Science.gov

Sample records for combined computational chemistry

  1. Computational chemistry

    NASA Technical Reports Server (NTRS)

    Arnold, J. O.

    1987-01-01

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

  2. Computational quantum chemistry website

    SciTech Connect

    1997-08-22

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

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

    SciTech Connect

    Sugimoto, Manabu; Ideo, Toshihiro; Iwane, Ryo

    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 the 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.

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

    NASA Astrophysics Data System (ADS)

    Sugimoto, Manabu; Ideo, Toshihiro; Iwane, Ryo

    2015-12-01

    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 the 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.

  5. Computational chemistry research

    NASA Technical Reports Server (NTRS)

    Levin, Eugene

    1987-01-01

    Task 41 is composed of two parts: (1) analysis and design studies related to the Numerical Aerodynamic Simulation (NAS) Extended Operating Configuration (EOC) and (2) computational chemistry. During the first half of 1987, Dr. Levin served as a member of an advanced system planning team to establish the requirements, goals, and principal technical characteristics of the NAS EOC. A paper entitled 'Scaling of Data Communications for an Advanced Supercomputer Network' is included. The high temperature transport properties (such as viscosity, thermal conductivity, etc.) of the major constituents of air (oxygen and nitrogen) were correctly determined. The results of prior ab initio computer solutions of the Schroedinger equation were combined with the best available experimental data to obtain complete interaction potentials for both neutral and ion-atom collision partners. These potentials were then used in a computer program to evaluate the collision cross-sections from which the transport properties could be determined. A paper entitled 'High Temperature Transport Properties of Air' is included.

  6. Computational chemistry at Janssen

    NASA Astrophysics Data System (ADS)

    van Vlijmen, Herman; Desjarlais, Renee L.; Mirzadegan, Tara

    2016-12-01

    Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.

  7. Computational chemistry at Janssen.

    PubMed

    van Vlijmen, Herman; Desjarlais, Renee L; Mirzadegan, Tara

    2017-03-01

    Computer-aided drug discovery activities at Janssen are carried out by scientists in the Computational Chemistry group of the Discovery Sciences organization. This perspective gives an overview of the organizational and operational structure, the science, internal and external collaborations, and the impact of the group on Drug Discovery at Janssen.

  8. Chemistry by Computer.

    ERIC Educational Resources Information Center

    Garmon, Linda

    1981-01-01

    Describes the features of various computer chemistry programs. Utilization of computer graphics, color, digital imaging, and other innovations are discussed in programs including those which aid in the identification of unknowns, predict whether chemical reactions are feasible, and predict the biological activity of xenobiotic compounds. (CS)

  9. Chemistry by Computer.

    ERIC Educational Resources Information Center

    Garmon, Linda

    1981-01-01

    Describes the features of various computer chemistry programs. Utilization of computer graphics, color, digital imaging, and other innovations are discussed in programs including those which aid in the identification of unknowns, predict whether chemical reactions are feasible, and predict the biological activity of xenobiotic compounds. (CS)

  10. Using Computers in Chemistry.

    ERIC Educational Resources Information Center

    Pankuch, Brian

    1985-01-01

    Describes the use of two interactive computer programs in a college chemistry course. The first is a commercially-available simulation program (for Apple microcomputers with game paddles) which demonstrates gas laws. The second is a teacher-developed molecular bonding simulation program. (JN)

  11. Using Computers in Chemistry.

    ERIC Educational Resources Information Center

    Pankuch, Brian

    1985-01-01

    Describes the use of two interactive computer programs in a college chemistry course. The first is a commercially-available simulation program (for Apple microcomputers with game paddles) which demonstrates gas laws. The second is a teacher-developed molecular bonding simulation program. (JN)

  12. Extensible Computational Chemistry Environment

    SciTech Connect

    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 the 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.

  13. Corrosion chemistry closing comments: opportunities in corrosion science facilitated by operando experimental characterization combined with multi-scale computational modelling.

    PubMed

    Scully, John R

    2015-01-01

    Recent advances in characterization tools, computational capabilities, and theories have created opportunities for advancement in understanding of solid-fluid interfaces at the nanoscale in corroding metallic systems. The Faraday Discussion on Corrosion Chemistry in 2015 highlighted some of the current needs, gaps and opportunities in corrosion science. Themes were organized into several hierarchical categories that provide an organizational framework for corrosion. Opportunities to develop fundamental physical and chemical data which will enable further progress in thermodynamic and kinetic modelling of corrosion were discussed. These will enable new and better understanding of unit processes that govern corrosion at the nanoscale. Additional topics discussed included scales, films and oxides, fluid-surface and molecular-surface interactions, selected topics in corrosion science and engineering as well as corrosion control. Corrosion science and engineering topics included complex alloy dissolution, local corrosion, and modelling of specific corrosion processes that are made up of collections of temporally and spatially varying unit processes such as oxidation, ion transport, and competitive adsorption. Corrosion control and mitigation topics covered some new insights on coatings and inhibitors. Further advances in operando or in situ experimental characterization strategies at the nanoscale combined with computational modelling will enhance progress in the field, especially if coupling across length and time scales can be achieved incorporating the various phenomena encountered in corrosion. Readers are encouraged to not only to use this ad hoc organizational scheme to guide their immersion into the current opportunities in corrosion chemistry, but also to find value in the information presented in their own ways.

  14. Charge-assisted triel bonding interactions in solid state chemistry: A combined computational and crystallographic study

    NASA Astrophysics Data System (ADS)

    Bauzá, Antonio; García-Llinás, Xavier; Frontera, Antonio

    2016-12-01

    A combined energetic and geometric study of a series of triel bond complexes involving haloborane salts has been carried out at the M06-2X/def2-QZVPD level of theory. We have used 1-(dihaloboranyl)pyridin-1-ium compounds Py+BX2 (X = Cl, Br and I) as triel bond donors and Cl-, Br-, HCO2-, BF4- and ClO4- as electron donor moieties. In addition we have used Bader's theory of 'atoms in molecules' to further characterize the noncovalent interactions described herein. Finally, several examples were retrieved from the CSD (Cambridge Structural Database) in order to provide experimental support to the results presented in this work.

  15. Overview of positron emission tomography chemistry: clinical and technical considerations and combination with computed tomography.

    PubMed

    Koukourakis, G; Maravelis, G; Koukouraki, S; Padelakos, P; Kouloulias, V

    2009-01-01

    The concept of emission and transmission tomography was introduced by David Kuhl and Roy Edwards in the late 1950s. Their work later led to the design and construction of several tomographic instruments at the University of Pennsylvania. Tomographic imaging techniques were further developed by Michel Ter-Pogossian, Michael E. Phelps and others at the Washington University School of Medicine. Positron emission tomography (PET) is a nuclear medicine imaging technique which produces a 3-dimensional image or map of functional processes in the body. The system detects pairs of gamma rays emitted indirectly by a positron-emitting radionuclide (tracer), which is introduced into the body on a biologically active molecule. Images of tracer concentration in 3-dimensional space within the body are then reconstructed by computer analysis. In modern scanners, this reconstruction is often accomplished with the aid of a CT X-ray scan performed on the patient during the same session, in the same machine. If the biologically active molecule chosen for PET is 18F-fluorodeoxyglucose (FDG), an analogue of glucose, the concentrations of tracer imaged give tissue metabolic activity in terms of regional glucose uptake. Although use of this tracer results in the most common type of PET scan, other tracer molecules are used in PET to image the tissue concentration of many other types of molecules of interest. The main role of this article was to analyse the available types of radiopharmaceuticals used in PET-CT along with the principles of its clinical and technical considerations.

  16. Computational Chemistry and Lubrication

    NASA Technical Reports Server (NTRS)

    Zehe, Michael J.

    1998-01-01

    Members of NASA Lewis Research Center's Tribology and Surface Science Branch are applying high-level computational chemistry techniques to the development of new lubrication systems for space applications and for future advanced aircraft engines. The next generation of gas turbine engines will require a liquid lubricant to function at temperatures in excess of 350 C in oxidizing environments. Conventional hydrocarbon-based lubricants are incapable of operating in these extreme environments, but a class of compounds known as the perfluoropolyether (PFAE) liquids (see the preceding illustration) shows promise for such applications. These commercially available products are already being used as lubricants in conditions where low vapor pressure and chemical stability are crucial, such as in satellite bearings and composite disk platters. At higher temperatures, however, these compounds undergo a decomposition process that is assisted (catalyzed) by metal and metal oxide bearing surfaces. This decomposition process severely limits the applicability of PFAE's at higher temperatures. A great deal of laboratory experimentation has revealed that the extent of fluid degradation depends on the chemical properties of the bearing surface materials. Lubrication engineers would like to understand the chemical breakdown mechanism to design a less vulnerable PFAE or to develop a chemical additive to block this degradation.

  17. Quantum computation for quantum chemistry

    NASA Astrophysics Data System (ADS)

    Aspuru-Guzik, Alan

    2010-03-01

    Numerically exact simulation of quantum systems on classical computers is in general, an intractable computational problem. Computational chemists have made progress in the development of approximate methods to tackle complex chemical problems. The downside of these approximate methods is that their failure for certain important cases such as long-range charge transfer states in the case of traditional density functional theory. In 1982, Richard Feynman suggested that a quantum device should be able to simulate quantum systems (in our case, molecules) exactly using quantum computers in a tractable fashion. Our group has been working in the development of quantum chemistry algorithms for quantum devices. In this talk, I will describe how quantum computers can be employed to carry out numerically exact quantum chemistry and chemical reaction dynamics calculations, as well as molecular properties. Finally, I will describe our recent experimental quantum computation of the energy of the hydrogen molecule using an optical quantum computer.

  18. Theoretical and computational chemistry.

    PubMed

    Meuwly, Markus

    2010-01-01

    Computer-based and theoretical approaches to chemical problems can provide atomistic understanding of complex processes at the molecular level. Examples ranging from rates of ligand-binding reactions in proteins to structural and energetic investigations of diastereomers relevant to organo-catalysis are discussed in the following. They highlight the range of application of theoretical and computational methods to current questions in chemical research.

  19. Recent computational chemistry

    SciTech Connect

    Onishi, Taku

    2015-12-31

    Now we can investigate quantum phenomena for the real materials and molecules, and can design functional materials by computation, due to the previous developments of quantum theory and calculation methods. As there still exist the limit and problem in theory, the cooperation between theory and computation is getting more important to clarify the unknown quantum mechanism, and discover more efficient functional materials. It would be next-generation standard. Finally, our theoretical methodology for boundary solid is introduced.

  20. Cuby: An integrative framework for computational chemistry.

    PubMed

    Řezáč, Jan

    2016-05-15

    Cuby is a computational chemistry framework written in the Ruby programming language. It provides unified access to a wide range of computational methods by interfacing external software and it implements various protocols that operate on their results. Using structured input files, elementary calculations can be combined into complex workflows. For users, Cuby provides a unified and userfriendly way to automate their work, seamlessly integrating calculations carried out in different computational chemistry programs. For example, the QM/MM module allows combining methods across the interfaced programs and the builtin molecular dynamics engine makes it possible to run a simulation on the resulting potential. For programmers, it provides high-level, object-oriented environment that allows rapid development and testing of new methods and computational protocols. The Cuby framework is available for download at http://cuby4.molecular.cz. © 2016 Wiley Periodicals, Inc.

  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. Understanding MAOS through computational chemistry.

    PubMed

    Prieto, P; de la Hoz, A; Díaz-Ortiz, A; Rodríguez, A M

    2017-01-23

    The importance of microwave irradiation in organic synthesis today is unquestionable, but in many cases the nature of these improvements remains unknown. Exploiting the benefits that microwave irradiation has in chemistry is still hindered by a lack of understanding of the physical principles of the interaction of microwave irradiation with the components of a reaction. Moreover, dielectric properties vary with temperature and along the reaction coordinate and this makes the situation more complex. Experimental determinations employed to date in Microwave-Assisted Organic Chemistry (MAOS) are characterized by the importance of thermal heating. In this way the separation of thermal heating from any other effect of electromagnetic radiation is completely impossible. This review provides an overview of the use of Computational Chemistry in MAOS to provide a theoretical understanding of the factors that can be used to explain the improvements in MAOS and how computational calculations can be used as a predictive tool.

  3. Advancing manufacturing through computational chemistry

    SciTech Connect

    Noid, D.W.; Sumpter, B.G.; Tuzun, R.E.

    1995-12-31

    The capabilities of nanotechnology and computational chemistry are reaching a point of convergence. New computer hardware and novel computational methods have created opportunities to test proposed nanometer-scale devices, investigate molecular manufacturing and model and predict properties of new materials. Experimental methods are also beginning to provide new capabilities that make the possibility of manufacturing various devices with atomic precision tangible. In this paper, we will discuss some of the novel computational methods we have used in molecular dynamics simulations of polymer processes, neural network predictions of new materials, and simulations of proposed nano-bearings and fluid dynamics in nano- sized devices.

  4. Combining supramolecular chemistry with biology.

    PubMed

    Uhlenheuer, Dana A; Petkau, Katja; Brunsveld, Luc

    2010-08-01

    Supramolecular chemistry has primarily found its inspiration in biological molecules, such as proteins and lipids, and their interactions. Currently the supramolecular assembly of designed compounds can be controlled to great extent. This provides the opportunity to combine these synthetic supramolecular elements with biomolecules for the study of biological phenomena. This tutorial review focuses on the possibilities of the marriage of synthetic supramolecular architectures and biological systems. It highlights that synthetic supramolecular elements are for example ideal platforms for the recognition and modulation of proteins and cells. The unique features of synthetic supramolecular systems with control over size, shape, valency, and interaction strength allow the generation of structures fitting the demands to approach the biological problems at hand. Supramolecular chemistry has come full circle, studying the biology and its molecules which initially inspired its conception.

  5. Outlook Bright for Computers in Chemistry.

    ERIC Educational Resources Information Center

    Baum, Rudy M.

    1981-01-01

    Discusses the recent decision to close down the National Resource for Computation in Chemistry (NRCC), implications of that decision, and various alternatives in the field of computational chemistry. (CS)

  6. Deep learning for computational chemistry.

    PubMed

    Goh, Garrett B; Hodas, Nathan O; Vishnu, Abhinav

    2017-06-15

    The rise and fall of artificial neural networks is well documented in the scientific literature of both computer science and computational chemistry. Yet almost two decades later, we are now seeing a resurgence of interest in deep learning, a machine learning algorithm based on multilayer neural networks. Within the last few years, we have seen the transformative impact of deep learning in many domains, particularly in speech recognition and computer vision, to the extent that the majority of expert practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. In this review, we provide an introductory overview into the theory of deep neural networks and their unique properties that distinguish them from traditional machine learning algorithms used in cheminformatics. By providing an overview of the variety of emerging applications of deep neural networks, we highlight its ubiquity and broad applicability to a wide range of challenges in the field, including quantitative structure activity relationship, virtual screening, protein structure prediction, quantum chemistry, materials design, and property prediction. In reviewing the performance of deep neural networks, we observed a consistent outperformance against non-neural networks state-of-the-art models across disparate research topics, and deep neural network-based models often exceeded the "glass ceiling" expectations of their respective tasks. Coupled with the maturity of GPU-accelerated computing for training deep neural networks and the exponential growth of chemical data on which to train these networks on, we anticipate that deep learning algorithms will be a valuable tool for computational chemistry. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  7. Plug Pulled on Chemistry Computer Center.

    ERIC Educational Resources Information Center

    Robinson, Arthur L.

    1980-01-01

    Discusses the controversy surrounding the initial decision to establish, and the current decision to phase out, the National Resource for Computation in Chemistry (NRCC), a computational chemistry center jointly sponsored by the National Science Foundation and the Department of Energy. (CS)

  8. Plug Pulled on Chemistry Computer Center.

    ERIC Educational Resources Information Center

    Robinson, Arthur L.

    1980-01-01

    Discusses the controversy surrounding the initial decision to establish, and the current decision to phase out, the National Resource for Computation in Chemistry (NRCC), a computational chemistry center jointly sponsored by the National Science Foundation and the Department of Energy. (CS)

  9. Computational Chemistry Comparison and Benchmark Database

    National Institute of Standards and Technology Data Gateway

    SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

  10. Informatics, machine learning and computational medicinal chemistry.

    PubMed

    Mitchell, John B O

    2011-03-01

    This article reviews the use of informatics and computational chemistry methods in medicinal chemistry, with special consideration of how computational techniques can be adapted and extended to obtain more and higher-quality information. Special consideration is given to the computation of protein-ligand binding affinities, to the prediction of off-target bioactivities, bioactivity spectra and computational toxicology, and also to calculating absorption-, distribution-, metabolism- and excretion-relevant properties, such as solubility.

  11. 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.

  12. ATOMIC-SCALE DESIGN OF IRON FISCHER-TROPSCH CATALYSTS: A COMBINED COMPUTATIONAL CHEMISTRY, EXPERIMENTAL, AND MICROKINETIC MODELING APPROACH

    SciTech Connect

    Manos Mavrikakis; James A. Dumesic; Amit A. Gokhale; Rahul P. Nabar; Calvin H. Bartholomew; Hu Zou; Brian Critchfield

    2005-03-22

    Efforts during this first year focused on four areas: (1) searching/summarizing published FTS mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) construction of mass spectrometer-TPD and Berty CSTR reactor systems; (3) preparation and characterization of unsupported iron and alumina-supported iron catalysts at various iron loadings (4) Determination of thermochemical parameters such as binding energies of reactive intermediates, heat of FTS elementary reaction steps, and kinetic parameters such as activation energies, and frequency factors of FTS elementary reaction steps on a number of model surfaces. Literature describing mechanistic and kinetic studies of Fischer-Tropsch synthesis on iron catalysts was compiled in a draft review. Construction of the mass spectrometer-TPD system is 90% complete and of a Berty CSTR reactor system 98% complete. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by nonaqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2}, thus ideal for kinetic and mechanistic studies. The alumina-supported iron catalysts will be used for kinetic and mechanistic studies. In the coming year, adsorption/desorption properties, rates of elementary steps, and global reaction rates will be measured for these catalysts, with and without promoters, providing a database for understanding effects of dispersion, metal loading, and support on elementary kinetic parameters and for validation of computational models that incorporate effects of surface structure and promoters. Furthermore, using state-of-the-art self-consistent Density Functional Theory (DFT) methods, we have extensively studied the thermochemistry and kinetics of various elementary steps on

  13. Atomic-Scale Design of Iron Fischer-Tropsch Catalysts; A Combined Computational Chemistry, Experimental, and Microkinetic Modeling Approach

    SciTech Connect

    Manos Mavrikakis; James Dumesic; Rahul Nabar; Calvin Bartholonew; Hu Zou; Uchenna Paul

    2008-09-29

    This work focuses on (1) searching/summarizing published Fischer-Tropsch synthesis (FTS) mechanistic and kinetic studies of FTS reactions on iron catalysts; (2) preparation and characterization of unsupported iron catalysts with/without potassium/platinum promoters; (3) measurement of H{sub 2} and CO adsorption/dissociation kinetics on iron catalysts using transient methods; (3) analysis of the transient rate data to calculate kinetic parameters of early elementary steps in FTS; (4) construction of a microkinetic model of FTS on iron, and (5) validation of the model from collection of steady-state rate data for FTS on iron catalysts. Three unsupported iron catalysts and three alumina-supported iron catalysts were prepared by non-aqueous-evaporative deposition (NED) or aqueous impregnation (AI) and characterized by chemisorption, BET, temperature-programmed reduction (TPR), extent-of-reduction, XRD, and TEM methods. These catalysts, covering a wide range of dispersions and metal loadings, are well-reduced and relatively thermally stable up to 500-600 C in H{sub 2} and thus ideal for kinetic and mechanistic studies. Kinetic parameters for CO adsorption, CO dissociation, and surface carbon hydrogenation on these catalysts were determined from temperature-programmed desorption (TPD) of CO and temperature programmed surface hydrogenation (TPSR), temperature-programmed hydrogenation (TPH), and isothermal, transient hydrogenation (ITH). A microkinetic model was constructed for the early steps in FTS on polycrystalline iron from the kinetic parameters of elementary steps determined experimentally in this work and from literature values. Steady-state rate data were collected in a Berty reactor and used for validation of the microkinetic model. These rate data were fitted to 'smart' Langmuir-Hinshelwood rate expressions derived from a sequence of elementary steps and using a combination of fitted steady-state parameters and parameters specified from the transient

  14. Computer Shift Chemistry to More Mathematical Basis.

    ERIC Educational Resources Information Center

    Haggin, Joseph

    1983-01-01

    Discusses use and applications of computer technology in chemistry, indicating that the importance of the computer has not been fully realized in the realm of organic synthesis. Includes discussions of various computer programs and systems currently used, supplemented by tables highlighting, for example, features of major computer-aided synthesis…

  15. Parallel computing in atmospheric chemistry models

    SciTech Connect

    Rotman, D.

    1996-02-01

    Studies of atmospheric chemistry are of high scientific interest, involve computations that are complex and intense, and require enormous amounts of I/O. Current supercomputer computational capabilities are limiting the studies of stratospheric and tropospheric chemistry and will certainly not be able to handle the upcoming coupled chemistry/climate models. To enable such calculations, the authors have developed a computing framework that allows computations on a wide range of computational platforms, including massively parallel machines. Because of the fast paced changes in this field, the modeling framework and scientific modules have been developed to be highly portable and efficient. Here, the authors present the important features of the framework and focus on the atmospheric chemistry module, named IMPACT, and its capabilities. Applications of IMPACT to aircraft studies will be presented.

  16. Computing Advances in the Teaching of Chemistry.

    ERIC Educational Resources Information Center

    Baskett, W. P.; Matthews, G. P.

    1984-01-01

    Discusses three trends in computer-oriented chemistry instruction: (1) availability of interfaces to integrate computers with experiments; (2) impact of the development of higher resolution graphics and greater memory capacity; and (3) role of videodisc technology on computer assisted instruction. Includes program listings for auto-titration and…

  17. Computing Advances in the Teaching of Chemistry.

    ERIC Educational Resources Information Center

    Baskett, W. P.; Matthews, G. P.

    1984-01-01

    Discusses three trends in computer-oriented chemistry instruction: (1) availability of interfaces to integrate computers with experiments; (2) impact of the development of higher resolution graphics and greater memory capacity; and (3) role of videodisc technology on computer assisted instruction. Includes program listings for auto-titration and…

  18. Company Offers Computer-Assisted Chemistry.

    ERIC Educational Resources Information Center

    Waldrop, Mitch

    1979-01-01

    Discusses the possibilities and the potentials of advancing the state of the art in computer chemistry. Explains that the fears will be extrapolating new compounds from existing ones, and predicting new activities based on chemical structure. (GA)

  19. 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.

  20. Formulating and Solving Problems in Computational Chemistry.

    ERIC Educational Resources Information Center

    Norris, A. C.

    1980-01-01

    Considered are the main elements of computational chemistry problems and how these elements can be used to formulate the problems mathematically. Techniques that are useful in devising an appropriate solution are also considered. (Author/TG)

  1. 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.

  2. 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.

  3. 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

  4. 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…

  5. 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…

  6. Computational Chemistry of Adhesive Bonds

    NASA Technical Reports Server (NTRS)

    Phillips, Donald H.

    1999-01-01

    This investigation is intended to determine the electrical mechanical, and chemical properties of adhesive bonds at the molecular level. The initial determinations will be followed by investigations of the effects of environmental effects on the chemistry and properties of the bond layer.

  7. Medicinal electrochemistry: integration of electrochemistry, medicinal chemistry and computational chemistry.

    PubMed

    Almeida, M O; Maltarollo, V G; de Toledo, R A; Shim, H; Santos, M C; Honorio, K M

    2014-01-01

    Over the last centuries, there were many important discoveries in medicine that were crucial for gaining a better understanding of several physiological processes. Molecular modelling techniques are powerful tools that have been successfully used to analyse and interface medicinal chemistry studies with electrochemical experimental results. This special combination can help to comprehend medicinal chemistry problems, such as predicting biological activity and understanding drug action mechanisms. Electrochemistry has provided better comprehension of biological reactions and, as a result of many technological improvements, the combination of electrochemical techniques and biosensors has become an appealing choice for pharmaceutical and biomedical analyses. Therefore, this review will briefly outline the present scope and future advances related to the integration of electrochemical and medicinal chemistry approaches based on various applications from recent studies.

  8. Chemistry of combined residual chlorination

    SciTech Connect

    Leao, S.F.; Selleck, R.E.

    1982-01-01

    The decay of the combined chlorine residual was investigated in this work. Recent concerns about the formation of undesirable compounds such as chloroform with free residual chlorination have focused attention on the alternative use of combined residual chlorination. This work investigates the applicability of reactions proposed to describe the transformations and decay of the combined residual with time. Sodium hypochlorite was added to buffered solutions of ammonia with the chlorine residual being monitored over periods extending up to 10 days. The reaction was studied at four initial concentrations of hypochlorite of 100, 50, 25 and 10 mg/L as Cl/sub 2/ with molar application ratios of chlorine to ammonia, defined herein as M ratios, of 0.90, 0.50, 0.25 and 0.05 at each hypochlorite dose. Sixty-eight experiments were conducted at the pH of 6.6 and 7.2. The conclusions are: (1) in the absence of free chlorine, the concentration of NH/sub 3/ does not seem to affect the rate of disappearance of the residual other than through the formation of NHCl/sub 2/ by NH/sub 2/Cl hydrolysis; (2) the reaction between NHCl/sub 2/ and NH/sub 4//sup +/ to form NH/sub 2/Cl is either much slower than reported by Gray et. al. or the mechanism is different with a rate limiting step not involving NH/sub 3/ or NH/sub 4//sup +/; (3) a redox reaction in addition to the first-order decomposition of NHCl/sub 2/ appears necessary. Model simulation results indicated that a reaction of the type NH/sub 2/Cl + NHCl/sub 2/ ..-->.. P added to the first-order NHCl/sub 2/ decomposition can explain the results observed except at the higher chlorine doses.

  9. THE INTEGRATED USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY, AND VIRTUAL REALITY TO PREDICT THE CHEMICAL REACTIVITY OF ENVIRONMENTAL SURFACES

    EPA Science Inventory

    In the last decade three new techniques scanning probe microscopy (SPM), virtual reality (YR) and computational chemistry ave emerged with the combined capability of a priori predicting the chemically reactivity of environmental surfaces. Computational chemistry provides the cap...

  10. THE INTEGRATED USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY, AND VIRTUAL REALITY TO PREDICT THE CHEMICAL REACTIVITY OF ENVIRONMENTAL SURFACES

    EPA Science Inventory

    In the last decade three new techniques scanning probe microscopy (SPM), virtual reality (YR) and computational chemistry ave emerged with the combined capability of a priori predicting the chemically reactivity of environmental surfaces. Computational chemistry provides the cap...

  11. Computational chemistry and aeroassisted orbital transfer vehicles

    NASA Technical Reports Server (NTRS)

    Cooper, D. M.; Jaffe, R. L.; Arnold, J. O.

    1985-01-01

    An analysis of the radiative heating phenomena encountered during a typical aeroassisted orbital transfer vehicle (AOTV) trajectory was made to determine the potential impact of computational chemistry on AOTV design technology. Both equilibrium and nonequilibrium radiation mechanisms were considered. This analysis showed that computational chemistry can be used to predict (1) radiative intensity factors and spectroscopic data; (2) the excitation rates of both atoms and molecules; (3) high-temperature reaction rate constants for metathesis and charge exchange reactions; (4) particle ionization and neutralization rates and cross sections; and (5) spectral line widths.

  12. Computational chemistry and aeroassisted orbital transfer vehicles

    NASA Technical Reports Server (NTRS)

    Cooper, D. M.; Jaffe, R. L.; Arnold, J. O.

    1985-01-01

    An analysis of the radiative heating phenomena encountered during a typical aeroassisted orbital transfer vehicle (AOTV) trajectory was made to determine the potential impact of computational chemistry on AOTV design technology. Both equilibrium and nonequilibrium radiation mechanisms were considered. This analysis showed that computational chemistry can be used to predict (1) radiative intensity factors and spectroscopic data; (2) the excitation rates of both atoms and molecules; (3) high-temperature reaction rate constants for metathesis and charge exchange reactions; (4) particle ionization and neutralization rates and cross sections; and (5) spectral line widths.

  13. 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.

  14. Computational chemistry on Cray supercomputers

    SciTech Connect

    Freeman, A.J.

    1988-09-01

    The unique and significant scientific results possible from the (happy) union of advanced computational methods and algorithms (software) on (CRAY) supercomputers (hardware) are described using, as illustrative examples, the new high-temperature superconducting oxides and the high-temperature intermetallic alloys of importance for potential aerospace applications.

  15. Computational Chemistry Studies on the Carbene Hydroxymethylene

    ERIC Educational Resources Information Center

    Marzzacco, Charles J.; Baum, J. Clayton

    2011-01-01

    A density functional theory computational chemistry exercise on the structure and vibrational spectrum of the carbene hydroxymethylene is presented. The potential energy curve for the decomposition reaction of the carbene to formaldehyde and the geometry of the transition state are explored. The results are in good agreement with recent…

  16. Computational Chemistry Studies on the Carbene Hydroxymethylene

    ERIC Educational Resources Information Center

    Marzzacco, Charles J.; Baum, J. Clayton

    2011-01-01

    A density functional theory computational chemistry exercise on the structure and vibrational spectrum of the carbene hydroxymethylene is presented. The potential energy curve for the decomposition reaction of the carbene to formaldehyde and the geometry of the transition state are explored. The results are in good agreement with recent…

  17. Aqueous Boron Removal by Using Electrospun Poly(vinyl alcohol) (PVA) Mats: A Combined Study of IR/Raman Spectroscopy and Computational Chemistry.

    PubMed

    Lee, Kwan Sik; Eom, Ki Heon; Lim, Jun-Heok; Ryu, Hyunwook; Kim, Suhan; Lee, Dong-Kyu; Won, Yong Sun

    2017-03-23

    We report the use of a novel and efficient method to remove aqueous boron by using electrospun, water-resistant poly(vinyl alcohol) (PVA) mats stabilized in methanol. The removal of the primary aqueous boron species as (B(OH)3), was accomplished by chemical adsorption in reactions with -OH (hydroxyl) groups on the PVA mat surface. The chemical adsorption of B(OH)3 was qualitatively confirmed by the analysis of IR and Raman spectra. The bands, corresponding to the molecular vibration modes of chemically bonded boron in PVA, were identified by using the frequency calculation from the computational chemistry for the first time. The adsorption capacities of PVA mats for aqueous boron were then quantitated at a low boron concentration (range: 0.0010 to 0.0025 g of aqueous boron per g of PVA mats) by the Carmine method. The PVA mats were prepared by a well-established electrospinning technique, which make these substrates promising potential candidates for use as boron-selective sorbent media in applications such as reverse osmosis desalination processes.

  18. Algorithms versus architectures for computational chemistry

    NASA Technical Reports Server (NTRS)

    Partridge, H.; Bauschlicher, C. W., Jr.

    1986-01-01

    The algorithms employed are computationally intensive and, as a result, increased performance (both algorithmic and architectural) is required to improve accuracy and to treat larger molecular systems. Several benchmark quantum chemistry codes are examined on a variety of architectures. While these codes are only a small portion of a typical quantum chemistry library, they illustrate many of the computationally intensive kernels and data manipulation requirements of some applications. Furthermore, understanding the performance of the existing algorithm on present and proposed supercomputers serves as a guide for future programs and algorithm development. The algorithms investigated are: (1) a sparse symmetric matrix vector product; (2) a four index integral transformation; and (3) the calculation of diatomic two electron Slater integrals. The vectorization strategies are examined for these algorithms for both the Cyber 205 and Cray XMP. In addition, multiprocessor implementations of the algorithms are looked at on the Cray XMP and on the MIT static data flow machine proposed by DENNIS.

  19. Mathematical challenges from theoretical/computational chemistry

    SciTech Connect

    1995-12-31

    The committee believes that this report has relevance and potentially valuable suggestions for a wide range of readers. Target audiences include: graduate departments in the mathematical and chemical sciences; federal and private agencies that fund research in the mathematical and chemical sciences; selected industrial and government research and development laboratories; developers of software and hardware for computational chemistry; and selected individual researchers. Chapter 2 of this report covers some history of computational chemistry for the nonspecialist, while Chapter 3 illustrates the fruits of some past successful cross-fertilization between mathematical scientists and computational/theoretical chemists. In Chapter 4 the committee has assembled a representative, but not exhaustive, survey of research opportunities. Most of these are descriptions of important open problems in computational/theoretical chemistry that could gain much from the efforts of innovative mathematical scientists, written so as to be accessible introductions to the nonspecialist. Chapter 5 is an assessment, necessarily subjective, of cultural differences that must be overcome if collaborative work is to be encouraged between the mathematical and the chemical communities. Finally, the report ends with a brief list of conclusions and recommendations that, if followed, could promote accelerated progress at this interface. Recognizing that bothersome language issues can inhibit prospects for collaborative research at the interface between distinctive disciplines, the committee has attempted throughout to maintain an accessible style, in part by using illustrative boxes, and has included at the end of the report a glossary of technical terms that may be familiar to only a subset of the target audiences listed above.

  20. 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.

  1. 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…

  2. 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…

  3. 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

  4. [Basic principles of computational chemistry for medical biologists].

    PubMed

    Ivanov, A S

    2005-01-01

    The lecture describes the basic principles of computational chemistry underlying the methods of molecular modelling used in bioinformatics area. The basic positions, methods of molecular and quantum mechanics and combined approaches are considered. This lecture is from theoretical cycle "Bioinformatics and Computer-Aided Drug Design" for fourth year students of Medico-Biological Department of Russian State Medical University (specialty--biochemistry, biophysics and medical cybernetics). It can also be advised for all students and post-graduate students of medico-biological specialties.

  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. Integrating Computational Chemistry into the Physical Chemistry Laboratory Curriculum: A Wet Lab/Dry Lab Approach

    ERIC Educational Resources Information Center

    Karpen, Mary E.; Henderleiter, Julie; Schaertel, Stephanie A.

    2004-01-01

    The usage of computational chemistry in a pedagogically effective manner in the undergraduate chemistry curriculum is described. The changes instituted for an effective course structure and the assessment of the course efficacy are discussed.

  7. Introducing the Practical Aspects of Computational Chemistry to Undergraduate Chemistry Students

    ERIC Educational Resources Information Center

    Pearson, Jason K.

    2007-01-01

    Various efforts are being made to introduce the different physical aspects and uses of computational chemistry to the undergraduate chemistry students. A new laboratory approach that demonstrates all such aspects via experiments has been devised for the purpose.

  8. Network visualization system for computational chemistry.

    PubMed

    Kozhin, Mikhail; Yanov, Ilya; Leszczynski, Jerzy

    2003-10-01

    Network Visualization System for Computational Chemistry (NVSCC) is a molecular graphics program designed for the visualization of molecular assemblies. NVSCC accepts the output files from the most popular ab initio quantum chemical programs, GAUSSIAN and GAMESS, and provides visualization of molecular structures based on atomic coordinates. The main differences between NVSCC and other programs are: Network support due to built-in FTP and telnet clients, which allows for the processing of output from and the sending of input to different computer systems and operating systems. The possibility of working with output files in real time mode. The possibility of animation from an output file during all steps of optimization. The quick processing of huge volumes of data. The development of custom interfaces. Copyright 2003 Wiley Periodicals, Inc.

  9. Five Applications of Computers in the Chemistry Curriculum.

    ERIC Educational Resources Information Center

    Johnson, K. Jeffrey

    1981-01-01

    Describes the use of computer courseware in an undergraduate chemistry curriculum for (1) a tutorial program, (2) a computer assisted test construction (CATC) system, (3) a set of simulation and data reduction programs, (4) a "Numerical Methods in Chemistry" course, and (5) a library of computer managed instruction (CMI) programs. (JL)

  10. Scalable Computational Chemistry: New Developments and Applications

    SciTech Connect

    Alexeev, Yuri

    2002-01-01

    The computational part of the thesis is the investigation of titanium chloride (II) as a potential catalyst for the bis-silylation reaction of ethylene with hexaclorodisilane at different levels of theory. Bis-silylation is an important reaction for producing bis(silyl) compounds and new C-Si bonds, which can serve as monomers for silicon containing polymers and silicon carbides. Ab initio calculations on the steps involved in a proposed mechanism are presented. This choice of reactants allows them to study this reaction at reliable levels of theory without compromising accuracy. The calculations indicate that this is a highly exothermic barrierless reaction. The TiCl2 catalyst removes a 50 kcal/mol activation energy barrier required for the reaction without the catalyst. The first step is interaction of TiCl2 with ethylene to form an intermediate that is 60 kcal/mol below the energy of the reactants. This is the driving force for the entire reaction. Dynamic correlation plays a significant role because RHF calculations indicate that the net barrier for the catalyzed reaction is 50 kcal/mol. They conclude that divalent Ti has the potential to become an important industrial catalyst for silylation reactions. In the programming part of the thesis, parallelization of different quantum chemistry methods is presented. The parallelization of code is becoming important aspects of quantum chemistry code development. Two trends contribute to it: the overall desire to study large chemical systems and the desire to employ highly correlated methods which are usually computationally and memory expensive. In the presented distributed data algorithms computation is parallelized and the largest arrays are evenly distributed among CPUs. First, the parallelization of the Hartree-Fock self-consistent field (SCF) method is considered. SCF method is the most common starting point for more accurate calculations. The Fock build (sub step of SCF) from AO integrals is

  11. JACOB: An Enterprise Framework for Computational Chemistry

    PubMed Central

    Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

    2013-01-01

    Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: http://www.wallerlab.org/jacob. © 2013 Wiley Periodicals, Inc. PMID:23553271

  12. JACOB: an enterprise framework for computational chemistry.

    PubMed

    Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

    2013-06-15

    Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob.

  13. Computational Chemistry in the Pharmaceutical Industry: From Childhood to Adolescence.

    PubMed

    Hillisch, Alexander; Heinrich, Nikolaus; Wild, Hanno

    2015-12-01

    Computational chemistry within the pharmaceutical industry has grown into a field that proactively contributes to many aspects of drug design, including target selection and lead identification and optimization. While methodological advancements have been key to this development, organizational developments have been crucial to our success as well. In particular, the interaction between computational and medicinal chemistry and the integration of computational chemistry into the entire drug discovery process have been invaluable. Over the past ten years we have shaped and developed a highly efficient computational chemistry group for small-molecule drug discovery at Bayer HealthCare that has significantly impacted the clinical development pipeline. In this article we describe the setup and tasks of the computational group and discuss external collaborations. We explain what we have found to be the most valuable and productive methods and discuss future directions for computational chemistry method development. We share this information with the hope of igniting interesting discussions around this topic.

  14. Computationally efficient implementation of combustion chemistry in parallel PDF calculations

    SciTech Connect

    Lu Liuyan Lantz, Steven R.; Ren Zhuyin; Pope, Stephen B.

    2009-08-20

    In parallel calculations of combustion processes with realistic chemistry, the serial in situ adaptive tabulation (ISAT) algorithm [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combustion Theory and Modelling, 1 (1997) 41-63; L. Lu, S.B. Pope, An improved algorithm for in situ adaptive tabulation, Journal of Computational Physics 228 (2009) 361-386] substantially speeds up the chemistry calculations on each processor. To improve the parallel efficiency of large ensembles of such calculations in parallel computations, in this work, the ISAT algorithm is extended to the multi-processor environment, with the aim of minimizing the wall clock time required for the whole ensemble. Parallel ISAT strategies are developed by combining the existing serial ISAT algorithm with different distribution strategies, namely purely local processing (PLP), uniformly random distribution (URAN), and preferential distribution (PREF). The distribution strategies enable the queued load redistribution of chemistry calculations among processors using message passing. They are implemented in the software x2f{sub m}pi, which is a Fortran 95 library for facilitating many parallel evaluations of a general vector function. The relative performance of the parallel ISAT strategies is investigated in different computational regimes via the PDF calculations of multiple partially stirred reactors burning methane/air mixtures. The results show that the performance of ISAT with a fixed distribution strategy strongly depends on certain computational regimes, based on how much memory is available and how much overlap exists between tabulated information on different processors. No one fixed strategy consistently achieves good performance in all the regimes. Therefore, an adaptive distribution strategy, which blends PLP, URAN and PREF, is devised and implemented. It yields consistently good performance in all regimes. In the adaptive

  15. Computationally efficient implementation of combustion chemistry in parallel PDF calculations

    NASA Astrophysics Data System (ADS)

    Lu, Liuyan; Lantz, Steven R.; Ren, Zhuyin; Pope, Stephen B.

    2009-08-01

    In parallel calculations of combustion processes with realistic chemistry, the serial in situ adaptive tabulation (ISAT) algorithm [S.B. Pope, Computationally efficient implementation of combustion chemistry using in situ adaptive tabulation, Combustion Theory and Modelling, 1 (1997) 41-63; L. Lu, S.B. Pope, An improved algorithm for in situ adaptive tabulation, Journal of Computational Physics 228 (2009) 361-386] substantially speeds up the chemistry calculations on each processor. To improve the parallel efficiency of large ensembles of such calculations in parallel computations, in this work, the ISAT algorithm is extended to the multi-processor environment, with the aim of minimizing the wall clock time required for the whole ensemble. Parallel ISAT strategies are developed by combining the existing serial ISAT algorithm with different distribution strategies, namely purely local processing (PLP), uniformly random distribution (URAN), and preferential distribution (PREF). The distribution strategies enable the queued load redistribution of chemistry calculations among processors using message passing. They are implemented in the software x2f_mpi, which is a Fortran 95 library for facilitating many parallel evaluations of a general vector function. The relative performance of the parallel ISAT strategies is investigated in different computational regimes via the PDF calculations of multiple partially stirred reactors burning methane/air mixtures. The results show that the performance of ISAT with a fixed distribution strategy strongly depends on certain computational regimes, based on how much memory is available and how much overlap exists between tabulated information on different processors. No one fixed strategy consistently achieves good performance in all the regimes. Therefore, an adaptive distribution strategy, which blends PLP, URAN and PREF, is devised and implemented. It yields consistently good performance in all regimes. In the adaptive parallel

  16. Making the Computer Make a Difference in College Chemistry.

    ERIC Educational Resources Information Center

    Lower, Stephen K.

    Both failures and successes have been experienced in the application of the computer to the teaching of introductory chemistry at Simon Fraser University. Chemistry teachers looked to computer assisted instruction (CAI) to improve instruction because CAI effectively dealt with chemical concepts and their practical application and with the wide…

  17. Triclosan Computational Conformational Chemistry Analysis for Antimicrobial Properties in Polymers.

    PubMed

    Petersen, Richard C

    2015-03-01

    Triclosan is a diphenyl ether antimicrobial that has been analyzed by computational conformational chemistry for an understanding of Mechanomolecular Theory. Subsequent energy profile analysis combined with easily seen three-dimensional chemistry structure models for the nonpolar molecule Triclosan show how single bond rotations can alternate rapidly at a polar and nonpolar interface. Bond rotations for the center ether oxygen atom of the two aromatic rings then expose or hide nonbonding lone-pair electrons for the oxygen atom depending on the polar nature of the immediate local molecular environment. Rapid bond movements can subsequently produce fluctuations as vibration energy. Consequently, related mechanical molecular movements calculated as energy relationships by forces acting through different bond positions can help improve on current Mechanomolecular Theory. A previous controversy reported as a discrepancy in literature contends for a possible bacterial resistance from Triclosan antimicrobial. However, findings in clinical settings have not reported a single case for Triclosan bacterial resistance in over 40 years that has been documented carefully in government reports. As a result, Triclosan is recommended whenever there is a health benefit consistent with a number of approvals for use of Triclosan in healthcare devices. Since Triclosan is the most researched antimicrobial ever, literature meta analysis with computational chemistry can best describe new molecular conditions that were previously impossible by conventional chemistry methods. Triclosan vibrational energy can now explain the molecular disruption of bacterial membranes. Further, Triclosan mechanomolecular movements help illustrate use in polymer matrix composites as an antimicrobial with two new additive properties as a toughening agent to improve matrix fracture toughness from microcracking and a hydrophobic wetting agent to help incorporate strengthening fibers. Interrelated

  18. Triclosan Computational Conformational Chemistry Analysis for Antimicrobial Properties in Polymers

    PubMed Central

    Petersen, Richard C.

    2015-01-01

    Triclosan is a diphenyl ether antimicrobial that has been analyzed by computational conformational chemistry for an understanding of Mechanomolecular Theory. Subsequent energy profile analysis combined with easily seen three-dimensional chemistry structure models for the nonpolar molecule Triclosan show how single bond rotations can alternate rapidly at a polar and nonpolar interface. Bond rotations for the center ether oxygen atom of the two aromatic rings then expose or hide nonbonding lone-pair electrons for the oxygen atom depending on the polar nature of the immediate local molecular environment. Rapid bond movements can subsequently produce fluctuations as vibration energy. Consequently, related mechanical molecular movements calculated as energy relationships by forces acting through different bond positions can help improve on current Mechanomolecular Theory. A previous controversy reported as a discrepancy in literature contends for a possible bacterial resistance from Triclosan antimicrobial. However, findings in clinical settings have not reported a single case for Triclosan bacterial resistance in over 40 years that has been documented carefully in government reports. As a result, Triclosan is recommended whenever there is a health benefit consistent with a number of approvals for use of Triclosan in healthcare devices. Since Triclosan is the most researched antimicrobial ever, literature meta analysis with computational chemistry can best describe new molecular conditions that were previously impossible by conventional chemistry methods. Triclosan vibrational energy can now explain the molecular disruption of bacterial membranes. Further, Triclosan mechanomolecular movements help illustrate use in polymer matrix composites as an antimicrobial with two new additive properties as a toughening agent to improve matrix fracture toughness from microcracking and a hydrophobic wetting agent to help incorporate strengthening fibers. Interrelated

  19. Combining experimental and computational studies to understand and predict reactivities of relevance to homogeneous catalysis.

