Sample records for quantum chemistry calculations

  1. Computing protein infrared spectroscopy with quantum chemistry.

    PubMed

    Besley, Nicholas A

    2007-12-15

    Quantum chemistry is a field of science that has undergone unprecedented advances in the last 50 years. From the pioneering work of Boys in the 1950s, quantum chemistry has evolved from being regarded as a specialized and esoteric discipline to a widely used tool that underpins much of the current research in chemistry today. This achievement was recognized with the award of the 1998 Nobel Prize in Chemistry to John Pople and Walter Kohn. As the new millennium unfolds, quantum chemistry stands at the forefront of an exciting new era. Quantitative calculations on systems of the magnitude of proteins are becoming a realistic possibility, an achievement that would have been unimaginable to the early pioneers of quantum chemistry. In this article we will describe ongoing work towards this goal, focusing on the calculation of protein infrared amide bands directly with quantum chemical methods.

  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. Exploiting Locality in Quantum Computation for Quantum Chemistry.

    PubMed

    McClean, Jarrod R; Babbush, Ryan; Love, Peter J; Aspuru-Guzik, Alán

    2014-12-18

    Accurate prediction of chemical and material properties from first-principles quantum chemistry is a challenging task on traditional computers. Recent developments in quantum computation offer a route toward highly accurate solutions with polynomial cost; however, this solution still carries a large overhead. In this Perspective, we aim to bring together known results about the locality of physical interactions from quantum chemistry with ideas from quantum computation. We show that the utilization of spatial locality combined with the Bravyi-Kitaev transformation offers an improvement in the scaling of known quantum algorithms for quantum chemistry and provides numerical examples to help illustrate this point. We combine these developments to improve the outlook for the future of quantum chemistry on quantum computers.

  4. Calculating Potential Energy Curves with Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Powell, Andrew D.; Dawes, Richard

    2014-06-01

    Quantum Monte Carlo (QMC) is a computational technique that can be applied to the electronic Schrödinger equation for molecules. QMC methods such as Variational Monte Carlo (VMC) and Diffusion Monte Carlo (DMC) have demonstrated the capability of capturing large fractions of the correlation energy, thus suggesting their possible use for high-accuracy quantum chemistry calculations. QMC methods scale particularly well with respect to parallelization making them an attractive consideration in anticipation of next-generation computing architectures which will involve massive parallelization with millions of cores. Due to the statistical nature of the approach, in contrast to standard quantum chemistry methods, uncertainties (error-bars) are associated with each calculated energy. This study focuses on the cost, feasibility and practical application of calculating potential energy curves for small molecules with QMC methods. Trial wave functions were constructed with the multi-configurational self-consistent field (MCSCF) method from GAMESS-US.[1] The CASINO Monte Carlo quantum chemistry package [2] was used for all of the DMC calculations. An overview of our progress in this direction will be given. References: M. W. Schmidt et al. J. Comput. Chem. 14, 1347 (1993). R. J. Needs et al. J. Phys.: Condensed Matter 22, 023201 (2010).

  5. Virtually going green: The role of quantum computational chemistry in reducing pollution and toxicity in chemistry

    NASA Astrophysics Data System (ADS)

    Stevens, Jonathan

    2017-07-01

    Continuing advances in computational chemistry has permitted quantum mechanical calculation to assist in research in green chemistry and to contribute to the greening of chemical practice. Presented here are recent examples illustrating the contribution of computational quantum chemistry to green chemistry, including the possibility of using computation as a green alternative to experiments, but also illustrating contributions to greener catalysis and the search for greener solvents. Examples of applications of computation to ambitious projects for green synthetic chemistry using carbon dioxide are also presented.

  6. Computations and interpretations: The growth of quantum chemistry, 1927-1967

    NASA Astrophysics Data System (ADS)

    Park, Buhm Soon

    1999-10-01

    This dissertation is a contribution to the historical study of scientific disciplines in the twentieth century. It seeks to examine the development of quantum chemistry during the four decades after its inception in 1927. This development was manifest in theories, tools, scientists, and institutions, all of which constituted the disciplinary identity of quantum chemistry. To characterize its identity, I deal with the origins of key ideas and concepts; the change of computational tools from desk calculators to digital computers; the formation of a network among research groups and individuals; and the institutionalization of annual meetings. The dissertation's thesis is three-fold. First, in the pre- World War II years, there were individual contributions to the development of theories in quantum chemistry, but the founding fathers worked in their disciplinary contexts of physics or chemistry with little interest in building a quantum chemistry community. Second, the introduction of electronic digital computers in the postwar years affected the resurgence of the ab initio approach-the attempt to solve the Schrödinger equation without recourse to empirical data-and also the emergence of a community of quantum chemists. But the use of computers did not give rise to a consensus over the aims, methods, or content of the discipline. Third, quantum chemistry exerted a significant influence upon the transformation of chemical education and research in general, thanks to ``chemical translators,'' who sought to explain the gist of quantum chemistry in a language that chemists could understand. In sum, quantum chemistry has been a discipline characterized by diverse traditions, and the whole of chemistry has been under the influence of computations and interpretations made by quantum chemists.

  7. 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.

  8. Quantum chemistry simulation on quantum computers: theories and experiments.

    PubMed

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

    2012-07-14

    It has been claimed that quantum computers can mimic quantum systems efficiently in the polynomial scale. Traditionally, those simulations are carried out numerically on classical computers, which are inevitably confronted with the exponential growth of required resources, with the increasing size of quantum systems. Quantum computers avoid this problem, and thus provide a possible solution for large quantum systems. In this paper, we first discuss the ideas of quantum simulation, the background of quantum simulators, their categories, and the development in both theories and experiments. We then present a brief introduction to quantum chemistry evaluated via classical computers followed by typical procedures of quantum simulation towards quantum chemistry. Reviewed are not only theoretical proposals but also proof-of-principle experimental implementations, via a small quantum computer, which include the evaluation of the static molecular eigenenergy and the simulation of chemical reaction dynamics. Although the experimental development is still behind the theory, we give prospects and suggestions for future experiments. We anticipate that in the near future quantum simulation will become a powerful tool for quantum chemistry over classical computations.

  9. 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.

  10. 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.

  11. Serenity: A subsystem quantum chemistry program.

    PubMed

    Unsleber, Jan P; Dresselhaus, Thomas; Klahr, Kevin; Schnieders, David; Böckers, Michael; Barton, Dennis; Neugebauer, Johannes

    2018-05-15

    We present the new quantum chemistry program Serenity. It implements a wide variety of functionalities with a focus on subsystem methodology. The modular code structure in combination with publicly available external tools and particular design concepts ensures extensibility and robustness with a focus on the needs of a subsystem program. Several important features of the program are exemplified with sample calculations with subsystem density-functional theory, potential reconstruction techniques, a projection-based embedding approach and combinations thereof with geometry optimization, semi-numerical frequency calculations and linear-response time-dependent density-functional theory. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  12. Per-Olov Löwdin - father of quantum chemistry

    NASA Astrophysics Data System (ADS)

    Brändas, Erkki J.

    2017-09-01

    During 2016, we celebrate the 100th anniversary of the birth of Per-Olov Löwdin. He was appointed to the first Lehrstuhl in quantum chemistry at Uppsala University in 1960. Löwdin introduced quantum chemistry as a field in its own right by formulating its goals, establishing fundamental concepts, like the correlation energy, the method of configuration interaction, reduced density matrices, natural spin orbitals, charge and bond order matrices, symmetric orthogonalisation, and generalised self-consistent fields. His exposition of partitioning technique and perturbation theory, wave and reaction operators and associated non-linear summation techniques, introduced mathematical rigour and deductive order in the interpretative organisation of the new field. He brought the first computer to Uppsala University and pioneered the initiation of 'electronic brains' and anticipated their significance for quantum chemistry. Perhaps his single most influential contribution to the field was his education of two generations of future faculty in quantum chemistry through Summer Schools in the Scandinavian Mountains, Winter Institutes at Sanibel Island in the Gulf of Mexico. Per-Olov Löwdin founded the book series Advances in Quantum Chemistry and the International Journal of Quantum Chemistry. The evolution of quantum chemistry is appraised, starting from a collection of cross-disciplinary applications of quantum mechanics to the technologically advanced and predominant field of today, virtually used in all branches of chemistry. The scientific work of Per-Olov Löwdin has been crucial for the development of this new important province of science.

  13. Efficient hybrid-symbolic methods for quantum mechanical calculations

    NASA Astrophysics Data System (ADS)

    Scott, T. C.; Zhang, Wenxing

    2015-06-01

    We present hybrid symbolic-numerical tools to generate optimized numerical code for rapid prototyping and fast numerical computation starting from a computer algebra system (CAS) and tailored to any given quantum mechanical problem. Although a major focus concerns the quantum chemistry methods of H. Nakatsuji which has yielded successful and very accurate eigensolutions for small atoms and molecules, the tools are general and may be applied to any basis set calculation with a variational principle applied to its linear and non-linear parameters.

  14. Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Bertoni, Colleen

    Computational chemistry uses the theoretical advances of quantum mechanics and the algorithmic and hardware advances of computer science to give insight into chemical problems. It is currently possible to do highly accurate quantum chemistry calculations, but the most accurate methods are very computationally expensive. Thus it is only feasible to do highly accurate calculations on small molecules, since typically more computationally efficient methods are also less accurate. The overall goal of my dissertation work has been to try to decrease the computational expense of calculations without decreasing the accuracy. In particular, my dissertation work focuses on fragmentation methods, intermolecular interactionsmore » methods, analytic gradients, and taking advantage of new hardware.« less

  15. Dielectric response of periodic systems from quantum Monte Carlo calculations.

    PubMed

    Umari, P; Willamson, A J; Galli, Giulia; Marzari, Nicola

    2005-11-11

    We present a novel approach that allows us to calculate the dielectric response of periodic systems in the quantum Monte Carlo formalism. We employ a many-body generalization for the electric-enthalpy functional, where the coupling with the field is expressed via the Berry-phase formulation for the macroscopic polarization. A self-consistent local Hamiltonian then determines the ground-state wave function, allowing for accurate diffusion quantum Monte Carlo calculations where the polarization's fixed point is estimated from the average on an iterative sequence, sampled via forward walking. This approach has been validated for the case of an isolated hydrogen atom and then applied to a periodic system, to calculate the dielectric susceptibility of molecular-hydrogen chains. The results found are in excellent agreement with the best estimates obtained from the extrapolation of quantum-chemistry calculations.

  16. 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)

  17. Quantum Mechanical Calculations in Collaborations with Experimental Chemistry: The Theoretical Organic Chemistry Perspective

    NASA Astrophysics Data System (ADS)

    Nguyen, Quynh Nhu Ngoc

    The results of quantum chemical calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols by significantly increasing basicity of the substrate hydroxyl group. The energy barrier for cyclization of the pentadienyl cation after water loss is already low in the background reaction and is altered fairly little by the cage. The calculations for other non-alcohol substrates also suggest that the cage increases the basicity of amine and phosphine groups, though to a lesser extend comparing to the alcohol substrate. Due to their twisting patterns, alpha-helical peptides are known to have overall "macrodipoles" along the principal axes as the result of the backbone carbonyl groups pointing toward the C-terminus. As the dipoles have implications in helical bundles, interactions with lipid bilayers, and distribution of charge, chemists have long been interested in employing the macrodipole in modifications of peptides' catalytic activities. In this studied, we examined the impact of both global and local noncovalent interactions between peptide catalysts and substrates in the first transesterification step, in hope of designing a better peptide catalysts to aid in ester metabolism. Quantum mechanical calculations helped predict whether the targeted medium-sized cyclic peptide products would more likely be the major products, before the experimental team invested extensive resources and time to carry out the syntheses. Many systems were found to favor the medium-sized cyclic peptides, whereas one system was predicted to result in polycyclic product, and the latter experimental observations agreed with these predictions. Naturally occurring cyclic peptides display various biological activities due to their diverse structures. Understanding the dominant structures of these peptides could help give insight into protein-protein interactions or substrate-protein binding. With the experimental NMR data obtained for the

  18. UTChem - A Program for Ab Initio Quantum Chemistry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yanai, Takeshi; Nakano, Haruyuki; Nakajima, Takahito

    2003-06-18

    UTChem is a quantum chemistry software developed by Hirao's group at the University of Tokyo. UTChem is a research product of our work to develop new and better theoretical methods in quantum chemistry.

  19. Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree-Fock.

    PubMed

    Tamayo-Mendoza, Teresa; Kreisbeck, Christoph; Lindh, Roland; Aspuru-Guzik, Alán

    2018-05-23

    Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult , a Hartree-Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

  20. Automatic Differentiation in Quantum Chemistry with Applications to Fully Variational Hartree–Fock

    PubMed Central

    2018-01-01

    Automatic differentiation (AD) is a powerful tool that allows calculating derivatives of implemented algorithms with respect to all of their parameters up to machine precision, without the need to explicitly add any additional functions. Thus, AD has great potential in quantum chemistry, where gradients are omnipresent but also difficult to obtain, and researchers typically spend a considerable amount of time finding suitable analytical forms when implementing derivatives. Here, we demonstrate that AD can be used to compute gradients with respect to any parameter throughout a complete quantum chemistry method. We present DiffiQult, a Hartree–Fock implementation, entirely differentiated with the use of AD tools. DiffiQult is a software package written in plain Python with minimal deviation from standard code which illustrates the capability of AD to save human effort and time in implementations of exact gradients in quantum chemistry. We leverage the obtained gradients to optimize the parameters of one-particle basis sets in the context of the floating Gaussian framework.

  1. Quantum Chemistry, 5th Edition by Ira N. Levine

    NASA Astrophysics Data System (ADS)

    Hinde, Robert J.

    2000-12-01

    Of course, there is no one- or two-week shortcut by which nonspecialists can master enough quantum mechanics to become informed users of quantum chemical techniques. Nevertheless, a text that integrated the fundamentals of quantum theory with a rigorous introduction to quantum chemistry could help instructors design a class that would benefit both these nonspecialists and graduate students in physical chemistry. Could such a class overcome the (undeserved) stigma associated with the physical chemistry curriculum? That remains to be seen.

  2. 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,…

  3. 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.

  4. 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…

  5. Accurate quantum chemical calculations

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

    1989-01-01

    An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

  6. 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:

  7. 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

  8. 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.

  9. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Turi, László, E-mail: turi@chem.elte.hu

    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 withmore » 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.« less

  11. From transistor to trapped-ion computers for quantum chemistry.

    PubMed

    Yung, M-H; Casanova, J; Mezzacapo, A; McClean, J; Lamata, L; Aspuru-Guzik, A; Solano, E

    2014-01-07

    Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology.

  12. From transistor to trapped-ion computers for quantum chemistry

    PubMed Central

    Yung, M.-H.; Casanova, J.; Mezzacapo, A.; McClean, J.; Lamata, L.; Aspuru-Guzik, A.; Solano, E.

    2014-01-01

    Over the last few decades, quantum chemistry has progressed through the development of computational methods based on modern digital computers. However, these methods can hardly fulfill the exponentially-growing resource requirements when applied to large quantum systems. As pointed out by Feynman, this restriction is intrinsic to all computational models based on classical physics. Recently, the rapid advancement of trapped-ion technologies has opened new possibilities for quantum control and quantum simulations. Here, we present an efficient toolkit that exploits both the internal and motional degrees of freedom of trapped ions for solving problems in quantum chemistry, including molecular electronic structure, molecular dynamics, and vibronic coupling. We focus on applications that go beyond the capacity of classical computers, but may be realizable on state-of-the-art trapped-ion systems. These results allow us to envision a new paradigm of quantum chemistry that shifts from the current transistor to a near-future trapped-ion-based technology. PMID:24395054

  13. 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…

  14. Towards quantum chemistry on a quantum computer.

    PubMed

    Lanyon, B P; Whitfield, J D; Gillett, G G; Goggin, M E; Almeida, M P; Kassal, I; Biamonte, J D; Mohseni, M; Powell, B J; Barbieri, M; Aspuru-Guzik, A; White, A G

    2010-02-01

    Exact first-principles calculations of molecular properties are currently intractable because their computational cost grows exponentially with both the number of atoms and basis set size. A solution is to move to a radically different model of computing by building a quantum computer, which is a device that uses quantum systems themselves to store and process data. Here we report the application of the latest photonic quantum computer technology to calculate properties of the smallest molecular system: the hydrogen molecule in a minimal basis. We calculate the complete energy spectrum to 20 bits of precision and discuss how the technique can be expanded to solve large-scale chemical problems that lie beyond the reach of modern supercomputers. These results represent an early practical step toward a powerful tool with a broad range of quantum-chemical applications.

  15. Synthesis, crystal structure, vibrational spectra and theoretical calculations of quantum chemistry of a potential antimicrobial Meldrum's acid derivative

    NASA Astrophysics Data System (ADS)

    Campelo, M. J. M.; Freire, P. T. C.; Mendes Filho, J.; de Toledo, T. A.; Teixeira, A. M. R.; da Silva, L. E.; Bento, R. R. F.; Faria, J. L. B.; Pizani, P. S.; Gusmão, G. O. M.; Coutinho, H. D. M.; Oliveira, M. T. A.

    2017-10-01

    A new derivative of Meldrum's acid 5-((5-chloropyridin-2-ylamino)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione (CYMM) of molecular formula C12H11ClN2O4 was synthesized and structurally characterized using single crystal X-ray diffraction technique. The vibrational properties of the crystal were studied by Fourier Transform infrared (FT-IR), Fourier Transform Raman (FT-Raman) techniques and theoretical calculations of quantum chemistry using Density functional theory (DFT) and Density functional perturbation theory (DFPT). A comparison with experimental spectra allowed the assignment of all the normal modes. The descriptions of the normal modes were carried by means of potential energy distribution (PED). Additionally, analysis of the antimicrobial activity and antibiotic resistance modulatory activity was carried out to evaluate the antibacterial potential of the CYMM.

  16. 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).

  17. Quantum chemistry in environmental pesticide risk assessment.

    PubMed

    Villaverde, Juan J; López-Goti, Carmen; Alcamí, Manuel; Lamsabhi, Al Mokhtar; Alonso-Prados, José L; Sandín-España, Pilar

    2017-11-01

    The scientific community and regulatory bodies worldwide, currently promote the development of non-experimental tests that produce reliable data for pesticide risk assessment. The use of standard quantum chemistry methods could allow the development of tools to perform a first screening of compounds to be considered for the experimental studies, improving the risk assessment. This fact results in a better distribution of resources and in better planning, allowing a more exhaustive study of the pesticides and their metabolic products. The current paper explores the potential of quantum chemistry in modelling toxicity and environmental behaviour of pesticides and their by-products by using electronic descriptors obtained computationally. Quantum chemistry has potential to estimate the physico-chemical properties of pesticides, including certain chemical reaction mechanisms and their degradation pathways, allowing modelling of the environmental behaviour of both pesticides and their by-products. In this sense, theoretical methods can contribute to performing a more focused risk assessment of pesticides used in the market, and may lead to higher quality and safer agricultural products. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  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

    2016-02-03

    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.

  19. Spiers Memorial Lecture. Quantum chemistry: the first seventy years.

    PubMed

    McWeeny, Roy

    2007-01-01

    Present-day theoretical chemistry is rooted in Quantum Mechanics. The aim of the opening lecture is to trace the evolution of Quantum Chemistry from the Heitler-London paper of 1927 up to the end of the last century, emphasizing concepts rather than calculations. The importance of symmetry concepts became evident in the early years: one thinks of the necessary anti-symmetry of the wave function under electron permutations, the Pauli principle, the aufbau scheme, and the classification of spectroscopic states. But for chemists perhaps the key concept is embodied in the Hellmann-Feynman theorem, which provides a pictorial interpretation of chemical bonding in terms of classical electrostatic forces exerted on the nuclei by the electron distribution. Much of the lecture is concerned with various electron distribution functions--the electron density, the current density, the spin density, and other 'property densities'--and with their use in interpreting both molecular structure and molecular properties. Other topics touched upon include Response theory and propagators; Chemical groups in molecules and the group function approach; Atoms in molecules and Bader's theory; Electron correlation and the 'pair function'. Finally, some long-standing controversies, in particular the EPR paradox, are re-examined in the context of molecular dissociation. By admitting the concept of symmetry breaking, along with the use of the von Neumann-Dirac statistical ensemble, orthodox quantum mechanics can lead to a convincing picture of the dissociation mechanism.

  20. Quantum Chemistry; A concise introduction for students of physics, chemistry, biochemistry and materials science

    NASA Astrophysics Data System (ADS)

    Thakkar, Ajit J.

    2017-09-01

    This book provides non-specialists with a basic understanding of the underlying concepts of quantum chemistry. It is both a text for second- or third-year undergraduates and a reference for researchers who need a quick introduction or refresher. All chemists and many biochemists, materials scientists, engineers, and physicists routinely use spectroscopic measurements and electronic structure computations in their work. The emphasis of Quantum Chemistry on explaining ideas rather than enumerating facts or presenting procedural details makes this an excellent foundation text/reference.

  1. 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.

  2. 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.

  3. Quantum chemistry study of dielectric materials deposition

    NASA Astrophysics Data System (ADS)

    Widjaja, Yuniarto

    The drive to continually decrease the device dimensions of integrated circuits in the microelectronics industry requires that deposited films approach subnanometer thicknesses. Hence, a fundamental understanding of the physics and chemistry of film deposition is important to obtain better control of the properties of the deposited film. We use ab initio quantum chemistry calculations to explore chemical reactions at the atomic level. Important thermodynamic and kinetic parameters are then obtained, which can then be used as inputs in constructing first-principles based reactor models. Studies of new systems for which data are not available can be conducted as well. In this dissertation, we use quantum chemistry simulations to study the deposition of gate dielectrics for metal-oxide-semiconductor (MOS) devices. The focus of this study is on heterogeneous reactions between gaseous precursors and solid surfaces. Adsorbate-surface interactions introduce additional degrees of complexity compared to the corresponding gas-phase or solid-state reactions. The applicability and accuracy of cluster approximations to represent solid surfaces are first investigated. The majority of our results are obtained using B3LYP density functional theory (DFT). The structures of reactants, products, and transition states are obtained, followed by calculations of thermochemical and kinetic properties. Whenever experimental data are available, qualitative and/or quantitative comparisons are drawn. Atomistic mechanisms and the energetics of several reactions leading to the deposition of SiO2, Si3N4, and potential new high-kappa materials such as ZrO2, HfO2, and Al 2O3 have been explored in this dissertation. Competing reaction pathways are explored for each of the deposition reactions studied. For example, the potential energy surface (PES) for ZrO2 ALD shows that the reactions proceed through a trapping-mediated mechanism, which results in a competition between desorption and decomposition

  4. Simulating chemistry using quantum computers.

    PubMed

    Kassal, Ivan; Whitfield, James D; Perdomo-Ortiz, Alejandro; Yung, Man-Hong; Aspuru-Guzik, Alán

    2011-01-01

    The difficulty of simulating quantum systems, well known to quantum chemists, prompted the idea of quantum computation. One can avoid the steep scaling associated with the exact simulation of increasingly large quantum systems on conventional computers, by mapping the quantum system to another, more controllable one. In this review, we discuss to what extent the ideas in quantum computation, now a well-established field, have been applied to chemical problems. We describe algorithms that achieve significant advantages for the electronic-structure problem, the simulation of chemical dynamics, protein folding, and other tasks. Although theory is still ahead of experiment, we outline recent advances that have led to the first chemical calculations on small quantum information processors.

  5. Let Students Derive, by Themselves, Two-Dimensional Atomic and Molecular Quantum Chemistry from Scratch

    ERIC Educational Resources Information Center

    Ge, Yingbin

    2016-01-01

    Hands-on exercises are designed for undergraduate physical chemistry students to derive two-dimensional quantum chemistry from scratch for the H atom and H[subscript 2] molecule, both in the ground state and excited states. By reducing the mathematical complexity of the traditional quantum chemistry teaching, these exercises can be completed…

  6. 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.

  7. Assignment of absolute stereostructures through quantum mechanics electronic and vibrational circular dichroism calculations.

    PubMed

    Dai, Peng; Jiang, Nan; Tan, Ren-Xiang

    2016-01-01

    Elucidation of absolute configuration of chiral molecules including structurally complex natural products remains a challenging problem in organic chemistry. A reliable method for assigning the absolute stereostructure is to combine the experimental circular dichroism (CD) techniques such as electronic and vibrational CD (ECD and VCD), with quantum mechanics (QM) ECD and VCD calculations. The traditional QM methods as well as their continuing developments make them more applicable with accuracy. Taking some chiral natural products with diverse conformations as examples, this review describes the basic concepts and new developments of QM approaches for ECD and VCD calculations in solution and solid states.

  8. Cold molecules: Progress in quantum engineering of chemistry and quantum matter

    NASA Astrophysics Data System (ADS)

    Bohn, John L.; Rey, Ana Maria; Ye, Jun

    2017-09-01

    Cooling atoms to ultralow temperatures has produced a wealth of opportunities in fundamental physics, precision metrology, and quantum science. The more recent application of sophisticated cooling techniques to molecules, which has been more challenging to implement owing to the complexity of molecular structures, has now opened the door to the longstanding goal of precisely controlling molecular internal and external degrees of freedom and the resulting interaction processes. This line of research can leverage fundamental insights into how molecules interact and evolve to enable the control of reaction chemistry and the design and realization of a range of advanced quantum materials.

  9. Energetic factors determining the binding of type I inhibitors to c-Met kinase: experimental studies and quantum mechanical calculations.

    PubMed

    Yu, Zhe; Ma, Yu-chi; Ai, Jing; Chen, Dan-qi; Zhao, Dong-mei; Wang, Xin; Chen, Yue-lei; Geng, Mei-yu; Xiong, Bing; Cheng, Mao-sheng; Shen, Jing-Kang

    2013-11-01

    To decipher the molecular interactions between c-Met and its type I inhibitors and to facilitate the design of novel c-Met inhibitors. Based on the prototype model inhibitor 1, four ligands with subtle differences in the fused aromatic rings were synthesized. Quantum chemistry was employed to calculate the binding free energy for each ligand. Symmetry-adapted perturbation theory (SAPT) was used to decompose the binding energy into several fundamental forces to elucidate the determinant factors. Binding free energies calculated from quantum chemistry were correlated well with experimental data. SAPT calculations showed that the predominant driving force for binding was derived from a sandwich π-π interaction with Tyr-1230. Arg-1208 was the differentiating factor, interacting with the 6-position of the fused aromatic ring system through the backbone carbonyl with a force pattern similar to hydrogen bonding. Therefore, a hydrogen atom must be attached at the 6-position, and changing the carbon atom to nitrogen caused unfavorable electrostatic interactions. The theoretical studies have elucidated the determinant factors involved in the binding of type I inhibitors to c-Met.

  10. High-Level Spectroscopy, Quantum Chemistry, and Catalysis: Not just a Passing Fad.

    PubMed

    Neese, Frank

    2017-09-04

    Quantum chemistry can be used as a powerful link between theory and experiment for studying reactions in all areas of catalysis. The key feature of this approach is the combination of quantum chemistry with a range of high-level spectroscopic methods. This allows for conclusions to be reached that neither theory nor experiment would have been able to obtain in isolation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. 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.

  12. 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

    2011-10-14

    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

  13. 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

  14. Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

    PubMed

    Rappoport, Dmitrij; Galvin, Cooper J; Zubarev, Dmitry Yu; Aspuru-Guzik, Alán

    2014-03-11

    While structures and reactivities of many small molecules can be computed efficiently and accurately using quantum chemical methods, heuristic approaches remain essential for modeling complex structures and large-scale chemical systems. Here, we present a heuristics-aided quantum chemical methodology applicable to complex chemical reaction networks such as those arising in cell metabolism and prebiotic chemistry. Chemical heuristics offer an expedient way of traversing high-dimensional reactive potential energy surfaces and are combined here with quantum chemical structure optimizations, which yield the structures and energies of the reaction intermediates and products. Application of heuristics-aided quantum chemical methodology to the formose reaction reproduces the experimentally observed reaction products, major reaction pathways, and autocatalytic cycles.

  15. 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

  16. Energetic factors determining the binding of type I inhibitors to c-Met kinase: experimental studies and quantum mechanical calculations

    PubMed Central

    Yu, Zhe; Ma, Yu-chi; Ai, Jing; Chen, Dan-qi; Zhao, Dong-mei; Wang, Xin; Chen, Yue-lei; Geng, Mei-yu; Xiong, Bing; Cheng, Mao-sheng; Shen, Jing-kang

    2013-01-01

    Aim: To decipher the molecular interactions between c-Met and its type I inhibitors and to facilitate the design of novel c-Met inhibitors. Methods: Based on the prototype model inhibitor 1, four ligands with subtle differences in the fused aromatic rings were synthesized. Quantum chemistry was employed to calculate the binding free energy for each ligand. Symmetry-adapted perturbation theory (SAPT) was used to decompose the binding energy into several fundamental forces to elucidate the determinant factors. Results: Binding free energies calculated from quantum chemistry were correlated well with experimental data. SAPT calculations showed that the predominant driving force for binding was derived from a sandwich π–π interaction with Tyr-1230. Arg-1208 was the differentiating factor, interacting with the 6-position of the fused aromatic ring system through the backbone carbonyl with a force pattern similar to hydrogen bonding. Therefore, a hydrogen atom must be attached at the 6-position, and changing the carbon atom to nitrogen caused unfavorable electrostatic interactions. Conclusion: The theoretical studies have elucidated the determinant factors involved in the binding of type I inhibitors to c-Met. PMID:24056705

  17. Challenges in large scale quantum mechanical calculations: Challenges in large scale quantum mechanical calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ratcliff, Laura E.; Mohr, Stephan; Huhs, Georg

    2016-11-07

    During the past decades, quantum mechanical methods have undergone an amazing transition from pioneering investigations of experts into a wide range of practical applications, made by a vast community of researchers. First principles calculations of systems containing up to a few hundred atoms have become a standard in many branches of science. The sizes of the systems which can be simulated have increased even further during recent years, and quantum-mechanical calculations of systems up to many thousands of atoms are nowadays possible. This opens up new appealing possibilities, in particular for interdisciplinary work, bridging together communities of different needs andmore » sensibilities. In this review we will present the current status of this topic, and will also give an outlook on the vast multitude of applications, challenges and opportunities stimulated by electronic structure calculations, making this field an important working tool and bringing together researchers of many different domains.« less

  18. Parallel algorithms for quantum chemistry. I. Integral transformations on a hypercube multiprocessor

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Whiteside, R.A.; Binkley, J.S.; Colvin, M.E.

    1987-02-15

    For many years it has been recognized that fundamental physical constraints such as the speed of light will limit the ultimate speed of single processor computers to less than about three billion floating point operations per second (3 GFLOPS). This limitation is becoming increasingly restrictive as commercially available machines are now within an order of magnitude of this asymptotic limit. A natural way to avoid this limit is to harness together many processors to work on a single computational problem. In principle, these parallel processing computers have speeds limited only by the number of processors one chooses to acquire. Themore » usefulness of potentially unlimited processing speed to a computationally intensive field such as quantum chemistry is obvious. If these methods are to be applied to significantly larger chemical systems, parallel schemes will have to be employed. For this reason we have developed distributed-memory algorithms for a number of standard quantum chemical methods. We are currently implementing these on a 32 processor Intel hypercube. In this paper we present our algorithm and benchmark results for one of the bottleneck steps in quantum chemical calculations: the four index integral transformation.« less

  19. Human development VIII: a theory of "deep" quantum chemistry and cell consciousness: quantum chemistry controls genes and biochemistry to give cells and higher organisms consciousness and complex behavior.

    PubMed

    Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Nielsen, Maj Lyck; Merrick, Joav

    2006-11-14

    Deep quantum chemistry is a theory of deeply structured quantum fields carrying the biological information of the cell, making it able to remember, intend, represent the inner and outer world for comparison, understand what it "sees", and make choices on its structure, form, behavior and division. We suggest that deep quantum chemistry gives the cell consciousness and all the qualities and abilities related to consciousness. We use geometric symbolism, which is a pre-mathematical and philosophical approach to problems that cannot yet be handled mathematically. Using Occam's razor we have started with the simplest model that works; we presume this to be a many-dimensional, spiral fractal. We suggest that all the electrons of the large biological molecules' orbitals make one huge "cell-orbital", which is structured according to the spiral fractal nature of quantum fields. Consciousness of single cells, multi cellular structures as e.g. organs, multi-cellular organisms and multi-individual colonies (like ants) and human societies can thus be explained by deep quantum chemistry. When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. The top level of information is the consciousness of the cell or organism, which controls all the biochemical processes. By this speculative work inspired by Penrose and Hameroff we hope to inspire other researchers to formulate more strict and mathematically correct hypothesis on the complex and coherence nature of matter, life and consciousness.

  20. Green Synthesis, Spectrofluorometric Characterization and Antibacterial Activity of Heterocyclic Compound from Chalcone on the Basis of in Vitro and Quantum Chemistry Calculation.

    PubMed

    Khan, Salman A

    2017-05-01

    2-amino-4-(4-bromophenyl)-8-methoxy-5,6-dihydrobenzo[h]quinoline-3-carbonitrile (ABDC) was synthesized by the reaction of (2E)-2-(4 bromobenzylidene) - 6 -methoxy-3,4-dihydronaphthalen-1(2H)-one (Chalcone) with malononitrile and ammonium acetate under microwave irradiation. Chalcone was synthesised by the reaction 4-bromobenzaldehyd, 6-methoxy-1,2,3,4-tetrahydro-naphthalin-1-one under the same condition. Structure of ABDC was conformed by 1 H and 13 C NMR, FT-IR, EI-MS spectral studies and elemental analysis. The electronic absorption and fluorescence spectra of ABDC have been studied in solvents of different polarities, and the data were used to study the solvatochromic properties such as excitation coefficient, stokes shift, oscillator strength, transition dipole moment and fluorescence quantum yield. The absorption maximum and fluorescence emission maximum was observed red shift when increase solvent polarity n-Hexane to DMSO. ABDC undergoes solubilization in different micelles and may be used as a probe and quencher to determine the critical micelle concentration (CMC) of CTAB and SDS. The anti-bacterial activity of chalcone and its cyclized product ABDC was tested in vitro by the disk diffusion assay against two Gram-positive and two Gram-negative bacteria was determined with the reference of standard drug Tetracycline. Results showed that the ABDC is better anti-bacterial agent as compared to chalcone. The anti-bacterial activity was further supported by the quantum chemistry calculation.

  1. Human Development VIII: A Theory of “Deep” Quantum Chemistry and Cell Consciousness: Quantum Chemistry Controls Genes and Biochemistry to Give Cells and Higher Organisms Consciousness and Complex Behavior

    PubMed Central

    Ventegodt, Søren; Hermansen, Tyge Dahl; Flensborg-Madsen, Trine; Nielsen, Maj Lyck; Merrick, Joav

    2006-01-01

    Deep quantum chemistry is a theory of deeply structured quantum fields carrying the biological information of the cell, making it able to remember, intend, represent the inner and outer world for comparison, understand what it “sees”, and make choices on its structure, form, behavior and division. We suggest that deep quantum chemistry gives the cell consciousness and all the qualities and abilities related to consciousness. We use geometric symbolism, which is a pre-mathematical and philosophical approach to problems that cannot yet be handled mathematically. Using Occams razor we have started with the simplest model that works; we presume this to be a many-dimensional, spiral fractal. We suggest that all the electrons of the large biological molecules orbitals make one huge “cell-orbital”, which is structured according to the spiral fractal nature of quantum fields. Consciousness of single cells, multi cellular structures as e.g. organs, multi-cellular organisms and multi-individual colonies (like ants) and human societies can thus be explained by deep quantum chemistry. When biochemical activity is strictly controlled by the quantum-mechanical super-orbital of the cell, this orbital can deliver energetic quanta as biological information, distributed through many fractal levels of the cell to guide form and behavior of an individual single or a multi-cellular organism. The top level of information is the consciousness of the cell or organism, which controls all the biochemical processes. By this speculative work inspired by Penrose and Hameroff we hope to inspire other researchers to formulate more strict and mathematically correct hypothesis on the complex and coherence nature of matter, life and consciousness. PMID:17115084

  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.

  3. 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.

  4. 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.

  5. The molecular structure of 4-methylpyridine-N-oxide: Gas-phase electron diffraction and quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Belova, Natalya V.; Girichev, Georgiy V.; Kotova, Vitaliya E.; Korolkova, Kseniya A.; Trang, Nguyen Hoang

    2018-03-01

    The molecular structure of 4-methylpiridine-N-oxide, 4-MePyO, has been studied by gas-phase electron diffraction monitored by mass spectrometry (GED/MS) and quantum chemical (DFT) calculations. Both, quantum chemistry and GED analyses resulted in CS molecular symmetry with the planar pyridine ring. Obtained molecular parameters confirm the hyperconjugation in the pyridine ring and the sp2 hybridization concept of the nitrogen and carbon atoms in the ring. The experimental geometric parameters are in a good agreement with the parameters for non-substituted N-oxide and reproduced very closely by DFT calculations. The presence of the electron-donating CH3 substituent in 4-MePyO leads to a decrease of the ipso-angle and to an increase of r(N→O) in comparison with the non-substituted PyO. Electron density distribution analysis has been performed in terms of natural bond orbitals (NBO) scheme. The nature of the semipolar N→O bond is discussed.

  6. Quantum kernel applications in medicinal chemistry.

    PubMed

    Huang, Lulu; Massa, Lou

    2012-07-01

    Progress in the quantum mechanics of biological molecules is being driven by computational advances. The notion of quantum kernels can be introduced to simplify the formalism of quantum mechanics, making it especially suitable for parallel computation of very large biological molecules. The essential idea is to mathematically break large biological molecules into smaller kernels that are calculationally tractable, and then to represent the full molecule by a summation over the kernels. The accuracy of the kernel energy method (KEM) is shown by systematic application to a great variety of molecular types found in biology. These include peptides, proteins, DNA and RNA. Examples are given that explore the KEM across a variety of chemical models, and to the outer limits of energy accuracy and molecular size. KEM represents an advance in quantum biology applicable to problems in medicine and drug design.

  7. Adsorption Energies of Carbon, Nitrogen, and Oxygen Atoms on the Low-temperature Amorphous Water Ice: A Systematic Estimation from Quantum Chemistry Calculations

    NASA Astrophysics Data System (ADS)

    Shimonishi, Takashi; Nakatani, Naoki; Furuya, Kenji; Hama, Tetsuya

    2018-03-01

    We propose a new simple computational model to estimate the adsorption energies of atoms and molecules to low-temperature amorphous water ice, and we present the adsorption energies of carbon (3 P), nitrogen (4 S), and oxygen (3 P) atoms based on quantum chemistry calculations. The adsorption energies were estimated to be 14,100 ± 420 K for carbon, 400 ± 30 K for nitrogen, and 1440 ± 160 K for oxygen. The adsorption energy of oxygen is consistent with experimentally reported values. We found that the binding of a nitrogen atom is purely physisorption, while that of a carbon atom is chemisorption, in which a chemical bond to an O atom of a water molecule is formed. That of an oxygen atom has a dual character, with both physisorption and chemisorption. The chemisorption of atomic carbon also implies the possibility of further chemical reactions to produce molecules bearing a C–O bond, though this may hinder the formation of methane on water ice via sequential hydrogenation of carbon atoms. These properties would have a large impact on the chemical evolution of carbon species in interstellar environments. We also investigated the effects of newly calculated adsorption energies on the chemical compositions of cold dense molecular clouds with the aid of gas-ice astrochemical simulations. We found that abundances of major nitrogen-bearing molecules, such as N2 and NH3, are significantly altered by applying the calculated adsorption energy, because nitrogen atoms can thermally diffuse on surfaces, even at 10 K.

  8. Learning Quantum Chemistry via a Visual-Conceptual Approach: Students' Bidirectional Textual and Visual Understanding

    ERIC Educational Resources Information Center

    Dangur, Vered; Avargil, Shirly; Peskin, Uri; Dori, Yehudit Judy

    2014-01-01

    Most undergraduate chemistry courses and a few high school honors courses, which focus on physical chemistry and quantum mechanics, are highly mathematically-oriented. At the Technion, Israel Institute of Technology, we developed a new module for high school students, titled "Chemistry--From 'the Hole' to 'the Whole': From the Nanoscale to…

  9. 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

  10. 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.

  11. 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.

  12. 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.

  13. The promise of quantum simulation

    DOE PAGES

    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.

  14. Semiempirical and ab initio Calculations of Charged Species Used in the Physical Organic Chemistry Course.

    ERIC Educational Resources Information Center

    Gilliom, Richard D.

    1989-01-01

    Concentrates on the semiempirical methods MINDO/3, MNDO, and AMI available in the program AMPAC from the Quantum Chemistry Program Exchange at Indiana University. Uses charged ions in the teaching of computational chemistry. Finds that semiempirical methods are accurate enough for the general use of the bench chemist. (MVL)

  15. Quantum-chemical Calculations in the Study of Antitumour Compounds

    NASA Astrophysics Data System (ADS)

    Luzhkov, V. B.; Bogdanov, G. N.

    1986-01-01

    The results of quantum-chemical calculations on antitumour preparations concerning the mechanism of their action at the electronic and molecular levels and structure-activity correlations are discussed in this review. Preparations whose action involves alkylating and free-radial mechanisms, complex-forming agents, and antimetabolites are considered. Modern quantum-chemical methods for calculations on biologically active substances are described. The bibliography includes 106 references.

  16. Neutron scattering, solid state NMR and quantum chemistry studies of 11-keto-progesterone

    NASA Astrophysics Data System (ADS)

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

    2004-07-01

    The molecule geometry, frequency and intensity of the IINS and IR vibrational bands of 11-ketoprogesterone have been obtained by the HF, PM3 and density functional theory (DFT) with the B3LYP functionals and 6-31G(d,p) basis set. The optimised bond lengths and bond angles of the steroid skeleton are in good agreement with the X-ray data. The IR and IINS spectra of ketoprogesterone, computed at the DFT level, well reproduce the vibrational wavenumbers and intensities to an accuracy allowing reliable vibrational assignments. The molecular dynamic study by 1H NMR has confirmed the sequence of onset of reorientations of subsequent methyl groups indicated by the results of quantum chemistry calculations and INS spectra.

  17. Atoms and molecules in cavities, from weak to strong coupling in quantum-electrodynamics (QED) chemistry

    PubMed Central

    Flick, Johannes; Ruggenthaler, Michael; Appel, Heiko

    2017-01-01

    In this work, we provide an overview of how well-established concepts in the fields of quantum chemistry and material sciences have to be adapted when the quantum nature of light becomes important in correlated matter–photon problems. We analyze model systems in optical cavities, where the matter–photon interaction is considered from the weak- to the strong-coupling limit and for individual photon modes as well as for the multimode case. We identify fundamental changes in Born–Oppenheimer surfaces, spectroscopic quantities, conical intersections, and efficiency for quantum control. We conclude by applying our recently developed quantum-electrodynamical density-functional theory to spontaneous emission and show how a straightforward approximation accurately describes the correlated electron–photon dynamics. This work paves the way to describe matter–photon interactions from first principles and addresses the emergence of new states of matter in chemistry and material science. PMID:28275094

  18. Introducing Quantum Mechanics into General Chemistry

    NASA Astrophysics Data System (ADS)

    Popkowski, Iwona; Bascal, Hafed

    2008-10-01

    Periodicity has long been recognized as the tool that chemists can use to bring some order to investigating the chemistry of more than one hundred elements. Such studies provide useful tools for understanding a wide array of chemical principles. The advances in computational chemistry make it possible to study and teach such trends with hands on approach. In this study we utilize recently acquired software Spartan Pro to illustrate theoretical measurements of bond length, bond angle and dipole as compared to experimental data. We constructed a matrix of values obtained from the theoretical calculations and obtained trends in bond length, bond angle and dipoles for the several periodic groups.

  19. Communication: Calculation of interatomic forces and optimization of molecular geometry with auxiliary-field quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Motta, Mario; Zhang, Shiwei

    2018-05-01

    We propose an algorithm for accurate, systematic, and scalable computation of interatomic forces within the auxiliary-field quantum Monte Carlo (AFQMC) method. The algorithm relies on the Hellmann-Feynman theorem and incorporates Pulay corrections in the presence of atomic orbital basis sets. We benchmark the method for small molecules by comparing the computed forces with the derivatives of the AFQMC potential energy surface and by direct comparison with other quantum chemistry methods. We then perform geometry optimizations using the steepest descent algorithm in larger molecules. With realistic basis sets, we obtain equilibrium geometries in agreement, within statistical error bars, with experimental values. The increase in computational cost for computing forces in this approach is only a small prefactor over that of calculating the total energy. This paves the way for a general and efficient approach for geometry optimization and molecular dynamics within AFQMC.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    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 tomore » 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.« less

  1. Inverse problems in quantum chemistry

    NASA Astrophysics Data System (ADS)

    Karwowski, Jacek

    Inverse problems constitute a branch of applied mathematics with well-developed methodology and formalism. A broad family of tasks met in theoretical physics, in civil and mechanical engineering, as well as in various branches of medical and biological sciences has been formulated as specific implementations of the general theory of inverse problems. In this article, it is pointed out that a number of approaches met in quantum chemistry can (and should) be classified as inverse problems. Consequently, the methodology used in these approaches may be enriched by applying ideas and theorems developed within the general field of inverse problems. Several examples, including the RKR method for the construction of potential energy curves, determining parameter values in semiempirical methods, and finding external potentials for which the pertinent Schrödinger equation is exactly solvable, are discussed in detail.

  2. 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.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chandrasekaran, Suryanarayanan; Aghtar, Mortaza; Valleau, Stéphanie

    2015-08-06

    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 orbitalmore » (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.« less

  4. Calculations of condensation and chemistry in an aircraft contrail

    NASA Technical Reports Server (NTRS)

    Miake-Lye, Richard C.; Brown, R. C.; Anderson, M. R.; Kolb, C. E.

    1994-01-01

    The flow field, chemistry, and condensation nucleation behind a transport airplane are calculated in two regimes using two separate reacting flow codes: first the axisymmetric plume, then the three dimensional vortex wake. The included chemical kinetics equations follow the evolution of the NO(y) and SO(x) chemical families. In the plume regime, the chemistry is coupled with the binary homogeneous formation of sulfate condensation nuclei, where the calculated nucleation rates predict that copious quantities of H2SO4/H2O nuclei are produced in subnanometer sizes. These sulfate aerosols could play a major role in the subsequent condensation of water vapor and the formation of contrails under favorable atmospheric conditions.

