PMID:26026300

  14. Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

    NASA Astrophysics Data System (ADS)

    Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

    2015-01-01

    A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

  15. Programmability of the HPCS Languages: A Case Study with a Quantum Chemistry Kernel

    SciTech Connect

    Shet, Aniruddha G; Elwasif, Wael R; Harrison, Robert J; Bernholdt, David E

    2008-01-01

    As high-end computer systems present users with rapidly increasing numbers of processors, possibly also incorporating attached co-processors, programmers are increasingly challenged to express the necessary levels of concurrency with the dominant parallel programming model, Fortran+MPI+OpenMP (or minor variations). In this paper, we examine the languages developed under the DARPA High-Productivity Computing Systems (HPCS) program (Chapel, Fortress, and X10) as representatives of a different parallel programming model which might be more effective on coming high-performance systems. The application used in this study is the Hartree-Fock method from quantum chemistry, which combines access to distributed data with a task-parallel algorithm and is characterized by significant irregularity in the computational tasks. We present several different implementation strategies for load balancing of the task parallel computation, as well as distributed array operations, in each of the three languages. We conclude that the HPCS languages provide a wide variety of mechanisms for expressing parallelism, which can be combined at multiple levels, making them quite expressive for this problem.

  16. Progesterone and testosterone studies by neutron-scattering methods and quantum chemistry calculations

    NASA Astrophysics Data System (ADS)

    Holderna-Natkaniec, K.; Szyczewski, A.; Natkaniec, I.; Khavryutchenko, V. D.; Pawlukojc, A.

    Inelastic incoherent neutron scattering (IINS) and neutron diffraction spectra of progesterone and testosterone were measured simultaneously on the NERA spectrometer at the IBR-2 pulsed reactor in Dubna. Both studied samples do not indicate any phase transition in the temperature range from 20 to 290K. The IINS spectra have been transformed to the phonon density of states (PDS) in the one-phonon scattering approximation. The PDS spectra display well-resolved peaks of low-frequency internal vibration modes up to 600cm-1. The assignment of these modes was proposed taking into account the results of calculations of the structure and dynamics of isolated molecules of the investigated substances. The quantum chemistry calculations were performed by the semi-empirical PM3 method and at the restricted Hartree-Fock level with the 6-31* basis set. The lower internal modes assigned to torsional vibration of the androstane skeleton mix with the lattice vibrations. The intense bands in the PDS spectra in the frequency range from 150 to 300cm-1 are related to librations of structurally inequivalent methyl groups.

  17. IR spectrum simulation of molecular structure model of Shendong coal vitrinite by using quantum chemistry method.

    PubMed

    Jia, Jian-Bo; Wang, Ying; Li, Feng-Hai; Yi, Gui-Yun; Zeng, Fan-Gui; Guo, Hong-Yu

    2014-01-01

    The structure of coal needs to be understood from a molecular point of view for clean, effective and high value-added utilization of coal. In the literature, molecular structure model of Shendong coal vitrinite (SV) was established by the authors on the basis of experimental results of ultimate analysis and 13C NMR, and the calculated 13C NMR spectrum of SV model was consistent with the experimental spectrum. In order to further verify the accuracy of SV structure model established by the authors, the infrared spectrum of SV structure model was calculated using quantum chemistry semi-empirical VAMP in this thesis. The results showed that the peak shape of calculated IR spectrum of SV structure model was similar to the experiment's, but the wave number of calculated IR spectrum was obviously higher than that of experimental spectrum. According to the calculated results for model compounds by using the same method, calculated vibrational frequency was higher than that of experiment for the same functional groups. Hence, the calculated IR spectrum should be corrected. After correction the calculated IR spectrum of SV structure model matched well with the experimental spectrum. In other words, the SV structure model can truly reflect the structure characteristics of SV. PMID:24783531

  18. Programmability of the HPCS Languages: A Case Study with a Quantum Chemistry Kernel (Extended Version)

    SciTech Connect

    Shet, Aniruddha G; Elwasif, Wael R; Harrison, Robert J; Bernholdt, David E

    2008-04-01

    As high-end computer systems present users with rapidly increasing numbers of processors, possibly also incorporating attached co-processors, programmers are increasingly challenged to express the necessary levels of concurrency with the dominant parallel programming model, Fortran+MPI+OpenMP (or minor variations). In this paper, we examine the languages developed under the DARPA High-Productivity Computing Systems (HPCS) program (Chapel, Fortress, and X10) as representatives of a different parallel programming model which might be more effective on coming high-performance systems. The application used in this study is the Hartree-Fock method from quantum chemistry, which combines access to distributed data with a task-parallel algorithm and is characterized by significant irregularity in the computational tasks. We present several different implementation strategies for load balancing of the task parallel computation, as well as distributed array operations, in each of the three languages. We conclude that the HPCS languages provide a wide variety of mechanisms for expressing parallelism, which can be combined at multiple levels, making them quite expressive for this problem.

  19. Merging quantum-chemistry with B-splines to describe molecular photoionization

    NASA Astrophysics Data System (ADS)

    Argenti, L.; Marante, C.; Klinker, M.; Corral, I.; Gonzalez, J.; Martin, F.

    2016-05-01

    Theoretical description of observables in attosecond pump-probe experiments requires a good representation of the system's ionization continuum. For polyelectronic atoms and molecules, however, this is still a challenge, due to the complicated short-range structure of correlated electronic wavefunctions. Whereas quantum chemistry packages (QCP) implementing sophisticated methods to compute bound electronic molecular states are well established, comparable tools for the continuum are not widely available yet. To tackle this problem, we have developed a new approach that, by means of a hybrid Gaussian-B-spline basis, interfaces existing QCPs with close-coupling scattering methods. To illustrate the viability of this approach, we report results for the multichannel ionization of the helium atom and of the hydrogen molecule that are in excellent agreement with existing accurate benchmarks. These findings, together with the flexibility of QCPs, make of this approach a good candidate for the theoretical study of the ionization of poly-electronic systems. FP7/ERC Grant XCHEM 290853.

  20. Time-dependent quantum chemistry of laser driven many-electron molecules

    SciTech Connect

    Nguyen-Dang, Thanh-Tung; Couture-Bienvenue, Étienne; Viau-Trudel, Jérémy; Sainjon, Amaury

    2014-12-28

    A Time-Dependent Configuration Interaction approach using multiple Feshbach partitionings, corresponding to multiple ionization stages of a laser-driven molecule, has recently been proposed [T.-T. Nguyen-Dang and J. Viau-Trudel, J. Chem. Phys. 139, 244102 (2013)]. To complete this development toward a fully ab-initio method for the calculation of time-dependent electronic wavefunctions of an N-electron molecule, we describe how tools of multiconfiguration quantum chemistry such as the management of the configuration expansion space using Graphical Unitary Group Approach concepts can be profitably adapted to the new context, that of time-resolved electronic dynamics, as opposed to stationary electronic structure. The method is applied to calculate the detailed, sub-cycle electronic dynamics of BeH{sub 2}, treated in a 3–21G bound-orbital basis augmented by a set of orthogonalized plane-waves representing continuum-type orbitals, including its ionization under an intense λ = 800 nm or λ = 80 nm continuous-wave laser field. The dynamics is strongly non-linear at the field-intensity considered (I ≃ 10{sup 15} W/cm{sup 2}), featuring important ionization of an inner-shell electron and strong post-ionization bound-electron dynamics.

  1. Performance optimization of tensor contraction expressions for many-body methods in quantum chemistry.

    PubMed

    Hartono, Albert; Lu, Qingda; Henretty, Thomas; Krishnamoorthy, Sriram; Zhang, Huaijian; Baumgartner, Gerald; Bernholdt, David E; Nooijen, Marcel; Pitzer, Russell; Ramanujam, J; Sadayappan, P

    2009-11-12

    Complex tensor contraction expressions arise in accurate electronic structure models in quantum chemistry, such as the coupled cluster method. This paper addresses two complementary aspects of performance optimization of such tensor contraction expressions. Transformations using algebraic properties of commutativity and associativity can be used to significantly decrease the number of arithmetic operations required for evaluation of these expressions. The identification of common subexpressions among a set of tensor contraction expressions can result in a reduction of the total number of operations required to evaluate the tensor contractions. The first part of the paper describes an effective algorithm for operation minimization with common subexpression identification and demonstrates its effectiveness on tensor contraction expressions for coupled cluster equations. The second part of the paper highlights the importance of data layout transformation in the optimization of tensor contraction computations on modern processors. A number of considerations, such as minimization of cache misses and utilization of multimedia vector instructions, are discussed. A library for efficient index permutation of multidimensional tensors is described, and experimental performance data is provided that demonstrates its effectiveness. PMID:19888780

  2. Comparison of Oxygen Gauche Effects in Poly(Oxyethylene) and Poly(ethylene terephtylene) Based on Quantum Chemistry Calculations

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    The so-called oxygen gauche effect in poly(oxyethylene) (POE) and its model molecules such as 1,2-dimethoxyethane (DME) and diglyme (CH3OC2H4OC2H4OCH3) is manifested in the preference for gauche C-C bond conformations over trans. This has also been observed for poly(ethylene terephthalate) (PET). Our previous quantum chemistry calculations demonstrated that the large C-C gauche population in DME is due, in part, to a low-lying tg +/- g+ conformer that exhibits a substantial 1,5 CH ... O attraction. New calculations will be described that demonstrate the accuracy of the original quantum chemistry calculations. In addition, an extension of this work to model molecules for PET will be presented. It is seen that the C-C gauche preference is much stronger in 1,2 diacetoxyethane than in DME. In addition, there exist low-lying tg +/- g+/- and g+/-g+/-g+/- conformers that exhibit 1,5 CH ... O attractions involving the carbonyl oxygens. It is expected that the -O-C-C-O- torsional properties will be quite different in these two polymers. The quantum chemistry results are used to parameterize rotational isomeric states models (RIS) and force fields for molecular dynamics simulations of these polymers.

  3. Influence of Force Fields and Quantum Chemistry Approach on Spectral Densities of BChl a in Solution and in FMO Proteins.

    PubMed

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie; Aspuru-Guzik, Alán; Kleinekathöfer, Ulrich

    2015-08-01

    Studies on light-harvesting (LH) systems have attracted much attention after the finding of long-lived quantum coherences in the exciton dynamics of the Fenna-Matthews-Olson (FMO) complex. In this complex, excitation energy transfer occurs between the bacteriochlorophyll a (BChl a) pigments. Two quantum mechanics/molecular mechanics (QM/MM) studies, each with a different force-field and quantum chemistry approach, reported different excitation energy distributions for the FMO complex. To understand the reasons for these differences in the predicted excitation energies, we have carried out a comparative study between the simulations using the CHARMM and AMBER force field and the Zerner intermediate neglect of differential orbital (ZINDO)/S and time-dependent density functional theory (TDDFT) quantum chemistry methods. The calculations using the CHARMM force field together with ZINDO/S or TDDFT always show a wider spread in the energy distribution compared to those using the AMBER force field. High- or low-energy tails in these energy distributions result in larger values for the spectral density at low frequencies. A detailed study on individual BChl a molecules in solution shows that without the environment, the density of states is the same for both force field sets. Including the environmental point charges, however, the excitation energy distribution gets broader and, depending on the applied methods, also asymmetric. The excitation energy distribution predicted using TDDFT together with the AMBER force field shows a symmetric, Gaussian-like distribution. PMID:26156758

  4. Applying and assessing some semi-local density functionals for condensed matter physics and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Hao, Pan

    Density functional theory (DFT) is a widely used quantum mechanical method for the simulation of the electronic structure of atoms, molecules, and solids. The only part that needs to be approximated is the exchange-correlation energy as a functional of the electron density. After many-year development, there is a huge variety of exchange-correlation functionals. According to the ingredients, an exchange-correlation functional can be classified as a semi-local functional or beyond. A semi-local functional can be nonempirical or empirical and only uses locality information, such as electron density, gradient of the density, Laplacian of the density, and kinetic energy density. Unlike a non-local functional that uses non-locality information, a semi-local functional is computationally efficient and can be applied to large systems. The meta-generalized gradient approximation (meta-GGA), which is the highest-level semi-local functional, has the potential to give a good description for condensed matter physics and quantum chemistry. We built the self-consistent revised Tao-Perdew-Staroverov-Scuseria (revTPSS) meta-GGA into the band-structure program BAND to test the performances of some self-consistent semi-local functionals on lattice constant with a 58-solid test set. The self-consistent effect of revTPSS was also discussed. The vibration of a crystal has a contribution to the ground state energy of a system, which is the zero-point energy at zero temperature. It has anharmonicity at the equilibrium geometry. The standard DFT doesn't consider the zero-point energy of a crystal. We used density functional perturbation theory (DFPT), which is a powerful and flexible theoretical technique within the density functional framework, to study the zero-point energy and make a correction to the lattice constant. The method was compared to a traditional zero-point anharmonic expansion method that is based on the Debye and Dugdale-MacDonald approximations. We also tested some new

  5. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters?

    PubMed

    Yuan, Dandan; Shen, Xiaoling; Li, Wei; Li, Shuhua

    2016-06-28

    Fragment-based quantum chemistry methods are either based on the many-body expansion or the inclusion-exclusion principle. To compare the applicability of these two categories of methods, we have systematically evaluated the performance of the generalized energy based fragmentation (GEBF) method (J. Phys. Chem. A, 2007, 111, 2193) and the electrostatically embedded many-body (EE-MB) method (J. Chem. Theory Comput., 2007, 3, 46) for medium-sized water clusters (H2O)n (n = 10, 20, 30). Our calculations demonstrate that the GEBF method provides uniformly accurate ground-state energies for 10 low-energy isomers of three water clusters under study at a series of theory levels, while the EE-MB method (with one water molecule as a fragment and without using the cutoff distance) shows a poor convergence for (H2O)20 and (H2O)30 when the basis set contains diffuse functions. Our analysis shows that the neglect of the basis set superposition error for each subsystem has little effect on the accuracy of the GEBF method, but leads to much less accurate results for the EE-MB method. The accuracy of the EE-MB method can be dramatically improved by using an appropriate cutoff distance and using two water molecules as a fragment. For (H2O)30, the average deviation of the EE-MB method truncated up to the three-body level calculated using this strategy (relative to the conventional energies) is about 0.003 hartree at the M06-2X/6-311++G** level, while the deviation of the GEBF method with a similar computational cost is less than 0.001 hartree. The GEBF method is demonstrated to be applicable for electronic structure calculations of water clusters at any basis set. PMID:27263629

  6. Final report summary of LDRD 02-LW-022''Quantum Vibrations in Molecules: A New Frontier in Computational Chemistry''

    SciTech Connect

    Glaesemann, K R

    2004-01-22

    With the trend towards needing information about chemistry at conditions significantly different from 298K and 1 atm., methods need to be developed to generate and interpret this data. This demand for information about chemistry at extreme conditions comes from many fields. The study of atmospheric chemistry requires knowledge of unusual species that are formed when molecules are exposed to ultraviolet radiation. Studying of energetic materials requires knowledge of the thermochemical and structural properties of a myriad of chemical species under a wide range of temperatures. Basic scientific understanding of the very nature of a chemical bond requires detailed information. Studying these problems computationally requires multiple capabilities. The methodology used must provide both high accuracy and computational efficiency. Studying extreme chemistry also suffers from all the challenges of studying chemistry under non-extreme conditions. Therefore, either a new method must be developed or an old method must be applied in an innovative way. The method we have chosen to use is path integral Monte Carlo (PIMC) for the nuclear degrees of freedom and ab initio electronic structure methods for the electronic degrees of freedom. PIMC and ab initio electronic structure are methods of treating the quantum nature of particles. These methods have been chosen, because an accurate treatment requires treating both the electrons and the nuclei as quantum particles. We developed new ''projected'' methods that reduce the computational demands. These methods along with PIMC in general are described in two Journal of Chemical Physics articles (UCRL-JC-144960 and UCRL-JC-147423). This methodology was implemented into a PIMC code developed as part of this LDRD. The code was parallelized in order to utilize the computational resources of LLNL.

  7. Nobel Prizes in Physics and Chemistry 2014: Celebrating the International Year of Light 2015, commemorating the Old Quantum Theory

    NASA Astrophysics Data System (ADS)

    Shi, Yu

    2015-01-01

    2015 is the International Year of Light and Light-based Technologies (IYL), while the physics and chemistry Nobel Prizes 2014 are both about light. The work leading to the two prizes share the same basic theoretical foundation: when an electron jumps from a higher energy level to a lower energy level, the energy difference is transformed into a photon. This basic way of light generation is a key part of the Old Quantum Theory. Interestingly, the date of announcing the 2014 Nobel Prize for physics coincided with the birthdays of Niels Bohr and, especially, of Planck's blackbody radiation formula. In connection with the two 2014 Nobel Prizes, we recall the development of the Old Quantum Theory by Planck, Einstein and Bohr.

  8. Spiers memorial lecture. The quantum chemistry of d- and f-element complexes: from an approximate existence to functional happiness.

    PubMed

    Bursten, Bruce E; Drummond, Michael L; Li, Jun

    2003-01-01

    The field of modern quantum inorganic chemistry is just over 50 years old, dating back to 1951, when quantitative LCAO molecular orbital theory was developed and ferrocene was discovered. This Lecture provides a survey of the development of the field through about 1980, which has led to its current state. The application of modern quantum chemical techniques are illustrated via two disparate examples from the authors' research group. First, the recent discovery of uranium-noble gas bonds is discussed including the synergy between the theoretical and experimental investigations of this phenomenon. New theoretical results using coupled-cluster [CCSD(T)] methodology is contrasted to the original scalar-relativistic density functional theory results. Second, new applications of time-dependent density functional theory to the rich photochemistry of a dinuclear organometallic complex, (eta5-C5H5)2Fe2(mu-CO)2(CO)2, are discussed. PMID:14527206

  9. THE IONIC PATHWAYS OF LITHIUM CHEMISTRY IN THE EARLY UNIVERSE: QUANTUM CALCULATIONS FOR LiH{sup +} REACTING WITH H

    SciTech Connect

    Bovino, S.; Gianturco, F. A.; Stoecklin, T.

    2010-01-10

    To better understand the overall role of lithium chemistry in the early universe, reactive quantum calculations involving LiH{sup +} have been carried out and rate coefficients have been obtained. The reactive quantum calculations have been performed using a negative imaginary potential method. Infinite-order sudden approximation and the coupled state approximation have been used to simplify the angular coupling dynamics. Rate coefficients are obtained from the reactive cross sections by further integration over Boltzmann distribution of velocities. The results from the present calculations suggest that, at low redshifts (z), LiH{sup +} should be amenable to observation as imprinted on the cosmic background radiation, in contrast with its neutral counterpart. At higher z, the ionic species may disappear through both depletion reaction and three-body break-up processes.

