extensible computational chemistry: Topics by Science.gov

Sample records for extensible computational chemistry

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...
[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.
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)).
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.
Instrumental Analysis Chemistry Laboratory

ERIC Educational Resources Information Center

Munoz de la Pena, Arsenio; Gonzalez-Gomez, David; Munoz de la Pena, David; Gomez-Estern, Fabio; Sequedo, Manuel Sanchez

2013-01-01

designed for automating the collection and assessment of laboratory exercises is presented. This Web-based system has been extensively used in engineering courses such as control systems, mechanics, and computer programming. Goodle GMS allows the students to submit their results to a…
Kudi: A free open-source python library for the analysis of properties along reaction paths.

PubMed

Vogt-Geisse, Stefan

2016-05-01

With increasing computational capabilities, an ever growing amount of data is generated in computational chemistry that contains a vast amount of chemically relevant information. It is therefore imperative to create new computational tools in order to process and extract this data in a sensible way. Kudi is an open source library that aids in the extraction of chemical properties from reaction paths. The straightforward structure of Kudi makes it easy to use for users and allows for effortless implementation of new capabilities, and extension to any quantum chemistry package. A use case for Kudi is shown for the tautomerization reaction of formic acid. Kudi is available free of charge at www.github.com/stvogt/kudi.
Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

NASA Technical Reports Server (NTRS)

Liechty, Derek S.; Lewis, Mark J.

2010-01-01

Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.
Extensible Computational Chemistry Environment

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

2012-08-09

ECCE provides a sophisticated graphical user interface, scientific visualization tools, and the underlying data management framework enabling scientists to efficiently set up calculations and store, retrieve, and analyze the rapidly growing volumes of data produced by computational chemistry studies. ECCE was conceived as part of the Environmental Molecular Sciences Laboratory construction to solve the problem of researchers being able to effectively utilize complex computational chemistry codes and massively parallel high performance compute resources. Bringing the power of these codes and resources to the desktops of researcher and thus enabling world class research without users needing a detailed understanding of themore » inner workings of either the theoretical codes or the supercomputers needed to run them was a grand challenge problem in the original version of the EMSL. ECCE allows collaboration among researchers using a web-based data repository where the inputs and results for all calculations done within ECCE are organized. ECCE is a first of kind end-to-end problem solving environment for all phases of computational chemistry research: setting up calculations with sophisticated GUI and direct manipulation visualization tools, submitting and monitoring calculations on remote high performance supercomputers without having to be familiar with the details of using these compute resources, and performing results visualization and analysis including creating publication quality images. ECCE is a suite of tightly integrated applications that are employed as the user moves through the modeling process.« less
FermiLib v0.1

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

MCCLEAN, JARROD; HANER, THOMAS; STEIGER, DAMIAN

FermiLib is an open source software package designed to facilitate the development and testing of algorithms for simulations of fermionic systems on quantum computers. Fermionic simulations represent an important application of early quantum devices with a lot of potential high value targets, such as quantum chemistry for the development of new catalysts. This software strives to provide a link between the required domain expertise in specific fermionic applications and quantum computing to enable more users to directly interface with, and develop for, these applications. It is an extensible Python library designed to interface with the high performance quantum simulator, ProjectQ,more » as well as application specific software such as PSI4 from the domain of quantum chemistry. Such software is key to enabling effective user facilities in quantum computation research.« less
Acceleration of the chemistry solver for modeling DI engine combustion using dynamic adaptive chemistry (DAC) schemes

NASA Astrophysics Data System (ADS)

Shi, Yu; Liang, Long; Ge, Hai-Wen; Reitz, Rolf D.

2010-03-01

Acceleration of the chemistry solver for engine combustion is of much interest due to the fact that in practical engine simulations extensive computational time is spent solving the fuel oxidation and emission formation chemistry. A dynamic adaptive chemistry (DAC) scheme based on a directed relation graph error propagation (DRGEP) method has been applied to study homogeneous charge compression ignition (HCCI) engine combustion with detailed chemistry (over 500 species) previously using an R-value-based breadth-first search (RBFS) algorithm, which significantly reduced computational times (by as much as 30-fold). The present paper extends the use of this on-the-fly kinetic mechanism reduction scheme to model combustion in direct-injection (DI) engines. It was found that the DAC scheme becomes less efficient when applied to DI engine simulations using a kinetic mechanism of relatively small size and the accuracy of the original DAC scheme decreases for conventional non-premixed combustion engine. The present study also focuses on determination of search-initiating species, involvement of the NOx chemistry, selection of a proper error tolerance, as well as treatment of the interaction of chemical heat release and the fuel spray. Both the DAC schemes were integrated into the ERC KIVA-3v2 code, and simulations were conducted to compare the two schemes. In general, the present DAC scheme has better efficiency and similar accuracy compared to the previous DAC scheme. The efficiency depends on the size of the chemical kinetics mechanism used and the engine operating conditions. For cases using a small n-heptane kinetic mechanism of 34 species, 30% of the computational time is saved, and 50% for a larger n-heptane kinetic mechanism of 61 species. The paper also demonstrates that by combining the present DAC scheme with an adaptive multi-grid chemistry (AMC) solver, it is feasible to simulate a direct-injection engine using a detailed n-heptane mechanism with 543 species with practical computer time.
Students' use of atomic and molecular models in learning chemistry

NASA Astrophysics Data System (ADS)

O'Connor, Eileen Ann

1997-09-01

The objective of this study was to investigate the development of introductory college chemistry students' use of atomic and molecular models to explain physical and chemical phenomena. The study was conducted during the first semester of the course at a University and College II. Public institution (Carnegie Commission of Higher Education, 1973). Students' use of models was observed during one-on-one interviews conducted over the course of the semester. The approach to introductory chemistry emphasized models. Students were exposed to over two-hundred and fifty atomic and molecular models during lectures, were assigned text readings that used over a thousand models, and worked interactively with dozens of models on the computer. These models illustrated various features of the spatial organization of valence electrons and nuclei in atoms and molecules. Despite extensive exposure to models in lectures, in textbook, and in computer-based activities, the students in the study based their explanation in large part on a simple Bohr model (electrons arranged in concentric circles around the nuclei)--a model that had not been introduced in the course. Students used visual information from their models to construct their explanation, while overlooking inter-atomic and intra-molecular forces which are not represented explicitly in the models. In addition, students often explained phenomena by adding separate information about the topic without either integrating or logically relating this information into a cohesive explanation. The results of the study demonstrate that despite the extensive use of models in chemistry instruction, students do not necessarily apply them appropriately in explaining chemical and physical phenomena. The results of this study suggest that for the power of models as aids to learning to be more fully realized, chemistry professors must give more attention to the selection, use, integration, and limitations of models in their instruction.
Extension of a Kinetic Approach to Chemical Reactions to Electronic Energy Levels and Reactions Involving Charged Species with Application to DSMC Simulations

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2014-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for near-equilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion.
Exploring Do-It-Yourself Approaches in Computational Quantum Chemistry: The Pedagogical Benefits of the Classical Boys Algorithm

ERIC Educational Resources Information Center

Orsini, Gabriele

2015-01-01

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

NASA Astrophysics Data System (ADS)

1996-02-01

Computational Chemistry for the Masses Not long ago, chemical computation was considered a specialty area requiring extensive computer knowledge, power, and time. Over the past decade, however, it has changed from the arcane pursuit of a few advanced university researchers in the area of physical chemistry to a familiar tool used by a wide range of chemists. Nevertheless, it has required its practitioners to have extensive knowledge of computer programming and a thorough understanding of theoretical chemical concepts and as a result usually was reserved for the graduate curriculum. Now a further metamorphosis is in progress, as computational chemistry moves into the undergraduate curriculum, often using off-the-shelf software--commercial packages or adaptations of them that are readily shared by their creators. As we put this issue together, we realized that many of the articles involved sophisticated computations that would not have been possible a few years ago in the courses described. Further, the hard and software used was widely available at a reasonable cost. Some of the articles focus on the teaching of computational methods and others simply incorporate it as a facet in their overall strategy; however, taken together, they reflect a strong trend to utilize a diverse set of readily available methods and products in the undergraduate curriculum. The most familiar recent use of computational chemistry is the computer design of molecules in organic, medicinal, and biochemistry. However, computational chemistry is useful for inorganic chemists as well and is now migrating to undergraduate courses. Lipkowitz, Pearl, Robertson, and Schultz (page 105) make a strong case for its inclusion and present a two-week component they have developed for their senior-level laboratory course. Comba and Zimmer (page 108) offer a review of inorganic molecular mechanics calculations, which is designed for the novice and includes the basic equations, their application to inorganic molecules, and a discussion of the how to evaluate the reliability of the results. A computational experiment has been specifically designed for the undergraduate laboratory by Bakalbassis, Stiakaki, Tsipis, and Tsipis (page 111). The students use an atom-superposition and electron-delocalization molecular orbital model to predict the structural, spectroscopic, and energetic properties of highly ionic metal-containing systems. The exercise introduces students to the value of computational experiments as an alternative to wet-lab work and teaches enough quantum theory to make them comfortable with current literature. For teachers of organic chemistry, Delaware and Fountain (page 116) analyze how models can actually hinder learning in the introductory course if presented passively and describe how to use computer visualizations of reactions in an active, cooperative learning mode. They argue that these computational exercises need to be embedded in a carefully planned learning system to be effective. In similar fashion, Sauers (page 114) finds that a computer-assisted molecular modeling experiment is an effective way of making the concept of "steric interactions" more accessible. The theoretical number of isomers and derivatives of organic compounds is another concept difficult to visualize, and the calculations that would used for enumeration are complex enough that they are not usually brought into the undergraduate curriculum. However, Novak (page 120) demonstrates that widely available PC software, such as Mathematica, can be used by undergraduates along with the Polya enumeration method to enumerate derivatives and see the connection between these numbers and the symmetry of the parent molecule. A different use of computational software in biochemistry than the usual computer-assisted design of molecules is the main focus of a Computer Series article by Letkeman (page 165), who models the complex interactions of metal ions in human blood serum.
Evaluation of an Integrated Curriculum in Physics, Mathematics, Engineering, and Chemistry

NASA Astrophysics Data System (ADS)

Beichner, Robert

1997-04-01

An experimental, student centered, introductory curriculum called IMPEC (for Integrated Mathematics, Physics, Engineering, and Chemistry curriculum) is in its third year of pilot-testing at NCSU. The curriculum is taught by a multidisciplinary team of professors using a combination of traditional lecturing and alternative instructional methods including cooperative learning, activity-based class sessions, and extensive use of computer modeling, simulations, and the world wide web. This talk will discuss the research basis for our design and implementation of the curriculum, the qualitative and quantitative methods we have been using to assess its effectiveness, and the educational outcomes we have noted so far.
Employing OpenCL to Accelerate Ab Initio Calculations on Graphics Processing Units.

PubMed

Kussmann, Jörg; Ochsenfeld, Christian

2017-06-13

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

NASA Technical Reports Server (NTRS)

Liechty, Derek S.

2013-01-01

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties are extended in the current work to include electronic energy level transitions and reactions involving charged particles. These extensions are shown to agree favorably with reported transition and reaction rates from the literature for nearequilibrium conditions. Also, the extensions are applied to the second flight of the Project FIRE flight experiment at 1634 seconds with a Knudsen number of 0.001 at an altitude of 76.4 km. In order to accomplish this, NASA's direct simulation Monte Carlo code DAC was rewritten to include the ability to simulate charge-neutral ionized flows, take advantage of the recently introduced chemistry model, and to include the extensions presented in this work. The 1634 second data point was chosen for comparisons to be made in order to include a CFD solution. The Knudsen number at this point in time is such that the DSMC simulations are still tractable and the CFD computations are at the edge of what is considered valid because, although near-transitional, the flow is still considered to be continuum. It is shown that the inclusion of electronic energy levels in the DSMC simulation is necessary for flows of this nature and is required for comparison to the CFD solution. The flow field solutions are also post-processed by the nonequilibrium radiation code HARA to compute the radiative portion of the heating and is then compared to the total heating measured in flight.
Optimizing Performance of Combustion Chemistry Solvers on Intel's Many Integrated Core (MIC) Architectures

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

Sitaraman, Hariswaran; Grout, Ray W

This work investigates novel algorithm designs and optimization techniques for restructuring chemistry integrators in zero and multidimensional combustion solvers, which can then be effectively used on the emerging generation of Intel's Many Integrated Core/Xeon Phi processors. These processors offer increased computing performance via large number of lightweight cores at relatively lower clock speeds compared to traditional processors (e.g. Intel Sandybridge/Ivybridge) used in current supercomputers. This style of processor can be productively used for chemistry integrators that form a costly part of computational combustion codes, in spite of their relatively lower clock speeds. Performance commensurate with traditional processors is achieved heremore » through the combination of careful memory layout, exposing multiple levels of fine grain parallelism and through extensive use of vendor supported libraries (Cilk Plus and Math Kernel Libraries). Important optimization techniques for efficient memory usage and vectorization have been identified and quantified. These optimizations resulted in a factor of ~ 3 speed-up using Intel 2013 compiler and ~ 1.5 using Intel 2017 compiler for large chemical mechanisms compared to the unoptimized version on the Intel Xeon Phi. The strategies, especially with respect to memory usage and vectorization, should also be beneficial for general purpose computational fluid dynamics codes.« less
An intermediate level of abstraction for computational systems chemistry.

PubMed

Andersen, Jakob L; Flamm, Christoph; Merkle, Daniel; Stadler, Peter F

2017-12-28

Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems. The formalization of chemical reactions as graph grammars provides a generative system, well grounded in category theory, at the right level of abstraction for the analysis of large and complex reaction networks. An extension of the basic formalism into the realm of integer hyperflows allows for the identification of complex reaction patterns, such as autocatalysis, in large reaction networks using optimization techniques.This article is part of the themed issue 'Reconceptualizing the origins of life'. © 2017 The Author(s).
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.

Component-based integration of chemistry and optimization software.

PubMed

Kenny, Joseph P; Benson, Steven J; Alexeev, Yuri; Sarich, Jason; Janssen, Curtis L; McInnes, Lois Curfman; Krishnan, Manojkumar; Nieplocha, Jarek; Jurrus, Elizabeth; Fahlstrom, Carl; Windus, Theresa L

2004-11-15

Typical scientific software designs make rigid assumptions regarding programming language and data structures, frustrating software interoperability and scientific collaboration. Component-based software engineering is an emerging approach to managing the increasing complexity of scientific software. Component technology facilitates code interoperability and reuse. Through the adoption of methodology and tools developed by the Common Component Architecture Forum, we have developed a component architecture for molecular structure optimization. Using the NWChem and Massively Parallel Quantum Chemistry packages, we have produced chemistry components that provide capacity for energy and energy derivative evaluation. We have constructed geometry optimization applications by integrating the Toolkit for Advanced Optimization, Portable Extensible Toolkit for Scientific Computation, and Global Arrays packages, which provide optimization and linear algebra capabilities. We present a brief overview of the component development process and a description of abstract interfaces for chemical optimizations. The components conforming to these abstract interfaces allow the construction of applications using different chemistry and mathematics packages interchangeably. Initial numerical results for the component software demonstrate good performance, and highlight potential research enabled by this platform.
Evolution of computational chemistry, the "launch pad" to scientific computational models: The early days from a personal account, the present status from the TACC-2012 congress, and eventual future applications from the global simulation approach

NASA Astrophysics Data System (ADS)

Clementi, Enrico

2012-06-01

This is the introductory chapter to the AIP Proceedings volume "Theory and Applications of Computational Chemistry: The First Decade of the Second Millennium" where we discuss the evolution of "computational chemistry". Very early variational computational chemistry developments are reported in Sections 1 to 7, and 11, 12 by recalling some of the computational chemistry contributions by the author and his collaborators (from late 1950 to mid 1990); perturbation techniques are not considered in this already extended work. Present day's computational chemistry is partly considered in Sections 8 to 10 where more recent studies by the author and his collaborators are discussed, including the Hartree-Fock-Heitler-London method; a more general discussion on present day computational chemistry is presented in Section 14. The following chapters of this AIP volume provide a view of modern computational chemistry. Future computational chemistry developments can be extrapolated from the chapters of this AIP volume; further, in Sections 13 and 15 present an overall analysis on computational chemistry, obtained from the Global Simulation approach, by considering the evolution of scientific knowledge confronted with the opportunities offered by modern computers.
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.
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…
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

PubMed Central

2012-01-01

Background The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. Results The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Conclusions Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net. PMID:22889332
Avogadro: an advanced semantic chemical editor, visualization, and analysis platform.

PubMed

Hanwell, Marcus D; Curtis, Donald E; Lonie, David C; Vandermeersch, Tim; Zurek, Eva; Hutchison, Geoffrey R

2012-08-13

The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types. The work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here. Avogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics.

PubMed

Fukunishi, Yoshifumi; Mashimo, Tadaaki; Misoo, Kiyotaka; Wakabayashi, Yoshinori; Miyaki, Toshiaki; Ohta, Seiji; Nakamura, Mayu; Ikeda, Kazuyoshi

2016-01-01

Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design.
Miscellaneous Topics in Computer-Aided Drug Design: Synthetic Accessibility and GPU Computing, and Other Topics

PubMed Central

Fukunishi, Yoshifumi; Mashimo, Tadaaki; Misoo, Kiyotaka; Wakabayashi, Yoshinori; Miyaki, Toshiaki; Ohta, Seiji; Nakamura, Mayu; Ikeda, Kazuyoshi

2016-01-01

Abstract: Background Computer-aided drug design is still a state-of-the-art process in medicinal chemistry, and the main topics in this field have been extensively studied and well reviewed. These topics include compound databases, ligand-binding pocket prediction, protein-compound docking, virtual screening, target/off-target prediction, physical property prediction, molecular simulation and pharmacokinetics/pharmacodynamics (PK/PD) prediction. Message and Conclusion: However, there are also a number of secondary or miscellaneous topics that have been less well covered. For example, methods for synthesizing and predicting the synthetic accessibility (SA) of designed compounds are important in practical drug development, and hardware/software resources for performing the computations in computer-aided drug design are crucial. Cloud computing and general purpose graphics processing unit (GPGPU) computing have been used in virtual screening and molecular dynamics simulations. Not surprisingly, there is a growing demand for computer systems which combine these resources. In the present review, we summarize and discuss these various topics of drug design. PMID:27075578
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…
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)
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.
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)
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…
Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

2017-06-01

Atomistic modeling of chemistry at extreme conditions remains a challenge, despite continuing advances in computing resources and simulation tools. While first principles methods provide a powerful predictive tool, the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
Publication and Retrieval of Computational Chemical-Physical Data Via the Semantic Web. Final Technical Report

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

Ostlund, Neil

This research showed the feasibility of applying the concepts of the Semantic Web to Computation Chemistry. We have created the first web portal (www.chemsem.com) that allows data created in the calculations of quantum chemistry, and other such chemistry calculations to be placed on the web in a way that makes the data accessible to scientists in a semantic form never before possible. The semantic web nature of the portal allows data to be searched, found, and used as an advance over the usual approach of a relational database. The semantic data on our portal has the nature of a Giantmore » Global Graph (GGG) that can be easily merged with related data and searched globally via a SPARQL Protocol and RDF Query Language (SPARQL) that makes global searches for data easier than with traditional methods. Our Semantic Web Portal requires that the data be understood by a computer and hence defined by an ontology (vocabulary). This ontology is used by the computer in understanding the data. We have created such an ontology for computational chemistry (purl.org/gc) that encapsulates a broad knowledge of the field of computational chemistry. We refer to this ontology as the Gainesville Core. While it is perhaps the first ontology for computational chemistry and is used by our portal, it is only a start of what must be a long multi-partner effort to define computational chemistry. In conjunction with the above efforts we have defined a new potential file standard (Common Standard for eXchange – CSX for computational chemistry data). This CSX file is the precursor of data in the Resource Description Framework (RDF) form that the semantic web requires. Our portal translates CSX files (as well as other computational chemistry data files) into RDF files that are part of the graph database that the semantic web employs. We propose a CSX file as a convenient way to encapsulate computational chemistry data.« less
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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Transuranic Computational Chemistry.

PubMed

Kaltsoyannis, Nikolas

2018-02-26

Recent developments in the chemistry of the transuranic elements are surveyed, with particular emphasis on computational contributions. Examples are drawn from molecular coordination and organometallic chemistry, and from the study of extended solid systems. The role of the metal valence orbitals in covalent bonding is a particular focus, especially the consequences of the stabilization of the 5f orbitals as the actinide series is traversed. The fledgling chemistry of transuranic elements in the +II oxidation state is highlighted. Throughout, the symbiotic interplay of experimental and computational studies is emphasized; the extraordinary challenges of experimental transuranic chemistry afford computational chemistry a particularly valuable role at the frontier of the periodic table. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
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.
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…
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.

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
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. Copyright Â© 2011 Elsevier Inc. All rights reserved.
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less
Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1993-01-01

The period from Jan. 1993 thru Aug. 1993 is covered. The primary tasks during this period were the development of a single and multi-vibrational temperature preferential vibration-dissociation coupling model, the development of a normal shock nonequilibrium radiation-gasdynamic coupling model based upon the blunt body model, and the comparison of results obtained with these models with experimental data. In addition, an extensive series of computations were conducted using the blunt body model to develop a set of reference results covering a wide range of vehicle sizes, altitudes, and entry velocities.
Equipment for linking the AutoAnalyzer on-line to a computer

PubMed Central

Simpson, D.; Sims, G. E.; Harrison, M. I.; Whitby, L. G.

1971-01-01

An Elliott 903 computer with 8K central core store and magnetic tape backing store has been operated for approximately 20 months in a clinical chemistry laboratory. Details of the equipment designed for linking AutoAnalyzers on-line to the computer are described, and data presented concerning the time required by the computer for different processes. The reliability of the various components in daily operation is discussed. Limitations in the system's capabilities have been defined, and ways of overcoming these are delineated. At present, routine operations include the preparation of worksheets for a limited range of tests (five channels), monitoring of up to 11 AutoAnalyzer channels at a time on a seven-day week basis (with process control and automatic calculation of results), and the provision of quality control data. Cumulative reports can be printed out on those analyses for which computer-prepared worksheets are provided but the system will require extension before these can be issued sufficiently rapidly for routine use. PMID:5551384
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.
A Communication-Optimal Framework for Contracting Distributed Tensors

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

Rajbhandari, Samyam; NIkam, Akshay; Lai, Pai-Wei

Tensor contractions are extremely compute intensive generalized matrix multiplication operations encountered in many computational science fields, such as quantum chemistry and nuclear physics. Unlike distributed matrix multiplication, which has been extensively studied, limited work has been done in understanding distributed tensor contractions. In this paper, we characterize distributed tensor contraction algorithms on torus networks. We develop a framework with three fundamental communication operators to generate communication-efficient contraction algorithms for arbitrary tensor contractions. We show that for a given amount of memory per processor, our framework is communication optimal for all tensor contractions. We demonstrate performance and scalability of our frameworkmore » on up to 262,144 cores of BG/Q supercomputer using five tensor contraction examples.« less
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.
Environmental chemistry: Volume A

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

Yen, T.F.

1999-08-01

This is an extensive introduction to environmental chemistry for engineering and chemical professionals. The contents of Volume A include a brief review of basic chemistry prior to coverage of litho, atmo, hydro, pedo, and biospheres.
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...
Comptox Chemistry Dashboard: Web-Based Data Integration Hub for Environmental Chemistry and Toxicology Data (ACS Fall meeting 4 of 12)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and da...
The selectivity of protein-imprinted gels and its relation to protein properties: A computer simulation study.

PubMed

Yankelov, Rami; Yungerman, Irena; Srebnik, Simcha

2017-07-01

Polymer-based protein recognition systems have enormous potential within clinical and diagnostic fields due to their reusability, biocompatibility, ease of manufacturing, and potential specificity. Imprinted polymer matrices have been extensively studied and applied as a simple technique for creating artificial polymer-based recognition gels for a target molecule. Although this technique has been proven effective when targeting small molecules (such as drugs), imprinting of proteins have so far resulted in materials with limited selectivity due to the large molecular size of the protein and aqueous environment. Using coarse-grained molecular simulation, we investigate the relation between protein makeup, polymer properties, and the selectivity of imprinted gels. Nonspecific binding that results in poor selectivity is shown to be strongly dependent on surface chemistry of the template and competitor proteins as well as on polymer chemistry. Residence time distributions of proteins diffusing within the gels provide a transparent picture of the relation between polymer constitution, protein properties, and the nonspecific interactions with the imprinted gel. The pronounced effect of protein surface chemistry on imprinted gel specificity is demonstrated. Copyright © 2017 John Wiley & Sons, Ltd.
Kraft lignin chain extension chemistry via propargylation, oxidative coupling, and Claisen rearrangement.

PubMed

Sen, Sanghamitra; Sadeghifar, Hasan; Argyropoulos, Dimitris S

2013-10-14

Despite its aromatic and polymeric nature, the heterogeneous, stochastic, and reactive characteristics of softwood kraft lignin seriously limit its potential for thermoplastic applications. Our continuing efforts toward creating thermoplastic lignin polymers are now focused at exploring propargylation derivatization chemistry and its potential as a versatile novel route for the eventual utilization of technical lignins with a significant amount of molecular control. To do this, we initially report the systematic propargylation of softwood kraft lignin. The synthesized derivatives were extensively characterized with thermal methods (DSC, TGA), (1)H, (13)C, and quantitative (31)P NMR and IR spectroscopies. Further on, we explore the versatile nature of the lignin pendant propargyl groups by demonstrating two distinct chain extension chemistries; the solution-based, copper-mediated, oxidative coupling and the thermally induced, solid-state, Claissen rearrangement polymerization chemistries. Overall, we show that it is possible to modulate the reactivity of softwood kraft lignin via a combination of methylation and chain extension providing a rational means for the creation of higher molecular weight polymers with the potential for thermoplastic materials and carbon fibers with the desired control of structure-property relations.
Preconditioning for the Navier-Stokes equations with finite-rate chemistry

NASA Technical Reports Server (NTRS)

Godfrey, Andrew G.

1993-01-01

The extension of Van Leer's preconditioning procedure to generalized finite-rate chemistry is discussed. Application to viscous flow is begun with the proper preconditioning matrix for the one-dimensional Navier-Stokes equations. Eigenvalue stiffness is resolved and convergence-rate acceleration is demonstrated over the entire Mach-number range from nearly stagnant flow to hypersonic. Specific benefits are realized at the low and transonic flow speeds typical of complete propulsion-system simulations. The extended preconditioning matrix necessarily accounts for both thermal and chemical nonequilibrium. Numerical analysis reveals the possible theoretical improvements from using a preconditioner for all Mach number regimes. Numerical results confirm the expectations from the numerical analysis. Representative test cases include flows with previously troublesome embedded high-condition-number areas. Van Leer, Lee, and Roe recently developed an optimal, analytic preconditioning technique to reduce eigenvalue stiffness over the full Mach-number range. By multiplying the flux-balance residual with the preconditioning matrix, the acoustic wave speeds are scaled so that all waves propagate at the same rate, an essential property to eliminate inherent eigenvalue stiffness. This session discusses a synthesis of the thermochemical nonequilibrium flux-splitting developed by Grossman and Cinnella and the characteristic wave preconditioning of Van Leer into a powerful tool for implicitly solving two and three-dimensional flows with generalized finite-rate chemistry. For finite-rate chemistry, the state vector of unknowns is variable in length. Therefore, the preconditioning matrix extended to generalized finite-rate chemistry must accommodate a flexible system of moving waves. Fortunately, no new kind of wave appears in the system. The only existing waves are entropy and vorticity waves, which move with the fluid, and acoustic waves, which propagate in Mach number dependent directions. The nonequilibrium vibrational energies and species densities in the unknown state vector act strictly as convective waves. The essential concept for extending the preconditioning to generalized chemistry models is determining the differential variables which symmetrize the flux Jacobians. The extension is then straight-forward. This algorithm research effort will be released in a future version of the production level computational code coined the General Aerodynamic Simulation Program (GASP), developed by Walters, Slack, and McGrory.
The ChemViz Project: Using a Supercomputer To Illustrate Abstract Concepts in Chemistry.

ERIC Educational Resources Information Center

Beckwith, E. Kenneth; Nelson, Christopher

1998-01-01

Describes the Chemistry Visualization (ChemViz) Project, a Web venture maintained by the University of Illinois National Center for Supercomputing Applications (NCSA) that enables high school students to use computational chemistry as a technique for understanding abstract concepts. Discusses the evolution of computational chemistry and provides a…
Stochastic and Deterministic Approaches to Gas-grain Modeling of Interstellar Sources

NASA Astrophysics Data System (ADS)

Vasyunin, Anton; Herbst, Eric; Caselli, Paola

During the last decade, our understanding of the chemistry on surfaces of interstellar grains has been significantly enchanced. Extensive laboratory studies have revealed complex structure and dynamics in interstellar ice analogues, thus making our knowledge much more detailed. In addition, the first qualitative investigations of new processes were made, such as non-thermal chemical desorption of species from dust grains into the gas. Not surprisingly, the rapid growth of knowledge about the physics and chemistry of interstellar ices led to the development of a new generation of astrochemical models. The models are typically characterized by more detailed treatments of the ice physics and chemistry than previously. The utilized numerical approaches vary greatly from microscopic models, in which every single molecule is traced, to ``mean field'' macroscopic models, which simulate the evolution of averaged characteristics of interstellar ices, such as overall bulk composition. While microscopic models based on a stochastic Monte Carlo approach are potentially able to simulate the evolution of interstellar ices with an account of most subtle effects found in a laboratory, their use is often impractical due to limited knowledge about star-forming regions and huge computational demands. On the other hand, deterministic macroscopic models that often utilize kinetic rate equations are computationally efficient but experience difficulties in incorporation of such potentially important effects as ice segregation or discreteness of surface chemical reactions. In my talk, I will review the state of the art in the development of gas-grain astrochemical models. I will discuss how to incorporate key features of ice chemistry and dynamics in the gas-grain astrochemical models, and how the incorporation of recent laboratory findings into gas-grain models helps to better match observations.
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…
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…
Defined Host–Guest Chemistry on Nanocarbon for Sustained Inhibition of Cancer

PubMed Central

Ostadhossein, Fatemeh; Misra, Santosh K.; Mukherjee, Prabuddha; Ostadhossein, Alireza; Daza, Enrique; Tiwari, Saumya; Mittal, Shachi; Gryka, Mark C.; Bhargava, Rohit

2017-01-01

Signal transducer and activator of transcription factor 3 (STAT-3) is known to be overexpressed in cancer stem cells. Poor solubility and variable drug absorption are linked to low bioavailability and decreased efficacy. Many of the drugs regulating STAT-3 expression lack aqueous solubility; hence hindering efficient bioavailability. A theranostics nanoplatform based on luminescent carbon particles decorated with cucurbit[6]uril is introduced for enhancing the solubility of niclosamide, a STAT-3 inhibitor. The host–guest chemistry between cucurbit[6]uril and niclosamide makes the delivery of the hydrophobic drug feasible while carbon nanoparticles enhance cellular internalization. Extensive physicochemical characterizations confirm successful synthesis. Subsequently, the host–guest chemistry of niclosamide and cucurbit[6]uril is studied experimentally and computationally. In vitro assessments in human breast cancer cells indicate approximately twofold enhancement in IC50 of drug. Fourier transform infrared and fluorescence imaging demonstrate efficient cellular internalization. Furthermore, the catalytic biodegradation of the nanoplatforms occur upon exposure to human myeloperoxidase in short time. In vivo studies on athymic mice with MCF-7 xenograft indicate the size of tumor in the treatment group is half of the controls after 40 d. Immunohistochemistry corroborates the downregulation of STAT-3 phosphorylation. Overall, the host–guest chemistry on nanocarbon acts as a novel arsenal for STAT-3 inhibition. PMID:27545321
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.

The Distribution of Macromolecular Principles throughout Introductory Organic Chemistry

ERIC Educational Resources Information Center

Shulman, Joel I.

2017-01-01

Many of the principles of organic polymer chemistry are direct extensions of the information contained in the standard introductory organic chemistry course. Often, however, the discussion of macromolecules is relegated to a chapter at the end of the organic chemistry text and is covered briefly, if at all. Connecting the organic-chemical…
Historical Analysis of the Inorganic Chemistry Curriculum Using ACS Examinations as Artifacts

ERIC Educational Resources Information Center

Srinivasan, Shalini; Reisner, Barbara A.; Smith, Sheila R.; Stewart, Joanne L.; Johnson, Adam R.; Lin, Shirley; Marek, Keith A.; Nataro, Chip; Murphy, Kristen L.; Raker, Jeffrey R.

2018-01-01

ACS Examinations provide a lens through which to examine historical changes in topic coverage via analyses of course-specific examinations. This study is an extension of work completed previously by the ACS Exams Research Staff and collaborators in general chemistry, organic chemistry, and physical chemistry to explore content changes in the…
Global Futures: a multithreaded execution model for Global Arrays-based applications

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

Chavarría-Miranda, Daniel; Krishnamoorthy, Sriram; Vishnu, Abhinav

2012-05-31

We present Global Futures (GF), an execution model extension to Global Arrays, which is based on a PGAS-compatible Active Message-based paradigm. We describe the design and implementation of Global Futures and illustrate its use in a computational chemistry application benchmark (Hartree-Fock matrix construction using the Self-Consistent Field method). Our results show how we used GF to increase the scalability of the Hartree-Fock matrix build to up to 6,144 cores of an Infiniband cluster. We also show how GF's multithreaded execution has comparable performance to the traditional process-based SPMD model.
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…
Structure-based classification and ontology in chemistry

PubMed Central

2012-01-01

Background Recent years have seen an explosion in the availability of data in the chemistry domain. With this information explosion, however, retrieving relevant results from the available information, and organising those results, become even harder problems. Computational processing is essential to filter and organise the available resources so as to better facilitate the work of scientists. Ontologies encode expert domain knowledge in a hierarchically organised machine-processable format. One such ontology for the chemical domain is ChEBI. ChEBI provides a classification of chemicals based on their structural features and a role or activity-based classification. An example of a structure-based class is 'pentacyclic compound' (compounds containing five-ring structures), while an example of a role-based class is 'analgesic', since many different chemicals can act as analgesics without sharing structural features. Structure-based classification in chemistry exploits elegant regularities and symmetries in the underlying chemical domain. As yet, there has been neither a systematic analysis of the types of structural classification in use in chemistry nor a comparison to the capabilities of available technologies. Results We analyze the different categories of structural classes in chemistry, presenting a list of patterns for features found in class definitions. We compare these patterns of class definition to tools which allow for automation of hierarchy construction within cheminformatics and within logic-based ontology technology, going into detail in the latter case with respect to the expressive capabilities of the Web Ontology Language and recent extensions for modelling structured objects. Finally we discuss the relationships and interactions between cheminformatics approaches and logic-based approaches. Conclusion Systems that perform intelligent reasoning tasks on chemistry data require a diverse set of underlying computational utilities including algorithmic, statistical and logic-based tools. For the task of automatic structure-based classification of chemical entities, essential to managing the vast swathes of chemical data being brought online, systems which are capable of hybrid reasoning combining several different approaches are crucial. We provide a thorough review of the available tools and methodologies, and identify areas of open research. PMID:22480202
Using Bad Science to Teach Good Chemistry.

ERIC Educational Resources Information Center

Epstein, Michael S.

1998-01-01

Describes the integration of topics dealing with "bad science"--pseudo, pathological, or deviant science--into introductory undergraduate courses in general and analytical chemistry, and provides extensive references for the chemistry instructor interested in these topics. The approach is to incorporate specific cases that address…
Molecular computational elements encode large populations of small objects

NASA Astrophysics Data System (ADS)

Prasanna de Silva, A.; James, Mark R.; McKinney, Bernadine O. F.; Pears, David A.; Weir, Sheenagh M.

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1nm) and large `on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100μm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a `wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.
Molecular computational elements encode large populations of small objects.

PubMed

de Silva, A Prasanna; James, Mark R; McKinney, Bernadine O F; Pears, David A; Weir, Sheenagh M

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1 nm) and large 'on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100 microm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a 'wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.
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…
The performance of low-cost commercial cloud computing as an alternative in computational chemistry.