  5. Efficient free energy calculations of quantum systems through computer simulations

    NASA Astrophysics Data System (ADS)

    Antonelli, Alex; Ramirez, Rafael; Herrero, Carlos; Hernandez, Eduardo

    2009-03-01

    In general, the classical limit is assumed in computer simulation calculations of free energy. This approximation, however, is not justifiable for a class of systems in which quantum contributions for the free energy cannot be neglected. The inclusion of quantum effects is important for the determination of reliable phase diagrams of these systems. In this work, we present a new methodology to compute the free energy of many-body quantum systems [1]. This methodology results from the combination of the path integral formulation of statistical mechanics and efficient non-equilibrium methods to estimate free energy, namely, the adiabatic switching and reversible scaling methods. A quantum Einstein crystal is used as a model to show the accuracy and reliability the methodology. This new method is applied to the calculation of solid-liquid coexistence properties of neon. Our findings indicate that quantum contributions to properties such as, melting point, latent heat of fusion, entropy of fusion, and slope of melting line can be up to 10% of the calculated values using the classical approximation. [1] R. M. Ramirez, C. P. Herrero, A. Antonelli, and E. R. Hernández, Journal of Chemical Physics 129, 064110 (2008)

  6. Compressed Sensing for Chemistry

    NASA Astrophysics Data System (ADS)

    Sanders, Jacob Nathan

    Many chemical applications, from spectroscopy to quantum chemistry, involve measuring or computing a large amount of data, and then compressing this data to retain the most chemically-relevant information. In contrast, compressed sensing is an emergent technique that makes it possible to measure or compute an amount of data that is roughly proportional to its information content. In particular, compressed sensing enables the recovery of a sparse quantity of information from significantly undersampled data by solving an ℓ 1-optimization problem. This thesis represents the application of compressed sensing to problems in chemistry. The first half of this thesis is about spectroscopy. Compressed sensing is used to accelerate the computation of vibrational and electronic spectra from real-time time-dependent density functional theory simulations. Using compressed sensing as a drop-in replacement for the discrete Fourier transform, well-resolved frequency spectra are obtained at one-fifth the typical simulation time and computational cost. The technique is generalized to multiple dimensions and applied to two-dimensional absorption spectroscopy using experimental data collected on atomic rubidium vapor. Finally, a related technique known as super-resolution is applied to open quantum systems to obtain realistic models of a protein environment, in the form of atomistic spectral densities, at lower computational cost. The second half of this thesis deals with matrices in quantum chemistry. It presents a new use of compressed sensing for more efficient matrix recovery whenever the calculation of individual matrix elements is the computational bottleneck. The technique is applied to the computation of the second-derivative Hessian matrices in electronic structure calculations to obtain the vibrational modes and frequencies of molecules. When applied to anthracene, this technique results in a threefold speed-up, with greater speed-ups possible for larger molecules. The

  7. Recent advances in quantum scattering calculations on polyatomic bimolecular reactions.

    PubMed

    Fu, Bina; Shan, Xiao; Zhang, Dong H; Clary, David C

    2017-12-11

    This review surveys quantum scattering calculations on chemical reactions of polyatomic molecules in the gas phase published in the last ten years. These calculations are useful because they provide highly accurate information on the dynamics of chemical reactions which can be compared in detail with experimental results. They also serve as quantum mechanical benchmarks for testing approximate theories which can more readily be applied to more complicated reactions. This review includes theories for calculating quantities such as rate constants which have many important scientific applications.

  8. Infinite variance in fermion quantum Monte Carlo calculations.

    PubMed

    Shi, Hao; Zhang, Shiwei

    2016-03-01

    For important classes of many-fermion problems, quantum Monte Carlo (QMC) methods allow exact calculations of ground-state and finite-temperature properties without the sign problem. The list spans condensed matter, nuclear physics, and high-energy physics, including the half-filled repulsive Hubbard model, the spin-balanced atomic Fermi gas, and lattice quantum chromodynamics calculations at zero density with Wilson Fermions, and is growing rapidly as a number of problems have been discovered recently to be free of the sign problem. In these situations, QMC calculations are relied on to provide definitive answers. Their results are instrumental to our ability to understand and compute properties in fundamental models important to multiple subareas in quantum physics. It is shown, however, that the most commonly employed algorithms in such situations have an infinite variance problem. A diverging variance causes the estimated Monte Carlo statistical error bar to be incorrect, which can render the results of the calculation unreliable or meaningless. We discuss how to identify the infinite variance problem. An approach is then proposed to solve the problem. The solution does not require major modifications to standard algorithms, adding a "bridge link" to the imaginary-time path integral. The general idea is applicable to a variety of situations where the infinite variance problem may be present. Illustrative results are presented for the ground state of the Hubbard model at half-filling.

  9. LEGO-Method--New Strategy for Chemistry Calculation

    ERIC Educational Resources Information Center

    Molnar, Jozsef; Molnar-Hamvas, Livia

    2011-01-01

    The presented strategy of chemistry calculation is based on mole-concept, but it uses only one fundamental relationship of the amounts of substance as a basic panel. The name of LEGO-method comes from the famous toy of LEGO[R] because solving equations by grouping formulas is similar to that. The relations of mole and the molar amounts, as small…

  10. Multi-level meta-workflows: new concept for regularly occurring tasks in quantum chemistry.

    PubMed

    Arshad, Junaid; Hoffmann, Alexander; Gesing, Sandra; Grunzke, Richard; Krüger, Jens; Kiss, Tamas; Herres-Pawlis, Sonja; Terstyanszky, Gabor

    2016-01-01

    In Quantum Chemistry, many tasks are reoccurring frequently, e.g. geometry optimizations, benchmarking series etc. Here, workflows can help to reduce the time of manual job definition and output extraction. These workflows are executed on computing infrastructures and may require large computing and data resources. Scientific workflows hide these infrastructures and the resources needed to run them. It requires significant efforts and specific expertise to design, implement and test these workflows. Many of these workflows are complex and monolithic entities that can be used for particular scientific experiments. Hence, their modification is not straightforward and it makes almost impossible to share them. To address these issues we propose developing atomic workflows and embedding them in meta-workflows. Atomic workflows deliver a well-defined research domain specific function. Publishing workflows in repositories enables workflow sharing inside and/or among scientific communities. We formally specify atomic and meta-workflows in order to define data structures to be used in repositories for uploading and sharing them. Additionally, we present a formal description focused at orchestration of atomic workflows into meta-workflows. We investigated the operations that represent basic functionalities in Quantum Chemistry, developed the relevant atomic workflows and combined them into meta-workflows. Having these workflows we defined the structure of the Quantum Chemistry workflow library and uploaded these workflows in the SHIWA Workflow Repository.Graphical AbstractMeta-workflows and embedded workflows in the template representation.

  11. Creative Uses for Calculator-based Laboratory (CBL) Technology in Chemistry.

    ERIC Educational Resources Information Center

    Sales, Cynthia L.; Ragan, Nicole M.; Murphy, Maureen Kendrick

    1999-01-01

    Reviews three projects that use a graphing calculator linked to a calculator-based laboratory device as a portable data-collection system for students in chemistry classes. Projects include Isolation, Purification and Quantification of Buckminsterfullerene from Woodstove Ashes; Determination of the Activation Energy Associated with the…

  12. The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

    PubMed

    Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

    2012-08-07

    : This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

  13. The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

    PubMed Central

    2012-01-01

    This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

  14. The Application of Computational Chemistry to Problems in Mass Spectrometry

    EPA Science Inventory

    Quantum chemistry is capable of calculating a wide range of electronic and thermodynamic properties of interest to a chemist or physicist. Calculations can be used both to predict the results of future experiments and to aid in the interpretation of existing results. This paper w...

  15. Predicted phototoxicities of carbon nano-material by quantum mechanical calculations.

    PubMed

    Betowski, Don

    2017-08-01

    The purpose of this research was to develop a predictive model for the phototoxicity potential of carbon nanomaterials (fullerenols and single-walled carbon nanotubes). This model is based on the quantum mechanical (ab initio) calculations on these carbon-based materials and comparison of the triplet excited states of these materials to published work relating phototoxicity of polynuclear aromatic hydrocarbons (PAH) to their predictive triplet excited state energy. A successful outcome will add another tool to the arsenal of predictive methods for the U.S. EPA program offices as they assess the toxicity of compounds in use or coming into commerce. The basis of this research was obtaining the best quantum mechanical structure of the carbon nanomaterial and was fundamental in determining the triplet excited state energy. The triplet excited state, in turn, is associated with the phototoxicity of the material. This project relies heavily on the interaction of the predictive results (physical chemistry) and the experimental results obtained by biologists and toxicologists. The results of the experiments (toxicity testing) will help refine the predictive model, while the predictions will alert the scientists to red flag compounds. It is hoped that a guidance document for the U.S. EPA will be forthcoming to help determine the toxicity of compounds. This can be a screening tool that would rely on further testing for those compounds found by these predictions to be a phototoxic danger to health and the environment. Copyright © 2017. Published by Elsevier Inc.

  16. Quantum Monte Carlo tunneling from quantum chemistry to quantum annealing

    NASA Astrophysics Data System (ADS)

    Mazzola, Guglielmo; Smelyanskiy, Vadim N.; Troyer, Matthias

    2017-10-01

    Quantum tunneling is ubiquitous across different fields, from quantum chemical reactions and magnetic materials to quantum simulators and quantum computers. While simulating the real-time quantum dynamics of tunneling is infeasible for high-dimensional systems, quantum tunneling also shows up in quantum Monte Carlo (QMC) simulations, which aim to simulate quantum statistics with resources growing only polynomially with the system size. Here we extend the recent results obtained for quantum spin models [Phys. Rev. Lett. 117, 180402 (2016), 10.1103/PhysRevLett.117.180402], and we study continuous-variable models for proton transfer reactions. We demonstrate that QMC simulations efficiently recover the scaling of ground-state tunneling rates due to the existence of an instanton path, which always connects the reactant state with the product. We discuss the implications of our results in the context of quantum chemical reactions and quantum annealing, where quantum tunneling is expected to be a valuable resource for solving combinatorial optimization problems.

  17. A photoelectron imaging and quantum chemistry study of the deprotonated indole anion.

    PubMed

    Parkes, Michael A; Crellin, Jonathan; Henley, Alice; Fielding, Helen H

    2018-05-29

    Indole is an important molecular motif in many biological molecules and exists in its deprotonated anionic form in the cyan fluorescent protein, an analogue of green fluorescent protein. However, the electronic structure of the deprotonated indole anion has been relatively unexplored. Here, we use a combination of anion photoelectron velocity-map imaging measurements and quantum chemistry calculations to probe the electronic structure of the deprotonated indole anion. We report vertical detachment energies (VDEs) of 2.45 ± 0.05 eV and 3.20 ± 0.05 eV, respectively. The value for D0 is in agreement with recent high-resolution measurements whereas the value for D1 is a new measurement. We find that the first electronically excited singlet state of the anion, S1(ππ*), lies above the VDE and has shape resonance character with respect to the D0 detachment continuum and Feshbach resonance character with respect to the D1 continuum.

  18. Heats of Segregation of BCC Binaries from ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2004-01-01

    We compare dilute-limit heats of segregation for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent LMTO-based parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation, while the ab initio calculations are performed without relaxation. Results are discussed within the context of a segregation model driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  19. The calculation of aquifer chemistry in hot-water geothermal systems

    USGS Publications Warehouse

    Truesdell, Alfred H.; Singers, Wendy

    1974-01-01

    The temperature and chemical conditions (pH, gas pressure, and ion activities) in a geothermal aquifer supplying a producing bore can be calculated from the enthalpy of the total fluid (liquid + vapor) produced and chemical analyses of water and steam separated and collected at known pressures. Alternatively, if a single water phase exists in the aquifer, the complete analysis (including gases) of a sample collected from the aquifer by a downhole sampler is sufficient to determine the aquifer chemistry without a measured value of the enthalpy. The assumptions made are that the fluid is produced from a single aquifer and is homogeneous in enthalpy and chemical composition. These calculations of aquifer chemistry involving large amounts of ancillary information and many iterations require computer methods. A computer program in PL-1 to perform these calculations is available from the National Technical Information Service as document PB-219 376.

  20. Integrating Free Computer Software in Chemistry and Biochemistry Instruction: An International Collaboration

    ERIC Educational Resources Information Center

    Cedeno, David L.; Jones, Marjorie A.; Friesen, Jon A.; Wirtz, Mark W.; Rios, Luz Amalia; Ocampo, Gonzalo Taborda

    2010-01-01

    At the Universidad de Caldas, Manizales, Colombia, we used their new computer facilities to introduce chemistry graduate students to biochemical database mining and quantum chemistry calculations using freeware. These hands-on workshops allowed the students a strong introduction to easily accessible software and how to use this software to begin…

  1. Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

  2. The Nature of Infinity in Quantum Field Calculations

    NASA Astrophysics Data System (ADS)

    Kriske, Richard

    2011-05-01

    In many textbooks on Quantum Field Theory it has been noted that an infinity is taken a circle and the flux is calculated from the A field in that manner. There are of course many such examples of this sort of calculation using infinity as a circle. This author would like to point out that if the three dimensions of space are curved and the one dimension of time is not, in say a four space, infinity is the horizon, which is not a circle but rather a sphere; as long as space-time is curved uniformly, smoothly and has positive curvature. This author believes the math may be in error, since maps of the CMBR seem to indicate a ``Swiss-Cheese'' type of topology, wherein the Sphere at infinity (the Horizon of the Universe), has holes in it that can readily be seen. This author believes that these irregularities most certainly have a calculable effect on QED, QCD and Quantum Field Theory.

  3. Quantum chemistry calculation of resveratrol and related stilbenes

    NASA Astrophysics Data System (ADS)

    Del Nero, J.; de Melo, C. P.

    2003-01-01

    We report a semiempirical investigation of the first excited states and of the spectroscopic properties of resveratrol, a phytoalexin with well-known antioxidative properties, and of structurally related stilbenes. The analysis of the calculated bond length and charge rearrangements resulting from the photoexcitation and of the corresponding theoretical spectra gives us some insight of how chemical modifications of these molecules could affect the possible physiological properties of resveratrol.

  4. Modeling Alkyl p-Methoxy Cinnamate (APMC) as UV absorber based on electronic transition using semiempirical quantum mechanics ZINDO/s calculation

    NASA Astrophysics Data System (ADS)

    Salmahaminati; Azis, Muhlas Abdul; Purwiandono, Gani; Arsyik Kurniawan, Muhammad; Rubiyanto, Dwiarso; Darmawan, Arif

    2017-11-01

    In this research, modeling several alkyl p-methoxy cinnamate (APMC) based on electronic transition by using semiempirical mechanical quantum ZINDO/s calculation is performed. Alkyl cinnamates of C1 (methyl) up to C7 (heptyl) homolog with 1-5 example structures of each homolog are used as materials. Quantum chemistry-package software Hyperchem 8.0 is used to simulate the drawing of the structure, geometry optimization by a semiempirical Austin Model 1 algorithm and single point calculation employing a semiempirical ZINDO/s technique. ZINDO/s calculations use a defined criteria that singly excited -Configuration Interaction (CI) where a gap of HOMO-LUMO energy transition and maximum degeneracy level are 7 and 2, respectively. Moreover, analysis of the theoretical spectra is focused on the UV-B (290-320 nm) and UV-C (200-290 nm) area. The results show that modeling of the compound can be used to predict the type of UV protection activity depends on the electronic transition in the UV area. Modification of the alkyl homolog relatively does not change the value of wavelength absorption to indicate the UV protection activity. Alkyl cinnamate compounds are predicted as UV-B and UV-C sunscreen.

  5. 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.

  6. Quantum-chemistry based calibration of the alkali metal cation series (Li(+)-Cs(+)) for large-scale polarizable molecular mechanics/dynamics simulations.

    PubMed

    Dudev, Todor; Devereux, Mike; Meuwly, Markus; Lim, Carmay; Piquemal, Jean-Philip; Gresh, Nohad

    2015-02-15

    The alkali metal cations in the series Li(+)-Cs(+) act as major partners in a diversity of biological processes and in bioinorganic chemistry. In this article, we present the results of their calibration in the context of the SIBFA polarizable molecular mechanics/dynamics procedure. It relies on quantum-chemistry (QC) energy-decomposition analyses of their monoligated complexes with representative O-, N-, S-, and Se- ligands, performed with the aug-cc-pVTZ(-f) basis set at the Hartree-Fock level. Close agreement with QC is obtained for each individual contribution, even though the calibration involves only a limited set of cation-specific parameters. This agreement is preserved in tests on polyligated complexes with four and six O- ligands, water and formamide, indicating the transferability of the procedure. Preliminary extensions to density functional theory calculations are reported. © 2014 Wiley Periodicals, Inc.

  7. Quantum chemistry-assisted synthesis route development

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 thatmore » observed. The summary of transition state data base (TSDB) is also provided. TSDB is the key to reducing time of in silico screenings.« less

  8. Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory.

    PubMed

    Wu, Tao; Sun, Lei; Shi, Qi; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

    2016-12-21

    Charge mobilities of six DNAs and RNAs have been computed using quantum chemistry calculation combined with the Marcus-Hush theory. Based on this simulation model, we obtained quite reasonable results when compared with the experiment, and the obtained charge mobility strongly depends on the molecular reorganization and electronic coupling. Besides, we find that hole mobilities are larger than electron mobilities no matter in DNAs or in RNAs, and the hole mobility of 2L8I can reach 1.09 × 10 -1 cm 2 V -1 s -1 which can be applied in the molecular wire. The findings also show that our theoretical model can be regarded as a promising candidate for screening DNA- and RNA-based molecular electronic devices.

  9. Carrier mobility in double-helix DNA and RNA: A quantum chemistry study with Marcus-Hush theory

    NASA Astrophysics Data System (ADS)

    Wu, Tao; Sun, Lei; Shi, Qi; Deng, Kaiming; Deng, Weiqiao; Lu, Ruifeng

    2016-12-01

    Charge mobilities of six DNAs and RNAs have been computed using quantum chemistry calculation combined with the Marcus-Hush theory. Based on this simulation model, we obtained quite reasonable results when compared with the experiment, and the obtained charge mobility strongly depends on the molecular reorganization and electronic coupling. Besides, we find that hole mobilities are larger than electron mobilities no matter in DNAs or in RNAs, and the hole mobility of 2L8I can reach 1.09 × 10-1 cm2 V-1 s-1 which can be applied in the molecular wire. The findings also show that our theoretical model can be regarded as a promising candidate for screening DNA- and RNA-based molecular electronic devices.

  10. Heats of Segregation of BCC Binaries from Ab Initio and Quantum Approximate Calculations

    NASA Technical Reports Server (NTRS)

    Good, Brian S.

    2003-01-01

    We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy methods. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameters. Quantum approximate segregation energies are computed with and without atomistic relaxation. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with full-potential quantum calculations and with available experimental results.

  11. A perspective on quantum mechanics calculations in ADMET predictions.

    PubMed

    Bowen, J Phillip; Güner, Osman F

    2013-01-01

    Understanding the molecular basis of drug action has been an important objective for pharmaceutical scientists. With the increasing speed of computers and the implementation of quantum chemistry methodologies, pharmacodynamic and pharmacokinetic problems have become more computationally tractable. Historically the former has been the focus of drug design, but within the last two decades efforts to understand the latter have increased. It takes about fifteen years and over $1 billion dollars for a drug to go from laboratory hit, through lead optimization, to final approval by the U.S. Food and Drug Administration. While the costs have increased substantially, the overall clinical success rate for a compound to emerge from clinical trials is approximately 10%. Most of the attrition rate can be traced to ADMET (absorption, distribution, metabolism, excretion, and toxicity) problems, which is a powerful impetus to study these issues at an earlier stage in drug discovery. Quantum mechanics offers pharmaceutical scientists the opportunity to investigate pharmacokinetic problems at the molecular level prior to laboratory preparation and testing. This review will provide a perspective on the use of quantum mechanics or a combination of quantum mechanics coupled with other classical methods in the pharmacokinetic phase of drug discovery. A brief overview of the essential features of theory will be discussed, and a few carefully selected examples will be given to highlight the computational methods.

  12. 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…

  13. First-principles anharmonic quantum calculations for peptide spectroscopy: VSCF calculations and comparison with experiments.

    PubMed

    Roy, Tapta Kanchan; Sharma, Rahul; Gerber, R Benny

    2016-01-21

    First-principles quantum calculations for anharmonic vibrational spectroscopy of three protected dipeptides are carried out and compared with experimental data. Using hybrid HF/MP2 potentials, the Vibrational Self-Consistent Field with Second-Order Perturbation Correction (VSCF-PT2) algorithm is used to compute the spectra without any ad hoc scaling or fitting. All of the vibrational modes (135 for the largest system) are treated quantum mechanically and anharmonically using full pair-wise coupling potentials to represent the interaction between different modes. In the hybrid potential scheme the MP2 method is used for the harmonic part of the potential and a modified HF method is used for the anharmonic part. The overall agreement between computed spectra and experiment is very good and reveals different signatures for different conformers. This study shows that first-principles spectroscopic calculations of good accuracy are possible for dipeptides hence it opens possibilities for determination of dipeptide conformer structures by comparison of spectroscopic calculations with experiment.

  14. Double quantum coherence ESR spectroscopy and quantum chemical calculations on a BDPA biradical.

    PubMed

    Haeri, Haleh Hashemi; Spindler, Philipp; Plackmeyer, Jörn; Prisner, Thomas

    2016-10-26

    Carbon-centered radicals are interesting alternatives to otherwise commonly used nitroxide spin labels for dipolar spectroscopy techniques because of their narrow ESR linewidth. Herein, we present a novel BDPA biradical, where two BDPA (α,α,γ,γ-bisdiphenylene-β-phenylallyl) radicals are covalently tethered by a saturated biphenyl acetylene linker. The inter-spin distance between the two spin carrier fragments was measured using double quantum coherence (DQC) ESR methodology. The DQC experiment revealed a mean distance of only 1.8 nm between the two unpaired electron spins. This distance is shorter than the predictions based on a simple modelling of the biradical geometry with the electron spins located at the central carbon atoms. Therefore, DFT (density functional theory) calculations were performed to obtain a picture of the spin delocalization, which may give rise to a modified dipolar interaction tensor, and to find those conformations that correspond best to the experimentally observed inter-spin distance. Quantum chemical calculations showed that the attachment of the biphenyl acetylene linker at the second position of the fluorenyl ring of BDPA did not affect the spin population or geometry of the BDPA radical. Therefore, spin delocalization and geometry optimization of each BDPA moiety could be performed on the monomeric unit alone. The allylic dihedral angle θ 1 between the fluorenyl rings in the monomer subunit was determined to be 30° or 150° using quantum chemical calculations. The proton hyperfine coupling constant calculated from both energy minima was in very good agreement with literature values. Based on the optimal monomer geometries and spin density distributions, the dipolar coupling interaction between both BDPA units could be calculated for several dimer geometries. It was shown that the rotation of the BDPA units around the linker axis (θ 2 ) does not significantly influence the dipolar coupling strength when compared to the allylic

  15. The fourth age of quantum chemistry: molecules in motion.

    PubMed

    Császár, Attila G; Fábri, Csaba; Szidarovszky, Tamás; Mátyus, Edit; Furtenbacher, Tibor; Czakó, Gábor

    2012-01-21

    Developments during the last two decades in nuclear motion theory made it possible to obtain variational solutions to the time-independent, nuclear-motion Schrödinger equation of polyatomic systems as "exact" as the potential energy surface (PES) is. Nuclear motion theory thus reached a level whereby this branch of quantum chemistry started to catch up with the well developed and widely applied other branch, electronic structure theory. It seems to be fair to declare that we are now in the fourth age of quantum chemistry, where the first three ages are principally defined by developments in electronic structure techniques (G. Richards, Nature, 1979, 278, 507). In the fourth age we are able to incorporate into our quantum chemical treatment the motion of nuclei in an exact fashion and, for example, go beyond equilibrium molecular properties and compute accurate, temperature-dependent, effective properties, thus closing the gap between measurements and electronic structure computations. In this Perspective three fundamental algorithms for the variational solution of the time-independent nuclear-motion Schrödinger equation employing exact kinetic energy operators are presented: one based on tailor-made Hamiltonians, one on the Eckart-Watson Hamiltonian, and one on a general internal-coordinate Hamiltonian. It is argued that the most useful and most widely applicable procedure is the third one, based on a Hamiltonian containing a kinetic energy operator written in terms of internal coordinates and an arbitrary embedding of the body-fixed frame of the molecule. This Hamiltonian makes it feasible to treat the nuclear motions of arbitrary quantum systems, irrespective of whether they exhibit a single well-defined minimum or not, and of arbitrary reduced-dimensional models. As a result, molecular spectroscopy, an important field for the application of nuclear motion theory, has almost black-box-type tools at its disposal. Variational nuclear motion computations, based on

  16. Witnessing eigenstates for quantum simulation of Hamiltonian spectra

    PubMed Central

    Santagati, Raffaele; Wang, Jianwei; Gentile, Antonio A.; Paesani, Stefano; Wiebe, Nathan; McClean, Jarrod R.; Morley-Short, Sam; Shadbolt, Peter J.; Bonneau, Damien; Silverstone, Joshua W.; Tew, David P.; Zhou, Xiaoqi; O’Brien, Jeremy L.; Thompson, Mark G.

    2018-01-01

    The efficient calculation of Hamiltonian spectra, a problem often intractable on classical machines, can find application in many fields, from physics to chemistry. We introduce the concept of an “eigenstate witness” and, through it, provide a new quantum approach that combines variational methods and phase estimation to approximate eigenvalues for both ground and excited states. This protocol is experimentally verified on a programmable silicon quantum photonic chip, a mass-manufacturable platform, which embeds entangled state generation, arbitrary controlled unitary operations, and projective measurements. Both ground and excited states are experimentally found with fidelities >99%, and their eigenvalues are estimated with 32 bits of precision. We also investigate and discuss the scalability of the approach and study its performance through numerical simulations of more complex Hamiltonians. This result shows promising progress toward quantum chemistry on quantum computers. PMID:29387796

  17. 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…

  18. 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.

  19. 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. © 2011 American Chemical Society

  20. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    NASA Technical Reports Server (NTRS)

    Kahn, L. R.

    1982-01-01

    Metal atom clusters are studied based on the application of ab initio quantum mechanical approaches. Because these large 'molecular' systems pose special practical computational problems in the application of the quantum mechanical methods, there is a special need to find simplifying techniques that do not compromise the reliability of the calculations. Research is therefore directed towards various aspects of the implementation of the effective core potential technique for the removal of the metal atom core electrons from the calculations.

  1. 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.

  2. 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

  3. Adiabatic quantum simulation of quantum chemistry.

    PubMed

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

    2014-10-13

    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.

  4. Theoretical Studies of the Extraterrestrial Chemistry of Biogenic Elements and Compounds

    NASA Technical Reports Server (NTRS)

    Woon, D. E.

    1998-01-01

    The report discusses modeling gas-grain chemistry with ab initio quantum chemical cluster calculations which include heterogeneous hydrogenation of CO and H2CO on icy grain mantles, and ammonia-catalyzed, water-enhanced polymerization of formaldehyde in laboratory studies of astrophysical ices.

  5. Multi-million atom electronic structure calculations for quantum dots

    NASA Astrophysics Data System (ADS)

    Usman, Muhammad

    Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined

  6. Ab Initio Calculations Applied to Problems in Metal Ion Chemistry

    NASA Technical Reports Server (NTRS)

    Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Partridge, Harry; Arnold, James O. (Technical Monitor)

    1994-01-01

    Electronic structure calculations can provide accurate spectroscopic data (such as molecular structures) vibrational frequencies, binding energies, etc.) that have been very useful in explaining trends in experimental data and in identifying incorrect experimental measurements. In addition, ab initio calculations. have given considerable insight into the many interactions that make the chemistry of transition metal systems so diverse. In this review we focus on cases where calculations and experiment have been used to solve interesting chemical problems involving metal ions. The examples include cases where theory was used to differentiate between disparate experimental values and cases where theory was used to explain unexpected experimental results.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Li, Wei-Li; Jian, Tian; Lopez, Gary V.

    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 themore » 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.« less

  8. Large scale exact quantum dynamics calculations: Ten thousand quantum states of acetonitrile

    NASA Astrophysics Data System (ADS)

    Halverson, Thomas; Poirier, Bill

    2015-03-01

    'Exact' quantum dynamics (EQD) calculations of the vibrational spectrum of acetonitrile (CH3CN) are performed, using two different methods: (1) phase-space-truncated momentum-symmetrized Gaussian basis and (2) correlated truncated harmonic oscillator basis. In both cases, a simple classical phase space picture is used to optimize the selection of individual basis functions-leading to drastic reductions in basis size, in comparison with existing methods. Massive parallelization is also employed. Together, these tools-implemented into a single, easy-to-use computer code-enable a calculation of tens of thousands of vibrational states of CH3CN to an accuracy of 0.001-10 cm-1.

  9. Fast and accurate calculation of dilute quantum gas using Uehling–Uhlenbeck model equation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yano, Ryosuke, E-mail: ryosuke.yano@tokiorisk.co.jp

    The Uehling–Uhlenbeck (U–U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U–U model equation. DSMC analysis based on the U–U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U–U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculatingmore » the viscosity coefficient of a Bose gas on the basis of the Green–Kubo expression and the shock layer of a dilute Bose gas around a cylinder.« less

  10. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives.

    PubMed

    Rokob, Tibor András; Srnec, Martin; Rulíšek, Lubomír

    2012-05-21

    In the last decade, we have witnessed substantial progress in the development of quantum chemical methodologies. Simultaneously, robust solvation models and various combined quantum and molecular mechanical (QM/MM) approaches have become an integral part of quantum chemical programs. Along with the steady growth of computer power and, more importantly, the dramatic increase of the computer performance to price ratio, this has led to a situation where computational chemistry, when exercised with the proper amount of diligence and expertise, reproduces, predicts, and complements the experimental data. In this perspective, we review some of the latest achievements in the field of theoretical (quantum) bioinorganic chemistry, concentrating mostly on accurate calculations of the spectroscopic and physico-chemical properties of open-shell bioinorganic systems by wave-function (ab initio) and DFT methods. In our opinion, the one-to-one mapping between the calculated properties and individual molecular structures represents a major advantage of quantum chemical modelling since this type of information is very difficult to obtain experimentally. Once (and only once) the physico-chemical, thermodynamic and spectroscopic properties of complex bioinorganic systems are quantitatively reproduced by theoretical calculations may we consider the outcome of theoretical modelling, such as reaction profiles and the various decompositions of the calculated parameters into individual spatial or physical contributions, to be reliable. In an ideal situation, agreement between theory and experiment may imply that the practical problem at hand, such as the reaction mechanism of the studied metalloprotein, can be considered as essentially solved.

  11. Teaching Safety: Using Mole Calculations To Teach Aspects of Safety in Post-16 Chemistry.

    ERIC Educational Resources Information Center

    Borrows, Peter; Vincent, Ray; Cochrane, Allen

    1998-01-01

    Recommends beginning certain chemistry courses with revision and consolidation of mole calculations. Argues that by choosing examples related to health and safety, mole calculations can be made less academic while raising student awareness of important issues. (DDR)

  12. Using machine learning and quantum chemistry descriptors to predict the toxicity of ionic liquids.

    PubMed

    Cao, Lingdi; Zhu, Peng; Zhao, Yongsheng; Zhao, Jihong

    2018-06-15

    Large-scale application of ionic liquids (ILs) hinges on the advancement of designable and eco-friendly nature. Research of the potential toxicity of ILs towards different organisms and trophic levels is insufficient. Quantitative structure-activity relationships (QSAR) model is applied to evaluate the toxicity of ILs towards the leukemia rat cell line (ICP-81). The structures of 57 cations and 21 anions were optimized by quantum chemistry. The electrostatic potential surface area (S EP ) and charge distribution area (S σ-profile ) descriptors are calculated and used to predict the toxicity of ILs. The performance and predictive aptitude of extreme learning machine (ELM) model are analyzed and compared with those of multiple linear regression (MLR) and support vector machine (SVM) models. The highest R 2 and the lowest AARD% and RMSE of the training set, test set and total set for the ELM are observed, which validates the superior performance of the ELM than that of obtained by the MLR and SVM. The applicability domain of the model is assessed by the Williams plot. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Finite element method for calculating spectral and optical characteristics of axially symmetric quantum dots

    NASA Astrophysics Data System (ADS)

    Gusev, A. A.; Chuluunbaatar, O.; Vinitsky, S. I.; Derbov, V. L.; Hai, L. L.; Kazaryan, E. M.; Sarkisyan, H. A.

    2018-04-01

    We present new calculation schemes using high-order finite element method implemented on unstructured grids with triangle elements for solving boundary-value problems that describe axially symmetric quantum dots. The efficiency of the algorithms and software is demonstrated by benchmark calculations of the energy spectrum, the envelope eigenfunctions of electron, hole and exciton states, and the direct interband light absorption in conical and spheroidal impenetrable quantum dots.

  14. 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.

  15. O+OH-->O(2)+H: A key reaction for interstellar chemistry. New theoretical results and comparison with experiment.

    PubMed

    Lique, F; Jorfi, M; Honvault, P; Halvick, P; Lin, S Y; Guo, H; Xie, D Q; Dagdigian, P J; Kłos, J; Alexander, M H

    2009-12-14

    We report extensive, fully quantum, time-independent (TID) calculations of cross sections at low collision energies and rate constants at low temperatures for the O+OH reaction, of key importance in the production of molecular oxygen in cold, dark, interstellar clouds and in the chemistry of the Earth's atmosphere. Our calculations are compared with TID calculations within the J-shifting approximation, with wave-packet calculations, and with quasiclassical trajectory calculations. The fully quantum TID calculations yield rate constants higher than those from the more approximate methods and are qualitatively consistent with a low-temperature extrapolation of earlier experimental values but not with the most recent experiments at the lowest temperatures.

  16. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    PubMed

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  17. 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.

  18. The bond rupture force for sulfur chains calculated from quantum chemistry simulations and its relevance to the tensile strength of vulcanized rubber

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Hanson, David Edward; Barber, John L.

    From quantum chemistry simulations using density functional theory, we obtain the total electronic energy of an eight-atom sulfur chain as its end-to-end distance is extended until S–S bond rupture occurs. We find that a sulfur chain can be extended by about 40% beyond its nominally straight conformation, where it experiences rupture at an end-to-end tension of about 1.5 nN. Using this rupture force as the chain failure limit in an explicit polymer network simulation model (EPnet), we predict the tensile failure stress for sulfur crosslinked (vulcanized) natural rubber. Furthermore, quantitative agreement with published experimental data for the failure stress ismore » obtained in these simulations if we assume that only about 30% of the sulfur chains produce viable network crosslinks. Surprisingly, we also find that the failure stress of a rubber network does not scale linearly with the chain failure force limit.« less

  19. The bond rupture force for sulfur chains calculated from quantum chemistry simulations and its relevance to the tensile strength of vulcanized rubber

    DOE PAGES

    Hanson, David Edward; Barber, John L.

    2017-11-20

    From quantum chemistry simulations using density functional theory, we obtain the total electronic energy of an eight-atom sulfur chain as its end-to-end distance is extended until S–S bond rupture occurs. We find that a sulfur chain can be extended by about 40% beyond its nominally straight conformation, where it experiences rupture at an end-to-end tension of about 1.5 nN. Using this rupture force as the chain failure limit in an explicit polymer network simulation model (EPnet), we predict the tensile failure stress for sulfur crosslinked (vulcanized) natural rubber. Furthermore, quantitative agreement with published experimental data for the failure stress ismore » obtained in these simulations if we assume that only about 30% of the sulfur chains produce viable network crosslinks. Surprisingly, we also find that the failure stress of a rubber network does not scale linearly with the chain failure force limit.« less

  20. Hybrid Grid and Basis Set Approach to Quantum Chemistry DMRG

    NASA Astrophysics Data System (ADS)

    Stoudenmire, Edwin Miles; White, Steven

    We present a new approach for using DMRG for quantum chemistry that combines the advantages of a basis set with that of a grid approximation. Because DMRG scales linearly for quasi-one-dimensional systems, it is feasible to approximate the continuum with a fine grid in one direction while using a standard basis set approach for the transverse directions. Compared to standard basis set methods, we reach larger systems and achieve better scaling when approaching the basis set limit. The flexibility and reduced costs of our approach even make it feasible to incoporate advanced DMRG techniques such as simulating real-time dynamics. Supported by the Simons Collaboration on the Many-Electron Problem.

  1. 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

  2. Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units.

    PubMed

    Kussmann, Jörg; Ochsenfeld, Christian

    2017-06-13

    We present an extension of our graphics processing units (GPU)-accelerated quantum chemistry package to employ OpenCL compute kernels, which can be executed on a wide range of computing devices like CPUs, Intel Xeon Phi, and AMD GPUs. Here, we focus on the use of AMD GPUs and discuss differences as compared to CUDA-based calculations on NVIDIA GPUs. First illustrative timings are presented for hybrid density functional theory calculations using serial as well as parallel compute environments. The results show that AMD GPUs are as fast or faster than comparable NVIDIA GPUs and provide a viable alternative for quantum chemical applications.

  3. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra

    NASA Astrophysics Data System (ADS)

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-01

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pKa‧. The determination of pKa‧ is performed for various ionic strengths, which reveals the thermodynamic acid constant (pKa = 7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of - 1 and the blue form that of - 2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed.

  4. 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)

  5. Predicted phototoxicities of carbon nano-material by quantum mechanical calculations

    EPA Science Inventory

    The purpose of this research is to develop a predictive model for the phototoxicity potential of carbon nanomaterials (fullerenols and single-walled carbon nanotubes). This model is based on the quantum mechanical (ab initio) calculations on these carbon-based materials and compa...

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

    PubMed

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

    2016-07-08

    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.

  7. Calculation of metamorphic two-dimensional quantum energy system: Application to wetting layer states in InAs/InGaAs metamorphic quantum dot nanostructures

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Seravalli, L.; Trevisi, G.; Frigeri, P.

    In this work, we calculate the two-dimensional quantum energy system of the In(Ga)As wetting layer that arises in InAs/InGaAs/GaAs metamorphic quantum dot structures. Model calculations were carried on the basis of realistic material parameters taking in consideration their dependence on the strain relaxation of the metamorphic buffer; results of the calculations were validated against available literature data. Model results confirmed previous hypothesis on the extrinsic nature of the disappearance of wetting layer emission in metamorphic structures with high In composition. We also show how, by adjusting InGaAs metamorphic buffer parameters, it could be possible: (i) to spatially separate carriers confinedmore » in quantum dots from wetting layer carriers, (ii) to create an hybrid 0D-2D system, by tuning quantum dot and wetting layer levels. These results are interesting not only for the engineering of quantum dot structures but also for other applications of metamorphic structures, as the two design parameters of the metamorphic InGaAs buffer (thickness and composition) provide additional degrees of freedom to control properties of interest.« less

  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. Multiconfiguration Molecular Mechanics Based on Combined Quantum Mechanical and Molecular Mechanical Calculations.

    PubMed

    Lin, Hai; Zhao, Yan; Tishchenko, Oksana; Truhlar, Donald G

    2006-09-01

    The multiconfiguration molecular mechanics (MCMM) method is a general algorithm for generating potential energy surfaces for chemical reactions by fitting high-level electronic structure data with the help of molecular mechanical (MM) potentials. It was previously developed as an extension of standard MM to reactive systems by inclusion of multidimensional resonance interactions between MM configurations corresponding to specific valence bonding patterns, with the resonance matrix element obtained from quantum mechanical (QM) electronic structure calculations. In particular, the resonance matrix element is obtained by multidimensional interpolation employing a finite number of geometries at which electronic-structure calculations of the energy, gradient, and Hessian are carried out. In this paper, we present a strategy for combining MCMM with hybrid quantum mechanical molecular mechanical (QM/MM) methods. In the new scheme, electronic-structure information for obtaining the resonance integral is obtained by means of hybrid QM/MM calculations instead of fully QM calculations. As such, the new strategy can be applied to the studies of very large reactive systems. The new MCMM scheme is tested for two hydrogen-transfer reactions. Very encouraging convergence is obtained for rate constants including tunneling, suggesting that the new MCMM method, called QM/MM-MCMM, is a very general, stable, and efficient procedure for generating potential energy surfaces for large reactive systems. The results are found to converge well with respect to the number of Hessians. The results are also compared to calculations in which the resonance integral data are obtained by pure QM, and this illustrates the sensitivity of reaction rate calculations to the treatment of the QM-MM border. For the smaller of the two systems, comparison is also made to direct dynamics calculations in which the potential energies are computed quantum mechanically on the fly.

  10. Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

    NASA Astrophysics Data System (ADS)

    Huang, Jiayu; Liu, Shu; Zhang, Dong H.; Krems, Roman V.

    2018-04-01

    Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

  11. Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules.

    PubMed

    Huang, Jiayu; Liu, Shu; Zhang, Dong H; Krems, Roman V

    2018-04-06

    Because the de Broglie wavelength of ultracold molecules is very large, the cross sections for collisions of molecules at ultracold temperatures are always computed by the time-independent quantum scattering approach. Here, we report the first accurate time-dependent wave packet dynamics calculation for reactive scattering of ultracold molecules. Wave packet dynamics calculations can be applied to molecular systems with more dimensions and provide real-time information on the process of bond rearrangement and/or energy exchange in molecular collisions. Our work thus makes possible the extension of rigorous quantum calculations of ultracold reaction properties to polyatomic molecules and adds a new powerful tool for the study of ultracold chemistry.

  12. Linear Scaling Density Functional Calculations with Gaussian Orbitals

    NASA Technical Reports Server (NTRS)

    Scuseria, Gustavo E.

    1999-01-01

    Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.

  13. Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.

    PubMed

    Muddana, Hari S; Gilson, Michael K

    2012-06-12

    The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.

  14. Extending Halogen-based Medicinal Chemistry to Proteins

    PubMed Central

    El Hage, Krystel; Pandyarajan, Vijay; Phillips, Nelson B.; Smith, Brian J.; Menting, John G.; Whittaker, Jonathan; Lawrence, Michael C.; Meuwly, Markus; Weiss, Michael A.

    2016-01-01

    Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (TyrB26) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-TyrB26]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (TyrB16, PheB24, PheB25, 3-I-TyrB26, and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-TyrB26]insulin analog (determined as an R6 zinc hexamer). Given that residues B24–B30 detach from the core on receptor binding, the environment of 3-I-TyrB26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a “micro-receptor” complex, we predict that 3-I-TyrB26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such “halogen engineering” promises to extend principles of medicinal chemistry to proteins. PMID:27875310

  15. A new algorithm to handle finite nuclear mass effects in electronic calculations: the ISOTOPE program.

    PubMed

    Gonçalves, Cristina P; Mohallem, José R

    2004-11-15

    We report the development of a simple algorithm to modify quantum chemistry codes based on the LCAO procedure, to account for the isotope problem in electronic structure calculations. No extra computations are required compared to standard Born-Oppenheimer calculations. An upgrade of the Gamess package called ISOTOPE is presented, and its applicability is demonstrated in some examples.

  16. Quantum computing applied to calculations of molecular energies: CH2 benchmark.

    PubMed

    Veis, Libor; Pittner, Jiří

    2010-11-21

    Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.

  17. Determination of equilibrium structures of bromothymol blue revealed by using quantum chemistry with an aid of multivariate analysis of electronic absorption spectra.

    PubMed

    Shimada, Toru; Hasegawa, Takeshi

    2017-10-05

    The pH dependent chemical structures of bromothymol blue (BTB), which have long been under controversy, are determined by employing a combined technique of multivariate analysis of electronic absorption spectra and quantum chemistry. Principle component analysis (PCA) of the pH dependent spectra apparently reveals that only two chemical species are adequate to fully account for the color changes, with which the spectral decomposition is readily performed by using augmented alternative least-squares (ALS) regression analysis. The quantity variation by the ALS analysis also reveals the practical acid dissociation constant, pK a '. The determination of pK a ' is performed for various ionic strengths, which reveals the thermodynamic acid constant (pK a =7.5) and the number of charge on each chemical species; the yellow form is negatively charged species of -1 and the blue form that of -2. On this chemical information, the quantum chemical calculation is carried out to find that BTB molecules take the pure quinoid form in an acid solution and the quinoid-phenolate form in an alkaline solution. The time-dependent density functional theory (TD-DFT) calculations for the theoretically determined chemical structures account for the peak shift of the electronic spectra. In this manner, the structures of all the chemical species appeared in equilibrium have finally been confirmed. Copyright © 2017 Elsevier B.V. All rights reserved.

  18. A gist of comprehensive review of hadronic chemistry and its applications

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Tangde, Vijay M.

    20{sup th} century theories of Quantum Mechanics and Quantum Chemistry are exactly valid only when considered to represent the atomic structures. While considering the more general aspects of atomic combinations these theories fail to explain all the related experimental data from first unadulterated axiomatic principles. According to Quantum Chemistry two valence electrons should repel each other and as such there is no mathematical representation of a strong attractive forces between such valence electrons. In view of these and other insufficiencies of Quantum Chemistry, an Italian-American Scientist Professor Ruggero Maria Santilli during his more than five decades of dedicated and sustainedmore » research has denounced the fact that quantum chemistry is mostly based on mere nomenclatures. Professor R M Santilli first formulated the iso-, geno- and hyper- mathematics [1, 2, 3, 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, 4, 5] for the first time has removed the very fundamental limitations of quantum chemistry [2, 6, 7, 8]. In the present discussion, a comprehensive review of Hadronic Chemistry is presented 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, stepwise successes of Hadronic Chemistry and its application in development of a new chemical species called Magnecules.« less

  19. 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

  20. Is Mathematics to Blame? An Investigation into High School Students' Difficulty in Performing Calculations in Chemistry

    ERIC Educational Resources Information Center

    Scott, Fraser J.

    2012-01-01

    Mathematical ability is a major contributory factor to the success of a student in any science course. This paper aims to determine the source of the difficulty that students often find when performing calculations in chemistry. Through the design and analysis of a set of chemistry questions and analogous mathematics questions, set in a Standard…

  1. Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

    PubMed Central

    Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; McNichols, Brett W.; Miller, Elisa M.; Gu, Jing; Nozik, Arthur J.; Sellinger, Alan; Galli, Giulia; Beard, Matthew C.

    2017-01-01

    Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the band edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. We expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications. PMID:28508866

  2. Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

    DOE PAGES

    Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; ...

    2017-05-16

    Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the bandmore » edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. As a result, we expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.« less

  3. Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.

    Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the bandmore » edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. As a result, we expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.« less

  4. Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

    NASA Astrophysics Data System (ADS)

    Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; McNichols, Brett W.; Miller, Elisa M.; Gu, Jing; Nozik, Arthur J.; Sellinger, Alan; Galli, Giulia; Beard, Matthew C.

    2017-05-01

    Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the band edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. We expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.

  5. Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

    PubMed

    Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

    2018-06-13

    An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

  6. Quantum Monte Carlo calculations of NiO

    NASA Astrophysics Data System (ADS)

    Maezono, Ryo; Towler, Mike D.; Needs, Richard. J.

    2008-03-01

    We describe variational and diffusion quantum Monte Carlo (VMC and DMC) calculations [1] of NiO using a 1024-electron simulation cell. We have used a smooth, norm-conserving, Dirac-Fock pseudopotential [2] in our work. Our trial wave functions were of Slater-Jastrow form, containing orbitals generated in Gaussian-basis UHF periodic calculations. Jastrow factor is optimized using variance minimization with optimized cutoff lengths using the same scheme as our previous work. [4] We apply the lattice regulated scheme [5] to evaluate non-local pseudopotentials in DMC and find the scheme improves the smoothness of the energy-volume curve. [1] CASINO ver.2.1 User Manual, University of Cambridge (2007). [2] J.R. Trail et.al., J. Chem. Phys. 122, 014112 (2005). [3] CRYSTAL98 User's Manual, University of Torino (1998). [4] Ryo Maezono et.al., Phys. Rev. Lett., 98, 025701 (2007). [5] Michele Casula, Phys. Rev. B 74, 161102R (2006).

  7. Synthesis and DFT calculations of some 2-aminothiazoles

    NASA Astrophysics Data System (ADS)

    Rezania, Jafar; Behzadi, Hadi; Shockravi, Abbas; Ehsani, Morteza; Akbarzadeh, Elahe

    2018-04-01

    A series of 2-aminothiazole derivatives have been synthesized by the reaction of acetyl compounds with thiourea and iodine as catalyst under solvent-free condition, a green chemistry method. The quantum chemical calculations at the DFT/B3LYP level of theory in gas phase were carried out for starting acetyl derivatives. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) and related reactivity descriptor of acetyl derivatives, as well as, enthalpy of reactions are calculated in order to investigate the reaction properties of acetyl compounds and yields of the reactions. The calculated reactivity descriptors are well correlated to activity of different acetyl derivatives.