    PubMed

    Tsang, Althea S-K; Sanhueza, Italo A; Schoenebeck, Franziska

    2014-12-08

    This article showcases three major uses of computational chemistry in reactivity studies: the application after, in combination with, and before experiment. Following a brief introduction of suitable computational tools, challenges and opportunities in the implementation of computational chemistry in reactivity studies are discussed, exemplified with selected case studies from our and other laboratories.

  20. 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.

  1. Cheminformatics and Computational Chemistry: A Powerful ...

    EPA Pesticide Factsheets

    The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural ecosystems. The purpose of this presentation is to demonstrate how cheminformatics using chemical terms language in combination with the output of physicochemical property calculators can be employed to encode this knowledge and make it available to the appropriate decision makers. The encoded process science is realized through the execution of reaction libraries in simulators such as EPA’s Chemical Transformation Simulator (CTS). In support of the CTS, reaction libraries have or are currently being developed for a number of transformation processes including hydrolysis, abiotic reduction, photolysis and disinfection by-product formation. Examples of how the process science available in the peer-reviewed literature is being encoded will be presented. Presented at the 252nd American Chemical Society National Meeting:Aquatic Chemistry: Symposium in Honor of Professor Alan T. Stone

  2. Cheminformatics and Computational Chemistry: A Powerful ...

    EPA Pesticide Factsheets

    The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural ecosystems. The purpose of this presentation is to demonstrate how cheminformatics using chemical terms language in combination with the output of physicochemical property calculators can be employed to encode this knowledge and make it available to the appropriate decision makers. The encoded process science is realized through the execution of reaction libraries in simulators such as EPA’s Chemical Transformation Simulator (CTS). In support of the CTS, reaction libraries have or are currently being developed for a number of transformation processes including hydrolysis, abiotic reduction, photolysis and disinfection by-product formation. Examples of how the process science available in the peer-reviewed literature is being encoded will be presented. Presented at the 252nd American Chemical Society National Meeting:Aquatic Chemistry: Symposium in Honor of Professor Alan T. Stone

  3. Computational Chemistry Data Management Platform Based on the Semantic Web.

    PubMed

    Wang, Bing; Dobosh, Paul A; Chalk, Stuart; Sopek, Mirek; Ostlund, Neil S

    2017-01-12

    This paper presents a formal data publishing platform for computational chemistry using semantic web technologies. This platform encapsulates computational chemistry data from a variety of packages in an Extensible Markup Language (XML) file called CSX (Common Standard for eXchange). On the basis of a Gainesville Core (GC) ontology for computational chemistry, a CSX XML file is converted into the JavaScript Object Notation for Linked Data (JSON-LD) format using an XML Stylesheet Language Transformation (XSLT) file. Ultimately the JSON-LD file is converted to subject-predicate-object triples in a Turtle (TTL) file and published on the web portal. By leveraging semantic web technologies, we are able to place computational chemistry data onto web portals as a component of a Giant Global Graph (GGG) such that computer agents, as well as individual chemists, can access the data.

  4. Allenes and computational chemistry: from bonding situations to reaction mechanisms.

    PubMed

    Soriano, Elena; Fernández, Israel

    2014-05-07

    The present review is focused on the application of computational/theoretical methods to the wide and rich chemistry of allenes. Special emphasis is made on the interplay and synergy between experimental and computational methodologies, rather than on recent developments in methods and algorithms. Therefore, this review covers the state-of-the-art applications of computational chemistry to understand and rationalize the bonding situation and vast reactivity of allenes. Thus, the contents of this review span from the most fundamental studies on the equilibrium structure and chirality of allenes to recent advances in the study of complex reaction mechanisms involving allene derivatives in organic and organometallic chemistry.

  5. Molecular Modeling and Computational Chemistry at Humboldt State University.

    ERIC Educational Resources Information Center

    Paselk, Richard A.; Zoellner, Robert W.

    2002-01-01

    Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

  6. Molecular Modeling and Computational Chemistry at Humboldt State University.

    ERIC Educational Resources Information Center

    Paselk, Richard A.; Zoellner, Robert W.

    2002-01-01

    Describes a molecular modeling and computational chemistry (MM&CC) facility for undergraduate instruction and research at Humboldt State University. This facility complex allows the introduction of MM&CC throughout the chemistry curriculum with tailored experiments in general, organic, and inorganic courses as well as a new molecular modeling…

  7. Integrating medicinal chemistry, organic/combinatorial chemistry, and computational chemistry for the discovery of selective estrogen receptor modulators with Forecaster, a novel platform for drug discovery.

    PubMed

    Therrien, Eric; Englebienne, Pablo; Arrowsmith, Andrew G; Mendoza-Sanchez, Rodrigo; Corbeil, Christopher R; Weill, Nathanael; Campagna-Slater, Valérie; Moitessier, Nicolas

    2012-01-23

    As part of a large medicinal chemistry program, we wish to develop novel selective estrogen receptor modulators (SERMs) as potential breast cancer treatments using a combination of experimental and computational approaches. However, one of the remaining difficulties nowadays is to fully integrate computational (i.e., virtual, theoretical) and medicinal (i.e., experimental, intuitive) chemistry to take advantage of the full potential of both. For this purpose, we have developed a Web-based platform, Forecaster, and a number of programs (e.g., Prepare, React, Select) with the aim of combining computational chemistry and medicinal chemistry expertise to facilitate drug discovery and development and more specifically to integrate synthesis into computer-aided drug design. In our quest for potent SERMs, this platform was used to build virtual combinatorial libraries, filter and extract a highly diverse library from the NCI database, and dock them to the estrogen receptor (ER), with all of these steps being fully automated by computational chemists for use by medicinal chemists. As a result, virtual screening of a diverse library seeded with active compounds followed by a search for analogs yielded an enrichment factor of 129, with 98% of the seeded active compounds recovered, while the screening of a designed virtual combinatorial library including known actives yielded an area under the receiver operating characteristic (AU-ROC) of 0.78. The lead optimization proved less successful, further demonstrating the challenge to simulate structure activity relationship studies.

  8. From computational quantum chemistry to computational biology: experiments and computations are (full) partners.

    PubMed

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  9. PERSPECTIVE: From computational quantum chemistry to computational biology: experiments and computations are (full) partners

    NASA Astrophysics Data System (ADS)

    Ma, Buyong; Nussinov, Ruth

    2004-12-01

    Computations are being integrated into biological research at an increasingly fast pace. This has not only changed the way in which biological information is managed; it has also changed the way in which experiments are planned in order to obtain information from nature. Can experiments and computations be full partners? Computational chemistry has expanded over the years, proceeding from computations of a hydrogen molecule toward the challenging goal of systems biology, which attempts to handle the entire living cell. Applying theories from ab initio quantum mechanics to simplified models, the virtual worlds explored by computations provide replicas of real-world phenomena. At the same time, the virtual worlds can affect our perception of the real world. Computational biology targets a world of complex organization, for which a unified theory is unlikely to exist. A computational biology model, even if it has a clear physical or chemical basis, may not reduce to physics and chemistry. At the molecular level, computational biology and experimental biology have already been partners, mutually benefiting from each other. For the perception to become reality, computation and experiment should be united as full partners in biological research.

  10. Computer Series, 101: Accurate Equations of State in Computational Chemistry Projects.

    ERIC Educational Resources Information Center

    Albee, David; Jones, Edward

    1989-01-01

    Discusses the use of computers in chemistry courses at the United States Military Academy. Provides two examples of computer projects: (1) equations of state, and (2) solving for molar volume. Presents BASIC and PASCAL listings for the second project. Lists 10 applications for physical chemistry. (MVL)

  11. High performance computing in chemistry and massively parallel computers: A simple transition?

    SciTech Connect

    Kendall, R.A.

    1993-03-01

    A review of the various problems facing any software developer targeting massively parallel processing (MPP) systems is presented. Issues specific to computational chemistry application software will be also outlined. Computational chemistry software ported to and designed for the Intel Touchstone Delta Supercomputer will be discussed. Recommendations for future directions will also be made.

  12. Computational quantum chemistry and adaptive ligand modeling in mechanistic QSAR.

    PubMed

    De Benedetti, Pier G; Fanelli, Francesca

    2010-10-01

    Drugs are adaptive molecules. They realize this peculiarity by generating different ensembles of prototropic forms and conformers that depend on the environment. Among the impressive amount of available computational drug discovery technologies, quantitative structure-activity relationship approaches that rely on computational quantum chemistry descriptors are the most appropriate to model adaptive drugs. Indeed, computational quantum chemistry descriptors are able to account for the variation of the intramolecular interactions of the training compounds, which reflect their adaptive intermolecular interaction propensities. This enables the development of causative, interpretive and reasonably predictive quantitative structure-activity relationship models, and, hence, sound chemical information finalized to drug design and discovery.

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

    NASA Astrophysics Data System (ADS)

    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.

  14. 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.

  15. Computer-Based Learning in Chemistry Classes

    ERIC Educational Resources Information Center

    Pietzner, Verena

    2014-01-01

    Currently not many people would doubt that computers play an essential role in both public and private life in many countries. However, somewhat surprisingly, evidence of computer use is difficult to find in German state schools although other countries have managed to implement computer-based teaching and learning in their schools. This paper…

  16. Computer-Based Learning in Chemistry Classes

    ERIC Educational Resources Information Center

    Pietzner, Verena

    2014-01-01

    Currently not many people would doubt that computers play an essential role in both public and private life in many countries. However, somewhat surprisingly, evidence of computer use is difficult to find in German state schools although other countries have managed to implement computer-based teaching and learning in their schools. This paper…

  17. Computational solution of atmospheric chemistry problems

    NASA Technical Reports Server (NTRS)

    Jafri, J.; Ake, R. L.

    1986-01-01

    Extensive studies were performed on problems of interest in atmospheric chemistry. In addition to several minor projects, four major projects were performed and described (theoretical studies of ground and low-lying excited states of ClO2; ground and excited state potential energy surfaces of the methyl peroxy radical; electronic states ot the FO radical; and theoretical studies S02 (H2O) (sub n)).

  18. A Program of Computational Chemistry Exercises for the First-Semester General Chemistry Course

    ERIC Educational Resources Information Center

    Feller, Scott E.; Dallinger, Richard F.; McKinney, Paul Caylor

    2004-01-01

    The computer systems available for molecular modeling are described, along with a discussion of a molecular modeling program created and supported by computational techniques for the first-semester general chemistry course. Various exercises are listed, which direct the learner from a beginner's course in software practice to more complex…

  19. Software and resources for computational medicinal chemistry

    PubMed Central

    Liao, Chenzhong; Sitzmann, Markus; Pugliese, Angelo; Nicklaus, Marc C

    2011-01-01

    Computer-aided drug design plays a vital role in drug discovery and development and has become an indispensable tool in the pharmaceutical industry. Computational medicinal chemists can take advantage of all kinds of software and resources in the computer-aided drug design field for the purposes of discovering and optimizing biologically active compounds. This article reviews software and other resources related to computer-aided drug design approaches, putting particular emphasis on structure-based drug design, ligand-based drug design, chemical databases and chemoinformatics tools. PMID:21707404

  20. Interdisciplinary Educational Collaborations: Chemistry and Computer Science

    ERIC Educational Resources Information Center

    Haines, Ronald S.; Woo, Daniel T.; Hudson, Benjamin T.; Mori, Joji C.; Ngan, Evey S. M.; Pak, Wing-Yee

    2007-01-01

    Research collaborations between chemists and other scientists resulted in significant outcomes such as development of software. Such collaboration provided a realistic learning experience for computer science students.

  1. Interdisciplinary Educational Collaborations: Chemistry and Computer Science

    ERIC Educational Resources Information Center

    Haines, Ronald S.; Woo, Daniel T.; Hudson, Benjamin T.; Mori, Joji C.; Ngan, Evey S. M.; Pak, Wing-Yee

    2007-01-01

    Research collaborations between chemists and other scientists resulted in significant outcomes such as development of software. Such collaboration provided a realistic learning experience for computer science students.

  2. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  3. Probing Student Teachers' Subject Content Knowledge in Chemistry: Case Studies Using Dynamic Computer Models

    ERIC Educational Resources Information Center

    Toplis, Rob

    2008-01-01

    This paper reports case study research into the knowledge and understanding of chemistry for six secondary science student teachers. It combines innovative student-generated computer animations, using "ChemSense" software, with interviews to probe understanding of four common chemical processes used in the secondary school curriculum. Findings…

  4. Combining Dynamical Decoupling with Fault-Tolerant Quantum Computation

    DTIC Science & Technology

    2009-11-17

    ar X iv :0 91 1. 32 02 v1 [ qu an t- ph ] 1 7 N ov 2 00 9 Combining dynamical decoupling with fault-tolerant quantum computation Hui Khoon Ng,1...Daniel A. Lidar,2 and John Preskill1 1Institute for Quantum Information, California Institute of Technology, Pasadena, CA 91125, USA 2Departments...of Chemistry, Electrical Engineering, and Physics, and Center for Quantum Information Science & Technology, University of Southern California, Los

  5. 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.

  6. Virtual drug discovery: beyond computational chemistry?

    PubMed

    Gilardoni, Francois; Arvanites, Anthony C

    2010-02-01

    This editorial looks at how a fully integrated structure that performs all aspects in the drug discovery process, under one company, is slowly disappearing. The steps in the drug discovery paradigm have been slowly increasing toward virtuality or outsourcing at various phases of product development in a company's candidate pipeline. Each step in the process, such as target identification and validation and medicinal chemistry, can be managed by scientific teams within a 'virtual' company. Pharmaceutical companies to biotechnology start-ups have been quick in adopting this new research and development business strategy in order to gain flexibility, access the best technologies and technical expertise, and decrease product developmental costs. In today's financial climate, the term virtual drug discovery has an organizational meaning. It represents the next evolutionary step in outsourcing drug development.

  7. New reagents, new reactions: Computers in chemistry

    SciTech Connect

    Dessy, R.E.

    1996-12-31

    There is a new reagent in chemical reaction vessels-the computer. From data collection, through information processing, to knowledge creation the computer is an integral partner of today`s chemist. Despite its ability to be a Sorcerer`s Apprentice, it has become a leading weapon in overcoming some of the fiscal and technical demands placed upon research and development teams by global competition. In the process it is forcing changes in our work habits that arc, stressing both the Corporation and the individual, this article explores the uses, abuses, and possible future of the new reagent, and explores the meta-physics of the electronic web. 42 refs.

  8. National Resource for Computation in Chemistry (NRCC). Attached scientific processors for chemical computations: a report to the chemistry community

    SciTech Connect

    Ostlund, N.S.

    1980-01-01

    The demands of chemists for computational resources are well known and have been amply documented. The best and most cost-effective means of providing these resources is still open to discussion, however. This report surveys the field of attached scientific processors (array processors) and attempts to indicate their present and possible future use in computational chemistry. Array processors have the possibility of providing very cost-effective computation. This report attempts to provide information that will assist chemists who might be considering the use of an array processor for their computations. It describes the general ideas and concepts involved in using array processors, the commercial products that are available, and the experiences reported by those currently using them. In surveying the field of array processors, the author makes certain recommendations regarding their use in computational chemistry. 5 figures, 1 table (RWR)

  9. [Computational chemistry in structure-based drug design].

    PubMed

    Cao, Ran; Li, Wei; Sun, Han-Zi; Zhou, Yu; Huang, Niu

    2013-07-01

    Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains challenging to rationally design small molecular ligands with desired biological characteristics based on the structural information of the drug targets, which demands more accurate calculation of ligand binding free-energy. With the rapid advances in computer power and extensive efforts in algorithm development, physics-based computational chemistry approaches have played more important roles in structure-based drug design. Here we reviewed the newly developed computational chemistry methods in structure-based drug design as well as the elegant applications, including binding-site druggability assessment, large scale virtual screening of chemical database, and lead compound optimization. Importantly, here we address the current bottlenecks and propose practical solutions.

  10. Applied Computational Chemistry for the Blind and Visually Impaired

    ERIC Educational Resources Information Center

    Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

    2012-01-01

    We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

  11. Computational chemistry as an integral component of lead generation.

    PubMed

    Roche, Olivier; Guba, Wolfgang

    2005-07-01

    From library shaping to ADME-Tox prediction via virtual screening, computational chemistry is an integral component of Lead Generation. It provides a series of tools that help focusing on compounds with a balanced pharmacodynamic and ADME-Tox profile together with a high potential to optimize potency and selectivity.

  12. Investigating the Effectiveness of Computer Simulations for Chemistry Learning

    ERIC Educational Resources Information Center

    Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

    2012-01-01

    Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

  13. Incorporating Computational Chemistry into the Chemical Engineering Curriculum

    ERIC Educational Resources Information Center

    Wilcox, Jennifer

    2006-01-01

    A graduate-level computational chemistry course was designed and developed and carried out in the Department of Chemical Engineering at Worcester Polytechnic Institute in the Fall of 2005. The thrust of the course was a reaction assignment that led students through a series of steps, beginning with energetic predictions based upon fundamental…

  14. One Instructor's Approach to Computer Assisted Instruction in General Chemistry.

    ERIC Educational Resources Information Center

    DeLorenzo, Ronald

    1982-01-01

    Discusses advantages of using computer-assisted instruction in a college general chemistry course. Advantages include using programs which generate random equations with double arrows (equilibrium systems) or generate alkane structural formula, asking for the correct IUPAC name of the structure. (Author/JN)

  15. Incorporating Computational Chemistry into the Chemical Engineering Curriculum

    ERIC Educational Resources Information Center

    Wilcox, Jennifer

    2006-01-01

    A graduate-level computational chemistry course was designed and developed and carried out in the Department of Chemical Engineering at Worcester Polytechnic Institute in the Fall of 2005. The thrust of the course was a reaction assignment that led students through a series of steps, beginning with energetic predictions based upon fundamental…

  16. Applied Computational Chemistry for the Blind and Visually Impaired

    ERIC Educational Resources Information Center

    Wedler, Henry B.; Cohen, Sarah R.; Davis, Rebecca L.; Harrison, Jason G.; Siebert, Matthew R.; Willenbring, Dan; Hamann, Christian S.; Shaw, Jared T.; Tantillo, Dean J.

    2012-01-01

    We describe accommodations that we have made to our applied computational-theoretical chemistry laboratory to provide access for blind and visually impaired students interested in independent investigation of structure-function relationships. Our approach utilizes tactile drawings, molecular model kits, existing software, Bash and Perl scripts…

  17. Investigating the Effectiveness of Computer Simulations for Chemistry Learning

    ERIC Educational Resources Information Center

    Plass, Jan L.; Milne, Catherine; Homer, Bruce D.; Schwartz, Ruth N.; Hayward, Elizabeth O.; Jordan, Trace; Verkuilen, Jay; Ng, Florrie; Wang, Yan; Barrientos, Juan

    2012-01-01

    Are well-designed computer simulations an effective tool to support student understanding of complex concepts in chemistry when integrated into high school science classrooms? We investigated scaling up the use of a sequence of simulations of kinetic molecular theory and associated topics of diffusion, gas laws, and phase change, which we designed…

  18. Dissociation of the Ethyl Radical: An Exercise in Computational Chemistry

    ERIC Educational Resources Information Center

    Nassabeh, Nahal; Tran, Mark; Fleming, Patrick E.

    2014-01-01

    A set of exercises for use in a typical physical chemistry laboratory course are described, modeling the unimolecular dissociation of the ethyl radical to form ethylene and atomic hydrogen. Students analyze the computational results both qualitatively and quantitatively. Qualitative structural changes are compared to approximate predicted values…

  19. Dissociation of the Ethyl Radical: An Exercise in Computational Chemistry

    ERIC Educational Resources Information Center

    Nassabeh, Nahal; Tran, Mark; Fleming, Patrick E.

    2014-01-01

    A set of exercises for use in a typical physical chemistry laboratory course are described, modeling the unimolecular dissociation of the ethyl radical to form ethylene and atomic hydrogen. Students analyze the computational results both qualitatively and quantitatively. Qualitative structural changes are compared to approximate predicted values…

  20. 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.

  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. 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…

  3. Computational Tools To Model Halogen Bonds in Medicinal Chemistry.

    PubMed

    Ford, Melissa Coates; Ho, P Shing

    2016-03-10

    The use of halogens in therapeutics dates back to the earliest days of medicine when seaweed was used as a source of iodine to treat goiters. The incorporation of halogens to improve the potency of drugs is now fairly standard in medicinal chemistry. In the past decade, halogens have been recognized as direct participants in defining the affinity of inhibitors through a noncovalent interaction called the halogen bond or X-bond. Incorporating X-bonding into structure-based drug design requires computational models for the anisotropic distribution of charge and the nonspherical shape of halogens, which lead to their highly directional geometries and stabilizing energies. We review here current successes and challenges in developing computational methods to introduce X-bonding into lead compound discovery and optimization during drug development. This fast-growing field will push further development of more accurate and efficient computational tools to accelerate the exploitation of halogens in medicinal chemistry.

  4. A Lewis Acid-Base Computational Chemistry Exercise for Advanced Inorganic Chemistry

    NASA Astrophysics Data System (ADS)

    Anderson, Wayne P.

    2000-02-01

    A computational chemistry exercise dealing with Lewis acids and bases has been developed for use in advanced inorganic chemistry courses. The exercise employs ab initio or semiempirical quantum mechanical calculations to investigate the adducts of the Lewis acids BH3, BF3, BCl3, AlH3, and AlCl3 with the Lewis bases NH3 and PH3. Adducts of BCl3 with pyridine, 3,5-dimethylpyridine, and 2,6-dimethylpyridine are also investigated. Binding energies, geometric changes upon adduct formation, structural reorganizational energies, and partial atomic charges are calculated. Factors influencing binding energies between Lewis acids and bases can be inferred from the results.

  5. 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

  6. ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

    EPA Science Inventory

    Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...

  7. ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING: APPLICATION OF COMPUTATIONAL BIOPHYSICAL TRANSPORT, COMPUTATIONAL CHEMISTRY, AND COMPUTATIONAL BIOLOGY

    EPA Science Inventory

    Computational toxicology (CompTox) leverages the significant gains in computing power and computational techniques (e.g., numerical approaches, structure-activity relationships, bioinformatics) realized over the last few years, thereby reducing costs and increasing efficiency i...

  8. Computational Exploration of Molecular Scaffolds in Medicinal Chemistry.

    PubMed

    Hu, Ye; Stumpfe, Dagmar; Bajorath, Jürgen

    2016-05-12

    The scaffold concept is widely applied in medicinal chemistry. Scaffolds are mostly used to represent core structures of bioactive compounds. Although the scaffold concept has limitations and is often viewed differently from a chemical and computational perspective, it has provided a basis for systematic investigations of molecular cores and building blocks, going far beyond the consideration of individual compound series. Over the past 2 decades, alternative scaffold definitions and organization schemes have been introduced and scaffolds have been studied in a variety of ways and increasingly on a large scale. Major applications of the scaffold concept include the generation of molecular hierarchies, structural classification, association of scaffolds with biological activities, and activity prediction. This contribution discusses computational approaches for scaffold generation and analysis, with emphasis on recent developments impacting medicinal chemistry. A variety of scaffold-based studies are discussed, and a perspective on scaffold methods is provided.

  9. Computational chemistry in Argonne`s Reactor Analysis Division

    SciTech Connect

    Gelbard, E.; Agrawal, R.; Fanning, T.

    1997-08-01

    Roughly 3 years ago work on Argonne`s Integral Fast Reactor ({open_quotes}IFR{close_quotes}) was terminated and at that time, ANL funding was redirected to a number of alternative programs. One such alternative was waste management and, since disposal of spent fuel from ANL`s EBR-II reactor presents some special problems, this seemed an appropriate area for ANL work. Methods for the treatment and disposal of spent fuel (particularly from EBR-II but also from other sources) are now under very active investigation at ANL. The very large waste form development program is mainly experimental at this point, but within the Reactor Analysis ({open_quotes}RA{close_quotes}) Division a small computational chemistry program is underway, designed to supplement the experimental program. One of the most popular proposals for the treatment of much of our high-level wastes is vitrification. As noted below, this approach has serious drawbacks for EBR-II spent fuel. ANL has proposed, instead, that spent fuel first be pretreated by a special metallurgical process which produces, as waste, chloride salts of the various fission products; these salts would then be adsorbed in zeolite A, which is subsequently bonded with glass to produce a waste form suitable for disposal. So far it has been the main mission of RA`s computational chemistry program to study the process by which leaching occurs when the glass-bonded zeolite waste form is exposed to water. It is the purpose of this paper to describe RA`s computational chemistry program, to discuss the computational techniques involved in such a program, and in general to familiarize the M. and C. Division with a computational area which is probably unfamiliar to most of its member. 11 refs., 2 figs.

  10. Introductory College Chemistry Students' Understanding of Stoichiometry: Connections between Conceptual and Computational Understandings and Instruction.

    ERIC Educational Resources Information Center

    Wolfer, Adam J.; Lederman, Norman G.

    Many studies of college chemistry students have found a gap between students' success in solving computational chemistry problems and their success in solving conceptual chemistry problems. This paper examines college students' understanding of the concept of stoichiometry, the particulate nature of matter, and chemistry problem solving. This…

  11. Using the computer to understand the chemistry of conical intersections.

    PubMed

    Schapiro, Igor; Melaccio, Federico; Laricheva, Elena N; Olivucci, Massimo

    2011-06-01

    The application of computational chemistry in resolving photochemical and photobiological problems depends on theoretical models and calculation strategies that allow an understanding of how and when the energy contained in a photon can be used or dissipated by a molecule. Progress in this arena has been the result of a scientific journey that can be traced from the 1960s and 1970s with the development of the concept of the "photochemical funnel", and again from the 1980s and 1990s with the development and application of ab initio multiconfigurational quantum chemistry. Mainly following the viewpoint and contributions of the corresponding author (together with others), here we show that both the early and the ongoing research points to a central role of conical intersections in the molecular-level control of the selectivity and efficiency of photochemical reactions and internal conversion processes.

  12. Development and Assessment of a Chemistry-Based Computer Video Game as a Learning Tool

    ERIC Educational Resources Information Center

    Martinez-Hernandez, Kermin Joel

    2010-01-01

    The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning…

  13. In-Service Chemistry Teachers Training: The Impact of Introducing Computer Technology on Teachers' Attitudes.

    ERIC Educational Resources Information Center

    Dori, Y. J.; Barnea, N.

    A computer-assisted instruction (CAI) module on polymers was used to introduce chemistry teachers (n=64) to the variety of possibilities and benefits of using courseware in the current chemistry curriculum in Israel. From an analysis of a pre-and post-attitude questionnaire regarding the use of computers in chemistry teaching, it was concluded…

  14. Development and Assessment of a Chemistry-Based Computer Video Game as a Learning Tool

    ERIC Educational Resources Information Center

    Martinez-Hernandez, Kermin Joel

    2010-01-01

    The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning…

  15. Investigating the Medium Effect in Computer-Aided Assessment of School Chemistry and College Computing National Examinations

    ERIC Educational Resources Information Center

    Ashton, Helen S.; Beevers, Cliff E.; Korabinski, Athol A.; Youngson, Martin A.

    2005-01-01

    This article presents results of a comparison between paper and computer tests of ability in Chemistry and Computing. A statistical model is employed to analyse the experimental data from almost 200 candidates. It is shown that there is no medium effect when specific traditional paper examinations in Chemistry and Computing are transferred into…

  16. 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.

  17. Computational chemistry meets cultural heritage: challenges and perspectives.

    PubMed

    Fantacci, Simona; Amat, Anna; Sgamellotti, Antonio

    2010-06-15

    Chemistry is central to addressing topics of interest in the cultural heritage field, offering particular insight into the nature and composition of the original materials, the degradation processes that have occurred over the years, and the attendant physical and chemical changes. On the one hand, the chemical characterization of the constituting materials allows researchers to unravel the rich information enclosed in a work of art, providing insight into the manufacturing techniques and revealing aspects of artistic, chronological, historical, and sociocultural significance. On the other hand, despite the recognized contribution of computational chemistry in many branches of materials science, this tool has only recently been applied to cultural heritage, largely because of the inherent complexity of art materials. In this Account, we present a brief overview of the available computational methods, classified on the basis of accuracy level and dimension of the system to be simulated. Among the discussed methodologies, density functional theory (DFT) and time-dependent DFT represent a good compromise between accuracy and computational cost, allowing researchers to model the structural, electronic, and spectroscopic properties of complex extended systems in condensed phase. We then discuss the results of recent research devoted to the computer simulation of prototypical systems in cultural heritage, namely, indigo and Maya Blue, weld and weld lake, and the pigment minium (red lead). These studies provide insight into the basic interactions underlying the materials properties and, in some cases, permit the assignment of the material composition. We discuss properties of interest in the cultural heritage field, ranging from structural geometries and acid-base properties to IR-Raman vibrational spectra and UV-vis absorption-emission spectra (including excited-state deactivation pathways). We particularly highlight how computational chemistry applications in cultural

  18. A nascent proteome study combining click chemistry with 2DE.

    PubMed

    Osterman, Ilya A; Ustinov, Alexey V; Evdokimov, Denis V; Korshun, Vladimir A; Sergiev, Petr V; Serebryakova, Marina V; Demina, Irina A; Galyamina, Maria A; Govorun, Vadim M; Dontsova, Olga A

    2013-01-01

    To investigate the dynamic cellular response to a condition change, selective labeling of the nascent proteome is necessary. Here, we report a method combining click chemistry protein labeling with 2D DIGE. To test the relevance of the method, we compared nascent proteomes of actively growing bacterial cells with that of cells exposed to protein synthesis inhibitor, erythromycin. Cells were incubated with methionine analog, homopropargyl glycin, and their nascent proteome was selectively labeled with monosulfonated neutral Cy3 and Cy5 azides specially synthesized for this purpose. Following fluorescent labeling, the protein samples were mixed and subjected to standard 2D DIGE separation. The method allowed us to reveal a dramatic reduction of newly synthesized proteins upon erythromycin treatment, while the total proteome was not significantly affected. Additionally, several proteins, whose synthesis was resistant to erythromycin, were identified. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Is there a future for computational chemistry in drug research?

    NASA Astrophysics Data System (ADS)

    Maggiora, Gerald M.

    2012-01-01

    Improvements in computational chemistry methods have had a growing impact on drug research. But will incremental improvements be sufficient to ensure this continues? Almost all existing efforts to discover new drugs depend on the classic one target, one drug paradigm, although the situation is changing slowly. A new paradigm that focuses on a more systems biology approach and takes account of the reality that most drugs exhibit some level of polypharmacology is beginning to emerge. This will bring about dramatic changes that can significantly influence the role that computational methods play in future drug research. But these changes require that current methods be augmented with those from bioinformatics and engineering if the field is to have a significant impact on future drug research.

  20. Opportunities and challenges of high-performance computing in chemistry

    SciTech Connect

    Guest, M.F.; Kendall, R.A.; Nichols, J.A.

    1995-06-01

    The field of high-performance computing is developing at an extremely rapid pace. Massively parallel computers offering orders of magnitude increase in performance are under development by all the major computer vendors. Many sites now have production facilities that include massively parallel hardware. Molecular modeling methodologies (both quantum and classical) are also advancing at a brisk pace. The transition of molecular modeling software to a massively parallel computing environment offers many exciting opportunities, such as the accurate treatment of larger, more complex molecular systems in routine fashion, and a viable, cost-effective route to study physical, biological, and chemical `grand challenge` problems that are impractical on traditional vector supercomputers. This will have a broad effect on all areas of basic chemical science at academic research institutions and chemical, petroleum, and pharmaceutical industries in the United States, as well as chemical waste and environmental remediation processes. But, this transition also poses significant challenges: architectural issues (SIMD, MIMD, local memory, global memory, etc.) remain poorly understood and software development tools (compilers, debuggers, performance monitors, etc.) are not well developed. In addition, researchers that understand and wish to pursue the benefits offered by massively parallel computing are often hindered by lack of expertise, hardware, and/or information at their site. A conference and workshop organized to focus on these issues was held at the National Institute of Health, Bethesda, Maryland (February 1993). This report is the culmination of the organized workshop. The main conclusion: a drastic acceleration in the present rate of progress is required for the chemistry community to be positioned to exploit fully the emerging class of Teraflop computers, even allowing for the significant work to date by the community in developing software for parallel architectures.

  1. Theoretical Hammett Plot for the Gas-Phase Ionization of Benzoic Acid versus Phenol: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Ziegler, Blake E.

    2013-01-01

    Computational chemistry undergraduate laboratory courses are now part of the chemistry curriculum at many universities. However, there remains a lack of computational chemistry exercises available to instructors. This exercise is presented for students to develop skills using computational chemistry software while supplementing their knowledge of…

  2. Theoretical Hammett Plot for the Gas-Phase Ionization of Benzoic Acid versus Phenol: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Ziegler, Blake E.

    2013-01-01

    Computational chemistry undergraduate laboratory courses are now part of the chemistry curriculum at many universities. However, there remains a lack of computational chemistry exercises available to instructors. This exercise is presented for students to develop skills using computational chemistry software while supplementing their knowledge of…

  3. An improved computer model of struvite solution chemistry.

    PubMed

    Wrigley, T J; Scott, W D; Webb, K M

    1992-12-01

    The computer model of the solution chemistry of struvite has been improved. Firstly, with ammonia as the prime calculation point in the liquid phase, the algorithm is smaller and faster. Secondly, the incorporation of distilled magnesium hydrogen phosphate in the model significantly increased the concentrations in solution. Thirdly, estimates of the activity coefficients are included. These improvements have but a marginal (5-10%) improvement in the fit. However, proceeding with this flexible modelling procedure using the symbolic manipulator, Maple, easily allows the inclusion of all possible species. The addition of associated ammonium phosphates improves the fit. The relative standard deviation of the fit of both Taylor's data and the data of Webb is improved from 0.5 to 0.2. Estimates of the association constants are included.

  4. Supramolecular Chemistry: Computer-Assisted Instruction in Undergraduate and Graduate Chemistry Courses

    NASA Astrophysics Data System (ADS)

    Varnek, Alexandre A.; Dietrich, Bernard; Wipff, Georges; Lehn, Jean-Marie; Boldyreva, Elena V.

    2000-02-01

    An interactive electronic textbook (SC-WEB) based on Supramolecular Chemistry, by J.-M. Lehn, is described. It includes the text, which has been specially adapted for teaching, and data on the structures of molecules and supermolecules. The list includes about 100 structures retrieved from the Cambridge Structural Database (version 1997) as well as those obtained from molecular dynamics simulations in solution. The structures can be retrieved either from the text or, independently, from the list. SC-WEB uses two types of programs: the first one reads files in HTML format (Word97, Netscape, or Internet Explorer), and WebLab Viewer Lite is used for visualizing and manipulating the structures. It can run on any PC (W95/NT4.0) computer. The application of SC-WEB for a course in supramolecular chemistry, as well as in other chemical courses, is discussed. A few examples related to the binding of alkali cations by organic and inorganic receptors, and of R-NH3+ cations by organic receptors, are considered in more detail.

  5. Computational Chemistry for Nuclear Waste Characterization and Processing: Relativistic Quantum Chemistry of Actinides

    SciTech Connect

    Harrison, Robert J.; Bernholdt, David E.; Bursten, Bruce E.; De Jong, Wibe A.; Dixon, David A.; Dyall, Kenneth G.; Ermler, Walter V.; Fann, George I.; Hay, P. J.; Ismail Buchner, Nina; Kendall, Ricky A.; Li, Jun; Marino, Maria M.; Marsden, Colin J.; Martin, Richard L.; Minkoff, Michael; Nichols, Jeffrey A.; Nieplocha, Jarek; Pitzer, Russell M.; Pratt, Lawrence R.; Schreckenbach, Hans Georg; Seth, Michael C.; Shepard, Ron; Stevens, Rick L.; Tilson, Jeffrey L.; Wagner, Albert F.; Wang, Qi; Windus, Theresa L.; Wong, Adrian; Zhang, Zhiyong

    2002-08-02

    In the course of the 3 years we have conducted calculations on molecular structures containing actinides, lanthanides, and other heavy elements. Our calculations were done at the relativistically-correct, all-electron, 4-component calculations (DHF, MP2, and CCSD(T)), using density functional theory (DFT) with relativistic effective core potentials (RECPs), and various other methodologies. We studied the ground- and excited state structures, energetics, vibrational frequencies, and NMR, excitation and ionization spectra. In addition a considerable amount of codes and methodologies have been developed during the GC3 period, enabling us to do the extensive research described in this final report, and providing researchers worldwide with new computational chemistry tools. In this section we will give a brief overview of our activities and accomplishments, grouped by each research institution. A more extensive overview can be found in the appendices containing the full yearly reports.

  6. Hydration of pure and base-Containing sulfuric acid clusters studied by computational chemistry methods

    NASA Astrophysics Data System (ADS)

    Henschel, Henning; Ortega, Ismael K.; Kupiainen, Oona; Olenius, Tinja; Kurtén, Theo; Vehkamäki, Hanna

    2013-05-01

    The formation of hydrates of small molecular sulfuric acid clusters and cluster containing both sulfuric acid and base (ammonia or dimethylamine) has been studied by means of computational chemistry. Using a combined ab initio/density functional approach, formation energies of clusters with up to four sulfuric acid molecules, and up to two base molecules, have been calculated. Consequences for the hydration level of the corresponding clusters have been modelled. While the majority of pure sulfuric acid cluster are comparatively strongly hydrated, base containing cluster were found to be less hydrophilic. Dimethylamine is particularly effective in lowering the hydrophilicity of the cluster. Implications of the hydration profiles on atmospheric processes are discussed.

  7. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry

    PubMed Central

    Petraglia, Riccardo; Nicolaï, Adrien; Wodrich, Matthew D.

    2016-01-01

    Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica‐exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature‐dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD‐DFTB methodology at the heart of this study is powered by i‐PI, which efficiently handles the interface between the DFTB and REMD codes. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26228927

  8. Item Design Considerations for Computer-Based Testing of Student Learning in Chemistry

    NASA Astrophysics Data System (ADS)

    Bowen, Craig W.

    1998-09-01

    The focus of this paper is an examination of how chemistry test items may be designed for use in a computer-testing environment. It begins by examining ideas from cognitive psychology and research on problem solving in chemistry. It also consider previous ways computers have been used to measure student learning in chemistry. The paper ends by providing a framework for developing test items (and examples of items) across macroscopic, particulate, symbolic and integrated levels of chemical understanding.

  9. Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

    ERIC Educational Resources Information Center

    Perri, M. J.; Weber, S. H.

    2014-01-01

    A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

  10. Web-Based Job Submission Interface for the GAMESS Computational Chemistry Program

    ERIC Educational Resources Information Center

    Perri, M. J.; Weber, S. H.

    2014-01-01

    A Web site is described that facilitates use of the free computational chemistry software: General Atomic and Molecular Electronic Structure System (GAMESS). Its goal is to provide an opportunity for undergraduate students to perform computational chemistry experiments without the need to purchase expensive software.

  11. Crossing the Boundaries within Computational Chemistry: From Molecular Dynamics to Cheminformatics and back.

    PubMed

    Riniker, Sereina

    2014-09-01

    The research in the group for computational chemistry at the ETH Zurich focuses on the development of methods and software for classical molecular dynamics simulations and cheminformatics, and their application to biological and chemical questions. Here, important advances and challenges in these subfields of computational chemistry are reviewed and potential opportunities for cross-fertilization are outlined.

  12. Computers in Chemistry Teaching: A Bibliography and Index of CAL Packages.

    ERIC Educational Resources Information Center

    Rushby, N. J.

    This resource document lists 36 books, papers, and reports dealing with various uses of computers in chemistry instruction; and describes several computer program packages available for use in teaching undergraduate, experimental laboratory, physical, and nuclear and X-ray chemistry, including biochemistry. Each program package is presented by…

  13. High performance computational chemistry: Towards fully distributed parallel algorithms

    SciTech Connect

    Guest, M.F.; Apra, E.; Bernholdt, D.E.

    1994-07-01

    An account is given of work in progress within the High Performance Computational Chemistry Group (HPCC) at the Pacific Northwest Laboratory (PNL) to develop molecular modeling software applications for massively parallel processors (MPPs). A discussion of the issues in developing scalable parallel algorithms is presented, with a particular focus on the distribution, as opposed to the replication, of key data structures. Replication of large data structures limits the maximum calculation size by imposing a low ratio of processors to memory. Only applications that distribute both data and computation across processors are truly scalable. The use of shared data structures, which may be independently accessed by each process even in a distributed-memory environment, greatly simplifies development and provides a significant performance enhancement. In describing tools to support this programming paradigm, an outline is given of the implementation and performance of a highly efficient and scalable algorithm to perform quadratically convergent, self-consistent field calculations on molecular systems. A brief account is given of the development of corresponding MPP capabilities in the areas of periodic Hartree Fock, Moeller-Plesset perturbation theory (MP2), density functional theory, and molecular dynamics. Performance figures are presented using both the Intel Touchstone Delta and Kendall Square Research KSR-2 supercomputers.

  14. Computational Study of Nonequilibrium Chemistry in High Temperature Flows

    NASA Astrophysics Data System (ADS)

    Doraiswamy, Sriram

    Recent experimental measurements in the reflected shock tunnel CUBRC LENS-I facility raise questions about our ability to correctly model the recombination processes in high enthalpy flows. In the carbon dioxide flow, the computed shock standoff distance over the Mars Science Laboratory (MSL) shape was less than half of the experimental result. For the oxygen flows, both pressure and heat transfer data on the double cone geometry were not correctly predicted. The objective of this work is to investigate possible reasons for these discrepancies. This process involves systematically addressing different factors that could possibly explain the differences. These factors include vibrational modeling, role of electronic states and chemistry-vibrational coupling in high enthalpy flows. A state-specific vibrational model for CO2, CO, O2 and O system is devised by taking into account the first few vibrational states of each species. All vibrational states with energies at or below 1 eV are included in the present work. Of the three modes of vibration in CO2 , the antisymmetric mode is considered separately from the symmetric stretching mode and the doubly degenerate bending modes. The symmetric and the bending modes are grouped together since the energy transfer rates between the two modes are very large due to Fermi resonance. The symmetric and bending modes are assumed to be in equilibrium with the translational and rotational modes. The kinetic rates for the vibrational-translation energy exchange reactions, and the intermolecular and intramolecular vibrational-vibrational energy exchange reactions are based on experimental data to the maximum extent possible. Extrapolation methods are employed when necessary. This vibrational model is then coupled with an axisymmetric computational fluid dynamics code to study the expansion of CO2 in a nozzle. The potential role of low lying electronic states is also investigated. Carbon dioxide has a single excited state just below

  15. Interactive Computer Visualization in the Introductory Chemistry Curriculum

    NASA Astrophysics Data System (ADS)

    Bragin, Victoria M.

    1996-08-01

    Increasingly, chemistry instructors, especially in two-year colleges, find themselves teaching classes where there is great disparity in the academic preparation of the students and where even those students with good mathematics and basic science backgrounds have poor English language and communication skills. This project explores the use of technological innovations to facilitate learning in introductory chemistry courses by those with a poor academic background, while also challenging those prepared to master the curriculum. An additional objective is to improve the communication skills of all students. Material is presented visually and in as engaging a fashion as possible, students are provided ready access to relevant information about the course content in ways that are adapted to their individual learning styles, and collaborative learning is encouraged, especially among those who work and live at a distance from campus. The chief tactics employed are: Development of software that can be customized to meet the varying needs of individual students, courses, and instructors. Use of simulations that, while not replacing laboratory bench experiments, allow students to practice important laboratory techniques and observe the physical behavior of chemical systems. Use of software that allows students to explore the molecular basis of chemical phenomena. Use of software that allows students to display and analyze data in ways that facilitate drawing general conclusions about the quantitative relationships between observable properties. Use of the computer as a communications device. The ability to customize software is important in adapting to different learning styles and in encouraging students to learn by discovery. For example, TitrationLab was developed so that the material may merely be presented empirically or in ways in which the principles of equilibrium are demonstrated. At the advanced level, automatically generated titration curves are used to

  16. Modeling molecular computing systems by an artificial chemistry - its expressive power and application.

    PubMed

    Tominaga, Kazuto; Watanabe, Tooru; Kobayashi, Keiji; Nakamura, Masaki; Kishi, Koji; Kazuno, Mitsuyoshi

    2007-01-01

    Artificial chemistries are mainly used to construct virtual systems that are expected to show behavior similar to living systems. In this study, we explore possibilities of applying an artificial chemistry to modeling natural biochemical systems-or, to be specific, molecular computing systems-and show that it may be a useful modeling tool for molecular computation. We previously proposed an artificial chemistry based on string pattern matching and recombination. This article first demonstrates that this artificial chemistry is computationally universal if it has only rules that have one reactant or two reactants. We think this is a good property of an artificial chemistry that models molecular computing, because natural elementary chemical reactions, on which molecular computing is based, are mostly unimolecular or bimolecular. Then we give two illustrative example models for DNA computing in our artificial chemistry: one is for the type of computation called the Adleman-Lipton paradigm, and the other is for a DNA implementation of a finite automaton. Through the construction of these models we observe preferred properties of the artificial chemistry for modeling molecular computing, such as having no spatial structure and being flexible in choosing levels of abstraction.