  10. Laboratory study of nitrate photolysis in Antarctic snow. I. Observed quantum yield, domain of photolysis, and secondary chemistry

    SciTech Connect

    Meusinger, Carl; Johnson, Matthew S.; Berhanu, Tesfaye A.; Erbland, Joseph; Savarino, Joel

    2014-06-28

    Post-depositional processes alter nitrate concentration and nitrate isotopic composition in the top layers of snow at sites with low snow accumulation rates, such as Dome C, Antarctica. Available nitrate ice core records can provide input for studying past atmospheres and climate if such processes are understood. It has been shown that photolysis of nitrate in the snowpack plays a major role in nitrate loss and that the photolysis products have a significant influence on the local troposphere as well as on other species in the snow. Reported quantum yields for the main reaction spans orders of magnitude – apparently a result of whether nitrate is located at the air-ice interface or in the ice matrix – constituting the largest uncertainty in models of snowpack NO{sub x} emissions. Here, a laboratory study is presented that uses snow from Dome C and minimizes effects of desorption and recombination by flushing the snow during irradiation with UV light. A selection of UV filters allowed examination of the effects of the 200 and 305 nm absorption bands of nitrate. Nitrate concentration and photon flux were measured in the snow. The quantum yield for loss of nitrate was observed to decrease from 0.44 to 0.003 within what corresponds to days of UV exposure in Antarctica. The superposition of photolysis in two photochemical domains of nitrate in snow is proposed: one of photolabile nitrate, and one of buried nitrate. The difference lies in the ability of reaction products to escape the snow crystal, versus undergoing secondary (recombination) chemistry. Modeled NO{sub x} emissions may increase significantly above measured values due to the observed quantum yield in this study. The apparent quantum yield in the 200 nm band was found to be ∼1%, much lower than reported for aqueous chemistry. A companion paper presents an analysis of the change in isotopic composition of snowpack nitrate based on the same samples as in this study.

  11. Laboratory study of nitrate photolysis in Antarctic snow. I. Observed quantum yield, domain of photolysis, and secondary chemistry

    NASA Astrophysics Data System (ADS)

    Meusinger, Carl; Berhanu, Tesfaye A.; Erbland, Joseph; Savarino, Joel; Johnson, Matthew S.

    2014-06-01

    Post-depositional processes alter nitrate concentration and nitrate isotopic composition in the top layers of snow at sites with low snow accumulation rates, such as Dome C, Antarctica. Available nitrate ice core records can provide input for studying past atmospheres and climate if such processes are understood. It has been shown that photolysis of nitrate in the snowpack plays a major role in nitrate loss and that the photolysis products have a significant influence on the local troposphere as well as on other species in the snow. Reported quantum yields for the main reaction spans orders of magnitude - apparently a result of whether nitrate is located at the air-ice interface or in the ice matrix - constituting the largest uncertainty in models of snowpack NOx emissions. Here, a laboratory study is presented that uses snow from Dome C and minimizes effects of desorption and recombination by flushing the snow during irradiation with UV light. A selection of UV filters allowed examination of the effects of the 200 and 305 nm absorption bands of nitrate. Nitrate concentration and photon flux were measured in the snow. The quantum yield for loss of nitrate was observed to decrease from 0.44 to 0.003 within what corresponds to days of UV exposure in Antarctica. The superposition of photolysis in two photochemical domains of nitrate in snow is proposed: one of photolabile nitrate, and one of buried nitrate. The difference lies in the ability of reaction products to escape the snow crystal, versus undergoing secondary (recombination) chemistry. Modeled NOx emissions may increase significantly above measured values due to the observed quantum yield in this study. The apparent quantum yield in the 200 nm band was found to be ˜1%, much lower than reported for aqueous chemistry. A companion paper presents an analysis of the change in isotopic composition of snowpack nitrate based on the same samples as in this study.

  12. Laboratory study of nitrate photolysis in Antarctic snow. I. Observed quantum yield, domain of photolysis, and secondary chemistry.

    PubMed

    Meusinger, Carl; Berhanu, Tesfaye A; Erbland, Joseph; Savarino, Joel; Johnson, Matthew S

    2014-06-28

    Post-depositional processes alter nitrate concentration and nitrate isotopic composition in the top layers of snow at sites with low snow accumulation rates, such as Dome C, Antarctica. Available nitrate ice core records can provide input for studying past atmospheres and climate if such processes are understood. It has been shown that photolysis of nitrate in the snowpack plays a major role in nitrate loss and that the photolysis products have a significant influence on the local troposphere as well as on other species in the snow. Reported quantum yields for the main reaction spans orders of magnitude - apparently a result of whether nitrate is located at the air-ice interface or in the ice matrix - constituting the largest uncertainty in models of snowpack NOx emissions. Here, a laboratory study is presented that uses snow from Dome C and minimizes effects of desorption and recombination by flushing the snow during irradiation with UV light. A selection of UV filters allowed examination of the effects of the 200 and 305 nm absorption bands of nitrate. Nitrate concentration and photon flux were measured in the snow. The quantum yield for loss of nitrate was observed to decrease from 0.44 to 0.003 within what corresponds to days of UV exposure in Antarctica. The superposition of photolysis in two photochemical domains of nitrate in snow is proposed: one of photolabile nitrate, and one of buried nitrate. The difference lies in the ability of reaction products to escape the snow crystal, versus undergoing secondary (recombination) chemistry. Modeled NOx emissions may increase significantly above measured values due to the observed quantum yield in this study. The apparent quantum yield in the 200 nm band was found to be ∼1%, much lower than reported for aqueous chemistry. A companion paper presents an analysis of the change in isotopic composition of snowpack nitrate based on the same samples as in this study. PMID:24985636

  13. How Iron-Containing Proteins Control Dioxygen Chemistry: A Detailed Atomic Level Description Via Accurate Quantum Chemical and Mixed Quantum Mechanics/Molecular Mechanics Calculations.

    SciTech Connect

    Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.

    2003-03-01

    Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.

  14. Quantum chemistry and dynamics of the abstraction reaction of H atoms from formaldehyde

    NASA Astrophysics Data System (ADS)

    Siaï, A.; Oueslati, I.; Kerkeni, Boutheïna

    2016-08-01

    This work reports a reduced dimensionality rate constant calculation of the H-abstraction reaction from formaldehyde. Quantum scattering calculations are performed treating explicitly the bonds being broken and formed. Geometry optimisations and frequency calculations are done at the MP2/cc-pVTZ level while energies are calculated with the CCSD(T) method. An analytical potential energy surface was developed from a relatively small number of grid points. When compared to semi-classical approaches, the quantum scattering calculations show that quantum tunnelling yields large contributions at low temperatures. At 200 K, we note a difference of about 5 orders of magnitude between transition state theory (TST) and quantum rate constants. Our predicted results show that the quantum and the CVT/SCT rate constants are in reasonable agreement with the available experiment at high temperatures, but that the last one gives better agreement to experimental results at low temperatures.

  15. Characterizing Surface Acidic Sites in Mesoporous-Silica-Supported Tungsten Oxide Catalysts Using Solid State NMR and Quantum Chemistry Calculations

    SciTech Connect

    Hu, Jian Z.; Kwak, Ja Hun; Wang, Yong; Hu, Mary Y.; Turcu, Romulus VF; Peden, Charles HF

    2011-10-18

    The acidic sites in dispersed tungsten oxide supported on SBA-15 mesoporous silica were investigated using a combination of pyridine titration, both fast-, and slow-MAS {sup 15}N NMR, static {sup 2}H NMR, and quantum chemistry calculations. It is found that the bridged acidic -OH groups in surface adsorbed tungsten dimers (i.e., W-OH-W) are the Broensted acid sites. The unusually strong acidity of these Broensted acid sites is confirmed by quantum chemistry calculations. In contrast, terminal W-OH sites are very stable and only weakly acidic as are terminal Si-OH sites. Furthermore, molecular interactions between pyridine molecules and the dimer Broensted and terminal W-OH sites for dispersed tungsten oxide species is strong. This results in restricted molecular motion for the interacting pyridine molecules even at room temperature, i.e., a reorientation mainly about the molecular 2-fold axis. This restricted reorientation makes it possible to estimate the relative ratio of the Broensted (tungsten dimer) to the weakly acidic terminal W-OH sites in the catalyst using the slow-MAS {sup 1}H-{sup 15}N CP PASS method.

  16. A Component Approach to Collaborative Scientific Software Development: Tools and Techniques Utilized by the Quantum Chemistry Science Application Partnership

    DOE PAGESBeta

    Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; Sosonkina, Masha; Windus, Theresa L.

    2008-01-01

    Cutting-edge scientific computing software is complex, increasingly involving the coupling of multiple packages to combine advanced algorithms or simulations at multiple physical scales. Component-based software engineering (CBSE) has been advanced as a technique for managing this complexity, and complex component applications have been created in the quantum chemistry domain, as well as several other simulation areas, using the component model advocated by the Common Component Architecture (CCA) Forum. While programming models do indeed enable sound software engineering practices, the selection of programming model is just one building block in a comprehensive approach to large-scale collaborative development which must also addressmore » interface and data standardization, and language and package interoperability. We provide an overview of the development approach utilized within the Quantum Chemistry Science Application Partnership, identifying design challenges, describing the techniques which we have adopted to address these challenges and highlighting the advantages which the CCA approach offers for collaborative development.« less

  17. Efficient tree tensor network states (TTNS) for quantum chemistry: Generalizations of the density matrix renormalization group algorithm

    NASA Astrophysics Data System (ADS)

    Nakatani, Naoki; Chan, Garnet Kin-Lic

    2013-04-01

    We investigate tree tensor network states for quantum chemistry. Tree tensor network states represent one of the simplest generalizations of matrix product states and the density matrix renormalization group. While matrix product states encode a one-dimensional entanglement structure, tree tensor network states encode a tree entanglement structure, allowing for a more flexible description of general molecules. We describe an optimal tree tensor network state algorithm for quantum chemistry. We introduce the concept of half-renormalization which greatly improves the efficiency of the calculations. Using our efficient formulation we demonstrate the strengths and weaknesses of tree tensor network states versus matrix product states. We carry out benchmark calculations both on tree systems (hydrogen trees and π-conjugated dendrimers) as well as non-tree molecules (hydrogen chains, nitrogen dimer, and chromium dimer). In general, tree tensor network states require much fewer renormalized states to achieve the same accuracy as matrix product states. In non-tree molecules, whether this translates into a computational savings is system dependent, due to the higher prefactor and computational scaling associated with tree algorithms. In tree like molecules, tree network states are easily superior to matrix product states. As an illustration, our largest dendrimer calculation with tree tensor network states correlates 110 electrons in 110 active orbitals.

  18. A Surface Chemistry Approach to Enhancing Colloidal Quantum Dot Solids for Photovoltaics

    NASA Astrophysics Data System (ADS)

    Carey, Graham Hamilton

    Colloidal quantum dot (CQD) photovoltaic devices have improved rapidly over the past decade of research. By taking advantage of the quantum confinement effect, solar cells constructed using films of infrared-bandgap nanoparticles are able to capture previously untapped ranges of the solar energy spectrum. Additionally, films are fabricated using simple, cheap, reproducible solution processing techniques, enabling the creation of low-cost, flexible photovoltaic devices. A key factor limiting the creation of high efficiency CQD solar cells is the short charge carrier diffusion length in films. Driven by a combination of limited carrier mobility, poor nanoparticle surface passivation, and the presence of unexamined electrically active impurities throughout the film, the poor diffusion length limits the active layer thickness in CQD solar cells, leading to lower-than-desired light absorption, and curtailing the photocurrent generated by such devices. This thesis seeks to address poor diffusion length by addressing each of the limiting factors in turn. Electrical transport in quantum dot solids is examined in the context of improved quantum dot packing; methods are developed to improve packing by using actively densifying components, or by dramatically lowering the volume change required between quantum dots in solution and in solid state. Quantum dot surface passivation is improved by introducing a crucial secondary, small halide ligand source, and by surveying the impact of the processing environment on the final quality of the quantum dot surface. A heretofore unidentified impurity present in quantum dot solids is identified, characterized, and chemically eliminated. Finally, lessons learned through these experiments are combined into a single, novel materials system, leading to quantum dot devices with a significantly improved diffusion length (enhanced from 70 to 230 nm). This enabled thick, high current density (30 mA cm -2, compared to typical values in the 20

  19. Quantum Chemistry on Quantum Computers: A Polynomial-Time Quantum Algorithm for Constructing the Wave Functions of Open-Shell Molecules.

    PubMed

    Sugisaki, Kenji; Yamamoto, Satoru; Nakazawa, Shigeaki; Toyota, Kazuo; Sato, Kazunobu; Shiomi, Daisuke; Takui, Takeji

    2016-08-18

    Quantum computers are capable to efficiently perform full configuration interaction (FCI) calculations of atoms and molecules by using the quantum phase estimation (QPE) algorithm. Because the success probability of the QPE depends on the overlap between approximate and exact wave functions, efficient methods to prepare accurate initial guess wave functions enough to have sufficiently large overlap with the exact ones are highly desired. Here, we propose a quantum algorithm to construct the wave function consisting of one configuration state function, which is suitable for the initial guess wave function in QPE-based FCI calculations of open-shell molecules, based on the addition theorem of angular momentum. The proposed quantum algorithm enables us to prepare the wave function consisting of an exponential number of Slater determinants only by a polynomial number of quantum operations. PMID:27499026

  20. A Writing and Ethics Component for a Quantum Mechanics, Physical Chemistry Course

    ERIC Educational Resources Information Center

    Reilly, John T.; Strickland, Michael

    2010-01-01

    A writing-across-the-curriculum and ethics component is presented for a second-semester, physical chemistry course. The activity involves introducing ethical issues pertinent to scientists. Students are asked to read additional material, participate in discussions, and write essays and a paper on an ethical issue. The writing and discussion…

  1. Comparison of Chain Conformation of Poly(vinyl alcohol) in Solutions and Melts from Quantum Chemistry Based Molecular Dynamics Simulations

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Matsuda, Tsunetoshi; Yoon, Do; Langhoff, Stephen R. (Technical Monitor)

    1997-01-01

    Confirmations of 2,4-dihydroxypentane (DHP), a model molecule for poly(vinyl alcohol), have been studied by quantum chemistry (QC) calculations and molecular dynamics (MD) simulations. QC calculations at the 6-311G MP2 level show the meso tt conformer to be lowest in energy followed by the racemic tg, due to intramolecular hydrogen bond between the hydroxy groups. The Dreiding force field has been modified to reproduce the QC conformer energies for DHP. MD simulations using this force field have been carried out for DHP molecules in the gas phase, melt, and CHCl3 and water solutions. Extensive intramolecular hydrogen bonding is observed for the gas phase and CHCl3 solution, but not for the melt or aqueous solution, Such a condensed phase effect due to intermolecular interactions results in a drastic change in chain conformations, in agreement with experiments.

  2. Picture this: The value of multiple visual representations for student learning of quantum concepts in general chemistry

    NASA Astrophysics Data System (ADS)

    Allen, Emily Christine

    Mental models for scientific learning are often defined as, "cognitive tools situated between experiments and theories" (Duschl & Grandy, 2012). In learning, these cognitive tools are used to not only take in new information, but to help problem solve in new contexts. Nancy Nersessian (2008) describes a mental model as being "[loosely] characterized as a representation of a system with interactive parts with representations of those interactions. Models can be qualitative, quantitative, and/or simulative (mental, physical, computational)" (p. 63). If conceptual parts used by the students in science education are inaccurate, then the resulting model will not be useful. Students in college general chemistry courses are presented with multiple abstract topics and often struggle to fit these parts into complete models. This is especially true for topics that are founded on quantum concepts, such as atomic structure and molecular bonding taught in college general chemistry. The objectives of this study were focused on how students use visual tools introduced during instruction to reason with atomic and molecular structure, what misconceptions may be associated with these visual tools, and how visual modeling skills may be taught to support students' use of visual tools for reasoning. The research questions for this study follow from Gilbert's (2008) theory that experts use multiple representations when reasoning and modeling a system, and Kozma and Russell's (2005) theory of representational competence levels. This study finds that as students developed greater command of their understanding of abstract quantum concepts, they spontaneously provided additional representations to describe their more sophisticated models of atomic and molecular structure during interviews. This suggests that when visual modeling with multiple representations is taught, along with the limitations of the representations, it can assist students in the development of models for reasoning about

  3. Strong electron correlation in UO{sub 2}{sup −}: A photoelectron spectroscopy and relativistic quantum chemistry study

    SciTech Connect

    Li, Wei-Li; Jian, Tian; Lopez, Gary V.; Wang, Lai-Sheng; Su, Jing; Hu, Han-Shi; Cao, Guo-Jin; Li, Jun

    2014-03-07

    The electronic structures of actinide systems are extremely complicated and pose considerable challenges both experimentally and theoretically because of significant electron correlation and relativistic effects. Here we report an investigation of the electronic structure and chemical bonding of uranium dioxides, UO{sub 2}{sup −} and UO{sub 2}, using photoelectron spectroscopy and relativistic quantum chemistry. The electron affinity of UO{sub 2} is measured to be 1.159(20) eV. Intense detachment bands are observed from the UO{sub 2}{sup −} low-lying (7sσ{sub g}){sup 2}(5fϕ{sub u}){sup 1} orbitals and the more deeply bound O2p-based molecular orbitals which are separated by a large energy gap from the U-based orbitals. Surprisingly, numerous weak photodetachment transitions are observed in the gap region due to extensive two-electron transitions, suggesting strong electron correlations among the (7sσ{sub g}){sup 2}(5fϕ{sub u}){sup 1} electrons in UO{sub 2}{sup −} and the (7sσ{sub g}){sup 1}(5fϕ{sub u}){sup 1} electrons in UO{sub 2}. These observations are interpreted using multi-reference ab initio calculations with inclusion of spin-orbit coupling. The strong electron correlations and spin-orbit couplings generate orders-of-magnitude more detachment transitions from UO{sub 2}{sup −} than expected on the basis of the Koopmans’ theorem. The current experimental data on UO{sub 2}{sup −} provide a long-sought opportunity to arbitrating various relativistic quantum chemistry methods aimed at handling systems with strong electron correlations.

  4. Monte-Carlo Quantum Chemistry of Biogene Amines. Laser and Neutron Capture Effects

    SciTech Connect

    Glushkov, A. V.; Malinovskaya, S. V.; Khetselius, O. Yu.; Loboda, A. V.

    2009-03-09

    Monte-Carlo quantum calculation of the cluster consisting of the serotonine ST (histamine HM) molecules and 100 molecules of water is carried out. It is found that the zwitterion appears as expected to be strongly favoured with respect to neutral molecule. The perspective possibilities of laser and neutron capture action on different biomolecules are indicated.

  5. Monte-Carlo Quantum Chemistry of Biogene Amines. Laser and Neutron Capture Effects

    NASA Astrophysics Data System (ADS)

    Glushkov, A. V.; Malinovskaya, S. V.; Khetselius, O. Yu.; Loboda, A. V.

