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)

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.

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.

[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.

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

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.

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.

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...

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.

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…

[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.

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).

Estimations of global warming potentials from computational chemistry calculations for CH(2)F(2) and other fluorinated methyl species verified by comparison to experiment.

PubMed

Blowers, Paul; Hollingshead, Kyle

2009-05-21

In this work, the global warming potential (GWP) of methylene fluoride (CH(2)F(2)), or HFC-32, is estimated through computational chemistry methods. We find our computational chemistry approach reproduces well all phenomena important for predicting global warming potentials. Geometries predicted using the B3LYP/6-311g** method were in good agreement with experiment, although some other computational methods performed slightly better. Frequencies needed for both partition function calculations in transition-state theory and infrared intensities needed for radiative forcing estimates agreed well with experiment compared to other computational methods. A modified CBS-RAD method used to obtain energies led to superior results to all other previous heat of reaction estimates and most barrier height calculations when the B3LYP/6-311g** optimized geometry was used as the base structure. Use of the small-curvature tunneling correction and a hindered rotor treatment where appropriate led to accurate reaction rate constants and radiative forcing estimates without requiring any experimental data. Atmospheric lifetimes from theory at 277 K were indistinguishable from experimental results, as were the final global warming potentials compared to experiment. This is the first time entirely computational methods have been applied to estimate a global warming potential for a chemical, and we have found the approach to be robust, inexpensive, and accurate compared to prior experimental results. This methodology was subsequently used to estimate GWPs for three additional species [methane (CH(4)); fluoromethane (CH(3)F), or HFC-41; and fluoroform (CHF(3)), or HFC-23], where estimations also compare favorably to experimental values.

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.

Integrating computational methods to retrofit enzymes to synthetic pathways.

PubMed

Brunk, Elizabeth; Neri, Marilisa; Tavernelli, Ivano; Hatzimanikatis, Vassily; Rothlisberger, Ursula

2012-02-01

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target compounds with high yields and turnover rates. We use integrated computational methods to generate and quantify the performance of novel biosynthetic routes that contain highly optimized catalysts. Engineering a novel reaction pathway entails addressing feasibility on multiple levels, which involves handling the complexity of large-scale biochemical networks while respecting the critical chemical phenomena at the atomistic scale. To pursue this multi-layer challenge, our strategy merges knowledge-based metabolic engineering methods with computational chemistry methods. By bridging multiple disciplines, we provide an integral computational framework that could accelerate the discovery and implementation of novel biosynthetic production routes. Using this approach, we have identified and optimized a novel biosynthetic route for the production of 3HP from pyruvate. Copyright © 2011 Wiley Periodicals, Inc.

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…

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.

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.

Plane-Wave DFT Methods for Chemistry

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

Bylaska, Eric J.

A detailed description of modern plane-wave DFT methods and software (contained in the NWChem package) are described that allow for both geometry optimization and ab initio molecular dynamics simulations. Significant emphasis is placed on aspects of these methods that are of interest to computational chemists and useful for simulating chemistry, including techniques for calculating charged systems, exact exchange (i.e. hybrid DFT methods), and highly efficient AIMD/MM methods. Sample applications on the structure of the goethite+water interface and the hydrolysis of nitroaromatic molecules are described.

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.

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...

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.

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.…

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.

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

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.

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…

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 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 new computational method for reacting hypersonic flows

NASA Astrophysics Data System (ADS)

Niculescu, M. L.; Cojocaru, M. G.; Pricop, M. V.; Fadgyas, M. C.; Pepelea, D.; Stoican, M. G.

2017-07-01

Hypersonic gas dynamics computations are challenging due to the difficulties to have reliable and robust chemistry models that are usually added to Navier-Stokes equations. From the numerical point of view, it is very difficult to integrate together Navier-Stokes equations and chemistry model equations because these partial differential equations have different specific time scales. For these reasons, almost all known finite volume methods fail shortly to solve this second order partial differential system. Unfortunately, the heating of Earth reentry vehicles such as space shuttles and capsules is very close linked to endothermic chemical reactions. A better prediction of wall heat flux leads to smaller safety coefficient for thermal shield of space reentry vehicle; therefore, the size of thermal shield decreases and the payload increases. For these reasons, the present paper proposes a new computational method based on chemical equilibrium, which gives accurate prediction of hypersonic heating in order to support the Earth reentry capsule design.

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

Teaching Inorganic Photophysics and Photochemistry with Three Ruthenium(II) Polypyridyl Complexes: A Computer-Based Exercise

ERIC Educational Resources Information Center

Garino, Claudio; Terenzi, Alessio; Barone, Giampaolo; Salassa, Luca

2016-01-01

Among computational methods, DFT (density functional theory) and TD-DFT (time-dependent DFT) are widely used in research to describe, "inter alia," the optical properties of transition metal complexes. Inorganic/physical chemistry courses for undergraduate students treat such methods, but quite often only from the theoretical point of…

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.

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.

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.

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

PubMed

Ramabhadran, Raghunath O; Raghavachari, Krishnan

2014-12-16

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

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;

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

Balancing Chemical Reactions With Matrix Methods and Computer Assistance. Applications of Linear Algebra to Chemistry. Modules and Monographs in Undergraduate Mathematics and Its Applications Project. UMAP Unit 339.

ERIC Educational Resources Information Center

Grimaldi, Ralph P.

This material was developed to provide an application of matrix mathematics in chemistry, and to show the concepts of linear independence and dependence in vector spaces of dimensions greater than three in a concrete setting. The techniques presented are not intended to be considered as replacements for such chemical methods as oxidation-reduction…

Connecting the virtual world of computers to the real world of medicinal chemistry.

PubMed

Glen, Robert C

2011-03-01

Drug discovery involves the simultaneous optimization of chemical and biological properties, usually in a single small molecule, which modulates one of nature's most complex systems: the balance between human health and disease. The increased use of computer-aided methods is having a significant impact on all aspects of the drug-discovery and development process and with improved methods and ever faster computers, computer-aided molecular design will be ever more central to the discovery process.

Assessment of Molecular Modeling & Simulation

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

None

2002-01-03

This report reviews the development and applications of molecular and materials modeling in Europe and Japan in comparison to those in the United States. Topics covered include computational quantum chemistry, molecular simulations by molecular dynamics and Monte Carlo methods, mesoscale modeling of material domains, molecular-structure/macroscale property correlations like QSARs and QSPRs, and related information technologies like informatics and special-purpose molecular-modeling computers. The panel's findings include the following: The United States leads this field in many scientific areas. However, Canada has particular strengths in DFT methods and homogeneous catalysis; Europe in heterogeneous catalysis, mesoscale, and materials modeling; and Japan in materialsmore » modeling and special-purpose computing. Major government-industry initiatives are underway in Europe and Japan, notably in multi-scale materials modeling and in development of chemistry-capable ab-initio molecular dynamics codes.« less

 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...

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.

MIANN models in medicinal, physical and organic chemistry.

PubMed

González-Díaz, Humberto; Arrasate, Sonia; Sotomayor, Nuria; Lete, Esther; Munteanu, Cristian R; Pazos, Alejandro; Besada-Porto, Lina; Ruso, Juan M

2013-01-01

Reducing costs in terms of time, animal sacrifice, and material resources with computational methods has become a promising goal in Medicinal, Biological, Physical and Organic Chemistry. There are many computational techniques that can be used in this sense. In any case, almost all these methods focus on few fundamental aspects including: type (1) methods to quantify the molecular structure, type (2) methods to link the structure with the biological activity, and others. In particular, MARCH-INSIDE (MI), acronym for Markov Chain Invariants for Networks Simulation and Design, is a well-known method for QSAR analysis useful in step (1). In addition, the bio-inspired Artificial-Intelligence (AI) algorithms called Artificial Neural Networks (ANNs) are among the most powerful type (2) methods. We can combine MI with ANNs in order to seek QSAR models, a strategy which is called herein MIANN (MI & ANN models). One of the first applications of the MIANN strategy was in the development of new QSAR models for drug discovery. MIANN strategy has been expanded to the QSAR study of proteins, protein-drug interactions, and protein-protein interaction networks. In this paper, we review for the first time many interesting aspects of the MIANN strategy including theoretical basis, implementation in web servers, and examples of applications in Medicinal and Biological chemistry. We also report new applications of the MIANN strategy in Medicinal chemistry and the first examples in Physical and Organic Chemistry, as well. In so doing, we developed new MIANN models for several self-assembly physicochemical properties of surfactants and large reaction networks in organic synthesis. In some of the new examples we also present experimental results which were not published up to date.

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.

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)

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.

Using Q-Chem on the Peregrine System | High-Performance Computing | NREL

Science.gov Websites

initio quantum chemistry package with special strengths in excited state methods, non-adiabatic coupling , solvation models, explicitly correlated wavefunction methods, and cutting-edge DFT. Running Q-Chem on

QSAR Methods.

PubMed

Gini, Giuseppina

2016-01-01

In this chapter, we introduce the basis of computational chemistry and discuss how computational methods have been extended to some biological properties and toxicology, in particular. Since about 20 years, chemical experimentation is more and more replaced by modeling and virtual experimentation, using a large core of mathematics, chemistry, physics, and algorithms. Then we see how animal experiments, aimed at providing a standardized result about a biological property, can be mimicked by new in silico methods. Our emphasis here is on toxicology and on predicting properties through chemical structures. Two main streams of such models are available: models that consider the whole molecular structure to predict a value, namely QSAR (Quantitative Structure Activity Relationships), and models that find relevant substructures to predict a class, namely SAR. The term in silico discovery is applied to chemical design, to computational toxicology, and to drug discovery. We discuss how the experimental practice in biological science is moving more and more toward modeling and simulation. Such virtual experiments confirm hypotheses, provide data for regulation, and help in designing new chemicals.

Self-consistent field for fragmented quantum mechanical model of large molecular systems.

PubMed

Jin, Yingdi; Su, Neil Qiang; Xu, Xin; Hu, Hao

2016-01-30

Fragment-based linear scaling quantum chemistry methods are a promising tool for the accurate simulation of chemical and biomolecular systems. Because of the coupled inter-fragment electrostatic interactions, a dual-layer iterative scheme is often employed to compute the fragment electronic structure and the total energy. In the dual-layer scheme, the self-consistent field (SCF) of the electronic structure of a fragment must be solved first, then followed by the updating of the inter-fragment electrostatic interactions. The two steps are sequentially carried out and repeated; as such a significant total number of fragment SCF iterations is required to converge the total energy and becomes the computational bottleneck in many fragment quantum chemistry methods. To reduce the number of fragment SCF iterations and speed up the convergence of the total energy, we develop here a new SCF scheme in which the inter-fragment interactions can be updated concurrently without converging the fragment electronic structure. By constructing the global, block-wise Fock matrix and density matrix, we prove that the commutation between the two global matrices guarantees the commutation of the corresponding matrices in each fragment. Therefore, many highly efficient numerical techniques such as the direct inversion of the iterative subspace method can be employed to converge simultaneously the electronic structure of all fragments, reducing significantly the computational cost. Numerical examples for water clusters of different sizes suggest that the method shall be very useful in improving the scalability of fragment quantum chemistry methods. © 2015 Wiley Periodicals, Inc.

A priori and a posteriori analyses of the flamelet/progress variable approach for supersonic combustion

NASA Astrophysics Data System (ADS)

Saghafian, Amirreza; Pitsch, Heinz

2012-11-01

A compressible flamelet/progress variable approach (CFPV) has been devised for high-speed flows. Temperature is computed from the transported total energy and tabulated species mass fractions and the source term of the progress variable is rescaled with pressure and temperature. The combustion is thus modeled by three additional scalar equations and a chemistry table that is computed in a pre-processing step. Three-dimensional direct numerical simulation (DNS) databases of reacting supersonic turbulent mixing layer with detailed chemistry are analyzed to assess the underlying assumptions of CFPV. Large eddy simulations (LES) of the same configuration using the CFPV method have been performed and compared with the DNS results. The LES computations are based on the presumed subgrid PDFs of mixture fraction and progress variable, beta function and delta function respectively, which are assessed using DNS databases. The flamelet equation budget is also computed to verify the validity of CFPV method for high-speed flows.

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.

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.

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.

Results of a National Survey of Biochemistry Instructors to Determine the Prevalence and Types of Representations Used during Instruction and Assessment

ERIC Educational Resources Information Center

Linenberger, Kimberly J.; Holme, Thomas A.

2014-01-01

Chemists and chemistry educators have long sought meaningful ways to visualize fundamentally abstract components, such as atoms and molecules, of their trade. As technology has improved, computer-based visualization methods have infused both research and education in chemistry. Biochemistry, in particular, has become highly dependent on ways that…

Probing Nucleobase Interactions and Predicting Mechanisms of Synthetic Interest Using Computational Chemistry, and Furthering the Development of BVI Education in Chemistry

ERIC Educational Resources Information Center

Harrison, Jason Gordon

2013-01-01

Quantum mechanical (QM) and molecular docking methods are used to probe systems of biological and synthetic interest. Probing interactions of nucleobases within proteins, and properly modeling said interactions toward novel nucleobase development, is extremely difficult, and of great utility in RNA interference (RNAi) therapeutics. The issues in…

Exploring the Nature of the H[subscript 2] Bond. 1. Using Spreadsheet Calculations to Examine the Valence Bond and Molecular Orbital Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.; Glendening, Eric D.

2013-01-01

A three-part project for students in physical chemistry, computational chemistry, or independent study is described in which they explore applications of valence bond (VB) and molecular orbital-configuration interaction (MO-CI) treatments of H[subscript 2]. Using a scientific spreadsheet, students construct potential-energy (PE) curves for several…

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.

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.

Derek Vigil-Fowler | NREL

Science.gov Websites

simulation methods for materials physics and chemistry, with particular expertise in post-DFT, high accuracy methods such as the GW approximation for electronic structure and random phase approximation (RPA) total the art in computational methods, including efficient methods for including the effects of substrates

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…

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.

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.

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.

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.

Computer program determines chemical composition of physical system at equilibrium

NASA Technical Reports Server (NTRS)

Kwong, S. S.

1966-01-01

FORTRAN 4 digital computer program calculates equilibrium composition of complex, multiphase chemical systems. This is a free energy minimization method with solution of the problem reduced to mathematical operations, without concern for the chemistry involved. Also certain thermodynamic properties are determined as byproducts of the main calculations.

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…

Problem-based learning on quantitative analytical chemistry course

NASA Astrophysics Data System (ADS)

Fitri, Noor

2017-12-01

This research applies problem-based learning method on chemical quantitative analytical chemistry, so called as "Analytical Chemistry II" course, especially related to essential oil analysis. The learning outcomes of this course include aspects of understanding of lectures, the skills of applying course materials, and the ability to identify, formulate and solve chemical analysis problems. The role of study groups is quite important in improving students' learning ability and in completing independent tasks and group tasks. Thus, students are not only aware of the basic concepts of Analytical Chemistry II, but also able to understand and apply analytical concepts that have been studied to solve given analytical chemistry problems, and have the attitude and ability to work together to solve the problems. Based on the learning outcome, it can be concluded that the problem-based learning method in Analytical Chemistry II course has been proven to improve students' knowledge, skill, ability and attitude. Students are not only skilled at solving problems in analytical chemistry especially in essential oil analysis in accordance with local genius of Chemistry Department, Universitas Islam Indonesia, but also have skilled work with computer program and able to understand material and problem in English.

Quantum chemical studies of estrogenic compounds

USDA-ARS?s Scientific Manuscript database

Quantum chemical methods are potent tools to provide information on the chemical structure and electronic properties of organic molecules. Modern computational chemistry methods have provided a great deal of insight into the binding of estrogenic compounds to estrogenic receptors (ER), an important ...

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.

Organic chemistry as a language and the implications of chemical linguistics for structural and retrosynthetic analyses.

PubMed

Cadeddu, Andrea; Wylie, Elizabeth K; Jurczak, Janusz; Wampler-Doty, Matthew; Grzybowski, Bartosz A

2014-07-28

Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics-based analysis appears well-suited to the analysis of complex structural and reactivity patterns within organic molecules. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

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

PubMed

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

2018-06-11

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

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.

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 © 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

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.

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.

Advances in visual representation of molecular potentials.

PubMed

Du, Qi-Shi; Huang, Ri-Bo; Chou, Kuo-Chen

2010-06-01

The recent advances in visual representations of molecular properties in 3D space are summarized, and their applications in molecular modeling study and rational drug design are introduced. The visual representation methods provide us with detailed insights into protein-ligand interactions, and hence can play a major role in elucidating the structure or reactivity of a biomolecular system. Three newly developed computation and visualization methods for studying the physical and chemical properties of molecules are introduced, including their electrostatic potential, lipophilicity potential and excess chemical potential. The newest application examples of visual representations in structure-based rational drug are presented. The 3D electrostatic potentials, calculated using the empirical method (EM-ESP), in which the classical Coulomb equation and traditional atomic partial changes are discarded, are highly consistent with the results by the higher level quantum chemical method. The 3D lipophilicity potentials, computed by the heuristic molecular lipophilicity potential method based on the principles of quantum mechanics and statistical mechanics, are more accurate and reliable than those by using the traditional empirical methods. The 3D excess chemical potentials, derived by the reference interaction site model-hypernetted chain theory, provide a new tool for computational chemistry and molecular modeling. For structure-based drug design, the visual representations of molecular properties will play a significant role in practical applications. It is anticipated that the new advances in computational chemistry will stimulate the development of molecular modeling methods, further enriching the visual representation techniques for rational drug design, as well as other relevant fields in life science.

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...

Inner-shell chemistry under high pressure

NASA Astrophysics Data System (ADS)

Miao, Maosheng; Botana, Jorge; Pravica, Michael; Sneed, Daniel; Park, Changyong

2017-05-01

Chemistry at ambient conditions has implicit boundaries rooted in the atomic shell structure: the inner-shell electrons and the unoccupied outer-shell orbitals do not contribute as the major component to chemical reactions and in chemical bonds. These general rules govern our understanding of chemical structures and reactions. We review the recent progresses in high-pressure chemistry demonstrating that the above rules can be violated under extreme conditions. Using a first principles computation method and crystal structure search algorithm, we demonstrate that stable compounds involving inner shell electrons such as CsF3, CsF5, HgF3, and HgF4 can form under high external pressure and may present exotic properties. We also discuss experimental studies that have sought to confirm these predictions. Employing our recently developed hard X-ray photochemistry methods in a diamond anvil cell, we show promising early results toward realizing inner shell chemistry experimentally.

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.

On the equivalence of LIST and DIIS methods for convergence acceleration

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

Garza, Alejandro J.; Scuseria, Gustavo E.

2015-04-28

Self-consistent field extrapolation methods play a pivotal role in quantum chemistry and electronic structure theory. We, here, demonstrate the mathematical equivalence between the recently proposed family of LIST methods [Wang et al., J. Chem. Phys. 134, 241103 (2011); Y. K. Chen and Y. A. Wang, J. Chem. Theory Comput. 7, 3045 (2011)] and the general form of Pulay’s DIIS [Chem. Phys. Lett. 73, 393 (1980); J. Comput. Chem. 3, 556 (1982)] with specific error vectors. Our results also explain the differences in performance among the various LIST methods.

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.

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.

DEVELOPMENT OF EPA'S TOXCAST PROGRAM FOR PRIORITIZING THE TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS.

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS)and genomic technologies to predict potential toxicity and prioritize the use of limited testing resources.

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.

Supercomputers Of The Future

NASA Technical Reports Server (NTRS)

Peterson, Victor L.; Kim, John; Holst, Terry L.; Deiwert, George S.; Cooper, David M.; Watson, Andrew B.; Bailey, F. Ron

1992-01-01

Report evaluates supercomputer needs of five key disciplines: turbulence physics, aerodynamics, aerothermodynamics, chemistry, and mathematical modeling of human vision. Predicts these fields will require computer speed greater than 10(Sup 18) floating-point operations per second (FLOP's) and memory capacity greater than 10(Sup 15) words. Also, new parallel computer architectures and new structured numerical methods will make necessary speed and capacity available.

Cumulative reports and publications through December 31, 1989

NASA Technical Reports Server (NTRS)

1990-01-01

A complete list of reports from the Institute for Computer Applications in Science and Engineering (ICASE) is presented. The major categories of the current ICASE research program are: numerical methods, with particular emphasis on the development and analysis of basic numerical algorithms; control and parameter identification problems, with emphasis on effectual numerical methods; computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, structural analysis, and chemistry; computer systems and software, especially vector and parallel computers, microcomputers, and data management. Since ICASE reports are intended to be preprints of articles that will appear in journals or conference proceedings, the published reference is included when it is available.

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…

Effect of Material Ion Exchanges on the Mechanical Stiffness Properties and Shear Deformation of Hydrated Cement Material Chemistry Structure C-S-H Jennite -- A Computational Modeling Study

NASA Astrophysics Data System (ADS)

Adebiyi, Babatunde Mattew

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 modeling methodology is investigated and demonstrated for a key cement hydrated component material chemistry structure of Calcium-Silicate-Hydrate (C-S-H) Jennite in this work. The effect of material ion exchanges on the mechanical stiffness properties and shear deformation behavior of hydrated cement material chemistry structure of Calcium Silicate Hydrate (C-S-H) Jennite was studied. Calcium ions were replaced with Magnesium ions in Jennite structure of the C-S-H gel. Different level of substitution of the ions was used. The traditional Jennite structure was obtained from the American Mineralogist Crystal Structure Database and super cells of the structures were created using a Molecular Dynamics Analyzer and Visualizer Material Studio. Molecular dynamics parameters used in the modeling analysis were determined by carrying out initial dynamic studies. 64 unit cell of C-S-H Jennite was used in material modeling analysis studies based on convergence results obtained from the elastic modulus and total energies. NVT forcite dynamics using COMPASS force field based on 200 ps dynamics time was used to determine mechanical modulus of the traditional C-S-H gel and the Magnesium ion modified structures. NVT Discover dynamics using COMPASS forcefield was used in the material modeling studies to investigate the influence of ionic exchange on the shear deformation of the associated material chemistry structures. A prior established quasi-static deformation method to emulate shear deformation of C-S-H material chemistry structure that is based on a triclinic crystal structure was used, by deforming the triclinic crystal structure at 0.2 degree per time step for 75 steps of deformation. It was observed that there is a decrease in the total energies of the systems as the percentage of magnesium ion increases in the C-S-H Jennite molecular structure systems. Investigation of effect of ion exchange on the elastic modulus shows that the elastic stiffness modulus tends to decrease as the amount of Mg in the systems increases, using either COMPASS or universal force field. On the other hand, shear moduli obtained after deforming the structures computed from the stress-strain curve obtained from material modeling increases as the amount of Mg increases in the system. The present investigations also showed that ultimate shear stress obtained from predicted shear stress---strain also increases with amount of Mg in the chemistry structure. Present study clearly demonstrates that computational material modeling following molecular dynamics analysis methodology is an effective way to predict and understand the effective material chemistry and additive changes on the stiffness and deformation characteristics in cementitious materials, and the results suggest that this method can be extended to other materials.

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…

Computer Series, 39.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1983-01-01

Describes use of Warnier-Orr program design method for preparing general chemistry tutorial on ideal gas calculations. This program (BASIC-PLUS) is available from the author. Also describes a multipurpose computerized class record system at the University of Toledo. (JN)

Receptor Surface Models in the Classroom: Introducing Molecular Modeling to Students in a 3-D World

ERIC Educational Resources Information Center

Geldenhuys, Werner J.; Hayes, Michael; Van der Schyf, Cornelis J.; Allen, David D.; Malan, Sarel F.

2007-01-01

A simple, novel and generally applicable method to demonstrate structure-activity associations of a group of biologically interesting compounds in relation to receptor binding is described. This method is useful for undergraduates and graduate students in medicinal chemistry and computer modeling programs.

Plumbing the depths of batholiths

USGS Publications Warehouse

Zen, E.-A.

1989-01-01

Knowledge of the pressure of consolidation of a pluton and the pressure-time history of magmatic evolution should allow better understanding of the tectonic and thermal history of the crust. Available methods to estimate pressures of plutons are mainly for those of consolidation. These are either extrinsic, based on geological context, or intrinsic, based on mineral texture, mineral assemblage, fluid inclusions, mineral inclusions, apparent cooling rates, and mineral chemistry. The methods of lattice-dimension matching of mineral inclusions and of detailed chemistry for zoned minerals could lead to pressure-time reconstructions. Future barometers based on mineral chemistry should use atomic species that have low diffusion coefficients and whose values are not sensitive to computational schemes and cumulative analytical errors. Aluminum and silicon in coexisting hornblende, biotite, pyroxene, plagioclase, or garnet are reasonable candidate phases for barometry. -from Author

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

NASA Astrophysics Data System (ADS)

Shoemaker, James Richard

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

Investigation of chemically-reacting supersonic internal flows

NASA Technical Reports Server (NTRS)

Chitsomboon, T.; Tiwari, S. N.

1985-01-01

This report covers work done on the research project Analysis and Computation of Internal Flow Field in a Scramjet Engine. The work is supported by the NASA Langley Research Center (Computational Methods Branch of the High-Speed Aerodynamics Division) through research grant NAG1-423. The governing equations of two-dimensional chemically-reacting flows are presented together with the global two-step chemistry model. The finite-difference algorithm used is illustrated and the method of circumventing the stiffness is discussed. The computer program developed is used to solve two model problems of a premixed chemically-reacting flow. The results obtained are physically reasonable.

Case Study: The Use of a Hypercard Simulation to Aid in the Teaching of Laboratory Apparatus Operation.