PubMed

Thackston, Russell; Fortenberry, Ryan C

2015-05-05

The growth of commercial cloud computing (CCC) as a viable means of computational infrastructure is largely unexplored for the purposes of quantum chemistry. In this work, the PSI4 suite of computational chemistry programs is installed on five different types of Amazon World Services CCC platforms. The performance for a set of electronically excited state single-point energies is compared between these CCC platforms and typical, "in-house" physical machines. Further considerations are made for the number of cores or virtual CPUs (vCPUs, for the CCC platforms), but no considerations are made for full parallelization of the program (even though parallelization of the BLAS library is implemented), complete high-performance computing cluster utilization, or steal time. Even with this most pessimistic view of the computations, CCC resources are shown to be more cost effective for significant numbers of typical quantum chemistry computations. Large numbers of large computations are still best utilized by more traditional means, but smaller-scale research may be more effectively undertaken through CCC services. © 2015 Wiley Periodicals, Inc.
What Chemists (or Chemistry Students) Need to Know about Computing.

ERIC Educational Resources Information Center

Swift, Mary L.; Zielinski, Theresa Julia

1995-01-01

Presents key points of an on-line conference discussion and integrates them with information from the literature. Key points included: computer as a tool for learning, study, research, and communication; hardware, software, computing concepts, and other teaching concerns; and the appropriate place for chemistry computer-usage instruction. (45…
An Educational Approach to Computationally Modeling Dynamical Systems

ERIC Educational Resources Information Center

Chodroff, Leah; O'Neal, Tim M.; Long, David A.; Hemkin, Sheryl

2009-01-01

Chemists have used computational science methodologies for a number of decades and their utility continues to be unabated. For this reason we developed an advanced lab in computational chemistry in which students gain understanding of general strengths and weaknesses of computation-based chemistry by working through a specific research problem.…
Enhancement of DFT-calculations at petascale: Nuclear Magnetic Resonance, Hybrid Density Functional Theory and Car-Parrinello calculations

NASA Astrophysics Data System (ADS)

Varini, Nicola; Ceresoli, Davide; Martin-Samos, Layla; Girotto, Ivan; Cavazzoni, Carlo

2013-08-01

One of the most promising techniques used for studying the electronic properties of materials is based on Density Functional Theory (DFT) approach and its extensions. DFT has been widely applied in traditional solid state physics problems where periodicity and symmetry play a crucial role in reducing the computational workload. With growing compute power capability and the development of improved DFT methods, the range of potential applications is now including other scientific areas such as Chemistry and Biology. However, cross disciplinary combinations of traditional Solid-State Physics, Chemistry and Biology drastically improve the system complexity while reducing the degree of periodicity and symmetry. Large simulation cells containing of hundreds or even thousands of atoms are needed to model these kind of physical systems. The treatment of those systems still remains a computational challenge even with modern supercomputers. In this paper we describe our work to improve the scalability of Quantum ESPRESSO (Giannozzi et al., 2009 [3]) for treating very large cells and huge numbers of electrons. To this end we have introduced an extra level of parallelism, over electronic bands, in three kernels for solving computationally expensive problems: the Sternheimer equation solver (Nuclear Magnetic Resonance, package QE-GIPAW), the Fock operator builder (electronic ground-state, package PWscf) and most of the Car-Parrinello routines (Car-Parrinello dynamics, package CP). Final benchmarks show our success in computing the Nuclear Magnetic Response (NMR) chemical shift of a large biological assembly, the electronic structure of defected amorphous silica with hybrid exchange-correlation functionals and the equilibrium atomic structure of height Porphyrins anchored to a Carbon Nanotube, on many thousands of CPU cores.
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…
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…
Conformational Analysis of Drug Molecules: A Practical Exercise in the Medicinal Chemistry Course

ERIC Educational Resources Information Center

Yuriev, Elizabeth; Chalmers, David; Capuano, Ben

2009-01-01

Medicinal chemistry is a specialized, scientific discipline. Computational chemistry and structure-based drug design constitute important themes in the education of medicinal chemists. This problem-based task is associated with structure-based drug design lectures. It requires students to use computational techniques to investigate conformational…
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)
Earth System Chemistry integrated Modelling (ESCiMo) with the Modular Earth Submodel System (MESSy) version 2.51

NASA Astrophysics Data System (ADS)

Jöckel, Patrick; Tost, Holger; Pozzer, Andrea; Kunze, Markus; Kirner, Oliver; Brenninkmeijer, Carl A. M.; Brinkop, Sabine; Cai, Duy S.; Dyroff, Christoph; Eckstein, Johannes; Frank, Franziska; Garny, Hella; Gottschaldt, Klaus-Dirk; Graf, Phoebe; Grewe, Volker; Kerkweg, Astrid; Kern, Bastian; Matthes, Sigrun; Mertens, Mariano; Meul, Stefanie; Neumaier, Marco; Nützel, Matthias; Oberländer-Hayn, Sophie; Ruhnke, Roland; Runde, Theresa; Sander, Rolf; Scharffe, Dieter; Zahn, Andreas

2016-03-01

Three types of reference simulations, as recommended by the Chemistry-Climate Model Initiative (CCMI), have been performed with version 2.51 of the European Centre for Medium-Range Weather Forecasts - Hamburg (ECHAM)/Modular Earth Submodel System (MESSy) Atmospheric Chemistry (EMAC) model: hindcast simulations (1950-2011), hindcast simulations with specified dynamics (1979-2013), i.e. nudged towards ERA-Interim reanalysis data, and combined hindcast and projection simulations (1950-2100). The manuscript summarizes the updates of the model system and details the different model set-ups used, including the on-line calculated diagnostics. Simulations have been performed with two different nudging set-ups, with and without interactive tropospheric aerosol, and with and without a coupled ocean model. Two different vertical resolutions have been applied. The on-line calculated sources and sinks of reactive species are quantified and a first evaluation of the simulation results from a global perspective is provided as a quality check of the data. The focus is on the intercomparison of the different model set-ups. The simulation data will become publicly available via CCMI and the Climate and Environmental Retrieval and Archive (CERA) database of the German Climate Computing Centre (DKRZ). This manuscript is intended to serve as an extensive reference for further analyses of the Earth System Chemistry integrated Modelling (ESCiMo) simulations.
Defined Host-Guest Chemistry on Nanocarbon for Sustained Inhibition of Cancer.

PubMed

Ostadhossein, Fatemeh; Misra, Santosh K; Mukherjee, Prabuddha; Ostadhossein, Alireza; Daza, Enrique; Tiwari, Saumya; Mittal, Shachi; Gryka, Mark C; Bhargava, Rohit; Pan, Dipanjan

2016-08-22

Signal transducer and activator of transcription factor 3 (STAT-3) is known to be overexpressed in cancer stem cells. Poor solubility and variable drug absorption are linked to low bioavailability and decreased efficacy. Many of the drugs regulating STAT-3 expression lack aqueous solubility; hence hindering efficient bioavailability. A theranostics nanoplatform based on luminescent carbon particles decorated with cucurbit[6]uril is introduced for enhancing the solubility of niclosamide, a STAT-3 inhibitor. The host-guest chemistry between cucurbit[6]uril and niclosamide makes the delivery of the hydrophobic drug feasible while carbon nanoparticles enhance cellular internalization. Extensive physicochemical characterizations confirm successful synthesis. Subsequently, the host-guest chemistry of niclosamide and cucurbit[6]uril is studied experimentally and computationally. In vitro assessments in human breast cancer cells indicate approximately twofold enhancement in IC 50 of drug. Fourier transform infrared and fluorescence imaging demonstrate efficient cellular internalization. Furthermore, the catalytic biodegradation of the nanoplatforms occur upon exposure to human myeloperoxidase in short time. In vivo studies on athymic mice with MCF-7 xenograft indicate the size of tumor in the treatment group is half of the controls after 40 d. Immunohistochemistry corroborates the downregulation of STAT-3 phosphorylation. Overall, the host-guest chemistry on nanocarbon acts as a novel arsenal for STAT-3 inhibition. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Concept-Oriented Task Design: Making Purposeful Case Comparisons in Organic Chemistry

ERIC Educational Resources Information Center

Graulich, Nicole; Schween, Michael

2018-01-01

Acquiring conceptual understanding seems to be one of the main challenges students face when studying organic chemistry. Traditionally, organic chemistry presents an extensive variety of chemical transformations, which often lead students to recall an organic transformation rather than apply conceptual knowledge. Strong surface level focus and…

75 FR 67711 - Extension of Scoping Period for the Supplemental Environmental Impact Statement for the Nuclear...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-03

... Statement for the Nuclear Facility Portion of the Chemistry and Metallurgy Research Building Replacement... Statement for the Nuclear Facility Portion of the Chemistry and Metallurgy Research Building Replacement... facility portion of the Chemistry and Metallurgy Research Building Replacement Project (CMRR-NF) at Los...
76 FR 28222 - Extension of the Public Review and Comment Period and Announcement of an Additional Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-16

... Impact Statement for the Nuclear Facility Portion of the Chemistry and Metallurgy Research Building... Chemistry and Metallurgy Research Building Replacement Project at Los Alamos National Laboratory, Los Alamos... Chemistry and Metallurgy Research Building Replacement Project (CMRR-NF) at Los Alamos National Laboratory...
Computer-aided drug discovery research at a global contract research organization

NASA Astrophysics Data System (ADS)

Kitchen, Douglas B.

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.
Computer-aided drug discovery research at a global contract research organization.

PubMed

Kitchen, Douglas B

2017-03-01

Computer-aided drug discovery started at Albany Molecular Research, Inc in 1997. Over nearly 20 years the role of cheminformatics and computational chemistry has grown throughout the pharmaceutical industry and at AMRI. This paper will describe the infrastructure and roles of CADD throughout drug discovery and some of the lessons learned regarding the success of several methods. Various contributions provided by computational chemistry and cheminformatics in chemical library design, hit triage, hit-to-lead and lead optimization are discussed. Some frequently used computational chemistry techniques are described. The ways in which they may contribute to discovery projects are presented based on a few examples from recent publications.
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…
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…
iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957
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.
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.
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
ChemoPy: freely available python package for computational biology and chemoinformatics.

PubMed

Cao, Dong-Sheng; Xu, Qing-Song; Hu, Qian-Nan; Liang, Yi-Zeng

2013-04-15

Molecular representation for small molecules has been routinely used in QSAR/SAR, virtual screening, database search, ranking, drug ADME/T prediction and other drug discovery processes. To facilitate extensive studies of drug molecules, we developed a freely available, open-source python package called chemoinformatics in python (ChemoPy) for calculating the commonly used structural and physicochemical features. It computes 16 drug feature groups composed of 19 descriptors that include 1135 descriptor values. In addition, it provides seven types of molecular fingerprint systems for drug molecules, including topological fingerprints, electro-topological state (E-state) fingerprints, MACCS keys, FP4 keys, atom pairs fingerprints, topological torsion fingerprints and Morgan/circular fingerprints. By applying a semi-empirical quantum chemistry program MOPAC, ChemoPy can also compute a large number of 3D molecular descriptors conveniently. The python package, ChemoPy, is freely available via http://code.google.com/p/pychem/downloads/list, and it runs on Linux and MS-Windows. Supplementary data are available at Bioinformatics online.
Reflections on my career in analytical chemistry and biochemistry

PubMed Central

SWEELEY, Charles C.

2010-01-01

My career has been focused in two major areas, analytical chemistry and biochemistry of complex lipids and glycoconjugates. Included here are the pioneering work on the gas chromatography of long-chain sphingolipid bases, carbohydrates, steroids and urinary organic acids. Mass spectrometry was utilized extensively in structural studies of sphingolipids, fatty acids, carbohydrates, steroids, urinary organic acids, polyisoprenoid alcohols, and juvenile hormone. Computer systems were developed for the acquisition and analysis of mass spectra, and were used for development of automated metabolic profiling of complex mixtures of metabolites. Fabry’s disease was discovered to be a glycosphingolipidosis. Enzymes of lysosomal metabolism of glycosphingolipids were purified, characterized, and used in one of the first demonstrations of the feasibility of enzyme replacement therapy in a lysosomal storage disorder (Fabry’s disease). Extracellular sialidases were studied to evaluate the hypothesis that they might be involved in the regulation of membrane growth factor receptors. The enzyme for hematoside synthesis was purified and characterized. PMID:20948176
The EPA CompTox Chemistry Dashboard - an online resource for environmental chemists (ACS Spring Meeting)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...
The EPA Comptox Chemistry Dashboard: A Web-Based Data Integration Hub for Toxicology Data (SOT)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...
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.
Computer Simulations of Quantum Theory of Hydrogen Atom for Natural Science Education Students in a Virtual Lab

ERIC Educational Resources Information Center

Singh, Gurmukh

2012-01-01

The present article is primarily targeted for the advanced college/university undergraduate students of chemistry/physics education, computational physics/chemistry, and computer science. The most recent software system such as MS Visual Studio .NET version 2010 is employed to perform computer simulations for modeling Bohr's quantum theory of…
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
Probing the Question Order Effect While Developing a Chemistry Concept Inventory

ERIC Educational Resources Information Center

Undersander, Molly A.; Lund, Travis J.; Langdon, Laurie S.; Stains, Marilyne

2017-01-01

The design of assessment tools is critical to accurately evaluate students' understanding of chemistry. Although extensive research has been conducted on various aspects of assessment tool design, few studies in chemistry have focused on the impact of the order in which questions are presented to students on the measurement of students'…
Go Chemistry: A Card Game to Help Students Learn Chemical Formulas

ERIC Educational Resources Information Center

Morris, Todd A.

2011-01-01

For beginning chemistry students, the basic tasks of writing chemical formulas and naming covalent and ionic compounds often pose difficulties and are only sufficiently grasped after extensive practice with homework sets. An enjoyable card game that can replace or, at least, complement nomenclature homework sets is described. "Go Chemistry" is…
Ambarish Nag | NREL

Science.gov Websites

|Mathematical biology Education Ph.D., Computational Chemistry, University of Chicago M.S., Chemistry , University of Chicago M.S., (2-Year) Chemistry, Indian Institute of Technology, Kanpur, India B.S., Chemistry

The journey from forensic to predictive materials science using density functional theory

DOE PAGES

Schultz, Peter A.

2017-09-12

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.
The journey from forensic to predictive materials science using density functional theory

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

Schultz, Peter A.

Approximate methods for electronic structure, implemented in sophisticated computer codes and married to ever-more powerful computing platforms, have become invaluable in chemistry and materials science. The maturing and consolidation of quantum chemistry codes since the 1980s, based upon explicitly correlated electronic wave functions, has made them a staple of modern molecular chemistry. Here, the impact of first principles electronic structure in physics and materials science had lagged owing to the extra formal and computational demands of bulk calculations.
Introduction of Digital Computer Technology Into the Undergraduate Chemistry Laboratory. Final Technical Report.

ERIC Educational Resources Information Center

Perone, Sam P.

The objective of this project has been the development of a successful approach for the incorporation of on-line computer technology into the undergraduate chemistry laboratory. This approach assumes no prior programing, electronics or instrumental analysis experience on the part of the student; it does not displace the chemistry content with…
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…
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.
Computational chemistry at Janssen

NASA Astrophysics Data System (ADS)

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.
Using Games To Teach Chemistry: An Annotated Bibliography

NASA Astrophysics Data System (ADS)

Russell, Jeanne V.

1999-04-01

A list of published or marketed games based on a chemistry motif is presented. Each game is listed according to its level, subject matter, and title. A bibliographic notation and a short description are given for each game. For Introductory/High School/General Chemistry, 45 games are listed under the subjects General Knowledge; Elements & Atomic Structure (not Symbols); Nomenclature, Formulas, & Equation Writing; Chemical Reactions: Solutions & Solubilities; and Other Subjects. Seventeen games are listed under Organic Chemistry and 4 games under Other Chemistry Games. Computer games designed for outdated computers (PDP-11, TRS-80, and Apple II) are not included.
Computers in Science: Thinking Outside the Discipline.

ERIC Educational Resources Information Center

Hamilton, Todd M.

2003-01-01

Describes the Computers in Science course which integrates computer-related techniques into the science disciplines of chemistry, physics, biology, and Earth science. Uses a team teaching approach and teaches students how to solve chemistry problems with spreadsheets, identify minerals with X-rays, and chemical and force analysis. (Contains 14…
Computer-Based Molecular Modelling: Finnish School Teachers' Experiences and Views

ERIC Educational Resources Information Center

Aksela, Maija; Lundell, Jan

2008-01-01

Modern computer-based molecular modelling opens up new possibilities for chemistry teaching at different levels. This article presents a case study seeking insight into Finnish school teachers' use of computer-based molecular modelling in teaching chemistry, into the different working and teaching methods used, and their opinions about necessary…
Overview of the NCC

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey

2001-01-01

A multi-disciplinary design/analysis tool for combustion systems is critical for optimizing the low-emission, high-performance combustor design process. Based on discussions between then NASA Lewis Research Center and the jet engine companies, an industry-government team was formed in early 1995 to develop the National Combustion Code (NCC), which is an integrated system of computer codes for the design and analysis of combustion systems. NCC has advanced features that address the need to meet designer's requirements such as "assured accuracy", "fast turnaround", and "acceptable cost". The NCC development team is comprised of Allison Engine Company (Allison), CFD Research Corporation (CFDRC), GE Aircraft Engines (GEAE), NASA Glenn Research Center (LeRC), and Pratt & Whitney (P&W). The "unstructured mesh" capability and "parallel computing" are fundamental features of NCC from its inception. The NCC system is composed of a set of "elements" which includes grid generator, main flow solver, turbulence module, turbulence and chemistry interaction module, chemistry module, spray module, radiation heat transfer module, data visualization module, and a post-processor for evaluating engine performance parameters. Each element may have contributions from several team members. Such a multi-source multi-element system needs to be integrated in a way that facilitates inter-module data communication, flexibility in module selection, and ease of integration. The development of the NCC beta version was essentially completed in June 1998. Technical details of the NCC elements are given in the Reference List. Elements such as the baseline flow solver, turbulence module, and the chemistry module, have been extensively validated; and their parallel performance on large-scale parallel systems has been evaluated and optimized. However the scalar PDF module and the Spray module, as well as their coupling with the baseline flow solver, were developed in a small-scale distributed computing environment. As a result, the validation of the NCC beta version as a whole was quite limited. Current effort has been focused on the validation of the integrated code and the evaluation/optimization of its overall performance on large-scale parallel systems.
Case Studies in Systems Chemistry. Final Report. [Includes Complete Case Study, Carboxylic Acid Equilibria

ERIC Educational Resources Information Center

Fleck, George

This publication was produced as a teaching tool for college chemistry. The book is a text for a computer-based unit on the chemistry of acid-base titrations, and is designed for use with FORTRAN or BASIC computer systems, and with a programmable electronic calculator, in a variety of educational settings. The text attempts to present computer…
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…
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…
Workshop report on large-scale matrix diagonalization methods in chemistry theory institute

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

Bischof, C.H.; Shepard, R.L.; Huss-Lederman, S.

The Large-Scale Matrix Diagonalization Methods in Chemistry theory institute brought together 41 computational chemists and numerical analysts. The goal was to understand the needs of the computational chemistry community in problems that utilize matrix diagonalization techniques. This was accomplished by reviewing the current state of the art and looking toward future directions in matrix diagonalization techniques. This institute occurred about 20 years after a related meeting of similar size. During those 20 years the Davidson method continued to dominate the problem of finding a few extremal eigenvalues for many computational chemistry problems. Work on non-diagonally dominant and non-Hermitian problems asmore » well as parallel computing has also brought new methods to bear. The changes and similarities in problems and methods over the past two decades offered an interesting viewpoint for the success in this area. One important area covered by the talks was overviews of the source and nature of the chemistry problems. The numerical analysts were uniformly grateful for the efforts to convey a better understanding of the problems and issues faced in computational chemistry. An important outcome was an understanding of the wide range of eigenproblems encountered in computational chemistry. The workshop covered problems involving self- consistent-field (SCF), configuration interaction (CI), intramolecular vibrational relaxation (IVR), and scattering problems. In atomic structure calculations using the Hartree-Fock method (SCF), the symmetric matrices can range from order hundreds to thousands. These matrices often include large clusters of eigenvalues which can be as much as 25% of the spectrum. However, if Cl methods are also used, the matrix size can be between 10{sup 4} and 10{sup 9} where only one or a few extremal eigenvalues and eigenvectors are needed. Working with very large matrices has lead to the development of« less
Using quantum chemistry muscle to flex massive systems: How to respond to something perturbing

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

Bertoni, Colleen

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

ERIC Educational Resources Information Center

Matsumoto, Paul S.; Cao, Jiankang

2017-01-01

Computational thinking is a component of the Science and Engineering Practices in the Next Generation Science Standards, which were adopted by some states. We describe the activities in a high school chemistry course that may develop students' computational thinking skills by primarily using Excel, a widely available spreadsheet software. These…
Proceedings: Conference on Computers in Chemical Education and Research, Dekalb, Illinois, 19-23 July 1971.

ERIC Educational Resources Information Center

1971

Computers have effected a comprehensive transformation of chemistry. Computers have greatly enhanced the chemist's ability to do model building, simulations, data refinement and reduction, analysis of data in terms of models, on-line data logging, automated control of experiments, quantum chemistry and statistical and mechanical calculations, and…
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…

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.
Pair 2-electron reduced density matrix theory using localized orbitals

NASA Astrophysics Data System (ADS)

Head-Marsden, Kade; Mazziotti, David A.

2017-08-01

Full configuration interaction (FCI) restricted to a pairing space yields size-extensive correlation energies but its cost scales exponentially with molecular size. Restricting the variational two-electron reduced-density-matrix (2-RDM) method to represent the same pairing space yields an accurate lower bound to the pair FCI energy at a mean-field-like computational scaling of O (r3) where r is the number of orbitals. In this paper, we show that localized molecular orbitals can be employed to generate an efficient, approximately size-extensive pair 2-RDM method. The use of localized orbitals eliminates the substantial cost of optimizing iteratively the orbitals defining the pairing space without compromising accuracy. In contrast to the localized orbitals, the use of canonical Hartree-Fock molecular orbitals is shown to be both inaccurate and non-size-extensive. The pair 2-RDM has the flexibility to describe the spectra of one-electron RDM occupation numbers from all quantum states that are invariant to time-reversal symmetry. Applications are made to hydrogen chains and their dissociation, n-acene from naphthalene through octacene, and cadmium telluride 2-, 3-, and 4-unit polymers. For the hydrogen chains, the pair 2-RDM method recovers the majority of the energy obtained from similar calculations that iteratively optimize the orbitals. The localized-orbital pair 2-RDM method with its mean-field-like computational scaling and its ability to describe multi-reference correlation has important applications to a range of strongly correlated phenomena in chemistry and physics.
National resource for computation in chemistry, phase I: evaluation and recommendations

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

Not Available

1980-05-01

The National Resource for Computation in Chemistry (NRCC) was inaugurated at the Lawrence Berkeley Laboratory (LBL) in October 1977, with joint funding by the Department of Energy (DOE) and the National Science Foundation (NSF). The chief activities of the NRCC include: assembling a staff of eight postdoctoral computational chemists, establishing an office complex at LBL, purchasing a midi-computer and graphics display system, administering grants of computer time, conducting nine workshops in selected areas of computational chemistry, compiling a library of computer programs with adaptations and improvements, initiating a software distribution system, providing user assistance and consultation on request. This reportmore » presents assessments and recommendations of an Ad Hoc Review Committee appointed by the DOE and NSF in January 1980. The recommendations are that NRCC should: (1) not fund grants for computing time or research but leave that to the relevant agencies, (2) continue the Workshop Program in a mode similar to Phase I, (3) abandon in-house program development and establish instead a competitive external postdoctoral program in chemistry software development administered by the Policy Board and Director, and (4) not attempt a software distribution system (leaving that function to the QCPE). Furthermore, (5) DOE should continue to make its computational facilities available to outside users (at normal cost rates) and should find some way to allow the chemical community to gain occasional access to a CRAY-level computer.« less
Time-Dependent Wave Packet Dynamics Calculations of Cross Sections for Ultracold Scattering of Molecules

NASA Astrophysics Data System (ADS)

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

2018-04-01

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

PubMed

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

2018-04-06

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

ERIC Educational Resources Information Center

Cavin, Claudia S.; Cavin, E. D.

1978-01-01

This article describes the design, preparation, and initial evaluation of a set of computer-simulated chemistry experiments. The experiments entailed the use of an atomic emission spectroscope and a single-beam visible absorption spectrophometer. (Author/IRT)
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.
The Computer Bulletin Board.

ERIC Educational Resources Information Center

Batt, Russell H., Ed.

1989-01-01

Describes two chemistry computer programs: (1) "Eureka: A Chemistry Problem Solver" (problem files may be written by the instructor, MS-DOS 2.0, IBM with 384K); and (2) "PC-File+" (database management, IBM with 416K and two floppy drives). (MVL)
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…
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…
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…
The Use of Modular Computer-Based Lessons in a Modification of the Classical Introductory Course in Organic Chemistry.

ERIC Educational Resources Information Center

Stotter, Philip L.; Culp, George H.

An experimental course in organic chemistry utilized computer-assisted instructional (CAI) techniques. The CAI lessons provided tutorial drill and practice and simulated experiments and reactions. The Conversational Language for Instruction and Computing was used, along with a CDC 6400-6600 system; students scheduled and completed the lessons at…
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.…
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…
BLT-EC (Breach, Leach and Transport-Equilibrium Chemistry) data input guide. A computer model for simulating release and coupled geochemical transport of contaminants from a subsurface disposal facility

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

MacKinnon, R.J.; Sullivan, T.M.; Kinsey, R.R.

1997-05-01

The BLT-EC computer code has been developed, implemented, and tested. BLT-EC is a two-dimensional finite element computer code capable of simulating the time-dependent release and reactive transport of aqueous phase species in a subsurface soil system. BLT-EC contains models to simulate the processes (container degradation, waste-form performance, transport, chemical reactions, and radioactive production and decay) most relevant to estimating the release and transport of contaminants from a subsurface disposal system. Water flow is provided through tabular input or auxiliary files. Container degradation considers localized failure due to pitting corrosion and general failure due to uniform surface degradation processes. Waste-form performancemore » considers release to be limited by one of four mechanisms: rinse with partitioning, diffusion, uniform surface degradation, and solubility. Transport considers the processes of advection, dispersion, diffusion, chemical reaction, radioactive production and decay, and sources (waste form releases). Chemical reactions accounted for include complexation, sorption, dissolution-precipitation, oxidation-reduction, and ion exchange. Radioactive production and decay in the waste form is simulated. To improve the usefulness of BLT-EC, a pre-processor, ECIN, which assists in the creation of chemistry input files, and a post-processor, BLTPLOT, which provides a visual display of the data have been developed. BLT-EC also includes an extensive database of thermodynamic data that is also accessible to ECIN. This document reviews the models implemented in BLT-EC and serves as a guide to creating input files and applying BLT-EC.« less
Commentary: Prerequisite Knowledge

ERIC Educational Resources Information Center

Taylor, Ann T. S.

2013-01-01

Most biochemistry, genetics, cell biology, and molecular biology classes have extensive prerequisite or co-requisite requirements, often including introductory chemistry, introductory biology, and organic chemistry coursework. But what is the function of these prerequisites? While it seems logical that a basic understanding of biological and…
Programs for Fundamentals of Chemistry.

ERIC Educational Resources Information Center

Gallardo, Julio; Delgado, Steven

This document provides computer programs, written in BASIC PLUS, for presenting fundamental or remedial college chemistry students with chemical problems in a computer assisted instructional program. Programs include instructions, a sample run, and 14 separate practice sessions covering: mathematical operations, using decimals, solving…
[Advancements of computer chemistry in separation of Chinese medicine].

PubMed

Li, Lingjuan; Hong, Hong; Xu, Xuesong; Guo, Liwei

2011-12-01

Separating technique of Chinese medicine is not only a key technique in the field of Chinese medicine' s research and development, but also a significant step in the modernization of Chinese medicinal preparation. Computer chemistry can build model and look for the regulations from Chinese medicine system which is full of complicated data. This paper analyzed the applicability, key technology, basic mode and common algorithm of computer chemistry applied in the separation of Chinese medicine, introduced the mathematic mode and the setting methods of Extraction kinetics, investigated several problems which based on traditional Chinese medicine membrane procession, and forecasted the application prospect.
Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

PubMed Central

2013-01-01

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341
SDA 7: A modular and parallel implementation of the simulation of diffusional association software

PubMed Central

Martinez, Michael; Romanowska, Julia; Kokh, Daria B.; Ozboyaci, Musa; Yu, Xiaofeng; Öztürk, Mehmet Ali; Richter, Stefan

2015-01-01

The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:26123630

Protein Engineering: Development of a Metal Ion Dependent Switch

DTIC Science & Technology

2017-05-22

Society of Chemistry Royal Society of Chemistry Biochemistry PNAS Escherichia coli Journal of Biotechnology Biochemistry Nature Protocols Journal of...Molecular Biology Biochemistry Royal Society of Chemistry Proteins: Structure, Function, and Bioinformatics Journal of Molecular Biology Biophysical...Biophysical Journal Protein Science Journal of Computational Chemistry Current Opinion in Chemical Biology Royal Society of Chemistry
Efficient 3D kinetic Monte Carlo method for modeling of molecular structure and dynamics.

PubMed

Panshenskov, Mikhail; Solov'yov, Ilia A; Solov'yov, Andrey V

2014-06-30

Self-assembly of molecular systems is an important and general problem that intertwines physics, chemistry, biology, and material sciences. Through understanding of the physical principles of self-organization, it often becomes feasible to control the process and to obtain complex structures with tailored properties, for example, bacteria colonies of cells or nanodevices with desired properties. Theoretical studies and simulations provide an important tool for unraveling the principles of self-organization and, therefore, have recently gained an increasing interest. The present article features an extension of a popular code MBN EXPLORER (MesoBioNano Explorer) aiming to provide a universal approach to study self-assembly phenomena in biology and nanoscience. In particular, this extension involves a highly parallelized module of MBN EXPLORER that allows simulating stochastic processes using the kinetic Monte Carlo approach in a three-dimensional space. We describe the computational side of the developed code, discuss its efficiency, and apply it for studying an exemplary system. Copyright © 2014 Wiley Periodicals, Inc.
Computational chemistry for NH 3 synthesis, hydrotreating, and NO x reduction: Three topics of special interest to Haldor Topsøe

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

Elnabawy, Ahmed O.; Rangarajan, Srinivas; Mavrikakis, Manos

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 NO x reduction. Furthermore, wemore » 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.« less
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

2015-06-05

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 NO x reduction. Furthermore, wemore » 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.« less
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,…
Current state of aerosol nucleation parameterizations for air-quality and climate modeling

NASA Astrophysics Data System (ADS)

Semeniuk, Kirill; Dastoor, Ashu

2018-04-01

Aerosol nucleation parameterization models commonly used in 3-D air quality and climate models have serious limitations. This includes classical nucleation theory based variants, empirical models and other formulations. Recent work based on detailed and extensive laboratory measurements and improved quantum chemistry computation has substantially advanced the state of nucleation parameterizations. In terms of inorganic nucleation involving BHN and THN including ion effects these new models should be considered as worthwhile replacements for the old models. However, the contribution of organic species to nucleation remains poorly quantified. New particle formation consists of a distinct post-nucleation growth regime which is characterized by a strong Kelvin curvature effect and is thus dependent on availability of very low volatility organic species or sulfuric acid. There have been advances in the understanding of the multiphase chemistry of biogenic and anthropogenic organic compounds which facilitate to overcome the initial aerosol growth barrier. Implementation of processes influencing new particle formation is challenging in 3-D models and there is a lack of comprehensive parameterizations. This review considers the existing models and recent innovations.
Force Field Accelerated Density Functional Theory Molecular Dynamics for Simulation of Reactive Systems at Extreme Conditions

NASA Astrophysics Data System (ADS)

Lindsey, Rebecca; Goldman, Nir; Fried, Laurence

Understanding chemistry at extreme conditions is crucial in fields including geochemistry, astrobiology, and alternative energy. First principles methods can provide valuable microscopic insights into such systems while circumventing the risks of physical experiments, however the time and length scales associated with chemistry at extreme conditions (ns and μm, respectively) largely preclude extension of such models to molecular dynamics. In this work, we develop a simulation approach that retains the accuracy of density functional theory (DFT) while decreasing computational effort by several orders of magnitude. We generate n-body descriptions for atomic interactions by mapping forces arising from short density functional theory (DFT) trajectories on to simple Chebyshev polynomial series. We examine the importance of including greater than 2-body interactions, model transferability to different state points, and discuss approaches to ensure smooth and reasonable model shape outside of the distance domain sampled by the DFT training set. This work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.
LABORATORY AND COMPUTATIONAL INVESTIGATIONS OF THE ATMOSPHERIC CHEMISTRY OF KEY OXIDATION PRODUCTS CONTROLLING TROPOSPHERIC OZONE FORMATION

EPA Science Inventory

Major uncertainties remain in our ability to identify the key reactions and primary oxidation products of volatile hydrocarbons that contribute to ozone formation in the troposphere. To reduce these uncertainties, computational chemistry, mechanistic and process analysis techniqu...
Chemical calculations on Cray computers

NASA Technical Reports Server (NTRS)

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

1989-01-01

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

NASA Technical Reports Server (NTRS)

Kutler, Paul; Yee, Helen

1987-01-01

Topics addressed include: numerical aerodynamic simulation; computational mechanics; supercomputers; aerospace propulsion systems; computational modeling in ballistics; turbulence modeling; computational chemistry; computational fluid dynamics; and computational astrophysics.
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…
Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennit - A Computational Modeling Study

DTIC Science & Technology

2014-01-01

Study Material properties and performance are governed by material molecular chemistry structures and molecular level interactions. Methods to...understand relationships between the material properties and performance and their correlation to the molecular level chemistry and morphology, and thus...find ways of manipulating and adjusting matters at the atomistic level in order to improve material performance are required. A computational material
U.S. EPA’s Computational Toxicology Program: Innovation Powered by Chemistry (Dalton State College presentation)

EPA Science Inventory

Invited presentation at Dalton College, Dalton, GA to the Alliance for Innovation & Sustainability, April 20, 2017. U.S. EPA’s Computational Toxicology Program: Innovation Powered by Chemistry It is estimated that tens of thousands of commercial and industrial chemicals are ...
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…
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language.

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.
From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

PubMed Central

2013-01-01

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910
Chemistry Division: Annual progress report for period ending March 31, 1987

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

Not Available

1987-08-01

This report is divided into the following sections: coal chemistry; aqueous chemistry at high temperatures and pressures; geochemistry of crustal processes to high temperatures and pressures; chemistry of advanced inorganic materials; structure and dynamics of advanced polymeric materials; chemistry of transuranium elements and compounds; separations chemistry; reactions and catalysis in molten salts; surface science related to heterogeneous catalysis; electron spectroscopy; chemistry related to nuclear waste disposal; computational modeling of security document printing; and special topics. (DLC)
Development of the Connected Chemistry as Formative Assessment Pedagogy for High School Chemistry Teaching

ERIC Educational Resources Information Center

Park, Mihwa; Liu, Xiufeng; Waight, Noemi

2017-01-01

This paper describes the development of Connected Chemistry as Formative Assessment (CCFA) pedagogy, which integrates three promising teaching and learning approaches, computer models, formative assessments, and learning progressions, to promote student understanding in chemistry. CCFA supports student learning in making connections among the…
Indoor chemistry: research opportunities and challenges.

PubMed

Nazaroff, W W; Goldstein, A H

2015-08-01

In this editorial, we have highlighted key research opportunities and challenges in four topical themes for indoor chemistry: human occupants as agents influencing indoor chemistry; oxidative chemistry; surface phenomena; and semivolatile organic compounds. In each case, enough prior work has been done to demonstrate the importance of the theme and to create a foundation for future studies. Extensive achievements and ongoing progress in (outdoor) atmospheric chemistry—both in the analytical methods developed and in the scientific knowledge created—also contribute to a strong foundation from which to achieve rapid research progress in this exciting new domain.
Teaching Triple Science: GCSE Chemistry

ERIC Educational Resources Information Center

Learning and Skills Network (NJ3), 2007

2007-01-01

The Department for Children, Schools and Families (DCSF) has contracted with the Learning and Skills Network to support awareness and take-up of Triple Science GCSEs through the Triple Science Support Programme. This publication provides an introduction to teaching and learning approaches for the extension topics within GCSE Chemistry. It…

Medical Laboratory Technician (Chemistry and Urinalysis). (AFSC 92470).

ERIC Educational Resources Information Center

Thompson, Joselyn H.