  17. Promoting Intrinsic and Extrinsic Motivation among Chemistry Students Using Computer-Assisted Instruction

    ERIC Educational Resources Information Center

    Gambari, Isiaka A.; Gbodi, Bimpe E.; Olakanmi, Eyitao U.; Abalaka, Eneojo N.

    2016-01-01

    The role of computer-assisted instruction in promoting intrinsic and extrinsic motivation among Nigerian secondary school chemistry students was investigated in this study. The study employed two modes of computer-assisted instruction (computer simulation instruction and computer tutorial instructional packages) and two levels of gender (male and…

  18. A Timesharing Computer Program for a General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Cutler, Gary L.; Drum, Donald A.

    1975-01-01

    Describes an experiment in which general and physical chemistry students can determine the heat of vaporization of a volatile substance from experimental laboratory data using timesharing techniques. (MLH)

  19. A Timesharing Computer Program for a General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Cutler, Gary L.; Drum, Donald A.

    1975-01-01

    Describes an experiment in which general and physical chemistry students can determine the heat of vaporization of a volatile substance from experimental laboratory data using timesharing techniques. (MLH)

  20. Guide for Teaching Chemistry-Physics Combined 1-2, 3-4 (PSSC - CHEMS).

    ERIC Educational Resources Information Center

    Millstone, H. George

    This guide is written for a combined physics-chemistry course taught over a two-year period. The subject matter contains the major ideas in Chemical Education Materials Study (CHEMS) Chemistry and Physical Science Study Committee (PSSC) Physics. The guide includes discussion of text references, laboratory experiments, films, testing and evaluation…

  1. Computational investigation of rocket based combined cycle

    NASA Astrophysics Data System (ADS)

    Zhang, Xiao-bo; Wang, Zhan-xue; Liu, Zeng-wen

    2013-03-01

    Based on Computational Fluid Dynamic technology, the mixing process of Rocket Based Combined Cycle (RBCC) propulsion system is researched. The idea of RBCC propulsion system means combining rocket engine with ramjet engine effectively, which can flight from sea level to high altitude in wide Mach ranges. In order to analyze how the length of the mixing part affects mixing process, different length of mixing part are researched. As it is indicated, with a constant Mach number, increasing the length of mixing part makes main flow and second flow mix more evenly. Moreover, the length of mixing part has a slight impact on the thrust. Obviously the main consequence of increasing the length of mixing part is promoting the mix of main flow and second flow. Therefore, in order to decrease the weight of aircraft, it is of importance to reduce the length. Through comparing distribution of different cases, when working in the situation of maximum power, the flow in the nozzle of rocket engine is under expansion, while that in the nozzle is fully expanded. Nevertheless, in the case of high altitude and high Mach number, there exists a vortex in the nozzle of rocket engine because of over expansion; meanwhile, the flow in the nozzle is under expansion. Therefore, it is necessary to adjust nozzle throat area in order to increase the thrust of RBCC at high altitude.

  2. Using Computational Chemistry Activities to Promote Learning and Retention in a Secondary School General Chemistry Setting

    ERIC Educational Resources Information Center

    Ochterski, Joseph W.

    2014-01-01

    This article describes the results of using state-of-the-art, research-quality software as a learning tool in a general chemistry secondary school classroom setting. I present three activities designed to introduce fundamental chemical concepts regarding molecular shape and atomic orbitals to students with little background in chemistry, such as…

  3. Using Computational Chemistry Activities to Promote Learning and Retention in a Secondary School General Chemistry Setting

    ERIC Educational Resources Information Center

    Ochterski, Joseph W.

    2014-01-01

    This article describes the results of using state-of-the-art, research-quality software as a learning tool in a general chemistry secondary school classroom setting. I present three activities designed to introduce fundamental chemical concepts regarding molecular shape and atomic orbitals to students with little background in chemistry, such as…

  4. 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

  5. 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.

  6. Effects of Computer Based Learning on Students' Attitudes and Achievements towards Analytical Chemistry

    ERIC Educational Resources Information Center

    Akcay, Hüsamettin; Durmaz, Asli; Tüysüz, Cengiz; Feyzioglu, Burak

    2006-01-01

    The aim of this study was to compare the effects of computer-based learning and traditional method on students' attitudes and achievement towards analytical chemistry. Students from Chemistry Education Department at Dokuz Eylul University (D.E.U) were selected randomly and divided into three groups; two experimental (Eg-1 and Eg-2) and a control…

  7. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

    ERIC Educational Resources Information Center

    Albrecht, Birgit

    2014-01-01

    The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

  8. 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…

  9. 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…

  10. Computational Chemistry in the Undergraduate Laboratory: A Mechanistic Study of the Wittig Reaction

    ERIC Educational Resources Information Center

    Albrecht, Birgit

    2014-01-01

    The Wittig reaction is one of the most useful reactions in organic chemistry. Despite its prominence early in the organic chemistry curriculum, the exact mechanism of this reaction is still under debate, and this controversy is often neglected in the classroom. Introducing a simple computational study of the Wittig reaction illustrates the…

  11. The Use of Computer-Based Instruction in Undergraduate Organic Chemistry.

    ERIC Educational Resources Information Center

    Culp, George H.

    Thirty-two computer-based lesson modules in organic chemistry were developed at the University of Texas (Austin) over an 18-month period and evaluated in varying classroom situations for three semesters starting in the Fall of 1972. The modules were designed as supplements to the traditional organic chemistry course of the University. As such,…

  12. Effects of Computer Based Learning on Students' Attitudes and Achievements towards Analytical Chemistry

    ERIC Educational Resources Information Center

    Akcay, Husamettin; Durmaz, Asli; Tuysuz, Cengiz; Feyzioglu, Burak

    2006-01-01

    The aim of this study was to compare the effects of computer-based learning and traditional method on students' attitudes and achievement towards analytical chemistry. Students from Chemistry Education Department at Dokuz Eylul University (D.E.U) were selected randomly and divided into three groups; two experimental (Eg-1 and Eg-2) and a control…

  13. 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…

  14. Drug repurposing: translational pharmacology, chemistry, computers and the clinic.

    PubMed

    Issa, Naiem T; Byers, Stephen W; Dakshanamurthy, Sivanesan

    2013-01-01

    The process of discovering a pharmacological compound that elicits a desired clinical effect with minimal side effects is a challenge. Prior to the advent of high-performance computing and large-scale screening technologies, drug discovery was largely a serendipitous endeavor, as in the case of thalidomide for erythema nodosum leprosum or cancer drugs in general derived from flora located in far-reaching geographic locations. More recently, de novo drug discovery has become a more rationalized process where drug-target-effect hypotheses are formulated on the basis of already known compounds/protein targets and their structures. Although this approach is hypothesis-driven, the actual success has been very low, contributing to the soaring costs of research and development as well as the diminished pharmaceutical pipeline in the United States. In this review, we discuss the evolution in computational pharmacology as the next generation of successful drug discovery and implementation in the clinic where high-performance computing (HPC) is used to generate and validate drug-target-effect hypotheses completely in silico. The use of HPC would decrease development time and errors while increasing productivity prior to in vitro, animal and human testing. We highlight approaches in chemoinformatics, bioinformatics as well as network biopharmacology to illustrate potential avenues from which to design clinically efficacious drugs. We further discuss the implications of combining these approaches into an integrative methodology for high-accuracy computational predictions within the context of drug repositioning for the efficient streamlining of currently approved drugs back into clinical trials for possible new indications.

  15. Systems Theory as a Conceptual and Organizational Framework for Computational and Inferential Chemistry.

    ERIC Educational Resources Information Center

    Lacy, Mark E.

    1986-01-01

    Provides general background on basic concepts of systems theory. Discusses applications of systems theory to computational and inferential chemistry in molecular and reaction systems, systems analysis, and synthesis. Describes methodology for studying chemical systems by computer and gives advantages of an integrated computational environment. (JM)

  16. On combining computational differentiation and toolkits for parallel scientific computing.

    SciTech Connect

    Bischof, C. H.; Buecker, H. M.; Hovland, P. D.

    2000-06-08

    Automatic differentiation is a powerful technique for evaluating derivatives of functions given in the form of a high-level programming language such as Fortran, C, or C++. The program is treated as a potentially very long sequence of elementary statements to which the chain rule of differential calculus is applied over and over again. Combining automatic differentiation and the organizational structure of toolkits for parallel scientific computing provides a mechanism for evaluating derivatives by exploiting mathematical insight on a higher level. In these toolkits, algorithmic structures such as BLAS-like operations, linear and nonlinear solvers, or integrators for ordinary differential equations can be identified by their standardized interfaces and recognized as high-level mathematical objects rather than as a sequence of elementary statements. In this note, the differentiation of a linear solver with respect to some parameter vector is taken as an example. Mathematical insight is used to reformulate this problem into the solution of multiple linear systems that share the same coefficient matrix but differ in their right-hand sides. The experiments reported here use ADIC, a tool for the automatic differentiation of C programs, and PETSC, an object-oriented toolkit for the parallel solution of scientific problems modeled by partial differential equations.

  17. COMPUTATIONAL CHEMISTRY: AN EMERGING TECHNOLOGY FOR SOLVING PROBLEMS IN ATMOSPHERIC CHEMISTRY

    EPA Science Inventory

    Over the past three decades, atmospheric chemistry has served as an important component in developing strategies for reducing ambient concentrations of air pollutants. Laboratory studies are carried out to investigate the key chemical reactions that determine the fates and lif...

  18. COMPUTATIONAL CHEMISTRY: AN EMERGING TECHNOLOGY FOR SOLVING PROBLEMS IN ATMOSPHERIC CHEMISTRY

    EPA Science Inventory

    Over the past three decades, atmospheric chemistry has served as an important component in developing strategies for reducing ambient concentrations of air pollutants. Laboratory studies are carried out to investigate the key chemical reactions that determine the fates and lif...

  19. Using Computer-Assisted Personalized Assignments for Freshman Chemistry.

    ERIC Educational Resources Information Center

    Morrissey, D. J.; And Others

    1995-01-01

    Describes the Computer-Assisted Personalized Assignment (CAPA) system which offers a way to apply computers to assist instructors and students in the framework of lectures and assigned problem sets without students being forced to use the computer system. (DDR)

  20. Comparison of seven packages that compute ocean carbonate chemistry

    NASA Astrophysics Data System (ADS)

    Orr, J. C.; Epitalon, J.-M.; Gattuso, J.-P.

    2014-04-01

    To study ocean acidification and the carbon cycle, marine scientists often use two measured or modeled carbonate system variables to compute others. These carbonate chemistry calculations, based on well-known thermodynamic equilibria, are now available from seven public packages: CO2SYS, csys, seacarb, swco2, CO2calc, ODV, and mocsy. We compared results from these packages using common input data and the set of equilibrium constants recommended for best practices. All packages agree within ±0.00025 units for pH and ±0.5 μmol kg-1 for CO32-, and six packages agree within ±0.2 μatm for pCO2 in terms of zonal-mean surface values. In the remaining package (csys), the surface pCO2 variable is up to 1.4 μatm lower than in other packages, but that is because it is mislabeled. When compared to surface fCO2, it differs by less than 0.2 μatm. The csys deviations in fCO2, pH, and CO32- grow with depth but remain small. Another package (swco2) also diverges significantly but only in warm deep waters as found in the Mediterranean Sea. Discrepancies between packages derive largely from their code for the equilibrium constants. Analysis of the sensitivity of each computed variable to changes in each constant showed the expected dominance of K1 and K2, while also revealing comparable sensitivity to KB, e.g., with the AT-CT input pair. Best-practice formulations for K1 and K2 are implemented consistently among packages, except those in csys deviate slightly at depth (e.g., 0.5% larger values at 4000 db) due to its pressure corrections made on the total instead of the seawater pH scale. With more recent formulations for K1 and K2 designed to cover a wider range of salinities, packages disagree more, e.g., by 8 μatm in pCO2, 1 μmol kg-1 in CO32-, and 0.006 units in pH under typical surface conditions. These discrepancies stem from packages using different sets of coefficients for the corresponding salinity dependence of the new formulations. Although each set should be

  1. 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.

  2. The optimal combination of substrate chemistry with physiological fluid shear stress.

    PubMed

    Li, Yan; Luo, Yanfeng; Xie, Zhao; Xing, Juan; Lin, Manping; Yang, Li; Wang, Yuanliang; Huang, Ke

    2013-12-01

    Osteoblasts on implanted biomaterials sense both substrate chemistry and mechanical stimulus. The effects of substrate chemistry alone and mechanical stimulus alone on osteoblasts have been widely studied. This study investigates the optimal combination of substrate chemistry and 12dyn/cm(2) physiological flow shear stress (FSS) by examining their influences on primary rat osteoblasts (ROBs), including the releases of ATP, nitric oxide (NO), and prostaglandin E2 (PGE2). Self-assembled monolayers (SAMs) on glass slides with -OH, -CH3, and -NH2 were employed to provide various substrate chemistries, whereas a parallel-plate fluid flow system produced the physiological FSS. Substrate chemistry alone exerted no observable effects on the releases of ATP, NO, and PGE2. Nevertheless, when ROBs were exposed to both substrate chemistry and FSS, the ATP releases of NH2 were upregulated about 12-fold compared to substrate chemistry alone, while the ATP releases of CH3 and OH was similarly increased 7-fold at the peak. Similar trends were observed for the releases of NO and PGE2. The expressions of ATP, NO, and PGE2 followed the pattern of NH2-FSS>Glass-FSS>CH3-FSS≈OH-FSS. ROBs on NH2 produced the optimal combination of substrate chemistry with the physiological FSS. The F-actin organization and focal adhesion (FA) formation of ROBs on various SAMs without FSS were examined. NH2 produced the best results whereas CH3 and OH produced the worst ones. Inhibition of FAs and/or disruption of F-actin significantly decreased the releases of FSS-induced PGE2, NO, and/or ATP. Consequently, a mechanism was proposed that the best F-actin organization and FA formation of ROBs on NH2 lead to the optimal combination of substrate chemistry with the 12dyn/cm(2) physiological FSS. This mechanism gives guidance for the design of implanted biomaterials and bioreactors for bone tissue engineering.

  3. Combined volatolomics for monitoring of human body chemistry.

    PubMed

    Broza, Yoav Y; Zuri, Liat; Haick, Hossam

    2014-04-09

    Analysis of volatile organic compounds (VOCs) is a promising approach for non-invasive, fast and potentially inexpensive diagnostics. Here, we present a new methodology for profiling the body chemistry by using the volatile fraction of molecules in various body fluids. Using mass spectrometry and cross-reactive nanomaterial-based sensors array, we demonstrate that simultaneous VOC detection from breath and skin would provide complementary, non-correlated information of the body's volatile metabolites profile. Eventually with further wide population validation studies, such a methodology could provide more accurate monitoring of pathological changes compared to the information provided by a single body fluid. The qualitative and quantitative methods presented here offers a variety of options for novel mapping of the metabolic properties of complex organisms, including humans.

  4. Combining research in physical chemistry and chemical education: Part A. The femtosecond molecular dynamics of small gas-phase anion clusters. Part B. Surveying student beliefs about chemistry and the development of physical chemistry learning tutorials

    NASA Astrophysics Data System (ADS)

    Barbera, Jack

    2007-12-01

    This dissertation combines work in the areas of experimental physical chemistry and chemical education. In the area of physical chemistry, femtosecond pump-probe spectroscopy is used to interrogate the time-dependence for energy redistribution, solvent reorientation, and dissociation dynamics in small gas-phase anion clusters. The chemical education research addressed in this manuscript include the development and validation of a survey to measure students' beliefs about chemistry and the learning of chemistry and the development and testing of learning tutorials for use in undergraduate physical chemistry courses in thermodynamics and kinetics. In the first part of this dissertation, the Cu(CD3OD) dynamics are investigated using a combination of femtosecond pump-probe experiments and ab initio calculations. Dissociation of this complex into Cu and CD3OD occurs on two distinct time scales: 3 and 30 ps, which arise, respectively, from the coupling of intermolecular solvent rotations and excited methyl rotor rotation into the Cu-O dissociation component upon electron photodetachment of the precursor anion. In the second part of this dissertation, the time-resolved recombination of photodissociated IBr-(CO2)n (n = 5 - 10) cluster anions is investigated. Upon excitation to the A' 2pi 1/2 state of the chromophore, the bare anion results in I- and Br products, upon solvation with CO2, the IBr- chromophore regains near-IR absorption after recombination and vibrational relaxation on the ground electronic state. The recombination times vary with the number of solvent molecules from 12 ps for n = 5 to 900 ps for n = 10. Extensive electronic structure and non-adiabatic molecular dynamic simulations provide a framework to understand this behavior. In the third part of this dissertation, the modification and validation of the Colorado Learning Attitudes about Science Survey (CLASS) for use in chemistry is presented in detail. The CLASS survey is designed to measure student

  5. Beyond static structures: Putting forth REMD as a tool to solve problems in computational organic chemistry.

    PubMed

    Petraglia, Riccardo; Nicolaï, Adrien; Wodrich, Matthew D; Ceriotti, Michele; Corminboeuf, Clemence

    2016-01-05

    Computational studies of organic systems are frequently limited to static pictures that closely align with textbook style presentations of reaction mechanisms and isomerization processes. Of course, in reality chemical systems are dynamic entities where a multitude of molecular conformations exists on incredibly complex potential energy surfaces (PES). Here, we borrow a computational technique originally conceived to be used in the context of biological simulations, together with empirical force fields, and apply it to organic chemical problems. Replica-exchange molecular dynamics (REMD) permits thorough exploration of the PES. We combined REMD with density functional tight binding (DFTB), thereby establishing the level of accuracy necessary to analyze small molecular systems. Through the study of four prototypical problems: isomer identification, reaction mechanisms, temperature-dependent rotational processes, and catalysis, we reveal new insights and chemistry that likely would be missed using static electronic structure computations. The REMD-DFTB methodology at the heart of this study is powered by i-PI, which efficiently handles the interface between the DFTB and REMD codes.

  6. On the Impact of Execution Models: A Case Study in Computational Chemistry

    SciTech Connect

    Chavarría-Miranda, Daniel; Halappanavar, Mahantesh; Krishnamoorthy, Sriram; Manzano Franco, Joseph B.; Vishnu, Abhinav; Hoisie, Adolfy

    2015-05-25

    Efficient utilization of high-performance computing (HPC) platforms is an important and complex problem. Execution models, abstract descriptions of the dynamic runtime behavior of the execution stack, have significant impact on the utilization of HPC systems. Using a computational chemistry kernel as a case study and a wide variety of execution models combined with load balancing techniques, we explore the impact of execution models on the utilization of an HPC system. We demonstrate a 50 percent improvement in performance by using work stealing relative to a more traditional static scheduling approach. We also use a novel semi-matching technique for load balancing that has comparable performance to a traditional hypergraph-based partitioning implementation, which is computationally expensive. Using this study, we found that execution model design choices and assumptions can limit critical optimizations such as global, dynamic load balancing and finding the correct balance between available work units and different system and runtime overheads. With the emergence of multi- and many-core architectures and the consequent growth in the complexity of HPC platforms, we believe that these lessons will be beneficial to researchers tuning diverse applications on modern HPC platforms, especially on emerging dynamic platforms with energy-induced performance variability.

  7. Parallel Computation Chemistry Using Constraints: Final Report, LDRD 97-0301, Case 3504140000

    SciTech Connect

    Todd D. Plantenga

    1998-11-01

    Computer modeling to estimate material properties, design chem/bio sensors, and evaluate protein-protein interactions all require solving force field equations for molecular structures that contain tens of thousands of covalently connected atoms. Potential energy minimization is a key step in the calculation, but stiff covalent bonding forces make optimization difficult and expensive. This two-year LDRD developed two classes of advanced minimization algorithms that were specialized for chemistry applications and distributed computing machines. The project led to two successful algorithms that were implemented in three Sandia computational chemistry codes to support various users.

  8. The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

    ERIC Educational Resources Information Center

    Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

    2008-01-01

    It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

  9. The Impact of Learner's Prior Knowledge on Their Use of Chemistry Computer Simulations: A Case Study

    ERIC Educational Resources Information Center

    Liu, Han-Chin; Andre, Thomas; Greenbowe, Thomas

    2008-01-01

    It is complicated to design a computer simulation that adapts to students with different characteristics. This study documented cases that show how college students' prior chemistry knowledge level affected their interaction with peers and their approach to solving problems with the use of computer simulations that were designed to learn…

  10. 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…

  11. Computer Based Instructional Techniques in Undergraduate Introductory Organic Chemistry: Rationale, Developmental Techniques, Programming Strategies and Evaluation.

    ERIC Educational Resources Information Center

    Culp, G. H.; And Others

    Over 100 interactive computer programs for use in general and organic chemistry at the University of Texas at Austin have been prepared. The rationale for the programs is based upon the belief that computer-assisted instruction (CAI) can improve education by, among other things, freeing teachers from routine tasks, measuring entry skills,…

  12. Using Free Computational Resources to Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

    ERIC Educational Resources Information Center

    Rodrigues, Ricardo P.; Andrade, Saulo F.; Mantoani, Susimaire P.; Eifler-Lima, Vera L.; Silva, Vinicius B.; Kawano, Daniel F.

    2015-01-01

    Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted "in silico" drug design…

  13. Using Free Computational Resources to Illustrate the Drug Design Process in an Undergraduate Medicinal Chemistry Course

    ERIC Educational Resources Information Center

    Rodrigues, Ricardo P.; Andrade, Saulo F.; Mantoani, Susimaire P.; Eifler-Lima, Vera L.; Silva, Vinicius B.; Kawano, Daniel F.

    2015-01-01

    Advances in, and dissemination of, computer technologies in the field of drug research now enable the use of molecular modeling tools to teach important concepts of drug design to chemistry and pharmacy students. A series of computer laboratories is described to introduce undergraduate students to commonly adopted "in silico" drug design…

  14. Development of an Undergraduate Course in the Use of Digital Computers With Chemistry Instrumentation.

    ERIC Educational Resources Information Center

    Wilkins, Charles L.

    Computer-assisted instruction (CAI) has proven useful in teaching chemistry instrumentation techniques to undergraduate students. The work completed at the time of this interim report has clearly shown that a general purpose laboratory computer system, equipped with suitable devices to allow direct data input from experiments, can be an effective…

  15. Chemistry Problem-Solving Abilities: Gender, Reasoning Level and Computer-Simulated Experiments.

    ERIC Educational Resources Information Center

    Suits, Jerry P.; Lagowski, J. J.

    Two studies were conducted to determine the effects of gender, reasoning level, and inductive and deductive computer-simulated experiments (CSE) on problem-solving abilities in introductory general chemistry. In the pilot study, 254 subjects were randomly assigned to control (computer-assisted-instruction tutorials), inductive or deductive CSE…

  16. Development of an Undergraduate Course in the Use of Digital Computers With Chemistry Instrumentation.

    ERIC Educational Resources Information Center

    Wilkins, Charles L.

    Computer-assisted instruction (CAI) has proven useful in teaching chemistry instrumentation techniques to undergraduate students. The work completed at the time of this interim report has clearly shown that a general purpose laboratory computer system, equipped with suitable devices to allow direct data input from experiments, can be an effective…

  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. Development and assessment of a chemistry-based computer video game as a learning tool

    NASA Astrophysics Data System (ADS)

    Martinez-Hernandez, Kermin Joel

    The chemistry-based computer video game is a multidisciplinary collaboration between chemistry and computer graphics and technology fields developed to explore the use of video games as a possible learning tool. This innovative approach aims to integrate elements of commercial video game and authentic chemistry context environments into a learning experience through gameplay. The project consists of three areas: development, assessment, and implementation. However, the foci of this study were the development and assessment of the computer video game including possible learning outcomes and game design elements. A chemistry-based game using a mixed genre of a single player first-person game embedded with action-adventure and puzzle components was developed to determine if students' level of understanding of chemistry concepts change after gameplay intervention. Three phases have been completed to assess students' understanding of chemistry concepts prior and after gameplay intervention. Two main assessment instruments (pre/post open-ended content survey and individual semi-structured interviews) were used to assess student understanding of concepts. In addition, game design elements were evaluated for future development phases. Preliminary analyses of the interview data suggest that students were able to understand most of the chemistry challenges presented in the game and the game served as a review for previously learned concepts as well as a way to apply such previous knowledge. To guarantee a better understanding of the chemistry concepts, additions such as debriefing and feedback about the content presented in the game seem to be needed. The use of visuals in the game to represent chemical processes, game genre, and game idea appear to be the game design elements that students like the most about the current computer video game.

  19. Combinatorial computational chemistry approach for materials design: applications in deNOx catalysis, Fischer-Tropsch synthesis, lanthanoid complex, and lithium ion secondary battery.

    PubMed

    Koyama, Michihisa; Tsuboi, Hideyuki; Endou, Akira; Takaba, Hiromitsu; Kubo, Momoji; Del Carpio, Carlos A; Miyamoto, Akira

    2007-02-01

    Computational chemistry can provide fundamental knowledge regarding various aspects of materials. While its impact in scientific research is greatly increasing, its contributions to industrially important issues are far from satisfactory. In order to realize industrial innovation by computational chemistry, a new concept "combinatorial computational chemistry" has been proposed by introducing the concept of combinatorial chemistry to computational chemistry. This combinatorial computational chemistry approach enables theoretical high-throughput screening for materials design. In this manuscript, we review the successful applications of combinatorial computational chemistry to deNO(x) catalysts, Fischer-Tropsch catalysts, lanthanoid complex catalysts, and cathodes of the lithium ion secondary battery.

  20. Computers in Undergraduate Education: Mathematics, Physics, Statistics, and Chemistry.

    ERIC Educational Resources Information Center

    Lockard, J. David

    This is the report of a conference which was initiated by the National Science Foundation's Office of Computing Activities and which explored and summarized current thinking about the role of the computer for undergraduate curricula in the physical and mathematical sciences. The conference focused on deciding which goals of the existing…

  1.  The application of computational chemistry to lignin

    Treesearch

    Thomas Elder; Laura Berstis; Nele Sophie Zwirchmayr; Gregg T. Beckham; Michael F. Crowley

    2017-01-01

    Computational chemical methods have become an important technique in the examination of the structure and reactivity of lignin. The calculations can be based either on classical or quantum mechanics, with concomitant differences in computational intensity and size restrictions. The current paper will concentrate on results developed from the latter type of calculations...

  2. Computer-based, Jeopardy™-like game in general chemistry for engineering majors

    NASA Astrophysics Data System (ADS)

    Ling, S. S.; Saffre, F.; Kadadha, M.; Gater, D. L.; Isakovic, A. F.

    2013-03-01

    We report on the design of Jeopardy™-like computer game for enhancement of learning of general chemistry for engineering majors. While we examine several parameters of student achievement and attitude, our primary concern is addressing the motivation of students, which tends to be low in a traditionally run chemistry lectures. The effect of the game-playing is tested by comparing paper-based game quiz, which constitutes a control group, and computer-based game quiz, constituting a treatment group. Computer-based game quizzes are Java™-based applications that students run once a week in the second part of the last lecture of the week. Overall effectiveness of the semester-long program is measured through pretest-postest conceptual testing of general chemistry. The objective of this research is to determine to what extent this ``gamification'' of the course delivery and course evaluation processes may be beneficial to the undergraduates' learning of science in general, and chemistry in particular. We present data addressing gender-specific difference in performance, as well as background (pre-college) level of general science and chemistry preparation. We outline the plan how to extend such approach to general physics courses and to modern science driven electives, and we offer live, in-lectures examples of our computer gaming experience. We acknowledge support from Khalifa University, Abu Dhabi

  3. Construction of a robust, large-scale, collaborative database for raw data in computational chemistry: the Collaborative Chemistry Database Tool (CCDBT).

    PubMed

    Chen, Mingyang; Stott, Amanda C; Li, Shenggang; Dixon, David A

    2012-04-01

    A robust metadata database called the Collaborative Chemistry Database Tool (CCDBT) for massive amounts of computational chemistry raw data has been designed and implemented. It performs data synchronization and simultaneously extracts the metadata. Computational chemistry data in various formats from different computing sources, software packages, and users can be parsed into uniform metadata for storage in a MySQL database. Parsing is performed by a parsing pyramid, including parsers written for different levels of data types and sets created by the parser loader after loading parser engines and configurations.

  4. Art, Meet Chemistry; Chemistry, Meet Art: Case Studies, Current Literature, and Instrumental Methods Combined to Create a Hands-On Experience for Nonmajors and Instrumental Analysis Students

    ERIC Educational Resources Information Center

    Nivens, Delana A.; Padgett, Clifford W.; Chase, Jeffery M.; Verges, Katie J.; Jamieson, Deborah S.

    2010-01-01

    Case studies and current literature are combined with spectroscopic analysis to provide a unique chemistry experience for art history students and to provide a unique inquiry-based laboratory experiment for analytical chemistry students. The XRF analysis method was used to demonstrate to nonscience majors (art history students) a powerful…

  5. Art, Meet Chemistry; Chemistry, Meet Art: Case Studies, Current Literature, and Instrumental Methods Combined to Create a Hands-On Experience for Nonmajors and Instrumental Analysis Students

    ERIC Educational Resources Information Center

    Nivens, Delana A.; Padgett, Clifford W.; Chase, Jeffery M.; Verges, Katie J.; Jamieson, Deborah S.

    2010-01-01

    Case studies and current literature are combined with spectroscopic analysis to provide a unique chemistry experience for art history students and to provide a unique inquiry-based laboratory experiment for analytical chemistry students. The XRF analysis method was used to demonstrate to nonscience majors (art history students) a powerful…

  6. CHEMEX; Understanding and Solving Problems in Chemistry. A Computer-Assisted Instruction Program for General Chemistry.

    ERIC Educational Resources Information Center

    Lower, Stephen K.

    A brief overview of CHEMEX--a problem-solving, tutorial style computer-assisted instructional course--is provided and sample problems are offered. In CHEMEX, students receive problems in advance and attempt to solve them before moving through the computer program, which assists them in overcoming difficulties and serves as a review mechanism.…

  7. The role of computational chemistry in the science and measurements of the atmosphere

    NASA Technical Reports Server (NTRS)

    Phillips, D. H.

    1978-01-01

    The role of computational chemistry in determining the stability, photochemistry, spectroscopic parameters, and parameters for estimating reaction rates of atmospheric constituents is discussed. Examples dealing with the photolysis cross sections of HOCl and (1 Delta g) O2 and with the stability of gaseous NH4Cl and asymmetric ClO3 are presented. It is concluded that computational chemistry can play an important role in the study of atmospheric constituents, particularly reactive and short-lived species which are difficult to investigate experimentally.

  8. Computational chemistry in pharmaceutical research: at the crossroads.

    PubMed

    Bajorath, Jürgen

    2012-01-01

    Computational approaches are an integral part of pharmaceutical research. However, there are many of unsolved key questions that limit the scientific progress in the still evolving computational field and its impact on drug discovery. Importantly, a number of these questions are not new but date back many years. Hence, it might be difficult to conclusively answer them in the foreseeable future. Moreover, the computational field as a whole is characterized by a high degree of heterogeneity and so is, unfortunately, the quality of its scientific output. In light of this situation, it is proposed that changes in scientific standards and culture should be seriously considered now in order to lay a foundation for future progress in computational research.

  9. A computer-aided drug discovery system for chemistry teaching.

    PubMed

    Gledhill, Robert; Kent, Sarah; Hudson, Brian; Richards, W Graham; Essex, Jonathan W; Frey, Jeremy G

    2006-01-01

    The Schools Malaria Project (http://emalaria.soton.ac.uk/) brings together school students with university researchers in the hunt for a new antimalaria drug. The design challenge being offered to students is to use a distributed drug search and selection system to design potential antimalaria drugs. The system is accessed via a Web interface. This e-science project displays the results of the trials in an accessible manner, giving students an opportunity for discussion and debate both with peers and with the university contacts. The project has been implemented by using distributed computing techniques, spreading computer load over a network of machines that cross institutional boundaries, forming a grid. This provides access to greater computing power and allows a much more complex and detailed formulation of the drug design problem to be tackled for research, teaching, and learning.

  10. Computational chemistry and cheminformatics: an essay on the future

    NASA Astrophysics Data System (ADS)

    Glen, Robert Charles

    2012-01-01

    Computers have changed the way we do science. Surrounded by a sea of data and with phenomenal computing capacity, the methodology and approach to scientific problems is evolving into a partnership between experiment, theory and data analysis. Given the pace of change of the last twenty-five years, it seems folly to speculate on the future, but along with unpredictable leaps of progress there will be a continuous evolution of capability, which points to opportunities and improvements that will certainly appear as our discipline matures.

  11. Computational chemistry and cheminformatics: an essay on the future.

    PubMed

    Glen, Robert Charles

    2012-01-01

    Computers have changed the way we do science. Surrounded by a sea of data and with phenomenal computing capacity, the methodology and approach to scientific problems is evolving into a partnership between experiment, theory and data analysis. Given the pace of change of the last twenty-five years, it seems folly to speculate on the future, but along with unpredictable leaps of progress there will be a continuous evolution of capability, which points to opportunities and improvements that will certainly appear as our discipline matures.

  12. Computer Programs for Chemistry Experiments I and II.

    ERIC Educational Resources Information Center

    Reynard, Dale C.

    This unit of instruction includes nine laboratory experiments. All of the experiments are from the D.C. Health Revision of the Chemical Education Materials Study (CHEMS) with one exception. Program six is the lab from the original version of the CHEMS program. Each program consists of three parts (1) the lab and computer hints, (2) the description…

  13. The Use of Computers to Aid Instruction in Beginning Chemistry

    ERIC Educational Resources Information Center

    Grandey, Robert C.

    1971-01-01

    Describes computer-aided lessons for determining chemical formulas from composition by weight, quantities from chemical equations, and balancing equations for oxidation-reduction reactions. Lessons were developed and used on the PLATO system at the University of Illinois. A brief analysis of student attitudes and of effectiveness of the programs…

  14. Computer Programs for Chemistry Experiments I and II.

    ERIC Educational Resources Information Center

    Reynard, Dale C.

    This unit of instruction includes nine laboratory experiments. All of the experiments are from the D.C. Health Revision of the Chemical Education Materials Study (CHEMS) with one exception. Program six is the lab from the original version of the CHEMS program. Each program consists of three parts (1) the lab and computer hints, (2) the description…

  15. A Computer Based Problem Solving Environment in Chemistry

    ERIC Educational Resources Information Center

    Bilgin, Ibrahim; Karakirik, Erol

    2005-01-01

    The purpose of this study was to introduce the Mole Solver, a computer based system that facilitates monitors and improves the students' problems solving skills on mole concept. The system has three distinct modes that: i) finds step by step solutions to the word problems on the mole concept ii) enable students' to solve word problems on their own…

  16. A Computer Based Problem Solving Environment in Chemistry

    ERIC Educational Resources Information Center

    Bilgin, Ibrahim; Karakirik, Erol

    2005-01-01

    The purpose of this study was to introduce the Mole Solver, a computer based system that facilitates monitors and improves students' problem solving skills on mole concept. The system has three distinct modes that: (1) find step by step solutions to the word problems on the mole concept; (2) enable students to solve word problems on their own by…

  17. Spectroscopic and computational investigation of actinium coordination chemistry

    DOE PAGES

    Ferrier, Maryline Ghislaine; Batista, Enrique Ricardo; Berg, John M.; ...

    2016-08-17

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac–Cl and Ac–OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-raymore » absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1– ligands (3.2±1.1) than AmIII (0.8±0.3). Finally, these results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour.« less

  18. Spectroscopic and computational investigation of actinium coordination chemistry

    SciTech Connect

    Ferrier, Maryline Ghislaine; Batista, Enrique Ricardo; Berg, John M.; Birnbaum, Eva R.; Cross, Justin Neil; Engle, Jonathan Ward; La Pierre, Henry S.; Kozimor, Stosh Anthony; Lezama Pacheco, Juan S.; Stein, Benjamin W.; Stieber, S. Chantal E.; Wilson, Justin J.

    2016-08-17

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac–Cl and Ac–OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1– ligands (3.2±1.1) than AmIII (0.8±0.3). Finally, these results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour.

  19. Spectroscopic and computational investigation of actinium coordination chemistry

    PubMed Central

    Ferrier, Maryline G.; Batista, Enrique R.; Berg, John M.; Birnbaum, Eva R.; Cross, Justin N.; Engle, Jonathan W.; La Pierre, Henry S.; Kozimor, Stosh A.; Lezama Pacheco, Juan S.; Stein, Benjamin W.; Stieber, S. Chantal E.; Wilson, Justin J.

    2016-01-01

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac–Cl and Ac–OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1– ligands (3.2±1.1) than AmIII (0.8±0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour. PMID:27531582

  20. Spectroscopic and computational investigation of actinium coordination chemistry.

    PubMed

    Ferrier, Maryline G; Batista, Enrique R; Berg, John M; Birnbaum, Eva R; Cross, Justin N; Engle, Jonathan W; La Pierre, Henry S; Kozimor, Stosh A; Lezama Pacheco, Juan S; Stein, Benjamin W; Stieber, S Chantal E; Wilson, Justin J

    2016-08-17

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, Ac(III) reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac-Cl and Ac-OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between Ac(III) and Am(III) in HCl solutions indicate Ac(III) coordinates more inner-sphere Cl(1-) ligands (3.2±1.1) than Am(III) (0.8±0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique Ac(III) chemical behaviour.

  1. Spectroscopic and computational investigation of actinium coordination chemistry

    NASA Astrophysics Data System (ADS)

    Ferrier, Maryline G.; Batista, Enrique R.; Berg, John M.; Birnbaum, Eva R.; Cross, Justin N.; Engle, Jonathan W.; La Pierre, Henry S.; Kozimor, Stosh A.; Lezama Pacheco, Juan S.; Stein, Benjamin W.; Stieber, S. Chantal E.; Wilson, Justin J.

    2016-08-01

    Actinium-225 is a promising isotope for targeted-α therapy. Unfortunately, progress in developing chelators for medicinal applications has been hindered by a limited understanding of actinium chemistry. This knowledge gap is primarily associated with handling actinium, as it is highly radioactive and in short supply. Hence, AcIII reactivity is often inferred from the lanthanides and minor actinides (that is, Am, Cm), with limited success. Here we overcome these challenges and characterize actinium in HCl solutions using X-ray absorption spectroscopy and molecular dynamics density functional theory. The Ac-Cl and Ac-OH2O distances are measured to be 2.95(3) and 2.59(3) Å, respectively. The X-ray absorption spectroscopy comparisons between AcIII and AmIII in HCl solutions indicate AcIII coordinates more inner-sphere Cl1- ligands (3.2+/-1.1) than AmIII (0.8+/-0.3). These results imply diverse reactivity for the +3 actinides and highlight the unexpected and unique AcIII chemical behaviour.

  2. Detection of combined occurrences. [computer algorithms

    NASA Technical Reports Server (NTRS)

    Zobrist, A. L.; Carlson, F. R., Jr.

    1977-01-01

    In this paper it is supposed that the variables x sub 1,...,x sub n each have finite range with the variable x sub i taking on p sub i possible values and that the values of the variables are changing with time. It is supposed further that it is desired to detect occurrences in which some subset of the variables achieve particular values. Finally, it is supposed that the problem involves the detection of a large number of combined occurrences for a large number of changes of values of variables. Two efficient solutions for this problem are described. Both methods have the unusual property of being faster for systems where the sum p sub 1 +...+ p sub n is larger. The first solution is error-free and suitable for most cases. The second solution is slightly more elegant and allows negation as well as conjunction, but is subject to the possibility of errors. An error analysis is given for the second method and an empirical study is reported.

  3. A Compilation of Postgraduate Theses Written in Turkey on Computer Assisted Instruction in Chemistry Education

    ERIC Educational Resources Information Center

    Bozdogan, Aykut Emre; Demirbas, Murat

    2014-01-01

    The purpose of the study conducted is to present in-depth information about the postgraduate theses written within the context of Computer Assisted Instruction in Chemistry Education in Turkey. The theses collected in National Thesis Centre of Turkish Council of Higher Education were examined. As a result of an examination, it was found that about…

  4. Factors Affecting Energy Barriers for Pyramidal Inversion in Amines and Phosphines: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Montgomery, Craig D.

    2013-01-01

    An undergraduate exercise in computational chemistry that investigates the energy barrier for pyramidal inversion of amines and phosphines is presented. Semiempirical calculations (PM3) of the ground-state and transition-state energies for NR[superscript 1]R[superscript 2]R[superscript 3] and PR[superscript 1]R[superscript 2]R[superscript 3] allow…

  5. A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry

    ERIC Educational Resources Information Center

    Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew

    2012-01-01

    In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…

  6. Students' Cognitive Focus during a Chemistry Laboratory Exercise: Effects of a Computer-Simulated Prelab

    ERIC Educational Resources Information Center

    Winberg, T. Mikael; Berg, C. Anders R.

    2007-01-01

    To enhance the learning outcomes achieved by students, learners undertook a computer-simulated activity based on an acid-base titration prior to a university-level chemistry laboratory activity. Students were categorized with respect to their attitudes toward learning. During the laboratory exercise, questions that students asked their assistant…

  7. Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

    ERIC Educational Resources Information Center

    Simpson, Scott; Autschbach, Jochen; Zurek, Eva

    2013-01-01

    A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

  8. Students' Cognitive Focus during a Chemistry Laboratory Exercise: Effects of a Computer-Simulated Prelab

    ERIC Educational Resources Information Center

    Winberg, T. Mikael; Berg, C. Anders R.

    2007-01-01

    To enhance the learning outcomes achieved by students, learners undertook a computer-simulated activity based on an acid-base titration prior to a university-level chemistry laboratory activity. Students were categorized with respect to their attitudes toward learning. During the laboratory exercise, questions that students asked their assistant…

  9. A Computer Algebra Approach to Solving Chemical Equilibria in General Chemistry

    ERIC Educational Resources Information Center

    Kalainoff, Melinda; Lachance, Russ; Riegner, Dawn; Biaglow, Andrew

    2012-01-01

    In this article, we report on a semester-long study of the incorporation into our general chemistry course, of advanced algebraic and computer algebra techniques for solving chemical equilibrium problems. The method presented here is an alternative to the commonly used concentration table method for describing chemical equilibria in general…

  10. Annotated List of Chemistry Laboratory Experiments with Computer Access. Final Report.

    ERIC Educational Resources Information Center

    Bunce, S. C.; And Others

    Project Chemlab was designed to prepare an "Annotated List of Laboratory Experiments in Chemistry from the Journal of Chemical Education (1957-1979)" and to develop a computer file and program to search for specific types of experiments. Provided in this document are listings (photoreduced copies of printouts) of over 1500 entries…

  11. Computational Modeling of the Optical Rotation of Amino Acids: An "in Silico" Experiment for Physical Chemistry

    ERIC Educational Resources Information Center

    Simpson, Scott; Autschbach, Jochen; Zurek, Eva

    2013-01-01

    A computational experiment that investigates the optical activity of the amino acid valine has been developed for an upper-level undergraduate physical chemistry laboratory course. Hybrid density functional theory calculations were carried out for valine to confirm the rule that adding a strong acid to a solution of an amino acid in the l…

  12. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    ERIC Educational Resources Information Center

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  13. Exploring Interactive and Dynamic Simulations Using a Computer Algebra System in an Advanced Placement Chemistry Course

    ERIC Educational Resources Information Center

    Matsumoto, Paul S.

    2014-01-01

    The article describes the use of Mathematica, a computer algebra system (CAS), in a high school chemistry course. Mathematica was used to generate a graph, where a slider controls the value of parameter(s) in the equation; thus, students can visualize the effect of the parameter(s) on the behavior of the system. Also, Mathematica can show the…

  14. Factors Affecting Energy Barriers for Pyramidal Inversion in Amines and Phosphines: A Computational Chemistry Lab Exercise

    ERIC Educational Resources Information Center

    Montgomery, Craig D.

    2013-01-01

    An undergraduate exercise in computational chemistry that investigates the energy barrier for pyramidal inversion of amines and phosphines is presented. Semiempirical calculations (PM3) of the ground-state and transition-state energies for NR[superscript 1]R[superscript 2]R[superscript 3] and PR[superscript 1]R[superscript 2]R[superscript 3] allow…

  15. Combination of Cyclodextrin and Ionic Liquid in Analytical Chemistry: Current and Future Perspectives.

    PubMed

    Hui, Boon Yih; Raoov, Muggundha; Zain, Nur Nadhirah Mohamad; Mohamad, Sharifah; Osman, Hasnah

    2017-09-03

    The growth in driving force and popularity of cyclodextrin (CDs) and ionic liquids (ILs) as promising materials in the field of analytical chemistry has resulted in an exponentially increase of their exploitation and production in analytical chemistry field. CDs belong to the family of cyclic oligosaccharides composing of α-(1,4) linked glucopyranose subunits and possess a cage-like supramolecular structure. This structure enables chemical reactions to proceed between interacting ions, radical or molecules in the absence of covalent bonds. Conversely, ILs are an ionic fluids comprising of only cation and anion often with immeasurable vapor pressure making them as green or designer solvent. The cooperative effect between CD and IL due to their fascinating properties, have nowadays contributed their footprints for a better development in analytical chemistry nowadays. This comprehensive review serves to give an overview on some of the recent studies and provides an analytical trend for the application of CDs with the combination of ILs that possess beneficial and remarkable effects in analytical chemistry including their use in various sample preparation techniques such as solid phase extraction, magnetic solid phase extraction, cloud point extraction, microextraction, and separation techniques which includes gas chromatography, high-performance liquid chromatography, capillary electrophoresis as well as applications of electrochemical sensors as electrode modifiers with references to recent applications. This review will highlight the nature of interactions and synergic effects between CDs, ILs, and analytes. It is hoped that this review will stimulate further research in analytical chemistry.

