Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides.
Sastre, S; Casasnovas, R; Muñoz, F; Frau, J
2016-04-20
Theoretical and quantitative prediction of pKa values at low computational cost is a current challenge in computational chemistry. We report that the isodesmic reaction scheme provides semi-quantitative predictions (i.e. mean absolute errors of 0.5-1.0 pKa unit) for the pKa1 (α-carboxyl), pKa2 (α-amino) and pKa3 (sidechain groups) of a broad set of amino acids and peptides. This method fills the gaps of thermodynamic cycles for the computational pKa calculation of molecules that are unstable in the gas phase or undergo proton transfer reactions or large conformational changes from solution to the gas phase. We also report the key criteria to choose a reference species to make accurate predictions. This method is computationally inexpensive and makes use of standard density functional theory (DFT) and continuum solvent models. It is also conceptually simple and easy to use for researchers not specialized in theoretical chemistry methods. PMID:27052591
Accurate quantum chemical calculations
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.
1989-01-01
An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.
How Accurately can we Calculate Thermal Systems?
Cullen, D; Blomquist, R N; Dean, C; Heinrichs, D; Kalugin, M A; Lee, M; Lee, Y; MacFarlan, R; Nagaya, Y; Trkov, A
2004-04-20
I would like to determine how accurately a variety of neutron transport code packages (code and cross section libraries) can calculate simple integral parameters, such as K{sub eff}, for systems that are sensitive to thermal neutron scattering. Since we will only consider theoretical systems, we cannot really determine absolute accuracy compared to any real system. Therefore rather than accuracy, it would be more precise to say that I would like to determine the spread in answers that we obtain from a variety of code packages. This spread should serve as an excellent indicator of how accurately we can really model and calculate such systems today. Hopefully, eventually this will lead to improvements in both our codes and the thermal scattering models that they use in the future. In order to accomplish this I propose a number of extremely simple systems that involve thermal neutron scattering that can be easily modeled and calculated by a variety of neutron transport codes. These are theoretical systems designed to emphasize the effects of thermal scattering, since that is what we are interested in studying. I have attempted to keep these systems very simple, and yet at the same time they include most, if not all, of the important thermal scattering effects encountered in a large, water-moderated, uranium fueled thermal system, i.e., our typical thermal reactors.
Accurate theoretical chemistry with coupled pair models.
Neese, Frank; Hansen, Andreas; Wennmohs, Frank; Grimme, Stefan
2009-05-19
Quantum chemistry has found its way into the everyday work of many experimental chemists. Calculations can predict the outcome of chemical reactions, afford insight into reaction mechanisms, and be used to interpret structure and bonding in molecules. Thus, contemporary theory offers tremendous opportunities in experimental chemical research. However, even with present-day computers and algorithms, we cannot solve the many particle Schrodinger equation exactly; inevitably some error is introduced in approximating the solutions of this equation. Thus, the accuracy of quantum chemical calculations is of critical importance. The affordable accuracy depends on molecular size and particularly on the total number of atoms: for orientation, ethanol has 9 atoms, aspirin 21 atoms, morphine 40 atoms, sildenafil 63 atoms, paclitaxel 113 atoms, insulin nearly 800 atoms, and quaternary hemoglobin almost 12,000 atoms. Currently, molecules with up to approximately 10 atoms can be very accurately studied by coupled cluster (CC) theory, approximately 100 atoms with second-order Møller-Plesset perturbation theory (MP2), approximately 1000 atoms with density functional theory (DFT), and beyond that number with semiempirical quantum chemistry and force-field methods. The overwhelming majority of present-day calculations in the 100-atom range use DFT. Although these methods have been very successful in quantum chemistry, they do not offer a well-defined hierarchy of calculations that allows one to systematically converge to the correct answer. Recently a number of rather spectacular failures of DFT methods have been found-even for seemingly simple systems such as hydrocarbons, fueling renewed interest in wave function-based methods that incorporate the relevant physics of electron correlation in a more systematic way. Thus, it would be highly desirable to fill the gap between 10 and 100 atoms with highly correlated ab initio methods. We have found that one of the earliest (and now
Accurate radiative transfer calculations for layered media.
Selden, Adrian C
2016-07-01
Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics. PMID:27409700
Accurate calculation of diffraction-limited encircled and ensquared energy.
Andersen, Torben B
2015-09-01
Mathematical properties of the encircled and ensquared energy functions for the diffraction-limited point-spread function (PSF) are presented. These include power series and a set of linear differential equations that facilitate the accurate calculation of these functions. Asymptotic expressions are derived that provide very accurate estimates for the relative amount of energy in the diffraction PSF that fall outside a square or rectangular large detector. Tables with accurate values of the encircled and ensquared energy functions are also presented. PMID:26368873
Strategy Guideline. Accurate Heating and Cooling Load Calculations
Burdick, Arlan
2011-06-01
This guide presents the key criteria required to create accurate heating and cooling load calculations and offers examples of the implications when inaccurate adjustments are applied to the HVAC design process. The guide shows, through realistic examples, how various defaults and arbitrary safety factors can lead to significant increases in the load estimate. Emphasis is placed on the risks incurred from inaccurate adjustments or ignoring critical inputs of the load calculation.
Strategy Guideline: Accurate Heating and Cooling Load Calculations
Burdick, A.
2011-06-01
This guide presents the key criteria required to create accurate heating and cooling load calculations and offers examples of the implications when inaccurate adjustments are applied to the HVAC design process. The guide shows, through realistic examples, how various defaults and arbitrary safety factors can lead to significant increases in the load estimate. Emphasis is placed on the risks incurred from inaccurate adjustments or ignoring critical inputs of the load calculation.
Theoretical Calculations of Atomic Data for Spectroscopy
NASA Technical Reports Server (NTRS)
Bautista, Manuel A.
2000-01-01
Several different approximations and techniques have been developed for the calculation of atomic structure, ionization, and excitation of atoms and ions. These techniques have been used to compute large amounts of spectroscopic data of various levels of accuracy. This paper presents a review of these theoretical methods to help non-experts in atomic physics to better understand the qualities and limitations of various data sources and assess how reliable are spectral models based on those data.
A general, accurate procedure for calculating molecular interaction force.
Yang, Pinghai; Qian, Xiaoping
2009-09-15
The determination of molecular interaction forces, e.g., van der Waals force, between macroscopic bodies is of fundamental importance for understanding sintering, adhesion and fracture processes. In this paper, we develop an accurate, general procedure for van der Waals force calculation. This approach extends a surface formulation that converts a six-dimensional (6D) volume integral into a 4D surface integral for the force calculation. It uses non-uniform rational B-spline (NURBS) surfaces to represent object surfaces. Surface integrals are then done on the parametric domain of the NURBS surfaces. It has combined advantages of NURBS surface representation and surface formulation, including (1) molecular interactions between arbitrary-shaped objects can be represented and evaluated by the NURBS model further common geometries such as spheres, cones, planes can be represented exactly and interaction forces are thus calculated accurately; (2) calculation efficiency is improved by converting the volume integral to the surface integral. This approach is implemented and validated via its comparison with analytical solutions for simple geometries. Calculation of van der Waals force between complex geometries with surface roughness is also demonstrated. A tutorial on the NURBS approach is given in Appendix A. PMID:19596335
Fast and accurate Coulomb calculation with Gaussian functions.
Füsti-Molnár, László; Kong, Jing
2005-02-15
Coulomb interaction is one of the major time-consuming components in a density functional theory (DFT) calculation. In the last decade, dramatic progresses have been made to improve the efficiency of Coulomb calculation, including continuous fast multipole method (CFMM) and J-engine method, all developed first inside Q-Chem. The most recent development is the advent of Fourier transform Coulomb method developed by Fusti-Molnar and Pulay, and an improved version of the method has been recently implemented in Q-Chem. It replaces the least efficient part of the previous Coulomb methods with an accurate numerical integration scheme that scales in O(N2) instead of O(N4) with the basis size. The result is a much smaller slope in the linear scaling with respect to the molecular size and we will demonstrate through a series of benchmark calculations that it speeds up the calculation of Coulomb energy by several folds over the efficient existing code, i.e., the combination of CFMM and J-engine, without loss of accuracy. Furthermore, we will show that it is complementary to the latter and together the three methods offer the best performance for Coulomb part of DFT calculations, making the DFT calculations affordable for very large systems involving thousands of basis functions. PMID:15743222
Accurate pressure gradient calculations in hydrostatic atmospheric models
NASA Technical Reports Server (NTRS)
Carroll, John J.; Mendez-Nunez, Luis R.; Tanrikulu, Saffet
1987-01-01
A method for the accurate calculation of the horizontal pressure gradient acceleration in hydrostatic atmospheric models is presented which is especially useful in situations where the isothermal surfaces are not parallel to the vertical coordinate surfaces. The present method is shown to be exact if the potential temperature lapse rate is constant between the vertical pressure integration limits. The technique is applied to both the integration of the hydrostatic equation and the computation of the slope correction term in the horizontal pressure gradient. A fixed vertical grid and a dynamic grid defined by the significant levels in the vertical temperature distribution are employed.
Accurate and efficient linear scaling DFT calculations with universal applicability.
Mohr, Stephan; Ratcliff, Laura E; Genovese, Luigi; Caliste, Damien; Boulanger, Paul; Goedecker, Stefan; Deutsch, Thierry
2015-12-21
Density functional theory calculations are computationally extremely expensive for systems containing many atoms due to their intrinsic cubic scaling. This fact has led to the development of so-called linear scaling algorithms during the last few decades. In this way it becomes possible to perform ab initio calculations for several tens of thousands of atoms within reasonable walltimes. However, even though the use of linear scaling algorithms is physically well justified, their implementation often introduces some small errors. Consequently most implementations offering such a linear complexity either yield only a limited accuracy or, if one wants to go beyond this restriction, require a tedious fine tuning of many parameters. In our linear scaling approach within the BigDFT package, we were able to overcome this restriction. Using an ansatz based on localized support functions expressed in an underlying Daubechies wavelet basis - which offers ideal properties for accurate linear scaling calculations - we obtain an amazingly high accuracy and a universal applicability while still keeping the possibility of simulating large system with linear scaling walltimes requiring only a moderate demand of computing resources. We prove the effectiveness of our method on a wide variety of systems with different boundary conditions, for single-point calculations as well as for geometry optimizations and molecular dynamics. PMID:25958954
Accurate calculations of bound rovibrational states for argon trimer
Brandon, Drew; Poirier, Bill
2014-07-21
This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar{sub 3}), using the ScalIT suite of parallel codes. The Ar{sub 3} rovibrational energy levels are computed to a very high level of accuracy (10{sup −3} cm{sup −1} or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar{sub 3} are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar{sub 3} is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar{sub 3} may be found in the current literature—and only for the lowest-lying rotational excitations.
Accurate calculations of bound rovibrational states for argon trimer.
Brandon, Drew; Poirier, Bill
2014-07-21
This work presents a comprehensive quantum dynamics calculation of the bound rovibrational eigenstates of argon trimer (Ar3), using the ScalIT suite of parallel codes. The Ar3 rovibrational energy levels are computed to a very high level of accuracy (10(-3) cm(-1) or better), and up to the highest rotational and vibrational excitations for which bound states exist. For many of these rovibrational states, wavefunctions are also computed. Rare gas clusters such as Ar3 are interesting because the interatomic interactions manifest through long-range van der Waals forces, rather than through covalent chemical bonding. As a consequence, they exhibit strong Coriolis coupling between the rotational and vibrational degrees of freedom, as well as highly delocalized states, all of which renders accurate quantum dynamical calculation difficult. Moreover, with its (comparatively) deep potential well and heavy masses, Ar3 is an especially challenging rare gas trimer case. There are a great many rovibrational eigenstates to compute, and a very high density of states. Consequently, very few previous rovibrational state calculations for Ar3 may be found in the current literature-and only for the lowest-lying rotational excitations. PMID:25053315
Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations.
Schröder, Heiner; Schwabe, Tobias
2016-08-15
We evaluate embedding potentials, obtained via various methods, used for polarizable embedding computations of excitation energies of para-nitroaniline in water and organic solvents as well as of the green fluorescent protein. We found that isotropic polarizabilities derived from DFTD3 dispersion coefficients correlate well with those obtained via the LoProp method. We show that these polarizabilities in conjunction with appropriately derived point charges are in good agreement with calculations employing static multipole moments up to quadrupoles and anisotropic polarizabilities for both computed systems. The (partial) use of these easily-accessible parameters drastically reduces the computational effort to obtain accurate embedding potentials especially for proteins. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27317509
Highly Accurate Calculations of the Phase Diagram of Cold Lithium
NASA Astrophysics Data System (ADS)
Shulenburger, Luke; Baczewski, Andrew
The phase diagram of lithium is particularly complicated, exhibiting many different solid phases under the modest application of pressure. Experimental efforts to identify these phases using diamond anvil cells have been complemented by ab initio theory, primarily using density functional theory (DFT). Due to the multiplicity of crystal structures whose enthalpy is nearly degenerate and the uncertainty introduced by density functional approximations, we apply the highly accurate many-body diffusion Monte Carlo (DMC) method to the study of the solid phases at low temperature. These calculations span many different phases, including several with low symmetry, demonstrating the viability of DMC as a method for calculating phase diagrams for complex solids. Our results can be used as a benchmark to test the accuracy of various density functionals. This can strengthen confidence in DFT based predictions of more complex phenomena such as the anomalous melting behavior predicted for lithium at high pressures. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.
Accurate theoretical and experimental characterization of optical grating coupler.
Fesharaki, Faezeh; Hossain, Nadir; Vigne, Sebastien; Chaker, Mohamed; Wu, Ke
2016-09-01
Periodic structures, acting as reflectors, filters, and couplers, are a fundamental building block section in many optical devices. In this paper, a three-dimensional simulation of a grating coupler, a well-known periodic structure, is conducted. Guided waves and leakage characteristics of an out-of-plane grating coupler are studied in detail, and its coupling efficiency is examined. Furthermore, a numerical calibration analysis is applied through a commercial software package on the basis of a full-wave finite-element method to calculate the complex propagation constant of the structure and to evaluate the radiation pattern. For experimental evaluation, an optimized grating coupler is fabricated using electron-beam lithography technique and plasma etching. An excellent agreement between simulations and measurements is observed, thereby validating the demonstrated method. PMID:27607706
Accurate ionization potential of semiconductors from efficient density functional calculations
NASA Astrophysics Data System (ADS)
Ye, Lin-Hui
2016-07-01
Despite its huge successes in total-energy-related applications, the Kohn-Sham scheme of density functional theory cannot get reliable single-particle excitation energies for solids. In particular, it has not been able to calculate the ionization potential (IP), one of the most important material parameters, for semiconductors. We illustrate that an approximate exact-exchange optimized effective potential (EXX-OEP), the Becke-Johnson exchange, can be used to largely solve this long-standing problem. For a group of 17 semiconductors, we have obtained the IPs to an accuracy similar to that of the much more sophisticated G W approximation (GWA), with the computational cost of only local-density approximation/generalized gradient approximation. The EXX-OEP, therefore, is likely as useful for solids as for finite systems. For solid surfaces, the asymptotic behavior of the vx c has effects similar to those of finite systems which, when neglected, typically cause the semiconductor IPs to be underestimated. This may partially explain why standard GWA systematically underestimates the IPs and why using the same GWA procedures has not been able to get an accurate IP and band gap at the same time.
Accurate calculation of field and carrier distributions in doped semiconductors
NASA Astrophysics Data System (ADS)
Yang, Wenji; Tang, Jianping; Yu, Hongchun; Wang, Yanguo
2012-06-01
We use the numerical squeezing algorithm(NSA) combined with the shooting method to accurately calculate the built-in fields and carrier distributions in doped silicon films (SFs) in the micron and sub-micron thickness range and results are presented in graphical form for variety of doping profiles under different boundary conditions. As a complementary approach, we also present the methods and the results of the inverse problem (IVP) - finding out the doping profile in the SFs for given field distribution. The solution of the IVP provides us the approach to arbitrarily design field distribution in SFs - which is very important for low dimensional (LD) systems and device designing. Further more, the solution of the IVP is both direct and much easy for all the one-, two-, and three-dimensional semiconductor systems. With current efforts focused on the LD physics, knowing of the field and carrier distribution details in the LD systems will facilitate further researches on other aspects and hence the current work provides a platform for those researches.
Accurate calculation of (31)P NMR chemical shifts in polyoxometalates.
Pascual-Borràs, Magda; López, Xavier; Poblet, Josep M
2015-04-14
We search for the best density functional theory strategy for the determination of (31)P nuclear magnetic resonance (NMR) chemical shifts, δ((31)P), in polyoxometalates. Among the variables governing the quality of the quantum modelling, we tackle herein the influence of the functional and the basis set. The spin-orbit and solvent effects were routinely included. To do so we analysed the family of structures α-[P2W18-xMxO62](n-) with M = Mo(VI), V(V) or Nb(V); [P2W17O62(M'R)](n-) with M' = Sn(IV), Ge(IV) and Ru(II) and [PW12-xMxO40](n-) with M = Pd(IV), Nb(V) and Ti(IV). The main results suggest that, to date, the best procedure for the accurate calculation of δ((31)P) in polyoxometalates is the combination of TZP/PBE//TZ2P/OPBE (for NMR//optimization step). The hybrid functionals (PBE0, B3LYP) tested herein were applied to the NMR step, besides being more CPU-consuming, do not outperform pure GGA functionals. Although previous studies on (183)W NMR suggested that the use of very large basis sets like QZ4P were needed for geometry optimization, the present results indicate that TZ2P suffices if the functional is optimal. Moreover, scaling corrections were applied to the results providing low mean absolute errors below 1 ppm for δ((31)P), which is a step forward in order to confirm or predict chemical shifts in polyoxometalates. Finally, via a simplified molecular model, we establish how the small variations in δ((31)P) arise from energy changes in the occupied and virtual orbitals of the PO4 group. PMID:25738630
Spectroscopically Accurate Calculations of the Rovibrational Energies of Diatomic Hydrogen
NASA Astrophysics Data System (ADS)
Perry, Jason
2005-05-01
The Born-Oppenheimer approximation has been used to calculate the rotational and vibrational states of diatomic hydrogen. Because it is an approximation, our group now wants to use a Born-Oppenheimer potential to calculate the electronic energy that has been corrected to match closely with spectroscopic results. We are using a code that has corrections for adiabatic, relativistic, radiative, and non-adiabatic effects. The rovibrational energies have now been calculated for both bound and quasi-bound states. We also want to compute quadrupole transition probabilities for diatomic hydrogen. These calculations aspire to investigate diatomic hydrogen in astrophysical environments.
Theoretical Calculations of Equations of State
NASA Astrophysics Data System (ADS)
Prakash, Madappa
2016-07-01
The modeling of core-collapse supernovae, neutron stars from their birth to old age, and binary mergers of compact stars requires a detailed knowledge of the equation of state (EOS) of matter at finite temperature. Thermodynamic state variables such as the free energy, energy per baryon, pressure, entropy per baryon, specific heats, chemical potentials of the various species and their derivatives with respect to number densities, thermal and adiabatic indices, etc., all play distinct roles in large-scale computer simulations involving compact objects. In this talk, recent developments in the calculation of the thermal properties of dense matter will be reviewed. Recent results from beyond relativistic mean field theory will be discussed. Highlights will include the role of non-nucleonic degrees of freedom at finite temperature, and possible avenues for future investigations.
Time-accurate Navier-Stokes calculations with multigrid acceleration
NASA Technical Reports Server (NTRS)
Melson, N. D.; Sanetrik, Mark D.; Atkins, Harold L.
1993-01-01
An efficient method for calculating unsteady flows is presented, with emphasis on a modified version of the thin-layer Navier-Stokes equations. Fourier stability analysis is used to illustrate the effect of treating the source term implicitly instead of explicity, as well as to illustrate other algorithmic choices. A 2D circular cylinder (with a Reynolds number of 1200 and a Mach number of 0.3) is calculated. The present scheme requires only about 10 percent of the computer time required by global minimum time stepping.
General formula for accurate calculation of halofullerenes polarizability
NASA Astrophysics Data System (ADS)
Sabirov, D. Sh.; Garipova, R. R.; Bulgakov, R. G.
2012-01-01
At the first time mean polarizabilities of fluoro-, chloro-, bromo[60]fullerenes have been calculated. The dependences of halofullerenes polarizabilities on the structure and the number of halogen atoms in a molecule have been analyzed. The phenomenon of polarizability depression is typical for all compounds under study. General formula for calculation of all classes of halofullerenes mean polarizabilities has been derived based on polarizability depression. Its applicability to related compounds (C70 fullerene choro-derivatives and hypothetical iodo[60]fullerenes) has been shown.
Machine learning of parameters for accurate semiempirical quantum chemical calculations
Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter
2015-04-14
We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempiricalmore » OM2 method using a set of 6095 constitutional isomers C7H10O2, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.« less
Machine learning of parameters for accurate semiempirical quantum chemical calculations
Dral, Pavlo O.; von Lilienfeld, O. Anatole; Thiel, Walter
2015-04-14
We investigate possible improvements in the accuracy of semiempirical quantum chemistry (SQC) methods through the use of machine learning (ML) models for the parameters. For a given class of compounds, ML techniques require sufficiently large training sets to develop ML models that can be used for adapting SQC parameters to reflect changes in molecular composition and geometry. The ML-SQC approach allows the automatic tuning of SQC parameters for individual molecules, thereby improving the accuracy without deteriorating transferability to molecules with molecular descriptors very different from those in the training set. The performance of this approach is demonstrated for the semiempirical OM2 method using a set of 6095 constitutional isomers C_{7}H_{10}O_{2}, for which accurate ab initio atomization enthalpies are available. The ML-OM2 results show improved average accuracy and a much reduced error range compared with those of standard OM2 results, with mean absolute errors in atomization enthalpies dropping from 6.3 to 1.7 kcal/mol. They are also found to be superior to the results from specific OM2 reparameterizations (rOM2) for the same set of isomers. The ML-SQC approach thus holds promise for fast and reasonably accurate high-throughput screening of materials and molecules.
The Calculation of Accurate Metal-Ligand Bond Energies
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W.; Partridge, Harry, III; Ricca, Alessandra; Arnold, James O. (Technical Monitor)
1997-01-01
The optimization of the geometry and calculation of zero-point energies are carried out at the B3LYP level of theory. The bond energies are determined at this level, as well as at the CCSD(T) level using very large basis sets. The successive OH bond energies to the first row transition metal cations are reported. For most systems there has been an experimental determination of the first OH. In general, the CCSD(T) values are in good agreement with experiment. The bonding changes from mostly covalent for the early metals to mostly electrostatic for the late transition metal systems.
How Accurately Can We Calculate Neutrons Slowing Down In Water ?
Cullen, D E; Blomquist, R; Greene, M; Lent, E; MacFarlane, R; McKinley, S; Plechaty, E; Sublet, J C
2006-03-30
We have compared the results produced by a variety of currently available Monte Carlo neutron transport codes for the relatively simple problem of a fast source of neutrons slowing down and thermalizing in water. Initial comparisons showed rather large differences in the calculated flux; up to 80% differences. By working together we iterated to improve the results by: (1) insuring that all codes were using the same data, (2) improving the models used by the codes, and (3) correcting errors in the codes; no code is perfect. Even after a number of iterations we still found differences, demonstrating that our Monte Carlo and supporting codes are far from perfect; in particularly we found that the often overlooked nuclear data processing codes can be the weakest link in our systems of codes. The results presented here represent the today's state-of-the-art, in the sense that all of the Monte Carlo codes are modern, widely available and used codes. They all use the most up-to-date nuclear data, and the results are very recent, weeks or at most a few months old; these are the results that current users of these codes should expect to obtain from them. As such, the accuracy and limitations of the codes presented here should serve as guidelines to code users in interpreting their results for similar problems. We avoid crystal ball gazing, in the sense that we limit the scope of this report to what is available to code users today, and we avoid predicting future improvements that may or may not actual come to pass. An exception that we make is in presenting results for an improved thermal scattering model currently being testing using advanced versions of NJOY and MCNP that are not currently available to users, but are planned for release in the not too distant future. The other exception is to show comparisons between experimentally measured water cross sections and preliminary ENDF/B-VII thermal scattering law, S({alpha},{beta}) data; although these data are strictly
Theoretical Calculation and Validation of the Water Vapor Continuum Absorption
NASA Technical Reports Server (NTRS)
Ma, Qiancheng; Tipping, Richard H.
1998-01-01
The primary objective of this investigation is the development of an improved parameterization of the water vapor continuum absorption through the refinement and validation of our existing theoretical formalism. The chief advantage of our approach is the self-consistent, first principles, basis of the formalism which allows us to predict the frequency, temperature and pressure dependence of the continuum absorption as well as provide insights into the physical mechanisms responsible for the continuum absorption. Moreover, our approach is such that the calculated continuum absorption can be easily incorporated into satellite retrieval algorithms and climate models. Accurate determination of the water vapor continuum is essential for the next generation of retrieval algorithms which propose to use the combined constraints of multi-spectral measurements such as those under development for EOS data analysis (e.g., retrieval algorithms based on MODIS and AIRS measurements); current Pathfinder activities which seek to use the combined constraints of infrared and microwave (e.g., HIRS and MSU) measurements to improve temperature and water profile retrievals, and field campaigns which seek to reconcile spectrally-resolved and broad-band measurements such as those obtained as part of FIRE. Current widely used continuum treatments have been shown to produce spectrally dependent errors, with the magnitude of the error dependent on temperature and abundance which produces errors with a seasonal and latitude dependence. Translated into flux, current water vapor continuum parameterizations produce flux errors of order 10 W/ml, which compared to the 4 W/m' magnitude of the greenhouse gas forcing and the 1-2 W/m' estimated aerosol forcing is certainly climatologically significant and unacceptably large. While it is possible to tune the empirical formalisms, the paucity of laboratory measurements, especially at temperatures of interest for atmospheric applications, preclude tuning
Theoretical Calculation and Validation of the Water Vapor Continuum Absorption
NASA Technical Reports Server (NTRS)
Ma, Qiancheng; Tipping, Richard H.
1998-01-01
The primary objective of this investigation is the development of an improved parameterization of the water vapor continuum absorption through the refinement and validation of our existing theoretical formalism. The chief advantage of our approach is the self-consistent, first principles, basis of the formalism which allows us to predict the frequency, temperature and pressure dependence of the continuum absorption as well as provide insights into the physical mechanisms responsible for the continuum absorption. Moreover, our approach is such that the calculated continuum absorption can be easily incorporated into satellite retrieval algorithms and climate models. Accurate determination of the water vapor continuum is essential for the next generation of retrieval algorithms which propose to use the combined constraints of multispectral measurements such as those under development for EOS data analysis (e.g., retrieval algorithms based on MODIS and AIRS measurements); current Pathfinder activities which seek to use the combined constraints of infrared and microwave (e.g., HIRS and MSU) measurements to improve temperature and water profile retrievals, and field campaigns which seek to reconcile spectrally-resolved and broad-band measurements such as those obtained as part of FIRE. Current widely used continuum treatments have been shown to produce spectrally dependent errors, with the magnitude of the error dependent on temperature and abundance which produces errors with a seasonal and latitude dependence. Translated into flux, current water vapor continuum parameterizations produce flux errors of order 10 W/sq m, which compared to the 4 W/sq m magnitude of the greenhouse gas forcing and the 1-2 W/sq m estimated aerosol forcing is certainly climatologically significant and unacceptably large. While it is possible to tune the empirical formalisms, the paucity of laboratory measurements, especially at temperatures of interest for atmospheric applications, preclude
NASA Technical Reports Server (NTRS)
Liu, Yen; Vinokur, Marcel
1989-01-01
This paper treats the accurate and efficient calculation of thermodynamic properties of arbitrary gas mixtures for equilibrium flow computations. New improvements in the Stupochenko-Jaffe model for the calculation of thermodynamic properties of diatomic molecules are presented. A unified formulation of equilibrium calculations for gas mixtures in terms of irreversible entropy is given. Using a highly accurate thermo-chemical data base, a new, efficient and vectorizable search algorithm is used to construct piecewise interpolation procedures with generate accurate thermodynamic variable and their derivatives required by modern computational algorithms. Results are presented for equilibrium air, and compared with those given by the Srinivasan program.
SMARTIES: User-friendly codes for fast and accurate calculations of light scattering by spheroids
NASA Astrophysics Data System (ADS)
Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.
2016-05-01
We provide a detailed user guide for SMARTIES, a suite of MATLAB codes for the calculation of the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. SMARTIES is a MATLAB implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. The theory behind the improvements in numerical accuracy and convergence is briefly summarized, with reference to the original publications. Instructions of use, and a detailed description of the code structure, its range of applicability, as well as guidelines for further developments by advanced users are discussed in separate sections of this user guide. The code may be useful to researchers seeking a fast, accurate and reliable tool to simulate the near-field and far-field optical properties of elongated particles, but will also appeal to other developers of light-scattering software seeking a reliable benchmark for non-spherical particles with a challenging aspect ratio and/or refractive index contrast.
Discretely disordered photonic bandgap structures: a more accurate invariant measure calculation
NASA Astrophysics Data System (ADS)
Kissel, Glen J.
2009-02-01
In the one-dimensional optical analog to Anderson localization, a periodically layered medium has one or more parameters randomly disordered. Such a randomized system can be modeled by an infinite product of 2x2 random transfer matrices with the upper Lyapunov exponent of the matrix product identified as the localization factor (inverse localization length) for the model. The theorem of Furstenberg allows us, at least theoretically, to calculate this upper Lyapunov exponent. In Furstenberg's formula we not only integrate with respect to the probability measure of the random matrices, but also with respect to the invariant probability measure of the direction of the vector propagated by the random matrices. This invariant measure is difficult to find analytically, and, as a result, the most successful approach is to determine the invariant measure numerically. A Monte Carlo simulation which uses accumulated bin counts to track the direction of the propagated vector through a long chain of random matrices does a good job of estimating the invariant probability measure, but with a level of uncertainty. A potentially more accurate numerical technique by Froyland and Aihara obtains the invariant measure as a left eigenvector of a large sparse matrix containing probability values determined by the action of the random matrices on input vectors. We first apply these two techniques to a random Fibonacci sequence whose Lyapunov exponent was determined by Viswanath. We then demonstrate these techniques on a quarter-wave stack model with binary discrete disorder in layer thickness, and compare results to the continuously disordered counterpart.
An Effective Method to Accurately Calculate the Phase Space Factors for β - β - Decay
Neacsu, Andrei; Horoi, Mihai
2016-01-01
Accurate calculations of the electron phase space factors are necessary for reliable predictions of double-beta decay rates and for the analysis of the associated electron angular and energy distributions. We present an effective method to calculate these phase space factors that takes into account the distorted Coulomb field of the daughter nucleus, yet it allows one to easily calculate the phase space factors with good accuracy relative to the most exact methods available in the recent literature.
Potential theoretic methods for far field sound radiation calculations
NASA Technical Reports Server (NTRS)
Hariharan, S. I.; Stenger, Edward J.; Scott, J. R.