ERIC Educational Resources Information Center

Waddick, John

1994-01-01

Compares the effect of a chemistry computer simulation, written by the author, with the effect of an instructor demonstration. The study indicates that in this particular situation the operation of a spectrophotometer can be effectively taught by computer simulation method. The program is written using HyperTalk, the HyperCard programming…

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

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

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

1987-02-15

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

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…

Modeling of Biomaterials for Non-Linear Optical Applications.

DTIC Science & Technology

1995-01-01

Computational chemistry methods were used to explore the molecular conformations of a variety of optoelectronic biopolymers -spiropyran chromophore...investigated. These polypeptides are compositionally representative of the naturally occurring amino acid sequences in silk and wool, having respectively

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (S)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

THE TOXCAST PROGRAM FOR PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

The United States Environmental Protection Agency (EPA) is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals...

Efficient hybrid-symbolic methods for quantum mechanical calculations

NASA Astrophysics Data System (ADS)

Scott, T. C.; Zhang, Wenxing

2015-06-01

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

Comparisons of Lagrangian and Eulerian PDF methods in simulations of non-premixed turbulent jet flames with moderate-to-strong turbulence-chemistry interactions

NASA Astrophysics Data System (ADS)

Jaishree, J.; Haworth, D. C.

2012-06-01

Transported probability density function (PDF) methods have been applied widely and effectively for modelling turbulent reacting flows. In most applications of PDF methods to date, Lagrangian particle Monte Carlo algorithms have been used to solve a modelled PDF transport equation. However, Lagrangian particle PDF methods are computationally intensive and are not readily integrated into conventional Eulerian computational fluid dynamics (CFD) codes. Eulerian field PDF methods have been proposed as an alternative. Here a systematic comparison is performed among three methods for solving the same underlying modelled composition PDF transport equation: a consistent hybrid Lagrangian particle/Eulerian mesh (LPEM) method, a stochastic Eulerian field (SEF) method and a deterministic Eulerian field method with a direct-quadrature-method-of-moments closure (a multi-environment PDF-MEPDF method). The comparisons have been made in simulations of a series of three non-premixed, piloted methane-air turbulent jet flames that exhibit progressively increasing levels of local extinction and turbulence-chemistry interactions: Sandia/TUD flames D, E and F. The three PDF methods have been implemented using the same underlying CFD solver, and results obtained using the three methods have been compared using (to the extent possible) equivalent physical models and numerical parameters. Reasonably converged mean and rms scalar profiles are obtained using 40 particles per cell for the LPEM method or 40 Eulerian fields for the SEF method. Results from these stochastic methods are compared with results obtained using two- and three-environment MEPDF methods. The relative advantages and disadvantages of each method in terms of accuracy and computational requirements are explored and identified. In general, the results obtained from the two stochastic methods (LPEM and SEF) are very similar, and are in closer agreement with experimental measurements than those obtained using the MEPDF method, while MEPDF is the most computationally efficient of the three methods. These and other findings are discussed in detail.

Theoretical investigation of cyromazine tautomerism using density functional theory and Møller–Plesset perturbation theory methods

USDA-ARS?s Scientific Manuscript database

A computational chemistry analysis of six unique tautomers of cyromazine, a pesticide used for fly control, was performed with density functional theory (DFT) and canonical second order Møller–Plesset perturbation theory (MP2) methods to gain insight into the contributions of molecular structure to ...

Dispersion Interactions between Rare Gas Atoms: Testing the London Equation Using ab Initio Methods

ERIC Educational Resources Information Center

Halpern, Arthur M.

2011-01-01

A computational chemistry experiment is described in which students can use advanced ab initio quantum mechanical methods to test the ability of the London equation to account quantitatively for the attractive (dispersion) interactions between rare gas atoms. Using readily available electronic structure applications, students can calculate the…

Microgravity Diode Laser Spectroscopy Measurements in a Reacting Vortex Ring

NASA Technical Reports Server (NTRS)

Chen, Shin-Juh; Dahm, Werner J. A.; Silver, Joel A.; Piltch, Nancy D.

2001-01-01

The technique of Diode Laser Spectroscopy (DLS) with wavelength modulation is utilized to measure the concentration of methane in reacting vortex rings under microgravity conditions. From the measured concentration of methane, other major species such as water, carbon dioxide, nitrogen, and oxygen can be easily computed under the assumption of equilibrium chemistry with the method of Interactive Temperature with Assumed Chemistry (ITAC). The conserved scalar approach in modelling the coupling between fluid dynamics and combustion is utilized to represent the unknown variables in terms of the mixture fraction and scalar dissipation rate in conjunction with ITAC. Post-processing of the DLS measurements and the method of ITAC used in computing the species concentration are discussed. From the flame luminosity results, the increase in ring circulation appears to increase the fuel consumption rate inside the reacting vortex ring and the flame height for cases with similar fuel volumes. Preliminary results and application of ITAC show some potential capabilities of ITAC in DLS. The measured concentration of methane, and computed concentrations of water and carbon dioxide agree well with available results from numerical simulations.

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.

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…

Computational design of soft materials for the capture of Cs-137 in contaminated environments: From 2D covalent cucurbituril networks to 3D supramolecular materials

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

Pichierri, Fabio, E-mail: fabio@che.tohoku.ac.jp

Using computational quantum chemistry methods we design novel 2D and 3D soft materials made of cucurbituril macrocycles covalently connected with each other via rigid linkers. Such covalent cucurbituril networks might be useful for the capture of radioactive Cs-137 (present as Cs{sup +}) in the contaminated environment.

Computer analysis of potentiometric data of complexes formation in the solution

NASA Astrophysics Data System (ADS)

Jastrzab, Renata; Kaczmarek, Małgorzata T.; Tylkowski, Bartosz; Odani, Akira

2018-02-01

The determination of equilibrium constants is an important process for many branches of chemistry. In this review we provide the readers with a discussion on computer methods which have been applied for elaboration of potentiometric experimental data generated during complexes formation in solution. The review describes both: general basis of modeling tools and examples of the use of calculated stability constants.

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

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

Tensor contractions represent the most compute-intensive core kernels in ab initio computational quantum chemistry and nuclear physics. Symmetries in these tensor contractions makes them difficult to load balance and scale to large distributed systems. In this paper, we develop an efficient and scalable algorithm to contract symmetric tensors. We introduce a novel approach that avoids data redistribution in contracting symmetric tensors while also avoiding redundant storage and maintaining load balance. We present experimental results on two parallel supercomputers for several symmetric contractions that appear in the CCSD quantum chemistry method. We also present a novel approach to tensor redistribution thatmore » can take advantage of parallel hyperplanes when the initial distribution has replicated dimensions, and use collective broadcast when the final distribution has replicated dimensions, making the algorithm very efficient.« less

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.…

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.

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.

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…

Estimation of Radiative Efficiency of Chemicals with Potentially Significant Global Warming Potential.

PubMed

Betowski, Don; Bevington, Charles; Allison, Thomas C

2016-01-19

Halogenated chemical substances are used in a broad array of applications, and new chemical substances are continually being developed and introduced into commerce. While recent research has considerably increased our understanding of the global warming potentials (GWPs) of multiple individual chemical substances, this research inevitably lags behind the development of new chemical substances. There are currently over 200 substances known to have high GWP. Evaluation of schemes to estimate radiative efficiency (RE) based on computational chemistry are useful where no measured IR spectrum is available. This study assesses the reliability of values of RE calculated using computational chemistry techniques for 235 chemical substances against the best available values. Computed vibrational frequency data is used to estimate RE values using several Pinnock-type models, and reasonable agreement with reported values is found. Significant improvement is obtained through scaling of both vibrational frequencies and intensities. The effect of varying the computational method and basis set used to calculate the frequency data is discussed. It is found that the vibrational intensities have a strong dependence on basis set and are largely responsible for differences in computed RE values.

ToxCast: Using high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Applications of high throughput screening to identify profiles of biological activity

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

Predictive In Vitro Screening of Environmental Chemicals – The ToxCast Project

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

EPA'S TOXCAST PROGRAM FOR PREDICTING HAZARD AND PRIORITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

EPA is developing methods for utilizing computational chemistry, high-throughput screening (HTS) and various toxicogenomic technologies to predict potential for toxicity and prioritize limited testing resources towards chemicals that likely represent the greatest hazard to human ...

Research in computational fluid dynamics

NASA Technical Reports Server (NTRS)

Murman, Earll M.

1987-01-01

The numerical integration of quasi-one-dimensional unsteady flow problems which involve finite rate chemistry are discussed, and are expressed in terms of conservative form Euler and species conservation equations. Hypersonic viscous calculations for delta wing geometries is also examined. The conical Navier-Stokes equations model was selected in order to investigate the effects of viscous-inviscid interations. The more complete three-dimensional model is beyond the available computing resources. The flux vector splitting method with van Leer's MUSCL differencing is being used. Preliminary results were computed for several conditions.

Designing Artificial Enzymes by Intuition and Computation

PubMed Central

Nanda, Vikas; Koder, Ronald L.

2012-01-01

The rational design of artificial enzymes either by applying physio-chemical intuition of protein structure and function or with the aid of computation methods is a promising area of research with the potential to tremendously impact medicine, industrial chemistry and energy production. Designed proteins also provide a powerful platform for dissecting enzyme mechanisms of natural systems. Artificial enzymes have come a long way, from simple α-helical peptide catalysts to proteins that facilitate multi-step chemical reactions designed by state-of-the-art computational methods. Looking forward, we examine strategies employed by natural enzymes which could be used to improve the speed and selectivity of artificial catalysts. PMID:21124375

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)

[Global Atmospheric Chemistry/Transport Modeling and Data-Analysis

NASA Technical Reports Server (NTRS)

Prinn, Ronald G.

1999-01-01

This grant supported a global atmospheric chemistry/transport modeling and data- analysis project devoted to: (a) development, testing, and refining of inverse methods for determining regional and global transient source and sink strengths for trace gases; (b) utilization of these inverse methods which use either the Model for Atmospheric Chemistry and Transport (MATCH) which is based on analyzed observed winds or back- trajectories calculated from these same winds for determining regional and global source and sink strengths for long-lived trace gases important in ozone depletion and the greenhouse effect; (c) determination of global (and perhaps regional) average hydroxyl radical concentrations using inverse methods with multiple "titrating" gases; and (d) computation of the lifetimes and spatially resolved destruction rates of trace gases using 3D models. Important ultimate goals included determination of regional source strengths of important biogenic/anthropogenic trace gases and also of halocarbons restricted by the Montreal Protocol and its follow-on agreements, and hydrohalocarbons now used as alternatives to the above restricted halocarbons.

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…

Computational chemistry in 25 years

NASA Astrophysics Data System (ADS)

Abagyan, Ruben

2012-01-01

Here we are making some predictions based on three methods: a straightforward extrapolations of the existing trends; a self-fulfilling prophecy; and picking some current grievances and predicting that they will be addressed or solved. We predict the growth of multicore computing and dramatic growth of data, as well as the improvements in force fields and sampling methods. We also predict that effects of therapeutic and environmental molecules on human body, as well as complex natural chemical signalling will be understood in terms of three dimensional models of their binding to specific pockets.

Transient Macroscopic Chemistry in the DSMC Method

NASA Astrophysics Data System (ADS)

Goldsworthy, M. J.; Macrossan, M. N.; Abdel-Jawad, M.

2008-12-01

In the Direct Simulation Monte Carlo method, a combination of statistical and deterministic procedures applied to a finite number of `simulator' particles are used to model rarefied gas-kinetic processes. Traditionally, chemical reactions are modelled using information from specific colliding particle pairs. In the Macroscopic Chemistry Method (MCM), the reactions are decoupled from the specific particle pairs selected for collisions. Information from all of the particles within a cell is used to determine a reaction rate coefficient for that cell. MCM has previously been applied to steady flow DSMC simulations. Here we show how MCM can be used to model chemical kinetics in DSMC simulations of unsteady flow. Results are compared with a collision-based chemistry procedure for two binary reactions in a 1-D unsteady shock-expansion tube simulation and during the unsteady development of 2-D flow through a cavity. For the shock tube simulation, close agreement is demonstrated between the two methods for instantaneous, ensemble-averaged profiles of temperature and species mole fractions. For the cavity flow, a high degree of thermal non-equilibrium is present and non-equilibrium reaction rate correction factors are employed in MCM. Very close agreement is demonstrated for ensemble averaged mole fraction contours predicted by the particle and macroscopic methods at three different flow-times. A comparison of the accumulated number of net reactions per cell shows that both methods compute identical numbers of reaction events. For the 2-D flow, MCM required similar CPU and memory resources to the particle chemistry method. The Macroscopic Chemistry Method is applicable to any general DSMC code using any viscosity or non-reacting collision models and any non-reacting energy exchange models. MCM can be used to implement any reaction rate formulations, whether these be from experimental or theoretical studies.

TOXCAST: A PROGRAM FOR PRIORTITIZING TOXICITY TESTING OF ENVIRONMENTAL CHEMICALS

EPA Science Inventory

Evaluating the potential of tens of thousands of chemicals for risk to human health and the environment is beyond the resource limits of the Environmental Protection Agency. The EPA's ToxCast program will explore alternative methods comprising computational chemistry, high-throug...

Applications of high throughput screening to identify profiles of biological activity relevant to carcinogenesis

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry and bioactivity profiling to predict potential for toxicity and prioritize limited testing resources (www.epa.gov/toc...

ExpoCast: Exposure Science for Prioritization and Toxicity Testing (S)

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCast. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize limi...

ExpoCast: Exposure Science for Prioritization and Toxicity Testing

EPA Science Inventory

The US EPA is completing the Phase I pilot for a chemical prioritization research program, called ToxCastTM. Here EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomic technologies to predict potential toxicity and prioritize l...

Navigating through the domains of biology and chemistry

EPA Science Inventory

Developing computational toxicology methods to assist the risk assessment process has recently gained much attention both in regulatory agencies and industries. The FDA Center for Food Safety and Applied Nutrition’s Office of Food Additive Safety (CFSAN OFAS) uses (Q)SAR approach...

Soft computing methods in design of superalloys

NASA Technical Reports Server (NTRS)

Cios, K. J.; Berke, L.; Vary, A.; Sharma, S.

1995-01-01

Soft computing techniques of neural networks and genetic algorithms are used in the design of superalloys. The cyclic oxidation attack parameter K(sub a), generated from tests at NASA Lewis Research Center, is modeled as a function of the superalloy chemistry and test temperature using a neural network. This model is then used in conjunction with a genetic algorithm to obtain an optimized superalloy composition resulting in low K(sub a) values.

Soft Computing Methods in Design of Superalloys

NASA Technical Reports Server (NTRS)

Cios, K. J.; Berke, L.; Vary, A.; Sharma, S.

1996-01-01

Soft computing techniques of neural networks and genetic algorithms are used in the design of superalloys. The cyclic oxidation attack parameter K(sub a), generated from tests at NASA Lewis Research Center, is modelled as a function of the superalloy chemistry and test temperature using a neural network. This model is then used in conjunction with a genetic algorithm to obtain an optimized superalloy composition resulting in low K(sub a) values.

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.

Automated Transition State Search and Its Application to Diverse Types of Organic Reactions.

PubMed

Jacobson, Leif D; Bochevarov, Art D; Watson, Mark A; Hughes, Thomas F; Rinaldo, David; Ehrlich, Stephan; Steinbrecher, Thomas B; Vaitheeswaran, S; Philipp, Dean M; Halls, Mathew D; Friesner, Richard A

2017-11-14

Transition state search is at the center of multiple types of computational chemical predictions related to mechanistic investigations, reactivity and regioselectivity predictions, and catalyst design. The process of finding transition states in practice is, however, a laborious multistep operation that requires significant user involvement. Here, we report a highly automated workflow designed to locate transition states for a given elementary reaction with minimal setup overhead. The only essential inputs required from the user are the structures of the separated reactants and products. The seamless workflow combining computational technologies from the fields of cheminformatics, molecular mechanics, and quantum chemistry automatically finds the most probable correspondence between the atoms in the reactants and the products, generates a transition state guess, launches a transition state search through a combined approach involving the relaxing string method and the quadratic synchronous transit, and finally validates the transition state via the analysis of the reactive chemical bonds and imaginary vibrational frequencies as well as by the intrinsic reaction coordinate method. Our approach does not target any specific reaction type, nor does it depend on training data; instead, it is meant to be of general applicability for a wide variety of reaction types. The workflow is highly flexible, permitting modifications such as a choice of accuracy, level of theory, basis set, or solvation treatment. Successfully located transition states can be used for setting up transition state guesses in related reactions, saving computational time and increasing the probability of success. The utility and performance of the method are demonstrated in applications to transition state searches in reactions typical for organic chemistry, medicinal chemistry, and homogeneous catalysis research. In particular, applications of our code to Michael additions, hydrogen abstractions, Diels-Alder cycloadditions, carbene insertions, and an enzyme reaction model involving a molybdenum complex are shown and discussed.

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...

Probabilistic performance estimators for computational chemistry methods: The empirical cumulative distribution function of absolute errors

NASA Astrophysics Data System (ADS)

Pernot, Pascal; Savin, Andreas

2018-06-01

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely, (1) the probability for a new calculation to have an absolute error below a chosen threshold and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the standard error on all benchmarking statistics depends on the size of the reference dataset. Systematic publication of these standard errors would be very helpful to assess the statistical reliability of benchmarking conclusions.

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

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

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.

A stochastic multi-scale method for turbulent premixed combustion

NASA Astrophysics Data System (ADS)

Cha, Chong M.

2002-11-01

The stochastic chemistry algorithm of Bunker et al. and Gillespie is used to perform the chemical reactions in a transported probability density function (PDF) modeling approach of turbulent combustion. Recently, Kraft & Wagner have demonstrated a 100-fold gain in computational speed (for a 100 species mechanism) using the stochastic approach over the conventional, direct integration method of solving for the chemistry. Here, the stochastic chemistry algorithm is applied to develop a new transported PDF model of turbulent premixed combustion. The methodology relies on representing the relevant spatially dependent physical processes as queuing events. The canonical problem of a one-dimensional premixed flame is used for validation. For the laminar case, molecular diffusion is described by a random walk. For the turbulent case, one of two different material transport submodels can provide the necessary closure: Taylor dispersion or Kerstein's one-dimensional turbulence approach. The former exploits ``eddy diffusivity'' and hence would be much more computationally tractable for practical applications. Various validation studies are performed. Results from the Monte Carlo simulations compare well to asymptotic solutions of laminar premixed flames, both with and without high activation temperatures. The correct scaling of the turbulent burning velocity is predicted in both Damköhler's small- and large-scale turbulence limits. The effect of applying the eddy diffusivity concept in the various regimes is discussed.

ToxCast: Developing Predictive Signatures of Chemically Induced Toxicity (Developing Predictive Bioactivity Signatures from ToxCasts HTS Data)

EPA Science Inventory

ToxCast, the United States Environmental Protection Agency’s chemical prioritization research program, is developing methods for utilizing computational chemistry, bioactivity profiling and toxicogenomic data to predict potential for toxicity and prioritize limited testing resour...

Computer Series, 61: Bits & Pieces, 24.

ERIC Educational Resources Information Center

Moore, John W., Ed.

1985-01-01

Describes: (1) laboratory information science in the clinical chemistry curriculum; (2) testing Boyle's Law, a context for statistical methods in undergraduate laboratories; (3) acquiring chemical concepts using microcomputers as tutees; and (4) using Data Interchange Format files for Apple microcomputers. Includes feedback from a previous article…

Source-to-Dose Modeling of Phthalates: Lessons for Prioritization

EPA Science Inventory

Globally there is a need to characterize potential risk to human health and the environment that arises from the manufacture and use of tens of thousands of chemicals. The US EPA is developing methods for using computational chemistry, high-throughput screening, and toxicogenomi...

Microgravity Diode Laser Spectroscopy Measurements in a Reacting Vortex Ring

NASA Technical Reports Server (NTRS)

Chen, Shin-Juh; Dahm, Werner J. A.; Silver, Joel A.; Piltch, Nancy D.; VanderWal, R. (Technical Monitor)

2001-01-01

The technique of Diode Laser Spectroscopy (DLS) with wavelength modulation is utilized to measure the concentration of methane in reacting vortex rings under microgravity conditions. From the measured concentration of methane, other major species such as water, carbon dioxide, nitrogen, and oxygen can be easily computed under the assumption of equilibrium chemistry with an iterative method called ITAC (Iterative Temperature with Assumed Chemistry). The conserved scalar approach in modelling the coupling between fluid dynamics and combustion is utilized to represent the unknown variables in terms of the mixture fraction and scalar dissipation rate in conjunction with ITAC. Post-processing of the DLS and the method used to compute the species concentration are discussed. From the flame luminosity results, ring circulation appears to increase the fuel consumption rate inside the reacting vortex ring and the flame height for cases with similar fuel volumes but different ring circulations. The concentrations of methane, water, and carbon dioxide agree well with available results from numerical simulations.

Computational Prediction and Validation of an Expert's Evaluation of Chemical Probes

PubMed Central

Litterman, Nadia K.; Lipinski, Christopher A.; Bunin, Barry A.; Ekins, Sean

2016-01-01

In a decade with over half a billion dollars of investment, more than 300 chemical probes have been identified to have biological activity through NIH funded screening efforts. We have collected the evaluations of an experienced medicinal chemist on the likely chemistry quality of these probes based on a number of criteria including literature related to the probe and potential chemical reactivity. Over 20% of these probes were found to be undesirable. Analysis of the molecular properties of these compounds scored as desirable suggested higher pKa, molecular weight, heavy atom count and rotatable bond number. We were particularly interested whether the human evaluation aspect of medicinal chemistry due diligence could be computationally predicted. We used a process of sequential Bayesian model building and iterative testing as we included additional probes. Following external validation of these methods and comparing different machine learning methods we identified Bayesian models with accuracy comparable to other measures of drug-likeness and filtering rules created to date. PMID:25244007

Quantum chemistry in environmental pesticide risk assessment.

PubMed

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

2017-11-01

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

NASA/DoD Aerospace Knowledge Diffusion Research Project. Report Number 19. The U. S. Government Technical Report and the Transfer of Federally Funded Aerospace R&D: An Analysis of Five Studies

DTIC Science & Technology

1994-01-01

defined etymologically , according to report content and method (U.S. Department of Defense, 1964); behaviorally, according to the influence on the reader...SCIENCES 2 ASTRONAUTICS 7 MATERIALS & CHEMISTRY 3 ENGINEERING 8 PHYSICS 4 GEOSCIENCES 9 SPACE SCIENCES 5 LIFE SCIENCES 10 OTHER (specify) 63. IsANYof...YOUR work? (Circle ONLY one number) I AERONAUTICS 6 MATHEMATICAL & COMPUTER SCIENCES 2 ASTRONAUTICS 7 MATERIALS & CHEMISTRY 3 ENGINEERING 8 PHYSICS 4

International Journal of Quantum Chemistry. Quantum Chemistry Symposium Number 27: Proceedings of the International Symposium on Atomic, Molecular, and Condensed Matter Theory and Computational Methods Held in St. Augustine, Florida on 13-20 March 1993

DTIC Science & Technology

1993-03-20

photochromic glasses, x - ray absorbing television glasses, extrudablc oriented ceramics, and the ultra-pure materials for optical fibers. While...quartz through the analysis of x - ray diffraction experiments. The repeating nature of the quartz crystal give, many diffraction peaks which allow the...fused silica, which serves as a backbone for most of the silicate glasses. Doris Evans, an x - ray crystallographer at Corning, built a model of fused

Navier-Stokes computations with finite-rate chemistry for LO2/LH2 rocket engine plume flow studies

NASA Technical Reports Server (NTRS)

Dougherty, N. Sam; Liu, Baw-Lin

1991-01-01

Computational fluid dynamics methods have been developed and applied to Space Shuttle Main Engine LO2/LH2 plume flow simulation/analysis of airloading and convective base heating effects on the vehicle at high flight velocities and altitudes. New methods are described which were applied to the simulation of a Return-to-Launch-Site abort where the vehicle would fly briefly at negative angles of attack into its own plume. A simplified two-perfect-gases-mixing approach is used where one gas is the plume and the other is air at 180-deg and 135-deg flight angle of attack. Related research has resulted in real gas multiple-plume interaction methods with finite-rate chemistry described herein which are applied to the same high-altitude-flight conditions of 0 deg angle of attack. Continuing research plans are to study Orbiter wake/plume flows at several Mach numbers and altitudes during ascent and then to merge this model with the Shuttle 'nose-to-tail' aerodynamic and SRB plume models for an overall 'nose-to-plume' capability. These new methods are also applicable to future launch vehicles using clustered-engine LO2/LH2 propulsion.

Soot and Spectral Radiation Modeling for a High-Pressure Turbulent Spray Flame

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

Ferreryo-Fernandez, Sebastian; Paul, Chandan; Sircar, Arpan

Simulations are performed of a transient high-pressure turbulent n-dodecane spray flame under engine-relevant conditions. An unsteady RANS formulation is used, with detailed chemistry, a semi-empirical two-equation soot model, and a particle-based transported composition probability density function (PDF) method to account for unresolved turbulent fluctuations in composition and temperature. Results from the PDF model are compared with those from a locally well-stirred reactor (WSR) model to quantify the effects of turbulence-chemistry-soot interactions. Computed liquid and vapor penetration versus time, ignition delay, and flame lift-off height are in good agreement with experiment, and relatively small differences are seen between the WSR andmore » PDF models for these global quantities. Computed soot levels and spatial soot distributions from the WSR and PDF models show large differences, with PDF results being in better agreement with experimental measurements. An uncoupled photon Monte Carlo method with line-by-line spectral resolution is used to compute the spectral intensity distribution of the radiation leaving the flame. This provides new insight into the relative importance of molecular gas radiation versus soot radiation, and the importance of turbulent fluctuations on radiative heat transfer.« less

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

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 aided drug design

NASA Astrophysics Data System (ADS)

Jain, A.