This four-volume student text is designed for use by Air Force personnel enrolled in a self-study extension course for medical laboratory technicians. Covered in the individual volumes are medical laboratory administration and clinical chemistry (career opportunities, general laboratory safety and materials, general medical laboratory…
Writing and Computing across the USM Chemistry Curriculum

NASA Astrophysics Data System (ADS)

Gordon, Nancy R.; Newton, Thomas A.; Rhodes, Gale; Ricci, John S.; Stebbins, Richard G.; Tracy, Henry J.

2001-01-01

The faculty of the University of Southern Maine believes the ability to communicate effectively is one of the most important skills required of successful chemists. To help students achieve that goal, the faculty has developed a Writing and Computer Program consisting of writing and computer assignments of gradually increasing sophistication for all our laboratory courses. The assignments build in complexity until, at the junior level, students are writing full journal-quality laboratory reports. Computer assignments also increase in difficulty as students attack more complicated subjects. We have found the program easy to initiate and our part-time faculty concurs as well. The Writing and Computing across the Curriculum Program also serves to unite the entire chemistry curriculum. We believe the program is helping to reverse what the USM chemistry faculty and other educators have found to be a steady deterioration in the writing skills of many of today's students.
Biennial Conference on Chemical Education: Abstracts of Papers (9th, Bozeman, Montana, July 27-August 2, 1986).

ERIC Educational Resources Information Center

1986

This document includes summaries of conference presentations dealing with a wide variety of topics, including chemistry units for the elementary classroom, science experimentation in the secondary school, computer simulations, computer interfaces, videodisc technology, correspondence teaching of general chemistry, interdisciplinary energy courses,…
Using Computer Simulations in Chemistry Problem Solving

ERIC Educational Resources Information Center

Avramiotis, Spyridon; Tsaparlis, Georgios

2013-01-01

This study is concerned with the effects of computer simulations of two novel chemistry problems on the problem solving ability of students. A control-experimental group, equalized by pair groups (n[subscript Exp] = n[subscript Ctrl] = 78), research design was used. The students had no previous experience of chemical practical work. Student…
RESEARCH STRATEGIES FOR THE APPLICATION OF THE TECHNIQUES OF COMPUTATIONAL BIOLOGICAL CHEMISTRY TO ENVIRONMENTAL PROBLEMS

EPA Science Inventory

On October 25 and 26, 1984, the U.S. EPA sponsored a workshop to consider the potential applications of the techniques of computational biological chemistry to problems in environmental health. Eleven extramural scientists from the various related disciplines and a similar number...
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...
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…
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…
Intrafen and interfen variation of Indiana fens: water chemistry

USGS Publications Warehouse

Stewart, Paul M.; Kessler, Katrina; Dunbar, Richard

1993-01-01

This study establishes a baseline of water chemistry information for selected Indiana fens over the course of one year. Fens are peatlands fed by groundwater seepage and are characterized by their dominant plant communities. Most of the fens discussed in this paper are located on property controlled and protected by the State of Indiana or the Federal government. Comparisons were made of variability in water chemistry data between fens located in the same area and those located some distance away. This survey indicated extensive variability in fen water chemistry with greater variability in water chemistry between fens in separate locations than in yearly variation within individual fens.
[On teaching the chemistry of pharmaceutical auxiliary substances within the framework of pharmaceutical education in the Czech and Slovak Republics].

PubMed

Jan, Subert

2011-02-01

The paper emphasizes the need of the introduction of the subject Chemistry of Pharmaceutical Auxiliaries into the Pharmacy study programme at more colleges in the Czech and Slovak Republics. It also introduces and discusses some topics for possible extension of the content of the courses of the subject (the presented examples are taken form the field of analytical chemistry of pharmaceutical auxiliaries).
Interdisciplinarity and Education: Towards Principles of Pedagogical Practice

ERIC Educational Resources Information Center

Mulder, Martin

2012-01-01

Disciplines play a major role in agricultural education and extension. Biology, chemistry and physics are all essential to understand nature and to improve the quality of agricultural production. During the past centuries, disciplines have evolved, and a multitude of specialisations emerged, like cell biology, colloid chemistry and geophysics. The…
75 FR 18784 - FY 2010 NIST Center for Neutron Research (NCNR) Comprehensive Grants Program

Federal Register 2010, 2011, 2012, 2013, 2014

2010-04-13

... extensive publications and invited lectures in condensed matter physics, chemistry, material science... science, particularly in the areas of macromolecular science, condensed matter physics, and chemistry (20... these topics must be in compliance with any statutory requirements imposed upon the Department of Health...
Mineral Analysis of Whole Grain Total Cereal

ERIC Educational Resources Information Center

Hooker, Paul

2005-01-01

The quantitative analysis of elemental iron in Whole Grain Total Cereal using visible spectroscopy is suitable for a general chemistry course for science or nonscience majors. The more extensive mineral analysis, specifically for the elements iron, calcium and zinc, is suitable for an instrumental or quantitative analysis chemistry course.
Chemistry of Meridiani Outcrops

NASA Technical Reports Server (NTRS)

Clark, B. C.; Squyres, S. W.; Ming, D. W.; Morris, R. V.; Yen, A.; Gellert, R.; Knoll, A.H.; Arvidson, R. E.

2006-01-01

The chemistry and mineralogy of the sulfate-rich sandstone outcrops at Meridiani Planum, Mars, have been inferred from data obtained by the Opportunity rover of the MER mission and reported in recent publications [1-6]. Here, we provide an update on more recent samples and results derived from this extensive data set.
Fundamentals of ISCO Using Hydrogen Peroxide

EPA Science Inventory

Hydrogen peroxide is a common oxidant that has been applied extensively with in situ chemical oxidation (ISCO). Because of its widespread use in this and other fields, it has been extensively researched. This research has revealed that hydrogen peroxide has very complex chemistry...
New developments in theoretical thermochemistry and electronic structure applications in supramolecular chemistry and cluster science

NASA Astrophysics Data System (ADS)

Ramabhadran, Raghunath Ozhapakkam

In a concise display of the power and diversity of electronic structure theory (EST), the work presented herein involves the development of new computational methods to advance the practical utility of quantum chemistry, as well as solving different types of challenging chemical problems by applying existing EST tools. The research presented is highly interdisciplinary in nature and features synergistic collaborations to solve real-life problems such as regulating toxic chemicals and generating alternative sources of energy. In the first chapter of this dissertation, the solution to a long-standing problem in theoretical thermochemistry is accomplished by the development of the automated, chemically intuitive and generalized thermochemical hierarchy, Connectivity-Based Hierarchy (CBH) to accurately predict the thermochemical properties of organic molecules. The extension of the hierarchy to predict the enthalpies of formations of biomonomers such as amino acids is also presented. The development of a computationally efficient protocol to accurately extrapolate to high CCSD(T) energies based on MP2 and DFT energies using CBH is presented in the second chapter, thus merging theoretical thermochemistry with fragment-based methods in quantum chemistry. This merger drastically reduces the computational cost involved in a CCSD(T) calculation, while retaining the impeccable accuracy it offers. The practical utility of the CH hydrogen bond, commonly thought as being too weak to be used in supramolecular applications has been demonstrated by DFT calculations (along with experimental results from the Flood group) in the third chapter. This is accomplished by systematically studying the binding of monoatomic chloride, diatomic and toxic cyanide and the polyatomic bi-fluoride anions for the first time using only CH hydrogen bonds within a triazolophane macrocycle. The fourth chapter contains the introduction of the concept of fluxionality in the chemical reactions of transition metal oxide clusters. This is useful to develop a systematic paradigm for discussing the mechanisms in the reactions of larger transition metal oxide clusters with small molecules. Additionally, DFT calculations (along with experimental results from the C. C. Jarrold group) are shown to be useful to provide new insights on hydrogen liberation from water, thus aiding in the generation of alternative sources of energy.
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…
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…
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…
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…

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…
Mass spectrometry. [in organic chemistry

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Shackleton, C. H. L.; Howe, I.; Chizhov, O. S.

1978-01-01

A review of mass spectrometry in organic chemistry is given, dealing with advances in instrumentation and computer techniques, selected topics in gas-phase ion chemistry, and applications in such fields as biomedicine, natural-product studies, and environmental pollution analysis. Innovative techniques and instrumentation are discussed, along with chromatographic-mass spectrometric on-line computer techniques, mass spectral interpretation and management techniques, and such topics in gas-phase ion chemistry as electron-impact ionization and decomposition, photoionization, field ionization and desorption, high-pressure mass spectrometry, ion cyclotron resonance, and isomerization reactions of organic ions. Applications of mass spectrometry are examined with respect to bio-oligomers and their constituents, biomedically important substances, microbiology, environmental organic analysis, and organic geochemistry.
Experimental Investigation of Turbulence-Chemistry Interaction in High-Reynolds-Number Turbulent Partially Premixed Flames

DTIC Science & Technology

2016-06-23

4 . TITLE AND SUBTITLE [U] Experimental investigation of turbulence-chemistry interaction in high-Reynolds-number 5a. CONTRACT NUMBER turbulent...nonpremixed/partially premixed flames and turbulence-chemistry interaction. Turbulent mixing of mixture fraction has been studied extensively [ 4 , 14]. In a...two-feed non-premixed flame, the mixture fraction is defined as: ξ = Y − Yo YF − Yo (1) where Y is a conserved quantity such as the mass fraction of any
A detailed analysis of inviscid flux splitting algorithms for real gases with equilibrium or finite-rate chemistry

NASA Technical Reports Server (NTRS)

Shuen, Jian-Shun; Liou, Meng-Sing; Van Leer, Bram

1989-01-01

The extension of the known flux-vector and flux-difference splittings to real gases via rigorous mathematical procedures is demonstrated. Formulations of both equilibrium and finite-rate chemistry for real-gas flows are described, with emphasis on derivations of finite-rate chemistry. Split-flux formulas from other authors are examined. A second-order upwind-based TVD scheme is adopted to eliminate oscillations and to obtain a sharp representation of discontinuities.
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…
Symbolic Mathematics Engines in Teaching Chemistry: A Symposium Report

ERIC Educational Resources Information Center

Ellison, Mark

2004-01-01

The use of Symbolic Mathematics Engines (SMEs) in chemical education as a part of the Division of Computers in Chemistry was discussed by a panel of educators at the Symbolic Calculation in Chemistry symposium in Philadelphia in 2004. The panelists agreed that many more topics in chemistry are amenable to SME's exploration and that symbolic…
The FREZCHEM Model

NASA Astrophysics Data System (ADS)

Marion, Giles M.; Kargel, Jeffrey S.

Implementation of the Pitzer approach is through the FREZCHEM (FREEZING CHEMISTRY) model, which is at the core of this work. This model was originally designed to simulate salt chemistries and freezing processes at low temperatures (-54 to 25°C) and 1 atm pressure. Over the years, this model has been broadened to include more chemistries (from 16 to 58 solid phases), a broader temperature range for some chemistries (to 113°C), and incorporation of a pressure dependence (1 to 1000 bars) into the model. Implementation, parameterization, validation, and limitations of the FREZCHEM model are extensively discussed in Chapter 3.
Modeling ecohydrologic processes at Hubbard Brook: Initial results for Watershed 6 stream discharge and chemistry

EPA Science Inventory

The Hubbard Brook Long Term Ecological Research site has produced some of the most extensive and long-running databases on the hydrology, biology and chemistry of forest ecosystem responses to climate and forest harvest. We used these long-term databases to calibrate and apply G...
Supramolecular Based Membrane Sensors

PubMed Central

Ganjali, Mohammad Reza; Norouzi, Parviz; Rezapour, Morteza; Faridbod, Farnoush; Pourjavid, Mohammad Reza

2006-01-01

Supramolecular chemistry can be defined as a field of chemistry, which studies the complex multi-molecular species formed from molecular components that have relatively simpler structures. This field has been subject to extensive research over the past four decades. This review discusses classification of supramolecules and their application in design and construction of ion selective sensors.
The Chemical and Educational Appeal of the Orange Juice Clock.

ERIC Educational Resources Information Center

Kelter, Paul B.; And Others

1996-01-01

Describes the recent history, chemistry, and educational uses of the Orange Juice Clock demonstration in which a galvanic cell is made from the combination of a magnesium strip, a copper strip, and juice in a beaker. Discusses the chemistry basics, extensions for more advanced students, questions for student/teacher workshop participants, and…
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...
Development and Application of Computational/In Vitro Toxicological Methods for Chemical Hazard Risk Reduction of New Materials for Advanced Weapon Systems

NASA Technical Reports Server (NTRS)

Frazier, John M.; Mattie, D. R.; Hussain, Saber; Pachter, Ruth; Boatz, Jerry; Hawkins, T. W.

2000-01-01

The development of quantitative structure-activity relationship (QSAR) is essential for reducing the chemical hazards of new weapon systems. The current collaboration between HEST (toxicology research and testing), MLPJ (computational chemistry) and PRS (computational chemistry, new propellant synthesis) is focusing R&D efforts on basic research goals that will rapidly transition to useful products for propellant development. Computational methods are being investigated that will assist in forecasting cellular toxicological end-points. Models developed from these chemical structure-toxicity relationships are useful for the prediction of the toxicological endpoints of new related compounds. Research is focusing on the evaluation tools to be used for the discovery of such relationships and the development of models of the mechanisms of action. Combinations of computational chemistry techniques, in vitro toxicity methods, and statistical correlations, will be employed to develop and explore potential predictive relationships; results for series of molecular systems that demonstrate the viability of this approach are reported. A number of hydrazine salts have been synthesized for evaluation. Computational chemistry methods are being used to elucidate the mechanism of action of these salts. Toxicity endpoints such as viability (LDH) and changes in enzyme activity (glutahoione peroxidase and catalase) are being experimentally measured as indicators of cellular damage. Extrapolation from computational/in vitro studies to human toxicity, is the ultimate goal. The product of this program will be a predictive tool to assist in the development of new, less toxic propellants.
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…
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…
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…
Software platform virtualization in chemistry research and university teaching

PubMed Central

2009-01-01

Background Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Results Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Conclusion Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide. PMID:20150997
Software platform virtualization in chemistry research and university teaching.

PubMed

Kind, Tobias; Leamy, Tim; Leary, Julie A; Fiehn, Oliver

2009-11-16

Modern chemistry laboratories operate with a wide range of software applications under different operating systems, such as Windows, LINUX or Mac OS X. Instead of installing software on different computers it is possible to install those applications on a single computer using Virtual Machine software. Software platform virtualization allows a single guest operating system to execute multiple other operating systems on the same computer. We apply and discuss the use of virtual machines in chemistry research and teaching laboratories. Virtual machines are commonly used for cheminformatics software development and testing. Benchmarking multiple chemistry software packages we have confirmed that the computational speed penalty for using virtual machines is low and around 5% to 10%. Software virtualization in a teaching environment allows faster deployment and easy use of commercial and open source software in hands-on computer teaching labs. Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.
Markstein Numbers of Negatively-Stretched Premixed Flames: Microgravity Measurements and Computations

NASA Technical Reports Server (NTRS)

Ibarreta, Alfonso F.; Driscoll, James F.; Feikema, Douglas A.; Salzman, Jack (Technical Monitor)

2001-01-01

The effect of flame stretch, composed of strain and curvature, plays a major role in the propagation of turbulent premixed flames. Although all forms of stretch (positive and negative) are present in turbulent conditions, little research has been focused on the stretch due to curvature. The present study quantifies the Markstein number (which characterizes the sensitivity of the flame propagation speed to the imposed stretch rate) for an inwardly-propagating flame (IPF). This flame is of interest because it is negatively stretched, and is subjected to curvature effects alone, without the competing effects of strain. In an extension of our previous work, microgravity experiments were run using a vortex-flame interaction to create a pocket of reactants surrounded by an IPF. Computations using the RUN-1DL code of Rogg were also performed in order to explain the measurements. It was found that the Markstein number of an inwardly-propagating flame, for both the microgravity experiment and the computations, is significantly larger than that of an outwardly-propagating flame. Further insight was gained by running the computations for the simplified (hypothetical) cases of one step chemistry, unity Lewis number, and negligible heat release. Results provide additional evidence that the Markstein numbers associated with strain and curvature have different values.
Development and application of the GIM code for the Cyber 203 computer

NASA Technical Reports Server (NTRS)

Stainaker, J. F.; Robinson, M. A.; Rawlinson, E. G.; Anderson, P. G.; Mayne, A. W.; Spradley, L. W.

1982-01-01

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.
Mobilizing EPA's Comptox Chemistry Dashboard Data on Mobile Devices (ACS Spring Meeting)

EPA Science Inventory

The EPA’s National Center of Computational Toxicology (NCCT) Chemistry Dashboard provides access to chemistry data for about 720,000 chemical substances. The application is used to source, for example: physicochemical property data, bioassay screening data and functional use, and...

Software Applications on the Peregrine System | High-Performance Computing

Science.gov Websites

programming and optimization. Gaussian Chemistry Program for calculating molecular electronic structure and Materials Science Open-source classical molecular dynamics program designed for massively parallel systems framework Q-Chem Chemistry ab initio quantum chemistry package for predictin molecular structures
Students' Learning with the Connected Chemistry (CC1) Curriculum: Navigating the Complexities of the Particulate World

ERIC Educational Resources Information Center

Levy, Sharona T.; Wilensky, Uri

2009-01-01

The focus of this study is students' learning with a Connected Chemistry unit, CC1 (denotes Connected Chemistry, chapter 1), a computer-based environment for learning the topics of gas laws and kinetic molecular theory in chemistry (Levy and Wilensky 2009). An investigation was conducted into high-school students' learning with Connected…
A survey of upwind methods for flows with equilibrium and non-equilibrium chemistry and thermodynamics

NASA Technical Reports Server (NTRS)

Grossman, B.; Garrett, J.; Cinnella, P.

1989-01-01

Several versions of flux-vector split and flux-difference split algorithms were compared with regard to general applicability and complexity. Test computations were performed using curve-fit equilibrium air chemistry for an M = 5 high-temperature inviscid flow over a wedge, and an M = 24.5 inviscid flow over a blunt cylinder for test computations; for these cases, little difference in accuracy was found among the versions of the same flux-split algorithm. For flows with nonequilibrium chemistry, the effects of the thermodynamic model on the development of flux-vector split and flux-difference split algorithms were investigated using an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Several numerical examples are presented, including nonequilibrium air chemistry in a high-temperature shock tube and nonequilibrium hydrogen-air chemistry in a supersonic diffuser.
Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

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

2015-01-01

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

NASA Technical Reports Server (NTRS)

Eppard, W. M.; Grossman, B.

1993-01-01

We have developed new upwind kinetic difference schemes for flows with non-equilibrium thermodynamics and chemistry. These schemes are derived from the Boltzmann equation with the resulting Euler schemes developed as moments of the discretized Boltzmann scheme with a locally Maxwellian velocity distribution. Splitting the velocity distribution at the Boltzmann level is seen to result in a flux-split Euler scheme and is called Kinetic Flux Vector Splitting (KFVS). Extensions to flows with finite-rate chemistry and vibrational relaxation is accomplished utilizing nonequilibrium kinetic theory. Computational examples are presented comparing KFVS with the schemes of Van Leer and Roe for a quasi-one-dimensional flow through a supersonic diffuser, inviscid flow through two-dimensional inlet, and viscous flow over a cone at zero angle-of-attack. Calculations are also shown for the transonic flow over a bump in a channel and the transonic flow over an NACA 0012 airfoil. The results show that even though the KFVS scheme is a Riemann solver at the kinetic level, its behavior at the Euler level is more similar to the existing flux-vector splitting algorithms than to the flux-difference splitting scheme of Roe.
Chemistry on the Go: Review of Chemistry Apps on Smartphones

ERIC Educational Resources Information Center

Libman, Diana; Huang, Ling

2013-01-01

touch-controlled computers such as smartphones and iPods are seeing dramatic growth with increasing adoption rates. This review covers about 30 popular and mostly free apps that can be used to learn chemistry and to serve as reference or research tools. The target…
Richard J. French, Ph.D. | NREL

Science.gov Websites

J. French, Ph.D. Photo of Richard J. French Rick French Researcher IV-Chemistry Richard.French Laboratory equipment design and construction Computer-aided design (CAD) Education Ph.D., Chemistry, Oregon State University B.S., Chemistry, Wheaton College Professional Experience Research Scientist, National
Effectiveness of Using Computer-Assisted Supplementary Instruction for Teaching the Mole Concept

NASA Astrophysics Data System (ADS)

Yalçinalp, Serpil; Geban, Ömer; Özkan, Ilker

This study examined the effect of computer-assisted instruction (CAI), used as a problem-solving supplement to classroom instruction, on students' understanding of chemical formulas and mole concept, their attitudes toward chemistry subjects, and CAI. The objective was to assess the effectiveness of CAI over recitation hours when both teaching methods were used as a supplement to the traditional chemistry instruction. We randomly selected two classes in a secondary school. Each teaching strategy was randomly assigned to one class. The experimental group received supplementary instruction delivered via CAI, while the control group received similar instruction through recitation hours. The data were analyzed using two-way analysis of variance and t-test. It was found that the students who used the CAI accompanied with lectures scored significantly higher than those who attended recitation hours, in terms of school subject achievement in chemistry and attitudes toward chemistry subjects. In addition, there was a significant improvement in the attitudes of students in the experimental group toward the use of computers in a chemistry course. There was no significant difference between the performances of females versus males in each treatment group.Received: 26 April 1994; Revised: 6 April 1995;
Wetfall deposition and precipitation chemistry for a central Appalachian forest

Treesearch

Frank S. Gilliam; Mary Beth Adams

1996-01-01

Although extensive research on acidic deposition has been directed toward spruce-fir forests, less research has been done on the impacts of air pollution on eastern montane hardwood forests. The purpose of this study was to describe precipitation chemistry for several Appalachian hardwood forest sites at or near the Fernow Experimental Forest (FEF) to assess the...
Open Source Molecular Modeling

PubMed Central

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-01-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. PMID:27631126
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…
Using a Tablet PC to Enhance Student Engagement and Learning in an Introductory Organic Chemistry Course

ERIC Educational Resources Information Center

Derting, Terry L.; Cox, James R.

2008-01-01

Over the past three decades, computer-based technologies have influenced all aspects of chemistry, including chemical education. Pen-based computing applications, such as the tablet PC, have reemerged in the past few years and are providing new ways for educators to deliver content and engage students inside and outside the classroom and…
Implementing a Computer Program that Captures Students' Work on Customizable, Periodic-System Data Assignments

ERIC Educational Resources Information Center

Wiediger, Susan D.

2009-01-01

The periodic table and the periodic system are central to chemistry and thus to many introductory chemistry courses. A number of existing activities use various data sets to model the development process for the periodic table. This paper describes an image arrangement computer program developed to mimic a paper-based card sorting periodic table…
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…
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…
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…
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…
Networked Instructional Chemistry: Using Technology To Teach Chemistry

NASA Astrophysics Data System (ADS)

Smith, Stanley; Stovall, Iris

1996-10-01

Networked multimedia microcomputers provide new ways to help students learn chemistry and to help instructors manage the learning environment. This technology is used to replace some traditional laboratory work, collect on-line experimental data, enhance lectures and quiz sections with multimedia presentations, provide prelaboratory training for beginning nonchemistry- major organic laboratory, provide electronic homework for organic chemistry students, give graduate students access to real NMR data for analysis, and provide access to molecular modeling tools. The integration of all of these activities into an active learning environment is made possible by a client-server network of hundreds of computers. This requires not only instructional software but also classroom and course management software, computers, networking, and room management. Combining computer-based work with traditional course material is made possible with software management tools that allow the instructor to monitor the progress of each student and make available an on-line gradebook so students can see their grades and class standing. This client-server based system extends the capabilities of the earlier mainframe-based PLATO system, which was used for instructional computing. This paper outlines the components of a technology center used to support over 5,000 students per semester.
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.
Static Chemistry in Disks or Clouds

NASA Astrophysics Data System (ADS)

Semenov, D.; Wiebe, D.

2006-11-01

This FORTRAN77 code can be used to model static, time-dependent chemistry in ISM and circumstellar disks. Current version is based on the OSU'06 gas-grain astrochemical network with all updates to the reaction rates, and includes surface chemistry from Hasegawa & Herbst (1993) and Hasegawa, Herbst, and Leung (1992). Surface chemistry can be modeled either with the standard rate equation approach or modified rate equation approach (useful in disks). Gas-grain interactions include sticking of neutral molecules to grains, dissociative recombination of ions on grains as well as thermal, UV, X-ray, and CRP-induced desorption of frozen species. An advanced X-ray chemistry and 3 grain sizes with power-law size distribution are also included. An deuterium extension to this chemical model is available.

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...
Laboratory Sequence in Computational Methods for Introductory Chemistry

NASA Astrophysics Data System (ADS)

Cody, Jason A.; Wiser, Dawn C.

2003-07-01

A four-exercise laboratory sequence for introductory chemistry integrating hands-on, student-centered experience with computer modeling has been designed and implemented. The progression builds from exploration of molecular shapes to intermolecular forces and the impact of those forces on chemical separations made with gas chromatography and distillation. The sequence ends with an exploration of molecular orbitals. The students use the computers as a tool; they build the molecules, submit the calculations, and interpret the results. Because of the construction of the sequence and its placement spanning the semester break, good laboratory notebook practices are reinforced and the continuity of course content and methods between semesters is emphasized. The inclusion of these techniques in the first year of chemistry has had a positive impact on student perceptions and student learning.
77 FR 5852 - Proposal Review Panel for Chemistry; Notice of Meeting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-06

... NATIONAL SCIENCE FOUNDATION Proposal Review Panel for Chemistry; Notice of Meeting In accordance with the Federal Advisory Committee Act (Pub. L. 92- 463, as amended), the National Science Foundation... and Computation for Chemistry Presentations. 11:45 a.m.-1 p.m. Closed--Executive Session, review and...
Public Access to Environmental Chemistry Data via the CompTox Chemistry Dashboard (ACS Fall Meeting 6 of 12)

EPA Science Inventory

The National Center for Computational Toxicology (NCCT) has assembled and delivered an enormous quantity and diversity of data for the environmental sciences through the CompTox Chemistry Dashboard. These data include high-throughput in vitro screening data, in vivo and functiona...
Mathematical Description of Complex Chemical Kinetics and Application to CFD Modeling Codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.
Mathematical description of complex chemical kinetics and application to CFD modeling codes

NASA Technical Reports Server (NTRS)

Bittker, D. A.

1993-01-01

A major effort in combustion research at the present time is devoted to the theoretical modeling of practical combustion systems. These include turbojet and ramjet air-breathing engines as well as ground-based gas-turbine power generating systems. The ability to use computational modeling extensively in designing these products not only saves time and money, but also helps designers meet the quite rigorous environmental standards that have been imposed on all combustion devices. The goal is to combine the very complex solution of the Navier-Stokes flow equations with realistic turbulence and heat-release models into a single computer code. Such a computational fluid-dynamic (CFD) code simulates the coupling of fluid mechanics with the chemistry of combustion to describe the practical devices. This paper will focus on the task of developing a simplified chemical model which can predict realistic heat-release rates as well as species composition profiles, and is also computationally rapid. We first discuss the mathematical techniques used to describe a complex, multistep fuel oxidation chemical reaction and develop a detailed mechanism for the process. We then show how this mechanism may be reduced and simplified to give an approximate model which adequately predicts heat release rates and a limited number of species composition profiles, but is computationally much faster than the original one. Only such a model can be incorporated into a CFD code without adding significantly to long computation times. Finally, we present some of the recent advances in the development of these simplified chemical mechanisms.
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…
Integrating a Single Tablet PC in Chemistry, Engineering, and Physics Courses

ERIC Educational Resources Information Center

Rogers, James W.; Cox, James R.

2008-01-01

A tablet PC is a versatile computer that combines the computing power of a notebook with the pen functionality of a PDA (Cox and Rogers 2005b). The authors adopted tablet PC technology in order to improve the process and product of the lecture format in their chemistry, engineering, and physics courses. In this high-tech model, a single tablet PC…
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…
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…
The Role of Crustal Strength in Controlling Magmatism and Melt Chemistry During Rifting and Breakup

NASA Astrophysics Data System (ADS)

Armitage, John J.; Petersen, Kenni D.; Pérez-Gussinyé, Marta

2018-02-01

The strength of the crust has a strong impact on the evolution of continental extension and breakup. Strong crust may promote focused narrow rifting, while wide rifting might be due to a weaker crustal architecture. The strength of the crust also influences deeper processes within the asthenosphere. To quantitatively test the implications of crustal strength on the evolution of continental rift zones, we developed a 2-D numerical model of lithosphere extension that can predict the rare Earth element (REE) chemistry of erupted lava. We find that a difference in crustal strength leads to a different rate of depletion in light elements relative to heavy elements. By comparing the model predictions to rock samples from the Basin and Range, USA, we can demonstrate that slow extension of a weak continental crust can explain the observed depletion in melt chemistry. The same comparison for the Main Ethiopian Rift suggests that magmatism within this narrow rift zone can be explained by the localization of strain caused by a strong lower crust. We demonstrate that the slow extension of a strong lower crust above a mantle of potential temperature of 1,350 °C can fit the observed REE trends and the upper mantle seismic velocity for the Main Ethiopian Rift. The thermo-mechanical model implies that melt composition could provide quantitative information on the style of breakup and the initial strength of the continental crust.
Using Structured Chemistry Examinations (SCHemEs) as an Assessment Method to Improve Undergraduate Students' Generic, Practical, and Laboratory-Based Skills

ERIC Educational Resources Information Center

Kirton, Stewart B.; Al-Ahmad, Abdullah; Fergus, Suzanne

2014-01-01

Increase in tuition fees means there will be renewed pressure on universities to provide "value for money" courses that provide extensive training in both subject-specific and generic skills. For graduates of chemistry this includes embedding the generic, practical, and laboratory-based skills associated with industrial research as an…
Colloidal characterization of ultrafine silicon carbide and silicon nitride powders

NASA Technical Reports Server (NTRS)

Whitman, Pamela K.; Feke, Donald L.

1986-01-01

The effects of various powder treatment strategies on the colloid chemistry of aqueous dispersions of silicon carbide and silicon nitride are examined using a surface titration methodology. Pretreatments are used to differentiate between the true surface chemistry of the powders and artifacts resulting from exposure history. Silicon nitride powders require more extensive pretreatment to reveal consistent surface chemistry than do silicon carbide powders. As measured by titration, the degree of proton adsorption from the suspending fluid by pretreated silicon nitride and silicon carbide powders can both be made similar to that of silica.
Numerical computation of linear instability of detonations

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry; Kasimov, Aslan

2017-11-01

We propose a method to study linear stability of detonations by direct numerical computation. The linearized governing equations together with the shock-evolution equation are solved in the shock-attached frame using a high-resolution numerical algorithm. The computed results are processed by the Dynamic Mode Decomposition technique to generate dispersion relations. The method is applied to the reactive Euler equations with simple-depletion chemistry as well as more complex multistep chemistry. The results are compared with those known from normal-mode analysis. We acknowledge financial support from King Abdullah University of Science and Technology.
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.
Computational Investigations for Undergraduate Organic Chemistry: Predicting the Mechanism of the Ritter Reaction

NASA Astrophysics Data System (ADS)

Hessley, Rita K.

2000-02-01

In an effort to engage students more deeply in their laboratory work and provide them with valuable learning experiences in the applications and limitations of computational chemistry as a research tool, students are instructed to carry out a computational pre-lab exercise. Before carrying out a laboratory experiment that investigates the mechanism for the formation of N-t-butylbenzamide, students construct and obtain heats of formation for reactants, products, postulated reaction intermediates, and one transition state structure for each proposed mechanism. This is designed as a companion to an open-ended laboratory experiment that hones skills learned early in most traditional organic chemistry courses. The incorporation of a preliminary computational exercise enables students to move beyond guessing what the outcome of the reaction will be. It challenges them to test what they believe they "know" about such fundamental concepts as stability of carbocations, or the significance and utility of thermodynamic data relative to kinetic data. On the basis of their computations and their own experimental data, students then verify or dispute their hypothesis, finally arriving at a defensible and logical conclusion about the course of the reaction mechanism. The manner of implementation of the exercise and typical computational data are described.
Structure Identification Using High Resolution Mass Spectrometry Data and the EPAs Chemistry Dashboard (ACS Fall meeting)

EPA Science Inventory

The iCSS Chemistry Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and Exp...
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 beliefs about chemistry and the learning of chemistry. This instrument is a modification of the original CLASS-Phys survey designed for use in physics. Statements on the chemistry version (CLASS-Chem) are validated using chemistry students with a broad range of experience levels to ensure clarity in wording and meaning. The chemistry version addresses additional belief areas important in learning chemistry but not physics, specifically, beliefs about reactions and molecular structure. Statements are grouped into statistically robust categories using reduced basis factor analysis. The final part of this dissertation addresses the development and testing of learning tutorials for use in undergraduate physical chemistry. The tutorials are designed to promote the active mental engagement of students in the process of learning. Questions within the pencil-paper format guide students through the reasoning needed to apply concepts to real-world situations. Each tutorial is connected to a physical model or computer simulation providing students with additional hands-on investigations to strengthen their connection with the concepts addressed in the tutorial. Currently tutorials connected with the First and Second Laws of Thermodynamics as well as Kinetics have been developed and tested.
Two-Center/Three-Electron Sigma Half-Bonds in Main Group and Transition Metal Chemistry.

PubMed

Berry, John F

2016-01-19

First proposed in a classic Linus Pauling paper, the two-center/three-electron (2c/3e) σ half-bond challenges the extremes of what may or may not be considered a chemical bond. Two electrons occupying a σ bonding orbital and one electron occupying the antibonding σ* orbital results in bond orders of ∼0.5 that are characteristic of metastable and exotic species, epitomized in the fleetingly stable He2(+) ion. In this Account, I describe the use of coordination chemistry to stabilize such fugacious three-electron bonded species at disparate ends of the periodic table. A recent emphasis in the chemistry of metal-metal bonds has been to prepare compounds with extremely short metal-metal distances and high metal-metal bond orders. But similar chemistry can be used to explore metal-metal bond orders less than one, including 2c/3e half-bonds. Bimetallic compounds in the Ni2(II,III) and Pd2(II,III) oxidation states were originally examined in the 1980s, but the evidence collected at that time suggested that they did not contain 2c/3e σ bonds. Both classes of compounds have been re-examined using EPR spectroscopy and modern computational methods that show the unpaired electron of each compound to occupy a M-M σ* orbital, consistent with 2c/3e Ni-Ni and Pd-Pd σ half-bonds. Elsewhere on the periodic table, a seemingly unrelated compound containing a trigonal bipyramidal Cu3S2 core caused a stir, leaving prominent theorists at odds with one another as to whether the compound contains a S-S bond. Due to my previous experience with 2c/3e metal-metal bonds, I suggested that the Cu3S2 compound could contain a 2c/3e S-S σ half-bond in the previously unknown oxidation state of S2(3-). By use of the Cambridge Database, a number of other known compounds were identified as potentially containing S2(3-) ligands, including a noteworthy set of cyclopentadienyl-supported compounds possessing diamond-shaped Ni2E2 units with E = S, Se, and Te. These compounds were subjected to extensive studies using X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, density functional theory, and wave function-based computational methods, as well as chemical oxidation and reduction. The compounds contain E-E 2c/3e σ half-bonds and unprecedented E2(3-) "subchalcogenide" ligands, ushering in a new oxidation state paradigm for transition metal-chalcogen chemistry.
Upwind MacCormack Euler solver with non-equilibrium chemistry

NASA Technical Reports Server (NTRS)

Sherer, Scott E.; Scott, James N.

1993-01-01

A computer code, designated UMPIRE, is currently under development to solve the Euler equations in two dimensions with non-equilibrium chemistry. UMPIRE employs an explicit MacCormack algorithm with dissipation introduced via Roe's flux-difference split upwind method. The code also has the capability to employ a point-implicit methodology for flows where stiffness is introduced through the chemical source term. A technique consisting of diagonal sweeps across the computational domain from each corner is presented, which is used to reduce storage and execution requirements. Results depicting one dimensional shock tube flow for both calorically perfect gas and thermally perfect, dissociating nitrogen are presented to verify current capabilities of the program. Also, computational results from a chemical reactor vessel with no fluid dynamic effects are presented to check the chemistry capability and to verify the point implicit strategy.