    2009-03-01

    Monte-Carlo quantum calculation of the cluster consisting of the serotonine ST (histamine HM) molecules and 100 molecules of water is carried out. It is found that the zwitterion appears as expected to be strongly favoured with respect to neutral molecule. The perspective possibilities of laser and neutron capture action on different biomolecules are indicated.

  6. The Variation Theorem Applied to H-2+: A Simple Quantum Chemistry Computer Project

    ERIC Educational Resources Information Center

    Robiette, Alan G.

    1975-01-01

    Describes a student project which requires limited knowledge of Fortran and only minimal computing resources. The results illustrate such important principles of quantum mechanics as the variation theorem and the virial theorem. Presents sample calculations and the subprogram for energy calculations. (GS)

  7. Linear and nonlinear optical properties of functionalized CdSe quantum dots prepared by plasma sputtering and wet chemistry.

    PubMed

    Humbert, Christophe; Dahi, Abdellatif; Dalstein, Laetitia; Busson, Bertrand; Lismont, Marjorie; Colson, Pierre; Dreesen, Laurent

    2015-05-01

    We develop an innovative manufacturing process, based on radio-frequency magnetron sputtering (RFMS), to prepare neat CdSe quantum dots (QDs) on glass and silicon substrates and further chemically functionalize them. In order to validate the fabrication protocol, their optical properties are compared with those of QDs obtained from commercial solutions and deposited by wet chemistry on the substrates. Firstly, AFM measurements attest that nano-objects with a mean diameter around 13 nm are located on the substrate after RFMS treatment. Secondly, the UV-Vis absorption study of this deposited layer shows a specific optical absorption band, located at 550 nm, which is related to a discrete energy level of QDs. Thirdly, by using two-color sum-frequency generation (2C-SFG) nonlinear optical spectroscopy, we show experimentally the functionalization efficiency of the RFMS CdSe QDs layer with thiol derived molecules, which is not possible on the QDs layer prepared by wet chemistry due to the surfactant molecules from the native solution. Finally, 2C-SFG spectroscopy, performed at different visible wavelengths, highlights modifications of the vibration mode shape whatever the QDs deposition method, which is correlated to the discrete energy level of the QDs. PMID:25596370

  8. Interfacial Atmospheric Chemistry: Quantum Chemical Calculations on the Mechanism of Protonation and Oligomerization of Isoprene on Aqueous Surfaces

    NASA Astrophysics Data System (ADS)

    Mishra, H.; Colussi, A. J.; Enami, S.; Nielsen, R. J.; Hoffmann, M. R.; Goddard, W. A.

    2012-12-01

    It has become increasingly apparent that atmospheric chemistry involves more than gas-phase reactions. Key processes, such as the decay of NO2 in urban plumes and the associated daytime formation of HONO, and the rapid chemistries observed in and over forest canopies at nighttime defy explanation by conventional atmospheric chemistry mechanisms. We have recently reported experimental results on several gas-liquid reactions of atmospheric interest, such as the facile protonation of gaseous isoprene on mildly acidic (pH < 4) water. Although interfacial proton transfers, such as the one involved in the protonation of gaseous isoprene, also participate in cloud and ocean acidification, bioenergetics coupling, 'on-water' catalysis, self-assembly and molecular recognition, little is known about the molecular mechanisms of such reactions. Herein we apply quantum mechanics to investigate how biogenic or anthropogenic olefins may get protonated and undergo oligomerization at the air-water interface by performing model calculations on small water clusters carrying an excess proton as surrogates for the surface of mildly acidic water as sensed by gaseous isoprene (ISO). We find that ISO binds weakly to the surface of water and accepts a proton from H+(H2O)3, leading to ISOH+ via a proton transfer hindered by a ΔG1‡ = 5.6 kcal mol-1 kinetic barrier. Subsequently, another ISO attaches loosely to this ensemble, before being attacked by the ISOH+. This process, which represents the first step of the cationic polymerization of ISO, is hindered by a similar ΔG2‡ = 5.7 kcal mol-1 barrier. Our theoretical results are consistent with experimental (~ 10-4) uptake coefficients for ISO measured on acidic water.

  9. A potential from quantum chemistry for thermodynamic property predictions for methanethiol

    NASA Astrophysics Data System (ADS)

    Garrison, Stephen L.; Sandler, Stanley I.

    2005-08-01

    An ab initio potential for methanethiol is determined by computing quantum-chemical interaction energies for a range of orientations and center-of-mass separation distances. These energies are initially fitted to a pairwise-additive, site-site Morse-C6 intermolecular potential. Additional interaction energies were then calculated at separation distances determined to be important from the angle-averaged Mayer f function calculated with the initial potential. This expanded set of interaction energies is then fitted using Boltzmann-type weighting to obtain the final intermolecular potential. Although there are some discrepancies in the fit for a particular type of orientation, the phase behavior calculated from Gibbs ensemble Monte Carlo simulations using this final potential is in very good agreement with experimental data. The prescription used here for obtaining the optimum potential from quantum-chemical methods should be applicable to other systems.

  10. Abstract Data Types In The Construction Of Knowledge-Based Quantum Chemistry Software

    NASA Astrophysics Data System (ADS)

    Kilpatrick, P. L.; Scott, N. S.

    Recently, Diercksen and Hall (1) presented the OpenMol Program: a proposal for an open, flexible and intelligent software system for performing quantum chemical computations. Central to their proposal was the observation that there is a close relationship between an abstract data type operation and a production rule in a rule-based expert system. The aim of this paper is to explore the establishment of a sound theoretical foundation for this relationship.

  11. Yb-based heavy fermion compounds and field tuned quantum chemistry

    SciTech Connect

    Mun, Eundeok

    2010-01-01

    The motivation of this dissertation was to advance the study of Yb-based heavy fermion (HF) compounds especially ones related to quantum phase transitions. One of the topics of this work was the investigation of the interaction between the Kondo and crystalline electric field (CEF) energy scales in Yb-based HF systems by means of thermoelectric power (TEP) measurements. In these systems, the Kondo interaction and CEF excitations generally give rise to large anomalies such as maxima in ρ(T) and as minima in S(T). The TEP data were use to determine the evolution of Kondo and CEF energy scales upon varying transition metals for YbT2Zn20 (T = Fe, Ru, Os, Ir, Rh, and Co) compounds and applying magnetic fields for YbAgGe and YbPtBi. For YbT2Zn20 and YbPtBi, the Kondo and CEF energy scales could not be well separated in S(T), presumably because of small CEF level splittings. A similar effect was observed for the magnetic contribution to the resistivity. For YbAgGe, S(T) has been successfully applied to determine the Kondo and CEF energy scales due to the clear separation between the ground state and thermally excited CEF states. The Kondo temperature, TK, inferred from the local maximum in S(T), remains finite as magnetic field increases up to 140 kOe. In this dissertation we have examined the heavy quasi-particle behavior, found near the field tuned AFM quantum critical point (QCP), with YbAgGe and YbPtBi. Although the observed nFL behaviors in the vicinity of the QCP are different between YbAgGe and YbPtBi, the constructed H-T phase diagram including the two crossovers are similar. For both YbAgGe and YbPtBi, the details of the quantum criticality turn out to be complicated. We expect that YbPtBi will provide an additional example of field tuned quantum criticality, but clearly there are further experimental investigations left and more ideas needed to understand the basic physics of field-induced quantum

  12. Spectroscopic accuracy directly from quantum chemistry: Application to ground and excited states of beryllium dimer

    SciTech Connect

    Sharma, Sandeep; Booth, George H.; Chan, Garnet Kin-Lic; Yanai, Takeshi; Umrigar, C. J.

    2014-03-14

    We combine explicit correlation via the canonical transcorrelation approach with the density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods to compute a near-exact beryllium dimer curve, without the use of composite methods. In particular, our direct density matrix renormalization group calculations produce a well-depth of D{sub e} = 931.2 cm{sup −1} which agrees very well with recent experimentally derived estimates D{sub e} = 929.7±2 cm{sup −1} [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D{sub e}= 934.6 cm{sup −1} [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D{sub e} = 938±15 cm{sup −1} [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D{sub e}=935.1±10 cm{sup −1} [J. Koput, Phys. Chem. Chem. Phys. 13, 20311 (2011)]. Our results suggest possible inaccuracies in the functional form of the potential used at shorter bond lengths to fit the experimental data [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)]. With the density matrix renormalization group we also compute near-exact vertical excitation energies at the equilibrium geometry. These provide non-trivial benchmarks for quantum chemical methods for excited states, and illustrate the surprisingly large error that remains for 1 {sup 1}Σ{sub g}{sup −} state with approximate multi-reference configuration interaction and equation-of-motion coupled cluster methods. Overall, we demonstrate that explicitly correlated density matrix renormalization group and initiator full configuration interaction quantum Monte Carlo methods allow us to fully converge to the basis set and correlation limit of the non-relativistic Schrödinger equation in small molecules.

  13. Two Conformers of N,N-Diethylpropionamide As Observed by Microwave Spectroscopy and Quantum Chemistry.

    PubMed

    Kannengießer, Raphaela; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2016-08-01

    The microwave spectra of two conformers of N,N-diethylpropionamide were recorded using a molecular beam Fourier transform microwave spectrometer operating in the frequency range 2-26.5 GHz. Hyperfine splittings arising from the (14)N quadrupole coupling effect were observed and analyzed. Fits using a rigid rotor model with centrifugal distortion correction and first-order perturbation approach for the quadrupole coupling yielded highly accurate molecular parameters and standard deviations within the measurement accuracy for both conformers. Complementary quantum chemical calculations were carried out for a conformational analysis, theoretical values of the spectroscopic constants, and the (14)N nuclear quadrupole coupling constants. PMID:27412132

  14. Visually impaired researchers get their hands on quantum chemistry: application to a computational study on the isomerization of a sterol.

    PubMed

    Lounnas, Valère; Wedler, Henry B; Newman, Timothy; Schaftenaar, Gijs; Harrison, Jason G; Nepomuceno, Gabriella; Pemberton, Ryan; Tantillo, Dean J; Vriend, Gert

    2014-11-01

    In molecular sciences, articles tend to revolve around 2D representations of 3D molecules, and sighted scientists often resort to 3D virtual reality software to study these molecules in detail. Blind and visually impaired (BVI) molecular scientists have access to a series of audio devices that can help them read the text in articles and work with computers. Reading articles published in this journal, though, is nearly impossible for them because they need to generate mental 3D images of molecules, but the article-reading software cannot do that for them. We have previously designed AsteriX, a web server that fully automatically decomposes articles, detects 2D plots of low molecular weight molecules, removes meta data and annotations from these plots, and converts them into 3D atomic coordinates. AsteriX-BVI goes one step further and converts the 3D representation into a 3D printable, haptic-enhanced format that includes Braille annotations. These Braille-annotated physical 3D models allow BVI scientists to generate a complete mental model of the molecule. AsteriX-BVI uses Molden to convert the meta data of quantum chemistry experiments into BVI friendly formats so that the entire line of scientific information that sighted people take for granted-from published articles, via printed results of computational chemistry experiments, to 3D models-is now available to BVI scientists too. The possibilities offered by AsteriX-BVI are illustrated by a project on the isomerization of a sterol, executed by the blind co-author of this article (HBW). PMID:25091066

  15. Quantum science in secondary chemistry: Influence of teachers' beliefs and knowledge on the use of interactive computer models

    NASA Astrophysics Data System (ADS)

    Robblee, Karen M.

    Current science education reform efforts promote inquiry-based learning, a goal that requires appropriate tools and instructional approaches. This study investigated the influence of the beliefs and knowledge of four experienced secondary chemistry teachers in their use of new instructional software that generates models of atoms and molecules based on quantum mechanics. The software, which was developed through a National Science Foundation funded project, Quantum Science Across Disciplines (QSAD), was designed to promote inquiry learning. Qualitative research methods were used for this multiple case study. Data from surveys, interviews, and extended classroom observations revealed a close correlation between a teacher's model of the learner and his or her model of teaching. Combined models of learner and teacher had the greatest influence on their decisions about implementing QSAD software. Teachers who espoused a constructivist model of learning and related models of teaching used the software to promote student investigations and inductive approaches to learning. Other factors that appeared to support the use of inquiry methods included sufficient time for students to investigate phenomena, the extent of the teacher's pedagogical content knowledge, and the amount of training using QSAD software. The Views-On-Science-Technology-Society (VOSTS) instrument was used to compare the informants' beliefs about the epistemology of science to their classroom practices. Data related to the role of teachers' beliefs about scientific knowledge were inconclusive, and VOSTS results were inconsistent with the informants' stated beliefs. All four cases revealed that the teachers acted as agents of the school culture. In schools that promoted development of critical thinking, questioning, and self-direction in students, teachers were more likely to use a variety of instructional methods and emphasize construction of knowledge. These findings suggest that educational reform

  16. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry

    PubMed Central

    Frutos, Luis Manuel; Andruniów, Tadeusz; Santoro, Fabrizio; Ferré, Nicolas; Olivucci, Massimo

    2007-01-01

    The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at ≈60-fs delay, initiates a space saving “asynchronous bicycle-pedal or crankshaft” motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy. PMID:17470789

  17. Solution Structure of Azidoalcohols Studied by IR Spectroscopy and Quantum Chemistry

    NASA Astrophysics Data System (ADS)

    Karpov, S. V.; Lodygina, V. P.; Malkov, G. V.

    2014-03-01

    Features of the association of azidoalcohols in CH2Cl2 were studied by IR spectroscopy using 1,3-diazidopropan-2-ol and 1-azidoethan-2-ol as examples. It was established that the investigated compounds could exist as two types of [OH…N3] associates. In the fi rst instance, the OH group was affected by strong intermolecular interactions like in common alcohols; in the second, the interactions were much weaker. Density functional theory and quantum theory of atoms-in-molecules were used to determine the structures of such associates and the energy parameters of the observed intermolecular interactions. Also, the experimental and calculated frequencies of OH stretching vibrations were correlated.

  18. Extended Lagrangian quantum molecular dynamics simulations of shock-induced chemistry in hydrocarbons

    SciTech Connect

    Sanville, Edward J; Bock, Nicolas; Challacombe, William M; Cawkwell, Marc J; Niklasson, Anders M N; Dattelbaum, Dana M; Sheffield, Stephen; Sewell, Thomas D

    2010-01-01

    A set of interatomic potentials for hydrocarbons that are based upon the self-consistent charge transfer tight-binding approximation to density functional theory have been developed and implemented into the quantum molecular dynamics code ''LATTE''. The interatomic potentials exhibit an outstanding level of transferability and have been applied in molecular dynamics simulations of tert-butylacetylene under thermodynamic conditions that correspond to its single-shock Hugoniot. We have achieved precise conservation of the total energy during microcanonical molecular dynamics trajectories under incomplete convergence via the extended Lagrangian Born-Oppenheimer molecular dynamics formalism. In good agreement with the results of a series of flyer-plate impact experiments, our SCC-TB molecular dynamics simulations show that tert-butylactylene molecules polymerize at shock pressures around 6.1 GPa.

  19. Tracking the excited-state time evolution of the visual pigment with multiconfigurational quantum chemistry.

    PubMed

    Frutos, Luis Manuel; Andruniów, Tadeusz; Santoro, Fabrizio; Ferré, Nicolas; Olivucci, Massimo

    2007-05-01

    The primary event that initiates vision is the photoinduced isomerization of retinal in the visual pigment rhodopsin (Rh). Here, we use a scaled quantum mechanics/molecular mechanics potential that reproduces the isomerization path determined with multiconfigurational perturbation theory to follow the excited-state evolution of bovine Rh. The analysis of a 140-fs trajectory provides a description of the electronic and geometrical changes that prepare the system for decay to the ground state. The data uncover a complex change of the retinal backbone that, at approximately 60-fs delay, initiates a space saving "asynchronous bicycle-pedal or crankshaft" motion, leading to a conical intersection on a 110-fs time scale. It is shown that the twisted structure achieved at decay features a momentum that provides a natural route toward the photoRh structure recently resolved by using femtosecond-stimulated Raman spectroscopy. PMID:17470789

  20. Quantum chemistry study of molecular structure and vibrational spectrum of naproxen

    NASA Astrophysics Data System (ADS)

    Liu, Lekun; Gao, Hongwei

    2012-02-01

    The purpose of this research was to compare the performance of different DFT methods at different basis sets in predicting geometry and vibrational spectrum of naproxen. The molecular structure and infrared spectrum of naproxen was studied. Quantum chemical calculations using density functional theory (DFT) with functions LSDA, B3LYP, B3PW91, BPV86, mPW1PW91 and PBEPBE at various basis set levels (LANL2DZ, SDD, 3-21G, 6-31G, 6-311G and STO-3G) were performed. The computed result indicates that LSDA/6-311G level is distinctly superior to all the remaining DFT methods in predicting molecular structure of naproxen. The vibrational spectral analysis indicates the LSDA/3-21G level and LSDA/6-311G level are both better than the other methods at all the remaining basis sets.

  1. Acetyl Methyl Torsion in N-Ethylacetamide: A Challenge for Microwave Spectroscopy and Quantum Chemistry.

    PubMed

    Kannengießer, Raphaela; Lach, Marcel J; Stahl, Wolfgang; Nguyen, Ha Vinh Lam

    2015-06-22

    The gas-phase structures and parameters describing acetyl methyl torsion of N-ethylacetamide are determined with high accuracy, using a combination of molecular beam Fourier-transform microwave spectroscopy and quantum chemical calculations. Conformational studies at the MP2 level of theory yield four minima on the energy surface. The most energetically favorable conformer, which possesses C1 symmetry, is assigned. Due to the torsional barrier of 73.4782(1) cm(-1) of the acetyl methyl group, fine splitting up to 4.9 GHz is found in the spectrum. The conformational structure is not only confirmed by the rotational constants, but also by the orientation of the internal rotor. The (14) N quadrupole hyperfine splittings are analyzed and the deduced coupling constants are compared with the calculated values. PMID:25916631

  2. High-throughput quantum chemistry and virtual screening for OLED material components

    NASA Astrophysics Data System (ADS)

    Halls, Mathew D.; Giesen, David J.; Hughes, Thomas F.; Goldberg, Alexander; Cao, Yixiang

    2013-09-01

    Computational structure enumeration, analysis using an automated simulation workflow and filtering of large chemical structure libraries to identify lead systems, has become a central paradigm in drug discovery research. Transferring this paradigm to challenges in materials science is now possible due to advances in the speed of computational resources and the efficiency and stability of chemical simulation packages. State-of-the-art software tools that have been developed for drug discovery can be applied to efficiently explore the chemical design space to identify solutions for problems such as organic light-emitting diode material components. In this work, virtual screening for OLED materials based on intrinsic quantum mechanical properties is illustrated. Also, a new approach to more reliably identify candidate systems is introduced that is based on the chemical reaction energetics of defect pathways for OLED materials.