  16. Application of lightweight threading techniques to computational chemistry

    NASA Astrophysics Data System (ADS)

    Thornley, John; Muller, Richard P.; Mainz, Daniel T.; Çağin, Tahir; Goddard, William A.

    2001-05-01

    The recent advent of inexpensive commodity multiprocessor computers with standardized operating system support for lightweight threads provides computational chemists and other scientists with an exciting opportunity to develop sophisticated new approaches to materials simulation. We contrast the flexible performance characteristics of lightweight threading with the restrictions of traditional scientific supercomputing, based on our experiences with multithreaded molecular dynamics simulation. Motivated by the results of our molecular dynamics experiments, we propose an approach to multi-scale materials simulation using highly dynamic thread creation and synchronization within and between concurrent simulations at many different scales. This approach will enable extremely realistic simulations, with computing resources dynamically directed to areas where they are needed. Multi-scale simulations of this kind require large amounts of processing power, but are too sophisticated to be expressed using traditional supercomputing programming models. As a result, we have developed a high-level programming system called Sthreads that allows highly dynamic, nested multithreaded algorithms to be expressed. Program development is simplified through the use of innovative synchronization operations that allow multithreaded programs to be tested and debugged using standard sequential methods and tools. For this reason, Sthreads is very well suited to the complex multi-scale simulation applications that we are developing.

  17. Parallelism in computational chemistry: Applications in quantum and statistical mechanics

    NASA Astrophysics Data System (ADS)

    Clementi, E.; Corongiu, G.; Detrich, J. H.; Kahnmohammadbaigi, H.; Chin, S.; Domingo, L.; Laaksonen, A.; Nguyen, N. L.

    1985-08-01

    Often very fundamental biochemical and biophysical problems defy simulations because of limitation in today's computers. We present and discuss a distributed system composed of two IBM-4341 and one IBM-4381, as front-end processors, and ten FPS-164 attached array processors. This parallel system-called LCAP-has presently a peak performance of about 120 MFlops; extensions to higher performance are discussed. Presently, the system applications use a modified version of VM/SP as the operating system: description of the modifications is given. Three applications programs have migrated from sequential to parallel; a molecular quantum mechanical, a Metropolis-Monte Carlo and a Molecular Dynamics program. Descriptions of the parallel codes are briefly outlined. As examples and tests of these applications we report on a study for proton tunneling in DNA base-pairs, very relevant to spontaneous mutations in genetics. As a second example, we present a Monte Carlo study of liquid water at room temperature where not only two- and three-body interactions are considered but-for the first time-also four-body interactions are included. Finally we briefly summarize a molecular dynamics study where two- and three-body interactions have been considered. These examples, and very positive performance comparison with today's supercomputers allow us to conclude that parallel computers and programming of the type we have considered, represent a pragmatic answer to many computer intensive problems.

  18. Computational carbohydrate chemistry: what theoretical methods can tell us

    PubMed Central

    Woods, Robert J.

    2014-01-01

    Computational methods have had a long history of application to carbohydrate systems and their development in this regard is discussed. The conformational analysis of carbohydrates differs in several ways from that of other biomolecules. Many glycans appear to exhibit numerous conformations coexisting in solution at room temperature and a conformational analysis of a carbohydrate must address both spatial and temporal properties. When solution nuclear magnetic resonance data are used for comparison, the simulation must give rise to ensemble-averaged properties. In contrast, when comparing to experimental data obtained from crystal structures a simulation of a crystal lattice, rather than of an isolated molecule, is appropriate. Molecular dynamics simulations are well suited for such condensed phase modeling. Interactions between carbohydrates and other biological macromolecules are also amenable to computational approaches. Having obtained a three-dimensional structure of the receptor protein, it is possible to model with accuracy the conformation of the carbohydrate in the complex. An example of the application of free energy perturbation simulations to the prediction of carbohydrate-protein binding energies is presented. PMID:9579797

  19. Recent developments in computer vision-based analytical chemistry: A tutorial review.

    PubMed

    Capitán-Vallvey, Luis Fermín; López-Ruiz, Nuria; Martínez-Olmos, Antonio; Erenas, Miguel M; Palma, Alberto J

    2015-10-29

    Chemical analysis based on colour changes recorded with imaging devices is gaining increasing interest. This is due to its several significant advantages, such as simplicity of use, and the fact that it is easily combinable with portable and widely distributed imaging devices, resulting in friendly analytical procedures in many areas that demand out-of-lab applications for in situ and real-time monitoring. This tutorial review covers computer vision-based analytical (CVAC) procedures and systems from 2005 to 2015, a period of time when 87.5% of the papers on this topic were published. The background regarding colour spaces and recent analytical system architectures of interest in analytical chemistry is presented in the form of a tutorial. Moreover, issues regarding images, such as the influence of illuminants, and the most relevant techniques for processing and analysing digital images are addressed. Some of the most relevant applications are then detailed, highlighting their main characteristics. Finally, our opinion about future perspectives is discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Effects of a test taking strategy on postsecondary computer assisted chemistry assessments

    NASA Astrophysics Data System (ADS)

    Manco, Sharon Ann

    Metacognitive test taking strategies have proven advantageous in improving content-based test scores in a wide variety of disciplines and age/grade levels using traditional paper-and-pencil tests. However, despite the increase in computer assisted assessment (CAA), little research has examined whether these test taking strategies are effective for computer assisted tests. Research was conducted to determine if learning a proven test taking strategy would improve the online quiz scores of six university students in an introductory chemistry course intended for science, technology, engineering and math majors. Participants completed six to ten chemistry quizzes prior to intervention---learning the test taking strategy---and four to eight chemistry quizzes after intervention. Results indicated that, while students learned the strategy, it had little effect on their online chemistry quiz scores. Additionally, at the end of the semester, participants completed a satisfaction survey indicating general satisfaction with having learned the test taking strategy and generalization to other courses and types of tests. Furthermore, results suggest that adaptations to the on-line delivery method of the quizzes and to the test taking strategies may improve the robustness of the effect. Due to the increased use of computer assisted assessment, additional research is warranted to determine appropriate test taking strategies for online tests.

  1. Conceptual change in an organic chemistry laboratory: A comparison of computer simulations and traditional laboratory experiments

    NASA Astrophysics Data System (ADS)

    Gaddis, Barbara A.

    2001-12-01

    This quasi-experimental research study examined the effect of computer simulations and hands-on laboratory experiments in enhancing conceptual understanding and alleviating misconceptions of organic chemistry reaction mechanisms. Subjects were sixty-nine sophomore-level organic chemistry students enrolled in four laboratory sections. Laboratory sections were stratified across instructor and randomly assigned to serve as a control or treatment laboratory. Students in the control group performed all hands-on experiments. Students in the treatment group performed hands-on experiments for the first and last part of the semester but performed computer simulations for a five-week period in the middle of the semester. Prior to treatment, groups were equivalent with respect to academic orientation, motivation, formal reasoning ability, and spatial visualization ability. Fifteen common misconceptions held by beginning organic chemistry students were identified from the Covalent Bonding and Structures Test. At the end of the semester, thirteen of these misconceptions persisted. Molecular geometry was the only category of misconceptions that significantly improved as a result of computer simulations, F(1,58) = 6.309, p = .015. No significant differential change was observed in misconceptions about bond polarity, molecular polarity, intermolecular forces, lattice structures, or the octet rule. Computer simulations were found to result in significantly greater conceptual understanding of organic chemistry reactions on two of the experiments, Stereochemistry, F(1,55) = 6.174, p = .016, and Nucleophilic Substitution, F(1,57) = 6.093, p = .017. The other three experiments, Infrared Spectroscopy, Elimination, and Oxymercuration, did not show a significant differential effect between types of laboratory experiences. No significant differences were observed on long-term retention of concepts. Overall conclusions from the study are that neither computer simulations nor hands

  2. Lookup tables to compute high energy cosmic ray induced atmospheric ionization and changes in atmospheric chemistry

    SciTech Connect

    Atri, Dimitra; Melott, Adrian L.; Thomas, Brian C. E-mail: melott@ku.edu

    2010-05-01

    A variety of events such as gamma-ray bursts and supernovae may expose the Earth to an increased flux of high-energy cosmic rays, with potentially important effects on the biosphere. Existing atmospheric chemistry software does not have the capability of incorporating the effects of substantial cosmic ray flux above 10 GeV. An atmospheric code, the NASA-Goddard Space Flight Center two-dimensional (latitude, altitude) time-dependent atmospheric model (NGSFC), is used to study atmospheric chemistry changes. Using CORSIKA, we have created tables that can be used to compute high energy cosmic ray (10 GeV–1 PeV) induced atmospheric ionization and also, with the use of the NGSFC code, can be used to simulate the resulting atmospheric chemistry changes. We discuss the tables, their uses, weaknesses, and strengths.

  3. Cl2O4 in the Stratosphere: A Collaborative Computational Physical Chemistry Project

    NASA Astrophysics Data System (ADS)

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

    2000-12-01

    Computational software is moving into the chemistry mainstream and should be introduced into the undergraduate curriculum. This paper describes a collaborative computational project involving the implications of Cl2O4 for the stratospheric degradation of ozone. The project would be appropriate for physical chemistry, advanced inorganic chemistry, and an upper-level integrated laboratory or environmental chemistry course. After an initial WWW search for information on stratospheric ozone, students use group theory, IR and Raman spectra data from the literature, and formal charges to determine the most likely structure of Cl2O4. They then use pooled results of RHF calculations with different basis sets to study the effect of changing basis sets on ab initio calculations of the structure of this molecule. In the next phase of the project, the students pool results of MP2/6-31G(d) level calculations to predict the spontaneity of a possible ozone-destroying reaction. In the last phase, they engage in an online discussion of the kinetics of a potential mechanism for which this reaction is one step. Calculations in this project were done with Gaussian 98W on 266- and 450-MHz Pentium II PCs. Communication during the project was primarily by electronic mail and the WWW.

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

    NASA Astrophysics Data System (ADS)

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

    2010-10-01

    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 to explore computer modeling. Each workshop was scheduled for 2 h and each included a tutorial exercise to familiarize the students with the main menus and features of the software. In addition, accompanying lectures and practical laboratory sections were provided. Both courses were taught in Spanish although the written instructions were in English. This was not a problem since these students have a comfort level with reading English. Student feedback following these workshops was highly enthusiastic and positive. This international collaborative will impact both the teaching and research goals for this cohort of graduate students.

  5. Computational chemistry for graphene-based energy applications: progress and challenges.

    PubMed

    Hughes, Zak E; Walsh, Tiffany R

    2015-04-28

    Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

  6. A numerical method for parameterization of atmospheric chemistry - Computation of tropospheric OH

    NASA Technical Reports Server (NTRS)

    Spivakovsky, C. M.; Wofsy, S. C.; Prather, M. J.

    1990-01-01

    An efficient and stable computational scheme for parameterization of atmospheric chemistry is described. The 24-hour-average concentration of OH is represented as a set of high-order polynomials in variables such as temperature, densities of H2O, CO, O3, and NO(t) (defined as NO + NO2 + NO3 + 2N2O5 + HNO2 + HNO4) as well as variables determining solar irradiance: cloud cover, density of the overhead ozone column, surface albedo, latitude, and solar declination. This parameterization of OH chemistry was used in the three-dimensional study of global distribution of CH3CCl3. The proposed computational scheme can be used for parameterization of rates of chemical production and loss or of any other output of a full chemical model.

  7. Computational chemistry for graphene-based energy applications: progress and challenges

    NASA Astrophysics Data System (ADS)

    Hughes, Zak E.; Walsh, Tiffany R.

    2015-04-01

    Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.

  8. 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.

  9. Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology.

    PubMed

    González-Nilo, Fernando; Pérez-Acle, Tomás; Guínez-Molinos, Sergio; Geraldo, Daniela A; Sandoval, Claudia; Yévenes, Alejandro; Santos, Leonardo S; Laurie, V Felipe; Mendoza, Hegaly; Cachau, Raúl E

    2011-01-01

    After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.

  10. Enabling drug discovery project decisions with integrated computational chemistry and informatics

    NASA Astrophysics Data System (ADS)

    Tsui, Vickie; Ortwine, Daniel F.; Blaney, Jeffrey M.

    2017-03-01

    Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.

  11. Drug Guru: a computer software program for drug design using medicinal chemistry rules.

    PubMed

    Stewart, Kent D; Shiroda, Melisa; James, Craig A

    2006-10-15

    Drug Guru (drug generation using rules) is a new web-based computer software program for medicinal chemists that applies a set of transformations, that is, rules, to an input structure. The transformations correspond to medicinal chemistry design rules-of-thumb taken from the historical lore of drug discovery programs. The output of the program is a list of target analogs that can be evaluated for possible future synthesis. A discussion of the features of the program is followed by an example of the software applied to sildenafil (Viagra) in generating ideas for target analogs for phosphodiesterase inhibition. Comparison with other computer-assisted drug design software is given.

  12. Enabling drug discovery project decisions with integrated computational chemistry and informatics

    NASA Astrophysics Data System (ADS)

    Tsui, Vickie; Ortwine, Daniel F.; Blaney, Jeffrey M.

    2016-10-01

    Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.

  13. Enabling drug discovery project decisions with integrated computational chemistry and informatics.

    PubMed

    Tsui, Vickie; Ortwine, Daniel F; Blaney, Jeffrey M

    2017-03-01

    Computational chemistry/informatics scientists and software engineers in Genentech Small Molecule Drug Discovery collaborate with experimental scientists in a therapeutic project-centric environment. Our mission is to enable and improve pre-clinical drug discovery design and decisions. Our goal is to deliver timely data, analysis, and modeling to our therapeutic project teams using best-in-class software tools. We describe our strategy, the organization of our group, and our approaches to reach this goal. We conclude with a summary of the interdisciplinary skills required for computational scientists and recommendations for their training.

  14. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

  15. Introduction to Computational Chemistry: Teaching Hu¨ckel Molecular Orbital Theory Using an Excel Workbook for Matrix Diagonalization

    ERIC Educational Resources Information Center

    Litofsky, Joshua; Viswanathan, Rama

    2015-01-01

    Matrix diagonalization, the key technique at the heart of modern computational chemistry for the numerical solution of the Schrödinger equation, can be easily introduced in the physical chemistry curriculum in a pedagogical context using simple Hückel molecular orbital theory for p bonding in molecules. We present details and results of…

  16. Reaction of formaldehyde at the ortho- and para-positions of phenol: exploration of mechanisms using computational chemistry.

    Treesearch

    Anthony H. Conner; Melissa S. Reeves

    2001-01-01

    Computational chemistry methods can be used to explore the theoretical chemistry behind reactive systems, to compare the relative chemical reactivity of different systems, and, by extension, to predict the reactivity of new systems. Ongoing research has focused on the reactivity of a wide variety of phenolic compounds with formaldehyde using semi-empirical and ab...

  17. Microscopes and computers combined for analysis of chromosomes

    NASA Technical Reports Server (NTRS)

    Butler, J. W.; Butler, M. K.; Stroud, A. N.

    1969-01-01

    Scanning machine CHLOE, developed for photographic use, is combined with a digital computer to obtain quantitative and statistically significant data on chromosome shapes, distribution, density, and pairing. CHLOE permits data acquisition about a chromosome complement to be obtained two times faster than by manual pairing.

  18. Combining Cases and Computer Simulations in Strategic Management Courses

    ERIC Educational Resources Information Center

    Mitchell, Rex C.

    2004-01-01

    In this study, the author compared the effectiveness of two different strategic management course designs: one centered on case discussions and the other combining a computer-based simulation with some cases. In addition to evaluation of the research literature, the study involved experiments with six course sections composed of 130 students, Both…

  19. Combining computer and manual overlays—Willamette River Greenway Study

    Treesearch

    Asa Hanamoto; Lucille Biesbroeck

    1979-01-01

    We will present a method of combining computer mapping with manual overlays. An example of its use is the Willamette River Greenway Study produced for the State of Oregon Department of Transportation in 1974. This one year planning study included analysis of data relevant to a 286-mile river system. The product is a "wise use" plan which conserves the basic...

  20. Computational chemistry approach to protein kinase recognition using 3D stochastic van der Waals spectral moments.

    PubMed

    González-Díaz, Humberto; Saíz-Urra, Liane; Molina, Reinaldo; González-Díaz, Yenny; Sánchez-González, Angeles

    2007-04-30

    Three-dimensional (3D) protein structures now frequently lack functional annotations because of the increase in the rate at which chemical structures are solved with respect to experimental knowledge of biological activity. As a result, predicting structure-function relationships for proteins is an active research field in computational chemistry and has implications in medicinal chemistry, biochemistry and proteomics. In previous studies stochastic spectral moments were used to predict protein stability or function (González-Díaz, H. et al. Bioorg Med Chem 2005, 13, 323; Biopolymers 2005, 77, 296). Nevertheless, these moments take into consideration only electrostatic interactions and ignore other important factors such as van der Waals interactions. The present study introduces a new class of 3D structure molecular descriptors for folded proteins named the stochastic van der Waals spectral moments ((o)beta(k)). Among many possible applications, recognition of kinases was selected due to the fact that previous computational chemistry studies in this area have not been reported, despite the widespread distribution of kinases. The best linear model found was Kact = -9.44 degrees beta(0)(c) +10.94 degrees beta(5)(c) -2.40 degrees beta(0)(i) + 2.45 degrees beta(5)(m) + 0.73, where core (c), inner (i) and middle (m) refer to specific spatial protein regions. The model with a high Matthew's regression coefficient (0.79) correctly classified 206 out of 230 proteins (89.6%) including both training and predicting series. An area under the ROC curve of 0.94 differentiates our model from a random classifier. A subsequent principal components analysis of 152 heterogeneous proteins demonstrated that beta(k) codifies information different to other descriptors used in protein computational chemistry studies. Finally, the model recognizes 110 out of 125 kinases (88.0%) in a virtual screening experiment and this can be considered as an additional validation study (these proteins

  1. Research and Teaching: Computational Methods in General Chemistry--Perceptions of Programming, Prior Experience, and Student Outcomes

    ERIC Educational Resources Information Center

    Wheeler, Lindsay B.; Chiu, Jennie L.; Grisham, Charles M.

    2016-01-01

    This article explores how integrating computational tools into a general chemistry laboratory course can influence student perceptions of programming and investigates relationships among student perceptions, prior experience, and student outcomes.

  2. Research and Teaching: Computational Methods in General Chemistry--Perceptions of Programming, Prior Experience, and Student Outcomes

    ERIC Educational Resources Information Center

    Wheeler, Lindsay B.; Chiu, Jennie L.; Grisham, Charles M.

    2016-01-01

    This article explores how integrating computational tools into a general chemistry laboratory course can influence student perceptions of programming and investigates relationships among student perceptions, prior experience, and student outcomes.

  3. Computational Materials Science and Chemistry: Accelerating Discovery and Innovation through Simulation-Based Engineering and Science

    SciTech Connect

    Crabtree, George; Glotzer, Sharon; McCurdy, Bill; Roberto, Jim

    2010-07-26

    This report is based on a SC Workshop on Computational Materials Science and Chemistry for Innovation on July 26-27, 2010, to assess the potential of state-of-the-art computer simulations to accelerate understanding and discovery in materials science and chemistry, with a focus on potential impacts in energy technologies and innovation. The urgent demand for new energy technologies has greatly exceeded the capabilities of today's materials and chemical processes. To convert sunlight to fuel, efficiently store energy, or enable a new generation of energy production and utilization technologies requires the development of new materials and processes of unprecedented functionality and performance. New materials and processes are critical pacing elements for progress in advanced energy systems and virtually all industrial technologies. Over the past two decades, the United States has developed and deployed the world's most powerful collection of tools for the synthesis, processing, characterization, and simulation and modeling of materials and chemical systems at the nanoscale, dimensions of a few atoms to a few hundred atoms across. These tools, which include world-leading x-ray and neutron sources, nanoscale science facilities, and high-performance computers, provide an unprecedented view of the atomic-scale structure and dynamics of materials and the molecular-scale basis of chemical processes. For the first time in history, we are able to synthesize, characterize, and model materials and chemical behavior at the length scale where this behavior is controlled. This ability is transformational for the discovery process and, as a result, confers a significant competitive advantage. Perhaps the most spectacular increase in capability has been demonstrated in high performance computing. Over the past decade, computational power has increased by a factor of a million due to advances in hardware and software. This rate of improvement, which shows no sign of abating, has

  4. A Computational Approach for Identifying Synergistic Drug Combinations

    PubMed Central

    Gayvert, Kaitlyn M.; Aly, Omar; Bosenberg, Marcus W.; Stern, David F.; Elemento, Olivier

    2017-01-01

    A promising alternative to address the problem of acquired drug resistance is to rely on combination therapies. Identification of the right combinations is often accomplished through trial and error, a labor and resource intensive process whose scale quickly escalates as more drugs can be combined. To address this problem, we present a broad computational approach for predicting synergistic combinations using easily obtainable single drug efficacy, no detailed mechanistic understanding of drug function, and limited drug combination testing. When applied to mutant BRAF melanoma, we found that our approach exhibited significant predictive power. Additionally, we validated previously untested synergy predictions involving anticancer molecules. As additional large combinatorial screens become available, this methodology could prove to be impactful for identification of drug synergy in context of other types of cancers. PMID:28085880

  5. Water chemistry of a combined-cycle power plant's auxiliary equipment cooling system

    NASA Astrophysics Data System (ADS)

    Larin, B. M.; Korotkov, A. N.; Oparin, M. Yu.; Larin, A. B.

    2013-04-01

    Results from an analysis of methods aimed at reducing the corrosion rate of structural metal used in heat-transfer systems with water coolant are presented. Data from examination of the closed-circuit system for cooling the auxiliary mechanisms of a combined-cycle plant-based power unit and the results from adjustment of its water chemistry are given. A conclusion is drawn about the possibility of using a reagent prepared on the basis of sodium sulfite for reducing the corrosion rate when the loss of coolant is replenished with nondeaerated water.

  6. Application of computer assisted combinatorial chemistry in antivirial, antimalarial and anticancer agents design

    NASA Astrophysics Data System (ADS)

    Burello, E.; Bologa, C.; Frecer, V.; Miertus, S.

    Combinatorial chemistry and technologies have been developed to a stage where synthetic schemes are available for generation of a large variety of organic molecules. The innovative concept of combinatorial design assumes that screening of a large and diverse library of compounds will increase the probability of finding an active analogue among the compounds tested. Since the rate at which libraries are screened for activity currently constitutes a limitation to the use of combinatorial technologies, it is important to be selective about the number of compounds to be synthesized. Early experience with combinatorial chemistry indicated that chemical diversity alone did not result in a significant increase in the number of generated lead compounds. Emphasis has therefore been increasingly put on the use of computer assisted combinatorial chemical techniques. Computational methods are valuable in the design of virtual libraries of molecular models. Selection strategies based on computed physicochemical properties of the models or of a target compound are introduced to reduce the time and costs of library synthesis and screening. In addition, computational structure-based library focusing methods can be used to perform in silico screening of the activity of compounds against a target receptor by docking the ligands into the receptor model. Three case studies are discussed dealing with the design of targeted combinatorial libraries of inhibitors of HIV-1 protease, P. falciparum plasmepsin and human urokinase as potential antivirial, antimalarial and anticancer drugs. These illustrate library focusing strategies.

  7. Managing the computational chemistry big data problem: the ioChem-BD platform.

    PubMed

    Álvarez-Moreno, M; de Graaf, C; López, N; Maseras, F; Poblet, J M; Bo, C

    2015-01-26

    We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  9. An Open Environment to Support the Development of Computational Chemistry Solutions

    NASA Astrophysics Data System (ADS)

    Bejarano, Bernardo Palacios; Ruiz, Irene Luque; Gómez-Nieto, Miguel Ángel

    2009-08-01

    In this paper we present an open software environment devoted to support the investigations in computational chemistry. The software, named CoChiSE (Computational Chimica Software Environment) is fully developed in Java using Eclipse as IDE; in this way, the system is integrated by different perspectives oriented to solve different aspects of the computational chemistry research. CoChiSE is able to manage large chemical databases, maintaining information about molecules and properties as well; this information can be exported and imported to/from the most popular standard file formats. The system also allows the user to perform the calculation of different type of isomorphism and molecular similarity. Besides, CoChiSE incorporates a perspective in charge of the calculation of molecular descriptors, considering more than four hundred descriptors of different categories. All the information and system perspectives are integrated in the same environment, so a huge amount of information is managed by the user. The characteristics of the developed system permit the easy integration of either user, proprietary and free software.

  10. Computational Chemistry Approach to Interpret the Crystal Violet Adsorption on Golbasi Lignite Activated Carbon

    NASA Astrophysics Data System (ADS)

    Depci, Tolga; Sarikaya, Musa; Prisbrey, Keith A.; Yucel, Aysegul

    2016-10-01

    In this paper, adsorption mechanism of Crystal Violet (CV) dye from the aqueous solution on the activated carbon prepared from Golbasi lignite was explained and interpreted by a computational chemistry approach and experimental studies. Molecular dynamic simulations and Ab initio frontier orbital analysis indicated relatively high energy and electron transfer processes during adsorption, and molecular dynamics simulations showed CV dye molecules moving around on the activated carbon surface after adsorption, facilitating penetration into cracks and pores. The experimental results supported to molecular dynamic simulation and showed that the monolayer coverage occurred on the activated carbon surface and each CV dye ion had equal sorption activation energy.

  11. Energy-Efficient Computational Chemistry: Comparison of x86 and ARM Systems.

    PubMed

    Keipert, Kristopher; Mitra, Gaurav; Sunriyal, Vaibhav; Leang, Sarom S; Sosonkina, Masha; Rendell, Alistair P; Gordon, Mark S

    2015-11-10

    The computational efficiency and energy-to-solution of several applications using the GAMESS quantum chemistry suite of codes is evaluated for 32-bit and 64-bit ARM-based computers, and compared to an x86 machine. The x86 system completes all benchmark computations more quickly than either ARM system and is the best choice to minimize time to solution. The ARM64 and ARM32 computational performances are similar to each other for Hartree-Fock and density functional theory energy calculations. However, for memory-intensive second-order perturbation theory energy and gradient computations the lower ARM32 read/write memory bandwidth results in computation times as much as 86% longer than on the ARM64 system. The ARM32 system is more energy efficient than the x86 and ARM64 CPUs for all benchmarked methods, while the ARM64 CPU is more energy efficient than the x86 CPU for some core counts and molecular sizes.

  12. Predicting chemical kinetics with computational chemistry: is QOO&(H)rarr;HOQO important in fuel ignition?

    NASA Astrophysics Data System (ADS)

    Green, William H.; Wijaya, Catherina D.; Yelvington, Paul E.; Sumathi, R.

    An overview of predictive chemical kinetics is presented, with an application to the simulation and design of homogeneous charge compression ignition (HCCI) engines. The engine simulations are sensitive to the details of hydroperoxyalkyl (QOOH) radical chemistry, which are only partially understood, and there is a significant discrepancy between the simulations and experiment that limits the usefulness of the simulations. One possible explanation is that QOOH decomposes by other channels not considered in existing combustion chemistry models. Rate constants for one of these neglected channels, the intramolecular radical attack on the QOOH peroxide linkage to form hydroxyalkoxyl (HOQO) radicals, are predicted using quantum chemistry (CBS-QB3), to test whether or not this proposed channel can explain the observed discrepancies in the engine simulations. Although this channel has a significant rate, the competing attack on the other O atom in the peroxide to form a cyclic ether+OH is computed to be an order of magnitude faster, so the HOQO channel does not appear to be fast enough to explain the discrepancy. Definitive judgement on the importance of this reaction channel will require a careful reconsideration of all the coupled chemically activated QOOH reaction channels using modern predictive chemical kinetics software.

  13. Post-16 Physics and Chemistry Uptake: Combining Large-Scale Secondary Analysis with In-Depth Qualitative Methods

    ERIC Educational Resources Information Center

    Hampden-Thompson, Gillian; Lubben, Fred; Bennett, Judith

    2011-01-01

    Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served…

  14. Post-16 Physics and Chemistry Uptake: Combining Large-Scale Secondary Analysis with In-Depth Qualitative Methods

    ERIC Educational Resources Information Center

    Hampden-Thompson, Gillian; Lubben, Fred; Bennett, Judith

    2011-01-01

    Quantitative secondary analysis of large-scale data can be combined with in-depth qualitative methods. In this paper, we discuss the role of this combined methods approach in examining the uptake of physics and chemistry in post compulsory schooling for students in England. The secondary data analysis of the National Pupil Database (NPD) served…

  15. Combining the GRID with Cloud for Earth Science Computing

    NASA Astrophysics Data System (ADS)

    Mishin, Dmitry; Levchenko, Oleg; Groudnev, Andrei; Zhizhin, Mikhail

    2010-05-01

    Cloud computing is a new economic model of using large cluster computing resources which were earlier managed by GRID. Reusing existing GRID infrastructure gives an opportunity to combine the Cloud and GRID technologies on the same hardware and to provide GRID users with functionality for running high performance computing tasks inside virtual machines. In this case Cloud works "above" GRID, sharing computing power and utilizing unused processor time. We manage virtual machines with Eucalyptus elastic cloud and we use Torque system from gLite infrastructure for spreading Cloud jobs in GRID computing nodes to scale the parallel computing tasks on virtual machines created by elastic cloud. For this purpose we have added new types of tasks to the standard GRID task list: to run a virtual node and to run a job on a virtual node. This gives a possibility to seamlessly upscale the Cloud with the new tasks when needed and to shrink it when the tasks are completed. Using GRID components for managing the size of a virtual cloud simplifies building the billing system to charge the Cloud users for the processor time, disk space and outer traffic consumed. A list of Earth Science computing problems that can be solved by using the elastic Cloud include repetitive tasks of downloading, converting and storing in a database of large arrays of data (e.g. weather forecast); creating a pyramid of lower resolution images from a very large one for fast distributed browsing; processing and analyzing the large distributed amounts of data by running Earth Science numerical models.

  16. Chemical Equilibrium, Unit 2: Le Chatelier's Principle. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Jameson, A. Keith

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on Le Chatelier's principle includes objectives, prerequisites, pretest, instructions for executing the computer program, and…

  17. Computational organic chemistry: bridging theory and experiment in establishing the mechanisms of chemical reactions.

    PubMed

    Cheng, Gui-Juan; Zhang, Xinhao; Chung, Lung Wa; Xu, Liping; Wu, Yun-Dong

    2015-02-11

    Understanding the mechanisms of chemical reactions, especially catalysis, has been an important and active area of computational organic chemistry, and close collaborations between experimentalists and theorists represent a growing trend. This Perspective provides examples of such productive collaborations. The understanding of various reaction mechanisms and the insight gained from these studies are emphasized. The applications of various experimental techniques in elucidation of reaction details as well as the development of various computational techniques to meet the demand of emerging synthetic methods, e.g., C-H activation, organocatalysis, and single electron transfer, are presented along with some conventional developments of mechanistic aspects. Examples of applications are selected to demonstrate the advantages and limitations of these techniques. Some challenges in the mechanistic studies and predictions of reactions are also analyzed.

  18. Computational chemistry modeling and design of photoswitchable alignment materials for optically addressable liquid crystal devices

    NASA Astrophysics Data System (ADS)

    Marshall, K. L.; Sekera, E. R.; Xiao, K.

    2015-09-01

    Photoalignment technology based on optically switchable "command surfaces" has been receiving increasing interest for liquid crystal optics and photonics device applications. Azobenzene compounds in the form of low-molar-mass, watersoluble salts deposited either directly on the substrate surface or after dispersion in a polymer binder have been almost exclusively employed for these applications, and ongoing research in the area follows a largely empirical materials design and development approach. Recent computational chemistry advances now afford unprecedented opportunities to develop predictive capabilities that will lead to new photoswitchable alignment layer materials with low switching energies, enhanced bistability, write/erase fatigue resistance, and high laser-damage thresholds. In the work described here, computational methods based on the density functional theory and time-dependent density functional theory were employed to study the impact of molecular structure on optical switching properties in photoswitchable methacrylate and acrylamide polymers functionalized with azobenzene and spiropyran pendants.

  19. Intermolecular Forces in Introductory Chemistry Studied by Gas Chromatography, Computer Models, and Viscometry

    NASA Astrophysics Data System (ADS)

    Wedvik, Jonathan C.; McManaman, Charity; Anderson, Janet S.; Carroll, Mary K.

    1998-07-01

    An experiment on intermolecular forces for first-term introductory college chemistry is presented. The experiment integrates traditional viscometry-based measurements with modern chromatographic analysis and use of computer-based molecular models. Students performing gas chromatographic (GC) analyses of mixtures of n-alkanes and samples that simulate crime scene evidence discover that liquid mixtures can be separated rapidly into their components based upon intermolecular forces. Each group of students is given a liquid sample that simulates one collected at an arson scene, and the group is required to determine the identity of the accelerant. Students also examine computer models to better visualize how molecular structure affects intermolecular forces: London forces, dipole-dipole interactions, and hydrogen bonding. The relative viscosities of organic liquids are also measured to relate physical properties to intermolecular forces.

  20. plasmaFoam: An OpenFOAM framework for computational plasma physics and chemistry

    NASA Astrophysics Data System (ADS)

    Venkattraman, Ayyaswamy; Verma, Abhishek Kumar

    2016-09-01

    As emphasized in the 2012 Roadmap for low temperature plasmas (LTP), scientific computing has emerged as an essential tool for the investigation and prediction of the fundamental physical and chemical processes associated with these systems. While several in-house and commercial codes exist, with each having its own advantages and disadvantages, a common framework that can be developed by researchers from all over the world will likely accelerate the impact of computational studies on advances in low-temperature plasma physics and chemistry. In this regard, we present a finite volume computational toolbox to perform high-fidelity simulations of LTP systems. This framework, primarily based on the OpenFOAM solver suite, allows us to enhance our understanding of multiscale plasma phenomenon by performing massively parallel, three-dimensional simulations on unstructured meshes using well-established high performance computing tools that are widely used in the computational fluid dynamics community. In this talk, we will present preliminary results obtained using the OpenFOAM-based solver suite with benchmark three-dimensional simulations of microplasma devices including both dielectric and plasma regions. We will also discuss the future outlook for the solver suite.

  1. Thermodynamics of natural selection III: Landauer's principle in computation and chemistry.

    PubMed

    Smith, Eric

    2008-05-21

    This is the third in a series of three papers devoted to energy flow and entropy changes in chemical and biological processes, and their relations to the thermodynamics of computation. The previous two papers have developed reversible chemical transformations as idealizations for studying physiology and natural selection, and derived bounds from the second law of thermodynamics, between information gain in an ensemble and the chemical work required to produce it. This paper concerns the explicit mapping of chemistry to computation, and particularly the Landauer decomposition of irreversible computations, in which reversible logical operations generating no heat are separated from heat-generating erasure steps which are logically irreversible but thermodynamically reversible. The Landauer arrangement of computation is shown to produce the same entropy-flow diagram as that of the chemical Carnot cycles used in the second paper of the series to idealize physiological cycles. The specific application of computation to data compression and error-correcting encoding also makes possible a Landauer analysis of the somewhat different problem of optimal molecular recognition, which has been considered as an information theory problem. It is shown here that bounds on maximum sequence discrimination from the enthalpy of complex formation, although derived from the same logical model as the Shannon theorem for channel capacity, arise from exactly the opposite model for erasure.

  2. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

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

  3. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

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

  4. Heterogeneous processes at the intersection of chemistry and biology: A computational approach

    SciTech Connect

    Kuo, I W; Mundy, C J

    2008-02-11

    Heterogeneous processes hold the key to understanding many problems in biology and atmospheric science. In particular, recent experiments have shown that heterogeneous chemistry at the surface of sea-salt aerosols plays a large role in important atmospheric processes with far reaching implications towards understanding of the fate and transport of aerosolized chemical weapons (i.e. organophosphates such as sarin and VX). Unfortunately, the precise mechanistic details of the simplest surface enhanced chemical reactions remain unknown. Understanding heterogeneous processes also has implications in the biological sciences. Traditionally, it is accepted that enzymes catalyze reactions by stabilizing the transition state, thereby lowering the free energy barrier. However, recent findings have shown that a multitude of phenomena likely contribute to the efficiency of enzymes, such as coupled protein motion, quantum mechanical tunneling, or strong electrostatic binding. The objective of this project was to develop and validate a single computational framework based on first principles simulations using tera-scale computational resources to answer fundamental scientific questions about heterogeneous chemical processes relevant to atmospheric chemistry and biological sciences.

  5. Addressing genetic tumor heterogeneity through computationally predictive combination therapy.

    PubMed

    Zhao, Boyang; Pritchard, Justin R; Lauffenburger, Douglas A; Hemann, Michael T

    2014-02-01

    Recent tumor sequencing data suggest an urgent need to develop a methodology to directly address intratumoral heterogeneity in the design of anticancer treatment regimens. We use RNA interference to model heterogeneous tumors, and demonstrate successful validation of computational predictions for how optimized drug combinations can yield superior effects on these tumors both in vitro and in vivo. Importantly, we discover here that for many such tumors knowledge of the predominant subpopulation is insufficient for determining the best drug combination. Surprisingly, in some cases, the optimal drug combination does not include drugs that would treat any particular subpopulation most effectively, challenging straightforward intuition. We confirm examples of such a case with survival studies in a murine preclinical lymphoma model. Altogether, our approach provides new insights about design principles for combination therapy in the context of intratumoral diversity, data that should inform the development of drug regimens superior for complex tumors. This study provides the first example of how combination drug regimens, using existing chemotherapies, can be rationally designed to maximize tumor cell death, while minimizing the outgrowth of clonal subpopulations. 2013 AACR

  6. Major Successes of Theory-and-Experiment-Combined Studies in Surface Chemistry and Heterogeneous Catalysis.

    SciTech Connect

    Somorjai, Gabor A.; Li, Yimin

    2009-11-21

    Experimental discoveries followed by theoretical interpretations that pave the way of further advances by experimentalists is a developing pattern in modern surface chemistry and catalysis. The revolution of modern surface science started with the development of surface-sensitive techniques such as LEED, XPS, AES, ISS and SIMS, in which the close collaboration between experimentalists and theorists led to the quantitative determination of surface structure and composition. The experimental discovery of the chemical activity of surface defects and the trends in the reactivity of transitional metals followed by the explanations from the theoretical studies led to the molecular level understanding of active sites in catalysis. The molecular level knowledge, in turn, provided a guide for experiments to search for new generation of catalysts. These and many other examples of successes in experiment-and-theory-combined studies demonstrate the importance of the collaboration between experimentalists and theorists in the development of modern surface science.

  7. 4D sequential actuation: combining ionoprinting and redox chemistry in hydrogels

    NASA Astrophysics Data System (ADS)

    Baker, Anna B.; Wass, Duncan F.; Trask, Richard S.

    2016-10-01

    The programmable sequential actuation of two-dimensional hydrogel membranes into three-dimensional folded architectures has been achieved by combining ionoprinting and redox chemistry; this methodology permits the programmed evolution of complex architectures triggered through localized out-of-plane deformations. In our study we describe a soft actuator which utilizes ionoprinting of iron and vanadium, with the selective reduction of iron through a mild reducing agent, to achieve chemically controlled sequential folding. Through the optimization of solvent polarity and ionoprinting variables (voltage, duration and anode composition), we have shown how the actuation pathways, rate-of-movement and magnitude of angular rotation can be controlled for the design of a 4D sequential actuator.

  8. Computer simulation of combination extrusion of ENAW1050A aluminum

    NASA Astrophysics Data System (ADS)

    Thomas, P.

    2017-02-01

    Computer simulation of the combination extrusion process for ENAW-1050A aluminum alloy is presented. The tests were carried out for three values of relative strain in forward direction ε1: 0.77, 0.69 and 0.59. For each value of relative strain ε1, three different values of strain in backward direction, ε2, were taken: 0.41, 0.52, 0.64. The effect of the relative strain degree on the development and values of the punch force was determined. It was demonstrated that the punch force increases with the increasing degree of relative strain in both forward and backward directions.

  9. The Combined Effects of Classroom Teaching and Learning Strategy Use on Students' Chemistry Self-Efficacy

    ERIC Educational Resources Information Center

    Cheung, Derek

    2015-01-01

    For students to be successful in school chemistry, a strong sense of self-efficacy is essential. Chemistry self-efficacy can be defined as students' beliefs about the extent to which they are capable of performing specific chemistry tasks. According to Bandura ("Psychol. Rev." 84:191-215, 1977), students acquire information about their…

  10. The Combined Effects of Classroom Teaching and Learning Strategy Use on Students' Chemistry Self-Efficacy

    ERIC Educational Resources Information Center

    Cheung, Derek

    2015-01-01

    For students to be successful in school chemistry, a strong sense of self-efficacy is essential. Chemistry self-efficacy can be defined as students' beliefs about the extent to which they are capable of performing specific chemistry tasks. According to Bandura ("Psychol. Rev." 84:191-215, 1977), students acquire information about their…

  11. Protein Engineering by Combined Computational and In Vitro Evolution Approaches.

    PubMed

    Rosenfeld, Lior; Heyne, Michael; Shifman, Julia M; Papo, Niv

    2016-05-01

    Two alternative strategies are commonly used to study protein-protein interactions (PPIs) and to engineer protein-based inhibitors. In one approach, binders are selected experimentally from combinatorial libraries of protein mutants that are displayed on a cell surface. In the other approach, computational modeling is used to explore an astronomically large number of protein sequences to select a small number of sequences for experimental testing. While both approaches have some limitations, their combination produces superior results in various protein engineering applications. Such applications include the design of novel binders and inhibitors, the enhancement of affinity and specificity, and the mapping of binding epitopes. The combination of these approaches also aids in the understanding of the specificity profiles of various PPIs.

  12. Computational Material Modeling of Hydrated Cement Paste Calcium Silicate Hydrate (C-S-H) Chemistry Structure - Influence of Magnesium Exchange on Mechanical Stiffness: C-S-H Jennite

    DTIC Science & Technology

    2015-04-27

    material chemistry structure are studied following a molecular dynamics (MD) computational modeling methodology. Calcium ions are replaced with... chemistry structure. Conference Name: 1st Pan-American Conference on Computational Mechanics Conference Date: April 27, 2015 1st Pan-American Congress on...MODELING OF C-S-H Material chemistry level modeling following the principles and techniques commonly grouped under Computational Material Science is

  13. Characterizing Molecular Structure by Combining Experimental Measurements with Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Lopez-Encarnacion, Juan M.

    2016-06-01

    In this talk, the power and synergy of combining experimental measurements with density functional theory computations as a single tool to unambiguously characterize the molecular structure of complex atomic systems is shown. Here, we bring three beautiful cases where the interaction between the experiment and theory is in very good agreement for both finite and extended systems: 1) Characterizing Metal Coordination Environments in Porous Organic Polymers: A Joint Density Functional Theory and Experimental Infrared Spectroscopy Study 2) Characterization of Rhenium Compounds Obtained by Electrochemical Synthesis After Aging Process and 3) Infrared Study of H(D)2 + Co4+ Chemical Reaction: Characterizing Molecular Structures. J.M. López-Encarnación, K.K. Tanabe, M.J.A. Johnson, J. Jellinek, Chemistry-A European Journal 19 (41), 13646-13651 A. Vargas-Uscategui, E. Mosquera, J.M. López-Encarnación, B. Chornik, R. S. Katiyar, L. Cifuentes, Journal of Solid State Chemistry 220, 17-21

  14. FOREWORD: Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology and Mathematics

    NASA Astrophysics Data System (ADS)

    Kaski, K.; Salomaa, M.

    1990-01-01

    These are Proceedings of the Third Nordic Symposium on Computer Simulation in Physics, Chemistry, Biology, and Mathematics, held August 25-26, 1989, at Lahti (Finland). The Symposium belongs to an annual series of Meetings, the first one of which was arranged in 1987 at Lund (Sweden) and the second one in 1988 at Kolle-Kolle near Copenhagen (Denmark). Although these Symposia have thus far been essentially Nordic events, their international character has increased significantly; the trend is vividly reflected through contributions in the present Topical Issue. The interdisciplinary nature of Computational Science is central to the activity; this fundamental aspect is also responsible, in an essential way, for its rapidly increasing impact. Crucially important to a wide spectrum of superficially disparate fields is the common need for extensive - and often quite demanding - computational modelling. For such theoretical models, no closed-form (analytical) solutions are available or they would be extremely difficult to find; hence one must rather resort to the Art of performing computational investigations. Among the unifying features in the computational research are the methods of simulation employed; methods which frequently are quite closely related with each other even for faculties of science that are quite unrelated. Computer simulation in Natural Sciences is presently apprehended as a discipline on its own right, occupying a broad region somewhere between the experimental and theoretical methods, but also partially overlapping with and complementing them. - Whichever its proper definition may be, the computational approach serves as a novel and an extremely versatile tool with which one can equally well perform "pure" experimental modelling and conduct "computational theory". Computational studies that have earlier been made possible only through supercomputers have opened unexpected, as well as exciting, novel frontiers equally in mathematics (e.g., fractals

  15. 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.

  16. Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding

    PubMed Central

    Schalk, Vinushka; Lerner, Michael G.; Woodcock, H. Lee; Brooks, Bernard R.

    2014-01-01

    A lesson utilizing a coarse-grained (CG) G-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the G-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG G model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field. PMID:25058338

  17. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding.