Impact of Chemistry Teachers' Knowledge and Practices on Student Achievement

NASA Astrophysics Data System (ADS)

Scantlebury, Kathryn

2008-10-01

Professional development programs promoting inquiry-based teaching are challenged with providing teachers content knowledge and using pedagogical approaches that model standards based instruction. Inquiry practices are also important for undergraduate students. This paper focuses on the evaluation of an extensive professional development program for chemistry teachers that included chemistry content tests for students and the teachers and the impact of undergraduate research experiences on college students' attitudes towards chemistry. Baseline results for the students showed that there were no gender differences on the achievement test but white students scored significantly higher than non-white students. However, parent/adult involvement with chemistry homework and projects, was a significant negative predictor of 11th grade students' test chemistry achievement score. This paper will focus on students' achievement and attitude results for teachers who are mid-way through the program providing evidence that on-going, sustained professional development in content and pedagogy is critical for improving students' science achievement.
Students' perceptions of academic dishonesty in the chemistry classroom laboratory

NASA Astrophysics Data System (ADS)

del Carlo, Dawn I.; Bodner, George M.

2004-01-01

Although the literature on both academic dishonesty and scientific misconduct is extensive, research on academic dishonesty has focused on quizzes, exams, and papers, with the virtual exclusion of the classroom laboratory. This study examined the distinctions undergraduate chemistry majors made between academic dishonesty in the classroom laboratory and scientific misconduct in the research laboratory. Across the spectrum of undergraduate chemistry courses, from the introductory course for first-semester chemistry majors to the capstone course in instrumental analysis, we noted that students believe the classroom lab is fundamentally different from a research or industrial lab. This difference is so significant that it carries over into students' perceptions of dishonesty in these two environments.
Exploring the Nature of the H[subscript 2] Bond. 2. Using Ab Initio Molecular Orbital Calculations to Obtain the Molecular Constants

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A project for students in an upper-level course in quantum or computational chemistry is described in which they are introduced to the concepts and applications of a high quality, ab initio treatment of the ground-state potential energy curve (PEC) for H[subscript 2] and D[subscript 2]. Using a commercial computational chemistry application and a…
The international water conference proceedings

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

Guseman, J.R.

1984-10-01

This book provides information on computer applications to water chemistry control, groundwater, membrane technology, instrumentation/analytical techniques and ion exchange. Other topics of discussion include cooling water, biocontrol, the hydraulic properties of ion exchange resins, steam electric power plant aqueous discharges and colorimetric determination of trace benzotriazole or tolytriazole. Water chemistry guidelines for large steam generating power plants is discussed, as well as wastewater treatment, boiler water conditioning and ion exchange/computer related topics.
The EPA Comptox Chemistry Dashboard: A Web-Based Data ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data but recent developments have focused on the development of a new software architecture that assembles the resources into a single platform. A new web application, the CompTox Chemistry Dashboard provides access to data associated with ~720,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, product and functional use information and a myriad of related data of value to environmental scientists. The dashboard provides chemical-based searching based on chemical names, synonyms and CAS Registry Numbers. Flexible search capabilities allow for chemical identificati
Extension of the quantum-kinetic model to lunar and Mars return physics

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

Liechty, D. S.; Lewis, M. J.

The ability to compute rarefied, ionized hypersonic flows is becoming more important as missions such as Earth reentry, landing high-mass payloads on Mars, and the exploration of the outer planets and their satellites are being considered. A recently introduced molecular-level chemistry model, the quantum-kinetic, or Q-K, model that predicts reaction rates for gases in thermal equilibrium and non-equilibrium using only kinetic theory and fundamental molecular properties, is extended in the current work to include electronic energy level transitions and reactions involving charged particles. Like the Q-K procedures for neutral species chemical reactions, these new models are phenomenological procedures that aimmore » to reproduce the reaction/transition rates but do not necessarily capture the exact physics. These engineering models are necessarily efficient due to the requirement to compute billions of simulated collisions in direct simulation Monte Carlo (DSMC) simulations. The new models are shown to generally agree within the spread of reported transition and reaction rates from the literature for near equilibrium conditions.« less
Work stealing for GPU-accelerated parallel programs in a global address space framework: WORK STEALING ON GPU-ACCELERATED SYSTEMS

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

Arafat, Humayun; Dinan, James; Krishnamoorthy, Sriram

Task parallelism is an attractive approach to automatically load balance the computation in a parallel system and adapt to dynamism exhibited by parallel systems. Exploiting task parallelism through work stealing has been extensively studied in shared and distributed-memory contexts. In this paper, we study the design of a system that uses work stealing for dynamic load balancing of task-parallel programs executed on hybrid distributed-memory CPU-graphics processing unit (GPU) systems in a global-address space framework. We take into account the unique nature of the accelerator model employed by GPUs, the significant performance difference between GPU and CPU execution as a functionmore » of problem size, and the distinct CPU and GPU memory domains. We consider various alternatives in designing a distributed work stealing algorithm for CPU-GPU systems, while taking into account the impact of task distribution and data movement overheads. These strategies are evaluated using microbenchmarks that capture various execution configurations as well as the state-of-the-art CCSD(T) application module from the computational chemistry domain.« less
Work stealing for GPU-accelerated parallel programs in a global address space framework

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

Arafat, Humayun; Dinan, James; Krishnamoorthy, Sriram

Task parallelism is an attractive approach to automatically load balance the computation in a parallel system and adapt to dynamism exhibited by parallel systems. Exploiting task parallelism through work stealing has been extensively studied in shared and distributed-memory contexts. In this paper, we study the design of a system that uses work stealing for dynamic load balancing of task-parallel programs executed on hybrid distributed-memory CPU-graphics processing unit (GPU) systems in a global-address space framework. We take into account the unique nature of the accelerator model employed by GPUs, the significant performance difference between GPU and CPU execution as a functionmore » of problem size, and the distinct CPU and GPU memory domains. We consider various alternatives in designing a distributed work stealing algorithm for CPU-GPU systems, while taking into account the impact of task distribution and data movement overheads. These strategies are evaluated using microbenchmarks that capture various execution configurations as well as the state-of-the-art CCSD(T) application module from the computational chemistry domain« less
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.
19. VIEW OF THE GENERAL CHEMISTRY LABORATORY IN BUILDING 881. ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

19. VIEW OF THE GENERAL CHEMISTRY LABORATORY IN BUILDING 881. (4/12/62) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO
10 CFR 76.74 - Computation and extension of time.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 2 2011-01-01 2011-01-01 false Computation and extension of time. 76.74 Section 76.74 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) CERTIFICATION OF GASEOUS DIFFUSION PLANTS Certification § 76.74 Computation and extension of time. (a) In computing any period of time, the day of the act...
10 CFR 76.74 - Computation and extension of time.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 2 2012-01-01 2012-01-01 false Computation and extension of time. 76.74 Section 76.74 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) CERTIFICATION OF GASEOUS DIFFUSION PLANTS Certification § 76.74 Computation and extension of time. (a) In computing any period of time, the day of the act...
10 CFR 76.74 - Computation and extension of time.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 2 2013-01-01 2013-01-01 false Computation and extension of time. 76.74 Section 76.74 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) CERTIFICATION OF GASEOUS DIFFUSION PLANTS Certification § 76.74 Computation and extension of time. (a) In computing any period of time, the day of the act...
10 CFR 76.74 - Computation and extension of time.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Computation and extension of time. 76.74 Section 76.74 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) CERTIFICATION OF GASEOUS DIFFUSION PLANTS Certification § 76.74 Computation and extension of time. (a) In computing any period of time, the day of the act...
10 CFR 76.74 - Computation and extension of time.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 2 2014-01-01 2014-01-01 false Computation and extension of time. 76.74 Section 76.74 Energy NUCLEAR REGULATORY COMMISSION (CONTINUED) CERTIFICATION OF GASEOUS DIFFUSION PLANTS Certification § 76.74 Computation and extension of time. (a) In computing any period of time, the day of the act...
Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-01-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.
Surveys of research in the Chemistry Division, Argonne National Laboratory

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

Grazis, B.M.

1992-11-01

Research reports are presented on reactive intermediates in condensed phase (radiation chemistry, photochemistry), electron transfer and energy conversion, photosynthesis and solar energy conversion, metal cluster chemistry, chemical dynamics in gas phase, photoionization-photoelectrons, characterization and reactivity of coal and coal macerals, premium coal sample program, chemical separations, heavy elements coordination chemistry, heavy elements photophysics/photochemistry, f-electron interactions, radiation chemistry of high-level wastes (gas generation in waste tanks), ultrafast molecular electronic devices, and nuclear medicine. Separate abstracts have been prepared. Accelerator activites and computer system/network services are also reported.
Report on the NEACT Conference: "The Chemistry Lab and Its Future."

ERIC Educational Resources Information Center

Pickering, Miles

1988-01-01

Reports on the session at the New England Association of Chemistry Teachers meeting on chemistry laboratories in March 1987. Speakers included Leonard K. Nash and Audrey Champagne on values and goals; Howard Ende on regulation; Stanley Smith and Jerry Bell on the uses of computers; and Miles Pickering on the human dimension. (CW)
Semiempirical and ab initio Calculations of Charged Species Used in the Physical Organic Chemistry Course.

ERIC Educational Resources Information Center

Gilliom, Richard D.

1989-01-01

Concentrates on the semiempirical methods MINDO/3, MNDO, and AMI available in the program AMPAC from the Quantum Chemistry Program Exchange at Indiana University. Uses charged ions in the teaching of computational chemistry. Finds that semiempirical methods are accurate enough for the general use of the bench chemist. (MVL)
ConfChem Conference on Select 2016 BCCE Presentations: Twentieth Year of the OLCC

ERIC Educational Resources Information Center

Belford, Robert E.

2017-01-01

The ACS CHED Committee on Computers in Chemical Education (CCCE) ran the first intercollegiate OnLine Chemistry Course (OLCC) on Environmental and Industrial Chemistry in 1996, and is offering the seventh OLCC on Cheminformatics and Public Compound Databases: An Introduction to Big Data in Chemistry in 2017. This Communication summarizes the past,…

Rotational Energy Transfer of N2 Determined Using a New Ab Initio Potential Energy Surface

NASA Technical Reports Server (NTRS)

Huo, Winifred M.; Stallcop, James R.; Partridge, Harry; Langhoff, Stephen R. (Technical Monitor)

1997-01-01

A new N2-N2 rigid-rotor surface has been determined using extensive Ab Initio quantum chemistry calculations together with recent experimental data for the second virial coefficient. Rotational energy transfer is studied using the new potential energy surface (PES) employing the close coupling method below 200 cm(exp -1) and coupled state approximation above that. Comparing with a previous calculation based on the PES of van der Avoird et al.,3 it is found that the new PES generally gives larger cross sections for large (delta)J transitions, but for small (delta)J transitions the cross sections are either comparable or smaller. Correlation between the differences in the cross sections and the two PES will be attempted. The computed cross sections will also be compared with available experimental data.
Li-Doped Ionic Liquid Electrolytes: From Bulk Phase to Interfacial Behavior

NASA Technical Reports Server (NTRS)

Haskins, Justin B.; Lawson, John W.

2016-01-01

Ionic liquids have been proposed as candidate electrolytes for high-energy density, rechargeable batteries. We present an extensive computational analysis supported by experimental comparisons of the bulk and interfacial properties of a representative set of these electrolytes as a function of Li-salt doping. We begin by investigating the bulk electrolyte using quantum chemistry and ab initio molecular dynamics to elucidate the solvation structure of Li(+). MD simulations using the polarizable force field of Borodin and coworkers were then performed, from which we obtain an array of thermodynamic and transport properties. Excellent agreement is found with experiments for diffusion, ionic conductivity, and viscosity. Combining MD simulations with electronic structure computations, we computed the electrochemical window of the electrolytes across a range of Li(+)-doping levels and comment on the role of the liquid environment. Finally, we performed a suite of simulations of these Li-doped electrolytes at ideal electrified interfaces to evaluate the differential capacitance and the equilibrium Li(+) distribution in the double layer. The magnitude of differential capacitance is in good agreement with our experiments and exhibits the characteristic camel-shaped profile. In addition, the simulations reveal Li(+) to be highly localized to the second molecular layer of the double layer, which is supported by additional computations that find this layer to be a free energy minimum with respect to Li(+) translation.
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), physics (fluid-dynamical and quantum-mechanical calculations; extensive numerical simulations of various condensed-matter systems; the development of stellar constellations, even the early Universe), chemistry (quantum-chemical calculations on the structures of new chemical compounds; chemical reactions and reaction dynamics), and biology (various models, for example, in population dynamics). We succeeded in our effort to assemble several internationally recognized researchers of Computational Science to deliver invited talks on a couple of exceptionally beautiful late-summer days in the modern premises of the Adult Education Center at Lahti. Among the plenary speakers, Per Bak described his highly original work on self-organized criticality. David Ceperley discussed pioneering numerical simulations of superfluid helium in which, for the first time, Feynman's path-integral formulation of quantum mechanics has been implemented on a computer. Jim Gunton presented his comprehensive studies of the Cahn-Hilliard equation for the dynamics of ordering in a condensed-matter system far from equilibrium, while Alex Hansen explained those on nonlinear breakdown in disordered materials. Representing the important field of computational chemistry, Bo Jönsson dealt with attractive forces between polyelectrolytes. Kurt Kremer gave an interesting account on computer-simulation studies of complex polymer systems, while Ole Mouritsen reviewed studies of interfacial fluctuations in lipid membranes. Pekka Pyykkö introduced his pioneering work which has led to predictions of completely novel chemical species. Annette Zippelius gave an expert introduction to the highly active field of neural networks. It is evident from each of these intriguing plenary contributions that, indeed, the computational approach is a frontier field of science, possibly providing the most versatile research method available today. We also arranged a competition for the best Posters presented at the Symposium; the Prizes were some of the newest books on the beauty of fractals. The First Prize was won by Hanna Viertio, the Second Prize by Miguel Zendejas and the Third Prize was shared by Leo Kärkkäinen and Kari Rummukainen. As for the future of Computational Science, we identify two principal avenues: (a) big science - large centers with ultrafast supercomputers, and (b) small science - active groups utilizing personal minisupercomputers or supenvorkstations. At present, it appears that the latter already compete extremely favourably in their performance with the massive supercomputers - at least in their throughput and, especially, in tasks where a broad range of diverse software support is not absolutely necessary. In view of this important emergence of "personal supercomputing", we envisage that the role and the development of large computer centers will have to be reviewed critically and modified accordingly. Furthermore, a promise for some radically new approaches to Computational Science could be provided by massively parallel computers; among them, maybe solutions based on ideas of neural computing could be utilized, especially for restricted applications. Therefore, in order not to overlook any important advances within such a forefront field, one should rather choose the strategy of actively following each and every one of these routes. In perspective of the large variety of simultaneous developments, we want to emphasize the importance of Nordic collaboration in sharing expertise and experience in the rapidly progressing research - it ought to be cultivated and could be expanded. Therefore, we think that it is vitally important to continue with and to further promote the kind of Nordic Symposia that have been held at Lund, Kolle-Kolle, and Lahti. We want to thank most cordially the plenary and invited speakers, contributors, students, and in particular the Conference Secretary, Ms Ulla Ahlfors and Dr Milja Mäkelä, who was responsible for the local arrangements. The work that they did served to make this Symposium a scientific success and a useful and pleasant experience for all the well over 100 participants. We also thank the City of Lahti for kindly arranging a refreshing reception at the Town Hall. We wish to express our gratitude to Nordiska Kulturfonden, NORDITA, the Research Institute for Theoretical Physics at the University of Helsinki, the Finnish Ministry of Education and the Academy of Finland for their financial support. March 1990
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…
Current status and future prospects for enabling chemistry technology in the drug discovery process.

PubMed

Djuric, Stevan W; Hutchins, Charles W; Talaty, Nari N

2016-01-01

This review covers recent advances in the implementation of enabling chemistry technologies into the drug discovery process. Areas covered include parallel synthesis chemistry, high-throughput experimentation, automated synthesis and purification methods, flow chemistry methodology including photochemistry, electrochemistry, and the handling of "dangerous" reagents. Also featured are advances in the "computer-assisted drug design" area and the expanding application of novel mass spectrometry-based techniques to a wide range of drug discovery activities.
Time-Filtered Navier-Stokes Approach and Emulation of Turbulence-Chemistry Interaction

NASA Technical Reports Server (NTRS)

Liu, Nan-Suey; Wey, Thomas; Shih, Tsan-Hsing

2013-01-01

This paper describes the time-filtered Navier-Stokes approach capable of capturing unsteady flow structures important for turbulent mixing and an accompanying subgrid model directly accounting for the major processes in turbulence-chemistry interaction. They have been applied to the computation of two-phase turbulent combustion occurring in a single-element lean-direct-injection combustor. Some of the preliminary results from this computational effort are presented in this paper.
Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery.

PubMed

St-Gallay, Steve A; Sambrook-Smith, Colin P

2017-03-01

Computer-aided drug design encompasses a wide variety of tools and techniques, and can be implemented with a range of organisational structures and focus in different organisations. Here we outline the computational chemistry skills within Sygnature Discovery, along with the software and hardware at our disposal, and briefly discuss the methods that are not employed and why. The goal of the group is to provide support for design and analysis in order to improve the quality of compounds synthesised and reduce the timelines of drug discovery projects, and we reveal how this is achieved at Sygnature. Impact on medicinal chemistry is vital to demonstrating the value of computational chemistry, and we discuss the approaches taken to influence the list of compounds for synthesis, and how we recognise success. Finally we touch on some of the areas being developed within the team in order to provide further value to the projects and clients.
Tools, techniques, organisation and culture of the CADD group at Sygnature Discovery

NASA Astrophysics Data System (ADS)

St-Gallay, Steve A.; Sambrook-Smith, Colin P.

2017-03-01

Computer-aided drug design encompasses a wide variety of tools and techniques, and can be implemented with a range of organisational structures and focus in different organisations. Here we outline the computational chemistry skills within Sygnature Discovery, along with the software and hardware at our disposal, and briefly discuss the methods that are not employed and why. The goal of the group is to provide support for design and analysis in order to improve the quality of compounds synthesised and reduce the timelines of drug discovery projects, and we reveal how this is achieved at Sygnature. Impact on medicinal chemistry is vital to demonstrating the value of computational chemistry, and we discuss the approaches taken to influence the list of compounds for synthesis, and how we recognise success. Finally we touch on some of the areas being developed within the team in order to provide further value to the projects and clients.
COMPUTATIONAL TOXICOLOGY

EPA Science Inventory

Over the last several years, there has been increased pressure to utilize novel technologies derived from computational chemistry, molecular biology and systems biology in toxicological risk assessment. This new area has been referred to as "Computational Toxicology". Our resear...
Mass spectrometry. [review of techniques

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Kimble, B. J.; Derrick, P. J.

1976-01-01

Advances in mass spectrometry (MS) and its applications over the past decade are reviewed in depth, with annotated literature references. New instrumentation and techniques surveyed include: modulated-beam MS, chromatographic MS on-line computer techniques, digital computer-compatible quadrupole MS, selected ion monitoring (mass fragmentography), and computer-aided management of MS data and interpretation. Areas of application surveyed include: organic MS and electron impact MS, field ionization kinetics, appearance potentials, translational energy release, studies of metastable species, photoionization, calculations of molecular orbitals, chemical kinetics, field desorption MS, high pressure MS, ion cyclotron resonance, biochemistry, medical/clinical chemistry, pharmacology, and environmental chemistry and pollution studies.
Computer Series, 13: Bits and Pieces, 11.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (with ordering information) on various topics including, among others, modeling of thermodynamics and economics of solar energy, radioactive decay simulation, stoichiometry drill/tutorial (in Spanish), computer-generated safety quiz, medical chemistry computer game, medical biochemistry question bank, generation of…
Kent and Riegel's Handbook of industrial chemistry and biotechnology. 11th ed.

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

Kent, James A.

2007-07-01

This handbook provides extensive information on plastics, rubber, adhesives, textile fibers, pharmaceutical chemistry, synthetic organic chemicals, soaps and detergents, as well as various other major classes of industrial chemistry. There is detailed coverage of coal utilization technology, dyes and dye intermediates, chlor-alkali and heavy chemicals, paints and pigments, chemical explosives, propellants, petroleum and petrochemicals, natural gas, industrial gases, synthetic nitrogen products, fats and oils, sulfur and sulfuric acid, phosphorous and phosphates, wood products, and sweeteners. The chapter on coal is entitled: coal technology for power, liquid fuels and chemicals. 100 ills.
Duct flow nonuniformities for Space Shuttle Main Engine (SSME)

NASA Technical Reports Server (NTRS)

1987-01-01

A three-duct Space Shuttle Main Engine (SSME) Hot Gas Manifold geometry code was developed for use. The methodology of the program is described, recommendations on its implementation made, and an input guide, input deck listing, and a source code listing provided. The code listing is strewn with an abundance of comments to assist the user in following its development and logic. A working source deck will be provided. A thorough analysis was made of the proper boundary conditions and chemistry kinetics necessary for an accurate computational analysis of the flow environment in the SSME fuel side preburner chamber during the initial startup transient. Pertinent results were presented to facilitate incorporation of these findings into an appropriate CFD code. The computation must be a turbulent computation, since the flow field turbulent mixing will have a profound effect on the chemistry. Because of the additional equations demanded by the chemistry model it is recommended that for expediency a simple algebraic mixing length model be adopted. Performing this computation for all or selected time intervals of the startup time will require an abundance of computer CPU time regardless of the specific CFD code selected.
Delivering The Benefits of Chemical-Biological Integration in ...

EPA Pesticide Factsheets

Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intention of this research program is to quickly evaluate thousands of chemicals for potential risk but with much reduced cost relative to historical approaches. This work involves computational and data driven approaches including high-throughput screening, modeling, text-mining and the integration of chemistry, exposure and biological data. We have developed a number of databases and applications that are delivering on the vision of developing a deeper understanding of chemicals and their effects on exposure and biological processes that are supporting a large community of scientists in their research efforts. This presentation will provide an overview of our work to bring together diverse large scale data from the chemical and biological domains, our approaches to integrate and disseminate these data, and the delivery of models supporting computational toxicology. This abstract does not reflect U.S. EPA policy. Presentation at ACS TOXI session on Computational Chemistry and Toxicology in Chemical Discovery and Assessement (QSARs).
Improving Chemistry Education by Offering Salient Technology Training to Preservice Teachers: A Graduate-Level Course on Using Software to Teach Chemistry

ERIC Educational Resources Information Center

Tofan, Daniel C.

2009-01-01

This paper describes an upper-level undergraduate and graduate-level course on computers in chemical education that was developed and offered for the first time in Fall 2007. The course provides future chemistry teachers with exposure to current software tools that can improve productivity in teaching, curriculum development, and education…
| NREL

Science.gov Websites

of NREL's Computational Science Center, where he uses electronic structure calculations and other introductory chemistry and physical chemistry. Research Interests Electronic structure and dynamics in the quantum/classical molecular dynamics simulation|Coupling of molecular electronic structure to
Labeled Nucleoside Triphosphates with Reversibly Terminating Aminoalkoxyl Groups

PubMed Central

Hutter, Daniel; Kim, Myong-Jung; Karalkar, Nilesh; Leal, Nicole A.; Chen, Fei; Guggenheim, Evan; Visalakshi, Visa; Olejnik, Jerzy; Gordon, Steven; Benner, Steven A.

2013-01-01

Nucleoside triphosphates having a 3′-ONH2 blocking group have been prepared with and without fluorescent tags on their nucleobases. DNA polymerases were identified that accepted these, adding a single nucleotide to the 3′-end of a primer in a template-directed extension reaction that then stops. Nitrite chemistry was developed to cleave the 3′-ONH2 group under mild conditions to allow continued primer extension. Extension-cleavage-extension cycles in solution were demonstrated with untagged nucleotides and mixtures of tagged and untagged nucleotides. Multiple extension-cleavage-extension cycles were demonstrated on an Intelligent Bio-Systems Sequencer, showing the potential of the 3′-ONH2 blocking group in “next generation sequencing”. PMID:21128174
Purchase of a Raman and Photoluminescence Imaging System for Characterization of Advanced Electrochemical and Electronic Materials

DTIC Science & Technology

2016-01-05

regularly used the Raman imaging system to characterize the doping chemistry of colloidal indium nitride nanoparticles . This material shows an interesting...regularly used the Raman imaging system to characterize the doping chemistry of colloidal indium nitride nanoparticles . This material shows an...analysis of thin film coatings, bulk materials, powders and nanoparticles . The instrument is extensively used to characterize advanced electrochemical and
Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents biology, chemistry, physics, and health activities, experiments, demonstrations, and computer programs. Includes mechanism of stomatal opening, using aquatic plants to help demonstrate chemical buffering, microbial activity/contamination in milk samples, computer computation of fitness scores, reservoir project, complexes of transition…
Current status and future prospects for enabling chemistry technology in the drug discovery process

PubMed Central

Djuric, Stevan W.; Hutchins, Charles W.; Talaty, Nari N.

2016-01-01

This review covers recent advances in the implementation of enabling chemistry technologies into the drug discovery process. Areas covered include parallel synthesis chemistry, high-throughput experimentation, automated synthesis and purification methods, flow chemistry methodology including photochemistry, electrochemistry, and the handling of “dangerous” reagents. Also featured are advances in the “computer-assisted drug design” area and the expanding application of novel mass spectrometry-based techniques to a wide range of drug discovery activities. PMID:27781094

Quality assurance for health and environmental chemistry: 1990

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

Gautier, M.A.; Gladney, E.S.; Koski, N.L.

1991-10-01

This report documents the continuing quality assurance efforts of the Health and Environmental Chemistry Group (HSE-9) at the Los Alamos National Laboratory. The philosophy, methodology, computing resources, and laboratory information management system used by the quality assurance program to encompass the diversity of analytical chemistry practiced in the group are described. Included in the report are all quality assurance reference materials used, along with their certified or consensus concentrations, and all analytical chemistry quality assurance measurements made by HSE-9 during 1990.
Mass spectrometry. [in organic ion and biorganic chemistry and medicine

NASA Technical Reports Server (NTRS)

Burlingame, A. L.; Cox, R. E.; Derrick, P. J.

1974-01-01

Review of the present status of mass spectrometry in the light of pertinent recent publications spanning the period from December 1971 to January 1974. Following an initial survey of techniques, instruments, and computer applications, a sharp distinction is made between the chemistry of organic (radical-)ions and analytical applications in biorganic chemistry and medicine. The emphasis is on the chemistry of organic (radical-)ions at the expense of inorganic, organometallic, and surface ion chemistry. Biochemistry and medicine are chosen because of their contemporary importance and because of the stupendous contributions of mass spectroscopy to these fields in the past two years. In the review of gas-phase organic ion chemistry, special attention is given to studies making significant contributions to the understanding of ion chemistry.
Assessing Changes in High School Students' Conceptual Understanding through Concept Maps before and after the Computer-Based Predict-Observe-Explain (CB-POE) Tasks on Acid-Base Chemistry at the Secondary Level

ERIC Educational Resources Information Center

Yaman, Fatma; Ayas, Alipasa

2015-01-01

Although concept maps have been used as alternative assessment methods in education, there has been an ongoing debate on how to evaluate students' concept maps. This study discusses how to evaluate students' concept maps as an assessment tool before and after 15 computer-based Predict-Observe-Explain (CB-POE) tasks related to acid-base chemistry.…
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.
Improve Outcomes Study subjects Chemistry Teaching and Learning Strategies through independent study with the help of computer-based media

NASA Astrophysics Data System (ADS)

Sugiharti, Gulmah

2018-03-01

This study aims to see the improvement of student learning outcomes by independent learning using computer-based learning media in the course of STBM (Teaching and Learning Strategy) Chemistry. Population in this research all student of class of 2014 which take subject STBM Chemistry as many as 4 class. While the sample is taken by purposive as many as 2 classes, each 32 students, as control class and expriment class. The instrument used is the test of learning outcomes in the form of multiple choice with the number of questions as many as 20 questions that have been declared valid, and reliable. Data analysis techniques used one-sided t test and improved learning outcomes using a normalized gain test. Based on the learning result data, the average of normalized gain values for the experimental class is 0,530 and for the control class is 0,224. The result of the experimental student learning result is 53% and the control class is 22,4%. Hypothesis testing results obtained t count> ttable is 9.02> 1.6723 at the level of significance α = 0.05 and db = 58. This means that the acceptance of Ha is the use of computer-based learning media (CAI Computer) can improve student learning outcomes in the course Learning Teaching Strategy (STBM) Chemistry academic year 2017/2018.
Computational materials chemistry for carbon capture using porous materials

NASA Astrophysics Data System (ADS)

Sharma, Abhishek; Huang, Runhong; Malani, Ateeque; Babarao, Ravichandar

2017-11-01

Control over carbon dioxide (CO2) release is extremely important to decrease its hazardous effects on the environment such as global warming, ocean acidification, etc. For CO2 capture and storage at industrial point sources, nanoporous materials offer an energetically viable and economically feasible approach compared to chemisorption in amines. There is a growing need to design and synthesize new nanoporous materials with enhanced capability for carbon capture. Computational materials chemistry offers tools to screen and design cost-effective materials for CO2 separation and storage, and it is less time consuming compared to trial and error experimental synthesis. It also provides a guide to synthesize new materials with better properties for real world applications. In this review, we briefly highlight the various carbon capture technologies and the need of computational materials design for carbon capture. This review discusses the commonly used computational chemistry-based simulation methods for structural characterization and prediction of thermodynamic properties of adsorbed gases in porous materials. Finally, simulation studies reported on various potential porous materials, such as zeolites, porous carbon, metal organic frameworks (MOFs) and covalent organic frameworks (COFs), for CO2 capture are discussed.
Development of high performance scientific components for interoperability of computing packages

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

Gulabani, Teena Pratap

2008-01-01

Three major high performance quantum chemistry computational packages, NWChem, GAMESS and MPQC have been developed by different research efforts following different design patterns. The goal is to achieve interoperability among these packages by overcoming the challenges caused by the different communication patterns and software design of each of these packages. A chemistry algorithm is hard to develop as well as being a time consuming process; integration of large quantum chemistry packages will allow resource sharing and thus avoid reinvention of the wheel. Creating connections between these incompatible packages is the major motivation of the proposed work. This interoperability is achievedmore » by bringing the benefits of Component Based Software Engineering through a plug-and-play component framework called Common Component Architecture (CCA). In this thesis, I present a strategy and process used for interfacing two widely used and important computational chemistry methodologies: Quantum Mechanics and Molecular Mechanics. To show the feasibility of the proposed approach the Tuning and Analysis Utility (TAU) has been coupled with NWChem code and its CCA components. Results show that the overhead is negligible when compared to the ease and potential of organizing and coping with large-scale software applications.« less
Implementation of Premixed Equilibrium Chemistry Capability in OVERFLOW

NASA Technical Reports Server (NTRS)

Olsen, M. E.; Liu, Y.; Vinokur, M.; Olsen, T.

2003-01-01

An implementation of premixed equilibrium chemistry has been completed for the OVERFLOW code, a chimera capable, complex geometry flow code widely used to predict transonic flowfields. The implementation builds on the computational efficiency and geometric generality of the solver.
Implementation of Premixed Equilibrium Chemistry Capability in OVERFLOW

NASA Technical Reports Server (NTRS)

Olsen, Mike E.; Liu, Yen; Vinokur, M.; Olsen, Tom

2004-01-01

An implementation of premixed equilibrium chemistry has been completed for the OVERFLOW code, a chimera capable, complex geometry flow code widely used to predict transonic flowfields. The implementation builds on the computational efficiency and geometric generality of the solver.
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.
Using Technology to Enhance the Effectiveness of General Chemistry Laboratory Courses

ERIC Educational Resources Information Center

Carvalho-Knighton, Kathleen M.; Keen-Rocha, Linda

2007-01-01

The effectiveness of two different laboratory techniques is compared to teach students majoring in science in a general chemistry laboratory. The results demonstrated that student laboratory activities with computer-interface systems could improve student understanding.
Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career.

PubMed

Anslyn, Eric V

2016-01-01

While the strict definition of supramolecular chemistry is "chemistry beyond the molecule", meaning having a focus on non-covalent interactions, the field is primarily associated with the creation of synthetic receptors and self-assembly. For synthetic ease, the receptors and assemblies routinely possess a high degree of symmetry, which lends them an aspect of aesthetic beauty. Pictures of electron orbitals similarly can be seen as akin to works of art. This similarity was an early draw for me to the fields of supramolecular chemistry and molecular orbital theory, because I grew up in a household filled with art. In addition to art, my childhood was filled with repairing and constructing mechanical entities, such as internal combustion motors, where many components work together to achieve a function. Analogously, the field of supramolecular chemistry creates systems of high complexity that achieve functions or perform tasks. Therefore, in retrospect a career in supramolecular chemistry appears to be simply an extension of childhood hobbies involving art and auto-mechanics.
Art, auto-mechanics, and supramolecular chemistry. A merging of hobbies and career

PubMed Central

2016-01-01

Summary While the strict definition of supramolecular chemistry is “chemistry beyond the molecule”, meaning having a focus on non-covalent interactions, the field is primarily associated with the creation of synthetic receptors and self-assembly. For synthetic ease, the receptors and assemblies routinely possess a high degree of symmetry, which lends them an aspect of aesthetic beauty. Pictures of electron orbitals similarly can be seen as akin to works of art. This similarity was an early draw for me to the fields of supramolecular chemistry and molecular orbital theory, because I grew up in a household filled with art. In addition to art, my childhood was filled with repairing and constructing mechanical entities, such as internal combustion motors, where many components work together to achieve a function. Analogously, the field of supramolecular chemistry creates systems of high complexity that achieve functions or perform tasks. Therefore, in retrospect a career in supramolecular chemistry appears to be simply an extension of childhood hobbies involving art and auto-mechanics. PMID:26977197
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.
Prospectus 2000

NASA Astrophysics Data System (ADS)

Holmes, Jon L.; Gettys, Nancy S.