2017-08-01

Computer based method can help in discovery of leads and can potentially eliminate chemical synthesis and screening of many irrelevant compounds, and in this way, it save time as well as cost. Molecular modeling systems are powerful tools for building, visualizing, analyzing and storing models of complex molecular structure that can help to interpretate structure activity relationship. The use of various techniques of molecular mechanics and dynamics and software in Computer aided drug design along with statistics analysis is powerful tool for the medicinal chemistry to synthesis therapeutic and effective drugs with minimum side effect.

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…

Predicting the reactivity of adhesive starting materials

Treesearch

Anthony H. Conner

1999-01-01

Phenolic compounds are important in the production of bonded-wood products. Phenolic compounds in addition to phenol and resorcinol are potential alternative feedstocks for producing adhesives. The reactivity of a wide variety of phenolic compounds with formaldehyde was investigated using semi-empirical and ab initio computational chemistry methods...

Teaching Chemistry with Electron Density Models.

ERIC Educational Resources Information Center

Shusterman, Gwendolyn P.; Shusterman, Alan J.

1997-01-01

Describes a method for teaching electronic structure and its relevance to chemical phenomena that relies on computer-generated three-dimensional models of electron density distributions. Discusses the quantum mechanical background needed and presents ways of using models of electronic ground states to teach electronic structure, bonding concepts,…

Testing electronic structure methods for describing intermolecular H...H interactions in supramolecular chemistry.

PubMed

Casadesús, Ricard; Moreno, Miquel; González-Lafont, Angels; Lluch, José M; Repasky, Matthew P

2004-01-15

In this article a wide variety of computational approaches (molecular mechanics force fields, semiempirical formalisms, and hybrid methods, namely ONIOM calculations) have been used to calculate the energy and geometry of the supramolecular system 2-(2'-hydroxyphenyl)-4-methyloxazole (HPMO) encapsulated in beta-cyclodextrin (beta-CD). The main objective of the present study has been to examine the performance of these computational methods when describing the short range H. H intermolecular interactions between guest (HPMO) and host (beta-CD) molecules. The analyzed molecular mechanics methods do not provide unphysical short H...H contacts, but it is obvious that their applicability to the study of supramolecular systems is rather limited. For the semiempirical methods, MNDO is found to generate more reliable geometries than AM1, PM3 and the two recently developed schemes PDDG/MNDO and PDDG/PM3. MNDO results only give one slightly short H...H distance, whereas the NDDO formalisms with modifications of the Core Repulsion Function (CRF) via Gaussians exhibit a large number of short to very short and unphysical H...H intermolecular distances. In contrast, the PM5 method, which is the successor to PM3, gives very promising results. Our ONIOM calculations indicate that the unphysical optimized geometries from PM3 are retained when this semiempirical method is used as the low level layer in a QM:QM formulation. On the other hand, ab initio methods involving good enough basis sets, at least for the high level layer in a hybrid ONIOM calculation, behave well, but they may be too expensive in practice for most supramolecular chemistry applications. Finally, the performance of the evaluated computational methods has also been tested by evaluating the energetic difference between the two most stable conformations of the host(beta-CD)-guest(HPMO) system. Copyright 2003 Wiley Periodicals, Inc. J Comput Chem 25: 99-105, 2004

Dichloro-Cycloazatriphosphane: The Missing Link between N2 P2 and P4 Ring Systems in the Systematic Development of NP Chemistry.

PubMed

Bresien, Jonas; Hinz, Alexander; Schulz, Axel; Suhrbier, Tim; Thomas, Max; Villinger, Alexander

2017-10-20

A dichloro-cycloazatriphosphane that incorporates a cyclic NP 3 backbone could be synthesized using knowledge gained from the chemistry of N 2 P 2 and P 4 ring systems. It fills the gap between the congeneric compounds [ClP(μ-NR)] 2 and [ClP(μ-PR)] 2 (R=sterically demanding substituent), and thus contributes to the systematic development of nitrogen-phosphorus chemistry in general. The title compound was studied with respect to its formation via a labile aminodiphosphene, which readily underwent different rearrangement reactions depending on the solvent. All compounds were fully characterized by experimental and computational methods. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Medicinal chemistry for 2020

PubMed Central

Satyanarayanajois, Seetharama D; Hill, Ronald A

2011-01-01

Rapid advances in our collective understanding of biomolecular structure and, in concert, of biochemical systems, coupled with developments in computational methods, have massively impacted the field of medicinal chemistry over the past two decades, with even greater changes appearing on the horizon. In this perspective, we endeavor to profile some of the most prominent determinants of change and speculate as to further evolution that may consequently occur during the next decade. The five main angles to be addressed are: protein–protein interactions; peptides and peptidomimetics; molecular diversity and pharmacological space; molecular pharmacodynamics (significance, potential and challenges); and early-stage clinical efficacy and safety. We then consider, in light of these, the future of medicinal chemistry and the educational preparation that will be required for future medicinal chemists. PMID:22004084

Physical Principle for Generation of Randomness

NASA Technical Reports Server (NTRS)

Zak, Michail

2009-01-01

A physical principle (more precisely, a principle that incorporates mathematical models used in physics) has been conceived as the basis of a method of generating randomness in Monte Carlo simulations. The principle eliminates the need for conventional random-number generators. The Monte Carlo simulation method is among the most powerful computational methods for solving high-dimensional problems in physics, chemistry, economics, and information processing. The Monte Carlo simulation method is especially effective for solving problems in which computational complexity increases exponentially with dimensionality. The main advantage of the Monte Carlo simulation method over other methods is that the demand on computational resources becomes independent of dimensionality. As augmented by the present principle, the Monte Carlo simulation method becomes an even more powerful computational method that is especially useful for solving problems associated with dynamics of fluids, planning, scheduling, and combinatorial optimization. The present principle is based on coupling of dynamical equations with the corresponding Liouville equation. The randomness is generated by non-Lipschitz instability of dynamics triggered and controlled by feedback from the Liouville equation. (In non-Lipschitz dynamics, the derivatives of solutions of the dynamical equations are not required to be bounded.)

Massively parallel sparse matrix function calculations with NTPoly

NASA Astrophysics Data System (ADS)

Dawson, William; Nakajima, Takahito

2018-04-01

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

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

NASA Astrophysics Data System (ADS)

Motta, Mario; Zhang, Shiwei

2018-05-01

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

Computer Assisted Design, Prediction, and Execution of Economical Organic Syntheses

NASA Astrophysics Data System (ADS)

Gothard, Nosheen Akber

The synthesis of useful organic molecules via simple and cost-effective routes is a core challenge in organic chemistry. In industry or academia, organic chemists use their chemical intuition, technical expertise and published procedures to determine an optimal pathway. This approach, not only takes time and effort, but also is cost prohibitive. Many potential optimal routes scratched on paper fail to get experimentally tested. In addition, with new methods being discovered daily are often overlooked by established techniques. This thesis reports a computational technique that assist the discovery of economical synthetic routes to useful organic targets. Organic chemistry exists as a network where chemicals are connected by reactions, analogous to citied connected by roads in a geographic map. This network topology of organic reactions in the network of organic chemistry (NOC) allows the application of graph-theory to devise algorithms for synthetic optimization of organic targets. A computational approach comprised of customizable algorithms, pre-screening filters, and existing chemoinformatic techniques is capable of answering complex questions and perform mechanistic tasks desired by chemists such as optimization of organic syntheses. One-pot reactions are central to modern synthesis since they save resources and time by avoiding isolation, purification, characterization, and production of chemical waste after each synthetic step. Sometimes, such reactions are identified by chance or, more often, by careful inspection of individual steps that are to be wired together. Algorithms are used to discover one-pot reactions and validated experimentally. Which demonstrate that the computationally predicted sequences can indeed by carried out experimentally in good overall yields. The experimental examples are chosen to from small networks of reactions around useful chemicals such as quinoline scaffolds, quinoline-based inhibitors of phosphoinositide 3-kinase delta (PI3Kdelta) enzyme, and thiophene derivatives. In this way, we replace individual synthetic connections with two-, three-, or even four-step one-pot sequences. Lastly, the computational method is utilized to devise hypothetical synthetic route to popular pharmaceutical drugs like NaproxenRTM and TaxolRTM. The algorithmically generated optimal pathways are evaluated with chemistry logic. By applying labor/cost factor It was revealed that not all shorter synthesis routes are economical, sometimes "Longest way round is the shortest way home" lengthier routes are found to be more economical and environmentally friendly.

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…

SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules

PubMed Central

Daina, Antoine; Michielin, Olivier; Zoete, Vincent

2017-01-01

To be effective as a drug, a potent molecule must reach its target in the body in sufficient concentration, and stay there in a bioactive form long enough for the expected biologic events to occur. Drug development involves assessment of absorption, distribution, metabolism and excretion (ADME) increasingly earlier in the discovery process, at a stage when considered compounds are numerous but access to the physical samples is limited. In that context, computer models constitute valid alternatives to experiments. Here, we present the new SwissADME web tool that gives free access to a pool of fast yet robust predictive models for physicochemical properties, pharmacokinetics, drug-likeness and medicinal chemistry friendliness, among which in-house proficient methods such as the BOILED-Egg, iLOGP and Bioavailability Radar. Easy efficient input and interpretation are ensured thanks to a user-friendly interface through the login-free website http://www.swissadme.ch. Specialists, but also nonexpert in cheminformatics or computational chemistry can predict rapidly key parameters for a collection of molecules to support their drug discovery endeavours. PMID:28256516

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.

Fourier Transforms Simplified: Computing an Infrared Spectrum from an Interferogram

ERIC Educational Resources Information Center

Hanley, Quentin S.

2012-01-01

Fourier transforms are used widely in chemistry and allied sciences. Examples include infrared, nuclear magnetic resonance, and mass spectroscopies. A thorough understanding of Fourier methods assists the understanding of microscopy, X-ray diffraction, and diffraction gratings. The theory of Fourier transforms has been presented in this "Journal",…

Improving chemical education from high school to college using a more hands-on approach

NASA Astrophysics Data System (ADS)

Ruddick, Kristie Winfield

In this work, various alternative teaching methods and activities for chemical education are developed, presented, and evaluated. In the first study, an original hands-on activity using LEGO® blocks to model ionic chemical formulas is presented together with quantitative and qualitative data regarding its educational effectiveness. Students explore cation to anion ratios using LEGO® blocks to represent trivalent, divalent and monovalent cations and anions. High school chemistry students who participated in the LEGO® lab showed significantly higher post-test scores than other students. The second study grows out of the creation of a computational lab module that is shown to significantly increase student learning in the subject of molecular orbital theory in first semester college General Chemistry. The third and final study presented is a course redesign project for college CHEM 1100, Preparation for General Chemistry. In this project the classroom is “flipped”. Students watch video lectures at home, and spend class time working with peers and the instructor on problem solving activities. The results presented here are one of the first quantitative studies showing the effectiveness of “flipping the classroom”. Students who were taught using the Reverse-Instruction (RI) method had significantly higher success in both the Preparation for General Chemistry course and traditionally taught General Chemistry I the following semester.

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

A Fresh Math Perspective Opens New Possibilities for Computational Chemistry

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

Vu, Linda; Govind, Niranjan; Yang, Chao

2017-05-26

By reformulating the TDDFT problem as a matrix function approximation, making use of a special transformation and taking advantage of the underlying symmetry with respect to a non-Euclidean metric, Yang and his colleagues were able to apply the Lanczos algorithm and a Kernal Polynomial Method (KPM) to approximate the absorption spectrum of several molecules. Both of these algorithms require relatively low-memory compared to non-symmetrical alternatives, which is the key to the computational savings.

The synergistic use of computation, chemistry and biology to discover novel peptide-based drugs: the time is right.

PubMed

Audie, J; Boyd, C

2010-01-01

The case for peptide-based drugs is compelling. Due to their chemical, physical and conformational diversity, and relatively unproblematic toxicity and immunogenicity, peptides represent excellent starting material for drug discovery. Nature has solved many physiological and pharmacological problems through the use of peptides, polypeptides and proteins. If nature could solve such a diversity of challenging biological problems through the use of peptides, it seems reasonable to infer that human ingenuity will prove even more successful. And this, indeed, appears to be the case, as a number of scientific and methodological advances are making peptides and peptide-based compounds ever more promising pharmacological agents. Chief among these advances are powerful chemical and biological screening technologies for lead identification and optimization, methods for enhancing peptide in vivo stability, bioavailability and cell-permeability, and new delivery technologies. Other advances include the development and experimental validation of robust computational methods for peptide lead identification and optimization. Finally, scientific analysis, biology and chemistry indicate the prospect of designing relatively small peptides to therapeutically modulate so-called 'undruggable' protein-protein interactions. Taken together a clear picture is emerging: through the synergistic use of the scientific imagination and the computational, chemical and biological methods that are currently available, effective peptide therapeutics for novel targets can be designed that surpass even the proven peptidic designs of nature.

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)

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…

SPRAI: coupling of radiative feedback and primordial chemistry in moving mesh hydrodynamics

NASA Astrophysics Data System (ADS)

Jaura, O.; Glover, S. C. O.; Klessen, R. S.; Paardekooper, J.-P.

2018-04-01

In this paper, we introduce a new radiative transfer code SPRAI (Simplex Photon Radiation in the Arepo Implementation) based on the SIMPLEX radiation transfer method. This method, originally used only for post-processing, is now directly integrated into the AREPO code and takes advantage of its adaptive unstructured mesh. Radiated photons are transferred from the sources through the series of Voronoi gas cells within a specific solid angle. From the photon attenuation, we derive corresponding photon fluxes and ionization rates and feed them to a primordial chemistry module. This gives us a self-consistent method for studying dynamical and chemical processes caused by ionizing sources in primordial gas. Since the computational cost of the SIMPLEX method does not scale directly with the number of sources, it is convenient for studying systems such as primordial star-forming haloes that may form multiple ionizing sources.

Computational intelligence approaches for pattern discovery in biological systems.

PubMed

Fogel, Gary B

2008-07-01

Biology, chemistry and medicine are faced by tremendous challenges caused by an overwhelming amount of data and the need for rapid interpretation. Computational intelligence (CI) approaches such as artificial neural networks, fuzzy systems and evolutionary computation are being used with increasing frequency to contend with this problem, in light of noise, non-linearity and temporal dynamics in the data. Such methods can be used to develop robust models of processes either on their own or in combination with standard statistical approaches. This is especially true for database mining, where modeling is a key component of scientific understanding. This review provides an introduction to current CI methods, their application to biological problems, and concludes with a commentary about the anticipated impact of these approaches in bioinformatics.

Nonequilibrium radiation and chemistry models for aerocapture vehicle flowfields, volume 3

NASA Technical Reports Server (NTRS)

Carlson, Leland A.

1991-01-01

The computer programs developed to calculate the shock wave precursor and the method of using them are described. This method calculated the precursor flow field in a nitrogen gas including the effects of emission and absorption of radiation on the energy and composition of gas. The radiative transfer is calculated including the effects of absorption and emission through the line as well as the continuum process in the shock layer and through the continuum processes only in the precursor. The effects of local thermodynamic nonequilibrium in the shock layer and precursor regions are also included in the radiative transfer calculations. Three computer programs utilized by this computational scheme to calculate the precursor flow field solution for a given shock layer flow field are discussed.

Recommendations for evaluation of computational methods

NASA Astrophysics Data System (ADS)

Jain, Ajay N.; Nicholls, Anthony

2008-03-01

The field of computational chemistry, particularly as applied to drug design, has become increasingly important in terms of the practical application of predictive modeling to pharmaceutical research and development. Tools for exploiting protein structures or sets of ligands known to bind particular targets can be used for binding-mode prediction, virtual screening, and prediction of activity. A serious weakness within the field is a lack of standards with respect to quantitative evaluation of methods, data set preparation, and data set sharing. Our goal should be to report new methods or comparative evaluations of methods in a manner that supports decision making for practical applications. Here we propose a modest beginning, with recommendations for requirements on statistical reporting, requirements for data sharing, and best practices for benchmark preparation and usage.

Computation of iodine species concentrations in water

NASA Technical Reports Server (NTRS)

Schultz, John R.; Mudgett, Paul D.; Flanagan, David T.; Sauer, Richard L.

1994-01-01

During an evaluation of the use of iodine as a water disinfectant and the development of methods for measuring various iodine species in water onboard Space Freedom, it became necessary to compute the concentration of the various species based on equilibrium principles alone. Of particular concern was the case when various amounts of iodine, iodide, strong acid, and strong base are added to water. Such solutions can be used to evaluate the performance of various monitoring methods being considered. The authors of this paper present an overview of aqueous iodine chemistry, a set of nonlinear equations which can be used to model the above case, and a computer program for solving this system of equations using the Newton-Raphson method. The program was validated by comparing results over a range of concentrations and pH values with those previously presented by Gottardi for a given pH. Use of this program indicated that there are multiple roots to many cases and selecting an appropriate initial guess is important. Comparison of program results with laboratory results for the case when only iodine is added to water indicates the program gives high pH values for the iodine concentrations normally used for water disinfection. Extending the model to include the effects of iodate formation results in the computer pH values being closer to those observed, but the model with iodate does not agree well for the case in which base is added in addition to iodine to raise the pH. Potential explanations include failure to obtain equilibrium conditions in the lab, inaccuracies in published values for the equilibrium constants, and inadequate model of iodine chemistry and/or the lack of adequate analytical methods for measuring the various iodine species in water.

Flux-split algorithms for flows with non-equilibrium chemistry and vibrational relaxation

NASA Technical Reports Server (NTRS)

Grossman, B.; Cinnella, P.

1990-01-01

The present consideration of numerical computation methods for gas flows with nonequilibrium chemistry thermodynamics gives attention to an equilibrium model, a general nonequilibrium model, and a simplified model based on vibrational relaxation. Flux-splitting procedures are developed for the fully-coupled inviscid equations encompassing fluid dynamics and both chemical and internal energy-relaxation processes. A fully coupled and implicit large-block structure is presented which embodies novel forms of flux-vector split and flux-difference split algorithms valid for nonequilibrium flow; illustrative high-temperature shock tube and nozzle flow examples are given.

Reports of the second All-Union conference on the chemistry of transplutonium elements (Dmitrovgrad, June 21-23, 1963)

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

Not Available

1987-05-01

The nine papers presented at this conference cover the following topics: the systematization, condensed description, and prediction of sets of anion exchange extraction constants on the basis of their statistical computer treatment; characteristics and uses of solid extractants containing D2EHPA and TBP for separating the transplutonium elements; enrichment of americium 242m and americium 242 by the Szilard-Chalmers method; an x-ray diffraction pattern analysis for transplutonium compounds; the radiation chemistry of americium; and the effects of alpha irradiation on the behavior of americium in perchlorate solutions.

International Journal of Quantum Chemistry. Quantum Chemistry Symposium Number 26: Proceedings of the International Symposium on Atomic, Molecular, and Condensed Matter Theory and Computational Methods Held in St. Augustine, Florida on 14-21 March 1992

DTIC Science & Technology

1993-02-01

Spectrum The vibrational IR spectra of formaldeh.de and its deuterated species have been measured by a number of groups and analyzed in several studies ... studies [23-28]. The order of the frontier (r) orbitals, a textbook example for simple group theory arguments, is determined by the high symmetry (Dy...simplexes will give a structure with octahedral symmetr\\ since the subgroup of the Coxeter group which leaves one component of a four -vector invariant

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…

Validation of chemistry models employed in a particle simulation method

NASA Technical Reports Server (NTRS)

Haas, Brian L.; Mcdonald, Jeffrey D.

1991-01-01

The chemistry models employed in a statistical particle simulation method, as implemented in the Intel iPSC/860 multiprocessor computer, are validated and applied. Chemical relaxation of five-species air in these reservoirs involves 34 simultaneous dissociation, recombination, and atomic-exchange reactions. The reaction rates employed in the analytic solutions are obtained from Arrhenius experimental correlations as functions of temperature for adiabatic gas reservoirs in thermal equilibrium. Favorable agreement with the analytic solutions validates the simulation when applied to relaxation of O2 toward equilibrium in reservoirs dominated by dissociation and recombination, respectively, and when applied to relaxation of air in the temperature range 5000 to 30,000 K. A flow of O2 over a circular cylinder at high Mach number is simulated to demonstrate application of the method to multidimensional reactive flows.

Optical characterization of shock-induced chemistry in the explosive nitromethane using DFT and time-dependent DFT

NASA Astrophysics Data System (ADS)

Pellouchoud, Lenson; Reed, Evan

2014-03-01

With continual improvements in ultrafast optical spectroscopy and new multi-scale methods for simulating chemistry for hundreds of picoseconds, the opportunity is beginning to exist to connect experiments with simulations on the same timescale. We compute the optical properties of the liquid phase energetic material nitromethane (CH3NO2) for the first 100 picoseconds behind the front of a simulated shock at 6.5km/s, close to the experimentally observed detonation shock speed. We utilize molecular dynamics trajectories computed using the multi-scale shock technique (MSST) for time-resolved optical spectrum calculations based on both linear response time-dependent DFT (TDDFT) and the Kubo-Greenwood (KG) formula within Kohn-Sham DFT. We find that TDDFT predicts optical conductivities 25-35% lower than KG-based values and provides better agreement with the experimentally measured index of refraction of unreacted nitromethane. We investigate the influence of electronic temperature on the KG spectra and find no significant effect at optical wavelengths. With all methods, the spectra evolve non-monotonically in time as shock-induced chemistry takes place. We attribute the time-resolved absorption at optical wavelengths to time-dependent populations of molecular decomposition products, including NO, CNO, CNOH, H2O, and larger molecules. Supported by NASA Space Technology Research Fellowship (NSTRF) #NNX12AM48H.

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

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,…

Progress in computational toxicology.

PubMed

Ekins, Sean

2014-01-01

Computational methods have been widely applied to toxicology across pharmaceutical, consumer product and environmental fields over the past decade. Progress in computational toxicology is now reviewed. A literature review was performed on computational models for hepatotoxicity (e.g. for drug-induced liver injury (DILI)), cardiotoxicity, renal toxicity and genotoxicity. In addition various publications have been highlighted that use machine learning methods. Several computational toxicology model datasets from past publications were used to compare Bayesian and Support Vector Machine (SVM) learning methods. The increasing amounts of data for defined toxicology endpoints have enabled machine learning models that have been increasingly used for predictions. It is shown that across many different models Bayesian and SVM perform similarly based on cross validation data. Considerable progress has been made in computational toxicology in a decade in both model development and availability of larger scale or 'big data' models. The future efforts in toxicology data generation will likely provide us with hundreds of thousands of compounds that are readily accessible for machine learning models. These models will cover relevant chemistry space for pharmaceutical, consumer product and environmental applications. Copyright © 2013 Elsevier Inc. All rights reserved.

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

Freitez, Juan A.; Sanchez, Morella; Ruette, Fernando

Application of simulated annealing (SA) and simplified GSA (SGSA) techniques for parameter optimization of parametric quantum chemistry method (CATIVIC) was performed. A set of organic molecules were selected for test these techniques. Comparison of the algorithms was carried out for error function minimization with respect to experimental values. Results show that SGSA is more efficient than SA with respect to computer time. Accuracy is similar in both methods; however, there are important differences in the final set of parameters.

Computational Nanotechnology Program

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1997-01-01

The objectives are: (1) development of methodological and computational tool for the quantum chemistry study of carbon nanostructures and (2) development of the fundamental understanding of the bonding, reactivity, and electronic structure of carbon nanostructures. Our calculations have continued to play a central role in understanding the outcome of the carbon nanotube macroscopic production experiment. The calculations on buckyonions offer the resolution of a long controversy between experiment and theory. Our new tight binding method offers increased speed for realistic simulations of large carbon nanostructures.

Parallel Performance of a Combustion Chemistry Simulation

DOE PAGES

Skinner, Gregg; Eigenmann, Rudolf

1995-01-01

We used a description of a combustion simulation's mathematical and computational methods to develop a version for parallel execution. The result was a reasonable performance improvement on small numbers of processors. We applied several important programming techniques, which we describe, in optimizing the application. This work has implications for programming languages, compiler design, and software engineering.

Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback

ERIC Educational Resources Information Center

Gunersel, Adalet Baris; Fleming, Steven

2014-01-01

Research shows that computer animations are especially helpful in fields such as chemistry and in this mixed-methods study, we investigate the educational effectiveness of Bio-Organic Reaction Animations (BioORA), a 3-D software, in four undergraduate biochemistry classes at different universities. Statistically significant findings indicate that…

IMPROVEMENT OF SMVGEAR II ON VECTOR AND SCALAR MACHINES THROUGH ABSOLUTE ERROR TOLERANCE CONTROL (R823186)

EPA Science Inventory

The computer speed of SMVGEAR II was improved markedly on scalar and vector machines with relatively little loss in accuracy. The improvement was due to a method of frequently recalculating the absolute error tolerance instead of keeping it constant for a given set of chemistry. ...