1995-01-01
In the area of computational acoustics, procedures which accurately predict the far-field sound radiation are much sought after. A systematic development of such procedures are found in a sequence of papers by Atassi. The method presented here is an alternate approach to predicting far field sound based on simple layer potential theoretic methods. The main advantages of this method are: it requires only a simple free space Green's function, it can accommodate arbitrary shapes of Kirchoff surfaces, and is readily extendable to three-dimensional problems. Moreover, the procedure presented here, though tested for unsteady lifting airfoil problems, can easily be adapted to other areas of interest, such as jet noise radiation problems. Results are presented for lifting airfoil problems and comparisons are made with the results reported by Atassi. Direct comparisons are also made for the flat plate case.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH(+) ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations. PMID:24697449
NASA Astrophysics Data System (ADS)
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-01
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH+ ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
Accurate calculation of conductive conductances in complex geometries for spacecrafts thermal models
NASA Astrophysics Data System (ADS)
Garmendia, Iñaki; Anglada, Eva; Vallejo, Haritz; Seco, Miguel
2016-02-01
The thermal subsystem of spacecrafts and payloads is always designed with the help of Thermal Mathematical Models. In the case of the Thermal Lumped Parameter (TLP) method, the non-linear system of equations that is created is solved to calculate the temperature distribution and the heat power that goes between nodes. The accuracy of the results depends largely on the appropriate calculation of the conductive and radiative conductances. Several established methods for the determination of conductive conductances exist but they present some limitations for complex geometries. Two new methods are proposed in this paper to calculate accurately these conductive conductances: The Extended Far Field method and the Mid-Section method. Both are based on a finite element calculation but while the Extended Far Field method uses the calculation of node mean temperatures, the Mid-Section method is based on assuming specific temperature values. They are compared with traditionally used methods showing the advantages of these two new methods.
Ab Initio Potential Energy Surfaces and the Calculation of Accurate Vibrational Frequencies
NASA Technical Reports Server (NTRS)
Lee, Timothy J.; Dateo, Christopher E.; Martin, Jan M. L.; Taylor, Peter R.; Langhoff, Stephen R. (Technical Monitor)
1995-01-01
Due to advances in quantum mechanical methods over the last few years, it is now possible to determine ab initio potential energy surfaces in which fundamental vibrational frequencies are accurate to within plus or minus 8 cm(exp -1) on average, and molecular bond distances are accurate to within plus or minus 0.001-0.003 Angstroms, depending on the nature of the bond. That is, the potential energy surfaces have not been scaled or empirically adjusted in any way, showing that theoretical methods have progressed to the point of being useful in analyzing spectra that are not from a tightly controlled laboratory environment, such as vibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy will be presented and discussed. These include the HNO, CH4, C2H4, and ClCN molecules. The HNO molecule is interesting due to the very large H-N anharmonicity, while ClCN has a very large Fermi resonance. The ab initio studies for the CH4 and C2H4 molecules present the first accurate full quartic force fields of any kind (i.e., whether theoretical or empirical) for a five-atom and six-atom system, respectively.
NASA Astrophysics Data System (ADS)
Purwanto, Wirawan; Krakauer, Henry; Zhang, Shiwei; Virgus, Yudistira
2011-03-01
Weak H2 physisorption energies present a significant challenge to first-principle theoretical modeling and prediction of materials for H storage. There has been controversy regarding the accuracy of DFT on systems involving Ca cations. We use the auxiliary-field quantum Monte Carlo (AFQMC) method to accurately predict the binding energy of Ca + , - 4{H}2 . AFQMC scales as Nbasis3and has demonstrated accuracy similar to or better than the gold-standard coupled cluster CCSD(T) method. We apply a modified Cholesky decomposition to achieve efficient Hubbard-Stratonovich transformation in AFQMC at large basis sizes. We employ the largest correlation consistent basis sets available, up to Ca/cc-pCV5Z, to extrapolate to the complete basis limit. The calculated potential energy curve exhibits binding with a double-well structure. Supported by DOE and NSF. Calculations were performed at OLCF Jaguar and CPD.
NASA Technical Reports Server (NTRS)
Avrett, E. H.
1984-01-01
Models and spectra of sunspots were studied, because they are important to energy balance and variability discussions. Sunspot observations in the ultraviolet region 140 to 168 nn was obtained by the NRL High Resolution Telescope and Spectrograph. Extensive photometric observations of sunspot umbrae and prenumbrae in 10 chanels covering the wavelength region 387 to 3800 nm were made. Cool star opacities and model atmospheres were computed. The Sun is the first testcase, both to check the opacity calculations against the observed solar spectrum, and to check the purely theoretical model calculation against the observed solar energy distribution. Line lists were finally completed for all the molecules that are important in computing statistical opacities for energy balance and for radiative rate calculations in the Sun (except perhaps for sunspots). Because many of these bands are incompletely analyzed in the laboratory, the energy levels are not well enough known to predict wavelengths accurately for spectrum synthesis and for detailed comparison with the observations.
NASA Astrophysics Data System (ADS)
Skone, Jonathan; Govoni, Marco; Galli, Giulia
Dielectric-dependent hybrid [DDH] functionals have recently been shown to yield highly accurate energy gaps and dielectric constants for a wide variety of solids, at a computational cost considerably less than standard GW calculations. The fraction of exact exchange included in the definition of DDH functionals depends (self-consistently) on the dielectric constant of the material. In the present talk we introduce a range-separated (RS) version of DDH functionals where short and long-range components are matched using material dependent, non-empirical parameters. Comparing with state of the art GW calculations and experiment, we show that such RS hybrids yield accurate electronic properties of both molecules and solids, including energy gaps, photoelectron spectra and absolute ionization potentials. This work was supported by NSF-CCI Grant Number NSF-CHE-0802907 and DOE-BES.
Accurate near-field calculation in the rigorous coupled-wave analysis method
NASA Astrophysics Data System (ADS)
Weismann, Martin; Gallagher, Dominic F. G.; Panoiu, Nicolae C.
2015-12-01
The rigorous coupled-wave analysis (RCWA) is one of the most successful and widely used methods for modeling periodic optical structures. It yields fast convergence of the electromagnetic far-field and has been adapted to model various optical devices and wave configurations. In this article, we investigate the accuracy with which the electromagnetic near-field can be calculated by using RCWA and explain the observed slow convergence and numerical artifacts from which it suffers, namely unphysical oscillations at material boundaries due to the Gibbs phenomenon. In order to alleviate these shortcomings, we also introduce a mathematical formulation for accurate near-field calculation in RCWA, for one- and two-dimensional straight and slanted diffraction gratings. This accurate near-field computational approach is tested and evaluated for several representative test-structures and configurations in order to illustrate the advantages provided by the proposed modified formulation of the RCWA.
Accurate calculation of phase shifts for electron collisions with positive ions
NASA Astrophysics Data System (ADS)
Gien, T. T.
2003-06-01
The Harris-Nesbet variational method was considered for the calculation of phase shifts of electron collisions with hydrogen-like ions (Li2+, Be3+, and B4+). Calculations were carried out for both singlet and triplet scattering. Very accurate results of phase shift of electron collisions with these ionic targets were obtained for the first time for partial waves of L up to six. The phase shifts that we obtained for low partial wave (S, P, and D) scattering were compared with those available in the literature by a few other research groups employing different numerical methods.
A localized basis that allows fast and accurate second order Moller-Plesset calculations
Subotnik, Joseph E.; Head-Gordon, Martin
2004-10-27
We present a method for computing a basis of localized orthonormal orbitals (both occupied and virtual), in whose representation the Fock matrix is extremely diagonal-dominant. The existence of these orbitals is shown empirically to be sufficient for achieving highly accurate MP@ energies, calculated according to Kapuy's method. This method (which we abbreviate KMP2), which involves a different partitioning of the n-electron Hamiltonian, scales at most quadratically with potential for linearity in the number of electrons. As such, we believe the KMP2 algorithm presented here could be the basis of a viable approach to local correlation calculations.
Theoretical model for calculation of helicity in solar active regions
NASA Astrophysics Data System (ADS)
Chatterjee, P.
We (Choudhuri, Chatterjee and Nandy, 2005) calculate helicities of solar active regions based on the idea of Choudhuri (2003) that poloidal flux lines get wrapped around a toroidal flux tube rising through the convection zone, thereby giving rise to the helicity. Rough estimates based on this idea compare favourably with the observed magnitude of helicity. We use our solar dynamo model based on the Babcock--Leighton α-effect to study how helicity varies with latitude and time. At the time of solar maximum, our theoretical model gives negative helicity in the northern hemisphere and positive helicity in the south, in accordance with observed hemispheric trends. However, we find that, during a short interval at the beginning of a cycle, helicities tend to be opposite of the preferred hemispheric trends. Next we (Chatterjee, Choudhuri and Petrovay 2006) use the above idea along with the sunspot decay model of Petrovay and Moreno-Insertis, (1997) to estimate the distribution of helicity inside a flux tube as it keeps collecting more azimuthal flux during its rise through the convection zone and as turbulent diffusion keeps acting on it. By varying parameters over reasonable ranges in our simple 1-d model, we find that the azimuthal flux penetrates the flux tube to some extent instead of being confined to a narrow sheath outside.
Accurate variational calculations and analysis of the HOCl vibrational energy spectrum
Skokov, S.; Qi, J.; Bowman, J.M.; Yang, C.; Gray, S.K.; Peterson, K.A. |; Mandelshtam, V.A.
1998-12-01
Large scale variational calculations for the vibrational states of HOCl are performed using a recently developed, accurate {ital ab initio} potential energy surface. Three different approaches for obtaining vibrational states are employed and contrasted; a truncation/recoupling scheme with direct diagonalization, the Lanczos method, and Chebyshev iteration with filter diagonalization. The complete spectrum of bound states for nonrotating HOCl is computed and analyzed within a random matrix theory framework. This analysis indicates almost entirely regular dynamics with only a small degree of chaos. The nearly regular spectral structure allows us to make assignments for the most significant part of the spectrum, based on analysis of coordinate expectation values and eigenfunctions. Ground state dipole moments and dipole transition probabilities are also calculated using accurate {ital ab initio} data. Computed values are in good agreement with available experimental data. Some exact rovibrational calculations for J=1, including Coriolis coupling, are performed. The exact results are nearly identical with those obtained from the adiabatic rotation approximation and very close to those from the centrifugal sudden approximation, thus indicating a very small degree of asymmetry and Coriolis coupling for the HOCl molecule. {copyright} {ital 1998 American Institute of Physics.}
Accurate calculation of computer-generated holograms using angular-spectrum layer-oriented method.
Zhao, Yan; Cao, Liangcai; Zhang, Hao; Kong, Dezhao; Jin, Guofan
2015-10-01
Fast calculation and correct depth cue are crucial issues in the calculation of computer-generated hologram (CGH) for high quality three-dimensional (3-D) display. An angular-spectrum based algorithm for layer-oriented CGH is proposed. Angular spectra from each layer are synthesized as a layer-corresponded sub-hologram based on the fast Fourier transform without paraxial approximation. The proposed method can avoid the huge computational cost of the point-oriented method and yield accurate predictions of the whole diffracted field compared with other layer-oriented methods. CGHs of versatile formats of 3-D digital scenes, including computed tomography and 3-D digital models, are demonstrated with precise depth performance and advanced image quality. PMID:26480062
Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.
Neal, Stephen; Nip, Alex M; Zhang, Haiyan; Wishart, David S
2003-07-01
A computer program (SHIFTX) is described which rapidly and accurately calculates the diamagnetic 1H, 13C and 15N chemical shifts of both backbone and sidechain atoms in proteins. The program uses a hybrid predictive approach that employs pre-calculated, empirically derived chemical shift hypersurfaces in combination with classical or semi-classical equations (for ring current, electric field, hydrogen bond and solvent effects) to calculate 1H, 13C and 15N chemical shifts from atomic coordinates. The chemical shift hypersurfaces capture dihedral angle, sidechain orientation, secondary structure and nearest neighbor effects that cannot easily be translated to analytical formulae or predicted via classical means. The chemical shift hypersurfaces were generated using a database of IUPAC-referenced protein chemical shifts--RefDB (Zhang et al., 2003), and a corresponding set of high resolution (<2.1 A) X-ray structures. Data mining techniques were used to extract the largest pairwise contributors (from a list of approximately 20 derived geometric, sequential and structural parameters) to generate the necessary hypersurfaces. SHIFTX is rapid (<1 CPU second for a complete shift calculation of 100 residues) and accurate. Overall, the program was able to attain a correlation coefficient (r) between observed and calculated shifts of 0.911 (1Halpha), 0.980 (13Calpha), 0.996 (13Cbeta), 0.863 (13CO), 0.909 (15N), 0.741 (1HN), and 0.907 (sidechain 1H) with RMS errors of 0.23, 0.98, 1.10, 1.16, 2.43, 0.49, and 0.30 ppm, respectively on test data sets. We further show that the agreement between observed and SHIFTX calculated chemical shifts can be an extremely sensitive measure of the quality of protein structures. Our results suggest that if NMR-derived structures could be refined using heteronuclear chemical shifts calculated by SHIFTX, their precision could approach that of the highest resolution X-ray structures. SHIFTX is freely available as a web server at http
On the accurate theoretical determination of the static hyperpolarizability of trans-butadiene
NASA Astrophysics Data System (ADS)
Maroulis, George
1999-07-01
Finite-field many-body perturbation theory and coupled cluster calculations are reported for the static second dipole hyperpolarizability γαβγδ of trans-butadiene. A very large basis set of [9s6p4d1f/6s3p1d] size (336 contracted Gaussian-type functions) should lead to self-consistent field (SCF) values of near-Hartree-Fock quality. We report γxxxx=6.19, γxxxz=-0.44, γxxyy=3.42, γzzxx=2.07, γxyyz=-0.50, γxzzz=1.73, γyyyy=14.72, γyyzz=8.46, γzzzz=24.10 and γ¯=14.58 for 10-3×γαβγδ/e4a04Eh-3 at the experimental geometry (molecule on the xz plane with z as the main axis). γ¯=(14.6±0.4)×103e4a04Eh-3 should be a very reliable estimate of the Hartree-Fock limit of the mean hyperpolarizability. Keeping all other molecular geometry parameters constant, we find that near the Hartree-Fock limit the mean hyperpolarizability varies with the C=C bond length as 10-3×γ¯(RC=C)/e4a04Eh-3=14.93+31.78ΔR+30.88ΔR2-2.96ΔR3 and with the C-C bond length as 10-3×γ¯(RC-C)/e4a04Eh-3=14.93-7.20ΔR+3.04ΔR2, where ΔR/a0 is the displacement from the respective experimental value. The dependence of the components of γαβγδ on the molecular geometry parameters is not uniform. Electron correlation corrections have been calculated at various molecular geometries at the coupled-cluster single, double and perturbatively linked triple excitations level of theory for all independent components of γαβγδ. In absolute terms, electron correlation affects strongly the γzzzz, less strongly the γxxxx, and even less strongly the out-of-plane component γyyyy. The present analysis suggests a conservative estimate of (3.0±0.6)×103e4a04Eh-3 for the electron correlation correction to γ¯ at the experimental molecular geometry. Most of this value is appropriate to γzzzz. A static limit of γ¯=(17.6±1.0)×103e4a04Eh-3 is advanced (neglecting vibrational averaging). Even if a crude theoretical estimate of the dispersion of γ¯ at 1064 nm is added to this value, the
Abate-Pella, Daniel; Freund, Dana M; Ma, Yan; Simón-Manso, Yamil; Hollender, Juliane; Broeckling, Corey D; Huhman, David V; Krokhin, Oleg V; Stoll, Dwight R; Hegeman, Adrian D; Kind, Tobias; Fiehn, Oliver; Schymanski, Emma L; Prenni, Jessica E; Sumner, Lloyd W; Boswell, Paul G
2015-09-18
Identification of small molecules by liquid chromatography-mass spectrometry (LC-MS) can be greatly improved if the chromatographic retention information is used along with mass spectral information to narrow down the lists of candidates. Linear retention indexing remains the standard for sharing retention data across labs, but it is unreliable because it cannot properly account for differences in the experimental conditions used by various labs, even when the differences are relatively small and unintentional. On the other hand, an approach called "retention projection" properly accounts for many intentional differences in experimental conditions, and when combined with a "back-calculation" methodology described recently, it also accounts for unintentional differences. In this study, the accuracy of this methodology is compared with linear retention indexing across eight different labs. When each lab ran a test mixture under a range of multi-segment gradients and flow rates they selected independently, retention projections averaged 22-fold more accurate for uncharged compounds because they properly accounted for these intentional differences, which were more pronounced in steep gradients. When each lab ran the test mixture under nominally the same conditions, which is the ideal situation to reproduce linear retention indices, retention projections still averaged 2-fold more accurate because they properly accounted for many unintentional differences between the LC systems. To the best of our knowledge, this is the most successful study to date aiming to calculate (or even just to reproduce) LC gradient retention across labs, and it is the only study in which retention was reliably calculated under various multi-segment gradients and flow rates chosen independently by labs. PMID:26292625
Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry
NASA Astrophysics Data System (ADS)
Umer, Muhammad; Kopp, Wassja A.; Leonhard, Kai
2015-12-01
We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 — both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably.
Efficient yet accurate approximations for ab initio calculations of alcohol cluster thermochemistry.
Umer, Muhammad; Kopp, Wassja A; Leonhard, Kai
2015-12-01
We have calculated the binding enthalpies and entropies of gas phase alcohol clusters from ethanol to 1-decanol. In addition to the monomers, we have investigated dimers, tetramers, and pentamers. Geometries have been obtained at the B3LYP/TZVP level and single point energy calculations have been performed with the Resolution of the Identity-MP2 (RIMP2) method and basis set limit extrapolation using aug-cc-pVTZ and aug-cc-pVQZ basis sets. Thermochemistry is calculated with decoupled hindered rotor treatment for large amplitude motions. The results show three points: First, it is more accurate to transfer the rigid-rotor harmonic oscillator entropies from propanol to longer alcohols than to compute them with an ultra-fine grid and tight geometry convergence criteria. Second, the computational effort can be reduced considerably by using dimerization energies of longer alcohols at density functional theory (B3LYP) level plus a RIMP2 correction obtained from 1-propanol. This approximation yields results almost with the same accuracy as RIMP2 - both methods differ for 1-decanol only 0.4 kJ/mol. Third, the entropy of dimerization including the hindered rotation contribution is converged at 1-propanol with respect to chain length. This allows for a transfer of hindered rotation contributions from smaller alcohols to longer ones which reduces the required computational and man power considerably. PMID:26646881
Takahashi, F; Endo, A
2007-01-01
A system utilising radiation transport codes has been developed to derive accurate dose distributions in a human body for radiological accidents. A suitable model is quite essential for a numerical analysis. Therefore, two tools were developed to setup a 'problem-dependent' input file, defining a radiation source and an exposed person to simulate the radiation transport in an accident with the Monte Carlo calculation codes-MCNP and MCNPX. Necessary resources are defined by a dialogue method with a generally used personal computer for both the tools. The tools prepare human body and source models described in the input file format of the employed Monte Carlo codes. The tools were validated for dose assessment in comparison with a past criticality accident and a hypothesized exposure. PMID:17510203
Temperature dependent effective potential method for accurate free energy calculations of solids
NASA Astrophysics Data System (ADS)
Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.
2013-03-01
We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.
Accurate calculation of Coulomb sums: Efficacy of Pade-like methods
Sarkar, B. ); Bhattacharyya, K. )
1993-09-01
The adequacy of numerical sequence accelerative transforms in providing accurate estimates of Coulomb sums is considered, referring particularly to distorted lattices. Performance of diagonal Pade approximants (DPA) in this context is critically assessed. Failure in the case of lattice vacancies is also demonstrated. The method of multiple-point Pade approximants (MPA) has been introduced for slowly convergent sequences and is shown to work well for both regular and distorted lattices, the latter being due either to impurities or vacancies. Viability of the two methods is also compared. In divergent situations with distortions owing to vacancies, a strategy of obtaining reliable results by separate applications of both DPA and MPA at appropriate places is also sketched. Representative calculations involve two basic cubic-lattice sums, one slowly convergent and the other divergent, from which very good quality estimates of Madelung constants for a number of common lattices follow.
Accurate band gaps of semiconductors and insulators from Quantum Monte Carlo calculations
NASA Astrophysics Data System (ADS)
Nazarov, Roman; Hood, Randolph; Morales, Miguel
2015-03-01
Ab initio calculations are useful tools in developing materials with targeted band gaps for semiconductor industry. Unfortunately, the main workhorse of ab initio calculations - density functional theory (DFT) in local density approximation (LDA) or generalized gradient approximation (GGA) underestimates band gaps. Several approaches have been proposed starting from empirical corrections to more elaborate exchange-correlation functionals to deal with this problem. But none of these work well for the entire range of semiconductors and insulators. Deficiencies of DFT as a mean field method can be overcome using many-body techniques. Quantum Monte Carlo (QMC) methods can obtain a nearly exact numerical solutions of both total energies and spectral properties. Diffusion Monte Carlo (DMC), the most widely used QMC method, has been shown to provide gold standard results for different material properties, including spectroscopic constants of dimers and clusters, equation of state for solids, accurate descriptions of defects in metals and insulators. To test DMC's accuracy in a wider range of semiconductors and insulators we have computed band gaps of several semiconductors and insulators. We show that DMC can provide superior agreement with experiment compared with more traditional DFT approaches including high level exchange-correlation functionals (e.g. HSE).
Accurate calculation of the dissociation energy of the highly anharmonic system ClHCl(-).
Stein, Christopher; Oswald, Rainer; Botschwina, Peter; Peterson, Kirk A
2015-05-28
Accurate bond dissociation energies (D0) are reported for different isotopologues of the highly anharmonic system ClHCl(-). The mass-independent equilibrium dissociation energy De was obtained by a composite method with frozen-core (fc) CCSD(T) as the basic contribution. Basis sets as large as aug-cc-pV8(+d)Z were employed, and extrapolation to the complete basis set (CBS) limit was carried out. Explicitly correlated calculations with the CCSD(T)-F12b method were also performed to support the conventionally calculated values. Core-core and core-valence correlation, scalar relativity, and higher-order correlation were considered as well. Two mass-dependent contributions, namely, the diagonal Born-Oppenheimer correction and the difference in zero-point energies between the complex and the HCl fragment, were then added in order to arrive at precise D0 values. Results for (35)ClH(35)Cl(-) and (35)ClD(35)Cl(-) are 23.81 and 23.63 kcal/mol, respectively, with estimated uncertainties of 0.05 kcal/mol. In contrast to FHF(-) ( Stein , C. ; Oswald , R. ; Sebald , P. ; Botschwina , P. ; Stoll , H. , Peterson , K. A. Mol. Phys. 2013 , 111 , 2647 - 2652 ), the D0 values of the bichloride species are larger than their De counterparts, which is an unusual situation in hydrogen-bonded systems. PMID:25405989
Accurate 2d finite element calculations for hydrogen in magnetic fields of arbitrary strength
NASA Astrophysics Data System (ADS)
Schimeczek, C.; Wunner, G.
2014-02-01
Recent observations of hundreds of hydrogen-rich magnetic white dwarf stars with magnetic fields up to 105 T (103 MG) have called for more comprehensive and accurate databases for wavelengths and oscillator strengths of the H atom in strong magnetic fields for all states evolving from the field-free levels with principal quantum numbers n≤10. We present a code to calculate the energy eigenvalues and wave functions of such states which is capable of covering the entire regime of field strengths B=0 T to B˜109 T. We achieve this high flexibility by using a two-dimensional finite element expansion of the wave functions in terms of B-splines in the directions parallel and perpendicular to the magnetic field, instead of using asymptotically valid basis expansions in terms of spherical harmonics or Landau orbitals. We have paid special attention to the automation of the program such that the data points for the magnetic field strengths at which the energy of a given state are calculated can be selected automatically. Furthermore, an elaborate method for varying the basis parameters is applied to ensure that the results reach a pre-selected precision, which also can be adjusted freely. Energies and wave functions are stored in a convenient format for further analysis, e.g. for the calculation of transition energies and oscillator strengths. The code has been tested to work for 300 states with an accuracy of better than 10-6 Rydberg across several symmetry subspaces over the entire regime of magnetic field strengths.
NASA Astrophysics Data System (ADS)
Kopparla, P.; Natraj, V.; Spurr, R. J. D.; Shia, R. L.; Yung, Y. L.
2014-12-01
Radiative transfer (RT) computations are an essential component of energy budget calculations in climate models. However, full treatment of RT processes is computationally expensive, prompting usage of 2-stream approximations in operational climate models. This simplification introduces errors of the order of 10% in the top of the atmosphere (TOA) fluxes [Randles et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT simulations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those (few) optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Here, we extend the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Comparisons between the new model, called Universal Principal Component Analysis model for Radiative Transfer (UPCART), 2-stream models (such as those used in climate applications) and line-by-line RT models are performed, in order for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the TOA for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and solar and viewing geometries. We demonstrate that very accurate radiative forcing estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases as compared to an exact line-by-line RT model. The model is comparable in speeds to 2-stream models, potentially rendering UPCART useful for operational General Circulation Models (GCMs). The operational speed and accuracy of UPCART can be further
Morales, Giovanni; Martínez, Ramiro
2009-07-30
This research's main goals were to analyze ketene dimers' relative stability and expand group additivity value (GAV) methodology for estimating the thermochemical properties of high-weight ketene polymers (up to tetramers). The CBS-Q multilevel procedure and statistical thermodynamics were used for calculating the thermochemical properties of 20 cyclic structures, such as diketenes, cyclobutane-1,3-diones, cyclobut-2-enones and pyran-4-ones, as well as 57 acyclic base compounds organized into five groups. According to theoretical heat of formation predictions, diketene was found to be thermodynamically favored over cyclobutane-1,3-dione and its enol-tautomeric form (3-hydroxycyclobut-2-enone). This result did not agree with old combustion experiments. 3-Hydroxycyclobut-2-enone was found to be the least stable dimer and its reported experimental detection in solution may have been due to solvent effects. Substituted diketenes had lower stability than substituted cyclobutane-1,3-diones with an increased number of methyl substituents, suggesting that cyclobutane-1,3-dione type dimers are the major products because of thermodynamic control of alkylketene dimerization. Missing GAVs for the ketene dimers and related structures were calculated through linear regression on the 57 acyclic base compounds. Corrections for non next neighbor interactions (such as gauche, eclipses, and internal hydrogen bond) were needed for obtaining a highly accurate and precise regression model. To the best of our knowledge, the hydrogen bond correction for GAV methodology is the first reported in the literature; this correction was correlated to MP2/6-31Gdagger and HF/6-31Gdagger derived geometries to facilitate its application. GAVs assessed by the linear regression model were able to reproduce acyclic compounds' theoretical thermochemical properties and experimental heat of formation for acetylacetone. Ring formation and substituent position corrections were calculated by consecutively
The focus of light - theoretical calculation and experimental tomographic reconstruction
NASA Astrophysics Data System (ADS)
Quabis, S.; Dorn, R.; Eberler, M.; Glöckl, O.; Leuchs, G.
2001-01-01
We present numerical calculations on the field distribution in the focus of an optical system with high numerical aperture. The diffraction integrals which are based on the Debye approximation are derived and evaluated for a radially polarized input field with a doughnut-shaped intensity distribution. It is shown that this mode focusses down to a spot size significantly smaller as compared to the case of linear polarization. An experimental setup to measure the three-dimensional intensity distribution in the focal region is presented, which is based on the knife-edge method and on tomographic reconstruction.
Calorimetric determinations and theoretical calculations of polymorphs of thalidomide
NASA Astrophysics Data System (ADS)
Lara-Ochoa, F.; Pérez, G. Espinosa; Mijangos-Santiago, F.
2007-09-01
The analysis of the thermograms of thalidomide obtained for the two reported polymorphs α and β by differential scanning calorimetry (DSC) shows some inconsistencies that are discussed in the present work. The conception of a new polymorph form, named β ∗, allowed us to explain the observed thermal behavior more satisfactorily. This new polymorph shows enantiotropy with both α and β polymorphs, reflected in the unique endotherm obtained in the DSC-thermograms, when a heating rate of 10 °C/min is applied. Several additional experiments, such as re-melting of both polymorph forms, showed that there is indeed a new polymorph with an endotherm located between the endotherms of α and β. IR, Raman, and powder X-ray permit us to characterize the isolated compound, resulting from the re-melting of both polymorph forms. Mechanical calculations were performed to elucidate the conformations of each polymorph, and ab initio quantum chemical calculations were performed to determine the energy of the more stable conformers and the spatial cell energy for both polymorphs α and β. These results suggested a possible conformation for the newly discovered polymorph β ∗.
Theoretical calculation of spectra of dibutyl phthalate and dioctyl phthalate
NASA Astrophysics Data System (ADS)
Du, Jian-Bin; Tang, Yan-Lin; Long, Zheng-Wen; Hu, Shuang-Hui; Li, Tao
2014-05-01
Dibutyl phthalate DBP and dioctyl phthalate DOP are the main components of the plasticizers. In order to investigate their molecular structure, chemical bond and spectrum, the geometrical parameters of the ground state and infrared (IR) spectrum are calculated using the density functional theory B3LYP method at the level of 6-311++G( d, p). On this basis, the first twenty-six excited states and the UV-Vis absorption spectra of DBP and DOP are studied using the time-dependent density functional theory (TDDFT) in the same fundamental group and compared with the ultraviolet absorption peak of the molecules measured with UNICO UV-Vis spectrophotometer. The two kinds of molecular spectra are then classified and compared with that in reference. The results show that the strong absorption of IR spectra of DOP and DBP are produced by C-H bending in-plane vibration and C=O telescopic vibration producing. The most absorption of UV-Vis absorption spectra appears in the end absorption belt from n to σ* transition, and the stronger absorption in the E belt of benzene electronic transition from π to π*. There are blue shift for DOP end absorption belt from n to σ* transition and red shift for DOP E absorption belt from π to π* transition relative to that of DBP. This calculation results are better in accord with the spectral data measured by UNICO ultraviolet and visible spectrophotometer.
Plasmon spectroscopy: Theoretical and numerical calculations, and optimization techniques
NASA Astrophysics Data System (ADS)
Rodríguez-Oliveros, Rogelio; Paniagua-Domínguez, Ramón; Sánchez-Gil, José A.; Macías, Demetrio
2016-02-01
We present an overview of recent advances in plasmonics, mainly concerning theoretical and numerical tools required for the rigorous determination of the spectral properties of complex-shape nanoparticles exhibiting strong localized surface plasmon resonances (LSPRs). Both quasistatic approaches and full electrodynamic methods are described, providing a thorough comparison of their numerical implementations. Special attention is paid to surface integral equation formulations, giving examples of their performance in complicated nanoparticle shapes of interest for their LSPR spectra. In this regard, complex (single) nanoparticle configurations (nanocrosses and nanorods) yield a hierarchy of multiple-order LSPR s with evidence of a rich symmetric or asymmetric (Fano-like) LSPR line shapes. In addition, means to address the design of complex geometries to retrieve LSPR spectra are commented on, with special interest in biologically inspired algorithms. Thewealth of LSPRbased applications are discussed in two choice examples, single-nanoparticle surface-enhanced Raman scattering (SERS) and optical heating, and multifrequency nanoantennas for fluorescence and nonlinear optics.
NASA Astrophysics Data System (ADS)
Kopparla, P.; Natraj, V.; Shia, R. L.; Spurr, R. J. D.; Crisp, D.; Yung, Y. L.