2000-01-01

We begin 2000 with a message about our plans for JCE Software and what you will be seeing in this column as the year progresses. Floppy Disk --> CD-ROM Most software today is distributed on CD-ROM or by downloading from the Internet. Several new computers no longer include a floppy disk drive as "standard equipment". Today's software no longer fits on one or two floppies (the installation software alone can require two disks) and the cost of reproducing and distributing several disks is prohibitive. In short, distribution of software on floppy disks is no longer practical. Therefore, JCE Software will distribute all new software publications on CD-ROM rather than on disks. Regular Issues --> Collections Distribution of all our software on CD-ROM allows us to extend our concept of software collections that we started with the General Chemistry Collection. Such collections will contain all the previously published software that is still "in print" (i.e., is compatible with current operating systems and hardware) and any new programs that fall under the topic of the collection. Proposed topics in addition to General Chemistry currently include Advanced Chemistry, Instrument and Laboratory Simulations, and Spectroscopy. Eventually, all regular issues will be replaced by these collections, which will be updated annually or semiannually with new programs and updates to existing programs. Abstracts for all new programs will continue to appear in this column when a collection or its update is ready for publication. We will continue to offer special issues of single larger programs (e.g. Periodic Table Live!, Chemistry Comes Alive! volumes) on CD-ROM and video on videotape. Connect with Your Students outside Class JCE Software has always offered network licenses to allow instructors to make our software available to students in computer labs, but that model no longer fits the way many instructors and students work with computers. Many students (or their families) own a personal computer allowing them much more flexibility than a campus computer lab. Many instructors utilize the World Wide Web, creating HTML pages for students to use. JCE Software has options available to take advantage of both of these developments. Software Adoption To provide students who own computers access to JCE Software programs, consider adopting one or more of our CD-ROMs as you would a textbook. The General Chemistry Collection has been adopted by several general chemistry courses. We can arrange to bundle CDs with laboratory manuals or to be sold separately to students through the campus bookstore. The cost per CD can be quite low (as little as $5) when large numbers are ordered, making this a cost-effective method of allowing students access to the software they need whenever and wherever they desire. Web-Ready Publications Several JCE Software programs use HTML to present the material. Viewed with the ubiquitous Internet Browser, HTML is compatible with both Mac OS and Windows (as well most other current operating systems) and provides a flexible hypermedia interface that is familiar to an increasing number of instructors and students. HTML-based publications are also ready for use on local intranets, with appropriate licensing, and can be readily incorporated into other HTML-based materials. Already published in this format are: Chemistry Comes Alive!, Volumes 1 and 2 (Special Issues 18 and 21), Flying over Atoms (Special Issue 19), and Periodic Table Live! Second Edition (Special Issue 17). Solid State Resources Second Edition (Special Issue 12) and Chemistry Comes Alive!, Volume 3 (Special Issue 23) will be available soon. Other submissions being developed in HTML format include ChemPages Laboratory and Multimedia General Chemistry Problems. Contact the JCE Software office to learn about licensing alternatives that take advantage of the World Wide Web. Periodic Table Live! 2nd ed. is one of JCE Software's "Web-ready" publications. Publication Plans for 2000 We have several exciting new issues planned for publication in the coming year. Chemistry Comes Alive! The Chemistry Comes Alive! (CCA!) series continues with additional CD-ROMs for Mac OS and Windows. Each volume in this series contains video and animations of chemical reactions that can be easily incorporated into your own computer-based presentations. Our digital video now uses state-of-the-art compression that yields higher quality video with smaller file sizes and data rates more suited for WWW delivery. Video for Periodic Table Live! 2nd edition, Chemistry Comes Alive! Volumes 3, ChemPages Laboratory, and Multimedia General Chemistry Problems use this new format. We will be releasing updates of CCA! Volumes 1 and 2 to take advantage of this new technology. We are very pleased with the results and think you will be also. The reaction of aluminum with chlorine is included in Chemistry Comes Alive! Volume 3. ChemPages Laboratory ChemPages Laboratory, developed by the New Traditions Curriculum Project at the University of Wisconsin-Madison, is an HTML-based CD-ROM for Mac OS and Windows that contains lessons and tutorials to prepare introductory chemistry students to work in the laboratory. It includes text, photographs, computer graphics, animations, digital video, and voice narration to introduce students to the laboratory equipment and procedures. ChemPages Laboratory teaches introductory chemistry students about laboratory instruments, equipment, and procedures. Versatile Video Video demonstrating the "drinking bird" is included in the Chemistry Comes Alive! video collection. Video from this collection can be incorporated into many other projects. As an example, David Whisnant has used the drinking bird in his Multimedia General Chemistry Problems, where students view the video and are asked to explain why the bird bobs up and down. JCE Software anticipates publication of Multimedia General Chemistry Problems on CD-ROM for Mac OS and Windows in 2000. It will be "Web-ready". General Chemistry Collection, 4th Edition The General Chemistry Collection will be revised early in the summer and CDs will be shipped in time for fall adoptions. The 4th edition will include JCE Software publications for general chemistry published in 1999, as well as any programs for general chemistry accepted in 2000. Regular Issues We have had many recent submissions and submissions of work in progress. In 2000 we will work with the authors and our peer-reviewers to complete and publish these submissions individually or as part of a software collection on CD-ROM. An Invitation In collaboration with JCE Online we plan to make available in 2000 more support files for JCE Software. These will include not only troubleshooting tips and technical support notes, but also supporting information submitted by users such as lessons, specific assignments, and activities using JCE Software publications. All JCE Software users are invited to contribute to this area. Get in touch with JCE Software and let us know how you are using our materials so that we can share your ideas with others! Although the word software is in our name, many of our publications are not traditional software. We also publish video on videotape, videodisc, and CD-ROM and electronic documents (Mathcad and Mathematica, spreadsheet files and macros, HTML documents, and PowerPoint presentations). Most chemistry instructors who use a computer in their teaching have created or considered creating one or more of these for their classes. If you have an original computer presentation, electronic document, animation, video, or any other item that is not printed text it is probably an appropriate submission for JCE Software. By publishing your work in any branch of the Journal of Chemical Education, you will share your efforts with chemistry instructors and students all over the world and get professional recognition for your achievements. All JCE Software publications are Y2K compliant.
Industrial medicinal chemistry insights: neuroscience hit generation at Janssen.

PubMed

Tresadern, Gary; Rombouts, Frederik J R; Oehlrich, Daniel; Macdonald, Gregor; Trabanco, Andres A

2017-10-01

The role of medicinal chemistry has changed over the past 10 years. Chemistry had become one step in a process; funneling the output of high-throughput screening (HTS) on to the next stage. The goal to identify the ideal clinical compound remains, but the means to achieve this have changed. Modern medicinal chemistry is responsible for integrating innovation throughout early drug discovery, including new screening paradigms, computational approaches, novel synthetic chemistry, gene-family screening, investigating routes of delivery, and so on. In this Foundation Review, we show how a successful medicinal chemistry team has a broad impact and requires multidisciplinary expertise in these areas. Copyright © 2017 Elsevier Ltd. All rights reserved.
Mathematical challenges from theoretical/computational chemistry

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

NONE

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 assembledmore » 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.« less
Research in bioanalysis and separations at the University of Nebraska - Lincoln.

PubMed

Hage, David S; Dodds, Eric D; Du, Liangcheng; Powers, Robert

2011-05-01

The Chemistry Department at the University of Nebraska - Lincoln (UNL) is located in Hamilton Hall on the main campus of UNL in Lincoln, NE, USA. This department houses the primary graduate and research program in chemistry in the state of Nebraska. This program includes the traditional fields of analytical chemistry, biochemistry, inorganic chemistry, organic chemistry and physical chemistry. However, this program also contains a great deal of multidisciplinary research in fields that range from bioanalytical and biophysical chemistry to nanomaterials, energy research, catalysis and computational chemistry. Current research in bioanalytical and biophysical chemistry at UNL includes work with separation methods such as HPLC and CE, as well as with techniques such as MS and LC-MS, NMR spectroscopy, electrochemical biosensors, scanning probe microscopy and laser spectroscopy. This article will discuss several of these areas, with an emphasis being placed on research in bioanalytical separations, binding assays and related fields.
An approach to quality and performance control in a computer-assisted clinical chemistry laboratory.

PubMed Central

Undrill, P E; Frazer, S C

1979-01-01

A locally developed, computer-based clinical chemistry laboratory system has been in operation since 1970. This utilises a Digital Equipment Co Ltd PDP 12 and an interconnected PDP 8/F computer. Details are presented of the performance and quality control techniques incorporated into the system. Laboratory performance is assessed through analysis of results from fixed-level control sera as well as from cumulative sum methods. At a simple level the presentation may be considered purely indicative, while at a more sophisticated level statistical concepts have been introduced to aid the laboratory controller in decision-making processes. PMID:438340
Computer Series, 88.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Describes two experiments in college chemistry which use microcomputers. One experiment deals with chemical oscillations, while the other involves colorimeter titration with laser excitation and computer-interfaced endpoint detection. (TW)

OrChem - An open source chemistry search engine for Oracle(R).

PubMed

Rijnbeek, Mark; Steinbeck, Christoph

2009-10-22

Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net.
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.
Medicinal chemistry in drug discovery in big pharma: past, present and future.

PubMed

Campbell, Ian B; Macdonald, Simon J F; Procopiou, Panayiotis A

2018-02-01

The changes in synthetic and medicinal chemistry and related drug discovery science as practiced in big pharma over the past few decades are described. These have been predominantly driven by wider changes in society namely the computer, internet and globalisation. Thoughts about the future of medicinal chemistry are also discussed including sharing the risks and costs of drug discovery and the future of outsourcing. The continuing impact of access to substantial computing power and big data, the use of algorithms in data analysis and drug design are also presented. The next generation of medicinal chemists will communicate in ways that reflect social media and the results of constantly being connected to each other and data. Copyright © 2017. Published by Elsevier Ltd.
Methane and Methanol Oxidation in Supercritical Water: Chemical Kinetics and Hydrothermal Flame Studies

DTIC Science & Technology

1996-01-01

water at 270 bar and at temperatures from 390 to 442 ’C. The initial methane concentration was nominally 0.15 gmol/L, a level representa- tive of...compounds appropriate for treatment with SCWO technology (Modell, 1989). Since then, the need to understand reaction chemistry has motivated extensive...understand the physics and chemistry controlling oxidation in supercritical water; to contribute to combustion science by performing fundamental studies in a
Effects of hurricane disturbance on stream water concentrations and fluxes in eight tropical forest watersheds of the Luquillo Experimental Forest, Puerto Rico.

Treesearch

DOUGLAS. A. SCHAEFER; WILLIAM H. McDOWELL; FREDRICK N. SCATENA; CLYDE E. ASBURY

2000-01-01

Stream water chemistry responds substantially to watershed disturbances, but hurricane effects have not been extensively investigated in tropical regions. This study presents a long-term (2.5Â±11 y) weekly record of stream water chemistry on eight forested watersheds (catchment basins) in the Luquillo Mountains of Puerto Rico. This includes a period before and at least...
Investigating Impact Metrics for Performance for the US EPA National Center for Computational Toxicology (ACS Fall meeting)

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...
NASA/DoD Aerospace Knowledge Diffusion Research Project. Report Number 20. The Use of Selected Information Products and Services by U.S. Aerospace Engineers and Scientists: Results of Two Surveys.

DTIC Science & Technology

1994-02-01

within and between organizations. The technical report has been defined etymologically , according to report content and method (U.S. Department of...number) I AERONAUTICS 6 MATHEMATICAL & COMPUTER SCIENCES 2 ASTRONAUTICS 7 MATERIALS & CHEMISTRY 3 ENGINEERING 8 PHYSICS 4 GEOSCIENCES 9 SPACE SCIENCES 5...the application of your work? (Circle ONLY one number) 1 AERONAUTICS 6 MATHEMATICAL & COMPUTER SCIENCES 2 ASTRONAUTICS 7 MATERIALS & CHEMISTRY 3
Open source molecular modeling.

PubMed

Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

2016-09-01

The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.
Computer Series, 29: Bits and Pieces, 10.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Describes computer programs (available from authors) including molecular input to computer, programs for quantum chemistry, library orientation to technical literature, plotting potentiometric titration data, simulating oscilloscope curves, organic qualitative analysis with dynamic graphics, extended Huckel calculations, and calculator programs…
Computer Series, 78.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1986-01-01

Presents six brief articles dealing with the use of computers in teaching various topics in chemistry. Describes hardware and software applications which relate to protein graphics, computer simulated metabolism, interfaces between microcomputers and measurement devices, courseware available for spectrophotometers, and the calculation of elemental…
Clinical chemistry through Clinical Chemistry: a journal timeline.

PubMed

Rej, Robert

2004-12-01

The establishment of the modern discipline of clinical chemistry was concurrent with the foundation of the journal Clinical Chemistry and that of the American Association for Clinical Chemistry in the late 1940s and early 1950s. To mark the 50th volume of this Journal, I chronicle and highlight scientific milestones, and those within the discipline, as documented in the pages of Clinical Chemistry. Amazing progress has been made in the field of laboratory diagnostics over these five decades, in many cases paralleling-as well as being bolstered by-the rapid pace in the development of computer technologies. Specific areas of laboratory medicine particularly well represented in Clinical Chemistry include lipids, endocrinology, protein markers, quality of laboratory measurements, molecular diagnostics, and general advances in methodology and instrumentation.
Robin Ganellin gives his views on medicinal chemistry and drug discovery. Interview by Stephen L. Carney.

PubMed

Ganellin, C Robin

2004-02-15

Robin Ganellin was born in East London and studied chemistry at Queen Mary College, London, receiving a PhD in 1958 under Professor Michael Dewar for his research on tropylium chemistry. He joined Smith Kline & French Laboratories (SK&F) in the UK in 1958 and was one of the co-inventors of the revolutionary drug cimetidine (Tagamet(R)) He subsequently became Vice-President for Research at the company's Welwyn facility. In 1986 he was awarded a DSc from London University for his work on the medicinal chemistry of drugs acting at histamine receptors and was also made a Fellow of the Royal Society and appointed to the SK&F Chair of Medicinal Chemistry at University College London, where he is now Emeritus Professor of Medicinal Chemistry. Professor Ganellin has been honoured extensively, including such awards as the Royal Society of Chemistry Award for Medicinal Chemistry, their Tilden Medal and Lectureship and their Adrien Albert Medal and Lectureship, Le Prix Charles Mentzer de France, the ACS Division of Medicinal Chemistry Award, the Society of Chemical Industry Messel Medal and the Society for Drug Research Award for Drug Discovery. He is a past Chairman of the Society for Drug Research, was President of the Medicinal Chemistry Section of IUPAC, and is currently Chairman of the IUPAC Subcommittee on Medicinal Chemistry and Drug Development.
Carbohydrate CuAAC click chemistry for therapy and diagnosis.

PubMed

He, Xiao-Peng; Zeng, Ya-Li; Zang, Yi; Li, Jia; Field, Robert A; Chen, Guo-Rong

2016-06-24

Carbohydrates are important as signaling molecules and for cellular recognition events, therefore offering scope for the development of carbohydrate-mimetic diagnostics and drug candidates. As a consequence, the construction of carbohydrate-based bioactive compounds and sensors has become an active research area. While the advent of click chemistry has greatly accelerated the progress of medicinal chemistry and chemical biology, recent literature has seen an extensive use of such approaches to construct functionally diverse carbohydrate derivatives. Here we summarize some of the progress, covering the period 2010 to mid-2015, in Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition CuAAC "click chemistry" of carbohydrate derivatives, in the context of potential therapeutic and diagnostic tool development. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.
4D bioprinting: the next-generation technology for biofabrication enabled by stimuli-responsive materials.

PubMed

Li, Yi-Chen; Zhang, Yu Shrike; Akpek, Ali; Shin, Su Ryon; Khademhosseini, Ali

2016-12-02

Four-dimensional (4D) bioprinting, encompassing a wide range of disciplines including bioengineering, materials science, chemistry, and computer sciences, is emerging as the next-generation biofabrication technology. By utilizing stimuli-responsive materials and advanced three-dimensional (3D) bioprinting strategies, 4D bioprinting aims to create dynamic 3D patterned biological structures that can transform their shapes or behavior under various stimuli. In this review, we highlight the potential use of various stimuli-responsive materials for 4D printing and their extension into biofabrication. We first discuss the state of the art and limitations associated with current 3D printing modalities and their transition into the inclusion of the additional time dimension. We then suggest the potential use of different stimuli-responsive biomaterials as the bioink that may achieve 4D bioprinting where transformation of fabricated biological constructs can be realized. We finally conclude with future perspectives.
Performance prediction of a ducted rocket combustor

NASA Astrophysics Data System (ADS)

Stowe, Robert

2001-07-01

The ducted rocket is a supersonic flight propulsion system that takes the exhaust from a solid fuel gas generator, mixes it with air, and burns it to produce thrust. To develop such systems, the use of numerical models based on Computational Fluid Dynamics (CFD) is increasingly popular, but their application to reacting flow requires specific attention and validation. Through a careful examination of the governing equations and experimental measurements, a CFD-based method was developed to predict the performance of a ducted rocket combustor. It uses an equilibrium-chemistry Probability Density Function (PDF) combustion model, with a gaseous and a separate stream of 75 nm diameter carbon spheres to represent the fuel. After extensive validation with water tunnel and direct-connect combustion experiments over a wide range of geometries and test conditions, this CFD-based method was able to predict, within a good degree of accuracy, the combustion efficiency of a ducted rocket combustor.
IGI (the Italian Grid initiative) and its impact on the Astrophysics community

NASA Astrophysics Data System (ADS)

Pasian, F.; Vuerli, C.; Taffoni, G.

IGI - the Association for the Italian Grid Infrastructure - has been established as a consortium of 14 different national institutions to provide long term sustainability to the Italian Grid. Its formal predecessor, the Grid.it project, has come to a close in 2006; to extend the benefits of this project, IGI has taken over and acts as the national coordinator for the different sectors of the Italian e-Infrastructure present in EGEE. IGI plans to support activities in a vast range of scientificdisciplines - e.g. Physics, Astrophysics, Biology, Health, Chemistry, Geophysics, Economy, Finance - and any possible extensions to other sectors such as Civil Protection, e-Learning, dissemination in Universities and secondary schools. Among these, the Astrophysics community is active as a user, by porting applications of various kinds, but also as a resource provider in terms of computing power and storage, and as middleware developer.
The Future of Ethenolysis in Biobased Chemistry.

PubMed

Spekreijse, Jurjen; Sanders, Johan P M; Bitter, Johannes H; Scott, Elinor L

2017-02-08

The desire to utilise biobased feedstocks and develop more sustainable chemistry poses new challenges in catalysis. A synthetically useful catalytic conversion is ethenolysis, a cross metathesis reaction with ethylene. In this Review, the state of the art of ethenolysis in biobased chemistry was extensively examined using methyl oleate as a model compound for fatty acids. Allied to this, the ethenolysis of fatty acid, polymers and more challenging substrates are reviewed. To determine the limiting factors for the application of ethenolysis on biomass, the influence of reaction parameters were investigated and the bottlenecks for reaching high turnover numbers identified. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Compressed Sensing for Chemistry

NASA Astrophysics Data System (ADS)

Sanders, Jacob Nathan

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

NASA Astrophysics Data System (ADS)

Kundu, Prithwish

Turbulent non-premixed flames play a very important role in the field of engineering ranging from power generation to propulsion. The coupling of fluid mechanics and complicated combustion chemistry of fuels pose a challenge for the numerical modeling of these type of problems. Combustion modeling in Computational Fluid Dynamics (CFD) is one of the most important tools used for predictive modeling of complex systems and to understand the basic fundamentals of combustion. Traditional combustion models solve a transport equation of each species with a source term. In order to resolve the complex chemistry accurately it is important to include a large number of species. However, the computational cost is generally proportional to the cube of number of species. The presence of a large number of species in a flame makes the use of CFD computationally expensive and beyond reach for some applications or inaccurate when solved with simplified chemistry. For highly turbulent flows, it also becomes important to incorporate the effects of turbulence chemistry interaction (TCI). The aim of this work is to develop high fidelity combustion models based on the flamelet concept and to significantly advance the existing capabilities. A thorough investigation of existing models (Finite-rate chemistry and Representative Interactive Flamelet (RIF)) and comparative study of combustion models was done initially on a constant volume combustion chamber with diesel fuel injection. The CFD modeling was validated with experimental results and was also successfully applied to a single cylinder diesel engine. The effect of number of flamelets on the RIF model and flamelet initialization strategies were studied. The RIF model with multiple flamelets is computationally expensive and a model was proposed on the frame work of RIF. The new model was based on tabulated chemistry and incorporated TCI effects. A multidimensional tabulated chemistry database generation code was developed based on the 1D diffusion flame solver. The proposed model did not use progress variables like the traditional chemistry tabulation methods. The resulting model demonstrated an order of magnitude computational speed up over the RIF model. The results were validated across a wide range of operating conditions for diesel injections and the results were in close agreement to those of the experimental data. History of scalar dissipation rates plays a very important role in non premixed flames. However, tabulated methods have not been able to incorporate this physics in their models. A comparative approach is developed that can quantify these effects and find correlations with flow variables. A new model is proposed to include these effects in tabulated combustion models. The model is initially validated for 1D counterflow diffusion flame problems at engine conditions. The model is further implemented and validated in a 3D RANS code across a range of operating conditions for spray flames.
Technical Highlights

Science.gov Websites

Hopkins) Summary of data on computational modeling and experimental validation of correlations between targetr chemistries and carry out plasma etching assessment 2014: Jane Chang (UCLA) Non-PFC plasma varying physiochemical ENs 2013: Shyam Aravamudhan (NC A&T) Non-PFC plasma chemistries for patterning

Implementation of Finite Rate Chemistry Capability in OVERFLOW

NASA Technical Reports Server (NTRS)

Olsen, M. E.; Venkateswaran, S.; Prabhu, D. K.

2004-01-01

An implementation of both finite rate and equilibrium chemistry have been completed for the OVERFLOW code, a chimera capable, complex geometry flow code widely used to predict transonic flow fields. The implementation builds on the computational efficiency and geometric generality of the solver.
Evaluation of Three Instructional Methods for Teaching General Chemistry.

ERIC Educational Resources Information Center

Jackman, Lance E.; And Others

1987-01-01

Reports on a study designed to determine the relative effectiveness of different instructional approaches on chemistry laboratory achievement. Investigated differences in achievement in spectrophotometry among college freshmen who received either traditional, learning cycle, or computer simulation instruction. Results indicated that students…
9 CFR 439.1 - Definitions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE REGULATORY... four food chemistry analytes (protein, moisture, fat, and salt); or a determination by FSIS that a.... For purposes of computing the comparison mean, a laboratory's “result” for a food chemistry analyte is...
9 CFR 439.1 - Definitions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE REGULATORY... four food chemistry analytes (protein, moisture, fat, and salt); or a determination by FSIS that a.... For purposes of computing the comparison mean, a laboratory's “result” for a food chemistry analyte is...
9 CFR 439.1 - Definitions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE REGULATORY... four food chemistry analytes (protein, moisture, fat, and salt); or a determination by FSIS that a.... For purposes of computing the comparison mean, a laboratory's “result” for a food chemistry analyte is...
9 CFR 439.1 - Definitions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF AGRICULTURE REGULATORY... four food chemistry analytes (protein, moisture, fat, and salt); or a determination by FSIS that a.... For purposes of computing the comparison mean, a laboratory's “result” for a food chemistry analyte is...
UNDERSTANDING, DERIVING, AND COMPUTING BUFFER CAPACITY

EPA Science Inventory

Derivation and systematic calculation of buffer capacity is a topic that seems often to be neglected in chemistry courses and given minimal treatment in most texts. However, buffer capacity is very important in the chemistry of natural waters and potable water. It affects corro...
Delivering an Informational Hub for Data at the National Center for Computational Toxicology (ACS Spring Meeting) 7 of 7

EPA Science Inventory

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data drive...
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…
Use of Computer-Based Case Studies in a Problem-Solving Curriculum.

ERIC Educational Resources Information Center

Haworth, Ian S.; And Others

1997-01-01

Describes the use of three case studies, on computer, to enhance problem solving and critical thinking among doctoral pharmacy students in a physical chemistry course. Students are expected to use specific computer programs, spreadsheets, electronic mail, molecular graphics, word processing, online literature searching, and other computer-based…
Developing Computer Model-Based Assessment of Chemical Reasoning: A Feasibility Study

ERIC Educational Resources Information Center

Liu, Xiufeng; Waight, Noemi; Gregorius, Roberto; Smith, Erica; Park, Mihwa

2012-01-01

This paper reports a feasibility study on developing computer model-based assessments of chemical reasoning at the high school level. Computer models are flash and NetLogo environments to make simultaneously available three domains in chemistry: macroscopic, submicroscopic, and symbolic. Students interact with computer models to answer assessment…
Quantum Chemistry; A concise introduction for students of physics, chemistry, biochemistry and materials science

NASA Astrophysics Data System (ADS)

Thakkar, Ajit J.

2017-09-01

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

NASA Astrophysics Data System (ADS)

Fianchini, Mauro

2017-11-01

Chemical synthesis has its roots in the empirical approach of alchemy. Nonetheless, the birth of the scientific method, the technical and technological advances (exploiting revolutionary discoveries in physics) and the improved management and sharing of growing databases greatly contributed to the evolution of chemistry from an esoteric ground into a mature scientific discipline during these last 400 years. Furthermore, thanks to the evolution of computational resources, platforms and media in the last 40 years, theoretical chemistry has added to the puzzle the final missing tile in the process of "rationalizing" chemistry. The use of mathematical models of chemical properties, behaviors and reactivities is nowadays ubiquitous in literature. Theoretical chemistry has been successful in the difficult task of complementing and explaining synthetic results and providing rigorous insights when these are otherwise unattainable by experiment. The first part of this review walks the reader through a concise historical overview on the evolution of the "model" in chemistry. Salient milestones have been highlighted and briefly discussed. The second part focuses more on the general description of recent state-of-the-art computational techniques currently used worldwide by chemists to produce synergistic models between theory and experiment. Each section is complemented by key-examples taken from the literature that illustrate the application of the technique discussed therein.
Big Data Meets Quantum Chemistry Approximations: The Δ-Machine Learning Approach.

PubMed

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

2015-05-12

Chemically accurate and comprehensive studies of the virtual space of all possible molecules are severely limited by the computational cost of quantum chemistry. We introduce a composite strategy that adds machine learning corrections to computationally inexpensive approximate legacy quantum methods. After training, highly accurate predictions of enthalpies, free energies, entropies, and electron correlation energies are possible, for significantly larger molecular sets than used for training. For thermochemical properties of up to 16k isomers of C7H10O2 we present numerical evidence that chemical accuracy can be reached. We also predict electron correlation energy in post Hartree-Fock methods, at the computational cost of Hartree-Fock, and we establish a qualitative relationship between molecular entropy and electron correlation. The transferability of our approach is demonstrated, using semiempirical quantum chemistry and machine learning models trained on 1 and 10% of 134k organic molecules, to reproduce enthalpies of all remaining molecules at density functional theory level of accuracy.
Convection and chemistry effects in CVD: A 3-D analysis for silicon deposition

NASA Technical Reports Server (NTRS)

Gokoglu, S. A.; Kuczmarski, M. A.; Tsui, P.; Chait, A.

1989-01-01

The computational fluid dynamics code FLUENT has been adopted to simulate the entire rectangular-channel-like (3-D) geometry of an experimental CVD reactor designed for Si deposition. The code incorporated the effects of both homogeneous (gas phase) and heterogeneous (surface) chemistry with finite reaction rates of important species existing in silane dissociation. The experiments were designed to elucidate the effects of gravitationally-induced buoyancy-driven convection flows on the quality of the grown Si films. This goal is accomplished by contrasting the results obtained from a carrier gas mixture of H2/Ar with the ones obtained from the same molar mixture ratio of H2/He, without any accompanying change in the chemistry. Computationally, these cases are simulated in the terrestrial gravitational field and in the absence of gravity. The numerical results compare favorably with experiments. Powerful computational tools provide invaluable insights into the complex physicochemical phenomena taking place in CVD reactors. Such information is essential for the improved design and optimization of future CVD reactors.
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.
Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes.

PubMed

Semighini, Evandro P; Resende, Jonathan A; de Andrade, Peterson; Morais, Pedro A B; Carvalho, Ivone; Taft, Carlton A; Silva, Carlos H T P

2011-04-01

The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.
'Click chemistry' for diagnosis: a patent review on exploitation of its emerging trends.

PubMed

Mandhare, Anita; Banerjee, Paromita; Bhutkar, Smita; Hirwani, Rajkumar

2014-12-01

Click chemistry is the novel synthetic approach towards developing reactions with large thermodynamic driving forces to give almost complete conversion of new molecular reagents to a single product. Thus, click chemistry describes the chemistry for making carbon-heteroatom-carbon bonds in benign solvents, especially in water, and having a plethora of chemical and biological applications. This has played an important role in early detection of diseases, real-time monitoring of drug delivery and investigating the biomolecular functions in vivo. This review aims at highlighting the research advancements in click chemistry published in the patent literature and categorizing the patents according to the technological progress. An extensive search was carried out to collect and analyze the patent information claiming the use of click chemistry in biotechnology, especially for diagnosis. The study further concentrates on licensing of the click chemistry patents and defining the recent breakthroughs. Different databases like Espacenet, ISI Web of Science, Patbase and Thomson Innovation are used to compile the relevant literature. In recent years, considerable development in the click concept has encouraged researchers in using click reactions in almost every branch of industry that uses chemistry. Click chemistry for chemical ligation has been immensely explored in the field of biotechnology especially for detection, diagnosis and therapeutics.
Development and Performance of the Modularized, High-performance Computing and Hybrid-architecture Capable GEOS-Chem Chemical Transport Model

NASA Astrophysics Data System (ADS)

Long, M. S.; Yantosca, R.; Nielsen, J.; Linford, J. C.; Keller, C. A.; Payer Sulprizio, M.; Jacob, D. J.

2014-12-01

The GEOS-Chem global chemical transport model (CTM), used by a large atmospheric chemistry research community, has been reengineered to serve as a platform for a range of computational atmospheric chemistry science foci and applications. Development included modularization for coupling to general circulation and Earth system models (ESMs) and the adoption of co-processor capable atmospheric chemistry solvers. This was done using an Earth System Modeling Framework (ESMF) interface that operates independently of GEOS-Chem scientific code to permit seamless transition from the GEOS-Chem stand-alone serial CTM to deployment as a coupled ESM module. In this manner, the continual stream of updates contributed by the CTM user community is automatically available for broader applications, which remain state-of-science and directly referenceable to the latest version of the standard GEOS-Chem CTM. These developments are now available as part of the standard version of the GEOS-Chem CTM. The system has been implemented as an atmospheric chemistry module within the NASA GEOS-5 ESM. The coupled GEOS-5/GEOS-Chem system was tested for weak and strong scalability and performance with a tropospheric oxidant-aerosol simulation. Results confirm that the GEOS-Chem chemical operator scales efficiently for any number of processes. Although inclusion of atmospheric chemistry in ESMs is computationally expensive, the excellent scalability of the chemical operator means that the relative cost goes down with increasing number of processes, making fine-scale resolution simulations possible.
An investigation comparing traditional recitation instruction to computer tutorials which combine three-dimensional animation with varying levels of visual complexity, including digital video in teaching various chemistry topics

NASA Astrophysics Data System (ADS)

Graves, A. Palmer

This study examines the effect of increasing the visual complexity used in computer assisted instruction in general chemistry. Traditional recitation instruction was used as a control for the experiment. One tutorial presented a chemistry topic using 3-D animation showing molecular activity and symbolic representation of the macroscopic view of a chemical phenomenon. A second tutorial presented the same topic but simultaneously presented students with a digital video movie showing the phenomena and 3-D animation showing the molecular view of the phenomena. This experimental set-up was used in two different experiments during the first semester of college level general chemistry course. The topics covered were the molecular effect of heating water through the solid-liquid phase change and the kinetic molecular theory used in explaining pressure changes. The subjects used in the experiment were 236 college students enrolled in a freshman chemistry course at a large university. The data indicated that the simultaneous presentation of digital video, showing the solid to liquid phase change of water, with a molecular animation, showing the molecular behavior during the phase change, had a significant effect on student particulate understanding when compared to traditional recitation. Although the effect of the KMT tutorial was not statistically significant, there was a positive effect on student particulate understanding. The use of computer tutorial also had a significant effect on student attitude toward their comprehension of the lesson.

The Computer Revolution and Physical Chemistry.

ERIC Educational Resources Information Center

O'Brien, James F.

1989-01-01

Describes laboratory-oriented software programs that are short, time-saving, eliminate computational errors, and not found in public domain courseware. Program availability for IBM and Apple microcomputers is included. (RT)
CARES/LIFE Software Commercialization

NASA Technical Reports Server (NTRS)

1995-01-01

The NASA Lewis Research Center has entered into a letter agreement with BIOSYM Technologies Inc. (now merged with Molecular Simulations Inc. (MSI)). Under this agreement, NASA will provide a developmental copy of the CARES/LIFE computer program to BIOSYM for evaluation. This computer code predicts the time-dependent reliability of a thermomechanically loaded component. BIOSYM will become familiar with CARES/LIFE, provide results of computations useful in validating the code, evaluate it for potential commercialization, and submit suggestions for improvements or extensions to the code or its documentation. If BIOSYM/Molecular Simulations reaches a favorable evaluation of CARES/LIFE, NASA will enter into negotiations for a cooperative agreement with BIOSYM/Molecular Simulations to further develop the code--adding features such as a user-friendly interface and other improvements. This agreement would give BIOSYM intellectual property rights in the modified codes, which they could protect and then commercialize. NASA would provide BIOSYM with the NASA-developed source codes and would agree to cooperate with BIOSYM in further developing the code. In return, NASA would receive certain use rights in the modified CARES/LIFE program. Presently BIOSYM Technologies Inc. has been involved with integration issues concerning its merger with Molecular Simulations Inc., since both companies used to compete in the computational chemistry market, and to some degree, in the materials market. Consequently, evaluation of the CARES/LIFE software is on hold for a month or two while the merger is finalized. Their interest in CARES continues, however, and they expect to get back to the evaluation by early November 1995.
The CompTox Chemistry Dashboard - A Community Data Resource for Environmental Chemistry

EPA Science Inventory

Despite an abundance of online databases providing access to chemical data, there is increasing demand for high-quality, structure-curated, open data to meet the various needs of the environmental sciences and computational toxicology communities. The U.S. Environmental Protectio...
Integrating Mathematics into the Introductory Biology Laboratory Course

ERIC Educational Resources Information Center

White, James D.; Carpenter, Jenna P.

2008-01-01

Louisiana Tech University has an integrated science curriculum for its mathematics, chemistry, physics, computer science, biology-research track and secondary mathematics and science education majors. The curriculum focuses on the calculus sequence and introductory labs in biology, physics, and chemistry. In the introductory biology laboratory…
What a Chemist Needs to Know--Other than Chemistry.

ERIC Educational Resources Information Center

Chemical and Engineering News, 1980

1980-01-01

Recommends a range of courses of study which may be important for one pursuing a career in chemistry. Discusses courses in computer science, statistics, public speaking, technical writing, mathematics, physics, economics, market research, psychology, chemical engineering, toxicology, history, foreign language, and science history. (CS)
ADVANCED COMPUTATIONAL METHODS IN DOSE MODELING

EPA Science Inventory

The overall goal of the EPA-ORD NERL research program on Computational Toxicology (CompTox) is to provide the Agency with the tools of modern chemistry, biology, and computing to improve quantitative risk assessments and reduce uncertainties in the source-to-adverse outcome conti...
ENVIRONMENTAL ANALYSIS BY AB INITIO QUANTUM MECHANICAL COMPUTATION AND GAS CHROMATOGRAPHY/FOURIER TRANSFORM INFRARED SPECTROMETRY.

EPA Science Inventory

Computational chemistry, in conjunction with gas chromatography/mass spectrometry/Fourier transform infrared spectrometry (GC/MS/FT-IR), was used to tentatively identify seven tetrachlorobutadiene (TCBD) isomers detected in an environmental sample. Computation of the TCBD infrare...
Shock simulations of a single-site coarse-grain RDX model using the dissipative particle dynamics method with reactivity

NASA Astrophysics Data System (ADS)

Sellers, Michael S.; Lísal, Martin; Schweigert, Igor; Larentzos, James P.; Brennan, John K.

2017-01-01

In discrete particle simulations, when an atomistic model is coarse-grained, a tradeoff is made: a boost in computational speed for a reduction in accuracy. The Dissipative Particle Dynamics (DPD) methods help to recover lost accuracy of the viscous and thermal properties, while giving back a relatively small amount of computational speed. Since its initial development for polymers, one of the most notable extensions of DPD has been the introduction of chemical reactivity, called DPD-RX. In 2007, Maillet, Soulard, and Stoltz introduced implicit chemical reactivity in DPD through the concept of particle reactors and simulated the decomposition of liquid nitromethane. We present an extended and generalized version of the DPD-RX method, and have applied it to solid hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX). Demonstration simulations of reacting RDX are performed under shock conditions using a recently developed single-site coarse-grain model and a reduced RDX decomposition mechanism. A description of the methods used to simulate RDX and its transition to hot product gases within DPD-RX is presented. Additionally, we discuss several examples of the effect of shock speed and microstructure on the corresponding material chemistry.
Droplet evaporation and combustion in a liquid-gas multiphase system

NASA Astrophysics Data System (ADS)

Muradoglu, Metin; Irfan, Muhammad

2017-11-01

Droplet evaporation and combustion in a liquid-gas multiphase system are studied computationally using a front-tracking method. One field formulation is used to solve the flow, energy and species equations with suitable jump conditions. Both phases are assumed to be incompressible; however, the divergence-free velocity field condition is modified to account for the phase change at the interface. Both temperature and species gradient driven phase change processes are simulated. Extensive validation studies are performed using the benchmark cases: The Stefan and the sucking interface problems, d2 law and wet bulb temperature comparison with the psychrometric chart values. The phase change solver is then extended to incorporate the burning process following the evaporation as a first step towards the development of a computational framework for spray combustion. We used detailed chemistry, variable transport properties and ideal gas behaviour for a n-heptane droplet combustion; the chemical kinetics being handled by the CHEMKIN. An operator-splitting approach is used to advance temperature and species mass fraction in time. The numerical results of the droplet burning rate, flame temperature and flame standoff ratio show good agreement with the experimental and previous numeric.
Modeling RF-induced Plasma-Surface Interactions with VSim

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Smithe, David N.; Pankin, Alexei Y.; Roark, Christine M.; Stoltz, Peter H.; Zhou, Sean C.-D.; Kruger, Scott E.

2014-10-01

An overview of ongoing enhancements to the Plasma Discharge (PD) module of Tech-X's VSim software tool is presented. A sub-grid kinetic sheath model, developed for the accurate computation of sheath potentials near metal and dielectric-coated walls, enables the physical effects of DC and RF sheath dynamics to be included in macroscopic-scale plasma simulations that need not explicitly resolve sheath scale lengths. Sheath potential evolution, together with particle behavior near the sheath (e.g. sputtering), can thus be simulated in complex, experimentally relevant geometries. Simulations of RF sheath-enhanced impurity production near surfaces of the C-Mod field-aligned ICRF antenna are presented to illustrate the model; impurity mitigation techniques are also explored. Model extensions to capture the physics of secondary electron emission and of multispecies plasmas are summarized, together with a discussion of improved tools for plasma chemistry and IEDF/EEDF visualization and modeling. The latter tools are also highly relevant for commercial plasma processing applications. Ultimately, we aim to establish VSimPD as a robust, efficient computational tool for modeling fusion and industrial plasma processes. Supported by U.S. DoE SBIR Phase I/II Award DE-SC0009501.
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.
Routine operation of an Elliott 903 computer in a clinical chemistry laboratory

PubMed Central

Whitby, L. G.; Simpson, D.