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

    DOE PAGES

    Kenny, Joseph P.; Janssen, Curtis L.; Gordon, Mark S.; ...

    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

  9. Quantum biological channel modeling and capacity calculation.

    PubMed

    Djordjevic, Ivan B

    2012-12-10

    Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general.

  10. Molcas 8: New capabilities for multiconfigurational quantum chemical calculations across the periodic table.

    PubMed

    Aquilante, Francesco; Autschbach, Jochen; Carlson, Rebecca K; Chibotaru, Liviu F; Delcey, Mickaël G; De Vico, Luca; Fdez Galván, Ignacio; Ferré, Nicolas; Frutos, Luis Manuel; Gagliardi, Laura; Garavelli, Marco; Giussani, Angelo; Hoyer, Chad E; Li Manni, Giovanni; Lischka, Hans; Ma, Dongxia; Malmqvist, Per Åke; Müller, Thomas; Nenov, Artur; Olivucci, Massimo; Pedersen, Thomas Bondo; Peng, Daoling; Plasser, Felix; Pritchard, Ben; Reiher, Markus; Rivalta, Ivan; Schapiro, Igor; Segarra-Martí, Javier; Stenrup, Michael; Truhlar, Donald G; Ungur, Liviu; Valentini, Alessio; Vancoillie, Steven; Veryazov, Valera; Vysotskiy, Victor P; Weingart, Oliver; Zapata, Felipe; Lindh, Roland

    2016-02-15

    In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization. © 2015 Wiley Periodicals, Inc.

  11. Combined use of computational chemistry and chemoinformatics methods for chemical discovery

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sugimoto, Manabu, E-mail: sugimoto@kumamoto-u.ac.jp; Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585; CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012

    2015-12-31

    Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of “cancer”. Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be “cancer”-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of themore » density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.« less

  12. Renyi entanglement entropy of interacting fermions calculated using the continuous-time quantum Monte Carlo method.

    PubMed

    Wang, Lei; Troyer, Matthias

    2014-09-12

    We present a new algorithm for calculating the Renyi entanglement entropy of interacting fermions using the continuous-time quantum Monte Carlo method. The algorithm only samples the interaction correction of the entanglement entropy, which by design ensures the efficient calculation of weakly interacting systems. Combined with Monte Carlo reweighting, the algorithm also performs well for systems with strong interactions. We demonstrate the potential of this method by studying the quantum entanglement signatures of the charge-density-wave transition of interacting fermions on a square lattice.

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

    USDA-ARS?s Scientific Manuscript database

    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...

  14. First-principles calculations of Ti and O NMR chemical shift tensors in ferroelectric perovskites

    NASA Astrophysics Data System (ADS)

    Pechkis, Daniel; Walter, Eric; Krakauer, Henry

    2011-03-01

    Complementary chemical shift calculations were carried out with embedded clusters, using quantum chemistry methods, and with periodic boundary conditions, using the GIPAW approach within the Quantum Espresso package. Compared to oxygen chemical shifts, δ̂ (O), cluster calculations for δ̂ (Ti) were found to be more sensitive to size effects, termination, and choice of gaussian-type atomic basis set, while GIPAW results were found to be more sensitive to the pseudopotential construction. The two approaches complemented each other in optimizing these factors. We show that the two approaches yield comparable chemical shifts for suitably converged simulations, and results are compared with available experimental measurements. Supported by ONR.

  15. "Shut up and calculate": the available discursive positions in quantum physics courses

    NASA Astrophysics Data System (ADS)

    Johansson, Anders; Andersson, Staffan; Salminen-Karlsson, Minna; Elmgren, Maja

    2018-03-01

    Educating new generations of physicists is often seen as a matter of attracting good students, teaching them physics and making sure that they stay at the university. Sometimes, questions are also raised about what could be done to increase diversity in recruitment. Using a discursive perspective, in this study of three introductory quantum physics courses at two Swedish universities, we instead ask what it means to become a physicist, and whether certain ways of becoming a physicist and doing physics is privileged in this process. Asking the question of what discursive positions are made accessible to students, we use observations of lectures and problem solving sessions together with interviews with students to characterize the discourse in the courses. Many students seem to have high expectations for the quantum physics course and generally express that they appreciate the course more than other courses. Nevertheless, our analysis shows that the ways of being a "good quantum physics student" are limited by the dominating focus on calculating quantum physics in the courses. We argue that this could have negative consequences both for the education of future physicists and the discipline of physics itself, in that it may reproduce an instrumental "shut up and calculate"-culture of physics, as well as an elitist physics education. Additionally, many students who take the courses are not future physicists, and the limitation of discursive positions may also affect these students significantly.

  16. Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical Concepts.

    PubMed

    Knizia, Gerald

    2013-11-12

    Modern quantum chemistry can make quantitative predictions on an immense array of chemical systems. However, the interpretation of those predictions is often complicated by the complex wave function expansions used. Here we show that an exceptionally simple algebraic construction allows for defining atomic core and valence orbitals, polarized by the molecular environment, which can exactly represent self-consistent field wave functions. This construction provides an unbiased and direct connection between quantum chemistry and empirical chemical concepts, and can be used, for example, to calculate the nature of bonding in molecules, in chemical terms, from first principles. In particular, we find consistency with electronegativities (χ), C 1s core-level shifts, resonance substituent parameters (σR), Lewis structures, and oxidation states of transition-metal complexes.

  17. Applying Quantum Monte Carlo to the Electronic Structure Problem

    NASA Astrophysics Data System (ADS)

    Powell, Andrew D.; Dawes, Richard

    2016-06-01

    Two distinct types of Quantum Monte Carlo (QMC) calculations are applied to electronic structure problems such as calculating potential energy curves and producing benchmark values for reaction barriers. First, Variational and Diffusion Monte Carlo (VMC and DMC) methods using a trial wavefunction subject to the fixed node approximation were tested using the CASINO code.[1] Next, Full Configuration Interaction Quantum Monte Carlo (FCIQMC), along with its initiator extension (i-FCIQMC) were tested using the NECI code.[2] FCIQMC seeks the FCI energy for a specific basis set. At a reduced cost, the efficient i-FCIQMC method can be applied to systems in which the standard FCIQMC approach proves to be too costly. Since all of these methods are statistical approaches, uncertainties (error-bars) are introduced for each calculated energy. This study tests the performance of the methods relative to traditional quantum chemistry for some benchmark systems. References: [1] R. J. Needs et al., J. Phys.: Condensed Matter 22, 023201 (2010). [2] G. H. Booth et al., J. Chem. Phys. 131, 054106 (2009).

  18. 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

  19. Calculation of exchange interaction for modified Gaussian coupled quantum dots

    NASA Astrophysics Data System (ADS)

    Khordad, R.

    2017-08-01

    A system of two laterally coupled quantum dots with modified Gaussian potential has been considered. Each quantum dot has an electron under electric and magnetic field. The quantum dots have been considered as hydrogen-like atoms. The physical picture has translated into the Heisenberg spin Hamiltonian. The Schrödinger equation using finite element method has been numerically solved. The exchange energy factor has been calculated as a functions of electric field, magnetic field, and the separation distance between the centers of the dots ( d). According to the results, it is found that there is the transition from anti-ferromagnetic to ferromagnetic for constant electric field. Also, the transition occurs from ferromagnetic to anti-ferromagnetic for constant magnetic field (B>1 T). With decreasing the distance between the centers of the dots and increasing magnetic field, the transition occurs from anti-ferromagnetic to ferromagnetic. It is found that a switching of exchange energy factor is presented without canceling the interactions of the electric and magnetic fields on the system.

  20. Quantum Monte Carlo calculations of van der Waals interactions between aromatic benzene rings

    NASA Astrophysics Data System (ADS)

    Azadi, Sam; Kühne, T. D.

    2018-05-01

    The magnitude of finite-size effects and Coulomb interactions in quantum Monte Carlo simulations of van der Waals interactions between weakly bonded benzene molecules are investigated. To that extent, two trial wave functions of the Slater-Jastrow and Backflow-Slater-Jastrow types are employed to calculate the energy-volume equation of state. We assess the impact of the backflow coordinate transformation on the nonlocal correlation energy. We found that the effect of finite-size errors in quantum Monte Carlo calculations on energy differences is particularly large and may even be more important than the employed trial wave function. In addition to the cohesive energy, the singlet excitonic energy gap and the energy gap renormalization of crystalline benzene at different densities are computed.

  1. Artificial Intelligence Support for Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Duch, Wlodzislaw

    Possible forms of artificial intelligence (AI) support for quantum chemistry are discussed. Questions addressed include: what kind of support is desirable, what kind of support is feasible, what can we expect in the coming years. Advantages and disadvantages of current AI techniques are presented and it is argued that at present the memory-based systems are the most effective for large scale applications. Such systems may be used to predict the accuracy of calculations and to select the least expensive methods and basis sets belonging to the same accuracy class. Advantages of the Feature Space Mapping as an improvement on the memory based systems are outlined and some results obtained in classification problems given. Relevance of such classification systems to computational chemistry is illustrated with two examples showing similarity of results obtained by different methods that take electron correlation into account.

  2. REVIEWS OF TOPICAL PROBLEMS: Analytic calculations on digital computers for applications in physics and mathematics

    NASA Astrophysics Data System (ADS)

    Gerdt, V. P.; Tarasov, O. V.; Shirkov, Dmitrii V.

    1980-01-01

    The present state of analytic calculations on computers is reviewed. Several programming systems which are used for analytic calculations are discussed: SCHOONSCHIP, CLAM, REDUCE-2, SYMBAL, CAMAL, AVTO-ANALITIK, MACSYMA, etc. It is shown that these systems can be used to solve a wide range of problems in physics and mathematics. Some physical applications are discussed in celestial mechanics, the general theory of relativity, quantum field theory, plasma physics, hydrodynamics, atomic and molecular physics, and quantum chemistry. Some mathematical applications which are discussed are evaluating indefinite integrals, solving differential equations, and analyzing mathematical expressions. This review is addressed to physicists and mathematicians working in a wide range of fields.

  3. Parallel scalability of Hartree-Fock calculations

    NASA Astrophysics Data System (ADS)

    Chow, Edmond; Liu, Xing; Smelyanskiy, Mikhail; Hammond, Jeff R.

    2015-03-01

    Quantum chemistry is increasingly performed using large cluster computers consisting of multiple interconnected nodes. For a fixed molecular problem, the efficiency of a calculation usually decreases as more nodes are used, due to the cost of communication between the nodes. This paper empirically investigates the parallel scalability of Hartree-Fock calculations. The construction of the Fock matrix and the density matrix calculation are analyzed separately. For the former, we use a parallelization of Fock matrix construction based on a static partitioning of work followed by a work stealing phase. For the latter, we use density matrix purification from the linear scaling methods literature, but without using sparsity. When using large numbers of nodes for moderately sized problems, density matrix computations are network-bandwidth bound, making purification methods potentially faster than eigendecomposition methods.

  4. Quantum dot properties in the multiband envelope-function approximation using boundary conditions based upon first-principles quantum calculations

    NASA Astrophysics Data System (ADS)

    Flory, Curt A.; Musgrave, Charles B.; Zhang, Zhiyong

    2008-05-01

    A number of physical processes involving quantum dots depend critically upon the “evanescent” electron eigenstate wave function that extends outside of the material surface into the surrounding region. These processes include electron tunneling through quantum dots, as well as interactions between multiple quantum dot structures. In order to unambiguously determine these evanescent fields, appropriate boundary conditions have been developed to connect the electronic solutions interior to the semiconductor quantum dot to exterior vacuum solutions. In standard envelope function theory, the interior wave function consists of products of band edge and envelope functions, and both must be considered when matching to the external solution. While the envelope functions satisfy tractable equations, the band edge functions are generally not known. In this work, symmetry arguments in the spherically symmetric approximation are used in conjunction with the known qualitative behavior of bonding and antibonding orbitals to catalog the behavior of the band edge functions at the unit cell boundary. This physical approximation allows consolidation of the influence of the band edge functions to two simple surface parameters that are incorporated into the boundary conditions and are straightforwardly computed by using numerical first-principles quantum techniques. These new boundary conditions are employed to analyze an isolated spherically symmetric semiconductor quantum dot in vacuum within the analytical model of Sercel and Vahala [Phys. Rev. Lett. 65, 239 (1990); Phys. Rev. B 42, 3690 (1990)]. Results are obtained for quantum dots made of GaAs and InP, which are compared with ab initio calculations that have appeared in the literature.

  5. A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations

    NASA Astrophysics Data System (ADS)

    Romero, Jonathan; Posada, Edwin; Flores-Moreno, Roberto; Reyes, Andrés

    2012-08-01

    In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.

  6. Simple way to calculate a UV-finite one-loop quantum energy in the Randall-Sundrum model

    NASA Astrophysics Data System (ADS)

    Altshuler, Boris L.

    2017-04-01

    The surprising simplicity of Barvinsky-Nesterov or equivalently Gelfand-Yaglom methods of calculation of quantum determinants permits us to obtain compact expressions for a UV-finite difference of one-loop quantum energies for two arbitrary values of the parameter of the double-trace asymptotic boundary conditions. This result generalizes the Gubser and Mitra calculation for the particular case of difference of "regular" and "irregular" one-loop energies in the one-brane Randall-Sundrum model. The approach developed in the paper also allows us to get "in one line" the one-loop quantum energies in the two-brane Randall-Sundrum model. The relationship between "one-loop" expressions corresponding to the mixed Robin and to double-trace asymptotic boundary conditions is traced.

  7. Secondary Structures in Phe-Containing Isolated Dipeptide Chains: Laser Spectroscopy vs Quantum Chemistry.

    PubMed

    Loquais, Yohan; Gloaguen, Eric; Habka, Sana; Vaquero-Vara, Vanesa; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel

    2015-06-11

    The intrinsic conformational landscape of two phenylalanine-containing protein chain models (-Gly-Phe- and -Ala-Phe- sequences) has been investigated theoretically and experimentally in the gas phase. The near UV spectroscopy (first ππ* transition of the Phe ring) is obtained experimentally under jet conditions where the conformational features can be resolved. Single-conformation IR spectroscopy in the NH stretch region is then obtained by IR/UV double resonance in the ground state, leading to resolved vibrational spectra that are assigned in terms of conformation and H-bonding content from comparison with quantum chemistry calculations. For the main conformer, whose UV spectrum exhibits a significant Franck-Condon activity in low frequency modes involving peptide backbone motions relative to the Phe chromophore, excited state IR spectroscopy has also been recorded in a UV/IR/UV experiment. The NH stretch spectral changes observed in such a ππ* labeling experiment enable us to determine those NH bonds that are coupled to the phenyl ring; they are compared to CC2 excited state calculations to quantify the geometry change upon ππ* excitation. The complete and consistent series of data obtained enable us to propose an unambiguous assignment for the gallery of conformers observed and to demonstrate that, in these two sequences, three conceptually important local structural motifs of proteins (β-strands, 27 ribbons, and β-turns) are represented. The satisfactory agreement between the experimental conformational distribution and the predicted landscape anticipated from the DFT-D approach demonstrates the capabilities of a theoretical method that accounts for dispersive interactions. It also shows that the flaws, inherent to a resonant two-photon ionization detection scheme, often evoked for aromatic chromophores, do not seem to be significant in the case of Phe.

  8. Importance of parametrizing constraints in quantum-mechanical variational calculations

    NASA Technical Reports Server (NTRS)

    Chung, Kwong T.; Bhatia, A. K.

    1992-01-01

    In variational calculations of quantum mechanics, constraints are sometimes imposed explicitly on the wave function. These constraints, which are deduced by physical arguments, are often not uniquely defined. In this work, the advantage of parametrizing constraints and letting the variational principle determine the best possible constraint for the problem is pointed out. Examples are carried out to show the surprising effectiveness of the variational method if constraints are parameterized. It is also shown that misleading results may be obtained if a constraint is not parameterized.

  9. SU-E-T-191: First Principle Calculation of Quantum Yield in Photodynamic Therapy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Abolfath, R; Guo, F; Chen, Z

    Purpose: We present a first-principle method to calculate the spin transfer efficiency in oxygen induced by any photon fields especially in MeV energy range. The optical pumping is mediated through photosensitizers, e.g., porphyrin and/or ensemble of quantum dots. Methods: Under normal conditions, oxygen molecules are in the relatively non-reactive triplet state. In the presence of certain photosensitizer compounds such as porphyrins, electromagnetic radiation of specific wavelengths can excite oxygen to highly reactive singlet state. With selective uptake of photosensitizers by certain malignant cells, photon irradiation of phosensitized tumors can lead to selective killing of cancer cells. This is the basismore » of photodynamic therapy (PDT). Despite several attempts, PDT has not been clinically successful except in limited superficial cancers. Many parameters such as photon energy, conjugation with quantum dots etc. can be potentially combined with PDT in order to extend the role of PDT in cancer management. The key quantity for this optimization is the spin transfer efficiency in oxygen by any photon field. The first principle calculation model presented here, is an attempt to fill this need. We employ stochastic density matrix description of the quantum jumps and the rate equation methods in quantum optics based on Markov/Poisson processes and calculate time evolution of the population of the optically pumped singlet oxygen. Results: The results demonstrate the feasibility of our model in showing the dependence of the optical yield in generating spin-singlet oxygen on the experimental conditions. The adjustable variables can be tuned to maximize the population of the singlet oxygen hence the efficacy of the photodynamic therapy. Conclusion: The present model can be employed to fit and analyze the experimental data and possibly to assist researchers in optimizing the experimental conditions in photodynamic therapy.« less

  10. Annular tautomerism: experimental observations and quantum mechanics calculations.

    PubMed

    Cruz-Cabeza, Aurora J; Schreyer, Adrian; Pitt, William R

    2010-06-01

    The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein-small molecule crystal structures.

  11. Annular tautomerism: experimental observations and quantum mechanics calculations

    NASA Astrophysics Data System (ADS)

    Cruz-Cabeza, Aurora J.; Schreyer, Adrian; Pitt, William R.

    2010-06-01

    The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein—small molecule crystal structures.

  12. Influence of single particle orbital sets and configuration selection on multideterminant wavefunctions in quantum Monte Carlo

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Clay, Raymond C.; Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550; Morales, Miguel A., E-mail: moralessilva2@llnl.gov

    2015-06-21

    Multideterminant wavefunctions, while having a long history in quantum chemistry, are increasingly being used in highly accurate quantum Monte Carlo calculations. Since the accuracy of QMC is ultimately limited by the quality of the trial wavefunction, multi-Slater determinants wavefunctions offer an attractive alternative to Slater-Jastrow and more sophisticated wavefunction ansatz for several reasons. They can be efficiently calculated, straightforwardly optimized, and systematically improved by increasing the number of included determinants. In spite of their potential, however, the convergence properties of multi-Slater determinant wavefunctions with respect to orbital set choice and excited determinant selection are poorly understood, which hinders the applicationmore » of these wavefunctions to large systems and solids. In this paper, by performing QMC calculations on the equilibrium and stretched carbon dimer, we find that convergence of the recovered correlation energy with respect to number of determinants can depend quite strongly on basis set and determinant selection methods, especially where there is strong correlation. We demonstrate that properly chosen orbital sets and determinant selection techniques from quantum chemistry methods can dramatically reduce the required number of determinants (and thus the computational cost) to reach a given accuracy, which we argue shows clear need for an automatic QMC-only method for selecting determinants and generating optimal orbital sets.« less

  13. Peptide-Decorated Tunable-Fluorescence Graphene Quantum Dots.

    PubMed

    Sapkota, Bedanga; Benabbas, Abdelkrim; Lin, Hao-Yu Greg; Liang, Wentao; Champion, Paul; Wanunu, Meni

    2017-03-22

    We report here the synthesis of graphene quantum dots with tunable size, surface chemistry, and fluorescence properties. In the size regime 15-35 nm, these quantum dots maintain strong visible light fluorescence (mean quantum yield of 0.64) and a high two-photon absorption (TPA) cross section (6500 Göppert-Mayer units). Furthermore, through noncovalent tailoring of the chemistry of these quantum dots, we obtain water-stable quantum dots. For example, quantum dots with lysine groups bind strongly to DNA in solution and inhibit polymerase-based DNA strand synthesis. Finally, by virtue of their mesoscopic size, the quantum dots exhibit good cell permeability into living epithelial cells, but they do not enter the cell nucleus.

  14. Continuous-time quantum Monte Carlo calculation of multiorbital vertex asymptotics

    NASA Astrophysics Data System (ADS)

    Kaufmann, Josef; Gunacker, Patrik; Held, Karsten

    2017-07-01

    We derive the equations for calculating the high-frequency asymptotics of the local two-particle vertex function for a multiorbital impurity model. These relate the asymptotics for a general local interaction to equal-time two-particle Green's functions, which we sample using continuous-time quantum Monte Carlo simulations with a worm algorithm. As specific examples we study the single-orbital Hubbard model and the three t2 g orbitals of SrVO3 within dynamical mean-field theory (DMFT). We demonstrate how the knowledge of the high-frequency asymptotics reduces the statistical uncertainties of the vertex and further eliminates finite-box-size effects. The proposed method benefits the calculation of nonlocal susceptibilities in DMFT and diagrammatic extensions of DMFT.

  15. Quantum Monte Carlo Calculations Applied to Magnetic Molecules

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Engelhardt, Larry

    2006-01-01

    We have calculated the equilibrium thermodynamic properties of Heisenberg spin systems using a quantum Monte Carlo (QMC) method. We have used some of these systems as models to describe recently synthesized magnetic molecules, and-upon comparing the results of these calculations with experimental data-have obtained accurate estimates for the basic parameters of these models. We have also performed calculations for other systems that are of more general interest, being relevant both for existing experimental data and for future experiments. Utilizing the concept of importance sampling, these calculations can be carried out in an arbitrarily large quantum Hilbert space, while still avoidingmore » any approximations that would introduce systematic errors. The only errors are statistical in nature, and as such, their magnitudes are accurately estimated during the course of a simulation. Frustrated spin systems present a major challenge to the QMC method, nevertheless, in many instances progress can be made. In this chapter, the field of magnetic molecules is introduced, paying particular attention to the characteristics that distinguish magnetic molecules from other systems that are studied in condensed matter physics. We briefly outline the typical path by which we learn about magnetic molecules, which requires a close relationship between experiments and theoretical calculations. The typical experiments are introduced here, while the theoretical methods are discussed in the next chapter. Each of these theoretical methods has a considerable limitation, also described in Chapter 2, which together serve to motivate the present work. As is shown throughout the later chapters, the present QMC method is often able to provide useful information where other methods fail. In Chapter 3, the use of Monte Carlo methods in statistical physics is reviewed, building up the fundamental ideas that are necessary in order to understand the method that has been used in this work. With

  16. Artificial Bee Colony Optimization of Capping Potentials for Hybrid Quantum Mechanical/Molecular Mechanical Calculations.

    PubMed

    Schiffmann, Christoph; Sebastiani, Daniel

    2011-05-10

    We present an algorithmic extension of a numerical optimization scheme for analytic capping potentials for use in mixed quantum-classical (quantum mechanical/molecular mechanical, QM/MM) ab initio calculations. Our goal is to minimize bond-cleavage-induced perturbations in the electronic structure, measured by means of a suitable penalty functional. The optimization algorithm-a variant of the artificial bee colony (ABC) algorithm, which relies on swarm intelligence-couples deterministic (downhill gradient) and stochastic elements to avoid local minimum trapping. The ABC algorithm outperforms the conventional downhill gradient approach, if the penalty hypersurface exhibits wiggles that prevent a straight minimization pathway. We characterize the optimized capping potentials by computing NMR chemical shifts. This approach will increase the accuracy of QM/MM calculations of complex biomolecules.

  17. Rethinking Undergraduate Physical Chemistry Curricula

    ERIC Educational Resources Information Center

    Miller, Stephen R.

    2016-01-01

    A summary of fundamental changes made to the undergraduate physical chemistry curriculum in the Chemistry Department at Gustavus Adolphus College (beginning in the 2013-2014 academic year) is presented. The yearlong sequence now consists of an introductory semester covering both quantum mechanics and thermodynamics/kinetics, followed by a second…

  18. Linear and Non-Linear Dielectric Response of Periodic Systems from Quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Umari, Paolo

    2006-03-01

    We present a novel approach that allows to calculate the dielectric response of periodic systems in the quantum Monte Carlo formalism. We employ a many-body generalization for the electric enthalpy functional, where the coupling with the field is expressed via the Berry-phase formulation for the macroscopic polarization. A self-consistent local Hamiltonian then determines the ground-state wavefunction, allowing for accurate diffusion quantum Monte Carlo calculations where the polarization's fixed point is estimated from the average on an iterative sequence. The polarization is sampled through forward-walking. This approach has been validated for the case of the polarizability of an isolated hydrogen atom, and then applied to a periodic system. We then calculate the linear susceptibility and second-order hyper-susceptibility of molecular-hydrogen chains whith different bond-length alternations, and assess the quality of nodal surfaces derived from density-functional theory or from Hartree-Fock. The results found are in excellent agreement with the best estimates obtained from the extrapolation of quantum-chemistry calculations.P. Umari, A.J. Williamson, G. Galli, and N. MarzariPhys. Rev. Lett. 95, 207602 (2005).

  19. Density Functional Theory Calculations of the Quantum Capacitance of Graphene Oxide as a Supercapacitor Electrode.

    PubMed

    Song, Ce; Wang, Jinyan; Meng, Zhaoliang; Hu, Fangyuan; Jian, Xigao

    2018-03-31

    Graphene oxide has become an attractive electrode-material candidate for supercapacitors thanks to its higher specific capacitance compared to graphene. The quantum capacitance makes relative contributions to the specific capacitance, which is considered as the major limitation of graphene electrodes, while the quantum capacitance of graphene oxide is rarely concerned. This study explores the quantum capacitance of graphene oxide, which bears epoxy and hydroxyl groups on its basal plane, by employing density functional theory (DFT) calculations. The results demonstrate that the total density of states near the Fermi level is significantly enhanced by introducing oxygen-containing groups, which is beneficial for the improvement of the quantum capacitance. Moreover, the quantum capacitances of the graphene oxide with different concentrations of these two oxygen-containing groups are compared, revealing that more epoxy and hydroxyl groups result in a higher quantum capacitance. Notably, the hydroxyl concentration has a considerable effect on the capacitive behavior. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  20. User's Guide to Handlens - A Computer Program that Calculates the Chemistry of Minerals in Mixtures

    USGS Publications Warehouse

    Eberl, D.D.

    2008-01-01

    HandLens is a computer program, written in Excel macro language, that calculates the chemistry of minerals in mineral mixtures (for example, in rocks, soils and sediments) for related samples from inputs of quantitative mineralogy and chemistry. For best results, the related samples should contain minerals having the same chemical compositions; that is, the samples should differ only in the proportions of minerals present. This manual describes how to use the program, discusses the theory behind its operation, and presents test results of the program's accuracy. Required input for HandLens includes quantitative mineralogical data, obtained, for example, by RockJock analysis of X-ray diffraction (XRD) patterns, and quantitative chemical data, obtained, for example, by X-ray florescence (XRF) analysis of the same samples. Other quantitative data, such as sample depth, temperature, surface area, also can be entered. The minerals present in the samples are selected from a list, and the program is started. The results of the calculation include: (1) a table of linear coefficients of determination (r2's) which relate pairs of input data (for example, Si versus quartz weight percents); (2) a utility for plotting all input data, either as pairs of variables, or as sums of up to eight variables; (3) a table that presents the calculated chemical formulae for minerals in the samples; (4) a table that lists the calculated concentrations of major, minor, and trace elements in the various minerals; and (5) a table that presents chemical formulae for the minerals that have been corrected for possible systematic errors in the mineralogical and/or chemical analyses. In addition, the program contains a method for testing the assumption of constant chemistry of the minerals within a sample set.

  1. The SOA formation model combined with semiempirical quantum chemistry for predicting UV-Vis absorption of secondary organic aerosols.

    PubMed

    Zhong, Min; Jang, Myoseon; Oliferenko, Alexander; Pillai, Girinath G; Katritzky, Alan R

    2012-07-07

    A new model for predicting the UV-visible absorption spectra of secondary organic aerosols (SOA) has been developed. The model consists of two primary parts: a SOA formation model and a semiempirical quantum chemistry method. The mass of SOA is predicted using the PHRCSOA (Partitioning Heterogeneous Reaction Consortium Secondary Organic Aerosol) model developed by Cao and Jang [Environ. Sci. Technol., 2010, 44, 727]. The chemical composition is estimated using a combination of the kinetic model (MCM) and the PHRCSOA model. The absorption spectrum is obtained by taking the sum of the spectrum of each SOA product calculated using a semiempirical NDDO (Neglect of Diatomic Differential Overlap)-based method. SOA was generated from the photochemical reaction of toluene or α-pinene at different NO(x) levels (low NO(x): 24-26 ppm, middle NO(x): 49 ppb, high NO(x): 104-105 ppb) using a 2 m(3) indoor Teflon film chamber. The model simulation reasonably agrees with the measured absorption spectra of α-pinene SOA but underestimates toluene SOA under high and middle NO(x) conditions. The absorption spectrum of toluene SOA is moderately enhanced with increasing NO(x) concentrations, while that of α-pinene SOA is not affected. Both measured and calculated UV-visible spectra show that the light absorption of toluene SOA is much stronger than that of α-pinene SOA.

  2. Molecular Studies of Complex Soil Organic Matter Interactions with Metal Ions and Mineral Surfaces using Classical Molecular Dynamics and Quantum Chemistry Methods

    NASA Astrophysics Data System (ADS)

    Andersen, A.; Govind, N.; Laskin, A.

    2017-12-01

    Mineral surfaces have been implicated as potential protectors of soil organic matter (SOM) against decomposition and ultimate mineralization to small molecules which can provide nutrients for plants and soil microbes and can also contribute to the Earth's elemental cycles. SOM is a complex mixture of organic molecules of biological origin at varying degrees of decomposition and can, itself, self-assemble in such a way as to expose some biomolecule types to biotic and abiotic attack while protecting other biomolecule types. The organization of SOM and SOM with mineral surfaces and solvated metal ions is driven by an interplay of van der Waals and electrostatic interactions leading to partitioning of hydrophilic (e.g. sugars) and hydrophobic (e.g., lipids) SOM components that can be bridged with amphiphilic molecules (e.g., proteins). Classical molecular dynamics simulations can shed light on assemblies of organic molecules alone or complexation with mineral surfaces. The role of chemical reactions is also an important consideration in potential chemical changes of the organic species such as oxidation/reduction, degradation, chemisorption to mineral surfaces, and complexation with solvated metal ions to form organometallic systems. For the study of chemical reactivity, quantum chemistry methods can be employed and combined with structural insight provided by classical MD simulations. Moreover, quantum chemistry can also simulate spectroscopic signatures based on chemical structure and is a valuable tool in interpreting spectra from, notably, x-ray absorption spectroscopy (XAS). In this presentation, we will discuss our classical MD and quantum chemistry findings on a model SOM system interacting with mineral surfaces and solvated metal ions.

  3. Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory

    NASA Technical Reports Server (NTRS)

    Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.

    1990-01-01

    New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.

  4. Preface: Special Topic: From Quantum Mechanics to Force Fields.

    PubMed

    Piquemal, Jean-Philip; Jordan, Kenneth D

    2017-10-28

    This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

  5. Preface: Special Topic: From Quantum Mechanics to Force Fields

    NASA Astrophysics Data System (ADS)

    Piquemal, Jean-Philip; Jordan, Kenneth D.

    2017-10-01

    This Special Topic issue entitled "From Quantum Mechanics to Force Fields" is dedicated to the ongoing efforts of the theoretical chemistry community to develop a new generation of accurate force fields based on data from high-level electronic structure calculations and to develop faster electronic structure methods for testing and designing force fields as well as for carrying out simulations. This issue includes a collection of 35 original research articles that illustrate recent theoretical advances in the field. It provides a timely snapshot of recent developments in the generation of approaches to enable more accurate molecular simulations of processes important in chemistry, physics, biophysics, and materials science.

  6. Molecular Quantum Mechanics: Analytic Gradients and Beyond - Program and Abstracts

    DTIC Science & Technology

    2007-06-03

    Kutzelnigg (Bochum, Germany) Chair: Pekka Pyykko (Helsinki, Finland) Which Masses are Vibrating or Rotating in a Molecule? 15:40-16:15 O30...Krylov (Los Angeles, CA, U.S.A.) Multiconfigurational Quantum Chemistry for Actinide Containing Systems: From Isolated Molecules to Condensed...the genetic algorithm will be critically assessed. For B4n, the double rings are notably stable. The DFT calculations provide strong indications of

  7. 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…

  8. Using the Chebychev expansion in quantum transport calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Popescu, Bogdan; Rahman, Hasan; Kleinekathöfer, Ulrich, E-mail: u.kleinekathoefer@jacobs-university.de

    2015-04-21

    Irradiation by laser pulses and a fluctuating surrounding liquid environment can, for example, lead to time-dependent effects in the transport through molecular junctions. From the theoretical point of view, time-dependent theories of quantum transport are still challenging. In one of these existing transport theories, the energy-dependent coupling between molecule and leads is decomposed into Lorentzian functions. This trick has successfully been combined with quantum master approaches, hierarchical formalisms, and non-equilibrium Green’s functions. The drawback of this approach is, however, its serious limitation to certain forms of the molecule-lead coupling and to higher temperatures. Tian and Chen [J. Chem. Phys. 137,more » 204114 (2012)] recently employed a Chebychev expansion to circumvent some of these latter problems. Here, we report on a similar approach also based on the Chebychev expansion but leading to a different set of coupled differential equations using the fact that a derivative of a zeroth-order Bessel function can again be given in terms of Bessel functions. Test calculations show the excellent numerical accuracy and stability of the presented formalism. The time span for which this Chebychev expansion scheme is valid without any restrictions on the form of the spectral density or temperature can be determined a priori.« less

  9. Vibrational analysis and quantum chemical calculations of 2,2‧-bipyridine Zinc(II) halide complexes

    NASA Astrophysics Data System (ADS)

    Ozel, Aysen E.; Kecel, Serda; Akyuz, Sevim

    2007-05-01

    In this study the molecular structure and vibrational spectra of Zn(2,2'-bipyridine)X 2 (X = Cl and Br) complexes were studied in their ground states by computational vibrational study and scaled quantum mechanical (SQM) analysis. The geometry optimization, vibrational wavenumber and intensity calculations of free and coordinated 2,2'-bipyridine were carried out with the Gaussian03 program package by using Hartree-Fock (HF) and Density Functional Theory (DFT) with B3LYP functional and 6-31G (d,p) basis set. The total energy distributions (TED) of the vibrational modes were calculated by using Scaled Quantum Mechanical (SQM) analysis. Fundamentals were characterised by their total energy distributions. Coordination sensitive modes of 2,2'-bipyridine were determined.

  10. Application of fermionic marginal constraints to hybrid quantum algorithms

    NASA Astrophysics Data System (ADS)

    Rubin, Nicholas C.; Babbush, Ryan; McClean, Jarrod

    2018-05-01

    Many quantum algorithms, including recently proposed hybrid classical/quantum algorithms, make use of restricted tomography of the quantum state that measures the reduced density matrices, or marginals, of the full state. The most straightforward approach to this algorithmic step estimates each component of the marginal independently without making use of the algebraic and geometric structure of the marginals. Within the field of quantum chemistry, this structure is termed the fermionic n-representability conditions, and is supported by a vast amount of literature on both theoretical and practical results related to their approximations. In this work, we introduce these conditions in the language of quantum computation, and utilize them to develop several techniques to accelerate and improve practical applications for quantum chemistry on quantum computers. As a general result, we demonstrate how these marginals concentrate to diagonal quantities when measured on random quantum states. We also show that one can use fermionic n-representability conditions to reduce the total number of measurements required by more than an order of magnitude for medium sized systems in chemistry. As a practical demonstration, we simulate an efficient restoration of the physicality of energy curves for the dilation of a four qubit diatomic hydrogen system in the presence of three distinct one qubit error channels, providing evidence these techniques are useful for pre-fault tolerant quantum chemistry experiments.

  11. Bohm's Quantum Potential and the Visualization of Molecular Structure

    NASA Technical Reports Server (NTRS)

    Levit, Creon; Chancellor, Marisa K. (Technical Monitor)

    1997-01-01

    David Bohm's ontological interpretation of quantum theory can shed light on otherwise counter-intuitive quantum mechanical phenomena including chemical bonding. In the field of quantum chemistry, Richard Bader has shown that the topology of the Laplacian of the electronic charge density characterizes many features of molecular structure and reactivity. Visual and computational examination suggests that the Laplacian of Bader and the quantum potential of Bohm are morphologically equivalent. It appears that Bohmian mechanics and the quantum potential can make chemistry as clear as they makes physics.

  12. Linear and nonlinear susceptibilities from diffusion quantum Monte Carlo: application to periodic hydrogen chains.

    PubMed

    Umari, P; Marzari, Nicola

    2009-09-07

    We calculate the linear and nonlinear susceptibilities of periodic longitudinal chains of hydrogen dimers with different bond-length alternations using a diffusion quantum Monte Carlo approach. These quantities are derived from the changes in electronic polarization as a function of applied finite electric field--an approach we recently introduced and made possible by the use of a Berry-phase, many-body electric-enthalpy functional. Calculated susceptibilities and hypersusceptibilities are found to be in excellent agreement with the best estimates available from quantum chemistry--usually extrapolations to the infinite-chain limit of calculations for chains of finite length. It is found that while exchange effects dominate the proper description of the susceptibilities, second hypersusceptibilities are greatly affected by electronic correlations. We also assess how different approximations to the nodal surface of the many-body wave function affect the accuracy of the calculated susceptibilities.

  13. Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

    PubMed

    Smith, Daniel G A; Burns, Lori A; Sirianni, Dominic A; Nascimento, Daniel R; Kumar, Ashutosh; James, Andrew M; Schriber, Jeffrey B; Zhang, Tianyuan; Zhang, Boyi; Abbott, Adam S; Berquist, Eric J; Lechner, Marvin H; Cunha, Leonardo A; Heide, Alexander G; Waldrop, Jonathan M; Takeshita, Tyler Y; Alenaizan, Asem; Neuhauser, Daniel; King, Rollin A; Simmonett, Andrew C; Turney, Justin M; Schaefer, Henry F; Evangelista, Francesco A; DePrince, A Eugene; Crawford, T Daniel; Patkowski, Konrad; Sherrill, C David

    2018-06-11

    Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

  14. Protactinium and the intersection of actinide and transition metal chemistry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wilson, Richard E.; De Sio, Stephanie; Vallet, Valérie

    The role of the 5f and 6d orbitals in the chemistry of the actinide elements has been of considerable interest since their discovery and synthesis. Relativistic effects cause the energetics of the 5f and 6d orbitals to change as the actinide series is traversed left to right imparting a rich and complex chemistry. The 5f and 6d atomic states cross in energy at protactinium (Pa), making it a potential intersection between transition metal and actinide chemistries. Herein, we report the synthesis of a Pa-peroxo cluster, A(6)(Pa4O(O-2)(6)F-12) [A = Rb, Cs, (CH3)(4)N], formed in pursuit of an actinide polyoxometalate. Quantum chemicalmore » calculations at the density functional theory level demonstrate equal 5f and 6d orbital participation in the chemistry of Pa and increasing 5f orbital participation for the heavier actinides. Periodic changes in orbital character to the bonding in the early actinides highlights the influence of the 5f orbitals in their reactivity and chemical structure.« less

  15. Young’s modulus calculations for cellulose Iß by MM3 and quantum mechanics

    USDA-ARS?s Scientific Manuscript database

    Quantum mechanics (QM) and molecular mechanics (MM) calculations were performed to elucidate Young’s moduli for a series of cellulose Iß models. Computations using the second generation empirical force field MM3 with a disaccharide cellulose model, 1,4'-O-dimethyl-ß-cellobioside (DMCB), and an analo...

  16. Single colloidal quantum dots as sources of single photons for quantum cryptography

    NASA Astrophysics Data System (ADS)

    Pisanello, Ferruccio; Qualtieri, Antonio; Leménager, Godefroy; Martiradonna, Luigi; Stomeo, Tiziana; Cingolani, Roberto; Bramati, Alberto; De Vittorio, Massimo

    2011-02-01

    Colloidal nanocrystals, i.e. quantum dots synthesized trough wet-chemistry approaches, are promising nanoparticles for photonic applications and, remarkably, their quantum nature makes them very promising for single photon emission at room temperature. In this work we describe two approaches to engineer the emission properties of these nanoemitters in terms of radiative lifetime and photon polarization, drawing a viable strategy for their exploitation as room-temperature single photon sources for quantum information and quantum telecommunications.

  17. Generalized Bloch theorem for complex periodic potentials: A powerful application to quantum transport calculations

    NASA Astrophysics Data System (ADS)

    Zhang, X.-G.; Varga, Kalman; Pantelides, Sokrates T.

    2007-07-01

    Band-theoretic methods with periodically repeated supercells have been a powerful approach for ground-state electronic structure calculations but have not so far been adapted for quantum transport problems with open boundary conditions. Here, we introduce a generalized Bloch theorem for complex periodic potentials and use a transfer-matrix formulation to cast the transmission probability in a scattering problem with open boundary conditions in terms of the complex wave vectors of a periodic system with absorbing layers, allowing a band technique for quantum transport calculations. The accuracy and utility of the method are demonstrated by the model problems of the transmission of an electron over a square barrier and the scattering of a phonon in an inhomogeneous nanowire. Application to the resistance of a twin boundary in nanocrystalline copper yields excellent agreement with recent experimental data.

  18. Communication: Reactivity borrowing in the mode selective chemistry of H + CHD3 → H2 + CD3

    NASA Astrophysics Data System (ADS)

    Ellerbrock, Roman; Manthe, Uwe

    2017-12-01

    Quantum state-resolved reaction probabilities for the H + CHD3 → H2 + CD3 reaction are calculated by accurate full-dimensional quantum dynamics calculations using the multi-layer multi-configurational time-dependent Hartree approach and the quantum transition state concept. Reaction probabilities of various ro-vibrational states of the CHD3 reactant are investigated for vanishing total angular momentum. While the reactivity of the different vibrational states of CHD3 mostly follows intuitive patterns, an unusually large reaction probability is found for CHD3 molecules triply excited in the CD3 umbrella-bending vibration. This surprising reactivity can be explained by a Fermi resonance-type mixing of the single CH-stretch excited and the triple CD3 umbrella-bend excited vibrational states of CHD3. These findings show that resonant energy transfer can significantly affect the mode-selective chemistry of CHD3 and result in counter-intuitive reactivity patterns.

  19. Teaching Introductory Quantum Physics and Chemistry: Caveats from the History of Science and Science Teaching to the Training of Modern Chemists

    ERIC Educational Resources Information Center

    Greca, Ileana M.; Freire, Olival, Jr.

    2014-01-01

    Finding the best ways to introduce quantum physics to undergraduate students in all scientific areas, in particular for chemistry students, is a pressing, but hardly a simple task. In this paper, we discuss the relevance of taking into account lessons from the history of the discipline and the ongoing controversy over its interpretations and…

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Meusinger, Carl; Johnson, Matthew S.; Berhanu, Tesfaye A.

    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 amore » 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.« less

  1. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    ERIC Educational Resources Information Center

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  2. Bond additivity corrections for quantum chemistry methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    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 duemore » 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.« less

  3. Insight into He diffusion in apatite by ion beam experiments and quantum calculations: implication for the (U-Th)/He thermochronometer

    NASA Astrophysics Data System (ADS)

    Gautheron, C.; Mbongo-Djimbi, D.; Gerin, C.; Roques, J.; Bachelet, C.; Oliviero, E.; Tassan-Got, L.

    2015-12-01

    The apatite (U-Th)/He (AHe) system has rapidly become a very popular thermochronometer, however, interpretation of AHe age depends on a precise knowledge of He diffusion. Several studies suggest that He retention is function of the amount of damage that is controlled by U-Th concentration, grain chemistry and thermal history. Still, the models are not well constrained and do not fully explain the mechanism of He retention. In order to have a deeper insight into this issue, a multidisciplinary study on apatite combining physical methods such as multi-scale theoretical diffusion calculations based on Density Functional Theory (DFT) with diffusion experiments by ion beam Elastic Recoil Diffusion Analysis (ERDA) were performed. Quantum calculations permit to quantify He diffusivity base level for damage-free crystal and to estimate the additional energy cost to extract He atoms trapped in point defects (i.e. vacancies). On the other hand ion beam ERDA experiments allow to measure He diffusivity in artificially damaged crystals. We show that damage-free apatite crystals are characterized by low retention behavior and closure temperature of ~35°C for pure F-apatite to higher value for Cl rich apatite (up to 12°C higher), for typical grain size and cooling rate (Mbongo-Djimbi et al., 2015). Our computed closure temperature is slightly lower than previously reported experimental values (~50°C). Using ERDA and DFT modeling of damage, we show how He diffusivity is influenced by damage. Finally, we are able to propose a new modeling of He diffusion incorporating mechanisms not included in classical damage models, and taking into account the level of damage and apatite chemistry. We show that it could affect significantly AHe age interpretation. Mbongo-Djimbi D. et al. 2015. Apatite composition effect on (U-Th)/He thermochronometer: an atomistic point of view. Geohimica Cosmochim. Acta.

  4. Role of Precursor-Conversion Chemistry in the Crystal-Phase Control of Catalytically Grown Colloidal Semiconductor Quantum Wires.

    PubMed

    Wang, Fudong; Buhro, William E

    2017-12-26

    Crystal-phase control is one of the most challenging problems in nanowire growth. We demonstrate that, in the solution-phase catalyzed growth of colloidal cadmium telluride (CdTe) quantum wires (QWs), the crystal phase can be controlled by manipulating the reaction chemistry of the Cd precursors and tri-n-octylphosphine telluride (TOPTe) to favor the production of either a CdTe solute or Te, which consequently determines the composition and (liquid or solid) state of the Bi x Cd y Te z catalyst nanoparticles. Growth of single-phase (e.g., wurtzite) QWs is achieved only from solid catalysts (y ≪ z) that enable the solution-solid-solid growth of the QWs, whereas the liquid catalysts (y ≈ z) fulfill the solution-liquid-solid growth of the polytypic QWs. Factors that affect the precursor-conversion chemistry are systematically accounted for, which are correlated with a kinetic study of the composition and state of the catalyst nanoparticles to understand the mechanism. This work reveals the role of the precursor-reaction chemistry in the crystal-phase control of catalytically grown colloidal QWs, opening the possibility of growing phase-pure QWs of other compositions.

  5. Relativistic quantum mechanical calculations of electron-impact broadening for spectral lines in Be-like ions

    NASA Astrophysics Data System (ADS)

    Duan, B.; Bari, M. A.; Wu, Z. Q.; Jun, Y.; Li, Y. M.; Wang, J. G.

    2012-11-01

    Aims: We present relativistic quantum mechanical calculations of electron-impact broadening of the singlet and triplet transition 2s3s ← 2s3p in four Be-like ions from N IV to Ne VII. Methods: In our theoretical calculations, the K-matrix and related symmetry information determined by the colliding systems are generated by the DARC codes. Results: A careful comparison between our calculations and experimental results shows good agreement. Our calculated widths of spectral lines also agree with earlier theoretical results. Our investigations provide new methods of calculating electron-impact broadening parameters for plasma diagnostics.

  6. Quantum chemical determination of young?s modulus of lignin. Calculations on ß-O-4' model compound

    Treesearch

    Thomas Elder

    2007-01-01

    The calculation of Young?s modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in...

  7. Accelerating atomistic calculations of quantum energy eigenstates on graphic cards

    NASA Astrophysics Data System (ADS)

    Rodrigues, Walter; Pecchia, A.; Lopez, M.; Auf der Maur, M.; Di Carlo, A.