2015-12-01
Radiative transfer (RT) computations form the engine of atmospheric retrieval codes. However, full treatment of RT processes is computationally expensive, prompting usage of two-stream approximations in current exoplanetary atmospheric retrieval codes [Line et al., 2013]. Natraj et al. [2005, 2010] and Spurr and Natraj [2013] demonstrated the ability of a technique using principal component analysis (PCA) to speed up RT computations. In the PCA method for RT performance enhancement, empirical orthogonal functions are developed for binned sets of inherent optical properties that possess some redundancy; costly multiple-scattering RT calculations are only done for those few optical states corresponding to the most important principal components, and correction factors are applied to approximate radiation fields. Kopparla et al. [2015, in preparation] extended the PCA method to a broadband spectral region from the ultraviolet to the shortwave infrared (0.3-3 micron), accounting for major gas absorptions in this region. Here, we apply the PCA method to a some typical (exo-)planetary retrieval problems. Comparisons between the new model, called Universal Principal Component Analysis Radiative Transfer (UPCART) model, two-stream models and line-by-line RT models are performed, for spectral radiances, spectral fluxes and broadband fluxes. Each of these are calculated at the top of the atmosphere for several scenarios with varying aerosol types, extinction and scattering optical depth profiles, and stellar and viewing geometries. We demonstrate that very accurate radiance and flux estimates can be obtained, with better than 1% accuracy in all spectral regions and better than 0.1% in most cases, as compared to a numerically exact line-by-line RT model. The accuracy is enhanced when the results are convolved to typical instrument resolutions. The operational speed and accuracy of UPCART can be further improved by optimizing binning schemes and parallelizing the codes, work
NASA Technical Reports Server (NTRS)
Du, Ping
1993-01-01
As a theoretical component of the joint effort with the laboratory of Dr. Lou Allamandola to search for potential candidates for interstellar organic carbon compound that are responsible for the visible diffuse interstellar absorption bands (DIB's), quantum mechanical calculations were performed on the electron absorption spectra of selected polycyclic aromatic hydrocarbons (PAH) and derivatives. In the completed project, 15 different species of naphthalene, its hydrogen abstraction and addition derivatives, and corresponding cations and anions were studied. Using semiempirical quantum mechanical method INDO/S, the ground electronic state of each species was evaluated with restricted Hartree-Fock scheme and limited configuration interaction. The lowest energy spin state for each species was used for electron absorption calculations. Results indicate that these calculations are accurate enough to reproduce the spectra of naphthalene cation and anion observed in neon matrix. The spectral pattern of the hydrogen abstraction and addition derivatives predicted based on these results indicate that the electron configuration of the pi orbitals of these species is the dominant determinant. A combined list of 19 absorptions calculated from 4500 A to 10,400 A were compiled and suggested as potential candidates that are relevant for the DIB's absorptions. Continued studies on pyrene and derivatives revealed the ground state symmetries and multiplicities of its neutral, anionic, and cationic species. Spectral calculations show that the cation (B(sub 3g)-2) and the anion (A(sub u)-2) are more likely to have low energy absorptions in the regions between 10 kK and 20 kK, similar to naphthalene. These absorptions, together with those to be determined from the hydrogen abstraction and addition derivatives of pyrene, can be used to provide additional candidates and suggest experimental work in the search for interstellar compounds that are responsible for DIB's.
Properties of Solar Thermal Fuels by Accurate Quantum Monte Carlo Calculations
NASA Astrophysics Data System (ADS)
Saritas, Kayahan; Ataca, Can; Grossman, Jeffrey C.
2014-03-01
Efficient utilization of the sun as a renewable and clean energy source is one of the major goals of this century due to increasing energy demand and environmental impact. Solar thermal fuels are materials that capture and store the sun's energy in the form of chemical bonds, which can then be released as heat on demand and charged again. Previous work on solar thermal fuels faced challenges related to the cyclability of the fuel over time, as well as the need for higher energy densities. Recently, it was shown that by templating photoswitches onto carbon nanostructures, both high energy density as well as high stability can be achieved. In this work, we explore alternative molecules to azobenzene in such a nano-templated system. We employ the highly accurate quantum Monte Carlo (QMC) method to predict the energy storage potential for each molecule. Our calculations show that in many cases the level of accuracy provided by density functional theory (DFT) is sufficient. However, in some cases, such as dihydroazulene, the drastic change in conjugation upon light absorption causes the DFT predictions to be inconsistent and incorrect. For this case, we compare our QMC results for the geometric structure, band gap and reaction enthalpy with different DFT functionals.
Aryl sulfoxide radical cations. Generation, spectral properties, and theoretical calculations.
Baciocchi, Enrico; Del Giacco, Tiziana; Gerini, Maria Francesca; Lanzalunga, Osvaldo
2006-08-17
Aromatic sulfoxide radical cations have been generated by pulse radiolysis and laser flash photolysis techniques. In water (pulse radiolysis) the radical cations showed an intense absorption band in the UV region (ca. 300 nm) and a broad less intense band in the visible region (from 500 to 1000 nm) whose position depends on the nature of the ring substituent. At very low pulse energy, the radical cations decayed by first-order kinetics, the decay rate increasing as the pH increases. It is suggested that the decay involves a nucleophilic attack of H(2)O or OH(-) (in basic solutions) to the positively charged sulfur atom to give the radical ArSO(OH)CH(3)(*). By sensitized [N-methylquinolinium tetrafluoborate (NMQ(+))] laser flash photolysis (LFP) the aromatic sulfoxide radical cations were generated in acetonitrile. In these experiments, however, only the band of the radical cation in the visible region could be observed, the UV band being covered by the UV absorption of NMQ(+). The lambda(max) values of the bands in the visible region resulted almost identical to those observed in water for the same radical cations. In the LFP experiments the sulfoxide radical cations decayed by second-order kinetics at a diffusion-controlled rate, and the decay is attributed to the back electron transfer between the radical cation and NMQ(*). DFT calculations were also carried out for a number of 4-X ring substituted (X = H, Me, Br, OMe, CN) aromatic sulfoxide radical cations (and their neutral parents). In all radical cations, the conformation with the S-O bond almost coplanar with the aromatic ring is the only one corresponding to the energy minimum. The maximum of energy corresponds to the conformation where the S-O bond is perpendicular to the aromatic ring. The rotational energy barriers are not very high, ranging from 3.9 to 6.9 kcal/mol. In all radical cations, the major fraction of charge and spin density is localized on the SOMe group. However, a substantial delocalization
Kouznetsov, Alexei; Tambasco, Mauro
2011-03-15
Purpose: To develop and validate a fast and accurate method that uses computed tomography (CT) voxel data to estimate absorbed radiation dose at a point of interest (POI) or series of POIs from a kilovoltage (kV) imaging procedure. Methods: The authors developed an approach that computes absorbed radiation dose at a POI by numerically evaluating the linear Boltzmann transport equation (LBTE) using a combination of deterministic and Monte Carlo (MC) techniques. This hybrid approach accounts for material heterogeneity with a level of accuracy comparable to the general MC algorithms. Also, the dose at a POI is computed within seconds using the Intel Core i7 CPU 920 2.67 GHz quad core architecture, and the calculations are performed using CT voxel data, making it flexible and feasible for clinical applications. To validate the method, the authors constructed and acquired a CT scan of a heterogeneous block phantom consisting of a succession of slab densities: Tissue (1.29 cm), bone (2.42 cm), lung (4.84 cm), bone (1.37 cm), and tissue (4.84 cm). Using the hybrid transport method, the authors computed the absorbed doses at a set of points along the central axis and x direction of the phantom for an isotropic 125 kVp photon spectral point source located along the central axis 92.7 cm above the phantom surface. The accuracy of the results was compared to those computed with MCNP, which was cross-validated with EGSnrc, and served as the benchmark for validation. Results: The error in the depth dose ranged from -1.45% to +1.39% with a mean and standard deviation of -0.12% and 0.66%, respectively. The error in the x profile ranged from -1.3% to +0.9%, with standard deviations of -0.3% and 0.5%, respectively. The number of photons required to achieve these results was 1x10{sup 6}. Conclusions: The voxel-based hybrid method evaluates the LBTE rapidly and accurately to estimate the absorbed x-ray dose at any POI or series of POIs from a kV imaging procedure.
NASA Astrophysics Data System (ADS)
Kripal, Ram; Yadav, Awadhesh Kumar
2015-06-01
Zero field splitting parameters (ZFSPs) D and E of Cr3+ ion doped ammonium oxalate monohydrate (AOM) are calculated with formula using the superposition model. The theoretically calculated ZFSPs for Cr3+ in AOM crystal are compared with the experimental value obtained by electron paramagnetic resonance (EPR). Theoretical ZFSPs are in good agreement with the experimental ones. The energy band positions of optical absorption spectra of Cr3+ in AOM crystal calculated with CFA package are in good match with the experimental values.
Accurate calculation and modeling of the adiabatic connection in density functional theory
NASA Astrophysics Data System (ADS)
Teale, A. M.; Coriani, S.; Helgaker, T.
2010-04-01
AC. When parametrized in terms of the same input data, the AC-CI model offers improved performance over the corresponding AC-D model, which is shown to be the lowest-order contribution to the AC-CI model. The utility of the accurately calculated AC curves for the analysis of standard density functionals is demonstrated for the BLYP exchange-correlation functional and the interaction-strength-interpolation (ISI) model AC integrand. From the results of this analysis, we investigate the performance of our proposed two-parameter AC-D and AC-CI models when a simple density functional for the AC at infinite interaction strength is employed in place of information at the fully interacting point. The resulting two-parameter correlation functionals offer a qualitatively correct behavior of the AC integrand with much improved accuracy over previous attempts. The AC integrands in the present work are recommended as a basis for further work, generating functionals that avoid spurious error cancellations between exchange and correlation energies and give good accuracy for the range of densities and types of correlation contained in the systems studied here.
Accurate and efficient calculation of discrete correlation functions and power spectra
NASA Astrophysics Data System (ADS)
Xu, Y. F.; Liu, J. M.; Zhu, W. D.
2015-07-01
Operational modal analysis (OMA), or output-only modal analysis, has been widely conducted especially when excitation applied on a structure is unknown or difficult to measure. Discrete cross-correlation functions and cross-power spectra between a reference data series and measured response data series are bases for OMA to identify modal properties of a structure. Such functions and spectra can be efficiently transformed from each other using the discrete Fourier transform (DFT) and inverse DFT (IDFT) based on the cross-correlation theorem. However, a direct application of the theorem and transforms, including the DFT and IDFT, can yield physically erroneous results due to periodic extension of the DFT on a function of a finite length to be transformed, which is false most of the time. Padding zero series to ends of data series before applying the theorem and transforms can reduce the errors, but the results are still physically erroneous. A new methodology is developed in this work to calculate discrete cross-correlation functions of non-negative time delays and associated cross-power spectra, referred to as half spectra, for OMA. The methodology can be extended to cross-correlation functions of any time delays and associated cross-power spectra, referred to as full spectra. The new methodology is computationally efficient due to use of the transforms. Data series are properly processed to avoid the errors caused by the periodic extension, and the resulting cross-correlation functions and associated cross-power spectra perfectly comply with their definitions. A coherence function, a convergence function, and a convergence index are introduced to evaluate qualities of measured cross-correlation functions and associated cross-power spectra. The new methodology was numerically and experimentally applied to an ideal two-degree-of-freedom (2-DOF) mass-spring-damper system and a damaged aluminum beam, respectively, and OMA was conducted using half spectra to estimate
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Zhu, Zun-Lue; Yang, Xiang-Dong
2006-12-01
The reasonable dissociation limit of the second excited singlet state B1Π of 7LiH molecule is obtained. The accurate dissociation energy and equilibrium geometry of the B1Π state are calculated using a symmetry-adapted-cluster configuration-interaction method in full active space. The whole potential energy curve for the B1Π state is obtained over the internuclear distance ranging from about 0.10 nm to 0.54 nm, and has a least-square fit to the analytic Murrell-Sorbie function form. The vertical excitation energy is calculated from the ground state to the B1Π state and compared with previous theoretical results. The equilibrium internuclear distance obtained by geometry optimization is found to be quite different from that obtained by single-point energy scanning under the same calculation condition. Based on the analytic potential energy function, the harmonic frequency value of the B1Π state is estimated. A comparison of the theoretical calculations of dissociation energies, equilibrium interatomic distances and the analytic potential energy function with those obtained by previous theoretical results clearly shows that the present work is more comprehensive and in better agreement with experiments than previous theories, thus it is an improvement on previous theories.
Tung, Wei-Cheng; Adamowicz, Ludwik
2014-03-28
Very accurate calculations of the ground-state potential energy curve (PEC) of the LiH{sup +} ion performed with all-electron explicitly correlated Gaussian functions with shifted centers are presented. The variational method is employed. The calculations involve optimization of nonlinear exponential parameters of the Gaussians performed with the aid of the analytical first derivatives of the energy determined with respect to the parameters. The diagonal adiabatic correction is also calculated for each PEC point. The PEC is then used to calculate the vibrational energies of the system. In that calculation, the non-adiabatic effects are accounted for by using an effective vibrational mass obtained by the minimization of the difference between the vibrational energies obtained from the calculations where the Born-Oppenheimer approximation was not assumed and the results of the present calculations.
NASA Astrophysics Data System (ADS)
Moreira, Rafael Y. O.; Brasil, Davi S. B.; Alves, Cláudio N.; Guilhon, Giselle M. S. P.; Santos, Lourivaldo S.; Arruda, Mara S. P.; Müller, Adolfo H.; Barbosa, Patrícia S.; Abreu, Alcicley S.; Silva, Edilene O.; Rumjanek, Victor M.; Souza, Jaime, Jr.; da Silva, Albérico B. F.; Santos, Regina H. De A.
Julocrotine, N-(2,6-dioxo-1-phenethyl-piperidin-3-yl)-2-methyl-butyramide, is a potent antiproliferative agent against the promastigote and amastigote forms of Leishmania amazonensis (L.). In this work, the crystal structure of Julocrotine was solved by X-ray diffraction, and its geometrical parameters were compared with theoretical calculations at the B3LYP and HF level of theory. IR and NMR spectra also have been obtained and compared with theoretical calculations. IR absorptions calculated with the B3LYP level of theory employed together with the 6-311G+(d,p) basis set, are close to those observed experimentally. Theoretical NMR calculations show little deviation from experimental results. The results show that the theory is in accordance with the experimental data.0
DICOM organ dose does not accurately represent calculated dose in mammography
NASA Astrophysics Data System (ADS)
Suleiman, Moayyad E.; Brennan, Patrick C.; McEntee, Mark F.
2016-03-01
This study aims to analyze the agreement between the mean glandular dose estimated by the mammography unit (organ dose) and mean glandular dose calculated using Dance et al published method (calculated dose). Anonymised digital mammograms from 50 BreastScreen NSW centers were downloaded and exposure information required for the calculation of dose was extracted from the DICOM header along with the organ dose estimated by the system. Data from quality assurance annual tests for the included centers were collected and used to calculate the mean glandular dose for each mammogram. Bland-Altman analysis and a two-tailed paired t-test were used to study the agreement between calculated and organ dose and the significance of any differences. A total of 27,869 dose points from 40 centers were included in the study, mean calculated dose and mean organ dose (+/- standard deviation) were 1.47 (+/-0.66) and 1.38 (+/-0.56) mGy respectively. A statistically significant 0.09 mGy bias (t = 69.25; p<0.0001) with 95% limits of agreement between calculated and organ doses ranging from -0.34 and 0.52 were shown by Bland-Altman analysis, which indicates a small yet highly significant difference between the two means. The use of organ dose for dose audits is done at the risk of over or underestimating the calculated dose, hence, further work is needed to identify the causal agents for differences between organ and calculated doses and to generate a correction factor for organ dose.
Baer, M.R.; Hobbs, M.L.; McGee, B.C.
1998-11-03
Exponential-13,6 (EXP-13,6) potential pammeters for 750 gases composed of 48 elements were determined and assembled in a database, referred to as the JCZS database, for use with the Jacobs Cowperthwaite Zwisler equation of state (JCZ3-EOS)~l) The EXP- 13,6 force constants were obtained by using literature values of Lennard-Jones (LJ) potential functions, by using corresponding states (CS) theory, by matching pure liquid shock Hugoniot data, and by using molecular volume to determine the approach radii with the well depth estimated from high-pressure isen- tropes. The JCZS database was used to accurately predict detonation velocity, pressure, and temperature for 50 dif- 3 Accurate predictions were also ferent explosives with initial densities ranging from 0.25 glcm3 to 1.97 g/cm . obtained for pure liquid shock Hugoniots, static properties of nitrogen, and gas detonations at high initial pressures.
Myint, P. C.; Hao, Y.; Firoozabadi, A.
2015-03-27
Thermodynamic property calculations of mixtures containing carbon dioxide (CO_{2}) and water, including brines, are essential in theoretical models of many natural and industrial processes. The properties of greatest practical interest are density, solubility, and enthalpy. Many models for density and solubility calculations have been presented in the literature, but there exists only one study, by Spycher and Pruess, that has compared theoretical molar enthalpy predictions with experimental data [1]. In this report, we recommend two different models for enthalpy calculations: the CPA equation of state by Li and Firoozabadi [2], and the CO_{2} activity coefficient model by Duan and Sun [3]. We show that the CPA equation of state, which has been demonstrated to provide good agreement with density and solubility data, also accurately calculates molar enthalpies of pure CO_{2}, pure water, and both CO_{2}-rich and aqueous (H_{2}O-rich) mixtures of the two species. It is applicable to a wider range of conditions than the Spycher and Pruess model. In aqueous sodium chloride (NaCl) mixtures, we show that Duan and Sun’s model yields accurate results for the partial molar enthalpy of CO_{2}. It can be combined with another model for the brine enthalpy to calculate the molar enthalpy of H_{2}O-CO_{2}-NaCl mixtures. We conclude by explaining how the CPA equation of state may be modified to further improve agreement with experiments. This generalized CPA is the basis of our future work on this topic.
Wills, John M; Mattsson, Ann E
2012-06-06
Brooks, Johansson, and Skriver, using the LMTO-ASA method and considerable insight, were able to explain many of the ground state properties of the actinides. In the many years since this work was done, electronic structure calculations of increasing sophistication have been applied to actinide elements and compounds, attempting to quantify the applicability of DFT to actinides and actinide compounds and to try to incorporate other methodologies (i.e. DMFT) into DFT calculations. Through these calculations, the limits of both available density functionals and ad hoc methodologies are starting to become clear. However, it has also become clear that approximations used to incorporate relativity are not adequate to provide rigorous tests of the underlying equations of DFT, not to mention ad hoc additions. In this talk, we describe the result of full-potential LMTO calculations for the elemental actinides, comparing results obtained with a full Dirac basis with those obtained from scalar-relativistic bases, with and without variational spin-orbit. This comparison shows that the scalar relativistic treatment of actinides does not have sufficient accuracy to provide a rigorous test of theory and that variational spin-orbit introduces uncontrolled errors in the results of electronic structure calculations on actinide elements.
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Arnold, James O. (Technical Monitor)
1996-01-01
The vibrational frequencies and infrared intensities of naphthalene neutral and cation are studied at the self-consistent-field (SCF), second-order Moller-Plesset (MP2), and density functional theory (DFT) levels using a variety of one-particle basis sets. Very accurate frequencies can be obtained at the DFT level in conjunction with large basis sets if they are scaled with two factors, one for the C-H stretches and a second for all other modes. We also find remarkably good agreement at the B3LYP/4-31G level using only one scale factor. Unlike the neutral PAHs where all methods do reasonably well for the intensities, only the DFT results are accurate for the PAH cations. The failure of the SCF and MP2 methods is caused by symmetry breaking and an inability to describe charge delocalization. We present several interesting cases of symmetry breaking in this study. An assessment is made as to whether an ensemble of PAH neutrals or cations could account for the unidentified infrared bands observed in many astronomical sources.
Do Bond Functions Help for the Calculation of Accurate Bond Energies?
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Arnold, James (Technical Monitor)
1998-01-01
The bond energies of 8 chemically bound diatomics are computed using several basis sets with and without bond functions (BF). The bond energies obtained using the aug-pVnZ+BF basis sets (with a correction for basis set superposition error, BSSE) tend to be slightly smaller that the results obtained using the aug-pV(n+I)Z basis sets, but slightly larger than the BSSE corrected aug-pV(n+I)Z results. The aug-cc-pVDZ+BF and aug-cc-pVTZ+BF basis sets yield reasonable estimates of bond energies, but, in most cases, these results cannot be considered highly accurate. Extrapolation of the results obtained with basis sets including bond functions appears to be inferior to the results obtained by extrapolation using atom-centered basis sets. Therefore bond functions do not appear to offer a path for obtaining highly accurate results for chemically bound systems at a lower computational cost than atom centered basis sets.
PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra
NASA Astrophysics Data System (ADS)
Sibaev, Marat; Crittenden, Deborah L.
2016-06-01
The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).
Validation of the new code package APOLLO2.8 for accurate PWR neutronics calculations
Santamarina, A.; Bernard, D.; Blaise, P.; Leconte, P.; Palau, J. M.; Roque, B.; Vaglio, C.; Vidal, J. F.
2013-07-01
This paper summarizes the Qualification work performed to demonstrate the accuracy of the new APOLLO2.S/SHEM-MOC package based on JEFF3.1.1 nuclear data file for the prediction of PWR neutronics parameters. This experimental validation is based on PWR mock-up critical experiments performed in the EOLE/MINERVE zero-power reactors and on P.I. Es on spent fuel assemblies from the French PWRs. The Calculation-Experiment comparison for the main design parameters is presented: reactivity of UOX and MOX lattices, depletion calculation and fuel inventory, reactivity loss with burnup, pin-by-pin power maps, Doppler coefficient, Moderator Temperature Coefficient, Void coefficient, UO{sub 2}-Gd{sub 2}O{sub 3} poisoning worth, Efficiency of Ag-In-Cd and B4C control rods, Reflector Saving for both standard 2-cm baffle and GEN3 advanced thick SS reflector. From this qualification process, calculation biases and associated uncertainties are derived. This code package APOLLO2.8 is already implemented in the ARCADIA new AREVA calculation chain for core physics and is currently under implementation in the future neutronics package of the French utility Electricite de France. (authors)
Frolov, Andrey I
2015-05-12
Accurate calculation of solvation free energies (SFEs) is a fundamental problem of theoretical chemistry. In this work we perform a careful validation of the theory of solutions in energy representation (ER method) developed by Matubayasi et al. [J. Chem. Phys. 2000, 113, 6070-6081] for SFE calculations in supercritical solvents. This method can be seen as a bridge between the molecular simulations and the classical (not quantum) density functional theory (DFT) formulated in energy representation. We performed extensive calculations of SFEs of organic molecules of different chemical natures in pure supercritical CO2 (sc-CO2) and in sc-CO2 with addition of 6 mol % of ethanol, acetone, and n-hexane as cosolvents. We show that the ER method reproduces SFE data calculated by a method free of theoretical approximations (the Bennett's acceptance ratio) with the mean absolute error of only 0.05 kcal/mol. However, the ER method requires by an order less computational resources. Also, we show that the quality of ER calculations should be carefully monitored since the lack of sampling can result into a considerable bias in predictions. The present calculations reproduce the trends in the cosolvent-induced solubility enhancement factors observed in experimental data. Thus, we think that molecular simulations coupled with the ER method can be used for quick calculations of the effect of variation of temperature, pressure, and cosolvent concentration on SFE and hence solubility of bioactive compounds in supercritical fluids. This should dramatically reduce the burden of experimental work on optimizing solvency of supercritical solvents. PMID:26574423
Theoretical calculation of light-induced forces and torques on complex microrotors
NASA Astrophysics Data System (ADS)
Liu, Yuxiang; Zhu, Anding; Huang, Wenhao
2004-12-01
In this letter, we propose the new theoretical investigation on the optical forces and torques on complex microrotors. On the basis of R. C. Gauthier"s hybrid ray-wave model, the optical forces and toques on two complex asymmetric micro-objects, the conical microrotor and the helical microrotor, are analyzed. The viscous drag torque is estimated by Stokes flow to obtain the rotational speed. The results of our computation agree well with the previously published experimental results, which indicates that our approach of the optical torque calculation is suitable for other complex microrotors and that the theoretical calculation is very helpful to optimum design of light-driven microrotors.
Kuwada, Takeshi; Fukui, Miyako; Hata, Toshiyuki; Choshi, Tominari; Nobuhiro, Junko; Ono, Yukio; Hibino, Satoshi
2003-01-01
The specific optical rotations of (R)-oxopropaline D calculated by two ab initio MO methods were +52+/-31 degrees and +61+/-29 degrees, respectively, and (+)-oxopropaline D (3) was presumed to have an R-configuration. On the basis of this theoretical result, the reaction of 1-litio-beta-carboline with (R)-glyceraldehyde acetonide followed by oxidation with MnO(2) gave (R)-oxopropaline D acetonide (4a), which was consistent with the previously synthesized (+)-oxopropaline D acetonide (4) in all respects. From the results of theoretical calculations and the experimental synthesis, we determined that natural (+)-oxopropaline D (3) has an R-configuration. PMID:12520122
NASA Technical Reports Server (NTRS)
Boughner, Robert E.
1986-01-01
A method for calculating the photodissociation rates needed for photochemical modeling of the stratosphere, which includes the effects of molecular scattering, is described. The procedure is based on Sokolov's method of averaging functional correction. The radiation model and approximations used to calculate the radiation field are examined. The approximated diffuse fields and photolysis rates are compared with exact data. It is observed that the approximate solutions differ from the exact result by 10 percent or less at altitudes above 15 km; the photolysis rates differ from the exact rates by less than 5 percent for altitudes above 10 km and all zenith angles, and by less than 1 percent for altitudes above 15 km.
Santiago, Régis Tadeu; Haiduke, Roberto Luiz Andrade
2015-10-30
This research provides a performance investigation of density functional theory and also proposes new functional parameterizations to deal with electric field gradient (EFG) calculations at nuclear positions. The entire procedure is conducted within the four-component formalism. First, we noticed that traditional hybrid and long-range corrected functionals are more efficient in the description of EFG variations for a set of elements (indium, antimony, iodine, lutetium, and hafnium) among linear molecules. Thus, we selected the PBE0, B3LYP, and CAM-B3LYP functionals and promoted a reoptimization of their parameters for a better description of these EFG changes. The PBE0q variant developed here showed an overall promising performance in a validation test conducted with potassium, iodine, copper, and gold. In general, the correlation coefficients found in linear regressions between experimental nuclear quadrupole coupling constants and calculated EFGs are improved while the systematic EFG errors also decrease as a result of this reparameterization. PMID:26284820
Accurate Calculation of Oscillator Strengths for CI II Lines Using Non-orthogonal Wavefunctions
NASA Technical Reports Server (NTRS)
Tayal, S. S.
2004-01-01
Non-orthogonal orbitals technique in the multiconfiguration Hartree-Fock approach is used to calculate oscillator strengths and transition probabilities for allowed and intercombination lines in Cl II. The relativistic corrections are included through the Breit-Pauli Hamiltonian. The Cl II wave functions show strong term dependence. The non-orthogonal orbitals are used to describe the term dependence of radial functions. Large sets of spectroscopic and correlation functions are chosen to describe adequately strong interactions in the 3s(sup 2)3p(sup 3)nl (sup 3)Po, (sup 1)Po and (sup 3)Do Rydberg series and to properly account for the important correlation and relaxation effects. The length and velocity forms of oscillator strength show good agreement for most transitions. The calculated radiative lifetime for the 3s3p(sup 5) (sup 3)Po state is in good agreement with experiment.
Accurate calculations of the high-pressure elastic constants based on the first-principles
NASA Astrophysics Data System (ADS)
Wang, Chen-Ju; Gu, Jian-Bing; Kuang, Xiao-Yu; Yang, Xiang-Dong
2015-08-01
The energy term corresponding to the first order of the strain in Taylor series expansion of the energy with respect to strain is always ignored when high-pressure elastic constants are calculated. Whether the modus operandi would affect the results of the high-pressure elastic constants is still unsolved. To clarify this query, we calculate the high-pressure elastic constants of tantalum and rhenium when the energy term mentioned above is considered and neglected, respectively. Results show that the neglect of the energy term corresponding to the first order of the strain indeed would influence the veracity of the high-pressure elastic constants, and this influence becomes larger with pressure increasing. Therefore, the energy term corresponding to the first-order of the strain should be considered when the high-pressure elastic constants are calculated. Project supported by the National Natural Science Foundation of China (Grant No. 11274235), the Young Scientist Fund of the National Natural Science Foundation of China (Grant No. 11104190), and the Doctoral Education Fund of Education Ministry of China (Grant Nos. 20100181110086 and 20110181120112).
Ab-initio Calculations of Accurate Electronic Properties of ZnS
NASA Astrophysics Data System (ADS)
Khamala, Bethuel; Franklin, Loushanda; Malozovski, Yuriy; Stewart, Anthony; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present the results from ab-initio, self consistent, local density approximation (LDA) calculations of the electronic and related properties of zinc-blende zinc sulphide (zb-ZnS). We employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism in our non-relativistic computations. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method includes a methodical search for the optimal basis set that yields the minima of the occupied energies. This search entails increasing the size of the basis set and related modifications of angular symmetry and of radial orbitals. Our calculated, direct gap of 3.725 eV, at the Γ point, is in excellent agreement with experiment. We have also calculated the total (DOS) and partial (pDOS) densities of states, electron and hole effective masses and total energies that agree very well with available, corresponding experimental results. Acknowledgement: This research is funded in part by the National Science Foundation (NSF) and the Louisiana Board of Regents, through LASiGMA [Award Nos. EPS- 1003897, NSF (2010-15)-RII-SUBR] and NSF HRD-1002541, the US Department of Energy - National, Nuclear Security Administration (NNSA) (Award No. DE-NA0001861), LaSPACE, and LONI-SUBR.
Ab-initio Calculations of Accurate Electronic Properties of Wurzite AlN
NASA Astrophysics Data System (ADS)
Nwigboji, Ifeanyi; Malozovsky, Yuriy; Bagayoko, Diola; Bagayoko Research Group Team
2014-03-01
We present results from ab-initio, self consistent local density approximation (LDA) calculations of electronic and related properties of wurtzite Aluminum Nitride (w-AlN). Our non-relativistic computations employed the Ceperley and Alder LDA potential and the linear combination of atomic orbital (LCAO) formalism. The implementation of the LCAO formalism followed the Bagayoko, Zhao, and Williams' method as enhanced by Ekuma and Franklin (BZW-EF). The BZW-EF method verifiably obtains the minima of the occupied energies; these minima provide the most variationally and physically valid density functional theory (DFT) description of the ground states of materials under study. Our preliminary results for w-AlN show that w-AlN has a direct band gap of 5.82 eV at the Γ point. The preliminary energy bands were obtained with a basis set comprising 48 functions. None of the several, larger basis sets tested to date led to occupied energies lower than those obtained with the above 48. While most previous LDA calculations are 2 eV smaller or more than the experimental value of 5.9 eV that is in excellent agreement with our finding, considering the typical experimental uncertainty of 0.2 eV for absorption measurements on AlN. We also discuss our calculated density of states (DOS) and partial densities of states (pDOS).
Accurate calculation of Stokes drag for point-particle tracking in two-way coupled flows
NASA Astrophysics Data System (ADS)
Horwitz, J. A. K.; Mani, A.