  3. Introducing phase transitions to quantum chemistry: from Trouton's rule to first principles vaporization entropies.

    PubMed

    Spickermann, Christian; Lehmann, Sebastian B C; Kirchner, Barbara

    2008-06-28

    In the present study, we employ quantum cluster equilibrium calculations on a small water cluster set in order to derive thermochemical equilibrium properties of the liquid phase as well as the liquid-vapor phase transition. The focus is set on the calculation of liquid phase entropies, from which entropies of vaporization at the normal boiling point of water are derived. Different electronic structure methods are compared and the influences of basis set size and of cooperative effects are discussed. In line with a previous study on the subject [B. Kirchner, J. Chem. Phys. 123, 204116 (2005)], we find that the neglect of cooperativity leads to large errors in the equilibrium cluster populations as well as in the obtained entropy values. In contrast, a correct treatment of the intermolecular many-body interaction yields liquid phase entropies and phase transition entropies being in very good agreement with the experimental reference, thus demonstrating that the quantum cluster equilibrium partition function intrinsically accounts for the shortcomings of the ideal gas partition function often employed in first principles entropy calculations. Comparing the calculated vaporization entropies to the value predicted by Trouton's rule, it is observed that for entropy calculations the consideration of intracluster cooperative effects is more important than the explicit treatment of the intercluster association even in a highly associated liquid such as water. The decomposition of entropy into contributions due to different degrees of freedom implies the need for the accurate treatment of particle indistinguishability and free volume of translation, whereas minor influences should be expected from the vibrational and rotational degrees of freedom and none from the electronic degrees of freedom. PMID:18618941

  4. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design

    PubMed Central

    Xie, Neng-Zhong; Du, Qi-Shi; Li, Jian-Xiu; Huang, Ri-Bo

    2015-01-01

    Objectives Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. Methods Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. Results The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. Conclusion (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions. PMID:26339784

  5. Ab initio quantum chemistry in parallel-portable tools and applications

    SciTech Connect

    Harrison, R.J.; Shepard, R. ); Kendall, R.A. )

    1991-01-01

    In common with many of the computational sciences, ab initio chemistry faces computational constraints to which a partial solution is offered by the prospect of highly parallel computers. Ab initio codes are large and complex (O(10{sup 5}) lines of FORTRAN), representing a significant investment of communal effort. The often conflicting requirements of portability and efficiency have been successfully resolved on vector computers by reliance on matrix oriented kernels. This proves inadequate even upon closely-coupled shared-memory parallel machines. We examine the algorithms employed during a typical sequence of calculations. Then we investigate how efficient portable parallel implementations may be derived, including the complex multi-reference singles and doubles configuration interaction algorithm. A portable toolkit, modeled after the Intel iPSC and the ANL-ACRF PARMACS, is developed, using shared memory and TCP/IP sockets. The toolkit is used as an initial platform for programs portable between LANS, Crays and true distributed-memory MIMD machines. Timings are presented. 53 refs., 4 tabs.

  6. The chemical mechanism of the limonene ozonolysis reaction in the SOA formation: A quantum chemistry and direct dynamic study

    NASA Astrophysics Data System (ADS)

    Sun, Tingli; Wang, Yudong; Zhang, Chenxi; Sun, Xiaomin; Wang, Wenxing

    2011-03-01

    The ozonolysis of limonene is one of the most important processes for secondary organic aerosol formation and a detailed understanding of the atmospheric chemistry of d-limonene is highly urgent. In this paper, the reaction of d-limonene with O 3 has been studied using high level molecular orbital theory. A detailed description of the possible ozonolysis mechanism in the presence of H 2O or NO is provided. The main products obtained are keto-limonene, limononic acid and 7OH-lim, which are low vapor pressure compounds. On the basis of the quantum chemical information, the direct dynamic calculation is performed and the rate constants are calculated over a temperature range of 200˜800 K using the transition state theory and canonical varitional transition state theory with small-curvature tunneling effect. The four-parameter formula of rate constants with the temperature is fitted and the lifetimes of the reaction species in the troposphere are estimated according to the rate constants, which can provide helpful information to the model simulation study.

  7. Comments on the molecular geometry of ferrocene: The dangers of using quantum chemistry programs as black boxes.

    PubMed

    Martin, Jason; Baker, Jon; Pulay, Peter

    2009-04-30

    The dangers of using standard quantum chemistry programs as black boxes is illustrated by analyzing some results in a recent paper published in this journal (Zhang et al., J Comput Chem 2007, 28, 2260). The main danger is that nonlinear optimizations of both the wavefunction and the molecular geometry may converge to higher local minima or to saddle points, producing misleading results. For instance, some of the calculated molecular geometries of ferrocene in the aforementioned paper correspond to an SCF solution that converged to an excited state. This is the cause of the apparent large variation in the calculated iron-ring distance with the basis set. Another problem we noticed is that the source of the diffuse functions used in the earlier work in connection with the 6-31G and 6-311G basis sets for transition metals is not specified in the literature or the program manual. They are also a poor match for the 6-31G basis set. We re-emphasize that the 6-31G basis set used in this paper lacks the necessary diffuse d-type functions for the late first-row transition metals, and ought to be replaced by the m6-31G basis that offers a more balanced description of the atomic valence states. PMID:18780342

  8. RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium

    PubMed Central

    Dutra, José Diogo L.; Filho, Manoel A. M.; Rocha, Gerd B.; Simas, Alfredo M.; Freire, Ricardo O.

    2015-01-01

    The RM1 model for the lanthanides is parameterized for complexes of the trications of lanthanum, cerium, and praseodymium. The semiempirical quantum chemical model core stands for the [Xe]4fn electronic configuration, with n =0,1,2 for La(III), Ce(III), and Pr(III), respectively. In addition, the valence shell is described by three electrons in a set of 5d, 6s, and 6p orbitals. Results indicate that the present model is more accurate than the previous sparkle models, although these are still very good methods provided the ligands only possess oxygen or nitrogen atoms directly coordinated to the lanthanide ion. For all other different types of coordination, the present RM1 model for the lanthanides is much superior and must definitely be used. Overall, the accuracy of the model is of the order of 0.07Å for La(III) and Pr(III), and 0.08Å for Ce(III) for lanthanide-ligand atom distances which lie mostly around the 2.3Å to 2.6Å interval, implying an error around 3% only. PMID:26132289

  9. Communication: Towards ab initio self-energy embedding theory in quantum chemistry.

    PubMed

    Lan, Tran Nguyen; Kananenka, Alexei A; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces. PMID:26723581

  10. Gas-Phase Reactivity of Cesium-Containing Species by Quantum Chemistry.

    PubMed

    Šulková, Katarína; Cantrel, Laurent; Louis, Florent

    2015-09-01

    Thermodynamics and kinetics of cesium species reactions have been studied by using high-level quantum chemical tools. A systematic theoretical study has been done to find suitable methodology for calculation of reliable thermodynamic properties, allowing us to determine bimolecular rate constants with appropriate kinetic theories of gas-phase reactions. Four different reactions have been studied in this work: CsO + H2 = CsOH + H (R1), Cs + HI = CsI + H (R2), CsI + H2O = CsOH + HI (R3), and CsI + OH = CsOH + I (R4). All reactions involve steam, hydrogen, and iodine in addition of cesium. Most of the reactions are fast and (R3) and (R4) proceed even without energetic barrier. In terms of chemical reactivity in the reactor coolant system (RCS) in the case of severe accident, it can be expected that there will be no kinetic limitations for main cesium species (CsOH and CsI) transported along the RCS. Cs chemical speciation inside the RCS should be governed by the thermodynamics. PMID:26237575

  11. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    NASA Astrophysics Data System (ADS)

    Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika

    2015-12-01

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green's function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  12. RM1 Semiempirical Quantum Chemistry: Parameters for Trivalent Lanthanum, Cerium and Praseodymium.

    PubMed

    Dutra, José Diogo L; Filho, Manoel A M; Rocha, Gerd B; Simas, Alfredo M; Freire, Ricardo O

    2015-01-01

    The RM1 model for the lanthanides is parameterized for complexes of the trications of lanthanum, cerium, and praseodymium. The semiempirical quantum chemical model core stands for the [Xe]4fn electronic configuration, with n =0,1,2 for La(III), Ce(III), and Pr(III), respectively. In addition, the valence shell is described by three electrons in a set of 5d, 6s, and 6p orbitals. Results indicate that the present model is more accurate than the previous sparkle models, although these are still very good methods provided the ligands only possess oxygen or nitrogen atoms directly coordinated to the lanthanide ion. For all other different types of coordination, the present RM1 model for the lanthanides is much superior and must definitely be used. Overall, the accuracy of the model is of the order of 0.07Å for La(III) and Pr(III), and 0.08Å for Ce(III) for lanthanide-ligand atom distances which lie mostly around the 2.3Å to 2.6Å interval, implying an error around 3% only. PMID:26132289

  13. Neural network approach to quantum-chemistry data: Accurate prediction of density functional theory energies

    NASA Astrophysics Data System (ADS)

    Balabin, Roman M.; Lomakina, Ekaterina I.

    2009-08-01

    Artificial neural network (ANN) approach has been applied to estimate the density functional theory (DFT) energy with large basis set using lower-level energy values and molecular descriptors. A total of 208 different molecules were used for the ANN training, cross validation, and testing by applying BLYP, B3LYP, and BMK density functionals. Hartree-Fock results were reported for comparison. Furthermore, constitutional molecular descriptor (CD) and quantum-chemical molecular descriptor (QD) were used for building the calibration model. The neural network structure optimization, leading to four to five hidden neurons, was also carried out. The usage of several low-level energy values was found to greatly reduce the prediction error. An expected error, mean absolute deviation, for ANN approximation to DFT energies was 0.6±0.2 kcal mol-1. In addition, the comparison of the different density functionals with the basis sets and the comparison of multiple linear regression results were also provided. The CDs were found to overcome limitation of the QD. Furthermore, the effective ANN model for DFT/6-311G(3df,3pd) and DFT/6-311G(2df,2pd) energy estimation was developed, and the benchmark results were provided.

  14. Communication: Towards ab initio self-energy embedding theory in quantum chemistry

    SciTech Connect

    Lan, Tran Nguyen; Kananenka, Alexei A.; Zgid, Dominika

    2015-12-28

    The self-energy embedding theory (SEET), in which the active space self-energy is embedded in the self-energy obtained from a perturbative method treating the non-local correlation effects, was recently developed in our group. In SEET, the double counting problem does not appear and the accuracy can be improved either by increasing the perturbation order or by enlarging the active space. This method was first calibrated for the 2D Hubbard lattice showing promising results. In this paper, we report an extension of SEET to quantum chemical ab initio Hamiltonians for applications to molecular systems. The self-consistent second-order Green’s function method is used to describe the non-local correlations, while the full configuration interaction method is carried out to capture strong correlation within the active space. Using few proof-of-concept examples, we show that SEET yields results of comparable quality to n-electron valence state second-order perturbation theory with the same active space, and furthermore, the full active space can be split into smaller active spaces without further implementation. Moreover, SEET avoids intruder states and does not require any high-order reduced density matrices. These advantages show that SEET is a promising method to describe physical and chemical properties of challenging molecules requiring large active spaces.

  15. Quantum dot surface chemistry and functionalization for cell targeting and imaging.

    PubMed

    Bilan, Regina; Fleury, Fabrice; Nabiev, Igor; Sukhanova, Alyona

    2015-04-15

    Quantum dots (QDs) are highly fluorescent nanoscale crystals with size-dependent emission spectra. Due to their excellent photophysical properties, QDs are a promising alternative to organic fluorescent dyes and fluorescent proteins for cell targeting, imaging, and drug delivery. For biomedical applications, QDs should be chemically modified to be stable in aqueous solutions and tagged with the recognition molecules or drugs. Here, we review surface modification approaches to, and strategies for, conjugation of bioactive molecules with QDs. There are a variety of methods of QD surface modification and QD incorporation into larger delivery systems that yield fluorescent nanocarriers from 10 nm to several micrometers. Conjugates of QDs with peptides, proteins, antibodies, oligonucleotides, and small molecules have been used for fluorescent targeting, tracking, and imaging both in vitro and in vivo. Due to an extremely high stability to photobleaching, QDs were used for long-term visualization. QD applications pave the way for new generations of ultrasensitive detection, diagnostic systems, as well as drug delivery approaches, combining accurate targeting, delivery, and imaging in a single assay. PMID:25710410

  16. Control of PbSe Quantum Dot Surface Chemistry and Photophysics Using an Alkylselenide Ligand

    SciTech Connect

    Hughes, B. K.; Ruddy, D. A.; Blackburn, J. L.; Smith, D. K.; Bergren, M. R.; Nozik, A. J.; Johnson, J. C.; Beard, M. C.

    2012-06-26

    We have synthesized alkylselenide reagents to replace the native oleate ligand on PbSe quantum dots (QDs) in order to investigate the effect of surface modification on their stoichiometry, photophysics, and air stability. The alkylselenide reagent removes all of the oleate on the QD surface and results in Se addition; however, complete Se enrichment does not occur, achieving a 53% decrease in the amount of excess Pb for 2 nm diameter QDs and a 23% decrease for 10 nm QDs. Our analysis suggests that the Se ligand preferentially binds to the {l_brace}111{r_brace} faces, which are more prevalent in smaller QDs. We find that attachment of the alkylselenide ligand to the QD surface enhances oxidative resistance, likely resulting from a more stable bond between surface Pb atoms and the alkylselenide ligand compared to Pb-oleate. However, binding of the alkylselenide ligand produces a separate nonradiative relaxation route that partially quenches PL, suggesting the formation of a dark hole-trap.

  17. Quantum Chemistry for Solvated Molecules on Graphical Processing Units Using Polarizable Continuum Models.

    PubMed

    Liu, Fang; Luehr, Nathan; Kulik, Heather J; Martínez, Todd J

    2015-07-14

    The conductor-like polarization model (C-PCM) with switching/Gaussian smooth discretization is a widely used implicit solvation model in chemical simulations. However, its application in quantum mechanical calculations of large-scale biomolecular systems can be limited by computational expense of both the gas phase electronic structure and the solvation interaction. We have previously used graphical processing units (GPUs) to accelerate the first of these steps. Here, we extend the use of GPUs to accelerate electronic structure calculations including C-PCM solvation. Implementation on the GPU leads to significant acceleration of the generation of the required integrals for C-PCM. We further propose two strategies to improve the solution of the required linear equations: a dynamic convergence threshold and a randomized block-Jacobi preconditioner. These strategies are not specific to GPUs and are expected to be beneficial for both CPU and GPU implementations. We benchmark the performance of the new implementation using over 20 small proteins in solvent environment. Using a single GPU, our method evaluates the C-PCM related integrals and their derivatives more than 10× faster than that with a conventional CPU-based implementation. Our improvements to the linear solver provide a further 3× acceleration. The overall calculations including C-PCM solvation require, typically, 20-40% more effort than that for their gas phase counterparts for a moderate basis set and molecule surface discretization level. The relative cost of the C-PCM solvation correction decreases as the basis sets and/or cavity radii increase. Therefore, description of solvation with this model should be routine. We also discuss applications to the study of the conformational landscape of an amyloid fibril. PMID:26575750

  18. From C60 to Infinity: Large-Scale Quantum Chemistry Calculations of the Heats of Formation of Higher Fullerenes.

    PubMed

    Chan, Bun; Kawashima, Yukio; Katouda, Michio; Nakajima, Takahito; Hirao, Kimihiko

    2016-02-01

    We have carried out large-scale computational quantum chemistry calculations on the K computer to obtain heats of formation for C60 and some higher fullerenes with the DSD-PBE-PBE/cc-pVQZ double-hybrid density functional theory method. Our best estimated values are 2520.0 ± 20.7 (C60), 2683.4 ± 17.7 (C70), 2862.0 ± 18.5 (C76), 2878.8 ± 13.3 (C78), 2946.4 ± 14.5 (C84), 3067.3 ± 15.4 (C90), 3156.6 ± 16.2 (C96), 3967.7 ± 33.4 (C180), 4364 (C240) and 5415 (C320) kJ mol(-1). In our assessment, we also find that the B3-PW91-D3BJ and BMK-D3(BJ) functionals perform reasonably well. Using the convergence behavior for the calculated per-atom heats of formation, we obtained the formula ΔfH per carbon = 722n(-0.72) + 5.2 kJ mol(-1) (n = the number of carbon atoms), which enables an estimation of ΔfH for higher fullerenes more generally. A slow convergence to the graphene limit is observed, which we attribute to the relatively small proportion of fullerene carbons that are in "low-strain" regions. We further propose that it would take tens, if not hundreds, of thousands of carbons for a fullerene to roughly approach the limit. Such a distinction may be a contributing factor to the discrete properties between the two types of nanomaterials. During the course of our study, we also observe a fairly reliable means for the theoretical calculation of heats of formation for medium-sized fullerenes. This involves the use of isodesmic-type reactions with fullerenes of similar sizes to provide a good balance of the chemistry and to minimize the use of accompanying species. PMID:26799740

  19. Combustion chemistry

    SciTech Connect

    Brown, N.J.

    1993-12-01

    This research is concerned with the development and use of sensitivity analysis tools to probe the response of dependent variables to model input variables. Sensitivity analysis is important at all levels of combustion modeling. This group`s research continues to be focused on elucidating the interrelationship between features in the underlying potential energy surface (obtained from ab initio quantum chemistry calculations) and their responses in the quantum dynamics, e.g., reactive transition probabilities, cross sections, and thermal rate coefficients. The goals of this research are: (i) to provide feedback information to quantum chemists in their potential surface refinement efforts, and (ii) to gain a better understanding of how various regions in the potential influence the dynamics. These investigations are carried out with the methodology of quantum functional sensitivity analysis (QFSA).

  20. Deposition kinetics of quantum dots and polystyrene latex nanoparticles onto alumina: role of water chemistry and particle coating.