1973-01-01

Experience gained in the last four years concerning the capabilities and limitations of an 8K Elliott 903 (18-bit word) computer with magnetic tape backing store in the routine operation of a clinical chemistry laboratory is described. Designed as a total system, routine operation has latterly had to be confined to data acquisition and process control functions, due primarily to limitations imposed by the choice of hardware early in the project. In this final report of a partially successful experiment the opportunity is taken to review mistakes made, especially at the start of the project, to warn potential computer users of pitfalls to be avoided. PMID:4580240
Turbulent reacting flow computations including turbulence-chemistry interactions

NASA Technical Reports Server (NTRS)

Narayan, J. R.; Girimaji, S. S.

1992-01-01

A two-equation (k-epsilon) turbulence model has been extended to be applicable for compressible reacting flows. A compressibility correction model based on modeling the dilatational terms in the Reynolds stress equations has been used. A turbulence-chemistry interaction model is outlined. In this model, the effects of temperature and species mass concentrations fluctuations on the species mass production rates are decoupled. The effect of temperature fluctuations is modeled via a moment model, and the effect of concentration fluctuations is included using an assumed beta-pdf model. Preliminary results obtained using this model are presented. A two-dimensional reacting mixing layer has been used as a test case. Computations are carried out using the Navier-Stokes solver SPARK using a finite rate chemistry model for hydrogen-air combustion.
Effects of Computer-Based Simulations Teaching Approach on Students' Achievement in the Learning of Chemistry among Secondary School Students in Nakuru Sub County, Kenya

ERIC Educational Resources Information Center

Mihindo, W. Jane; Wachanga, S.W.; Anditi, Z. O.

2017-01-01

Science education should help develop student's interest in science as today's society depends largely on output of science and technology. Chemistry is one of the branches of science. Chemistry education helps to expand the pupil's knowledge of the universe and of his/her position in it. It helps in the appreciation and enjoyment of nature and…
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 developments from the field of compressed sensing to find compact representations of ground states. As an application we study electronic systems and find solutions dramatically more compact than traditional configuration interaction expansions, offering hope to extend this methodology to challenging systems in chemical and material design.
Reviews.

ERIC Educational Resources Information Center

Newland, Robert J.; And Others

1988-01-01

Reviews four organic chemistry computer programs and three books. Software includes: (1) NMR Simulator 7--for IBM or Macintosh, (2) Nucleic Acid Structure and Synthesis--for IBM, (3) Molecular Design Editor--for Apple II, and (4) Synthetic Adventure--for Apple II and IBM. Book topics include physical chemistry, polymer pioneers, and the basics of…
The Application of Computational Chemistry to Problems in Mass Spectrometry

EPA Science Inventory

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

ERIC Educational Resources Information Center

Goddard, William A., III

1985-01-01

The expected thrust for theoretical chemistry in the next decade will be to combine knowledge of fundamental chemical steps/interactions with advances in chemical dynamics, irreversible statistical mechanics, and computer technology to produce simulations of chemical systems with reaction site competition. A sample simulation (using the enzyme…
Dynamic combinatorial libraries: from exploring molecular recognition to systems chemistry.

PubMed

Li, Jianwei; Nowak, Piotr; Otto, Sijbren

2013-06-26

Dynamic combinatorial chemistry (DCC) is a subset of combinatorial chemistry where the library members interconvert continuously by exchanging building blocks with each other. Dynamic combinatorial libraries (DCLs) are powerful tools for discovering the unexpected and have given rise to many fascinating molecules, ranging from interlocked structures to self-replicators. Furthermore, dynamic combinatorial molecular networks can produce emergent properties at systems level, which provide exciting new opportunities in systems chemistry. In this perspective we will highlight some new methodologies in this field and analyze selected examples of DCLs that are under thermodynamic control, leading to synthetic receptors, catalytic systems, and complex self-assembled supramolecular architectures. Also reviewed are extensions of the principles of DCC to systems that are not at equilibrium and may therefore harbor richer functional behavior. Examples include self-replication and molecular machines.
GenIce: Hydrogen-Disordered Ice Generator.

PubMed

Matsumoto, Masakazu; Yagasaki, Takuma; Tanaka, Hideki

2018-01-05

GenIce is an efficient and user-friendly tool to generate hydrogen-disordered ice structures. It makes ice and clathrate hydrate structures in various file formats. More than 100 kinds of structures are preset. Users can install their own crystal structures, guest molecules, and file formats as plugins. The algorithm certifies that the generated structures are completely randomized hydrogen-disordered networks obeying the ice rule with zero net polarization. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Apoc Social: A Mobile Interactive and Social Learning Platform for Collaborative Solving of Advanced Problems in Organic Chemistry.

PubMed

Sievertsen, Niels; Carreira, Erick M

2018-02-01

Mobile devices such as smartphones are carried in the pockets of university students around the globe and are increasingly cheap to come by. These portable devices have evolved into powerful and interconnected handheld computers, which, among other applications, can be used as advanced learning tools and providers of targeted, curated content. Herein, we describe Apoc Social (Advanced Problems in Organic Chemistry Social), a mobile application that assists both learning and teaching college-level organic chemistry both in the classroom and on the go. With more than 750 chemistry exercises available, Apoc Social facilitates collaborative learning through discussion boards and fosters enthusiasm for complex organic chemistry.
Computer Series, 83. Bits and Pieces, 34.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1987-01-01

Contains seven articles about computer applications to chemistry instruction. Includes descriptions of a three-dimensional animation of a potential energy surface, numerical solutions of kinetic equations, applications for spectroscopy courses, a computer-controlled experiment on the tin/lead solid/liquid phase diagram, an inexpensive thermistor…
The Computer Bulletin Board.

ERIC Educational Resources Information Center

Batt, Russell H., Ed.

1989-01-01

Discussed are some uses of computers in chemistry classrooms. Described are: (1) interactive chromatographic analysis software; (2) computer interface for a digital frequency-period-counter-ratio meter and analog interface based on a voltage-to-frequency converter; and (3) use of spectrometer/microcomputer arrangement for teaching atomic theory.…
Computational Nanotechnology Molecular Electronics, Materials and Machines

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Biegel, Bryan A. (Technical Monitor)

2002-01-01

This presentation covers research being performed on computational nanotechnology, carbon nanotubes and fullerenes at the NASA Ames Research Center. Topics cover include: nanomechanics of nanomaterials, nanotubes and composite materials, molecular electronics with nanotube junctions, kinky chemistry, and nanotechnology for solid-state quantum computers using fullerenes.
A database of georeferenced nutrient chemistry data for mountain lakes of the Western United States

PubMed Central

Williams, Jason; Labou, Stephanie G.

2017-01-01

Human activities have increased atmospheric nitrogen and phosphorus deposition rates relative to pre-industrial background. In the Western U.S., anthropogenic nutrient deposition has increased nutrient concentrations and stimulated algal growth in at least some remote mountain lakes. The Georeferenced Lake Nutrient Chemistry (GLNC) Database was constructed to create a spatially-extensive lake chemistry database needed to assess atmospheric nutrient deposition effects on Western U.S. mountain lakes. The database includes nitrogen and phosphorus water chemistry data spanning 1964–2015, with 148,336 chemistry results from 51,048 samples collected across 3,602 lakes in the Western U.S. Data were obtained from public databases, government agencies, scientific literature, and researchers, and were formatted into a consistent table structure. All data are georeferenced to a modified version of the National Hydrography Dataset Plus version 2. The database is transparent and reproducible; R code and input files used to format data are provided in an appendix. The database will likely be useful to those assessing spatial patterns of lake nutrient chemistry associated with atmospheric deposition or other environmental stressors. PMID:28509907
Spectroscopic and Computational Investigation of Room-Temperature Decomposition of a Chemical Warfare Agent Simulant on Polycrystalline Cupric Oxide

DOE PAGES

Trotochaud, Lena; Tsyshevsky, Roman; Holdren, Scott; ...

2017-08-21

Certain organophosphorus molecules are infamous due to their use as highly toxic nerve agents. The filtration materials currently in common use for protection against chemical warfare agents were designed before organophosphorus compounds were used as chemical weapons. A better understanding of the surface chemistry between simulant molecules and the individual filtration-material components is a critical precursor to the development of more effective materials for filtration, destruction, decontamination, and/or sensing of nerve agents. Here, we report on the surface adsorption and reactions of a sarin simulant molecule, dimethyl methylphosphonate (DMMP), with cupric oxide surfaces. In situ ambient pressure X-ray photoelectron andmore » infrared spectroscopies are coupled with density functional calculations to propose mechanisms for DMMP decomposition on CuO. We find extensive room temperature decomposition of DMMP on CuO, with the majority of decomposition fragments bound to the CuO surface. We observe breaking of PO-CH3, P-OCH3, and P-CH3bonds at room temperature. On the basis of these results, we identify specific DMMP decomposition mechanisms not seen on other metal oxides. Participation of lattice oxygen in the decomposition mechanism leads to significant changes in chemical and electronic surface environment, which are manifest in the spectroscopic and computational data. This study establishes a computational baseline for the study of highly toxic organophosphorous compounds on metal oxide surfaces.« less
Spectroscopic and Computational Investigation of Room-Temperature Decomposition of a Chemical Warfare Agent Simulant on Polycrystalline Cupric Oxide

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

Trotochaud, Lena; Tsyshevsky, Roman; Holdren, Scott

Certain organophosphorus molecules are infamous due to their use as highly toxic nerve agents. The filtration materials currently in common use for protection against chemical warfare agents were designed before organophosphorus compounds were used as chemical weapons. A better understanding of the surface chemistry between simulant molecules and the individual filtration-material components is a critical precursor to the development of more effective materials for filtration, destruction, decontamination, and/or sensing of nerve agents. Here, we report on the surface adsorption and reactions of a sarin simulant molecule, dimethyl methylphosphonate (DMMP), with cupric oxide surfaces. In situ ambient pressure X-ray photoelectron andmore » infrared spectroscopies are coupled with density functional calculations to propose mechanisms for DMMP decomposition on CuO. We find extensive room temperature decomposition of DMMP on CuO, with the majority of decomposition fragments bound to the CuO surface. We observe breaking of PO-CH3, P-OCH3, and P-CH3bonds at room temperature. On the basis of these results, we identify specific DMMP decomposition mechanisms not seen on other metal oxides. Participation of lattice oxygen in the decomposition mechanism leads to significant changes in chemical and electronic surface environment, which are manifest in the spectroscopic and computational data. This study establishes a computational baseline for the study of highly toxic organophosphorous compounds on metal oxide surfaces.« less
Sensitivity of chemistry-transport model simulations to the duration of chemical and transport operators: a case study with GEOS-Chem v10-01

NASA Astrophysics Data System (ADS)

Philip, Sajeev; Martin, Randall V.; Keller, Christoph A.

2016-05-01

Chemistry-transport models involve considerable computational expense. Fine temporal resolution offers accuracy at the expense of computation time. Assessment is needed of the sensitivity of simulation accuracy to the duration of chemical and transport operators. We conduct a series of simulations with the GEOS-Chem chemistry-transport model at different temporal and spatial resolutions to examine the sensitivity of simulated atmospheric composition to operator duration. Subsequently, we compare the species simulated with operator durations from 10 to 60 min as typically used by global chemistry-transport models, and identify the operator durations that optimize both computational expense and simulation accuracy. We find that longer continuous transport operator duration increases concentrations of emitted species such as nitrogen oxides and carbon monoxide since a more homogeneous distribution reduces loss through chemical reactions and dry deposition. The increased concentrations of ozone precursors increase ozone production with longer transport operator duration. Longer chemical operator duration decreases sulfate and ammonium but increases nitrate due to feedbacks with in-cloud sulfur dioxide oxidation and aerosol thermodynamics. The simulation duration decreases by up to a factor of 5 from fine (5 min) to coarse (60 min) operator duration. We assess the change in simulation accuracy with resolution by comparing the root mean square difference in ground-level concentrations of nitrogen oxides, secondary inorganic aerosols, ozone and carbon monoxide with a finer temporal or spatial resolution taken as "truth". Relative simulation error for these species increases by more than a factor of 5 from the shortest (5 min) to longest (60 min) operator duration. Chemical operator duration twice that of the transport operator duration offers more simulation accuracy per unit computation. However, the relative simulation error from coarser spatial resolution generally exceeds that from longer operator duration; e.g., degrading from 2° × 2.5° to 4° × 5° increases error by an order of magnitude. We recommend prioritizing fine spatial resolution before considering different operator durations in offline chemistry-transport models. We encourage chemistry-transport model users to specify in publications the durations of operators due to their effects on simulation accuracy.
Systematic Changes in the Undergraduate Chemistry Curriculum Progam Award and Course and Curriculum Development Program Awards

NASA Astrophysics Data System (ADS)

1996-06-01

Eight awards in chemistry curriculum development for FY1996 have been announced. One award, to a consortium centered at the University of California-Los Angeles, represents the fifth award in the Systemic Changes in the Undergraduate Chemistry Curriculum program. Although no proposals will be accepted in this program for either planning or full grants for FY1997, it is anticipated that proposals will be accepted in June of 1997 for projects that would adapt and adopt materials developed by the five funded consortia: Molecular Science centered at the University of California-Los Angeles; ChemLinks centered at Beloit College; MolecularChem Consortium centered at the University of California-Berkeley; Workshop Chemistry centered at CUNY City College; and New Traditions centered at the University of Wisconsin-Madison. Seven awards have been made in the Course and Curriculum Development program. This ongoing program continues to accept proposals in chemistry as usual. Systemic Changes in the Undergraduate Chemistry Curriculum Program Award. Molecular Science. Orville L. Chapman University of California-Los Angeles DUE 9555605 FY96 725,000 FY97 575,000, FY98 575,000 FY99 275,000, FY00 275,000 The UCLA-CSUF-Community College Alliance (24 area community colleges that have worked together for more than 15 years) proposes a sweeping restructuring of the lower division chemistry curriculum and the auxiliary learning and assessment processes. In forming our new curriculum, we reject the positivist approach to science education in favor of a constructivist approach that emphasizes problem solving and exploratory learning. We make this change in order to focus on the developing key skills, traits, and abilities of our students. Our new curriculum, the Molecular Science Curriculum, cuts across departments and disciplines to embrace all activities that involve the study of atoms and molecules. In particular, environmental science, materials science, and molecular life science have important positions in the lower-division chemistry curriculum. The new curriculum reflects accurately current practice in research and the chemical industry where growth is occurring in these new fields. Today information-technology-based learning enables a practical approach to discovery learning, which educational theorists have long favored. Students can learn science by doing science. In particular, we will produce problem-based modular learning units that define the molecular science curriculum; data sets organized for exploratory learning; prepackaged molecular, mathematical, and schematic models illustrating important principles and phenomena; and a client/server system that manages education. Client/server technology enables individualized courses and frees students from rigid time constraints. The learning units will be used immediately by several of the community colleges in technology programs, such as those for science technicians and hazardous materials technicians at Mount San Antonio CC. New assessment vehicles including cumulative electronic portfolios of group and individual work provide new insight into student development and potential. The project also addresses the preparation of primary and secondary science teachers by involving them as active participants in the lower division courses of the molecular science curriculum. At both UCLA and CSUF, these students will gain experience with the modules, associated learning methods, and electronic delivery system. These experiences should result in teachers with a practical perspective on science teaching as well as the ability to utilize current technology to direct learning activities. The electronic delivery system will allow students at UCLA to work with the science education faculty at CSUF to obtain certification. Since 1990 two high schools (Aliso Niguel and Crossroads) have become members of the Alliance. These schools have the facilities to expose students, experienced teachers, and future teachers to both the content and learning methods of the molecular science curriculum. Course and Curriculum Development Program Awards. Studio General Chemistry with Full Merging of the Laboratory and Classroom Experiences. Thomas M. Apple Rensselaer Polytechnic Institute DUE 9555069 114,000 A workshop general chemistry class is being developed that includes experimental work during every meeting. Lab work is merged with classroom discussion. Students working in groups are challenged to link their macroscopic observations to chemical principles. The merger of thirty-minute, concept-based discovery labs with discussion and lateral development material provides a unique perspective of chemistry. In modernizing the general chemistry curriculum, fewer topics are treated and the more esoteric aspects of physical chemistry that are inappropriate for freshmen are eliminated. More time is allocated to materials chemistry, organic and biological chemistry, and environmental science. The course material is organized into modules or case-studies that contain material that is developed with the specific aim of showing the relevance of the material to problems to which the students already have been exposed. Societal relevance is built into every module of the syllabus by incorporating laboratories, discussion and "lateral development" problems for each topic. Dynamic Visualization in Chemistry. James P. Birk Arizona State University DUE 9555098 175,000 This project will produce real images of chemical and physical changes occurring at the microscopic and atomic levels. These images, from different instruments (optical, electron, and scanning probe microscopes), will be captured electronically (video tapes and CD ROMs) and used in conjunction with molecular modeling as instructional aids in introductory chemistry courses. The objective is to introduce students to the relationships between macroscopic changes in materials and the corresponding changes in the arrangements of their atoms and molecules. The graphic images will be combined with interactive benchtop demonstrations and computer animations to produce dynamic visual instructional components (dynamic visualization modules, DVMs) for introductory chemistry courses. The existing instrumentation and modeling facilities required for the project are currently in place. Once developed the DVMs will be tested with approximately 4000 general chemistry students at Arizona State University and the Maricopa Community College system. There is a goal of national dissemination by a commercial publisher once the DVMs have been tested in the local environment. An Introductory Course in Modeling Dynamic Chemical and Ecological Systems. Joseph E. Earley Georgetown University DUE 9554932 99,996 An introductory course in modeling of dynamic systems, with special emphasis on chemical and ecological problems, will be developed. The target student population will be first- and second-year social science and humanities students, but upper division students and interested science majors will not be excluded. Rather than placing emphasis on mathematical methods and techniques used in modeling, attention will be centered on salient aspects of complex-system behavior as illustrated by models constructed using the commercially available software-package STELLA II. Relatively straightforward models dealing with chemical reactions will be used to introduce fundamental features of complex-system dynamics. Problems of ecological and demographic interest, at moderate level of difficulty, will then be covered. The origin and behavior of "deterministic chaos" will be treated using examples from both chemistry and ecology. In the last third of the course, students will work in small groups (or individually) developing their own models, each related to a specific problem of current interest, preferably in fields of the students' major academic interest. Opportunity will be provided for some outstanding students to use less "user-friendly" software such as ODEPACK to deal with models involving "stiff" differential equations. The last exercise of the course will be a poster session, at which individuals and groups will present their project models to other members of the class and to guests. The main aims of the course will be to facilitate development of the students' insight with respect to types of functioning to be expected of complex networks of relationships, and therefore in important natural systems, and also to engender an appreciation of the power and limitations of modeling techniques. VizChem-Visualizing Chemistry. Leonard W. Fine Columbia University DUE 9555122 209,000 Multimedia computer modules suitable for undergraduate chemistry lecture and laboratory courses are being designed. The modules are both content and skills oriented, interdisciplinary and multidimensional, and take full advantage of the benefits of simulation, computation, and visualization. They are being designed and created as tools for the teacher and for the student and are primarily directed at general chemistry, organic chemistry, physical chemistry, inorganic chemistry, and materials science. Module topics will include the next version of IR Tutor and applicable and important spectroscopies and diagnostic devices such as electronic absorption (UV-vis) and electronic emission (fluorescence and phosphorescence); proton and carbon-13 nuclear magnetic resonance; atomic absorption; thermal analysis; topics in polymer chemistry and materials science; and PCR technology. Secondary objectives of the project include: a broadening of the chemistry curriculum beyond traditional disciplinary boundaries, new undergraduate courses, enhanced effectiveness of teaching assistants, an expanded role for postdoctoral students in undergraduate education, and improved performance by classes of students. Connecting Undergraduate/Analytical Courses to Modern Analytical Chemistry. Thomas R. Gilbert Northeastern University DUE 9554906 200,000 Application modules in the form of projects and active learning techniques to provide a strong foundation in the principles of chemical measurement and to pique the interest of both chemistry majors and nonmajors will be developed for use in introductory analytical courses. The modules will address an analytical problem drawn from current research in biological, environmental, or materials science. Students will be responsible for proposing and evaluating analytical protocols to solve the problems: they will conduct workshops and design their own laboratory experiments. A multidisciplinary Advisory Council will guide the PIs in problem selection and module development. A two-week faculty workshop will provide training in the use of these modules. A World Wide Web home page will be used to distribute information about the modules and will allow users to share experiences using them. Modules will ultimately be distributed by a commercial publisher. Process Workshops for General Chemistry. David M. Hanson SUNY at Stony Brook DUE 9555142 150,000 The process skills needed by students will be addressed by developing innovations in both content and methodology to replace recitation sessions associated with large lecture courses by process workshops, specifically for introductory chemistry courses. The novel format involves process skills, student participation, and active learning at the forefront. Students will work in cooperative-learning groups on lessons that involve discovery learning, critical thinking, problem solving, reporting, and assessment. Computer-based technology will be used to provide personalized quizzes, and the workshop lessons will be transported to a computer network, multi-media format. The objectives of this project are to develop teaching strategies that support a successful cooperative-learning environment, develop lessons that enhance the understanding of concepts and promote learning and problem solving through the use of higher order thinking skills, develop lessons incorporating interdisciplinary and real world perspectives, enhance learning with computer-driven technology, develop process skills in key areas, promote positive attitudes toward chemistry and science, help students develop confidence in their ability to learn and perform well, create a supportive social environment that will encourage students to involve themselves seriously and successfully in learning, and promote a culture where the university is a community of learners. The transformation of recitation sessions into workshops introduces the missing element in large lecture courses. The lectures structure information and make it available to the students, and the workshops complement that component by facilitating the construction of understanding, the application of knowledge, and the development of process skills. Such development is extremely significant because introductory chemistry courses involve large numbers of students early in their college careers. Among other things, summer teaching and authoring institutes will be held to excite the interest of others in this approach and to share ideas on the methodology, strategies, and lesson content. Forensic Science: An Interactive Multimedia Laboratory Program to Enhance Introductory Chemistry (Science) Courses. Lawrence J. Kaplan Williams College DUE 9554875 234,539 While major changes have taken place in all areas of the natural sciences, introductory instruction in both the lecture hall and the laboratory has not changed significantly in many years. The PI instituted innovative teaching techniques in an elementary chemistry course called "Chemistry and Crime: From Sherlock Holmes to Modern Forensic Science" for the nonscience major. The techniques used in the laboratory have received national attention and many colleagues have instituted similar innovations. However, many institutions do not have the resources to develop laboratory programs along these lines and, as times have changed, are increasingly concerned with exposing the students to situations now recognized as potentially dangerous. Since the PI has proven that forensics can be used to spark interest in science and since it is given that young people are intrigued by computer graphics, it was decided to use computer-animated simulations to allow extensive, intensive investigation of scientific evidence collected at simulated crime scenes and studied using simulated scientific instruments. These animated modules will enhance not only the laboratory program in the forensic science course but also the programs in introductory science courses for majors. The PI will guide the development of the computer-animated modules, develop the story board and oversee the computer interfacing and the integration of the components into the curriculum. The actual modules will be created by Engineering Animation, Inc. EAI, using their Vislab software, is one of the premier computer animation companies in the world. It is anticipated that implementing this innovative and creative approach, as part of an overall multimedia program including actual laboratory experience, will enhance science education by stimulating interest and engendering enthusiasm instead of promoting the stereotype that science is boring and hard.
Comparison of nine different real-time PCR chemistries for qualitative and quantitative applications in GMO detection.

PubMed

Buh Gasparic, Meti; Tengs, Torstein; La Paz, Jose Luis; Holst-Jensen, Arne; Pla, Maria; Esteve, Teresa; Zel, Jana; Gruden, Kristina

2010-03-01

Several techniques have been developed for detection and quantification of genetically modified organisms, but quantitative real-time PCR is by far the most popular approach. Among the most commonly used real-time PCR chemistries are TaqMan probes and SYBR green, but many other detection chemistries have also been developed. Because their performance has never been compared systematically, here we present an extensive evaluation of some promising chemistries: sequence-unspecific DNA labeling dyes (SYBR green), primer-based technologies (AmpliFluor, Plexor, Lux primers), and techniques involving double-labeled probes, comprising hybridization (molecular beacon) and hydrolysis (TaqMan, CPT, LNA, and MGB) probes, based on recently published experimental data. For each of the detection chemistries assays were included targeting selected loci. Real-time PCR chemistries were subsequently compared for their efficiency in PCR amplification and limits of detection and quantification. The overall applicability of the chemistries was evaluated, adding practicability and cost issues to the performance characteristics. None of the chemistries seemed to be significantly better than any other, but certain features favor LNA and MGB technology as good alternatives to TaqMan in quantification assays. SYBR green and molecular beacon assays can perform equally well but may need more optimization prior to use.
Ice Chemistry in Interstellar Dense Molecular Clouds, Protostellar Disks, and Comets

NASA Technical Reports Server (NTRS)

Sandford, Scott A.

2015-01-01

Despite the low temperatures (T less than 20K), low pressures, and low molecular densities found in much of the cosmos, considerable chemistry is expected to occur in many astronomical environments. Much of this chemistry happens in icy grain mantles on dust grains and is driven by ionizing radiation. This ionizing radiation breaks chemical bonds of molecules in the ices and creates a host of ions and radicals that can react at the ambient temperature or when the parent ice is subsequently warmed. Experiments that similar these conditions have demonstrated a rich chemistry associated with these environments that leads to a wide variety of organic products. Many of these products are of considerable interest to astrobiology. For example, the irradiation of simple ices has been shown to abiotically produce amino acids, nucleobases, quinones, and amphiphiles, all compounds that play key roles in modern biochemistry. This suggests extraterrestrial chemistry could have played a role in the origin of life on Earth and, by extension, do so on planets in other stellar systems.
The Influence of Modern Instrumentation on the Analytical and General Chemistry Curriculum at Bates College

NASA Astrophysics Data System (ADS)

Wenzel, Thomas J.

2001-09-01

The availability of state-of-the-art instruments such as high performance liquid chromatograph, gas chromatograph-mass spectrometer, inductively coupled plasma-atomic emission spectrometer, capillary electrophoresis system, and ion chromatograph obtained through four Instructional Laboratory Improvement and one Course, Curriculum, and Laboratory Improvement grants from the National Science Foundation has led to a profound change in the structure of the analytical and general chemistry courses at Bates College. Students in both sets of courses now undertake ambitious, semester-long, small-group projects. The general chemistry course, which fulfills the prerequisite requirement for all upper-level chemistry courses, focuses on the connection between chemistry and the study of the environment. The projects provide students with an opportunity to conduct a real scientific investigation. The projects emphasize problem solving, team work, and communication, while still fostering the development of important laboratory skills. Cooperative learning is also used extensively in the classroom portion of these courses.
Gradient gravitational search: An efficient metaheuristic algorithm for global optimization.

PubMed

Dash, Tirtharaj; Sahu, Prabhat K

2015-05-30

The adaptation of novel techniques developed in the field of computational chemistry to solve the concerned problems for large and flexible molecules is taking the center stage with regard to efficient algorithm, computational cost and accuracy. In this article, the gradient-based gravitational search (GGS) algorithm, using analytical gradients for a fast minimization to the next local minimum has been reported. Its efficiency as metaheuristic approach has also been compared with Gradient Tabu Search and others like: Gravitational Search, Cuckoo Search, and Back Tracking Search algorithms for global optimization. Moreover, the GGS approach has also been applied to computational chemistry problems for finding the minimal value potential energy of two-dimensional and three-dimensional off-lattice protein models. The simulation results reveal the relative stability and physical accuracy of protein models with efficient computational cost. © 2015 Wiley Periodicals, Inc.
Technology for the Organic Chemist: Three Exploratory Modules

ERIC Educational Resources Information Center

Esteb, John J.; McNulty, LuAnne M.; Magers, John; Morgan, Paul; Wilson, Anne M.

2010-01-01

The ability to use computer-based technology is an essential skill set for students majoring in chemistry. This exercise details the introduction of appropriate uses for this technology in the organic chemistry series. The incorporation of chemically appropriate online resources (module 1), scientific databases (module 2), and the use of a…
Connecting Biology and Organic Chemistry Introductory Laboratory Courses through a Collaborative Research Project

ERIC Educational Resources Information Center

Boltax, Ariana L.; Armanious, Stephanie; Kosinski-Collins, Melissa S.; Pontrello, Jason K.

2015-01-01

Modern research often requires collaboration of experts in fields, such as math, chemistry, biology, physics, and computer science to develop unique solutions to common problems. Traditional introductory undergraduate laboratory curricula in the sciences often do not emphasize connections possible between the various disciplines. We designed an…
Report of Ninth Biennial Conference on Chemical Education.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1987

1987-01-01

Provides a summary of the events occurring at the Ninth Biennial Conference on Chemical Education, held in Bozeman, Montana, on July 27-August 2, 1986. Contains brief descriptions of sessions on the role of chemists, demonstrations of laboratory experiences, learning chemistry with computers, teacher training, and chemistry for elementary school…
BASIC Simulation Programs; Volumes I and II. Biology, Earth Science, Chemistry.

ERIC Educational Resources Information Center

Digital Equipment Corp., Maynard, MA.

Computer programs which teach concepts and processes related to biology, earth science, and chemistry are presented. The seven biology problems deal with aspects of genetics, evolution and natural selection, gametogenesis, enzymes, photosynthesis, and the transport of material across a membrane. Four earth science problems concern climates, the…
Foreign-Language Study Still Required for Chemistry.

ERIC Educational Resources Information Center

Chemical and Engineering News, 1983

1983-01-01

Results of a survey of schools granting American Chemical Society-approved degrees indicate that most chemistry departments still require graduate students to understand a foreign language, despite much discussion in the past few years that the requirement might be outdated or that competency with computers is more relevant to chemists. (Author/JN)
COMPUTATIONAL CHEMISTRY METHOD FOR PREDICTING VAPOR PRESSURES AND ACTIVITY COEFFICIENTS OF POLAR ORGANIC OXYGENATES IN PM2.5

EPA Science Inventory

Parameterizations of interactions of polar multifunctional organic oxygenates in PM2.5 must be included in aerosol chemistry models for evaluating control strategies for reducing ambient concentrations of PM2.5 compounds. Vapor pressures and activity coefficients of these compo...
A Statistics Curriculum for the Undergraduate Chemistry Major

ERIC Educational Resources Information Center

Schlotter, Nicholas E.

2013-01-01

Our ability to statistically analyze data has grown significantly with the maturing of computer hardware and software. However, the evolution of our statistics capabilities has taken place without a corresponding evolution in the curriculum for the undergraduate chemistry major. Most faculty understands the need for a statistical educational…

High fidelity chemistry and radiation modeling for oxy -- combustion scenarios

NASA Astrophysics Data System (ADS)

Abdul Sater, Hassan A.

To account for the thermal and chemical effects associated with the high CO2 concentrations in an oxy-combustion atmosphere, several refined gas-phase chemistry and radiative property models have been formulated for laminar to highly turbulent systems. This thesis examines the accuracies of several chemistry and radiative property models employed in computational fluid dynamic (CFD) simulations of laminar to transitional oxy-methane diffusion flames by comparing their predictions against experimental data. Literature review about chemistry and radiation modeling in oxy-combustion atmospheres considered turbulent systems where the predictions are impacted by the interplay and accuracies of the turbulence, radiation and chemistry models. Thus, by considering a laminar system we minimize the impact of turbulence and the uncertainties associated with turbulence models. In the first section of this thesis, an assessment and validation of gray and non-gray formulations of a recently proposed weighted-sum-of-gray gas model in oxy-combustion scenarios was undertaken. Predictions of gas, wall temperatures and flame lengths were in good agreement with experimental measurements. The temperature and flame length predictions were not sensitive to the radiative property model employed. However, there were significant variations between the gray and non-gray model radiant fraction predictions with the variations in general increasing with decrease in Reynolds numbers possibly attributed to shorter flames and steeper temperature gradients. The results of this section confirm that non-gray model predictions of radiative heat fluxes are more accurate than gray model predictions especially at steeper temperature gradients. In the second section, the accuracies of three gas-phase chemistry models were assessed by comparing their predictions against experimental measurements of temperature, species concentrations and flame lengths. The chemistry was modeled employing the Eddy Dissipation Concept (EDC) employing a 41-step detailed chemistry mechanism, the non-adiabatic extension of the equilibrium Probability Density Function (PDF) based mixture-fraction model and a two-step global finite rate chemistry model with modified rate constants proposed to work well in oxy-methane flames. Based on the results from this section, the equilibrium PDF model in conjunction with a high-fidelity non-gray model for the radiative properties of the gas-phase may be deemed as accurate to capture the major gas species concentrations, temperatures and flame lengths in oxy-methane flames. The third section examines the variations in radiative transfer predictions due to the choice of chemistry and gas-phase radiative property models. The radiative properties were estimated employing four weighted-sum-of-gray-gases models (WSGGM) that were formulated employing different spectroscopic/model databases. An average variation of 14 -- 17% in the wall incident radiative fluxes was observed between the EDC and equilibrium mixture fraction chemistry models, due to differences in their temperature predictions within the flame. One-dimensional, line-of-sight radiation calculations showed a 15 -- 25 % reduction in the directional radiative fluxes at lower axial locations as a result of ignoring radiation from CO and CH4. Under the constraints of fixed temperature and species distributions, the flame radiant power estimates and average wall incident radiative fluxes varied by nearly 60% and 11% respectively among the different WSGG models.
Deep learning for computational chemistry

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

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

The rise and fall of artificial neural networks is well documented in the scientific literature of both the fields of 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 “deep” neural networks. Within the last few years, we have seen the transformative impact of deep learning the computer science domain, notably in speech recognition and computer vision, to the extent that the majority of practitioners in those field are now regularly eschewing prior established models in favor of deep learning models. Inmore » this review, we provide an introductory overview into the theory of deep neural networks and their unique properties as compared to 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 QSAR, virtual screening, protein structure modeling, QM calculations, materials synthesis 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 useful tool and may grow into a pivotal role for various challenges in the computational chemistry field.« less
The Diazo Copying Process.

ERIC Educational Resources Information Center

Osterby, Bruce

1989-01-01

Described is an activity which demonstrates an organic-based reprographic method that is used extensively for the duplication of microfilm and engineering drawings. Discussed are the chemistry of the process and how to demonstrate the process for students. (CW)
A Computational Experiment on Single-Walled Carbon Nanotubes

ERIC Educational Resources Information Center

Simpson, Scott; Lonie, David C.; Chen, Jiechen; Zurek, Eva

2013-01-01

A computational experiment that investigates single-walled carbon nanotubes (SWNTs) has been developed and employed in an upper-level undergraduate physical chemistry laboratory course. Computations were carried out to determine the electronic structure, radial breathing modes, and the influence of the nanotube's diameter on the…
OrChem - An open source chemistry search engine for Oracle®

PubMed Central

2009-01-01

Background Registration, indexing and searching of chemical structures in relational databases is one of the core areas of cheminformatics. However, little detail has been published on the inner workings of search engines and their development has been mostly closed-source. We decided to develop an open source chemistry extension for Oracle, the de facto database platform in the commercial world. Results Here we present OrChem, an extension for the Oracle 11G database that adds registration and indexing of chemical structures to support fast substructure and similarity searching. The cheminformatics functionality is provided by the Chemistry Development Kit. OrChem provides similarity searching with response times in the order of seconds for databases with millions of compounds, depending on a given similarity cut-off. For substructure searching, it can make use of multiple processor cores on today's powerful database servers to provide fast response times in equally large data sets. Availability OrChem is free software and can be redistributed and/or modified under the terms of the GNU Lesser General Public License as published by the Free Software Foundation. All software is available via http://orchem.sourceforge.net. PMID:20298521
Interplay between theory and experiment: computational organometallic and transition metal chemistry.