Methods and Applications of Computational Chemistry

DTIC Science & Technology

2007-07-04

RFFXUVYLDWKHGRPLQDQWµDQFKRULQJ¶$X< < ) 2 1 ERQG DW WKH HGJH RI WKH $XP ENWUVGT =? YJGTG VJG IQNF ENWUVGT .7/1OQUVN...WKH JROGFOXVWHU#U C TGUWNV VJGTG CRRGCTU H[FHVV QHJDWLYH FKDUJHV RQ WKH XQDQFKRUHG HGJH JROG DWRPV WKDWPDNHVWKHFRUUHVSRQGLQJ...FRQGLWLRQVVKRXOGEHVDWLVILHGIRU HGJH DWRPV6LQFHWKHPRVWRILQRUJDQLF FRPSRXQGV LV FKDUDFWHUL]HG E\\ D K\\SHUYDOHQW VWUXFWXUH ZKHUH

Investigation of thermal protection systems effects on viscid and inviscid flow fields for manned entry systems

NASA Technical Reports Server (NTRS)

Bartlett, E. P.; Morse, H. L.; Tong, H.

1971-01-01

Procedures and methods for predicting aerothermodynamic heating to delta orbiter shuttle vehicles were reviewed. A number of approximate methods were found to be adequate for large scale parameter studies, but are considered inadequate for final design calculations. It is recommended that final design calculations be based on a computer code which accounts for nonequilibrium chemistry, streamline spreading, entropy swallowing, and turbulence. It is further recommended that this code be developed with the intent that it can be directly coupled with an exact inviscid flow field calculation when the latter becomes available. A nonsimilar, equilibrium chemistry computer code (BLIMP) was used to evaluate the effects of entropy swallowing, turbulence, and various three dimensional approximations. These solutions were compared with available wind tunnel data. It was found study that, for wind tunnel conditions, the effect of entropy swallowing and three dimensionality are small for laminar boundary layers but entropy swallowing causes a significant increase in turbulent heat transfer. However, it is noted that even small effects (say, 10-20%) may be important for the shuttle reusability concept.

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...

Pharmacophore screening of the protein data bank for specific binding site chemistry.

PubMed

Campagna-Slater, Valérie; Arrowsmith, Andrew G; Zhao, Yong; Schapira, Matthieu

2010-03-22

A simple computational approach was developed to screen the Protein Data Bank (PDB) for putative pockets possessing a specific binding site chemistry and geometry. The method employs two commonly used 3D screening technologies, namely identification of cavities in protein structures and pharmacophore screening of chemical libraries. For each protein structure, a pocket finding algorithm is used to extract potential binding sites containing the correct types of residues, which are then stored in a large SDF-formatted virtual library; pharmacophore filters describing the desired binding site chemistry and geometry are then applied to screen this virtual library and identify pockets matching the specified structural chemistry. As an example, this approach was used to screen all human protein structures in the PDB and identify sites having chemistry similar to that of known methyl-lysine binding domains that recognize chromatin methylation marks. The selected genes include known readers of the histone code as well as novel binding pockets that may be involved in epigenetic signaling. Putative allosteric sites were identified on the structures of TP53BP1, L3MBTL3, CHEK1, KDM4A, and CREBBP.

High pressure jet flame numerical analysis of CO emissions by means of the flamelet generated manifolds technique

NASA Astrophysics Data System (ADS)

Donini, A.; Martin, S. M.; Bastiaans, R. J. M.; van Oijen, J. A.; de Goey, L. P. H.

2013-10-01

In the present paper a computational analysis of a high pressure confined premixed turbulent methane/air jet flames is presented. In this scope, chemistry is reduced by the use of the Flamelet Generated Manifold method [1] and the fluid flow is modeled in an LES and RANS context. The reaction evolution is described by the reaction progress variable, the heat loss is described by the enthalpy and the turbulence effect on the reaction is represented by the progress variable variance. The interaction between chemistry and turbulence is considered through a presumed probability density function (PDF) approach. The use of FGM as a combustion model shows that combustion features at gas turbine conditions can be satisfactorily reproduced with a reasonable computational effort. Furthermore, the present analysis indicates that the physical and chemical processes controlling carbon monoxide (CO) emissions can be captured only by means of unsteady simulations.

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).

Combined use of computational chemistry and chemoinformatics methods for chemical discovery

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

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

2015-12-31

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

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…

Triclosan Computational Conformational Chemistry Analysis for Antimicrobial Properties in Polymers.

PubMed

Petersen, Richard C

2015-03-01

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

Computer-Aided Drug Design in Epigenetics

NASA Astrophysics Data System (ADS)

Lu, Wenchao; Zhang, Rukang; Jiang, Hao; Zhang, Huimin; Luo, Cheng

2018-03-01

Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.

Computer-Aided Drug Design in Epigenetics

PubMed Central

Lu, Wenchao; Zhang, Rukang; Jiang, Hao; Zhang, Huimin; Luo, Cheng

2018-01-01

Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field. PMID:29594101

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

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

Jing Yanfei, E-mail: yanfeijing@uestc.edu.c; Huang Tingzhu, E-mail: tzhuang@uestc.edu.c; Duan Yong, E-mail: duanyong@yahoo.c

This study is mainly focused on iterative solutions with simple diagonal preconditioning to two complex-valued nonsymmetric systems of linear equations arising from a computational chemistry model problem proposed by Sherry Li of NERSC. Numerical experiments show the feasibility of iterative methods to some extent when applied to the problems and reveal the competitiveness of our recently proposed Lanczos biconjugate A-orthonormalization methods to other classic and popular iterative methods. By the way, experiment results also indicate that application specific preconditioners may be mandatory and required for accelerating convergence.

Time-dependent solution for axisymmetric flow over a blunt body with ideal gas, CF4, or equilibrium air chemistry

NASA Technical Reports Server (NTRS)

Hamilton, H. H., II; Spall, J. R.

1986-01-01

A time-asymptotic method has been used to obtain steady-flow solutions for axisymmetric inviscid flow over several blunt bodies including spheres, paraboloids, ellipsoids, and spherically blunted cones. Comparisons with experimental data and results of other computational methods have demonstrated that accurate solutions can be obtained using this approach. The method should prove useful as an analysis tool for comparing with experimental data and for making engineering calculations for blunt reentry vehicles.

Time-dependent solution for axisymmetric flow over a blunt body with ideal gas, CF4, or equilibrium air chemistry

NASA Astrophysics Data System (ADS)

Hamilton, H. H., II; Spall, J. R.

1986-07-01

A time-asymptotic method has been used to obtain steady-flow solutions for axisymmetric inviscid flow over several blunt bodies including spheres, paraboloids, ellipsoids, and spherically blunted cones. Comparisons with experimental data and results of other computational methods have demonstrated that accurate solutions can be obtained using this approach. The method should prove useful as an analysis tool for comparing with experimental data and for making engineering calculations for blunt reentry vehicles.

Automated Discovery of Elementary Chemical Reaction Steps Using Freezing String and Berny Optimization Methods.

PubMed

Suleimanov, Yury V; Green, William H

2015-09-08

We present a simple protocol which allows fully automated discovery of elementary chemical reaction steps using in cooperation double- and single-ended transition-state optimization algorithms--the freezing string and Berny optimization methods, respectively. To demonstrate the utility of the proposed approach, the reactivity of several single-molecule systems of combustion and atmospheric chemistry importance is investigated. The proposed algorithm allowed us to detect without any human intervention not only "known" reaction pathways, manually detected in the previous studies, but also new, previously "unknown", reaction pathways which involve significant atom rearrangements. We believe that applying such a systematic approach to elementary reaction path finding will greatly accelerate the discovery of new chemistry and will lead to more accurate computer simulations of various chemical processes.

Generalized theoretical method for the interaction between arbitrary nonuniform electric field and molecular vibrations: Toward near-field infrared spectroscopy and microscopy

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

Iwasa, Takeshi, E-mail: tiwasa@mail.sci.hokudai.ac.jp; Takenaka, Masato; Taketsugu, Tetsuya

A theoretical method to compute infrared absorption spectra when a molecule is interacting with an arbitrary nonuniform electric field such as near-fields is developed and numerically applied to simple model systems. The method is based on the multipolar Hamiltonian where the light-matter interaction is described by a spatial integral of the inner product of the molecular polarization and applied electric field. The computation scheme is developed under the harmonic approximation for the molecular vibrations and the framework of modern electronic structure calculations such as the density functional theory. Infrared reflection absorption and near-field infrared absorption are considered as model systems.more » The obtained IR spectra successfully reflect the spatial structure of the applied electric field and corresponding vibrational modes, demonstrating applicability of the present method to analyze modern nanovibrational spectroscopy using near-fields. The present method can use arbitral electric fields and thus can integrate two fields such as computational chemistry and electromagnetics.« less

Generalized theoretical method for the interaction between arbitrary nonuniform electric field and molecular vibrations: Toward near-field infrared spectroscopy and microscopy.

PubMed

Iwasa, Takeshi; Takenaka, Masato; Taketsugu, Tetsuya

2016-03-28

A theoretical method to compute infrared absorption spectra when a molecule is interacting with an arbitrary nonuniform electric field such as near-fields is developed and numerically applied to simple model systems. The method is based on the multipolar Hamiltonian where the light-matter interaction is described by a spatial integral of the inner product of the molecular polarization and applied electric field. The computation scheme is developed under the harmonic approximation for the molecular vibrations and the framework of modern electronic structure calculations such as the density functional theory. Infrared reflection absorption and near-field infrared absorption are considered as model systems. The obtained IR spectra successfully reflect the spatial structure of the applied electric field and corresponding vibrational modes, demonstrating applicability of the present method to analyze modern nanovibrational spectroscopy using near-fields. The present method can use arbitral electric fields and thus can integrate two fields such as computational chemistry and electromagnetics.

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…

Development of a Computational Chemical Vapor Deposition Model: Applications to Indium Nitride and Dicyanovinylaniline

NASA Technical Reports Server (NTRS)

Cardelino, Carlos

1999-01-01

A computational chemical vapor deposition (CVD) model is presented, that couples chemical reaction mechanisms with fluid dynamic simulations for vapor deposition experiments. The chemical properties of the systems under investigation are evaluated using quantum, molecular and statistical mechanics models. The fluid dynamic computations are performed using the CFD-ACE program, which can simulate multispecies transport, heat and mass transfer, gas phase chemistry, chemistry of adsorbed species, pulsed reactant flow and variable gravity conditions. Two experimental setups are being studied, in order to fabricate films of: (a) indium nitride (InN) from the gas or surface phase reaction of trimethylindium and ammonia; and (b) 4-(1,1)dicyanovinyl-dimethylaminoaniline (DCVA) by vapor deposition. Modeling of these setups requires knowledge of three groups of properties: thermodynamic properties (heat capacity), transport properties (diffusion, viscosity, and thermal conductivity), and kinetic properties (rate constants for all possible elementary chemical reactions). These properties are evaluated using computational methods whenever experimental data is not available for the species or for the elementary reactions. The chemical vapor deposition model is applied to InN and DCVA. Several possible InN mechanisms are proposed and analyzed. The CVD model simulations of InN show that the deposition rate of InN is more efficient when pulsing chemistry is used under conditions of high pressure and microgravity. An analysis of the chemical properties of DCVA show that DCVA dimers may form under certain conditions of physical vapor transport. CVD simulations of the DCVA system suggest that deposition of the DCVA dimer may play a small role in the film and crystal growth processes.

A study of health effects of long-distance ocean voyages on seamen using a data classification approach

PubMed Central

2010-01-01

Background Long-distance ocean voyages may have substantial impacts on seamen's health, possibly causing malnutrition and other illness. Measures can possibly be taken to prevent such problems from happening through preparing special diet and making special precautions prior or during the sailing if a detailed understanding can be gained about what specific health effects such voyages may have on the seamen. Methods We present a computational study on 200 seamen using 41 chemistry indicators measured on their blood samples collected before and after the sailing. Our computational study is done using a data classification approach with a support vector machine-based classifier in conjunction with feature selections using a recursive feature elimination procedure. Results Our analysis results suggest that among the 41 blood chemistry measures, nine are most likely to be affected during the sailing, which provide important clues about the specific effects of ocean voyage on seamen's health. Conclusions The identification of the nine blood chemistry measures provides important clues about the effects of long-distance voyage on seamen's health. These findings will prove to be useful to guide in improving the living and working environment, as well as food preparation on ships. PMID:20219089

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

PubMed

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

2018-05-23

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

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

PubMed Central

2018-01-01

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

3D chemical imaging in the laboratory by hyperspectral X-ray computed tomography

PubMed Central

Egan, C. K.; Jacques, S. D. M.; Wilson, M. D.; Veale, M. C.; Seller, P.; Beale, A. M.; Pattrick, R. A. D.; Withers, P. J.; Cernik, R. J.

2015-01-01

We report the development of laboratory based hyperspectral X-ray computed tomography which allows the internal elemental chemistry of an object to be reconstructed and visualised in three dimensions. The method employs a spectroscopic X-ray imaging detector with sufficient energy resolution to distinguish individual elemental absorption edges. Elemental distributions can then be made by K-edge subtraction, or alternatively by voxel-wise spectral fitting to give relative atomic concentrations. We demonstrate its application to two material systems: studying the distribution of catalyst material on porous substrates for industrial scale chemical processing; and mapping of minerals and inclusion phases inside a mineralised ore sample. The method makes use of a standard laboratory X-ray source with measurement times similar to that required for conventional computed tomography. PMID:26514938

Advances in rapid compression machine studies of low- and intermediate-temperature autoignition phenomena

DOE PAGES

Goldsborough, S. Scott; Hochgreb, Simone; Vanhove, Guillaume; ...

2017-07-10

Rapid compression machines (RCMs) are widely-used to acquire experimental insights into fuel autoignition and pollutant formation chemistry, especially at conditions relevant to current and future combustion technologies. RCM studies emphasize important experimental regimes, characterized by low- to intermediate-temperatures (600–1200 K) and moderate to high pressures (5–80 bar). At these conditions, which are directly relevant to modern combustion schemes including low temperature combustion (LTC) for internal combustion engines and dry low emissions (DLE) for gas turbine engines, combustion chemistry exhibits complex and experimentally challenging behaviors such as the chemistry attributed to cool flame behavior and the negative temperature coefficient regime. Challengesmore » for studying this regime include that experimental observations can be more sensitive to coupled physical-chemical processes leading to phenomena such as mixed deflagrative/autoignitive combustion. Experimental strategies which leverage the strengths of RCMs have been developed in recent years to make RCMs particularly well suited for elucidating LTC and DLE chemistry, as well as convolved physical-chemical processes. Specifically, this work presents a review of experimental and computational efforts applying RCMs to study autoignition phenomena, and the insights gained through these efforts. A brief history of RCM development is presented towards the steady improvement in design, characterization, instrumentation and data analysis. Novel experimental approaches and measurement techniques, coordinated with computational methods are described which have expanded the utility of RCMs beyond empirical studies of explosion limits to increasingly detailed understanding of autoignition chemistry and the role of physical-chemical interactions. Fundamental insight into the autoignition chemistry of specific fuels is described, demonstrating the extent of knowledge of low-temperature chemistry derived from RCM studies, from simple hydrocarbons to multi-component blends and full-boiling range fuels. In conclusion, emerging needs and further opportunities are suggested, including investigations of under-explored fuels and the implementation of increasingly higher fidelity diagnostics.« less

Advances in rapid compression machine studies of low- and intermediate-temperature autoignition phenomena

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

Goldsborough, S. Scott; Hochgreb, Simone; Vanhove, Guillaume

Rapid compression machines (RCMs) are widely-used to acquire experimental insights into fuel autoignition and pollutant formation chemistry, especially at conditions relevant to current and future combustion technologies. RCM studies emphasize important experimental regimes, characterized by low- to intermediate-temperatures (600–1200 K) and moderate to high pressures (5–80 bar). At these conditions, which are directly relevant to modern combustion schemes including low temperature combustion (LTC) for internal combustion engines and dry low emissions (DLE) for gas turbine engines, combustion chemistry exhibits complex and experimentally challenging behaviors such as the chemistry attributed to cool flame behavior and the negative temperature coefficient regime. Challengesmore » for studying this regime include that experimental observations can be more sensitive to coupled physical-chemical processes leading to phenomena such as mixed deflagrative/autoignitive combustion. Experimental strategies which leverage the strengths of RCMs have been developed in recent years to make RCMs particularly well suited for elucidating LTC and DLE chemistry, as well as convolved physical-chemical processes. Specifically, this work presents a review of experimental and computational efforts applying RCMs to study autoignition phenomena, and the insights gained through these efforts. A brief history of RCM development is presented towards the steady improvement in design, characterization, instrumentation and data analysis. Novel experimental approaches and measurement techniques, coordinated with computational methods are described which have expanded the utility of RCMs beyond empirical studies of explosion limits to increasingly detailed understanding of autoignition chemistry and the role of physical-chemical interactions. Fundamental insight into the autoignition chemistry of specific fuels is described, demonstrating the extent of knowledge of low-temperature chemistry derived from RCM studies, from simple hydrocarbons to multi-component blends and full-boiling range fuels. In conclusion, emerging needs and further opportunities are suggested, including investigations of under-explored fuels and the implementation of increasingly higher fidelity diagnostics.« less

Electron-correlated fragment-molecular-orbital calculations for biomolecular and nano systems.

PubMed

Tanaka, Shigenori; Mochizuki, Yuji; Komeiji, Yuto; Okiyama, Yoshio; Fukuzawa, Kaori

2014-06-14

Recent developments in the fragment molecular orbital (FMO) method for theoretical formulation, implementation, and application to nano and biomolecular systems are reviewed. The FMO method has enabled ab initio quantum-mechanical calculations for large molecular systems such as protein-ligand complexes at a reasonable computational cost in a parallelized way. There have been a wealth of application outcomes from the FMO method in the fields of biochemistry, medicinal chemistry and nanotechnology, in which the electron correlation effects play vital roles. With the aid of the advances in high-performance computing, the FMO method promises larger, faster, and more accurate simulations of biomolecular and related systems, including the descriptions of dynamical behaviors in solvent environments. The current status and future prospects of the FMO scheme are addressed in these contexts.

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.

Perspective: Ring-polymer instanton theory

NASA Astrophysics Data System (ADS)

Richardson, Jeremy O.

2018-05-01

Since the earliest explorations of quantum mechanics, it has been a topic of great interest that quantum tunneling allows particles to penetrate classically insurmountable barriers. Instanton theory provides a simple description of these processes in terms of dominant tunneling pathways. Using a ring-polymer discretization, an efficient computational method is obtained for applying this theory to compute reaction rates and tunneling splittings in molecular systems. Unlike other quantum-dynamics approaches, the method scales well with the number of degrees of freedom, and for many polyatomic systems, the method may provide the most accurate predictions which can be practically computed. Instanton theory thus has the capability to produce useful data for many fields of low-temperature chemistry including spectroscopy, atmospheric and astrochemistry, as well as surface science. There is however still room for improvement in the efficiency of the numerical algorithms, and new theories are under development for describing tunneling in nonadiabatic transitions.

Incorporation of local structure into kriging models for the prediction of atomistic properties in the water decamer.

PubMed

Davie, Stuart J; Di Pasquale, Nicodemo; Popelier, Paul L A

2016-10-15

Machine learning algorithms have been demonstrated to predict atomistic properties approaching the accuracy of quantum chemical calculations at significantly less computational cost. Difficulties arise, however, when attempting to apply these techniques to large systems, or systems possessing excessive conformational freedom. In this article, the machine learning method kriging is applied to predict both the intra-atomic and interatomic energies, as well as the electrostatic multipole moments, of the atoms of a water molecule at the center of a 10 water molecule (decamer) cluster. Unlike previous work, where the properties of small water clusters were predicted using a molecular local frame, and where training set inputs (features) were based on atomic index, a variety of feature definitions and coordinate frames are considered here to increase prediction accuracy. It is shown that, for a water molecule at the center of a decamer, no single method of defining features or coordinate schemes is optimal for every property. However, explicitly accounting for the structure of the first solvation shell in the definition of the features of the kriging training set, and centring the coordinate frame on the atom-of-interest will, in general, return better predictions than models that apply the standard methods of feature definition, or a molecular coordinate frame. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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…

Per-Olov Löwdin - father of quantum chemistry

NASA Astrophysics Data System (ADS)

Brändas, Erkki J.

2017-09-01

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

CAG12 - A CSCM based procedure for flow of an equilibrium chemically reacting gas

NASA Technical Reports Server (NTRS)

Green, M. J.; Davy, W. C.; Lombard, C. K.

1985-01-01

The Conservative Supra Characteristic Method (CSCM), an implicit upwind Navier-Stokes algorithm, is extended to the numerical simulation of flows in chemical equilibrium. The resulting computer code known as Chemistry and Gasdynamics Implicit - Version 2 (CAG12) is described. First-order accurate results are presented for inviscid and viscous Mach 20 flows of air past a hemisphere-cylinder. The solution procedure captures the bow shock in a chemically reacting gas, a technique that is needed for simulating high altitude, rarefied flows. In an initial effort to validate the code, the inviscid results are compared with published gasdynamic and chemistry solutions and satisfactorily agreement is obtained.

A Simple Computer-Aided Three-Dimensional Molecular Modeling for the Octant Rule

ERIC Educational Resources Information Center

Kang, Yinan; Kang, Fu-An

2011-01-01

The Moffitt-Woodward-Moscowitz-Klyne-Djerassi octant rule is one of the most successful empirical rules in organic chemistry. However, the lack of a simple effective modeling method for the octant rule in the past 50 years has posed constant difficulties for researchers, teachers, and students, particularly the young generations, to learn and…

Development of efficient time-evolution method based on three-term recurrence relation

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

Akama, Tomoko, E-mail: a.tomo---s-b-l-r@suou.waseda.jp; Kobayashi, Osamu; Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp

The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function.more » Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.« less

Elucidating Hyperconjugation from Electronegativity to Predict Drug Conformational Energy in a High Throughput Manner.

PubMed

Liu, Zhaomin; Pottel, Joshua; Shahamat, Moeed; Tomberg, Anna; Labute, Paul; Moitessier, Nicolas

2016-04-25

Computational chemists use structure-based drug design and molecular dynamics of drug/protein complexes which require an accurate description of the conformational space of drugs. Organic chemists use qualitative chemical principles such as the effect of electronegativity on hyperconjugation, the impact of steric clashes on stereochemical outcome of reactions, and the consequence of resonance on the shape of molecules to rationalize experimental observations. While computational chemists speak about electron densities and molecular orbitals, organic chemists speak about partial charges and localized molecular orbitals. Attempts to reconcile these two parallel approaches such as programs for natural bond orbitals and intrinsic atomic orbitals computing Lewis structures-like orbitals and reaction mechanism have appeared. In the past, we have shown that encoding and quantifying chemistry knowledge and qualitative principles can lead to predictive methods. In the same vein, we thought to understand the conformational behaviors of molecules and to encode this knowledge back into a molecular mechanics tool computing conformational potential energy and to develop an alternative to atom types and training of force fields on large sets of molecules. Herein, we describe a conceptually new approach to model torsion energies based on fundamental chemistry principles. To demonstrate our approach, torsional energy parameters were derived on-the-fly from atomic properties. When the torsional energy terms implemented in GAFF, Parm@Frosst, and MMFF94 were substituted by our method, the accuracy of these force fields to reproduce MP2-derived torsional energy profiles and their transferability to a variety of functional groups and drug fragments were overall improved. In addition, our method did not rely on atom types and consequently did not suffer from poor automated atom type assignments.

[Towards computer-aided catalyst design: Three effective core potential studies of C-H activation]. Final report

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

NONE

1998-12-31

Research in the initial grant period focused on computational studies relevant to the selective activation of methane, the prime component of natural gas. Reaction coordinates for methane activation by experimental models were delineated, as well as the bonding and structure of complexes that effect this important reaction. This research, highlighted in the following sections, also provided the impetus for further development, and application of methods for modeling metal-containing catalysts. Sections of the report describe the following: methane activation by multiple-bonded transition metal complexes; computational lanthanide chemistry; and methane activation by non-imido, multiple-bonded ligands.

Bioinformatics by Example: From Sequence to Target

NASA Astrophysics Data System (ADS)

Kossida, Sophia; Tahri, Nadia; Daizadeh, Iraj

2002-12-01

With the completion of the human genome, and the imminent completion of other large-scale sequencing and structure-determination projects, computer-assisted bioscience is aimed to become the new paradigm for conducting basic and applied research. The presence of these additional bioinformatics tools stirs great anxiety for experimental researchers (as well as for pedagogues), since they are now faced with a wider and deeper knowledge of differing disciplines (biology, chemistry, physics, mathematics, and computer science). This review targets those individuals who are interested in using computational methods in their teaching or research. By analyzing a real-life, pharmaceutical, multicomponent, target-based example the reader will experience this fascinating new discipline.

A Framework for Load Balancing of Tensor Contraction Expressions via Dynamic Task Partitioning

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

Lai, Pai-Wei; Stock, Kevin; Rajbhandari, Samyam

In this paper, we introduce the Dynamic Load-balanced Tensor Contractions (DLTC), a domain-specific library for efficient task parallel execution of tensor contraction expressions, a class of computation encountered in quantum chemistry and physics. Our framework decomposes each contraction into smaller unit of tasks, represented by an abstraction referred to as iterators. We exploit an extra level of parallelism by having tasks across independent contractions executed concurrently through a dynamic load balancing run- time. We demonstrate the improved performance, scalability, and flexibility for the computation of tensor contraction expressions on parallel computers using examples from coupled cluster methods.

Cumulative reports and publications through 31 December 1983

NASA Technical Reports Server (NTRS)

1983-01-01

All reports for the calendar years 1975 through December 1983 are listed by author. Since ICASE reports are intended to be preprints of articles for journals and conference proceedings, the published reference is included when available. Thirteen older journal and conference proceedings references are included as well as five additional reports by ICASE personnel. Major categories of research covered include: (1) numerical methods, with particular emphasis on the development and analysis of basic algorithms; (2) computational problems in engineering and the physical sciences, particularly fluid dynamics, acoustics, structural analysis, and chemistry; and (3) computer systems and software, especially vector and parallel computers, microcomputers, and data management.