    2014-10-01

    Electronic properties of nanoscale materials require the calculation of eigenvalues and eigenvectors of large matrices. This bottleneck can be overcome by parallel computing techniques or the introduction of faster algorithms. In this paper we report a custom implementation of the Lanczos algorithm with simple restart, optimized for graphical processing units (GPUs). The whole algorithm has been developed using CUDA and runs entirely on the GPU, with a specialized implementation that spares memory and reduces at most machine-to-device data transfers. Furthermore parallel distribution over several GPUs has been attained using the standard message passing interface (MPI). Benchmark calculations performed on a GaN/AlGaN wurtzite quantum dot with up to 600,000 atoms are presented. The empirical tight-binding (ETB) model with an sp3d5s∗+spin-orbit parametrization has been used to build the system Hamiltonian (H).

  8. Quantum chemical calculations of Cr2O3/SnO2 using density functional theory method

    NASA Astrophysics Data System (ADS)

    Jawaher, K. Rackesh; Indirajith, R.; Krishnan, S.; Robert, R.; Das, S. Jerome

    2018-03-01

    Quantum chemical calculations have been employed to study the molecular effects produced by Cr2O3/SnO2 optimised structure. The theoretical parameters of the transparent conducting metal oxides were calculated using DFT / B3LYP / LANL2DZ method. The optimised bond parameters such as bond lengths, bond angles and dihedral angles were calculated using the same theory. The non-linear optical property of the title compound was calculated using first-order hyperpolarisability calculation. The calculated HOMO-LUMO analysis explains the charge transfer interaction between the molecule. In addition, MEP and Mulliken atomic charges were also calculated and analysed.

  9. Modeling Stretching Modes of Common Organic Molecules with the Quantum Mechanical Harmonic Oscillator: An Undergraduate Vibrational Spectroscopy Laboratory Exercise

    ERIC Educational Resources Information Center

    Parnis, J. Mark; Thompson, Matthew G. K.

    2004-01-01

    An introductory undergraduate physical organic chemistry exercise that introduces the harmonic oscillator's use in vibrational spectroscopy is developed. The analysis and modeling exercise begins with the students calculating the stretching modes of common organic molecules with the help of the quantum mechanical harmonic oscillator (QMHO) model.

  10. Performance of quantum Monte Carlo for calculating molecular bond lengths

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Cleland, Deidre M., E-mail: deidre.cleland@csiro.au; Per, Manolo C., E-mail: manolo.per@csiro.au

    2016-03-28

    This work investigates the accuracy of real-space quantum Monte Carlo (QMC) methods for calculating molecular geometries. We present the equilibrium bond lengths of a test set of 30 diatomic molecules calculated using variational Monte Carlo (VMC) and diffusion Monte Carlo (DMC) methods. The effect of different trial wavefunctions is investigated using single determinants constructed from Hartree-Fock (HF) and Density Functional Theory (DFT) orbitals with LDA, PBE, and B3LYP functionals, as well as small multi-configurational self-consistent field (MCSCF) multi-determinant expansions. When compared to experimental geometries, all DMC methods exhibit smaller mean-absolute deviations (MADs) than those given by HF, DFT, and MCSCF.more » The most accurate MAD of 3 ± 2 × 10{sup −3} Å is achieved using DMC with a small multi-determinant expansion. However, the more computationally efficient multi-determinant VMC method has a similar MAD of only 4.0 ± 0.9 × 10{sup −3} Å, suggesting that QMC forces calculated from the relatively simple VMC algorithm may often be sufficient for accurate molecular geometries.« less

  11. First-principles calculation of intrinsic defect chemistry and self-doping in PbTe

    DOE PAGES

    Goyal, Anuj; Gorai, Prashun; Toberer, Eric S.; ...

    2017-11-10

    Semiconductor dopability is inherently limited by intrinsic defect chemistry. In many thermoelectric materials, narrow band gaps due to strong spin-orbit interactions make accurate atomic level predictions of intrinsic defect chemistry and self-doping computationally challenging. For this study, we use different levels of theory to model point defects in PbTe, and compare and contrast the results against each other and a large body of experimental data. We find that to accurately reproduce the intrinsic defect chemistry and known self-doping behavior of PbTe, it is essential to (a) go beyond the semi-local GGA approximation to density functional theory, (b) include spin-orbit coupling,more » and (c) utilize many-body GW theory to describe the positions of individual band edges. The hybrid HSE functional with spin-orbit coupling included, in combination with the band edge shifts from G0W0 is the only approach that accurately captures both the intrinsic conductivity type of PbTe as function of synthesis conditions as well as the measured charge carrier concentrations, without the need for experimental inputs. Our results reaffirm the critical role of the position of individual band edges in defect calculations, and demonstrate that dopability can be accurately predicted in such challenging narrow band gap materials.« less

  12. First-principles calculation of intrinsic defect chemistry and self-doping in PbTe

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goyal, Anuj; Gorai, Prashun; Toberer, Eric S.

    Semiconductor dopability is inherently limited by intrinsic defect chemistry. In many thermoelectric materials, narrow band gaps due to strong spin-orbit interactions make accurate atomic level predictions of intrinsic defect chemistry and self-doping computationally challenging. For this study, we use different levels of theory to model point defects in PbTe, and compare and contrast the results against each other and a large body of experimental data. We find that to accurately reproduce the intrinsic defect chemistry and known self-doping behavior of PbTe, it is essential to (a) go beyond the semi-local GGA approximation to density functional theory, (b) include spin-orbit coupling,more » and (c) utilize many-body GW theory to describe the positions of individual band edges. The hybrid HSE functional with spin-orbit coupling included, in combination with the band edge shifts from G0W0 is the only approach that accurately captures both the intrinsic conductivity type of PbTe as function of synthesis conditions as well as the measured charge carrier concentrations, without the need for experimental inputs. Our results reaffirm the critical role of the position of individual band edges in defect calculations, and demonstrate that dopability can be accurately predicted in such challenging narrow band gap materials.« less

  13. First-principles calculation of intrinsic defect chemistry and self-doping in PbTe

    NASA Astrophysics Data System (ADS)

    Goyal, Anuj; Gorai, Prashun; Toberer, Eric S.; Stevanović, Vladan

    2017-10-01

    Semiconductor dopability is inherently limited by intrinsic defect chemistry. In many thermoelectric materials, narrow band gaps due to strong spin-orbit interactions make accurate atomic level predictions of intrinsic defect chemistry and self-doping computationally challenging. Here we use different levels of theory to model point defects in PbTe, and compare and contrast the results against each other and a large body of experimental data. We find that to accurately reproduce the intrinsic defect chemistry and known self-doping behavior of PbTe, it is essential to (a) go beyond the semi-local GGA approximation to density functional theory, (b) include spin-orbit coupling, and (c) utilize many-body GW theory to describe the positions of individual band edges. The hybrid HSE functional with spin-orbit coupling included, in combination with the band edge shifts from G0W0 is the only approach that accurately captures both the intrinsic conductivity type of PbTe as function of synthesis conditions as well as the measured charge carrier concentrations, without the need for experimental inputs. Our results reaffirm the critical role of the position of individual band edges in defect calculations, and demonstrate that dopability can be accurately predicted in such challenging narrow band gap materials.

  14. Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

    NASA Astrophysics Data System (ADS)

    Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

    1997-07-01

    Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

  15. Calculating work in weakly driven quantum master equations: Backward and forward equations

    NASA Astrophysics Data System (ADS)

    Liu, Fei

    2016-01-01

    I present a technical report indicating that the two methods used for calculating characteristic functions for the work distribution in weakly driven quantum master equations are equivalent. One involves applying the notion of quantum jump trajectory [Phys. Rev. E 89, 042122 (2014), 10.1103/PhysRevE.89.042122], while the other is based on two energy measurements on the combined system and reservoir [Silaev et al., Phys. Rev. E 90, 022103 (2014), 10.1103/PhysRevE.90.022103]. These represent backward and forward methods, respectively, which adopt a very similar approach to that of the Kolmogorov backward and forward equations used in classical stochastic theory. The microscopic basis for the former method is also clarified. In addition, a previously unnoticed equality related to the heat is also revealed.

  16. Extending Halogen-based Medicinal Chemistry to Proteins: IODO-INSULIN AS A CASE STUDY.

    PubMed

    El Hage, Krystel; Pandyarajan, Vijay; Phillips, Nelson B; Smith, Brian J; Menting, John G; Whittaker, Jonathan; Lawrence, Michael C; Meuwly, Markus; Weiss, Michael A

    2016-12-30

    Insulin, a protein critical for metabolic homeostasis, provides a classical model for protein design with application to human health. Recent efforts to improve its pharmaceutical formulation demonstrated that iodination of a conserved tyrosine (Tyr B26 ) enhances key properties of a rapid-acting clinical analog. Moreover, the broad utility of halogens in medicinal chemistry has motivated the use of hybrid quantum- and molecular-mechanical methods to study proteins. Here, we (i) undertook quantitative atomistic simulations of 3-[iodo-Tyr B26 ]insulin to predict its structural features, and (ii) tested these predictions by X-ray crystallography. Using an electrostatic model of the modified aromatic ring based on quantum chemistry, the calculations suggested that the analog, as a dimer and hexamer, exhibits subtle differences in aromatic-aromatic interactions at the dimer interface. Aromatic rings (Tyr B16 , Phe B24 , Phe B25 , 3-I-Tyr B26 , and their symmetry-related mates) at this interface adjust to enable packing of the hydrophobic iodine atoms within the core of each monomer. Strikingly, these features were observed in the crystal structure of a 3-[iodo-Tyr B26 ]insulin analog (determined as an R 6 zinc hexamer). Given that residues B24-B30 detach from the core on receptor binding, the environment of 3-I-Tyr B26 in a receptor complex must differ from that in the free hormone. Based on the recent structure of a "micro-receptor" complex, we predict that 3-I-Tyr B26 engages the receptor via directional halogen bonding and halogen-directed hydrogen bonding as follows: favorable electrostatic interactions exploiting, respectively, the halogen's electron-deficient σ-hole and electronegative equatorial band. Inspired by quantum chemistry and molecular dynamics, such "halogen engineering" promises to extend principles of medicinal chemistry to proteins. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  17. Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

    NASA Astrophysics Data System (ADS)

    Aquilanti, Vincenzo; Bitencourt, Ana Carla P.; Ferreira, Cristiane da S.; Marzuoli, Annalisa; Ragni, Mirco

    2008-11-01

    The mathematical apparatus of quantum-mechanical angular momentum (re)coupling, developed originally to describe spectroscopic phenomena in atomic, molecular, optical and nuclear physics, is embedded in modern algebraic settings which emphasize the underlying combinatorial aspects. SU(2) recoupling theory, involving Wigner's 3nj symbols, as well as the related problems of their calculations, general properties, asymptotic limits for large entries, nowadays plays a prominent role also in quantum gravity and quantum computing applications. We refer to the ingredients of this theory—and of its extension to other Lie and quantum groups—by using the collective term of 'spin networks'. Recent progress is recorded about the already established connections with the mathematical theory of discrete orthogonal polynomials (the so-called Askey scheme), providing powerful tools based on asymptotic expansions, which correspond on the physical side to various levels of semi-classical limits. These results are useful not only in theoretical molecular physics but also in motivating algorithms for the computationally demanding problems of molecular dynamics and chemical reaction theory, where large angular momenta are typically involved. As for quantum chemistry, applications of these techniques include selection and classification of complete orthogonal basis sets in atomic and molecular problems, either in configuration space (Sturmian orbitals) or in momentum space. In this paper, we list and discuss some aspects of these developments—such as for instance the hyperquantization algorithm—as well as a few applications to quantum gravity and topology, thus providing evidence of a unifying background structure.

  18. Quantum calculations of the carrier mobility: Methodology, Matthiessen's rule, and comparison with semi-classical approaches

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Niquet, Yann-Michel, E-mail: yniquet@cea.fr; Nguyen, Viet-Hung; Duchemin, Ivan

    2014-02-07

    We discuss carrier mobilities in the quantum Non-Equilibrium Green's Functions (NEGF) framework. We introduce a method for the extraction of the mobility that is free from contact resistance contamination and with minimal needs for ensemble averages. We focus on silicon thin films as an illustration, although the method can be applied to various materials such as semiconductor nanowires or carbon nanostructures. We then introduce a new paradigm for the definition of the partial mobility μ{sub M} associated with a given elastic scattering mechanism “M,” taking phonons (PH) as a reference (μ{sub M}{sup −1}=μ{sub PH+M}{sup −1}−μ{sub PH}{sup −1}). We argue thatmore » this definition makes better sense in a quantum transport framework as it is free from long range interference effects that can appear in purely ballistic calculations. As a matter of fact, these mobilities satisfy Matthiessen's rule for three mechanisms [e.g., surface roughness (SR), remote Coulomb scattering (RCS) and phonons] much better than the usual, single mechanism calculations. We also discuss the problems raised by the long range spatial correlations in the RCS disorder. Finally, we compare semi-classical Kubo-Greenwood (KG) and quantum NEGF calculations. We show that KG and NEGF are in reasonable agreement for phonon and RCS, yet not for SR. We discuss the reasons for these discrepancies.« less

  19. Ab initio calculation of transport properties between PbSe quantum dots facets with iodide ligands

    NASA Astrophysics Data System (ADS)

    Wang, B.; Patterson, R.; Chen, W.; Zhang, Z.; Yang, J.; Huang, S.; Shrestha, S.; Conibeer, G.

    2018-01-01

    The transport properties between Lead Selenide (PbSe) quantum dots decorated with iodide ligands has been studied using density functional theory (DFT). Quantum conductance at each selected energy levels has been calculated along with total density of states and projected density of states. The DFT calculation is carried on using a grid-based planar augmented wave (GPAW) code incorporated with the linear combination of atomic orbital (LCAO) mode and Perdew Burke Ernzerhof (PBE) exchange-correlation functional. Three iodide ligand attached low index facets including (001), (011), (111) are investigated in this work. P-orbital of iodide ligand majorly contributes to density of state (DOS) at near top valence band resulting a significant quantum conductance, whereas DOS of Pb p-orbital shows minor influence. Various values of quantum conductance observed along different planes are possibly reasoned from a combined effect electrical field over topmost surface and total distance between adjacent facets. Ligands attached to (001) and (011) planes possess similar bond length whereas it is significantly shortened in (111) plane, whereas transport between (011) has an overall low value due to newly formed electric field. On the other hand, (111) plane with a net surface dipole perpendicular to surface layers leading to stronger electron coupling suggests an apparent increase of transport probability. Apart from previously mentioned, the maximum transport energy levels located several eVs (1 2 eVs) from the edge of valence band top.

  20. EVALUATING METRICS FOR GREEN CHEMISTRIES: INFORMATION AND CALCULATION NEEDS

    EPA Science Inventory

    Research within the U.S. EPA's National Risk Management Research Laboratory is developing a methodology for the evaluation of green chemistries. This methodology called GREENSCOPE (Gauging Reaction Effectiveness for the ENvironmental Sustainability of Chemistries with a multi-Ob...

  1. General Procedure for the Easy Calculation of pH in an Introductory Course of General or Analytical Chemistry

    ERIC Educational Resources Information Center

    Cepriá, Gemma; Salvatella, Luis

    2014-01-01

    All pH calculations for simple acid-base systems used in introductory courses on general or analytical chemistry can be carried out by using a general procedure requiring the use of predominance diagrams. In particular, the pH is calculated as the sum of an independent term equaling the average pK[subscript a] values of the acids involved in the…

  2. Quantum Mechanical Calculations of Cytosine, Thiocytosine and Their Radical Ions

    NASA Astrophysics Data System (ADS)

    Singh, Rashmi

    2010-08-01

    The RNA and DNA are polymer that share some interesting similarities, for instance it is well known that cytosine is the one of the common nucleic acid base. The sulfur is characterized as a very reactive element and it has been used, in chemical warfare agents. Since the genetic information is based on the sequence of the nucleic acid bases. The quantum mechanical calculations of the energies, geometries, charges and vibrational characteristics of the cytosine and thiocytosine. and their corresponding radicals were carried out by using DFT method with b3lyp/6-311++g** basis set.

  3. Improving the accuracy of Density Functional Theory (DFT) calculation for homolysis bond dissociation energies of Y-NO bond: generalized regression neural network based on grey relational analysis and principal component analysis.

    PubMed

    Li, Hong Zhi; Tao, Wei; Gao, Ting; Li, Hui; Lu, Ying Hua; Su, Zhong Min

    2011-01-01

    We propose a generalized regression neural network (GRNN) approach based on grey relational analysis (GRA) and principal component analysis (PCA) (GP-GRNN) to improve the accuracy of density functional theory (DFT) calculation for homolysis bond dissociation energies (BDE) of Y-NO bond. As a demonstration, this combined quantum chemistry calculation with the GP-GRNN approach has been applied to evaluate the homolysis BDE of 92 Y-NO organic molecules. The results show that the ull-descriptor GRNN without GRA and PCA (F-GRNN) and with GRA (G-GRNN) approaches reduce the root-mean-square (RMS) of the calculated homolysis BDE of 92 organic molecules from 5.31 to 0.49 and 0.39 kcal mol(-1) for the B3LYP/6-31G (d) calculation. Then the newly developed GP-GRNN approach further reduces the RMS to 0.31 kcal mol(-1). Thus, the GP-GRNN correction on top of B3LYP/6-31G (d) can improve the accuracy of calculating the homolysis BDE in quantum chemistry and can predict homolysis BDE which cannot be obtained experimentally.

  4. An Analytical Quantum Model to Calculate Fluorescence Enhancement of a Molecule in Vicinity of a Sub-10 nm Metal Nanoparticle.

    PubMed

    Bagheri, Zahra; Massudi, Reza

    2017-05-01

    An analytical quantum model is used to calculate electrical permittivity of a metal nanoparticle located in an adjacent molecule. Different parameters, such as radiative and non-radiative decay rates, quantum yield, electrical field enhancement factor, and fluorescence enhancement are calculated by such a model and they are compared with those obtained by using the classical Drude model. It is observed that using an analytical quantum model presents a higher enhancement factor, up to 30%, as compared to classical model for nanoparticles smaller than 10 nm. Furthermore, the results are in better agreement with those experimentally realized.

  5. Line Coupling Effects in the Isotropic Raman Spectra of N2: A Quantum Calculation at Room Temperature

    NASA Technical Reports Server (NTRS)

    Thibault, Franck; Boulet, Christian; Ma, Qiancheng

    2014-01-01

    We present quantum calculations of the relaxation matrix for the Q branch of N2 at room temperature using a recently proposed N2-N2 rigid rotor potential. Close coupling calculations were complemented by coupled states studies at high energies and provide about 10200 two-body state-to state cross sections from which the needed one-body cross-sections may be obtained. For such temperatures, convergence has to be thoroughly analyzed since such conditions are close to the limit of current computational feasibility. This has been done using complementary calculations based on the energy corrected sudden formalism. Agreement of these quantum predictions with experimental data is good, but the main goal of this work is to provide a benchmark relaxation matrix for testing more approximate methods which remain of a great utility for complex molecular systems at room (and higher) temperatures.

  6. Recent advances in jointed quantum mechanics and molecular mechanics calculations of biological macromolecules: schemes and applications coupled to ab initio calculations.

    PubMed

    Hagiwara, Yohsuke; Tateno, Masaru

    2010-10-20

    We review the recent research on the functional mechanisms of biological macromolecules using theoretical methodologies coupled to ab initio quantum mechanical (QM) treatments of reaction centers in proteins and nucleic acids. Since in most cases such biological molecules are large, the computational costs of performing ab initio calculations for the entire structures are prohibitive. Instead, simulations that are jointed with molecular mechanics (MM) calculations are crucial to evaluate the long-range electrostatic interactions, which significantly affect the electronic structures of biological macromolecules. Thus, we focus our attention on the methodologies/schemes and applications of jointed QM/MM calculations, and discuss the critical issues to be elucidated in biological macromolecular systems. © 2010 IOP Publishing Ltd

  7. Error Sensitivity to Environmental Noise in Quantum Circuits for Chemical State Preparation.

    PubMed

    Sawaya, Nicolas P D; Smelyanskiy, Mikhail; McClean, Jarrod R; Aspuru-Guzik, Alán

    2016-07-12

    Calculating molecular energies is likely to be one of the first useful applications to achieve quantum supremacy, performing faster on a quantum than a classical computer. However, if future quantum devices are to produce accurate calculations, errors due to environmental noise and algorithmic approximations need to be characterized and reduced. In this study, we use the high performance qHiPSTER software to investigate the effects of environmental noise on the preparation of quantum chemistry states. We simulated 18 16-qubit quantum circuits under environmental noise, each corresponding to a unitary coupled cluster state preparation of a different molecule or molecular configuration. Additionally, we analyze the nature of simple gate errors in noise-free circuits of up to 40 qubits. We find that, in most cases, the Jordan-Wigner (JW) encoding produces smaller errors under a noisy environment as compared to the Bravyi-Kitaev (BK) encoding. For the JW encoding, pure dephasing noise is shown to produce substantially smaller errors than pure relaxation noise of the same magnitude. We report error trends in both molecular energy and electron particle number within a unitary coupled cluster state preparation scheme, against changes in nuclear charge, bond length, number of electrons, noise types, and noise magnitude. These trends may prove to be useful in making algorithmic and hardware-related choices for quantum simulation of molecular energies.

  8. 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

  9. Photodissociation of ultracold diatomic strontium molecules with quantum state control.

    PubMed

    McDonald, M; McGuyer, B H; Apfelbeck, F; Lee, C-H; Majewska, I; Moszynski, R; Zelevinsky, T

    2016-07-07

    Chemical reactions at ultracold temperatures are expected to be dominated by quantum mechanical effects. Although progress towards ultracold chemistry has been made through atomic photoassociation, Feshbach resonances and bimolecular collisions, these approaches have been limited by imperfect quantum state selectivity. In particular, attaining complete control of the ground or excited continuum quantum states has remained a challenge. Here we achieve this control using photodissociation, an approach that encodes a wealth of information in the angular distribution of outgoing fragments. By photodissociating ultracold (88)Sr2 molecules with full control of the low-energy continuum, we access the quantum regime of ultracold chemistry, observing resonant and nonresonant barrier tunnelling, matter-wave interference of reaction products and forbidden reaction pathways. Our results illustrate the failure of the traditional quasiclassical model of photodissociation and instead are accurately described by a quantum mechanical model. The experimental ability to produce well-defined quantum continuum states at low energies will enable high-precision studies of long-range molecular potentials for which accurate quantum chemistry models are unavailable, and may serve as a source of entangled states and coherent matter waves for a wide range of experiments in quantum optics.

  10. 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.

  11. 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.

  12. An efficient solver for large structured eigenvalue problems in relativistic quantum chemistry

    NASA Astrophysics Data System (ADS)

    Shiozaki, Toru

    2017-01-01

    We report an efficient program for computing the eigenvalues and symmetry-adapted eigenvectors of very large quaternionic (or Hermitian skew-Hamiltonian) matrices, using which structure-preserving diagonalisation of matrices of dimension N > 10, 000 is now routine on a single computer node. Such matrices appear frequently in relativistic quantum chemistry owing to the time-reversal symmetry. The implementation is based on a blocked version of the Paige-Van Loan algorithm, which allows us to use the Level 3 BLAS subroutines for most of the computations. Taking advantage of the symmetry, the program is faster by up to a factor of 2 than state-of-the-art implementations of complex Hermitian diagonalisation; diagonalising a 12, 800 × 12, 800 matrix took 42.8 (9.5) and 85.6 (12.6) minutes with 1 CPU core (16 CPU cores) using our symmetry-adapted solver and Intel Math Kernel Library's ZHEEV that is not structure-preserving, respectively. The source code is publicly available under the FreeBSD licence.

  13. 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)

  14. Bismuth as a versatile cation for luminescence in coordination polymers from BiX3/4,4'-bipy: understanding of photophysics by quantum chemical calculations and structural parallels to lanthanides.

    PubMed

    Sorg, Jens R; Wehner, Tobias; Matthes, Philipp R; Sure, Rebecca; Grimme, Stefan; Heine, Johanna; Müller-Buschbaum, Klaus

    2018-05-16

    Coordination polymers (CPs) with bismuth(iii) as a connectivity centre have been prepared from BiX3 (X = Cl-I) and 4,4'-bipyridine (bipy) in order to implement Bi-based luminescence. The products were obtained via different synthetic routes such as solution chemistry, melt syntheses or mechanochemical reactions. Five neutral and anionic 1D-CPs are presented that show a chemical parallel to trivalent lanthanides forming isostructural or closely related 1D-CPs, of which five additional compounds are described. Bi3+ proves to be a versatile cation for luminescence resulting from energy transfer processes between a metal and a ligand in the presented CPs. Quantum chemical calculations were carried out to investigate Bi3+-participation in the luminescence processes. The calculated results allow an assignment of the bright transitions composed of mainly metal-to-ligand-charge transfer (MLCT) character. These results show that Bi3+ can form strongly luminescent coordination compounds with N-donor ligands.

  15. 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…

  16. QmeQ 1.0: An open-source Python package for calculations of transport through quantum dot devices

    NASA Astrophysics Data System (ADS)

    Kiršanskas, Gediminas; Pedersen, Jonas Nyvold; Karlström, Olov; Leijnse, Martin; Wacker, Andreas

    2017-12-01

    QmeQ is an open-source Python package for numerical modeling of transport through quantum dot devices with strong electron-electron interactions using various approximate master equation approaches. The package provides a framework for calculating stationary particle or energy currents driven by differences in chemical potentials or temperatures between the leads which are tunnel coupled to the quantum dots. The electronic structures of the quantum dots are described by their single-particle states and the Coulomb matrix elements between the states. When transport is treated perturbatively to lowest order in the tunneling couplings, the possible approaches are Pauli (classical), first-order Redfield, and first-order von Neumann master equations, and a particular form of the Lindblad equation. When all processes involving two-particle excitations in the leads are of interest, the second-order von Neumann approach can be applied. All these approaches are implemented in QmeQ. We here give an overview of the basic structure of the package, give examples of transport calculations, and outline the range of applicability of the different approximate approaches.

  17. On the validity of microscopic calculations of double-quantum-dot spin qubits based on Fock-Darwin states

    NASA Astrophysics Data System (ADS)

    Chan, GuoXuan; Wang, Xin

    2018-04-01

    We consider two typical approximations that are used in the microscopic calculations of double-quantum dot spin qubits, namely, the Heitler-London (HL) and the Hund-Mulliken (HM) approximations, which use linear combinations of Fock-Darwin states to approximate the two-electron states under the double-well confinement potential. We compared these results to a case in which the solution to a one-dimensional Schr¨odinger equation was exactly known and found that typical microscopic calculations based on Fock-Darwin states substantially underestimate the value of the exchange interaction, which is the key parameter that controls the quantum dot spin qubits. This underestimation originates from the lack of tunneling of Fock-Darwin states, which is accurate only in the case with a single potential well. Our results suggest that the accuracies of the current two-dimensional molecular- orbit-theoretical calculations based on Fock-Darwin states should be revisited since underestimation could only deteriorate in dimensions that are higher than one.

  18. Time-dependent quantum wave packet calculation for nonadiabatic F(2P3/2,2P1/2)+H2 reaction

    NASA Astrophysics Data System (ADS)

    Zhang, Yan; Xie, Ting-Xian; Han, Ke-Li; Zhang, John Z. H.

    2003-12-01

    In this paper we present a time-dependent quantum wave packet calculation for the reaction of F(2P3/2,2P1/2)+H2 on the Alexander-Stark-Werner potential energy surface. The reaction probabilities and the integral cross sections for the reaction of F(2P3/2,2P1/2)+H2 (v=j=0) are computed using time-dependent quantum methods with the centrifugal sudden approximate. The results are compared with recent time-independent quantum calculations. The two-surface reaction probability for the initial ground spin-orbit state of J=0.5 is similar to the time-independent result obtained by Alexander et al. [J. Chem. Phys. 113, 11084 (2000)]. Our calculation also shows that electronic coupling has a relatively minor effect on the reactivity from the 2P3/2 state but a non-negligible one from the 2P1/2 state. By comparison with exact time-independent calculations, it is found that the Coriolis coupling plays a relatively minor role. In addition, most of the reactivity of the excited state of fluorine atom results from the spin-orbit coupling.

  19. InAs Colloidal Quantum Dots Synthesis via Aminopnictogen Precursor Chemistry.

    PubMed

    Grigel, Valeriia; Dupont, Dorian; De Nolf, Kim; Hens, Zeger; Tessier, Mickael D

    2016-10-05

    Despite their various potential applications, InAs colloidal quantum dots have attracted considerably less attention than more classical II-VI materials because of their complex syntheses that require hazardous precursors. Recently, amino-phosphine has been introduced as a cheap, easy-to-use and efficient phosphorus precursor to synthesize InP quantum dots. Here, we use aminopnictogen precursors to implement a similar approach for synthesizing InAs quantum dots. We develop a two-step method based on the combination of aminoarsine as the arsenic precursor and aminophosphine as the reducing agent. This results in state-of-the-art InAs quantum dots with respect to the size dispersion and band-gap range. Moreover, we present shell coating procedures that lead to the formation of InAs/ZnS(e) core/shell quantum dots that emit in the infrared region. This innovative synthesis approach can greatly facilitate the research on InAs quantum dots and may lead to synthesis protocols for a wide range of III-V quantum dots.

  20. Calculated quantum yield of photosynthesis of phytoplankton in the Marine Light-Mixed Layers (59 deg N, 21 deg W)

    NASA Technical Reports Server (NTRS)

    Carder, K. L.; Lee, Z. P.; Marra, John; Steward, R. G.; Perry, M. J.

    1995-01-01

    The quantum yield of photosynthesis (mol C/mol photons) was calculated at six depths for the waters of the Marine Light-Mixed Layer (MLML) cruise of May 1991. As there were photosynthetically available radiation (PAR) but no spectral irradiance measurements for the primary production incubations, three ways are presented here for the calculation of the absorbed photons (AP) by phytoplankton for the purpose of calculating phi. The first is based on a simple, nonspectral model; the second is based on a nonlinear regression using measured PAR values with depth; and the third is derived through remote sensing measurements. We show that the results of phi calculated using the nonlinear regreesion method and those using remote sensing are in good agreement with each other, and are consistent with the reported values of other studies. In deep waters, however, the simple nonspectral model may cause quantum yield values much higher than theoretically possible.

  1. Chemical accuracy from quantum Monte Carlo for the benzene dimer.

    PubMed

    Azadi, Sam; Cohen, R E

    2015-09-14

    We report an accurate study of interactions between benzene molecules using variational quantum Monte Carlo (VMC) and diffusion quantum Monte Carlo (DMC) methods. We compare these results with density functional theory using different van der Waals functionals. In our quantum Monte Carlo (QMC) calculations, we use accurate correlated trial wave functions including three-body Jastrow factors and backflow transformations. We consider two benzene molecules in the parallel displaced geometry, and find that by highly optimizing the wave function and introducing more dynamical correlation into the wave function, we compute the weak chemical binding energy between aromatic rings accurately. We find optimal VMC and DMC binding energies of -2.3(4) and -2.7(3) kcal/mol, respectively. The best estimate of the coupled-cluster theory through perturbative triplets/complete basis set limit is -2.65(2) kcal/mol [Miliordos et al., J. Phys. Chem. A 118, 7568 (2014)]. Our results indicate that QMC methods give chemical accuracy for weakly bound van der Waals molecular interactions, comparable to results from the best quantum chemistry methods.

  2. Nontrivial Quantum Effects in Biology: A Skeptical Physicists' View

    NASA Astrophysics Data System (ADS)

    Wiseman, Howard; Eisert, Jens

    The following sections are included: * Introduction * A Quantum Life Principle * A quantum chemistry principle? * The anthropic principle * Quantum Computing in the Brain * Nature did everything first? * Decoherence as the make or break issue * Quantum error correction * Uselessness of quantum algorithms for organisms * Quantum Computing in Genetics * Quantum search * Teleological aspects and the fast-track to life * Quantum Consciousness * Computability and free will * Time scales * Quantum Free Will * Predictability and free will * Determinism and free will * Acknowledgements * References

  3. Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

    PubMed

    Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

    2011-06-02

    Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS.

  4. Quasi-classical modeling of molecular quantum-dot cellular automata multidriver gates

    NASA Astrophysics Data System (ADS)

    Rahimi, Ehsan; Nejad, Shahram Mohammad

    2012-05-01

    Molecular quantum-dot cellular automata (mQCA) has received considerable attention in nanoscience. Unlike the current-based molecular switches, where the digital data is represented by the on/off states of the switches, in mQCA devices, binary information is encoded in charge configuration within molecular redox centers. The mQCA paradigm allows high device density and ultra-low power consumption. Digital mQCA gates are the building blocks of circuits in this paradigm. Design and analysis of these gates require quantum chemical calculations, which are demanding in computer time and memory. Therefore, developing simple models to probe mQCA gates is of paramount importance. We derive a semi-classical model to study the steady-state output polarization of mQCA multidriver gates, directly from the two-state approximation in electron transfer theory. The accuracy and validity of this model are analyzed using full quantum chemistry calculations. A complete set of logic gates, including inverters and minority voters, are implemented to provide an appropriate test bench in the two-dot mQCA regime. We also briefly discuss how the QCADesigner tool could find its application in simulation of mQCA devices.

  5. Wave packet and statistical quantum calculations for the He + NeH⁺ → HeH⁺ + Ne reaction on the ground electronic state.

    PubMed

    Koner, Debasish; Barrios, Lizandra; González-Lezana, Tomás; Panda, Aditya N

    2014-09-21

    A real wave packet based time-dependent method and a statistical quantum method have been used to study the He + NeH(+) (v, j) reaction with the reactant in various ro-vibrational states, on a recently calculated ab initio ground state potential energy surface. Both the wave packet and statistical quantum calculations were carried out within the centrifugal sudden approximation as well as using the exact Hamiltonian. Quantum reaction probabilities exhibit dense oscillatory pattern for smaller total angular momentum values, which is a signature of resonances in a complex forming mechanism for the title reaction. Significant differences, found between exact and approximate quantum reaction cross sections, highlight the importance of inclusion of Coriolis coupling in the calculations. Statistical results are in fairly good agreement with the exact quantum results, for ground ro-vibrational states of the reactant. Vibrational excitation greatly enhances the reaction cross sections, whereas rotational excitation has relatively small effect on the reaction. The nature of the reaction cross section curves is dependent on the initial vibrational state of the reactant and is typical of a late barrier type potential energy profile.

  6. Numerical renormalization group calculation of impurity internal energy and specific heat of quantum impurity models

    NASA Astrophysics Data System (ADS)

    Merker, L.; Costi, T. A.

    2012-08-01

    We introduce a method to obtain the specific heat of quantum impurity models via a direct calculation of the impurity internal energy requiring only the evaluation of local quantities within a single numerical renormalization group (NRG) calculation for the total system. For the Anderson impurity model we show that the impurity internal energy can be expressed as a sum of purely local static correlation functions and a term that involves also the impurity Green function. The temperature dependence of the latter can be neglected in many cases, thereby allowing the impurity specific heat Cimp to be calculated accurately from local static correlation functions; specifically via Cimp=(∂Eionic)/(∂T)+(1)/(2)(∂Ehyb)/(∂T), where Eionic and Ehyb are the energies of the (embedded) impurity and the hybridization energy, respectively. The term involving the Green function can also be evaluated in cases where its temperature dependence is non-negligible, adding an extra term to Cimp. For the nondegenerate Anderson impurity model, we show by comparison with exact Bethe ansatz calculations that the results recover accurately both the Kondo induced peak in the specific heat at low temperatures as well as the high-temperature peak due to the resonant level. The approach applies to multiorbital and multichannel Anderson impurity models with arbitrary local Coulomb interactions. An application to the Ohmic two-state system and the anisotropic Kondo model is also given, with comparisons to Bethe ansatz calculations. The approach could also be of interest within other impurity solvers, for example, within quantum Monte Carlo techniques.

  7. Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU-GPU Computing Platform.

    PubMed

    Wu, Xin; Koslowski, Axel; Thiel, Walter

    2012-07-10

    In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

  8. Wintertime nitric acid chemistry - Implications from three-dimensional model calculations

    NASA Technical Reports Server (NTRS)

    Rood, Richard B.; Kaye, Jack A.; Douglass, Anne R.; Allen, Dale J.; Steenford, Stephen

    1990-01-01

    A three-dimensional simulation of the evolution of HNO3 has been run for the winter of 1979. Winds and temperatures are taken from a stratospheric data assimilation analysis, and the chemistry is based on Limb Infrared Monitor of the Stratosphere (LIMS) observations. The model is compared to LIMS observations to investigate the problem of 'missing' nitric acid chemistry in the winter hemisphere. Both the model and observations support the contention that a nitric acid source is needed outside of the polar vortex and north of the subtropics. Observations suggest that HNO3 is not dynamically controlled in middle latitudes. The model shows that given the time scales of conventional chemistry, dynamical control is expected. Therefore, an error exists in the conventional chemistry or additional processes are needed to bring the model and data into agreement. Since the polar vortex is dynamically isolated from the middle latitudes, and since the highest HNO3 values are observed in October and November, a source associated solely with polar stratospheric clouds cannot explain the deficiencies in the chemistry. The role of heterogeneous processes on background aerosols is reviewed in light of these results.

  9. Sol-Gel Chemistry for Carbon Dots.

    PubMed

    Malfatti, Luca; Innocenzi, Plinio

    2018-03-14

    Carbon dots are an emerging class of carbon-based nanostructures produced by low-cost raw materials which exhibit a widely-tunable photoluminescence and a high quantum yield. The potential of these nanomaterials as a substitute of semiconductor quantum dots in optoelectronics and biomedicine is very high, however they need a customized chemistry to be integrated in host-guest systems or functionalized in core-shell structures. This review is focused on recent advances of the sol-gel chemistry applied to the C-dots technology. The surface modification, the fine tailoring of the chemical composition and the embedding into a complex nanostructured material are the main targets of combining sol-gel processing with C-dots chemistry. In addition, the synergistic effect of the sol-gel precursor combined with the C-dots contribute to modify the intrinsic chemo-physical properties of the dots, empowering the emission efficiency or enabling the tuning of the photoluminescence over a wide range of the visible spectrum. © 2018 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    NASA Astrophysics Data System (ADS)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

  11. Quantum mechanical calculation of electric fields and vibrational Stark shifts at active site of human aldose reductase

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wang, Xianwei; State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai 200062; Zhang, John Z. H.

    2015-11-14

    Recent advance in biophysics has made it possible to directly measure site-specific electric field at internal sites of proteins using molecular probes with C = O or C≡N groups in the context of vibrational Stark effect. These measurements directly probe changes of electric field at specific protein sites due to, e.g., mutation and are very useful in protein design. Computational simulation of the Stark effect based on force fields such as AMBER and OPLS, while providing good insight, shows large errors in comparison to experimental measurement due to inherent difficulties associated with point charge based representation of force fields. Inmore » this study, quantum mechanical calculation of protein’s internal electrostatic properties and vibrational Stark shifts was carried out by using electrostatically embedded generalized molecular fractionation with conjugate caps method. Quantum calculated change of mutation-induced electric field and vibrational Stark shift is reported at the internal probing site of enzyme human aldose reductase. The quantum result is in much better agreement with experimental data than those predicted by force fields, underscoring the deficiency of traditional point charge models describing intra-protein electrostatic properties.« less

  12. Ab initio quantum chemistry: methodology and applications.

    PubMed

    Friesner, Richard A

    2005-05-10

    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.

  13. Free Energies of Quantum Particles: The Coupled-Perturbed Quantum Umbrella Sampling Method.

    PubMed

    Glover, William J; Casey, Jennifer R; Schwartz, Benjamin J

    2014-10-14

    We introduce a new simulation method called Coupled-Perturbed Quantum Umbrella Sampling that extends the classical umbrella sampling approach to reaction coordinates involving quantum mechanical degrees of freedom. The central idea in our method is to solve coupled-perturbed equations to find the response of the quantum system's wave function along a reaction coordinate of interest. This allows for propagation of the system's dynamics under the influence of a quantum biasing umbrella potential and provides a method to rigorously undo the effects of the bias to compute equilibrium ensemble averages. In this way, one can drag electrons into regions of high free energy where they would otherwise not go, thus enabling chemistry by fiat. We demonstrate the applicability of our method for two condensed-phase systems of interest. First, we consider the interaction of a hydrated electron with an aqueous sodium cation, and we calculate a potential of mean force that shows that an e(-):Na(+) contact pair is the thermodynamically favored product starting from either a neutral sodium atom or the separate cation and electron species. Second, we present the first determination of a hydrated electron's free-energy profile relative to an air/water interface. For the particular model parameters used, we find that the hydrated electron is more thermodynamically stable in the bulk rather than at the interface. Our analysis suggests that the primary driving force keeping the electron away from the interface is the long-range electron-solvent polarization interaction rather than the short-range details of the chosen pseudopotential.

  14. Machine Learning of Parameters for Accurate Semiempirical Quantum Chemical Calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-05-12

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  15. Machine learning of parameters for accurate semiempirical quantum chemical calculations

    DOE PAGES

    Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter

    2015-04-14

    We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C 7H 10O 2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less

  16. Multireference quantum chemistry through a joint density matrix renormalization group and canonical transformation theory.

    PubMed

    Yanai, Takeshi; Kurashige, Yuki; Neuscamman, Eric; Chan, Garnet Kin-Lic

    2010-01-14

    We describe the joint application of the density matrix renormalization group and canonical transformation theory to multireference quantum chemistry. The density matrix renormalization group provides the ability to describe static correlation in large active spaces, while the canonical transformation theory provides a high-order description of the dynamic correlation effects. We demonstrate the joint theory in two benchmark systems designed to test the dynamic and static correlation capabilities of the methods, namely, (i) total correlation energies in long polyenes and (ii) the isomerization curve of the [Cu(2)O(2)](2+) core. The largest complete active spaces and atomic orbital basis sets treated by the joint DMRG-CT theory in these systems correspond to a (24e,24o) active space and 268 atomic orbitals in the polyenes and a (28e,32o) active space and 278 atomic orbitals in [Cu(2)O(2)](2+).

  17. Reducing Projection Calculation in Quantum Teleportation by Virtue of the IWOP Technique and Schmidt Decomposition of |η〉 State

    NASA Astrophysics Data System (ADS)

    Fan, Hong-Yi; Fan, Yue

    2002-01-01

    By virtue of the technique of integration within an ordered product of operators and the Schmidt decomposition of the entangled state |η〉, we reduce the general projection calculation in the theory of quantum teleportation to a as simple as possible form and present a general formalism for teleportating quantum states of continuous variable. The project supported by National Natural Science Foundation of China and Educational Ministry Foundation of China

  18. User's guide for vectorized code EQUIL for calculating equilibrium chemistry on Control Data STAR-100 computer

    NASA Technical Reports Server (NTRS)

    Kumar, A.; Graves, R. A., Jr.; Weilmuenster, K. J.

    1980-01-01

    A vectorized code, EQUIL, was developed for calculating the equilibrium chemistry of a reacting gas mixture on the Control Data STAR-100 computer. The code provides species mole fractions, mass fractions, and thermodynamic and transport properties of the mixture for given temperature, pressure, and elemental mass fractions. The code is set up for the electrons H, He, C, O, N system of elements. In all, 24 chemical species are included.

  19. Making a molecular gas in the quantum regime

    NASA Astrophysics Data System (ADS)

    Ni, Kang-Kuen

    2017-04-01

    Ultracold molecules are exciting systems for a large range of scientific explorations including studies of novel phases of matter and precision measurement. In this talk, I will present a brief story of the first quantum gas of molecules, KRb, created under my PhD advisor, Deborah Jin, in 2008. A complete surprise was finding ultracold chemistry in such a system through measurements of reactant losses. In particular, long-range physics that determines KRb reactant collision rates, including van der Waals interactions, quantum statistics, and dipolar interactions, were studied extensively. However, the short-range behavior of these chemical reactions remains unknown. A legacy of her work is carried out in my lab at Harvard, where we are integrating physical chemistry tools with cold atom techniques to study ultracold chemistry with KRb molecules. In particular, we aim to elucidate the four-center reaction 2 KRb ->K2 + Rb2 by detecting the reaction products through ionization - both identify the product species and mapping out their complete quantum states.

  20. Synthesis of Cesium Lead Halide Perovskite Quantum Dots

    ERIC Educational Resources Information Center

    Shekhirev, Mikhail; Goza, John; Teeter, Jacob D.; Lipatov, Alexey; Sinitskii, Alexander

    2017-01-01

    Synthesis of quantum dots is a valuable experiment for demonstration and discussion of quantum phenomena in undergraduate chemistry curricula. Recently, a new class of all-inorganic perovskite quantum dots (QDs) with a formula of CsPbX[subscript 3] (X = Cl, Br, I) was presented and attracted tremendous attention. Here we adapt the synthesis of…

  1. Multicomponent Density Functional Theory: Impact of Nuclear Quantum Effects on Proton Affinities and Geometries.

    PubMed

    Brorsen, Kurt R; Yang, Yang; Hammes-Schiffer, Sharon

    2017-08-03

    Nuclear quantum effects such as zero point energy play a critical role in computational chemistry and often are included as energetic corrections following geometry optimizations. The nuclear-electronic orbital (NEO) multicomponent density functional theory (DFT) method treats select nuclei, typically protons, quantum mechanically on the same level as the electrons. Electron-proton correlation is highly significant, and inadequate treatments lead to highly overlocalized nuclear densities. A recently developed electron-proton correlation functional, epc17, has been shown to provide accurate nuclear densities for molecular systems. Herein, the NEO-DFT/epc17 method is used to compute the proton affinities for a set of molecules and to examine the role of nuclear quantum effects on the equilibrium geometry of FHF - . The agreement of the computed results with experimental and benchmark values demonstrates the promise of this approach for including nuclear quantum effects in calculations of proton affinities, pK a 's, optimized geometries, and reaction paths.

  2. Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.

    PubMed

    Yilmazer, Nusret Duygu; Korth, Martin

    2016-05-16

    We review the first successes and failures of a "new wave" of quantum chemistry-based approaches to the treatment of protein/ligand interactions. These approaches share the use of "enhanced", dispersion (D), and/or hydrogen-bond (H) corrected density functional theory (DFT) or semi-empirical quantum mechanical (SQM) methods, in combination with ensemble weighting techniques of some form to capture entropic effects. Benchmark and model system calculations in comparison to high-level theoretical as well as experimental references have shown that both DFT-D (dispersion-corrected density functional theory) and SQM-DH (dispersion and hydrogen bond-corrected semi-empirical quantum mechanical) perform much more accurately than older DFT and SQM approaches and also standard docking methods. In addition, DFT-D might soon become and SQM-DH already is fast enough to compute a large number of binding modes of comparably large protein/ligand complexes, thus allowing for a more accurate assessment of entropic effects.

  3. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations.