    PubMed

    Pickard, Frank C; Miller, Benjamin T; Schalk, Vinushka; Lerner, Michael G; Woodcock, H Lee; Brooks, Bernard R

    2014-07-01

    A lesson utilizing a coarse-grained (CG) Gō-like model has been implemented into the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org) to the Chemistry at HARvard Macromolecular Mechanics (CHARMM) molecular simulation package. While widely used to model various biophysical processes, such as protein folding and aggregation, CG models can also serve as an educational tool because they can provide qualitative descriptions of complex biophysical phenomena for a relatively cheap computational cost. As a proof of concept, this lesson demonstrates the construction of a CG model of a small globular protein, its simulation via Langevin dynamics, and the analysis of the resulting data. This lesson makes connections between modern molecular simulation techniques and topics commonly presented in an advanced undergraduate lecture on physical chemistry. It culminates in a straightforward analysis of a short dynamics trajectory of a small fast folding globular protein; we briefly describe the thermodynamic properties that can be calculated from this analysis. The assumptions inherent in the model and the data analysis are laid out in a clear, concise manner, and the techniques used are consistent with those employed by specialists in the field of CG modeling. One of the major tasks in building the Gō-like model is determining the relative strength of the nonbonded interactions between coarse-grained sites. New functionality has been added to CHARMMing to facilitate this process. The implementation of these features into CHARMMing helps automate many of the tedious aspects of constructing a CG Gō model. The CG model builder and its accompanying lesson should be a valuable tool to chemistry students, teachers, and modelers in the field.

  18. Combined experiment and theory approach in surface chemistry: Stairway to heaven?

    NASA Astrophysics Data System (ADS)

    Exner, Kai S.; Heß, Franziska; Over, Herbert; Seitsonen, Ari Paavo

    2015-10-01

    In this perspective we discuss how an intimate interaction of experiments with theory is able to deepen our insight into the catalytic reaction system on the molecular level. This strategy is illustrated by discussing various examples from our own research of surface chemistry and model catalysis. The particular examples were carefully chosen to balance the specific strength of both approaches - theory and experiment - and emphasize the benefit of this combined approach. We start with the determination of complex surface structures, where diffraction techniques in combination with theory are clear-cut. The promoter action of alkali metals in heterogeneous catalysis is rationalized with theory and experiment for the case of CO coadsorption. Predictive power of theory is limited as demonstrated with the apparent activity of chlorinated TiO2(110) in the oxidation of HCl: Even if we know all elementary reaction steps of a catalytic reaction mechanism, the overall kinetics may remain elusive and require the application kinetic Monte Carlo simulations. Catalysts are not always stable under reaction conditions and may chemically transform as discussed for the CO oxidation reaction over ruthenium. Under oxidizing reaction conditions ruthenium transforms into RuO2, a process which is hardly understood on the molecular level. Lastly we focus on electrochemical reactions. Here theory is clearly ahead since spectroscopic methods are not available to resolve the processes at the electrode surface.

  19. Heat-induced-radiolabeling and click chemistry: A powerful combination for generating multifunctional nanomaterials

    PubMed Central

    Wilks, Moses Q.; El Fakhri, Georges; Normandin, Marc D.; Kaittanis, Charalambos; Josephson, Lee

    2017-01-01

    A key advantage of nanomaterials for biomedical applications is their ability to feature multiple small reporter groups (multimodality), or combinations of reporter groups and therapeutic agents (multifunctionality), while being targeted to cell surface receptors. Here a facile combination of techniques for the syntheses of multimodal, targeted nanoparticles (NPs) is presented, whereby heat-induced-radiolabeling (HIR) labels NPs with radiometals and so-called click chemistry is used to attach bioactive groups to the NP surface. Click-reactive alkyne or azide groups were first attached to the nonradioactive clinical Feraheme (FH) NPs. Resulting “Alkyne-FH” and “Azide-FH” intermediates, like the parent NP, tolerated 89Zr labeling by the HIR method previously described. Subsequently, biomolecules were quickly conjugated to the radioactive NPs by either copper-catalyzed or copper-free click reactions with high efficiency. Synthesis of the Alkyne-FH or Azide-FH intermediates, followed by HIR and then by click reactions for biomolecule attachment, provides a simple and potentially general path for the synthesis of multimodal, multifunctional, and targeted NPs for biomedical applications. PMID:28225818

  20. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

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

  1. Chemistry Notes

    ERIC Educational Resources Information Center

    School Science Review, 1972

    1972-01-01

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

  2. The multiple roles of computational chemistry in fragment-based drug design

    NASA Astrophysics Data System (ADS)

    Law, Richard; Barker, Oliver; Barker, John J.; Hesterkamp, Thomas; Godemann, Robert; Andersen, Ole; Fryatt, Tara; Courtney, Steve; Hallett, Dave; Whittaker, Mark

    2009-08-01

    Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.

  3. The multiple roles of computational chemistry in fragment-based drug design.

    PubMed

    Law, Richard; Barker, Oliver; Barker, John J; Hesterkamp, Thomas; Godemann, Robert; Andersen, Ole; Fryatt, Tara; Courtney, Steve; Hallett, Dave; Whittaker, Mark

    2009-08-01

    Fragment-based drug discovery (FBDD) represents a change in strategy from the screening of molecules with higher molecular weights and physical properties more akin to fully drug-like compounds, to the screening of smaller, less complex molecules. This is because it has been recognised that fragment hit molecules can be efficiently grown and optimised into leads, particularly after the binding mode to the target protein has been first determined by 3D structural elucidation, e.g. by NMR or X-ray crystallography. Several studies have shown that medicinal chemistry optimisation of an already drug-like hit or lead compound can result in a final compound with too high molecular weight and lipophilicity. The evolution of a lower molecular weight fragment hit therefore represents an attractive alternative approach to optimisation as it allows better control of compound properties. Computational chemistry can play an important role both prior to a fragment screen, in producing a target focussed fragment library, and post-screening in the evolution of a drug-like molecule from a fragment hit, both with and without the available fragment-target co-complex structure. We will review many of the current developments in the area and illustrate with some recent examples from successful FBDD discovery projects that we have conducted.

  4. Thiol-ene click chemistry: computational and kinetic analysis of the influence of alkene functionality.

    PubMed

    Northrop, Brian H; Coffey, Roderick N

    2012-08-22

    The influence of alkene functionality on the energetics and kinetics of radical initiated thiol-ene click chemistry has been studied computationally at the CBS-QB3 level. Relative energetics (ΔH°, ΔH(++), ΔG°, ΔG(++)) have been determined for all stationary points along the step-growth mechanism of thiol-ene reactions between methyl mercaptan and a series of 12 alkenes: propene, methyl vinyl ether, methyl allyl ether, norbornene, acrylonitrile, methyl acrylate, butadiene, methyl(vinyl)silanediamine, methyl crotonate, dimethyl fumarate, styrene, and maleimide. Electronic structure calculations reveal the underlying factors that control activation barriers for propagation and chain-transfer processes of the step-growth mechanism. Results are further extended to predict rate constants for forward and reverse propagation and chain-transfer steps (k(P), k(-P), k(CT), k(-CT)) and used to model overall reaction kinetics. A relationship between alkene structure and reactivity in thiol-ene reactions is derived from the results of kinetic modeling and can be directly related to the relative energetics of stationary points obtained from electronic structure calculations. The results predict the order of reactivity of alkenes and have broad implications for the use and applications of thiol-ene click chemistry.

  5. A Unique Master's Program in Combined Nuclear Technology and Nuclear Chemistry at Chalmers University of Technology, Sweden

    NASA Astrophysics Data System (ADS)

    Skarnemark, Gunnar; Allard, Stefan; Ekberg, Christian; Nordlund, Anders

    2009-08-01

    The need for engineers and scientists who can ensure safe and secure use of nuclear energy is large in Sweden and internationally. Chalmers University of Technology is therefore launching a new 2-year master's program in Nuclear Engineering, with start from the autumn of 2009. The program is open to Swedish and foreign students. The program starts with compulsory courses dealing with the basics of nuclear chemistry and physics, radiation protection, nuclear power and reactors, nuclear fuel supply, nuclear waste management and nuclear safety and security. There are also compulsory courses in nuclear industry applications and sustainable energy futures. The subsequent elective courses can be chosen freely but there is also a possibility to choose informal tracks that concentrate on nuclear chemistry or reactor technology and physics. The nuclear chemistry track comprises courses in e.g. chemistry of lanthanides, actinides and transactinides, solvent extraction, radioecology and radioanalytical chemistry and radiopharmaceuticals. The program is finished with a one semester thesis project. This is probably a unique master program in the sense of its combination of deep courses in both nuclear technology and nuclear chemistry.

  6. A Unique Master's Program in Combined Nuclear Technology and Nuclear Chemistry at Chalmers University of Technology, Sweden

    SciTech Connect

    Skarnemark, Gunnar; Allard, Stefan; Ekberg, Christian; Nordlund, Anders

    2009-08-19

    The need for engineers and scientists who can ensure safe and secure use of nuclear energy is large in Sweden and internationally. Chalmers University of Technology is therefore launching a new 2-year master's program in Nuclear Engineering, with start from the autumn of 2009. The program is open to Swedish and foreign students. The program starts with compulsory courses dealing with the basics of nuclear chemistry and physics, radiation protection, nuclear power and reactors, nuclear fuel supply, nuclear waste management and nuclear safety and security. There are also compulsory courses in nuclear industry applications and sustainable energy futures. The subsequent elective courses can be chosen freely but there is also a possibility to choose informal tracks that concentrate on nuclear chemistry or reactor technology and physics. The nuclear chemistry track comprises courses in e.g. chemistry of lanthanides, actinides and transactinides, solvent extraction, radioecology and radioanalytical chemistry and radiopharmaceuticals. The program is finished with a one semester thesis project. This is probably a unique master program in the sense of its combination of deep courses in both nuclear technology and nuclear chemistry.

  7. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    ERIC Educational Resources Information Center

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  8. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    ERIC Educational Resources Information Center

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  9. Large-Scale Parallel Simulations of Turbulent Combustion using Combined Dimension Reduction and Tabulation of Chemistry

    DTIC Science & Technology

    2012-05-22

    redistributing the chemistry workload, namely (a) PLP, purely local processing; (b) URAN , the uniform random distribution of chemistry com- putations among...all cores following an early stage of PLP; and (c) P- URAN , a Partitioned URAN strategy that redistributes the workload within parti- tions or subsets...parallel strate- gies for redistributing the chemistry workload, namely (a) PLP, purely local processing; (b) URAN , the uniform random distribution

  10. A Combined Experimental/Computational Investigation of a Rocket Based Combined Cycle Inlet

    NASA Technical Reports Server (NTRS)

    Smart, Michael K.; Trexler, Carl A.; Goldman, Allen L.

    2001-01-01

    A rocket based combined cycle inlet geometry has undergone wind tunnel testing and computational analysis with Mach 4 flow at the inlet face. Performance parameters obtained from the wind tunnel tests were the mass capture, the maximum back-pressure, and the self-starting characteristics of the inlet. The CFD analysis supplied a confirmation of the mass capture, the inlet efficiency and the details of the flowfield structure. Physical parameters varied during the test program were cowl geometry, cowl position, body-side bleed magnitude and ingested boundary layer thickness. An optimum configuration was determined for the inlet as a result of this work.

  11. Technetium chemistry in the fuel cycle: combining basic and applied studies.

    PubMed

    Poineau, Frederic; Mausolf, Edward; Jarvinen, Gordon D; Sattelberger, Alfred P; Czerwinski, Kenneth R

    2013-04-01

    Technetium is intimately linked with nuclear reactions. The ultraminute natural levels in the environment are due to the spontaneous fission of uranium isotopes. The discovery of technetium was born from accelerator reactions, and its use and presence in the modern world are directly due to nuclear reactors. While occupying a central location in the periodic table, the chemistry of technetium is poorly explored, especially when compared to its neighboring elements, i.e., molybdenum, ruthenium, and rhenium. This state of affairs, which is tied to the small number of laboratories equipped to work with the long-lived (99)Tc isotope, provides a remarkable opportunity to combine basic studies with applications for the nuclear fuel cycle. An example is given through examination of the technetium halide compounds. Binary metal halides represent some of the most fundamental of inorganic compounds. The synthesis of new technetium halides demonstrates trends with structure, coordination number, and speciation that can be utilized in the nuclear fuel cycle. Examples are provided for technetium-zirconium alloys as waste forms and the formation of reduced technetium species in separations.

  12. New Combined Laser Ablation Platform Determines Cell Wall Chemistry (Fact Sheet)

    SciTech Connect

    Not Available

    2011-09-01

    NREL has designed and developed a combined laser ablation/pulsed sample introduction/mass spectrometry platform that integrates pyrolysis and/or laser ablation with resonance-enhanced multiphoton ionization (REMPI) time-of-flight mass spectrometry. Using this apparatus, we can measure the cell wall chemical composition of untreated biomass materials. Understanding the chemical composition of untreated biomass is key to both the biochemical and thermochemical conversion of lignocellulosic biomass to biofuels. In the biochemical conversion process, the new technique provides a better understanding of the chemistry of lignin and will improve accessibility to plant sugars. In thermochemical conversion, the information provided by the new technique may help to reduce the formation of unwanted byproducts during gasification. NREL validated the ability of the system to detect pyrolysis products from plant materials using poplar, a potentially high-impact bioenergy feedstock. In the technique, biomass vapors are produced by laser ablation using the 3rd harmonic of an Nd:YAG laser (355 nm). The resulting vapors are entrained in a free jet expansion of helium, then skimmed and introduced into an ionization region. REMPI is used to ionize the vapors because it is highly sensitive for detecting lignin and aromatic metabolites. The laser ablation method was used to selectively volatilize specific plant tissues and detect lignin-based products from the vapors with enhanced sensitivity. This will allow the determination of lignin distribution in future biomass studies.

  13. Combining Click Chemistry-Based Proteomics With Dox-Inducible Gene Expression.

    PubMed

    Gebert, J; Schnölzer, M; Warnken, U; Kopitz, J

    2017-01-01

    Inactivating mutations in single genes can trigger, prevent, promote, or alleviate diseases. Identifying such disease-related genes is a main pillar of medical research. Since proteins play a crucial role in mediating these effects, their impact on the diseased cells' proteome including posttranslational modifications has to be elucidated for a detailed understanding of the role of these genes in the disease process. In complex disorders, like cancer, several genes contribute to the disease process, thereby hampering the assignment of a proteomic change to the corresponding causative gene. To enable comprehensive screening for the impact of inactivation of a gene, e.g., loss of a tumor suppressor in cancer, on the cellular proteome, we present a strategy based on combination of three technologies that is recombinase-mediated cassette exchange, click chemistry, and mass spectrometry. The methodology is exemplified by the analysis of the proteomic changes induced by the loss of a tumor suppressor gene in colorectal cancer cells. To demonstrate the applicability to screen for posttranslational modification changes, we also describe the analysis of protein glycosylation changes caused by the tumor suppressor inactivation. In principle, this strategy can be applied to analyze the effects of any gene of interest on protein expression as well as posttranslational modification by glycosylation. Moreover adaptation of the strategy to an appropriate cell culture model has the potential for application on a broad range of diseases where the disease-promoting mutations have been identified. © 2017 Elsevier Inc. All rights reserved.

  14. PREDICTING CHEMICAL REACTIVITY OF HUMIC SUBSTANCES FOR MINERALS AND XENOBIOTICS: USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY AND VIRTUAL REALITY

    EPA Science Inventory

    In this chapter we review the literature on scanning probe microscopy (SPM), virtual reality (VR), and computational chemistry and our earlier work dealing with modeling lignin, lignin-carbohydrate complexes (LCC), humic substances (HSs) and non-bonded organo-mineral interactions...

  15. Solutions, Unit 2: Molarity, Molality, Concentration Conversions. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Bader, Morris

    Presented are the teacher's guide and student manual for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student module for this solution concentration unit includes objectives, prerequisites, pretest, discussion, and 20 problem sets. Included in the teacher's guide…

  16. Using an Advanced Computational Laboratory Experiment to Extend and Deepen Physical Chemistry Students' Understanding of Atomic Structure

    ERIC Educational Resources Information Center

    Hoffman, Gary G.

    2015-01-01

    A computational laboratory experiment is described, which involves the advanced study of an atomic system. The students use concepts and techniques typically covered in a physical chemistry course but extend those concepts and techniques to more complex situations. The students get a chance to explore the study of atomic states and perform…

  17. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

    ERIC Educational Resources Information Center

    Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

  18. Using an Advanced Computational Laboratory Experiment to Extend and Deepen Physical Chemistry Students' Understanding of Atomic Structure

    ERIC Educational Resources Information Center

    Hoffman, Gary G.

    2015-01-01

    A computational laboratory experiment is described, which involves the advanced study of an atomic system. The students use concepts and techniques typically covered in a physical chemistry course but extend those concepts and techniques to more complex situations. The students get a chance to explore the study of atomic states and perform…

  19. Solutions, Unit 5: Colligative Properties of Solutions. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Bader, Morris

    Presented are the teacher's guide and student manual for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on the colligative properties of solutions includes objectives, prerequisites, pretest, discussion, and 20 problem sets. Included in…

  20. PREDICTING CHEMICAL REACTIVITY OF HUMIC SUBSTANCES FOR MINERALS AND XENOBIOTICS: USE OF COMPUTATIONAL CHEMISTRY, SCANNING PROBE MICROSCOPY AND VIRTUAL REALITY

    EPA Science Inventory

    In this chapter we review the literature on scanning probe microscopy (SPM), virtual reality (VR), and computational chemistry and our earlier work dealing with modeling lignin, lignin-carbohydrate complexes (LCC), humic substances (HSs) and non-bonded organo-mineral interactions...

  1. Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling: Experiments for Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Bumpus, John A.; Lewis, Anne; Stotts, Corey; Cramer, Christopher J.

    2007-01-01

    Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of…

  2. Chemical Equilibrium, Unit 3: Chemical Equilibrium Calculations. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Jameson, Cynthia J.

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this unit on chemical equilibrium calculations includes objectives, prerequisites, a discussion of the equilibrium constant (K), and ten…

  3. Introductory Molecular Orbital Theory: An Honors General Chemistry Computational Lab as Implemented Using Three-Dimensional Modeling Software

    ERIC Educational Resources Information Center

    Ruddick, Kristie R.; Parrill, Abby L.; Petersen, Richard L.

    2012-01-01

    In this study, a computational molecular orbital theory experiment was implemented in a first-semester honors general chemistry course. Students used the GAMESS (General Atomic and Molecular Electronic Structure System) quantum mechanical software (as implemented in ChemBio3D) to optimize the geometry for various small molecules. Extended Huckel…

  4. Characterization of High Explosives and Other Energetic Compounds by Computational Chemistry and Molecular Modeling: Experiments for Undergraduate Curriculum

    ERIC Educational Resources Information Center

    Bumpus, John A.; Lewis, Anne; Stotts, Corey; Cramer, Christopher J.

    2007-01-01

    Experiments suited for the undergraduate instructional laboratory in which the heats of formation of several aliphatic and aromatic compounds are calculated, are described. The experiments could be used to introduce students to commercially available computational chemistry and its thermodynamics, while assess and compare the energy content of…

  5. Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

    ERIC Educational Resources Information Center

    Springer, Michael T.

    2014-01-01

    Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

  6. Improving Students' Understanding of Molecular Structure through Broad-Based Use of Computer Models in the Undergraduate Organic Chemistry Lecture

    ERIC Educational Resources Information Center

    Springer, Michael T.

    2014-01-01

    Several articles suggest how to incorporate computer models into the organic chemistry laboratory, but relatively few papers discuss how to incorporate these models broadly into the organic chemistry lecture. Previous research has suggested that "manipulating" physical or computer models enhances student understanding; this study…

  7. A molecular-modeling toolbox aimed at bridging the gap between medicinal chemistry and computational sciences.

    PubMed

    Eid, Sameh; Zalewski, Adam; Smieško, Martin; Ernst, Beat; Vedani, Angelo

    2013-01-04

    In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand-protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin.

  8. Uquantchem: A versatile and easy to use quantum chemistry computational software

    NASA Astrophysics Data System (ADS)

    Souvatzis, Petros

    2014-01-01

    In this paper we present the Uppsala Quantum Chemistry package (UQUANTCHEM), a new and versatile computational platform with capabilities ranging from simple Hartree-Fock calculations to state of the art First principles Extended Lagrangian Born-Oppenheimer Molecular Dynamics (XL-BOMD) and diffusion quantum Monte Carlo (DMC). The UQUANTCHEM package is distributed under the general public license and can be directly downloaded from the code web-site (http://www.anst.uu.se/pesou087/DOWNLOAD-UQUANTCHEM/DOWNLOAD-UQUANTCHEM/DOWNLOAD-SITE-UQUANTCHEM.html) [1]. Together with a presentation of the different capabilities of the uquantchem code and a more technical discussion on how these capabilities have been implemented, a presentation of the user-friendly aspect of the package on the basis of the large number of default settings will also be presented. Furthermore, since the code has been parallelized within the framework of the message passing interface (MPI), the timing of some benchmark calculations are reported to illustrate how the code scales with the number of computational nodes for different levels of chemical theory.

  9. A Molecular-Modeling Toolbox Aimed at Bridging the Gap between Medicinal Chemistry and Computational Sciences

    PubMed Central

    Eid, Sameh; Zalewski, Adam; Smieško, Martin; Ernst, Beat; Vedani, Angelo

    2013-01-01

    In the current era of high-throughput drug discovery and development, molecular modeling has become an indispensable tool for identifying, optimizing and prioritizing small-molecule drug candidates. The required background in computational chemistry and the knowledge of how to handle the complex underlying protocols, however, might keep medicinal chemists from routinely using in silico technologies. Our objective is to encourage those researchers to exploit existing modeling technologies more frequently through easy-to-use graphical user interfaces. In this account, we present two innovative tools (which we are prepared to share with academic institutions) facilitating computational tasks commonly utilized in drug discovery and development: (1) the VirtualDesignLab estimates the binding affinity of small molecules by simulating and quantifying their binding to the three-dimensional structure of a target protein; and (2) the MD Client launches molecular dynamics simulations aimed at exploring the time-dependent stability of ligand–protein complexes and provides residue-based interaction energies. This allows medicinal chemists to identify sites of potential improvement in their candidate molecule. As a case study, we present the application of our tools towards the design of novel antagonists for the FimH adhesin. PMID:23344039

  10. The Combined Effects of Classroom Teaching and Learning Strategy Use on Students' Chemistry Self-Efficacy

    NASA Astrophysics Data System (ADS)

    Cheung, Derek

    2015-02-01

    For students to be successful in school chemistry, a strong sense of self-efficacy is essential. Chemistry self-efficacy can be defined as students' beliefs about the extent to which they are capable of performing specific chemistry tasks. According to Bandura (Psychol. Rev. 84:191-215, 1977), students acquire information about their level of self-efficacy from four sources: performance accomplishments, vicarious experiences, verbal persuasion, and physiological states. No published studies have investigated how instructional strategies in chemistry lessons can provide students with positive experiences with these four sources of self-efficacy information and how the instructional strategies promote students' chemistry self-efficacy. In this study, questionnaire items were constructed to measure student perceptions about instructional strategies, termed efficacy-enhancing teaching, which can provide positive experiences with the four sources of self-efficacy information. Structural equation modeling was then applied to test a hypothesized mediation model, positing that efficacy-enhancing teaching positively affects students' chemistry self-efficacy through their use of deep learning strategies such as metacognitive control strategies. A total of 590 chemistry students at nine secondary schools in Hong Kong participated in the survey. The mediation model provided a good fit to the student data. Efficacy-enhancing teaching had a direct effect on students' chemistry self-efficacy. Efficacy-enhancing teaching also directly affected students' use of deep learning strategies, which in turn affected students' chemistry self-efficacy. The implications of these findings for developing secondary school students' chemistry self-efficacy are discussed.

  11. Combining Chemistry and Music to Engage Student Interest: Using Songs to Accompany Selected Chemical Topics

    ERIC Educational Resources Information Center

    Last, Arthur M.

    2009-01-01

    The use of recorded music to add interest to a variety of lecture topics is described. Topics include the periodic table, the formation of ionic compounds, thermodynamics, carbohydrates, nuclear chemistry, and qualitative analysis. (Contains 1 note.)

  12. Combining Chemistry and Music to Engage Student Interest: Using Songs to Accompany Selected Chemical Topics

    ERIC Educational Resources Information Center

    Last, Arthur M.

    2009-01-01

    The use of recorded music to add interest to a variety of lecture topics is described. Topics include the periodic table, the formation of ionic compounds, thermodynamics, carbohydrates, nuclear chemistry, and qualitative analysis. (Contains 1 note.)

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

    SciTech Connect

    Glaesemann, K R

    2004-01-22

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

  14. Many Body Methods from Chemistry to Physics: Novel Computational Techniques for Materials-Specific Modelling: A Computational Materials Science and Chemistry Network

    SciTech Connect

    Millis, Andrew

    2016-11-17

    Understanding the behavior of interacting electrons in molecules and solids so that one can predict new superconductors, catalysts, light harvesters, energy and battery materials and optimize existing ones is the ``quantum many-body problem’’. This is one of the scientific grand challenges of the 21st century. A complete solution to the problem has been proven to be exponentially hard, meaning that straightforward numerical approaches fail. New insights and new methods are needed to provide accurate yet feasible approximate solutions. This CMSCN project brought together chemists and physicists to combine insights from the two disciplines to develop innovative new approaches. Outcomes included the Density Matrix Embedding method, a new, computationally inexpensive and extremely accurate approach that may enable first principles treatment of superconducting and magnetic properties of strongly correlated materials, new techniques for existing methods including an Adaptively Truncated Hilbert Space approach that will vastly expand the capabilities of the dynamical mean field method, a self-energy embedding theory and a new memory-function based approach to the calculations of the behavior of driven systems. The methods developed under this project are now being applied to improve our understanding of superconductivity, to calculate novel topological properties of materials and to characterize and improve the properties of nanoscale devices.

  15. 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

  16. The use of computer-aided learning in chemistry laboratory instruction

    NASA Astrophysics Data System (ADS)

    Allred, Brian Robert Tracy

    This research involves developing and implementing computer software for chemistry laboratory instruction. The specific goal is to design the software and investigate whether it can be used to introduce concepts and laboratory procedures without a lecture format. This would allow students to conduct an experiment even though they may not have been introduced to the chemical concept in their lecture course. This would also allow for another type of interaction for those students who respond more positively to a visual approach to instruction. The first module developed was devoted to using computer software to help introduce students to the concepts related to thin-layer chromatography and setting up and running an experiment. This was achieved through the use of digitized pictures and digitized video clips along with written information. A review quiz was used to help reinforce the learned information. The second module was devoted to the concept of the "dry lab". This module presented students with relevant information regarding the chemical concepts and then showed them the outcome of mixing solutions. By these observations, they were to determine the composition of unknown solutions based on provided descriptions and comparison with their written observations. The third piece of the software designed was a computer game. This program followed the first two modules in providing information the students were to learn. The difference here, though, was incorporating a game scenario for students to use to help reinforce the learning. Students were then assessed to see how much information they retained after playing the game. In each of the three cases, a control group exposed to the traditional lecture format was used. Their results were compared to the experimental group using the computer modules. Based upon the findings, it can be concluded that using technology to aid in the instructional process is definitely of benefit and students were more successful in

  17. Computing gas solubility in reservoir waters for environmental chemistry applications: the role of satellite observations

    NASA Astrophysics Data System (ADS)

    Rosa, R.; Lima, I.; Ramos, F.; Bambace, L.; Assireu, A.; Stech, J.; Novo, E.; Lorenzeti, L.

    Atmospheric greenhouse gases concentration has increased during the past centuries basically due to biogenic and pyrogenic anthopogenic emissions Recent investigations have shown that gas emission methane as an important example from tropical hydroelectric reservoirs may comprise a considerable fraction of the total anthropogenic bulk In order to evaluate the concentration of gases of potential importance in environmental chemistry the solubility of such gases have been collected and converted into a uniform format using the Henry s law which states that the solubility of a gas in a liquid is directly proportional to its partial pressure However the Henry s law can be derived as a function of temperature density molar mixing ratio in the aqueous phase and molar mass of water In this paper we show that due to the complex temperature variation and water composition measured in brazilian tropical reservoirs as Serra da Mesa and Manso expressive secular variation on the traditional solubility constants concentration of a species in the aqueous phase by the partial pressure of that species in the gas phase can change in a rate of approximately 30 in 6 decades This estimation comes from a computational analysis of temperature variation measured during 6 months in Serra da Mesa and Manso reservoirs taking into account a simulated density and molar mass variation of the aqueous composition in these environments As an important global change issue from this preliminary analysis we discuss its role in the current estimations on the concentration emission rates

  18. The nucleation rate surfaces design over diagram of phase equilibria and their applications for computational chemistry

    NASA Astrophysics Data System (ADS)

    Anisimov, M. P.

    2016-12-01

    One can find in scientific literature a pretty fresh idea of the nucleation rate surfaces design over the diagrams of phase equilibria. That idea looks like profitable for the nucleation theory development and for various practical applications where predictions of theory have no high enough accuracy for today. The common thermodynamics has no real ability to predict parameters of the first order phase transition. Nucleation experiment can be provided in very local nucleation conditions even the nucleation takes place from the critical line (in two-component case) down to the absolute zero temperature limit and from zero nucleation rates at phase equilibria up to the spinodal conditions. Theory predictions have low reliability as a rule. The computational chemistry has chance to make solution of that problem easier when a set of the used axiomatic statements will adapt enough progressive assumptions [1]. Semiempirical design of the nucleation rate surfaces over diagrams of phase equilibria have a potential ability to provide a reasonable quality information on nucleation rate for each channel of nucleation. Consideration and using of the nucleation rate surface topologies to optimize synthesis of a given phase of the target material can be available when data base on nucleation rates over diagrams of phase equilibria will be created.

  19. Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins.

    PubMed

    Perrin, B Scott; Miller, Benjamin T; Schalk, Vinushka; Woodcock, H Lee; Brooks, Bernard R; Ichiye, Toshiko

    2014-07-01

    A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.

  20. Generation of naphthoquinone radical anions by electrospray ionization: solution, gas-phase, and computational chemistry studies.

    PubMed

    Vessecchi, Ricardo; Naal, Zeki; Lopes, José N C; Galembeck, Sérgio E; Lopes, Norberto P

    2011-06-02

    Radical anions are present in several chemical processes, and understanding the reactivity of these species may be described by their thermodynamic properties. Over the last years, the formation of radical ions in the gas phase has been an important issue concerning electrospray ionization mass spectrometry studies. In this work, we report on the generation of radical anions of quinonoid compounds (Q) by electrospray ionization mass spectrometry. The balance between radical anion formation and the deprotonated molecule is also analyzed by influence of the experimental parameters (gas-phase acidity, electron affinity, and reduction potential) and solvent system employed. The gas-phase parameters for formation of radical species and deprotonated species were achieved on the basis of computational thermochemistry. The solution effects on the formation of radical anion (Q(•-)) and dianion (Q(2-)) were evaluated on the basis of cyclic voltammetry analysis and the reduction potentials compared with calculated electron affinities. The occurrence of unexpected ions [Q+15](-) was described as being a reaction between the solvent system and the radical anion, Q(•-). The gas-phase chemistry of the electrosprayed radical anions was obtained by collisional-induced dissociation and compared to the relative energy calculations. These results are important for understanding the formation and reactivity of radical anions and to establish their correlation with the reducing properties by electrospray ionization analyses.

  1. Assault on resistance: the use of computational chemistry in the development of anti-HIV drugs.

    PubMed

    Smith, Marilyn B Kroeger; Smith, Richard H; Jorgensen, William L

    2006-01-01

    While many inhibitors of the Human Immunodeficiency Virus (HIV), the causative agent of Acquired Immunodeficiency Syndrome (AIDS), have been developed, the problem of drug resistance has continued to plague the fight against the disease. The ability of computers to aid in the drug discovery process, and by default the resistance problem, has increased dramatically as the speed of computers and sophistication of associated calculation programs has grown. In particular, the capability of predicting a compound's ability to combat resistance prior to synthesis of drug candidates has proven particularly desirable. Since resistance can develop against a specific drug designed to inhibit only one stage of the viral cycle, combinations of drugs directed at more than one step have proven to be more effective than a single drug given alone. While the introduction of this combination therapy (termed highly active antiretroviral therapy (HAART)) has significantly decreased the death rate from HIV infections, resistance problems still arise. This paper will review previous approaches and address current and future computational strategies used in the design of second-generation and beyond drugs.

  2. Toward computational cumulative biology by combining models of biological datasets.

    PubMed

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations-for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database.

  3. Toward Computational Cumulative Biology by Combining Models of Biological Datasets

    PubMed Central

    Faisal, Ali; Peltonen, Jaakko; Georgii, Elisabeth; Rung, Johan; Kaski, Samuel

    2014-01-01

    A main challenge of data-driven sciences is how to make maximal use of the progressively expanding databases of experimental datasets in order to keep research cumulative. We introduce the idea of a modeling-based dataset retrieval engine designed for relating a researcher's experimental dataset to earlier work in the field. The search is (i) data-driven to enable new findings, going beyond the state of the art of keyword searches in annotations, (ii) modeling-driven, to include both biological knowledge and insights learned from data, and (iii) scalable, as it is accomplished without building one unified grand model of all data. Assuming each dataset has been modeled beforehand, by the researchers or automatically by database managers, we apply a rapidly computable and optimizable combination model to decompose a new dataset into contributions from earlier relevant models. By using the data-driven decomposition, we identify a network of interrelated datasets from a large annotated human gene expression atlas. While tissue type and disease were major driving forces for determining relevant datasets, the found relationships were richer, and the model-based search was more accurate than the keyword search; moreover, it recovered biologically meaningful relationships that are not straightforwardly visible from annotations—for instance, between cells in different developmental stages such as thymocytes and T-cells. Data-driven links and citations matched to a large extent; the data-driven links even uncovered corrections to the publication data, as two of the most linked datasets were not highly cited and turned out to have wrong publication entries in the database. PMID:25427176

  4. Personal computer versus personal computer/mobile device combination users' preclinical laboratory e-learning activity.

    PubMed

    Kon, Haruka; Kobayashi, Hiroshi; Sakurai, Naoki; Watanabe, Kiyoshi; Yamaga, Yoshiro; Ono, Takahiro

    2016-11-15

    The aim of the present study was to clarify differences between personal computer (PC)/mobile device combination and PC-only user patterns. We analyzed access frequency and time spent on a complete denture preclinical website in order to maximize website effectiveness. Fourth-year undergraduate students (N=41) in the preclinical complete denture laboratory course were invited to participate in this survey during the final week of the course to track login data. Students accessed video demonstrations and quizzes via our e-learning site/course program, and were instructed to view online demonstrations before classes. When the course concluded, participating students filled out a questionnaire about the program, their opinions, and devices they had used to access the site. Combination user access was significantly more frequent than PC-only during supplementary learning time, indicating that students with mobile devices studied during lunch breaks and before morning classes. Most students had favorable opinions of the e-learning site, but a few combination users commented that some videos were too long and that descriptive answers were difficult on smartphones. These results imply that mobile devices' increased accessibility encouraged learning by enabling more efficient time use between classes. They also suggest that e-learning system improvements should cater to mobile device users by reducing video length and including more short-answer questions. © 2016 John Wiley & Sons Australia, Ltd.

  5. Factors associated with computer and Internet technology implementation in biology, chemistry, and physics education in Turkish secondary schools

    NASA Astrophysics Data System (ADS)

    Ozer, Melike

    The main purposes of the research were to identify computer and Internet use by biology, chemistry and physics teachers in Turkish secondary schools and identify factors associated with computer and Internet technology. To this end, survey documents were sent by the Provincial Directorate of National Education to 250 selected schools' administrators for further distribution. Administrators were asked to complete the "Computer and Internet Use: School Survey," and to distribute the "Science Teacher Computer and Internet Use" surveys to the two teachers who teach science class. Surveys were then returned to the General Directorate of Educational Technologies. Research findings showed that computer and Internet use has not occurred effectively. Computers were first introduced to Turkish schools in 1984; unfortunately the current situation of computer and Internet use in science education is not at the projected earlier point in time. Considering the fact that science teachers' participation in technology-related professional development program is higher than other subject teachers, the use of computer and Internet technologies in Turkish secondary schools is still at its early stages. Lack of computer knowledge and not knowing how to integrate computers into education were the major factors reported. With regard to computer and Internet use, a regression model for Turkish schools, which includes access and knowledge, explains a large part of the variance in study results. There was a significant relationship between computer attitude (computer liking, usefulness, and confidence) and computer and Internet use. Although there was a significant negative relationship between Internet and computer uses and the attitudinal component, computer anxiety, it did not deter individuals from expressing a desire to engage in computer use in education.

  6. Chemistry for Kids: Generating Carbon Dioxide in Elementary School Chemistry and Using a Computer To Write about It.

    ERIC Educational Resources Information Center

    Schlenker, Richard M.; Yoshida, Sarah

    This material describes an activity using vinegar and baking soda to generate carbon dioxide, and writing a report using the Appleworks word processing program for grades 3 to 8 students. Time requirement, relevant process skills, vocabulary, mathematics skills, computer skills, and materials are listed. Activity procedures including class…

  7. The Effectiveness of a Computer-Assisted Instruction Package in High School Chemistry.

    ERIC Educational Resources Information Center

    Wainwright, Camille L.

    1989-01-01

    Evaluates the attributes of a microcomputer software package as a supplement to chemistry instruction. Reports higher scores among the students in a control group. Discovers no significant interaction between treatment and development stage. Discusses several implications for further research. Provides the General Chemistry Test and error analysis…

  8. Implementation of Protocols To Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student

    PubMed Central

    2016-01-01

    There exists a sparse representation of blind and low-vision students in science, technology, engineering and mathematics (STEM) fields. This is due in part to these individuals being discouraged from pursuing STEM degrees as well as a lack of appropriate adaptive resources in upper level STEM courses and research. Mona Minkara is a rising fifth year graduate student in computational chemistry at the University of Florida. She is also blind. This account presents efforts conducted by an expansive team of university and student personnel in conjunction with Mona to adapt different portions of the graduate student curriculum to meet Mona’s needs. The most important consideration is prior preparation of materials to assist with coursework and cumulative exams. Herein we present an account of the first four years of Mona’s graduate experience hoping this will assist in the development of protocols for future blind and low-vision graduate students in computational chemistry. PMID:26300560

  9. Implementation of Protocols To Enable Doctoral Training in Physical and Computational Chemistry of a Blind Graduate Student.

    PubMed

    Minkara, Mona S; Weaver, Michael N; Gorske, Jim; Bowers, Clifford R; Merz, Kenneth M

    2015-08-11

    There exists a sparse representation of blind and low-vision students in science, technology, engineering and mathematics (STEM) fields. This is due in part to these individuals being discouraged from pursuing STEM degrees as well as a lack of appropriate adaptive resources in upper level STEM courses and research. Mona Minkara is a rising fifth year graduate student in computational chemistry at the University of Florida. She is also blind. This account presents efforts conducted by an expansive team of university and student personnel in conjunction with Mona to adapt different portions of the graduate student curriculum to meet Mona's needs. The most important consideration is prior preparation of materials to assist with coursework and cumulative exams. Herein we present an account of the first four years of Mona's graduate experience hoping this will assist in the development of protocols for future blind and low-vision graduate students in computational chemistry.

  10. Computational Chemistry to the Rescue: Modern Toolboxes for the Assignment of Complex Molecules by GIAO NMR Calculations.

    PubMed

    Grimblat, Nicolas; Sarotti, Ariel M

    2016-08-22

    The calculations of NMR properties of molecules using quantum chemical methods have deeply impacted several branches of organic chemistry. They are particularly important in structural or stereochemical assignments of organic compounds, with implications in total synthesis, stereoselective reactions, and natural products chemistry. In studying the evolution of the strategies developed to support (or reject) a structural proposal, it becomes clear that the most effective and accurate ones involve sophisticated procedures to correlate experimental and computational data. Owing to their relatively high mathematical complexity, such calculations (CP3, DP4, ANN-PRA) are often carried out using additional computational resources provided by the authors (such as applets or Excel files). This Minireview will cover the state-of-the-art of these toolboxes in the assignment of organic molecules, including mathematical definitions, updates, and discussion of relevant examples.

  11. Computers and Calculators: A Strategy for Combined Usage in Trigonometry.

    ERIC Educational Resources Information Center

    Spero, Samuel W.

    The instructional strategy described was used to incorporate both the computer and the hand calculator into trigonometry courses at an Ohio community college. The computer was used to generate different problem sets for individual students and, at the same time, solution sets for the instructor. The students were required to use calculators to…

  12. Combining human and computer interpretation capabilities to analyze ERTS imagery

    NASA Technical Reports Server (NTRS)

    Nichols, J. D.

    1973-01-01

    The human photointerpreter and the computer have complementary capabilities that are exploited in a computer-based data analysis system developed at the Forestry Remote Sensing Laboratory, University of California. This system is designed to optimize the process of extracting resource information from ERTS images. The human has the ability to quickly delineate gross differences in land classes, such as wildland, urban, and agriculture on appropriate ERTS images, and to further break these gross classes into meaningful subclasses. The computer, however, can more efficiently analyze point-by-point spectral information and localized textural information which can result in a much more detailed agricultural or wildland classification based on species composition and/or plant association. These human and computer capabilities have been integrated through the use of an inexpensive small scale computer dedicated to the interactive preprocessing of the human inputs and the display of raw ERTS images and computer classified images. The small computer is linked to a large scale computer system wherein the bulk of the statistical work and the automatic point-by-point classification is done.

  13. Combining Computational and Social Effort for Collaborative Problem Solving.

    PubMed

    Wagy, Mark D; Bongard, Josh C

    2015-01-01

    Rather than replacing human labor, there is growing evidence that networked computers create opportunities for collaborations of people and algorithms to solve problems beyond either of them. In this study, we demonstrate the conditions under which such synergy can arise. We show that, for a design task, three elements are sufficient: humans apply intuitions to the problem, algorithms automatically determine and report back on the quality of designs, and humans observe and innovate on others' designs to focus creative and computational effort on good designs. This study suggests how such collaborations should be composed for other domains, as well as how social and computational dynamics mutually influence one another during collaborative problem solving.

  14. Combining high performance simulation, data acquisition, and graphics display computers

    NASA Technical Reports Server (NTRS)

    Hickman, Robert J.

    1989-01-01

    Issues involved in the continuing development of an advanced simulation complex are discussed. This approach provides the capability to perform the majority of tests on advanced systems, non-destructively. The controlled test environments can be replicated to examine the response of the systems under test to alternative treatments of the system control design, or test the function and qualification of specific hardware. Field tests verify that the elements simulated in the laboratories are sufficient. The digital computer is hosted by a Digital Equipment Corp. MicroVAX computer with an Aptec Computer Systems Model 24 I/O computer performing the communication function. An Applied Dynamics International AD100 performs the high speed simulation computing and an Evans and Sutherland PS350 performs on-line graphics display. A Scientific Computer Systems SCS40 acts as a high performance FORTRAN program processor to support the complex, by generating numerous large files from programs coded in FORTRAN that are required for the real time processing. Four programming languages are involved in the process, FORTRAN, ADSIM, ADRIO, and STAPLE. FORTRAN is employed on the MicroVAX host to initialize and terminate the simulation runs on the system. The generation of the data files on the SCS40 also is performed with FORTRAN programs. ADSIM and ADIRO are used to program the processing elements of the AD100 and its IOCP processor. STAPLE is used to program the Aptec DIP and DIA processors.

  15. New Mechanistic Insights on the Selectivity of Transition-Metal-Catalyzed Organic Reactions: The Role of Computational Chemistry.

    PubMed

    Zhang, Xinhao; Chung, Lung Wa; Wu, Yun-Dong

    2016-06-21

    With new advances in theoretical methods and increased computational power, applications of computational chemistry are becoming practical and routine in many fields of chemistry. In organic chemistry, computational chemistry plays an indispensable role in elucidating reaction mechanisms and the origins of various selectivities, such as chemo-, regio-, and stereoselectivities. Consequently, mechanistic understanding improves synthesis and assists in the rational design of new catalysts. In this Account, we present some of our recent works to illustrate how computational chemistry provides new mechanistic insights for improvement of the selectivities of several organic reactions. These examples include not only explanations for the existing experimental observations, but also predictions which were subsequently verified experimentally. This Account consists of three sections discuss three different kinds of selectivities. The first section discusses the regio- and stereoselectivities of hydrosilylations of alkynes, mainly catalyzed by [Cp*Ru(MeCN)3](+) or [CpRu(MeCN)3](+). Calculations suggest a new mechanism that involves a key ruthenacyclopropene intermediate. This mechanism not only explains the unusual Markovnikov regio-selectivity and anti-addition stereoselectivity observed by Trost and co-workers, but also motivated further experimental investigations. New intriguing experimental observations and further theoretical studies led to an extension of the reaction mechanism. The second section includes three cases of meta-selective C-H activation of aryl compounds. In the case of Cu-catalyzed selective meta-C-H activation of aniline, a new mechanism that involves a Cu(III)-Ar-mediated Heck-like transition state, in which the Ar group acts as an electrophile, was proposed. This mechanism predicted a higher reactivity for more electron-deficient Ar groups, which was supported by experiments. For two template-mediated, meta-selective C-H bond activations catalyzed by

  16. Coupled Lagrangian Monte Carlo PDF-CFD computation of gas turbine combustor flowfields with finite-rate chemistry

    SciTech Connect

    Tolpadi, A.K.; Hu, I.Z.; Correa, S.M.; Burrus, D.L.