2016-08-01
In this work, we propose and test a method for calculating Stokes drag applicable to particle-laden fluid flows where two-way momentum coupling is important. In the point-particle formulation, particle dynamics are coupled to fluid dynamics via a source term that appears in the respective momentum equations. When the particle Reynolds number is small and the particle diameter is smaller than the fluid scales, it is common to approximate the momentum coupling source term as the Stokes drag. The Stokes drag force depends on the difference between the undisturbed fluid velocity evaluated at the particle location, and the particle velocity. However, owing to two-way coupling, the fluid velocity is modified in the neighborhood of a particle, relative to its undisturbed value. This causes the computed Stokes drag force to be underestimated in two-way coupled point-particle simulations. We develop estimates for the drag force error as function of the particle size relative to the grid size. Because the disturbance field created by the particle contaminates the surrounding fluid, correctly calculating the drag force cannot be done solely by direct interpolation of the fluid velocity. Instead, we develop a correction method that calculates the undisturbed fluid velocity from the computed disturbed velocity field by adding an estimate of the velocity disturbance created by the particle. The correction scheme is tested for a particle settling in an otherwise quiescent fluid and is found to reduce the error in computed settling velocity by an order of magnitude compared with common interpolation schemes.
Shaughnessy, M C; Jones, R E
2016-02-01
We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825
A new class of atomic basis functions for accurate electronic structure calculations of molecules
NASA Astrophysics Data System (ADS)
Laikov, Dimitri N.
2005-11-01
A new general approach is developed for obtaining systematic sequences of atomic single-particle basis sets for use in correlated electronic structure calculations of molecules. All the constituent functions are defined as the solutions of variational problems and are of three types: a minimal Hartree-Fock set, additional functions to represent low-lying excited configurations, and general functions for describing electron correlation. The latter are determined to minimize a functional derived from the closed-shell second-order correlation energy expression. Generally-contracted Gaussian expansions are developed to approximate these general functions in the non-relativistic case and within a scalar-relativistic approximation.
NASA Astrophysics Data System (ADS)
Orwat, Justyna; Mielimaka, Ryszard
2016-06-01
The article demonstrates the comparison of prognosed values of deformation indicators with their values obtained from geodetic measurements. The value of correlation coefficient R between its theoretical and practical values was calculated for each indicator. Following the measured values as basic ones, the evaluation of efficiency of prognosis via the use of Knothe`s theory (a mathematical model, in which lowering of point is calculated as a double integral from Gauss error function with adequate parameters).
Accurate calculation of binding energies for molecular clusters - Assessment of different models
NASA Astrophysics Data System (ADS)
Friedrich, Joachim; Fiedler, Benjamin
2016-06-01
In this work we test different strategies to compute high-level benchmark energies for medium-sized molecular clusters. We use the incremental scheme to obtain CCSD(T)/CBS energies for our test set and carefully validate the accuracy for binding energies by statistical measures. The local errors of the incremental scheme are <1 kJ/mol. Since they are smaller than the basis set errors, we obtain higher total accuracy due to the applicability of larger basis sets. The final CCSD(T)/CBS benchmark values are ΔE = - 278.01 kJ/mol for (H2O)10, ΔE = - 221.64 kJ/mol for (HF)10, ΔE = - 45.63 kJ/mol for (CH4)10, ΔE = - 19.52 kJ/mol for (H2)20 and ΔE = - 7.38 kJ/mol for (H2)10 . Furthermore we test state-of-the-art wave-function-based and DFT methods. Our benchmark data will be very useful for critical validations of new methods. We find focal-point-methods for estimating CCSD(T)/CBS energies to be highly accurate and efficient. For foQ-i3CCSD(T)-MP2/TZ we get a mean error of 0.34 kJ/mol and a standard deviation of 0.39 kJ/mol.
NASA Astrophysics Data System (ADS)
Komsa, Hannu-Pekka; Berseneva, Natalia; Krasheninnikov, Arkady V.; Nieminen, Risto M.
2014-07-01
Impurities and defects frequently govern materials properties, with the most prominent example being the doping of bulk semiconductors where a minute amount of foreign atoms can be responsible for the operation of the electronic devices. Several computational schemes based on a supercell approach have been developed to get insights into types and equilibrium concentrations of point defects, which successfully work in bulk materials. Here, we show that many of these schemes cannot directly be applied to two-dimensional (2D) systems, as formation energies of charged point defects are dominated by large spurious electrostatic interactions between defects in inhomogeneous environments. We suggest two approaches that solve this problem and give accurate formation energies of charged defects in 2D systems in the dilute limit. Our methods, which are applicable to all kinds of charged defects in any 2D system, are benchmarked for impurities in technologically important h-BN and MoS2 2D materials, and they are found to perform equally well for substitutional and adatom impurities.
NASA Technical Reports Server (NTRS)
Mcgrath, W. R.; Richards, P. L.; Face, D. W.; Prober, D. E.; Lloyd, F. L.
1988-01-01
A systematic study of the gain and noise in superconductor-insulator-superconductor mixers employing Ta based, Nb based, and Pb-alloy based tunnel junctions was made. These junctions displayed both weak and strong quantum effects at a signal frequency of 33 GHz. The effects of energy gap sharpness and subgap current were investigated and are quantitatively related to mixer performance. Detailed comparisons are made of the mixing results with the predictions of a three-port model approximation to the Tucker theory. Mixer performance was measured with a novel test apparatus which is accurate enough to allow for the first quantitative tests of theoretical noise predictions. It is found that the three-port model of the Tucker theory underestimates the mixer noise temperature by a factor of about 2 for all of the mixers. In addition, predicted values of available mixer gain are in reasonable agreement with experiment when quantum effects are weak. However, as quantum effects become strong, the predicted available gain diverges to infinity, which is in sharp contrast to the experimental results. Predictions of coupled gain do not always show such divergences.
Rucker, Robert; Oelschlaeger, Peter; Warshel, Arieh
2010-01-01
DNA polymerase β (pol β) is a small eukaryotic enzyme with the ability to repair short single-stranded DNA gaps that has found use as a model system for larger replicative DNA polymerases. For all DNA polymerases, the factors determining their catalytic power and fidelity are the interactions between the bases of the base pair, amino acids near the active site, and the two magnesium ions. In this report, we study effects of all three aspects on human pol β transition state (TS) binding free energies by reproducing a consistent set of experimentally determined data for different structures. Our calculations comprise the combination of four different base pairs (incoming pyrimidine nucleotides incorporated opposite both matched and mismatched purines) with four different pol β structures (wild type and three separate mutations of ionized residues to alanine). We decompose the incoming deoxynucleoside 5′-triphosphate-TS, and run separate calculations for the neutral base part and the highly charged triphosphate part, using different dielectric constants in order to account for the specific electrostatic environments. This new approach improves our ability to predict the effect of matched and mismatched base pairing and of mutations in DNA polymerases on fidelity and may be a useful tool in studying the potential of DNA polymerase mutations in the development of cancer. It also supports our point of view with regards to the origin of the structural control of fidelity, allowing for a quantified description of the fidelity of DNA polymerases. PMID:19842163
Halverson, Thomas; Poirier, Bill
2012-12-14
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a 'weylet' basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality-the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).
Halverson, Thomas; Poirier, Bill
2012-12-14
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003); B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004); and ibid. 121, 1704 (2004)], a new method was introduced for performing exact quantum dynamics calculations. The method uses a "weylet" basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality--the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions). PMID:23248981
NASA Astrophysics Data System (ADS)
Halverson, Thomas; Poirier, Bill
2012-12-01
In a series of earlier articles [B. Poirier, J. Theor. Comput. Chem. 2, 65 (2003);, 10.1142/S0219633603000380 B. Poirier and A. Salam, J. Chem. Phys. 121, 1690 (2004);, 10.1063/1.1767511 B. Poirier and A. Salam, J. Chem. Phys. 121, 1704 (2004), 10.1063/1.1767512], a new method was introduced for performing exact quantum dynamics calculations. The method uses a "weylet" basis set (orthogonalized Weyl-Heisenberg wavelets) combined with phase space truncation, to defeat the exponential scaling of CPU effort with system dimensionality—the first method ever able to achieve this long-standing goal. Here, we develop another such method, which uses a much more convenient basis of momentum-symmetrized Gaussians. Despite being non-orthogonal, symmetrized Gaussians are collectively local, allowing for effective phase space truncation. A dimension-independent code for computing energy eigenstates of both coupled and uncoupled systems has been created, exploiting massively parallel algorithms. Results are presented for model isotropic uncoupled harmonic oscillators and coupled anharmonic oscillators up to 27 dimensions. These are compared with the previous weylet calculations (uncoupled harmonic oscillators up to 15 dimensions), and found to be essentially just as efficient. Coupled system results are also compared to corresponding exact results obtained using a harmonic oscillator basis, and also to approximate results obtained using first-order perturbation theory up to the maximum dimensionality for which the latter may be feasibly obtained (four dimensions).
NASA Astrophysics Data System (ADS)
Wang, Xinxin; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue
2016-08-01
The potential energy curves were calculated for the 21 states (X2Π, A2Π, 32Π, 42Π, 52Π, 12Σ+, 22Σ+, 32Σ+, 12Σ-, 22Σ-, 32Σ-, 12Δ, 22Δ, 32Δ, 12Φ, 14Σ+, a4Σ-, 24Σ-, 14Π, 24Π and 14Δ), which originated from the two lowest dissociation channels of ClO radical. The calculations were done for internuclear separations approximately from 0.08 to 1.10 nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV5Z basis set. Of these 21 states, the 14Π, 24Π, 32Δ, 42Π, 52Π, 12Φ, 32Σ+, 14Δ and 24Σ- states are repulsive. The 12Δ, 12Σ-, 14Σ+, 22Σ-, 12Σ+, 22Σ+, 22Δ and 32Σ- states are very weakly bound. Only the A2Π state has one barrier. The avoided crossing exists between the A2Π and the 32Π state. However, the avoided crossing does not generate any double wells. Core- valence correlation correction was accounted for at the level of an aug-cc-pCVQZ basis set. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pVQZ basis set. All the potential energy curves were extrapolated to the complete basis set limit. The spectroscopic parameters were determined. The 12Σ-, 22Σ-, 32Σ- and 14Σ+ states may be very difficult to be detected in an experiment, since each of these Λ-S states has only one or two vibrational states. The Franck-Condon factors and radiative lifetimes were calculated for several low vibrational levels of the A2Π - X2Π, 32Π - a4Σ-, 22Δ - a4Σ- and 32Σ- - 12Σ- transitions. The spin-orbit coupling effect on the spectroscopic parameters of the X2Π, A2Π, 32Π, a4Σ- and 22Σ+ states were discussed. The spectroscopic properties reported here can be expected to be reliably predicted ones.
NASA Astrophysics Data System (ADS)
Bačić, Z.
1991-09-01
We show that the triatomic adiabatic vibrational eigenstates (AVES) provide a convenient basis for accurate discrete variable representation (DVR) calculation and automatic assignment of highly excited, large amplitude motion vibrational states of floppy triatomic molecules. The DVR-AVES states are eigenvectors of the diagonal (in the stretch states) blocks of the adiabatically rearranged triatomic DVR-ray eigenvector (DVR-REV) Hamiltonian [J. C. Light and Z. Bačić, J. Chem. Phys. 87, 4008 (1987)]. The transformation of the full triatomic vibrational Hamiltonian from the DVR-REV basis to the new DVR-AVES basis is simple, and does not involve calculation of any new matrix elements. No dynamical approximation is made in the energy level calculation by the DVR-AVES approach; its accuracy and efficiency are identical to those of the DVR-REV method. The DVR-AVES states, as the adiabatic approximation to the vibrational states of a triatomic molecule, are labeled by three vibrational quantum numbers. Consequently, accurate large amplitude motion vibrational levels obtained by diagonalizing the full vibrational Hamiltonian transformed to the DVR-AVES basis, can be assigned automatically by the code, with the three quantum numbers of the dominant DVR-AVES state associated with the largest (by modulus) eigenvector element in the DVR-AVES basis. The DVR-AVES approach is used to calculate accurate highly excited localized and delocalized vibrational levels of HCN/HNC and LiCN/LiNC. A significant fraction of localized states of both systems, below and above the isomerization barrier, is assigned automatically, without inspection of wave function plots or separate approximate calculations.
Highly accurate incremental CCSD(T) calculations on aqua- and amine-complexes
NASA Astrophysics Data System (ADS)
Anacker, Tony; Friedrich, Joachim
2013-07-01
In this work, the accuracy of the second-order incremental expansion using the domain-specific basis set approach is tested for 20 cationic metal-aqua and 25 cationic metal-amine complexes. The accuracy of the approach is analysed by the statistical measures range, arithmetic mean, mean absolute deviation, root mean square deviation and standard deviation. Using these measures we find that the error due to the local approximations decreases with increasing basis set. Next we construct a local virtual space using projected atomic orbitals (PAOs). The accuracy of the incremental series in combination with a distance-based truncation of the PAO space is analysed and compared to the convergence of the incremental series within the domain-specific basis set approach. Furthermore, we establish the recently proposed incremental CCSD(T)|MP2 method as a benchmark method to obtain highly accurate CCSD(T) energies. In combination with a basis set of quintuple-ζ quality we establish benchmarks for the binding energies of the investigated complexes. Finally, we use the inc-CCSD(T)|MP2/aV5Z' binding energies of 45 complexes and 34 dissociation reactions to compute the accuracy of several state of the art density functional theory (DFT) functionals like BP86, B3LYP, CAM-B3LYP, M06, PBE0 and TPSSh. With our implementation of the incremental scheme it was possible to compute the inc-CCSD(T)|MP2/aV5Z' energy for Al(H2O)3+ 25 (6106 AOs).
Santra, Robin; Christ, Kevin V.; Greene, Chris H.
2004-04-01
The first three electronically excited states in the alkaline-earth-metal atoms magnesium, calcium, and strontium comprise the (nsnp){sup 3}P{sub J}{sup o}(J=0,1,2) fine-structure manifold. All three states are metastable and are of interest for optical atomic clocks as well as for cold-collision physics. An efficient technique--based on a physically motivated potential that models the presence of the ionic core--is employed to solve the Schroedinger equation for the two-electron valence shell. In this way, radiative lifetimes, laser-induced clock shifts, and long-range interaction parameters are calculated for metastable Mg, Ca, and Sr.
Structure and properties of electronic and hole centers in CsBr from theoretical calculations
Halliday, Matthew T.; Hess, Wayne P.; Shluger, Alexander L.
2015-06-24
The electronic structure, geometry, diffusion barriers and optical properties of fundamental defects of CsBr are calculated using hybrid functional DFT and TD- DFT methods. The B3LYP functional with a modified exchange contribution has been used in an embedded cluster scheme to model the structure and spectroscopic properties of self-trapped triplet exciton, interstitial Br atoms and ions, self-trapped holes and Br vacancies. The calculated migration barriers and positions of maxima of optical absorption bands are in good agreement with experiment, justifying the obtained defect geometries. The o*-center triplet exciton luminescence energy is also accurately calculated.
Accurate ab initio calculations which demonstrate a 3 Pi u ground state for Al2
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W., Jr.; Partridge, Harry; Langhoff, Stephen R.; Taylor, Peter R.; Walch, Stephen P.
1986-01-01
The spectroscopic parameters and separations between the three low-lying X 3 Pi u, A 3 Sigma g -, and a 1 Sigma g + states of Al2 are studied as a function of both the one-particle and n-particle basis set. Approximate correlation treatments are calibrated against full Cl calculations correlating the six valence electrons in a double-zeta plus two d-function basis set. Since the CASSCF/MRCI 3 Pi u to 3 Sigma g - separation is in excellent agreement wtih the FCI value, the MRCI calculations were carried out in an extended (20s13p6d4f)/(6s5p3d2f) gaussian basis. Including a small correction for relativistic effects, the best estimate is that 3 Sigma g - state lies 174/cm above the 3 Pi u ground state. The 1 Sigma g + state lies at least 2000/cm higher in energy. At the CPF level, inclusion of 2s and 2p correlation has little effect on D sub e, reduces T sub e by only 26/cm, and shortens the bond lengths by about 0.02 a sub o. Further strong support for a 3 Pi u ground state comes from the experimental absorption spectra, since both observed transitions can be convincingly assigned as 3 Pi u yields 3 Pi g. The (2) 3 Pi g state is observed to be sensitive to the level of correlation treatment, and to have its minimum shifted to shorter rho values, such that the strongest experimental absorption peak probably corresponds to the 0 yields 2 transition.
Technology Transfer Automated Retrieval System (TEKTRAN)
Time-dependent density functional theory (TDDFT) was employed for theoretical calculation of electronic circular dichroism (ECD) of a hexahydroxydiphenoyl (HHDP)-containing flavanone glycoside, mattucinol-7-O-[4'',6''-O-(aS)-hexahydroxydiphenoyl]-ß-d-glucopyranoside (2). It identified the roles of t...
Microcomputer Calculation of Theoretical Pre-Exponential Factors for Bimolecular Reactions.
ERIC Educational Resources Information Center
Venugopalan, Mundiyath
1991-01-01
Described is the application of microcomputers to predict reaction rates based on theoretical atomic and molecular properties taught in undergraduate physical chemistry. Listed is the BASIC program which computes the partition functions for any specific bimolecular reactants. These functions are then used to calculate the pre-exponential factor of…
Invariant-theoretic method for calculating Clebsch-Gordan coefficients for space groups
Aizenberg, A.Ya.; Gufan, Yu.M.
1995-03-01
A new invariant-theoretic method to directly calculate Clebsch-Gordan coefficients for space and point groups representations is proposed. The method is exemplified with the space groups O{sub h}{sup 5} and D{sub 6h}{sup 1}. 34 refs.
Efficiency and power loss in d. c. chopper circuits. [Theoretical calculation
Beck, M.O.
1981-01-01
The object of this paper was to investigate the efficiency and source of power losses of various classes of dc chopper circuits. The study involved a theoretical calculation of the power losses, supported by a considerable amount of practical work on full power-rated traction motor test bed. 3 refs.
Wang, Xinxin; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue
2016-08-01
The potential energy curves were calculated for the 21 states (X(2)Π, A(2)Π, 3(2)Π, 4(2)Π, 5(2)Π, 1(2)Σ(+), 2(2)Σ(+), 3(2)Σ(+), 1(2)Σ(-), 2(2)Σ(-), 3(2)Σ(-), 1(2)Δ, 2(2)Δ, 3(2)Δ, 1(2)Φ, 1(4)Σ(+), a(4)Σ(-), 2(4)Σ(-), 1(4)Π, 2(4)Π and 1(4)Δ), which originated from the two lowest dissociation channels of ClO radical. The calculations were done for internuclear separations approximately from 0.08 to 1.10nm using the CASSCF method, which was followed by the icMRCI approach with the aug-cc-pV5Z basis set. Of these 21 states, the 1(4)Π, 2(4)Π, 3(2)Δ, 4(2)Π, 5(2)Π, 1(2)Φ, 3(2)Σ(+), 1(4)Δ and 2(4)Σ(-) states are repulsive. The 1(2)Δ, 1(2)Σ(-), 1(4)Σ(+), 2(2)Σ(-), 1(2)Σ(+), 2(2)Σ(+), 2(2)Δ and 3(2)Σ(-) states are very weakly bound. Only the A(2)Π state has one barrier. The avoided crossing exists between the A(2)Π and the 3(2)Π state. However, the avoided crossing does not generate any double wells. Core- valence correlation correction was accounted for at the level of an aug-cc-pCVQZ basis set. Scalar relativistic correction was included by the third-order Douglas-Kroll Hamiltonian approximation at the level of an aug-cc-pVQZ basis set. All the potential energy curves were extrapolated to the complete basis set limit. The spectroscopic parameters were determined. The 1(2)Σ(-), 2(2)Σ(-), 3(2)Σ(-) and 1(4)Σ(+) states may be very difficult to be detected in an experiment, since each of these Λ-S states has only one or two vibrational states. The Franck-Condon factors and radiative lifetimes were calculated for several low vibrational levels of the A(2)Π - X(2)Π, 3(2)Π - a(4)Σ(-), 2(2)Δ - a(4)Σ(-) and 3(2)Σ(-) - 1(2)Σ(-) transitions. The spin-orbit coupling effect on the spectroscopic parameters of the X(2)Π, A(2)Π, 3(2)Π, a(4)Σ(-) and 2(2)Σ(+) states were discussed. The spectroscopic properties reported here can be expected to be reliably predicted ones. PMID:27111157
Theoretical basis for two-phase disengagement and vapor fraction calculations
Sheppard, C.M.
1995-12-31
This paper reviews the theoretical basis for disengagement calculations. That is the assumptions of pseudo-steady-state, volumetric gas production and applicable drift-flux correlations. Using these an axial void fraction profile can be calculated. The use of graphical, analytical, and simplified-equation-based correlations for vertical cylinders, horizontal cylinders, and spheres are covered. Before disengagement occurs the vent stream void fraction can be estimated using the coupling equation. The implications of the converging cross-sectional area of horizontal cylinders and spheres are discussed for both disengagement and two-phase flow calculations. 22 refs., 9 figs., 5 tabs.
NASA Astrophysics Data System (ADS)
Roberts, B. M.; Dzuba, V. A.; Flambaum, V. V.; Pospelov, M.; Stadnik, Y. V.
2016-06-01
We revisit the WIMP-type dark matter scattering on electrons that results in atomic ionization and can manifest itself in a variety of existing direct-detection experiments. Unlike the WIMP-nucleon scattering, where current experiments probe typical interaction strengths much smaller than the Fermi constant, the scattering on electrons requires a much stronger interaction to be detectable, which in turn requires new light force carriers. We account for such new forces explicitly, by introducing a mediator particle with scalar or vector couplings to dark matter and to electrons. We then perform state-of-the-art numerical calculations of atomic ionization relevant to the existing experiments. Our goals are to consistently take into account the atomic physics aspect of the problem (e.g., the relativistic effects, which can be quite significant) and to scan the parameter space—the dark matter mass, the mediator mass, and the effective coupling strength—to see if there is any part of the parameter space that could potentially explain the DAMA modulation signal. While we find that the modulation fraction of all events with energy deposition above 2 keV in NaI can be quite significant, reaching ˜50 %, the relevant parts of the parameter space are excluded by the XENON10 and XENON100 experiments.
Bubin, Sergiy; Stanke, Monika; Adamowicz, Ludwik
2011-08-21
In this work we report very accurate variational calculations of the complete pure vibrational spectrum of the D(2) molecule performed within the framework where the Born-Oppenheimer (BO) approximation is not assumed. After the elimination of the center-of-mass motion, D(2) becomes a three-particle problem in this framework. As the considered states correspond to the zero total angular momentum, their wave functions are expanded in terms of all-particle, one-center, spherically symmetric explicitly correlated Gaussian functions multiplied by even non-negative powers of the internuclear distance. The nonrelativistic energies of the states obtained in the non-BO calculations are corrected for the relativistic effects of the order of α(2) (where α = 1/c is the fine structure constant) calculated as expectation values of the operators representing these effects. PMID:21861559
Derenzo, Stephen E.; Klintenberg, Mattias K.; Weber, Marvin J.
2000-02-01
In performing atomic cluster calculations of local electronic structure defects in ionic crystals, the crystal is often modeled as a central cluster of 5-50 ions embedded in an array of point charges. For most crystals, however, a finite three-dimensional repeated array of unit cells generates electrostatic potentials that are in significant disagreement with the Madelung (infinite crystal) potentials computed by the Ewald method. This is illustrated for the cubic crystal CaF{sub 2}. We present a novel algorithm for solving this problem for any crystal whose unit cell information is known: (1) the unit cell is used to generate a neutral array containing typically 10 000 point charges at their normal crystallographic positions; (2) the array is divided into zone 1 (a volume defined by the atomic cluster of interest), zone 2 (several hundred additional point charges that together with zone 1 fill a spherical volume), and zone 3 (all other point charges); (3) the Ewald formula is used to compute the site potentials at all point charges in zones 1 and 2; (4) a system of simultaneous linear equations is solved to find the zone 3 charge values that make the zone 1 and zone 2 site potentials exactly equal to their Ewald values and the total charge and dipole moments equal to zero, and (5) the solution is checked at 1000 additional points randomly chosen in zone 1. The method is applied to 33 different crystal types with 50-71 ions in zone 1. In all cases the accuracy determined in step 5 steadily improves as the sizes of zones 2 and 3 are increased, reaching a typical rms error of 1 {mu}V in zone 1 for 500 point charges in zone 2 and 10 000 in zone 3. (c) 2000 American Institute of Physics.
NASA Astrophysics Data System (ADS)
Majumder, Moumita; Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker; Li, Jun; Guo, Hua; Manzhos, Sergei
2014-06-01
New potential energy surfaces for methane were constructed, represented as analytic fits to about 100,000 individual high-level ab initio data. Explicitly-correlated multireference data (MRCI-F12(AE)/CVQZ-F12) were computed using Molpro [1] and fit using multiple strategies. Fits with small to negligible errors were obtained using adaptations of the permutation-invariant-polynomials (PIP) approach [2,3] based on neural-networks (PIP-NN) [4,5] and the interpolative moving least squares (IMLS) fitting method [6] (PIP-IMLS). The PESs were used in full-dimensional vibrational calculations with an exact kinetic energy operator by representing the Hamiltonian in a basis of products of contracted bend and stretch functions and using a symmetry adapted Lanczos method to obtain eigenvalues and eigenvectors. Very close agreement with experiment was produced from the purely ab initio PESs. References 1- H.-J. Werner, P. J. Knowles, G. Knizia, 2012.1 ed. 2012, MOLPRO, a package of ab initio programs. see http://www.molpro.net. 2- Z. Xie and J. M. Bowman, J. Chem. Theory Comput 6, 26, 2010. 3- B. J. Braams and J. M. Bowman, Int. Rev. Phys. Chem. 28, 577, 2009. 4- J. Li, B. Jiang and Hua Guo, J. Chem. Phys. 139, 204103 (2013). 5- S Manzhos, X Wang, R Dawes and T Carrington, JPC A 110, 5295 (2006). 6- R. Dawes, X-G Wang, A.W. Jasper and T. Carrington Jr., J. Chem. Phys. 133, 134304 (2010).
NASA Astrophysics Data System (ADS)
Luo, Ye; Sorella, Sandro
2014-03-01
We introduce a general and efficient method for the calculation of vibrational frequencies of electronic systems, ranging from molecules to solids. By performing damped molecular dynamics with ab initio forces, we show that quantum vibrational frequencies can be evaluated by diagonalizing the time averaged position-position or force-force correlation matrices, although the ionic motion is treated on the classical level within the Born-Oppenheimer approximation. The novelty of our approach is to evaluate atomic forces with QMC by means of a highly accurate and correlated variational wave function which is optimized simultaneously during the dynamics. QMC is an accurate and promising many-body technique for electronic structure calculation thanks to massively parallel computers. However, since infinite statistics is not feasible, property evaluation may be affected by large noise that is difficult to harness. Our approach controls the QMC stochastic bias systematically and gives very accurate results with moderate computational effort, namely even with noisy forces. We prove the accuracy and efficiency of our method on the water monomer[A. Zen et al., JCTC 9 (2013) 4332] and dimer. We are currently working on the challenging problem of simulating liquid water at ambient conditions.
Bai, D.; Levine, S.L. ); Luoma, J.; Mahgerefteh, M. )
1992-01-01
The Three Mile Island unit 1 core reloads have been designed using fast but accurate scoping codes, PSUI-LEOPARD and ADMARC. PSUI-LEOPARD has been normalized to EPRI-CPM2 results and used to calculate the two-group constants, whereas ADMARC is a modern two-dimensional, two-group diffusion theory nodal code. Problems in accuracy were encountered for cycles 8 and higher as the core lifetime was increased beyond 500 effective full-power days. This is because the heavier loaded cores in both {sup 235}U and {sup 10}B have harder neutron spectra, which produces a change in the transport effect in the baffle reflector region, and the burnable poison (BP) simulations were not accurate enough for the cores containing the increased amount of {sup 10}B required in the BP rods. In the authors study, a technique has been developed to take into account the change in the transport effect in the baffle region by modifying the fast neutron diffusion coefficient as a function of cycle length and core exposure or burnup. A more accurate BP simulation method is also developed, using integral transport theory and CPM2 data, to calculate the BP contribution to the equivalent fuel assembly (supercell) two-group constants. The net result is that the accuracy of the scoping codes is as good as that produced by CASMO/SIMULATE or CPM2/SIMULATE when comparing with measured data.
Calculations of steady and transient channel flows with a time-accurate L-U factorization scheme
NASA Technical Reports Server (NTRS)
Kim, S.-W.
1991-01-01
Calculations of steady and unsteady, transonic, turbulent channel flows with a time accurate, lower-upper (L-U) factorization scheme are presented. The L-U factorization scheme is formally second-order accurate in time and space, and it is an extension of the steady state flow solver (RPLUS) used extensively to solve compressible flows. A time discretization method and the implementation of a consistent boundary condition specific to the L-U factorization scheme are also presented. The turbulence is described by the Baldwin-Lomax algebraic turbulence model. The present L-U scheme yields stable numerical results with the use of much smaller artificial dissipations than those used in the previous steady flow solver for steady and unsteady channel flows. The capability to solve time dependent flows is shown by solving very weakly excited and strongly excited, forced oscillatory, channel flows.
NASA Astrophysics Data System (ADS)
Santos, Marcela F.; Braga, Carolyne B.; Rozada, Thiago C.; Basso, Ernani A.; Fiorin, Barbara C.
2014-08-01
The geometries involved in the conformational equilibria of 2,2-dichloro-N-cyclohexyl-N-methyl-acetamide (DCCMA) and 2-chloro-N,N-dicyclohexylacetamide (CDCA) were investigated. Theoretical calculations at the B3LYP/cc-pVDZ level of theory showed that gauche forms (Clsbnd Csbnd Cdbnd O) are the most stable and the predominant conformers in isolated phase. Both compounds had the conformational behavior in solvents of different polarities estimated from theoretical calculations with the PCM (Polarizable Continuum Model), at the same level of theory, using infrared data from deconvolution of the carbonyl absorption bands and 13C NMR spectra. Their IR spectra showed two carbonyl absorptions and that the conformer with the highest dipole moment had its population increased when the most polar solvents were used, in accordance with the theoretical calculation in solution. 1JCH coupling constants were obtained from their NMR spectra, and revealed that there was population variation of conformers with solvent exchange. Experimental data (NMR and IR) as well as calculations including the solvent effects followed the same trend.
van Wyk, Marnus J; Bingle, Marianne; Meyer, Frans J C
2005-09-01
International bodies such as International Commission on Non-Ionizing Radiation Protection (ICNIRP) and the Institute for Electrical and Electronic Engineering (IEEE) make provision for human exposure assessment based on SAR calculations (or measurements) and basic restrictions. In the case of base station exposure this is mostly applicable to occupational exposure scenarios in the very near field of these antennas where the conservative reference level criteria could be unnecessarily restrictive. This study presents a variety of critical aspects that need to be considered when calculating SAR in a human body close to a mobile phone base station antenna. A hybrid FEM/MoM technique is proposed as a suitable numerical method to obtain accurate results. The verification of the FEM/MoM implementation has been presented in a previous publication; the focus of this study is an investigation into the detail that must be included in a numerical model of the antenna, to accurately represent the real-world scenario. This is accomplished by comparing numerical results to measurements for a generic GSM base station antenna and appropriate, representative canonical and human phantoms. The results show that it is critical to take the disturbance effect of the human phantom (a large conductive body) on the base station antenna into account when the antenna-phantom spacing is less than 300 mm. For these small spacings, the antenna structure must be modeled in detail. The conclusion is that it is feasible to calculate, using the proposed techniques and methodology, accurate occupational compliance zones around base station antennas based on a SAR profile and basic restriction guidelines. PMID:15931680
NASA Astrophysics Data System (ADS)
Teale, Andrew M.; Lutnæs, Ola B.; Helgaker, Trygve; Tozer, David J.; Gauss, Jürgen
2013-01-01
Accurate sets of benchmark nuclear-magnetic-resonance shielding constants and spin-rotation constants are calculated using coupled-cluster singles-doubles (CCSD) theory and coupled-cluster singles-doubles-perturbative-triples [CCSD(T)] theory, in a variety of basis sets consisting of (rotational) London atomic orbitals. The accuracy of the calculated coupled-cluster constants is established by a careful comparison with experimental data, taking into account zero-point vibrational corrections. Coupled-cluster basis-set convergence is analyzed and extrapolation techniques are employed to estimate basis-set-limit quantities, thereby establishing an accurate benchmark data set. Together with the set provided for rotational g-tensors and magnetizabilities in our previous work [O. B. Lutnæs, A. M. Teale, T. Helgaker, D. J. Tozer, K. Ruud, and J. Gauss, J. Chem. Phys. 131, 144104 (2009)], 10.1063/1.3242081, it provides a substantial source of consistently calculated high-accuracy data on second-order magnetic response properties. The utility of this benchmark data set is demonstrated by examining a wide variety of Kohn-Sham exchange-correlation functionals for the calculation of these properties. None of the existing approximate functionals provide an accuracy competitive with that provided by CCSD or CCSD(T) theory. The need for a careful consideration of vibrational effects is clearly illustrated. Finally, the pure coupled-cluster results are compared with the results of Kohn-Sham calculations constrained to give the same electronic density. Routes to future improvements are discussed in light of this comparison.