    PubMed

    Duan, Yong; Wu, Chun; Chowdhury, Shibasish; Lee, Mathew C; Xiong, Guoming; Zhang, Wei; Yang, Rong; Cieplak, Piotr; Luo, Ray; Lee, Taisung; Caldwell, James; Wang, Junmei; Kollman, Peter

    2003-12-01

    Molecular mechanics models have been applied extensively to study the dynamics of proteins and nucleic acids. Here we report the development of a third-generation point-charge all-atom force field for proteins. Following the earlier approach of Cornell et al., the charge set was obtained by fitting to the electrostatic potentials of dipeptides calculated using B3LYP/cc-pVTZ//HF/6-31G** quantum mechanical methods. The main-chain torsion parameters were obtained by fitting to the energy profiles of Ace-Ala-Nme and Ace-Gly-Nme di-peptides calculated using MP2/cc-pVTZ//HF/6-31G** quantum mechanical methods. All other parameters were taken from the existing AMBER data base. The major departure from previous force fields is that all quantum mechanical calculations were done in the condensed phase with continuum solvent models and an effective dielectric constant of epsilon = 4. We anticipate that this force field parameter set will address certain critical short comings of previous force fields in condensed-phase simulations of proteins. Initial tests on peptides demonstrated a high-degree of similarity between the calculated and the statistically measured Ramanchandran maps for both Ace-Gly-Nme and Ace-Ala-Nme di-peptides. Some highlights of our results include (1) well-preserved balance between the extended and helical region distributions, and (2) favorable type-II poly-proline helical region in agreement with recent experiments. Backward compatibility between the new and Cornell et al. charge sets, as judged by overall agreement between dipole moments, allows a smooth transition to the new force field in the area of ligand-binding calculations. Test simulations on a large set of proteins are also discussed. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1999-2012, 2003

  4. Exciton scattering approach for optical spectra calculations in branched conjugated macromolecules

    NASA Astrophysics Data System (ADS)

    Li, Hao; Wu, Chao; Malinin, Sergey V.; Tretiak, Sergei; Chernyak, Vladimir Y.

    2016-12-01

    The exciton scattering (ES) technique is a multiscale approach based on the concept of a particle in a box and developed for efficient calculations of excited-state electronic structure and optical spectra in low-dimensional conjugated macromolecules. Within the ES method, electronic excitations in molecular structure are attributed to standing waves representing quantum quasi-particles (excitons), which reside on the graph whose edges and nodes stand for the molecular linear segments and vertices, respectively. Exciton propagation on the linear segments is characterized by the exciton dispersion, whereas exciton scattering at the branching centers is determined by the energy-dependent scattering matrices. Using these ES energetic parameters, the excitation energies are then found by solving a set of generalized "particle in a box" problems on the graph that represents the molecule. Similarly, unique energy-dependent ES dipolar parameters permit calculations of the corresponding oscillator strengths, thus, completing optical spectra modeling. Both the energetic and dipolar parameters can be extracted from quantum-chemical computations in small molecular fragments and tabulated in the ES library for further applications. Subsequently, spectroscopic modeling for any macrostructure within a considered molecular family could be performed with negligible numerical effort. We demonstrate the ES method application to molecular families of branched conjugated phenylacetylenes and ladder poly-para-phenylenes, as well as structures with electron donor and acceptor chemical substituents. Time-dependent density functional theory (TD-DFT) is used as a reference model for electronic structure. The ES calculations accurately reproduce the optical spectra compared to the reference quantum chemistry results, and make possible to predict spectra of complex macromolecules, where conventional electronic structure calculations are unfeasible.

  5. 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…

  6. Massively parallel sparse matrix function calculations with NTPoly

    NASA Astrophysics Data System (ADS)

    Dawson, William; Nakajima, Takahito

    2018-04-01

    We present NTPoly, a massively parallel library for computing the functions of sparse, symmetric matrices. The theory of matrix functions is a well developed framework with a wide range of applications including differential equations, graph theory, and electronic structure calculations. One particularly important application area is diagonalization free methods in quantum chemistry. When the input and output of the matrix function are sparse, methods based on polynomial expansions can be used to compute matrix functions in linear time. We present a library based on these methods that can compute a variety of matrix functions. Distributed memory parallelization is based on a communication avoiding sparse matrix multiplication algorithm. OpenMP task parallellization is utilized to implement hybrid parallelization. We describe NTPoly's interface and show how it can be integrated with programs written in many different programming languages. We demonstrate the merits of NTPoly by performing large scale calculations on the K computer.

  7. Chemistry in the News: 1998 Nobel Prizes in Chemistry and Medicine

    NASA Astrophysics Data System (ADS)

    Miller, Jennifer B.

    1999-01-01

    The Royal Swedish Academy of Sciences has awarded the 1998 Nobel Prize in Chemistry to Walter Kohn (University of California at Santa Barbara) for his development of the density-functional theory and to John A. Pople (Northwestern University at Evanston, Illinois) for his development of computational methods in quantum chemistry. The Nobel Assembly at the Karolinska Institute has awarded the 1998 Nobel Prize in Physiology or Medicine jointly to Robert F. Fuchgott (State University of New York Health Science Center at Brooklyn), Louis J. Ignarro (University of California at Los Angeles), and Ferid Murad (University of Texas Medical School at Houston) for identifying nitric oxide as a key biological signaling molecule in the cardiovascular system.

  8. Studies on the Conformational Landscape of Tert-Butyl Acetate Using Microwave Spectroscopy and Quantum Chemical Calculations

    NASA Astrophysics Data System (ADS)

    Zhao, YueYue; Mouhib, Halima; Li, Guohua; Stahl, Wolfgang; Kleiner, Isabelle

    2014-06-01

    The tert-Butyl acetate molecule was studied using a combination of quantum chemical calculations and molecular beam Fourier transform microwave spectroscopy in the 9 to 14 GHz range. Due to its rather rigid frame, the molecule possesses only two different conformers: one of Cs and one of C1 symmetry. According to ab initio calculations, the Cs conformer is 46 kJ/mol lower in energy and is the one observed in the supersonic jet. We report on the structure and dynamics of the most abundant conformer of tert-butyl acetate, with accurate rotational and centrifugal distortion constants. Additionally, the barrier to internal rotation of the acetyl methyl group was determined. Splittings due to the internal rotation of the methyl group of up to 1.3 GHz were observed in the spectrum. Using the programs XIAM and BELGI-Cs, we determine the barrier height to be about 113 cm-1 and compare the molecular parameters obtained from these two codes. Additionally, the experimental rotational constants were used to validate numerous quantum chemical calculations. This study is part of a larger project which aims at determining the lowest energy conformers of organic esters and ketones which are of interest for flavor or perfume synthetic applications Project partly supported by the PHC PROCOPE 25059YB.

  9. Consistent Quantum Theory

    NASA Astrophysics Data System (ADS)

    Griffiths, Robert B.

    2001-11-01

    Quantum mechanics is one of the most fundamental yet difficult subjects in physics. Nonrelativistic quantum theory is presented here in a clear and systematic fashion, integrating Born's probabilistic interpretation with Schrödinger dynamics. Basic quantum principles are illustrated with simple examples requiring no mathematics beyond linear algebra and elementary probability theory. The quantum measurement process is consistently analyzed using fundamental quantum principles without referring to measurement. These same principles are used to resolve several of the paradoxes that have long perplexed physicists, including the double slit and Schrödinger's cat. The consistent histories formalism used here was first introduced by the author, and extended by M. Gell-Mann, J. Hartle and R. Omnès. Essential for researchers yet accessible to advanced undergraduate students in physics, chemistry, mathematics, and computer science, this book is supplementary to standard textbooks. It will also be of interest to physicists and philosophers working on the foundations of quantum mechanics. Comprehensive account Written by one of the main figures in the field Paperback edition of successful work on philosophy of quantum mechanics

  10. Substitution Structures of Large Molecules and Medium Range Correlations in Quantum Chemistry Calculations

    NASA Astrophysics Data System (ADS)

    Evangelisti, Luca; Pate, Brooks

    2017-06-01

    A study of the minimally exciting topic of agreement between experimental and measured rotational constants of molecules was performed on a set of large molecules with 16-18 heavy atoms (carbon and oxygen). The molecules are: nootkatone (C_{15}H_{22}O), cedrol (C_{15}H_{26}O), ambroxide (C_{16}H_{28}O), sclareolide (C_{16}H_{22}O_{2}), and dihydroartemisinic acid (C_{15}H_{24}O_{2}). For this set of molecules we obtained 13C-subsitution structures for six molecules (this includes two conformers of nootkatone). A comparison of theoretical structures and experimental substitution structures was performed in the spirit of the recent work of Grimme and Steinmetz.[1] Our analysis focused the center-of-mass distance of the carbon atoms in the molecules. Four different computational methods were studied: standard DFT (B3LYP), dispersion corrected DFT (B3LYP-D3BJ), hybrid DFT with dispersion correction (B2PLYP-D3), and MP2. A significant difference in these theories is how they handle medium range correlation of electrons that produce dispersion forces. For larger molecules, these dispersion forces produce an overall contraction of the molecule around the center-of-mass. DFT poorly treats this effect and produces structures that are too expanded. MP2 calculations overestimate the correction and produce structures that are too compact. Both dispersion corrected DFT methods produce structures in excellent agreement with experiment. The analysis shows that the difference in computational methods can be described by a linear error in the center-of-mass distance. This makes it possible to correct poorer performing calculations with a single scale factor. We also reexamine the issue of the "Costain error" in substitution structures and show that it is significantly larger in these systems than in the smaller molecules used by Costain to establish the error limits. [1] Stefan Grimme and Marc Steinmetz, "Effects of London dispersion correction in density functional theory on

  11. What History Tells Us about the Distinct Nature of Chemistry.

    PubMed

    Chang, Hasok

    2017-11-01

    Attention to the history of chemistry can help us recognise the characteristics of chemistry that have helped to maintain it as a separate scientific discipline with a unique identity. Three such features are highlighted in this paper. First, chemistry has maintained a distinct type of theoretical thinking, independent from that of physics even in the era of quantum chemistry. Second, chemical research has always been shaped by its ineliminable practical relevance and usefulness. Third, the lived experience of chemistry, spanning the laboratory, the classroom and everyday life, is distinctive in its multidimensional sensuousness. Furthermore, I argue that the combination of these three features makes chemistry an exemplary science.

  12. Chemical calculations on Cray computers

    NASA Technical Reports Server (NTRS)

    Taylor, Peter R.; Bauschlicher, Charles W., Jr.; Schwenke, David W.

    1989-01-01

    The influence of recent developments in supercomputing on computational chemistry is discussed with particular reference to Cray computers and their pipelined vector/limited parallel architectures. After reviewing Cray hardware and software the performance of different elementary program structures are examined, and effective methods for improving program performance are outlined. The computational strategies appropriate for obtaining optimum performance in applications to quantum chemistry and dynamics are discussed. Finally, some discussion is given of new developments and future hardware and software improvements.

  13. Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

    DTIC Science & Technology

    2015-07-15

    There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

  14. Quantum-enhanced absorption refrigerators

    PubMed Central

    Correa, Luis A.; Palao, José P.; Alonso, Daniel; Adesso, Gerardo

    2014-01-01

    Thermodynamics is a branch of science blessed by an unparalleled combination of generality of scope and formal simplicity. Based on few natural assumptions together with the four laws, it sets the boundaries between possible and impossible in macroscopic aggregates of matter. This triggered groundbreaking achievements in physics, chemistry and engineering over the last two centuries. Close analogues of those fundamental laws are now being established at the level of individual quantum systems, thus placing limits on the operation of quantum-mechanical devices. Here we study quantum absorption refrigerators, which are driven by heat rather than external work. We establish thermodynamic performance bounds for these machines and investigate their quantum origin. We also show how those bounds may be pushed beyond what is classically achievable, by suitably tailoring the environmental fluctuations via quantum reservoir engineering techniques. Such superefficient quantum-enhanced cooling realises a promising step towards the technological exploitation of autonomous quantum refrigerators. PMID:24492860

  15. Preparation of freezing quantum state for quantum coherence

    NASA Astrophysics Data System (ADS)

    Yang, Lian-Wu; Man, Zhong-Xiao; Zhang, Ying-Jie; Han, Feng; Du, Shao-jiang; Xia, Yun-Jie

    2018-06-01

    We provide a method to prepare the freezing quantum state for quantum coherence via unitary operations. The initial product state consists of the control qubit and target qubit; when it satisfies certain conditions, the initial product state converts into the particular Bell diagonal state under the unitary operations, which have the property of freezing of quantum coherence under quantum channels. We calculate the frozen quantum coherence and corresponding quantum correlations, and find that the quantities are determined by the control qubit only when the freezing phenomena occur.

  16. Spectroscopic, quantum chemical calculation and molecular docking of dipfluzine

    NASA Astrophysics Data System (ADS)

    Srivastava, Karnica; Srivastava, Anubha; Tandon, Poonam; Sinha, Kirti; Wang, Jing

    2016-12-01

    Molecular structure and vibrational analysis of dipfluzine (C27H29FN2O) were presented using FT-IR and FT-Raman spectroscopy and quantum chemical calculations. The theoretical ground state geometry and electronic structure of dipfluzine are optimized by the DFT/B3LYP/6-311++G (d,p) method and compared with those of the crystal data. The 1D potential energy scan was performed by varying the dihedral angle using B3LYP functional at 6-31G(d,p) level of theory and thus the most stable conformer of the compound were determined. Molecular electrostatic potential surface (MEPS), frontier orbital analysis and electronic reactivity descriptor were used to predict the chemical reactivity of molecule. Energies of intra- and inter-molecular hydrogen bonds in molecule and their electronic aspects were investigated by natural bond orbital (NBO). To find out the anti-apoptotic activity of the title compound molecular docking studies have been performed against protein Fas.

  17. Majorana-Based Fermionic Quantum Computation.

    PubMed

    O'Brien, T E; Rożek, P; Akhmerov, A R

    2018-06-01

    Because Majorana zero modes store quantum information nonlocally, they are protected from noise, and have been proposed as a building block for a quantum computer. We show how to use the same protection from noise to implement universal fermionic quantum computation. Our architecture requires only two Majorana modes to encode a fermionic quantum degree of freedom, compared to alternative implementations which require a minimum of four Majorana modes for a spin quantum degree of freedom. The fermionic degrees of freedom support both unitary coupled cluster variational quantum eigensolver and quantum phase estimation algorithms, proposed for quantum chemistry simulations. Because we avoid the Jordan-Wigner transformation, our scheme has a lower overhead for implementing both of these algorithms, allowing for simulation of the Trotterized Hubbard Hamiltonian in O(1) time per unitary step. We finally demonstrate magic state distillation in our fermionic architecture, giving a universal set of topologically protected fermionic quantum gates.

  18. Majorana-Based Fermionic Quantum Computation

    NASA Astrophysics Data System (ADS)

    O'Brien, T. E.; RoŻek, P.; Akhmerov, A. R.

    2018-06-01

    Because Majorana zero modes store quantum information nonlocally, they are protected from noise, and have been proposed as a building block for a quantum computer. We show how to use the same protection from noise to implement universal fermionic quantum computation. Our architecture requires only two Majorana modes to encode a fermionic quantum degree of freedom, compared to alternative implementations which require a minimum of four Majorana modes for a spin quantum degree of freedom. The fermionic degrees of freedom support both unitary coupled cluster variational quantum eigensolver and quantum phase estimation algorithms, proposed for quantum chemistry simulations. Because we avoid the Jordan-Wigner transformation, our scheme has a lower overhead for implementing both of these algorithms, allowing for simulation of the Trotterized Hubbard Hamiltonian in O (1 ) time per unitary step. We finally demonstrate magic state distillation in our fermionic architecture, giving a universal set of topologically protected fermionic quantum gates.

  19. Polyatomic molecular Dirac-Hartree-Fock calculations with Gaussian basis sets

    NASA Technical Reports Server (NTRS)

    Dyall, Kenneth G.; Faegri, Knut, Jr.; Taylor, Peter R.

    1990-01-01

    Numerical methods have been used successfully in atomic Dirac-Hartree-Fock (DHF) calculations for many years. Some DHF calculations using numerical methods have been done on diatomic molecules, but while these serve a useful purpose for calibration, the computational effort in extending this approach to polyatomic molecules is prohibitive. An alternative more in line with traditional quantum chemistry is to use an analytical basis set expansion of the wave function. This approach fell into disrepute in the early 1980's due to problems with variational collapse and intruder states, but has recently been put on firm theoretical foundations. In particular, the problems of variational collapse are well understood, and prescriptions for avoiding the most serious failures have been developed. Consequently, it is now possible to develop reliable molecular programs using basis set methods. This paper describes such a program and reports results of test calculations to demonstrate the convergence and stability of the method.

  20. The challenge of detecting gravitational radiation is creating a new chapter in quantum electronics: Quantum nondemolition measurements

    NASA Technical Reports Server (NTRS)

    Braginsky, V. B.; Vorontsov, Y. I.; Thorne, K. S.

    1979-01-01

    Future gravitational wave antennas will be approximately 100 kilogram cylinders, whose end-to-end vibrations must be measured so accurately (10 to the -19th power centimeters) that they behave quantum mechanically. Moreover, the vibration amplitude must be measured over and over again without perturbing it (quantum nondemolition measurement). This contrasts with quantum chemistry, quantum optics, or atomic, nuclear, and elementary particle physics where measurements are usually made on an ensemble of identical objects, and care is not given to whether any single object is perturbed or destroyed by the measurement. Electronic techniques required for quantum nondemolition measurements are described as well as the theory underlying them.

  1. Energy-consistent small-core pseudopotentials for 3d-transition metals adapted to quantum Monte Carlo calculations.

    PubMed

    Burkatzki, M; Filippi, Claudia; Dolg, M

    2008-10-28

    We extend our recently published set of energy-consistent scalar-relativistic Hartree-Fock pseudopotentials by the 3d-transition metal elements, scandium through zinc. The pseudopotentials do not exhibit a singularity at the nucleus and are therefore suitable for quantum Monte Carlo (QMC) calculations. The pseudopotentials and the accompanying basis sets (VnZ with n=T,Q) are given in standard Gaussian representation and their parameter sets are presented. Coupled cluster, configuration interaction, and QMC studies are carried out for the scandium and titanium atoms and their oxides, demonstrating the good performance of the pseudopotentials. Even though the choice of pseudopotential form is motivated by QMC, these pseudopotentials can also be employed in other quantum chemical approaches.

  2. Cold chemistry with cold molecules

    NASA Astrophysics Data System (ADS)

    Shagam, Yuval

    Low temperature chemistry has been predicted to be dominated by quantum effects, such as shape resonances, where colliding particles exhibit wave-like behavior and tunnel through potential barriers. Observation of these quantum effects provides valuable insight into the microscopic mechanism that governs scattering processes. Our recent advances in the control of neutral supersonic molecular beams, namely merged beam experiments, have enabled continuous tuning of collision energies from the classical regime at room temperature down to 0.01 kelvin, where a quantum description of the dynamics is necessary. I will discuss our use of this technique to study how the dynamics change when molecules participate in collisions, demonstrating the crucial role the molecular quantum rotor plays. We have found that at low temperatures rotational state of the molecule can strongly affect collision dynamics considerably changing reaction rates, due to the different symmetries of the molecular wavefunction.

  3. WavePacket: A Matlab package for numerical quantum dynamics. I: Closed quantum systems and discrete variable representations

    NASA Astrophysics Data System (ADS)

    Schmidt, Burkhard; Lorenz, Ulf

    2017-04-01

    WavePacket is an open-source program package for the numerical simulation of quantum-mechanical dynamics. It can be used to solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semiclassical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. The graphical capabilities allow visualization of quantum dynamics 'on the fly', including Wigner phase space representations. Being easy to use and highly versatile, WavePacket is well suited for the teaching of quantum mechanics as well as for research projects in atomic, molecular and optical physics or in physical or theoretical chemistry. The present Part I deals with the description of closed quantum systems in terms of Schrödinger equations. The emphasis is on discrete variable representations for spatial discretization as well as various techniques for temporal discretization. The upcoming Part II will focus on open quantum systems and dimension reduction; it also describes the codes for optimal control of quantum dynamics. The present work introduces the MATLAB version of WavePacket 5.2.1 which is hosted at the Sourceforge platform, where extensive Wiki-documentation as well as worked-out demonstration examples can be found.

  4. Quantum chemical determination of Young's modulus of lignin. Calculations on a beta-O-4' model compound.

    PubMed

    Elder, Thomas

    2007-11-01

    The calculation of Young's modulus of lignin has been examined by subjecting a dimeric model compound to strain, coupled with the determination of energy and stress. The computational results, derived from quantum chemical calculations, are in agreement with available experimental results. Changes in geometry indicate that modifications in dihedral angles occur in response to linear strain. At larger levels of strain, bond rupture is evidenced by abrupt changes in energy, structure, and charge. Based on the current calculations, the bond scission may be occurring through a homolytic reaction between aliphatic carbon atoms. These results may have implications in the reactivity of lignin especially when subjected to processing methods that place large mechanical forces on the structure.

  5. Intrinsic Folding Proclivities in Cyclic β-Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer-Selective Spectroscopy and Quantum Chemistry.

    PubMed

    Alauddin, Mohammad; Gloaguen, Eric; Brenner, Valérie; Tardivel, Benjamin; Mons, Michel; Zehnacker-Rentien, Anne; Declerck, Valérie; Aitken, David J

    2015-11-09

    This work describes the use of conformer-selective laser spectroscopy following supersonic expansion to probe the local folding proclivities of four-membered ring cyclic β-amino acid building blocks. Emphasis is placed on stereochemical effects as well as on the structural changes induced by the replacement of a carbon atom of the cycle by a nitrogen atom. The amide A IR spectra are obtained and interpreted with the help of quantum chemistry structure calculations. Results provide evidence that the building block with a trans-substituted cyclobutane ring has a predilection to form strong C8 hydrogen bonds. Nitrogen-atom substitution in the ring induces the formation of the hydrazino turn, with a related but distinct hydrogen-bonding network: the structure is best viewed as a bifurcated C8/C5 bond with the N heteroatom lone electron pair playing a significant acceptor role, which supports recent observations on the hydrazino turn structure in solution. Surprisingly, this study shows that the cis-substituted cyclobutane ring derivative also gives rise predominantly to a C8 hydrogen bond, although weaker than in the two former cases, a feature that is not often encountered for this building block. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO

    NASA Astrophysics Data System (ADS)

    Malakkal, Linu; Szpunar, Barbara; Zuniga, Juan Carlos; Siripurapu, Ravi Kiran; Szpunar, Jerzy A.

    2016-05-01

    In this work, we have used Quantum ESPRESSO (QE), an open source first principles code, based on density-functional theory, plane waves, and pseudopotentials, along with quasi-harmonic approximation (QHA) to calculate the thermo-mechanical properties of thorium dioxide (ThO2). Using Python programming language, our group developed qe-nipy-advanced, an interface to QE, which can evaluate the structural and thermo-mechanical properties of materials. We predicted the phonon contribution to thermal conductivity (kL) using the Slack model. We performed the calculations within local density approximation (LDA) and generalized gradient approximation (GGA) with the recently proposed version for solids (PBEsol). We employed a Monkhorst-Pack 5 × 5 × 5 k-points mesh in reciprocal space with a plane wave cut-off energy of 150 Ry to obtain the convergence of the structure. We calculated the dynamical matrices of the lattice on a 4 × 4 × 4 mesh. We have predicted the heat capacity, thermal expansion and the phonon contribution to thermal conductivity, as a function of temperature up to 1400K, and compared them with the previous work and known experimental results.

  7. Laboratory and Theoretical Studies of Tropospheric Iodine Chemistry (Invited)

    NASA Astrophysics Data System (ADS)

    Plane, J. M.; Saunders, R. W.; Kumar, R.; Gomez Martin, J.; Mahajan, A. S.; Murray, B. J.

    2009-12-01

    This paper will discuss progress in understanding two important properties of iodine in the marine boundary layer: ozone depletion and new particle formation. A variety of laboratory techniques have been employed to study the kinetics and growth of iodine oxide particles, their uptake of water, sulphuric and organic acids, and the recyling of iodine from them. The photochemistry of a variety of iodine oxides, which are central to catalytic O3 depletion and are involved in homogeneous condensation, will also be described. The use of high-level quantum chemistry calculations to underpin these experiments will then be discussed. Finally, the implications of this work for understanding the impact of iodine in both remote and polluted marine environments will be considered.

  8. Canonical partition functions: ideal quantum gases, interacting classical gases, and interacting quantum gases

    NASA Astrophysics Data System (ADS)

    Zhou, Chi-Chun; Dai, Wu-Sheng

    2018-02-01

    In statistical mechanics, for a system with a fixed number of particles, e.g. a finite-size system, strictly speaking, the thermodynamic quantity needs to be calculated in the canonical ensemble. Nevertheless, the calculation of the canonical partition function is difficult. In this paper, based on the mathematical theory of the symmetric function, we suggest a method for the calculation of the canonical partition function of ideal quantum gases, including ideal Bose, Fermi, and Gentile gases. Moreover, we express the canonical partition functions of interacting classical and quantum gases given by the classical and quantum cluster expansion methods in terms of the Bell polynomial in mathematics. The virial coefficients of ideal Bose, Fermi, and Gentile gases are calculated from the exact canonical partition function. The virial coefficients of interacting classical and quantum gases are calculated from the canonical partition function by using the expansion of the Bell polynomial, rather than calculated from the grand canonical potential.

  9. Adaptations in Electronic Structure Calculations in Heterogeneous Environments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Talamudupula, Sai

    Modern quantum chemistry deals with electronic structure calculations of unprecedented complexity and accuracy. They demand full power of high-performance computing and must be in tune with the given architecture for superior e ciency. To make such applications resourceaware, it is desirable to enable their static and dynamic adaptations using some external software (middleware), which may monitor both system availability and application needs, rather than mix science with system-related calls inside the application. The present work investigates scienti c application interlinking with middleware based on the example of the computational chemistry package GAMESS and middleware NICAN. The existing synchronous model ismore » limited by the possible delays due to the middleware processing time under the sustainable runtime system conditions. Proposed asynchronous and hybrid models aim at overcoming this limitation. When linked with NICAN, the fragment molecular orbital (FMO) method is capable of adapting statically and dynamically its fragment scheduling policy based on the computing platform conditions. Signi cant execution time and throughput gains have been obtained due to such static adaptations when the compute nodes have very di erent core counts. Dynamic adaptations are based on the main memory availability at run time. NICAN prompts FMO to postpone scheduling certain fragments, if there is not enough memory for their immediate execution. Hence, FMO may be able to complete the calculations whereas without such adaptations it aborts.« less

  10. Impact of Surface Functionalization on the Quantum Coherence of Nitrogen-Vacancy Centers in Nanodiamonds.

    PubMed

    Ryan, Robert G; Stacey, Alastair; O'Donnell, Kane M; Ohshima, Takeshi; Johnson, Brett C; Hollenberg, Lloyd C L; Mulvaney, Paul; Simpson, David A

    2018-04-18

    Nanoscale quantum probes such as the nitrogen-vacancy (NV) center in diamonds have demonstrated remarkable sensing capabilities over the past decade as control over fabrication and manipulation of these systems has evolved. The biocompatibility and rich surface chemistry of diamonds has added to the utility of these probes but, as the size of these nanoscale systems is reduced, the surface chemistry of diamond begins to impact the quantum properties of the NV center. In this work, we systematically study the effect of the diamond surface chemistry on the quantum coherence of the NV center in nanodiamonds (NDs) 50 nm in size. Our results show that a borane-reduced diamond surface can on average double the spin relaxation time of individual NV centers in nanodiamonds when compared to thermally oxidized surfaces. Using a combination of infrared and X-ray absorption spectroscopy techniques, we correlate the changes in quantum relaxation rates with the conversion of sp 2 carbon to C-O and C-H bonds on the diamond surface. These findings implicate double-bonded carbon species as a dominant source of spin noise for near surface NV centers. The link between the surface chemistry and quantum coherence indicates that through tailored engineering of the surface, the quantum properties and magnetic sensitivity of these nanoscale systems may approach that observed in bulk diamond.

  11. The calculation of quality indices of the water heat carrier and estimation of the condition of water chemistry of drum boilers

    NASA Astrophysics Data System (ADS)

    Larin, B. M.; Larin, A. B.; Kozyulina, E. V.; Kolegov, A. V.

    2012-07-01

    There is suggested a method for an indirect calculated identification of ionic impurities in water of drum boilers ( p b = 13.8 MPa) by means of measuring the electric conductivity of cooled samples (direct and H-cationized ones) of the feedwater and drum water. This paper reports the results of an industrial experiment carried out on the drum power boiler during the entire heating season. The possibility of evaluating the condition of the water chemistry, with plotting a phase diagram of the phosphate-based water chemistry and determining characteristic dependences, is shown.

  12. Benchmarking quantum mechanical calculations with experimental NMR chemical shifts of 2-HADNT

    NASA Astrophysics Data System (ADS)

    Liu, Yuemin; Junk, Thomas; Liu, Yucheng; Tzeng, Nianfeng; Perkins, Richard

    2015-04-01

    In this study, both GIAO-DFT and GIAO-MP2 calculations of nuclear magnetic resonance (NMR) spectra were benchmarked with experimental chemical shifts. The experimental chemical shifts were determined experimentally for carbon-13 (C-13) of seven carbon atoms for the TNT degradation product 2-hydroxylamino-4,6-dinitrotoluene (2-HADNT). Quantum mechanics GIAO calculations were implemented using Becke-3-Lee-Yang-Parr (B3LYP) and other six hybrid DFT methods (Becke-1-Lee-Yang-Parr (B1LYP), Becke-half-and-half-Lee-Yang-Parr (BH and HLYP), Cohen-Handy-3-Lee-Yang-Parr (O3LYP), Coulomb-attenuating-B3LYP (CAM-B3LYP), modified-Perdew-Wang-91-Lee-Yang-Parr (mPW1LYP), and Xu-3-Lee-Yang-Parr (X3LYP)) which use the same correlation functional LYP. Calculation results showed that the GIAO-MP2 method gives the most accurate chemical shift values, and O3LYP method provides the best prediction of chemical shifts among the B3LYP and other five DFT methods. Three types of atomic partial charges, Mulliken (MK), electrostatic potential (ESP), and natural bond orbital (NBO), were also calculated using MP2/aug-cc-pVDZ method. A reasonable correlation was discovered between NBO partial charges and experimental chemical shifts of carbon-13 (C-13).

  13. Hybrid quantum and molecular mechanics embedded cluster models for chemistry on silicon and silicon carbide surfaces

    NASA Astrophysics Data System (ADS)

    Shoemaker, James Richard

    Fabrication of silicon carbide (SiC) semiconductor devices are of interest for aerospace applications because of their high-temperature tolerance. Growth of an insulating SiO2 layer on SiC by oxidation is a poorly understood process, and sometimes produces interface defects that degrade device performance. Accurate theoretical models of surface chemistry, using quantum mechanics (QM), do not exist because of the huge computational cost of solving Schrodinger's equation for a molecular cluster large enough to represent a surface. Molecular mechanics (MM), which describes a molecule as a collection of atoms interacting through classical potentials, is a fast computational method, good at predicting molecular structure, but cannot accurately model chemical reactions. A new hybrid QM/MM computational method for surface chemistry was developed and applied to silicon and SiC surfaces. The addition of MM steric constraints was shown to have a large effect on the energetics of O atom adsorption on SiC. Adsorption of O atoms on Si-terminated SiC(111) favors above surface sites, in contrast to Si(111), but favors subsurface adsorption sites on C- terminated SiC(111). This difference, and the energetics of C atom etching via CO2 desorption, can explain the observed poor performance of SiC devices in which insulating layers were grown on C-terminated surfaces.

  14. Comment on "Modified quantum-speed-limit bounds for open quantum dynamics in quantum channels"

    NASA Astrophysics Data System (ADS)

    Mirkin, Nicolás; Toscano, Fabricio; Wisniacki, Diego A.

    2018-04-01

    In a recent paper [Phys. Rev. A 95, 052118 (2017), 10.1103/PhysRevA.95.052118], the authors claim that our criticism, in Phys. Rev. A 94, 052125 (2016), 10.1103/PhysRevA.94.052125, to some quantum speed limit bounds for open quantum dynamics that appeared recently in literature are invalid. According to the authors, the problem with our analysis would be generated by an artifact of the finite-precision numerical calculations. We analytically show here that it is not possible to have any inconsistency associated with the numerical precision of calculations. Therefore, our criticism of the quantum speed limit bounds continues to be valid.

  15. QMC Goes BOINC: Using Public Resource Computing to Perform Quantum Monte Carlo Calculations

    NASA Astrophysics Data System (ADS)

    Rainey, Cameron; Engelhardt, Larry; Schröder, Christian; Hilbig, Thomas

    2008-10-01

    Theoretical modeling of magnetic molecules traditionally involves the diagonalization of quantum Hamiltonian matrices. However, as the complexity of these molecules increases, the matrices become so large that this process becomes unusable. An additional challenge to this modeling is that many repetitive calculations must be performed, further increasing the need for computing power. Both of these obstacles can be overcome by using a quantum Monte Carlo (QMC) method and a distributed computing project. We have recently implemented a QMC method within the Spinhenge@home project, which is a Public Resource Computing (PRC) project where private citizens allow part-time usage of their PCs for scientific computing. The use of PRC for scientific computing will be described in detail, as well as how you can contribute to the project. See, e.g., L. Engelhardt, et. al., Angew. Chem. Int. Ed. 47, 924 (2008). C. Schröoder, in Distributed & Grid Computing - Science Made Transparent for Everyone. Principles, Applications and Supporting Communities. (Weber, M.H.W., ed., 2008). Project URL: http://spin.fh-bielefeld.de

  16. Elucidating Reaction Mechanisms on Quantum Computers

    NASA Astrophysics Data System (ADS)

    Wiebe, Nathan; Reiher, Markus; Svore, Krysta; Wecker, Dave; Troyer, Matthias

    We show how a quantum computer can be employed to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical-computer simulations for such problems, to significantly increase their accuracy and enable hitherto intractable simulations. Detailed resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. This demonstrates that quantum computers will realistically be able to tackle important problems in chemistry that are both scientifically and economically significant.

  17. Compression selective solid-state chemistry

    NASA Astrophysics Data System (ADS)

    Hu, Anguang

    Compression selective solid-state chemistry refers to mechanically induced selective reactions of solids under thermomechanical extreme conditions. Advanced quantum solid-state chemistry simulations, based on density functional theory with localized basis functions, were performed to provide a remarkable insight into bonding pathways of high-pressure chemical reactions in all agreement with experiments. These pathways clearly demonstrate reaction mechanisms in unprecedented structural details, showing not only the chemical identity of reactive intermediates but also how atoms move along the reaction coordinate associated with a specific vibrational mode, directed by induced chemical stress occurred during bond breaking and forming. It indicates that chemical bonds in solids can break and form precisely under compression as we wish. This can be realized through strongly coupling of mechanical work to an initiation vibrational mode when all other modes can be suppressed under compression, resulting in ultrafast reactions to take place isothermally in a few femtoseconds. Thermodynamically, such reactions correspond to an entropy minimum process on an isotherm where the compression can force thermal expansion coefficient equal to zero. Combining a significantly brief reaction process with specific mode selectivity, both statistical laws and quantum uncertainty principle can be bypassed to precisely break chemical bonds, establishing fundamental principles of compression selective solid-state chemistry. Naturally this leads to understand the ''alchemy'' to purify, grow, and perfect certain materials such as emerging novel disruptive energetics.

  18. Ab Initio Studies of Stratospheric Ozone Depletion Chemistry

    NASA Technical Reports Server (NTRS)

    Lee, Timothy J.; Head-Gordon, Martin; Langhoff, Stephen R. (Technical Monitor)

    1995-01-01

    An overview of the current understanding of ozone depletion chemistry, particularly with regards the formation of the so-called Antarctic ozone hole, will be presented together with an outline as to how ab initio quantum chemistry can be used to further our understanding of stratospheric chemistry. The ability of modern state-of-the art ab initio quantum chemical techniques to characterize reliably the gas-phase molecular structure, vibrational spectrum, electronic spectrum, and thermal stability of fluorine, chlorine, bromine and nitrogen oxide species will be demonstrated by presentation of some example studies. The ab initio results will be shown to be in excellent agreement with the available experimental data, and where the experimental data are either not known or are inconclusive, the theoretical results are shown to fill in the gaps and to resolve experimental controversies. In addition, ab initio studies in which the electronic spectra and the characterization of excited electronic states of halogen oxide species will also be presented. Again where available, the ab initio results are compared to experimental observations, and are used to aid in the interpretation of experimental studies.

  19. Spectroscopy and Chemistry of Cold Molecules

    NASA Astrophysics Data System (ADS)

    Momose, Takamasa

    2012-06-01

    Molecules at low temperatures are expected to behave quite differently from those at high temperatures because pronounced quantum effects emerge from thermal averages. Even at 10 K, a significant enhancement of reaction cross section is expected due to tunneling and resonance effects. Chemistry at this temperature is very important in order to understand chemical reactions in interstellar molecular clouds. At temperatures lower than 1 K, collisions and intermolecular interactions become qualitatively different from those at high temperatures because of the large thermal de Broglie wavelength of molecules. Collisions at these temperatures must be treated as the interference of molecular matter waves, but not as hard sphere collisions. A Bose-Einstein condensate is a significant state of matter as a result of coherent matter wave interaction. Especially, dense para-H_2 molecules are predicted to become a condensate even around 1 K. A convenient method to investigate molecules around 1 K is to dope molecules in cold matrices. Among various matrices, quantum hosts such as solid para-H_2 and superfluid He nano-droplets have been proven to be an excellent host for high-resolution spectroscopy. Rovibrational motion of molecules in these quantum hosts is well quantized on account of the weak interactions and the softness of quantum environment. The linewidths of infrared spectra of molecules in the quantum hosts are extremely narrow compared with those in other matrices. The sharp linewidths allow us to resolve fine spectral structures originated in subtle interactions between guest and host molecules. In this talk, I will describe how the splitting and lineshape of high-resolution spectra of molecules in quantum hosts give us new information on the static and dynamical interactions of molecules in quantum medium. The topics include dynamical response of superfluid environment upon rotational excitation, and possible superfluid phase of para-H_2 clusters. I will also

  20. 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)

  1. Quantum mechanical calculations related to ionization and charge transfer in DNA

    NASA Astrophysics Data System (ADS)

    Cauët, E.; Valiev, M.; Weare, J. H.; Liévin, J.

    2012-07-01

    Ionization and charge migration in DNA play crucial roles in mechanisms of DNA damage caused by ionizing radiation, oxidizing agents and photo-irradiation. Therefore, an evaluation of the ionization properties of the DNA bases is central to the full interpretation and understanding of the elementary reactive processes that occur at the molecular level during the initial exposure and afterwards. Ab initio quantum mechanical (QM) methods have been successful in providing highly accurate evaluations of key parameters, such as ionization energies (IE) of DNA bases. Hence, in this study, we performed high-level QM calculations to characterize the molecular energy levels and potential energy surfaces, which shed light on ionization and charge migration between DNA bases. In particular, we examined the IEs of guanine, the most easily oxidized base, isolated and embedded in base clusters, and investigated the mechanism of charge migration over two and three stacked guanines. The IE of guanine in the human telomere sequence has also been evaluated. We report a simple molecular orbital analysis to explain how modifications in the base sequence are expected to change the efficiency of the sequence as a hole trap. Finally, the application of a hybrid approach combining quantum mechanics with molecular mechanics brings an interesting discussion as to how the native aqueous DNA environment affects the IE threshold of nucleobases.

  2. Quantum mechanical calculations of vibrational population inversion in chemical reactions - Numerically exact L-squared-amplitude-density study of the H2Br reactive system

    NASA Technical Reports Server (NTRS)

    Zhang, Y. C.; Zhang, J. Z. H.; Kouri, D. J.; Haug, K.; Schwenke, D. W.

    1988-01-01

    Numerically exact, fully three-dimensional quantum mechanicl reactive scattering calculations are reported for the H2Br system. Both the exchange (H + H-prime Br to H-prime + HBr) and abstraction (H + HBR to H2 + Br) reaction channels are included in the calculations. The present results are the first completely converged three-dimensional quantum calculations for a system involving a highly exoergic reaction channel (the abstraction process). It is found that the production of vibrationally hot H2 in the abstraction reaction, and hence the extent of population inversion in the products, is a sensitive function of initial HBr rotational state and collision energy.

  3. Assessing Advanced High School and Undergraduate Students' Thinking Skills: The Chemistry--From the Nanoscale to Microelectronics Module

    ERIC Educational Resources Information Center

    Dori, Yehudit Judy; Dangur, Vered; Avargil, Shirly; Peskin, Uri

    2014-01-01

    Chemistry students in Israel have two options for studying chemistry: basic or honors (advanced placement). For instruction in high school honors chemistry courses, we developed a module focusing on abstract topics in quantum mechanics: Chemistry--From the Nanoscale to Microelectronics. The module adopts a visual-conceptual approach, which…

  4. The Use of Gas Chromatography and Mass Spectrometry to Introduce General Chemistry Students to Percent Mass and Atomic Mass Calculations

    ERIC Educational Resources Information Center

    Pfennig, Brian W.; Schaefer, Amy K.

    2011-01-01

    A general chemistry laboratory experiment is described that introduces students to instrumental analysis using gas chromatography-mass spectrometry (GC-MS), while simultaneously reinforcing the concepts of mass percent and the calculation of atomic mass. Working in small groups, students use the GC to separate and quantify the percent composition…

  5. 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

  6. Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

    PubMed

    Mazack, Michael J M; Gao, Jiali

    2014-05-28

    The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

  7. An Introduction to Quantum Theory

    NASA Astrophysics Data System (ADS)

    Greensite, Jeff

    2017-02-01

    Written in a lucid and engaging style, the author takes readers from an overview of classical mechanics and the historical development of quantum theory through to advanced topics. The mathematical aspects of quantum theory necessary for a firm grasp of the subject are developed in the early chapters, but an effort is made to motivate that formalism on physical grounds. Including animated figures and their respective Mathematica® codes, this book provides a complete and comprehensive text for students in physics, maths, chemistry and engineering needing an accessible introduction to quantum mechanics. Supplementary Mathematica codes available within Book Information

  8. Elucidating reaction mechanisms on quantum computers.

    PubMed

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M; Wecker, Dave; Troyer, Matthias

    2017-07-18

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  9. Elucidating reaction mechanisms on quantum computers

    PubMed Central

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-01-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources. PMID:28674011

  10. Elucidating reaction mechanisms on quantum computers

    NASA Astrophysics Data System (ADS)

    Reiher, Markus; Wiebe, Nathan; Svore, Krysta M.; Wecker, Dave; Troyer, Matthias

    2017-07-01

    With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

  11. Electronic structure calculations of PbS quantum rods and tubes

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pimachev, Artem; Dahnovsky, Yuri, E-mail: yurid@uwyo.edu

    2014-01-28

    We study absorption spectra, optical and HOMO-LUMO gaps, and the density of states for PbS quantum rods (QRs) and tubes (QTs). We find some similarities and also differences in QR and QT properties. For both QRs and QTs, the optical and HOMO-LUMO gaps reach the plateaus for small lengths. We find that tubes are as stable as rods. The optical spectra exhibit a peak that can be due to the electron-hole interaction or be a prototype of an S{sub e}–S{sub h} transition in the effective mass approximation. We also calculate the density of states by the density functional theory (DFT)more » and time-dependent density functional theory (TDDFT) methods. The TDDFT density of states function is shifted towards the red side by 0.5 eV indicating the strong e-h interaction.« less

  12. Wang-Landau method for calculating Rényi entropies in finite-temperature quantum Monte Carlo simulations.

    PubMed

    Inglis, Stephen; Melko, Roger G

    2013-01-01

    We implement a Wang-Landau sampling technique in quantum Monte Carlo (QMC) simulations for the purpose of calculating the Rényi entanglement entropies and associated mutual information. The algorithm converges an estimate for an analog to the density of states for stochastic series expansion QMC, allowing a direct calculation of Rényi entropies without explicit thermodynamic integration. We benchmark results for the mutual information on two-dimensional (2D) isotropic and anisotropic Heisenberg models, a 2D transverse field Ising model, and a three-dimensional Heisenberg model, confirming a critical scaling of the mutual information in cases with a finite-temperature transition. We discuss the benefits and limitations of broad sampling techniques compared to standard importance sampling methods.

  13. DOE pushes for useful quantum computing

    NASA Astrophysics Data System (ADS)

    Cho, Adrian

    2018-01-01

    The U.S. Department of Energy (DOE) is joining the quest to develop quantum computers, devices that would exploit quantum mechanics to crack problems that overwhelm conventional computers. The initiative comes as Google and other companies race to build a quantum computer that can demonstrate "quantum supremacy" by beating classical computers on a test problem. But reaching that milestone will not mean practical uses are at hand, and the new $40 million DOE effort is intended to spur the development of useful quantum computing algorithms for its work in chemistry, materials science, nuclear physics, and particle physics. With the resources at its 17 national laboratories, DOE could play a key role in developing the machines, researchers say, although finding problems with which quantum computers can help isn't so easy.

  14. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein.

    PubMed

    Nåbo, Lina J; Olsen, Jógvan Magnus Haugaard; Martínez, Todd J; Kongsted, Jacob

    2017-12-12

    The calculation of spectral properties for photoactive proteins is challenging because of the large cost of electronic structure calculations on large systems. Mixed quantum mechanical (QM) and molecular mechanical (MM) methods are typically employed to make such calculations computationally tractable. This study addresses the connection between the minimal QM region size and the method used to model the MM region in the calculation of absorption properties-here exemplified for calculations on the green fluorescent protein. We find that polarizable embedding is necessary for a qualitatively correct description of the MM region, and that this enables the use of much smaller QM regions compared to fixed charge electrostatic embedding. Furthermore, absorption intensities converge very slowly with system size and inclusion of effective external field effects in the MM region through polarizabilities is therefore very important. Thus, this embedding scheme enables accurate prediction of intensities for systems that are too large to be treated fully quantum mechanically.

  15. A quantum–quantum Metropolis algorithm

    PubMed Central

    Yung, Man-Hong; Aspuru-Guzik, Alán

    2012-01-01

    The classical Metropolis sampling method is a cornerstone of many statistical modeling applications that range from physics, chemistry, and biology to economics. This method is particularly suitable for sampling the thermal distributions of classical systems. The challenge of extending this method to the simulation of arbitrary quantum systems is that, in general, eigenstates of quantum Hamiltonians cannot be obtained efficiently with a classical computer. However, this challenge can be overcome by quantum computers. Here, we present a quantum algorithm which fully generalizes the classical Metropolis algorithm to the quantum domain. The meaning of quantum generalization is twofold: The proposed algorithm is not only applicable to both classical and quantum systems, but also offers a quantum speedup relative to the classical counterpart. Furthermore, unlike the classical method of quantum Monte Carlo, this quantum algorithm does not suffer from the negative-sign problem associated with fermionic systems. Applications of this algorithm include the study of low-temperature properties of quantum systems, such as the Hubbard model, and preparing the thermal states of sizable molecules to simulate, for example, chemical reactions at an arbitrary temperature. PMID:22215584

  16. Some foundational aspects of quantum computers and quantum robots.

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Benioff, P.; Physics

    1998-01-01

    This paper addresses foundational issues related to quantum computing. The need for a universally valid theory such as quantum mechanics to describe to some extent its own validation is noted. This includes quantum mechanical descriptions of systems that do theoretical calculations (i.e. quantum computers) and systems that perform experiments. Quantum robots interacting with an environment are a small first step in this direction. Quantum robots are described here as mobile quantum systems with on-board quantum computers that interact with environments. Included are discussions on the carrying out of tasks and the division of tasks into computation and action phases. Specificmore » models based on quantum Turing machines are described. Differences and similarities between quantum robots plus environments and quantum computers are discussed.« less

  17. The Effect of Non-equilibrium Kinetics on Oxygen Chemistry in the Interstellar Medium

    NASA Technical Reports Server (NTRS)

    Naduvalath, Balakrishnan

    2006-01-01

    It has been suggested that in photon-dominated regions, oxygen chemistry is initiated by the O+H2 yields OH+H reaction. The reaction has an energy barrier of about 0.4 eV with ground state reactants and it is slow at low temperatures. There is strong experimental evidence that vibrational excitation of the H2 molecule increases the reactivity significantly. We present extensive quantum calculations of cross sections and rate coefficients for the O+H2(v) reaction for v = 0 - 3 of the H2 molecule and show that the vibrational excitation of the molecule has a significant effect on reactivity, especially at low temperatures.