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.

Searching for life in the Universe: unconventional methods for an unconventional problem.

PubMed

Nealson, K H; Tsapin, A; Storrie-Lombardi, M

2002-12-01

The search for life, on and off our planet, can be done by conventional methods with which we are all familiar. These methods are sensitive and specific, and are often capable of detecting even single cells. However, if the search broadens to include life that may be different (even subtly different) in composition, the methods and even the approach must be altered. Here we discuss the development of what we call non-earthcentric life detection--detecting life with methods that could detect life no matter what its form or composition. To develop these methods, we simply ask, can we define life in terms of its general properties and particularly those that can be measured and quantified? Taking such an approach we can search for life using physics and chemistry to ask questions about structure, chemical composition, thermodynamics, and kinetics. Structural complexity can be searched for using computer algorithms that recognize complex structures. Once identified, these structures can be examined for a variety of chemical traits, including elemental composition, chirality, and complex chemistry. A second approach involves defining our environment in terms of energy sources (i.e., reductants), and oxidants (e.g. what is available to eat and breathe), and then looking for areas in which such phenomena are inexplicably out of chemical equilibrium. These disequilibria, when found, can then be examined in detail for the presence of the structural and chemical complexity that presumably characterizes any living systems. By this approach, we move the search for life to one that should facilitate the detection of any earthly life it encountered, as well as any non-conventional life forms that have structure, complex chemistry, and live via some form of redox chemistry.

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

PubMed

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

2016-06-30

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

Absolute Configuration of 3-METHYLCYCLOHEXANONE by Chiral Tag Rotational Spectroscopy and Vibrational Circular Dichroism

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Holdren, Martin S.; Mayer, Kevin J.; Smart, Taylor; West, Channing; Pate, Brooks

2017-06-01

The absolute configuration of 3-methylcyclohexanone was established by chiral tag rotational spectroscopy measurements using 3-butyn-2-ol as the tag partner. This molecule was chosen because it is a benchmark measurement for vibrational circular dichroism (VCD). A comparison of the analysis approaches of chiral tag rotational spectroscopy and VCD will be presented. One important issue in chiral analysis by both methods is the conformational flexibility of the molecule being analyzed. The analysis of conformational composition of samples will be illustrated. In this case, the high spectral resolution of molecular rotational spectroscopy and potential for spectral simplification by conformational cooling in the pulsed jet expansion are advantages for chiral tag spectroscopy. The computational chemistry requirements for the two methods will also be discussed. In this case, the need to perform conformer searches for weakly bound complexes and to perform reasonably high level quantum chemistry geometry optimizations on these complexes makes the computational time requirements less favorable for chiral tag rotational spectroscopy. Finally, the issue of reliability of the determination of the absolute configuration will be considered. In this case, rotational spectroscopy offers a "gold standard" analysis method through the determination of the ^{13}C-subsitution structure of the complex between 3-methylcyclohexanone and an enantiopure sample of the 3-butyn-2-ol tag.

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…

An Efficient Computational Model to Predict Protonation at the Amide Nitrogen and Reactivity along the C–N Rotational Pathway

PubMed Central

Szostak, Roman; Aubé, Jeffrey

2015-01-01

N-protonation of amides is critical in numerous biological processes, including amide bonds proteolysis and protein folding, as well as in organic synthesis as a method to activate amide bonds towards unconventional reactivity. A computational model enabling prediction of protonation at the amide bond nitrogen atom along the C–N rotational pathway is reported. Notably, this study provides a blueprint for the rational design and application of amides with a controlled degree of rotation in synthetic chemistry and biology. PMID:25766378

Thermodynamic equilibrium-air correlations for flowfield applications

NASA Technical Reports Server (NTRS)

Zoby, E. V.; Moss, J. N.

1981-01-01

Equilibrium-air thermodynamic correlations have been developed for flowfield calculation procedures. A comparison between the postshock results computed by the correlation equations and detailed chemistry calculations is very good. The thermodynamic correlations are incorporated in an approximate inviscid flowfield code with a convective heating capability for the purpose of defining the thermodynamic environment through the shock layer. Comparisons of heating rates computed by the approximate code and a viscous-shock-layer method are good. In addition to presenting the thermodynamic correlations, the impact of several viscosity models on the convective heat transfer is demonstrated.

Shape resonances of Be- and Mg- investigated with the method of analytic continuation

NASA Astrophysics Data System (ADS)

Čurík, Roman; Paidarová, I.; Horáček, J.

2018-05-01

The regularized method of analytic continuation is used to study the low-energy negative-ion states of beryllium (configuration 2 s2ɛ p 2P ) and magnesium (configuration 3 s2ɛ p 2P ) atoms. The method applies an additional perturbation potential and requires only routine bound-state multi-electron quantum calculations. Such computations are accessible by most of the free or commercial quantum chemistry software available for atoms and molecules. The perturbation potential is implemented as a spherical Gaussian function with a fixed width. Stability of the analytic continuation technique with respect to the width and with respect to the input range of electron affinities is studied in detail. The computed resonance parameters Er=0.282 eV, Γ =0.316 eV for the 2 p state of Be- and Er=0.188 eV, Γ =0.167 for the 3 p state of Mg- agree well with the best results obtained by much more elaborate and computationally demanding present-day methods.

Data-Driven Astrochemistry: One Step Further within the Origin of Life Puzzle.

PubMed

Ruf, Alexander; d'Hendecourt, Louis L S; Schmitt-Kopplin, Philippe

2018-06-01

Astrochemistry, meteoritics and chemical analytics represent a manifold scientific field, including various disciplines. In this review, clarifications on astrochemistry, comet chemistry, laboratory astrophysics and meteoritic research with respect to organic and metalorganic chemistry will be given. The seemingly large number of observed astrochemical molecules necessarily requires explanations on molecular complexity and chemical evolution, which will be discussed. Special emphasis should be placed on data-driven analytical methods including ultrahigh-resolving instruments and their interplay with quantum chemical computations. These methods enable remarkable insights into the complex chemical spaces that exist in meteorites and maximize the level of information on the huge astrochemical molecular diversity. In addition, they allow one to study even yet undescribed chemistry as the one involving organomagnesium compounds in meteorites. Both targeted and non-targeted analytical strategies will be explained and may touch upon epistemological problems. In addition, implications of (metal)organic matter toward prebiotic chemistry leading to the emergence of life will be discussed. The precise description of astrochemical organic and metalorganic matter as seeds for life and their interactions within various astrophysical environments may appear essential to further study questions regarding the emergence of life on a most fundamental level that is within the molecular world and its self-organization properties.

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.

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…

Simulation of a hydrocarbon fueled scramjet exhaust

NASA Technical Reports Server (NTRS)

Leng, J.

1982-01-01

Exhaust nozzle flow fields for a fully integrated, hydrocarbon burning scramjet were calculated for flight conditions of M (undisturbed free stream) = 4 at 6.1 km altitude and M (undisturbed free stream) = 6 at 30.5 km altitude. Equilibrium flow, frozen flow, and finite rate chemistry effects are considered. All flow fields were calculated by method of characteristics. Finite rate chemistry results were evaluated by a one dimensional code (Bittker) using streamtube area distributions extracted from the equilibrium flow field, and compared to very slow artificial rate cases for the same streamtube area distribution. Several candidate substitute gas mixtures, designed to simulate the gas dynamics of the real engine exhaust flow, were examined. Two mixtures are found to give excellent simulations of the specified exhaust flow fields when evaluated by the same method of characteristics computer code.

Identifying the relationship between feedback provided in computer-assisted instructional modules, science self-efficacy, and academic achievement

NASA Astrophysics Data System (ADS)

Mazingo, Diann Etsuko

Feedback has been identified as a key variable in developing academic self-efficacy. The types of feedback can vary from a traditional, objectivist approach that focuses on minimizing learner errors to a more constructivist approach, focusing on facilitating understanding. The influx of computer-based courses, whether online or through a series of computer-assisted instruction (CAI) modules require that the current research of effective feedback techniques in the classroom be extended to computer environments in order to impact their instructional design. In this study, exposure to different types of feedback during a chemistry CAI module was studied in relation to science self-efficacy (SSE) and performance on an objective-driven assessment (ODA) of the chemistry concepts covered in the unit. The quantitative analysis consisted of two separate ANCOVAs on the dependent variables, using pretest as the covariate and group as the fixed factor. No significant differences were found for either variable between the three groups on adjusted posttest means for the ODA and SSE measures (.95F(2, 106) = 1.311, p = 0.274 and .95F(2, 106) = 1.080, p = 0.344, respectively). However, a mixed methods approach yielded valuable qualitative insights into why only one overall quantitative effect was observed. These findings are discussed in relation to the need to further refine the instruments and methods used in order to more fully explore the possibility that type of feedback might play a role in developing SSE, and consequently, improve academic performance in science. Future research building on this study may reveal significance that could impact instructional design practices for developing online and computer-based instruction.

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...

Picking a Fight with Water, and Water Lost ... an Electron

NASA Astrophysics Data System (ADS)

Herr, Jonathan D.

The global need for energy is increasing, as is the importance of producing energy by green and renewable methodologies. This document outlines a research program dedicated to investigating a possible source for this form of energy generation and storage: solar fuels. The photon-induced splitting of water into molecular hydrogen and oxygen is currently hindered by large overpotentials from the oxidation half-reaction of water-splitting. This study concentrated on fundamental models of water-spitting chemistry, using a physical and computational chemistry analysis. The oxidation was first explored via ab initio electronic structure calculations of bare cationic water clusters, comprised of 2 to 21 molecules, in order to determine key electronic interactions that facilitate oxidation. Deeper understanding of these interactions could serve as guides for the development of viable water oxidation catalysts (WOC) designed to reduce overpotentials. The cationic water cluster study was followed by an investigation into hydrated copper (I) clusters, which acted as precursor models for real WOCs. Analyzing how the copper ion perturbed the properties of water clusters led to important electronic considerations for the development of WOCs, such as copper-water interactions that go beyond simple electrostatics. The importance of diagnostic thermodynamic properties, as well as anharmonic characteristics being persistent throughout oxidized water clusters, necessitated the use of quantum and classical molecular dynamics (MD) routines. Therefore, two new methods for accelerating computationally demanding classical and quantum MD methods were developed to increase their accessibility. The first method utilized a new form of electronic extrapolation - a linear prediction routine incorporating a Burg minimization - to decrease the iterations required for solving the electronic equations throughout the dynamics. The second method utilized a multiple-timestepping description of the potential energy term in the path integral molecular dynamics (PIMD) formalism. This method led to reductions of computational time by allowing the use of less computationally laborious methods for portions of the simulation and resulted in negligible increase of error. The determination of the fundamental driving forces within water oxidation and the development of acceleration techniques for important electronic structure methods will help drive progress into fully solar-initiated water oxidation.

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

Computational chemistry calculations of stability for bismuth nanotubes, fullerene-like structures and hydrogen-containing nanostructures.

PubMed

Kharissova, Oxana V; Osorio, Mario; Vázquez, Mario Sánchez; Kharisov, Boris I

2012-08-01

Using molecular mechanics (MM+), semi-empirical (PM6) and density functional theory (DFT) (B3LYP) methods we characterized bismuth nanotubes. In addition, we predicted the bismuth clusters {Bi(20)(C(5V)), Bi(24)(C(6v)), Bi(28)(C(1)), B(32)(D(3H)), Bi(60)(C(I))} and calculated their conductor properties.

Improved transition path sampling methods for simulation of rare events

NASA Astrophysics Data System (ADS)

Chopra, Manan; Malshe, Rohit; Reddy, Allam S.; de Pablo, J. J.

2008-04-01

The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.

Parallel scalability of Hartree-Fock calculations

NASA Astrophysics Data System (ADS)

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

2015-03-01

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

Quantitative collision induced mass spectrometry of substituted piperazines - A correlative analysis between theory and experiment

NASA Astrophysics Data System (ADS)

Ivanova, Bojidarka; Spiteller, Michael

2017-12-01

The present paper deals with quantitative kinetics and thermodynamics of collision induced dissociation (CID) reactions of piperazines under different experimental conditions together with a systematic description of effect of counter-ions on common MS fragment reactions of piperazines; and intra-molecular effect of quaternary cyclization of substituted piperazines yielding to quaternary salts. There are discussed quantitative model equations of rate constants as well as free Gibbs energies of series of m-independent CID fragment processes in GP, which have been evidenced experimentally. Both kinetic and thermodynamic parameters are also predicted by computational density functional theory (DFT) and ab initio both static and dynamic methods. The paper examines validity of Maxwell-Boltzmann distribution to non-Boltzmann CID processes in quantitatively as well. The experiments conducted within the latter framework yield to an excellent correspondence with theoretical quantum chemical modeling. The important property of presented model equations of reaction kinetics is the applicability in predicting unknown and assigning of known mass spectrometric (MS) patterns. The nature of "GP" continuum of CID-MS coupled scheme of measurements with electrospray ionization (ESI) source is discussed, performing parallel computations in gas-phase (GP) and polar continuum at different temperatures and ionic strengths. The effect of pressure is presented. The study contributes significantly to methodological and phenomenological developments of CID-MS and its analytical implementations for quantitative and structural analyses. It also demonstrates great prospective of a complementary application of experimental CID-MS and computational quantum chemistry studying chemical reactivity, among others. To a considerable extend this work underlies the place of computational quantum chemistry to the field of experimental analytical chemistry in particular highlighting the structural analysis.

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.

Empirical Force Fields for Mechanistic Studies of Chemical Reactions in Proteins.

PubMed

Das, A K; Meuwly, M

2016-01-01

Following chemical reactions in atomistic detail is one of the most challenging aspects of current computational approaches to chemistry. In this chapter the application of adiabatic reactive MD (ARMD) and its multistate version (MS-ARMD) are discussed. Both methods allow to study bond-breaking and bond-forming processes in chemical and biological processes. Particular emphasis is put on practical aspects for applying the methods to investigate the dynamics of chemical reactions. The chapter closes with an outlook of possible generalizations of the methods discussed. © 2016 Elsevier Inc. All rights reserved.

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.

Considerations for the independent reaction times and step-by-step methods for radiation chemistry simulations

NASA Astrophysics Data System (ADS)

Plante, Ianik; Devroye, Luc

2017-10-01

Ionizing radiation interacts with the water molecules of the tissues mostly by ionizations and excitations, which result in the formation of the radiation track structure and the creation of radiolytic species such as H.,.OH, H2, H2O2, and e-aq. After their creation, these species diffuse and may chemically react with the neighboring species and with the molecules of the medium. Therefore radiation chemistry is of great importance in radiation biology. As the chemical species are not distributed homogeneously, the use of conventional models of homogeneous reactions cannot completely describe the reaction kinetics of the particles. Actually, many simulations of radiation chemistry are done using the Independent Reaction Time (IRT) method, which is a very fast technique to calculate radiochemical yields but which do not calculate the positions of the radiolytic species as a function of time. Step-by-step (SBS) methods, which are able to provide such information, have been used only sparsely because these are time-consuming in terms of calculation. Recent improvements in computer performance now allow the regular use of the SBS method in radiation chemistry. The SBS and IRT methods are both based on the Green's functions of the diffusion equation (GFDE). In this paper, several sampling algorithms of the GFDE and for the IRT method are presented. We show that the IRT and SBS methods are exactly equivalent for 2-particles systems for diffusion and partially diffusion-controlled reactions between non-interacting particles. We also show that the results obtained with the SBS simulation method with periodic boundary conditions are in agreement with the predictions by classical reaction kinetics theory, which is an important step towards using this method for modelling of biochemical networks and metabolic pathways involved in oxidative stress. Finally, the first simulation results obtained with the code RITRACKS (Relativistic Ion Tracks) are 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

Part I: Reverse-docking studies of a squaramide-catalyzed conjugate addition of a diketone to a nitro-olefin Part II: The development of ChemSort: an education game for organic chemistry

NASA Astrophysics Data System (ADS)

Granger, Jenna Christine

Part 1: Reverse-docking studies of a squaramide-catalyzed conjugate addition of a diketone to a nitro-olefin. Asymmetric organocatalysis, the catalysis of asymmetric reactions by small organic molecules, is a rapidly growing field within organic synthesis. The ability to rationally design organocatalysts is therefore of increasing interest to organic chemists. Computational chemistry is quickly proving to be an extremely successful method for understanding and predicting the roles of organocatalysts, and therefore is certain to be of use in the rational design of such catalysts. A methodology for reverse-docking flexible organocatalysts to rigid transition state models of asymmetric reactions has been previously developed by the Deslongchamps group. The investigation of Rawal's squaramide-based organocatalyst for the addition of a diketone to a nitro-olefin is described, and the results of the reverse docking of Rawal's catalyst to the geometry optimized transition state models of the uncatalyzed reaction for both the R and S-product enantiomers are presented. The results of this study indicate a preference for binding of the organocatalyst to the R-enantiomer transition state model with a predicted enantiomeric excess of 99%, which is consistent with the experimental results. A plausible geometric model of the transition state for the catalyzed reaction is also presented. The success of this study demonstrates the credibility of using reverse docking methods for the rational design of asymmetric organocatalysts. Part 2: The development of ChemSort: an educational game for organic chemistry. With the advent of the millennial learner, we need to rethink traditional classroom approaches to science learning in terms of goals, approaches, and assessments. Digital simulations and games hold much promise in support of this educational shift. Although the idea of using games for education is not a new one, well-designed computer-based "serious games" are only beginning to emerge as exceptional tools for helping learners understand concepts and processes. The use of computer games for learning college-level organic chemistry is still relatively unexplored and underrepresented within the realm of "serious gaming". In this section, ideas for games as a way for teaching and learning organic chemistry will be introduced and the development process of ChemSort, a web-based Flash game for learning college-level organic chemistry topics, will be outlined. ChemSort is a path-based game, in which the player, or in this case the learner, must match the chemical structures with their appropriate functional groups. At the end of this section a 4-level useable prototype of ChemSort will be unveiled.

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 study of the rate-controlled constrained-equilibrium dimension reduction method and its different implementations

NASA Astrophysics Data System (ADS)

Hiremath, Varun; Pope, Stephen B.

2013-04-01

The Rate-Controlled Constrained-Equilibrium (RCCE) method is a thermodynamic based dimension reduction method which enables representation of chemistry involving n s species in terms of fewer n r constraints. Here we focus on the application of the RCCE method to Lagrangian particle probability density function based computations. In these computations, at every reaction fractional step, given the initial particle composition (represented using RCCE), we need to compute the reaction mapping, i.e. the particle composition at the end of the time step. In this work we study three different implementations of RCCE for computing this reaction mapping, and compare their relative accuracy and efficiency. These implementations include: (1) RCCE/TIFS (Trajectory In Full Space): this involves solving a system of n s rate-equations for all the species in the full composition space to obtain the reaction mapping. The other two implementations obtain the reaction mapping by solving a reduced system of n r rate-equations obtained by projecting the n s rate-equations for species evaluated in the full space onto the constrained subspace. These implementations include (2) RCCE: this is the classical implementation of RCCE which uses a direct projection of the rate-equations for species onto the constrained subspace; and (3) RCCE/RAMP (Reaction-mixing Attracting Manifold Projector): this is a new implementation introduced here which uses an alternative projector obtained using the RAMP approach. We test these three implementations of RCCE for methane/air premixed combustion in the partially-stirred reactor with chemistry represented using the n s=31 species GRI-Mech 1.2 mechanism with n r=13 to 19 constraints. We show that: (a) the classical RCCE implementation involves an inaccurate projector which yields large errors (over 50%) in the reaction mapping; (b) both RCCE/RAMP and RCCE/TIFS approaches yield significantly lower errors (less than 2%); and (c) overall the RCCE/TIFS approach is the most accurate, efficient (by orders of magnitude) and robust implementation.

Detailed and reduced chemical-kinetic descriptions for hydrocarbon combustion

NASA Astrophysics Data System (ADS)

Petrova, Maria V.

Numerical and theoretical studies of autoignition processes of fuels such as propane are in need of realistic simplified chemical-kinetic descriptions that retain the essential features of the detailed descriptions. These descriptions should be computationally feasible and cost-effective. Such descriptions are useful for investigating ignition processes that occur, for example, in homogeneous-charge compression-ignition engines, for studying the structures and dynamics of detonations and in fields such as multi-dimensional Computational Fluid Dynamics (CFD). Reduced chemistry has previously been developed successfully for a number of other hydrocarbon fuels, however, propane has not been considered in this manner. This work focuses on the fuels of propane, as well propene, allene and propyne, for several reasons. The ignition properties of propane resemble those of other higher hydrocarbons but are different from those of the lower hydrocarbons (e.g. ethylene and acetylene). Propane, therefore, may be the smallest hydrocarbon that is representative of higher hydrocarbons in ignition and detonation processes. Since the overall activation energy and ignition times for propane are similar to those of other higher hydrocarbons, including liquid fuels that are suitable for many applications, propane has been used as a model fuel for several numerical and experimental studies. The reason for studying elementary chemistry of propene and C3H4 (allene or propyne) is that during the combustion process, propane breaks down to propene and C3H4 before proceeding to products. Similarly, propene combustion includes C3H4 chemistry. In studying propane combustion, it is therefore necessary to understand the underlying combustion chemistry of propene as well as C3H 4. The first part of this thesis focuses on obtaining and testing a detailed chemical-kinetic description for autoignition of propane, propene and C 3H4, by comparing predictions obtained with this detailed mechanism against numerous experimental data available from shock-tube studies and flame-speed measurements. To keep the detailed mechanism small, attention is restricted to pressures below about 100 atm, temperatures above about 1000 K and equivalence ratios less than about 3. Based on this detailed chemistry description, short (or skeletal) mechanisms are then obtained for each of the three fuels by eliminating reactions that are unimportant for the autoignition process under conditions presented above. This was achieved by utilizing tools such as sensitivity and reaction pathway analyses. Two distinct methodologies were then used in order to obtain a reduced mechanism for autoignition from the short mechanisms. A Systematic Reduction approach is first taken that involves introducing steady-state approximations to as many species as analytically possible. To avoid resorting to numerical methods, the analysis for obtaining ignition times for heptane, presented by Peters and co-workers is followed in order to obtain a rough estimate for an expression of propane ignition time. The results from this expression are then compared to the ignition times obtained computationally with the detailed mechanism. The second method is an Empirical Approach in which chemistry is not derived formally, but rather postulated empirically on the basis of experimental, computational and theoretical observations. As a result, generalized reduced mechanisms are proposed for autoignition of propane, propene and C3H 4. Expressions for ignition times obtained via this empirical approach are compared to the computational results obtained from the detailed mechanism.

Complex Chemical Reaction Networks from Heuristics-Aided Quantum Chemistry.

PubMed

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

2014-03-11

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

Finite-Difference Solution for Laminar or Turbulent Boundary Layer Flow over Axisymmetric Bodies with Ideal Gas, CF4, or Equilibrium Air Chemistry

NASA Technical Reports Server (NTRS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-01-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

Finite-difference solution for laminar or turbulent boundary layer flow over axisymmetric bodies with ideal gas, CF4, or equilibrium air chemistry

NASA Astrophysics Data System (ADS)

Hamilton, H. Harris, II; Millman, Daniel R.; Greendyke, Robert B.

1992-12-01

A computer code was developed that uses an implicit finite-difference technique to solve nonsimilar, axisymmetric boundary layer equations for both laminar and turbulent flow. The code can treat ideal gases, air in chemical equilibrium, and carbon tetrafluoride (CF4), which is a useful gas for hypersonic blunt-body simulations. This is the only known boundary layer code that can treat CF4. Comparisons with experimental data have demonstrated that accurate solutions are obtained. The method should prove useful as an analysis tool for comparing calculations with wind tunnel experiments and for making calculations about flight vehicles where equilibrium air chemistry assumptions are valid.

The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.

PubMed

Xu, You; Villa, Alessandra; Nilsson, Lennart

2017-06-05

Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Nanodusty plasma chemistry: a mechanistic and variational transition state theory study of the initial steps of silyl anion-silane and silylene anion-silane polymerization reactions.

PubMed

Bao, Junwei Lucas; Seal, Prasenjit; Truhlar, Donald G

2015-06-28

The growth of nanodusty particles, which is critical in plasma chemistry, physics, and engineering. The aim of the present work is to understand the detailed reaction mechanisms of early steps in this growth. The polymerization of neutral silane with the silylene or silyl anion, which eliminates molecular hydrogen with the formation of their higher homologues, governs the silicon hydride clustering in nanodusty plasma chemistry. The detailed mechanisms of these important polymerization reactions in terms of elementary reactions have not been proposed yet. In the present work, we investigated the initial steps of these polymerization reactions, i.e., the SiH4 + Si2H4(-)/Si2H5(-) reactions, and we propose a three-step mechanism, which is also applicable to the following polymerization steps. CM5 charges of all the silicon-containing species were computed in order to analyze the character of the species in the proposed reaction mechanisms. We also calculated thermal rate constant of each step using multi-structural canonical variational transition state theory (MS-CVT) with the small-curvature tunneling (SCT) approximation, based on the minimum energy path computed using M08-HX/MG3S electronic structure method.