NASA Technical Reports Server (NTRS)
Srivastava, R. C.; Coen, J. L.
1992-01-01
The traditional explicit growth equation has been widely used to calculate the growth and evaporation of hydrometeors by the diffusion of water vapor. This paper reexamines the assumptions underlying the traditional equation and shows that large errors (10-30 percent in some cases) result if it is used carelessly. More accurate explicit equations are derived by approximating the saturation vapor-density difference as a quadratic rather than a linear function of the temperature difference between the particle and ambient air. These new equations, which reduce the error to less than a few percent, merit inclusion in a broad range of atmospheric models.
NASA Technical Reports Server (NTRS)
Gamache, Robert R.; Pollack, James B.
1995-01-01
Halfwidths were calculated for H2O with H2 as a broadening gas and were estimated for He as the broadening species. The calculations used the model of Robert and Bonamy with parabolic trajectories and all relevant terms in the interaction potential. The calculations investigated the dependence of the halfwidth on the order of the atom-atom expansion, the rotational states, and the temperature in the range 200 to 400K. Finally, calculations were performed for many transitions of interest in the 5 micrometer window region of the spectrum. The resulting data will be supplied to Dr. R. Freedman for extracting accurate water mixing ratios from the analysis of the thermal channels for the Net Flux experiment on the Galileo probe.
Takahashi, F; Shigemori, Y; Seki, A
2009-01-01
A system has been developed to assess radiation dose distribution inside the body of exposed persons in a radiological accident by utilising radiation transport calculation codes-MCNP and MCNPX. The system consists mainly of two parts, pre-processor and post-processor of the radiation transport calculation. Programs for the pre-processor are used to set up a 'problem-dependent' input file, which defines the accident condition and dosimetric quantities to be estimated. The program developed for the post-processor part can effectively indicate dose information based upon the output file of the code. All of the programs in the dosimetry system can be executed with a generally used personal computer and accurately give the dose profile to an exposed person in a radiological accident without complicated procedures. An experiment using a physical phantom was carried out to verify the availability of the dosimetry system with the developed programs in a gamma ray irradiation field. PMID:19181661
NASA Astrophysics Data System (ADS)
Fedorov, V. M.
2016-05-01
Based on the astronomical ephemerides DE-406, theoretical calculations have been performed of the interannual variability of the Earth's insolation related to celestial-mechanical processes for 365 points of a tropical year in the time period from 1900 to 2050. It has been determined that the average amplitude of variations of the interannual insolation is 0.310 W/m2 (0.023% of the solar constant). The calculated variations are characterized by strict periodicity that corresponds with the length of a synodic month. Connection between the extreme values of the calculated insolation variability and syzygies has been defined. The average amplitude of the calculated variability exceeds by 1.7 times (0.01% of the solar constant) the amplitude of the interannual variability in the 11-year variation of the total Earth's insolation.
Nuclear radii calculations in various theoretical approaches for nucleus-nucleus interactions
Merino, C.; Novikov, I. S.; Shabelski, Yu.
2009-12-15
The information about sizes and nuclear density distributions in unstable (radioactive) nuclei is usually extracted from the data on interaction of radioactive nuclear beams with a nuclear target. We show that in the case of nucleus-nucleus collisions the values of the parameters depend somewhat strongly on the considered theoretical approach and on the assumption about the parametrization of the nuclear density distribution. The obtained values of root-mean-square radii (R{sub rms}) for stable nuclei with atomic weights A=12-40 vary by approximately 0.1 fm when calculated in the optical approximation, in the rigid target approximation, and using the exact expression of the Glauber theory. We present several examples of R{sub rms} radii calculations using these three theoretical approaches and compare these results with the data obtained from electron-nucleus scattering.
NASA Astrophysics Data System (ADS)
Sievänen, Elina; Toušek, Jaromír; Lunerová, Kamila; Marek, Jaromír; Jankovská, Dagmar; Dvorská, Margita; Marek, Radek
2010-08-01
In this article we present a detailed structural investigation for five homoisoflavonoids, molecules important from the pharmacological point of view. For studying the electron distribution as well as its influence on the physicochemical properties, NMR spectroscopy, X-ray diffraction, and theoretical calculations have been used. Nuclear magnetic shieldings obtained by using DFT calculations for optimized molecular geometries are correlated with the experimentally determined chemical shifts. The theoretical data are well in agreement with the experimental values. The single crystal X-ray structures of homoisoflavonoid derivatives 1, 3, and 4 have been solved. The molecular geometries and crystal packing determined by X-ray diffraction are used for characterizing the intermolecular interactions. Electron distribution is crucial for the stability of radicals and hence the antioxidant efficiency of flavonoid structures. The hydrogen bonding governs the formation of complexes of homoisoflavonoids with biological targets.
Theoretical calculation of plane wave speeds for alkali metals under pressure.
NASA Technical Reports Server (NTRS)
Eftis, J.; Macdonald, D. E.; Arkilic, G. M.
1971-01-01
Theoretical calculations of the variation with pressure of small amplitude plane wave speeds are performed for sodium and potassium at zero temperature. The results obtained for wave speeds associated with volume dependent second-order elastic coefficients show better agreement with experimental data than for wave speeds associated with shear dependent coefficients. This result is believed to be due to omission of the band structure correction to the strain energy density.
Tian, Lian; Henningsen, Joseph; Salick, Max R; Crone, Wendy C; Gunderson, McLean; Dailey, Seth H; Chesler, Naomi C
2015-07-01
The mechanical properties of vascular tissues affect hemodynamics and can alter disease progression. The uniaxial tensile test is a simple and effective method for determining the stress-strain relationship in arterial tissue ex vivo. To enable calculation of strain, stretch can be measured directly with image tracking of markers on the tissue or indirectly from the distance between the grips used to hold the specimen. While the imaging technique is generally considered more accurate, it also requires more analysis, and the grip distance method is more widely used. The purpose of this study is to compare the stretch of the testing specimen calculated from the grip distance method to that obtained from the imaging method for canine descending aortas and large proximal pulmonary arteries. Our results showed a significant difference in stretch between the two methods; however, this difference was consistently less than 2%. Therefore, the grip distance method is an accurate approximation of the stretch in large elastic arteries in the uniaxial tensile test. PMID:25881308
Tian, Lian; Henningsen, Joseph; Salick, Max R.; Crone, Wendy C.; Gunderson, McLean; Dailey, Seth H.; Chesler, Naomi C.
2015-01-01
The mechanical properties of vascular tissues affect hemodynamics and can alter disease progression. The uniaxial tensile test is a simple and effective method for determining the stress-strain relationship in arterial tissue ex vivo. To enable calculation of strain, stretch can be measured directly with image tracking of markers on the tissue or indirectly from the distance between the grips used to hold the specimen. While the imaging technique is generally considered more accurate, it also requires more analysis, and the grip distance method is more widely used. The purpose of this study is to compare the stretch of the testing specimen calculated from the grip distance method to that obtained from the imaging method for canine descending aortas and large proximal pulmonary arteries. Our results showed a significant difference in stretch between the two methods; however, this difference was consistently less than 2%. Therefore, the grip distance method is an accurate approximation of the stretch in large elastic arteries in the uniaxial tensile test. PMID:25881308
Wu, Baolin; Guan, Weihua; Pankow, James S
2016-03-01
The objective of this paper is to discuss and develop alternative computational methods to accurately and efficiently calculate significance P-values for the commonly used sequence kernel association test (SKAT) and adaptive sum of SKAT and burden test (SKAT-O) for variant set association. We show that the existing software can lead to either conservative or inflated type I errors. We develop alternative and efficient computational algorithms that quickly compute the SKAT P-value and have well-controlled type I errors. In addition, we derive an alternative and simplified formula for calculating the significance P-value of SKAT-O, which sheds light on the development of efficient and accurate numerical algorithms. We implement the proposed methods in the publicly available R package that can be readily used or adapted to large-scale sequencing studies. Given that more and more large-scale exome and whole genome sequencing or re-sequencing studies are being conducted, the proposed methods are practically very important. We conduct extensive numerical studies to investigate the performance of the proposed methods. We further illustrate their usefulness with application to associations between rare exonic variants and fasting glucose levels in the Atherosclerosis Risk in Communities (ARIC) study. PMID:26757198
NASA Astrophysics Data System (ADS)
Moore, Keith; McLaughlin, Brendan M.; Lane, Ian C.
2016-04-01
BaH (and its isotopomers) is an attractive molecular candidate for laser cooling to ultracold temperatures and a potential precursor for the production of ultracold gases of hydrogen and deuterium. The theoretical challenge is to simulate the laser cooling cycle as reliably as possible and this paper addresses the generation of a highly accurate ab initio 2Σ+ potential for such studies. The performance of various basis sets within the multi-reference configuration-interaction (MRCI) approximation with the Davidson correction is tested and taken to the Complete Basis Set (CBS) limit. It is shown that the calculated molecular constants using a 46 electron effective core-potential and even-tempered augmented polarized core-valence basis sets (aug-pCVnZ-PP, n = 4 and 5) but only including three active electrons in the MRCI calculation are in excellent agreement with the available experimental values. The predicted dissociation energy De for the X2Σ+ state (extrapolated to the CBS limit) is 16 895.12 cm-1 (2.094 eV), which agrees within 0.1% of a revised experimental value of <16 910.6 cm-1, while the calculated re is within 0.03 pm of the experimental result.
NASA Technical Reports Server (NTRS)
Richards, P. G.; Torr, D. G.
1981-01-01
A simplified method for the evaluation of theoretical photoelectron fluxes in the upper atmosphere resulting from the solar radiation at 304 A is presented. The calculation is based on considerations of primary and cascade (secondary) photoelectron production in the two-stream model, where photoelectron transport is described by two electron streams, one moving up and one moving down, and of loss rates due to collisions with neutral gases and thermal electrons. The calculation is illustrated for the case of photoelectrons at an energy of 24.5 eV, and it is noted that the 24.5-eV photoelectron flux may be used to monitor variations in the solar 304 A flux. Theoretical calculations based on various ionization and excitation cross sections of Banks et al. (1974) are shown to be in generally good agreement with AE-E measurements taken between 200 and 235 km, however the use of more recent, larger cross sections leads to photoelectron values a factor of two smaller than observations but in agreement with previous calculations. It is concluded that a final resolution of the photoelectron problem may depend on a reevaluation of the inelastic electron collision cross sections.
NASA Astrophysics Data System (ADS)
He, C.; Liou, K. N.; Takano, Y.; Li, Q.; Yang, P.; Zhang, R.
2014-12-01
The optical properties of black carbon (BC) are significantly affected by its aging process in the atmosphere. We have built a conceptual model defining three BC aging stages, including freshly emitted BC aggregates, coating by soluble material and hygroscopic growth. We apply an improved geometric-optics surface-wave approach (Liou et al., 2011; Takano et al., 2013) to calculate the absorption and scattering properties of BC at each stage and compare the theoretical results with those obtained from laboratory experiments (Zhang et al., 2008; Khalizov et al., 2009). Preliminary results show a general agreement between calculated and measured BC absorption cross sections (bias < 10%) and scattering cross sections (bias < 30%) for BC aerosols with mobility diameters of 155, 245 and 320 nm at Stages 1 and 2, where BC is coated by sulfuric acid and its water solution, respectively. We find that the calculated scattering and absorption cross sections for fresh BC aggregates (Stage 0) with different sizes are invariably larger than experimental results partly because of the uncertainty in theoretical calculations for BC with size parameters less than 1. It appears that the uncertainty in the experiment could also contribute to the discrepancy, considering that the measuring instrument missed some scattering in certain angles (0-7° and 170-180°). Finally, we will apply the conceptual model and the single-scattering results to assess the effects of BC aging processes on direct radiative forcing using observed BC vertical profiles.
Lundahl, Gunnel
2007-01-01
When calculating of the physical F121.1 degrees c-value by the equation F121.1 degrees C = t x 10(T-121.1/z the temperature (T), in combination with the z-value, influences the F121.1 degrees c-value exponentially. Because the z-value for spores of Geobacillus stearothermophilus often varies between 6 and 9, the biological F-value (F(Bio) will not always correspond to the F0-value based on temperature records from the sterilization process calculated with a z-value of 10, even if the calibration of both of them are correct. Consequently an error in calibration of thermocouples and difference in z-values influences the F121.1 degrees c-values logarithmically. The paper describes how results from measurements with different z-values can be compared. The first part describes the mathematics of a calculation program, which makes it easily possible to compare F0-values based on temperature records with the F(BIO)-value based on analysis of bioindicators such as glycerin-water-suspension sensors. For biological measurements, a suitable bioindicator with a high D121-value can be used (such a bioindicator can be manufactured as described in the article "A Method of Increasing Test Range and Accuracy of Bioindicators-Geobacillus stearothermophilus Spores"). By the mathematics and calculations described in this macro program it is possible to calculate for every position the theoretical temperature difference (deltaT(th)) needed to explain the difference in results between the thermocouple and the biointegrator. Since the temperature difference is a linear function and constant all over the process this value is an indication of the magnitude of an error. A graph and table from these calculations gives a picture of the run. The second part deals with product characteristics, the sterilization processes, loading patterns. Appropriate safety margins have to be chosen in the development phase of a sterilization process to achieve acceptable safety limits. Case studies are
NASA Astrophysics Data System (ADS)
McCann, Kathleen; Laane, Jaan
2008-11-01
The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.
NASA Technical Reports Server (NTRS)
Binienda, W. K.; Arnold, S. M.; Tan, H. Q.
1992-01-01
An essential part of describing the damage state and predicting the damage growth in a multicracked plate is the accurate calculation of stress intensity factors (SIF's). Here, a methodology and rigorous solution formulation for SIF's of a multicracked plate, with fully interacting cracks, subjected to a far-field arbitrary stress state is presented. The fundamental perturbation problem is derived, and the steps needed to formulate the system of singular integral equations whose solution gives rise to the evaluation of the SIF's are identified. This analytical derivation and numerical solution are obtained by using intelligent application of symbolic computations and automatic FORTRAN generation capabilities (described in the second part of this paper). As a result, a symbolic/FORTRAN package, named SYMFRAC, that is capable of providing accurate SIF's at each crack tip was developed and validated.
Esque, Jeremy; Cecchini, Marco
2015-04-23
The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent. PMID:25807150
Sun, Y. Y.; Kim, Y. H.; Lee, K.; Zhang, S. B.
2008-01-01
Density functional theory (DFT) in the commonly used local density or generalized gradient approximation fails to describe van der Waals (vdW) interactions that are vital to organic, biological, and other molecular systems. Here, we propose a simple, efficient, yet accurate local atomic potential (LAP) approach, named DFT+LAP, for including vdW interactions in the framework of DFT. The LAPs for H, C, N, and O are generated by fitting the DFT+LAP potential energy curves of small molecule dimers to those obtained from coupled cluster calculations with single, double, and perturbatively treated triple excitations, CCSD(T). Excellent transferability of the LAPs is demonstrated by remarkable agreement with the JSCH-2005 benchmark database [P. Jurecka et al. Phys. Chem. Chem. Phys. 8, 1985 (2006)], which provides the interaction energies of CCSD(T) quality for 165 vdW and hydrogen-bonded complexes. For over 100 vdW dominant complexes in this database, our DFT+LAP calculations give a mean absolute deviation from the benchmark results less than 0.5 kcal/mol. The DFT+LAP approach involves no extra computational cost other than standard DFT calculations and no modification of existing DFT codes, which enables straightforward quantum simulations, such as ab initio molecular dynamics, on biomolecular systems, as well as on other organic systems.
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Yu-Fang; Sun, Jin-Feng; Yang, Xiang-Dong; Zhu, Zun-Lue
2006-05-01
The reasonable dissociation limit of the A1Σ+ state 7LiH molecule is obtained. The accurate dissociation energy and the equilibrium geometry of this state are calculated using a symmetry-adapted-cluster configuration-interaction method in complete active space for the first time. The whole potential energy curve and the dipole moment function for the A1Σ+ state are calculated over a wide internuclear separation range from about 0.1 to 1.4 nm. The calculated equilibrium geometry and dissociation energy of this potential energy curve are of Re=0.2487 nm and De=1.064 eV, respectively. The unusual negative values of the anharmonicity constant and the vibration-rotational coupling constant are of ωeχe=-4.7158cm-1 and αe=-0.08649cm-1, respectively. The vertical excitation energy from the ground to the A1Σ+ state is calculated and the value is of 3.613 eV at 0.15875 nm (the equilibrium position of the ground state). The highly anomalous shape of this potential energy curve, which is exceptionally flat over a wide radial range around the equilibrium position, is discussed in detail. The harmonic frequency value of 502.47cm-1 about this state is approximately estimated. Careful comparison of the theoretical determinations with those obtained by previous theories about the A1Σ+ state dissociation energy clearly shows that the present calculations are much closer to the experiments than previous theories, thus represents an improvement.
Mayhall, Nicholas J; Raghavachari, Krishnan
2011-05-10
We present a new extrapolated fragment-based approach, termed molecules-in-molecules (MIM), for accurate energy calculations on large molecules. In this method, we use a multilevel partitioning approach coupled with electronic structure studies at multiple levels of theory to provide a hierarchical strategy for systematically improving the computed results. In particular, we use a generalized hybrid energy expression, similar in spirit to that in the popular ONIOM methodology, that can be combined easily with any fragmentation procedure. In the current work, we explore a MIM scheme which first partitions a molecule into nonoverlapping fragments and then recombines the interacting fragments to form overlapping subsystems. By including all interactions with a cheaper level of theory, the MIM approach is shown to significantly reduce the errors arising from a single level fragmentation procedure. We report the implementation of energies and gradients and the initial assessment of the MIM method using both biological and materials systems as test cases. PMID:26610128
Son, Sang-Kil
2011-03-01
We introduce a new numerical grid-based method on unstructured grids in the three-dimensional real-space to investigate the electronic structure of polyatomic molecules. The Voronoi-cell finite difference (VFD) method realizes a discrete Laplacian operator based on Voronoi cells and their natural neighbors, featuring high adaptivity and simplicity. To resolve multicenter Coulomb singularity in all-electron calculations of polyatomic molecules, this method utilizes highly adaptive molecular grids which consist of spherical atomic grids. It provides accurate and efficient solutions for the Schroedinger equation and the Poisson equation with the all-electron Coulomb potentials regardless of the coordinate system and the molecular symmetry. For numerical examples, we assess accuracy of the VFD method for electronic structures of one-electron polyatomic systems, and apply the method to the density-functional theory for many-electron polyatomic molecules.
Rodgers, R P; Tannen, R
1983-01-01
Since its appearance in 1960, the method of Barnhard and associates for the determination of total lung capacity (TLC) from routine chest radiograms has been widely studied in normal and diseased subjects. The method appears to be as accurate as the current definitive procedure, total body plethysmography. The method is in routine use in major medical institutions where the procedure has been automated, but the method does not seem to have gained the wide use it deserves. This is likely due to the tedium of the technique when performed manually--a single determination can require 30 min. We present here an implementation of the Barnhard method for the HP41-C hand-held programmable calculator. In conjunction with the use of a transparent reticle used for obtaining the required measurements, the program allows a single measurement to be made in under 12 minutes. We hope this technique will make radiographic TLC measurements more broadly accessible to the medical profession. PMID:6872526
Han, Min Cheol; Yeom, Yeon Soo; Kim, Chan Hyeong; Kim, Seonghoon; Sohn, Jason W
2015-02-21
In the present study, to achieve accurate 4D Monte Carlo dose calculation in radiation therapy, we devised a new approach that combines (1) modeling of the patient body using tetrahedral-mesh geometry based on the patient's 4D CT data, (2) continuous movement/deformation of the tetrahedral patient model by interpolation of deformation vector fields acquired through deformable image registration, and (3) direct transportation of radiation particles during the movement and deformation of the tetrahedral patient model. The results of our feasibility study show that it is certainly possible to construct 4D patient models (= phantoms) with sufficient accuracy using the tetrahedral-mesh geometry and to directly transport radiation particles during continuous movement and deformation of the tetrahedral patient model. This new approach not only produces more accurate dose distribution in the patient but also replaces the current practice of using multiple 3D voxel phantoms and combining multiple dose distributions after Monte Carlo simulations. For routine clinical application of our new approach, the use of fast automatic segmentation algorithms is a must. In order to achieve, simultaneously, both dose accuracy and computation speed, the number of tetrahedrons for the lungs should be optimized. Although the current computation speed of our new 4D Monte Carlo simulation approach is slow (i.e. ~40 times slower than that of the conventional dose accumulation approach), this problem is resolvable by developing, in Geant4, a dedicated navigation class optimized for particle transportation in tetrahedral-mesh geometry. PMID:25615567
NASA Astrophysics Data System (ADS)
Lonardoni, D.; Pederiva, F.; Gandolfi, S.
2014-01-01
Background: An accurate assessment of the hyperon-nucleon interaction is of great interest in view of recent observations of very massive neutron stars. The challenge is to build a realistic interaction that can be used over a wide range of masses and in infinite matter starting from the available experimental data on the binding energy of light hypernuclei. To this end, accurate calculations of the hyperon binding energy in a hypernucleus are necessary. Purpose: We present a quantum Monte Carlo study of Λ and ΛΛ hypernuclei up to A =91. We investigate the contribution of two- and three-body Λ-nucleon forces to the Λ binding energy. Method: Ground state energies are computed solving the Schrödinger equation for nonrelativistic baryons by means of the auxiliary field diffusion Monte Carlo algorithm extended to the hypernuclear sector. Results: We show that a simple adjustment of the parameters of the ΛNN three-body force yields a very good agreement with available experimental data over a wide range of hypernuclear masses. In some cases no experiments have been performed yet, and we give new predictions. Conclusions: The newly fitted ΛNN force properly describes the physics of medium-heavy Λ hypernuclei, correctly reproducing the saturation property of the hyperon separation energy.
Theoretical calculation of the melting curve of Cu-Zr binary alloys
Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; Song, Xueyu
2014-11-14
Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu51Zr14(β), CuZr(B2), CuZr2(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which themore » melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.« less
Theoretical calculation of the melting curve of Cu-Zr binary alloys
Gunawardana, K. G.S.H.; Wilson, S. R.; Mendelev, M. I.; Song, Xueyu
2014-11-14
Helmholtz free energies of the dominant binary crystalline solids found in the Cu-Zr system at high temperatures close to the melting curve are calculated. This theoretical approach combines fundamental measure density functional theory (applied to the hard-sphere reference system) and a perturbative approach to include the attractive interactions. The studied crystalline solids are Cu(fcc), Cu_{51}Zr_{14}(β), CuZr(B_{2}), CuZr_{2}(C11b), Zr(hcp), and Zr(bcc). The calculated Helmholtz free energies of crystalline solids are in good agreement with results from molecular-dynamics (MD) simulations. Using the same perturbation approach, the liquid phase free energies are calculated as a function of composition and temperature, from which the melting curve of the entire composition range of this system can be obtained. Phase diagrams are determined in this way for two leading embedded atom method potentials, and the results are compared with experimental data. Furthermore, theoretical melting temperatures are compared both with experimental values and with values obtained directly from MD simulations at several compositions.
Theoretical study of the electronic structure with dipole moment calculations of barium monofluoride
NASA Astrophysics Data System (ADS)
Tohme, Samir N.; Korek, Mahmoud
2015-12-01
The potential energy curves have been investigated for the 41 lowest doublet and quartet electronic states in the 2s+1Λ± representation below 55,000 cm-1 of the molecule BaF via CASSCF and MRCI (single and double excitations with Davidson correction) calculations. Twenty-five electronic states have been studied here theoretically for the first time. The crossing and avoided crossing of 20 doublet electronic states have been studied in the region 30,000-50,000 cm-1. The harmonic frequency ωe, the internuclear distance Re, the rotational constant Be, the electronic energy with respect to the ground state Te, and the permanent and transition dipole moments have been calculated in addition to static dipole polarizability of the ground state. By using the canonical functions approach, the eigenvalue Ev, the rotational constant Bv, and the abscissas of the turning points Rmin and Rmax have been calculated for the electronic states up to the vibrational level v=98. The comparison of these values with the theoretical results available in the literature shows a very good agreement.
Hoo, Zhe Hui; Curley, Rachael; Campbell, Michael J; Walters, Stephen J; Hind, Daniel; Wildman, Martin J
2016-01-01
Background Preventative inhaled treatments in cystic fibrosis will only be effective in maintaining lung health if used appropriately. An accurate adherence index should therefore reflect treatment effectiveness, but the standard method of reporting adherence, that is, as a percentage of the agreed regimen between clinicians and people with cystic fibrosis, does not account for the appropriateness of the treatment regimen. We describe two different indices of inhaled therapy adherence for adults with cystic fibrosis which take into account effectiveness, that is, “simple” and “sophisticated” normative adherence. Methods to calculate normative adherence Denominator adjustment involves fixing a minimum appropriate value based on the recommended therapy given a person’s characteristics. For simple normative adherence, the denominator is determined by the person’s Pseudomonas status. For sophisticated normative adherence, the denominator is determined by the person’s Pseudomonas status and history of pulmonary exacerbations over the previous year. Numerator adjustment involves capping the daily maximum inhaled therapy use at 100% so that medication overuse does not artificially inflate the adherence level. Three illustrative cases Case A is an example of inhaled therapy under prescription based on Pseudomonas status resulting in lower simple normative adherence compared to unadjusted adherence. Case B is an example of inhaled therapy under-prescription based on previous exacerbation history resulting in lower sophisticated normative adherence compared to unadjusted adherence and simple normative adherence. Case C is an example of nebulizer overuse exaggerating the magnitude of unadjusted adherence. Conclusion Different methods of reporting adherence can result in different magnitudes of adherence. We have proposed two methods of standardizing the calculation of adherence which should better reflect treatment effectiveness. The value of these indices can
Bulut, N; Castillo, J F; Jambrina, P G; Kłos, J; Roncero, O; Aoiz, F J; Bañares, L
2015-12-17
Accurate quantum reactive scattering time-dependent wave packet close-coupling calculations have been carried out to determine total reaction probabilities and integral cross sections for the O(+) + H2 → OH(+) + H reaction in a range of collision energies from 10(-3) eV up to 1.0 eV for the H2 rovibrational states (v = 0; j = 0, 1, 2) and (v = 1; j = 0) using the potential energy surface (PES) by Martı́nez et al. As expected for a barrierless reaction, the reaction cross section decays rapidly with collision energy, Ec, following a behavior that nearly corresponds to that predicted by the Langevin model. Rotational excitation of H2 into j = 1, 2 has a very moderate effect on reactivity, similarly to what happens with vibrational excitation below Ec ≈ 0.3 eV. However, at higher collision energies the cross section increases notably when H2 is promoted to v = 1. This effect is explained by resorting to the effective potentials in the entrance channel. The integral cross sections have been used to calculate rate constants in the temperature range 200-1000 K. A good overall agreement has been found with the available experimental data on integral cross sections and rate constants. In addition, time-independent quantum mechanical and quasi-classical trajectory (QCT) calculations have been performed on the same PES aimed to compare the various methodologies and to discern the detailed mechanism of the title reaction. In particular, the analysis of individual trajectories has made it possible to explain, in terms of the coupling between reagent relative velocity and the topography of the PES, the presence of a series of alternating maxima and minima in the collision energy dependence of the QCT reaction probabilities for the reactions with H2(v=0,1,j=0), which are absent in the quantum mechanical calculations. PMID:25822338
Matsuzawa, Nobuyuki; Ishitani, Akihiko; Dixon, David A.; Uda, Tsuyoshi
2001-06-13
In order to aid in the design of transparent materials for use as photoresists for F2 lithography (157 nm), we have performed time-dependent density functional theory (TD-DFT) calculations of the photoabsorption of molecules in the vacuum ultraviolet region. The application of this TD-DFT method to the prediction of photoabsorption was benchmarked using model molecules such as formaldehyde, and an empirical equation for correcting the calculated transition energy was obtained. The TD-DFT method with the empirical correction equation provides dramatically more accurate results than those obtained with the CIS (single-excitation configuration interaction) method, which we employed in previous studies. We used it to predict the photoabsorption of various molecules such as methanol, t-butylalcohol, acetic acid, methyl acetate, cycloalkane, norbonane, tricyclodecane, tetrahydropyrane, adamantane, maleic anhydride and their fluorinated derivatives.
Experimental investigation and theoretical calculation for 3He induced nuclear reactions on vanadium
NASA Astrophysics Data System (ADS)
Ali, B. M.; Al-Abyad, M.; Seddik, U.; El-Kameesy, S. U.; Ditrói, F.; Takács, S.; Tárkányi, F.
2016-04-01
Using stacked-foil activation technique and gamma-ray spectrometry, excitation functions for 3He induced nuclear reactions on natV were measured. Cross-sections for natV(3He, xn)52m,gMn and natV(3He, pxn)51Cr nuclear reactions were measured up to 27 MeV utilizing the MGC-20E cyclotron of ATOMKI. The measurements establish for the first time consistent excitation curves. Comparisons with results for values derived from different theoretical codes were included. Integral yield were calculated.
Pavanello, Michele; Van Voorhis, Troy; Visscher, Lucas; Neugebauer, Johannes
2013-02-07
Quantum-mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those charge transfer excitations that take place between non-covalently bound molecules. In particular, we present a method that scales linearly with the number of non-covalently bound molecules in the system and is based on a two-pronged approach: The molecular electronic structure of broken-symmetry charge-localized states is obtained with the frozen density embedding formulation of subsystem density-functional theory; subsequently, in a post-SCF calculation, the full-electron Hamiltonian and overlap matrix elements among the charge-localized states are evaluated with an algorithm which takes full advantage of the subsystem DFT density partitioning technique. The method is benchmarked against coupled-cluster calculations and achieves chemical accuracy for the systems considered for intermolecular separations ranging from hydrogen-bond distances to tens of Angstroms. Numerical examples are provided for molecular clusters comprised of up to 56 non-covalently bound molecules.