  18. Quantum Foundations of Quantum Information

    NASA Astrophysics Data System (ADS)

    Griffiths, Robert

    2009-03-01

    The main foundational issue for quantum information is: What is quantum information about? What does it refer to? Classical information typically refers to physical properties, and since classical is a subset of quantum information (assuming the world is quantum mechanical), quantum information should--and, it will be argued, does--refer to quantum physical properties represented by projectors on appropriate subspaces of a quantum Hilbert space. All sorts of microscopic and macroscopic properties, not just measurement outcomes, can be represented in this way, and are thus a proper subject of quantum information. The Stern-Gerlach experiment illustrates this. When properties are compatible, which is to say their projectors commute, Shannon's classical information theory based on statistical correlations extends without difficulty or change to the quantum case. When projectors do not commute, giving rise to characteristic quantum effects, a foundation for the subject can still be constructed by replacing the ``measurement and wave-function collapse'' found in textbooks--an efficient calculational tool, but one giving rise to numerous conceptual difficulties--with a fully consistent and paradox free stochastic formulation of standard quantum mechanics. This formulation is particularly helpful in that it contains no nonlocal superluminal influences; the reason the latter carry no information is that they do not exist.

  19. Interactive Simulations to Support Quantum Mechanics Instruction for Chemistry Students

    ERIC Educational Resources Information Center

    Kohnle, Antje; Benfield, Cory; Hahner, Georg; Paetkau, Mark

    2017-01-01

    The QuVis Quantum Mechanics Visualization Project provides freely available research-based interactive simulations with accompanying activities for the teaching and learning of quantum mechanics across a wide range of topics and levels. This article gives an overview of some of the simulations and describes their use in an introductory physical…

  20. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    The application of the local basis equation (Ferenczy and Adams, J. Chem. Phys. 2009, 130, 134108) in mixed quantum mechanics/molecular mechanics (QM/MM) and quantum mechanics/quantum mechanics (QM/QM) methods is investigated. This equation is suitable to derive local basis nonorthogonal orbitals that minimize the energy of the system and it exhibits good convergence properties in a self-consistent field solution. These features make the equation appropriate to be used in mixed QM/MM and QM/QM methods to optimize orbitals in the field of frozen localized orbitals connecting the subsystems. Calculations performed for several properties in divers systems show that the method is robust with various choices of the frozen orbitals and frontier atom properties. With appropriate basis set assignment, it gives results equivalent with those of a related approach [G. G. Ferenczy previous paper in this issue] using the Huzinaga equation. Thus, the local basis equation can be used in mixed QM/MM methods with small size quantum subsystems to calculate properties in good agreement with reference Hartree-Fock-Roothaan results. It is shown that bond charges are not necessary when the local basis equation is applied, although they are required for the self-consistent field solution of the Huzinaga equation based method. Conversely, the deformation of the wave-function near to the boundary is observed without bond charges and this has a significant effect on deprotonation energies but a less pronounced effect when the total charge of the system is conserved. The local basis equation can also be used to define a two layer quantum system with nonorthogonal localized orbitals surrounding the central delocalized quantum subsystem. Copyright © 2013 Wiley Periodicals, Inc.

  1. On the Use of a Mixed Gaussian/Finite-Element Basis Set for the Calculation of Rydberg States

    NASA Technical Reports Server (NTRS)

    Thuemmel, Helmar T.; Langhoff, Stephen (Technical Monitor)

    1996-01-01

    Configuration-interaction studies are reported for the Rydberg states of the helium atom using mixed Gaussian/finite-element (GTO/FE) one particle basis sets. Standard Gaussian valence basis sets are employed, like those, used extensively in quantum chemistry calculations. It is shown that the term values for high-lying Rydberg states of the helium atom can be obtained accurately (within 1 cm -1), even for a small GTO set, by augmenting the n-particle space with configurations, where orthonormalized interpolation polynomials are singly occupied.

  2. Increasing the efficiency and accuracy of time-resolved electronic spectra calculations with on-the-fly ab initio quantum dynamics methods

    NASA Astrophysics Data System (ADS)

    Vanicek, Jiri

    2014-03-01

    Rigorous quantum-mechanical calculations of coherent ultrafast electronic spectra remain difficult. I will present several approaches developed in our group that increase the efficiency and accuracy of such calculations: First, we justified the feasibility of evaluating time-resolved spectra of large systems by proving that the number of trajectories needed for convergence of the semiclassical dephasing representation/phase averaging is independent of dimensionality. Recently, we further accelerated this approximation with a cellular scheme employing inverse Weierstrass transform and optimal scaling of the cell size. The accuracy of potential energy surfaces was increased by combining the dephasing representation with accurate on-the-fly ab initio electronic structure calculations, including nonadiabatic and spin-orbit couplings. Finally, the inherent semiclassical approximation was removed in the exact quantum Gaussian dephasing representation, in which semiclassical trajectories are replaced by communicating frozen Gaussian basis functions evolving classically with an average Hamiltonian. Among other examples I will present an on-the-fly ab initio semiclassical dynamics calculation of the dispersed time-resolved stimulated emission spectrum of the 54-dimensional azulene. This research was supported by EPFL and by the Swiss National Science Foundation NCCR MUST (Molecular Ultrafast Science and Technology) and Grant No. 200021124936/1.

  3. Improving Density Functionals with Quantum Harmonic Oscillators

    NASA Astrophysics Data System (ADS)

    Tkatchenko, Alexandre

    2013-03-01

    Density functional theory (DFT) is the most widely used and successful approach for electronic structure calculations. However, one of the pressing challenges for DFT is developing efficient functionals that can accurately capture the omnipresent long-range electron correlations, which determine the structure and stability of many molecules and materials. Here we show that, under certain conditions, the problem of computing the long-range correlation energy of interacting electrons can be mapped to a system of coupled quantum harmonic oscillators (QHOs). The proposed model allows us to synergistically combine concepts from DFT, quantum chemistry, and the widely discussed random-phase approximation for the correlation energy. In the dipole limit, the interaction energy for a system of coupled QHOs can be calculated exactly, thereby leading to an efficient and accurate model for the many-body dispersion energy of complex molecules and materials. The studied examples include intermolecular binding energies, the conformational hierarchy of DNA structures, the geometry and stability of molecular crystals, and supramolecular host-guest complexes (A. Tkatchenko, R. A. DiStasio Jr., R. Car, M. Scheffler, Phys. Rev. Lett. 108, 236402 (2012); R. A. DiStasio Jr., A. von Lilienfeld, A. Tkatchenko, PNAS 109, 14791 (2012); A. Tkatchenko, D. Alfe, K. S. Kim, J. Chem. Theory and Comp. (2012), doi: 10.1021/ct300711r; A. Tkatchenko, A. Ambrosetti, R. A. DiStasio Jr., arXiv:1210.8343v1).

  4. Inhibition of the checkpoint protein PD-1 by the therapeutic antibody pembrolizumab outlined by quantum chemistry.

    PubMed

    Tavares, Ana Beatriz M L A; Lima Neto, José X; Fulco, Umberto L; Albuquerque, Eudenilson L

    2018-01-30

    Much of the recent excitement in the cancer immunotherapy approach has been generated by the recognition that immune checkpoint proteins, like the receptor PD-1, can be blocked by antibody-based drugs with profound effects. Promising clinical data have already been released pointing to the efficiency of the drug pembrolizumab to block the PD-1 pathway, triggering the T-lymphocytes to destroy the cancer cells. Thus, a deep understanding of this drug/receptor complex is essential for the improvement of new drugs targeting the protein PD-1. In this context, by employing quantum chemistry methods based on the Density Functional Theory (DFT), we investigate in silico the binding energy features of the receptor PD-1 in complex with its drug inhibitor. Our computational results give a better understanding of the binding mechanisms, being also an efficient alternative towards the development of antibody-based drugs, pointing to new treatments for cancer therapy.

  5. Quantum chemical calculations in the structural analysis of phloretin

    NASA Astrophysics Data System (ADS)

    Gómez-Zavaglia, Andrea

    2009-07-01

    In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

  6. Communication: Quantum six-dimensional calculations of the coupled translation-rotation eigenstates of H{sub 2}O@C{sub 60}

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Felker, Peter M., E-mail: felker@chem.ucla.edu; Bačić, Zlatko, E-mail: zlatko.bacic@nyu.edu; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, 3663 Zhongshan Road North, Shanghai 200062

    2016-05-28

    We report rigorous quantum calculations of the translation-rotation (TR) eigenstates of para- and ortho-H{sub 2}O@C{sub 60}. They provide a comprehensive description of the dynamical behavior of H{sub 2}O inside the fullerene having icosahedral (I{sub h}) symmetry. The TR eigenstates are assigned in terms of the irreducible representations of the proper symmetry group of H{sub 2}O@C{sub 60}, as well as the appropriate translational and rotational quantum numbers. The coupling between the orbital and the rotational angular momenta of the caged H{sub 2}O gives rise to the total angular momentum λ, which additionally labels each TR level. The calculated TR levels allowmore » tentative assignments of a number of transitions in the recent experimental INS spectra of H{sub 2}O@C{sub 60} that have not been assigned previously.« less

  7. Water catalysis and anticatalysis in photochemical reactions: observation of a delayed threshold effect in the reaction quantum yield.

    PubMed

    Kramer, Zeb C; Takahashi, Kaito; Skodje, Rex T

    2010-11-03

    The possible catalysis of photochemical reactions by water molecules is considered. Using theoretical simulations, we investigate the HF-elimination reaction of fluoromethanol in small water clusters initiated by the overtone excitation of the hydroxyl group. The reaction occurs in competition with the process of water evaporation that dissipates the excitation and quenches the reaction. Although the transition state barrier is stabilized by over 20 kcal/mol through hydrogen bonding with water, the quantum yield versus energy shows a pronounced delayed threshold that effectively eliminates the catalytic effect. It is concluded that the quantum chemistry calculations of barrier lowering are not sufficient to infer water catalysis in some photochemical reactions, which instead require dynamical modeling.

  8. What's on the Surface? Physics and Chemistry of Delta-Doped Surfaces

    NASA Technical Reports Server (NTRS)

    Hoenk, Michael

    2011-01-01

    Outline of presentation: 1. Detector surfaces and the problem of stability 2. Delta-doped detectors 3. Physics of Delta-doped Silicon 4. Chemistry of the Si-SiO2 Interface 5. Physics and Chemistry of Delta-doped Surfaces a. Compensation b. Inversion c. Quantum exclusion. Conclusions: 1. Quantum confinement of electrons and holes dominates the behavior of delta-doped surfaces. 2. Stability of delta-doped detectors: Delta-layer creates an approx 1 eV tunnel barrier between bulk and surface. 3. At high surface charge densities, Tamm-Shockley states form at the surface. 4. Surface passivation by quantum exclusion: Near-surface delta-layer suppresses T-S trapping of minority carriers. 5. The Si-SiO2 interface compensates the surface 6. For delta-layers at intermediate depth, surface inversion layer forms 7. Density of Si-SiO2 interface charge can be extremely high (>10(exp 14)/sq cm)

  9. National Chemistry Week 2000: JCE Resources in Food Chemistry

    NASA Astrophysics Data System (ADS)

    Jacobsen, Erica K.

    2000-10-01

    November brings another National Chemistry Week, and this year's theme is food chemistry. I was asked to collect and evaluate JCE resources for use with this theme, a project that took me deep into past issues of JCE and yielded many treasures. Here we present the results of searches for food chemistry information and activities. While the selected articles are mainly at the high school and college levels, there are some excellent ones for the elementary school level and some that can be adapted for younger students. The focus of all articles is on the chemistry of food itself. Activities that only use food to demonstrate a principle other than food chemistry are not included. Articles that cover household products such as cleansers and pharmaceuticals are also not included. Each article has been characterized as a demonstration, experiment, calculation, activity, or informational item; several fit more than one classification. Also included are keywords and an evaluation as to which levels the article may serve.

  10. Using Computer Visualization Models in High School Chemistry: The Role of Teacher Beliefs.

    ERIC Educational Resources Information Center

    Robblee, Karen M.; Garik, Peter; Abegg, Gerald L.; Faux, Russell; Horwitz, Paul

    This paper discusses the role of high school chemistry teachers' beliefs in implementing computer visualization software to teach atomic and molecular structure from a quantum mechanical perspective. The informants in this study were four high school chemistry teachers with comparable academic and professional backgrounds. These teachers received…

  11. Toward extending photosynthetic biosignatures: quantum dynamics calculation of light harvesting complexes

    NASA Astrophysics Data System (ADS)

    Komatsu, Yu; Umemura, Masayuki; Shoji, Mitsuo; Kayanuma, Megumi; Yabana, Kazuhiro; Shiraishi, Kenji

    For detecting life from reflectance spectra on extrasolar planets, several indicators called surface biosignatures have been proposed. One of them is the vegetation red edge (VRE) which derives from surface vegetation. VRE is observed in 700-750 nm on the Earth, but there is no guarantee that exovegetation show the red edge in this wavelength. Therefore it is necessary to check the validity of current standards of VRE as the signatures. In facts, M stars (cooler than Sun) will be the main targets in future missions, it is significantly important to know on the fundamental mechanisms in photosynthetic organism such as purple bacteria which absorb longer wavelength radiation. We investigated light absorptions and excitation energy transfers (EETs) in light harvesting complexes in purple bacteria (LH2s) by using quantum dynamics simulations. In LH2, effective EET is accomplished by corporative electronic excitation of the pigments. In our theoretical model, a dipole-dipole approximation was used for the electronic interactions between pigment excitations. Quantum dynamics simulations were performed according to Liouville equation to examine the EET process. The calculated oscillator strength and the transfer time between LH2 were good agreement with the experimental values. As the system size increases, the absorption bands shifted longer and the transfer velocities became larger. When two pigments in a LHC were exchanged to another pigments with lower excitation energy, faster and intensive light collection were observed.

  12. 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

  13. Quantum scattering calculations for ro-vibrational de-excitation of CO by hydrogen atoms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Song, Lei; Avoird, Ad van der; Karman, Tijs

    2015-05-28

    We present quantum-mechanical scattering calculations for ro-vibrational relaxation of carbon monoxide (CO) in collision with hydrogen atoms. Collisional cross sections of CO ro-vibrational transitions from v = 1, j = 0 − 30 to v′ = 0, j′ are calculated using the close coupling method for collision energies between 0.1 and 15 000 cm{sup −1} based on the three-dimensional potential energy surface of Song et al. [J. Phys. Chem. A 117, 7571 (2013)]. Cross sections of transitions from v = 1, j ≥ 3 to v′ = 0, j′ are reported for the first time at this level of theory. Alsomore » calculations by the more approximate coupled states and infinite order sudden (IOS) methods are performed in order to test the applicability of these methods to H–CO ro-vibrational inelastic scattering. Vibrational de-excitation rate coefficients of CO (v = 1) are presented for the temperature range from 100 K to 3000 K and are compared with the available experimental and theoretical data. All of these results and additional rate coefficients reported in a forthcoming paper are important for including the effects of H–CO collisions in astrophysical models.« less

  14. 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

  15. A New Quantum Watermarking Based on Quantum Wavelet Transforms

    NASA Astrophysics Data System (ADS)

    Heidari, Shahrokh; Naseri, Mosayeb; Gheibi, Reza; Baghfalaki, Masoud; Rasoul Pourarian, Mohammad; Farouk, Ahmed

    2017-06-01

    Quantum watermarking is a technique to embed specific information, usually the owner’s identification, into quantum cover data such for copyright protection purposes. In this paper, a new scheme for quantum watermarking based on quantum wavelet transforms is proposed which includes scrambling, embedding and extracting procedures. The invisibility and robustness performances of the proposed watermarking method is confirmed by simulation technique. The invisibility of the scheme is examined by the peak-signal-to-noise ratio (PSNR) and the histogram calculation. Furthermore the robustness of the scheme is analyzed by the Bit Error Rate (BER) and the Correlation Two-Dimensional (Corr 2-D) calculation. The simulation results indicate that the proposed watermarking scheme indicate not only acceptable visual quality but also a good resistance against different types of attack. Supported by Kermanshah Branch, Islamic Azad University, Kermanshah, Iran

  16. A molecular quantum spin network controlled by a single qubit.

    PubMed

    Schlipf, Lukas; Oeckinghaus, Thomas; Xu, Kebiao; Dasari, Durga Bhaktavatsala Rao; Zappe, Andrea; de Oliveira, Felipe Fávaro; Kern, Bastian; Azarkh, Mykhailo; Drescher, Malte; Ternes, Markus; Kern, Klaus; Wrachtrup, Jörg; Finkler, Amit

    2017-08-01

    Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers. We demonstrate the collective readout and coherent manipulation of very few (≤ 6) of these S = 1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show that it is feasible to use spin-labeled peptides as a resource for a molecular qubit-based network, while at the same time providing simple optical readout of single quantum states through NV magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.

  17. Development and validation of an achievement test in introductory quantum mechanics: The Quantum Mechanics Visualization Instrument (QMVI)

    NASA Astrophysics Data System (ADS)

    Cataloglu, Erdat

    The purpose of this study was to construct a valid and reliable multiple-choice achievement test to assess students' understanding of core concepts of introductory quantum mechanics. Development of the Quantum Mechanics Visualization Instrument (QMVI) occurred across four successive semesters in 1999--2001. During this time 213 undergraduate and graduate students attending the Pennsylvania State University (PSU) at University Park and Arizona State University (ASU) participated in this development and validation study. Participating students were enrolled in four distinct groups of courses: Modern Physics, Undergraduate Quantum Mechanics, Graduate Quantum Mechanics, and Chemistry Quantum Mechanics. Expert panels of professors of physics experienced in teaching quantum mechanics courses and graduate students in physics and science education established the core content and assisted in the validating of successive versions of the 24-question QMVI. Instrument development was guided by procedures outlined in the Standards for Educational and Psychological Testing (AERA-APA-NCME, 1999). Data gathered in this study provided information used in the development of successive versions of the QMVI. Data gathered in the final phase of administration of the QMVI also provided evidence that the intended score interpretation of the QMVI achievement test is valid and reliable. A moderate positive correlation coefficient of 0.49 was observed between the students' QMVI scores and their confidence levels. Analyses of variance indicated that students' scores in Graduate Quantum Mechanics and Undergraduate Quantum Mechanics courses were significantly higher than the mean scores of students in Modern Physics and Chemistry Quantum Mechanics courses (p < 0.05). That finding is consistent with the additional understanding and experience that should be anticipated in graduate students and junior-senior level students over sophomore physics majors and majors in another field. The moderate

  18. Intramolecular hydrogen bonding in myricetin and myricitrin. Quantum chemical calculations and vibrational spectroscopy

    NASA Astrophysics Data System (ADS)

    Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens

    2017-03-01

    The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.

  19. Wavy carbon: A new series of carbon structures explored by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki; Tokoyama, Hiroaki; Yamakado, Hideo

    2015-10-01

    A new carbon family adopting wavy structures has been found by quantum chemical calculations. The key motif of this family is a condensed four-membered ring. Periodically wavy-carbon sheets (wavy-Cn sheets, n = 2, 6, and 8) as well as wavy-C36 tube were found to be very similar to the previously reported prism-Cn carbon tubes (n = 5, 6, and 8) in several respects, including the relative energies per one carbon atom with respect to graphene, CC bond lengths, and CCC bond angles. Because of very high relative energies with respect to graphene (206-253 kJ mol-1), the wavy-carbons may behave as energy reserving materials.

  20. Quantum close coupling calculation of transport and relaxation properties for Hg-H2 system

    NASA Astrophysics Data System (ADS)

    Nemati-Kande, Ebrahim; Maghari, Ali

    2016-11-01

    Quantum mechanical close coupling calculation of the state-to-state transport and relaxation cross sections have been done for Hg-H2 molecular system using a high-level ab initio potential energy surface. Rotationally averaged cross sections were also calculated to obtain the energy dependent Senftleben-Beenakker cross sections at the energy range of 0.005-25,000 cm-1. Boltzmann averaging of the energy dependent Senftleben-Beenakker cross sections showed the temperature dependency over a wide temperature range of 50-2500 K. Interaction viscosity and diffusion coefficients were also calculated using close coupling cross sections and full classical Mason-Monchick approximation. The results were compared with each other and with the available experimental data. It was found that Mason-Monchick approximation for viscosity is more reliable than diffusion coefficient. Furthermore, from the comparison of the experimental diffusion coefficients with the result of the close coupling and Mason-Monchick approximation, it was found that the Hg-H2 potential energy surface used in this work can reliably predict diffusion coefficient data.

  1. Interface behaviors of acetylene and ethylene molecules with 1-butyl-3-methylimidazolium acetate ionic liquid: a combined quantum chemistry calculation and molecular dynamics simulation study.

    PubMed

    Xu, Hao; Han, Zhe; Zhang, Dongju; Zhan, Jinhua

    2012-12-01

    Although imidazolium-based ionic liquids (ILs) combined with oxygen-containing anions were proposed as the potential solvents for the selective separation of acetylene (C(2)H(2)) and ethylene (C(2)H(4)), the detailed mechanism at the molecular level is still not well understood. The present work focuses on a most effective IL for removing C(2)H(2) from a C(2)H(4) stream, 1-butyl-3-methylimidazolium acetate ([BMIM][OAc]), aiming at understanding the first steps of the adsorption process of the molecules at the IL surface. We present a combined quantum mechanical (QM) calculation and molecular dynamics (MD) simulation study on the structure and property of the IL as well as its interaction with C(2)H(2) and C(2)H(4) molecules. The calculated results indicate that C(2)H(2) presents a stronger interaction with the IL than C(2)H(4) and the anion of the IL is mainly responsible for the stronger interaction. QM calculations show a stronger hydrogen-binding linkage between an acidic proton of C(2)H(2)/C(2)H(4) and the basic oxygen atom in [OAc](-) anion, in contrast to the relative weaker association via the C-H···π interaction between C(2)H(2)/C(2)H(4) and the cation. From MD simulations, it is observed that in the interfacial region, the butyl chain of cations and methyl of anions point into the vapor phase. The coming molecules on the IL surface may be initially wrapped by the extensive butyl chain and then devolved to the interface or caught into the bulk by the anion of IL. The introduction of guest molecules significantly influences the anion distribution and orientation on the interface, but the cations are not disturbed because of their larger volume and relatively weaker interaction with the changes in the guest molecules. The theoretical results provide insight into the molecular mechanism of the observed selective separation of C(2)H(2) form a C(2)H(4) stream by ILs.

  2. Designing, programming, and optimizing a (small) quantum computer

    NASA Astrophysics Data System (ADS)

    Svore, Krysta

    In 1982, Richard Feynman proposed to use a computer founded on the laws of quantum physics to simulate physical systems. In the more than thirty years since, quantum computers have shown promise to solve problems in number theory, chemistry, and materials science that would otherwise take longer than the lifetime of the universe to solve on an exascale classical machine. The practical realization of a quantum computer requires understanding and manipulating subtle quantum states while experimentally controlling quantum interference. It also requires an end-to-end software architecture for programming, optimizing, and implementing a quantum algorithm on the quantum device hardware. In this talk, we will introduce recent advances in connecting abstract theory to present-day real-world applications through software. We will highlight recent advancement of quantum algorithms and the challenges in ultimately performing a scalable solution on a quantum device.

  3. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    PubMed

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  4. Fixed-node quantum Monte Carlo

    NASA Astrophysics Data System (ADS)

    Anderson, James B.

    Quantum Monte Carlo methods cannot at present provide exact solutions of the Schrödinger equation for systems with more than a few electrons. But, quantum Monte Carlo calculations can provide very low energy, highly accurate solutions for many systems ranging up to several hundred electrons. These systems include atoms such as Be and Fe, molecules such as H2O, CH4, and HF, and condensed materials such as solid N2 and solid silicon. The quantum Monte Carlo predictions of their energies and structures may not be `exact', but they are the best available. Most of the Monte Carlo calculations for these systems have been carried out using approximately correct fixed nodal hypersurfaces and they have come to be known as `fixed-node quantum Monte Carlo' calculations. In this paper we review these `fixed node' calculations and the accuracies they yield.

  5. Early contributions to theoretical chemistry: Inga Fischer-Hjalmars, a founder of the Swedish school

    NASA Astrophysics Data System (ADS)

    Johansson, Adam Johannes

    2017-09-01

    Inga Fischer-Hjalmars was one of the pioneers in the creation of the Swedish school of theoretical chemistry. She started her scientific endeavours in pharmacy and biochemistry, but soon sought a deeper understanding of molecules and chemistry. With a genuine experimental background and quantum chemical skills learned from Charles Coulson in the late 1940s, Inga was well prepared to continue her research and to contribute to the establishment of theoretical chemistry as it was later defined by Coulson; the use of quantum mechanics to explain experimental phenomena in all branches of chemistry. During the 1950s and 1960s Inga made important contributions to our understanding of chemical bonding and reactivity. For example, she made key insights into the dissociation of molecular hydrogen, the influence of heteroatoms on dipole moments in organic compounds, the electronic configuration of ozone and on the validity of different approximations in molecular theory. Inga Fischer-Hjalmars and her students developed extensions of the Pariser-Parr-Pople method and during the latter part of her career, she returned to the biomolecules that once had brought her into science, now applying quantum chemical methods to understand bonding and spectral properties of these molecules at greater depth.

  6. Systematic study of imidazoles inhibiting IDO1 via the integration of molecular mechanics and quantum mechanics calculations.

    PubMed

    Zou, Yi; Wang, Fang; Wang, Yan; Guo, Wenjie; Zhang, Yihua; Xu, Qiang; Lai, Yisheng

    2017-05-05

    Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations. Secondly, molecular dynamics (MD) simulations and MM/PBSA free energy calculations were employed to determine the dynamic binding process and crucial residues were confirmed through close contact analysis, hydrogen-bond analysis and binding free energy decomposition calculations. Subsequent quantum mechanics and nonbonding interaction analysis were carried out to provide in-depth explanations on the critical role of those key residues, and Arg231 and 7-propionate of the heme group were major contributors to ligand binding, which lowed a great amount of interaction energy. We anticipate that these findings will be valuable for enzymatic studies and rational drug design. Copyright © 2017. Published by Elsevier Masson SAS.

  7. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies.

    PubMed

    Sodt, Alexander J; Mei, Ye; König, Gerhard; Tao, Peng; Steele, Ryan P; Brooks, Bernard R; Shao, Yihan

    2015-03-05

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton-Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin-luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.

  8. Effects of nonequilibrium ablation chemistry on Viking radio blackout.

    NASA Technical Reports Server (NTRS)

    Evans, J. S.; Schexnayder, C. J., Jr.; Grose, W. L.

    1973-01-01

    The length of the entry blackout period during descent of the Viking Lander into the Mars atmosphere is predicted from calculated profiles of electron density in the shock layer over the aeroshell. Nonequilibrium chemistry plays a key role in the calculation, both in the inviscid flow and in the boundary layer. This is especially true in the boundary layer contaminated with ablation material, for which nonequilibrium chemistry predicts electron densities two decades lower than the same case calculated with equilibrium chemistry.

  9. Variational method for calculating the binding energy of the base state of an impurity D- centered on a quantum dot of GaAs-Ga1-xAlxAs

    NASA Astrophysics Data System (ADS)

    Durán-Flórez, F.; Caicedo, L. C.; Gonzalez, J. E.

    2018-04-01

    In quantum mechanics it is very difficult to obtain exact solutions, therefore, it is necessary to resort to tools and methods that facilitate the calculations of the solutions of these systems, one of these methods is the variational method that consists in proposing a wave function that depend on several parameters that are adjusted to get close to the exact solution. Authors in the past have performed calculations applying this method using exponential and Gaussian orbital functions with linear and quadratic correlation factors. In this paper, a Gaussian function with a linear correlation factor is proposed, for the calculation of the binding energy of an impurity D ‑ centered on a quantum dot of radius r, the Gaussian function is dependent on the radius of the quantum dot.

  10. Effects of strain and quantum confinement in optically pumped nuclear magnetic resonance in GaAs: Interpretation guided by spin-dependent band structure calculations

    DOE PAGES

    Wood, R. M.; Saha, D.; McCarthy, L. A.; ...

    2014-10-29

    A combined experimental-theoretical study of optically pumped NMR (OPNMR) has been performed in a GaAs/Al 0.1Ga 0.9As quantum well film with thermally induced biaxial strain. The photon energy dependence of the Ga-71 OPNMR signal was recorded at magnetic fields of 4.9 and 9.4 T at a temperature of 4.8-5.4 K. The data were compared to the nuclear spin polarization calculated from differential absorption to spin-up and spin-down states of the conduction band using a modified Pidgeon Brown model. Reasonable agreement between theory and experiment is obtained, facilitating assignment of features in the OPNMR energy dependence to specific interband transitions. Despitemore » the approximations made in the quantum-mechanical model and the inexact correspondence between the experimental and calculated observables, the results provide insight into how effects of strain and quantum confinement are manifested in OPNMR signals« less

  11. Autonomy, explanation, and theoretical values: physicists and chemists on molecular quantum mechanics.

    PubMed

    Hendry, Robin Findlay

    2003-05-01

    The emergence of quantum chemistry in the early twentieth century was an international as well as an interdisciplinary affair, involving dialogue between physicists and chemists in Germany, the United States, and Britain. Historians of science have recently documented both the causes and effects of this internationalism and interdisciplinarity. Chemists and physicists involved in the development of quantum chemistry in its first few decades tended to argue for opposing views on acceptable standards of explanation in their field, although the debate did not divide along disciplinary lines. The purpose of this paper is to investigate these different positions, through the methodological reflections of John Clarke Slater, Linus Pauling, and Charles Coulson. Slater tended to argue for quantum-mechanical rigor and the application of fundamental principles as the values guiding models of molecular bonding. Although they were on different sides of the debate between the valence-bond and molecular-orbital approaches, Pauling and Coulson both emphasized the recovery of traditional chemical explanations and systematic explanatory power within chemistry.

  12. Entangled quantum electronic wavefunctions of the Mn₄CaO₅ cluster in photosystem II.

    PubMed

    Kurashige, Yuki; Chan, Garnet Kin-Lic; Yanai, Takeshi

    2013-08-01

    It is a long-standing goal to understand the reaction mechanisms of catalytic metalloenzymes at an entangled many-electron level, but this is hampered by the exponential complexity of quantum mechanics. Here, by exploiting the special structure of physical quantum states and using the density matrix renormalization group, we compute near-exact many-electron wavefunctions of the Mn4CaO5 cluster of photosystem II, with more than 1 × 10(18) quantum degrees of freedom. This is the first treatment of photosystem II beyond the single-electron picture of density functional theory. Our calculations support recent modifications to the structure determined by X-ray crystallography. We further identify multiple low-lying energy surfaces associated with the structural distortion seen using X-ray crystallography, highlighting multistate reactivity in the chemistry of the cluster. Direct determination of Mn spin-projections from our wavefunctions suggests that current candidates that have been recently distinguished using parameterized spin models should be reassessed. Through entanglement maps, we reveal rich information contained in the wavefunctions on bonding changes in the cycle.

  13. Quantum effects in the understanding of consciousness.

    PubMed

    Hameroff, Stuart R; Craddock, Travis J A; Tuszynski, Jack A

    2014-06-01

    This paper presents a historical perspective on the development and application of quantum physics methodology beyond physics, especially in biology and in the area of consciousness studies. Quantum physics provides a conceptual framework for the structural aspects of biological systems and processes via quantum chemistry. In recent years individual biological phenomena such as photosynthesis and bird navigation have been experimentally and theoretically analyzed using quantum methods building conceptual foundations for quantum biology. Since consciousness is attributed to human (and possibly animal) mind, quantum underpinnings of cognitive processes are a logical extension. Several proposals, especially the Orch OR hypothesis, have been put forth in an effort to introduce a scientific basis to the theory of consciousness. At the center of these approaches are microtubules as the substrate on which conscious processes in terms of quantum coherence and entanglement can be built. Additionally, Quantum Metabolism, quantum processes in ion channels and quantum effects in sensory stimulation are discussed in this connection. We discuss the challenges and merits related to quantum consciousness approaches as well as their potential extensions.

  14. Molecular structure and ring tunneling of phenyl formate as observed by microwave spectroscopy and quantum chemistry

    NASA Astrophysics Data System (ADS)

    Ferres, Lynn; Mouhib, Halima; Stahl, Wolfgang; Schwell, Martin; Nguyen, Ha Vinh Lam

    2017-07-01

    Phenyl formate has been investigated by molecular jet Fourier-transform microwave spectroscopy in the frequency range from 2 to 26.5 GHz. Quantum chemical calculations at the MP2/6-311++G(d,p) level of theory indicate that this molecule does not have a plane of symmetry at equilibrium, and that the phenyl ring performs a large amplitude tunneling motion from one side of the Cs configuration to the other. The tilt angle of the ring out of the Hsbnd (Cdbnd O)O plane is ±70° and the calculated tunneling barrier is only 28 cm-1. The two lowest torsional states vt = 0 and 1 are assigned in the experimental spectrum and fitted using the program SPFIT/SPCAT. The Coriolis splitting ΔE between these states is 46.2231(25) GHz, very close to the value of 48.24 GHz calculated using a simple two-top torsional Hamiltonian of the formate group and the phenyl ring.

  15. 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.

  16. Using Mathematical Software to Introduce Fourier Transforms in Physical Chemistry to Develop Improved Understanding of Their Applications in Analytical Chemistry

    ERIC Educational Resources Information Center

    Miller, Tierney C.; Richardson, John N.; Kegerreis, Jeb S.

    2016-01-01

    This manuscript presents an exercise that utilizes mathematical software to explore Fourier transforms in the context of model quantum mechanical systems, thus providing a deeper mathematical understanding of relevant information often introduced and treated as a "black-box" in analytical chemistry courses. The exercise is given to…

  17. Non-perturbative background field calculations

    NASA Astrophysics Data System (ADS)

    Stephens, C. R.

    1988-01-01

    New methods are developed for calculating one loop functional determinants in quantum field theory. Instead of relying on a calculation of all the eigenvalues of the small fluctuation equation, these techniques exploit the ability of the proper time formalism to reformulate an infinite dimensional field theoretic problem into a finite dimensional covariant quantum mechanical analog, thereby allowing powerful tools such as the method of Jacobi fields to be used advantageously in a field theory setting. More generally the methods developed herein should be extremely valuable when calculating quantum processes in non-constant background fields, offering a utilitarian alternative to the two standard methods of calculation—perturbation theory in the background field or taking the background field into account exactly. The formalism developed also allows for the approximate calculation of covariances of partial differential equations from a knowledge of the solutions of a homogeneous ordinary differential equation.

  18. Quantum Tunneling Contribution for the Activation Energy in Microwave-Induced Reactions.

    PubMed

    Kuhnen, Carlos A; Dall'Oglio, Evandro L; de Sousa, Paulo T

    2017-08-03

    In this study, a quantum approach is presented to explain microwave-enhanced reaction rates by considering the tunneling effects in chemical reactions. In the Arrhenius equation, the part of the Hamiltonian relative to the interaction energy during tunneling, between the particle that tunnels and the electrical field defined in the medium, whose spatial component is specified by its rms value, is taken into account. An approximate evaluation of the interaction energy leads to a linear dependence of the effective activation energy on the applied field. The evaluation of the rms value of the field for pure liquids and reaction mixtures, through their known dielectric properties, leads to an appreciable reduction in the activation energies for the proton transfer process in these liquids. The results indicate the need to move toward the use of more refined methods of modern quantum chemistry to calculate more accurately field-induced reaction rates and effective activation energies.

  19. Recovering a full dimensional quantum rate constant from a reduced dimensionality calculation: Application to the OH+CO{r_arrow}H+CO{sub 2} reaction

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Dzegilenko, F.N.; Bowman, J.M.

    1996-08-01

    Two reduced dimensionality theories are used to calculate the thermal rate constant for the OH+CO{r_arrow}H+CO{sub 2} reaction. The standard theory employs energy-shift approximations to extract the full six degree-of-freedom quantum rate constant for this reaction from the previous two degree-of-freedom (2-DOF) quantum calculations of Hernandez and Clary [M.I. Hernandez and D.C. Clary, J. Chem. Phys. {bold 101}, 2779 (1994)]. Three extra bending modes and one extra {open_quote}{open_quote}spectator{close_quote}{close_quote} CO stretch mode are treated adiabatically in the harmonic fashion. The parameters of the exit channel transition state are used to evaluate the frequencies of those additional modes. A new reduced dimensionality theorymore » is also applied to this reaction. This theory explicitly addresses the finding from the 2-DOF calculations that the reaction proceeds mainly via complex formation. A J-shifting approximation has been used to take into account the initial states with non-zero values of total angular momentum in both reduced dimensionality theories. Cumulative reaction probabilities and thermal rate constants are calculated and compared with the previous quasiclassical and reduced dimensionality quantum calculations and with experiment. The rate constant from the new reduced dimensionality theory is between a factor of 5 and 100 times smaller than the statistical transition state theory result, and is in much better agreement with experiment. {copyright} {ital 1996 American Institute of Physics.}« less

  20. Quantum Computation Using Optically Coupled Quantum Dot Arrays

    NASA Technical Reports Server (NTRS)

    Pradhan, Prabhakar; Anantram, M. P.; Wang, K. L.; Roychowhury, V. P.; Saini, Subhash (Technical Monitor)

    1998-01-01

    A solid state model for quantum computation has potential advantages in terms of the ease of fabrication, characterization, and integration. The fundamental requirements for a quantum computer involve the realization of basic processing units (qubits), and a scheme for controlled switching and coupling among the qubits, which enables one to perform controlled operations on qubits. We propose a model for quantum computation based on optically coupled quantum dot arrays, which is computationally similar to the atomic model proposed by Cirac and Zoller. In this model, individual qubits are comprised of two coupled quantum dots, and an array of these basic units is placed in an optical cavity. Switching among the states of the individual units is done by controlled laser pulses via near field interaction using the NSOM technology. Controlled rotations involving two or more qubits are performed via common cavity mode photon. We have calculated critical times, including the spontaneous emission and switching times, and show that they are comparable to the best times projected for other proposed models of quantum computation. We have also shown the feasibility of accessing individual quantum dots using the NSOM technology by calculating the photon density at the tip, and estimating the power necessary to perform the basic controlled operations. We are currently in the process of estimating the decoherence times for this system; however, we have formulated initial arguments which seem to indicate that the decoherence times will be comparable, if not longer, than many other proposed models.

  1. Ab initio calculations of torsionally mediated hyperfine splittings in E states of acetaldehyde

    NASA Astrophysics Data System (ADS)

    Xu, Li-Hong; Reid, E. M.; Guislain, B.; Hougen, J. T.; Alekseev, E. A.; Krapivin, I.

    2017-12-01

    Quantum chemistry packages can be used to predict with reasonable accuracy spin-rotation hyperfine interaction constants for methanol, which contains one methyl-top internal rotor. In this work we use one of these packages to calculate components of the spin-rotation interaction tensor for acetaldehyde. We then use torsion-rotation wavefunctions obtained from a fit to the acetaldehyde torsion-rotation spectrum to calculate the expected magnitude of hyperfine splittings analogous to those observed at relatively high J values in the E symmetry states of methanol. We find that theory does indeed predict doublet splittings at moderate J values in the acetaldehyde torsion-rotation spectrum, which closely resemble those seen in methanol, but that the factor of three decrease in hyperfine spin-rotation constants compared to methanol puts the largest of the acetaldehyde splittings a factor of two below presently available Lamb-dip resolution.

  2. Photon-assisted quantum transport in quantum point contacts

    NASA Astrophysics Data System (ADS)

    Hu, Qing

    1993-02-01

    We have studied the feasibility of photon-assisted quantum transport in semiconductor quantum point contacts or electron waveguides. Due to photon-induced intersubband transitions, it is expected that the drain/source conductance of the quantum point contacts can be modulated by far-infrared (f not less than 300 GHz) radiation, which is similar to the photon-assisted tunneling in superconducting tunnel junctions. An antenna/gate electrodes structure will be used to couple far-infrared photons into quantum point contacts of submicron dimensions. A calculation of the photon-induced drain/source current as a function of the far-infrared radiation power is also presented.

  3. Full-dimensional quantum calculations of the vibrational states of H5(+).

    PubMed

    Song, Hongwei; Lee, Soo-Ying; Yang, Minghui; Lu, Yunpeng

    2013-03-28

    Full-dimensional quantum calculations of the vibrational states of H5(+) have been performed on the accurate potential energy surface developed by Xie et al. [J. Chem. Phys. 122, 224307 (2005)]. The zero point energies of H5(+), H4D(+), D4H(+), and D5(+) and their ground-state geometries are presented and compared with earlier theoretical results. The first 10 low-lying excited states of H5(+) are assigned to the fundamental, overtone, and combination of the H2-H3(+) stretch, the shared proton hopping and the out-of-plane torsion. The ground-state torsional tunneling splitting, the fundamental of the photon hopping mode and the first overtone of the torsion mode are 87.3 cm(-1), 354.4 cm(-1), and 444.0 cm(-1), respectively. All of these values agree well with the diffusion Monte Carlo and multi-configuration time-dependent Hartree results where available.

  4. Quantum Monte Carlo: Faster, More Reliable, And More Accurate

    NASA Astrophysics Data System (ADS)

    Anderson, Amos Gerald

    2010-06-01

    The Schrodinger Equation has been available for about 83 years, but today, we still strain to apply it accurately to molecules of interest. The difficulty is not theoretical in nature, but practical, since we're held back by lack of sufficient computing power. Consequently, effort is applied to find acceptable approximations to facilitate real time solutions. In the meantime, computer technology has begun rapidly advancing and changing the way we think about efficient algorithms. For those who can reorganize their formulas to take advantage of these changes and thereby lift some approximations, incredible new opportunities await. Over the last decade, we've seen the emergence of a new kind of computer processor, the graphics card. Designed to accelerate computer games by optimizing quantity instead of quality in processor, they have become of sufficient quality to be useful to some scientists. In this thesis, we explore the first known use of a graphics card to computational chemistry by rewriting our Quantum Monte Carlo software into the requisite "data parallel" formalism. We find that notwithstanding precision considerations, we are able to speed up our software by about a factor of 6. The success of a Quantum Monte Carlo calculation depends on more than just processing power. It also requires the scientist to carefully design the trial wavefunction used to guide simulated electrons. We have studied the use of Generalized Valence Bond wavefunctions to simply, and yet effectively, captured the essential static correlation in atoms and molecules. Furthermore, we have developed significantly improved two particle correlation functions, designed with both flexibility and simplicity considerations, representing an effective and reliable way to add the necessary dynamic correlation. Lastly, we present our method for stabilizing the statistical nature of the calculation, by manipulating configuration weights, thus facilitating efficient and robust calculations. Our

  5. Spin-driven structural effects in alkali doped (4)He clusters from quantum calculations.

    PubMed

    Bovino, S; Coccia, E; Bodo, E; Lopez-Durán, D; Gianturco, F A

    2009-06-14

    In this paper, we carry out variational Monte Carlo and diffusion Monte Carlo (DMC) calculations for Li(2)((1)Sigma(g) (+))((4)He)(N) and Li(2)((3)Sigma(u) (+))((4)He)(N) with N up to 30 and discuss in detail the results of our computations. After a comparison between our DMC energies with the "exact" discrete variable representation values for the species with one (4)He, in order to test the quality of our computations at 0 K, we analyze the structural features of the whole range of doped clusters. We find that both species reside on the droplet surface, but that their orientation is spin driven, i.e., the singlet molecule is perpendicular and the triplet one is parallel to the droplet's surface. We have also computed quantum vibrational relaxation rates for both dimers in collision with a single (4)He and we find them to differ by orders of magnitude at the estimated surface temperature. Our results therefore confirm the findings from a great number of experimental data present in the current literature and provide one of the first attempts at giving an accurate, fully quantum picture for the nanoscopic properties of alkali dimers in (4)He clusters.

  6. Diffusion quantum Monte Carlo calculations of SrFeO 3 and LaFeO 3

    DOE PAGES

    Santana, Juan A.; Krogel, Jaron T.; Kent, Paul R. C.; ...

    2017-07-18

    The equations of state, formation energy, and migration energy barrier of the oxygen vacancy in SrFeO 3 and LaFeO 3 were calculated in this paper with the diffusion quantum Monte Carlo (DMC) method. Calculations were also performed with various Density Functional Theory (DFT) approximations for comparison. DMC reproduces the measured cohesive energies of these materials with errors below 0.23(5) eV and the structural properties within 1% of the experimental values. The DMC formation energies of the oxygen vacancy in SrFeO 3 and LaFeO 3 under oxygen-rich conditions are 1.3(1) and 6.24(7) eV, respectively. Similar calculations with semi-local DFT approximations formore » LaFeO 3 yielded vacancy formation energies 1.5 eV lower. Comparison of charge density evaluated with DMC and DFT approximations shows that DFT tends to overdelocalize the electrons in defected SrFeO 3 and LaFeO 3. Finally, calculations with DMC and local density approximation yield similar vacancy migration energy barriers, indicating that steric/electrostatic effects mainly determine migration barriers in these materials.« less

  7. Conformational analysis of a polyconjugated protein-binding ligand by joint quantum chemistry and polarizable molecular mechanics. Addressing the issues of anisotropy, conjugation, polarization, and multipole transferability.

    PubMed

    Goldwaser, Elodie; de Courcy, Benoit; Demange, Luc; Garbay, Christiane; Raynaud, Françoise; Hadj-Slimane, Reda; Piquemal, Jean-Philip; Gresh, Nohad

    2014-11-01

    We investigate the conformational properties of a potent inhibitor of neuropilin-1, a protein involved in cancer processes and macular degeneration. This inhibitor consists of four aromatic/conjugated fragments: a benzimidazole, a methylbenzene, a carboxythiourea, and a benzene-linker dioxane, and these fragments are all linked together by conjugated bonds. The calculations use the SIBFA polarizable molecular mechanics procedure. Prior to docking simulations, it is essential to ensure that variations in the ligand conformational energy upon rotations around its six main-chain torsional bonds are correctly represented (as compared to high-level ab initio quantum chemistry, QC). This is done in two successive calibration stages and one validation stage. In the latter, the minima identified following independent stepwise variations of each of the six main-chain torsion angles are used as starting points for energy minimization of all the torsion angles simultaneously. Single-point QC calculations of the minimized structures are then done to compare their relative energies ΔE conf to the SIBFA ones. We compare three different methods of deriving the multipoles and polarizabilities of the central, most critical moiety of the inhibitor: carboxythiourea (CTU). The representation that gives the best agreement with QC is the one that includes the effects of the mutual polarization energy E pol between the amide and thioamide moieties. This again highlights the critical role of this contribution. The implications and perspectives of these findings are discussed.

  8. Quantum capacity of quantum black holes

    NASA Astrophysics Data System (ADS)

    Adami, Chris; Bradler, Kamil

    2014-03-01

    The fate of quantum entanglement interacting with a black hole has been an enduring mystery, not the least because standard curved space field theory does not address the interaction of black holes with matter. We discuss an effective Hamiltonian of matter interacting with a black hole that has a precise analogue in quantum optics and correctly reproduces both spontaneous and stimulated Hawking radiation with grey-body factors. We calculate the quantum capacity of this channel in the limit of perfect absorption, as well as in the limit of a perfectly reflecting black hole (a white hole). We find that the white hole is an optimal quantum cloner, and is isomorphic to the Unruh channel with positive quantum capacity. The complementary channel (across the horizon) is entanglement-breaking with zero capacity, avoiding a violation of the quantum no-cloning theorem. The black hole channel on the contrary has vanishing capacity, while its complement has positive capacity instead. Thus, quantum states can be reconstructed faithfully behind the black hole horizon, but not outside. This work sheds new light on black hole complementarity because it shows that black holes can both reflect and absorb quantum states without violating the no-cloning theorem, and makes quantum firewalls obsolete.