Growing Applications of “Click Chemistry” for Bioconjugation in Contemporary Biomedical Research

PubMed Central

Nwe, Kido

2009-01-01

Summation This update summarizes the growing application of “click” chemistry in diverse areas such as bioconjugation, drug discovery, materials science, and radiochemistry. This update also discusses click chemistry reactions that proceed rapidly with high selectivity, specificity, and yield. Two important characteristics make click chemistry so attractive for assembling compounds, reagents, and biomolecules for preclinical and clinical applications. First, click reactions are bio-orthogonal; neither the reactants nor their product's functional groups interact with functionalized biomolecules. Second, the reactions proceed with ease under mild nontoxic conditions, such as at room temperature and, usually, in water. The copper-catalyzed Huisgen cycloaddition, azide-alkyne [3 + 2] dipolar cycloaddition, Staudinger ligation, and azide-phosphine ligation each possess these unique qualities. These reactions can be used to modify one cellular component while leaving others unharmed or untouched. Click chemistry has found increasing applications in all aspects of drug discovery in medicinal chemistry, such as for generating lead compounds through combinatorial methods. Bioconjugation via click chemistry is rigorously employed in proteomics and nucleic research. In radiochemistry, selective radiolabeling of biomolecules in cells and living organisms for imaging and therapy has been realized by this technology. Bifunctional chelating agents for several radionuclides useful for positron emission tomography and single-photon emission computed tomography imaging have also been prepared by using click chemistry. This review concludes that click chemistry is not the perfect conjugation and assembly technology for all applications, but provides a powerful, attractive alternative to conventional chemistry. This chemistry has proven itself to be superior in satisfying many criteria (e.g., biocompatibility, selectivity, yield, stereospecificity, and so forth); thus, one can expect it will consequently become a more routine strategy in the near future for a wide range of applications. PMID:19538051

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

Ethers on Si(001): A Prime Example for the Common Ground between Surface Science and Molecular Organic Chemistry.

PubMed

Pecher, Lisa; Laref, Slimane; Raupach, Marc; Tonner, Ralf

2017-11-20

By using computational chemistry it has been shown that the adsorption of ether molecules on Si(001) under ultrahigh vacuum conditions can be understood with classical concepts of organic chemistry. Detailed analysis of the two-step reaction mechanism-1) formation of a dative bond between the ether oxygen atom and a Lewis acidic surface atom and 2) nucleophilic attack of a nearby Lewis basic surface atom-shows that it mirrors acid-catalyzed ether cleavage in solution. The O-Si dative bond is the strongest of its kind, and the reactivity in step 2 defies the Bell-Evans-Polanyi principle. Electron rearrangement during C-O bond cleavage has been visualized with a newly developed method for analyzing bonding, which shows that the mechanism of nucleophilic substitutions on semiconductor surfaces is identical to molecular S N 2 reactions. Our findings illustrate how surface science and molecular chemistry can mutually benefit from each other and unexpected insight can be gained. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

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...

ANI-1, A data set of 20 million calculated off-equilibrium conformations for organic molecules

NASA Astrophysics Data System (ADS)

Smith, Justin S.; Isayev, Olexandr; Roitberg, Adrian E.

2017-12-01

One of the grand challenges in modern theoretical chemistry is designing and implementing approximations that expedite ab initio methods without loss of accuracy. Machine learning (ML) methods are emerging as a powerful approach to constructing various forms of transferable atomistic potentials. They have been successfully applied in a variety of applications in chemistry, biology, catalysis, and solid-state physics. However, these models are heavily dependent on the quality and quantity of data used in their fitting. Fitting highly flexible ML potentials, such as neural networks, comes at a cost: a vast amount of reference data is required to properly train these models. We address this need by providing access to a large computational DFT database, which consists of more than 20 M off equilibrium conformations for 57,462 small organic molecules. We believe it will become a new standard benchmark for comparison of current and future methods in the ML potential community.

Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide.

PubMed

Ingham, Richard J; Battilocchio, Claudio; Hawkins, Joel M; Ley, Steven V

2014-01-01

Here we describe the use of a new open-source software package and a Raspberry Pi(®) computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide - a component of Rifater(®), used in the treatment of tuberculosis - and its reduced derivative piperazine-2-carboxamide.

The use of computer simulations in whole-class versus small-group settings

NASA Astrophysics Data System (ADS)

Smetana, Lara Kathleen

This study explored the use of computer simulations in a whole-class as compared to small-group setting. Specific consideration was given to the nature and impact of classroom conversations and interactions when computer simulations were incorporated into a high school chemistry course. This investigation fills a need for qualitative research that focuses on the social dimensions of actual classrooms. Participants included a novice chemistry teacher experienced in the use of educational technologies and two honors chemistry classes. The study was conducted in a rural school in the south-Atlantic United States at the end of the fall 2007 semester. The study took place during one instructional unit on atomic structure. Data collection allowed for triangulation of evidence from a variety of sources approximately 24 hours of video- and audio-taped classroom observations, supplemented with the researcher's field notes and analytic journal; miscellaneous classroom artifacts such as class notes, worksheets, and assignments; open-ended pre- and post-assessments; student exit interviews; teacher entrance, exit and informal interviews. Four web-based simulations were used, three of which were from the ExploreLearning collection. Assessments were analyzed using descriptive statistics and classroom observations, artifacts and interviews were analyzed using Erickson's (1986) guidelines for analytic induction. Conversational analysis was guided by methods outlined by Erickson (1982). Findings indicated (a) the teacher effectively incorporated simulations in both settings (b) students in both groups significantly improved their understanding of the chemistry concepts (c) there was no statistically significant difference between groups' achievement (d) there was more frequent exploratory talk in the whole-class group (e) there were more frequent and meaningful teacher-student interactions in the whole-class group (f) additional learning experiences not measured on the assessment resulted from conversations and interactions in the whole-class setting (g) the potential benefits of exploratory talk in the whole-class setting were not fully realized. These findings suggest that both whole-class and small-group settings are appropriate for using computer simulations in science. The effective incorporation of simulations into whole-class instruction may provide a solution to the dilemma of technology penetration versus integration in today's classrooms.

Civil propulsion technology for the next twenty-five years

NASA Technical Reports Server (NTRS)

Rosen, Robert; Facey, John R.

1987-01-01

The next twenty-five years will see major advances in civil propulsion technology that will result in completely new aircraft systems for domestic, international, commuter and high-speed transports. These aircraft will include advanced aerodynamic, structural, and avionic technologies resulting in major new system capabilities and economic improvements. Propulsion technologies will include high-speed turboprops in the near term, very high bypass ratio turbofans, high efficiency small engines and advanced cycles utilizing high temperature materials for high-speed propulsion. Key fundamental enabling technologies include increased temperature capability and advanced design methods. Increased temperature capability will be based on improved composite materials such as metal matrix, intermetallics, ceramics, and carbon/carbon as well as advanced heat transfer techniques. Advanced design methods will make use of advances in internal computational fluid mechanics, reacting flow computation, computational structural mechanics and computational chemistry. The combination of advanced enabling technologies, new propulsion concepts and advanced control approaches will provide major improvements in civil aircraft.

Contributions of computational chemistry and biophysical techniques to fragment-based drug discovery.

PubMed

Gozalbes, Rafael; Carbajo, Rodrigo J; Pineda-Lucena, Antonio

2010-01-01

In the last decade, fragment-based drug discovery (FBDD) has evolved from a novel approach in the search of new hits to a valuable alternative to the high-throughput screening (HTS) campaigns of many pharmaceutical companies. The increasing relevance of FBDD in the drug discovery universe has been concomitant with an implementation of the biophysical techniques used for the detection of weak inhibitors, e.g. NMR, X-ray crystallography or surface plasmon resonance (SPR). At the same time, computational approaches have also been progressively incorporated into the FBDD process and nowadays several computational tools are available. These stretch from the filtering of huge chemical databases in order to build fragment-focused libraries comprising compounds with adequate physicochemical properties, to more evolved models based on different in silico methods such as docking, pharmacophore modelling, QSAR and virtual screening. In this paper we will review the parallel evolution and complementarities of biophysical techniques and computational methods, providing some representative examples of drug discovery success stories by using FBDD.

Simulation of ceramic materials relevant for nuclear waste management: Case of La1-xEuxPO4 solid solution

NASA Astrophysics Data System (ADS)

Kowalski, Piotr M.; Ji, Yaqi; Li, Yan; Arinicheva, Yulia; Beridze, George; Neumeier, Stefan; Bukaemskiy, Andrey; Bosbach, Dirk

2017-02-01

Using powerful computational resources and state-of-the-art methods of computational chemistry we contribute to the research on novel nuclear waste forms by providing atomic scale description of processes that govern the structural incorporation and the interactions of radionuclides in host materials. Here we present various results of combined computational and experimental studies on La1-xEuxPO4 monazite-type solid solution. We discuss the performance of DFT + U method with the Hubbard U parameter value derived ab initio, and the derivation of various structural, thermodynamic and radiation-damage related properties. We show a correlation between the cation displacement probabilities and the solubility data, indicating that the binding of cations is the driving factor behind both processes. The combined atomistic modeling and experimental studies result in a superior characterization of the investigated material.

Delta Clipper-Experimental In-Ground Effect on Base-Heating Environment

NASA Technical Reports Server (NTRS)

Wang, Ten-See

1998-01-01

A quasitransient in-ground effect method is developed to study the effect of vertical landing on a launch vehicle base-heating environment. This computational methodology is based on a three-dimensional, pressure-based, viscous flow, chemically reacting, computational fluid dynamics formulation. Important in-ground base-flow physics such as the fountain-jet formation, plume growth, air entrainment, and plume afterburning are captured with the present methodology. Convective and radiative base-heat fluxes are computed for comparison with those of a flight test. The influence of the laminar Prandtl number on the convective heat flux is included in this study. A radiative direction-dependency test is conducted using both the discrete ordinate and finite volume methods. Treatment of the plume afterburning is found to be very important for accurate prediction of the base-heat fluxes. Convective and radiative base-heat fluxes predicted by the model using a finite rate chemistry option compared reasonably well with flight-test data.

Preface: phys. stat. sol. (b) 243/5

NASA Astrophysics Data System (ADS)

Artacho, Emilio; Beck, Thomas L.; Hernández, Eduardo

Between 20 and 24 June 2005 the Centre Européen de Calcul Atomique et Moléculaire - or CECAM, as it is more widely known - hosted a workshop entitled State-of-the-art, developments and perspectives of real-space electronic structure methods in condensed-matter and chemical physics, organized with the support of CECAM itself and the ?k network. The workshop was attended by some forty participants coming from fifteen countries, and about thirty presentations were given. The workshop provided a lively forum for the discussion of recent methodological developments in electronic structure calculations, ranging from linear-scaling methods, mesh techniques, time-dependent density functional methods, and a long etcetera, which had been our ultimate objective when undertaking its organization.The first-principles simulation of solids, liquids and complex matter in general has jumped in the last few years from the relatively confined niches in condensed matter and materials physics and in quantum chemistry, to cover most of the sciences, including nano, bio, geo, environmental sciences and engineering. This effect has been propitiated by the ability of simulation techniques to deal with an ever larger degree of complexity. Although this is partially to be attributed to the steady increase in computer power, the main factor behind this change has been the coming of age of the main theoretical framework for most of the simulations performed today, together with an extremely active development of the basic algorithms for its computer implementation. It is this latter aspect that is the topic of this special issue of physica status solidi.There is a relentless effort in the scientific community seeking to achieve not only higher accuracy, but also more efficient, cost-effective and if possible simpler computational methods in electronic structure calculations [1]. From the early 1990s onwards there has been a keen interest in the computational condensed matter and chemical physics communities in methods that had the potential to overcome the unfavourable scaling of the computational cost with the system size, implicit in the momentum-space formalism familiar to solid-state physicists and the quantum chemistry approaches more common in chemical physics and physical chemistry. This interest was sparkled by the famous paper in which Weitao Yang [2] introduced the Divide and Conquer method. Soon afterwards several practical schemes aiming to achieve linear-scaling calculations, by exploiting what Walter Kohn called most aptly the near-sightedness of quantum mechanics [3], were proposed and explored (for a review on linear-scaling methods, see [4]). This search for novel, more efficient and better scaling algorithms proved to be fruitful in more than one way. Not only was it the start of several packages which are well-known today (such as Siesta, Conquest, etc.), but it also leads to new ways of representing electronic states and orbitals, such as grids [5, 6], wavelets [7], finite elements, etc. Also, the drive to exploit near-sightedness attracted computational solid state physicists to the type of atomic-like basis functions traditionally used in the quantum chemistry community. At the same time computational chemists learnt about plane waves and density functional theory, and thus a fruitful dialogue was started between two communities that hitherto had not had much contact.Another interesting development that has begun to take place over the last decade or so is the convergence of several branches of science, notably physics, chemistry and biology, at the nanoscale. Experimentalists in all these different fields are now performing highly sophisticated measurements on systems of nanometer size, the kind of systems that us theoreticians can address with our computational methods, and this convergence of experiment and theory at this scale has also been very fruitful, particularly in the fields of electronic transport and STM image simulation. It is now quite common to find papers at the cutting edge of nanoscience and nanotechnology co-authored by experimentalists and theorists, and it can only be expected that this fruitful interplay between theory and experiment will increase in the future.It was considerations such as these that moved us to propose to CECAM and ?k the celebration of a workshop devoted to the discussion of recent developments in electronic structure techniques, a proposal that was enthusiastically received, not just by CECAM and ?k, but also by our invited speakers and participants. Interest in novel electronic structure methods is now as high as ever, and we are therefore very happy that physica status solidi has given us the opportunity to devote a special issue to the topics covered in the workshop. This special issue of physica status solidi gathers invited contributions from several attendants to the workshop, contributions that are representative of the range of topics and issues discussed then, including progress in linear scaling methods, electronic transport, simulation of STM images, time-dependent DFT methods, etc. It rests for us to thank all the contributors to this special issue for their efforts, CECAM and ?k for funding the workshop, physica status solidi for agreeing to devote this special issue to the workshop, and last but not least Emmanuelle and Emilie, the CECAM secretaries, for their invaluable practical help in putting this workshop together

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…

Application of high level wavefunction methods in quantum mechanics/molecular mechanics hybrid schemes.

PubMed

Mata, Ricardo A

2010-05-21

In this Perspective, several developments in the field of quantum mechanics/molecular mechanics (QM/MM) approaches are reviewed. Emphasis is placed on the use of correlated wavefunction theory and new state of the art methods for the treatment of large quantum systems. Until recently, computational chemistry approaches to large/complex chemical problems have seldom been considered as tools for quantitative predictions. However, due to the tremendous development of computational resources and new quantum chemical methods, it is nowadays possible to describe the electronic structure of biomolecules at levels of theory which a decade ago were only possible for system sizes of up to 20 atoms. These advances are here outlined in the context of QM/MM. The article concludes with a short outlook on upcoming developments and possible bottlenecks for future applications.

A greedy algorithm for species selection in dimension reduction of combustion chemistry

NASA Astrophysics Data System (ADS)

Hiremath, Varun; Ren, Zhuyin; Pope, Stephen B.

2010-09-01

Computational calculations of combustion problems involving large numbers of species and reactions with a detailed description of the chemistry can be very expensive. Numerous dimension reduction techniques have been developed in the past to reduce the computational cost. In this paper, we consider the rate controlled constrained-equilibrium (RCCE) dimension reduction method, in which a set of constrained species is specified. For a given number of constrained species, the 'optimal' set of constrained species is that which minimizes the dimension reduction error. The direct determination of the optimal set is computationally infeasible, and instead we present a greedy algorithm which aims at determining a 'good' set of constrained species; that is, one leading to near-minimal dimension reduction error. The partially-stirred reactor (PaSR) involving methane premixed combustion with chemistry described by the GRI-Mech 1.2 mechanism containing 31 species is used to test the algorithm. Results on dimension reduction errors for different sets of constrained species are presented to assess the effectiveness of the greedy algorithm. It is shown that the first four constrained species selected using the proposed greedy algorithm produce lower dimension reduction error than constraints on the major species: CH4, O2, CO2 and H2O. It is also shown that the first ten constrained species selected using the proposed greedy algorithm produce a non-increasing dimension reduction error with every additional constrained species; and produce the lowest dimension reduction error in many cases tested over a wide range of equivalence ratios, pressures and initial temperatures.

Polarizable atomic multipole X-ray refinement: application to peptide crystals

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

Schnieders, Michael J.; Fenn, Timothy D.; Howard Hughes Medical Institute

2009-09-01

A method to accelerate the computation of structure factors from an electron density described by anisotropic and aspherical atomic form factors via fast Fourier transformation is described for the first time. Recent advances in computational chemistry have produced force fields based on a polarizable atomic multipole description of biomolecular electrostatics. In this work, the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) force field is applied to restrained refinement of molecular models against X-ray diffraction data from peptide crystals. A new formalism is also developed to compute anisotropic and aspherical structure factors using fast Fourier transformation (FFT) of Cartesian Gaussianmore » multipoles. Relative to direct summation, the FFT approach can give a speedup of more than an order of magnitude for aspherical refinement of ultrahigh-resolution data sets. Use of a sublattice formalism makes the method highly parallelizable. Application of the Cartesian Gaussian multipole scattering model to a series of four peptide crystals using multipole coefficients from the AMOEBA force field demonstrates that AMOEBA systematically underestimates electron density at bond centers. For the trigonal and tetrahedral bonding geometries common in organic chemistry, an atomic multipole expansion through hexadecapole order is required to explain bond electron density. Alternatively, the addition of interatomic scattering (IAS) sites to the AMOEBA-based density captured bonding effects with fewer parameters. For a series of four peptide crystals, the AMOEBA–IAS model lowered R{sub free} by 20–40% relative to the original spherically symmetric scattering model.« less

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

An abstraction layer for efficient memory management of tabulated chemistry and flamelet solutions

NASA Astrophysics Data System (ADS)

Weise, Steffen; Messig, Danny; Meyer, Bernd; Hasse, Christian

2013-06-01

A large number of methods for simulating reactive flows exist, some of them, for example, directly use detailed chemical kinetics or use precomputed and tabulated flame solutions. Both approaches couple the research fields computational fluid dynamics and chemistry tightly together using either an online or offline approach to solve the chemistry domain. The offline approach usually involves a method of generating databases or so-called Lookup-Tables (LUTs). As these LUTs are extended to not only contain material properties but interactions between chemistry and turbulent flow, the number of parameters and thus dimensions increases. Given a reasonable discretisation, file sizes can increase drastically. The main goal of this work is to provide methods that handle large database files efficiently. A Memory Abstraction Layer (MAL) has been developed that handles requested LUT entries efficiently by splitting the database file into several smaller blocks. It keeps the total memory usage at a minimum using thin allocation methods and compression to minimise filesystem operations. The MAL has been evaluated using three different test cases. The first rather generic one is a sequential reading operation on an LUT to evaluate the runtime behaviour as well as the memory consumption of the MAL. The second test case is a simulation of a non-premixed turbulent flame, the so-called HM1 flame, which is a well-known test case in the turbulent combustion community. The third test case is a simulation of a non-premixed laminar flame as described by McEnally in 1996 and Bennett in 2000. Using the previously developed solver 'flameletFoam' in conjunction with the MAL, memory consumption and the performance penalty introduced were studied. The total memory used while running a parallel simulation was reduced significantly while the CPU time overhead associated with the MAL remained low.

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.

Direct conversion of hydride- to siloxane-terminated silicon quantum dots

DOE PAGES

Anderson, Ryan T.; Zang, Xiaoning; Fernando, Roshan; ...

2016-10-20

Here, peripheral surface functionalization of hydride-terminated silicon quantum dots (SiQD) is necessary in order to minimize their oxidation/aggregation and allow for solution processability. Historically thermal hydrosilylation addition of alkenes and alkynes across the Si-H surface to form Si-C bonds has been the primary method to achieve this. Here we demonstrate a mild alternative approach to functionalize hydride-terminated SiQDs using bulky silanols in the presence of free-radical initiators to form stable siloxane (~Si-O-SiR 3) surfaces with hydrogen gas as a byproduct. This offers an alternative to existing methods of forming siloxane surfaces that require corrosive Si-Cl based chemistry with HCl byproducts.more » A 52 nm blue shift in the photoluminescent spectra of siloxane versus alkyl-functionalized SiQDs is observed that we explain using computational theory. Model compound synthesis of silane and silsesquioxane analogues is used to optimize surface chemistry and elucidate reaction mechanisms. Thorough characterization on the extent of siloxane surface coverage is provided using FTIR and XPS. As a result, TEM is used to demonstrate SiQD size and integrity after surface chemistry and product isolation.« less

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...

Bias-Free Chemically Diverse Test Sets from Machine Learning.

PubMed

Swann, Ellen T; Fernandez, Michael; Coote, Michelle L; Barnard, Amanda S

2017-08-14

Current benchmarking methods in quantum chemistry rely on databases that are built using a chemist's intuition. It is not fully understood how diverse or representative these databases truly are. Multivariate statistical techniques like archetypal analysis and K-means clustering have previously been used to summarize large sets of nanoparticles however molecules are more diverse and not as easily characterized by descriptors. In this work, we compare three sets of descriptors based on the one-, two-, and three-dimensional structure of a molecule. Using data from the NIST Computational Chemistry Comparison and Benchmark Database and machine learning techniques, we demonstrate the functional relationship between these structural descriptors and the electronic energy of molecules. Archetypes and prototypes found with topological or Coulomb matrix descriptors can be used to identify smaller, statistically significant test sets that better capture the diversity of chemical space. We apply this same method to find a diverse subset of organic molecules to demonstrate how the methods can easily be reapplied to individual research projects. Finally, we use our bias-free test sets to assess the performance of density functional theory and quantum Monte Carlo methods.

Effects of continuum breakdown on hypersonic aerothermodynamics for reacting flow

NASA Astrophysics Data System (ADS)

Holman, Timothy D.; Boyd, Iain D.

2011-02-01

This study investigates the effects of continuum breakdown on the surface aerothermodynamic properties (pressure, stress, and heat transfer rate) of a sphere in a Mach 25 flow of reacting air in regimes varying from continuum to a rarefied gas. Results are generated using both continuum [computational fluid dynamics (CFD)] and particle [direct simulation Monte Carlo (DSMC)] approaches. The DSMC method utilizes a chemistry model that calculates the backward rates from an equilibrium constant. A preferential dissociation model is modified in the CFD method to better compare with the vibrationally favored dissociation model that is utilized in the DSMC method. Tests of these models are performed to confirm their validity and to compare the chemistry models in both numerical methods. This study examines the effect of reacting air flow on continuum breakdown and the surface properties of the sphere. As the global Knudsen number increases, the amount of continuum breakdown in the flow and on the surface increases. This increase in continuum breakdown significantly affects the surface properties, causing an increase in the differences between CFD and DSMC. Explanations are provided for the trends observed.

Indirect photopatterning of functionalized organic monolayers via copper-catalyzed "click chemistry"

NASA Astrophysics Data System (ADS)

Williams, Mackenzie G.; Teplyakov, Andrew V.

2018-07-01

Solution-based lithographic surface modification of an organic monolayer on a solid substrate is attained based on selective area photo-reduction of copper (II) to copper (I) to catalyze the azide-alkyne dipolar cycloaddition "click" reaction. X-ray photoelectron spectroscopy is used to confirm patterning, and spectroscopic results are analyzed and supplemented with computational models to confirm the surface chemistry. It is determined that this surface modification approach requires irradiation of the solid substrate with all necessary components present in solution. This method requires only minutes of irradiation to result in spatial and temporal control of the covalent surface functionalization of a monolayer and offers the potential for wavelength tunability that may be desirable in many applications utilizing organic monolayers.

Adaptations in Electronic Structure Calculations in Heterogeneous Environments

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

Talamudupula, Sai

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

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

Research in Computational Astrobiology

NASA Technical Reports Server (NTRS)

Chaban, Galina; Jaffe, Richard; Liang, Shoudan; New, Michael H.; Pohorille, Andrew; Wilson, Michael A.

2002-01-01

We present results from several projects in the new field of computational astrobiology, which is devoted to advancing our understanding of the origin, evolution and distribution of life in the Universe using theoretical and computational tools. We have developed a procedure for calculating long-range effects in molecular dynamics using a plane wave expansion of the electrostatic potential. This method is expected to be highly efficient for simulating biological systems on massively parallel supercomputers. We have perform genomics analysis on a family of actin binding proteins. We have performed quantum mechanical calculations on carbon nanotubes and nucleic acids, which simulations will allow us to investigate possible sources of organic material on the early earth. Finally, we have developed a model of protobiological chemistry using neural networks.

Integration of enabling methods for the automated flow preparation of piperazine-2-carboxamide

PubMed Central

Ingham, Richard J; Battilocchio, Claudio; Hawkins, Joel M

2014-01-01

Summary Here we describe the use of a new open-source software package and a Raspberry Pi® computer for the simultaneous control of multiple flow chemistry devices and its application to a machine-assisted, multi-step flow preparation of pyrazine-2-carboxamide – a component of Rifater®, used in the treatment of tuberculosis – and its reduced derivative piperazine-2-carboxamide. PMID:24778715

Performance Evaluation of NWChem Ab-Initio Molecular Dynamics (AIMD) Simulations on the Intel® Xeon Phi™ Processor

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

Bylaska, Eric J.; Jacquelin, Mathias; De Jong, Wibe A.

2017-10-20

Ab-initio Molecular Dynamics (AIMD) methods are an important class of algorithms, as they enable scientists to understand the chemistry and dynamics of molecular and condensed phase systems while retaining a first-principles-based description of their interactions. Many-core architectures such as the Intel® Xeon Phi™ processor are an interesting and promising target for these algorithms, as they can provide the computational power that is needed to solve interesting problems in chemistry. In this paper, we describe the efforts of refactoring the existing AIMD plane-wave method of NWChem from an MPI-only implementation to a scalable, hybrid code that employs MPI and OpenMP tomore » exploit the capabilities of current and future many-core architectures. We describe the optimizations required to get close to optimal performance for the multiplication of the tall-and-skinny matrices that form the core of the computational algorithm. We present strong scaling results on the complete AIMD simulation for a test case that simulates 256 water molecules and that strong-scales well on a cluster of 1024 nodes of Intel Xeon Phi processors. We compare the performance obtained with a cluster of dual-socket Intel® Xeon® E5–2698v3 processors.« less

Theoretical Studies of Elementary Hydrocarbon Species and Their Reactions

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

Allen, Wesley D.; Schaefer, Henry F.