NASA Astrophysics Data System (ADS)
Mohr, Stephan; Genovese, Luigi; Ratcliff, Laura; Masella, Michel
The quantum mechanics/molecular mechanis (QM/MM) method is a popular approach that allows to perform atomistic simulations using different levels of accuracy. Since only the essential part of the simulation domain is treated using a highly precise (but also expensive) QM method, whereas the remaining parts are handled using a less accurate level of theory, this approach allows to considerably extend the total system size that can be simulated without a notable loss of accuracy. In order to couple the QM and MM regions we use an approximation of the electrostatic potential based on a multipole expansion. The multipoles of the QM region are determined based on the results of a linear scaling Density Functional Theory (DFT) calculation using a set of adaptive, localized basis functions, as implemented within the BigDFT software package. As this determination comes at virtually no extra cost compared to the QM calculation, the coupling between QM and MM region can be done very efficiently. In this presentation I will demonstrate the accuracy of both the linear scaling DFT approach itself as well as of the approximation of the electrostatic potential based on the multipole expansion, and show some first QM/MM applications using the aforementioned approach.
Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue
2016-11-01
The potential energy curves were calculated for the 24 Λ-S states correlating with the lowest four dissociation channels of the BO(+) cation. The potential energy curves were also computed for the 60 Ω states generated from the 24 Λ-S states. Calculations were made for internuclear separations from 0.08 to 1.05nm using the CASSCF method, which was followed by the icMRCI approach with the correlation-consistent basis sets. Core-valence correlation, scalar relativistic and basis extrapolation were accounted for. Of the 24 Λ-S states, only three states (2(5)Π, 1(5)Σ(-), and 2(5)Σ(-)) were found to be repulsive; only the 1(5)Δ state was found to be a very weakly-bound state; and the E(1)Π, 2(3)Π, and 1(5)Π states were found to be very strong bound. In addition, the B(1)Σ(+) and 3(1)Σ(+) states have double wells by the avoided crossing between the two states. The a(3)Π, 1(3)Σ(-), and 2(3)Σ(-) states are inverted with the spin-orbit coupling effect included. The spectroscopic parameters were determined and the vibrational properties of several Λ-S states were predicted. Comparison with available experimental data shows that the methodology employed is highly accurate for this system. PMID:27289351
NASA Astrophysics Data System (ADS)
Michalska, Katarzyna; Mizera, Mikołaj; Lewandowska, Kornelia; Cielecka-Piontek, Judyta
2016-07-01
Tedizolid is the newest antibacterial agent from the oxazolidinone class. For its identification, FT-IR (2000-400 cm-1) and Raman (2000-400 cm-1) analyses were proposed. Studies of the enantiomeric purity of tedizolid were conducted based on ultraviolet-circular dichroism (UV-CD) analysis. Density functional theory (DFT) with the B3LYP hybrid functional and 6-311G(2df,2pd) basis set was used for support of the analysis of the FT-IR and Raman spectra. Theoretical methods made it possible to conduct HOMO and LUMO analysis, which was used to determine the charge transfer for two tedizolid enantiomers. Molecular electrostatic potential maps were calculated with the DFT method for both tedizolid enantiomers. The relationship between the results of ab initio calculations and knowledge about the chemical-biological properties of R- and S-tedizolid enantiomers is also discussed.
Calculation of membrane bending rigidity using field-theoretic umbrella sampling.
Smirnova, Y G; Müller, M
2015-12-28
The free-energy change of membrane shape transformations can be small, e.g., as in the case of membrane bending. Therefore, the calculation of the free-energy difference between different membrane morphologies is a challenge. Here, we discuss a computational method - field-theoretic umbrella sampling - to compute the local chemical potential of a non-equilibrium configuration and illustrate how one can apply it to study free-energy changes of membrane transformations using simulations. Specifically, the chemical potential profile of the bent membrane and the bending rigidity of membrane are calculated for a soft, coarse-grained amphiphile model and the MARTINI model of a dioleoylphosphatidylcholine (DOPC) membrane. PMID:26723640
Synthesis, characterization, optical properties and theoretical calculations of 6-fluoro coumarin
NASA Astrophysics Data System (ADS)
Bai, Yihui; Du, Jinyan; Weng, Xuexiang
6-Fluoro coumarin is synthesized and characterized by 1H NMR and 13C NMR. The optical properties of the title compound are investigated by UV-vis absorption and fluorescence emission spectra, the results show the title compound can absorb UV-vis light at 319, 269 and 215 nm, moreover it exhibits blue-purple fluorescence emission at 416 nm. Theoretical studies on molecular structure, infrared spectra (IR), nuclear magnetic resonance (1H NMR, 13C NMR) chemical shifts, UV-vis absorption and fluorescence emission of the synthesized compound have been worked out. Most chemical calculations were performed by density functional theory (DFT) method at the B3LYP/6-311G(d,p) level (NMR at B3LYP/Aug-CC-Pvdz level) using Gaussian 09 program. The compared results reveal that the scaled theoretical vibrational frequencies are in good accordance with the observed spectra; computational chemical shifts are consistent with the experimental values in most parts, except for some minor deviations; the UV-vis absorption calculated matches the experimental one very well, and the fluorescence emission spectrum is in good agreement with the experimental one when the solute-solvent hydrogen-bonding interaction is considered. These good coincidences prove that the computational methods selected can be used to predict these properties of other similar materials where it is difficult to arrive at experimental results.
Investigation on the Gas-Phase Decomposition of Trichlorfon by GC-MS and Theoretical Calculation
Jiang, Kezhi; Zhang, Ningwen; Zhang, Hu; Wang, Jianmei; Qian, Mingrong
2015-01-01
The gas phase pyrolysis of trichlorfon was investigated by the on-line gas chromatography – mass spectrometry (GC-MS) pyrolysis and theoretical calculations. Two reaction channels were proposed in the pyrolytic reaction, by analyzing the detected pyrolytic products in the total ion chromatography, including 2,2,2-trichloroacetaldehyde, dimethyl phosphite, and dichlorvos. Theoretical calculations showed that there is an intramolecular hydrogen bond between the hydroxyl group and the phosphate O atom in trichlorfon, through which the hydroxyl H atom can be easily transferred to phosphate O atom to trigger two pyrolytic channels. In path-a, migration of H atom results in direct decomposition of trichlorfon to give 2,2,2-trichloroacetaldehyde and dimethyl phosphite in one step. In path-b, migration of H atom in trichlorfon is combined with formation of the O-P bond to give an intermediate, followed by HCl elimination to afford dichlorvos. Path-a is kinetically more favorable than path-b, which is consistent with the GC-MS results. PMID:25856549
NASA Technical Reports Server (NTRS)
Schwenke, David W.
1990-01-01
The dissociation and recombination of H2 over the temperature range 1000-5000 K are calculated in a nonempirical manner. The computation procedure involves the calculation of the state-to-state energy transfer rate coefficients, the solution of the 349 coupled equations which form the master equation, and the determination of the phenomenological rate coefficients. The nonempirical results presented here are in good agreement with experimental data at 1000 and 3000 K.
NASA Astrophysics Data System (ADS)
Lu, Hua; Zhang, Shushu; Liu, Hanzhuang; Wang, Yanwei; Shen, Zhen; Liu, Chungen; You, Xiaozeng
2009-12-01
A boron-dipyrromethene (BODIPY)-based fluorescence probe with a N,N'-(pyridine-2, 6-diylbis(methylene))-dianiline substituent (1) has been prepared by condensation of 2,6-pyridinedicarboxaldehyde with 8-(4-amino)-4,4-difluoro-1,3,5,7-tetramethyl-4-bora-3a,4a-diaza-s-indacene and reduction by NaBH4. The sensing properties of compound 1 toward various metal ions are investigated via fluorometric titration in methanol, which show highly selective fluorescent turn-on response in the presence of Hg2+ over the other metal ions, such as Li+, Na+, K+, Ca2+, Mg2+, Pb2+, Fe2+, Co2+, Ni2+, Cu2+, Zn2+, Cd2+, Ag+, and Mn2+. Computational approach has been carried out to investigate the mechanism why compound 1 provides different fluorescent signal for Hg2+ and other ions. Theoretic calculations of the energy levels show that the quenching of the bright green fluorescence of boradiazaindacene fluorophore is due to the reductive photoinduced electron transfer (PET) from the aniline subunit to the excited state of BODIPY fluorophore. In metal complexes, the frontier molecular orbital energy levels changes greatly. Binding Zn2+ or Cd2+ ion leads to significant decreasing of both the HOMO and LUMO energy levels of the receptor, thus inhibit the reductive PET process, whereas an oxidative PET from the excited state fluorophore to the receptor occurs, vice versa, which also quenches the fluorescence. However, for 1-Hg2+ complex, both the reductive and oxidative PETs are prohibited; therefore, strong fluorescence emission from the fluorophore can be observed experimentally. The agreement of the experimental results and theoretic calculations suggests that our calculation method can be applicable as guidance for the design of new chemosensors for other metal ions.
NASA Astrophysics Data System (ADS)
Infantino, Angelo; Marengo, Mario; Baschetti, Serafina; Cicoria, Gianfranco; Longo Vaschetto, Vittorio; Lucconi, Giulia; Massucci, Piera; Vichi, Sara; Zagni, Federico; Mostacci, Domiziano
2015-11-01
Biomedical cyclotrons for production of Positron Emission Tomography (PET) radionuclides and radiotherapy with hadrons or ions are widely diffused and established in hospitals as well as in industrial facilities and research sites. Guidelines for site planning and installation, as well as for radiation protection assessment, are given in a number of international documents; however, these well-established guides typically offer analytic methods of calculation of both shielding and materials activation, in approximate or idealized geometry set up. The availability of Monte Carlo codes with accurate and up-to-date libraries for transport and interactions of neutrons and charged particles at energies below 250 MeV, together with the continuously increasing power of nowadays computers, makes systematic use of simulations with realistic geometries possible, yielding equipment and site specific evaluation of the source terms, shielding requirements and all quantities relevant to radiation protection. In this work, the well-known Monte Carlo code FLUKA was used to simulate two representative models of cyclotron for PET radionuclides production, including their targetry; and one type of proton therapy cyclotron including the energy selection system. Simulations yield estimates of various quantities of radiological interest, including the effective dose distribution around the equipment, the effective number of neutron produced per incident proton and the activation of target materials, the structure of the cyclotron, the energy degrader, the vault walls and the soil. The model was validated against experimental measurements and comparison with well-established reference data. Neutron ambient dose equivalent H*(10) was measured around a GE PETtrace cyclotron: an average ratio between experimental measurement and simulations of 0.99±0.07 was found. Saturation yield of 18F, produced by the well-known 18O(p,n)18F reaction, was calculated and compared with the IAEA recommended
Li, Yongqing; Yuan, Jiuchuang; Chen, Maodu; Ma, Fengcai; Sun, Mengtao
2013-07-15
An accurate single-sheeted double many-body expansion potential energy surface is reported for the title system. A switching function formalism has been used to warrant the correct behavior at the H2(X1Σg+)+N(2D) and NH (X3Σ-)+H(2S) dissociation channels involving nitrogen in the ground N(4S) and first excited N(2D) states. The topographical features of the novel global potential energy surface are examined in detail, and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. The novel surface can be using to treat well the Renner-Teller degeneracy of the 12A″ and 12A' states of NH 2. Such a work can both be recommended for dynamics studies of the N(2D)+H2 reaction and as building blocks for constructing the double many-body expansion potential energy surface of larger nitrogen/hydrogen-containing systems. In turn, a test theoretical study of the reaction N(2D)+H2(X1Σg+)(ν=0,j=0)→NH (X3Σ-)+H(2S) has been carried out with the method of quantum wave packet on the new potential energy surface. Reaction probabilities, integral cross sections, and differential cross sections have been calculated. Threshold exists because of the energy barrier (68.5 meV) along the minimum energy path. On the curve of reaction probability for total angular momentum J = 0, there are two sharp peaks just above threshold. The value of integral cross section increases quickly from zero to maximum with the increase of collision energy, and then stays stable with small oscillations. The differential cross section result shows that the reaction is a typical forward and backward scatter in agreement with experimental measurement result. PMID:23666848
Theoretical calculations and vibrational potential energy surface of 4-silaspiro(3,3)heptane
Ocola, Esther J.; Medders, Cross; Laane, Jaan; Meinander, Niklas
2014-04-28
Theoretical computations have been carried out on 4-silaspiro(3,3)heptane (SSH) in order to calculate its molecular structure and conformational energies. The molecule has two puckered four-membered rings with dihedral angles of 34.2° and a tilt angle of 9.4° between the two rings. Energy calculations were carried out for different conformations of SSH. These results allowed the generation of a two-dimensional ring-puckering potential energy surface (PES) of the form V = a(x{sub 1}{sup 4} + x{sub 2}{sup 4}) – b(x{sub 1}{sup 2} + x{sub 2}{sup 2}) + cx{sub 1}{sup 2}x{sub 2}{sup 2}, where x{sub 1} and x{sub 2} are the ring-puckering coordinates for the two rings. The presence of sufficiently high potential energy barriers prevents the molecule from undergoing pseudorotation. The quantum states, wave functions, and predicted spectra resulting from the PESs were calculated.
Skokov, S.; Peterson, K.A.; Bowman, J.M.
1998-08-01
Accurate {ital ab initio} multireference configuration interaction (CI) calculations with large correlation-consistent basis sets are performed for HOCl. After extrapolation to the complete basis set limit, the {ital ab initio} data are precisely fit to give a semiglobal three-dimensional potential energy surface to describe HOCl{r_arrow}Cl+OH from high overtone excitation of the OH-stretch. The average absolute deviation between the {ital ab initio} and fitted energies is 4.2thinspcm{sup {minus}1} for energies up to 60 kcal/mol relative to the HOCl minimum. Vibrational energies of HOCl including the six overtones of the OH-stretch are computed using a vibrational-Cl method on the fitted potential and also on a slightly adjusted potential. Near-spectroscopic accuracy is obtained using the adjusted potential; the average absolute deviation between theory and experiment for 19 experimentally reported states is 4.8thinspcm{sup {minus}1}. Very good agreement with experiment is also obtained for numerous rotational energies for the ground vibrational state, the ClO-stretch fundamental, and the fifth overtone of the OH-stretch. {copyright} {ital 1998 American Institute of Physics.}
NASA Astrophysics Data System (ADS)
Deguchi, Daiki; Sato, Kazunori; Kino, Hiori; Kotani, Takao
2016-05-01
We have recently implemented a new version of the quasiparticle self-consistent GW (QSGW) method in the ecalj package released at http://github.com/tkotani/ecalj. Since the new version of the ecalj package is numerically stable and more accurate than the previous versions, we can perform calculations easily without being bothered with tuning input parameters. Here we examine its ability to describe energy band properties, e.g., band-gap energy, eigenvalues at special points, and effective mass, for a variety of semiconductors and insulators. We treat C, Si, Ge, Sn, SiC (in 2H, 3C, and 4H structures), (Al, Ga, In) × (N, P, As, Sb), (Zn, Cd, Mg) × (O, S, Se, Te), SiO2, HfO2, ZrO2, SrTiO3, PbS, PbTe, MnO, NiO, and HgO. We propose that a hybrid QSGW method, where we mix 80% of QSGW and 20% of LDA, gives universally good agreement with experiments for these materials.
Den, Takuya S.; Frey, Hans-Martin; Leutwyler, Samuel
2014-11-21
The gas-phase rotational motion of hexafluorobenzene has been measured in real time using femtosecond (fs) time-resolved rotational Raman coherence spectroscopy (RR-RCS) at T = 100 and 295 K. This four-wave mixing method allows to probe the rotation of non-polar gas-phase molecules with fs time resolution over times up to ∼5 ns. The ground state rotational constant of hexafluorobenzene is determined as B{sub 0} = 1029.740(28) MHz (2σ uncertainty) from RR-RCS transients measured in a pulsed seeded supersonic jet, where essentially only the v = 0 state is populated. Using this B{sub 0} value, RR-RCS measurements in a room temperature gas cell give the rotational constants B{sub v} of the five lowest-lying thermally populated vibrationally excited states ν{sub 7/8}, ν{sub 9}, ν{sub 11/12}, ν{sub 13}, and ν{sub 14/15}. Their B{sub v} constants differ from B{sub 0} by between −1.02 MHz and +2.23 MHz. Combining the B{sub 0} with the results of all-electron coupled-cluster CCSD(T) calculations of Demaison et al. [Mol. Phys. 111, 1539 (2013)] and of our own allow to determine the C-C and C-F semi-experimental equilibrium bond lengths r{sub e}(C-C) = 1.3866(3) Å and r{sub e}(C-F) = 1.3244(4) Å. These agree with the CCSD(T)/wCVQZ r{sub e} bond lengths calculated by Demaison et al. within ±0.0005 Å. We also calculate the semi-experimental thermally averaged bond lengths r{sub g}(C-C)=1.3907(3) Å and r{sub g}(C-F)=1.3250(4) Å. These are at least ten times more accurate than two sets of experimental gas-phase electron diffraction r{sub g} bond lengths measured in the 1960s.
NASA Astrophysics Data System (ADS)
Kashinski, D. O.; Nelson, R. G.; Chase, G. M.; di Nallo, O. E.; Byrd, E. F. C.
2016-05-01
We are investigating the accuracy of theoretical models used to predict the visible, ultraviolet, and infrared spectra, as well as other properties, of product materials ejected from the muzzle of currently fielded systems. Recent advances in solid propellants has made the management of muzzle signature (flash) a principle issue in weapons development across the calibers. A priori prediction of the electromagnetic spectra of formulations will allow researchers to tailor blends that yield desired signatures and determine spectrographic detection ranges. Quantum chemistry methods at various levels of sophistication have been employed to optimize molecular geometries, compute unscaled harmonic frequencies, and determine the optical spectra of specific gas-phase species. Electronic excitations are being computed using Time Dependent Density Functional Theory (TD-DFT). Calculation of approximate global harmonic frequency scaling factors for specific DFT functionals is also in progress. A full statistical analysis and reliability assessment of computational results is currently underway. Work supported by the ARL, DoD-HPCMP, and USMA.
NASA Astrophysics Data System (ADS)
da Silva, Julio Cesar A.; Ducati, Lucas C.; Rittner, Roberto
2012-05-01
NMR solvent effects and theoretical calculations showed muscarinic agonists present a large stability for their near synclinal conformations, indicating the presence of significant stabilization factors. Analysis of the results clearly indicated that this stability is not determined by the dihedral around the substituted C-C ethane bond, as stated by some authors, but a consequence of the geometry adopted in order to maximize N+/O interactions in this type of molecules. It can be assumed that acetylcholine and its muscarinic agonists exhibit their biologic activity when the positively charged nitrogen and the oxygen atoms are in the same side of the molecule within an interatomic distance ranging from 3.0 to 6.0 Å.
Theoretical calculations of a compound formed by Fe(+3) and tris(catechol).
Kara, İzzet; Kara, Yeşim; Öztürk Kiraz, Aslı; Mammadov, Ramazan
2015-10-01
Phenolic compounds generally have special smell, easily soluble in water, organic solvents (alcohols, esters, chloroform, ethyl acetate), in aqueous solutions of bases, colorless or colorful, crystalline and amorphous materials. Phenols form colorful complexes when they form compounds with heavy metals. In this study, the structural properties of a compound formed by catechol and Fe(+3) are investigated theoretically. The electronic and thermodynamic properties of the complex were also investigated in gas phase and organic solvents at B3LYP/6-31+G(d,p) and B3LYP/6-311++G(d,p) basis set. The formation of Fe-tris(catechol) complex compound is exothermic, and it is difficult to obtain the complex as the temperature increases. The observed and calculated FT-IR and geometric parameters spectra are in good agreement with empirical. PMID:25983060
Rokhina, Ekaterina V; Lahtinen, Manu; Makarova, Katerina; Jegatheesan, Veeriah; Virkutyte, Jurate
2012-06-01
The nitric acid-functionalized commercial carbon nanofibers (CNFs) were comprehensively studied by instrumental (XRD, BET, SEM, TGA) and theoretical (DFT calculations) methods. The detailed surface study revealed the variation in the characteristics of functionalized CNFs, such as a decreased (up to 34%) surface area and impacted structural, electronic and chemical properties. The effects of functional groups were studied by comparison with pristine nanofibers. The results showed that the C-C bond lengths of the modified CNFs varied significantly. Chemical functionalization altered the frontier orbitals of the pristine material, and therefore altered the nature of their interactions with other substances. Moreover, the pristine and modified CNFs were tested for the removal of phenol from aqueous solutions. It was observed that surface modification tuned the adsorption capacity of carbon nanofibers (up to 0.35 mmol g(-1)), whereas original fibers did not demonstrate any adsorption capacity of phenol. PMID:22209137
Bellazzini, R.; Brez, A.; Massai, M.M.; Torquati, M.R.
1985-02-01
A fast and accurate algorithm to calculate the charge and current induced on all the electrodes of wire chambers (MWPC, 'pad chambers', TPC. . . .) is presented. The algorithm is completely three dimensional so that it is possible to calculate the induced charge on anode wires and cathode strips or 'pads' regardless of their orientation in space.
A 3-D Theoretical Model for Calculating Plasma Effects in Germanium Detectors
NASA Astrophysics Data System (ADS)
Wei, Wenzhao; Liu, Jing; Mei, Dongming; Cubed Collaboration
2015-04-01
In the detection of WIMP-induced nuclear recoil with Ge detectors, the main background source is the electron recoil produced by natural radioactivity. The capability of discriminating nuclear recoil (n) from electron recoil (γ) is crucial to WIMP searches. Digital pulse shape analysis is an encouraging approach to the discrimination of nuclear recoil from electron recoil since nucleus is much heavier than electron and heavier particle generates ionization more densely along its path, which forms a plasma-like cloud of charge that shields the interior from the influence of the electric field. The time needed for total disintegration of this plasma region is called plasma time. The plasma time depends on the initial density and radius of the plasma-like cloud, diffusion constant for charge carriers, and the strength of electric field. In this work, we developed a 3-D theoretical model for calculating the plasma time in Ge detectors. Using this model, we calculated the plasma time for both nuclear recoils and electron recoils to study the possibility for Ge detectors to realize n/ γ discrimination and improve detector sensitivity in detecting low-mass WIMPs. This work is supported by NSF in part by the NSF PHY-0758120, DOE Grant DE-FG02-10ER46709, and the State of South Dakota.
Accuracy of Theoretical Calculations for Electron-Impact Ionization of atoms and Molecules
NASA Astrophysics Data System (ADS)
Madison, Don
2015-09-01
In the last two decades, there have been several close-coupling approaches developed which can accurately calculate the triply differential cross sections for electron impact ionization of effective one and two electron atoms. The agreement between experiment and theory is not particularly good for more complicated atoms and molecules. Very recently, a B-spline R-matrix with pseudostates (BSRPS) approach was used to investigate low energy electron impact ionization of neon and very good agreement with experiment was found. The perturbative 3-body distorted wave (3DW) approach which includes the exact final state electron-electron interaction (post collision interaction - PCI) gave comparably good agreement with experiment. For ionization of molecules, there have been numerous studies of high-energy electron impact. These studies are called EMS (Electron Momentum Spectroscopy) and they were very valuable in determining the accuracy of molecular wavefunctions since the measured cross sections were proportional to the momentum space molecular wavefunction. More recently, lower energy collisions have started to be measured and these cross sections are much more difficult for theory since the detailed kinematics of the experiment become important. So far, the only close coupling calculation reported for ionization of molecules is the time-dependent close-coupling calculation (TDCC) which has been developed for ionization of H2 and it yields relative good agreement with experiment. Again the molecular 3-body distorted wave (M3DW) gave equally good agreement with experiment. For polyatomic molecules, the only theory available is the M3DW. In this talk, I will show the current status of agreement between experiment and theory for low and intermediate energy single ionization of atoms and molecules. Work supported by the NSF and XSEDE.
NASA Astrophysics Data System (ADS)
Wei, Guangfei; Li, Xiongyao; Wang, Shijie
2015-02-01
Terrestrial radiation is another possible source of heat in lunar thermal environment at its nearside besides the solar illumination. On the basis of Clouds and the Earth's Radiant Energy System (CERES) data products, the effect of terrestrial radiation on the brightness temperature (TBe) of the lunar nearside has been theoretically calculated. It shows that the mafic lunar mare with high TBe is more sensitive to terrestrial radiation than the feldspathic highland with low TBe value. According to the synchronous rotation of the Moon, we extract TBe on lunar nearside using the microwave radiometer data from the first Chinese lunar probe Chang'E-1 (CE-1). Consistently, the average TBe at Mare Serenitatis is about 1.2 K while the highland around the Geber crater (19.4°S, 13.9°E) is relatively small at ∼0.4 K. Our results indicate that there is no significant effect of terrestrial radiation on TBe at the lunar nearside. However, to extract TBe accurately, effects of heat flow, rock abundance and subsurface rock fragments which are more significant should be considered in the future work.
NASA Astrophysics Data System (ADS)
Predoi-Cross, Adriana; Holladay, Christopher; Heung, Henry; Bouanich, Jean-Pierre; Mellau, Georg Ch.; Keller, Reimund; Hurtmans, Daniel R.
2008-09-01
We report measurements for N 2-broadening, pressure-shift and line mixing coefficients for 55 oxygen transitions in the A-band retrieved using a multispectrum fitting technique. Nineteen laboratory absorption spectra were recorded at 0.02 cm -1 resolution using a multi-pass absorption cell with path length of 1636.9 cm and the IFS 120 Fourier transform spectrometer located at Justus-Liebig-University in Giessen, Germany. The total sample pressures ranged from 8.8 to 3004.5 Torr with oxygen volume mixing ratios in nitrogen ranging between 0.057 and 0.62. An Exponential Power Gap (EPG) scaling law was used to calculate the N 2-broadening and N 2-line mixing coefficients. The line broadening and shift coefficients for the A-band of oxygen self-perturbed and perturbed by N 2 are modeled using semiclassical calculations based on the Robert-Bonamy formalism and two intermolecular potentials. These potentials involve electrostatic contributions including the hexadecapole moment of the molecules and (a) a simple dispersion contribution with one adjustable parameter to fit the broadening coefficients or (b) the atom-atom Lennard-Jones model without such adjustable parameters. The first potential leads to very weak broadening coefficients for high J transitions whereas the second potential gives much more improved results at medium and large J values, in reasonable agreement with the experimental data. For the line shifts which mainly arise in our calculation from the electronic state dependence of the isotropic potential, their general trends with increasing J values can be well predicted, especially from the first potential. From the theoretical results, we have derived air-broadening and air-induced shift coefficients with an agreement comparable to that obtained for O 2-O 2 and O 2-N 2.
Duan, Yuhua
2012-11-02
Since current technologies for capturing CO{sub 2} to fight global climate change are still too energy intensive, there is a critical need for development of new materials that can capture CO{sub 2} reversibly with acceptable energy costs. Accordingly, solid sorbents have been proposed to be used for CO{sub 2} capture applications through a reversible chemical transformation. By combining thermodynamic database mining with first principles density functional theory and phonon lattice dynamics calculations, a theoretical screening methodology to identify the most promising CO{sub 2} sorbent candidates from the vast array of possible solid materials has been proposed and validated. The calculated thermodynamic properties of different classes of solid materials versus temperature and pressure changes were further used to evaluate the equilibrium properties for the CO{sub 2} adsorption/desorption cycles. According to the requirements imposed by the pre- and post- combustion technologies and based on our calculated thermodynamic properties for the CO{sub 2} capture reactions by the solids of interest, we were able to screen only those solid materials for which lower capture energy costs are expected at the desired pressure and temperature conditions. Only those selected CO{sub 2} sorbent candidates were further considered for experimental validations. The ab initio thermodynamic technique has the advantage of identifying thermodynamic properties of CO{sub 2} capture reactions without any experimental input beyond crystallographic structural information of the solid phases involved. Such methodology not only can be used to search for good candidates from existing database of solid materials, but also can provide some guidelines for synthesis new materials. In this presentation, we first introduce our screening methodology and the results on a testing set of solids with known thermodynamic properties to validate our methodology. Then, by applying our computational method
NASA Astrophysics Data System (ADS)
Pavlov, A. V.; Sitnov, Iu. S.
1985-10-01
Pavlov's (1984) method is used to determine the relative errors (due to errors in measuring the input parameters of the model) in theoretical calculations of the main parameters of the daytime F2-layer under quiet conditions. The parameters calculated are the height of the F2-layer maximum and the electron density.
Habegger, Maria L; Motta, Philip J; Huber, Daniel R; Dean, Mason N
2012-12-01
Evaluations of bite force, either measured directly or calculated theoretically, have been used to investigate the maximum feeding performance of a wide variety of vertebrates. However, bite force studies of fishes have focused primarily on small species due to the intractable nature of large apex predators. More massive muscles can generate higher forces and many of these fishes attain immense sizes; it is unclear how much of their biting performance is driven purely by dramatic ontogenetic increases in body size versus size-specific selection for enhanced feeding performance. In this study, we investigated biting performance and feeding biomechanics of immature and mature individuals from an ontogenetic series of an apex predator, the bull shark, Carcharhinus leucas (73-285cm total length). Theoretical bite force ranged from 36 to 2128N at the most anterior bite point, and 170 to 5914N at the most posterior bite point over the ontogenetic series. Scaling patterns differed among the two age groups investigated; immature bull shark bite force scaled with positive allometry, whereas adult bite force scaled isometrically. When the bite force of C. leucas was compared to those of 12 other cartilaginous fishes, bull sharks presented the highest mass-specific bite force, greater than that of the white shark or the great hammerhead shark. A phylogenetic independent contrast analysis of anatomical and dietary variables as determinants of bite force in these 13 species indicated that the evolution of large adult bite forces in cartilaginous fishes is linked predominantly to the evolution of large body size. Multiple regressions based on mass-specific standardized contrasts suggest that the evolution of high bite forces in Chondrichthyes is further correlated with hypertrophication of the jaw adductors, increased leverage for anterior biting, and widening of the head. Lastly, we discuss the ecological significance of positive allometry in bite force as a possible
Theoretical calculations of nonlinear refraction and absorption coefficients of doped graphene
NASA Astrophysics Data System (ADS)
Margulis, Vl A.; Muryumin, E. E.; Gaiduk, E. A.
2014-12-01
In this study, we present the first theoretical predictions concerning the nonlinear refractive and absorptive properties of the doped graphene in which the Fermi energy {{E}F} of charge carriers (noninteracting massless Dirac fermions) is controlled by an external gate voltage. We base our study on the original perturbation theory technique developed by Genkin and Mednis (1968 Sov. Phys. JETP 27 609) for calculating the nonlinear-optical (NLO) response coefficients of bulk crystalline semiconductors with partially filled bands. Using a simple tight-binding model for the π-electron energy bands of graphene, we obtain analytic expressions for the nonlinear refractive index {{n}2}(ω ) and the nonlinear absorption coefficient {{α }2}(ω ) of the doped graphene at photon energies above twice the value of the Fermi energy (\\hbar ω \\gt 2{{E}F}). We show that in this spectral region, both the nonlinear refraction ant the nonlinear absorption are determined predominantly by the combined processes which simultaneously involve intraband and interband motion of π-electrons. Our calculations indicate that extremely large negative values of n2 (of the order of -{{10}-6} cm2 W-1) can be achieved in the graphene at a relatively low doping level (of about 1012 cm-2) provided that the excitation frequency slightly exceeds the threshold frequency corresponding to the onset of interband transitions. With a further increase of the radiation frequency, the {{n}2}(ω ) becomes positive and begins to decrease in its absolute magnitude. The peculiar frequency dispersion of n2 and a negative sign of the {{α }2} (absorption bleaching), as predicted by our theory, suggest that the doped graphene is a prospective NLO material to be used in practical optical switching applications.