  9. Hybrid quantum-classical modeling of quantum dot devices

    NASA Astrophysics Data System (ADS)

    Kantner, Markus; Mittnenzweig, Markus; Koprucki, Thomas

    2017-11-01

    The design of electrically driven quantum dot devices for quantum optical applications asks for modeling approaches combining classical device physics with quantum mechanics. We connect the well-established fields of semiclassical semiconductor transport theory and the theory of open quantum systems to meet this requirement. By coupling the van Roosbroeck system with a quantum master equation in Lindblad form, we introduce a new hybrid quantum-classical modeling approach, which provides a comprehensive description of quantum dot devices on multiple scales: it enables the calculation of quantum optical figures of merit and the spatially resolved simulation of the current flow in realistic semiconductor device geometries in a unified way. We construct the interface between both theories in such a way, that the resulting hybrid system obeys the fundamental axioms of (non)equilibrium thermodynamics. We show that our approach guarantees the conservation of charge, consistency with the thermodynamic equilibrium and the second law of thermodynamics. The feasibility of the approach is demonstrated by numerical simulations of an electrically driven single-photon source based on a single quantum dot in the stationary and transient operation regime.

  10. Quantum mechanical electronic structure calculation reveals orientation dependence of hydrogen bond energy in proteins.

    PubMed

    Mondal, Abhisek; Datta, Saumen

    2017-06-01

    Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  11. Quantum Dots in a Polymer Composite: A Convenient Particle-in-a-Box Laboratory Experiment

    ERIC Educational Resources Information Center

    Rice, Charles V.; Giffin, Guinevere A.

    2008-01-01

    Semiconductor quantum dots are at the forefront of materials science chemistry with applications in biological imaging and photovoltaic technologies. We have developed a simple laboratory experiment to measure the quantum-dot size from fluorescence spectra. A major roadblock of quantum-dot based exercises is the particle synthesis and handling;…

  12. Plasticity and Kinky Chemistry of Carbon Nanotubes

    NASA Technical Reports Server (NTRS)

    Srivastava, Deepak; Dzegilenko, Fedor

    2000-01-01

    Since their discovery in 1991, carbon nanotubes have been the subject of intense research interest based on early predictions of their unique mechanical, electronic, and chemical properties. Materials with the predicted unique properties of carbon nanotubes are of great interest for use in future generations of aerospace vehicles. For their structural properties, carbon nanotubes could be used as reinforcing fibers in ultralight multifunctional composites. For their electronic properties, carbon nanotubes offer the potential of very high-speed, low-power computing elements, high-density data storage, and unique sensors. In a continuing effort to model and predict the properties of carbon nanotubes, Ames accomplished three significant results during FY99. First, accurate values of the nanomechanics and plasticity of carbon nanotubes based on quantum molecular dynamics simulations were computed. Second, the concept of mechanical deformation catalyzed-kinky-chemistry as a means to control local chemistry of nanotubes was discovered. Third, the ease of nano-indentation of silicon surfaces with carbon nanotubes was established. The elastic response and plastic failure mechanisms of single-wall nanotubes were investigated by means of quantum molecular dynamics simulations.

  13. Divide and conquer approach to quantum Hamiltonian simulation

    NASA Astrophysics Data System (ADS)

    Hadfield, Stuart; Papageorgiou, Anargyros

    2018-04-01

    We show a divide and conquer approach for simulating quantum mechanical systems on quantum computers. We can obtain fast simulation algorithms using Hamiltonian structure. Considering a sum of Hamiltonians we split them into groups, simulate each group separately, and combine the partial results. Simulation is customized to take advantage of the properties of each group, and hence yield refined bounds to the overall simulation cost. We illustrate our results using the electronic structure problem of quantum chemistry, where we obtain significantly improved cost estimates under very mild assumptions.

  14. Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

    PubMed Central

    2015-01-01

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completely avoided at each configuration. They produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy. PMID:25321186

  15. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies

    DOE PAGES

    Sodt, Alexander J.; Mei, Ye; Konig, Gerhard; ...

    2014-10-16

    In combined quantum mechanical/molecular mechanical (QM/MM) free energy calculations, it is often advantageous to have a frozen geometry for the quantum mechanical (QM) region. For such multiple-environment single-system (MESS) cases, two schemes are proposed here for estimating the polarization energy: the first scheme, termed MESS-E, involves a Roothaan step extrapolation of the self-consistent field (SCF) energy; whereas the other scheme, termed MESS-H, employs a Newton–Raphson correction using an approximate inverse electronic Hessian of the QM region (which is constructed only once). Both schemes are extremely efficient, because the expensive Fock updates and SCF iterations in standard QM/MM calculations are completelymore » avoided at each configuration. Here, they produce reasonably accurate QM/MM polarization energies: MESS-E can predict the polarization energy within 0.25 kcal/mol in terms of the mean signed error for two of our test cases, solvated methanol and solvated β-alanine, using the M06-2X or ωB97X-D functionals; MESS-H can reproduce the polarization energy within 0.2 kcal/mol for these two cases and for the oxyluciferin–luciferase complex, if the approximate inverse electronic Hessians are constructed with sufficient accuracy.« less

  16. Variational calculations of subbands in a quantum well with uniform electric field - Gram-Schmidt orthogonalization approach

    NASA Technical Reports Server (NTRS)

    Ahn, Doyeol; Chuang, S. L.

    1986-01-01

    Variational calculations of subband eigenstates in an infinite quantum well with an applied electric field using Gram-Schmidt orthogonalized trial wave functions are presented. The results agree very well with the exact numerical solutions even up to 1200 kV/cm. It is also shown that, for increasing electric fields, the energy of the ground state decreases, while that of higher subband states increases slightly up to 1000 kV/cm and then decreases for a well size of 100 A.

  17. Quantum chemical studies of estrogenic compounds

    USDA-ARS?s Scientific Manuscript database

    Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

  18. A Safer, Easier, Faster Synthesis for CdSe Quantum Dot Nanocrystals

    ERIC Educational Resources Information Center

    Boatman, Elizabeth M.; Lisensky, George C.; Nordell, Karen J.

    2005-01-01

    The synthesis for CdSe quantum dot nanocrystals that vary in color and are a visually engaging way to demonstrate quantum effects in chemistry is presented. CdSe nanocrystals are synthesized from CdO and elemental Se using a kinetic growth method where particle size depends on reaction time.

  19. Auxiliary-field-based trial wave functions in quantum Monte Carlo calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Chang, Chia -Chen; Rubenstein, Brenda M.; Morales, Miguel A.

    2016-12-19

    Quantum Monte Carlo (QMC) algorithms have long relied on Jastrow factors to incorporate dynamic correlation into trial wave functions. While Jastrow-type wave functions have been widely employed in real-space algorithms, they have seen limited use in second-quantized QMC methods, particularly in projection methods that involve a stochastic evolution of the wave function in imaginary time. Here we propose a scheme for generating Jastrow-type correlated trial wave functions for auxiliary-field QMC methods. The method is based on decoupling the two-body Jastrow into one-body projectors coupled to auxiliary fields, which then operate on a single determinant to produce a multideterminant trial wavemore » function. We demonstrate that intelligent sampling of the most significant determinants in this expansion can produce compact trial wave functions that reduce errors in the calculated energies. Lastly, our technique may be readily generalized to accommodate a wide range of two-body Jastrow factors and applied to a variety of model and chemical systems.« less

  20. Linking molecular level chemistry to macroscopic combustion behavior for nano-energetic materials with halogen containing oxides.

    PubMed

    Farley, Cory W; Pantoya, Michelle L; Losada, Martin; Chaudhuri, Santanu

    2013-08-21

    Coupling molecular scale reaction kinetics with macroscopic combustion behavior is critical to understanding the influences of intermediate chemistry on energy propagation, yet bridging this multi-scale gap is challenging. This study integrates ab initio quantum chemical calculations and condensed phase density functional theory to elucidate factors contributing to experimentally measured high flame speeds (i.e., >900 m∕s) associated with halogen based energetic composites, such as aluminum (Al) and iodine pentoxide (I2O5). Experiments show a direct correlation between apparent activation energy and flame speed suggesting that flame speed is directly influenced by chemical kinetics. Toward this end, the first principle simulations resolve key exothermic surface and intermediate chemistries contributing toward the kinetics that promote high flame speeds. Linking molecular level exothermicity to macroscopic experimental investigations provides insight into the unique role of the alumina oxide shell passivating aluminum particles. In the case of Al reacting with I2O5, the alumina shell promotes exothermic surface chemistries that reduce activation energy and increase flame speed. This finding is in contrast to Al reaction with metal oxides that show the alumina shell does not participate exothermically in the reaction.

  1. Time-dependent interstellar chemistry

    NASA Technical Reports Server (NTRS)

    Glassgold, A. E.

    1985-01-01

    Some current problems in interstellar chemistry are considered in the context of time-dependent calculations. The limitations of steady-state models of interstellar gas-phase chemistry are discussed, and attempts to chemically date interstellar clouds are reviewed. The importance of studying the physical and chemical properties of interstellar dust is emphasized. Finally, the results of a series of studies of collapsing clouds are described.

  2. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis.

    PubMed

    Schmidt, Andrea; Gruber, Karl; Kratky, Christoph; Lamzin, Victor S

    2008-08-01

    Hydroxynitrile lyases are versatile enzymes that enantiospecifically cope with cyanohydrins, important intermediates in the production of various agrochemicals or pharmaceuticals. We determined four atomic resolution crystal structures of hydroxynitrile lyase from Hevea brasiliensis: one native and three complexes with acetone, isopropyl alcohol, and thiocyanate. We observed distinct distance changes among the active site residues related to proton shifts upon substrate binding. The combined use of crystallography and ab initio quantum chemical calculations allowed the determination of the protonation states in the enzyme active site. We show that His(235) of the catalytic triad must be protonated in order for catalysis to proceed, and we could reproduce the cyanohydrin synthesis in ab initio calculations. We also found evidence for the considerable pK(a) shifts that had been hypothesized earlier. We envision that this knowledge can be used to enhance the catalytic properties and the stability of the enzyme for industrial production of enantiomerically pure cyanohydrins.

  3. Demystifying Introductory Chemistry. Part 1: Electron Configurations from Experiment.

    ERIC Educational Resources Information Center

    Gillespie, Ronald J.; And Others

    1996-01-01

    Presents suggestions for alternative presentations of some of the material that usually forms part of the introductory chemistry course. Emphasizes development of concepts from experimental results. Discusses electronic configurations and quantum numbers, experimental evidence for electron configurations, deducing the shell model from the periodic…

  4. Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations.

    PubMed

    Shen, Lin; Yang, Weitao

    2016-04-12

    We developed a new multiresolution method that spans three levels of resolution with quantum mechanical, atomistic molecular mechanical, and coarse-grained models. The resolution-adapted all-atom and coarse-grained water model, in which an all-atom structural description of the entire system is maintained during the simulations, is combined with the ab initio quantum mechanics and molecular mechanics method. We apply this model to calculate the redox potentials of the aqueous ruthenium and iron complexes by using the fractional number of electrons approach and thermodynamic integration simulations. The redox potentials are recovered in excellent accordance with the experimental data. The speed-up of the hybrid all-atom and coarse-grained water model renders it computationally more attractive. The accuracy depends on the hybrid all-atom and coarse-grained water model used in the combined quantum mechanical and molecular mechanical method. We have used another multiresolution model, in which an atomic-level layer of water molecules around redox center is solvated in supramolecular coarse-grained waters for the redox potential calculations. Compared with the experimental data, this alternative multilayer model leads to less accurate results when used with the coarse-grained polarizable MARTINI water or big multipole water model for the coarse-grained layer.

  5. Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liao, Sing; Green, Michael E.

    2011-01-01

    Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 watermore » molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if

  6. A multi-standard approach for GIAO (13)C NMR calculations.

    PubMed

    Sarotti, Ariel M; Pellegrinet, Silvina C

    2009-10-02

    The influence of the reference standard employed in the calculation of (13)C NMR chemical shifts was investigated over a large variety of known organic compounds, using different quantum chemistry methods and basis sets. After detailed analysis of the collected data, we found that methanol and benzene are excellent reference standards for computing NMR shifts of sp(3)- and sp-sp(2)-hybridized carbon atoms, respectively. This multi-standard approach (MSTD) performs better than TMS in terms of accuracy and precision and also displays much lower dependence on the level of theory employed. The use of mPW1PW91/6-31G(d)//mPW1PW91/6-31G(d) level is recommended for accurate (13)C NMR chemical shift prediction at low computational cost.

  7. Entanglement in a quantum neural network based on quantum dots

    NASA Astrophysics Data System (ADS)

    Altaisky, M. V.; Zolnikova, N. N.; Kaputkina, N. E.; Krylov, V. A.; Lozovik, Yu E.; Dattani, N. S.

    2017-05-01

    We studied the quantum correlations between the nodes in a quantum neural network built of an array of quantum dots with dipole-dipole interaction. By means of the quasiadiabatic path integral simulation of the density matrix evolution in a presence of the common phonon bath we have shown the coherence in such system can survive up to the liquid nitrogen temperature of 77 K and above. The quantum correlations between quantum dots are studied by means of calculation of the entanglement of formation in a pair of quantum dots with the typical dot size of a few nanometers and interdot distance of the same order. We have shown that the proposed quantum neural network can keep the mixture of entangled states of QD pairs up to the above mentioned high temperatures.

  8. Quantum Chemical Examination of the Sequential Halogen Incorporation Scheme for the Modeling of Speciation of I/Br/Cl-Containing Trihalomethanes.

    PubMed

    Zhang, Chenyang; Li, Maodong; Han, Xuze; Yan, Mingquan

    2018-02-20

    The recently developed three-step ternary halogenation model interprets the incorporation of chlorine, bromine, and iodine ions into natural organic matter (NOM) and formation of iodine-, bromine-, and chlorine-containing trihalomethanes (THMs) based on the competition of iodine, bromine, and chlorine species at each node of the halogenation sequence. This competition is accounted for using the dimensionless ratios (denoted as γ) of kinetic rates of reactions of the initial attack sites or halogenated intermediates with chlorine, bromine, and iodine ions. However, correlations between the model predictions made and mechanistic aspects of the incorporation of halogen species need to be ascertained in more detail. In this study, quantum chemistry calculations were first used to probe the formation mechanism of 10 species of Cl-/Br-/I- THMs. The HOMO energy (E HOMO ) of each mono-, bi-, or trihalomethanes were calculated by B3LYP method in Gaussian 09 software. Linear correlations were found to exist between the logarithms of experimentally determined kinetic preference coefficients γ reported in prior research and, on the other hand, differences of E HOMO values between brominated/iodinated and chlorinated halomethanes. One notable exception from this trend was that observed for the incorporation of iodine into mono- and di-iodinated intermediates. These observations confirm the three-step halogen incorporation sequence and the factor γ in the statistical model. The combined use of quantum chemistry calculations and the ternary sequential halogenation model provides a new insight into the microscopic nature of NOM-halogen interactions and the trends seen in the behavior of γ factors incorporated in the THM speciation models.

  9. Using ‘particle in a box’ models to calculate energy levels in semiconductor quantum well structures

    NASA Astrophysics Data System (ADS)

    Ebbens, A. T.

    2018-07-01

    Although infinite potential ‘particle in a box’ models are widely used to introduce quantised energy levels their predictions cannot be quantitatively compared with atomic emission spectra. Here, this problem is overcome by describing how both infinite and finite potential well models can be used to calculate the confined energy levels of semiconductor quantum wells. This is done by using physics and mathematics concepts that are accessible to pre-university students. The results of the models are compared with experimental data and their accuracy discussed.

  10. Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

    PubMed

    Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

    2018-03-22

    Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

  11. Efficient Variational Quantum Simulator Incorporating Active Error Minimization

    NASA Astrophysics Data System (ADS)

    Li, Ying; Benjamin, Simon C.

    2017-04-01

    One of the key applications for quantum computers will be the simulation of other quantum systems that arise in chemistry, materials science, etc., in order to accelerate the process of discovery. It is important to ask the following question: Can this simulation be achieved using near-future quantum processors, of modest size and under imperfect control, or must it await the more distant era of large-scale fault-tolerant quantum computing? Here, we propose a variational method involving closely integrated classical and quantum coprocessors. We presume that all operations in the quantum coprocessor are prone to error. The impact of such errors is minimized by boosting them artificially and then extrapolating to the zero-error case. In comparison to a more conventional optimized Trotterization technique, we find that our protocol is efficient and appears to be fundamentally more robust against error accumulation.

  12. Quantum crystallographic charge density of urea

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Wall, Michael E.

    Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

  13. Quantum crystallographic charge density of urea

    DOE PAGES

    Wall, Michael E.

    2016-06-08

    Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

  14. Quantum chemical study of methane oxidation species

    NASA Technical Reports Server (NTRS)

    Jackels, Charles F.

    1993-01-01

    The research funded by this project has focused on quantum chemical investigations of molecular species thought to be important in the chemistry of the earth's upper and lower atmospheres. The body of this report contains brief discussions of the results of the several phases of this investigation. In many instances these results have been presented at scientific meetings and/or published in refereed journals. Those bibliographic references are given. In addition to the study of specific chemical systems, there were several phases during the course of this investigation where much of the effort went into the development and modification of computer codes necessary to carry out these calculations on the wide range of computer equipment used during this study. This type of code maintenance and development work did not generally result in publications and presentations, but a brief review is given.

  15. Mid-Infrared Quantum-Dot Quantum Cascade Laser: A Theoretical Feasibility Study

    DOE PAGES

    Michael, Stephan; Chow, Weng; Schneider, Hans

    2016-05-01

    In the framework of a microscopic model for intersubband gain from electrically pumped quantum-dot structures we investigate electrically pumped quantum-dots as active material for a mid-infrared quantum cascade laser. Our previous calculations have indicated that these structures could operate with reduced threshold current densities while also achieving a modal gain comparable to that of quantum well active materials. We study the influence of two important quantum-dot material parameters, here, namely inhomogeneous broadening and quantum-dot sheet density, on the performance of a proposed quantum cascade laser design. In terms of achieving a positive modal net gain, a high quantum-dot density canmore » compensate for moderately high inhomogeneous broadening, but at a cost of increased threshold current density. By minimizing quantum-dot density with presently achievable inhomogeneous broadening and total losses, significantly lower threshold densities than those reported in quantum-well quantum-cascade lasers are predicted by our theory.« less

  16. Quantum Monte Carlo Methods for First Principles Simulation of Liquid Water

    ERIC Educational Resources Information Center

    Gergely, John Robert

    2009-01-01

    Obtaining an accurate microscopic description of water structure and dynamics is of great interest to molecular biology researchers and in the physics and quantum chemistry simulation communities. This dissertation describes efforts to apply quantum Monte Carlo methods to this problem with the goal of making progress toward a fully "ab initio"…

  17. Molecular structure of tris(cyclopropylsilyl)amine as determined by gas electron diffraction and quantum-chemical calculations

    NASA Astrophysics Data System (ADS)

    Vishnevskiy, Yuri V.; Abaev, Maxim A.; Ivanov, Arkadii A.; Vilkov, Lev V.; Dakkouri, Marwan

    2008-10-01

    The molecular structure and conformation of tris(cyclopropylsilyl)amine (TCPSA) has been studied by means of gas-phase electron diffraction at 338 K and quantum-chemical calculations. A total of 12 relatively stable conformations of TCPSA molecule were considered. According to the experimental results and the DFT calculations the most stable conformer corresponds to a configuration (according to the Prelog-Klyne notation) of the type (-ac)(-ac)(+ac)-(-ac)(-ac)(+ac), where the first three parentheses describe the three different Si-N-Si-C torsional angles and the latter ones depict the rotation of the three cyclopropyl groups about the C ring-Si axes, respectively. The quantum-mechanical calculations were performed using various density functional (B3LYP, X3LYP and O3LYP) and perturbation MP2 methods in combination with double- and triple- ζ basis sets plus polarization and diffuse functions. The most important experimental geometrical parameters of TCPSA ( ra Å, ∠ h1 degrees) are: (Si-N) av = 1.741(3), (Si-C) av = 1.866(4), (C-C) av = 1.510(3), (C-C(Si)) av = 1.535(3), (N-Si-C) av = 115.1(18)°. For the purpose of comparison and searching for reasons leading to the planarity of the Si 3N moiety in trisilylated amines we carried out NBO analysis and optimized the geometries of numerous silylamines. Among these compounds was tris(allylsilyl)amine (TASA), which is isovalent and isoelectronic to TCPSA. Utilizing the structural results we obtained we could show that Si +⋯Si + electrostatic repulsive interaction is predominantly responsible for the planarity of the Si 3N skeleton in TCPSA and in all other trisilylamines we considered. We also found that regardless the size and partial charges of the substituents the Si-N-Si bond angle in various disilylamines amounts to 130 ± 2°.

  18. A model of CO-CH4 global transport/chemistry. I - Chemistry model

    NASA Technical Reports Server (NTRS)

    Peters, L. K.; Kitada, T.

    1980-01-01

    A simplified chemistry model was developed to incorporate the CO-CH4 chemistry into the global transport model of these compounds. CO is important because of its effects on atmospheric chemistry and is partly responsible for controlling the hydroxyl radical (OH) concentration in the troposphere. The model includes the photodissociation rate coefficients expressed as functions of solar zenith angle and altitude, and it was applied to determine the sensitivity of the OH concentration to trace gaseous species, such as NOx, O3, and H2O. Also, the concentrations and diurnal variations of OH and HO2, and the contribution of individual reactions to OH generation and consumption were calculated.

  19. Partition of unity finite element method for quantum mechanical materials calculations

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Pask, J. E.; Sukumar, N.

    The current state of the art for large-scale quantum-mechanical simulations is the planewave (PW) pseudopotential method, as implemented in codes such as VASP, ABINIT, and many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires significant nonlocal communications, which limit parallel efficiency. Real-space methods such as finite-differences (FD) and finite-elements (FE) have partially addressed both resolution and parallel-communications issues but have been plagued by one key disadvantage relative tomore » PW: excessive number of degrees of freedom (basis functions) needed to achieve the required accuracies. In this paper, we present a real-space partition of unity finite element (PUFE) method to solve the Kohn–Sham equations of density functional theory. In the PUFE method, we build the known atomic physics into the solution process using partition-of-unity enrichment techniques in finite element analysis. The method developed herein is completely general, applicable to metals and insulators alike, and particularly efficient for deep, localized potentials, as occur in calculations at extreme conditions of pressure and temperature. Full self-consistent Kohn–Sham calculations are presented for LiH, involving light atoms, and CeAl, involving heavy atoms with large numbers of atomic-orbital enrichments. We find that the new PUFE approach attains the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the PW method. As a result, we compute the equation of state of LiH and show that the computed lattice constant and bulk modulus are in excellent agreement with reference PW results, while requiring an order of magnitude fewer degrees of freedom to obtain.« less

  20. Partition of unity finite element method for quantum mechanical materials calculations

    DOE PAGES

    Pask, J. E.; Sukumar, N.

    2016-11-09

    The current state of the art for large-scale quantum-mechanical simulations is the planewave (PW) pseudopotential method, as implemented in codes such as VASP, ABINIT, and many others. However, since the PW method uses a global Fourier basis, with strictly uniform resolution at all points in space, it suffers from substantial inefficiencies in calculations involving atoms with localized states, such as first-row and transition-metal atoms, and requires significant nonlocal communications, which limit parallel efficiency. Real-space methods such as finite-differences (FD) and finite-elements (FE) have partially addressed both resolution and parallel-communications issues but have been plagued by one key disadvantage relative tomore » PW: excessive number of degrees of freedom (basis functions) needed to achieve the required accuracies. In this paper, we present a real-space partition of unity finite element (PUFE) method to solve the Kohn–Sham equations of density functional theory. In the PUFE method, we build the known atomic physics into the solution process using partition-of-unity enrichment techniques in finite element analysis. The method developed herein is completely general, applicable to metals and insulators alike, and particularly efficient for deep, localized potentials, as occur in calculations at extreme conditions of pressure and temperature. Full self-consistent Kohn–Sham calculations are presented for LiH, involving light atoms, and CeAl, involving heavy atoms with large numbers of atomic-orbital enrichments. We find that the new PUFE approach attains the required accuracies with substantially fewer degrees of freedom, typically by an order of magnitude or more, than the PW method. As a result, we compute the equation of state of LiH and show that the computed lattice constant and bulk modulus are in excellent agreement with reference PW results, while requiring an order of magnitude fewer degrees of freedom to obtain.« less

  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. Manipulating the Surface Chemistry of Quantum Dots for Sensitive Ratiometric Fluorescence Detection of Sulfur Dioxide.

    PubMed

    Li, Huihui; Zhu, Houjuan; Sun, Mingtai; Yan, Yehan; Zhang, Kui; Huang, Dejian; Wang, Suhua

    2015-08-11

    Herein, we report a novel approach to the rapid visual detection of gaseous sulfur dioxide (SO2) by manipulating the surface chemistry of 3-aminopropyltriethoxysilane (APTS)-modified quantum dots (QDs) using fluorescent coumarin-3-carboxylic acid (CCA) for specific reaction with SO2. The CCA molecules are attached to the surface amino groups of the QDs through electrostatic attraction, thus the fluorescence of CCA is greatly suppressed because of the formation of an ion-pair complex between the ATPS-modified QDs and CCA. Such an interaction is vulnerable to SO2 because SO2 can readily react with surface amino groups to form strong charge-transfer complexes and subsequently release the strongly fluorescent CCA molecules. The mechanism has been carefully verified through a series of control experiments. Upon exposure to different amounts of SO2, the fluorescent color of the nanoparticle-based sensor displays continuously changes from red to blue. Most importantly, the approach owns high selectivity for SO2 and a tolerance of interference, which enables the sensor to detect SO2 in a practical application. Using this fluorescence-based sensing method, we have achieved a visual detection limit of 6 ppb for gaseous SO2.

  3. Quantum Dynamics in Biological Systems

    NASA Astrophysics Data System (ADS)

    Shim, Sangwoo

    In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.

  4. Applications of Programmable Calculators in Chemistry Classes

    ERIC Educational Resources Information Center

    Holdsworth, David

    1977-01-01

    Described is the use of calculators in two experiments. In the first, students determine the relative atomic mass of magnesium. In the second, students use a calculator to determine a constant for gaseous concentrations of two reactants and the product at equilibrium. (AJ)

  5. Secure multi-party quantum summation based on quantum Fourier transform

    NASA Astrophysics Data System (ADS)

    Yang, Hui-Yi; Ye, Tian-Yu

    2018-06-01

    In this paper, we propose a novel secure multi-party quantum summation protocol based on quantum Fourier transform, where the traveling particles are transmitted in a tree-type mode. The party who prepares the initial quantum states is assumed to be semi-honest, which means that she may misbehave on her own but will not conspire with anyone. The proposed protocol can resist both the outside attacks and the participant attacks. Especially, one party cannot obtain other parties' private integer strings; and it is secure for the colluding attack performed by at most n - 2 parties, where n is the number of parties. In addition, the proposed protocol calculates the addition of modulo d and implements the calculation of addition in a secret-by-secret way rather than a bit-by-bit way.

  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. Inorganic Chemistry Solutions to Semiconductor Nanocrystal Problems

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Alvarado, Samuel R.; Guo, Yijun; Ruberu, T. Purnima A.

    2014-03-15

    The optoelectronic and chemical properties of semiconductor nanocrystals heavily depend on their composition, size, shape and internal structure, surface functionality, etc. Available strategies to alter these properties through traditional colloidal syntheses and ligand exchange methods place a premium on specific reaction conditions and surfactant combinations. In this invited review, we apply a molecular-level understanding of chemical precursor reactivity to reliably control the morphology, composition and intimate architecture (core/shell vs. alloyed) of semiconductor nanocrystals. We also describe our work aimed at achieving highly selective, low-temperature photochemical methods for the synthesis of semiconductor–metal and semiconductor–metal oxide photocatalytic nanocomposites. In addition, we describemore » our work on surface modification of semiconductor nanocrystal quantum dots using new approaches and methods that bypass ligand exchange, retaining the nanocrystal's native ligands and original optical properties, as well as on spectroscopic methods of characterization useful in determining surface ligand organization and chemistry. Using recent examples from our group and collaborators, we demonstrate how these efforts have lead to faster, wider and more systematic application of semiconductor nanocrystal-based materials to biological imaging and tracking, and to photocatalysis of unconventional substrates. We believe techniques and methods borrowed from inorganic chemistry (including coordination, organometallic and solid state chemistry) have much to offer in reaching a better understanding of the synthesis, functionalization and real-life application of such exciting materials as semiconductor nanocrystals (quantum dots, rods, tetrapods, etc.).« less

  8. An Assessment of the Accuracy of Semi-Empirical Quantum Chemistry Calculations of the Mechanical Properties of Polymers

    DTIC Science & Technology

    1991-03-01

    the crystal structure. The program Cerius 30 for Silicon Graphics workstations was used for this crystal simulation. A standard Lennard - Jones ...calculations ........... 16 2. General polymer stress-strain curve ......................... 23 3. Comparison of Morse and harmonic potentials ...a PE oligom er .......................................... 35 6. PE cluster strain dependent heat of formation potential ........... 36 7. Comparison

  9. Extensible Computational Chemistry Environment

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    2012-08-09

    ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less

  10. Simulated quantum computation of molecular energies.

    PubMed

    Aspuru-Guzik, Alán; Dutoi, Anthony D; Love, Peter J; Head-Gordon, Martin

    2005-09-09

    The calculation time for the energy of atoms and molecules scales exponentially with system size on a classical computer but polynomially using quantum algorithms. We demonstrate that such algorithms can be applied to problems of chemical interest using modest numbers of quantum bits. Calculations of the water and lithium hydride molecular ground-state energies have been carried out on a quantum computer simulator using a recursive phase-estimation algorithm. The recursive algorithm reduces the number of quantum bits required for the readout register from about 20 to 4. Mappings of the molecular wave function to the quantum bits are described. An adiabatic method for the preparation of a good approximate ground-state wave function is described and demonstrated for a stretched hydrogen molecule. The number of quantum bits required scales linearly with the number of basis functions, and the number of gates required grows polynomially with the number of quantum bits.

  11. Multiphase Equation of State and Strength Properties of Beryllium from AB INITIO and Quantum Molecular Dynamics Calculations.

    NASA Astrophysics Data System (ADS)

    Robert, G.; Sollier, A.; Legrand, Ph.

    2007-12-01

    In the framework of density functional theory, static properties and phonon spectra of beryllium have been calculated under high compression (for pressures up to 4 Mbar) for two solid phases: hexagonal compact (hcp) and body-centered cubic (bcc). The melting curve and some isotherms in the liquid phase have been calculated using quantum molecular dynamics. The coupling of these theoretical data to a quasi-harmonic approach (phonon moments) allows us to suggest a new theoretical phase diagram and to build a multiphase equation of state (EOS) valid in a large range of pressure and temperature. The resulting Hugoniot curves as well as the evolution of the longitudinal sound speed with both pressure and temperature are in good agreement with available experimental data.

  12. Physical Chemistry for the Chemical and Biological Sciences (by Raymond Chang)

    NASA Astrophysics Data System (ADS)

    Pounds, Andrew

    2001-05-01

    This book does offer an alternative approach to physical chemistry that is particularly well suited for those who want to pursue a course of study more focused on the biological sciences. It could also be an excellent choice for schools that mainly serve preprofessional programs or for schools that have split physical chemistry tracks to independently serve the B.S. and B.A. degrees. Since the book focuses on single-variable mathematics, schools that require only one year of calculus for their chemistry degree could also think about adopting it. However, in general, the use of the text as a drop-in replacement for physical chemistry for the B.S. degree is questionable owing to its lack of focus on quantum mechanics and its implications for spectroscopy.

  13. Learning that Prepares for More Learning: Symbolic Mathematics in Physical Chemistry

    ERIC Educational Resources Information Center

    Zielinski, Theresa Julia

    2004-01-01

    The well-crafted templates are useful to learn the new concepts of chemistry. The templates focus on pressure-volume work, the Boltzmann distribution, the Gibbs free energy function, intermolecular potentials, the second virial coefficient and quantum mechanical tunneling.

  14. WavePacket: A Matlab package for numerical quantum dynamics.II: Open quantum systems, optimal control, and model reduction

    NASA Astrophysics Data System (ADS)

    Schmidt, Burkhard; Hartmann, Carsten

    2018-07-01

    WavePacket is an open-source program package for numeric simulations in quantum dynamics. It can solve time-independent or time-dependent linear Schrödinger and Liouville-von Neumann-equations in one or more dimensions. Also coupled equations can be treated, which allows, e.g., to simulate molecular quantum dynamics beyond the Born-Oppenheimer approximation. Optionally accounting for the interaction with external electric fields within the semi-classical dipole approximation, WavePacket can be used to simulate experiments involving tailored light pulses in photo-induced physics or chemistry. Being highly versatile and offering visualization of quantum dynamics 'on the fly', WavePacket is well suited for teaching or research projects in atomic, molecular and optical physics as well as in physical or theoretical chemistry. Building on the previous Part I [Comp. Phys. Comm. 213, 223-234 (2017)] which dealt with closed quantum systems and discrete variable representations, the present Part II focuses on the dynamics of open quantum systems, with Lindblad operators modeling dissipation and dephasing. This part also describes the WavePacket function for optimal control of quantum dynamics, building on rapid monotonically convergent iteration methods. Furthermore, two different approaches to dimension reduction implemented in WavePacket are documented here. In the first one, a balancing transformation based on the concepts of controllability and observability Gramians is used to identify states that are neither well controllable nor well observable. Those states are either truncated or averaged out. In the other approach, the H2-error for a given reduced dimensionality is minimized by H2 optimal model reduction techniques, utilizing a bilinear iterative rational Krylov algorithm. The present work describes the MATLAB version of WavePacket 5.3.0 which is hosted and further developed at the Sourceforge platform, where also extensive Wiki-documentation as well as numerous

  15. Molecular structure of the trans and cis isomers of metal-free phthalocyanine studied by gas-phase electron diffraction and high-level quantum chemical calculations: NH tautomerization and calculated vibrational frequencies.

    PubMed

    Strenalyuk, Tatyana; Samdal, Svein; Volden, Hans Vidar

    2008-05-29

    The molecular structure of the trans isomer of metal-free phthalocyanine (H2Pc) is determined using the gas electron diffraction (GED) method and high-level quantum chemical calculations. B3LYP calculations employing the basis sets 6-31G**, 6-311++G**, and cc-pVTZ give two tautomeric isomers for the inner H atoms, a trans isomer having D2h symmetry and a cis isomer having C2v symmetry. The trans isomer is calculated to be 41.6 (B3LYP/6-311++G**, zero-point corrected) and 37.3 kJ/mol (B3LYP/cc-pVTZ, not zero-point corrected) more stable than the cis isomer. However, Hartree-Fock (HF) calculations using different basis sets predict that cis is preferred and that trans does not exist as a stable form of the molecule. The equilibrium composition in the gas phase at 471 degrees C (the temperature of the GED experiment) calculated at the B3LYP/6-311++G** level is 99.8% trans and 0.2% cis. This is in very good agreement with the GED data, which indicate that the mole fraction of the cis isomer is close to zero. The transition states for two mechanisms of the NH tautomerization have been characterized. A concerted mechanism where the two H atoms move simultaneously yields a transition state of D2h symmetry and an energy barrier of 95.8 kJ/mol. A two-step mechanism where a trans isomer is converted to a cis isomer, which is converted into another trans isomer, proceeds via two transition states of C(s) symmetry and an energy barrier of 64.2 kJ/mol according to the B3LYP/6-311++G** calculation. The molecular geometry determined from GED is in very good agreement with the geometry obtained from the quantum chemical calculations. Vibrational frequencies, IR, and Raman intensities have been calculated using B3LYP/6-311++G**. These calculations indicate that the molecule is rather flexible with six vibrational frequencies in the range of 20-84 cm(-1) for the trans isomer. The cis isomer might be detected by infrared matrix spectroscopy since the N-H stretching frequencies are

  16. Dilution physics modeling: Dissolution/precipitation chemistry

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Onishi, Y.; Reid, H.C.; Trent, D.S.

    This report documents progress made to date on integrating dilution/precipitation chemistry and new physical models into the TEMPEST thermal-hydraulics computer code. Implementation of dissolution/precipitation chemistry models is necessary for predicting nonhomogeneous, time-dependent, physical/chemical behavior of tank wastes with and without a variety of possible engineered remediation and mitigation activities. Such behavior includes chemical reactions, gas retention, solids resuspension, solids dissolution and generation, solids settling/rising, and convective motion of physical and chemical species. Thus this model development is important from the standpoint of predicting the consequences of various engineered activities, such as mitigation by dilution, retrieval, or pretreatment, that can affectmore » safe operations. The integration of a dissolution/precipitation chemistry module allows the various phase species concentrations to enter into the physical calculations that affect the TEMPEST hydrodynamic flow calculations. The yield strength model of non-Newtonian sludge correlates yield to a power function of solids concentration. Likewise, shear stress is concentration-dependent, and the dissolution/precipitation chemistry calculations develop the species concentration evolution that produces fluid flow resistance changes. Dilution of waste with pure water, molar concentrations of sodium hydroxide, and other chemical streams can be analyzed for the reactive species changes and hydrodynamic flow characteristics.« less

  17. Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

    PubMed

    Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

    2014-06-14

    Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

  18. Quantum radiation produced by the entanglement of quantum fields

    NASA Astrophysics Data System (ADS)

    Iso, Satoshi; Oshita, Naritaka; Tatsukawa, Rumi; Yamamoto, Kazuhiro; Zhang, Sen

    2017-01-01

    We investigate the quantum radiation produced by an Unruh-De Witt detector in a uniformly accelerating motion coupled to the vacuum fluctuations. Quantum radiation is nonvanishing, which is consistent with the previous calculation by Lin and Hu [Phys. Rev. D 73, 124018 (2006), 10.1103/PhysRevD.73.124018]. We infer that this quantum radiation from the Unruh-De Witt detector is generated by the nonlocal correlation of the Minkowski vacuum state, which has its origin in the entanglement of the state between the left and the right Rindler wedges.

  19. Efficient Calculation of Exact Exchange Within the Quantum Espresso Software Package

    NASA Astrophysics Data System (ADS)

    Barnes, Taylor; Kurth, Thorsten; Carrier, Pierre; Wichmann, Nathan; Prendergast, David; Kent, Paul; Deslippe, Jack

    Accurate simulation of condensed matter at the nanoscale requires careful treatment of the exchange interaction between electrons. In the context of plane-wave DFT, these interactions are typically represented through the use of approximate functionals. Greater accuracy can often be obtained through the use of functionals that incorporate some fraction of exact exchange; however, evaluation of the exact exchange potential is often prohibitively expensive. We present an improved algorithm for the parallel computation of exact exchange in Quantum Espresso, an open-source software package for plane-wave DFT simulation. Through the use of aggressive load balancing and on-the-fly transformation of internal data structures, our code exhibits speedups of approximately an order of magnitude for practical calculations. Additional optimizations are presented targeting the many-core Intel Xeon-Phi ``Knights Landing'' architecture, which largely powers NERSC's new Cori system. We demonstrate the successful application of the code to difficult problems, including simulation of water at a platinum interface and computation of the X-ray absorption spectra of transition metal oxides.

  20. Los Alamos Quantum Dots for Solar, Display Technology

    ScienceCinema

    Klimov, Victor

    2018-05-01

    Quantum dots are ultra-small bits of semiconductor matter that can be synthesized with nearly atomic precision via modern methods of colloidal chemistry. Their emission color can be tuned by simply varying their dimensions. Color tunability is combined with high emission efficiencies approaching 100 percent. These properties have recently become the basis of a new technology – quantum dot displays – employed, for example, in the newest generation of e-readers and video monitors.

  1. A quantum framework for likelihood ratios

    NASA Astrophysics Data System (ADS)

    Bond, Rachael L.; He, Yang-Hui; Ormerod, Thomas C.

    The ability to calculate precise likelihood ratios is fundamental to science, from Quantum Information Theory through to Quantum State Estimation. However, there is no assumption-free statistical methodology to achieve this. For instance, in the absence of data relating to covariate overlap, the widely used Bayes’ theorem either defaults to the marginal probability driven “naive Bayes’ classifier”, or requires the use of compensatory expectation-maximization techniques. This paper takes an information-theoretic approach in developing a new statistical formula for the calculation of likelihood ratios based on the principles of quantum entanglement, and demonstrates that Bayes’ theorem is a special case of a more general quantum mechanical expression.

  2. Quantum Game of Life

    NASA Astrophysics Data System (ADS)

    Glick, Aaron; Carr, Lincoln; Calarco, Tommaso; Montangero, Simone

    2014-03-01

    In order to investigate the emergence of complexity in quantum systems, we present a quantum game of life, inspired by Conway's classic game of life. Through Matrix Product State (MPS) calculations, we simulate the evolution of quantum systems, dictated by a Hamiltonian that defines the rules of our quantum game. We analyze the system through a number of measures which elicit the emergence of complexity in terms of spatial organization, system dynamics, and non-local mutual information within the network. Funded by NSF

  3. Electron-Phonon Systems on a Universal Quantum Computer

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Macridin, Alexandru; Spentzouris, Panagiotis; Amundson, James

    We present an algorithm that extends existing quantum algorithms forsimulating fermion systems in quantum chemistry and condensed matter physics toinclude phonons. The phonon degrees of freedom are represented with exponentialaccuracy on a truncated Hilbert space with a size that increases linearly withthe cutoff of the maximum phonon number. The additional number of qubitsrequired by the presence of phonons scales linearly with the size of thesystem. The additional circuit depth is constant for systems with finite-rangeelectron-phonon and phonon-phonon interactions and linear for long-rangeelectron-phonon interactions. Our algorithm for a Holstein polaron problem wasimplemented on an Atos Quantum Learning Machine (QLM) quantum simulatoremployingmore » the Quantum Phase Estimation method. The energy and the phonon numberdistribution of the polaron state agree with exact diagonalization results forweak, intermediate and strong electron-phonon coupling regimes.« less

  4. OpenFlow Extensions for Programmable Quantum Networks

    DTIC Science & Technology

    2017-06-19

    Extensions for Programmable Quantum Networks by Venkat Dasari, Nikolai Snow, and Billy Geerhart Computational and Information Sciences Directorate...distribution is unlimited. 1 1. Introduction Quantum networks and quantum computing have been receiving a surge of interest recently.1–3 However, there has...communicate using entangled particles and perform calculations using quantum logic gates. Additionally, quantum computing uses a quantum bit (qubit

  5. Quantum Dot Surface Engineering: Toward Inert Fluorophores with Compact Size and Bright, Stable Emission

    PubMed Central

    Lim, Sung Jun; Ma, Liang; Schleife, André; Smith, Andrew M.

    2016-01-01

    The surfaces of colloidal nanocrystals are complex interfaces between solid crystals, coordinating ligands, and liquid solutions. For fluorescent quantum dots, the properties of the surface vastly influence the efficiency of light emission, stability, and physical interactions, and thus determine their sensitivity and specificity when they are used to detect and image biological molecules. But after more than 30 years of study, the surfaces of quantum dots remain poorly understood and continue to be an important subject of both experimental and theoretical research. In this article, we review the physics and chemistry of quantum dot surfaces and describe approaches to engineer optimal fluorescent probes for applications in biomolecular imaging and sensing. We describe the structure and electronic properties of crystalline facets, the chemistry of ligand coordination, and the impact of ligands on optical properties. We further describe recent advances in compact coatings that have significantly improved their properties by providing small hydrodynamic size, high stability and fluorescence efficiency, and minimal nonspecific interactions with cells and biological molecules. While major progress has been made in both basic and applied research, many questions remain in the chemistry and physics of quantum dot surfaces that have hindered key breakthroughs to fully optimize their properties. PMID:28344357

  6. Raman spectrum, quantum mechanical calculations and vibrational assignments of (95% alpha-TeO2/5% Sm2O3) glass.

    PubMed

    Shaltout, I; Mohamed, Tarek A

    2007-06-01

    Chozen system of tellurite glasses doped with rare earth oxides (95% alpha-TeO(2)+5% Sm2O3) was prepared by melt quenching. Consequently, the Raman spectrum (150-1250 cm(-1)) of the modified tellurite have been recorded. As a continuation to our normal coordinate analysis, force constants and quantum mechanical (QM) calculations for tbp TeO4(4-) (triagonal bipyramid, C(2v)) and TeO(3+1); Te2O7(6-) (bridged tetrahedral), we have carried out ab initio frequency calculations for tpy TeO3(2-) (triagonal pyramidal, C(3v) and C(s)) and tp TeO3(2-) (triagonal planar, D(3h)) ions. The quantum mechanical calculations at the levels of RHF, B3LYP and MP2 allow confident vibrational assignments and structural identification in the binary oxide glass (95% alpha-TeO2 +5% Sm2O3). The dominant three-dimensional network structures in the modified glass are triagonal pyramidal TeO3 with minor features of short range distorted tbp TeO4 and bridged tetrahedral unit of TeO(3+1), leading to a structure of infinite chain. Therefore, alpha-TeO2/Sm2O3 (95/5%) glass experience structural changes from TeO4 (tbp); Te2O7 (TeO(3+1))-->TeO3 (tpy).

  7. Effects of quantum confinement and shape on band gap of core/shell quantum dots and nanowires

    NASA Astrophysics Data System (ADS)

    Gao, Faming

    2011-05-01

    A quantum confinement model for nanocrystals developed is extended to study for the optical gap shifts in core/shell quantum dots and nanowires. The chemical bond properties and gap shifts in the InP/ZnS, CdSe/CdS, CdSe/ZnS, and CdTe/ZnS core/shell quantum dots are calculated in detail. The calculated band gaps are in excellent agreement with experimental values. The effects of structural taping and twinning on quantum confinement of InP and Si nanowires are elucidated. It is found theoretically that a competition between the positive Kubo energy-gap shift and the negative surface energy shift plays the crucial role in the optical gaps of these nanosystems.

  8. Online Grading of Calculations in General Chemistry Laboratory Write-Ups

    ERIC Educational Resources Information Center

    Silva, Alexsandra; Gonzales, Robert; Brennan, Daniel P.

    2010-01-01

    In the past, there were frequently complaints about the grading of laboratory reports in our laboratory chemistry courses. This article discussed the implementation of an online submission of laboratory acquired data using LON-CAPA (The Learning Online Network with Computer-Assisted Personalized Approach), which is an open source management and…

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

    PubMed

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

    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(e) = 931.2 cm(-1) which agrees very well with recent experimentally derived estimates D(e) = 929.7±2 cm(-1) [J. M. Merritt, V. E. Bondybey, and M. C. Heaven, Science 324, 1548 (2009)] and D(e) = 934.6 cm(-1) [K. Patkowski, V. Špirko, and K. Szalewicz, Science 326, 1382 (2009)], as well the best composite theoretical estimates, D(e) = 938±15 cm(-1) [K. Patkowski, R. Podeszwa, and K. Szalewicz, J. Phys. Chem. A 111, 12822 (2007)] and D(e) = 935.1±10 cm(-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 ¹Σ(g)⁻ 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.