The research program supported by this DOE grant carried out both methodological development and computational applications of first-principles theoretical chemistry based on quantum mechanical wavefunctions, as directed toward understanding and harnessing the fundamental chemical physics of combustion. To build and refine the world’s database of thermochemistry, spectroscopy, and chemical kinetics, predictive and definitive computational methods are needed that push the envelope of modern electronic structure theory. The application of such methods has been made to gain comprehensive knowledge of the paradigmatic reaction networks by which the n- and i-propyl, t-butyl, and n-butyl radicals are oxidized by O 2. Numerous ROOmore » and QOOH intermediates in these R + O 2 reaction systems have been characterized along with the interconnecting isomerization transition states and the barriers leading to fragmentation. Other combustion-related intermediates have also been studied, including methylsulfinyl radical, cyclobutylidene, and radicals derived from acetaldehyde and vinyl alcohol. Theoretical advances have been achieved and made available to the scientific community by implementation into PSI4, an open-source electronic structure computer package emphasizing automation, advanced libraries, and interoperability. We have pursued the development of universal explicitly correlated methods applicable to general electronic wavefunctions, as well as a framework that allows multideterminant reference functions to be expressed as a single determinant from quasiparticle operators. Finally, a rigorous analytical tool for correlated wavefunctions has been created to elucidate dispersion interactions, which play essential roles in many areas of chemistry, but whose effects are often masked and enigmatic. Our research decomposes and analyzes the coupled-cluster electron correlation energy in molecular systems as a function of interelectronic distance. Concepts are emerging that can be used to explain the influence of dispersion on the thermochemistry of large hydrocarbons, including fuels important to combustion technologies.« 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

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.

Development of the general interpolants method for the CYBER 200 series of supercomputers

NASA Technical Reports Server (NTRS)

Stalnaker, J. F.; Robinson, M. A.; Spradley, L. W.; Kurzius, S. C.; Thoenes, J.

1988-01-01

The General Interpolants Method (GIM) is a 3-D, time-dependent, hybrid procedure for generating numerical analogs of the conservation laws. This study is directed toward the development and application of the GIM computer code for fluid dynamic research applications as implemented for the Cyber 200 series of supercomputers. An elliptic and quasi-parabolic version of the GIM code are discussed. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and an implicit finite difference scheme are also included.

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)

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,…

Environmental research program. 1995 Annual report

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

Brown, N.J.

1996-06-01

The objective of the Environmental Research Program is to enhance the understanding of, and mitigate the effects of pollutants on health, ecological systems, global and regional climate, and air quality. The program is multidisciplinary and includes fundamental research and development in efficient and environmentally benign combustion, pollutant abatement and destruction, and novel methods of detection and analysis of criteria and noncriteria pollutants. This diverse group conducts investigations in combustion, atmospheric and marine processes, flue-gas chemistry, and ecological systems. Combustion chemistry research emphasizes modeling at microscopic and macroscopic scales. At the microscopic scale, functional sensitivity analysis is used to explore themore » nature of the potential-to-dynamics relationships for reacting systems. Rate coefficients are estimated using quantum dynamics and path integral approaches. At the macroscopic level, combustion processes are modelled using chemical mechanisms at the appropriate level of detail dictated by the requirements of predicting particular aspects of combustion behavior. Parallel computing has facilitated the efforts to use detailed chemistry in models of turbulent reacting flow to predict minor species concentrations.« less

Advances in theory and their application within the field of zeolite chemistry.

PubMed

Van Speybroeck, Veronique; Hemelsoet, Karen; Joos, Lennart; Waroquier, Michel; Bell, Robert G; Catlow, C Richard A

2015-10-21

Zeolites are versatile and fascinating materials which are vital for a wide range of industries, due to their unique structural and chemical properties, which are the basis of applications in gas separation, ion exchange and catalysis. Given their economic impact, there is a powerful incentive for smart design of new materials with enhanced functionalities to obtain the best material for a given application. Over the last decades, theoretical modeling has matured to a level that model guided design has become within reach. Major hurdles have been overcome to reach this point and almost all contemporary methods in computational materials chemistry are actively used in the field of modeling zeolite chemistry and applications. Integration of complementary modeling approaches is necessary to obtain reliable predictions and rationalizations from theory. A close synergy between experimentalists and theoreticians has led to a deep understanding of the complexity of the system at hand, but also allowed the identification of shortcomings in current theoretical approaches. Inspired by the importance of zeolite characterization which can now be performed at the single atom and single molecule level from experiment, computational spectroscopy has grown in importance in the last decade. In this review most of the currently available modeling tools are introduced and illustrated on the most challenging problems in zeolite science. Directions for future model developments will be given.

Northwest Trajectory Analysis Capability: A Platform for Enhancing Computational Biophysics Analysis

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

Peterson, Elena S.; Stephan, Eric G.; Corrigan, Abigail L.

2008-07-30

As computational resources continue to increase, the ability of computational simulations to effectively complement, and in some cases replace, experimentation in scientific exploration also increases. Today, large-scale simulations are recognized as an effective tool for scientific exploration in many disciplines including chemistry and biology. A natural side effect of this trend has been the need for an increasingly complex analytical environment. In this paper, we describe Northwest Trajectory Analysis Capability (NTRAC), an analytical software suite developed to enhance the efficiency of computational biophysics analyses. Our strategy is to layer higher-level services and introduce improved tools within the user’s familiar environmentmore » without preventing researchers from using traditional tools and methods. Our desire is to share these experiences to serve as an example for effectively analyzing data intensive large scale simulation data.« less

Computational 3D structures of drug-targeting proteins in the 2009-H1N1 influenza A virus

NASA Astrophysics Data System (ADS)

Du, Qi-Shi; Wang, Shu-Qing; Huang, Ri-Bo; Chou, Kuo-Chen

2010-01-01

The neuraminidase (NA) and M2 proton channel of influenza virus are the drug-targeting proteins, based on which several drugs were developed. However these once powerful drugs encountered drug-resistant problem to the H5N1 and H1N1 flu. To address this problem, the computational 3D structures of NA and M2 proteins of 2009-H1N1 influenza virus were built using the molecular modeling technique and computational chemistry method. Based on the models the structure features of NA and M2 proteins were analyzed, the docking structures of drug-protein complexes were computed, and the residue mutations were annotated. The results may help to solve the drug-resistant problem and stimulate designing more effective drugs against 2009-H1N1 influenza pandemic.

Understanding the nanoparticle-protein corona complexes using computational and experimental methods.

PubMed

Kharazian, B; Hadipour, N L; Ejtehadi, M R

2016-06-01

Nanoparticles (NP) have capability to adsorb proteins from biological fluids and form protein layer, which is called protein corona. As the cell sees corona coated NPs, the protein corona can dictate biological response to NPs. The composition of protein corona is varied by physicochemical properties of NPs including size, shape, surface chemistry. Processing of protein adsorption is dynamic phenomena; to that end, a protein may desorb or leave a surface vacancy that is rapidly filled by another protein and cause changes in the corona composition mainly by the Vroman effect. In this review, we discuss the interaction between NP and proteins and the available techniques for identification of NP-bound proteins. Also we review current developed computational methods for understanding the NP-protein complex interactions. Copyright © 2016. Published by Elsevier Ltd.

Computing the Baker-Campbell-Hausdorff series and the Zassenhaus product

NASA Astrophysics Data System (ADS)

Weyrauch, Michael; Scholz, Daniel

2009-09-01

The Baker-Campbell-Hausdorff (BCH) series and the Zassenhaus product are of fundamental importance for the theory of Lie groups and their applications in physics and physical chemistry. Standard methods for the explicit construction of the BCH and Zassenhaus terms yield polynomial representations, which must be translated into the usually required commutator representation. We prove that a new translation proposed recently yields a correct representation of the BCH and Zassenhaus terms. This representation entails fewer terms than the well-known Dynkin-Specht-Wever representation, which is of relevance for practical applications. Furthermore, various methods for the computation of the BCH and Zassenhaus terms are compared, and a new efficient approach for the calculation of the Zassenhaus terms is proposed. Mathematica implementations for the most efficient algorithms are provided together with comparisons of efficiency.

Final Report: Main Group Element Chemistry in Service of Hydrogen Storage and Activation

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

David A. Dixon; Anthony J. Arduengo, III

2010-09-30

Replacing combustion of carbon-based fuels with alternative energy sources that have minimal environmental impact is one of the grand scientific and technological challenges of the early 21st century. Not only is it critical to capture energy from new, renewable sources, it is also necessary to store the captured energy efficiently and effectively for use at the point of service when and where it is needed, which may not be collocated with the collection site. There are many potential storage media but we focus on the storage of energy in chemical bonds. It is more efficient to store energy on amore » per weight basis in chemical bonds. This is because it is hard to pack electrons into small volumes with low weight without the use of chemical bonds. The focus of the project was the development of new chemistries to enable DOE to meet its technical objectives for hydrogen storage using chemical hydrogen storage systems. We provided computational chemistry support in terms of thermodynamics, kinetics, and properties prediction in support of the experimental efforts of the DOE Center of Excellence for Chemical Hydrogen Storage. The goal of the Center is to store energy in chemical bonds involving hydrogen atoms. Once the hydrogen is stored in a set of X-H/Y-H bonds, the hydrogen has to be easily released and the depleted fuel regenerated very efficiently. This differs substantially from our current use of fossil fuel energy sources where the reactant is converted to energy plus CO2 (coal) or CO2 and H2O (gasoline, natural gas), which are released into the atmosphere. In future energy storage scenarios, the spent fuel will be captured and the energy storage medium regenerated. This places substantial additional constraints on the chemistry. The goal of the computational chemistry work was to reduce the time to design new materials and develop materials that meet the 2010 and 2015 DOE objectives in terms of weight percent, volume, release time, and regeneration ability. This goal was met in terms of reducing the number of costly experiments and helping to focus the experimental effort on the potentially optimal targets. We have used computational chemistry approaches to predict the thermodynamic properties of a wide range of compounds containing boron, nitrogen, hydrogen, and other elements as appropriate including carbon. These calculations were done in most cases with high level molecular orbital theory methods that have small error bars on the order of ± 1 to 2 kcal/mol. The results were used to benchmark more approximate methods such as density functional theory for larger systems and for database development. We predicted reliable thermodynamics for thousands of compounds for release and regeneration schemes to aid/guide materials design and process design and simulation. These are the first reliable computed values for these compounds and for many represent the only available values. Overall, the computational results have provided us with new insights into the chemistry of main group and organic-base chemical hydrogen systems from the release of hydrogen to the regeneration of spent fuel. A number of experimental accomplishments were also made in this project. The experimental work on hydrogen storage materials centered on activated polarized σ- or π-bonded frameworks that hold the potential for ready dihydrogen activation, uptake, and eventually release. To this end, a large number of non-traditional valence systems including carbenes, cyanocarbons, and C-B and and B-N systems were synthesized and examined. During the course of these studies an important lead arose from the novel valency of a class of stable organic singlet bi-radical systems. A synthetic strategy to an “endless” hydrogen storage polymer has been developed based on our cyanocarbon chemistry. A key issue with the synthetic efforts was being able to link the kinetics of release with the size of the substituents as it was difficult to develop a low molecular weight molecule with the right kinetics. A novel hydrogen activation process has been developed which showed that Lewis acid-base pairs need not be “frustrated” in their reactivity towards activating H2. Reaction can occur at temperatures as low as -80 ºC. We established that the interaction of H2 with the electrophile is a key step in the activation process.« less

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

PubMed

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

2016-02-15

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

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.

4th Penn State Bioinorganic Workshop

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

Krebs, Carsten

The research area of biological inorganic chemistry encompasses a wide variety of subfields, including molecular biology, biochemistry, biophysics, inorganic chemistry, analytical chemistry, physical chemistry, and theoretical chemistry, as well as many different methods, such as biochemical characterization of enzymes, reaction kinetics, a plethora of spectroscopic techniques, and computational methods. The above methods are combined to understand the formation, function, and regulation of the many metallo-cofactors found in Nature as well as to identify novel metallo-cofactors. Many metalloenzyme-catalyzed reactions are extremely complex, but are of fundamental importance to science and society. Examples include (i) the reduction of the chemically inert molecule,more » dinitrogen, to ammonia by the enzyme nitrogenase (this reaction is fundamental for the production of nitrogen fertilizers); (ii) the oxidation of water to dioxygen by the Mn4Ca cluster found in photosystem II; and (iii) myriad reactions in which aliphatic, inert C-H bonds are cleaved for subsequent functionalization of the carbon atoms (the latter reactions are important in the biosynthesis of many natural products). Because of the broad range of areas and techniques employed in this field, research in bioinorganic chemistry is typically carried out collaboratively between two or more research groups. It is of paramount importance that researchers working in this field have a good, basic, working knowledge of many methods and approaches employed in the field, in order to design and discuss experiments with collaborators. Therefore, the training of students working in bioinorganic chemistry is an important aspect of this field. Hugely successful “bioinorganic workshops” were offered in the 1990s at The University of Georgia. These workshops laid the foundation for many of the extant collaborative research efforts in this area today. The large and diverse group of bioinorganic chemists at The Pennsylvania State University and our unique laboratory space are well suited for the continuation of such training workshops. The co-principal investigators of this award lead these efforts. After a smaller “trial workshop” in 2010, the Penn State bioinorganic group, led by the co-PIs, offers these workshops biennially. The 2012, 2014, and 2016 workshops provided training to 123, 162, and 153 participants, respectively, by offering (i) a series of lectures given by faculty experts on the given topic, (ii) hands-on training in small groups by experts in the various methods, and (iii) sharing research results of the participants by oral and poster presentations. The centerpiece of the workshops is the hands-on training, in which approximately half of the participants from all ranks (undergraduate students to faculty) served as teachers. In this section, the traditional roles of teachers and students were sometimes reversed to the extent that undergraduate students taught faculty in the students' areas of specialty. We anticipate that these workshops will facilitate research in bioinorganic chemistry and will help establish future collaborations among “workshop alumni” to carry out cutting-edge research in bioinorganic chemistry that will address many important topics relevant to our society.« less

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.

Crystal Structure and Properties of Imidazo-Pyridine Ionic Liquids.

PubMed

Farren-Dai, Marco; Cameron, Stanley; Johnson, Michel B; Ghandi, Khashayar

2018-07-05

Computational studies were performed on novel protic ionic liquids imidazolium-[1,2-a]-pyridine trifluoroacetate [ImPr][TFA] synthesized by the reaction of imidazo-[1,2a]-pyridine (ImPr) with trifluoroacetic acid (TFA), and on fused salt imidazolium-[1,2-a]-pyridine maleamic carbonate [ImPr][Mal] synthesized by reaction of ImPr with maleamic acid (Mal). Synthesis was performed as one-pot reactions, which applies green chemistry tenets. Both these compounds begin to decompose at 180°C. Our computational studies suggest another thermal reaction channel, in which [ImPr][Mal] can also thermally polymerizes to polyacrylamide which then cyclizes. This is thermal product remains stable up to 700 degrees, consistent with our thermogravimetric studies. [ImPr][TFA] exhibited good conductivity and ideal ionic behavior, as evaluated by a Walden plot. X-ray crystallography of [ImPr][TFA] revealed a tightly packed system for the crystals as a result of strong ionic interaction, pi-stacking, and fluorine-CH interactions. Both synthesized compounds exhibited some CO 2 absorptivity, with [ImPr][Mal] outperforming [ImPr][TFA] in this regard. The quantum chemistry based computational methods can shed light on many properties of these ionic liquids, but they are challenged in fully describing their ionic nature. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

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…

Assimilation of surface NO2 and O3 observations into the SILAM chemistry transport model

NASA Astrophysics Data System (ADS)

Vira, J.; Sofiev, M.

2014-08-01

This paper describes assimilation of trace gas observations into the chemistry transport model SILAM using the 3D-Var method. Assimilation results for year 2012 are presented for the prominent photochemical pollutants ozone (O3) and nitrogen dioxide (NO2). Both species are covered by the Airbase observation database, which provides the observational dataset used in this study. Attention is paid to the background and observation error covariance matrices, which are obtained primarily by iterative application of a posteriori diagnostics. The diagnostics are computed separately for two months representing summer and winter conditions, and further disaggregated by time of day. This allows deriving background and observation error covariance definitions which include both seasonal and diurnal variation. The consistency of the obtained covariance matrices is verified using χ2 diagnostics. The analysis scores are computed for a control set of observation stations withheld from assimilation. Compared to a free-running model simulation, the correlation coefficient for daily maximum values is improved from 0.8 to 0.9 for O3 and from 0.53 to 0.63 for NO2.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes

NASA Astrophysics Data System (ADS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-05-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Computational models for the viscous/inviscid analysis of jet aircraft exhaust plumes. [predicting afterbody drag

NASA Technical Reports Server (NTRS)

Dash, S. M.; Pergament, H. S.; Thorpe, R. D.

1980-01-01

Computational models which analyze viscous/inviscid flow processes in jet aircraft exhaust plumes are discussed. These models are component parts of an NASA-LaRC method for the prediction of nozzle afterbody drag. Inviscid/shock processes are analyzed by the SCIPAC code which is a compact version of a generalized shock capturing, inviscid plume code (SCIPPY). The SCIPAC code analyzes underexpanded jet exhaust gas mixtures with a self-contained thermodynamic package for hydrocarbon exhaust products and air. A detailed and automated treatment of the embedded subsonic zones behind Mach discs is provided in this analysis. Mixing processes along the plume interface are analyzed by two upgraded versions of an overlaid, turbulent mixing code (BOAT) developed previously for calculating nearfield jet entrainment. The BOATAC program is a frozen chemistry version of BOAT containing the aircraft thermodynamic package as SCIPAC; BOATAB is an afterburning version with a self-contained aircraft (hydrocarbon/air) finite-rate chemistry package. The coupling of viscous and inviscid flow processes is achieved by an overlaid procedure with interactive effects accounted for by a displacement thickness type correction to the inviscid plume interface.

Prediction of the Thrust Performance and the Flowfield of Liquid Rocket Engines

NASA Technical Reports Server (NTRS)

Wang, T.-S.

1990-01-01

In an effort to improve the current solutions in the design and analysis of liquid propulsive engines, a computational fluid dynamics (CFD) model capable of calculating the reacting flows from the combustion chamber, through the nozzle to the external plume, was developed. The Space Shuttle Main Engine (SSME) fired at sea level, was investigated as a sample case. The CFD model, FDNS, is a pressure based, non-staggered grid, viscous/inviscid, ideal gas/real gas, reactive code. An adaptive upwinding differencing scheme is employed for the spatial discretization. The upwind scheme is based on fourth order central differencing with fourth order damping for smooth regions, and second order central differencing with second order damping for shock capturing. It is equipped with a CHMQGM equilibrium chemistry algorithm and a PARASOL finite rate chemistry algorithm using the point implicit method. The computed flow results and performance compared well with those of other standard codes and engine hot fire test data. In addition, the transient nozzle flowfield calculation was also performed to demonstrate the ability of FDNS in capturing the flow separation during the startup process.

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.

Variational approach to direct and inverse problems of atmospheric pollution studies

NASA Astrophysics Data System (ADS)

Penenko, Vladimir; Tsvetova, Elena; Penenko, Alexey

2016-04-01

We present the development of a variational approach for solving interrelated problems of atmospheric hydrodynamics and chemistry concerning air pollution transport and transformations. The proposed approach allows us to carry out complex studies of different-scale physical and chemical processes using the methods of direct and inverse modeling [1-3]. We formulate the problems of risk/vulnerability and uncertainty assessment, sensitivity studies, variational data assimilation procedures [4], etc. A computational technology of constructing consistent mathematical models and methods of their numerical implementation is based on the variational principle in the weak constraint formulation specifically designed to account for uncertainties in models and observations. Algorithms for direct and inverse modeling are designed with the use of global and local adjoint problems. Implementing the idea of adjoint integrating factors provides unconditionally monotone and stable discrete-analytic approximations for convection-diffusion-reaction problems [5,6]. The general framework is applied to the direct and inverse problems for the models of transport and transformation of pollutants in Siberian and Arctic regions. The work has been partially supported by the RFBR grant 14-01-00125 and RAS Presidium Program I.33P. References: 1. V. Penenko, A.Baklanov, E. Tsvetova and A. Mahura . Direct and inverse problems in a variational concept of environmental modeling //Pure and Applied Geoph.(2012) v.169: 447-465. 2. V. V. Penenko, E. A. Tsvetova, and A. V. Penenko Development of variational approach for direct and inverse problems of atmospheric hydrodynamics and chemistry, Izvestiya, Atmospheric and Oceanic Physics, 2015, Vol. 51, No. 3, p. 311-319, DOI: 10.1134/S0001433815030093. 3. V.V. Penenko, E.A. Tsvetova, A.V. Penenko. Methods based on the joint use of models and observational data in the framework of variational approach to forecasting weather and atmospheric composition quality// Russian meteorology and hydrology, V. 40, Issue: 6, Pages: 365-373, DOI: 10.3103/S1068373915060023. 4. 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. 5. V.V. Penenko, E.A. Tsvetova, A.V. Penenko Variational approach and Euler's integrating factors for environmental studies// Computers and Mathematics with Applications, 2014, V.67, Issue 12, Pages 2240-2256, DOI:10.1016/j.camwa.2014.04.004 6. V.V. Penenko, E.A. Tsvetova. Variational methods of constructing monotone approximations for atmospheric chemistry models // Numerical analysis and applications, 2013, V. 6, Issue 3, pp 210-220, DOI 10.1134/S199542391303004X

Discontinuous Galerkin method for multicomponent chemically reacting flows and combustion

NASA Astrophysics Data System (ADS)

Lv, Yu; Ihme, Matthias

2014-08-01

This paper presents the development of a discontinuous Galerkin (DG) method for application to chemically reacting flows in subsonic and supersonic regimes under the consideration of variable thermo-viscous-diffusive transport properties, detailed and stiff reaction chemistry, and shock capturing. A hybrid-flux formulation is developed for treatment of the convective fluxes, combining a conservative Riemann-solver and an extended double-flux scheme. A computationally efficient splitting scheme is proposed, in which advection and diffusion operators are solved in the weak form, and the chemically stiff substep is advanced in the strong form using a time-implicit scheme. The discretization of the viscous-diffusive transport terms follows the second form of Bassi and Rebay, and the WENO-based limiter due to Zhong and Shu is extended to multicomponent systems. Boundary conditions are developed for subsonic and supersonic flow conditions, and the algorithm is coupled to thermochemical libraries to account for detailed reaction chemistry and complex transport. The resulting DG method is applied to a series of test cases of increasing physico-chemical complexity. Beginning with one- and two-dimensional multispecies advection and shock-fluid interaction problems, computational efficiency, convergence, and conservation properties are demonstrated. This study is followed by considering a series of detonation and supersonic combustion problems to investigate the convergence-rate and the shock-capturing capability in the presence of one- and multistep reaction chemistry. The DG algorithm is then applied to diffusion-controlled deflagration problems. By examining convergence properties for polynomial order and spatial resolution, and comparing these with second-order finite-volume solutions, it is shown that optimal convergence is achieved and that polynomial refinement provides advantages in better resolving the localized flame structure and complex flow-field features associated with multidimensional and hydrodynamic/thermo-diffusive instabilities in deflagration and detonation systems. Comparisons with standard third- and fifth-order WENO schemes are presented to illustrate the benefit of the DG scheme for application to detonation and multispecies flow/shock-interaction problems.

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

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…

Computerized approaches to enhance understanding of organic reaction mechanisms: CAN reaction mechanisms and CPLEX prelaboratory methodology

NASA Astrophysics Data System (ADS)

Al-Shammari, Abdulrahman G. Alhamzani

2008-10-01

Two approaches to enhance the understanding of organic reaction mechanisms are described. First, a new method for teaching organic reaction mechanisms that can be used in a Computer-Assisted Instruction (CAI) environment is proposed and tested (Chapter 1). The method concentrates upon the important intermediate structures, which are assumed to be on the reaction coordinate, and which can be evaluated and graded by currently available computer techniques. At the same time, the "curved arrows" that show the electron flow in a reaction mechanism are neglected, since they cannot be evaluated and graded with currently available computer techniques. By allowing student practice for learning organic reaction mechanisms using the Curved Arrow Neglect (CAN) method within a "Practice Makes Perfect" CAI method, student performance in the drawing of traditional reaction mechanisms, in which students had to include the "curved arrows" on their written classroom exams, was significantly enhanced. Second, computerized prelaboratory experiments (CPLEX) for organic chemistry laboratory 1 & 2 courses have been created, used, and evaluated (Chapters 2 and 3). These computerized prelabs are unique because they combine both "dry lab" actions with detailed animations of the actual chemistry occurring at the molecular level. The "dry lab" serves to simulate the actual physical manipulations of equipment and chemicals that occur in the laboratory experiment through the use of drag-and-drop computer technology. At the same time, these physical actions are accompanied on a separate part of the computer screen by animations showing the chemistry at the molecular level that is occurring in the experiment. These CPLEX modules were made into Internet accessible modules. The students were allowed to access the CPLEX modules prior to performing the actual laboratory experiment. A detailed evaluation of students' perception of the modules was accomplished via survey methodology during the entire implementation process over the course of three semesters. Results of the survey data indicate that students thought that they better understood the chemical principles and procedures of the laboratory experiment. Interestingly, students prefer the CPLEX prelaboratory materials, compared to the traditional textbooks, by a wide margin (Chapter 2). The utility of CPLEX was further demonstrated by enabling a study of the effectiveness of animated reaction mechanisms to promote student learning. While most instructors believe that animated mechanisms aid student understanding of reactions, there has been no quantitative data to-date to support this view. In this work, a quantitative study, using an experimental/control group study, was conducted to provide data on the effectiveness of animated reaction mechanisms to promote student learning. Analysis of student answers, using an appropriate rubric, demonstrated that there was a statistically significant improvement in students' scores in the mechanistic question of a pre-laboratory quiz in the post-treatment results of the experimental group which had had access to the animated reaction mechanisms (Chapter 3).