NASA Astrophysics Data System (ADS)
Rusakova, I. L.; Rusakov, Yu Yu; Krivdin, L. B.
2016-04-01
The theoretical grounds of the modern relativistic methods for quantum chemical calculation of spin–spin coupling constants in nuclear magnetic resonance spectra are considered. Examples and prospects of application of relativistic calculations of these constants in the structural studies of organic and heteroorganic compounds are discussed. Practical recommendations on relativistic calculations of spin–spin coupling constants using the available software are given. The bibliography includes 622 references.
Fu, Haohao; Shao, Xueguang; Chipot, Christophe; Cai, Wensheng
2016-08-01
Proper use of the adaptive biasing force (ABF) algorithm in free-energy calculations needs certain prerequisites to be met, namely, that the Jacobian for the metric transformation and its first derivative be available and the coarse variables be independent and fully decoupled from any holonomic constraint or geometric restraint, thereby limiting singularly the field of application of the approach. The extended ABF (eABF) algorithm circumvents these intrinsic limitations by applying the time-dependent bias onto a fictitious particle coupled to the coarse variable of interest by means of a stiff spring. However, with the current implementation of eABF in the popular molecular dynamics engine NAMD, a trajectory-based post-treatment is necessary to derive the underlying free-energy change. Usually, such a posthoc analysis leads to a decrease in the reliability of the free-energy estimates due to the inevitable loss of information, as well as to a drop in efficiency, which stems from substantial read-write accesses to file systems. We have developed a user-friendly, on-the-fly code for performing eABF simulations within NAMD. In the present contribution, this code is probed in eight illustrative examples. The performance of the algorithm is compared with traditional ABF, on the one hand, and the original eABF implementation combined with a posthoc analysis, on the other hand. Our results indicate that the on-the-fly eABF algorithm (i) supplies the correct free-energy landscape in those critical cases where the coarse variables at play are coupled to either each other or to geometric restraints or holonomic constraints, (ii) greatly improves the reliability of the free-energy change, compared to the outcome of a posthoc analysis, and (iii) represents a negligible additional computational effort compared to regular ABF. Moreover, in the proposed implementation, guidelines for choosing two parameters of the eABF algorithm, namely the stiffness of the spring and the mass
NASA Technical Reports Server (NTRS)
Cohen, S. C.
1979-01-01
A model of viscoelastic deformations associated with earthquakes is presented. A strike-slip fault is represented by a rectangular dislocation in a viscoelastic layer (lithosphere) lying over a viscoelastic half-space (asthenosphere). Deformations occur on three time scales. The initial response is governed by the instantaneous elastic properties of the earth. A slower response is associated with viscoelastic relaxation of the lithosphere and a yet slower response is due to viscoelastic relaxation of the asthenosphere. The major conceptual contribution is the inclusion of lithospheric viscoelastic properties into a dislocation model of earthquake related deformations and stresses. Numerical calculations using typical fault parameters reveal that the postseismic displacements and strains are small compared to the coseismic ones near the fault, but become significant further away. Moreover, the directional sense of the deformations attributable to the elastic response, the lithospheric viscoelastic softening, and the asthenospheric viscoelastic flow may differ and depend on location and model details. The results and theoretical arguments suggest that the stress changes accompanying lithospheric relaxation may also be in a different sense than and be larger than the strain changes.
Wu, Yanlin; Shi, Jin; Chen, Hongche; Zhao, Jianfu; Dong, Wenbo
2016-10-01
4-tert-butylphenol (4-t-BP), an endocrine disrupting chemical, is widely distributed in natural bodies of water but is difficult to biodegrade. In this study, we focused on the transformation of 4-t-BP in photo-initiated degradation processes. The steady-state photolysis and laser flash photolysis (LFP) experiments were conducted in order to elucidate its degradation mechanism. Identification of products was performed using the GC-MS, LC-MS and theoretical calculation techniques. The oxidation pathway of 4-t-BP by hydroxyl radical (HO) was also studied and H2O2 was added to produce HO. 4-tert-butylcatechol and 4-tert-butylphenol dimer were produced in 4-t-BP direct photolysis. 4-tert-butylcatechol and hydroquinone were produced by the oxidation of HO. But the formation mechanism of 4-tert-butylcatechol in the two processes was different. The benzene ring was fractured in 4-t-BP oxidation process and 29% of TOC was degraded after 16h irradiation. PMID:27213674
NASA Astrophysics Data System (ADS)
Takeshima, Tsuguhide; Takeuchi, Hiroshi; Egawa, Toru; Konaka, Shigehiro
2005-01-01
The molecular structure of arecoline (methyl 1,2,5,6-tetrahydro-1-methylnicotinate, ? has been determined by gas electron diffraction. Diffraction patterns were taken at about 370 K. Structural constraints for the data analysis were obtained from MP2/6-31G** calculations. Vibrational mean amplitudes and shrinkage corrections were calculated from the force constants obtained from the gas-phase vibrational frequencies and the B3LYP/6-31G** calculations. The electron diffraction data were well reproduced by assuming the mixture of four conformers. The determined structural parameters ( rg (Å) and ∠ (°)) for the main conformer with 3 σ in parentheses are as follows: < rg(N-C ring)>=1.456(4); rg(N-C methyl)=1.451 (d.p.); rg(C dbnd6 C)=1.339(9); < rg(C-C)>=1.512(3); rg(O-C methyl)=1.434(5); rg(C(O)-O)=1.355 (d.p.); rg(C dbnd6 O)=1.209(4); the out-of-plane angle of the methyl group=50.3(23); ∠C ringN ringC ring=112.8(30); ∠N ringC ringC ring(H 2)=110.5(16); <∠C ringC ringC ring>=118.4(5); ∠C dbnd6 CC(O)=116.8(7); ∠CC dbnd6 O=127.6(9); ∠CC-O=109.8(8), where the angle brackets denote averaged values and d.p. denotes dependent parameters. Fixing the abundances of the minor conformers, Ax-s- cis and Ax-s- trans, at the theoretical values (13% in total), those of the Eq-s- cis and Eq-s- trans conformers were determined to be 46(16) and 41(16)%, respectively. Here Ax and Eq denote the axial and equatorial directions of the N-CH 3 bond and s- cis and s- trans show the orientation of the methoxycarbonyl group expressed by the configuration of the C dbnd6 O and C dbnd6 C bonds. The N⋯O carbonyl distances of the Eq-s- cis and Ax-s- cis conformers are 4.832(13) and 4.874(16) Å, respectively. They are close to the N⋯N distance of the most abundant conformer of nicotine, 4.885(6) Å, suggesting that the Eq-s- cis and Ax-s- cis conformers have nicotinic activity.
Chen, Xiao-bo; Wang, Ce; Li, Song; Naruhito, Sawanobori; Kang, Dong-guo
2010-07-01
A photonic phenomenon of fluorescence intensity reverse between red and green fluorescence was studied theoretically and experimentally in the present article. It was found by experiment that Er(0.5) Yb(9.5) : FOV oxyfluoride vitroceramics exhibits strong fluorescence intensity reverse phenomenon. The range of the intensity reverse of Er(0.5) Yb(9.5) : FOV was measured to be 877. Moreover, all basic spectroscopic parameters were calculated. The theoretical basis of numerical calculation for dynamics processes of all levels was established. PMID:20827959
NASA Astrophysics Data System (ADS)
Sun, Yuansheng; Periasamy, Ammasi
2010-03-01
Förster resonance energy transfer (FRET) microscopy is commonly used to monitor protein interactions with filter-based imaging systems, which require spectral bleedthrough (or cross talk) correction to accurately measure energy transfer efficiency (E). The double-label (donor+acceptor) specimen is excited with the donor wavelength, the acceptor emission provided the uncorrected FRET signal and the donor emission (the donor channel) represents the quenched donor (qD), the basis for the E calculation. Our results indicate this is not the most accurate determination of the quenched donor signal as it fails to consider the donor spectral bleedthrough (DSBT) signals in the qD for the E calculation, which our new model addresses, leading to a more accurate E result. This refinement improves E comparisons made with lifetime and spectral FRET imaging microscopy as shown here using several genetic (FRET standard) constructs, where cerulean and venus fluorescent proteins are tethered by different amino acid linkers.
Theoretical methods for the calculation of Bragg curves and 3D distributions of proton beams
NASA Astrophysics Data System (ADS)
Ulmer, W.; Matsinos, E.
2010-12-01
buildup is explained by a theoretical analysis of impinging proton beamlets. In order to obtain a complete dose calculation model for proton treatment planning, some further aspects have to be accounted for: the decrease of the fluence of the primary protons due to nuclear interactions, the transport of released secondary protons, the dose contribution of heavy recoil nuclei, the inclusion of lateral scatter of the primary and secondary protons based on Molière's multiple-scatter theory, and the scatter contributions of collimators. This study also presents some results which go beyond proton dose calculation models; namely, the application of the relativistic generalization of the Bragg-Kleeman rule to electrons and, in an appendix, a method to determine inelastic cross-sections of therapeutic protons in media of therapeutic interest.
NASA Astrophysics Data System (ADS)
Umari, P.; Fabris, S.
2012-05-01
The quasi-particle energy levels of the Zn-Phthalocyanine (ZnPc) molecule calculated with the GW approximation are shown to depend sensitively on the explicit description of the metal-center semicore states. We find that the calculated GW energy levels are in good agreement with the measured experimental photoemission spectra only when explicitly including the Zn 3s and 3p semicore states in the valence. The main origin of this effect is traced back to the exchange term in the self-energy GW approximation. Based on this finding, we propose a simplified approach for correcting GW calculations of metal phthalocyanine molecules that avoids the time-consuming explicit treatment of the metal semicore states. Our method allows for speeding up the calculations without compromising the accuracy of the computed spectra.
Communication: An accurate calculation of the S1 C2H2 cis-trans isomerization barrier height
NASA Astrophysics Data System (ADS)
Baraban, Joshua H.; Matthews, Devin A.; Stanton, John F.
2016-03-01
A high level ab initio calculation of the cis-trans isomerization barrier height in the first excited singlet electronic state of acetylene is found to agree very well with a recent experimental determination.
Peterson, K.A.; Skokov, S.; Bowman, J.M.
1999-10-01
A new, global analytical potential energy surface is constructed for the X&hthinsp;{sup 1}A{sup {prime}} electronic ground state of HOCl that accurately includes the HClO isomer. The potential is obtained by using accurate {ital ab initio} data from a previously published surface [Skokov {ital et al.}, J. Chem. Phys. {bold 109}, 2662 (1998)], as well as a significant number of new data for the HClO region of the surface at the same multireference configuration interaction, complete basis set limit level of theory. Vibrational energy levels and intensities are computed for both HOCl and HClO up to the OH+Cl dissociation limit and above the isomerization barrier. After making only minor adjustments to the {ital ab initio} surface, the errors with respect to experiment for HOCl are generally within a few cm{sup {minus}1} for 22 vibrational levels with the largest error being 26 cm{sup {minus}1}. A total of 813 bound vibrational states are calculated for HOCl. The HClO potential well supports 57 localized states, of which only the first 3 are bound. The strongest dipole transitions for HClO were computed for the fundamentals{emdash}33, 2.9, and 25 km/mol for {nu}{sub 1}, {nu}{sub 2}, and {nu}{sub 3}, respectively. From exact J=1 ro-vibrational calculations, state dependent rotational constants have been calculated for HClO. Lastly, resonance calculations with the new potential demonstrate that the presence of the HClO minimum has a negligible effect on the resonance states of HOCl near the dissociation threshold due to the relatively high and wide isomerization barrier. {copyright} {ital 1999 American Institute of Physics.}
NASA Astrophysics Data System (ADS)
Takeshima, Tsuguhide; Takeuchi, Hiroshi; Egawa, Toru; Konaka, Shigehiro
2007-09-01
The molecular structure of cotinine (( S)-1-methyl-5-(3-pyridinyl)-2-pyrrolidinone), the major metabolite of nicotine, has been determined at about 182 °C by gas electron diffraction combined with MP2 and DFT calculations. The diffraction data are consistent with the existence of the (ax, sc), (ax, ap), (eq, sp) and (eq, ap) conformers, where ax and eq indicate the configuration of the pyrrolidinone ring by means of the position (axial and equatorial) of the pyridine ring, and sc, sp and ap distinguish the isomers arising from the internal rotation around the bond connecting the two rings. The (CH 3)NCCC(N) dihedral angles, ϕ, of the (ax, sc) and (eq, sp) conformers were determined independently to be 158(12)° and 129(13)°, respectively, where the numbers in parentheses are three times the standard errors, 3 σ. According to the MP2 calculations, the corresponding dihedral angles for the (ax, ap) and (eq, ap) conformers were assumed to differ by 180° from their syn counterparts. The ratios x(ax, sc)/ x(ax, ap) and x(eq, sp)/ x(eq, ap) were taken from the theoretically estimated free energy differences, Δ G, where x is the abundance of the conformer. The resultant abundances of (ax, sc), (ax, ap), (eq, sp) and (eq, ap) conformers are 34(6)%, 21% (d.p.), 28% (d.p.), and 17% (d.p.), respectively, where d.p. represents dependent parameters. The determined structural parameters ( rg (Å) and ∠ α (°)) of the most abundant conformer, (ax, sc), are as follows: r(N sbnd C) pyrrol = 1.463(5); r(N sbnd C methyl) = 1.457(←); r(N sbnd C( dbnd O)) = 1.384(12); r(C dbnd O) = 1.219(5); < r(C sbnd C) pyrrol> = 1.541(3); r(C pyrrolsbnd C pyrid) = 1.521(←); < r(C sbnd C) pyrid> = 1.396(2); < r(C sbnd N) pyrid> = 1.343(←); ∠(CNC) pyrrol = 113.9(11); ∠CCC pyrrol(-C pyrid) = 103.6(←); ∠NCO = 124.1(13); ∠NC pyrrolC pyrid = 113.1(12); ∠C pyrrolC pyrrolC pyrid = 113.3(←); ∠(CNC) pyrid = 117.1(2); <∠(NCC) pyrid> = 124.4(←); ∠C methylNC( dbnd O) =
NASA Astrophysics Data System (ADS)
Brawand, Nicholas; Vörös, Márton; Govoni, Marco; Galli, Giulia
The accurate prediction of optoelectronic properties of molecules and solids is a persisting challenge for current density functional theory (DFT) based methods. We propose a hybrid functional where the mixing fraction of exact and local exchange is determined by a non-empirical, system dependent function. This functional yields ionization potentials, fundamental and optical gaps of many, diverse systems in excellent agreement with experiments, including organic and inorganic molecules and nanocrystals. We further demonstrate that the newly defined hybrid functional gives the correct alignment between the energy level of the exemplary TTF-TCNQ donor-acceptor system. DOE-BES: DE-FG02-06ER46262.
Ishida, Toyokazu
2008-09-17
To further understand the catalytic role of the protein environment in the enzymatic process, the author has analyzed the reaction mechanism of the Claisen rearrangement of Bacillus subtilis chorismate mutase (BsCM). By introducing a new computational strategy that combines all-electron QM calculations with ab initio QM/MM modelings, it was possible to simulate the molecular interactions between the substrate and the protein environment. The electrostatic nature of the transition state stabilization was characterized by performing all-electron QM calculations based on the fragment molecular orbital technique for the entire enzyme.
Beare, Richard; Brown, Michael J. I.; Pimbblet, Kevin
2014-12-20
We describe an accurate new method for determining absolute magnitudes, and hence also K-corrections, that is simpler than most previous methods, being based on a quadratic function of just one suitably chosen observed color. The method relies on the extensive and accurate new set of 129 empirical galaxy template spectral energy distributions from Brown et al. A key advantage of our method is that we can reliably estimate random errors in computed absolute magnitudes due to galaxy diversity, photometric error and redshift error. We derive K-corrections for the five Sloan Digital Sky Survey filters and provide parameter tables for use by the astronomical community. Using the New York Value-Added Galaxy Catalog, we compare our K-corrections with those from kcorrect. Our K-corrections produce absolute magnitudes that are generally in good agreement with kcorrect. Absolute griz magnitudes differ by less than 0.02 mag and those in the u band by ∼0.04 mag. The evolution of rest-frame colors as a function of redshift is better behaved using our method, with relatively few galaxies being assigned anomalously red colors and a tight red sequence being observed across the whole 0.0 < z < 0.5 redshift range.
Nalli, Nicholas R; Minnett, Peter J; van Delst, Paul
2008-07-20
Although published sea surface infrared (IR) emissivity models have gained widespread acceptance for remote sensing applications, discrepancies have been identified against field observations obtained from IR Fourier transform spectrometers at view angles approximately > 40 degrees. We therefore propose, in this two-part paper, an alternative approach for calculating surface-leaving IR radiance that treats both emissivity and atmospheric reflection in a systematic yet practical manner. This first part presents the theoretical basis, development, and computations of the proposed model. PMID:18641735
Accurate calculation of the x-ray absorption spectrum of water via the GW/Bethe-Salpeter equation
NASA Astrophysics Data System (ADS)
Gilmore, Keith; Vinson, John; Kas, Josh; Vila, Fernando; Rehr, John
2014-03-01
We calculate x-ray absorption spectra (XAS) of water within the OCEAN code, which combines plane-wave, pseudopotential electronic structure, PAW transition elements, GW self-energy corrections, and the NIST BSE solver. Due to the computational demands of this approach, our initial XAS calculations were limited to 17 molecule super cells. This lead to unphysical, size dependent effects in the calculated spectra. To treat larger systems, we extended the OCEAN interface to support well-parallelized codes such as QuantumESPRESSO. We also implemented an efficient interpolation scheme of Shirley. We applied this large-scale GW/BSE approach to 64 molecule unit cell structures of water obtained from classical DFT/MD and PIMD simulations. In concurrence with previous work, we find the calculated spectrum both qualitatively and quantitatively reproduces the experimental features. The agreement implies that structures based on PIMD, which are similar to the traditional distorted tetrahedral view, are consistent with experimental observations. Supported by the DOE CMCSN through DOE award DE-SC0005180 (Princeton University) and in part by DOE Grant No. DE-FG03-97ER45623 (JJR) with computer support from NERSC.
NASA Astrophysics Data System (ADS)
Xu, Zhongnan; Joshi, Yogesh V.; Raman, Sumathy; Kitchin, John R.
2015-04-01
We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.
Xu, Zhongnan; Kitchin, John R.; Joshi, Yogesh V.; Raman, Sumathy
2015-04-14
We validate the usage of the calculated, linear response Hubbard U for evaluating accurate electronic and chemical properties of bulk 3d transition metal oxides. We find calculated values of U lead to improved band gaps. For the evaluation of accurate reaction energies, we first identify and eliminate contributions to the reaction energies of bulk systems due only to changes in U and construct a thermodynamic cycle that references the total energies of unique U systems to a common point using a DFT + U(V ) method, which we recast from a recently introduced DFT + U(R) method for molecular systems. We then introduce a semi-empirical method based on weighted DFT/DFT + U cohesive energies to calculate bulk oxidation energies of transition metal oxides using density functional theory and linear response calculated U values. We validate this method by calculating 14 reactions energies involving V, Cr, Mn, Fe, and Co oxides. We find up to an 85% reduction of the mean average error (MAE) compared to energies calculated with the Perdew-Burke-Ernzerhof functional. When our method is compared with DFT + U with empirically derived U values and the HSE06 hybrid functional, we find up to 65% and 39% reductions in the MAE, respectively.
NASA Technical Reports Server (NTRS)
Burr, D. M.; Emery, J. P.; Lorenz, R. D.
2005-01-01
The Cassini Imaging Science System (ISS) has been returning images of Titan, along with other Saturnian satellites. Images taken through the 938 nm methane window see down to Titan's surface. One of the purposes of the Cassini mission is to investigate possible fluid cycling on Titan. Lemniscate features shown recently and radar evidence of surface flow prompted us to consider theoretically the creation by methane fluid flow of streamlined forms on Titan. This follows work by other groups in theoretical consideration of fluid motion on Titan's surface.
Chikayama, Eisuke; Shimbo, Yudai; Komatsu, Keiko; Kikuchi, Jun
2016-04-14
NMR spectroscopy is a powerful method for analyzing metabolic mixtures. The information obtained from an NMR spectrum is in the form of physical parameters, such as chemical shifts, and construction of databases for many metabolites will be useful for data interpretation. To increase the accuracy of theoretical chemical shifts for development of a database for a variety of metabolites, the effects of sets of conformations (structural ensembles) and the levels of theory on computations of theoretical chemical shifts were systematically investigated for a set of 29 small molecules in the present study. For each of the 29 compounds, 101 structures were generated by classical molecular dynamics at 298.15 K, and then theoretical chemical shifts for 164 (1)H and 123 (13)C atoms were calculated by ab initio quantum chemical methods. Six levels of theory were used by pairing Hartree-Fock, B3LYP (density functional theory), or second order Møller-Plesset perturbation with 6-31G or aug-cc-pVDZ basis set. The six average fluctuations in the (1)H chemical shift were ±0.63, ± 0.59, ± 0.70, ± 0.62, ± 0.75, and ±0.66 ppm for the structural ensembles, and the six average errors were ±0.34, ± 0.27, ± 0.32, ± 0.25, ± 0.32, and ±0.25 ppm. The results showed that chemical shift fluctuations with changes in the conformation because of molecular motion were larger than the differences between computed and experimental chemical shifts for all six levels of theory. In conclusion, selection of an appropriate structural ensemble should be performed before theoretical chemical shift calculations for development of an accurate database for a variety of metabolites. PMID:26963288
NASA Astrophysics Data System (ADS)
Hsieh, Tiane-Jye; Su, Chia-Ching; Chen, Chung-Yi; Liou, Chyong-Huey; Lu, Li-Hwa
2005-05-01
Three natural products, Coumarin ( 1), p-hydroxybenzoic acid ( 2), trans-cinnamic acid ( 3) were isolated from the natural plant of indigenous cinnamon and the structures including relative stereochemistry were elucidated on the basis of spectroscopic data and theoretical calculations. Their sterochemical structures were determined by NMR spectroscopy, mass spectroscopy, and X-ray crystallography. The p-hydroxybenzoic acid complex with water is reported to show the existence of two hydrogen bonds. The two hydrogen bonds are formed in the water molecule of two hydrogen-accepting oxygen of carbonyl group of the p-hydroxybenzoic acid. The intermolecular interaction two hydrogen bond of the model system of the water- p-hydroxybenzoic acid was investigated. An experimental study and a theoretical analysis using the B3LYP/6-31G* method in the GAUSSIAN-03 package program were conducted on the three natural products. The theoretical results are supplemented by experimental data. Optimal geometric structures of three compounds were also determined. The calculated molecular mechanics compared quite well with those obtained from the experimental data. The ionization potentials, highest occupied molecular orbital energy, lowest unoccupied molecular orbital energy, energy gaps, heat of formation, atomization energies, and vibration frequencies of the compounds were also calculated. The results of the calculations show that three natural products are stable molecules with high reactive and various other physical properties. The study also provided an explicit understanding of the sterochemical structure and thermodynamic properties of the three natural products.
Karton, Amir; O'Reilly, Robert J; Radom, Leo
2012-04-26
Accurate electronic barrier heights are obtained for a set of nine proton-transfer tautomerization reactions, which are either (i) uncatalyzed, (ii) catalyzed by one water molecule, or (iii) catalyzed by two water molecules. The barrier heights for reactions (i) and (ii) are obtained by means of the high-level ab initio W2.2 thermochemical protocol, while those for reaction (iii) are obtained using the W1 protocol. These three sets of benchmark barrier heights allow an assessment of the performance of more approximate theoretical procedures for the calculation of barrier heights of uncatalyzed and water-catalyzed reactions. We evaluate initially the performance of the composite G4 procedure and variants thereof (e.g., G4(MP2) and G4(MP2)-6X), as well as that of standard ab initio procedures (e.g., MP2, SCS-MP2, and MP4). We find that the performance of the G4(MP2)-type thermochemical procedures deteriorates with the number of water molecules involved in the catalysis. This behavior is linked to deficiencies in the MP2-based basis-set-correction term in the G4(MP2)-type procedures. This is remedied in the MP4-based G4 procedure, which shows good performance for both the uncatalyzed and the water-catalyzed reactions, with mean absolute deviations (MADs) from the benchmark values lying below the threshold of "chemical accuracy" (arbitrarily defined as 1 kcal mol(-1) ≈ 4.2 kJ mol(-1)). We also examine the performance of a large number of density functional theory (DFT) and double-hybrid DFT (DHDFT) procedures. We find that, with few exceptions (most notably PW6-B95 and B97-2), the performance of the DFT procedures that give good results for the uncatalyzed reactions deteriorates with the number of water molecules involved in the catalysis. The DHDFT procedures, on the other hand, show excellent performance for both the uncatalyzed and catalyzed reactions. Specifically, almost all of them afford MADs below the "chemical accuracy" threshold, with ROB2-PLYP and B2K
Kanai, Y; Takeuchi, N
2009-10-14
We revisit the molecular line growth mechanism of styrene on the hydrogenated Si(001) 2x1 surface. In particular, we investigate the energetics of the radical chain reaction mechanism by means of diffusion quantum Monte Carlo (QMC) and density functional theory (DFT) calculations. For the exchange correlation (XC) functional we use the non-empirical generalized-gradient approximation (GGA) and meta-GGA. We find that the QMC result also predicts the intra dimer-row growth of the molecular line over the inter dimer-row growth, supporting the conclusion based on DFT results. However, the absolute magnitudes of the adsorption and reaction energies, and the heights of the energy barriers differ considerably between the QMC and DFT with the GGA/meta-GGA XC functionals.
Yamamoto, Atsushi; Matsui, Yasunori; Asada, Toshio; Kumeda, Motoki; Takagi, Kenichiro; Suenaga, Yu; Nagae, Kunihiko; Ohta, Eisuke; Sato, Hiroyasu; Koseki, Shiro; Naito, Hiroyoshi; Ikeda, Hiroshi
2016-04-15
The p-type organic semiconductor (OSC) material tetrathieno[2,3-a:3',2'-c:2″,3″-f:3‴,2‴-h]naphthalene (2TTN) and its alkyl-substituted derivatives Cn-2TTNs (n = 6, 8, and 10) have been developed based on the results of theoretical calculation-inspired investigation. A hole mobility for amorphous Cn-2TTNs (10(-2)-10(-3) cm(2) V(-1) s(-1)) was accurately predicted by using a novel statistical method in which the geometric mean of the mobilities for many individual small molecular flocks in an amorphous solid was obtained by using molecular mechanical molecular dynamics simulations and quantum chemical calculations. The simulation also suggests that upon increasing the length of alkyl chains in Cn-2TTNs the mobilities become smaller as a consequence of a decrease in transfer integral values. Cn-2TTNs are synthesized in a microflow reactor through photoreactions of the corresponding precursors. Cn-2TTNs are then utilized in the fabrication of organic field-effect transistors (OFETs). Although spin-coated thin films of Cn-2TTNs are crystalline, the hole mobilities (10(-2)-10(-3) cm(2) V(-1) s(-1)) of trial OFETs decrease upon elongation of the alkyl chains. This finding parallels the results of theoretical simulation. The simulation method for amorphous solids developed in this effort should become a useful tool in studies aimed at designing new OSC materials. PMID:27010327
Wood, R.F.; Wilson, T.M.
1981-01-01
The structure of the Hartree-Fock one-electron equations for simple point defects in ionic crystals are discussed. The importance of polarization effects due to the diffuse nature of the wavefunctions in the relaxed excited states are emphasized, and the usefulness of an effective mass approximation indicated. Several approaches to the calculation of the electronic structure are discussed and evaluated. The connection between electronic structure calculations and phonon perturbations are pointed out through a brief discussion of localized perturbation theory.
NASA Technical Reports Server (NTRS)
Mccluney, W. R.
1974-01-01
The development is considered of procedures for measuring a number of subsurface oceanographic parameters using remotely sensed ocean color data. It is proposed that the first step in this effort should be the development of adequate theoretical models relating the desired oceanographic parameters to the upwelling radiances to be observed. A portion of a contributory theoretical model is shown to be described by a modified single scattering approach based upon a simple treatment of multiple scattering. The resulting quasi-single scattering model can be used to predict the upwelling distribution of spectral radiance emerging from the sea. The shape of the radiance spectrum predicted by this model for clear ocean water shows encouraging agreement with measurments made at the edge of the Sargasso Sea off Cape Hatteras.
Theoretical calculations of emission of wolframite and scheelite-type tungstate crystals
Nikolaenko, T.; Hizhnyi, Y.; Nedilko, S.
2009-01-21
Tungstate crystals AWO{sub 4} (A = Zn,Cd,Pb) are well-known scintillation materials for various applications in science and technology. In recent years the optical properties of these crystals were intensively studied experimentally and theoretically. However, the origin of luminescence in lead, cadmium and zinc tungstates is still the subject of discussion. According to generally accepted view, the centers of luminescence in AWO{sub 4} crystals are in some or other way related to the tungstate anionic groups. We developed a cluster approach in theoretical investigation of the electronic structure of AWO{sub 4} tungstate crystals based on the configuration interaction (CI) computation in which the lattice vibrations were taken into account.
NASA Astrophysics Data System (ADS)
Badnell, N. R.; Spruck, K.; Krantz, C.; Novotný, O.; Becker, A.; Bernhardt, D.; Grieser, M.; Hahn, M.; Repnow, R.; Savin, D. W.; Wolf, A.; Müller, A.; Schippers, S.
2016-05-01
Experimentally measured and theoretically calculated rate coefficients for the recombination of W19 +([Kr ] 4 d10 4 f9 ) ions with free electrons (forming W18 +) are presented. At low electron-ion collision energies, the merged-beam rate coefficient is dominated by strong, mutually overlapping, recombination resonances as already found previously for the neighboring charge-state ions W18 + and W20 +. In the temperature range where W19 + is expected to form in a collisionally ionized plasma, the experimentally derived recombination rate coefficient deviates by up to a factor of about 20 from the theoretical rate coefficient obtained from the Atomic Data and Analysis Structure database. The present calculations, which employ a Breit-Wigner redistributive partitioning of autoionizing widths for dielectronic recombination via multi-electron resonances, reproduce the experimental findings over the entire temperature range.
Johnston, Ryne C.; Zhou, Jing; Smith, Jeremy C.; Parks, Jerry M.