PubMed

Lin, Zhenyang

2010-05-18

Computational and theoretical chemistry provide fundamental insights into the structures, properties, and reactivities of molecules. As a result, theoretical calculations have become indispensable in various fields of chemical research and development. In this Account, we present our research in the area of computational transition metal chemistry, using examples to illustrate how theory impacts our understanding of experimental results and how close collaboration between theoreticians and experimental chemists can be mutually beneficial. We begin by examining the use of computational chemistry to elucidate the details of some unusual chemical bonds. We consider the three-center, two-electron bonding in titanocene sigma-borane complexes and the five-center, four-electron bonding in a rhodium-bismuth complex. The bonding in metallabenzene complexes is also examined. In each case, theoretical calculations provide particular insight into the electronic structure of the chemical bonds. We then give an example of how theoretical calculations aided the structural determination of a kappa(2)-N,N chelate ruthenium complex formed upon heating an intermediate benzonitrile-coordinated complex. An initial X-ray diffraction structure proposed on the basis of a reasonable mechanism appeared to fit well, with an apparently acceptable R value of 0.0478. But when DFT calculations were applied, the optimized geometry differed significantly from the experimental data. By combining experimental and theoretical outlooks, we posited a new structure. Remarkably, a re-refining of the X-ray diffraction data based on the new structure resulted in a slightly lower R value of 0.0453. We further examine the use of computational chemistry in providing new insight into C-H bond activation mechanisms and in understanding the reactivity properties of nucleophilic boryl ligands, addressing experimental difficulties with calculations and vice versa. Finally, we consider the impact of theoretical insights in three very specific experimental studies of chemical reactions, illustrating how theoretical results prompt further experimental studies: (i) diboration of aldehydes catalyzed by copper(I) boryl complexes, (ii) ruthenium-catalyzed C-H amination of arylazides, and (iii) zinc reduction of a vinylcarbyne complex. The concepts and examples presented here are intended for nonspecialists, particularly experimentalists. Together, they illustrate some of the achievements that are possible with a fruitful union of experiment and theory.
Mono- and binuclear non-heme iron chemistry from a theoretical perspective.

PubMed

Rokob, Tibor András; Chalupský, Jakub; Bím, Daniel; Andrikopoulos, Prokopis C; Srnec, Martin; Rulíšek, Lubomír

2016-09-01

In this minireview, we provide an account of the current state-of-the-art developments in the area of mono- and binuclear non-heme enzymes (NHFe and NHFe2) and the smaller NHFe(2) synthetic models, mostly from a theoretical and computational perspective. The sheer complexity, and at the same time the beauty, of the NHFe(2) world represents a challenge for experimental as well as theoretical methods. We emphasize that the concerted progress on both theoretical and experimental side is a conditio sine qua non for future understanding, exploration and utilization of the NHFe(2) systems. After briefly discussing the current challenges and advances in the computational methodology, we review the recent spectroscopic and computational studies of NHFe(2) enzymatic and inorganic systems and highlight the correlations between various experimental data (spectroscopic, kinetic, thermodynamic, electrochemical) and computations. Throughout, we attempt to keep in mind the most fascinating and attractive phenomenon in the NHFe(2) chemistry, which is the fact that despite the strong oxidative power of many reactive intermediates, the NHFe(2) enzymes perform catalysis with high selectivity. We conclude with our personal viewpoint and hope that further developments in quantum chemistry and especially in the field of multireference wave function methods are needed to have a solid theoretical basis for the NHFe(2) studies, mostly by providing benchmarking and calibration of the computationally efficient and easy-to-use DFT methods.
Ignition in convective-diffusive systems

NASA Astrophysics Data System (ADS)

Fotache, Catalin Grig

The main goal of this work is understanding the controlling mechanisms and responses of forced ignition in an environment where chemistry and transport phenomena are intimately coupled. To analyze systematically this interaction the well-characterized counterflow configuration is selected whereupon a cold fuel jet impinges on a heated air jet, and ignites as the air temperature is raised gradually. In this configuration the ignition response is studied experimentally and numerically with extensive variations of the fuel dilution, flow strain rate, and ambient pressure, for hydrogen and Csb1{-}Csb4 paraffins. Experimentally, the temperatures are measured by thermocouple and Raman spectroscopy, while flow strain rates are determined through laser Doppler velocimetry. The experimental envelope comprises pressures of 0.1-8.0 atm, fuel concentrations from 0 to 100%, and strain rates between 50 and 700 ssp{-1}. Computations are performed using various detailed kinetic and transport models, whose adequacy is assessed by comparison with the experimental results. Through computational simulations, the controlling ignition mechanisms are isolated and analyzed. Simplified kinetic models are derived and evaluated, by using sensitivity/flux analyses and the Computational Singular Perturbation (CSP) method. The investigation demonstrates that the coupling chemistry-transport can produce unexpected responses, even for the arguably simplest Hsb2-air kinetic system. Here, up to three stable steady-states are identified experimentally for identical boundary conditions, corresponding to the distinct regimes of frozen flow, mild oxidation, and flaming combustion, respectively. These states can be accessed in a dual-staged ignition sequence, with radical runaway followed by thermokinetic ignition. The pattern, however, depends on the imposed parameters. Specifically, three ignition limits are found when pressure is varied; the first two are characterized by radical runaway only, whereas the third is thermokinetic in character, and may involve dual-staged ignition. The similarity with homogeneous pressure-temperature explosion limits is attributed to the dominance of similar chemistry. When this involves fast kinetics only the transport effects are minimal, such as occurs within the second limit. Conversely, the other two limits are transport-sensitive because of the relatively slower dominant chemistry. The homogeneous-heterogeneous analogy persists when studying the hydrocarbons. For example, increasing pressure uniformly facilitates ignition in both systems. The transport of heat and chemical species out of the reaction zone, however, requires higher temperatures for nonpremixed ignition. Furthermore, nonpremixed ignition is affected by preferential diffusion of light species such as Hsb2. As a result, the addition of relatively small amounts of hydrogen to the fuel jet dramatically reduces the ignition temperature for low ignitability fuels, such as methane. Finally, the presence of diffusive-convective losses results in a selection of the most efficient chemical branching modes. For hydrocarbons, this selection typically implies the dominance of high temperature kinetics, although the Csb4 alkanes show possible transition to a low-to-intermediate temperature branching mode in the limit of elevated pressures. Further research is suggested in this area, as well as in other related directions.
Computer-Aided Drug Discovery: Molecular Docking of Diminazene Ligands to DNA Minor Groove

ERIC Educational Resources Information Center

Kholod, Yana; Hoag, Erin; Muratore, Katlynn; Kosenkov, Dmytro

2018-01-01

The reported project-based laboratory unit introduces upper-division undergraduate students to the basics of computer-aided drug discovery as a part of a computational chemistry laboratory course. The students learn to perform model binding of organic molecules (ligands) to the DNA minor groove with computer-aided drug discovery (CADD) tools. The…
Artificial Intelligence Support for Computational Chemistry

NASA Astrophysics Data System (ADS)

Duch, Wlodzislaw

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

NASA Astrophysics Data System (ADS)

Kang, Congying

2012-04-01

Traditionally, college students always use flash cards as a tool to remember massive knowledge, such as nomenclature, structures, and reactions in chemistry. Educational and information technology have enabled flashcards viewed on computers, like Slides and PowerPoint, works as tunnels of drilling and feedback for the learners. The current generation of students is more capable of information technology and mobile computing devices. For example, they use their Mobile phones much more intensively everyday day. Trends of using Mobile phone as an educational tool is analyzed and a educational technology initiative is proposed, which use Mobile phone flash cards applications to help students learn biology and chemistry. Experiments show that users responded positively to these mobile flash cards.
48 CFR 6302.6 - Computation and extension of time limits (Rule 6).

Code of Federal Regulations, 2010 CFR

2010-10-01

... of time limits (Rule 6). 6302.6 Section 6302.6 Federal Acquisition Regulations System DEPARTMENT OF TRANSPORTATION BOARD OF CONTRACT APPEALS RULES OF PROCEDURE 6302.6 Computation and extension of time limits (Rule 6). (a) Computation. Except as otherwise provided by law, in computing any period of time prescribed...
Computer Series, 75: Bits and Pieces, 30.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1986-01-01

Identifies six computer-oriented approaches to teaching concepts in chemistry. Describes courseware and equipment involved in various experiments dealing with such topics as polymer configurations, stepper motors, conductometric titration, kinetic spectrophotometry, and overlap integrals. (TW)
Biomarkers in Computational Toxicology

EPA Science Inventory

Biomarkers are a means to evaluate chemical exposure and/or the subsequent impacts on toxicity pathways that lead to adverse health outcomes. Computational toxicology can integrate biomarker data with knowledge of exposure, chemistry, biology, pharmacokinetics, toxicology, and e...
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.
Recent advances in computational actinoid chemistry.

PubMed

Wang, Dongqi; van Gunsteren, Wilfred F; Chai, Zhifang

2012-09-07

We briefly review advances in computational actinoid (An) chemistry during the past ten years in regard to two issues: the geometrical and electronic structures, and reactions. The former addresses the An-O, An-C, and M-An (M is a metal atom including An) bonds in the actinoid molecular systems, including actinoid oxo and oxide species, actinoid-carbenoid, dinuclear and diatomic systems, and the latter the hydration and ligand exchange, the disproportionation, the oxidation, the reduction of uranyl, hydroamination, and the photolysis of uranium azide. Concerning their relevance to the electronic structures and reactions of actinoids and their importance in the development of an advanced nuclear fuel cycle, we also mentioned the work on actinoid carbides and nitrides, which have been proposed to be candidates of the next generation of nuclear fuel, and the oxidation of PuO(x), which is important to understand the speciation of actinoids in the environment, followed by a brief discussion on the urgent need for a heavier involvement of computational actinoid chemistry in developing advanced reprocessing protocols of spent nuclear fuel. The paper is concluded with an outlook.
Extraordinarily Adaptive Properties of the Genetically Encoded Amino Acids

PubMed Central

Ilardo, Melissa; Meringer, Markus; Freeland, Stephen; Rasulev, Bakhtiyor; Cleaves II, H. James

2015-01-01

Using novel advances in computational chemistry, we demonstrate that the set of 20 genetically encoded amino acids, used nearly universally to construct all coded terrestrial proteins, has been highly influenced by natural selection. We defined an adaptive set of amino acids as one whose members thoroughly cover relevant physico-chemical properties, or “chemistry space.” Using this metric, we compared the encoded amino acid alphabet to random sets of amino acids. These random sets were drawn from a computationally generated compound library containing 1913 alternative amino acids that lie within the molecular weight range of the encoded amino acids. Sets that cover chemistry space better than the genetically encoded alphabet are extremely rare and energetically costly. Further analysis of more adaptive sets reveals common features and anomalies, and we explore their implications for synthetic biology. We present these computations as evidence that the set of 20 amino acids found within the standard genetic code is the result of considerable natural selection. The amino acids used for constructing coded proteins may represent a largely global optimum, such that any aqueous biochemistry would use a very similar set. PMID:25802223
Computer-Based Self-Instructional Modules. Final Technical Report.

ERIC Educational Resources Information Center

Weinstock, Harold

Reported is a project involving seven chemists, six mathematicians, and six physicists in the production of computer-based, self-study modules for use in introductory college courses in chemistry, physics, and mathematics. These modules were designed to be used by students and instructors with little or no computer backgrounds, in institutions…
New Pedagogies on Teaching Science with Computer Simulations

ERIC Educational Resources Information Center

Khan, Samia

2011-01-01

Teaching science with computer simulations is a complex undertaking. This case study examines how an experienced science teacher taught chemistry using computer simulations and the impact of his teaching on his students. Classroom observations over 3 semesters, teacher interviews, and student surveys were collected. The data was analyzed for (1)…
Delivering The Benefits of Chemical-Biological Integration in Computational Toxicology at the EPA (ACS Fall meeting)

EPA Science Inventory

Abstract: Researchers at the EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The intent...

Computer Series, 102: Bits and Pieces, 40.

ERIC Educational Resources Information Center

Birk, James P., Ed.

1989-01-01

Discussed are seven computer programs: (1) a computer graphics experiment for organic chemistry laboratory; (2) a gel filtration simulation; (3) judging spelling correctness; (4) interfacing the TLC548 ADC; (5) a digitizing circuit for the Apple II game port; (6) a chemical information base; and (7) an IBM PC article database. (MVL)
New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA

EPA Science Inventory

Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this researc...
Chemistry Modeling for Aerothermodynamics and TPS

NASA Technical Reports Server (NTRS)

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

2005-01-01

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

PubMed Central

Baker, Angela K.; Sauvage, Carina; Thorenz, Ute R.; van Velthoven, Peter; Oram, David E.; Zahn, Andreas; Brenninkmeijer, Carl A. M.; Williams, Jonathan

2016-01-01

The chlorine radical is a potent atmospheric oxidant, capable of perturbing tropospheric oxidative cycles normally controlled by the hydroxyl radical. Significantly faster reaction rates allow chlorine radicals to expedite oxidation of hydrocarbons, including methane, and in polluted environments, to enhance ozone production. Here we present evidence, from the CARIBIC airborne dataset, for extensive chlorine radical chemistry associated with Asian pollution outflow, from airborne observations made over the Malaysian Peninsula in winter. This region is known for persistent convection that regularly delivers surface air to higher altitudes and serves as a major transport pathway into the stratosphere. Oxidant ratios inferred from hydrocarbon relationships show that chlorine radicals were regionally more important than hydroxyl radicals for alkane oxidation and were also important for methane and alkene oxidation (>10%). Our observations reveal pollution-related chlorine chemistry that is both widespread and recurrent, and has implications for tropospheric oxidizing capacity, stratospheric composition and ozone chemistry. PMID:27845366
Viscosity of Common Seed and Vegetable Oils

NASA Astrophysics Data System (ADS)

Wes Fountain, C.; Jennings, Jeanne; McKie, Cheryl K.; Oakman, Patrice; Fetterolf, Monty L.

1997-02-01

Viscosity experiments using Ostwald-type gravity flow viscometers are not new to the physical chemistry laboratory. Several physical chemistry laboratory texts (1 - 3) contain at least one experiment studying polymer solutions or other well-defined systems. Several recently published articles (4 - 8) indicated the continued interest in using viscosity measurements in the teaching lab to illustrate molecular interpretation of bulk phenomena. Most of these discussions and teaching experiments are designed around an extensive theory of viscous flow and models of molecular shape that allow a full data interpretation to be attempted. This approach to viscosity experiments may not be appropriate for all teaching situations (e.g., high schools, general chemistry labs, and nonmajor physical chemistry labs). A viscosity experiment is presented here that is designed around common seed and vegetable oils. With the importance of viscosity to foodstuffs (9) and the importance of fatty acids to nutrition (10), an experiment using these common, recognizable oils has broad appeal.
Dynamic adaptive chemistry for turbulent flame simulations

NASA Astrophysics Data System (ADS)

Yang, Hongtao; Ren, Zhuyin; Lu, Tianfeng; Goldin, Graham M.

2013-02-01

The use of large chemical mechanisms in flame simulations is computationally expensive due to the large number of chemical species and the wide range of chemical time scales involved. This study investigates the use of dynamic adaptive chemistry (DAC) for efficient chemistry calculations in turbulent flame simulations. DAC is achieved through the directed relation graph (DRG) method, which is invoked for each computational fluid dynamics cell/particle to obtain a small skeletal mechanism that is valid for the local thermochemical condition. Consequently, during reaction fractional steps, one needs to solve a smaller set of ordinary differential equations governing chemical kinetics. Test calculations are performed in a partially-stirred reactor (PaSR) involving both methane/air premixed and non-premixed combustion with chemistry described by the 53-species GRI-Mech 3.0 mechanism and the 129-species USC-Mech II mechanism augmented with recently updated NO x pathways, respectively. Results show that, in the DAC approach, the DRG reduction threshold effectively controls the incurred errors in the predicted temperature and species concentrations. The computational saving achieved by DAC increases with the size of chemical kinetic mechanisms. For the PaSR simulations, DAC achieves a speedup factor of up to three for GRI-Mech 3.0 and up to six for USC-Mech II in simulation time, while at the same time maintaining good accuracy in temperature and species concentration predictions.
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
High-Fidelity, Computational Modeling of Non-Equilibrium Discharges for Combustion Applications

DTIC Science & Technology

2013-10-01

gradient reconstruction)  4th order RK time integration  Domain decomposition parallel enabled Plasma chemistry mechanism 22  Methane-air... plasma chemistry mechanism  Species and pathways relevant to plasma time scale (~10’s ns)  26 Species : E, O, N2 , O2 , H , N2+ , O2+ , N4+ , O4...Photoionization (3-term Helmholtz equation model) 0.0067 0.0447 0.0346 0.1121 0.3059 0.5994 Plasma chemistry mechanism used in studies 81
The EPA CompTox Chemistry Dashboard - an online resource ...

EPA Pesticide Factsheets

The U.S. Environmental Protection Agency (EPA) Computational Toxicology Program integrates advances in biology, chemistry, and computer science to help prioritize chemicals for further research based on potential human health risks. This work involves computational and data driven approaches that integrate chemistry, exposure and biological data. As an outcome of these efforts the National Center for Computational Toxicology (NCCT) has measured, assembled and delivered an enormous quantity and diversity of data for the environmental sciences including high-throughput in vitro screening data, in vivo and functional use data, exposure models and chemical databases with associated properties. A series of software applications and databases have been produced over the past decade to deliver these data. Recent work has focused on the development of a new architecture that assembles the resources into a single platform. With a focus on delivering access to Open Data streams, web service integration accessibility and a user-friendly web application the CompTox Dashboard provides access to data associated with ~720,000 chemical substances. These data include research data in the form of bioassay screening data associated with the ToxCast program, experimental and predicted physicochemical properties, product and functional use information and related data of value to environmental scientists. This presentation will provide an overview of the CompTox Dashboard and its va
Computational Materials Science and Chemistry: Accelerating Discovery and Innovation through Simulation-Based Engineering and Science

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

Crabtree, George; Glotzer, Sharon; McCurdy, Bill

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. Newmore » 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 enabled the development of computer simulations and models of unprecedented fidelity. We are at the threshold of a new era where the integrated synthesis, characterization, and modeling of complex materials and chemical processes will transform our ability to understand and design new materials and chemistries with predictive power. In turn, this predictive capability will transform technological innovation by accelerating the development and deployment of new materials and processes in products and manufacturing. Harnessing the potential of computational science and engineering for the discovery and development of materials and chemical processes is essential to maintaining leadership in these foundational fields that underpin energy technologies and industrial competitiveness. Capitalizing on the opportunities presented by simulation-based engineering and science in materials and chemistry will require an integration of experimental capabilities with theoretical and computational modeling; the development of a robust and sustainable infrastructure to support the development and deployment of advanced computational models; and the assembly of a community of scientists and engineers to implement this integration and infrastructure. This community must extend to industry, where incorporating predictive materials science and chemistry into design tools can accelerate the product development cycle and drive economic competitiveness. The confluence of new theories, new materials synthesis capabilities, and new computer platforms has created an unprecedented opportunity to implement a "materials-by-design" paradigm with wide-ranging benefits in technological innovation and scientific discovery. The Workshop on Computational Materials Science and Chemistry for Innovation was convened in Bethesda, Maryland, on July 26-27, 2010. Sponsored by the Department of Energy (DOE) Offices of Advanced Scientific Computing Research and Basic Energy Sciences, the workshop brought together 160 experts in materials science, chemistry, and computational science representing more than 65 universities, laboratories, and industries, and four agencies. The workshop examined seven foundational challenge areas in materials science and chemistry: materials for extreme conditions, self-assembly, light harvesting, chemical reactions, designer fluids, thin films and interfaces, and electronic structure. Each of these challenge areas is critical to the development of advanced energy systems, and each can be accelerated by the integrated application of predictive capability with theory and experiment. The workshop concluded that emerging capabilities in predictive modeling and simulation have the potential to revolutionize the development of new materials and chemical processes. Coupled with world-leading materials characterization and nanoscale science facilities, this predictive capability provides the foundation for an innovation ecosystem that can accelerate the discovery, development, and deployment of new technologies, including advanced energy systems. Delivering on the promise of this innovation ecosystem requires the following: Integration of synthesis, processing, characterization, theory, and simulation and modeling. Many of the newly established Energy Frontier Research Centers and Energy Hubs are exploiting this integration. Achieving/strengthening predictive capability in foundational challenge areas. Predictive capability in the seven foundational challenge areas described in this report is critical to the development of advanced energy technologies. Developing validated computational approaches that span vast differences in time and length scales. This fundamental computational challenge crosscuts all of the foundational challenge areas. Similarly challenging is coupling of analytical data from multiple instruments and techniques that are required to link these length and time scales. Experimental validation and quantification of uncertainty in simulation and modeling. Uncertainty quantification becomes increasingly challenging as simulations become more complex. Robust and sustainable computational infrastructure, including software and applications. For modeling and simulation, software equals infrastructure. To validate the computational tools, software is critical infrastructure that effectively translates huge arrays of experimental data into useful scientific understanding. An integrated approach for managing this infrastructure is essential. Efficient transfer and incorporation of simulation-based engineering and science in industry. Strategies for bridging the gap between research and industrial applications and for widespread industry adoption of integrated computational materials engineering are needed.« less
The Inversion Potential of Ammonia: An Intrinsic Reaction Coordinate Calculation for Student Investigation

ERIC Educational Resources Information Center

Halpern, Arthur M.; Ramachandran, B. R.; Glendening, Eric D.

2007-01-01

A report is presented to describe how students can be empowered to construct the full, double minimum inversion potential for ammonia by performing intrinsic reaction coordinate calculations. This work can be associated with the third year physical chemistry lecture laboratory or an upper level course in computational chemistry.
First Encounters of the Close Kind: The Formation Process of Airline Flight Crews

DTIC Science & Technology

1987-01-01

process and aircrew performance, Foushee notes an interesting etymological parallel: "Webster’s New Collegiate Dictionary (1961) defines cockpit as ’a...here combines applications from the physical science of chemistry and the modern science of computers. In chemistry , a shell is a space occupied by
Learning Nuclear Chemistry through Practice: A High School Student Project Using PET in a Clinical Setting

ERIC Educational Resources Information Center

Liguori, Lucia; Adamsen, Tom Christian Holm

2013-01-01

Practical experience is vital for promoting interest in science. Several aspects of chemistry are rarely taught in the secondary school curriculum, especially nuclear and radiochemistry. Therefore, we introduced radiochemistry to secondary school students through positron emission tomography (PET) associated with computer tomography (CT). PET-CT…
Visualization and Interactivity in the Teaching of Chemistry to Science and Non-Science Students

ERIC Educational Resources Information Center

Venkataraman, Bhawani

2009-01-01

A series of interactive, instructional units have been developed that integrate computational molecular modelling and visualization to teach fundamental chemistry concepts and the relationship between the molecular and macro-scales. The units span the scale from atoms, small molecules to macromolecular systems, and introduce many of the concepts…
So Why Use Multimedia, the Internet, and Lotus Notes?

ERIC Educational Resources Information Center

Byers, Donnie N.

As part of an effort to begin offering a general chemistry course over the Internet, a project was undertaken at Kansas's Johnson County Community College to determine the possibilities of using a computer to incorporate the tools used in teaching organic chemistry. Using an interactive software package, original lectures were developed, with…
Real-time prediction of Physicochemical and Toxicological Endpoints Using the Web-based CompTox Chemistry Dashboard (ACS Fall meeting) 10 of 12

EPA Science Inventory

The EPA CompTox Chemistry Dashboard developed by the National Center for Computational Toxicology (NCCT) provides access to data for ~750,000 chemical substances. The data include experimental and predicted data for physicochemical, environmental fate and transport and toxicologi...
"SimChemistry" as an Active Learning Tool in Chemical Education

ERIC Educational Resources Information Center

Bolton, Kim; Saalman, Elisabeth; Christie, Michael; Ingerman, Ake; Linder, Cedric

2008-01-01

The publicly available free computer program, "SimChemistry," was used as an active learning tool in the chemical engineering curriculum at the University College of Boras, Sweden. The activity involved students writing their own simulation programs on topics in the area of molecular structure and interactions. Evaluation of the learning…
Online Grading of Calculations in General Chemistry Laboratory Write-Ups

ERIC Educational Resources Information Center

Silva, Alexsandra; Gonzales, Robert; Brennan, Daniel P.

2010-01-01

In the past, there were frequently complaints about the grading of laboratory reports in our laboratory chemistry courses. This article discussed the implementation of an online submission of laboratory acquired data using LON-CAPA (The Learning Online Network with Computer-Assisted Personalized Approach), which is an open source management and…
The use of ARL trajectories for the evaluation of precipitation chemistry data

Treesearch

John M. Miller; James N. Galloway; Gene E. Likens

1976-01-01

One of the major problems in interpreting precipitation chemistry data is determining the possible source areas of the materials found in the precipitation. To investigate this problem, the trajectory program developed at Air Resources Laboratories (NOAA) was used to compute five-day backward air trajectories from Ithaca, New York.

Moving an In-Class Module Online: A Case Study for Chemistry

ERIC Educational Resources Information Center

Seery, Michael K.

2012-01-01

This article summarises the author's experiences in running a module "Computers for Chemistry" entirely online for the past four years. The module, previously taught in a face-to-face environment, was reconfigured for teaching in an online environment. The rationale for moving online along with the design, implementation and evaluation of the…
NSSEFF COMPUTATIONAL AND THEORETICAL DESIGN OF PHOTO AND MECHANORESPONSIVE MOLECULAR DEVICES

DTIC Science & Technology

2016-11-10

R. McGibbon, F. Liu, V.S. Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014...Pande and T.J. Martinez, "Discovering Chemistry with an Ab Initio Nanoreactor," Nature Chem. 6, 1044 (2014). New discoveries, inventions, or patent
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

MODELING OF C-S-H Material chemistry level modeling following the principles and techniques commonly grouped under Computational Material Science is...Henmi, C. and Kusachi, I. Monoclinic tobermorite from fuka, bitchu-cho, Okoyama Perfecture. Japan J. Min. Petr. Econ . Geol. (1989)84:374-379. [22...31] Liu, Y. et al. First principles study of the stability and mechanical properties of MC (M=Ti, V, Zr, Nb, Hf and Ta) compounds. Journal of Alloys and Compounds. (2014) 582:500-504. 10
Modelling of Molecular Structures and Properties. Proceedings of the International Meeting of Physical Chemistry on Modeling of Molecular Structures and Properties in Physical Chemistry and Biophysics Organized by the Division de Chimie Physique of the Societe Francaise de Chimie Held in Nancy, France on 11-15 September 1989

DTIC Science & Technology

1990-01-01

expert systems, "intelligent" computer-aided instruction , symbolic learning . These aspects will be discussed, focusing on the specific problems the...VLSI chips) according to preliminary specifications. Finally ES are also used in computer-aided instruction (CAI) due to their ability of... instructions to process controllers), academic teaching (for mathematics , physics, foreign language, etc.). Domains of application The different
ESTIMATION OF PHYSIOCHEMICAL PROPERTIES OF ORGANIC COMPOUNDS BY SPARC

EPA Science Inventory

The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...
EPA CHEMICAL PRIORITIZATION COMMUNITY OF PRACTICE.

EPA Science Inventory

IN 2005 THE NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY (NCCT) ORGANIZED EPA CHEMICAL PRIORITIATION COMMUNITY OF PRACTICE (CPCP) TO PROVIDE A FORUM FOR DISCUSSING THE UTILITY OF COMPUTATIONAL CHEMISTRY, HIGH-THROUGHPUT SCREENIG (HTS) AND VARIOUS TOXICOGENOMIC TECHNOLOGIES FOR CH...
Molecular Modeling of Environmentally Important Processes: Reduction Potentials

ERIC Educational Resources Information Center

Lewis, Anne; Bumpus, John A.; Truhlar, Donald G.; Cramer, Christopher J.

2004-01-01

The increasing use of computational quantum chemistry in the modeling of environmentally important processes is described. The employment of computational quantum mechanics for the prediction of oxidation-reduction potential for solutes in an aqueous medium is discussed.
Magnetic polyoxometalates: from molecular magnetism to molecular spintronics and quantum computing.

PubMed

Clemente-Juan, Juan M; Coronado, Eugenio; Gaita-Ariño, Alejandro

2012-11-21

In this review we discuss the relevance of polyoxometalate (POM) chemistry to provide model objects in molecular magnetism. We present several potential applications in nanomagnetism, in particular, in molecular spintronics and quantum computing.
Computer Series, 13.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1981-01-01

Provides short descriptions of chemists' applications of computers in instruction: an interactive instructional program for Instrumental-Qualitative Organic Analysis; question-and-answer exercises in organic chemistry; computerized organic nomenclature drills; integration of theoretical and descriptive materials; acid-base titration simulation;…
Discovering chemistry with an ab initio nanoreactor

DOE PAGES

Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert; ...

2014-11-02

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
Discovering chemistry with an ab initio nanoreactor

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

Wang, Lee-Ping; Titov, Alexey; McGibbon, Robert

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provides detailed physical insight. While theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor – a highly accelerated, first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor we show new pathways for glycine synthesis frommore » primitive compounds proposed to exist on the early Earth, providing new insight into the classic Urey-Miller experiment. Ultimately, these results highlight the emergence of theoretical and computational chemistry as a tool for discovery in addition to its traditional role of interpreting experimental findings.« less
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.
Computing and the social organization of academic work

NASA Astrophysics Data System (ADS)

Shields, Mark A.; Graves, William; Nyce, James M.

1992-12-01

This article discusses the academic computing movement during the 1980s. We focus on the Faculty Workstations Project at Brown University, where major computing initiatives were undertaken during the 1980s. Six departments are compared: chemistry, cognitive and linguistic sciences, geology, music, neural science, and sociology. We discuss the theoretical implications of our study for conceptualizing the relationship of computing to academic work.
Enhancing the Scope of the Diels-Alder Reaction through Isonitrile Chemistry: Emergence of a New Class of Acyl-Activated Dienophiles

PubMed Central

Townsend, Steven D.; Wu, Xiangyang; Danishefsky, Samuel J.

2012-01-01

α,β-Unsaturated imides, formylated at the nitrogen atom, comprise a new and valuable family of dienophiles for servicing Diels-Alder reactions. These systems are assembled through extension of recently discovered isonitrile chemistry to the domain of α,β-unsaturated acids. Cycloadditions are facilitated by Et2AlCl, presumably via chelation between the two carbonyl groups of the N-formyl amide. Applications of the isonitrile/Diels-Alder logic to the IMDA reaction, as well as methodologies to modify the N-formyl amide of the resultant cycloaddition product, are described. It is expected that this easily executed chemistry will provide a significant enhancement for application of Diels-Alder reactions to many synthetic targets. PMID:22708980
A transported probability density function/photon Monte Carlo method for high-temperature oxy-natural gas combustion with spectral gas and wall radiation

NASA Astrophysics Data System (ADS)

Zhao, X. Y.; Haworth, D. C.; Ren, T.; Modest, M. F.

2013-04-01

A computational fluid dynamics model for high-temperature oxy-natural gas combustion is developed and exercised. The model features detailed gas-phase chemistry and radiation treatments (a photon Monte Carlo method with line-by-line spectral resolution for gas and wall radiation - PMC/LBL) and a transported probability density function (PDF) method to account for turbulent fluctuations in composition and temperature. The model is first validated for a 0.8 MW oxy-natural gas furnace, and the level of agreement between model and experiment is found to be at least as good as any that has been published earlier. Next, simulations are performed with systematic model variations to provide insight into the roles of individual physical processes and their interplay in high-temperature oxy-fuel combustion. This includes variations in the chemical mechanism and the radiation model, and comparisons of results obtained with versus without the PDF method to isolate and quantify the effects of turbulence-chemistry interactions and turbulence-radiation interactions. In this combustion environment, it is found to be important to account for the interconversion of CO and CO2, and radiation plays a dominant role. The PMC/LBL model allows the effects of molecular gas radiation and wall radiation to be clearly separated and quantified. Radiation and chemistry are tightly coupled through the temperature, and correct temperature prediction is required for correct prediction of the CO/CO2 ratio. Turbulence-chemistry interactions influence the computed flame structure and mean CO levels. Strong local effects of turbulence-radiation interactions are found in the flame, but the net influence of TRI on computed mean temperature and species profiles is small. The ultimate goal of this research is to simulate high-temperature oxy-coal combustion, where accurate treatments of chemistry, radiation and turbulence-chemistry-particle-radiation interactions will be even more important.
Computational neural networks in chemistry: Model free mapping devices for predicting chemical reactivity from molecular structure

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

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 ofmore » 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.« less
Quality improvement on chemistry practicum courses through implementation of 5E learning cycle

NASA Astrophysics Data System (ADS)

Merdekawati, Krisna

2017-03-01

Two of bachelor of chemical education's competences are having practical skills and mastering chemistry material. Practicum courses are organized to support the competency achievement. Based on observation and evaluation, many problems were found in the implementation of practicum courses. Preliminary study indicated that 5E Learning Cycle can be used as an alternative solution in order to improve the quality of chemistry practicum course. The 5E Learning Cycle can provide positive influence on the achievement of the competence, laboratory skills, and students' understanding. The aim of the research was to describe the feasibility of implementation of 5E Learning Cycle on chemistry practicum courses. The research was based on phenomenology method in qualitative approach. The participants of the research were 5 person of chemistry laboratory manager (lecturers at chemistry and chemistry education department). They concluded that the 5E Learning Cycle could be implemented to improve the quality of the chemistry practicum courses. Practicum guides and assistant competences were organized to support the implementation of 5E Learning Cycle. It needed training for assistants to understand and implement in the stages of 5E Learning Cycle. Preparation of practical guidelines referred to the stages of 5E Learning Cycle, started with the introduction of contextual and applicable materials, then followed with work procedures that accommodate the stage of engagement, exploration, explanation, extension, and evaluation
The calculation of aquifer chemistry in hot-water geothermal systems

USGS Publications Warehouse

Truesdell, Alfred H.; Singers, Wendy

1974-01-01

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

NASA Astrophysics Data System (ADS)

Costa, Paulo J.

2017-10-01

The halogen bond, corresponding to an attractive interaction between an electrophilic region in a halogen (X) and a nucleophile (B) yielding a R-X⋯B contact, found applications in many fields such as supramolecular chemistry, crystal engineering, medicinal chemistry, and chemical biology. Their large range of applications also led to an increased interest in their study using computational methods aiming not only at understanding the phenomena at a fundamental level, but also to help in the interpretation of results and guide the experimental work. Herein, a succinct overview of the recent theoretical and experimental developments is given starting by discussing the nature of the halogen bond and the latest theoretical insights on this topic. Then, the effects of the surrounding environment on halogen bonds are presented followed by a presentation of the available method benchmarks. Finally, recent experimental applications where the contribution of computational chemistry was fundamental are discussed, thus highlighting the synergy between the lab and modeling techniques.
Using Rasch Measurement to Develop a Computer Modeling-Based Instrument to Assess Students' Conceptual Understanding of Matter

ERIC Educational Resources Information Center

Wei, Silin; Liu, Xiufeng; Wang, Zuhao; Wang, Xingqiao

2012-01-01

Research suggests that difficulty in making connections among three levels of chemical representations--macroscopic, submicroscopic, and symbolic--is a primary reason for student alternative conceptions of chemistry concepts, and computer modeling is promising to help students make the connections. However, no computer modeling-based assessment…

How Science Students Can Learn about Unobservable Phenomena Using Computer-Based Analogies

ERIC Educational Resources Information Center

Trey, L.; Khan, S.

2008-01-01

A novel instructional computer simulation that incorporates a dynamic analogy to represent Le Chatelier's Principle was designed to investigate the contribution of this feature to students' understanding. Two groups of 12th grade Chemistry students (n=15) interacted with the computer simulation during the study. Both groups did the same…
Computation of Chemical Shifts for Paramagnetic Molecules: A Laboratory Experiment for the Undergraduate Curriculum

ERIC Educational Resources Information Center

Pritchard, Benjamin P.; Simpson, Scott; Zurek, Eva; Autschbach, Jochen

2014-01-01

A computational experiment investigating the [superscript 1]H and [superscript 13]C nuclear magnetic resonance (NMR) chemical shifts of molecules with unpaired electrons has been developed and implemented. This experiment is appropriate for an upper-level undergraduate laboratory course in computational, physical, or inorganic chemistry. The…
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…
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...
The Benefits of Making Data from the EPA National Center for Computational Toxicology available for reuse (ACS Fall meeting 3 of 12)

EPA Science Inventory

Researchers at EPA’s National Center for Computational Toxicology (NCCT) integrate advances in biology, chemistry, exposure and computer science to help prioritize chemicals for further research based on potential human health risks. The goal of this research is to quickly evalua...
Computer Augmented Lectures (CAL): A New Teaching Technique for Chemistry.