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

USGS Publications Warehouse

Eberl, D.D.

2008-01-01

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

A computational workflow for designing silicon donor qubits

DOE PAGES

Humble, Travis S.; Ericson, M. Nance; Jakowski, Jacek; ...

2016-09-19

Developing devices that can reliably and accurately demonstrate the principles of superposition and entanglement is an on-going challenge for the quantum computing community. Modeling and simulation offer attractive means of testing early device designs and establishing expectations for operational performance. However, the complex integrated material systems required by quantum device designs are not captured by any single existing computational modeling method. We examine the development and analysis of a multi-staged computational workflow that can be used to design and characterize silicon donor qubit systems with modeling and simulation. Our approach integrates quantum chemistry calculations with electrostatic field solvers to performmore » detailed simulations of a phosphorus dopant in silicon. We show how atomistic details can be synthesized into an operational model for the logical gates that define quantum computation in this particular technology. In conclusion, the resulting computational workflow realizes a design tool for silicon donor qubits that can help verify and validate current and near-term experimental devices.« less

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.

Effect of fullerenol surface chemistry on nanoparticle binding-induced protein misfolding

NASA Astrophysics Data System (ADS)

Radic, Slaven; Nedumpully-Govindan, Praveen; Chen, Ran; Salonen, Emppu; Brown, Jared M.; Ke, Pu Chun; Ding, Feng

2014-06-01

Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding.Fullerene and its derivatives with different surface chemistry have great potential in biomedical applications. Accordingly, it is important to delineate the impact of these carbon-based nanoparticles on protein structure, dynamics, and subsequently function. Here, we focused on the effect of hydroxylation -- a common strategy for solubilizing and functionalizing fullerene -- on protein-nanoparticle interactions using a model protein, ubiquitin. We applied a set of complementary computational modeling methods, including docking and molecular dynamics simulations with both explicit and implicit solvent, to illustrate the impact of hydroxylated fullerenes on the structure and dynamics of ubiquitin. We found that all derivatives bound to the model protein. Specifically, the more hydrophilic nanoparticles with a higher number of hydroxyl groups bound to the surface of the protein via hydrogen bonds, which stabilized the protein without inducing large conformational changes in the protein structure. In contrast, fullerene derivatives with a smaller number of hydroxyl groups buried their hydrophobic surface inside the protein, thereby causing protein denaturation. Overall, our results revealed a distinct role of surface chemistry on nanoparticle-protein binding and binding-induced protein misfolding. Electronic supplementary information (ESI) is available: Fluorescence spectra, ITC, CD spectra and other data as described in the text. See DOI: 10.1039/c4nr01544d

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.

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

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.

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

The Development and Comparison of Molecular Dynamics Simulation and Monte Carlo Simulation

NASA Astrophysics Data System (ADS)

Chen, Jundong

2018-03-01

Molecular dynamics is an integrated technology that combines physics, mathematics and chemistry. Molecular dynamics method is a computer simulation experimental method, which is a powerful tool for studying condensed matter system. This technique not only can get the trajectory of the atom, but can also observe the microscopic details of the atomic motion. By studying the numerical integration algorithm in molecular dynamics simulation, we can not only analyze the microstructure, the motion of particles and the image of macroscopic relationship between them and the material, but can also study the relationship between the interaction and the macroscopic properties more conveniently. The Monte Carlo Simulation, similar to the molecular dynamics, is a tool for studying the micro-molecular and particle nature. In this paper, the theoretical background of computer numerical simulation is introduced, and the specific methods of numerical integration are summarized, including Verlet method, Leap-frog method and Velocity Verlet method. At the same time, the method and principle of Monte Carlo Simulation are introduced. Finally, similarities and differences of Monte Carlo Simulation and the molecular dynamics simulation are discussed.

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.

Forebody and base region real gas flow in severe planetary entry by a factored implicit numerical method. II - Equilibrium reactive gas

NASA Technical Reports Server (NTRS)

Davy, W. C.; Green, M. J.; Lombard, C. K.

1981-01-01

The factored-implicit, gas-dynamic algorithm has been adapted to the numerical simulation of equilibrium reactive flows. Changes required in the perfect gas version of the algorithm are developed, and the method of coupling gas-dynamic and chemistry variables is discussed. A flow-field solution that approximates a Jovian entry case was obtained by this method and compared with the same solution obtained by HYVIS, a computer program much used for the study of planetary entry. Comparison of surface pressure distribution and stagnation line shock-layer profiles indicates that the two solutions agree well.

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.

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

PubMed

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

2017-08-03

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

The application of quantum mechanics in structure-based drug design.

PubMed

Mucs, Daniel; Bryce, Richard A

2013-03-01

Computational chemistry has become an established and valuable component in structure-based drug design. However the chemical complexity of many ligands and active sites challenges the accuracy of the empirical potentials commonly used to describe these systems. Consequently, there is a growing interest in utilizing electronic structure methods for addressing problems in protein-ligand recognition. In this review, the authors discuss recent progress in the development and application of quantum chemical approaches to modeling protein-ligand interactions. The authors specifically consider the development of quantum mechanics (QM) approaches for studying large molecular systems pertinent to biology, focusing on protein-ligand docking, protein-ligand binding affinities and ligand strain on binding. Although computation of binding energies remains a challenging and evolving area, current QM methods can underpin improved docking approaches and offer detailed insights into ligand strain and into the nature and relative strengths of complex active site interactions. The authors envisage that QM will become an increasingly routine and valued tool of the computational medicinal chemist.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional

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

Sun, Jianwei; Remsing, Richard C.; Zhang, Yubo

2016-06-13

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and vanmore » der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.« less

Kinetics and dynamics of near-resonant vibrational energy transfer in gas ensembles of atmospheric interest

NASA Astrophysics Data System (ADS)

McCaffery, Anthony J.

2018-03-01

This study of near-resonant, vibration-vibration (V-V) gas-phase energy transfer in diatomic molecules uses the theoretical/computational method, of Marsh & McCaffery (Marsh & McCaffery 2002 J. Chem. Phys. 117, 503 (doi:10.1063/1.1489998)) The method uses the angular momentum (AM) theoretical formalism to compute quantum-state populations within the component molecules of large, non-equilibrium, gas mixtures as the component species proceed to equilibration. Computed quantum-state populations are displayed in a number of formats that reveal the detailed mechanism of the near-resonant V-V process. Further, the evolution of quantum-state populations, for each species present, may be followed as the number of collision cycles increases, displaying the kinetics of evolution for each quantum state of the ensemble's molecules. These features are illustrated for ensembles containing vibrationally excited N2 in H2, O2 and N2 initially in their ground states. This article is part of the theme issue `Modern theoretical chemistry'.

Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional.

PubMed

Sun, Jianwei; Remsing, Richard C; Zhang, Yubo; Sun, Zhaoru; Ruzsinszky, Adrienn; Peng, Haowei; Yang, Zenghui; Paul, Arpita; Waghmare, Umesh; Wu, Xifan; Klein, Michael L; Perdew, John P

2016-09-01

One atom or molecule binds to another through various types of bond, the strengths of which range from several meV to several eV. Although some computational methods can provide accurate descriptions of all bond types, those methods are not efficient enough for many studies (for example, large systems, ab initio molecular dynamics and high-throughput searches for functional materials). Here, we show that the recently developed non-empirical strongly constrained and appropriately normed (SCAN) meta-generalized gradient approximation (meta-GGA) within the density functional theory framework predicts accurate geometries and energies of diversely bonded molecules and materials (including covalent, metallic, ionic, hydrogen and van der Waals bonds). This represents a significant improvement at comparable efficiency over its predecessors, the GGAs that currently dominate materials computation. Often, SCAN matches or improves on the accuracy of a computationally expensive hybrid functional, at almost-GGA cost. SCAN is therefore expected to have a broad impact on chemistry and materials science.

Characterization and Evaluation of Aged Chromium Nickel Niobium Stainless Steels

NASA Astrophysics Data System (ADS)

Dewar, Matthew

20Cr-32Ni-1Nb stainless steel alloys are commonly used in hydrogen reformer manifolds for transporting hot hydrogen by-products at 750-950°C. After long periods of exposure, embrittling secondary carbides and intermetallic phases can precipitate at the grain boundaries which can drastically reduce the ductility, and the repair weldability of the alloy. The intermetallic silicide, G-phase, is commonly observed in 20Cr-32Ni-1Nb stainless steels, and is prone to liquation cracking during welding operations. G-phase is deleterious to the material, where a high degree of G-phase coarsening will render the material unweldable. The present work will investigate various methods in mitigating G-phase precipitation. Variations in casting methods, wall thickness, homogenization treatments, and alloy chemistry will be examined by evaluating their microstructure after periodically aging the samples. Thermodynamic equilibrium modeling using computational thermodynamic tools will be used to optimize the 20Cr-32Ni-1Nb chemistry following ASTM specifications.

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.

An Analysis of Prospective Chemistry Teachers' Cognitive Structures through Flow Map Method: The Subject of Oxidation and Reduction

ERIC Educational Resources Information Center

Temel, Senar

2016-01-01

This study aims to analyse prospective chemistry teachers' cognitive structures related to the subject of oxidation and reduction through a flow map method. Purposeful sampling method was employed in this study, and 8 prospective chemistry teachers from a group of students who had taken general chemistry and analytical chemistry courses were…

Machine intelligence applications to securities production

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

Johnson, C.K.

1987-01-01

The production of security documents provides a cache of interesting problems ranging across a broad spectrum. Some of the problems do not have rigorous scientific solutions available at this time and provide opportunities for less structured approaches such as AI. AI methods can be used in conjunction with traditional scientific and computational methods. The most productive applications of AI occur when this marriage of methods can be carried out without motivation to prove that one method is better than the other. Fields such as ink chemistry and technology, and machine inspection of graphic arts printing offer interesting challenges which willmore » continue to intrigue current and future generations of researchers into the 21st century.« less

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

The Bravyi-Kitaev transformation for quantum computation of electronic structure

NASA Astrophysics Data System (ADS)

Seeley, Jacob T.; Richard, Martin J.; Love, Peter J.

2012-12-01

Quantum simulation is an important application of future quantum computers with applications in quantum chemistry, condensed matter, and beyond. Quantum simulation of fermionic systems presents a specific challenge. The Jordan-Wigner transformation allows for representation of a fermionic operator by O(n) qubit operations. Here, we develop an alternative method of simulating fermions with qubits, first proposed by Bravyi and Kitaev [Ann. Phys. 298, 210 (2002), 10.1006/aphy.2002.6254; e-print arXiv:quant-ph/0003137v2], that reduces the simulation cost to O(log n) qubit operations for one fermionic operation. We apply this new Bravyi-Kitaev transformation to the task of simulating quantum chemical Hamiltonians, and give a detailed example for the simplest possible case of molecular hydrogen in a minimal basis. We show that the quantum circuit for simulating a single Trotter time step of the Bravyi-Kitaev derived Hamiltonian for H2 requires fewer gate applications than the equivalent circuit derived from the Jordan-Wigner transformation. Since the scaling of the Bravyi-Kitaev method is asymptotically better than the Jordan-Wigner method, this result for molecular hydrogen in a minimal basis demonstrates the superior efficiency of the Bravyi-Kitaev method for all quantum computations of electronic structure.

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.

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)

Simulation of air pollution due to marine engines

NASA Astrophysics Data System (ADS)

Stan, L. C.

2017-08-01

This paperwork tried to simulate the combustion inside the marine engines using the newest computer methods and technologies with the result of a diverse and rich palette of solutions, extremely useful for the study and prediction of complex phenomena of the fuel combustion. The paperwork is contributing to the theoretical systematization of the area of interest bringing into attention a thoroughly inventory of the thermodynamic description of the phenomena which take place in the combustion process into the marine diesel engines; to the in depth multidimensional combustion models description along with the interdisciplinary phenomenology taking place in the combustion models; to the FEA (Finite Elements Method) modelling for the combustion chemistry in the nonpremixed mixtures approach considered too; the CFD (Computational Fluid Dynamics) model was issued for the combustion area and a rich palette of results interesting for any researcher of the process.

Gradient-based stochastic estimation of the density matrix

NASA Astrophysics Data System (ADS)

Wang, Zhentao; Chern, Gia-Wei; Batista, Cristian D.; Barros, Kipton

2018-03-01

Fast estimation of the single-particle density matrix is key to many applications in quantum chemistry and condensed matter physics. The best numerical methods leverage the fact that the density matrix elements f(H)ij decay rapidly with distance rij between orbitals. This decay is usually exponential. However, for the special case of metals at zero temperature, algebraic decay of the density matrix appears and poses a significant numerical challenge. We introduce a gradient-based probing method to estimate all local density matrix elements at a computational cost that scales linearly with system size. For zero-temperature metals, the stochastic error scales like S-(d+2)/2d, where d is the dimension and S is a prefactor to the computational cost. The convergence becomes exponential if the system is at finite temperature or is insulating.

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.

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...

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…

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.

Point-particle method to compute diffusion-limited cellular uptake.

PubMed

Sozza, A; Piazza, F; Cencini, M; De Lillo, F; Boffetta, G

2018-02-01

We present an efficient point-particle approach to simulate reaction-diffusion processes of spherical absorbing particles in the diffusion-limited regime, as simple models of cellular uptake. The exact solution for a single absorber is used to calibrate the method, linking the numerical parameters to the physical particle radius and uptake rate. We study the configurations of multiple absorbers of increasing complexity to examine the performance of the method by comparing our simulations with available exact analytical or numerical results. We demonstrate the potential of the method to resolve the complex diffusive interactions, here quantified by the Sherwood number, measuring the uptake rate in terms of that of isolated absorbers. We implement the method in a pseudospectral solver that can be generalized to include fluid motion and fluid-particle interactions. As a test case of the presence of a flow, we consider the uptake rate by a particle in a linear shear flow. Overall, our method represents a powerful and flexible computational tool that can be employed to investigate many complex situations in biology, chemistry, and related sciences.

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.

A data mining method to facilitate SAR transfer.

PubMed

Wassermann, Anne Mai; Bajorath, Jürgen

2011-08-22

A challenging practical problem in medicinal chemistry is the transfer of SAR information from one chemical series to another. Currently, there are no computational methods available to rationalize or support this process. Herein, we present a data mining approach that enables the identification of alternative analog series with different core structures, corresponding substitution patterns, and comparable potency progression. Scaffolds can be exchanged between these series and new analogs suggested that incorporate preferred R-groups. The methodology can be applied to search for alternative analog series if one series is known or, alternatively, to systematically assess SAR transfer potential in compound databases.

Artificial neural networks for efficient clustering of conformational ensembles and their potential for medicinal chemistry.

PubMed

Pandini, Alessandro; Fraccalvieri, Domenico; Bonati, Laura

2013-01-01

The biological function of proteins is strictly related to their molecular flexibility and dynamics: enzymatic activity, protein-protein interactions, ligand binding and allosteric regulation are important mechanisms involving protein motions. Computational approaches, such as Molecular Dynamics (MD) simulations, are now routinely used to study the intrinsic dynamics of target proteins as well as to complement molecular docking approaches. These methods have also successfully supported the process of rational design and discovery of new drugs. Identification of functionally relevant conformations is a key step in these studies. This is generally done by cluster analysis of the ensemble of structures in the MD trajectory. Recently Artificial Neural Network (ANN) approaches, in particular methods based on Self-Organising Maps (SOMs), have been reported performing more accurately and providing more consistent results than traditional clustering algorithms in various data-mining problems. In the specific case of conformational analysis, SOMs have been successfully used to compare multiple ensembles of protein conformations demonstrating a potential in efficiently detecting the dynamic signatures central to biological function. Moreover, examples of the use of SOMs to address problems relevant to other stages of the drug-design process, including clustering of docking poses, have been reported. In this contribution we review recent applications of ANN algorithms in analysing conformational and structural ensembles and we discuss their potential in computer-based approaches for medicinal chemistry.

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.

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.

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.

Computational studies of solid-state alkali conduction in rechargeable alkali-ion batteries

DOE PAGES

Deng, Zhi; Mo, Yifei; Ong, Shyue Ping

2016-03-25

The facile conduction of alkali ions in a crystal host is of crucial importance in rechargeable alkali-ion batteries, the dominant form of energy storage today. In this review, we provide a comprehensive survey of computational approaches to study solid-state alkali diffusion. We demonstrate how these methods have provided useful insights into the design of materials that form the main components of a rechargeable alkali-ion battery, namely the electrodes, superionic conductor solid electrolytes and interfaces. We will also provide a perspective on future challenges and directions. Here, the scope of this review includes the monovalent lithium- and sodium-ion chemistries that aremore » currently of the most commercial interest.« less

Semi-empirical quantum evaluation of peptide - MHC class II binding

NASA Astrophysics Data System (ADS)

González, Ronald; Suárez, Carlos F.; Bohórquez, Hugo J.; Patarroyo, Manuel A.; Patarroyo, Manuel E.

2017-01-01

Peptide presentation by the major histocompatibility complex (MHC) is a key process for triggering a specific immune response. Studying peptide-MHC (pMHC) binding from a structural-based approach has potential for reducing the costs of investigation into vaccine development. This study involved using two semi-empirical quantum chemistry methods (PM7 and FMO-DFTB) for computing the binding energies of peptides bonded to HLA-DR1 and HLA-DR2. We found that key stabilising water molecules involved in the peptide binding mechanism were required for finding high correlation with IC50 experimental values. Our proposal is computationally non-intensive, and is a reliable alternative for studying pMHC binding interactions.

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)

Development of the Next Generation of Biogeochemistry Simulations Using EMSL's NWChem Molecular Modeling Software

NASA Astrophysics Data System (ADS)

Bylaska, E. J.; Kowalski, K.; Apra, E.; Govind, N.; Valiev, M.

2017-12-01

Methods of directly simulating the behavior of complex strongly interacting atomic systems (molecular dynamics, Monte Carlo) have provided important insight into the behavior of nanoparticles, biogeochemical systems, mineral/fluid systems, nanoparticles, actinide systems and geofluids. The limitation of these methods to even wider applications is the difficulty of developing accurate potential interactions in these systems at the molecular level that capture their complex chemistry. The well-developed tools of quantum chemistry and physics have been shown to approach the accuracy required. However, despite the continuous effort being put into improving their accuracy and efficiency, these tools will be of little value to condensed matter problems without continued improvements in techniques to traverse and sample the high-dimensional phase space needed to span the ˜10^12 time scale differences between molecular simulation and chemical events. In recent years, we have made considerable progress in developing electronic structure and AIMD methods tailored to treat biochemical and geochemical problems, including very efficient implementations of many-body methods, fast exact exchange methods, electron-transfer methods, excited state methods, QM/MM, and new parallel algorithms that scale to +100,000 cores. The poster will focus on the fundamentals of these methods and the realities in terms of system size, computational requirements and simulation times that are required for their application to complex biogeochemical systems.

Large-eddy simulations of a solid-rocket booster jet

NASA Astrophysics Data System (ADS)

Paoli, Roberto; Poubeau, Adele; Cariolle, Daniel

2014-11-01

Emissions from solid-rocket boosters are responsible for a severe decrease in ozone concentration in the rocket plume during the first hours after a launch. The main source of ozone depletion is due to hydrogen chloride that is converted into chlorine in the high temperature regions of the jet (afterburning). The objective of this study is to evaluate the active chlorine concentration in the plume of a solid-rocket booster using large-eddy simulations. The gas is injected through the entire nozzle of the booster and a local time-stepping method based on coupling multi-instances of a fluid solver is used to extend the computational domain up to 600 nozzle exit diameters. The methodology is validated for a non-reactive case by analyzing the flow characteristics of supersonic co-flowing under expanded jets. Then, the chemistry of chlorine is studied offline using a complex chemistry solver and the LES data extracted from the mean trajectories of sample fluid particles. Finally, the online chemistry is analyzed by means of the multispecies version of the LES solver using a reduced chemistry scheme. The LES are able to capture the mixing of the exhaust with ambient air and the species concentrations, which is also useful to initialize atmospheric simulations on larger domains.

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)

M ssbauer spectroscopy

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

Hermann, Raphael P

2017-01-01

This most comprehensive and unrivaled compendium in the field provides an up-to-date account of the chemistry of solids, nanoparticles and hybrid materials. Following a valuable introductory chapter reviewing important synthesis techniques, the handbook presents a series of contributions by about 150 international leading experts -- the "Who's Who" of solid state science. Clearly structured, in six volumes it collates the knowledge available on solid state chemistry, starting from the synthesis, and modern methods of structure determination. Understanding and measuring the physical properties of bulk solids and the theoretical basis of modern computational treatments of solids are given ample space, asmore » are such modern trends as nanoparticles, surface properties and heterogeneous catalysis. Emphasis is placed throughout not only on the design and structure of solids but also on practical applications of these novel materials in real chemical situations.« less

Theoretical Design of Multilayer Dental Posts Using CAD-Based Approach and Sol-Gel Chemistry.

PubMed

Maietta, Saverio; De Santis, Roberto; Catauro, Michelina; Martorelli, Massimo; Gloria, Antonio

2018-05-07

A computer-aided design (CAD)-based approach and sol-gel chemistry were used to design a multilayer dental post with a compositional gradient and a Young’s modulus varying from 12.4 to 2.3 GPa in the coronal-apical direction. Specifically, we propose a theoretical multilayer post design, consisting of titanium dioxide (TiO₂) and TiO₂/poly(ε-caprolactone) (PCL) hybrid materials containing PCL up to 24% by weight obtained using the sol-gel method. The current study aimed to analyze the effect of the designed multilayer dental post in endodontically treated anterior teeth. Stress distribution was investigated along and between the post and the surrounding structures. In comparison to a metal post, the most uniform distributions with lower stress values and no significant stress concentration were found when using the multilayer post.

Witnessing eigenstates for quantum simulation of Hamiltonian spectra

PubMed Central

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

2018-01-01

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

Biomimetic molecular design tools that learn, evolve, and adapt.

PubMed

Winkler, David A

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known "S curve", with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine.

Biomimetic molecular design tools that learn, evolve, and adapt

PubMed Central

2017-01-01

A dominant hallmark of living systems is their ability to adapt to changes in the environment by learning and evolving. Nature does this so superbly that intensive research efforts are now attempting to mimic biological processes. Initially this biomimicry involved developing synthetic methods to generate complex bioactive natural products. Recent work is attempting to understand how molecular machines operate so their principles can be copied, and learning how to employ biomimetic evolution and learning methods to solve complex problems in science, medicine and engineering. Automation, robotics, artificial intelligence, and evolutionary algorithms are now converging to generate what might broadly be called in silico-based adaptive evolution of materials. These methods are being applied to organic chemistry to systematize reactions, create synthesis robots to carry out unit operations, and to devise closed loop flow self-optimizing chemical synthesis systems. Most scientific innovations and technologies pass through the well-known “S curve”, with slow beginning, an almost exponential growth in capability, and a stable applications period. Adaptive, evolving, machine learning-based molecular design and optimization methods are approaching the period of very rapid growth and their impact is already being described as potentially disruptive. This paper describes new developments in biomimetic adaptive, evolving, learning computational molecular design methods and their potential impacts in chemistry, engineering, and medicine. PMID:28694872

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...

Novel 3D/VR interactive environment for MD simulations, visualization and analysis.

PubMed

Doblack, Benjamin N; Allis, Tim; Dávila, Lilian P

2014-12-18

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced.

Novel 3D/VR Interactive Environment for MD Simulations, Visualization and Analysis

PubMed Central

Doblack, Benjamin N.; Allis, Tim; Dávila, Lilian P.

2014-01-01

The increasing development of computing (hardware and software) in the last decades has impacted scientific research in many fields including materials science, biology, chemistry and physics among many others. A new computational system for the accurate and fast simulation and 3D/VR visualization of nanostructures is presented here, using the open-source molecular dynamics (MD) computer program LAMMPS. This alternative computational method uses modern graphics processors, NVIDIA CUDA technology and specialized scientific codes to overcome processing speed barriers common to traditional computing methods. In conjunction with a virtual reality system used to model materials, this enhancement allows the addition of accelerated MD simulation capability. The motivation is to provide a novel research environment which simultaneously allows visualization, simulation, modeling and analysis. The research goal is to investigate the structure and properties of inorganic nanostructures (e.g., silica glass nanosprings) under different conditions using this innovative computational system. The work presented outlines a description of the 3D/VR Visualization System and basic components, an overview of important considerations such as the physical environment, details on the setup and use of the novel system, a general procedure for the accelerated MD enhancement, technical information, and relevant remarks. The impact of this work is the creation of a unique computational system combining nanoscale materials simulation, visualization and interactivity in a virtual environment, which is both a research and teaching instrument at UC Merced. PMID:25549300

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

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.