    PubMed

    Quevedo, Ivan R; Olsson, Adam L J; Tufenkji, Nathalie

    2013-03-01

    A clear understanding of the factors controlling the deposition behavior of engineered nanoparticles (ENPs), such as quantum dots (QDs), is necessary for predicting their transport and fate in natural subsurface environments and in water filtration processes. A quartz crystal microbalance with dissipation monitoring (QCM-D) was used to study the effect of particle surface coatings and water chemistry on the deposition of commercial QDs onto Al2O3. Two carboxylated QDs (CdSe and CdTe) with different surface coatings were compared with two model nanoparticles: sulfate-functionalized (sPL) and carboxyl-modified (cPL) polystyrene latex. Deposition rates were assessed over a range of ionic strengths (IS) in simple electrolyte (KCl) and in electrolyte supplemented with two organic molecules found in natural waters; namely, humic acid and rhamnolipid. The Al2O3 collector used here is selected to be representative of oxide patches found on the surface of aquifer or filter grains. Deposition studies showed that ENP deposition rates on bare Al2O3 generally decreased with increasing salt concentration, with the exception of the polyacrylic-acid (PAA) coated CdTe QD which exhibited unique deposition behavior due to changes in the conformation of the PAA coating. QD deposition rates on bare Al2O3 were approximately 1 order of magnitude lower than those of the polystyrene latex nanoparticles, likely as a result of steric stabilization imparted by the QD surface coatings. Adsorption of humic acid or rhamnolipid on the Al2O3 surface resulted in charge reversal of the collector and subsequent reduction in the deposition rates of all ENPs. Moreover, the ratio of the two QCM-D output parameters, frequency and dissipation, revealed key structural information of the ENP-collector interface; namely, on bare Al2O3, the latex particles were rigidly attached as compared to the more loosely attached QDs. This study emphasizes the importance of considering the nature of ENP coatings as well

  1. Quantum simulation

    NASA Astrophysics Data System (ADS)

    Georgescu, I. M.; Ashhab, S.; Nori, Franco

    2014-01-01

    Simulating quantum mechanics is known to be a difficult computational problem, especially when dealing with large systems. However, this difficulty may be overcome by using some controllable quantum system to study another less controllable or accessible quantum system, i.e., quantum simulation. Quantum simulation promises to have applications in the study of many problems in, e.g., condensed-matter physics, high-energy physics, atomic physics, quantum chemistry, and cosmology. Quantum simulation could be implemented using quantum computers, but also with simpler, analog devices that would require less control, and therefore, would be easier to construct. A number of quantum systems such as neutral atoms, ions, polar molecules, electrons in semiconductors, superconducting circuits, nuclear spins, and photons have been proposed as quantum simulators. This review outlines the main theoretical and experimental aspects of quantum simulation and emphasizes some of the challenges and promises of this fast-growing field.

  2. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    NASA Astrophysics Data System (ADS)

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-01

    environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

  3. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    SciTech Connect

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-21

    written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl+4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. By using these algorithms we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 seconds per time step to 6.9 seconds per time step.

  4. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations.

    PubMed

    Bylaska, Eric J; Weare, Jonathan Q; Weare, John H

    2013-08-21

    distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H2O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step. PMID:23968079

  5. Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations

    SciTech Connect

    Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.

    2013-08-21

    to 14.3. The parallel in time algorithms can be implemented in a distributed computing environment using very slow transmission control protocol/Internet protocol networks. Scripts written in Python that make calls to a precompiled quantum chemistry package (NWChem) are demonstrated to provide an actual speedup of 8.2 for a 2.5 ps AIMD simulation of HCl + 4H{sub 2}O at the MP2/6-31G* level. Implemented in this way these algorithms can be used for long time high-level AIMD simulations at a modest cost using machines connected by very slow networks such as WiFi, or in different time zones connected by the Internet. The algorithms can also be used with programs that are already parallel. Using these algorithms, we are able to reduce the cost of a MP2/6-311++G(2d,2p) simulation that had reached its maximum possible speedup in the parallelization of the electronic structure calculation from 32 s/time step to 6.9 s/time step.

  6. Low temperature synthesis of silicon quantum dots with plasma chemistry control in dual frequency non-thermal plasmas.

    PubMed

    Sahu, Bibhuti Bhusan; Yin, Yongyi; Han, Jeon Geon; Shiratani, Masaharu

    2016-06-21

    The advanced materials process by non-thermal plasmas with a high plasma density allows the synthesis of small-to-big sized Si quantum dots by combining low-temperature deposition with superior crystalline quality in the background of an amorphous hydrogenated silicon nitride matrix. Here, we make quantum dot thin films in a reactive mixture of ammonia/silane/hydrogen utilizing dual-frequency capacitively coupled plasmas with high atomic hydrogen and nitrogen radical densities. Systematic data analysis using different film and plasma characterization tools reveals that the quantum dots with different sizes exhibit size dependent film properties, which are sensitively dependent on plasma characteristics. These films exhibit intense photoluminescence in the visible range with violet to orange colors and with narrow to broad widths (∼0.3-0.9 eV). The observed luminescence behavior can come from the quantum confinement effect, quasi-direct band-to-band recombination, and variation of atomic hydrogen and nitrogen radicals in the film growth network. The high luminescence yields in the visible range of the spectrum and size-tunable low-temperature synthesis with plasma and radical control make these quantum dot films good candidates for light emitting applications. PMID:27226277

  7. Towards an ab initio description of the charge transfer between a proton and a lithium fluoride surface: A quantum chemistry approach

    NASA Astrophysics Data System (ADS)

    Tiwald, P.; Gräfe, S.; Burgdörfer, J.; Wirtz, L.

    2013-12-01

    We study the non-adiabatic charge transfer dynamics during the collision of a slow proton with a lithium fluoride surface employing a quantum-chemistry based dynamics approach. The surface is modeled by an Li5F1 + H+ cluster embedded in a large matrix of point charges. Going beyond the adiabatic (or Born-Oppenheimer) approximation, we apply multi-reference configuration-interaction methods that allow for the calculation of ground and excited states of the embedded cluster as well as of the non-adiabatic couplings between them. This information serves as input for the determination of the neutralization probability of a proton scattered off a LiF surface using Tully's semi-classical surface hopping algorithm.

  8. Exploring Do-It-Yourself Approaches in Computational Quantum Chemistry: The Pedagogical Benefits of the Classical Boys Algorithm

    ERIC Educational Resources Information Center

    Orsini, Gabriele

    2015-01-01

    The ever-increasing impact of molecular quantum calculations over chemical sciences implies a strong and urgent need for the elaboration of proper teaching strategies in university curricula. In such perspective, this paper proposes an extensive project for a student-driven, cooperative, from-scratch implementation of a general Hartree-Fock…

  9. F center in lithium fluoride revisited: Comparison of solid-state physics and quantum-chemistry approaches

    NASA Astrophysics Data System (ADS)

    Karsai, Ferenc; Tiwald, Paul; Laskowski, Robert; Tran, Fabien; Koller, David; Gräfe, Stefanie; Burgdörfer, Joachim; Wirtz, Ludger; Blaha, Peter

    2014-03-01

    We revisit the theoretical description of the F color center in lithium fluoride employing advanced complementary ab initio techniques. We compare the results from periodic supercell calculations involving density-functional theory (DFT) and post-DFT techniques with those from the embedded-cluster approach involving quantum-chemical many-electron wave-function techniques. These alternative approaches yield results in good agreement with each other and with the experimental data provided that correlation effects are properly taken into account.

  10. Quantum hydrodynamics with trajectories: The nonlinear conservation form mixed/discontinuous Galerkin method with applications in chemistry

    SciTech Connect

    Michoski, C. Evans, J.A.; Schmitz, P.G.; Vasseur, A.

    2009-12-10

    We present a solution to the conservation form (Eulerian form) of the quantum hydrodynamic equations which arise in chemical dynamics by implementing a mixed/discontinuous Galerkin (MDG) finite element numerical scheme. We show that this methodology is stable, showing good accuracy and a remarkable scale invariance in its solution space. In addition the MDG method is robust, adapting well to various initial-boundary value problems of particular significance in a range of physical and chemical applications. We further show explicitly how to recover the Lagrangian frame (or pathline) solutions.

  11. Low-temperature structural phase transitions in crystalline bromo and iodo 9-hydroxyphenalenone derivatives: Quantum chemistry employment

    NASA Astrophysics Data System (ADS)

    Dolin, S. P.; Khrulev, A. A.; Polyakov, E. V.; Mikhailova, T. Yu.; Levin, A. A.

    The model approaches and quantum chemical calculations are employed to explain the peculiarities of the ferroelectric behavior of new ?zero-dimensional? H-bonded materials, i.e., 5-bromo and 5-iodo derivatives of 9-hydroxyphenalenone (9HPO) and its deuteroxy analogue (9DPO). The tunneling parameters ? (H/D) and the Ising model coupling parameters Jij are evaluated and discussed. Analysis of these parameters for the hydroxy and deuteroxy species demonstrates the quantum paraelectric behavior of both Br and I 9HPO derivatives due to the large values of the ?(H)/J0 relation, where J0 is the molecular field parameter describing the coupling of any given H-bond proton with all rest ones. In contrast, small values ?(D)/J0 for their 9DPO analogues favor the low-temperature structural phase transition into an ordered phase, which has a rather antiferroelectric than ferroelectric character. The estimates obtained and the resulting conclusions are in line with the overall observed trends in behavior of the substances under examination that emerge from the available experimental data.

  12. Quantum chemical study of relative reactivities of a series of amines and nitriles - Relevance to prebiotic chemistry

    NASA Technical Reports Server (NTRS)

    Loew, G. H.; Berkowitz, D.; Chang, S.

    1975-01-01

    Using the Iterative Extended Huckel Theory (IEHT) calculations of the electron distribution and orbital energies of a series of thirteen amines, nitriles and amino-nitriles relevant to prebiotic and cosmo-chemistry have been carried out. Ground state properties such as the energy and nature of the highest occupied (HOMO) and lowest empty (LEMO) molecular orbitals, net atomic charges and number of nonbonding electrons have been identified as criteria for correlating the relative nucleophilicity of amine and nitrile nitrogens and the electrophilicity of nitrile and other unsaturated carbon atoms. The results of such correlations can be partially verified by known chemical behavior of these compounds and are used to predict and understand their role in prebiotic organic synthesis.

  13. CheMPS2: A free open-source spin-adapted implementation of the density matrix renormalization group for ab initio quantum chemistry

    NASA Astrophysics Data System (ADS)

    Wouters, Sebastian; Poelmans, Ward; Ayers, Paul W.; Van Neck, Dimitri

    2014-06-01

    The density matrix renormalization group (DMRG) has become an indispensable numerical tool to find exact eigenstates of finite-size quantum systems with strong correlation. In the fields of condensed matter, nuclear structure and molecular electronic structure, it has significantly extended the system sizes that can be handled compared to full configuration interaction, without losing numerical accuracy. For quantum chemistry (QC), the most efficient implementations of DMRG require the incorporation of particle number, spin and point group symmetries in the underlying matrix product state (MPS) ansatz, as well as the use of so-called complementary operators. The symmetries introduce a sparse block structure in the MPS ansatz and in the intermediary contracted tensors. If a symmetry is non-abelian, the Wigner-Eckart theorem allows to factorize a tensor into a Clebsch-Gordan coefficient and a reduced tensor. In addition, the fermion signs have to be carefully tracked. Because of these challenges, implementing DMRG efficiently for QC is not straightforward. Efficient and freely available implementations are therefore highly desired. In this work we present CheMPS2, our free open-source spin-adapted implementation of DMRG for ab initio QC. Around CheMPS2, we have implemented the augmented Hessian Newton-Raphson complete active space self-consistent field method, with exact Hessian. The bond dissociation curves of the 12 lowest states of the carbon dimer were obtained at the DMRG(28 orbitals, 12 electrons, DSU(2) = 2500)/cc-pVDZ level of theory. The contribution of 1 s core correlation to the X1Σg+ bond dissociation curve of the carbon dimer was estimated by comparing energies at the DMRG(36o, 12e, DSU(2) = 2500)/cc-pCVDZ and DMRG-SCF(34o, 8e, DSU(2) = 2500)/cc-pCVDZ levels of theory.

  14. Iridium Cyclometalated Complexes in Host-Guest Chemistry: A Strategy for Maximizing Quantum Yield in Aqueous Media.

    PubMed

    Alrawashdeh, Lubna R; Cronin, Michael P; Woodward, Clifford E; Day, Anthony I; Wallace, Lynne

    2016-07-01

    The weaker emission typically seen for iridium(III) cyclometalated complexes in aqueous medium can be reversed via encapsulation in cucurbit[10]uril (Q[10]). The Q[10] cavity is shown to effectively maximize quantum yields for the complexes, compared to any other medium. This may provide significant advantages for a number of sensor applications. NMR studies show that the complexes are accommodated similarly within the host molecule, even with cationic substituents attached to the ppy ligands, indicating that the hydrophobic effect is the dominant driving force for binding. Cavity-encapsulated 1:1 host-guest species dominate the emission, but 1:2 species are also indicated, which also give some enhancement of intensity. Results demonstrate that the enhancement is due primarily to much lower rates of nonradiative decay but also suggest that the encapsulation can cause a change in character of the emitting state. PMID:27315543

  15. The use of quantum molecular calculations to guide a genetic algorithm: a way to search for new chemistry.

    PubMed

    Durrant, Marcus C

    2007-01-01

    The process of gene-based molecular evolution has been simulated in silico by using massively parallel density functional theory quantum calculations, coupled with a genetic algorithm, to test for fitness with respect to a target chemical reaction in populations of genetically encoded molecules. The goal of this study was the identification of transition-metal complexes capable of mediating a known reaction, namely the cleavage of N(2) to give the metal nitride. Each complex within the search space was uniquely specified by a nanogene consisting of an eight-digit number. Propagation of an individual nanogene into successive generations was determined by the fitness of its phenotypic molecule to perform the target reaction and new generations were created by recombination and mutation of surviving nanogenes. In its simplest implementation, the quantum-directed genetic algorithm (QDGA) quickly located a local minimum on the evolutionary fitness hypersurface, but proved incapable of progressing towards the global minimum. A strategy for progressing beyond local minima consistent with the Darwinian paradigm by the use of environmental variations coupled with mass extinctions was therefore developed. This allowed for the identification of nitriding complexes that are very closely related to known examples from the chemical literature. Examples of mutations that appear to be beneficial at the genetic level but prove to be harmful at the phenotypic level are described. As well as revealing fundamental aspects of molecular evolution, QDGA appears to be a powerful tool for the identification of lead compounds capable of carrying out a target chemical reaction. PMID:17225228

  16. KiSThelP: a program to predict thermodynamic properties and rate constants from quantum chemistry results.

    PubMed

    Canneaux, Sébastien; Bohr, Frédéric; Henon, Eric

    2014-01-01

    Kinetic and Statistical Thermodynamical Package (KiSThelP) is a cross-platform free open-source program developed to estimate molecular and reaction properties from electronic structure data. To date, three computational chemistry software formats are supported (Gaussian, GAMESS, and NWChem). Some key features are: gas-phase molecular thermodynamic properties (offering hindered rotor treatment), thermal equilibrium constants, transition state theory rate coefficients (transition state theory (TST), variational transition state theory (VTST)) including one-dimensional (1D) tunnelling effects (Wigner, and Eckart) and Rice-Ramsperger-Kassel-Marcus (RRKM) rate constants, for elementary reactions with well-defined barriers. KiSThelP is intended as a working tool both for the general public and also for more expert users. It provides graphical front-end capabilities designed to facilitate calculations and interpreting results. KiSThelP enables to change input data and simulation parameters directly through the graphical user interface and to visually probe how it affects results. Users can access results in the form of graphs and tables. The graphical tool offers customizing of 2D plots, exporting images and data files. These features make this program also well-suited to support and enhance students learning and can serve as a very attractive courseware, taking the teaching content directly from results in molecular and kinetic modelling. PMID:24190715

  17. Thermodynamic behavior of the binaries 1-butylpyridinium tetrafluoroborate with water and alkanols: their interpretation using 1H NMR spectroscopy and quantum-chemistry calculations.

    PubMed

    Vreekamp, Remko; Castellano, Desire; Palomar, José; Ortega, Juan; Espiau, Fernando; Fernández, Luís; Penco, Eduvigis

    2011-07-14

    Here we present experimental data of different properties for a set of binary mixtures composed of water or alkanols (methanol to butanol) with an ionic liquid (IL), butylpyridinium tetrafluoroborate [bpy][BF(4)]. Solubility data (x(IL),T) are presented for each of the mixtures, including water, which is found to have a small interval of compositions in IL, x(IL), with immiscibility. In each case, the upper critical solubility temperature (UCST) is determined and a correlation was observed between the UCST and the nature of the compounds in the mixtures. Miscibility curves establish the composition and temperature intervals where thermodynamic properties of the mixtures, such as enthalpies H(m)(E) and volumes V(m)(E), can be determined. Hence, at 298.15 and 318.15 K these can only be found with the first four alkanols. All mixing properties are correlated with a suitable equation ξ (x(IL),T,Y(m)(E) = 0. An analysis on the influence of the temperature in the properties is shown, likewise a comparison between the results obtained here and those of analogous mixtures, discussing the position of the -CH(3) group in the pyridinic ring. The (1)H NMR spectra are determined to analyze the molecular interactions present, especially those due to hydrogen bonds. Additional information about the molecular interactions and their influence on the mixing properties is obtained by quantum chemistry calculations. PMID:21648473

  18. Effects of alkyl groups in the rate determining step of the Baeyer-Villiger reaction of phenyl alkyl ketones: a quantum chemistry study.

    PubMed

    Reyes, Lino; Díaz-Sánchez, Celestino; Iuga, Cristina

    2012-07-26

    In this work, we have studied the substituent effect of several alkyl groups in the rate-determining step of the catalyzed Baeyer-Villiger (BV) reaction of phenyl alkyl ketones with performic (PFA) and trifluoroperacetic (TFPAA) acids, using quantum chemistry methods. Our results reveal that the substituent effect is more pronounced in the migration step barriers than in the corresponding addition step; that could change the rate-determining step (RDS) of the reaction, as observed in the oxidation of phenyl tert-butyl ketone with both peracids. In addition, the effect of the acid/peracid pairs used is also analyzed. We have demonstrated that the addition step is less susceptible to the acid/peracid nature since the acid strength and the nucleophilicity of the peracid have opposite effects. The effect of the acid/peracid pair is much more pronounced in the migration step because it only depends on the leaving ability of the acid, which in turn depends on its strength. These observations are relevant for understanding the effects of the substrate, the peracid, and the catalyst on the switching of the RDS in the BV reaction. PMID:22738150

  19. Host-Guest Chemistry between Perylene Diimide (PDI) Derivatives and 18-Crown-6: Enhancement in Luminescence Quantum Yield and Electrical Conductivity.

    PubMed

    Lasitha, P; Prasad, Edamana

    2016-07-18

    Perylene diimide (PDI) derivatives exhibit a high propensity for aggregation, which causes the aggregation-induced quenching of emission from the system. Host-guest chemistry is one of the best-known methods for preventing aggregation through the encapsulation of guest molecules. Herein we report the use of 18-crown-6 (18-C-6) as a host system to disaggregate suitably substituted PDI derivatives in methanol. 18-C-6 formed complexes with amino-substituted PDIs in methanol, which led to disaggregation and enhanced emission from the systems. Furthermore, the embedding of the PDI⋅18-C-6 complexes in poly(vinyl alcohol) (PVA) films generated remarkably high emission quantum yields (60-70 %) from the PDI derivatives. More importantly, the host-guest systems were tested for their ability to conduct electricity in PVA films. The electrical conductivities of the self-assembled systems in PVA were measured by electrochemical impedance spectroscopy (EIS) and the highest conductivity observed was 2.42×10(-5)  S cm(-1) . PMID:27319975

  20. Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.