ERIC Educational Resources Information Center

Masten, F. A.; And Others

A new technique described as computer augmented lectures (CAL) is being used at the University of Texas at Austin. It involves the integration of on-line, interactive, time sharing computer terminals and theater size video projectors for large screen display. This paper covers the basic concept, pedagogical techniques, experiments conducted,…
Effect of Computer Simulations at the Particulate and Macroscopic Levels on Students' Understanding of the Particulate Nature of Matter

ERIC Educational Resources Information Center

Tang, Hui; Abraham, Michael R.

2016-01-01

Computer-based simulations can help students visualize chemical representations and understand chemistry concepts, but simulations at different levels of representation may vary in effectiveness on student learning. This study investigated the influence of computer activities that simulate chemical reactions at different levels of representation…
Evaluation of a computational model to predict elbow range of motion

PubMed Central

Nishiwaki, Masao; Johnson, James A.; King, Graham J. W.; Athwal, George S.

2014-01-01

Computer models capable of predicting elbow flexion and extension range of motion (ROM) limits would be useful for assisting surgeons in improving the outcomes of surgical treatment of patients with elbow contractures. A simple and robust computer-based model was developed that predicts elbow joint ROM using bone geometries calculated from computed tomography image data. The model assumes a hinge-like flexion-extension axis, and that elbow passive ROM limits can be based on terminal bony impingement. The model was validated against experimental results with a cadaveric specimen, and was able to predict the flexion and extension limits of the intact joint to 0° and 3°, respectively. The model was also able to predict the flexion and extension limits to 1° and 2°, respectively, when simulated osteophytes were inserted into the joint. Future studies based on this approach will be used for the prediction of elbow flexion-extension ROM in patients with primary osteoarthritis to help identify motion-limiting hypertrophic osteophytes, and will eventually permit real-time computer-assisted navigated excisions. PMID:24841799
The Computer Bulletin Board. Modified Gran Plots of Very Weak Acids on a Spreadsheet.

ERIC Educational Resources Information Center

Chau, F. T.; And Others

1990-01-01

Presented are two applications of computer technology to chemistry instruction: the use of a spreadsheet program to analyze acid-base titration curves and the use of database software to catalog stockroom inventories. (CW)
Science Notes.

ERIC Educational Resources Information Center

School Science Review, 1985

1985-01-01

Presents 23 experiments, demonstrations, activities, and computer programs in biology, chemistry, and physics. Topics include lead in petrol, production of organic chemicals, reduction of water, enthalpy, X-ray diffraction model, nuclear magnetic resonance spectroscopy, computer simulation for additive mixing of colors, Archimedes Principle, and…
Computer Series, 32.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1982-01-01

Ten computer programs (available from authors) and a noncomputer calculation of the electron in one-dimensional, one-Bohr box are described, including programs for analytical chemistry, space group generation using Pascal, mass-spectral search system (Applesoft), microcomputer-simulated liquid chromatography, voltammetry/amperometric titrations,…
Reviews.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1988

1988-01-01

Reviews three computer software packages for chemistry education including "Osmosis and Diffusion" and "E.M.E. Titration Lab" for Apple II and "Simplex-V: An Interactive Computer Program for Experimental Optimization" for IBM PC. Summary ratings include ease of use, content, pedagogic value, student reaction, and…
EPAS TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS(S).

EPA Science Inventory

EPAs National Center for Computational Toxicology is developing methods that apply computational chemistry, high-throughput screening (HTS) and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.
ESTIMATION OF PHYSICAL PROPERTIES AND CHEMICAL REACTIVITY PARAMETERS OF ORGANIC COMPOUNDS

EPA Science Inventory

The computer program SPARC (Sparc Performs Automated Reasoning in Chemistry)has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms ...
EnviroLand: A Simple Computer Program for Quantitative Stream Assessment.

ERIC Educational Resources Information Center

Dunnivant, Frank; Danowski, Dan; Timmens-Haroldson, Alice; Newman, Meredith

2002-01-01

Introduces the Enviroland computer program which features lab simulations of theoretical calculations for quantitative analysis and environmental chemistry, and fate and transport models. Uses the program to demonstrate the nature of linear and nonlinear equations. (Author/YDS)
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.
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.
Smart Phones, a Powerful Tool in the Chemistry Classroom

ERIC Educational Resources Information Center

Williams, Antony J.; Pence, Harry E.

2011-01-01

Cell phones, especially "smart phones", seem to have become ubiquitous. Actually, it is misleading to call many of these devices phones, as they are actually a portable and powerful computer that can be very valuable in the chemistry classroom. Currently, there are three major ways in which smart phones can be used for education. Smart phones…
Structure Identification Using High Resolution Mass Spectrometry Data and the EPA’s CompTox Chemistry Dashboard (EAS)

EPA Science Inventory

The iCSS CompTox Dashboard is a publicly accessible dashboard provided by the National Center for Computation Toxicology at the US-EPA. It serves a number of purposes, including providing a chemistry database underpinning many of our public-facing projects (e.g. ToxCast and ExpoC...
Bringing it all together: A Web-based Database for Chemical and Biological Data to Support Environmental Toxicology (ACS Fall meeting 8 of 12)

EPA Science Inventory

The EPA Comptox Chemistry Dashboard is a web-based application providing access to a set of data resources provided by the National Center of Computational Toxicology. Sitting on a foundation of chemistry data for ~750,000 chemical substances the application integrates bioassay s...

Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

ERIC Educational Resources Information Center

Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

2018-01-01

A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…
Study of the Kinetics of an S[subscript N]1 Reaction by Conductivity Measurement

ERIC Educational Resources Information Center

Marzluff, Elaine M.; Crawford, Mary A.; Reynolds, Helen

2011-01-01

Substitution reactions, a central part of organic chemistry, provide a model system in physical chemistry to study reaction rates and mechanisms. Here, the use of inexpensive and readily available commercial conductivity probes coupled with computer data acquisition for the study of the temperature and solvent dependence of the solvolysis of…
What Are They Thinking? Automated Analysis of Student Writing about Acid-Base Chemistry in Introductory Biology

ERIC Educational Resources Information Center

Haudek, Kevin C.; Prevost, Luanna B.; Moscarella, Rosa A.; Merrill, John; Urban-Lurain, Mark

2012-01-01

Students' writing can provide better insight into their thinking than can multiple-choice questions. However, resource constraints often prevent faculty from using writing assessments in large undergraduate science courses. We investigated the use of computer software to analyze student writing and to uncover student ideas about chemistry in an…
Adapting to Student Learning Styles: Engaging Students with Cell Phone Technology in Organic Chemistry Instruction

ERIC Educational Resources Information Center

Pursell, David P.

2009-01-01

Students of organic chemistry traditionally make 3 x 5 in. flash cards to assist learning nomenclature, structures, and reactions. Advances in educational technology have enabled flash cards to be viewed on computers, offering an endless array of drilling and feedback for students. The current generation of students is less inclined to use…
Medicinal Chemistry and Molecular Modeling: An Integration to Teach Drug Structure-Activity Relationship and the Molecular Basis of Drug Action

ERIC Educational Resources Information Center

Carvalho, Ivone; Borges, Aurea D. L.; Bernardes, Lilian S. C.

2005-01-01

The use of computational chemistry and the protein data bank (PDB) to understand and predict the chemical and molecular basis involved in the drug-receptor interactions is discussed. A geometrical and chemical overview of the great structural similarity in the substrate and inhibitor is provided.
A Procedure to Create a Pedagogic Conversational Agent in Secondary Physics and Chemistry Education

ERIC Educational Resources Information Center

Pérez-Marín, Diana; Boza, Antonio

2013-01-01

Pedagogic Conversational Agents are computer applications that can interact with students in natural language. They have been used with satisfactory results on the instruction of several domains. The authors believe that they could also be useful for the instruction of Secondary Physics and Chemistry Education. Therefore, in this paper, the…
Reactions. [Individualized Learning System (ILS) Chemistry Pac No. 5.

ERIC Educational Resources Information Center

Torop, William

This booklet is one of a set of eight designed to be used in a self-paced introductory chemistry course in conjunction with specified textbooks and computer-assisted instruction (CAI) modules. Each topic is introduced with a textbook reading assignment and additional readings are provided in the booklet. Also included are self-tests (and answers),…
Development of an Augmented Reality Game to Teach Abstract Concepts in Food Chemistry

ERIC Educational Resources Information Center

Crandall, Philip G.; Engler, Robert K.; Beck, Dennis E.; Killian, Susan A.; O'Bryan, Corliss A.; Jarvis, Nathan; Clausen, Ed

2015-01-01

One of the most pressing issues for many land grant institutions is the ever increasing cost to build and operate wet chemistry laboratories. A partial solution is to develop computer-based teaching modules that take advantage of animation, web-based or off-campus learning experiences directed at engaging students' creative experiences. We…
18. VIEW OF THE GENERAL CHEMISTRY LAB. THE LABORATORY PROVIDED ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

18. VIEW OF THE GENERAL CHEMISTRY LAB. THE LABORATORY PROVIDED GENERAL ANALYTICAL AND STANDARDS CALIBRATION, AS WELL AS DEVELOPMENT OPERATIONS INCLUDING WASTE TECHNOLOGY DEVELOPMENT AND DEVELOPMENT AND TESTING OF MECHANICAL SYSTEMS FOR WEAPONS SYSTEMS. (4/4/66) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO
Testing and Extending VSEPR with WebMO and MOPAC or GAMESS

ERIC Educational Resources Information Center

McNaught, Ian J.

2011-01-01

VSEPR is a topic that is commonly taught in undergraduate chemistry courses. The readily available Web-based program WebMO, in conjunction with the computational chemistry programs MOPAC and GAMESS, is used to quantitatively test a wide range of predictions of VSEPR. These predictions refer to the point group of the molecule, including the…
Qualitative Assessment of a 3D Simulation Program: Faculty, Students, and Bio-Organic Reaction Animations

ERIC Educational Resources Information Center

Günersel, Adalet B.; Fleming, Steven A.

2013-01-01

Research shows that computer-based simulations and animations are especially helpful in fields such as chemistry where concepts are abstract and cannot be directly observed. Bio-Organic Reaction Animations (BioORA) is a freely available 3D visualization software program developed to help students understand the chemistry of biomolecular events.…
Eppur Si Muove! The 2013 Nobel Prize in Chemistry

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

Smith, Jeremy C.; Roux, Benoit

2013-12-03

The 2013 Nobel Prize in Chemistry has been awarded to Martin Karplus, Michael Levitt, and Arieh Warshel for their work on developing computational methods to study complex chemical systems. Hence, their work has led to mechanistic critical insights into chemical systems both large and small and has enabled progress in a number of different fields, including structural biology.
Carbon. [Individualized Learning System (ILS) Chemistry Pac No. 7.

ERIC Educational Resources Information Center

Torop, William

This booklet is one of a set of eight designed to be used in a self-paced introductory chemistry course in conjunction with specified textbooks and computer-assisted instruction (CAI) modules. Each topic is introduced with a textbook reading assignment and additional readings are provided in the booklet. Also included are self-tests (and answers),…
A Computer Model for Red Blood Cell Chemistry

DTIC Science & Technology

1996-10-01

5012. 13. ABSTRACT (Maximum 200 There is a growing need for interactive computational tools for medical education and research. The most exciting...paradigm for interactive education is simulation. Fluid Mod is a simulation based computational tool developed in the late sixties and early seventies at...to a modern Windows, object oriented interface. This development will provide students with a useful computational tool for learning . More important
Reviews, Software.

ERIC Educational Resources Information Center

Science Teacher, 1988

1988-01-01

Reviews two computer software packages for use in physical science, physics, and chemistry classes. Includes "Physics of Model Rocketry" for Apple II, and "Black Box" for Apple II and IBM compatible computers. "Black Box" is designed to help students understand the concept of indirect evidence. (CW)
Computer Series, 115.

ERIC Educational Resources Information Center

Birk, James P., Ed.

1990-01-01

Reviewed are six computer programs which may be useful in teaching college level chemistry. Topics include dynamic data storage in FORTRAN, "KC?DISCOVERER," pH of acids and bases, calculating percent boundary surfaces for orbitals, and laboratory interfacing with PT Nomograph for the Macintosh. (CW)
Footwear Physics.

ERIC Educational Resources Information Center

Blaser, Mark; Larsen, Jamie

1996-01-01

Presents five interactive, computer-based activities that mimic scientific tests used by sport researchers to help companies design high-performance athletic shoes, including impact tests, flexion tests, friction tests, video analysis, and computer modeling. Provides a platform for teachers to build connections between chemistry (polymer science),…
A generalized chemistry version of SPARK

NASA Technical Reports Server (NTRS)

Carpenter, Mark H.

1988-01-01

An extension of the reacting H2-air computer code SPARK is presented, which enables the code to be used on any reacting flow problem. Routines are developed calculating in a general fashion, the reaction rates, and chemical Jacobians of any reacting system. In addition, an equilibrium routine is added so that the code will have frozen, finite rate, and equilibrium capabilities. The reaction rate for the species is determined from the law of mass action using Arrhenius expressions for the rate constants. The Jacobian routines are determined by numerically or analytically differentiating the law of mass action for each species. The equilibrium routine is based on a Gibbs free energy minimization routine. The routines are written in FORTRAN 77, with special consideration given to vectorization. Run times for the generalized routines are generally 20 percent slower than reaction specific routines. The numerical efficiency of the generalized analytical Jacobian, however, is nearly 300 percent better than the reaction specific numerical Jacobian used in SPARK.
Quantum Dynamics in Biological Systems

NASA Astrophysics Data System (ADS)

Shim, Sangwoo

In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.
A High School-Collegiate Outreach Program in Chemistry and Biology Delivering Modern Technology in a Mobile Van

NASA Astrophysics Data System (ADS)

Craney, Chris; Mazzeo, April; Lord, Kaye

1996-07-01

During the past five years the nation's concern for science education has expanded from a discussion about the future supply of Ph.D. scientists and its impact on the nation's scientific competitiveness to the broader consideration of the science education available to all students. Efforts to improve science education have led many authors to suggest greater collaboration between high school science teachers and their college/university colleagues. This article reviews the experience and outcomes of the Teachers + Occidental = Partnership in Science (TOPS) van program operating in the Los Angeles Metropolitan area. The program emphasizes an extensive ongoing staff development, responsiveness to teachers' concerns, technical and on-site support, and sustained interaction between participants and program staff. Access to modern technology, including computer-driven instruments and commercial data analysis software, coupled with increased teacher content knowledge has led to empowerment of teachers and changes in student interest in science. Results of student and teacher questionnaires are reviewed.

Flame Structure and Dynamics for an Array of Premixed Methane-Air Jets

NASA Astrophysics Data System (ADS)

Nigam, Siddharth P.; Lapointe, Caelan; Christopher, Jason D.; Wimer, Nicholas T.; Hayden, Torrey R. S.; Rieker, Gregory B.; Hamlington, Peter E.

2017-11-01

Premixed flames have been studied extensively, both experimentally and computationally, and their properties are reasonably well characterized for a range of conditions and configurations. However, the premixed combustion process is potentially much more difficult to predict when many such flames are arranged in a closely spaced array. These arrays must be better understood, in particular, for the design of industrial burners used in chemical and heat treatment processes. Here, the effects of geometric array parameters (e.g., angle and diameter of jet inlets, number of inlets and their respective orientation) and operating conditions (e.g., jet velocities, fuel-air ratio) on flame structure and dynamics are studied using large eddy simulations (LES). The simulations are performed in OpenFOAM using multi-step chemistry for a methane-air mixture, and temperature and chemical composition fields are characterized for a variety of configurations as functions of height above the array. Implications of these results for the design and operation of industrial burners are outlined.
Vascular endothelial growth factor receptor-2 (VEGFR-2) inhibitors: development and validation of predictive 3-D QSAR models through extensive ligand- and structure-based approaches

NASA Astrophysics Data System (ADS)

Ragno, Rino; Ballante, Flavio; Pirolli, Adele; Wickersham, Richard B.; Patsilinakos, Alexandros; Hesse, Stéphanie; Perspicace, Enrico; Kirsch, Gilbert

2015-08-01

Vascular endothelial growth factor receptor-2, (VEGFR-2), is a key element in angiogenesis, the process by which new blood vessels are formed, and is thus an important pharmaceutical target. Here, 3-D quantitative structure-activity relationship (3-D QSAR) were used to build a quantitative screening and pharmacophore model of the VEGFR-2 receptors for design of inhibitors with improved activities. Most of available experimental data information has been used as training set to derive optimized and fully cross-validated eight mono-probe and a multi-probe quantitative models. Notable is the use of 262 molecules, aligned following both structure-based and ligand-based protocols, as external test set confirming the 3-D QSAR models' predictive capability and their usefulness in design new VEGFR-2 inhibitors. From a survey on literature, this is the first generation of a wide-ranging computational medicinal chemistry application on VEGFR2 inhibitors.
Stepwise Nucleation of Aniline: Emergence of Spectroscopic Fingerprints of the Liquid Phase.

PubMed

Leon, Iker; Usabiaga, Imanol; Arnaiz, Pedro Felipe; Lesarri, Alberto; Fernández, Jose Andres

2018-06-11

We deal here with the controlled nucleation of aniline from the isolated molecule until formation of a moderately large aggregate: aniline nonamer. The structure of the cluster at each step of the nucleation was unravelled combining mass-resolved IR spectroscopy and computational chemistry, demonstrating that aggregation is primarily guided by formation of extensive N-H···N hydrogen bond networks that give the aggregates a sort of branched backbone, in clear competition with multiple N-H/C-H···pi and pi···pi interactions. The result is the co-existence of close nucleation paths connecting relational aggregates. The delicate balance of molecular forces makes the aniline clusters a challenge for molecular orbital calculations and an ideal system to refine the present nucleation models. Noticeably, spectroscopic signatures characteristic of the condensed phase are apparent in the nanometer-size aggregates formed in this work. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Ligand Electron Density Shape Recognition Using 3D Zernike Descriptors

NASA Astrophysics Data System (ADS)

Gunasekaran, Prasad; Grandison, Scott; Cowtan, Kevin; Mak, Lora; Lawson, David M.; Morris, Richard J.

We present a novel approach to crystallographic ligand density interpretation based on Zernike shape descriptors. Electron density for a bound ligand is expanded in an orthogonal polynomial series (3D Zernike polynomials) and the coefficients from this expansion are employed to construct rotation-invariant descriptors. These descriptors can be compared highly efficiently against large databases of descriptors computed from other molecules. In this manuscript we describe this process and show initial results from an electron density interpretation study on a dataset containing over a hundred OMIT maps. We could identify the correct ligand as the first hit in about 30 % of the cases, within the top five in a further 30 % of the cases, and giving rise to an 80 % probability of getting the correct ligand within the top ten matches. In all but a few examples, the top hit was highly similar to the correct ligand in both shape and chemistry. Further extensions and intrinsic limitations of the method are discussed.
Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells.

PubMed

Wagler, Patrick F; Tangen, Uwe; Maeke, Thomas; McCaskill, John S

2012-07-01

The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Free-radicals and advanced chemistries involved in cell membrane organization influence oxygen diffusion and pathology treatment.

PubMed

Petersen, Richard C

2017-01-01

A breakthrough has been discovered in pathology chemistry related to increasing molecular structure that can interfere with oxygen diffusion through cell membranes. Free radicals can crosslink unsaturated low-viscosity fatty acid oils by chain-growth polymerization into more viscous liquids and even solids. Free radicals are released by mitochondria in response to intermittent hypoxia that can increase membrane molecular organization to reduce fluidity and oxygen diffusion in a possible continuing vicious cycle toward pathological disease. Alternate computational chemistry demonstrates molecular bond dynamics in free energy for cell membrane physiologic movements. Paired electrons in oxygen and nitrogen atoms require that oxygen bonds rotate and nitrogen bonds invert to seek polar nano-environments and hide from nonpolar nano-environments thus creating fluctuating instability at a nonpolar membrane and polar biologic fluid interface. Subsequent mechanomolecular movements provide free energy to increase diffusion by membrane transport of molecules and oxygen into the cell, cell-membrane signaling/recognition/defense in addition to protein movements for enzyme mixing. In other chemistry calcium bonds to membrane phosphates primarily on the outer plasma cell membrane surface to influence the membrane firing threshold for excitability and better seal out water permeation. Because calcium is an excellent metal conductor and membrane phosphate headgroups form a semiconductor at the biologic fluid interface, excess electrons released by mitochondria may have more broad dissipation potential by safe conduction through calcium atomic-sized circuits on the outer membrane surface. Regarding medical conditions, free radicals are known to produce pathology especially in age-related disease in addition to aging. Because cancer cell membranes develop extreme polymorphism that has been extensively followed in research, accentuated easily-visualized free-radical models are developed. In terms of treatment, use of vitamin nutrient supplements purported to be antioxidants that remove free radicals has not proved worthwhile in clinical trials presumably due to errors with early antioxidant measurements based on inaccurate colorimetry tests. However, newer covalent-bond shrinkage tests now provide accurate measurements for free-radical inhibitor hydroquinone and other molecules toward drug therapy.
Free-radicals and advanced chemistries involved in cell membrane organization influence oxygen diffusion and pathology treatment

PubMed Central

Petersen, Richard C

2017-01-01

A breakthrough has been discovered in pathology chemistry related to increasing molecular structure that can interfere with oxygen diffusion through cell membranes. Free radicals can crosslink unsaturated low-viscosity fatty acid oils by chain-growth polymerization into more viscous liquids and even solids. Free radicals are released by mitochondria in response to intermittent hypoxia that can increase membrane molecular organization to reduce fluidity and oxygen diffusion in a possible continuing vicious cycle toward pathological disease. Alternate computational chemistry demonstrates molecular bond dynamics in free energy for cell membrane physiologic movements. Paired electrons in oxygen and nitrogen atoms require that oxygen bonds rotate and nitrogen bonds invert to seek polar nano-environments and hide from nonpolar nano-environments thus creating fluctuating instability at a nonpolar membrane and polar biologic fluid interface. Subsequent mechanomolecular movements provide free energy to increase diffusion by membrane transport of molecules and oxygen into the cell, cell-membrane signaling/recognition/defense in addition to protein movements for enzyme mixing. In other chemistry calcium bonds to membrane phosphates primarily on the outer plasma cell membrane surface to influence the membrane firing threshold for excitability and better seal out water permeation. Because calcium is an excellent metal conductor and membrane phosphate headgroups form a semiconductor at the biologic fluid interface, excess electrons released by mitochondria may have more broad dissipation potential by safe conduction through calcium atomic-sized circuits on the outer membrane surface. Regarding medical conditions, free radicals are known to produce pathology especially in age-related disease in addition to aging. Because cancer cell membranes develop extreme polymorphism that has been extensively followed in research, accentuated easily-visualized free-radical models are developed. In terms of treatment, use of vitamin nutrient supplements purported to be antioxidants that remove free radicals has not proved worthwhile in clinical trials presumably due to errors with early antioxidant measurements based on inaccurate colorimetry tests. However, newer covalent-bond shrinkage tests now provide accurate measurements for free-radical inhibitor hydroquinone and other molecules toward drug therapy. PMID:29202036
Variational fine-grained data assimilation schemes for atmospheric chemistry transport and transformation models

NASA Astrophysics Data System (ADS)

Penenko, Alexey; Penenko, Vladimir; Tsvetova, Elena

2015-04-01

The paper concerns data assimilation problem for an atmospheric chemistry transport and transformation models. Data assimilation is carried out within variation approach on a single time step of the approximated model. A control function is introduced into the model source term (emission rate) to provide flexibility to adjust to data. This function is evaluated as the minimum of the target functional combining control function norm to a misfit between measured and model-simulated analog of data. This provides a flow-dependent and physically-plausible structure of the resulting analysis and reduces the need to calculate model error covariance matrices that are sought within conventional approach to data assimilation. Extension of the atmospheric transport model with a chemical transformations module influences data assimilation algorithms performance. This influence is investigated with numerical experiments for different meteorological conditions altering convection-diffusion processes characteristics, namely strong, medium and low wind conditions. To study the impact of transformation and data assimilation, we compare results for a convection-diffusion model (without data assimilation), convection-diffusion with assimilation, convection-diffusion-reaction (without data assimilation) and convection-diffusion-reaction-assimilation models. Both high dimensionalities of the atmospheric chemistry models and a real-time mode of operation demand for computational efficiency of the algorithms. Computational issues with complicated models can be solved by using a splitting technique. As the result a model is presented as a set of relatively independent simple models equipped with a kind of coupling procedure. With regard to data assimilation two approaches can be identified. In a fine-grained approach data assimilation is carried out on the separate splitting stages [1,2] independently on shared measurement data. The same situation arises when constructing a hybrid model out of two models each having its own assimilation scheme. In integrated schemes data assimilation is carried out with respect to the split model as a whole. First approach is more efficient from computational point of view, for in some important cases it can be implemented without iterations [2]. Its shortcoming is that control functions in different part of the model are adjusted independently thus having less evident physical sense. With the aid of numerical experiments we compare the two approaches. Work has been partially supported by COST Action ES1004 STSM Grants #16817 and #21654, RFBR 14-01-31482 mol a and 14-01-00125, Programmes # 4 Presidium RAS and # 3 MSD RAS, integration projects SB RAS #8 and #35. References: [1] V. V. Penenko Variational methods of data assimilation and inverse problems for studying the atmosphere, ocean, and environment Num. Anal. and Appl., 2009 V 2 No 4, 341-351. [2] A.V. Penenko and V.V. Penenko. Direct data assimilation method for convection-diffusion models based on splitting scheme. Computational technologies, 19(4):69-83, 2014.
Assessing the Performance of Computationally Simple and Complex Representations of Aerosol Processes using a Testbed Methodology

NASA Astrophysics Data System (ADS)

Fast, J. D.; Ma, P.; Easter, R. C.; Liu, X.; Zaveri, R. A.; Rasch, P.

2012-12-01

Predictions of aerosol radiative forcing in climate models still contain large uncertainties, resulting from a poor understanding of certain aerosol processes, the level of complexity of aerosol processes represented in models, and the ability of models to account for sub-grid scale variability of aerosols and processes affecting them. In addition, comparing the performance and computational efficiency of new aerosol process modules used in various studies is problematic because different studies often employ different grid configurations, meteorology, trace gas chemistry, and emissions that affect the temporal and spatial evolution of aerosols. To address this issue, we have developed an Aerosol Modeling Testbed (AMT) to systematically and objectively evaluate aerosol process modules. The AMT consists of the modular Weather Research and Forecasting (WRF) model, a series of testbed cases for which extensive in situ and remote sensing measurements of meteorological, trace gas, and aerosol properties are available, and a suite of tools to evaluate the performance of meteorological, chemical, aerosol process modules. WRF contains various parameterizations of meteorological, chemical, and aerosol processes and includes interactive aerosol-cloud-radiation treatments similar to those employed by climate models. In addition, the physics suite from a global climate model, Community Atmosphere Model version 5 (CAM5), has also been ported to WRF so that these parameterizations can be tested at various spatial scales and compared directly with field campaign data and other parameterizations commonly used by the mesoscale modeling community. In this study, we evaluate simple and complex treatments of the aerosol size distribution and secondary organic aerosols using the AMT and measurements collected during three field campaigns: the Megacities Initiative Local and Global Observations (MILAGRO) campaign conducted in the vicinity of Mexico City during March 2006, the Carbonaceous Aerosol and Radiative Effects Study (CARES) conducted in the vicinity of Sacramento California during June 2010, and the California Nexus (CalNex) campaign conducted in southern California during May and June of 2010. For the aerosol size distribution, we compare the predictions from the GOCART bulk aerosol model, the MADE/SORGAM modal aerosol model, the Modal Aerosol Model (MAM) employed by CAM5, and the Model for Simulating Aerosol Interactions and Chemistry (MOSAIC) which uses a sectional representation. For secondary organic aerosols, we compare simple fixed mass yield approaches with the numerically complex volatility basis set approach. All simulations employ the same emissions, meteorology, trace gas chemistry (except for that involving condensable organic species), and initial and boundary conditions. Performance metrics from the AMT are used to assess performance in terms of simulated mass, composition, size distribution (except for GOCART), and aerosol optical properties in relation to computational expense. In addition to statistical measures, qualitative differences among the different aerosol models over the computational domain are presented to examine variations in how aerosols age among the aerosol models.
Chemistry in the News: 1998 Nobel Prizes in Chemistry and Medicine

NASA Astrophysics Data System (ADS)

Miller, Jennifer B.

1999-01-01

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

ERIC Educational Resources Information Center

Grandey, Robert C.

The development of computer-assisted instructional lessons on the following three topics is discussed: 1) the mole concept and chemical formulas, 2) concentration of solutions and quantities from chemical equations, and 3) balancing equations for oxidation-reduction reactions. Emphasis was placed on developing computer routines which interpret…
Acid base chemistry of luteolin and its methyl-ether derivatives: A DFT and ab initio investigation

NASA Astrophysics Data System (ADS)

Amat, Anna; De Angelis, Filippo; Sgamellotti, Antonio; Fantacci, Simona

2008-09-01

The acid-base chemistry of luteolin, a flavonoid with important pharmacological and dyeing properties, and of the related methyl ether derivatives have been investigated by DFT and MP2 methods, testing different computational setups. We calculate the pK's of all the possible deprotonation sites, for which no experimental assignment could be achieved. The calculated pK's deliver a different acidity order for the two most acidic deprotonation sites between luteolin and its methyl ether derivatives, due to intramolecular hydrogen bonding in luteolin. A lowest p Ka of 6.19 is computed for luteolin, in good agreement with available experimental data.
Boost-phase discrimination research activities

NASA Technical Reports Server (NTRS)

Cooper, David M.; Deiwert, George S.

1989-01-01

Theoretical research in two areas was performed. The aerothermodynamics research focused on the hard-body and rocket plume flows. Analytical real gas models to describe finite rate chemistry were developed and incorporated into the three-dimensional flow codes. New numerical algorithms capable of treating multi-species reacting gas equations and treating flows with large gradients were also developed. The computational chemistry research focused on the determination of spectral radiative intensity factors, transport properties and reaction rates. Ab initio solutions to the Schrodinger equation provided potential energy curves transition moments (radiative probabilities and strengths) and potential energy surfaces. These surfaces were then coupled with classical particle reactive trajectories to compute reaction cross-sections and rates.
Calculating Potential Energy Curves with Quantum Monte Carlo

NASA Astrophysics Data System (ADS)

Powell, Andrew D.; Dawes, Richard

2014-06-01

Quantum Monte Carlo (QMC) is a computational technique that can be applied to the electronic Schrödinger equation for molecules. QMC methods such as Variational Monte Carlo (VMC) and Diffusion Monte Carlo (DMC) have demonstrated the capability of capturing large fractions of the correlation energy, thus suggesting their possible use for high-accuracy quantum chemistry calculations. QMC methods scale particularly well with respect to parallelization making them an attractive consideration in anticipation of next-generation computing architectures which will involve massive parallelization with millions of cores. Due to the statistical nature of the approach, in contrast to standard quantum chemistry methods, uncertainties (error-bars) are associated with each calculated energy. This study focuses on the cost, feasibility and practical application of calculating potential energy curves for small molecules with QMC methods. Trial wave functions were constructed with the multi-configurational self-consistent field (MCSCF) method from GAMESS-US.[1] The CASINO Monte Carlo quantum chemistry package [2] was used for all of the DMC calculations. An overview of our progress in this direction will be given. References: M. W. Schmidt et al. J. Comput. Chem. 14, 1347 (1993). R. J. Needs et al. J. Phys.: Condensed Matter 22, 023201 (2010).
ASIS v1.0: an adaptive solver for the simulation of atmospheric chemistry

NASA Astrophysics Data System (ADS)

Cariolle, Daniel; Moinat, Philippe; Teyssèdre, Hubert; Giraud, Luc; Josse, Béatrice; Lefèvre, Franck

2017-04-01

This article reports on the development and tests of the adaptive semi-implicit scheme (ASIS) solver for the simulation of atmospheric chemistry. To solve the ordinary differential equation systems associated with the time evolution of the species concentrations, ASIS adopts a one-step linearized implicit scheme with specific treatments of the Jacobian of the chemical fluxes. It conserves mass and has a time-stepping module to control the accuracy of the numerical solution. In idealized box-model simulations, ASIS gives results similar to the higher-order implicit schemes derived from the Rosenbrock's and Gear's methods and requires less computation and run time at the moderate precision required for atmospheric applications. When implemented in the MOCAGE chemical transport model and the Laboratoire de Météorologie Dynamique Mars general circulation model, the ASIS solver performs well and reveals weaknesses and limitations of the original semi-implicit solvers used by these two models. ASIS can be easily adapted to various chemical schemes and further developments are foreseen to increase its computational efficiency, and to include the computation of the concentrations of the species in aqueous-phase in addition to gas-phase chemistry.
An extensible framework for capturing solvent effects in computer generated kinetic models.

PubMed

Jalan, Amrit; West, Richard H; Green, William H

2013-03-14

Detailed kinetic models provide useful mechanistic insight into a chemical system. Manual construction of such models is laborious and error-prone, which has led to the development of automated methods for exploring chemical pathways. These methods rely on fast, high-throughput estimation of species thermochemistry and kinetic parameters. In this paper, we present a methodology for extending automatic mechanism generation to solution phase systems which requires estimation of solvent effects on reaction rates and equilibria. The linear solvation energy relationship (LSER) method of Abraham and co-workers is combined with Mintz correlations to estimate ΔG(solv)°(T) in over 30 solvents using solute descriptors estimated from group additivity. Simple corrections are found to be adequate for the treatment of radical sites, as suggested by comparison with known experimental data. The performance of scaled particle theory expressions for enthalpic-entropic decomposition of ΔG(solv)°(T) is also presented along with the associated computational issues. Similar high-throughput methods for solvent effects on free-radical kinetics are only available for a handful of reactions due to lack of reliable experimental data, and continuum dielectric calculations offer an alternative method for their estimation. For illustration, we model liquid phase oxidation of tetralin in different solvents computing the solvent dependence for ROO• + ROO• and ROO• + solvent reactions using polarizable continuum quantum chemistry methods. The resulting kinetic models show an increase in oxidation rate with solvent polarity, consistent with experiment. Further work needed to make this approach more generally useful is outlined.
Quantum and semiclassical spin networks: from atomic and molecular physics to quantum computing and gravity

NASA Astrophysics Data System (ADS)

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

2008-11-01

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

NASA Astrophysics Data System (ADS)

Kumar, Vinay; Bedell, Julia Yang; Seed, Allen H.

1999-05-01

A DOE/KYEPSCoR-funded project enabled us to introduce a new curricular initiative aimed at improving the chemical education of pre-service elementary teachers. The new curriculum was developed in collaboration with the School of Education faculty. A new course for the pre-service teachers, "Discovering Chemistry with Lab" (CHE 105), was developed. The integrated lecture and lab course covers basic principles of chemistry and their applications in daily life. The course promotes reasoning and problem-solving skills and utilizes hands-on, discovery/guided-inquiry, and cooperative learning approaches. This paper describes the implementation of technology (computer-interfacing and simulation experiments) in the lab. Results of two assessment surveys conducted in the laboratory are also discussed. The key features of the lab course are eight new experiments, including four computer-interfacing/simulation experiments involving the use of Macintosh Power PCs, temperature and pH probes, and a serial box interface, and use of household materials. Several experiments and the midterm and final lab practical exams emphasize the discovery/guided-inquiry approach. The results of pre- and post-surveys showed very significant positive changes in students' attitude toward the relevancy of chemistry, use of technology (computers) in elementary school classrooms, and designing and teaching discovery-based units. Most students indicated that they would be very interested (52%) or interested (36%) in using computers in their science teaching.
The Ulam Index: Methods of Theoretical Computer Science Help in Identifying Chemical Substances

NASA Technical Reports Server (NTRS)

Beltran, Adriana; Salvador, James

1997-01-01

In this paper, we show how methods developed for solving a theoretical computer problem of graph isomorphism are used in structural chemistry. We also discuss potential applications of these methods to exobiology: the search for life outside Earth.
75 FR 15675 - Professional Research Experience Program in Chemical Science and Technology Laboratory...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-30

... in physics, chemistry, mathematics, computer science, or engineering. Institutions should have a 4..., mathematics, computer science, or engineering with work experiences in laboratories or other settings...-0141-01] Professional Research Experience Program in Chemical Science and Technology Laboratory...

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