    1997-07-01

    A coupled Lagrangian Monte Carlo Probability Density Function (PDF)-Eulerian Computational Fluid Dynamics (CFD) technique is presented for calculating steady three-dimensional turbulent reacting flow in a gas turbine combustor. PDF transport methods model turbulence-combustion interactions more accurately than conventional turbulence models with an assumed shape PDF. The PDF transport equation was solved using a Lagrangian particle tracking Monte Carlo (MC) method. The PDF modeled was over composition only. This MC module has been coupled with CONCERT, which is a fully elliptic three-dimensional body-fitted CFD code based on pressure correction techniques. In an earlier paper, this computational approach was described, but only fast chemistry calculations were presented in a typical aircraft engine combustor. In the present paper, reduced chemistry schemes were incorporated into the MC module that enabled the modeling of finite rate effects in gas turbine flames and therefore the prediction of CO and NO{sub x} emissions. With the inclusion of these finite rate effects, the gas temperatures obtained were also more realistic. Initially, a two scalar scheme was implemented that allowed validation against Raman data taken in a recirculation bluff body stabilized CO/H{sub 2}/N{sub 2}-air flame. Good agreement of the temperature and major species were obtained. Next, finite rate computations were performed in a single annular aircraft engine combustor by incorporating a simple three scalar reduced chemistry scheme for Jet A fuel. This three scalar scheme was an extension of the two scalar scheme for CO/H{sub 2}/N{sub 2} fuel. The solutions obtained using the present approach were compared with those obtained using the fast chemistry PDF transport approach as well as the presumed shape PDF method. The calculated exhaust gas temperature using the finite rate model showed the best agreement with measurements made by a thermocouple rake.

  17. Effects of Combined Hands-on Laboratory and Computer Modeling on Student Learning of Gas Laws: A Quasi-Experimental Study

    ERIC Educational Resources Information Center

    Liu, Xiufeng

    2006-01-01

    Based on current theories of chemistry learning, this study intends to test a hypothesis that computer modeling enhanced hands-on chemistry laboratories are more effective than hands-on laboratories or computer modeling laboratories alone in facilitating high school students' understanding of chemistry concepts. Thirty-three high school chemistry…

  18. Effects of Combined Hands-on Laboratory and Computer Modeling on Student Learning of Gas Laws: A Quasi-Experimental Study

    ERIC Educational Resources Information Center

    Liu, Xiufeng

    2006-01-01

    Based on current theories of chemistry learning, this study intends to test a hypothesis that computer modeling enhanced hands-on chemistry laboratories are more effective than hands-on laboratories or computer modeling laboratories alone in facilitating high school students' understanding of chemistry concepts. Thirty-three high school chemistry…

  19. Hybrid materials chemistry: Spectroscopic studies of molecular materials, nanoscale materials and their combinations

    NASA Astrophysics Data System (ADS)

    Marlatt, Craig W.

    Materials chemistry is a widely-used label within the overall field of chemistry, with a diverse range of possible applications. In this report, two classes of materials are discussed. Host-guest molecular systems that operate under supramolecular principles are examined via Raman spectroscopy and electrochemistry, and a sensing application for such systems is offered in the proof-of-principle detection of nitroaromatic explosives via host-guest binding. Next, metallic nanostructures that have tunable optical properties are synthesized and characterized to demonstrate that tunable nature, and the way such structures might be used for surface-enhanced Raman studies of the previously described host-guest systems is discussed by examining the current literature. Lastly, strategies to couple molecular systems and nanostructure systems are discussed and developed, and speculation on possible applications utilizing these coupled systems is made based on recent literature and the established themes of the research in this report.

  20. Combining Computational and Social Effort for Collaborative Problem Solving

    PubMed Central

    Wagy, Mark D.; Bongard, Josh C.

    2015-01-01

    Rather than replacing human labor, there is growing evidence that networked computers create opportunities for collaborations of people and algorithms to solve problems beyond either of them. In this study, we demonstrate the conditions under which such synergy can arise. We show that, for a design task, three elements are sufficient: humans apply intuitions to the problem, algorithms automatically determine and report back on the quality of designs, and humans observe and innovate on others’ designs to focus creative and computational effort on good designs. This study suggests how such collaborations should be composed for other domains, as well as how social and computational dynamics mutually influence one another during collaborative problem solving. PMID:26544199

  1. Computational Biology and Chemistry in MTi: Emphasis on the Prediction of Some ADMET Properties.

    PubMed

    Miteva, Maria A; Villoutreix, Bruno O

    2017-02-21

    Our research and teaching group called MTi (Molécules Thérapeutiques in silico) has developed numerous applications available online, thanks to the RPBS platform (Ressource Parisienne en Bioinformatique Structurale), in the field of chemoinformatics, structural bioinformatics and drug design. Since its opening in 2009, over 200 articles/reviews have been reported and involve virtual screening studies, prediction of druggability, analysis of protein-protein interaction inhibitors, development of databases, data mining and knowledge discovery, as well as combined in silico-in vitro work to search for new hits and chemical probes acting on original targets in several therapeutic areas. An international training program has also been developed pertaining to the field of in silico drug design. In this review, we present some tools developed in our laboratory with a special emphasis on the prediction of some ADMET properties, compound collection preparation and 3D-ADMET computations.

  2. Preparation of a tetrazolyl monolithic column via the combination of ATRP and click chemistry for the separation of proteins.

    PubMed

    Lei, Huan; Bai, Ligai; Zhang, Xiaoyan; Yang, Gengliang

    2014-01-01

    Tetrazolyl monolithic column is first prepared through the combination of atom transfer radical polymerization (ATRP) and "click chemistry" technique. In the ATRP fabrication process, vinyl ester resin is used as both the monomer and the cross-linking agent, and cetyl alcohol is used as the porogen, carbon tetrachloride as the initiator and ferrous chloride as the catalyst. The monolith is modified by click chemistry, which forms the tetrazolyl monolithic column. The chemical group of the prepared monolith is assayed by infrared spectroscopy, and its internal morphology is investigated by scanning electron microscopy. The pore size distribution is determined by a mercury porosimeter. What is more, the monolithic column was used as the stationary phase during high-performance liquid chromatography. Moreover, the monolith is used to separate lysozyme (Lys) from egg whites in a short time period (4 min). At the same time, the influences of buffer concentration and pH value on the elution of Lys are investigated. In addition, human serum albumin is successfully separated from human plasma by the prepared monoliths. The results show that click chemistry is an efficient method to modify the monoliths prepared by ATRP. © The Author [2014]. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Contention Bounds for Combinations of Computation Graphs and Network Topologies

    DTIC Science & Technology

    2014-08-08

    Google, Nokia , NVIDIA, Oracle, MathWorks and Samsung. Also funded by U.S. DOE Office of Science, Office of Advanced Scientific Computing Research...program sponsored by MARCO and DARPA, and ASPIRE Lab industrial sponsors and affiliates Intel, Google, Nokia , NVIDIA, Oracle, MathWorks and Samsung

  4. Designing a Scalable Fault Tolerance Model for High Performance Computational Chemistry: A Case Study with Coupled Cluster Perturbative Triples.

    PubMed

    van Dam, Hubertus J J; Vishnu, Abhinav; de Jong, Wibe A

    2011-01-11

    In the past couple of decades, the massive computational power provided by the most modern supercomputers has resulted in simulation of higher-order computational chemistry methods, previously considered intractable. As the system sizes continue to increase, the computational chemistry domain continues to escalate this trend using parallel computing with programming models such as Message Passing Interface (MPI) and Partitioned Global Address Space (PGAS) programming models such as Global Arrays. The ever increasing scale of these supercomputers comes at a cost of reduced Mean Time Between Failures (MTBF), currently on the order of days and projected to be on the order of hours for upcoming extreme scale systems. While traditional disk-based check pointing methods are ubiquitous for storing intermediate solutions, they suffer from high overhead of writing and recovering from checkpoints. In practice, checkpointing itself often brings the system down. Clearly, methods beyond checkpointing are imperative to handling the aggravating issue of reducing MTBF. In this paper, we address this challenge by designing and implementing an efficient fault tolerant version of the Coupled Cluster (CC) method with NWChem, using in-memory data redundancy. We present the challenges associated with our design, including an efficient data storage model, maintenance of at least one consistent data copy, and the recovery process. Our performance evaluation without faults shows that the current design exhibits a small overhead. In the presence of a simulated fault, the proposed design incurs negligible overhead in comparison to the state of the art implementation without faults.

  5. Development of antibacterial conjugates using sulfamethoxazole with monocyclic terpenes: A systematic medicinal chemistry based computational approach.

    PubMed

    Swain, Shasank S; Paidesetty, Sudhir K; Padhy, Rabindra N

    2017-03-01

    To develop 6 conjugate agents of the moribund antibiotic sulfamethoxazole (SMZ) joined to 6 individual monoterpenes, followed by protocols of medicinal chemistry as potent antibacterials, against multidrug resistant (MDR) human gruesome pathogenic bacteria. Antibacterial activities of the proposed conjugates were ascertained by the 'prediction of activity spectra of substances' (PASS) program. Drug-likeness parameters and toxicity profiles of conjugates were standardized with the Lipinski rule of five, using cheminformatic tools, Molsoft, molinspiration, OSIRIS and ProTox. Antibacterial activities of individual chemicals and conjugates were examined by targeting the bacterial folic acid biosynthesis enzyme, dihydropteroate synthases (DHPSs) of bacteria, Bacillus anthracis, Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae and Mycobacterium tuberculosis, with 3D structures of DHPSs from protein data bank. According to the PASS program, biological spectral values of conjugate-2, conjugate-5 and conjugate-6 were ascertained effective with 'probably active' or 'Pa' value > 0.5, for anti-infective and antituberculosic activities. Using molecular docking against 5 cited bacterial DHPSs, effective docking scores of 6 monoterpenes in the specified decreasing order (kcal/mol): -9.72 (eugenol against B. anthracis), -9.61 (eugenol against S. pneumoniae), -9. 42 (safrol, against B. anthracis), -9.39 (thymol, against M. tuberculosis), -9.34 (myristicin, against S. pneumoniae) and -9.29 (thymol, against B. anthracis); whereas the lowest docking score of SMZ was -8.46kcal/mol against S. aureus DHPS. Similarly, effective docking scores of conjugates were as specified (kcal/mol.): -10.80 (conjugate-4 consisting SMZ+safrol, against M. tuberculosis), -10.78 (conjugate-5 consisting SMZ+thymol, against M. tuberculosis), -10.60 (conjugate-5 against B. anthracis), -10.26 (conjugate-2 consisting SMZ+ eugenol, against M. tuberculosis), -10.25 (conjugate-5, against S

  6. Cathepsin B Inhibitors: Combining Dipeptide Nitriles with an Occluding Loop Recognition Element by Click Chemistry

    PubMed Central

    2015-01-01

    An active site mapping of human cathepsin B with dipeptide nitrile inhibitors was performed for a combinatorial approach by introducing several points of diversity and stepwise optimizing the inhibitor structure. To address the occluding loop of cathepsin B by a carboxylate moiety, click chemistry to generate linker-connected molecules was applied. Inhibitor 17 exhibited Ki values of 41.3 nM, 27.3 nM, or 19.2 nM, depending on the substrate and pH of the assay. Kinetic data were discussed with respect to the conformational selection and induced fit models. PMID:26985300

  7. Critical Evaluation of Thermodynamic Properties for Halobenzoic Acids Through Consistency Analyses for Results from Experiment and Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Chirico, Robert D.; Kazakov, Andrei; Bazyleva, Ala; Diky, Vladimir; Kroenlein, Kenneth; Emel′yanenko, Vladimir N.; Verevkin, Sergey P.

    2017-06-01

    Thermodynamic properties of the twelve monohalobenzoic acids are critically evaluated through the application of computational chemistry methods for the ideal-gas phase and thermodynamic consistency assessment of properties determined experimentally and reported in the literature, including enthalpies of combustion, enthalpies of sublimation, and enthalpies of fusion. The compounds of interest are the 2-, 3-, and 4-halo isomers of fluoro-, chloro-, bromo-, and iodobenzoic acids. Computations were validated by comparison with critically evaluated entropies and heat capacities in the ideal-gas state for benzoic acid, benzene, and some halobenzenes. Experimental enthalpies of formation for 2- and 3-bromobenzoic acids, measured by well-established research groups, are mutually inconsistent and further, are shown to be inconsistent with the computations and assessment in this work. Origins of the discrepancies are unknown, and recommended values for these compounds are based on computations and enthalpies of sublimation validated, in part, by a structure-property (i.e., group-additivity) analysis. Lesser, but significant, inconsistencies between experimental and computed results are demonstrated also for 3- and 4-iodobenzoic acids. The comparison of enthalpies of formation based on the experiment and computation for the ideal-gas state of 1- and 2-chloro-, bromo-, and iodonaphthalenes provides additional support for the findings for halobenzoic acids and also reveals some anomalous results in the experimental literature for chloronaphthalenes. Computations are discussed in detail to demonstrate the approach required to obtain optimal results with modern quantum chemical methods.

  8. Computer-Based Sentence-Combining Instruction. Final Report.

    ERIC Educational Resources Information Center

    Southwest Regional Laboratory for Educational Research and Development, Los Alamitos, CA.

    As part of a larger investigation into the use of microcomputers in composition instruction, this report focuses on one instructional technique--sentence combining. Consisting of four parts, the report first provides the courseware and operating manual developed from the project. The second part includes specifications for instruction and content.…

  9. Computer-Based Sentence-Combining Instruction. Final Report.

    ERIC Educational Resources Information Center

    Southwest Regional Laboratory for Educational Research and Development, Los Alamitos, CA.

    As part of a larger investigation into the use of microcomputers in composition instruction, this report focuses on one instructional technique--sentence combining. Consisting of four parts, the report first provides the courseware and operating manual developed from the project. The second part includes specifications for instruction and content.…

  10. A Titanium–Organic Framework as an Exemplar of Combining the Chemistry of Metal– and Covalent–Organic Frameworks

    SciTech Connect

    Nguyen, Ha L.; Gándara, Felipe; Furukawa, Hiroyasu; Doan, Tan L. H.; Cordova, Kyle E.; Yaghi, Omar M.

    2016-04-06

    A crystalline material with a two-dimensional structure, termed metal–organic framework-901 (MOF-901), was prepared using a strategy that combines the chemistry of MOFs and covalent–organic frameworks (COFs). This strategy involves in situ generation of an amine-functionalized titanium oxo cluster, Ti6O6(OCH3)6(AB)6 (AB = 4-aminobenzoate), which was linked with benzene-1,4-dialdehyde using imine condensation reactions, typical of COFs. The crystal structure of MOF-901 is composed of hexagonal porous layers that are likely stacked in staggered conformation (hxl topology). This MOF represents the first example of combining metal cluster chemistry with dynamic organic covalent bond formation to give a new crystalline, extended framework of titanium metal, which is rarely used in MOFs. The incorporation of Ti(IV) units made MOF-901 useful in the photocatalyzed polymerization of methyl methacrylate (MMA). The resulting polyMMA product was obtained with a high-number-average molar mass (26 850 g mol–1) and low polydispersity index (1.6), which in many respects are better than those achieved by the commercially available photocatalyst (P-25 TiO2). Additionally, the catalyst can be isolated, reused, and recycled with no loss in performance.

  11. Zwitterionic polymer functionalization of polysulfone membrane with improved antifouling property and blood compatibility by combination of ATRP and click chemistry.

    PubMed

    Xiang, Tao; Lu, Ting; Xie, Yi; Zhao, Wei-Feng; Sun, Shu-Dong; Zhao, Chang-Sheng

    2016-08-01

    The chemical compositions are very important for designing blood-contacting membranes with good antifouling property and blood compatibility. In this study, we propose a method combining ATRP and click chemistry to introduce zwitterionic polymer of poly(sulfobetaine methacrylate) (PSBMA), negatively charged polymers of poly(sodium methacrylate) (PNaMAA) and/or poly(sodium p-styrene sulfonate) (PNaSS), to improve the antifouling property and blood compatibility of polysulfone (PSf) membranes. Attenuated total reflectance-Fourier transform infrared spectra, X-ray photoelectron spectroscopy and water contact angle results confirmed the successful grafting of the functional polymers. The antifouling property and blood compatibility of the modified membranes were systematically investigated. The zwitterionic polymer (PSBMA) grafted membranes showed good resistance to protein adsorption and bacterial adhesion; the negatively charged polymer (PNaSS or PNaMAA) grafted membranes showed improved blood compatibility, especially the anticoagulant property. Moreover, the PSBMA/PNaMAA modified membrane showed both antifouling property and anticoagulant property, and exhibited a synergistic effect in inhibiting blood coagulation. The functionalization of membrane surfaces by a combination of ATRP and click chemistry is demonstrated as an effective route to improve the antifouling property and blood compatibility of membranes in blood-contact. Copyright © 2016 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

  12. A Titanium-Organic Framework as an Exemplar of Combining the Chemistry of Metal- and Covalent-Organic Frameworks.

    PubMed

    Nguyen, Ha L; Gándara, Felipe; Furukawa, Hiroyasu; Doan, Tan L H; Cordova, Kyle E; Yaghi, Omar M

    2016-04-06

    A crystalline material with a two-dimensional structure, termed metal-organic framework-901 (MOF-901), was prepared using a strategy that combines the chemistry of MOFs and covalent-organic frameworks (COFs). This strategy involves in situ generation of an amine-functionalized titanium oxo cluster, Ti6O6(OCH3)6(AB)6 (AB = 4-aminobenzoate), which was linked with benzene-1,4-dialdehyde using imine condensation reactions, typical of COFs. The crystal structure of MOF-901 is composed of hexagonal porous layers that are likely stacked in staggered conformation (hxl topology). This MOF represents the first example of combining metal cluster chemistry with dynamic organic covalent bond formation to give a new crystalline, extended framework of titanium metal, which is rarely used in MOFs. The incorporation of Ti(IV) units made MOF-901 useful in the photocatalyzed polymerization of methyl methacrylate (MMA). The resulting polyMMA product was obtained with a high-number-average molar mass (26 850 g mol(-1)) and low polydispersity index (1.6), which in many respects are better than those achieved by the commercially available photocatalyst (P-25 TiO2). Additionally, the catalyst can be isolated, reused, and recycled with no loss in performance.

  13. 2D-RNA-coupling numbers: a new computational chemistry approach to link secondary structure topology with biological function.

    PubMed

    González-Díaz, Humberto; Agüero-Chapin, Guillermín; Varona, Javier; Molina, Reinaldo; Delogu, Giovanna; Santana, Lourdes; Uriarte, Eugenio; Podda, Gianni

    2007-04-30

    Methods for prediction of proteins, DNA, or RNA function and mapping it onto sequence often rely on bioinformatics alignment approach instead of chemical structure. Consequently, it is interesting to develop computational chemistry approaches based on molecular descriptors. In this sense, many researchers used sequence-coupling numbers and our group extended them to 2D proteins representations. However, no coupling numbers have been reported for 2D-RNA topology graphs, which are highly branched and contain useful information. Here, we use a computational chemistry scheme: (a) transforming sequences into RNA secondary structures, (b) defining and calculating new 2D-RNA-coupling numbers, (c) seek a structure-function model, and (d) map biological function onto the folded RNA. We studied as example 1-aminocyclopropane-1-carboxylic acid (ACC) oxidases known as ACO, which control fruit ripening having importance for biotechnology industry. First, we calculated tau(k)(2D-RNA) values to a set of 90-folded RNAs, including 28 transcripts of ACO and control sequences. Afterwards, we compared the classification performance of 10 different classifiers implemented in the software WEKA. In particular, the logistic equation ACO = 23.8 . tau(1)(2D-RNA) + 41.4 predicts ACOs with 98.9%, 98.0%, and 97.8% of accuracy in training, leave-one-out and 10-fold cross-validation, respectively. Afterwards, with this equation we predict ACO function to a sequence isolated in this work from Coffea arabica (GenBank accession DQ218452). The tau(1)(2D-RNA) also favorably compare with other descriptors. This equation allows us to map the codification of ACO activity on different mRNA topology features. The present computational-chemistry approach is general and could be extended to connect RNA secondary structure topology to other functions.

  14. A Computer-Interfaced O2 Probe: Instrumentation for Undergraduate Chemistry Laboratories.

    ERIC Educational Resources Information Center

    Adamson, Gary E.; Nakhleh, Mary B.; Zimmerman, James R.

    1997-01-01

    Describes interfacing a hand-held oxygen probe with a microcomputer and suggests experiments for undergraduate chemistry courses that could facilitate student understanding of aquatic environmental processes which involve dissolved oxygen. Data can be analyzed through the program or exported into other software. Presents results of an experiment…

  15. A Computer-Interfaced O2 Probe: Instrumentation for Undergraduate Chemistry Laboratories.

    ERIC Educational Resources Information Center

    Adamson, Gary E.; Nakhleh, Mary B.; Zimmerman, James R.

    1997-01-01

    Describes interfacing a hand-held oxygen probe with a microcomputer and suggests experiments for undergraduate chemistry courses that could facilitate student understanding of aquatic environmental processes which involve dissolved oxygen. Data can be analyzed through the program or exported into other software. Presents results of an experiment…

  16. A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene.

    PubMed

    Jaraíz, Martín; Enríquez, Lourdes; Pinacho, Ruth; Rubio, José E; Lesarri, Alberto; López-Pérez, José L

    2017-04-07

    A novel DFT-based Reaction Kinetics (DFT-RK) simulation approach, employed in combination with real-time data from reaction monitoring instrumentation (like UV-vis, FTIR, Raman, and 2D NMR benchtop spectrometers), is shown to provide a detailed methodology for the analysis and design of complex synthetic chemistry schemes. As an example, it is applied to the opening of epoxides by titanocene in THF, a catalytic system with abundant experimental data available. Through a DFT-RK analysis of real-time IR data, we have developed a comprehensive mechanistic model that opens new perspectives to understand previous experiments. Although derived specifically from the opening of epoxides, the prediction capabilities of the model, built on elementary reactions, together with its practical side (reaction kinetics simulations of real experimental conditions) make it a useful simulation tool for the design of new experiments, as well as for the conception and development of improved versions of the reagents. From the perspective of the methodology employed, because both the computational (DFT-RK) and the experimental (spectroscopic data) components can follow the time evolution of several species simultaneously, it is expected to provide a helpful tool for the study of complex systems in synthetic chemistry.

  17. Anethole-Water a Combined Jet, Matrix, and Computational Study

    NASA Astrophysics Data System (ADS)

    Newby, Josh; Nesheiwat, Jackleen

    2016-06-01

    Anethole [(E)-1-methoxy-4-(1-propenyl)benzene] is a natural product molecule that is commonly recognized as the flavor component of anise, fennel, and licorice. Previously, we reported the jet-cooled, laser-induced fluorescence (LIF) and single vibronic level fluorescence (SVLF) spectra of anethole. In this work, several weak bands were observed and were tentatively assigned as van der Waals clusters of anethole with water. We have since confirmed this assignment and have conducted a more detailed study to determine the geometry of these clusters. Results from LIF, SVLF, and matrix isolation FTIR spectroscopy, as well as computational results will be presented in this talk. J. Phys. Chem. A, 2013, 117 (48), 12831-12841 Newly built system at Hobart and William Smith Colleges

  18. Combining Grid, SOA and Web Services for Smaller Computing Environments

    NASA Astrophysics Data System (ADS)

    Koschel, Arne; Kleiner, Carsten

    This paper describes practical experiences from a project to couple Grid and SOA technologies in smaller environments. Web services have been applied in two structurally different case studies to solve tasks with a Grid that is integrated into a SOA and vice versa. The case studies have revealed important insight on how and when to couple SOA and Grid technologies including monitoring aspects. Some interesting general rules are derived on what has to be observed when combining SOA and Grid in smaller environments. Performance and software technical analysis have been used in validating the results. They also clearly showed the benefits gained by employing SOA and Grid concepts form both a performance as well as an architectural perspective.

  19. Reveal protein dynamics by combining computer simulation and neutron scattering

    NASA Astrophysics Data System (ADS)

    Hong, Liang; Smith, Jeremy; CenterMolecular Biophysics Team

    2014-03-01

    Protein carries out most functions in living things on the earth through characteristic modulation of its three-dimensional structure over time. Understanding the microscopic nature of the protein internal motion and its connection to the function and structure of the biomolecule is a central topic in biophysics, and of great practical importance for drug design, study of diseases, and the development of renewable energy, etc. Under physiological conditions, protein exhibits a complex dynamics landscape, i.e., a variety of diffusive and conformational motions occur on similar time and length scales. This variety renders difficult the derivation of a simplified description of protein internal motions in terms of a small number of distinct, additive components. This difficulty is overcome by our work using a combined approach of Molecular Dynamics (MD) simulations and the Neutron Scattering experiments. Our approach enables distinct protein motions to be characterized separately, furnishing an in-depth understanding of the connection between protein structure, dynamics and function.

  20. A Summary Report of the Results of an Advertisement Placed in the "Journal of Chemical Education" Offering a Free Demonstration of Computer-Based Education in Chemistry.

    ERIC Educational Resources Information Center

    Texas Univ., Austin. Project C-BE.

    Project C-BE and CONDUIT had overlapping research objectives concerning the transferability of computer-related curriculum materials. In this regard, the projects co-sponsored an advertisement placed in the Journal of Chemical Education offering a "Free Demonstration of Computer Based Education in Chemistry." Forty packets were mailed.…

  1. Integration of Computational and Preparative Techniques to Demonstrate Physical Organic Concepts in Synthetic Organic Chemistry: An Example Using Diels-Alder Reaction

    ERIC Educational Resources Information Center

    Palmer, David R. J.

    2004-01-01

    The Diels-Alder reaction is used as an example for showing the integration of computational and preparative techniques, which help in demonstrating the physical organic concepts in synthetic organic chemistry. These experiments show that the students should not accept the computational results without questioning them and in many Diels-Alder…

  2. Integration of Computational and Preparative Techniques to Demonstrate Physical Organic Concepts in Synthetic Organic Chemistry: An Example Using Diels-Alder Reaction

    ERIC Educational Resources Information Center

    Palmer, David R. J.

    2004-01-01

    The Diels-Alder reaction is used as an example for showing the integration of computational and preparative techniques, which help in demonstrating the physical organic concepts in synthetic organic chemistry. These experiments show that the students should not accept the computational results without questioning them and in many Diels-Alder…

  3. Effectiveness of Computer-Based Chemistry Instruction in Enhancing the Learning of Content and Variable Control Under Guided versus Unguided Conditions.

    ERIC Educational Resources Information Center

    Ardac, Dilek; Sezen, Ali Hasan

    2002-01-01

    Examines the relative effectiveness of guided versus unguided computer-based instruction with regard to regular instruction in improving content knowledge and process skills among students with low and high chemistry achievement levels. The effectiveness of computer-based instruction increases when learning is supported by teacher-directed…

  4. Structural isomerization of the gas-phase 2-norbornyl cation revealed with infrared spectroscopy and computational chemistry.

    PubMed

    Mosley, Jonathan D; Young, Justin W; Agarwal, Jay; Schaefer, Henry F; Schleyer, Paul v R; Duncan, Michael A

    2014-06-02

    In an attempt to produce the 2-norbornyl cation (2NB(+)) in the gas phase, protonation of norbornene was accomplished in a pulsed discharge ion source coupled with a supersonic molecular beam. The C7H11(+) cation was size-selected in a time-of-flight mass spectrometer and investigated with infrared laser photodissociation spectroscopy using the method of "tagging" with argon. The resulting vibrational spectrum, containing sharp bands in the C-H stretching and fingerprint regions, was compared to that predicted by computational chemistry. However, the measured spectrum did not match that of 2NB(+), prompting a detailed computational study of other possible isomers of C7H11(+). This study finds five isomers more stable than 2NB(+). The spectrum obtained corresponds to the 1,3-dimethylcyclopentenyl cation, the global minimum-energy structure for C7H11(+), which is produced through an unanticipated ring-opening rearrangement path.

  5. Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data

    PubMed Central

    Salvadori, Andrea; Del Frate, Gianluca; Pagliai, Marco; Barone, Vincenzo

    2016-01-01

    Abstract The role of Virtual Reality (VR) tools in molecular sciences is analyzed in this contribution through the presentation of the Caffeine software to the quantum chemistry community. Caffeine, developed at Scuola Normale Superiore, is specifically tailored for molecular representation and data visualization with VR systems, such as VR theaters and helmets. Usefulness and advantages that can be gained by exploiting VR are here reported, considering few examples specifically selected to illustrate different level of theory and molecular representation. PMID:27867214

  6. A novel UV degradation product of Ebastine: isolation and characterization using Q-TOF, NMR, IR and computational chemistry.

    PubMed

    Rapolu, Ravi; Pandey, Avadhesh Kumar; Raju, Ch Krishnam; Ghosh, Kaushik; Srinivas, Kolupula; Awasthi, Atul; Navalgund, Sameer G; Surendranath, Koduru V

    2015-03-25

    Forced degradation of Ebastine (1-(4-(1,1-dimethylethyl)phenyl)-4-(4-(diphenylmethoxy) piperidin-1-yl)butan-1-one) drug substance in ultraviolet light condition resulted into an unknown significant degradation product. This degradation product was analyzed using a newly developed reverse-phase HPLC, where it was eluted at 2.73 relative retention time to Ebastine peak. UV degradation product was isolated from reaction mass using preparative HPLC and its structure was elucidated using high resolution MS, multidimensional NMR and FTIR spectroscopic techniques. UV degradation product has been characterized as 2-(4-(benzhydryloxy)piperidin-1-yl)-1-(4-(tert-butyl)phenyl)-2-methylcyclopropanol. (1)H and (13)C NMR chemical shift values were generated using computational chemistry for possible two diastereomers (7R10S and 7R10R) and later 7R10R was confirmed (and its enantiomer) as final structure given it showed close agreement with experimental NMR data. Formation of UV degradation product as a recemic mixture was further verified by computational chemistry evaluation, chiral HPLC and polarimetery. To best of our knowledge, this is a novel degradation product which is not discussed at any form of publication yet.

  7. Conformer Hunting: An Open-Ended Computational Chemistry Exercise That Expresses Real-World Complexity and Student Forethought

    NASA Astrophysics Data System (ADS)

    Lipkowitz, Kenny B.; Robertson, Daniel

    2000-02-01

    A computational chemistry project suitable for both graduate and undergraduate classes has been developed, tested, and implemented successfully over the course of 10 years. In this project we ask students the following simple question: "Which conformer searching strategy in Spartan is the best?" To answer this question the students need to develop a working definition of what "best" means within the context of the project, design their own experiments that can address that question most suitably, carry out the calculations to derive a compelling answer, and then write their results in the form of a research paper. In addition to teaching students about potential energy surfaces, molecular modeling techniques, and stereochemistry, the pedagogical advantages of this computational chemistry exercise compared to others published in this Journal are that it (i) requires a significant amount of student forethought in addition to afterthought by forcing students to design their own experiments, (ii) demonstrates real-world levels of complexity by using molecules having multiple rotatable bonds, (iii) allows for student creativity that is missing in most other published exercises, (iv) focuses on writing in the curriculum.

  8. Comprehensive mapping of protein N-glycosylation in human liver by combining hydrophilic interaction chromatography and hydrazide chemistry.

    PubMed

    Zhu, Jun; Sun, Zhen; Cheng, Kai; Chen, Rui; Ye, Mingliang; Xu, Bo; Sun, Deguang; Wang, Liming; Liu, Jing; Wang, Fangjun; Zou, Hanfa

    2014-03-07

    Although glycoproteomics is greatly developed in recent years, our knowledge about N-glycoproteome of human tissues is still very limited. In this study, we comprehensively mapped the N-glycosylation sites of human liver by combining click maltose-hydrophilic interaction chromatography (HILIC) and the improved hydrazide chemistry. The specificity could be as high as 90% for hydrazide chemistry and 80% for HILIC. Altogether, we identified 14,480 N-glycopeptides matched with N-!P-[S|T|C] sequence motif from human liver, corresponding to 2210 N-glycoproteins and 4783 N-glycosylation sites. These N-glycoproteins are widely involved into different types of biological processes, such as hepatic stellate cell activation and acute phase response of human liver, which all highly associate with the progression of liver diseases. Moreover, the exact N-glycosylation sites of some key-regulating proteins within different human liver physiological processes were also obtained, such as E-cadherin, transforming growth factor beta receptor and 29 members of G protein coupled receptors family.

  9. Computing the carbonate chemistry of the coral calcifying medium and its response to ocean acidification.

    PubMed

    Raybaud, Virginie; Tambutté, Sylvie; Ferrier-Pagès, Christine; Reynaud, Stéphanie; Venn, Alexander A; Tambutté, Éric; Nival, Paul; Allemand, Denis

    2017-07-07

    Critical to determining vulnerability or resilience of reef corals to Ocean Acidification (OA) is a clearer understanding of the extent to which corals can control carbonate chemistry in their Extracellular Calcifying Medium (ECM) where the CaCO3 skeleton is produced. Here, we employ a mathematical framework to calculate ECM aragonite saturation state (Ωarag.(ECM)) and carbonate system ion concentration using measurements of calcification rate, seawater characteristics (temperature, salinity and pH) and ECM pH (pH(ECM)). Our calculations of ECM carbonate chemistry at current-day seawater pH, indicate that Ωarag.(ECM) ranges from ∼10 to 38 (mean 20.41), i.e. about 5 to 6-fold higher than seawater. Accordingly, Dissolved Inorganic Carbon (DIC) and Total Alkalinity (TA) were calculated to be around 3 times higher in the ECM than in seawater. We also assessed the effects of acidification on ECM chemical properties of the coral Stylophora pistillata. At reduced seawater pH our calculations indicate that Ωarag.(ECM) remains almost constant. DIC(ECM) and TA(ECM) gradually increase as seawater pH declines, reaching values about 5 to 6-fold higher than in seawater, respectively for DIC and TA. We propose that these ECM characteristics buffer the effect of acidification and explain why certain corals continue to produce CaCO3 even when seawater chemistry is less favourable. Copyright © 2017 Elsevier Ltd. All rights reserved.

  10. Online Chemistry Modules: Interaction and Effective Faculty Facilitation

    ERIC Educational Resources Information Center

    Slocum, Laura E.; Towns Marcy Hamby; Zielinski, Theresa Julia

    2004-01-01

    Computer supported collaborative learning, cooperative learning combined with electronic communication, physical chemistry online modules, use of discussion boards, its advantages and limitations are experimented and discussed. The most important finding is the example of effective online faculty facilitation and interaction.

  11. Making the Earth: Combining dynamics and chemistry in the Solar System

    NASA Astrophysics Data System (ADS)

    Bond, Jade C.; Lauretta, Dante S.; O'Brien, David P.

    2010-02-01

    No terrestrial planet formation simulation completed to date has considered the detailed chemical composition of the planets produced. While many have considered possible water contents and late veneer compositions, none have examined the bulk elemental abundances of the planets produced as an important check of formation models. Here we report on the first study of this type. Bulk elemental abundances based on disk equilibrium studies have been determined for the simulated terrestrial planets of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58]. These abundances are in excellent agreement with observed planetary values, indicating that the models of O'Brien et al. [O'Brien, D.P., Morbidelli, A., Levison, H.F., 2006. Icarus 184, 39-58] are successfully producing planets comparable to those of the Solar System in terms of both their dynamical and chemical properties. Significant amounts of water are accreted in the present simulations, implying that the terrestrial planets form "wet" and do not need significant water delivery from other sources. Under the assumption of equilibrium controlled chemistry, the biogenic species N and C still need to be delivered to the Earth as they are not accreted in significant proportions during the formation process. Negligible solar photospheric pollution is produced by the planetary formation process. Assuming similar levels of pollution in other planetary systems, this in turn implies that the high metallicity trend observed in extrasolar planetary systems is in fact primordial.

  12. Combined surface micropatterning and reactive chemistry maximizes tissue adhesion with minimal inflammation

    PubMed Central

    Pereira, Maria J. N.; Sundback, Cathryn A.; Lang, Nora; Cho, Woo Kyung; Pomerantseva, Irina; Ouyang, Ben; Tao, Sarah L.; McHugh, Kevin; Mwizerwa, Olive; Vemula, Praveen K.; Mochel, Mark C.; Carter, David J.; Borenstein, Jeffrey T.; Langer, Robert; Ferreira, Lino S.; Karp, Jeffrey M.; Masiakos, Peter T.

    2014-01-01

    The use of tissue adhesives for internal clinical applications is limited due to a lack of materials that balance strong adhesion with biocompatibility. The use of substrate topography was explored to reduce the volume of a highly reactive and toxic glue without compromising adhesive strength. Micro-textured patches coated with a thin layer of cyanoacrylate glue achieved similar adhesion levels to patches employing large amounts of adhesive, and was superior to the level of adhesion achieved when a thin coating was applied to a non-textured patch. In vivo studies demonstrated reduced tissue inflammation and necrosis for patterned patches with a thinly coated layer of reactive glue, thus overcoming a significant challenge with existing tissue adhesives such as cyanoacrylate. Closure of surgical stomach and colon defects in a rat model was achieved without abdominal adhesions. Harnessing the synergy between surface topography and reactive chemistry enables controlled tissue adhesion with an improved biocompatibility profile without requiring changes in the chemical composition of reactive tissue glues. PMID:24106240

  13. Quantifying enzymatic lysis: estimating the combined effects of chemistry, physiology and physics

    NASA Astrophysics Data System (ADS)

    Mitchell, Gabriel J.; Nelson, Daniel C.; Weitz, Joshua S.

    2010-12-01

    The number of microbial pathogens resistant to antibiotics continues to increase even as the rate of discovery and approval of new antibiotic therapeutics steadily decreases. Many researchers have begun to investigate the therapeutic potential of naturally occurring lytic enzymes as an alternative to traditional antibiotics. However, direct characterization of lytic enzymes using techniques based on synthetic substrates is often difficult because lytic enzymes bind to the complex superstructure of intact cell walls. Here we present a new standard for the analysis of lytic enzymes based on turbidity assays which allow us to probe the dynamics of lysis without preparing a synthetic substrate. The challenge in the analysis of these assays is to infer the microscopic details of lysis from macroscopic turbidity data. We propose a model of enzymatic lysis that integrates the chemistry responsible for bond cleavage with the physical mechanisms leading to cell wall failure. We then present a solution to an inverse problem in which we estimate reaction rate constants and the heterogeneous susceptibility to lysis among target cells. We validate our model given simulated and experimental turbidity assays. The ability to estimate reaction rate constants for lytic enzymes will facilitate their biochemical characterization and development as antimicrobial therapeutics.

  14. Cheminformatics and Computational Chemistry: A Powerful Combination for the Encoding of Process Science

    EPA Science Inventory

    The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural...

  15. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose

    USDA-ARS?s Scientific Manuscript database

    The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially the molecular shape is inferred from the crystal structures of m...

  16. Cheminformatics and Computational Chemistry: A Powerful Combination for the Encoding of Process Science

    EPA Science Inventory

    The registration of new chemicals under the Toxicological Substances Control Act (TSCA) and new pesticides under the Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) requires knowledge of the process science underlying the transformation of organic chemicals in natural...

  17. Providing nearest neighbor point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer

    DOEpatents

    Archer, Charles J.; Faraj, Ahmad A.; Inglett, Todd A.; Ratterman, Joseph D.

    2012-10-23

    Methods, apparatus, and products are disclosed for providing nearest neighbor point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer, each compute node connected to each adjacent compute node in the global combining network through a link, that include: identifying each link in the global combining network for each compute node of the operational group; designating one of a plurality of point-to-point class routing identifiers for each link such that no compute node in the operational group is connected to two adjacent compute nodes in the operational group with links designated for the same class routing identifiers; and configuring each compute node of the operational group for point-to-point communications with each adjacent compute node in the global combining network through the link between that compute node and that adjacent compute node using that link's designated class routing identifier.

  18. Elucidating graphene - Ionic Liquid interfacial region: a combined experimental and computational study

    SciTech Connect

    Vijayakumar, M.; Schwenzer, Birgit; Shutthanandan, V.; Hu, Jian Z.; Liu, Jun; Aksay, Ilhan A.

    2014-01-10

    The interfacial region between graphene and an imidazolium based ionic liquid is studied using spectroscopic analysis and computational modelling. This combined approach reveals that the molecular level structure of the interfacial region is significantly influenced by functional group defects on the graphene surface.The combined experimental and computational study reveals that the molecular structure at interfacial region between graphene and imidazolium based ionic liquid is defined by the hydroxyl functional groups on the graphene surface

  19. Porous solids arising from synergistic and competing modes of assembly: combining coordination chemistry and covalent bond formation.

    PubMed

    Dutta, Ananya; Koh, Kyoungmoo; Wong-Foy, Antek G; Matzger, Adam J

    2015-03-23

    Design and synthesis of porous solids employing both reversible coordination chemistry and reversible covalent bond formation is described. The combination of two different linkage modes in a single material presents a link between two distinct classes of porous materials as exemplified by metal-organic frameworks (MOFs) and covalent organic frameworks (COFs). This strategy, in addition to being a compelling material-discovery method, also offers a platform for developing a fundamental understanding of the factors influencing the competing modes of assembly. We also demonstrate that even temporary formation of reversible connections between components may be leveraged to make new phases thus offering design routes to polymorphic frameworks. Moreover, this approach has the striking potential of providing a rich landscape of structurally complex materials from commercially available or readily accessible feedstocks.

  20. Synthesis of highly modified DNA by a combination of PCR with alkyne-bearing triphosphates and click chemistry.

    PubMed

    Gierlich, Johannes; Gutsmiedl, Katrin; Gramlich, Philipp M E; Schmidt, Alexandra; Burley, Glenn A; Carell, Thomas

    2007-01-01

    We report the combination of "click chemistry" with PCR by using alkyne-modified triphosphates for efficient and homogeneous labeling of DNA. A series of modified PCR products of different lengths (300, 900, and 2000 base pairs) were prepared by using a variety of alkyne- and azide-containing triphosphates and different polymerases. After intensive screening of real-time PCR methods, protocols were developed that allow the amplification of genes by using these modified triphosphates with similar efficiency to that of standard PCR. The click reaction on the highly modified PCR fragments provided conversion rates above 90 % and resulted in the functionalization of hundreds of alkynes on large DNA fragments with superb selectivity and efficiency.

  1. Connecting the virtual world of computers to the real world of medicinal chemistry.

    PubMed

    Glen, Robert C

    2011-03-01

    Drug discovery involves the simultaneous optimization of chemical and biological properties, usually in a single small molecule, which modulates one of nature's most complex systems: the balance between human health and disease. The increased use of computer-aided methods is having a significant impact on all aspects of the drug-discovery and development process and with improved methods and ever faster computers, computer-aided molecular design will be ever more central to the discovery process.

  2. Assessment of turbulence-chemistry interaction models in the computation of turbulent non-premixed flames

    NASA Astrophysics Data System (ADS)

    Lewandowski, M. T.; Pozorski, J.

    2016-10-01

    The present work reports on the assessment of different turbulence-chemistry interaction closures for the modelling of turbulent non-premixed combustion. Two-dimensional axisymmetric simulations have been carried out based on three different laboratory flames. The methane fueled, piloted jet flame Sandia D, the simple jet syngas flame and the so-called Delft Jet-in-Hot Coflow flame are studied. All the flames can be characterised as non-premixed but differ by some features which are taken into account through appropriate modelling approach.

  3. A diagonal implicit scheme for computing flows with finite-rate chemistry

    NASA Technical Reports Server (NTRS)

    Eberhardt, Scott; Imlay, Scott

    1990-01-01

    A new algorithm for solving steady, finite-rate chemistry, flow problems is presented. The new scheme eliminates the expense of inverting large block matrices that arise when species conservation equations are introduced. The source Jacobian matrix is replaced by a diagonal matrix which is tailored to account for the fastest reactions in the chemical system. A point-implicit procedure is discussed and then the algorithm is included into the LU-SGS scheme. Solutions are presented for hypervelocity reentry and Hydrogen-Oxygen combustion. For the LU-SGS scheme a CFL number in excess of 10,000 has been achieved.

  4. A Systematic Approach for Understanding Slater-Gaussian Functions in Computational Chemistry

    ERIC Educational Resources Information Center

    Stewart, Brianna; Hylton, Derrick J.; Ravi, Natarajan

    2013-01-01

    A systematic way to understand the intricacies of quantum mechanical computations done by a software package known as "Gaussian" is undertaken via an undergraduate research project. These computations involve the evaluation of key parameters in a fitting procedure to express a Slater-type orbital (STO) function in terms of the linear…

  5. A Systematic Approach for Understanding Slater-Gaussian Functions in Computational Chemistry

    ERIC Educational Resources Information Center

    Stewart, Brianna; Hylton, Derrick J.; Ravi, Natarajan

    2013-01-01

    A systematic way to understand the intricacies of quantum mechanical computations done by a software package known as "Gaussian" is undertaken via an undergraduate research project. These computations involve the evaluation of key parameters in a fitting procedure to express a Slater-type orbital (STO) function in terms of the linear…

  6. Heterofunctional Glycopolypeptides by Combination of Thiol-Ene Chemistry and NCA Polymerization.

    PubMed

    Krannig, Kai-Steffen; Schlaad, Helmut

    2016-01-01

    Glycopolypeptides are prepared either by the polymerization of glycosylated amino acid N-carboxyanhydrides (NCAs) or by the post-polymerization functionalization of polypeptides with suitable functional groups. Here we present a method for the in-situ functionalization and (co-) polymerization of allylglycine N-carboxyanhydride in a facile one-pot procedure, combining radical thiol-ene photochemistry and nucleophilic ring-opening polymerization techniques, to yield well-defined heterofunctional glycopolypeptides.