  10. Quantum information processing with superconducting circuits: a review.

    PubMed

    Wendin, G

    2017-10-01

    During the last ten years, superconducting circuits have passed from being interesting physical devices to becoming contenders for near-future useful and scalable quantum information processing (QIP). Advanced quantum simulation experiments have been shown with up to nine qubits, while a demonstration of quantum supremacy with fifty qubits is anticipated in just a few years. Quantum supremacy means that the quantum system can no longer be simulated by the most powerful classical supercomputers. Integrated classical-quantum computing systems are already emerging that can be used for software development and experimentation, even via web interfaces. Therefore, the time is ripe for describing some of the recent development of superconducting devices, systems and applications. As such, the discussion of superconducting qubits and circuits is limited to devices that are proven useful for current or near future applications. Consequently, the centre of interest is the practical applications of QIP, such as computation and simulation in Physics and Chemistry.

  11. Quantum information processing with superconducting circuits: a review

    NASA Astrophysics Data System (ADS)

    Wendin, G.

    2017-10-01

    During the last ten years, superconducting circuits have passed from being interesting physical devices to becoming contenders for near-future useful and scalable quantum information processing (QIP). Advanced quantum simulation experiments have been shown with up to nine qubits, while a demonstration of quantum supremacy with fifty qubits is anticipated in just a few years. Quantum supremacy means that the quantum system can no longer be simulated by the most powerful classical supercomputers. Integrated classical-quantum computing systems are already emerging that can be used for software development and experimentation, even via web interfaces. Therefore, the time is ripe for describing some of the recent development of superconducting devices, systems and applications. As such, the discussion of superconducting qubits and circuits is limited to devices that are proven useful for current or near future applications. Consequently, the centre of interest is the practical applications of QIP, such as computation and simulation in Physics and Chemistry.

  12. Integrating Particulate Representations into AP Chemistry and Introductory Chemistry Courses

    ERIC Educational Resources Information Center

    Prilliman, Stephen G.

    2014-01-01

    The College Board's recently revised curriculum for advanced placement (AP) chemistry places a strong emphasis on conceptual understanding, including representations of particle phenomena. This change in emphasis is informed by years of research showing that students could perform algorithmic calculations but not explain those calculations…

  13. Compressed Sensing Quantum Process Tomography for Superconducting Quantum Gates

    NASA Astrophysics Data System (ADS)

    Rodionov, Andrey

    An important challenge in quantum information science and quantum computing is the experimental realization of high-fidelity quantum operations on multi-qubit systems. Quantum process tomography (QPT) is a procedure devised to fully characterize a quantum operation. We first present the results of the estimation of the process matrix for superconducting multi-qubit quantum gates using the full data set employing various methods: linear inversion, maximum likelihood, and least-squares. To alleviate the problem of exponential resource scaling needed to characterize a multi-qubit system, we next investigate a compressed sensing (CS) method for QPT of two-qubit and three-qubit quantum gates. Using experimental data for two-qubit controlled-Z gates, taken with both Xmon and superconducting phase qubits, we obtain estimates for the process matrices with reasonably high fidelities compared to full QPT, despite using significantly reduced sets of initial states and measurement configurations. We show that the CS method still works when the amount of data is so small that the standard QPT would have an underdetermined system of equations. We also apply the CS method to the analysis of the three-qubit Toffoli gate with simulated noise, and similarly show that the method works well for a substantially reduced set of data. For the CS calculations we use two different bases in which the process matrix is approximately sparse (the Pauli-error basis and the singular value decomposition basis), and show that the resulting estimates of the process matrices match with reasonably high fidelity. For both two-qubit and three-qubit gates, we characterize the quantum process by its process matrix and average state fidelity, as well as by the corresponding standard deviation defined via the variation of the state fidelity for different initial states. We calculate the standard deviation of the average state fidelity both analytically and numerically, using a Monte Carlo method. Overall

  14. Quantum friction in arbitrarily directed motion

    DOE PAGES

    Klatt, J.; Farías, M. Belen; Dalvit, D. A. R.; ...

    2017-05-30

    In quantum friction, the electromagnetic fluctuation-induced frictional force decelerating an atom which moves past a macroscopic dielectric body, has so far eluded experimental evidence despite more than three decades of theoretical studies. Inspired by the recent finding that dynamical corrections to such an atom's internal dynamics are enhanced by one order of magnitude for vertical motion—compared with the paradigmatic setup of parallel motion—here we generalize quantum friction calculations to arbitrary angles between the atom's direction of motion and the surface in front of which it moves. Motivated by the disagreement between quantum friction calculations based on Markovian quantum master equationsmore » and time-dependent perturbation theory, we carry out our derivations of the quantum frictional force for arbitrary angles by employing both methods and compare them.« less

  15. Quantum simulation of quantum field theory using continuous variables

    DOE PAGES

    Marshall, Kevin; Pooser, Raphael C.; Siopsis, George; ...

    2015-12-14

    Much progress has been made in the field of quantum computing using continuous variables over the last couple of years. This includes the generation of extremely large entangled cluster states (10,000 modes, in fact) as well as a fault tolerant architecture. This has lead to the point that continuous-variable quantum computing can indeed be thought of as a viable alternative for universal quantum computing. With that in mind, we present a new algorithm for continuous-variable quantum computers which gives an exponential speedup over the best known classical methods. Specifically, this relates to efficiently calculating the scattering amplitudes in scalar bosonicmore » quantum field theory, a problem that is known to be hard using a classical computer. Thus, we give an experimental implementation based on cluster states that is feasible with today's technology.« less

  16. Quantum simulation of quantum field theory using continuous variables

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Marshall, Kevin; Pooser, Raphael C.; Siopsis, George

    Much progress has been made in the field of quantum computing using continuous variables over the last couple of years. This includes the generation of extremely large entangled cluster states (10,000 modes, in fact) as well as a fault tolerant architecture. This has lead to the point that continuous-variable quantum computing can indeed be thought of as a viable alternative for universal quantum computing. With that in mind, we present a new algorithm for continuous-variable quantum computers which gives an exponential speedup over the best known classical methods. Specifically, this relates to efficiently calculating the scattering amplitudes in scalar bosonicmore » quantum field theory, a problem that is known to be hard using a classical computer. Thus, we give an experimental implementation based on cluster states that is feasible with today's technology.« less

  17. Imaging the He2 quantum halo state using a free electron laser

    PubMed Central

    Zeller, Stefan; Kunitski, Maksim; Voigtsberger, Jörg; Kalinin, Anton; Schottelius, Alexander; Schober, Carl; Waitz, Markus; Sann, Hendrik; Hartung, Alexander; Bauer, Tobias; Pitzer, Martin; Trinter, Florian; Goihl, Christoph; Janke, Christian; Richter, Martin; Kastirke, Gregor; Weller, Miriam; Czasch, Achim; Kitzler, Markus; Braune, Markus; Grisenti, Robert E.; Schmidt, Lothar Ph. H.; Schöffler, Markus S.; Williams, Joshua B.; Jahnke, Till; Dörner, Reinhard

    2016-01-01

    Quantum tunneling is a ubiquitous phenomenon in nature and crucial for many technological applications. It allows quantum particles to reach regions in space which are energetically not accessible according to classical mechanics. In this “tunneling region,” the particle density is known to decay exponentially. This behavior is universal across all energy scales from nuclear physics to chemistry and solid state systems. Although typically only a small fraction of a particle wavefunction extends into the tunneling region, we present here an extreme quantum system: a gigantic molecule consisting of two helium atoms, with an 80% probability that its two nuclei will be found in this classical forbidden region. This circumstance allows us to directly image the exponentially decaying density of a tunneling particle, which we achieved for over two orders of magnitude. Imaging a tunneling particle shows one of the few features of our world that is truly universal: the probability to find one of the constituents of bound matter far away is never zero but decreases exponentially. The results were obtained by Coulomb explosion imaging using a free electron laser and furthermore yielded He2’s binding energy of 151.9±13.3 neV, which is in agreement with most recent calculations. PMID:27930299

  18. Algorithm for quantum-mechanical finite-nuclear-mass variational calculations of atoms with two p electrons using all-electron explicitly correlated Gaussian basis functions

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Sharkey, Keeper L.; Pavanello, Michele; Bubin, Sergiy

    2009-12-15

    A new algorithm for calculating the Hamiltonian matrix elements with all-electron explicitly correlated Gaussian functions for quantum-mechanical calculations of atoms with two p electrons or a single d electron have been derived and implemented. The Hamiltonian used in the approach was obtained by rigorously separating the center-of-mass motion and it explicitly depends on the finite mass of the nucleus. The approach was employed to perform test calculations on the isotopes of the carbon atom in their ground electronic states and to determine the finite-nuclear-mass corrections for these states.

  19. Quantum game theory

    NASA Astrophysics Data System (ADS)

    Stohler, Michael Lehman

    2002-01-01

    Non-cooperative quantum games have received much attention recently. This thesis defines and divides current works into two major categories of gaming techniques with close attention paid to Nash equilibria, form and possibilities for the payoff functions, and the benefits of using a quantum strategy. In addition to comparing and contrasting these techniques, new applications and calculations are discussed. Finally, the techniques are expanded into 3 x 3 games which allows the study of non-transitive strategies in quantum games.

  20. Facile synthesis of corticosteroids prodrugs from isolated hydrocortisone acetate and their quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Sethi, Arun; Singh, Ranvijay Pratap; Prakash, Rohit; Amandeep

    2017-02-01

    In the present research paper corticosteroids prodrugs of hydrocortisone acetate (1) have been synthesized, which was isolated from the flowers of Allamanda Violacea. The hydrocortisone acetate (1) was hydrolyzed to hydrocortisone (2) which was subsequently converted to prednisolone (3). Both the hydrocortisone (1) and prednisolone (2) underwent Steglich esterification with naproxen and Ibuprofen yielding compounds 11, 17 dihydroxy-21-(2-(6-methoxynaphthalene-2yl) propionoxy)-pregn-4-ene-3, 20-dione (4), 11, 17-dihydroxy-21-(2-(4-isobutylphenyl) propionoxy)-pregn-4-ene-3, 20-dione (5), 21-(2-(6-methoxynaphthalene-2-yl) propionoxy) 11,17-di-hydroxy-3,20-diketo-pregn-1,4-diene (6) and 11,17-di-hydroxy-3,20-diketo-pregn-1,4-diene-21-yl-2-(4-isobutylphenyl) propanoate (7). The synthesized compounds have been characterized with the help of spectroscopic techniques like 1H, 13C NMR, FT-IR spectroscopy and mass spectrometry. Density functional theory (DFT) with B3LYP functional and 6-31G (d, p) basis set has been used for the Quantum chemical calculations. The electronic properties such as frontier orbitals and band gap energies were calculated by TD-DFT approach. Intramolecular interactions have been identified by AIM (Atoms in Molecule) approach and vibrational wavenumbers have been calculated using DFT method. The reactivity and reactive site within the synthesized prodrugs have been examined with the help of reactivity descriptors. Dipole moment, polarizability and first static hyperpolarizability have been calculated to get a better insight of the properties of synthesized prodrugs. The molecular electrostatic potential (MEP) surface analysis has also been carried out.

  1. Full-dimensional Quantum Calculations of Rovibrational Transitions in CS induced by H2

    NASA Astrophysics Data System (ADS)

    Yang, Benhui; Zhang, Peng; Stancil, Phillip; Bowman, J.; Balakrishnan, N.; Forrey, R.

    2017-04-01

    Carbon monosulfide (CS), the sulfur analogue of carbon monoxide, has been widely observed in a variety interstellar regions. An accurate prediction of its abundance requires collisional rate coefficients with ambient gases. However, the collisional rate coefficients are largely unknown and primarily rely on theoretical scattering calculations. In interstellar clouds, the dominant collision partner is H2. Rate coefficient data on CS-H2 collisions are limited to pure rotational transitions and no data exist for rovibrational transitions. In this work we evaluate the first full-dimensional potential energy surface for the CS-H2 system using high-level electronic structure theory and perform explicit quantum close-coupling calculations of rovibrational transitions in CS induced by H2 collisions. Cross sections and rate coefficients for rotational transitions are compared with previous theoretical results obtained within a rigid-rotor model. For rovibrational transitions, state-to-state rate coefficients are evaluated for several low-lying rotational levels in the first excited vibrational level of CS. Results are presented for both para-H2 and ortho-H2 collision partners. Work at UGA and Emory are supported by NASA Grant No. NNX16AF09G, at UNLV by NSF Grant No. PHY-1505557, and at Penn State by NSF Grant No. PHY-1503615.

  2. Effect of self assembled quantum dots on carrier mobility, with application to modeling the dark current in quantum dot infrared photodetectors

    NASA Astrophysics Data System (ADS)

    Youssef, Sarah; El-Batawy, Yasser M.; Abouelsaood, Ahmed A.

    2016-09-01

    A theoretical method for calculating the electron mobility in quantum dot infrared photodetectors is developed. The mobility calculation is based on a time-dependent, finite-difference solution of the Boltzmann transport equation in a bulk semiconductor material with randomly positioned conical quantum dots. The quantum dots act as scatterers of current carriers (conduction-band electrons in our case), resulting in limiting their mobility. In fact, carrier scattering by quantum dots is typically the dominant factor in determining the mobility in the active region of the quantum dot device. The calculated values of the mobility are used in a recently developed generalized drift-diffusion model for the dark current of the device [Ameen et al., J. Appl. Phys. 115, 063703 (2014)] in order to fix the overall current scale. The results of the model are verified by comparing the predicted dark current characteristics to those experimentally measured and reported for actual InAs/GaAs quantum dot infrared photodetectors. Finally, the effect of the several relevant device parameters, including the operating temperature and the quantum dot average density, is studied.

  3. Quantum mechanical calculation of aqueuous uranium complexes: carbonate, phosphate, organic and biomolecular species

    PubMed Central

    Kubicki, James D; Halada, Gary P; Jha, Prashant; Phillips, Brian L

    2009-01-01

    Background Quantum mechanical calculations were performed on a variety of uranium species representing U(VI), U(V), U(IV), U-carbonates, U-phosphates, U-oxalates, U-catecholates, U-phosphodiesters, U-phosphorylated N-acetyl-glucosamine (NAG), and U-2-Keto-3-doxyoctanoate (KDO) with explicit solvation by H2O molecules. These models represent major U species in natural waters and complexes on bacterial surfaces. The model results are compared to observed EXAFS, IR, Raman and NMR spectra. Results Agreement between experiment and theory is acceptable in most cases, and the reasons for discrepancies are discussed. Calculated Gibbs free energies are used to constrain which configurations are most likely to be stable under circumneutral pH conditions. Reduction of U(VI) to U(IV) is examined for the U-carbonate and U-catechol complexes. Conclusion Results on the potential energy differences between U(V)- and U(IV)-carbonate complexes suggest that the cause of slower disproportionation in this system is electrostatic repulsion between UO2 [CO3]35- ions that must approach one another to form U(VI) and U(IV) rather than a change in thermodynamic stability. Calculations on U-catechol species are consistent with the observation that UO22+ can oxidize catechol and form quinone-like species. In addition, outer-sphere complexation is predicted to be the most stable for U-catechol interactions based on calculated energies and comparison to 13C NMR spectra. Outer-sphere complexes (i.e., ion pairs bridged by water molecules) are predicted to be comparable in Gibbs free energy to inner-sphere complexes for a model carboxylic acid. Complexation of uranyl to phosphorus-containing groups in extracellular polymeric substances is predicted to favor phosphonate groups, such as that found in phosphorylated NAG, rather than phosphodiesters, such as those in nucleic acids. PMID:19689800

  4. Quantum and quasi-classical calculations for the S+ + H2(v, j) →SH+(v′, j′)+H reactive collisions

    PubMed Central

    Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

    2016-01-01

    State-to-state cross sections for the S+ + H2(v, j) → SH+ (v′, j′) + H endothermic reaction are obtained with quantum wave packet(WP) and quasi-classical (QCT) methods for different initial rovibrational H2(v, j) over a wide range of translation energies. Final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient, that vibrational energy is the most favorable for reaction and rotational excitation significantly enhance reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid on an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2, An interesting resonant behaviour found in WP calculations is also discussed and is associated to the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al.[1] for S+ + HD and S+ +D2 reactions, finding a reasonably good agreement with those results. PMID:27055725

  5. Studies of quantum dots in the quantum Hall regime

    NASA Astrophysics Data System (ADS)

    Goldmann, Eyal

    We present two studies of quantum dots in the quantum Hall regime. In the first study, presented in Chapter 3, we investigate the edge reconstruction phenomenon believed to occur when the quantum dot filling fraction is n≲1 . Our approach involves the examination of large dots (≤40 electrons) using a partial diagonalization technique in which the occupancies of the deep interior orbitals are frozen. To interpret the results of this calculation, we evaluate the overlap between the diagonalized ground state and a set of trial wavefunctions which we call projected necklace (PN) states. A PN state is simply the angular momentum projection of a maximum density droplet surrounded by a ring of localized electrons. Our calculations reveal that PN states have up to 99% overlap with the diagonalized ground states, and are lower in energy than the states identified in Chamon and Wen's study of the edge reconstruction. In the second study, presented in Chapter 4, we investigate quantum dots in the fractional quantum Hall regime using a Hartree formulation of composite fermion theory. We find that under appropriate conditions, the chemical potential of the dots oscillates periodically with B due to the transfer of composite fermions between quasi-Landau bands. This effect is analogous the addition spectrum oscillations which occur in quantum dots in the integer quantum Hall regime. Period f0 oscillations are found in sharply confined dots with filling factors nu = 2/5 and nu = 2/3. Period 3 f0 oscillations are found in a parabolically confined nu = 2/5 dot. More generally, we argue that the oscillation period of dots with band pinning should vary continuously with B, whereas the period of dots without band pinning is f0 .

  6. Collisional breakup in a quantum system of three charged particles

    PubMed

    Rescigno; Baertschy; Isaacs; McCurdy

    1999-12-24

    Since the invention of quantum mechanics, even the simplest example of the collisional breakup of a system of charged particles, e(-) + H --> H(+) + e(-) + e(-) (where e(-) is an electron and H is hydrogen), has resisted solution and is now one of the last unsolved fundamental problems in atomic physics. A complete solution requires calculation of the energies and directions for a final state in which all three particles are moving away from each other. Even with supercomputers, the correct mathematical description of this state has proved difficult to apply. A framework for solving ionization problems in many areas of chemistry and physics is finally provided by a mathematical transformation of the Schrodinger equation that makes the final state tractable, providing the key to a numerical solution of this problem that reveals its full dynamics.

  7. Entanglement entropy of the Q≥4 quantum Potts chain.

    PubMed

    Lajkó, Péter; Iglói, Ferenc

    2017-01-01

    The entanglement entropy S is an indicator of quantum correlations in the ground state of a many-body quantum system. At a second-order quantum phase-transition point in one dimension S generally has a logarithmic singularity. Here we consider quantum spin chains with a first-order quantum phase transition, the prototype being the Q-state quantum Potts chain for Q>4 and calculate S across the transition point. According to numerical, density matrix renormalization group results at the first-order quantum phase transition point S shows a jump, which is expected to vanish for Q→4^{+}. This jump is calculated in leading order as ΔS=lnQ[1-4/Q-2/(QlnQ)+O(1/Q^{2})].

  8. Chern-Simons expectation values and quantum horizons from loop quantum gravity and the Duflo map.

    PubMed

    Sahlmann, Hanno; Thiemann, Thomas

    2012-03-16

    We report on a new approach to the calculation of Chern-Simons theory expectation values, using the mathematical underpinnings of loop quantum gravity, as well as the Duflo map, a quantization map for functions on Lie algebras. These new developments can be used in the quantum theory for certain types of black hole horizons, and they may offer new insights for loop quantum gravity, Chern-Simons theory and the theory of quantum groups.

  9. Absolute quantum yield measurement of powder samples.

    PubMed

    Moreno, Luis A

    2012-05-12

    Measurement of fluorescence quantum yield has become an important tool in the search for new solutions in the development, evaluation, quality control and research of illumination, AV equipment, organic EL material, films, filters and fluorescent probes for bio-industry. Quantum yield is calculated as the ratio of the number of photons absorbed, to the number of photons emitted by a material. The higher the quantum yield, the better the efficiency of the fluorescent material. For the measurements featured in this video, we will use the Hitachi F-7000 fluorescence spectrophotometer equipped with the Quantum Yield measuring accessory and Report Generator program. All the information provided applies to this system. Measurement of quantum yield in powder samples is performed following these steps: 1. Generation of instrument correction factors for the excitation and emission monochromators. This is an important requirement for the correct measurement of quantum yield. It has been performed in advance for the full measurement range of the instrument and will not be shown in this video due to time limitations. 2. Measurement of integrating sphere correction factors. The purpose of this step is to take into consideration reflectivity characteristics of the integrating sphere used for the measurements. 3. Reference and Sample measurement using direct excitation and indirect excitation. 4. Quantum Yield calculation using Direct and Indirect excitation. Direct excitation is when the sample is facing directly the excitation beam, which would be the normal measurement setup. However, because we use an integrating sphere, a portion of the emitted photons resulting from the sample fluorescence are reflected by the integrating sphere and will re-excite the sample, so we need to take into consideration indirect excitation. This is accomplished by measuring the sample placed in the port facing the emission monochromator, calculating indirect quantum yield and correcting the direct

  10. Towards a feasible implementation of quantum neural networks using quantum dots

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Altaisky, Mikhail V., E-mail: altaisky@mx.iki.rssi.ru, E-mail: nzolnik@iki.rssi.ru; Zolnikova, Nadezhda N., E-mail: altaisky@mx.iki.rssi.ru, E-mail: nzolnik@iki.rssi.ru; Kaputkina, Natalia E., E-mail: nataly@misis.ru

    2016-03-07

    We propose an implementation of quantum neural networks using an array of quantum dots with dipole-dipole interactions. We demonstrate that this implementation is both feasible and versatile by studying it within the framework of GaAs based quantum dot qubits coupled to a reservoir of acoustic phonons. Using numerically exact Feynman integral calculations, we have found that the quantum coherence in our neural networks survive for over a hundred ps even at liquid nitrogen temperatures (77 K), which is three orders of magnitude higher than current implementations, which are based on SQUID-based systems operating at temperatures in the mK range.

  11. Analytical scheme calculations of angular momentum coupling and recoupling coefficients

    NASA Astrophysics Data System (ADS)

    Deveikis, A.; Kuznecovas, A.

    2007-03-01

    We investigate the Scheme programming language opportunities to analytically calculate the Clebsch-Gordan coefficients, Wigner 6j and 9j symbols, and general recoupling coefficients that are used in the quantum theory of angular momentum. The considered coefficients are calculated by a direct evaluation of the sum formulas. The calculation results for large values of quantum angular momenta were compared with analogous calculations with FORTRAN and Java programming languages.

  12. Negative muon chemistry: the quantum muon effect and the finite nuclear mass effect.

    PubMed

    Posada, Edwin; Moncada, Félix; Reyes, Andrés

    2014-10-09

    The any-particle molecular orbital method at the full configuration interaction level has been employed to study atoms in which one electron has been replaced by a negative muon. In this approach electrons and muons are described as quantum waves. A scheme has been proposed to discriminate nuclear mass and quantum muon effects on chemical properties of muonic and regular atoms. This study reveals that the differences in the ionization potentials of isoelectronic muonic atoms and regular atoms are of the order of millielectronvolts. For the valence ionizations of muonic helium and muonic lithium the nuclear mass effects are more important. On the other hand, for 1s ionizations of muonic atoms heavier than beryllium, the quantum muon effects are more important. In addition, this study presents an assessment of the nuclear mass and quantum muon effects on the barrier of Heμ + H2 reaction.

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

    PubMed

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

    2015-01-01

    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. Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. 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. (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.

  14. Electronic Structure Calculations and Adaptation Scheme in Multi-core Computing Environments

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Seshagiri, Lakshminarasimhan; Sosonkina, Masha; Zhang, Zhao

    2009-05-20

    Multi-core processing environments have become the norm in the generic computing environment and are being considered for adding an extra dimension to the execution of any application. The T2 Niagara processor is a very unique environment where it consists of eight cores having a capability of running eight threads simultaneously in each of the cores. Applications like General Atomic and Molecular Electronic Structure (GAMESS), used for ab-initio molecular quantum chemistry calculations, can be good indicators of the performance of such machines and would be a guideline for both hardware designers and application programmers. In this paper we try to benchmarkmore » the GAMESS performance on a T2 Niagara processor for a couple of molecules. We also show the suitability of using a middleware based adaptation algorithm on GAMESS on such a multi-core environment.« less

  15. Topics in quantum chaos

    NASA Astrophysics Data System (ADS)

    Jordan, Andrew Noble

    2002-09-01

    In this dissertation, we study the quantum mechanics of classically chaotic dynamical systems. We begin by considering the decoherence effects a quantum chaotic system has on a simple quantum few state system. Typical time evolution of a quantum system whose classical limit is chaotic generates structures in phase space whose size is much smaller than Planck's constant. A naive application of Heisenberg's uncertainty principle indicates that these structures are not physically relevant. However, if we take the quantum chaotic system in question to be an environment which interacts with a simple two state quantum system (qubit), we show that these small phase-space structures cause the qubit to generically lose quantum coherence if and only if the environment has many degrees of freedom, such as a dilute gas. This implies that many-body environments may be crucial for the phenomenon of quantum decoherence. Next, we turn to an analysis of statistical properties of time correlation functions and matrix elements of quantum chaotic systems. A semiclassical evaluation of matrix elements of an operator indicates that the dominant contribution will be related to a classical time correlation function over the energy surface. For a highly chaotic class of dynamics, these correlation functions may be decomposed into sums of Ruelle resonances, which control exponential decay to the ergodic distribution. The theory is illustrated both numerically and theoretically on the Baker map. For this system, we are able to isolate individual Ruelle modes. We further consider dynamical systems whose approach to ergodicity is given by a power law rather than an exponential in time. We propose a billiard with diffusive boundary conditions, whose classical solution may be calculated analytically. We go on to compare the exact solution with an approximation scheme, as well calculate asympotic corrections. Quantum spectral statistics are calculated assuming the validity of the Again, Altshuler

  16. Exact quantum scattering calculation of transport properties for free radicals: OH(X2Π)-helium.

    PubMed

    Dagdigian, Paul J; Alexander, Millard H

    2012-09-07

    Transport properties for OH-He are computed through quantum scattering calculations using the ab initio potential energy surfaces determined by Lee et al. [J. Chem. Phys. 113, 5736 (2000)]. To gauge the importance of the open-shell character of OH and the anisotropy of the potential on the transport properties, including the collision integrals Ω((1,1)) and Ω((2,2)), as well as the diffusion coefficient, calculations were performed with the full potential, with the difference potential V(dif) set to zero, and with only the spherical average of the potential. Slight differences (3%-5%) in the computed diffusion coefficient were found between the values obtained using the full potential and the truncated potentials. The computed diffusion coefficients were compared to recent experimental measurements and those computed with a Lennard-Jones (LJ) 12-6 potential. The values obtained with the full potential were slightly higher than the experimental values. The LJ 12-6 potential was found to underestimate the variation in temperature as compared to that obtained using the full OH-He ab initio potential.

  17. Symbolic Mathematics Engines in Teaching Chemistry: A Symposium Report

    ERIC Educational Resources Information Center

    Ellison, Mark

    2004-01-01

    The use of Symbolic Mathematics Engines (SMEs) in chemical education as a part of the Division of Computers in Chemistry was discussed by a panel of educators at the Symbolic Calculation in Chemistry symposium in Philadelphia in 2004. The panelists agreed that many more topics in chemistry are amenable to SME's exploration and that symbolic…

  18. Frozen-Orbital and Downfolding Calculations with Auxiliary-Field Quantum Monte Carlo.

    PubMed

    Purwanto, Wirawan; Zhang, Shiwei; Krakauer, Henry

    2013-11-12

    We describe the implementation of the frozen-orbital and downfolding approximations in the auxiliary-field quantum Monte Carlo (AFQMC) method. These approaches can provide significant computational savings, compared to fully correlating all of the electrons. While the many-body wave function is never explicit in AFQMC, its random walkers are Slater determinants, whose orbitals may be expressed in terms of any one-particle orbital basis. It is therefore straightforward to partition the full N-particle Hilbert space into active and inactive parts to implement the frozen-orbital method. In the frozen-core approximation, for example, the core electrons can be eliminated in the correlated part of the calculations, greatly increasing the computational efficiency, especially for heavy atoms. Scalar relativistic effects are easily included using the Douglas-Kroll-Hess theory. Using this method, we obtain a way to effectively eliminate the error due to single-projector, norm-conserving pseudopotentials in AFQMC. We also illustrate a generalization of the frozen-orbital approach that downfolds high-energy basis states to a physically relevant low-energy sector, which allows a systematic approach to produce realistic model Hamiltonians to further increase efficiency for extended systems.

  19. New developments in theoretical thermochemistry and electronic structure applications in supramolecular chemistry and cluster science

    NASA Astrophysics Data System (ADS)

    Ramabhadran, Raghunath Ozhapakkam

    In a concise display of the power and diversity of electronic structure theory (EST), the work presented herein involves the development of new computational methods to advance the practical utility of quantum chemistry, as well as solving different types of challenging chemical problems by applying existing EST tools. The research presented is highly interdisciplinary in nature and features synergistic collaborations to solve real-life problems such as regulating toxic chemicals and generating alternative sources of energy. In the first chapter of this dissertation, the solution to a long-standing problem in theoretical thermochemistry is accomplished by the development of the automated, chemically intuitive and generalized thermochemical hierarchy, Connectivity-Based Hierarchy (CBH) to accurately predict the thermochemical properties of organic molecules. The extension of the hierarchy to predict the enthalpies of formations of biomonomers such as amino acids is also presented. The development of a computationally efficient protocol to accurately extrapolate to high CCSD(T) energies based on MP2 and DFT energies using CBH is presented in the second chapter, thus merging theoretical thermochemistry with fragment-based methods in quantum chemistry. This merger drastically reduces the computational cost involved in a CCSD(T) calculation, while retaining the impeccable accuracy it offers. The practical utility of the CH hydrogen bond, commonly thought as being too weak to be used in supramolecular applications has been demonstrated by DFT calculations (along with experimental results from the Flood group) in the third chapter. This is accomplished by systematically studying the binding of monoatomic chloride, diatomic and toxic cyanide and the polyatomic bi-fluoride anions for the first time using only CH hydrogen bonds within a triazolophane macrocycle. The fourth chapter contains the introduction of the concept of fluxionality in the chemical reactions of

  20. Thermodynamic integration from classical to quantum mechanics.

    PubMed

    Habershon, Scott; Manolopoulos, David E

    2011-12-14

    We present a new method for calculating quantum mechanical corrections to classical free energies, based on thermodynamic integration from classical to quantum mechanics. In contrast to previous methods, our method is numerically stable even in the presence of strong quantum delocalization. We first illustrate the method and its relationship to a well-established method with an analysis of a one-dimensional harmonic oscillator. We then show that our method can be used to calculate the quantum mechanical contributions to the free energies of ice and water for a flexible water model, a problem for which the established method is unstable. © 2011 American Institute of Physics

  1. Integration of Computational Chemistry into the Undergraduate Organic Chemistry Laboratory Curriculum

    ERIC Educational Resources Information Center

    Esselman, Brian J.; Hill, Nicholas J.

    2016-01-01

    Advances in software and hardware have promoted the use of computational chemistry in all branches of chemical research to probe important chemical concepts and to support experimentation. Consequently, it has become imperative that students in the modern undergraduate curriculum become adept at performing simple calculations using computational…

  2. Scaled Quantum Mechanical scale factors for vibrational calculations using alternate polarized and augmented basis sets with the B3LYP density functional calculation model

    NASA Astrophysics Data System (ADS)

    Legler, C. R.; Brown, N. R.; Dunbar, R. A.; Harness, M. D.; Nguyen, K.; Oyewole, O.; Collier, W. B.

    2015-06-01

    The Scaled Quantum Mechanical (SQM) method of scaling calculated force constants to predict theoretically calculated vibrational frequencies is expanded to include a broad array of polarized and augmented basis sets based on the split valence 6-31G and 6-311G basis sets with the B3LYP density functional. Pulay's original choice of a single polarized 6-31G(d) basis coupled with a B3LYP functional remains the most computationally economical choice for scaled frequency calculations. But it can be improved upon with additional polarization functions and added diffuse functions for complex molecular systems. The new scale factors for the B3LYP density functional and the 6-31G, 6-31G(d), 6-31G(d,p), 6-31G+(d,p), 6-31G++(d,p), 6-311G, 6-311G(d), 6-311G(d,p), 6-311G+(d,p), 6-311G++(d,p), 6-311G(2d,p), 6-311G++(2d,p), 6-311G++(df,p) basis sets are shown. The double d polarized models did not perform as well and the source of the decreased accuracy was investigated. An alternate system of generating internal coordinates that uses the out-of plane wagging coordinate whenever it is possible; makes vibrational assignments via potential energy distributions more meaningful. Automated software to produce SQM scaled vibrational calculations from different molecular orbital packages is presented.

  3. Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

    PubMed

    Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier

    2013-02-19

    Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of

  4. An Integrated, Statistical Molecular Approach to the Physical Chemistry Curriculum

    ERIC Educational Resources Information Center

    Cartier, Stephen F.

    2009-01-01

    As an alternative to the "thermodynamics first" or "quantum first" approaches to the physical chemistry curriculum, the statistical definition of entropy and the Boltzmann distribution are introduced in the first days of the course and the entire two-semester curriculum is then developed from these concepts. Once the tools of statistical mechanics…

  5. The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

    PubMed

    Thackston, Russell; Fortenberry, Ryan C

    2015-05-05

    The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. © 2015 Wiley Periodicals, Inc.

  6. Spectroscopic Characterization of Streptavidin Functionalized Quantum dots1

    PubMed Central

    Wu, Yang; Lopez, Gabriel P.; Sklar, Larry A.; Buranda, Tione

    2007-01-01

    The spectroscopic properties of quantum dots can be strongly influenced by the conditions of their synthesis. In this work we have characterized several spectroscopic properties of commercial, streptavidin functionalized quantum dots (QD525, lot#1005-0045 and QD585, Lot#0905-0031 from Invitrogen). This is the first step in the development of calibration beads, to be used in a generalizable quantification scheme of multiple fluorescent tags in flow cytometry or microscopy applications. We used light absorption, photoexcitation, and emission spectra, together with excited-state lifetime measurements to characterize their spectroscopic behavior, concentrating on the 400-500nm wavelength ranges that are important in biological applications. Our data show an anomalous dependence of emission spectrum, lifetimes, and quantum yield (QY) on excitation wavelength that is particularly pronounced in the QD525. For QD525, QY values ranged from 0.2 at 480nm excitation up to 0.4 at 450nm and down again to 0.15 at 350nm. For QD585, QY values were constant at 0.2 between 500nm and 400nm, but dropped to 0.1 at 350nm. We attribute the wavelength dependences to heterogeneity in size and surface defects in the QD525, consistent with characteristics previously described in the chemistry literature. The results are discussed in the context of bridging the gap between what is currently known in the physical chemistry literature of quantum dots, and the quantitative needs of assay development in biological applications. PMID:17368555

  7. Scrambling of quantum information in quantum many-body systems

    NASA Astrophysics Data System (ADS)

    Iyoda, Eiki; Sagawa, Takahiro

    2018-04-01

    We systematically investigate scrambling (or delocalizing) processes of quantum information encoded in quantum many-body systems by using numerical exact diagonalization. As a measure of scrambling, we adopt the tripartite mutual information (TMI) that becomes negative when quantum information is delocalized. We clarify that scrambling is an independent property of the integrability of Hamiltonians; TMI can be negative or positive for both integrable and nonintegrable systems. This implies that scrambling is a separate concept from conventional quantum chaos characterized by nonintegrability. Specifically, we argue that there are a few exceptional initial states that do not exhibit scrambling, and show that such exceptional initial states have small effective dimensions. Furthermore, we calculate TMI in the Sachdev-Ye-Kitaev (SYK) model, a fermionic toy model of quantum gravity. We find that disorder does not make scrambling slower but makes it smoother in the SYK model, in contrast to many-body localization in spin chains.

  8. Quantum Tunnelling to the Origin and Evolution of Life

    PubMed Central

    Trixler, Frank

    2013-01-01

    Quantum tunnelling is a phenomenon which becomes relevant at the nanoscale and below. It is a paradox from the classical point of view as it enables elementary particles and atoms to permeate an energetic barrier without the need for sufficient energy to overcome it. Tunnelling might seem to be an exotic process only important for special physical effects and applications such as the Tunnel Diode, Scanning Tunnelling Microscopy (electron tunnelling) or Near-field Optical Microscopy operating in photon tunnelling mode. However, this review demonstrates that tunnelling can do far more, being of vital importance for life: physical and chemical processes which are crucial in theories about the origin and evolution of life can be traced directly back to the effects of quantum tunnelling. These processes include the chemical evolution in stellar interiors and within the cold interstellar medium, prebiotic chemistry in the atmosphere and subsurface of planetary bodies, planetary habitability via insolation and geothermal heat as well as the function of biomolecular nanomachines. This review shows that quantum tunnelling has many highly important implications to the field of molecular and biological evolution, prebiotic chemistry and astrobiology. PMID:24039543

  9. Thiolated graphene - a new platform for anchoring CdSe quantum dots for hybrid heterostructures

    NASA Astrophysics Data System (ADS)

    Debgupta, Joyashish; Pillai, Vijayamohanan K.

    2013-04-01

    Effective organization of small CdSe quantum dots on graphene sheets has been achieved by a simple solution exchange with thiol terminated graphene prepared by diazonium salt chemistry. This generic methodology of CdSe QD attachment to any graphene surface has remarkable implications in designing hybrid heterostructures.Effective organization of small CdSe quantum dots on graphene sheets has been achieved by a simple solution exchange with thiol terminated graphene prepared by diazonium salt chemistry. This generic methodology of CdSe QD attachment to any graphene surface has remarkable implications in designing hybrid heterostructures. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr00363a

  10. Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.

    PubMed

    Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro

    2012-11-21

    In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.

  11. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation.

    PubMed

    Ferenczy, György G

    2013-04-05

    Mixed quantum mechanics/quantum mechanics (QM/QM) and quantum mechanics/molecular mechanics (QM/MM) methods make computations feasible for extended chemical systems by separating them into subsystems that are treated at different level of sophistication. In many applications, the subsystems are covalently bound and the use of frozen localized orbitals at the boundary is a possible way to separate the subsystems and to ensure a sensible description of the electronic structure near to the boundary. A complication in these methods is that orthogonality between optimized and frozen orbitals has to be warranted and this is usually achieved by an explicit orthogonalization of the basis set to the frozen orbitals. An alternative to this approach is proposed by calculating the wave-function from the Huzinaga equation that guaranties orthogonality to the frozen orbitals without basis set orthogonalization. The theoretical background and the practical aspects of the application of the Huzinaga equation in mixed methods are discussed. Forces have been derived to perform geometry optimization with wave-functions from the Huzinaga equation. Various properties have been calculated by applying the Huzinaga equation for the central QM subsystem, representing the environment by point charges and using frozen strictly localized orbitals to connect the subsystems. It is shown that a two to three bond separation of the chemical or physical event from the frozen bonds allows a very good reproduction (typically around 1 kcal/mol) of standard Hartree-Fock-Roothaan results. The proposed scheme provides an appropriate framework for mixed QM/QM and QM/MM methods. Copyright © 2012 Wiley Periodicals, Inc.

  12. How well can global chemistry models calculate the reactivity of short-lived greenhouse gases in the remote troposphere, knowing the chemical composition

    NASA Astrophysics Data System (ADS)

    Prather, Michael J.; Flynn, Clare M.; Zhu, Xin; Steenrod, Stephen D.; Strode, Sarah A.; Fiore, Arlene M.; Correa, Gustavo; Murray, Lee T.; Lamarque, Jean-Francois

    2018-05-01

    We develop a new protocol for merging in situ measurements with 3-D model simulations of atmospheric chemistry with the goal of integrating these data to identify the most reactive air parcels in terms of tropospheric production and loss of the greenhouse gases ozone and methane. Presupposing that we can accurately measure atmospheric composition, we examine whether models constrained by such measurements agree on the chemical budgets for ozone and methane. In applying our technique to a synthetic data stream of 14 880 parcels along 180° W, we are able to isolate the performance of the photochemical modules operating within their global chemistry-climate and chemistry-transport models, removing the effects of modules controlling tracer transport, emissions, and scavenging. Differences in reactivity across models are driven only by the chemical mechanism and the diurnal cycle of photolysis rates, which are driven in turn by temperature, water vapor, solar zenith angle, clouds, and possibly aerosols and overhead ozone, which are calculated in each model. We evaluate six global models and identify their differences and similarities in simulating the chemistry through a range of innovative diagnostics. All models agree that the more highly reactive parcels dominate the chemistry (e.g., the hottest 10 % of parcels control 25-30 % of the total reactivities), but do not fully agree on which parcels comprise the top 10 %. Distinct differences in specific features occur, including the spatial regions of maximum ozone production and methane loss, as well as in the relationship between photolysis and these reactivities. Unique, possibly aberrant, features are identified for each model, providing a benchmark for photochemical module development. Among the six models tested here, three are almost indistinguishable based on the inherent variability caused by clouds, and thus we identify four, effectively distinct, chemical models. Based on this work, we suggest that water vapor

  13. Quantum Theory of Jaynes' Principle, Bayes' Theorem, and Information

    NASA Astrophysics Data System (ADS)

    Haken, Hermann

    2014-12-01

    After a reminder of Jaynes' maximum entropy principle and of my quantum theoretical extension, I consider two coupled quantum systems A,B and formulate a quantum version of Bayes' theorem. The application of Feynman's disentangling theorem allows me to calculate the conditional density matrix ρ (A|B) , if system A is an oscillator (or a set of them), linearly coupled to an arbitrary quantum system B. Expectation values can simply be calculated by means of the normalization factor of ρ (A|B) that is derived.

  14. The Open Gate of the KV1.2 Channel: Quantum Calculations Show the Key Role of Hydration

    PubMed Central

    Kariev, Alisher M.; Njau, Philipa; Green, Michael E.

    2014-01-01

    The open gate of the Kv1.2 voltage-gated potassium channel can just hold a hydrated K+ ion. Quantum calculations starting from the x-ray coordinates of the channel confirm this, showing little change from the x-ray coordinates for the protein. Water molecules not in the x-ray coordinates, and the ion itself, are placed by the calculation. The water molecules, including their orientation and hydrogen bonding, with and without an ion, are critical for the path of the ion, from the solution to the gate. A sequence of steps is postulated in which the potential experienced by the ion in the pore is influenced by the position of the ion. The gate structure, with and without the ion, has been optimized. The charges on the atoms and bond lengths have been calculated using natural bond orbital calculations, giving K+ ∼0.77 charges, rather than 1.0. The PVPV hinge sequence has been mutated in silico to PVVV (P407V in the 2A79 numbering). The water structure around the ion becomes discontinuous, separated into two sections, above and below the ion. PVPV conservation closely relates to maintaining the water structure. Finally, these results have implications concerning gating. PMID:24507595

  15. Coupled harmonic oscillators and their quantum entanglement.

    PubMed

    Makarov, Dmitry N

    2018-04-01

    A system of two coupled quantum harmonic oscillators with the Hamiltonian H[over ̂]=1/2(1/m_{1}p[over ̂]_{1}^{2}+1/m_{2}p[over ̂]_{2}^{2}+Ax_{1}^{2}+Bx_{2}^{2}+Cx_{1}x_{2}) can be found in many applications of quantum and nonlinear physics, molecular chemistry, and biophysics. The stationary wave function of such a system is known, but its use for the analysis of quantum entanglement is complicated because of the complexity of computing the Schmidt modes. Moreover, there is no exact analytical solution to the nonstationary Schrodinger equation H[over ̂]Ψ=iℏ∂Ψ/∂t and Schmidt modes for such a dynamic system. In this paper we find a solution to the nonstationary Schrodinger equation; we also find in an analytical form a solution to the Schmidt mode for both stationary and dynamic problems. On the basis of the Schmidt modes, the quantum entanglement of the system under consideration is analyzed. It is shown that for certain parameters of the system, quantum entanglement can be very large.

  16. Coupled harmonic oscillators and their quantum entanglement

    NASA Astrophysics Data System (ADS)

    Makarov, Dmitry N.

    2018-04-01

    A system of two coupled quantum harmonic oscillators with the Hamiltonian H ̂=1/2 (1/m1p̂1 2+1/m2p̂2 2+A x12+B x22+C x1x2) can be found in many applications of quantum and nonlinear physics, molecular chemistry, and biophysics. The stationary wave function of such a system is known, but its use for the analysis of quantum entanglement is complicated because of the complexity of computing the Schmidt modes. Moreover, there is no exact analytical solution to the nonstationary Schrodinger equation H ̂Ψ =i ℏ ∂/Ψ ∂ t and Schmidt modes for such a dynamic system. In this paper we find a solution to the nonstationary Schrodinger equation; we also find in an analytical form a solution to the Schmidt mode for both stationary and dynamic problems. On the basis of the Schmidt modes, the quantum entanglement of the system under consideration is analyzed. It is shown that for certain parameters of the system, quantum entanglement can be very large.

  17. Quantum and quasi-classical calculations for the S⁺ + H₂(v,j) → SH⁺(v',j') + H reactive collisions.

    PubMed

    Zanchet, Alexandre; Roncero, Octavio; Bulut, Niyazi

    2016-04-28

    State-to-state cross-sections for the S(+) + H2(v,j) → SH(+)(v',j') + H endothermic reaction are obtained using quantum wave packet (WP) and quasi-classical (QCT) methods for different initial ro-vibrational H2(v,j) over a wide range of translation energies. The final state distribution as a function of the initial quantum number is obtained and discussed. Additionally, the effect of the internal excitation of H2 on the reactivity is carefully studied. It appears that energy transfer among modes is very inefficient that vibrational energy is the most favorable for the reaction, and rotational excitation significantly enhances the reactivity when vibrational energy is sufficient to reach the product. Special attention is also paid to an unusual discrepancy between classical and quantum dynamics for low rotational levels while agreement improves with rotational excitation of H2. An interesting resonant behaviour found in WP calculations is also discussed and associated with the existence of roaming classical trajectories that enhance the reactivity of the title reaction. Finally, a comparison with the experimental results of Stowe et al. for S(+) + HD and S(+) + D2 reactions exhibits a reasonably good agreement with those results.

  18. Entropic cohering power in quantum operations

    NASA Astrophysics Data System (ADS)

    Xi, Zhengjun; Hu, Ming-Liang; Li, Yongming; Fan, Heng

    2018-02-01

    Coherence is a basic feature of quantum systems and a common necessary condition for quantum correlations. It is also an important physical resource in quantum information processing. In this paper, using relative entropy, we consider a more general definition of the cohering power of quantum operations. First, we calculate the cohering power of unitary quantum operations and show that the amount of distributed coherence caused by non-unitary quantum operations cannot exceed the quantum-incoherent relative entropy between system of interest and its environment. We then find that the difference between the distributed coherence and the cohering power is larger than the quantum-incoherent relative entropy. As an application, we consider the distributed coherence caused by purification.

  19. A linearization of quantum channels

    NASA Astrophysics Data System (ADS)

    Crowder, Tanner

    2015-06-01

    Because the quantum channels form a compact, convex set, we can express any quantum channel as a convex combination of extremal channels. We give a Euclidean representation for the channels whose inverses are also valid channels; these are a subset of the extreme points. They form a compact, connected Lie group, and we calculate its Lie algebra. Lastly, we calculate a maximal torus for the group and provide a constructive approach to decomposing any invertible channel into a product of elementary channels.

  20. FastChem: An ultra-fast equilibrium chemistry

    NASA Astrophysics Data System (ADS)

    Kitzmann, Daniel; Stock, Joachim

    2018-04-01

    FastChem is an equilibrium chemistry code that calculates the chemical composition of the gas phase for given temperatures and pressures. Written in C++, it is based on a semi-analytic approach, and is optimized for extremely fast and accurate calculations.