    PubMed

    Gresh, Nohad; Sponer, Judit E; Devereux, Mike; Gkionis, Konstantinos; de Courcy, Benoit; Piquemal, Jean-Philip; Sponer, Jiri

    2015-07-30

    Until now, atomistic simulations of DNA and RNA and their complexes have been executed using well calibrated but conceptually simple pair-additive empirical potentials (force fields). Although such simulations provided many valuable results, it is well established that simple force fields also introduce errors into the description, underlying the need for development of alternative anisotropic, polarizable molecular mechanics (APMM) potentials. One of the most abundant forces in all kinds of nucleic acids topologies is base stacking. Intra- and interstrand stacking is assumed to be the most essential factor affecting local conformational variations of B-DNA. However, stacking also contributes to formation of all kinds of noncanonical nucleic acids structures, such as quadruplexes or folded RNAs. The present study focuses on 14 stacked cytosine (Cyt) dimers and the doubly H-bonded dimer. We evaluate the extent to which an APMM procedure, SIBFA, could account quantitatively for the results of high-level quantum chemistry (QC) on the total interaction energies, and the individual energy contributions and their nonisotropic behaviors. Good agreements are found at both uncorrelated HF and correlated DFT and CCSD(T) levels. Resorting in SIBFA to distributed QC multipoles and to an explicit representation of the lone pairs is essential to respectively account for the anisotropies of the Coulomb and of the exchange-repulsion QC contributions. PMID:26119247

  1. Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment.

    PubMed

    Sponer, Jiří; Sponer, Judit E; Mládek, Arnošt; Jurečka, Petr; Banáš, Pavel; Otyepka, Michal

    2013-12-01

    Base stacking is a major interaction shaping up and stabilizing nucleic acids. During the last decades, base stacking has been extensively studied by experimental and theoretical methods. Advanced quantum-chemical calculations clarified that base stacking is a common interaction, which in the first approximation can be described as combination of the three most basic contributions to molecular interactions, namely, electrostatic interaction, London dispersion attraction and short-range repulsion. There is not any specific π-π energy term associated with the delocalized π electrons of the aromatic rings that cannot be described by the mentioned contributions. The base stacking can be rather reasonably approximated by simple molecular simulation methods based on well-calibrated common force fields although the force fields do not include nonadditivity of stacking, anisotropy of dispersion interactions, and some other effects. However, description of stacking association in condensed phase and understanding of the stacking role in biomolecules remain a difficult problem, as the net base stacking forces always act in a complex and context-specific environment. Moreover, the stacking forces are balanced with many other energy contributions. Differences in definition of stacking in experimental and theoretical studies are explained. PMID:23784745

  2. Support vector machine regression (LS-SVM)--an alternative to artificial neural networks (ANNs) for the analysis of quantum chemistry data?

    PubMed

    Balabin, Roman M; Lomakina, Ekaterina I

    2011-06-28

    A multilayer feed-forward artificial neural network (MLP-ANN) with a single, hidden layer that contains a finite number of neurons can be regarded as a universal non-linear approximator. Today, the ANN method and linear regression (MLR) model are widely used for quantum chemistry (QC) data analysis (e.g., thermochemistry) to improve their accuracy (e.g., Gaussian G2-G4, B3LYP/B3-LYP, X1, or W1 theoretical methods). In this study, an alternative approach based on support vector machines (SVMs) is used, the least squares support vector machine (LS-SVM) regression. It has been applied to ab initio (first principle) and density functional theory (DFT) quantum chemistry data. So, QC + SVM methodology is an alternative to QC + ANN one. The task of the study was to estimate the Møller-Plesset (MPn) or DFT (B3LYP, BLYP, BMK) energies calculated with large basis sets (e.g., 6-311G(3df,3pd)) using smaller ones (6-311G, 6-311G*, 6-311G**) plus molecular descriptors. A molecular set (BRM-208) containing a total of 208 organic molecules was constructed and used for the LS-SVM training, cross-validation, and testing. MP2, MP3, MP4(DQ), MP4(SDQ), and MP4/MP4(SDTQ) ab initio methods were tested. Hartree-Fock (HF/SCF) results were also reported for comparison. Furthermore, constitutional (CD: total number of atoms and mole fractions of different atoms) and quantum-chemical (QD: HOMO-LUMO gap, dipole moment, average polarizability, and quadrupole moment) molecular descriptors were used for the building of the LS-SVM calibration model. Prediction accuracies (MADs) of 1.62 ± 0.51 and 0.85 ± 0.24 kcal mol(-1) (1 kcal mol(-1) = 4.184 kJ mol(-1)) were reached for SVM-based approximations of ab initio and DFT energies, respectively. The LS-SVM model was more accurate than the MLR model. A comparison with the artificial neural network approach shows that the accuracy of the LS-SVM method is similar to the accuracy of ANN. The extrapolation and interpolation results show that LS-SVM is

  3. Formation of Carbon Nanotube Based Gears: Quantum Chemistry and Molecular Mechanics Study of the Electrophilic Addition of o-Benzyne to Fullerenes, Graphene, and Nanotubes

    NASA Technical Reports Server (NTRS)

    Jaffe, Richard; Han, Jie; Globus, Al; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    Considerable progress has been made in recent years in chemical functionalization of fullerene molecules. In some cases, the predominant reaction products are different from those obtained (using the same reactants) from polycyclic aromatic hydrocarbons (PAHs). One such example is the cycloaddition of o-benzyne to C60. It is well established that benzyne adds across one of the rings in naphthalene, anthracene and other PAHs forming the [2+4] cycloaddition product (benzobicyclo[2.2.2.]-octatriene with naphthalene and triptycene with anthracene). However, Hoke et al demonstrated that the only reaction path for o-benzyne with C60 leads to the [2+2] cycloaddition product in which benzyne adds across one of the interpentagonal bonds (forming a cyclobutene ring in the process). Either reaction product results in a loss of aromaticity and distortion of the PAH or fullerene substrate, and in a loss of strain in the benzyne. It is not clear, however, why different products are preferred in these cases. In the current paper, we consider the stability of benzyne-nanotube adducts and the ability of Brenner's potential energy model to describe the structure and stability of these adducts. The Brenner potential has been widely used for describing diamondoid and graphitic carbon. Recently it has also been used for molecular mechanics and molecular dynamics simulations of fullerenes and nanotubes. However, it has not been tested for the case of functionalized fullerenes (especially with highly strained geometries). We use the Brenner potential for our companion nanogear simulations and believe that it should be calibrated to insure that those simulations are physically reasonable. In the present work, Density Functional theory (DFT) calculations are used to determine the preferred geometric structures and energetics for this calibration. The DFT method is a kind of ab initio quantum chemistry method for determining the electronic structure of molecules. For a given basis set

  4. Infrared and Raman spectroscopy and quantum chemistry calculation studies of C H⋯O hydrogen bondings and thermal behavior of biodegradable polyhydroxyalkanoate

    NASA Astrophysics Data System (ADS)

    Sato, Harumi; Dybal, Jiří; Murakami, Rumi; Noda, Isao; Ozaki, Yukihiro

    2005-06-01

    This review paper reports infrared (IR) and Raman spectroscopy and quantum chemistry calculation studies of C-H⋯O hydrogen bondings and thermal behavior of biodegradable polyhydroxyalkanoates. IR and Raman spectra were measured for poly(3-hydroxybutyrate) (PHB) and a new type of bacterial copolyester, poly(3-hydroxybutyrate- co-3-hydroxyhexanoate), P(HB- co-HHx) (HHx=12 mol%) over a temperature range of 20 °C to higher temperatures (PHB, 200 °C; HHx=12 mol%, 140 °C) to explore their structure and thermal behavior. One of bands due to the CH 3 asymmetric stretching modes appears near 3010 cm -1 in the IR and Raman spectra of PHB and P(HB- co-HHx) at 20 °C. These frequencies of IR and Raman CH 3 asymmetric stretching bands are much higher than usual. These anomalous frequencies of the CH 3 asymmetric stretching bands together with the X-ray crystallographic structure of PHB have suggested that there is an inter- or intra-molecular C-H⋯O hydrogen bond between the C dbnd6 O group in one helical structure and the CH 3 group in the other helical structure in PHB and P(HB- co-HHx). The quantum chemical calculation of model compounds of PHB also has suggested the existence of C-H⋯O hydrogen bonds in PHB and P(HB- co-HHx). It is very likely that a chain of C-H⋯O hydrogen bond pairs link two parallel helical structures in the crystalline parts. The temperature-dependent IR and Raman spectral variations have revealed that the crystallinity of P(HB- co-HHx) (HHx=12 mol%) decreases gradually from a fairly low temperature (about 60 °C), while the crystallinity of PHB remains almost unchanged until just below its melting temperature. It has also been found from the IR and Raman studies that for both PHB and P(HB- co-HHx) the weakening of the C-H⋯O hydrogen bonds starts from just above room temperature, but the deformation of helical structures occurs after the weakening of the C-H⋯O hydrogen bonds advances to some extent.

  5. Size distributions and geometries of alkali halide nanoclusters probed using ESI FT-ICR mass spectrometry and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Lemke, K.; Sadjadi, S.; Seward, T.

    2010-12-01

    The structures and energetic properties of ionic alkali metal halide clusters play a significant role in our understanding of aqueous geochemical processes such as salt dissolution, precipitation and neutralization reactions. Mass spectrometric and quantum chemical studies of such systems offer new opportunities to study the size-dependent evolution of cluster structures, the occurrence of magic number species as well as their fundamental properties. The work here presents new results for the stability, abundance and structure of pure [Na(NaClm)]+ , [K(KCl)m]+ and mixed [Na(NaCl)p(KCl)q]+ metal halide clusters with m<23 and p+q<14, respectively, using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR/MS) in combination with the Gn and CBS-x multistep ab initio methods. Ion-cluster experiments were conducted on a modified 7T Bruker FT-ICR/MS equipped with electrospray ionization (ESI) sources and a custom-designed solvent gas inlet interface. In ESI FT-ICR/MS experiments performed with solutions containing NaCl and KCl salts (1mM; 80/20 CH3CN/H2O), singly and doubly charged salt clusters were generated up to a cluster size of [Na(NaCl)22]+, [K(KCl)17]+ and [K2(KCl)21,23]2+, respectively, including “magic number” clusters that correspond to the completed cluster cuboids with the dimensions 3x3x1 (m=4), 3x3x2+3 (m=10) 3x3x3 (m=13) and 3x3x5 (m=22) (see Figure). On the other hand, no pure clusters except [K(KCl)1-3]+ were generated when alkali halides were electrosprayed from 1mM NaCl/KCl solutions. Instead, mixed [Na(NaCl)p(KCl)q]+ clusters are generated up to p+q=14, which are the largest mixed alkali halide clusters yet generated in mass spectrometric experiments, including a suite of ionic species that are generated via CH3CN fragmentation and charge transfer in [Na(CH3CN)n]+ to yield the clusters [Na(NaCN)(CH3CN)n-1]+. We describe our ESI FT-ICR/MS experiments and discuss ion cluster abundances and extent of clustering

  6. Matrix Isolation IR Spectroscopy and Quantum Chemistry Study of 1:1 Π-HYDROGEN Bonded Complexes of Benzene with a Series of Fluorophenols

    NASA Astrophysics Data System (ADS)

    Banerjee, Pujarini; Chakraborty, Tapas

    2015-06-01

    O-H stretching infrared fundamentals (νb{OH}) of phenol and a series of fluorophenol monomers and their 1:1 complexes with benzene have been measured under a matrix isolation condition (8K). For the phenol-benzene complex the measured shift of νb{OH} is 78 wn and for 3, 4, 5-trifluorophenol it is 98 wn. Although the cold matrix isolation environment is very different from an aqueous medium, the measured spectral shifts display an interesting linear correlation with the aqueous phase acid dissociation constants (pKa) of the phenols. The spectral shifts predicted by quantum chemistry calculations at several levels of theory are consistent with the observed values. Correlations of the shifts are also found with respect to energetic, geometric and several other electronic structure parameters of the complexes. Partitioning of binding energies of the complexes into components following the Morokuma-Kitaura scheme shows that dispersion is the predominant component of attractive interaction, and electrostatics, polarization and charge-transfer terms also have contributions to overall binding stability. NBO analysis reveals that hyperconjugative charge-transfers from the filled π-orbitals of the hydrogen bond acceptor (benzene) to the anti-bonding σ*(O-H) orbital of the donors (phenols) display correlations which are fully consistent with the observed variations of spectral shifts. The analysis also shows that the O-H bond dipole moments of all the phenolic species are nearly the same, implying that local electrostatics has only a little effect at the site of hydrogen bonding.

  7. Discovery of a general method of solving the Schrödinger and dirac equations that opens a way to accurately predictive quantum chemistry.

    PubMed

    Nakatsuji, Hiroshi

    2012-09-18

    Just as Newtonian law governs classical physics, the Schrödinger equation (SE) and the relativistic Dirac equation (DE) rule the world of chemistry. So, if we can solve these equations accurately, we can use computation to predict chemistry precisely. However, for approximately 80 years after the discovery of these equations, chemists believed that they could not solve SE and DE for atoms and molecules that included many electrons. This Account reviews ideas developed over the past decade to further the goal of predictive quantum chemistry. Between 2000 and 2005, I discovered a general method of solving the SE and DE accurately. As a first inspiration, I formulated the structure of the exact wave function of the SE in a compact mathematical form. The explicit inclusion of the exact wave function's structure within the variational space allows for the calculation of the exact wave function as a solution of the variational method. Although this process sounds almost impossible, it is indeed possible, and I have published several formulations and applied them to solve the full configuration interaction (CI) with a very small number of variables. However, when I examined analytical solutions for atoms and molecules, the Hamiltonian integrals in their secular equations diverged. This singularity problem occurred in all atoms and molecules because it originates from the singularity of the Coulomb potential in their Hamiltonians. To overcome this problem, I first introduced the inverse SE and then the scaled SE. The latter simpler idea led to immediate and surprisingly accurate solution for the SEs of the hydrogen atom, helium atom, and hydrogen molecule. The free complement (FC) method, also called the free iterative CI (free ICI) method, was efficient for solving the SEs. In the FC method, the basis functions that span the exact wave function are produced by the Hamiltonian of the system and the zeroth-order wave function. These basis functions are called complement

  8. Integrating Computational Chemistry into a Course in Classical Thermodynamics

    ERIC Educational Resources Information Center

    Martini, Sheridan R.; Hartzell, Cynthia J.

    2015-01-01

    Computational chemistry is commonly addressed in the quantum mechanics course of undergraduate physical chemistry curricula. Since quantum mechanics traditionally follows the thermodynamics course, there is a lack of curricula relating computational chemistry to thermodynamics. A method integrating molecular modeling software into a semester long…

  9. Role of gamma carboxylated Glu47 in connexin 26 hemichannel regulation by extracellular Ca{sup 2+}: Insight from a local quantum chemistry study

    SciTech Connect

    Zonta, Francesco; Mammano, Fabio; Torsello, Mauro; Fortunati, Nicola; Orian, Laura; Polimeno, Antonino

    2014-02-28

    Graphical abstract: - Highlights: • QM calculations show that Ca{sup 2+} binds to γGlu47 in connexin hemichannels. • Molecular models of increasing size are employed in hybrid DFT calculations. • Ca{sup 2+} binding affects the interaction between γGlu47 and Arg75, Arg184. • Ca{sup 2+} binding alters the structure in a critical region of connexin hemichannels. - Abstract: Connexin hemichannels are regulated by several gating mechanisms, some of which depend critically on the extracellular Ca{sup 2+} concentration ([Ca{sup 2+}]{sub e}). It is well established that hemichannel activity is inhibited at normal (∼1 mM) [Ca{sup 2+}]{sub e}, whereas lowering [Ca{sup 2+}]{sub e} to micromolar levels fosters hemichannel opening. Atomic force microscopy imaging shows significant and reversible changes of pore diameter at the extracellular mouth of Cx26 hemichannels exposed to different [Ca{sup 2+}]{sub e}, however, the underlying molecular mechanisms are not fully elucidated. Analysis of the crystal structure of connexin 26 (Cx26) gap junction channels, corroborated by molecular dynamics (MD) simulations, suggests that several negatively charged amino acids create a favorable environment for low-affinity Ca{sup 2+} binding within the extracellular vestibule of the Cx26 hemichannel. In particular a highly conserved glutammic acid, found in position 47 in most connexins, is thought to undergo post translational gamma carboxylation (γGlu47), and is thus likely to play an important role in Ca{sup 2+} coordination. γGlu47 may also form salt bridges with two conserved arginines (Arg75 and Arg184 in Cx26), which are considered important in stabilizing the structure of the extracellular region. Using a combination of quantum chemistry methods, we analyzed the interaction between γGlu47, Arg75 and Arg184 in a Cx26 hemichannel model both in the absence and in the presence of Ca{sup 2+}. We show that Ca{sup 2+} imparts significant local structural changes and speculate

  10. Determining the Quantum Efficiency for Activation of an Organometallic Photoinitiator for Cationic Polymerization: An Experiment for the Physical or Inorganic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Hayes, David M.; Mahar, Maura; Schnabel, R. Chris; Shah, Paras; Lees, Alistair J.; Jakubek, Vladimir

    2007-01-01

    We present a new laboratory experiment on the photochemistry of organometallic [eta][superscript 5],[eta][superscript 6]-mixed-sandwich compounds, which is suitable for both the physical chemistry and inorganic chemistry laboratory. Specifically, students use 1,10-phenanthroline to trap the intermediate formed when…

  11. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Described are eight chemistry experiments and demonstrations applicable to introductory chemistry courses. Activities include: measure of lattice enthalpy, Le Chatelier's principle, decarboxylation of soap, use of pocket calculators in pH measurement, and making nylon. (SL)

  12. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and chemistry experiments. Topics include sublimation, electronegativity, electrolysis, experimental aspects of strontianite, halide test, evaluation of present and future computer programs in chemistry, formula building, care of glass/saturated calomel…

  13. ENVIRONMENTAL CHEMISTRY

    EPA Science Inventory

    Environmental chemistry is applied to estimating the exposure of ecosystems and humans to various chemical environmental stressors. Among the stressors of concern are mercury, pesticides, and arsenic. Advanced analytical chemistry techniques are used to measure these stressors ...

  14. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Thirteen ideas are presented that may be of use to chemistry teachers. Topics covered include vitamin C, industrial chemistry, electrical conductivity, electrolysis, alkali metals, vibration modes infra-red, dynamic equilibrium, and some new demonstrations in gaseous combinations. (PS)

  15. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents background information, laboratory procedures, classroom materials/activities, and experiments for chemistry. Topics include superheavy elements, polarizing power and chemistry of alkali metals, particulate carbon from combustion, tips for the chemistry laboratory, interesting/colorful experiments, behavior of bismuth (III) iodine, and…

  16. The promise of quantum simulation

    SciTech Connect

    Muller, Richard P.; Blume-Kohout, Robin

    2015-07-21

    In this study, quantum simulations promise to be one of the primary applications of quantum computers, should one be constructed. This article briefly summarizes the history of quantum simulation in light of the recent result of Wang and co-workers, demonstrating calculation of the ground and excited states for a HeH+ molecule, and concludes with a discussion of why this and other recent progress in the field suggest that quantum simulations of quantum chemistry have a bright future.