  7. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Waltemath, Dagmar; Bergmann, Frank T.; Chaouiya, Claudine; Czauderna, Tobias; Gleeson, Padraig; Goble, Carole; Golebiewski, Martin; Hucka, Michael; Juty, Nick; Krebs, Olga; Le Novère, Nicolas; Mi, Huaiyu; Moraru, Ion I.; Myers, Chris J.; Nickerson, David; Olivier, Brett G.; Rodriguez, Nicolas; Schreiber, Falk; Smith, Lucian; Zhang, Fengkai; Bonnet, Eric

    2014-01-01

    The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report summarizes the topics and activities of the fourth edition of the annual COMBINE meeting, held in Paris during September 16-20 2013, and attended by a total of 96 people. This edition pioneered a first day devoted to modeling approaches in biology, which attracted a broad audience of scientists thanks to a panel of renowned speakers. During subsequent days, discussions were held on many subjects including the introduction of new features in the various COMBINE standards, new software tools that use the standards, and outreach efforts. Significant emphasis went into work on extensions of the SBML format, and also into community-building. This year’s edition once again demonstrated that the COMBINE community is thriving, and still manages to help coordinate activities between different standards in computational systems biology.

  8. Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

    DOE PAGES

    Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

    2015-08-01

    Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NOx reduction. We then discussmore » the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

  9. Computational chemistry for NH3 synthesis, hydrotreating, and NOx reduction: Three topics of special interest to Haldor Topsøe

    DOE PAGES

    Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

    2015-06-05

    Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NOx reduction. Furthermore, we thenmore » discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.« less

  10. Computational chemistry for NH3 synthesis, hydrotreating, and NOx reduction: Three topics of special interest to Haldor Topsøe

    SciTech Connect

    Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

    2015-06-05

    Computational chemistry, especially density functional theory, has experienced a remarkable growth in terms of application over the last few decades. This is attributed to the improvements in theory and computing infrastructure that enable the analysis of systems of unprecedented size and detail at an affordable computational expense. In this perspective, we discuss recent progress and current challenges facing electronic structure theory in the context of heterogeneous catalysis. We specifically focus on the impact of computational chemistry in elucidating and designing catalytic systems in three topics of interest to Haldor Topsøe – ammonia, synthesis, hydrotreating, and NOx reduction. Furthermore, we then discuss the common tools and concepts in computational catalysis that underline these topics and provide a perspective on the challenges and future directions of research in this area of catalysis research.

  11. Calcite sealing in a fractured geothermal reservoir: Insights from combined EBSD and chemistry mapping

    NASA Astrophysics Data System (ADS)

    McNamara, David D.; Lister, Aaron; Prior, Dave J.

    2016-09-01

    Fractures play an important role as fluid flow pathways in geothermal resources hosted in indurated greywacke basement of the Taupo Volcanic Zone, New Zealand, including the Kawerau Geothermal Field. Over time, the permeability of such geothermal reservoirs can be degraded by fracture sealing as minerals deposit out of transported geothermal fluids. Calcite is one such fracture sealing mineral. This study, for the first time, utilises combined data from electron backscatter diffraction and chemical mapping to characterise calcite vein fill morphologies, and gain insight into the mechanisms of calcite fracture sealing in the Kawerau Geothermal Field. Two calcite sealing mechanisms are identified 1) asymmetrical syntaxial growth of calcite, inferred by the presence of single, twinned, calcite crystals spanning the entire fracture width, and 2) 3D, interlocking growth of bladed vein calcite into free space as determined from chemical and crystallographic orientation mapping. This study also identifies other potential uses of combined EBSD and chemical mapping to understand geothermal field evolution including, potentially informing on levels of fluid supersaturation from the study of calcite lattice distortion, and providing information on a reservoir's history of stress, strain, and deformation through investigation of calcite crystal deformation and twinning patterns.

  12. 3D-Printing inside the Glovebox: A Versatile Tool for Inert-Gas Chemistry Combined with Spectroscopy.

    PubMed

    Lederle, Felix; Kaldun, Christian; Namyslo, Jan C; Hübner, Eike G

    2016-04-01

    3D-Printing with the well-established 'Fused Deposition Modeling' technology was used to print totally gas-tight reaction vessels, combined with printed cuvettes, inside the inert-gas atmosphere of a glovebox. During pauses of the print, the reaction flasks out of acrylonitrile butadiene styrene were filled with various reactants. After the basic test reactions to proof the oxygen tightness and investigations of the influence of printing within an inert-gas atmosphere, scope and limitations of the method are presented by syntheses of new compounds with highly reactive reagents, such as trimethylaluminium, and reaction monitoring via UV/VIS, IR, and NMR spectroscopy. The applicable temperature range, the choice of solvents, the reaction times, and the analytical methods have been investigated in detail. A set of reaction flasks is presented, which allow routine inert-gas syntheses and combined spectroscopy without modifications of the glovebox, the 3D-printer, or the spectrometers. Overall, this demonstrates the potential of 3D-printed reaction cuvettes to become a complementary standard method in inert-gas chemistry.

  13. The combined effect of surface chemistry and flow conditions on Staphylococcus epidermidis adhesion and ica operon expression.

    PubMed

    Foka, A; Katsikogianni, M G; Anastassiou, E D; Spiliopoulou, I; Missirlis, Y F

    2012-11-17

    The assessment of biomaterial susceptibility to infection relies mainly on the analysis of macroscopic bacterial responses to material interactions, usually under static conditions. However, new technologies permit a more profound understanding of the molecular basis of bacteria-biomaterial interactions. In this study, we combine both conventional phenotypic analysis - using confocal microscopy - and genotypic analysis - using the relative reverse transcription polymerase chain reaction (RT-PCR) - to examine the interaction of bacteria with OH- and CH3-terminated glass surfaces, under dynamic flow conditions. Bacterial adhesion, as well as slime production and biofilm formation, was much higher on the CH3-terminated than on the OH-terminated glass - for four Staphylococcus epidermidis strains. This was in agreement with the icaA and icaD gene expression results that showed increased expression for the bacteria adhering to the CH3-terminated substrate, especially under the higher shear rate. Therefore, the combined effect of the surface chemistry and shear significantly influence the adhesion and phenotype of interacting bacterial cells, while there are putative links between phenotypic responses to bacteria-material interactions and gene-expression profile alterations. This indicates that analysis of gene expression not only can greatly refine our knowledge of bacteria-material interactions, but also yield novel biomarkers for potential use in biocompatibility assessment.

  14. Synthesis of Zwitterionic Polymer Particles via Combined Distillation Precipitation Polymerization and Click Chemistry for Highly Efficient Enrichment of Glycopeptide.

    PubMed

    Liu, Jianxi; Yang, Kaiguang; Shao, Wenya; Li, Senwu; Wu, Qi; Zhang, Shen; Qu, Yanyan; Zhang, Lihua; Zhang, Yukui

    2016-08-31

    Because of the low abundance of glycopeptide in natural biological samples, methods for efficient and selective enrichment of glycopeptides play a significant role in mass spectrometry (MS)-based glycoproteomics. In this study, a novel kind of zwitterionic hydrophilic interaction chromatography polymer particles, namely, poly(N,N-methylenebisacrylamide-co-methacrylic acid)@l-Cys (poly(MBAAm-co-MAA)@l-Cys), for the enrichment of glycopeptides was synthesized by a facile and efficient approach that combined distillation precipitation polymerization (DPP) and "thiol-ene" click reaction. In the DPP approach, residual vinyl groups explored outside the core with high density, then the functional ligand cysteine was immobilized onto the surface of core particles by highly efficient thiol-ene click reaction. Taking advantage of the unique structure of poly(MBAAm-co-MAA)@l-Cys, the resulting particles possess remarkable enrichment selectivity for glycopeptides from the tryptic digested human immunoglobulin G. The polymer particles were successfully employed for the analysis of human plasma, and 208 unique glycopeptides corresponding to 121 glycoproteins were reliably identified in triple independent nano-LC-MS/MS runs. The selectivity toward glycopeptides of these particles poly(MBAAm-co-MAA)@l-Cys is ∼2 times than that of the commercial beads. These results demonstrated that these particles had great potential for large-scale glycoproteomics research. Moreover, the strategy with the combination of DPP and thiol-ene click chemistry might be a facile method to produce functional polymer particles for bioenrichment application.

  15. Combination of Synthetic Chemistry and Live-Cell Imaging Identified a Rapid Cell Division Inhibitor in Tobacco and Arabidopsis thaliana.

    PubMed

    Nambo, Masakazu; Kurihara, Daisuke; Yamada, Tomomi; Nishiwaki-Ohkawa, Taeko; Kadofusa, Naoya; Kimata, Yusuke; Kuwata, Keiko; Umeda, Masaaki; Ueda, Minako

    2016-11-01

    Cell proliferation is crucial to the growth of multicellular organisms, and thus the proper control of cell division is important to prevent developmental arrest or overgrowth. Nevertheless, tools for controlling cell proliferation are still poor in plant. To develop novel tools, we focused on a specific compound family, triarylmethanes, whose members show various antiproliferative activities in animals. By combining organic chemistry to create novel and diverse compounds containing the triarylmethyl moiety and biological screens based on live-cell imaging of a fluorescently labeled tobacco Bright Yellow-2 (BY-2) culture cell line (Nicotiana tabacum), we isolated (3-furyl)diphenylmethane as a strong but partially reversible inhibitor of plant cell division. We also found that this agent had efficient antiproliferative activity in developing organs of Arabidopsis thaliana without causing secondary defects in cell morphology, and induced rapid cell division arrest independent of the cell cycle stage. Given that (3-furyl)diphenylmethane did not affect the growth of a human cell line (HeLa) and a budding yeast (Saccharomyces cerevisiae), it should act specifically on plants. Taking our results together, we propose that the combination of desired chemical synthesis and detailed biological analysis is an effective tool to create novel drugs, and that (3-furyl)diphenylmethane is a specific antiproliferative agent for plants.

  16. Structural Isomerization of the Gas Phase 2-NORBORNYL Cation Revealed with Infrared Spectroscopy and Computational Chemistry

    NASA Astrophysics Data System (ADS)

    Mauney, Daniel; Mosley, Jonathan; Duncan, Michael A.

    2014-06-01

    The non-classical structure of the 2-norborny cation (C_7H11+) which was at the center of "the most heated chemical controversy of our time" has been observed in the condensed phase and recently using X-ray crystallography. However, no gas phase vibrational spectrum has been collected. The C_7H11+ cation is produced via H_3+ protonation of norbornene by pulsed discharge in a supersonic expansion of H_2/Ar. Ions are mass-selected and probed using infrared photodissociation spectroscopy. Due to high exothermicity, protonation via H_3+ leads to a structural isomerization to the global minimum structure 1,3-dimethylcyclopentenyl (DMCP+). Experiments are currently being conducted to find softer protonation techniques that could lead to the authentic 2-norbornyl cation. Schleyer,P.v.R. et. al.; Stable Carbocation Chemistry, John Wiley & Sons,Inc.; New York, 1997, Chapter 2

  17. Chemistry of protostellar envelopes and disks: computational testing of 2D abundances

    NASA Astrophysics Data System (ADS)

    Flores Rivera, Lizxandra; Willacy, Karen; Terebey, Susan

    2017-01-01

    Molecule formation is dynamic during the protostar collapse phase, driven by changes in temperature, density, and UV radiation as gas and dust flows from the envelope onto the forming protoplanetary disk. In this work, we use a chemistry model to generate fractional abundances of water and carbon monoxide using primarily as input parameters the temperature and density profile produced by the dust radiative transfer model HOCHUNK3D (Whitney et al. 2013). Contour maps are presented showing the meridional temperature, density, and fractional abundance at different outer radii. High concentrations of gas phase molecules are found within 5 AU of the star along with high temperatures in the same spatial region. Shielding by the disk leads to colder temperatures outside 10 AU near the disk mid-plane. In this region, CO freezes out onto grains and shows a much reduced abundance. Water remains solid almost everywhere during the infall and evaporates within ~10 AU.

  18. Matched molecular pair-based data sets for computer-aided medicinal chemistry.

    PubMed

    Hu, Ye; de la Vega de León, Antonio; Zhang, Bijun; Bajorath, Jürgen

    2014-01-01

    Matched molecular pairs (MMPs) are widely used in medicinal chemistry to study changes in compound properties including biological activity, which are associated with well-defined structural modifications. Herein we describe up-to-date versions of three MMP-based data sets that have originated from in-house research projects. These data sets include activity cliffs, structure-activity relationship (SAR) transfer series, and second generation MMPs based upon retrosynthetic rules. The data sets have in common that they have been derived from compounds included in the ChEMBL database (release 17) for which high-confidence activity data are available. Thus, the activity data associated with MMP-based activity cliffs, SAR transfer series, and retrosynthetic MMPs cover the entire spectrum of current pharmaceutical targets. Our data sets are made freely available to the scientific community.

  19. Open Data Management Solutions for Problem Solving Environments: Application of Distributed Authoring and Versioning to the Extensible Computational Chemistry Environment.

    SciTech Connect

    Schuchardt, Karen L. ); Myers, James D. ); Stephan, Eric G. ); IEEE Computer Society

    2001-01-01

    Next-generation problem solving environments (PSEs) promise significant advances over those now available. They will span scientific disciplines and incorporate collaboratory capabilities. They will host feature-detection and other agents, allow data mining and pedigree tracking, and provide access from a wide range of devices. Fundamental changes in PSE architecture are required to realize these and other PSE goals. This paper focuses specifically on issues related to data management and recommends an approach based on open, metadata-driven repositories with loosely defined, dynamic schemas. Benefits of this approach are discussed and the redesign of the Extensible Computational Chemistry Environment's (Ecce) data storage architecture to use such a repository is described, based on the distributed authoring and versioning (DAV) standard. The suitability of DAV for scientific data, the mapping of the Ecce scheme to DAV, and promising initial results are presented.

  20. Structural Characteristics and Reactivity Relationships of Nitroaromatic and Nitramine Explosives – A Review of Our Computational Chemistry and Spectroscopic Research

    PubMed Central

    Qasim, Mohammad M.; Moore, Brett; Taylor, Lyssa; Honea, Patricia; Gorb, Leonid; Leszczynski, Jerzy

    2007-01-01

    Although much has been discovered, discussed and written as to problems of contamination by various military unique compounds, particularly by the nitrogen based energetics (NOCs), remaining problems dictate further evaluation of actual and potential risk to the environment by these energetics and their derivatives and metabolites through determination of their environmental impact—transport, fate and toxicity. This work comprises an effort to understand structural relationships and degradation mechanisms of current and emerging explosives, including nitroaromatic; cyclic and cage cyclic nitramine; and a nitrocubane. This review of our computational chemistry and spectroscopic research describes and compares competitive degradation mechanisms by free radical oxidative, reductive and alkali hydrolysis, relating them, when possible, to environmental risk.

  1. Actinide chemistry using singlet-paired coupled cluster and its combinations with density functionals.

    PubMed

    Garza, Alejandro J; Sousa Alencar, Ana G; Scuseria, Gustavo E

    2015-12-28

    Singlet-paired coupled cluster doubles (CCD0) is a simplification of CCD that relinquishes a fraction of dynamic correlation in order to be able to describe static correlation. Combinations of CCD0 with density functionals that recover specifically the dynamic correlation missing in the former have also been developed recently. Here, we assess the accuracy of CCD0 and CCD0+DFT (and variants of these using Brueckner orbitals) as compared to well-established quantum chemical methods for describing ground-state properties of singlet actinide molecules. The f(0) actinyl series (UO2(2+), NpO2(3+), PuO2(4+)), the isoelectronic NUN, and thorium (ThO, ThO(2+)) and nobelium (NoO, NoO2) oxides are studied.

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

    NASA Astrophysics Data System (ADS)

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

    2014-11-01

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

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

    PubMed

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

    2014-11-01

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

  4. Degradable polyester scaffolds with controlled surface chemistry combining minimal protein adsorption with specific bioactivation

    NASA Astrophysics Data System (ADS)

    Grafahrend, Dirk; Heffels, Karl-Heinz; Beer, Meike V.; Gasteier, Peter; Möller, Martin; Boehm, Gabriele; Dalton, Paul D.; Groll, Jürgen

    2011-01-01

    Advanced biomaterials and scaffolds for tissue engineering place high demands on materials and exceed the passive biocompatibility requirements previously considered acceptable for biomedical implants. Together with degradability, the activation of specific cell-material interactions and a three-dimensional environment that mimics the extracellular matrix are core challenges and prerequisites for the organization of living cells to functional tissue. Moreover, although bioactive signalling combined with minimization of non-specific protein adsorption is an advanced modification technique for flat surfaces, it is usually not accomplished for three-dimensional fibrous scaffolds used in tissue engineering. Here, we present a one-step preparation of fully synthetic, bioactive and degradable extracellular matrix-mimetic scaffolds by electrospinning, using poly(D,L-lactide-co-glycolide) as the matrix polymer. Addition of a functional, amphiphilic macromolecule based on star-shaped poly(ethylene oxide) transforms current biomedically used degradable polyesters into hydrophilic fibres, which causes the suppression of non-specific protein adsorption on the fibres’ surface. The subsequent covalent attachment of cell-adhesion-mediating peptides to the hydrophilic fibres promotes specific bioactivation and enables adhesion of cells through exclusive recognition of the immobilized binding motifs. This approach permits synthetic materials to directly control cell behaviour, for example, resembling the binding of cells to fibronectin immobilized on collagen fibres in the extracellular matrix of connective tissue.

  5. Development of a Core-Course for College Science Majors Combining Material from Introductory Courses in Biology, Chemistry, and Physics-Phase II. Final Report.

    ERIC Educational Resources Information Center

    Pickar, Arnold D.

    Reported is the second phase of the development of a two-year college core science course for science majors. Materials were combined from introductory college courses in biology, chemistry, and physics. A revised lecture and laboratory syllabus was prepared incorporating improvements suggested after a pilot study of the first year course.…

  6. JINR CICC in computational chemistry and nanotechnology problems: DL_POLY performance for different communication architectures

    NASA Astrophysics Data System (ADS)

    Dushanov, E.; Kholmurodov, Kh.; Aru, G.; Korenkov, V.; Smith, W.; Ohno, Y.; Narumi, T.; Morimoto, G.; Taiji, M.; Yasuoka, K.

    2009-05-01

    This report compares the performance of the DL_POLY general-purpose molecular dynamics simulation package on the LIT JINR computing cluster CICC with various communication systems. The comparison involved two cluster architectures: Gigabit Ethernet and InfiniBand technologies, respectively. The code performance tests include some comparison of the CICC cluster with the special-purpose computer MDGRAPE-3 developed at RIKEN for a high-speed acceleration of the MD (molecular dynamics) without a fixed cutoff. The DL_POLY benchmark covers a set of typical MD system simulations detailed below.

  7. A Computational Approach to Understanding Aerosol Formation and Oxidant Chemistry in the Troposphere

    SciTech Connect

    Francisco, Joseph S.; Kathmann, Shawn M.; Schenter, Gregory K.; Dang, Liem X.; Xantheas, Sotiris S.; Garrett, Bruce C.; Du, Shiyu; Dixon, David A.; Bianco, Roberto; Wang, Shuzhi; Hynes, James T.; Morita, Akihiro; Peterson, Kirk A.

    2006-04-18

    An understanding of the mechanisms and kinetics of aerosol formation and ozone production in the troposphere is currently a high priority because these phenomena are recognized as two major effects of energy-related air pollution. Atmospheric aerosols are of concern because of their effect on visibility, climate, and human health. Equally important, aerosols can change the chemistry of the atmosphere, in dramatic fashion, by providing new chemical pathways (in the condensed phase) unavailable in the gas phase. The oxidation of volatile organic compounds (VOCs) and inorganic compounds (e.g., sulfuric acid, ammonia, nitric acid, ions, and mineral) can produce precursor molecules that act as nucleation seeds. The U.S. Department of Energy (DOE) Atmospheric Chemistry Program (ACP) has identified the need to evaluate the causes of variations in tropospheric aerosol chemical composition and concentrations, including determining the sources of aerosol particles and the fraction of such that are of primary and secondary origin. In particular, the ACP has called for a deeper understanding into aerosol formation because nucleation creates substantial concentrations of fresh particles that, via growth and coagulation, influence the Earth's radiation budget. Tropospheric ozone is also of concern primarily because of its impact on human health. Ozone levels are controlled by NOx and by VOCs in the lower troposphere. The VOCs can be either from natural emissions from such sources as vegetation and phytoplankton or from anthropogenic sources such as automobiles and oil-fueled power production plants. The major oxidant for VOCs in the atmosphere is the OH radical. With the increase in VOC emissions, there is rising concern regarding the available abundance of HOx species needed to initiate oxidation. Over the last five years, there have been four field studies aimed at initial measurements of HOx species (OH and HO? radicals). These measurements revealed HOx levels that are two to

  8. Computational medicinal chemistry in fragment-based drug discovery: what, how and when.

    PubMed

    Rabal, Obdulia; Urbano-Cuadrado, Manuel; Oyarzabal, Julen

    2011-01-01

    The use of fragment-based drug discovery (FBDD) has increased in the last decade due to the encouraging results obtained to date. In this scenario, computational approaches, together with experimental information, play an important role to guide and speed up the process. By default, FBDD is generally considered as a constructive approach. However, such additive behavior is not always present, therefore, simple fragment maturation will not always deliver the expected results. In this review, computational approaches utilized in FBDD are reported together with real case studies, where applicability domains are exemplified, in order to analyze them, and then, maximize their performance and reliability. Thus, a proper use of these computational tools can minimize misleading conclusions, keeping the credit on FBDD strategy, as well as achieve higher impact in the drug-discovery process. FBDD goes one step beyond a simple constructive approach. A broad set of computational tools: docking, R group quantitative structure-activity relationship, fragmentation tools, fragments management tools, patents analysis and fragment-hopping, for example, can be utilized in FBDD, providing a clear positive impact if they are utilized in the proper scenario - what, how and when. An initial assessment of additive/non-additive behavior is a critical point to define the most convenient approach for fragments elaboration.

  9. Glycolaldehyde monomer and oligomer equilibria in aqueous solution: comparing computational chemistry and NMR data.

    PubMed

    Kua, Jeremy; Galloway, Melissa M; Millage, Katherine D; Avila, Joseph E; De Haan, David O

    2013-04-11

    A computational protocol utilizing density functional theory calculations, including Poisson-Boltzmann implicit solvent and free energy corrections, is applied to study the thermodynamic and kinetic energy landscape of glycolaldehyde in solution. Comparison is made to NMR measurements of dissolved glycolaldehyde, where the initial dimeric ring structure interconverts among several species before reaching equilibrium where the hydrated monomer is dominant. There is good agreement between computation and experiment for the concentrations of all species in solution at equilibrium, that is, the calculated relative free energies represent the system well. There is also relatively good agreement between the calculated activation barriers and the estimated rate constants for the hydration reaction. The computational approach also predicted that two of the trimers would have a small but appreciable equilibrium concentration (>0.005 M), and this was confirmed by NMR measurements. Our results suggest that while our computational protocol is reasonable and may be applied to quickly map the energy landscape of more complex reactions, knowledge of the caveats and potential errors in this approach need to be taken into account.

  10. Computer Series, 82. The Application of Expert Systems in the General Chemistry Laboratory.

    ERIC Educational Resources Information Center

    Settle, Frank A., Jr.

    1987-01-01

    Describes the construction of expert computer systems using artificial intelligence technology and commercially available software, known as an expert system shell. Provides two applications; a simple one, the identification of seven white substances, and a more complicated one involving the qualitative analysis of six metal ions. (TW)

  11. 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)

  12. 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)

  13. Effect of Gender on Computer-Based Chemistry Problem Solving: Early Findings.

    ERIC Educational Resources Information Center

    Kumar, David D.; Helgeson, Stanley L.

    2000-01-01

    Studies the effect of gender on a computer-based approach to solving stoichiometric chemical equations. Implies that the feedback provided by the software might have had an effect on reducing the gender gap. However, upon closer examination, the results showed that the correctness means for males were higher than that for females, and the rate of…

  14. Providing full point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer

    DOEpatents

    Archer, Charles J; Faraj, Ahmad A; Inglett, Todd A; Ratterman, Joseph D

    2013-04-16

    Methods, apparatus, and products are disclosed for providing full point-to-point communications among compute nodes of an operational group in a global combining network of a parallel computer, each compute node connected to each adjacent compute node in the global combining network through a link, that include: receiving a network packet in a compute node, the network packet specifying a destination compute node; selecting, in dependence upon the destination compute node, at least one of the links for the compute node along which to forward the network packet toward the destination compute node; and forwarding the network packet along the selected link to the adjacent compute node connected to the compute node through the selected link.

  15. The Effectiveness of a Computer-Assisted Instruction Package in Supplementing Teaching of Selected Concepts in High School Chemistry: Writing Formulas and Balancing Chemical Equations.

    ERIC Educational Resources Information Center

    Wainwright, Camille L.

    Four classes of high school chemistry students (N=108) were randomly assigned to experimental and control groups to investigate the effectiveness of a computer assisted instruction (CAI) package during a unit on writing/naming of chemical formulas and balancing equations. Students in the experimental group received drill, review, and reinforcement…

  16. The Influence of Computer-Assisted Instruction on Students' Conceptual Understanding of Chemical Bonding and Attitude toward Chemistry: A Case for Turkey

    ERIC Educational Resources Information Center

    Ozmen, Haluk

    2008-01-01

    In this study, the effect of computer-assisted instruction on conceptual understanding of chemical bonding and attitude toward chemistry was investigated. The study employed a quasi-experimental design involving 11 grade students; 25 in an experimental and 25 in a control group. The Chemical Bonding Achievement Test (CBAT) consisting of 15…

  17. Chemical Equilibrium, Unit 4: Equilibria in Acid-Base Systems. A Computer-Enriched Module for Introductory Chemistry. Student's Guide and Teacher's Guide.

    ERIC Educational Resources Information Center

    Settle, Frank A., Jr.

    Presented are the teacher's guide and student materials for one of a series of self-instructional, computer-based learning modules for an introductory, undergraduate chemistry course. The student manual for this acid-base equilibria unit includes objectives, prerequisites, pretest, a discussion of equilibrium constants, and 20 problem sets.…

  18. Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

    SciTech Connect

    Elrod, D.W.

    1992-01-01

    Computational neural networks (CNNs) are a computational paradigm inspired by the brain's massively parallel network of highly interconnected neurons. The power of computational neural networks derives not so much from their ability to model the brain as from their ability to learn by example and to map highly complex, nonlinear functions, without the need to explicitly specify the functional relationship. Two central questions about CNNs were investigated in the context of predicting chemical reactions: (1) the mapping properties of neural networks and (2) the representation of chemical information for use in CNNs. Chemical reactivity is here considered an example of a complex, nonlinear function of molecular structure. CNN's were trained using modifications of the back propagation learning rule to map a three dimensional response surface similar to those typically observed in quantitative structure-activity and structure-property relationships. The computational neural network's mapping of the response surface was found to be robust to the effects of training sample size, noisy data and intercorrelated input variables. The investigation of chemical structure representation led to the development of a molecular structure-based connection-table representation suitable for neural network training. An extension of this work led to a BE-matrix structure representation that was found to be general for several classes of reactions. The CNN prediction of chemical reactivity and regiochemistry was investigated for electrophilic aromatic substitution reactions, Markovnikov addition to alkenes, Saytzeff elimination from haloalkanes, Diels-Alder cycloaddition, and retro Diels-Alder ring opening reactions using these connectivity-matrix derived representations. The reaction predictions made by the CNNs were more accurate than those of an expert system and were comparable to predictions made by chemists.

  19. Testing the Potential for Computational Chemistry to Quantify Biophysical Properties of the Non-Proteinaceous Amino Acids

    NASA Astrophysics Data System (ADS)

    Lu, Yi; Freeland, Stephen

    2006-08-01

    Although most proteins of most living organisms are constructed from the same set of 20 amino acids, all indications are that this standard alphabet represents a mere subset of what was available to life during early evolution. However, we currently lack an appropriate quantitative framework with which to test the qualitative hypotheses that have been offered to date as explanations for nature's "choices." Specifically, although many indices have been developed to describe the 20 standard amino acids, few or no comparable data extend to prebiotically plausible alternatives because of the costly and time-consuming bench experiments that would be required. Computational chemistry (specifically quantitative structure property relationship methods) offers a potentially fast, cost-effective remedy for this knowledge gap by predicting such molecular properties in silico. Thus, we investigated the use of various freely accessible programs to predict three key amino acid properties (hydrophobicity, charge, and size). We assessed the accuracy of these predictions by comparisons with experimentally determined counterparts for appropriate test data sets. In light of these results, and factors of software accessibility and transparency, we suggest a method for further computational assessments of prebiotically plausible amino acids. The results serve as a starting point for future quantitative analysis of amino acid alphabet evolution.

  20. Accuracy of color prediction of anthraquinone dyes in methanol solution estimated from first principle quantum chemistry computations.

    PubMed

    Cysewski, Piotr; Jeliński, Tomasz

    2013-10-01

    The electronic spectrum of four different anthraquinones (1,2-dihydroxyanthraquinone, 1-aminoanthraquinone, 2-aminoanthraquinone and 1-amino-2-methylanthraquinone) in methanol solution was measured and used as reference data for theoretical color prediction. The visible part of the spectrum was modeled according to TD-DFT framework with a broad range of DFT functionals. The convoluted theoretical spectra were validated against experimental data by a direct color comparison in terms of CIE XYZ and CIE Lab tristimulus model color. It was found, that the 6-31G** basis set provides the most accurate color prediction and there is no need to extend the basis set since it does not improve the prediction of color. Although different functionals were found to give the most accurate color prediction for different anthraquinones, it is possible to apply the same DFT approach for the whole set of analyzed dyes. Especially three functionals seem to be valuable, namely mPW1LYP, B1LYP and PBE0 due to very similar spectra predictions. The major source of discrepancies between theoretical and experimental spectra comes from L values, representing the lightness, and the a parameter, depicting the position on green→magenta axis. Fortunately, the agreement between computed and observed blue→yellow axis (parameter b) is very precise in the case of studied anthraquinone dyes in methanol solution. Despite discussed shortcomings, color prediction from first principle quantum chemistry computations can lead to quite satisfactory results, expressed in terms of color space parameters.

  1. Surface modification of carbon nanotubes via combination of mussel inspired chemistry and chain transfer free radical polymerization

    NASA Astrophysics Data System (ADS)

    Wan, Qing; Tian, Jianwen; Liu, Meiying; Zeng, Guangjian; Huang, Qiang; Wang, Ke; Zhang, Qingsong; Deng, Fengjie; Zhang, Xiaoyong; Wei, Yen

    2015-08-01

    In this work, a novel strategy for surface modification of carbon nanotubes (CNTs) was developed via combination of mussel inspired chemistry and chain transfer free radical polymerization. First, pristine CNTs were functionalized with polydopamine (PDA), which is formed via self-polymerization of dopamine in alkaline conditions. These PDA functionalized CNTs can be further reacted with amino-terminated polymers (named as PDMC), which was synthesized through chain transfer free radical polymerization using cysteamine hydrochloride as chain transfer agent and methacryloxyethyltrimethyl ammonium chloride as the monomer. PDMC perfectly conjugated with CNT-PDA was ascertained by a series of characterization techniques including transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS). The dispersibility of obtained CNT nanocomposites (named as CNT-PDA-PDMC) was further examined. Results showed that the dispersibility of CNT-PDA-PDMC in aqueous and organic solutions was obviously enhanced. Apart from PDMC, many other amino-terminated polymers can also be used to functionalization of CNTs via similar strategy. Therefore, the method described in this work should be a general strategy for fabrication various polymer nanocomposites.

  2. 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.

  3. Contributions of computational chemistry and biophysical techniques to fragment-based drug discovery.

    PubMed

    Gozalbes, Rafael; Carbajo, Rodrigo J; Pineda-Lucena, Antonio

    2010-01-01

    In the last decade, fragment-based drug discovery (FBDD) has evolved from a novel approach in the search of new hits to a valuable alternative to the high-throughput screening (HTS) campaigns of many pharmaceutical companies. The increasing relevance of FBDD in the drug discovery universe has been concomitant with an implementation of the biophysical techniques used for the detection of weak inhibitors, e.g. NMR, X-ray crystallography or surface plasmon resonance (SPR). At the same time, computational approaches have also been progressively incorporated into the FBDD process and nowadays several computational tools are available. These stretch from the filtering of huge chemical databases in order to build fragment-focused libraries comprising compounds with adequate physicochemical properties, to more evolved models based on different in silico methods such as docking, pharmacophore modelling, QSAR and virtual screening. In this paper we will review the parallel evolution and complementarities of biophysical techniques and computational methods, providing some representative examples of drug discovery success stories by using FBDD.

  4. Computational quantum chemistry for single Heisenberg spin couplings made simple: Just one spin flip required

    SciTech Connect

    Mayhall, Nicholas J.; Head-Gordon, Martin

    2014-10-07

    We highlight a simple strategy for computing the magnetic coupling constants, J, for a complex containing two multiradical centers. On the assumption that the system follows Heisenberg Hamiltonian physics, J is obtained from a spin-flip electronic structure calculation where only a single electron is excited (and spin-flipped), from the single reference with maximum S{sup ^}{sub z}, M, to the M − 1 manifold, regardless of the number of unpaired electrons, 2M, on the radical centers. In an active space picture involving 2M orbitals, only one β electron is required, together with only one α hole. While this observation is extremely simple, the reduction in the number of essential configurations from exponential in M to only linear provides dramatic computational benefits. This (M, M − 1) strategy for evaluating J is an unambiguous, spin-pure, wave function theory counterpart of the various projected broken symmetry density functional theory schemes, and likewise gives explicit energies for each possible spin-state that enable evaluation of properties. The approach is illustrated on five complexes with varying numbers of unpaired electrons, for which one spin-flip calculations are used to compute J. Some implications for further development of spin-flip methods are discussed.

  5. Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model Chemistries.

    PubMed

    Alecu, I M; Zheng, Jingjing; Zhao, Yan; Truhlar, Donald G

    2010-09-14

    Optimized scale factors for calculating vibrational harmonic and fundamental frequencies and zero-point energies have been determined for 145 electronic model chemistries, including 119 based on approximate functionals depending on occupied orbitals, 19 based on single-level wave function theory, three based on the neglect-of-diatomic-differential-overlap, two based on doubly hybrid density functional theory, and two based on multicoefficient correlation methods. Forty of the scale factors are obtained from large databases, which are also used to derive two universal scale factor ratios that can be used to interconvert between scale factors optimized for various properties, enabling the derivation of three key scale factors at the effort of optimizing only one of them. A reduced scale factor optimization model is formulated in order to further reduce the cost of optimizing scale factors, and the reduced model is illustrated by using it to obtain 105 additional scale factors. Using root-mean-square errors from the values in the large databases, we find that scaling reduces errors in zero-point energies by a factor of 2.3 and errors in fundamental vibrational frequencies by a factor of 3.0, but it reduces errors in harmonic vibrational frequencies by only a factor of 1.3. It is shown that, upon scaling, the balanced multicoefficient correlation method based on coupled cluster theory with single and double excitations (BMC-CCSD) can lead to very accurate predictions of vibrational frequencies. With a polarized, minimally augmented basis set, the density functionals with zero-point energy scale factors closest to unity are MPWLYP1M (1.009), τHCTHhyb (0.989), BB95 (1.012), BLYP (1.013), BP86 (1.014), B3LYP (0.986), MPW3LYP (0.986), and VSXC (0.986).

  6. What computational chemistry and magnetic resonance reveal concerning the oxygen evolving centre in Photosystem II.

    PubMed

    Terrett, Richard; Petrie, Simon; Stranger, Rob; Pace, Ron J

    2016-09-01

    Density Functional Theory (DFT) computational studies of the Mn4/Ca Oxygen Evolving Complex (OEC) region of Photosystem II in the paramagnetic S2 and S3 states of the water oxdizing catalytic cycle are described. These build upon recent advances in computationally understanding the detailed S1 state OEC geometries, revealed by the recent high resolution Photosystem II crystal structures of Shen et al., at 1.90Å and 1.95Å (Petrie et al., 2015, Angew. Chem. Int. Ed., 54, 7120). The models feature a 'Low Oxidation Paradigm' assumption for the mean Mn oxidation states in the functional enzyme, with the mean oxidation levels being 3.0, 3.25 and 3.5 in S1, S2 and S3, respectively. These calculations are used to infer magnetic exchange interactions within the coupled OEC cluster, particularly in the Electron Paramagnetic Resonance (EPR)-visible S2 and S3 states. Detailed computational estimates of the intrinsic magnitudes and molecular orientations of the (55)Mn hyperfine tensors in the S2 state are presented. These parameters, together with the resultant spin projected hyperfine values are compared with recent appropriate experimental EPR data (Continuous Wave (CW), Electron-Nuclear Double Resonance (ENDOR) and ELDOR (Electron-Electron Double Resonance)-Detected Nuclear Magnetic Resonance (EDNMR)) from the OEC. It is found that an effective Coupled Dimer magnetic organization of the four Mn in the OEC cluster in the S2 and S3 states is able to quantitatively rationalize the observed (55)Mn hyperfine data. This is consistent with structures we propose to represent the likely state of the OEC in the catalytically active form of the enzyme. Copyright © 2016 Elsevier Inc. All rights reserved.

  7. Drugging specific conformational states of GPCRs: challenges and opportunities for computational chemistry.

    PubMed

    Martí-Solano, Maria; Schmidt, Denis; Kolb, Peter; Selent, Jana

    2016-04-01

    Current advances in structural biology for membrane proteins support the existence of multiple Gprotein-coupled receptor (GPCR) conformations. These conformations can be associated to particular receptor states with definite coupling and signaling capacities. Drugging such receptor states represents an opportunity to discover a new generation of GPCR drugs with unprecedented specificity. However, exploiting recently available structural information to develop these drugs is still challenging. In this context, computational structure-based approaches can inform such drug development. In this review, we examine the potential of these approaches and the challenges they will need to overcome to guide the rational discovery of drugs targeting specific GPCR states.

  8. A City Parking Integration System Combined with Cloud Computing Technologies and Smart Mobile Devices

    ERIC Educational Resources Information Center

    Yeh, Her-Tyan; Chen, Bing-Chang; Wang, Bo-Xun

    2016-01-01

    The current study applied cloud computing technology and smart mobile devices combined with a streaming server for parking lots to plan a city parking integration system. It is also equipped with a parking search system, parking navigation system, parking reservation service, and car retrieval service. With this system, users can quickly find…

  9. A City Parking Integration System Combined with Cloud Computing Technologies and Smart Mobile Devices

    ERIC Educational Resources Information Center

    Yeh, Her-Tyan; Chen, Bing-Chang; Wang, Bo-Xun

    2016-01-01

    The current study applied cloud computing technology and smart mobile devices combined with a streaming server for parking lots to plan a city parking integration system. It is also equipped with a parking search system, parking navigation system, parking reservation service, and car retrieval service. With this system, users can quickly find…

  10. Combining Self-Explaining with Computer Architecture Diagrams to Enhance the Learning of Assembly Language Programming

    ERIC Educational Resources Information Center

    Hung, Y.-C.

    2012-01-01

    This paper investigates the impact of combining self explaining (SE) with computer architecture diagrams to help novice students learn assembly language programming. Pre- and post-test scores for the experimental and control groups were compared and subjected to covariance (ANCOVA) statistical analysis. Results indicate that the SE-plus-diagram…

  11. Computationally Efficient Modeling of Hydrocarbon Oxidation Chemistry and Flames Using Constituents and Species

    DTIC Science & Technology

    2012-02-10

    species, radicals , combination of radicals , etc.) having essential characteristic time scales (to be defined) and model the kinetics of the remaining...the light species set into a set of modeled quasi-steady species and a set of progress variable species. By definition, constituent radicals are those...both of which are radicals , may have the same chemical formula, the difference between constituents and these light species is that the later are

  12. X-ray solution scattering combined with computation characterizing protein folds and multiple conformational states : computation and application.

    SciTech Connect

    Yang, S.; Park, S.; Makowski, L.; Roux, B.

    2009-02-01

    Small angle X-ray scattering (SAXS) is an increasingly powerful technique to characterize the structure of biomolecules in solution. We present a computational method for accurately and efficiently computing the solution scattering curve from a protein with dynamical fluctuations. The method is built upon a coarse-grained (CG) representation of the protein. This CG approach takes advantage of the low-resolution character of solution scattering. It allows rapid determination of the scattering pattern from conformations extracted from CG simulations to obtain scattering characterization of the protein conformational landscapes. Important elements incorporated in the method include an effective residue-based structure factor for each amino acid, an explicit treatment of the hydration layer at the surface of the protein, and an ensemble average of scattering from all accessible conformations to account for macromolecular flexibility. The CG model is calibrated and illustrated to accurately reproduce the experimental scattering curve of Hen egg white lysozyme. We then illustrate the computational method by calculating the solution scattering pattern of several representative protein folds and multiple conformational states. The results suggest that solution scattering data, when combined with a reliable computational method, have great potential for a better structural description of multi-domain complexes in different functional states, and for recognizing structural folds when sequence similarity to a protein of known structure is low. Possible applications of the method are discussed.

  13. Studying the chemistry of cationized triacylglycerols using electrospray ionization mass spectrometry and density functional theory computations.

    PubMed

    Grossert, J Stuart; Cubero Herrera, Lisandra; Ramaley, Louis; Melanson, Jeremy E

    2014-08-01

    Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na(+)). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na(+), Li(+), K(+), Ag(+), NH4(+)). While most cations bind to oxygen, Ag(+) binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M](+) was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS(3)). These lactones can account for all the major product ions in the MS(3) spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

  14. A Case for Soft Error Detection and Correction in Computational Chemistry

    SciTech Connect

    van Dam, Hubertus JJ; Vishnu, Abhinav; De Jong, Wibe A.

    2013-09-10

    High performance computing platforms are expected to deliver 10(18) floating operations per second by the year 2022 through the deployment of millions of cores. Even if every core is highly reliable the sheer number of the them will mean that the mean time between failures will become so short that most applications runs will suffer at least one fault. In particular soft errors caused by intermittent incorrect behavior of the hardware are a concern as they lead to silent data corruption. In this paper we investigate the impact of soft errors on optimization algorithms using Hartree-Fock as a particular example. Optimization algorithms iteratively reduce the error in the initial guess to reach the intended solution. Therefore they may intuitively appear to be resilient to soft errors. Our results show that this is true for soft errors of small magnitudes but not for large errors. We suggest error detection and correction mechanisms for different classes of data structures. The results obtained with these mechanisms indicate that we can correct more than 95% of the soft errors at moderate increases in the computational cost.

  15. Studying the Chemistry of Cationized Triacylglycerols Using Electrospray Ionization Mass Spectrometry and Density Functional Theory Computations

    NASA Astrophysics Data System (ADS)

    Grossert, J. Stuart; Herrera, Lisandra Cubero; Ramaley, Louis; Melanson, Jeremy E.

    2014-08-01

    Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na+). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na+, Li+, K+, Ag+, NH4 +). While most cations bind to oxygen, Ag+ binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M]+ was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS3). These lactones can account for all the major product ions in the MS3 spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

  16. Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

    PubMed Central

    Miller, Benjamin T.; Singh, Rishi P.; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S.; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R.; Woodcock, H. Lee

    2014-01-01

    This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance. PMID:25057988

  17. The Effects of Study Tasks in a Computer-Based Chemistry Learning Environment

    NASA Astrophysics Data System (ADS)

    Urhahne, Detlef; Nick, Sabine; Poepping, Anna Christin; Schulz, Sarah Jayne

    2013-12-01

    The present study examines the effects of different study tasks on the acquisition of knowledge about acids and bases in a computer-based learning environment. Three different task formats were selected to create three treatment conditions: learning with gap-fill and matching tasks, learning with multiple-choice tasks, and learning only from text and figures without any additional tasks. Participants were 196 ninth-grade students who learned with a self-developed multimedia program in a pretest-posttest control group design. Research results reveal that gap-fill and matching tasks were most effective in promoting knowledge acquisition, followed by multiple-choice tasks, and no tasks at all. The findings are in line with previous research on this topic. The effects can possibly be explained by the generation-recognition model, which predicts that gap-fill and matching tasks trigger more encompassing learning processes than multiple-choice tasks. It is concluded that instructional designers should incorporate more challenging study tasks for enhancing the effectiveness of computer-based learning environments.

  18. Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

    PubMed

    Miller, Benjamin T; Singh, Rishi P; Schalk, Vinushka; Pevzner, Yuri; Sun, Jingjun; Miller, Carrie S; Boresch, Stefan; Ichiye, Toshiko; Brooks, Bernard R; Woodcock, H Lee

    2014-07-01

    This article describes the development, implementation, and use of web-based "lessons" to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that "point and click" simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.

  19. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

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

  20. Chemistry Notes.

    ERIC Educational Resources Information Center

    School Science Review, 1983

    1983-01-01

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

  1. Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)

    PubMed Central

    Le Novère, Nicolas; Hucka, Michael; Anwar, Nadia; Bader, Gary D; Demir, Emek; Moodie, Stuart; Sorokin, Anatoly

    2011-01-01

    The Computational Modeling in Biology Network (COMBINE), is an initiative to coordinate the development of the various community standards and formats in computational systems biology and related fields. This report summarizes the activities pursued at the first annual COMBINE meeting held in Edinburgh on October 6-9 2010 and the first HARMONY hackathon, held in New York on April 18-22 2011. The first of those meetings hosted 81 attendees. Discussions covered both official COMBINE standards-(BioPAX, SBGN and SBML), as well as emerging efforts and interoperability between different formats. The second meeting, oriented towards software developers, welcomed 59 participants and witnessed many technical discussions, development of improved standards support in community software systems and conversion between the standards. Both meetings were resounding successes and showed that the field is now mature enough to develop representation formats and related standards in a coordinated manner. PMID:22180826

  2. Freely available compound data sets and software tools for chemoinformatics and computational medicinal chemistry applications.