  17. The promise of quantum simulation

    DOE PAGESBeta

    Muller, Richard P.; Blume-Kohout, Robin

    2015-07-21

    In this study, quantum simulations promise to be one of the primary applications of quantum computers, should one be constructed. This article briefly summarizes the history of quantum simulation in light of the recent result of Wang and co-workers, demonstrating calculation of the ground and excited states for a HeH+ molecule, and concludes with a discussion of why this and other recent progress in the field suggest that quantum simulations of quantum chemistry have a bright future.

  18. The Promise of Quantum Simulation.

    PubMed

    Muller, Richard P; Blume-Kohout, Robin

    2015-08-25

    Quantum simulations promise to be one of the primary applications of quantum computers, should one be constructed. This article briefly summarizes the history of quantum simulation in light of the recent result of Wang and co-workers, demonstrating calculation of the ground and excited states for a HeH(+) molecule, and concludes with a discussion of why this and other recent progress in the field suggest that quantum simulations of quantum chemistry have a bright future. PMID:26197037

  19. Elementary and brief introduction of hadronic chemistry

    NASA Astrophysics Data System (ADS)

    Tangde, Vijay M.

    2013-10-01

    The discipline, today known as Quantum Chemistry for atomic and subatomic level interactions has no doubt made a significant historical contributions to the society. Despite of its significant achievements, quantum chemistry is also known for its widespread denial of insufficiencies it inherits. An Italian-American Scientist Professor Ruggero Maria Santilli during his more than five decades of dedicated and sustained research has denounced the fact that quantum chemistry is mostly based on mere nomenclatures without any quantitative scientific contents. Professor R M Santilli first formulated the iso-, geno- and hyper-mathematics [1-4] that helped in understanding numerous diversified problems and removing inadequacies in most of the established and celebrated theories of 20th century physics and chemistry. This involves the isotopic, genotopic, etc. lifting of Lie algebra that generated Lie admissible mathematics to properly describe irreversible processes. The studies on Hadronic Mechanics in general and chemistry in particular based on Santilli's mathematics[3-5] for the first time has removed the very fundamental limitations of quantum chemistry [2, 6-8]. In the present discussion, we have briefly reviewed the conceptual foundations of Hadronic Chemistry that imparts the completeness to the Quantum Chemistry via an addition of effects at distances of the order of 1 fm (only) which are assumed to be Non-linear, Non-local, Non-potential, Non-hamiltonian and thus Non-unitary and its application in development of a new chemical species called Magnecules.

  20. CLUSTER CHEMISTRY

    SciTech Connect

    Muetterties, Earl L.

    1980-05-01

    Metal cluster chemistry is one of the most rapidly developing areas of inorganic and organometallic chemistry. Prior to 1960 only a few metal clusters were well characterized. However, shortly after the early development of boron cluster chemistry, the field of metal cluster chemistry began to grow at a very rapid rate and a structural and a qualitative theoretical understanding of clusters came quickly. Analyzed here is the chemistry and the general significance of clusters with particular emphasis on the cluster research within my group. The importance of coordinately unsaturated, very reactive metal clusters is the major subject of discussion.

  1. Forensic Chemistry

    NASA Astrophysics Data System (ADS)

    Bell, Suzanne

    2009-07-01

    Forensic chemistry is unique among chemical sciences in that its research, practice, and presentation must meet the needs of both the scientific and the legal communities. As such, forensic chemistry research is applied and derivative by nature and design, and it emphasizes metrology (the science of measurement) and validation. Forensic chemistry has moved away from its analytical roots and is incorporating a broader spectrum of chemical sciences. Existing forensic practices are being revisited as the purview of forensic chemistry extends outward from drug analysis and toxicology into such diverse areas as combustion chemistry, materials science, and pattern evidence.

  2. Computational Chemistry Using Modern Electronic Structure Methods

    ERIC Educational Resources Information Center

    Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

    2007-01-01

    Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

  3. From Cathode Rays To Alpha Particles To Quantum of Action: A Rational Reconstruction of Structure of the Atom and Its Implications for Chemistry Textbooks.

    ERIC Educational Resources Information Center

    Niaz, Mansoor

    1998-01-01

    Reports on a study that involves the analysis of chemistry textbooks at the college freshman level to determine the degree to which they address developments in the history and philosophy of science. Twenty-three textbooks were evaluated on eight criteria. Contains 108 references. (DDR)

  4. A Mixed Quantum Mechanics/Molecular Mechanics (qm/mm) Method for Large-Scale Modeling of Chemistry in Protein Environments

    SciTech Connect

    Murphy, Robert B.; Philipp, Dean M.; Friesner, Richard A.

    2000-07-13

    A QM/MM method, using our previously developed frozen orbital QM/MM interface methodology, is presented as a general, accurate, and computationally efficient model for studying chemical problems in a protein environment. The method, its parameterization, and a preliminary application to modeling cytochrome P-450 chemistry are presented.

  5. Quantum Feynman Ratchet

    NASA Astrophysics Data System (ADS)

    Goyal, Ketan; Kawai, Ryoichi

    As nanotechnology advances, understanding of the thermodynamic properties of small systems becomes increasingly important. Such systems are found throughout physics, biology, and chemistry manifesting striking properties that are a direct result of their small dimensions where fluctuations become predominant. The standard theory of thermodynamics for macroscopic systems is powerless for such ever fluctuating systems. Furthermore, as small systems are inherently quantum mechanical, influence of quantum effects such as discreteness and quantum entanglement on their thermodynamic properties is of great interest. In particular, the quantum fluctuations due to quantum uncertainty principles may play a significant role. In this talk, we investigate thermodynamic properties of an autonomous quantum heat engine, resembling a quantum version of the Feynman Ratchet, in non-equilibrium condition based on the theory of open quantum systems. The heat engine consists of multiple subsystems individually contacted to different thermal environments.

  6. Technetium chemistry

    SciTech Connect

    Burns, C.; Bryan, J.; Cotton, F.; Ott, K.; Kubas, G.; Haefner, S.; Barrera, J.; Hall, K.; Burrell, A.

    1996-04-01

    Technetium chemistry is a young and developing field. Despite the limited knowledge of its chemistry, technetium is the workhorse for nuclear medicine. Technetium is also a significant environmental concern because it is formed as a byproduct of nuclear weapons production and fission-power generators. Development of new technetium radio-pharmaceuticals and effective environmental control depends strongly upon knowledge of basic technetium chemistry. The authors performed research into the basic coordination and organometallic chemistry of technetium and used this knowledge to address nuclear medicine and environmental applications. This is the final report of a three-year Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL).

  7. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Twelve new chemistry expermiments are described. Broad areas covered include atomic structure, solubility, gaseous diffusion, endothermic reactions, alcohols, equilibrium, atomic volumes, and some improvised apparatus. (PS)

  8. Integrating Computational Chemistry into the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Johnson, Lewis E.; Engel, Thomas

    2011-01-01

    Relatively few undergraduate physical chemistry programs integrate molecular modeling into their quantum mechanics curriculum owing to concerns about limited access to computational facilities, the cost of software, and concerns about increasing the course material. However, modeling exercises can be integrated into an undergraduate course at a…

  9. Conceptual versus Algorithmic Learning in High School Chemistry: The Case of Basic Quantum Chemical Concepts--Part 2. Students' Common Errors, Misconceptions and Difficulties in Understanding

    ERIC Educational Resources Information Center

    Papaphotis, Georgios; Tsaparlis, Georgios

    2008-01-01

    Part 2 of the findings are presented of a quantitative study (n = 125) on basic quantum chemical concepts taught at twelfth grade (age 17-18 years) in Greece. A paper-and-pencil test of fourteen questions was used that were of two kinds: five questions that tested recall of knowledge or application of algorithmic procedures (type-A questions);…

  10. Investigating Quantum Mechanical Tunneling at the Nanoscale via Analogy: Development and Assessment of a Teaching Tool for Upper-Division Chemistry

    ERIC Educational Resources Information Center

    Muniz, Marc N.; Oliver-Hoyo, Maria T.

    2014-01-01

    We report a novel educational activity designed to teach quantum mechanical tunneling to upper-division undergraduate students in the context of nanochemistry. The activity is based on a theoretical framework for analogy and is split into three parts that are linked pedagogically through the framework: classical ball-and-ramp system, tunneling…

  11. Using LEDs and Phosphorescent Materials to Teach High School Students Quantum Mechanics: A Guided-Inquiry Laboratory for Introductory High School Chemistry

    ERIC Educational Resources Information Center

    Green, William P.; Trotochaud, Alan; Sherman, Julia; Kazerounian, Kazem; Faraclas, Elias W.

    2009-01-01

    The quantization of electronic energy levels in atoms is foundational to a mechanistic explanation of the periodicity of elemental properties and behavior. This paper presents a hands-on, guided inquiry approach to teaching this concept as part of a broader treatment of quantum mechanics, and as a foundation for an understanding of chemical…

  12. Trace Chemistry

    NASA Technical Reports Server (NTRS)

    Radhakrishnan, Krishnan; Whitefield, Philip

    1999-01-01

    , in addition, of the pressure, temperature, and velocity. A near term goal of the experimental program should be to confirm the nonlinear effects of sulfur speciation, and if present, to provide an explanation for them. It is also desirable to examine if the particulate matter retains any sulfur. The recommendation is to examine the effects on SOx production of variations in fuel-bound sulfur and aromatic content (which may affect the amount of particulates formed). These experiments should help us to understand if there is a coupling between particulate formation and SO, concentration. Similarly, any coupling with NOx can be examined either by introducing NOx into the combustion air or by using fuel-bound nitrogen. Also of immediate urgency is the need to establish and validate a detailed mechanism for sulfur oxidation/aerosol formation, whose chemistry is concluded to be homogeneous, because there is not enough surface area for heterogeneous effects. It is envisaged that this work will involve both experimental and theoretical programs. The experimental work will require, in addition to the measurements described above, fundamental studies in devices such as flow reactors and shock tubes. Complementing this effort should be modeling and theoretical activities. One impediment to the successful modeling of sulfur oxidation is the lack of reliable data for thermodynamic and transport properties for several species, such as aqueous nitric acid, sulfur oxides, and sulfuric acid. Quantum mechanical calculations are recommended as a convenient means of deriving values for these properties. Such calculations would also help establish rate constants for several important reactions for which experimental measurements are inherently fraught with uncertainty. Efforts to implement sufficiently detailed chemistry into computational fluid dynamic codes should be continued. Zero- and one-dimensional flow models are also useful vehicles for elucidating the minimal set of species and

  13. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Outlines laboratory procedures, demonstrations, teaching suggestions, and content information related to chemistry. Topics include polarizing power; calorimetry and momentum; microcomputers in school chemistry; a constant-volume dispenser for liquids, floating magnets, and crystal lattices; preparation of chromium; and solvent polarity and…

  14. Circumstellar chemistry

    NASA Technical Reports Server (NTRS)

    Glassgold, Alfred E.; Huggins, Patrick J.

    1987-01-01

    The study of the outer envelopes of cool evolved stars has become an active area of research. The physical properties of CS envelopes are presented. Observations of many wavelengths bands are relevant. A summary of observations and a discussion of theoretical considerations concerning the chemistry are summarized. Recent theoretical considerations show that the thermal equilibrium model is of limited use for understanding the chemistry of the outer CS envelopes. The theoretical modeling of the chemistry of CS envelopes provides a quantitive test of chemical concepts which have a broader interest than the envelopes themselves.

  15. Quantum algorithms

    NASA Astrophysics Data System (ADS)

    Abrams, Daniel S.

    This thesis describes several new quantum algorithms. These include a polynomial time algorithm that uses a quantum fast Fourier transform to find eigenvalues and eigenvectors of a Hamiltonian operator, and that can be applied in cases (commonly found in ab initio physics and chemistry problems) for which all known classical algorithms require exponential time. Fast algorithms for simulating many body Fermi systems are also provided in both first and second quantized descriptions. An efficient quantum algorithm for anti-symmetrization is given as well as a detailed discussion of a simulation of the Hubbard model. In addition, quantum algorithms that calculate numerical integrals and various characteristics of stochastic processes are described. Two techniques are given, both of which obtain an exponential speed increase in comparison to the fastest known classical deterministic algorithms and a quadratic speed increase in comparison to classical Monte Carlo (probabilistic) methods. I derive a simpler and slightly faster version of Grover's mean algorithm, show how to apply quantum counting to the problem, develop some variations of these algorithms, and show how both (apparently distinct) approaches can be understood from the same unified framework. Finally, the relationship between physics and computation is explored in some more depth, and it is shown that computational complexity theory depends very sensitively on physical laws. In particular, it is shown that nonlinear quantum mechanics allows for the polynomial time solution of NP-complete and #P oracle problems. Using the Weinberg model as a simple example, the explicit construction of the necessary gates is derived from the underlying physics. Nonlinear quantum algorithms are also presented using Polchinski type nonlinearities which do not allow for superluminal communication. (Copies available exclusively from MIT Libraries, Rm. 14- 0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)

  16. Nuclear Chemistry.

    ERIC Educational Resources Information Center

    Chemical and Engineering News, 1979

    1979-01-01

    Provides a brief review of the latest developments in nuclear chemistry. Nuclear research today is directed toward increased activity in radiopharmaceuticals and formation of new isotopes by high-energy, heavy-ion collisions. (Author/BB)

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Describes equipment, activities, and experiments useful in chemistry instruction, including among others, a rapid method to determine available chlorine in bleach, simple flame testing apparatus, and a simple apparatus demonstrating the technique of flash photolysis. (SK)

  18. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1973

    1973-01-01

    Several ideas are proposed for chemistry teachers to try in their classrooms. Subjects included are polymerization of acrylate, polymerization of styrene, conductivity, pollution, preparation of chlorine, redox equations, chemiluminescence, and molecular sieves. (PS)

  19. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1981

    1981-01-01

    Describes 13 activities, experiments and demonstrations, including the preparation of iron (III) chloride, simple alpha-helix model, investigating camping gas, redox reactions of some organic compounds, a liquid crystal thermometer, and the oxidation number concept in organic chemistry. (JN)

  20. Catalytic Chemistry.

    ERIC Educational Resources Information Center

    Borer, Londa; And Others

    1996-01-01

    Describes an approach for making chemistry relevant to everyday life. Involves the study of kinetics using the decomposition of hydrogen peroxide by vegetable juices. Allows students to design and carry out experiments and then draw conclusions from their results. (JRH)

  1. Precolumbian Chemistry.

    ERIC Educational Resources Information Center

    Robinson, Janet Bond

    1995-01-01

    Describes the content and development of a curriculum that provides an approach to descriptive chemistry and the history of technology through consideration of the pottery, metallurgy, pigments, dyes, agriculture, and medicine of pre-Columbian people. (DDR)

  2. Stratospheric chemistry

    SciTech Connect

    Brune, W.H. )

    1991-01-01

    Advances in stratospheric chemistry made by investigators in the United States from 1987 to 1990 are reviewed. Subject areas under consideration include photochemistry of the polar stratosphere, photochemistry of the global stratosphere, and assessments of inadvertent modification of the stratosphere by anthropogenic activity. Particular attention is given to early observations and theories, gas phase chemistry, Antarctic observations, Arctic observations, odd-oxygen, odd-hydrogen, odd-nitrogen, halogens, aerosols, modeling of stratospheric ozone, and reactive nitrogen effects.

  3. Computing UV/vis spectra using a combined molecular dynamics and quantum chemistry approach: bis-triazin-pyridine (BTP) ligands studied in solution.

    PubMed

    Höfener, Sebastian; Trumm, Michael; Koke, Carsten; Heuser, Johannes; Ekström, Ulf; Skerencak-Frech, Andrej; Schimmelpfennig, Bernd; Panak, Petra J

    2016-03-21

    We report a combined computational and experimental study to investigate the UV/vis spectra of 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridine (BTP) ligands in solution. In order to study molecules in solution using theoretical methods, force-field parameters for the ligand-water interaction are adjusted to ab initio quantum chemical calculations. Based on these parameters, molecular dynamics (MD) simulations are carried out from which snapshots are extracted as input to quantum chemical excitation-energy calculations to obtain UV/vis spectra of BTP ligands in solution using time-dependent density functional theory (TDDFT) employing the Tamm-Dancoff approximation (TDA). The range-separated CAM-B3LYP functional is used to avoid large errors for charge-transfer states occurring in the electronic spectra. In order to study environment effects with theoretical methods, the frozen-density embedding scheme is applied. This computational procedure allows to obtain electronic spectra calculated at the (range-separated) DFT level of theory in solution, revealing solvatochromic shifts upon solvation of up to about 0.6 eV. Comparison to experimental data shows a significantly improved agreement compared to vacuum calculations and enables the analysis of relevant excitations for the line shape in solution. PMID:26907588

  4. Collaborative Physical Chemistry Projects Involving Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Whisnant, David M.; Howe, Jerry J.; Lever, Lisa S.

    2000-02-01

    The physical chemistry classes from three colleges have collaborated on two computational chemistry projects using Quantum CAChe 3.0 and Gaussian 94W running on Pentium II PCs. Online communication by email and the World Wide Web was an important part of the collaboration. In the first project, students used molecular modeling to predict benzene derivatives that might be possible hair dyes. They used PM3 and ZINDO calculations to predict the electronic spectra of the molecules and tested the predicted spectra by comparing some with experimental measurements. They also did literature searches for real hair dyes and possible health effects. In the final phase of the project they proposed a synthetic pathway for one compound. In the second project the students were asked to predict which isomer of a small carbon cluster (C3, C4, or C5) was responsible for a series of IR lines observed in the spectrum of a carbon star. After preliminary PM3 calculations, they used ab initio calculations at the HF/6-31G(d) and MP2/6-31G(d) level to model the molecules and predict their vibrational frequencies and rotational constants. A comparison of the predictions with the experimental spectra suggested that the linear isomer of the C5 molecule was responsible for the lines.

  5. Radiation Chemistry

    NASA Astrophysics Data System (ADS)

    Wojnárovits, L.

    Ionizing radiation causes chemical changes in the molecules of the interacting medium. The initial molecules change to new molecules, resulting in changes of the physical, chemical, and eventually biological properties of the material. For instance, water decomposes to its elements H2 and O2. In polymers, degradation and crosslinking take place. In biopolymers, e.g., DNS strand breaks and other alterations occur. Such changes are to be avoided in some cases (radiation protection), however, in other cases they are used for technological purposes (radiation processing). This chapter introduces radiation chemistry by discussing the sources of ionizing radiation (radionuclide sources, machine sources), absorption of radiation energy, techniques used in radiation chemistry research, and methods of absorbed energy (absorbed dose) measurements. Radiation chemistry of different classes of inorganic (water and aqueous solutions, inorganic solids, ionic liquids (ILs)) and organic substances (hydrocarbons, halogenated compounds, polymers, and biomolecules) is discussed in concise form together with theoretical and experimental backgrounds. An essential part of the chapter is the introduction of radiation processing technologies in the fields of polymer chemistry, food processing, and sterilization. The application of radiation chemistry to nuclear technology and to protection of environment (flue gas treatment, wastewater treatment) is also discussed.