    PubMed

    Hu, Ye; Bajorath, Jurgen

    2012-01-01

    We have generated a number of  compound data sets and programs for different types of applications in pharmaceutical research. These data sets and programs were originally designed for our research projects and are made publicly available. Without consulting original literature sources, it is difficult to understand specific features of data sets and software tools, basic ideas underlying their design, and applicability domains. Currently, 30 different entries are available for download from our website. In this data article, we provide an overview of the data and tools we make available and designate the areas of research for which they should be useful. For selected data sets and methods/programs, detailed descriptions are given. This article should help interested readers to select data and tools for specific computational investigations.

  3. Energy intensity of computer manufacturing: hybrid assessment combining process and economic input-output methods.

    PubMed

    Williams, Eric

    2004-11-15

    The total energy and fossil fuels used in producing a desktop computer with 17-in. CRT monitor are estimated at 6400 megajoules (MJ) and 260 kg, respectively. This indicates that computer manufacturing is energy intensive: the ratio of fossil fuel use to product weight is 11, an order of magnitude larger than the factor of 1-2 for many other manufactured goods. This high energy intensity of manufacturing, combined with rapid turnover in computers, results in an annual life cycle energy burden that is surprisingly high: about 2600 MJ per year, 1.3 times that of a refrigerator. In contrast with many home appliances, life cycle energy use of a computer is dominated by production (81%) as opposed to operation (19%). Extension of usable lifespan (e.g. by reselling or upgrading) is thus a promising approach to mitigating energy impacts as well as other environmental burdens associated with manufacturing and disposal.

  4. A Combined Geometric Approach for Computational Fluid Dynamics on Dynamic Grids

    NASA Technical Reports Server (NTRS)

    Slater, John W.

    1995-01-01

    A combined geometric approach for computational fluid dynamics is presented for the analysis of unsteady flow about mechanisms in which its components are in moderate relative motion. For a CFD analysis, the total dynamics problem involves the dynamics of the aspects of geometry modeling, grid generation, and flow modeling. The interrelationships between these three aspects allow for a more natural formulation of the problem and the sharing of information which can be advantageous to the computation of the dynamics. The approach is applied to planar geometries with the use of an efficient multi-block, structured grid generation method to compute unsteady, two-dimensional and axisymmetric flow. The applications presented include the computation of the unsteady, inviscid flow about a hinged-flap with flap deflections and a high-speed inlet with centerbody motion as part of the unstart / restart operation.

  5. Rapid Detection of Biological and Chemical Threat Agents Using Physical Chemistry, Active Detection, and Computational Analysis

    SciTech Connect

    Chung, Myung; Dong, Li; Fu, Rong; Liotta, Lance; Narayanan, Aarthi; Petricoin, Emanuel; Ross, Mark; Russo, Paul; Zhou, Weidong; Luchini, Alessandra; Manes, Nathan; Chertow, Jessica; Han, Suhua; Kidd, Jessica; Senina, Svetlana; Groves, Stephanie

    2007-01-01

    Basic technologies have been successfully developed within this project: rapid collection of aerosols and a rapid ultra-sensitive immunoassay technique. Water-soluble, humidity-resistant polyacrylamide nano-filters were shown to (1) capture aerosol particles as small as 20 nm, (2) work in humid air and (3) completely liberate their captured particles in an aqueous solution compatible with the immunoassay technique. The immunoassay technology developed within this project combines electrophoretic capture with magnetic bead detection. It allows detection of as few as 150-600 analyte molecules or viruses in only three minutes, something no other known method can duplicate. The technology can be used in a variety of applications where speed of analysis and/or extremely low detection limits are of great importance: in rapid analysis of donor blood for hepatitis, HIV and other blood-borne infections in emergency blood transfusions, in trace analysis of pollutants, or in search of biomarkers in biological fluids. Combined in a single device, the water-soluble filter and ultra-sensitive immunoassay technique may solve the problem of early warning type detection of aerosolized pathogens. These two technologies are protected with five patent applications and are ready for commercialization.

  6. Heat Transfer Computations of Internal Duct Flows With Combined Hydraulic and Thermal Developing Length

    NASA Technical Reports Server (NTRS)

    Wang, C. R.; Towne, C. E.; Hippensteele, S. A.; Poinsatte, P. E.

    1997-01-01

    This study investigated the Navier-Stokes computations of the surface heat transfer coefficients of a transition duct flow. A transition duct from an axisymmetric cross section to a non-axisymmetric cross section, is usually used to connect the turbine exit to the nozzle. As the gas turbine inlet temperature increases, the transition duct is subjected to the high temperature at the gas turbine exit. The transition duct flow has combined development of hydraulic and thermal entry length. The design of the transition duct required accurate surface heat transfer coefficients. The Navier-Stokes computational method could be used to predict the surface heat transfer coefficients of a transition duct flow. The Proteus three-dimensional Navier-Stokes numerical computational code was used in this study. The code was first studied for the computations of the turbulent developing flow properties within a circular duct and a square duct. The code was then used to compute the turbulent flow properties of a transition duct flow. The computational results of the surface pressure, the skin friction factor, and the surface heat transfer coefficient were described and compared with their values obtained from theoretical analyses or experiments. The comparison showed that the Navier-Stokes computation could predict approximately the surface heat transfer coefficients of a transition duct flow.

  7. To address accuracy and precision using methods from analytical chemistry and computational physics.

    PubMed

    Kozmutza, Cornelia; Picó, Yolanda

    2009-04-01

    In this work the pesticides were determined by liquid chromatography-mass spectrometry (LC-MS). In present study the occurrence of imidacloprid in 343 samples of oranges, tangerines, date plum, and watermelons from Valencian Community (Spain) has been investigated. The nine additional pesticides were chosen as they have been recommended for orchard treatment together with imidacloprid. The Mulliken population analysis has been applied to present the charge distribution in imidacloprid. Partitioned energy terms and the virial ratios have been calculated for certain molecules entering in interaction. A new technique based on the comparison of the decomposed total energy terms at various configurations is demonstrated in this work. The interaction ability could be established correctly in the studied case. An attempt is also made in this work to address accuracy and precision. These quantities are well-known in experimental measurements. In case precise theoretical description is achieved for the contributing monomers and also for the interacting complex structure some properties of this latter system can be predicted to quite a good accuracy. Based on simple hypothetical considerations we estimate the impact of applying computations on reducing the amount of analytical work.

  8. Scaffolding a Complex Task of Experimental Design in Chemistry with a Computer Environment

    NASA Astrophysics Data System (ADS)

    Girault, Isabelle; d'Ham, Cédric

    2014-08-01

    When solving a scientific problem through experimentation, students may have the responsibility to design the experiment. When students work in a conventional condition, with paper and pencil, the designed procedures stay at a very general level. There is a need for additional scaffolds to help the students perform this complex task. We propose a computer environment (copex-chimie) with embedded scaffolds in order to help students to design an experimental procedure. A pre-structuring of the procedure where the students have to choose the actions of their procedure among pre-defined actions and specify the parameters forces the students to face the complexity of the design. However, this is not sufficient for them to succeed; they look for some feedback to improve their procedure and finally abandon their task. In another condition, the students were provided with individualized feedbacks on the errors detected in their procedures by an artificial tutor. These feedbacks proved to be necessary to accompany the students throughout their experimental design without being discouraged. With this kind of scaffold, students worked longer and succeeded better to the task than all the other students.

  9. Cyclooctatetraene computational photo- and thermal chemistry: a reactivity model for conjugated hydrocarbons.

    PubMed

    Garavelli, Marco; Bernardi, Fernando; Cembran, Alessandro; Castaño, Obis; Frutos, Luis Manuel; Merchán, Manuela; Olivucci, Massimo

    2002-11-20

    We use ab initio CASSCF and CASPT2 computations to construct the composite multistate relaxation path relevant to cycloocta-1,3,5,7-tetraene singlet photochemistry. The results show that an efficient population of the dark excited state (S(1)) takes place after ultrafast decay from the spectroscopic excited state (S(2)). A planar D(8)(h)-symmetric minimum represents the collecting point on S(1). Nonadiabatic transitions to S(0) appear to be controlled by two different tetraradical-type conical intersections, which are directly accessible from the S(1) minimum following specific excited-state reaction paths. The higher-energy conical intersection belongs to the same type of intersections previously documented in linear and cyclic conjugated hydrocarbons and features a triangular -(CH)(3)- kink. This point mediates both cis --> trans photoisomerization and cyclopropanation reactions. The lowest energy conical intersection has a boat-shaped structure. This intersection accounts for production of semibullvalene or for double-bond shifting. The mapping of both photochemical and thermal reaction paths (including also Cope rearrangements, valence isomerizations, ring inversions, and double-bond shifting) has allowed us to draw a comprehensive reactivity scheme for cyclooctatetraene, which rationalizes the experimental observations and documents the complex network of photochemical and thermal reaction path interconnections. The factors controlling the selection and accessibility of a number of conjugated hydrocarbon prototype conical intersections and ground-state relaxation channels are discussed.

  10. Using computational chemistry to understand proton transfer in Green Fluorescent Protein

    NASA Astrophysics Data System (ADS)

    Hoskin, Christa; Champion, Paul; Sage, Timothy; Benabbas, Abdelkrim; Demidov, Alexander; Salna, Bridget

    2012-02-01

    Green Fluorescent Protein has been studied experimentally by the scientific community for years yet frustratingly little is known about the underlying proton transfer process that produces the green fluorescence. We are trying to elucidate more about this process using Density Functional Theory to prepare and run various calculations on GFP that we compare with kinetics data, Raman and vibrational coherence spectra. I am building a model of wild type GFP that is realistically sized for our computational power, yet still contains key residues that might affect the proton transport process. I will compare my results to those of the E222D GFP mutant. This comparison will allow us to see any differences in energy and normal modes that give insights regarding the proton transfer process. For example, how does it depend on a variety of factors such as temperature, buffer, pH, mutations, etc.? We also plan to examine if the proton transfer propagates through the three donor-acceptor pairs of the ``proton wire'' consecutively versus the three protons on the wire transferring simultaneously. Finally, we will consider how quantum tunneling may be involved in the proton transfer.

  11. Enhancing simulation of efficiency with analytical tools. [combining computer simulation and analytical techniques for cost reduction

    NASA Technical Reports Server (NTRS)

    Seltzer, S. M.

    1974-01-01

    Some means of combining both computer simulation and anlytical techniques are indicated in order to mutually enhance their efficiency as design tools and to motivate those involved in engineering design to consider using such combinations. While the idea is not new, heavy reliance on computers often seems to overshadow the potential utility of analytical tools. Although the example used is drawn from the area of dynamics and control, the principles espoused are applicable to other fields. In the example the parameter plane stability analysis technique is described briefly and extended beyond that reported in the literature to increase its utility (through a simple set of recursive formulas) and its applicability (through the portrayal of the effect of varying the sampling period of the computer). The numerical values that were rapidly selected by analysis were found to be correct for the hybrid computer simulation for which they were needed. This obviated the need for cut-and-try methods to choose the numerical values, thereby saving both time and computer utilization.

  12. Navier-Stokes computations with finite-rate chemistry for LO2/LH2 rocket engine plume flow studies

    NASA Technical Reports Server (NTRS)

    Dougherty, N. Sam; Liu, Baw-Lin

    1991-01-01

    Computational fluid dynamics methods have been developed and applied to Space Shuttle Main Engine LO2/LH2 plume flow simulation/analysis of airloading and convective base heating effects on the vehicle at high flight velocities and altitudes. New methods are described which were applied to the simulation of a Return-to-Launch-Site abort where the vehicle would fly briefly at negative angles of attack into its own plume. A simplified two-perfect-gases-mixing approach is used where one gas is the plume and the other is air at 180-deg and 135-deg flight angle of attack. Related research has resulted in real gas multiple-plume interaction methods with finite-rate chemistry described herein which are applied to the same high-altitude-flight conditions of 0 deg angle of attack. Continuing research plans are to study Orbiter wake/plume flows at several Mach numbers and altitudes during ascent and then to merge this model with the Shuttle 'nose-to-tail' aerodynamic and SRB plume models for an overall 'nose-to-plume' capability. These new methods are also applicable to future launch vehicles using clustered-engine LO2/LH2 propulsion.

  13. Hapten-antibody recognition studies in competitive immunoassay of α-zearalanol analogs by computational chemistry and Pearson Correlation analysis.

    PubMed

    Wang, Zhanhui; Luo, Pengjie; Cheng, Linli; Zhang, Suxia; Shen, Jianzhong

    2011-01-01

    The molecular recognition of hapten-antibody is a fundamental event in competitive immunoassay, which guarantees the sensitivity and specificity of immunoassay for the detection of haptens. The aim of this study is to investigate the correlation between binding ability of one monoclonal antibody, 1H9B4, recognizing and the molecular aspects of α-zearalanol analogs. The mouse-derived monoclonal antibody was produced by using α-zearalanol conjugated to bovine serum albumin as an immunogen. The antibody recognition abilities, expressed as IC(50) values, were determined by a competitive ELISA. All of the hapten molecules were optimized by Density Function Theory (DFT) at B3LYP/ 6-31G* level and the conformation and electrostatic molecular isosurface were employed to explain the molecular recognition between α-zearalanol analogs and antibody 1H9B4. Pearson Correlation analysis between molecular descriptors and IC(50) values was qualitatively undertaken and the results showed that one molecular descriptor, surface of the hapten molecule, clearly demonstrated linear relationship with antibody recognition ability, where the relationship coefficient was 0.88 and the correlation was significant at p < 0.05 level. The study shows that computational chemistry and Pearson Correlation analysis can be used as tool to help the immunochemistries better understand the processing of antibody recognition of hapten molecules in competitive immunoassay.

  14. Application of computational chemistry methods to the prediction of chirality and helical twisting power in liquid crystal systems

    NASA Astrophysics Data System (ADS)

    Noto, Anthony G.; Marshall, Kenneth L.

    2005-08-01

    Until recently, it has not been possible to determine, with any real certainty, a complete picture of "chirality" (absolute configuration, optical rotation direction, and helical twisting power) for new chiral compounds without first synthesizing, purifying, characterizing, and testing every new material. Recent advances in computational chemistry now allow the prediction of certain key chiral molecular properties prior to synthesis, which opens the possibility of predetermining the "chiroptical" properties of new liquid crystal dopants and mixtures for advanced optical and photonics applications. A key element to this activity was the development of both the chirality index (G0) by Osipov et al., and the scaled chirality index (G0S) by Solymosi et al., that can be used as a "figure of merit" for molecular chirality. Promising correlations between G0S and both circular dichroism (CD) and the helical twisting power (HTP) of a chiral dopant in a liquid crystal host have been shown by Neal et al., Osipov, and Kuball. Our work improves the predictive capabilities of G0S by taking into account the actual mass of each atom in the molecule in the calculations; in previous studies the mass of each atom was assumed to be equal. This "weighted" scaled chirality index (G0SW) was calculated and correlated to existing experimental HTP data for each member of a series of existing, well-known chiral compounds. The computed HTP using G0SW for these model systems correlated to the experimental data with remarkable accuracy. Weighted, scaled chiral indices were also calculated for the first time for a series of novel chiral transition metal dithiolene dyes for near-IR liquid crystal device applications.

  15. Combining Acceleration Techniques for Low-Dose X-Ray Cone Beam Computed Tomography Image Reconstruction.

    PubMed

    Huang, Hsuan-Ming; Hsiao, Ing-Tsung

    2017-01-01

    Over the past decade, image quality in low-dose computed tomography has been greatly improved by various compressive sensing- (CS-) based reconstruction methods. However, these methods have some disadvantages including high computational cost and slow convergence rate. Many different speed-up techniques for CS-based reconstruction algorithms have been developed. The purpose of this paper is to propose a fast reconstruction framework that combines a CS-based reconstruction algorithm with several speed-up techniques. First, total difference minimization (TDM) was implemented using the soft-threshold filtering (STF). Second, we combined TDM-STF with the ordered subsets transmission (OSTR) algorithm for accelerating the convergence. To further speed up the convergence of the proposed method, we applied the power factor and the fast iterative shrinkage thresholding algorithm to OSTR and TDM-STF, respectively. Results obtained from simulation and phantom studies showed that many speed-up techniques could be combined to greatly improve the convergence speed of a CS-based reconstruction algorithm. More importantly, the increased computation time (≤10%) was minor as compared to the acceleration provided by the proposed method. In this paper, we have presented a CS-based reconstruction framework that combines several acceleration techniques. Both simulation and phantom studies provide evidence that the proposed method has the potential to satisfy the requirement of fast image reconstruction in practical CT.

  16. A computational investigation of HCN2+ isomeric structures: implications for the chemistry of Titan's atmosphere.

    PubMed

    Antoniotti, Paola; Borocci, Stefano; Bronzolino, Nicoletta; Grandinetti, Felice

    2004-09-20

    The structure and stability of various HCN2+ isomeric structures have been investigated at the complete active space SCF (CASSCF) and multireference-configuration interaction [MR-Cl-SD(Q)] levels of theory with the 6-31G(d) and 6-311G(d,p) basis sets. The investigated species include the singlet (S) and triplet (T) open-chain H-N-C-N+ ions 1S, 1S', and 1T, the open-chain H-C-N-N+ ions 2S, 2S', and 2T, the HC-N2+ cyclic structures 3S and 3T, and the HN-CN+ cyclic structures 4S and 4T. All these species have been identified as true energy minima on the CASSCF(8,7)/6-31G(d) potential energy surface, and their optimised geometries, refined at the CASSCF(8,8)/6-31G(d) level of theory, have been used to perform single point calculations at the [MR-Cl-SD(Q]/6-311G(d,p) computational level. The most stable structure was the H-N-C-N+ ion 1T, whose absolute enthalpy of formation at 298.15 K has been estimated as 333.9 +/- 2 kcalmol(-1) using the Gaussian-3 (G3) procedure. The two species closest in energy to 1T are the triplet H-C-N-N+ ion 2T and the singlet diazirinyl cation 3S, whose G3 enthalpies of formation at 298.15 K are 343.5 +/- 2 and 340.6 +/- 2 kcalmol(-1), respectively. Finally, we have discussed the implications of our calculations for the detailed structure of the HCN2+ ions formed in the reaction between N3+ and HCN, experimentally observed by flowing after-glow-selected ion flow/drift tube mass spectrometry and possibly occurring in Titan's atmosphere.

  17. Hydration of atmospherically relevant molecular clusters: computational chemistry and classical thermodynamics.

    PubMed

    Henschel, Henning; Navarro, Juan C Acosta; Yli-Juuti, Taina; Kupiainen-Määttä, Oona; Olenius, Tinja; Ortega, Ismael K; Clegg, Simon L; Kurtén, Theo; Riipinen, Ilona; Vehkamäki, Hanna

    2014-04-10

    Formation of new particles through clustering of molecules from condensable vapors is a significant source for atmospheric aerosols. The smallest clusters formed in the very first steps of the condensation process are, however, not directly observable by experimental means. We present here a comprehensive series of electronic structure calculations on the hydrates of clusters formed by up to four molecules of sulfuric acid, and up to two molecules of ammonia or dimethylamine. Though clusters containing ammonia, and certainly dimethylamine, generally exhibit lower average hydration than the pure acid clusters, populations of individual hydrates vary widely. Furthermore, we explore the predictions obtained using a thermodynamic model for the description of these hydrates. The similar magnitude and trends of hydrate formation predicted by both methods illustrate the potential of combining them to obtain more comprehensive models. The stabilization of some clusters relative to others due to their hydration is highly likely to have significant effects on the overall processes that lead to formation of new particles in the atmosphere.

  18. Computational Chemistry-Based Identification of Ultra-Low Temperature Water-Gas-Shift Catalysts

    SciTech Connect

    Manos Mavrikakis

    2008-08-31

    The current work seeks to identify novel, catalytically-active, stable, poison-resistant LWGS catalysts that retain the superior activity typical of conventional Cu catalysts but can be operated at similar or lower temperatures. A database for the Binding Energies (BEs) of the LWGS relevant species, namely CO, O and OH on the most-stable, close-packed facets of a set of 17 catalytically relevant transition metals was established. This BE data and a database of previously established segregation energies was utilized to predict the stability of bimetallic NSAs that could be synthesized by combinations of the 17 parent transition metals. NSAs that were potentially stable both in vacuo and under the influence of strong-binding WGS intermediates were then selected for adsorption studies. A set of 40 NSAs were identified that satisfied all three screener criteria and the binding energies of CO, O and OH were calculated on a set of 66, 43 and 79 NSA candidates respectively. Several NSAs were found that bound intermediates weaker than the monometallic catalysts and were thus potentially poison-resistant. Finally, kinetic studies were performed and resulted in the discovery of a specific NSA-based bimetallic catalyst Cu/Pt that is potentially a promising LWGS catalyst. This stable Cu/Pt subsurface alloy is expected to provide facile H{sub 2}O activation and remain relatively resistant from the poisoning by CO, S and formate intermediates.

  19. [Computational fluid dynamics simulation of different impeller combinations in high viscosity fermentation and its application].

    PubMed

    Dong, Shuhao; Zhu, Ping; Xu, Xiaoying; Li, Sha; Jiang, Yongxiang; Xu, Hong

    2015-07-01

    Agitator is one of the essential factors to realize high efficient fermentation for high aerobic and viscous microorganisms, and the influence of different impeller combination on the fermentation process is very important. Welan gum is a microbial exopolysaccharide produced by Alcaligenes sp. under high aerobic and high viscos conditions. Computational fluid dynamics (CFD) numerical simulation was used for analyzing the distribution of velocity, shear rate and gas holdup in the welan fermentation reactor under six different impeller combinations. The best three combinations of impellers were applied to the fermentation of welan. By analyzing the fermentation performance, the MB-4-6 combination had better effect on dissolved oxygen and velocity. The content of welan was increased by 13%. Furthermore, the viscosity of production were also increased.

  20. Understanding the hydrolysis mechanism of ethyl acetate catalyzed by an aqueous molybdocene: a computational chemistry investigation.

    PubMed

    Tílvez, Elkin; Cárdenas-Jirón, Gloria I; Menéndez, María I; López, Ramón

    2015-02-16

    A thoroughly mechanistic investigation on the [Cp2Mo(OH)(OH2)](+)-catalyzed hydrolysis of ethyl acetate has been performed using density functional theory methodology together with continuum and discrete-continuum solvation models. The use of explicit water molecules in the PCM-B3LYP/aug-cc-pVTZ (aug-cc-pVTZ-PP for Mo)//PCM-B3LYP/aug-cc-pVDZ (aug-cc-pVDZ-PP for Mo) computations is crucial to show that the intramolecular hydroxo ligand attack is the preferred mechanism in agreement with experimental suggestions. Besides, the most stable intermediate located along this mechanism is analogous to that experimentally reported for the norbornenyl acetate hydrolysis catalyzed by molybdocenes. The three most relevant steps are the formation and cleavage of the tetrahedral intermediate immediately formed after the hydroxo ligand attack and the acetic acid formation, with the second one being the rate-determining step with a Gibbs energy barrier of 36.7 kcal/mol. Among several functionals checked, B3LYP-D3 and M06 give the best agreement with experiment as the rate-determining Gibbs energy barrier obtained only differs 0.2 and 0.7 kcal/mol, respectively, from that derived from the experimental kinetic constant measured at 296.15 K. In both cases, the acetic acid elimination becomes now the rate-determining step of the overall process as it is 0.4 kcal/mol less stable than the tetrahedral intermediate cleavage. Apart from clarifying the identity of the cyclic intermediate and discarding the tetrahedral intermediate formation as the rate-determining step for the mechanism of the acetyl acetate hydrolysis catalyzed by molybdocenes, the small difference in the Gibbs energy barrier found between the acetic acid formation and the tetrahedral intermediate cleavage also uncovers that the rate-determining step could change when studying the reactivity of carboxylic esters other than ethyl acetate substrate specific toward molybdocenes or other transition metal complexes. Therefore

  1. Combining associative computing and distributed arithmetic methods for efficient implementation of multiple inner products

    NASA Astrophysics Data System (ADS)

    Guevorkian, David; Yli-Pietilä, Timo; Liuha, Petri; Egiazarian, Karen

    2012-02-01

    Many multimedia processing algorithms as well as communication algorithms implemented in mobile devices are based on intensive implementation of linear algebra methods, in particular, implying implementation of a large number of inner products in real time. Among most efficient approaches to perform inner products are the Associative Computing (ASC) approach and Distributed Arithmetic (DA) approach. In ASC, computations are performed on Associative Processors (ASP), where Content-Addressable memories (CAMs) are used instead of traditional processing elements to perform basic arithmetic operations. In the DA approach, computations are reduced to look-up table reads with respect to binary planes of inputs. In this work, we propose a modification of Associative processors that supports efficient implementation of the DA method. Thus, the two powerful methods are combined to further improve the efficiency of multiple inner product computation. Computational complexity analysis of the proposed method illustrates significant speed-up when computing multiple inner products as compared both to the pure ASC method and to the pure DA method as well as to other state-of the art traditional methods for inner product calculation.

  2. Computational medicinal chemistry for rational drug design: Identification of novel chemical structures with potential anti-tuberculosis activity.

    PubMed

    Koseki, Yuji; Aoki, Shunsuke

    2014-01-01

    Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis and is a common infectious disease with high mortality and morbidity. The increasing prevalence of drug-resistant strains of TB presents a major public health problem. Due to the lack of effective drugs to treat these drug-resistant strains, the discovery or development of novel anti-TB drugs is important. Computer-aided drug design has become an established strategy for the identification of novel active chemicals through a combination of several drug design tools. In this review, we summarise the current chemotherapy for TB, describe attractive target proteins for the development of antibiotics against TB, and detail several computational drug design strategies that may contribute to the further identification of active chemicals for the treatment of not only TB but also other diseases.

  3. Emerging technology in surgical education: combining real-time augmented reality and wearable computing devices.

    PubMed

    Ponce, Brent A; Menendez, Mariano E; Oladeji, Lasun O; Fryberger, Charles T; Dantuluri, Phani K

    2014-11-01

    The authors describe the first surgical case adopting the combination of real-time augmented reality and wearable computing devices such as Google Glass (Google Inc, Mountain View, California). A 66-year-old man presented to their institution for a total shoulder replacement after 5 years of progressive right shoulder pain and decreased range of motion. Throughout the surgical procedure, Google Glass was integrated with the Virtual Interactive Presence and Augmented Reality system (University of Alabama at Birmingham, Birmingham, Alabama), enabling the local surgeon to interact with the remote surgeon within the local surgical field. Surgery was well tolerated by the patient and early surgical results were encouraging, with an improvement of shoulder pain and greater range of motion. The combination of real-time augmented reality and wearable computing devices such as Google Glass holds much promise in the field of surgery.

  4. Computational investigations on polymerase actions in gene transcription and replication: Combining physical modeling and atomistic simulations

    NASA Astrophysics Data System (ADS)

    Jin, Yu

    2016-01-01

    Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication fidelity through the non-equilibrium enzymatic cycles. We briefly review computational efforts that have been made toward understanding mechano-chemical coupling and fidelity control mechanisms of the polymerase elongation. The polymerases are regarded as molecular information motors during the elongation process. It requires a full spectrum of computational approaches from multiple time and length scales to understand the full polymerase functional cycle. We stay away from quantum mechanics based approaches to the polymerase catalysis due to abundant former surveys, while addressing statistical physics modeling approaches along with all-atom molecular dynamics simulation studies. We organize this review around our own modeling and simulation practices on a single subunit T7 RNA polymerase, and summarize commensurate studies on structurally similar DNA polymerases as well. For multi-subunit RNA polymerases that have been actively studied in recent years, we leave systematical reviews of the simulation achievements to latest computational chemistry surveys, while covering only representative studies published very recently, including our own work modeling structure-based elongation kinetic of yeast RNA polymerase II. In the end, we briefly go through physical modeling on elongation pauses and backtracking activities of the multi-subunit RNAPs. We emphasize on the fluctuation and control mechanisms of the polymerase actions, highlight the non-equilibrium nature of the operation system, and try to build some perspectives toward understanding the polymerase impacts from the single molecule level to a genome-wide scale. Project supported by the National Natural Science Foundation (Grant No. 11275022).

  5. UV-Photoelectron Spectroscopy of 1,2- and 1,3-Azaborines: A Combined Experimental and Computational Electronic Structure Analysis

    PubMed Central

    Chrostowska, Anna; Xu, Senmiao; Lamm, Ashley N.; Mazière, Audrey; Weber, Christopher D.; Dargelos, Alain; Baylère, Patrick; Graciaa, Alain; Liu, Shih-Yuan

    2012-01-01

    We present a comprehensive electronic structure analysis of structurally simple BN heterocycles using a combined UV-photoelectron spectroscopy (UV-PES) / computational chemistry approach. Gas-phase He I photoelectron spectra of 1,2-dihydro-1,2-azaborine 1, N-Me-1,2-BN-toluene 2, and N-Me-1,3-BN-toluene 3 have been recorded, assessed by density functional theory calculations, and compared with their corresponding carbonaceous analogues benzene and toluene. The first ionization energies of these BN heterocycles are in the order N-Me-1,3-BN-toluene 3 (8.0 eV) < N-Me-1,2-BN-toluene 2 (8.45 eV) < 1,2-dihydro-1,2-azaborine 1 (8.6 eV) < toluene (8.83 eV) < benzene (9.25 eV). The computationally determined molecular dipole moments are in the order 3 (4.577 Debye) > 2 (2.209 Debye) > 1 (2.154 Debye) > toluene (0.349 Debye) > benzene (0 Debye) and are consistent with experimental observations. The λmax in the UV-Vis absorption spectra are in the order 3 (297 nm) > 2 (278 nm) > 1 (269 nm) > toluene (262 nm) > benzene (255 nm). We also establish that the measured anodic peak potentials and electrophilic aromatic substitution (EAS) reactivity of BN heterocycles 1–3 are consistent with the electronic structure description determined by the combined UV-PES/computational chemistry approach. PMID:22616808

  6. Prediction of nitroxide hyperfine coupling constants in solution from combined nanosecond scale simulations and quantum computations

    NASA Astrophysics Data System (ADS)

    Houriez, Céline; Ferré, Nicolas; Masella, Michel; Siri, Didier

    2008-06-01

    We present a combined theoretical approach based on analyzing molecular dynamics trajectories (at the nanosecond scale) generated by use of classical polarizable force fields and on quantum calculations to compute averaged hyperfine coupling constants. That method is used to estimate the constant of a prototypical nitroxide: the dimethylnitroxide. The molecule is embedded during the simulations in a cubic box containing about 500 water molecules and the molecular dynamics is generated using periodic conditions. Once the trajectories are achieved, the nitroxide and its first hydration shell molecules are extracted, and the coupling constants are computed by considering the latter aggregates by means of quantum computations. However, all the water molecules of the bulk are also accounted for during those computations by means of the electrostatic potential fitted method. Our results exhibit that in order to predict accurate and reliable coupling constants, one needs to describe carefully the out-of-plane motion of the nitroxide nitrogen and to sample trajectories with a time interval of 400 fs at least to generate an uncorrelated large set of nitroxide structures. Compared to Car-Parrinello molecular dynamics techniques, our approach can be used readily to compute hyperfine coupling constants of large systems, such as nitroxides of great size interacting with macromolecules such as proteins or polymers.

  7. Computational identification of potential multi-drug combinations for reduction of microglial inflammation in Alzheimer disease

    PubMed Central

    Anastasio, Thomas J.

    2015-01-01

    Like other neurodegenerative diseases, Alzheimer Disease (AD) has a prominent inflammatory component mediated by brain microglia. Reducing microglial inflammation could potentially halt or at least slow the neurodegenerative process. A major challenge in the development of treatments targeting brain inflammation is the sheer complexity of the molecular mechanisms that determine whether microglia become inflammatory or take on a more neuroprotective phenotype. The process is highly multifactorial, raising the possibility that a multi-target/multi-drug strategy could be more effective than conventional monotherapy. This study takes a computational approach in finding combinations of approved drugs that are potentially more effective than single drugs in reducing microglial inflammation in AD. This novel approach exploits the distinct advantages of two different computer programming languages, one imperative and the other declarative. Existing programs written in both languages implement the same model of microglial behavior, and the input/output relationships of both programs agree with each other and with data on microglia over an extensive test battery. Here the imperative program is used efficiently to screen the model for the most efficacious combinations of 10 drugs, while the declarative program is used to analyze in detail the mechanisms of action of the most efficacious combinations. Of the 1024 possible drug combinations, the simulated screen identifies only 7 that are able to move simulated microglia at least 50% of the way from a neurotoxic to a neuroprotective phenotype. Subsequent analysis shows that of the 7 most efficacious combinations, 2 stand out as superior both in strength and reliability. The model offers many experimentally testable and therapeutically relevant predictions concerning effective drug combinations and their mechanisms of action. PMID:26097457

  8. Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic

    ERIC Educational Resources Information Center

    Jirat, Jiri; Cech, Petr; Znamenacek, Jiri; Simek, Miroslav; Skuta, Ctibor; Vanek, Tomas; Dibuszova, Eva; Nic, Miloslav; Svozil, Daniel

    2013-01-01

    Experience developing multidisciplinary bachelor's and master's curricula involving intertwined chemistry, informatics, and librarianship-editorship skills is described. The bachelor's curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chemical Technology Prague: a sole…

  9. Water as Life, Death, and Power: Building an Integrated Interdisciplinary Course Combining Perspectives from Anthropology, Biology, and Chemistry

    ERIC Educational Resources Information Center

    Willermet, Cathy; Mueller, Anja; Juris, Stephen J.; Drake, Eron; Upadhaya, Samik; Chhetri, Pratik

    2013-01-01

    In response to a request from a campus student organization, faculty from three fields came together to develop and teach an integrated interdisciplinary course on water issues and social activism. This course, "Water as Life, Death, and Power", brought together topics from the fields of anthropology, biology and chemistry to explore…

  10. Identification of Unknown Chloride Salts Using a Combination of Qualitative Analysis and Titration with Silver Nitrate: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Maines, Laina L.; Bruch, Martha D.

    2012-01-01

    General chemistry students often have difficulty writing balanced equations and performing stoichiometry calculations for precipitation reactions, in part because of difficulty understanding the symbolic notation used to represent chemical reactions. We have developed a problem-based experiment to improve student learning of these concepts, and…

  11. Identification of Unknown Chloride Salts Using a Combination of Qualitative Analysis and Titration with Silver Nitrate: A General Chemistry Laboratory

    ERIC Educational Resources Information Center

    Maines, Laina L.; Bruch, Martha D.

    2012-01-01

    General chemistry students often have difficulty writing balanced equations and performing stoichiometry calculations for precipitation reactions, in part because of difficulty understanding the symbolic notation used to represent chemical reactions. We have developed a problem-based experiment to improve student learning of these concepts, and…

  12. Developing and Implementing a Combined Chemistry and Informatics Curriculum for Undergraduate and Graduate Students in the Czech Republic

    ERIC Educational Resources Information Center

    Jirat, Jiri; Cech, Petr; Znamenacek, Jiri; Simek, Miroslav; Skuta, Ctibor; Vanek, Tomas; Dibuszova, Eva; Nic, Miloslav; Svozil, Daniel

    2013-01-01

    Experience developing multidisciplinary bachelor's and master's curricula involving intertwined chemistry, informatics, and librarianship-editorship skills is described. The bachelor's curriculum was created in close cooperation of academic staff, library staff, and the publishing house staff (Institute of Chemical Technology Prague: a sole…

  13. Combining label-free cell phenotypic profiling with computational approaches for novel drug discovery.

    PubMed

    Fang, Ye

    2015-04-01

    Drug discovery is a long and costly process. Innovations and paradigm shifts are essential for continuous improvement in the productivity of pharmaceutical R&D. The author reviews the progress of label-free cell phenotypic and computational approaches in early drug discovery since 2004 and proposes a novel paradigm, which combines both approaches. Label-free cell phenotypic profiling techniques offer an unprecedented and integrated approach to comprehend drug-target interactions in their native environments. However, these approaches have disadvantages associated with the lack of molecular details. Computational approaches, including ligand-, structure- and phenotype-based virtual screens, have become versatile tools in the early drug discovery process. However, these approaches mostly predict the binding of drug molecules to targets of interest and are limited to targets that are either well annotated for ligands or that are structurally resolved. Thus, combining label-free cell phenotypic profiling with computational approaches can provide a potential paradigm to accelerate novel drug discovery by taking advantages of the best of both approaches.

  14. The Description and Validation of a Computationally-Efficient CH4-CO-OH (ECCOHv1.01) Chemistry Module for 3D Model Applications

    NASA Technical Reports Server (NTRS)

    Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

    2016-01-01

    We present the Efficient CH4-CO-OH (ECCOH) chemistry module that allows for the simulation of the methane, carbon monoxide, and hydroxyl radical (CH4-CO- OH) system, within a chemistry climate model, carbon cycle model, or Earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO, and OH, and the concomitant impacts on climate. We implemented the ECCOH chemistry module in the NASA GEOS-5 atmospheric global circulation model (AGCM), performed multiple sensitivity simulations of the CH4-CO-OH system over 2 decades, and evaluated the model output with surface and satellite data sets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS- 5 AGCM) with observations demonstrates the fidelity of the module for use in scientific research.

  15. The description and validation of the computationally Efficient CH4-CO-OH (ECCOHv1.01) chemistry module for 3-D model applications

    NASA Astrophysics Data System (ADS)

    Elshorbany, Yasin F.; Duncan, Bryan N.; Strode, Sarah A.; Wang, James S.; Kouatchou, Jules

    2016-02-01

    We present the Efficient CH4-CO-OH (ECCOH) chemistry module that allows for the simulation of the methane, carbon monoxide, and hydroxyl radical (CH4-CO-OH) system, within a chemistry climate model, carbon cycle model, or Earth system model. The computational efficiency of the module allows many multi-decadal sensitivity simulations of the CH4-CO-OH system, which primarily determines the global atmospheric oxidizing capacity. This capability is important for capturing the nonlinear feedbacks of the CH4-CO-OH system and understanding the perturbations to methane, CO, and OH, and the concomitant impacts on climate. We implemented the ECCOH chemistry module in the NASA GEOS-5 atmospheric global circulation model (AGCM), performed multiple sensitivity simulations of the CH4-CO-OH system over 2 decades, and evaluated the model output with surface and satellite data sets of methane and CO. The favorable comparison of output from the ECCOH chemistry module (as configured in the GEOS-5 AGCM) with observations demonstrates the fidelity of the module for use in scientific research.

  16. Computational modelling of combining compressible flow through 30--150{degree} tee junction

    SciTech Connect

    Haidar, N.I.A.

    1994-12-31

    The present computational investigation is concerned with quantifying the influence of fluid compressibility on the additional total pressure losses in three-leg branched ducts. A fully-elliptic, control volume computational model is presented for the simulation of subsonic steady flow under combining conditions in 30--150{degree} sharp-cornered tee-junctions, in 300 increments, similar to those used in the secondary air cooling systems of gas turbine engines. For the main part of the flow the {kappa}-{epsilon} turbulence model is adopted, while wall functions are employed in the near wall region. A comparison is presented between computational and experimental results for the additional total pressure losses occurring in these tee-junctions using dry air as the working fluid. The Mach number of the average flow in the leg carrying the whole flow range between 0.2 and 0.6 in 0.1 increments. The successive refinement of the grid is found to bring the computed additional total pressure loss coefficients (i.e. pressure fields) into close accord with measurements. The comparison demonstrates that the adopted procedure is capable of predicting magnitude of pressure losses and extent of separation regions of low subsonic flows in branched ducts.

  17. The unimolecular chemistry of protonated and deprotonated 2,2-dinitroethene-1,1-diamine (FOX-7) studied by tandem mass spectrometry and computational chemistry.

    PubMed

    Žabka, Ján; Šimková, Ludmila; Jalový, Zdeněk; Polášek, Miroslav

    2014-01-01

    2,2-Dinitroethene-1,1-diamine (FOX-7) was studied by means of electrospray ionization (ESI) and chemical ionization (CI) mass spectrometry in both positive and negative ion mode. Detailed mechanisms of unimolecular fragmentations of protonated and deprotonated FOX-7 were investigated using high- and low- energy collision-induced dissociation (CID) mass spectrometry, neutral fragment reionization mass spectrometry and quantum chemistry calculations. In deprotonated FOX-7, elimination of the carbodiimide molecule was identified as the energetically most favored fragmentation channel, closely resembling the base hydrolysis of FOX-7. The dinitromethanide ion is formed during this fragmentation as revealed by comparison with CID mass spectra of an isobaric ion prepared by the ESI of authentic sodium dinitromethanide. The proton affinity of FOX-7 was estimated as 855 kJ mo(-1) by high-accuracy quantum chemistry calculations. This value corresponds to protonation at the C-2 position, though the oxygen-protonated tautomer was found to be nearly isoenergetic in the gas phase. In acetonitrile, the nitro group-protonated FOX-7 was found to be significantly less stable then its C-2 tautomer. These theoretical findings are clearly reflected in differences in fragmentations of ESI- and CI-generated [M+H(]+) ions. Interestingly, the consecutive losses of OH∙ and NO2∙ radicals instead of a whole HNO3 molecule were found to account for the most abundant fragment ion in the positive ESI CID mass spectra. In the CI-generated [M+H](+) and [M+D](+) ions, substantial internal energy effects upon the CID were observed.

  18. Computational thermodynamics, Gaussian processes and genetic algorithms: combined tools to design new alloys

    NASA Astrophysics Data System (ADS)

    Tancret, F.

    2013-06-01

    A new alloy design procedure is proposed, combining in a single computational tool several modelling and predictive techniques that have already been used and assessed in the field of materials science and alloy design: a genetic algorithm is used to optimize the alloy composition for target properties and performance on the basis of the prediction of mechanical properties (estimated by Gaussian process regression of data on existing alloys) and of microstructural constitution, stability and processability (evaluated by computational themodynamics). These tools are integrated in a unique Matlab programme. An example is given in the case of the design of a new nickel-base superalloy for future power plant applications (such as the ultra-supercritical (USC) coal-fired plant, or the high-temperature gas-cooled nuclear reactor (HTGCR or HTGR), where the selection criteria include cost, oxidation and creep resistance around 750 °C, long-term stability at service temperature, forgeability, weldability, etc.

  19. Design, development and characterization of a novel neutron and x-ray combined computed tomography system

    NASA Astrophysics Data System (ADS)

    Sinha, Vaibhav

    Visualizing the three dimensional structure of objects (e.g. nuclear fuel, nuclear materials, explosives and bio materials) and phenomena (e.g. particle tracking) can be very important in nondestructive testing applications. Computed tomography systems are indispensable tools for these types of applications because they provide a versatile non-destructive technique for analysis. A novel neutron and X-ray combined computed tomography (NXCT) system has been designed and developed at the Missouri University of Science & Technology. The neutron and X-ray combined computed tomography system holds much promise for non-destructive material detection and analysis where multiple materials having similar atomic number and differing thermal cross section or vice versa may be present within an object, exclusive neutron or X-ray analysis may exhibit shortcomings in distinguishing interfaces. However, fusing neutron image and X-ray image offers the strengths of both and may provide a superior method of analysis. In addition, a feasible design of a sample positioning system which allows the user to remotely and automatically manipulate the objects makes the NXCT system viable for commercial applications. Moreover, characterization of the newly developed digital imaging system is imperative to the performance evaluation, as well as for describing the associated parameters. The performance of a combined neutron/X-ray digital imaging system was evaluated in terms of modulation transfer function (MTF), noise power spectrum (NPS) and detective quantum efficiency (DQE). This dissertation is a complete overview of the design of the NXCT system, operation, algorithms, performance evaluation and results.

  20. a Look at Nitrile Chemistry in SGR B2(N) Using the Combined Power of the GBT and the VLA

    NASA Astrophysics Data System (ADS)

    Steber, Amanda; Zaleski, Daniel P.; Seifert, Nathan A.; Neill, Justin; Muckle, Matt; Pate, Brooks; Corby, Joanna F.; Remijan, Anthony

    2014-06-01

    Nitriles form the most prolific family of molecules known in the ISM, and laboratory work shows that radical-driven chemistry can account for the formation of a diverse set of nitrile and imine molecules. Broadband reaction screening of nitrile chemistry in a pulsed discharge nozzle coupled to a chirped-pulse Fourier transform rotational spectrometer has enabled detections of several new interstellar species including E- and Z-ethanimine and E-cyanomethanimine. The detections were made by direct comparisons of laboratory broadband rotational spectra with the Robert C. Byrd Green Bank Telescope (GBT) PRebiotic Interstellar MOlecule Survery (PRIMOS) survey towards Sgr B2(N), the most chemically complex interstellar region known. In order to probe nitrile chemistry in Sgr B2, we targeted low energy rotational transitions in the 18-21 GHz range of several nitriles with the Karl G. Jansky Very Large Array (VLA) at ˜1 arcsecond resolution. The data indicate that most nitriles and nitrile derivatives are co-spatial with shell shaped continuum features thought to be expanding ionization fronts. The CH2CN radical and imine species in particular are NOT associated with the hot core known as the "Large Molecule Heimat", where most large organic molecules are thought to reside. This result suggests radical driven nitrile chemistry may be promoted by near-UV radiation in moderate density regions of molecular clouds, and the data will be useful for evaluating possible formation mechanisms. R.A. Loomis et al. Ap. J. L., 765, (L9), 2013. D.P. Zaleski et al. Ap. J. L., 765, (L10), 2013.