  6. Perspectives on Computational Organic Chemistry

    PubMed Central

    Streitwieser, Andrew

    2009-01-01

    The author reviews how his early love for theoretical organic chemistry led to experimental research and the extended search for quantitative correlations between experiment and quantum calculations. The experimental work led to ion pair acidities of alkali-organic compounds and most recently to equilibria and reactions of lithium and cesium enolates in THF. This chemistry is now being modeled by ab initio calculations. An important consideration is the treatment of solvation in which coordination of the alkali cation with the ether solvent plays a major role. PMID:19518150

  7. Tropospheric chemistry

    NASA Technical Reports Server (NTRS)

    Mohnen, V. A.; Chameides, W.; Demerjian, K. L.; Lenschow, D. H.; Logan, J. A.; Mcneal, R. J.; Penkett, S. A.; Platt, U.; Schurath, U.; Dias, P. D.

    1985-01-01

    The chemistry of the background troposphere, the source region, and the transition regions are discussed. The troposphere is governed by heterogeneous chemistry far more so than the stratosphere. Heterogeneous processes of interest involve scavenging of trace gases by aerosols, cloud and precipitation elements leading to aqueous phase chemical reactions and to temporary and permanent removal of material from the gas phase. Dry deposition is a major removal process for ozone, as well as for other gases of importance in tropospheric photochemistry. These processes are also discussed.

  8. Chemistry Experiments

    NASA Technical Reports Server (NTRS)

    Brasseur, Guy; Remsberg, Ellis; Purcell, Patrick; Bhatt, Praful; Sage, Karen H.; Brown, Donald E.; Scott, Courtney J.; Ko, Malcolm K. W.; Tie, Xue-Xi; Huang, Theresa

    1999-01-01

    The purpose of the chemistry component of the model comparison is to assess to what extent differences in the formulation of chemical processes explain the variance between model results. Observed concentrations of chemical compounds are used to estimate to what degree the various models represent realistic situations. For readability, the materials for the chemistry experiment are reported in three separate sections. This section discussed the data used to evaluate the models in their simulation of the source gases and the Nitrogen compounds (NO(y)) and Chlorine compounds (Cl(y)) species.

  9. Polymer Chemistry

    NASA Technical Reports Server (NTRS)

    Williams, Martha; Roberson, Luke; Caraccio, Anne

    2010-01-01

    This viewgraph presentation describes new technologies in polymer and material chemistry that benefits NASA programs and missions. The topics include: 1) What are Polymers?; 2) History of Polymer Chemistry; 3) Composites/Materials Development at KSC; 4) Why Wiring; 5) Next Generation Wiring Materials; 6) Wire System Materials and Integration; 7) Self-Healing Wire Repair; 8) Smart Wiring Summary; 9) Fire and Polymers; 10) Aerogel Technology; 11) Aerogel Composites; 12) Aerogels for Oil Remediation; 13) KSC's Solution; 14) Chemochromic Hydrogen Sensors; 15) STS-130 and 131 Operations; 16) HyperPigment; 17) Antimicrobial Materials; 18) Conductive Inks Formulations for Multiple Applications; and 19) Testing and Processing Equipment.

  10. a Quantum Chemical Study of the Structure and Chemistry of HZnCH_3, a Transition Metal Compound with 4s^2 Recoupled Pair Bonding

    NASA Astrophysics Data System (ADS)

    Woon, D. E.; Dunning, T. H.; , Jr.

    2011-06-01

    A structure was recently reported by Flory et al. for methyl zinc hydride, HZnCH_3, a molecule that may be formed via the direct insertion of Zn into one of the CH bonds of methane. The experiments were not able to demonstrate the formation pathway conclusively. The structures, bond energies, and other properties of HZnCH_3, ZnH, and ZnCH_3 were determined with high level coupled-cluster theory and multireference configuration interaction calculations in order to better understand the nature of the chemistry of HZnCH_3. The Zn--H and Zn--C bonds in HZnCH_3(X^1A_1) were found to be formed through recoupling the 4s^2 pair of Zn(^1S) in a manner that is very similar to the bonding in HBeCH_3 and other compounds where the 2s^2 pair of Be is recoupled. Various formation pathways were characterized, such as the analogous family of exchange reactions H + CH_4 → CH_4 + H, Zn + CH_4 → ZnCH_3 + H, and Be + CH_4 → BeCH_3 + H. Direct insertion may involve an intersystem crossing from the Zn(^3P) + CH_4 triplet surface to the singlet surface, which has been explored. M. A. Flory, A. J. Apponi, L. N. Zack, and L. M. Ziurys, J. Am. Chem. Soc. 132, 17186 (2010).

  11. Fragment Assembly Approach Based on Graph/Network Theory with Quantum Chemistry Verifications for Assigning Multidimensional NMR Signals in Metabolite Mixtures.

    PubMed

    Ito, Kengo; Tsutsumi, Yu; Date, Yasuhiro; Kikuchi, Jun

    2016-04-15

    The abundant observation of chemical fragment information for molecular complexities is a major advantage of biological NMR analysis. Thus, the development of a novel technique for NMR signal assignment and metabolite identification may offer new possibilities for exploring molecular complexities. We propose a new signal assignment approach for metabolite mixtures by assembling H-H, H-C, C-C, and Q-C fragmental information obtained by multidimensional NMR, followed by the application of graph and network theory. High-speed experiments and complete automatic signal assignments were achieved for 12 combined mixtures of (13)C-labeled standards. Application to a (13)C-labeled seaweed extract showed 66 H-C, 60 H-H, 326 C-C, and 28 Q-C correlations, which were successfully assembled to 18 metabolites by the automatic assignment. The validity of automatic assignment was supported by quantum chemical calculations. This new approach can predict entire metabolite structures from peak networks of biological extracts. PMID:26789380

  12. Mechanistic Insights into Radical-Mediated Oxidation of Tryptophan from ab Initio Quantum Chemistry Calculations and QM/MM Molecular Dynamics Simulations.

    PubMed

    Wood, Geoffrey P F; Sreedhara, Alavattam; Moore, Jamie M; Wang, John; Trout, Bernhardt L

    2016-05-12

    An assessment of the mechanisms of (•)OH and (•)OOH radical-mediated oxidation of tryptophan was performed using density functional theory calculations and ab initio plane-wave Quantum Mechanics/Molecular Mechanics (QM/MM) molecular dynamics simulations. For the (•)OH reactions, addition to the pyrrole ring at position 2 is the most favored site with a barrierless reaction in the gas phase. The subsequent degradation of this adduct through a H atom transfer to water was intermittently observed in aqueous-phase molecular dynamics simulations. For the (•)OOH reactions, addition to the pyrrole ring at position 2 is the most favored pathway, in contrast to the situation in the model system ethylene, where concerted addition to the double bond is preferred. From the (•)OOH position 2 adduct QM/MM simulations show that formation of oxy-3-indolanaline occurs readily in an aqueous environment. The observed transformation starts from an initial rupture of the O-O bond followed by a H atom transfer with the accompanying loss of an (•)OH radical to solution. Finally, classical molecular dynamics simulations were performed to equate observed differential oxidation rates of various tryptophan residues in monoclonal antibody fragments. It was found that simple parameters derived from simulation correlate well with the experimental data. PMID:27082439

  13. Studying the adsorption and activation of benzene and chlorobenzene on Ni(12%)/Al2O3 by means of gas chromatography and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Pichugina, D. A.; Lanin, S. N.; Beletskaya, A. V.; Bannykh, A. A.; Peristyi, A. A.; Polyakova, M. V.; Kuz'menko, N. E.

    2012-12-01

    In studying the surface and adsorption properties of Al2O3 and Ni(12%)/Al2O3 with respect to C6H6 and C6H5Cl, it is found that adsorbate-adsorbent interaction is stronger than adsorbate-adsorbate interaction. It is shown that the calculated isosteric heats of adsorption vary in a range of 61 to 45 kJ/mol depending on adsorption magnitude; for Ni(12%)/γ-Al2O3, as in the case of γ-Al2O3, the heat of adsorption of chlorobenzene is higher at low degrees of filling than that of benzene. According to density functional theory quantum-chemical calculations of the structures of complexes (Ni nC6H5Cl) z and (Ni n C6H6) z ( n = 1, 4; z = -1, 0, +1), a nickel atom can penetrate into C6H5Cl along the C-Cl bond. It is concluded that a negative charge on nickel contributes to the efficient activation of the C-Cl bond and to an increase in the rate of desorption of benzene, a key step in the hydrodechlorination of chlorobenzene.

  14. Investigation of the azo-hydrazone tautomeric equilibrium in an azo dye involving the naphthalene moiety by UV-vis spectroscopy and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Ünal, Arslan; Eren, Bilge; Eren, Erdal

    2013-10-01

    Photophysical properties of the azo-hydrazone tautomerism of Eriochrome Blue Black B (1-(1-hydroxy-2-naphthylazo)-2-naphthol-4-sulphonic acid) in DMF, MeCN and water were investigated using UV-visible spectroscopy and quantum chemical calculations. The optimized molecular structure parameters, relative energies, mole fractions, electronic absorption spectra and HOMO-LUMO energies for possible stable tautomeric forms of EBB were theoretically calculated by using hybrid density functional theory, (B3LYP) methods with 6-31G(d) basis set level and polarizable continuum model (PCM) for solvation effect. The effects of varying pH-, dye concentration-, solvent-, temperature-, and time-dependences on the UV-vis spectra of Eriochrome Blue Black B were also investigated experimentally. The calculations showed that the dye exhibited acid-base, azo-hydrazone and aggregate equilibria in DMF solution, while the most probably preferred form in MeCN solution was azo form. Thermodynamic parameters of dimerization reaction in DMF solution proved that entropy was the driving force of this reaction.

  15. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, and classroom materials/activities. These include: experiments on colloids, processing of uranium ore, action of heat on carbonates; color test for phenols and aromatic amines; solvent properties of non-electrolytes; stereoscopic applications/methods; a valency balance;…

  16. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1978

    1978-01-01

    Describes some laboratory apparatus, chemistry experiments and demonstrations, such as a Kofler block melting point apparatus, chromatographic investigation of the phosphoric acid, x-ray diffraction, the fountain experiment, endothermic sherbet, the measurement of viscosity, ionization energies and electronic configurations. (GA)

  17. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1982

    1982-01-01

    Presents procedures, experiments, demonstrations, teaching suggestions, and information on a variety of chemistry topics including, for example, inert gases, light-induced reactions, calculators, identification of substituted acetophenones, the elements, analysis of copper minerals, extraction of metallic strontium, equilibrium, halogens, and…

  18. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Short articles on the kinetics of the hydrogen peroxide-iodide ion reaction, simulation of fluidization catalysis, the use of Newman projection diagrams to represent steric relationships in organic chemistry, the use of synthetic substrates for proteolytic enzyme reactions, and two simple clock reactions"--hydrolysis of halogenoalkanes and…

  19. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

    Presents chemistry experiments, laboratory procedures, demonstrations, teaching suggestions, and classroom materials/activities. These include: game for teaching ionic formulas; method for balancing equations; description of useful redox series; computer programs (with listings) for water electrolysis simulation and for determining chemical…

  20. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

    Short articles on the alkylation of aniline, the preparation and properties of perbromate, using scrap copper in chemistry instruction, a safe method of burning hydrogen, and the use of an ion-charge model as an alternative to the mole concept in secondary school instruction. (AL)

  1. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1976

    1976-01-01

    Describes several chemistry projects, including solubility, formula for magnesium oxide, dissociation of dinitrogen tetroxide, use of 1-chloro-2, 4-dinitrobenzene, migration of ions, heats of neutralizations, use of pocket calculators, sonic cleaning, oxidation states of manganese, and cell potentials. Includes an extract from Chemical Age on…

  2. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1980

    1980-01-01

    Presents 12 chemistry notes for British secondary school teachers. Some of these notes are: (1) a simple device for testing pH-meters; (2) portable fume cupboard safety screen; and (3) Mass spectroscopy-analysis of a mass peak. (HM)

  3. Quantum Computation and Quantum Information

    NASA Astrophysics Data System (ADS)

    Nielsen, Michael A.; Chuang, Isaac L.

    2010-12-01

    Part I. Fundamental Concepts: 1. Introduction and overview; 2. Introduction to quantum mechanics; 3. Introduction to computer science; Part II. Quantum Computation: 4. Quantum circuits; 5. The quantum Fourier transform and its application; 6. Quantum search algorithms; 7. Quantum computers: physical realization; Part III. Quantum Information: 8. Quantum noise and quantum operations; 9. Distance measures for quantum information; 10. Quantum error-correction; 11. Entropy and information; 12. Quantum information theory; Appendices; References; Index.

  4. Determination of Carbon Dioxide Cluster Structures and Binding Energies from Quantum Chemistry: Magic Number and Temperature Effects in (CO2)n with 2≤n≤16

    NASA Astrophysics Data System (ADS)

    Lemke, K.

    2014-12-01

    Weak intermolecular interactions play an important role in nature and are involved in the stabilization of a variety of different molecular aggregates. Carbon dioxide clusters (CO2)n are a good example in which monomers interact through London dispersion forces. The ability to accurately describe these types of interactions is crucial in understanding fundamental molecular-scale processes controlling the chemistry of carbon dioxide, ranging from CO2 self-organization into monolayer films on metal and mineral surfaces, formation of CO2 clouds and molecular interactions in supercritical CO2. Weak interactions in (CO2)n clusters pose a challenge for experimental techniques, and are therefore in many cases either difficult or impossible to explore. Density functional theory with dispersion correction (DFT-D), on the other hand, can provide insight into intermolecular interactions among CO2 molecules, provided that dispersion correction is properly accounted for. In this presentation results from dispersion sensitive DFT (M05-2X, B97-D, B2PLYPD) and MP2 theory will be shown, that describe interactions in (CO2)n clusters over a broad range of temperatures, and in particular, in those clusters with magic number sizes 6 and 13. Briefly, structure determinations and thermodynamic calculations for (CO2)n clustering reactions by DFT-D compare well against benchmark MP2 and CCSD(T)/CBS results, and therefore may be extended to significantly larger systems than accessible with highly correlated methods. The stepwise free energies of CO2 cluster formation at temperatures from 60-400K reveal valuable new insights, the most important being that the stacked cyclic hexamer and tridecameric cluster, consisting of a 3-6-3 ring structure with a centrally enclosed CO2 monomer, are highly stable clusters and therefore should be spectroscopically detectable. These results indicate that DFT-D provides an accurate and cost effective description of non-covalent interactions in (CO2) clusters

  5. Chemistry Modeling for Aerothermodynamics and TPS

    NASA Technical Reports Server (NTRS)

    Wang, Dun-You; Stallcop, James R.; Dateo, Christopher E.; Schwenke, David W.; Haliciogiu, Timur; Huo, Winifred

    2004-01-01

    Recent advances in supercomputers and highly scalable quantum chemistry software render computational chemistry methods a viable means of providing chemistry data for aerothermal analysis at a specific level of confidence. Four examples of first principles quantum chemistry calculations will be presented. The study of the highly nonequilibrium rotational distribution of nitrogen molecule from the exchange reaction N + N2 illustrates how chemical reactions can influence the rotational distribution. The reaction C2H + H2 is one example of a radical reaction that occurs during hypersonic entry into a methane containing atmosphere. A study of the etching of Si surface illustrates our approach to surface reactions. A recently developed web accessible database and software tool (DDD) that provides the radiation profile of diatomic molecules is also described.

  6. Chemistry Modeling for Aerothermodynamics and TPS

    NASA Technical Reports Server (NTRS)

    Wang, Dunyou; Stallcop, James R.; Dateo, Christopher e.; Schwenke, David W.; Halicioglu, Timur; Huo, winifred M.

    2005-01-01

    Recent advances in supercomputers and highly scalable quantum chemistry software render computational chemistry methods a viable means of providing chemistry data for aerothermal analysis at a specific level of confidence. Four examples of first principles quantum chemistry calculations will be presented. Study of the highly nonequilibrium rotational distribution of a nitrogen molecule from the exchange reaction N + N2 illustrates how chemical reactions can influence rotational distribution. The reaction C2H + H2 is one example of a radical reaction that occurs during hypersonic entry into an atmosphere containing methane. A study of the etching of a Si surface illustrates our approach to surface reactions. A recently developed web accessible database and software tool (DDD) that provides the radiation profile of diatomic molecules is also described.

  7. The Physics of Quantum Computation

    NASA Astrophysics Data System (ADS)

    Falci, Giuseppe; Paladino, Elisabette

    2015-10-01

    Quantum Computation has emerged in the past decades as a consequence of down-scaling of electronic devices to the mesoscopic regime and of advances in the ability of controlling and measuring microscopic quantum systems. QC has many interdisciplinary aspects, ranging from physics and chemistry to mathematics and computer science. In these lecture notes we focus on physical hardware, present day challenges and future directions for design of quantum architectures.

  8. Selected new developments in computational chemistry.

    PubMed Central

    Darden, T A; Bartolotti, L; Pedersen, L G

    1996-01-01

    Molecular dynamics is a general technique for simulating the time-dependent properties of molecules and their environments. Quantum mechanics, as applied to molecules or clusters of molecules, provides a prescription for predicting properties exactly (in principle). It is reasonable to expect that both will have a profound effect on our understanding of environmental chemistry in the future. In this review, we consider several recent advances and applications in computational chemistry. Images Figure 1. PMID:8722111

  9. Old Wine in New Bottles: Quantum Theory in Historical Perspective.

    ERIC Educational Resources Information Center

    Bent, Henry A.

    1984-01-01

    Discusses similarities between chemistry and three central concepts of quantum physics: (1) stationary states; (2) wave functions; and (3) complementarity. Based on these and other similarities, it is indicated that quantum physics is a chemical physics. (JN)

  10. Computational chemistry

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.

    1987-01-01

    With the advent of supercomputers, modern computational chemistry algorithms and codes, a powerful tool was created to help fill NASA's continuing need for information on the properties of matter in hostile or unusual environments. Computational resources provided under the National Aerodynamics Simulator (NAS) program were a cornerstone for recent advancements in this field. Properties of gases, materials, and their interactions can be determined from solutions of the governing equations. In the case of gases, for example, radiative transition probabilites per particle, bond-dissociation energies, and rates of simple chemical reactions can be determined computationally as reliably as from experiment. The data are proving to be quite valuable in providing inputs to real-gas flow simulation codes used to compute aerothermodynamic loads on NASA's aeroassist orbital transfer vehicles and a host of problems related to the National Aerospace Plane Program. Although more approximate, similar solutions can be obtained for ensembles of atoms simulating small particles of materials with and without the presence of gases. Computational chemistry has application in studying catalysis, properties of polymers, all of interest to various NASA missions, including those previously mentioned. In addition to discussing these applications of computational chemistry within NASA, the governing equations and the need for supercomputers for their solution is outlined.