2016-07-08
In redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. Moreover, a major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co ligand binding equilibrium constants (Kon/off), pKas and reduction potentials for models of aquacobalaminmore » in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for CoIII, CoII, and CoI species, respectively, and the second model features saturation of each vacant axial coordination site on CoII and CoI species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co axial ligand binding, leading to substantial errors in predicted
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
former. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861
Zhang, Xinyue; Lourenco, Daniela; Aguilar, Ignacio; Legarra, Andres; Misztal, Ignacy
2016-01-01
. Manhattan plots had higher resolution with 5 and 100 QTL. Using a common weight for a window of 20 SNP that sums or averages the SNP variance enhances accuracy of predicting GEBV and provides accurate estimation of marker effects. PMID:27594861
Johnston, Ryne C; Zhou, Jing; Smith, Jeremy C; Parks, Jerry M
2016-08-01
Redox processes in complex transition metal-containing species are often intimately associated with changes in ligand protonation states and metal coordination number. A major challenge is therefore to develop consistent computational approaches for computing pH-dependent redox and ligand dissociation properties of organometallic species. Reduction of the Co center in the vitamin B12 derivative aquacobalamin can be accompanied by ligand dissociation, protonation, or both, making these properties difficult to compute accurately. We examine this challenge here by using density functional theory and continuum solvation to compute Co-ligand binding equilibrium constants (Kon/off), pKas, and reduction potentials for models of aquacobalamin in aqueous solution. We consider two models for cobalamin ligand coordination: the first follows the hexa, penta, tetra coordination scheme for Co(III), Co(II), and Co(I) species, respectively, and the second model features saturation of each vacant axial coordination site on Co(II) and Co(I) species with a single, explicit water molecule to maintain six directly interacting ligands or water molecules in each oxidation state. Comparing these two coordination schemes in combination with five dispersion-corrected density functionals, we find that the accuracy of the computed properties is largely independent of the scheme used, but including only a continuum representation of the solvent yields marginally better results than saturating the first solvation shell around Co throughout. PBE performs best, displaying balanced accuracy and superior performance overall, with RMS errors of 80 mV for seven reduction potentials, 2.0 log units for five pKas and 2.3 log units for two log Kon/off values for the aquacobalamin system. Furthermore, we find that the BP86 functional commonly used in corrinoid studies suffers from erratic behavior and inaccurate descriptions of Co-axial ligand binding, leading to substantial errors in predicted pKas and
Hodder, Joanne N; La Delfa, Nicholas J; Potvin, Jim R
2016-08-01
To predict shoulder strength, most current ergonomics software assume independence of the strengths about each of the orthopedic axes. Using this independent axis approach (IAA), the shoulder can be predicted to have strengths as high as the resultant of the maximum moment about any two or three axes. We propose that shoulder strength is not independent between axes, and propose an approach that calculates the weighted average (WAA) between the strengths of the axes involved in the demand. Fifteen female participants performed maximum isometric shoulder exertions with their right arm placed in a rigid adjustable brace affixed to a tri-axial load cell. Maximum exertions were performed in 24 directions, including four primary directions, horizontal flexion-extension, abduction-adduction, and at 15° increments in between those axes. Moments were computed and comparisons made between the experimentally collected strengths and those predicted by the IAA and WAA methods. The IAA over-predicted strength in 14 of 20 non-primary exertions directions, while the WAA underpredicted strength in only 2 of these directions. Therefore, it is not valid to assume that shoulder axes are independent when predicting shoulder strengths between two orthopedic axes, and the WAA is an improvement over current methods for the posture tested. PMID:26145486
NASA Astrophysics Data System (ADS)
Rey, Michaël; Nikitin, Andrei V.; Tyuterev, Vladimir G.
2015-10-01
Accurate basis set convergence of first-principles predictions of rotationally resolved spectra at high energy range is a common challenging issue for variational methods. In this paper, a detailed convergence study for the methane spectra is presented both for vibrational and rotational degrees of freedom as well as for intensities. For this purpose, we use our previously reported nine-dimensional potential energy and dipole moment surfaces of the methane molecule [Nikitin et al. Chem Phys Lett 2011;501:179-86; 2013;565:5-11]. Vibration-rotation calculations were carried out using variational normal mode approach with a full account of the Td symmetry. The aim was to obtain accurate theoretical methane line lists for the wavenumber range beyond currently available spectra analyses. The focus of this paper is the complicated icosad range (6280-7900 cm-1) containing 20 bands and 134 sub-bands where over 90% of experimental lines still remain unassigned. We provide variational line lists converged to a "spectroscopic precision" for icosad transitions for T=80 K and T=296 K. The first one contains 70 300 lines and the second one 286 170 lines with the intensity cut-off 10-29cm-1 /(moleculecm-2) with Jmax=18. An average error in line positions of theoretical predictions up to J=15 is estimated as 0.2-0.5 cm-1 from the comparisons with currently analyzed bands. Ab initio line strength calculations give the integrated intensity 4.37 ×10-20cm-1 /(moleculecm-2) at T=80 K for the sum of all icosad bands. This is to be compared to the integrated intensity 4.36 ×10-20cm-1 /(moleculecm-2) of the experimental icosad line list recorded in Grenoble University [Campargue et al., J Mol Spectrosc 2013;291:16-22] using very sensitive laser techniques. The shapes of absorption bands are also in a good qualitative agreement with experimental spectra.
The Calculation of Theoretical Chromospheric Models and the Interpretation of the Solar Spectrum
NASA Technical Reports Server (NTRS)
Avrett, Eugene H.
1998-01-01
Since the early 1970s we have been developing the extensive computer programs needed to construct models of the solar atmosphere and to calculate detailed spectra for use in the interpretation of solar observations. This research involves two major related efforts: work by Avrett and Loeser on the Pandora computer program for non-LTE modeling of the solar atmosphere including a wide range of physical processes, and work by Rurucz on the detailed synthesis of the solar spectrum based on opacity data or over 58 million atomic and molecular lines. our goals are: to determine models of the various features observed on the Sun (sunspots, different components of quiet and active regions, and flares) by means of physically realistic models, and to calculate detailed spectra at all wavelengths that match observations of those features. These two goals are interrelated: discrepancies between calculated and observed spectra are used to determine improvements in the structure of the models, and in the detailed physical processes used in both the model calculations and the spectrum calculations. The atmospheric models obtained in this way provide not only the depth variation of various atmospheric parameters, but also a description of the internal physical processes that are responsible for non-radiative heating, and for solar activity in general.
Automated Routines for Calculating Whole-Stream Metabolism: Theoretical Background and User's Guide
Bales, Jerad D.; Nardi, Mark R.
2007-01-01
In order to standardize methods and facilitate rapid calculation and archival of stream-metabolism variables, the Stream Metabolism Program was developed to calculate gross primary production, net ecosystem production, respiration, and selected other variables from continuous measurements of dissolved-oxygen concentration, water temperature, and other user-supplied information. Methods for calculating metabolism from continuous measurements of dissolved-oxygen concentration and water temperature are fairly well known, but a standard set of procedures and computation software for all aspects of the calculations were not available previously. The Stream Metabolism Program addresses this deficiency with a stand-alone executable computer program written in Visual Basic.NET?, which runs in the Microsoft Windows? environment. All equations and assumptions used in the development of the software are documented in this report. Detailed guidance on application of the software is presented, along with a summary of the data required to use the software. Data from either a single station or paired (upstream, downstream) stations can be used with the software to calculate metabolism variables.
Theoretical calculation of the p-emitter length for snapback-free reverse-conducting IGBT
NASA Astrophysics Data System (ADS)
Liheng, Zhu; Xingbi, Chen
2014-06-01
A physically based equation for predicting required p-emitter length of a snapback-free reverse-conducting insulated gate bipolar transistor (RC-IGBT) with field-stop structure is proposed. The n-buffer resistances above the p-emitter region with anode geometries of linear strip, circular and annular type are calculated, and based on this, the minimum p-emitter lengths of those three geometries are given and verified by simulation. It is found that good agreement was achieved between the numerical calculation and simulation results. Moreover, the calculation results show that the annular case needs the shortest p-emitter length for RC-IGBT to be snapback-free.
Theoretical Calculation for the Ionization of Molecules by Short Strong Laser Pulses
Nagy, L.; Borbely, S.
2011-10-03
We have developed several calculation methods for the ionization of atoms and molecules by strong and ultrashort laser pulses, based on the numerical solution of the time dependent Schroedinger equation (TDSE) in the momentum space. We have performed calculations within the strong field approximation (Volkov) and using iterative and direct methods for solving the TDSE. The investigated molecules are H{sub 2}{sup +} and H{sub 2}O. In case of the ionization of diatomic molecules the interference effects in the ejected electron spectra due to the coherent addition of the waves associated to the electrons ejected from the vicinity of different nuclei were also analysed.
Vibrational spectra, structure, and theoretical calculations of 2-fluoro- and 3-fluoropyridine.
Boopalachandran, Praveenkumar; Laane, Jaan
2011-09-01
The infrared and Raman spectra of liquid and vapor-phase 2-fluoropyridine and 3-fluoropyridine have been recorded and assigned. Ab initio and DFT calculations were carried out to compute the molecular structures and to verify the vibrational assignments. The observed and calculated spectra agree extremely well. The ring bond distances of the fluoropyridines are very similar to those of pyridine except for a shortening of the C-N(F) bond in 2-fluoropyridine. The C-F bond stretching frequencies are similar to that in fluorobenzene reflecting the influence of the ring π bonding. PMID:21570895
Technology Transfer Automated Retrieval System (TEKTRAN)
Determination of absolute configuration (AC) is one of the most challenging features in the structure elucidation of chiral natural products, especially those with complex structures. With revolutionary advancements in the area of quantum chemical calculations of chiroptical spectroscopy over the pa...
NASA Astrophysics Data System (ADS)
Menapace, E.; Birattari, C.; Bonardi, M. L.; Groppi, F.; Morzenti, S.; Zona, C.
2005-05-01
The radionuclide production for biomedical applications has been brought up in the years, as a special nuclear application, at INFN LASA Laboratory, particularly in co-operation with the JRC-Ispra of EC. Mainly scientific aspects concerning radiation detection and the relevant instruments, the measurements of excitation functions of the involved nuclear reactions, the requested radiochemistry studies and further applications have been investigated. On the side of the nuclear data evaluations, based on nuclear model calculations and critically selected experimental data, the appropriate competence has been developed at ENEA Division for Advanced Physics Technologies. A series of high specific activity accelerator-produced radionuclides in no-carrier-added (NCA) form, for uses in metabolic radiotherapy and for PET radiodiagnostics, are investigated. In this work, last revised measurements and model calculations are reviewed for excitation functions of natZn(d,X)64Cu, 66Ga reactions, referring to irradiation experiments at K=38 variable energy Cyclotron of JRC-Ispra. Concerning the reaction data for producing 186gRe and 211At/211gPo (including significant emission spectra) and 210At, most recent and critically selected experimental results are considered and discussed in comparison with model calculations paying special care to pre-equilibrium effects estimate and to the appropriate overall parameterization. Model calculations are presented for 226Ra(p,2n)225Ac reaction, according to the working program of the ongoing IAEA CRP on the matter.
Menapace, E.; Birattari, C.; Bonardi, M.L.; Groppi, F.; Morzenti, S.; Zona, C.
2005-05-24
The radionuclide production for biomedical applications has been brought up in the years, as a special nuclear application, at INFN LASA Laboratory, particularly in co-operation with the JRC-Ispra of EC. Mainly scientific aspects concerning radiation detection and the relevant instruments, the measurements of excitation functions of the involved nuclear reactions, the requested radiochemistry studies and further applications have been investigated. On the side of the nuclear data evaluations, based on nuclear model calculations and critically selected experimental data, the appropriate competence has been developed at ENEA Division for Advanced Physics Technologies. A series of high specific activity accelerator-produced radionuclides in no-carrier-added (NCA) form, for uses in metabolic radiotherapy and for PET radiodiagnostics, are investigated. In this work, last revised measurements and model calculations are reviewed for excitation functions of natZn(d,X)64Cu, 66Ga reactions, referring to irradiation experiments at K=38 variable energy Cyclotron of JRC-Ispra. Concerning the reaction data for producing 186gRe and 211At/211gPo (including significant emission spectra) and 210At, most recent and critically selected experimental results are considered and discussed in comparison with model calculations paying special care to pre-equilibrium effects estimate and to the appropriate overall parameterization. Model calculations are presented for 226Ra(p,2n)225Ac reaction, according to the working program of the ongoing IAEA CRP on the matter.
Technology Transfer Automated Retrieval System (TEKTRAN)
Several flux-calculation (FC) schemes are available for determining soil-to-atmosphere emissions of nitrous oxide (N2O) and other trace gases using data from non-steady-state flux chambers. Recently developed methods claim to provide more accuracy in estimating the true pre-deployment flux (f0) comp...
Theoretical calculation of low-lying states of NaAr and NaXe
NASA Technical Reports Server (NTRS)
Laskowski, B. C.; Langhoff, S. R.; Stallcop, J. R.
1981-01-01
Potential curves as well as dipole moments and linking transition moments are calculated for the ground X 2 Sigma + and low lying excited A 2 Pi, B 2 Sigma +, C 2 Sigma +, (4) 2 Sigma +, (2) 2 Pi and (1) 2 Delta states of NaAr and NaXe. Calculations are performed using a self-consistent field plus configuration-interaction procedure with the core electrons replaced by an ab initio effective core potential. The potential curves obtained are found to be considerably less repulsive than the semiempirical curves of Pascale and Vandeplanque (1974) and to agree well with existing experimental data, although the binding energies of those states having potential minima due to van der Waals interactions are underestimated. Emission bands are also calculated for the X 2 Sigma + - C 2 Sigma + excimer transitions of NaAr and NaXe using the calculated transition moments and potential curves, and shown to agree well with experiment on the short-wavelength side of the maximum.
Calculations of band gaps in polyaniline from theoretical studies of oligomers
Kwon, O.; McKee, M.L.
2000-03-02
Geometries and band gaps of polyaniline oligomers up to decamer have been systematically calculated and analyzed using various computational techniques such as molecular mechanics, semiempirical, and ab initio methods. On the basis of fully optimized geometries of neural and charged forms of polyaniline oligomers, excitation energies are calculated at the semiempirical ZINDO (INDO/S) level and extrapolated to the band gap value of the infinite chain. Band gaps are also approximately by extrapolating the HOMO/LUMO difference calculated at the density functional level (B3LYP/6--31G*). The SINDO//AM1 band gaps in the reduced and oxidized form of polyaniline (4.3 and 2.7 eV) are in good agreement with experimental values (3.8 {+-} 2 and 1.8 {+-} 3 eV, respectively). The doped form of polyaniline (two positive charges per four aniline units) has been computed with a spin-unrestricted method (UAM1) and the band gap approximated from an extrapolation of the tetramer and octamer. The calculated band gap of 1.3 eV (UZINDO//UAM1) is in good agreement with experiment (1.5 eV). The influence of ring torsional angle and interchain interaction on the band gap of the polyaniline system are also discussed.
The three-fold theoretical basis of the Gravity Probe B gyro precession calculation
NASA Astrophysics Data System (ADS)
Adler, Ronald J.
2015-11-01
The Gravity Probe B (GP-B) experiment is complete and the results are in agreement with the predictions of general relativity (GR) for both the geodetic precession, 6.6 arcsec yr-1 to about 0.3%, and the Lense-Thirring precession, 39 marcsec to about 19%. This note is concerned with the theoretical basis for the predictions. The predictions depend on three elements of gravity theory, firstly that macroscopic gravity is described by a metric theory such as GR, secondly that the Lense-Thirring metric provides an approximate description of the gravitational field of the spinning Earth, and thirdly that the spin axis of a gyroscope is parallel displaced in spacetime, which gives its equation of motion. We look at each of these three elements to show how each is solidly based on previous experiments and well-tested theory. The agreement of GP-B with theory strengthens our belief that all three elements are correct and increases our confidence in applying GR to astrophysical phenomena. Conversely, if GP-B had not verified the predictions a major theoretical quandary would have occurred.
NASA Astrophysics Data System (ADS)
Latgé, A.; Porras-Montenegro, N.; de Dios-Leyva, M.; Oliveira, L. E.
1997-05-01
The acceptor-related photoluminescence of a GaAs-(Ga,Al)As superlattice, under the influence of a magnetic field applied parallel to the interfaces, is theoretically studied following a variational procedure within the effective-mass approximation. Electron and hole magnetic Landau levels and envelope wave functions were obtained by an expansion in terms of sine functions, whereas for the impurity levels the envelope functions were taken as products of sine and hydrogenic-like variational functions. Impurity binding energies and wave functions are obtained for acceptors at a general position in the superlattice and for different in-plane magnetic fields. Theoretical results corresponding to transitions from the conduction subband to states of acceptors (miniband-to-acceptor e-A0 transitions) at the edge and center positions of the GaAs quantum well compare well with available experimental data by Skromme et al. [Phys. Rev. Lett. 65, 2050 (1990)] on the magnetic-field dependence of the photoluminescence peak position of conduction miniband-to-acceptor transitions for different temperatures and values of the superlattice period.
Method and Basis Set Analysis of Oxorhenium(V) Complexes for Theoretical Calculations
Demoin, Dustin Wayne; Li, Yawen; Jurisson, Silvia S.; Deakyne, Carol A.
2012-01-01
A variety of method and basis set combinations has been evaluated for monooxorhenium(V) complexes with N, O, P, S, Cl, and Se donor atoms. The geometries and energies obtained are compared to both high-level computations and literature structures. These calculations show that the PBE0 method outperforms the B3LYP method with respect to both structure and energetics. The combination of 6-31G** basis set on the nonmetal atoms and LANL2TZ effective core potential on the rhenium center gives reliable equilibrium structures with minimal computational resources for both model and literature compounds. Single-point energy calculations at the PBE0/LANL2TZ,6-311+G* level of theory are recommended for energetics. PMID:23087847
Millimeterwave rotational spectrum and theoretical calculations of cis-propionic acid
NASA Astrophysics Data System (ADS)
Jaman, A. I.; Chakraborty, Shamik; Chakraborty, Rangana
2015-01-01
The millimeterwave rotational spectra of the cis conformer of propionic acid (C3H6O2) have been investigated in the ground vibrational state in the frequency range of 80.0-100.0 GHz. Many high J and K-1 (Jmax = 50, K-1 = 12) rotational lines have been assigned. A least-squares analysis of the measured and previously reported rotational transition frequencies resulted in the determination of an improved set of rotational and centrifugal distortion (CD) constants of the molecule. Detailed MP2 and DFT calculations were also carried out with various functional and basis sets to evaluate the spectroscopic constants, dipole moment, and various structural parameters of cis-propionic acid and compared with the corresponding experimental values. Potential energy surface has been calculated to identify other probable conformers in this molecule.
Theoretical Calculations of Refractive Properties for Hg3Te2Cl2 Crystals
NASA Astrophysics Data System (ADS)
Bokotey, O. V.
2016-05-01
This paper reviews the optical properties, such as refractive index, optical dielectric constant, and reflection coefficient of the Hg3Te2Cl2 crystals. The applications of the Hg3X2Y2 crystals as electronic, optical, and optoelectronic devices are very much determined by the nature and magnitude of these fundamental material properties. The origin of chemical bonding in the crystals is very important for definition of the physical and chemical properties. The main structural feature of the Hg3X2Y2 crystals is the presence of covalent pyramids [XHg3] and linear X-Hg-X groups. Optical properties are calculated according to the model proposed by Harrison. The refractive index in the spectral region far from the absorption edge is determined within the generalized single-oscillator model. The calculated results are found to be in good agreement with experimental data.
Theoretical Calculations of Refractive Properties for Hg3Te2Cl2 Crystals.
Bokotey, O V
2016-12-01
This paper reviews the optical properties, such as refractive index, optical dielectric constant, and reflection coefficient of the Hg3Te2Cl2 crystals. The applications of the Hg3X2Y2 crystals as electronic, optical, and optoelectronic devices are very much determined by the nature and magnitude of these fundamental material properties. The origin of chemical bonding in the crystals is very important for definition of the physical and chemical properties. The main structural feature of the Hg3X2Y2 crystals is the presence of covalent pyramids [XHg3] and linear X-Hg-X groups. Optical properties are calculated according to the model proposed by Harrison. The refractive index in the spectral region far from the absorption edge is determined within the generalized single-oscillator model. The calculated results are found to be in good agreement with experimental data. PMID:27184964
NASA Astrophysics Data System (ADS)
Ghazzali, Mohamed; Khattab, Sherine A. N.; Elnakady, Yasser A.; Al-Mekhlafi, Fahd A.; Al-Farhan, Khalid; El-Faham, Ayman
2013-08-01
A series of naphthyl and tolyl sulfonate ester were synthesized and characterized by H NMR. X-ray single crystal diffraction experiments established the molecular structure of three new sulfonate esters derivatives, and spectral data agree with these in solution. The observed hydrogen bonding is discussed on the basis of crystal structural analyses and DFT/MP2 geometry optimization quantum calculations. Antimicrobial activities were screened for selected compounds against three human cancer cell lines and Mosquito Culex pipiens larvae.
Shen, Ming; Roopchand, Rabia; Amoureux, Jean-Paul; Chen, Qun
2015-01-01
Quadrupolar echo NMR spectroscopy of solids often requires RF pulse excitation that covers spectral widths exceeding 100 kHz. In a recent work we found out that a four pulse, composite pulse COM-II ( 90180¯90135¯45 ), provided robust broadband excitation for deuterium quadrupolar echo spectroscopy. Moreover, when combined with an eight step phase cycle, spectral distortions arising from finite pulse widths were greatly supressed. In this paper we report on a theoretical analysis COM-II with 8-step phase cycle by average Hamiltonian theory. This treatment is combined with the fictitious spin-1 operator formalism, and the mechanism of the 8-step phase cycling that minimizes the spectral distortions is discussed. PMID:26681896
Silva, Mateus X; Galvão, Breno R L; Belchior, Jadson C
2014-05-21
Genetic algorithm is employed to survey an empirical potential energy surface for small Na(x)K(y) clusters with x + y ≤ 15, providing initial conditions for electronic structure methods. The minima of such empirical potential are assessed and corrected using high level ab initio methods such as CCSD(T), CR-CCSD(T)-L and MP2, and benchmark results are obtained for specific cases. The results are the first calculations for such small alloy clusters and may serve as a reference for further studies. The validity and choice of a proper functional and basis set for DFT calculations are then explored using the benchmark data, where it was found that the usual DFT approach may fail to provide the correct qualitative result for specific systems. The best general agreement to the benchmark calculations is achieved with def2-TZVPP basis set with SVWN5 functional, although the LANL2DZ basis set (with effective core potential) and SVWN5 functional provided the most cost-effective results. PMID:24691391
Theoretical calculations of ion acceleration in the vicinity of comet Giacobini-Zinner
NASA Technical Reports Server (NTRS)
Mckenzie, M. L.; Cravens, T. E.; Ye, G.
1994-01-01
Ionization of cometary neutral molecules produces ions which are picked up by the solar wind. The cometary ion pickup process for comet Giacobini-Zinner is studied in two ways: (1) with a test particle method in which trajectories are numerically calculated for several thousand ions whose initial locations were chosen randomly with probability proportional to the neutral density and (2) with a quasi-linear diffusion model. The cometary ion distribution function was calculated with the test particle model at several locations upstream of the bow shock and for several types of magnetic fluctuations (or waves). These waves were allowed to propagate in both directions along the magnetic field at the Alfven speed. Both pitch angle scattering and energy diffusion are evident in the derived ion distributions. The monochromatic waves result in less ion acceleration than turbulent fluctuations with about the same amplitude. The calculated ion distribution functions are in reasonable agreement with the distributions measured in the vicinity of comet Giacobini-Zinner in 1985 by particle detectors on the ICE spacecraft when the ratio of power in sunward propagating Alfven waves to the power in antisunward propagating waves is assumed to lie between about 20% and 50%. However, the quasi-linear diffusion model results agree best with the measured distribution functions when the power ratio is only about 3 percent.
Theoretical calculations on structural and electronic properties of BGaAsBi alloys
NASA Astrophysics Data System (ADS)
Aslan, Metin; Yalcin, Battal G.; Ustundag, Mehmet; Bagci, Sadik
2015-11-01
The structural and electronic properties of cubic B x Ga1- x As1- y Bi y alloys with bismuth (Bi) concentration of 0.0625, 0.125, 0.1875 and 0.25 are studied with various boron (B) compositions by means of density functional theory (DFT) within the Wu-Cohen (WC) exchange correlation potential based on generalized gradient approximation (GGA). For all studied alloy structures, we have implemented geometric optimization before the volume optimization calculations. The obtained equilibrium lattice constants and band gap of studied quaternary alloys are investigated for the first time in literature. While the lattice constant behavior changes linearly with boron concentration, increasing small amount of bismuth concentration alter the lattice constant nonlinearly. The present calculation shows that the band gap decreases with increasing bismuth concentration and direct band gap semiconductor alloy became an indirect band gap with increasing boron concentration. From the band offset calculation we have shown that increasing B and Bi concentration in host GaAs reduced the valance band offset in a heterostructure formed by GaAs and studied alloys.
Breiner, Joan; Gimeno, Benjamin S; Fenn, Mark
2007-01-01
Edaphic, foliar, and hydrologic forest nutrient status indicators from 15 mixed conifer forest stands in the Sierra Nevada, San Gabriel Mountains, and San Bernardino National Forest were used to estimate empirical or theoretical critical loads (CL) for nitrogen (N) as a nutrient. Soil acidification response to N deposition was also evaluated. Robust empirical relationships were found relating N deposition to plant N uptake (N in foliage), N fertility (litter C/N ratio), and soil acidification. However, no consistent empirical CL were obtained when the thresholds for parameters indicative of N excess from other types of ecosystems were used. Similarly, the highest theoretical CL for nutrient N calculated using the simple mass balance steady state model (estimates ranging from 1.4-8.8 kg N/ha/year) was approximately two times lower than the empirical observations. Further research is needed to derive the thresholds for indicators associated with the impairment of these mixed conifer forests exposed to chronic N deposition within a Mediterranean climate. Further development or parameterization of models for the calculation of theoretical critical loads suitable for these ecosystems will also be an important aspect of future critical loads research. PMID:17450298
Theoretical Model for the Calculation of Optical Properties of Gold Nanoparticles
NASA Astrophysics Data System (ADS)
Mendoza-García, A.; Romero-Depablos, A.; Ortega, M. A.; Paz, J. L.; Echevarría, L.
We have developed an analytical method to describe the optical properties of nanoparticles, whose results are in agreement with the observed experimental behavior according to the size of the nanoparticle under analysis. Our considerations to describe plasmonic absorption and dispersion are based on the combination of the two-level molecular system and the two-dimensional quantum box models. Employing the optical stochastic Bloch equations, we have determined the system's coherence, from which we have calculated expressions for the absorption coefficient and refractive index. The innovation of this methodology is that it allows us to take into account the solvent environment, which induce quantum effects not considered by classical treatments.
NASA Technical Reports Server (NTRS)
Avrett, E. H.
1985-01-01
Solar chromospheric models are described. The models included are based on the observed spectrum, and on the assumption of hydrostatic equilibrium. The calculations depend on realistic solutions of the radiative transfer and statistical equilibrium equations for optically thick lines and continua, and on including the effects of large numbers of lines throughout the spectrum. Although spectroheliograms show that the structure of the chromosphere is highly complex, one-dimensional models of particular features are reasonably successful in matching observed spectra. Such models were applied to the interpretation of chromospheric observations.
NASA Astrophysics Data System (ADS)
Arroudj, S.; Bouchouit, M.; Bouchouit, K.; Bouraiou, A.; Messaadia, L.; Kulyk, B.; Figa, V.; Bouacida, S.; Sofiani, Z.; Taboukhat, S.
2016-06-01
This paper explores the synthesis, structure characterization and optical properties of two new schiff bases. These compounds were obtained by condensation of o-tolidine with salicylaldehyde and cinnamaldehyde. The obtained ligands were characterized by UV, 1H and NMR. Their third-order NLO properties were measured using the third harmonic generation technique on thin films at 1064 nm. The electric dipole moment (μ), the polarizability (α) and the first hyperpolarizability (β) were calculated using the density functional B3LYP method with the lanl2dz basis set. For the results, the title compound shows nonzero β value revealing second order NLO behaviour.
NASA Astrophysics Data System (ADS)
Zhidong, Zhang; Zhiguang, Li; Jingli, Liu
The temperature-dependent pitch of a cholesteric phase is studied using both molecular field theory and the two-particle cluster theory. The interacting chiral molecules (as derived by van der Meer et al.) are placed at the sites of a three-dimensional, simple cubic lattice with orientations confined to two dimensions. The equilibrium pitch as functions of temperature is calculated and numerical results are compared with those predicted by Monte Carlo computer simulation. The two-particle cluster theory, taking into account short-range correlations between molecules, yields improved values compared with molecular field theory.
Munson, D.E.; Holcomb, D.J.; DeVries, K.L.; Brodsky, N.S.
1994-12-31
Cross-hole ultrasonic measurements were made in the immediate wall of the Air Intake Shaft of the Waste Isolation Pilot Plant facility. These measurements show that compressional wave speed markedly decreases at the shaft wall and then increases with radial distance from the shaft to eventually become that of solid or undamaged salt. This behavior is indicative of deformation damage or microfractures in the salt. These in situ data are compared to both laboratory measurements of wave speed as a function of volume dilatancy and to calculations based on the Multimechanism Deformation Coupled Fracture model, with reasonable agreement.
NASA Astrophysics Data System (ADS)
Kostko, Oleg; Troy, Tyler P.; Bandyopadhyay, Biswajit; Ahmed, Musahid
2015-03-01
Acetaldehyde, a probable human carcinogen and of environmental importance, upon solvation provides a test bed for understanding proton transfer pathways and catalytic mechanisms. In this study, we report on single photon vacuum ultraviolet photoionization of small acetaldehyde and acetaldehyde-water clusters. Appearance energies of protonated clusters are extracted from the experimental photoionization efficiency curves and compared to electronic structure calculations. The comparison of experimental data to computational results provides mechanistic insight into the fragmentation mechanisms of the observed mass spectra. Using deuterated water for isotopic tagging, we observe that proton transfer is mediated via acetaldehyde and not water in protonated acetaldehyde-water clusters.
Theoretical Calculations of the Catalytic Triad in Short-Chain Alcohol Dehydrogenases/Reductases
Gani, Osman A. B. S. M.; Adekoya, Olayiwola A.; Giurato, Laura; Spyrakis, Francesca; Cozzini, Pietro; Guccione, Salvatore; Winberg, Jan-Olof; Sylte, Ingebrigt
2008-01-01
Three highly conserved active site residues (Ser, Tyr, and Lys) of the family of short-chain alcohol dehydrogenases/reductases (SDRs) were demonstrated to be essential for catalytic activity and have been denoted the catalytic triad of SDRs. In this study computational methods were adopted to study the ionization properties of these amino acids in SDRs from Drosophila melanogaster and Drosophila lebanonensis. Three enzyme models, with different ionization scenarios of the catalytic triad that might be possible when inhibitors bind to the enzyme cofactor complex, were constructed. The binding of the two alcohol competitive inhibitors were studied using automatic docking by the Internal Coordinate Mechanics program, molecular dynamic (MD) simulations with the AMBER program package, calculation of the free energy of ligand binding by the linear interaction energy method, and the hydropathic interactions force field. The calculations indicated that deprotonated Tyr acts as a strong base in the binary enzyme-NAD+ complex. Molecular dynamic simulations for 5 ns confirmed that deprotonated Tyr is essential for anchoring and orientating the inhibitors at the active site, which might be a general trend for the family of SDRs. The findings here have implications for the development of therapeutically important SDR inhibitors. PMID:17981907
NASA Astrophysics Data System (ADS)
Barabash, Sergey V.; Pramanik, Dipankar
2015-03-01
Development of low-leakage dielectrics for semiconductor industry, together with many other areas of academic and industrial research, increasingly rely upon ab initio tunneling and transport calculations. Complex band structure (CBS) is a powerful formalism to establish the nature of tunneling modes, providing both a deeper understanding and a guided optimization of materials, with practical applications ranging from screening candidate dielectrics for lowest ``ultimate leakage'' to identifying charge-neutrality levels and Fermi level pinning. We demonstrate that CBS is prone to a particular type of spurious ``phantom'' solution, previously deemed true but irrelevant because of a very fast decay. We demonstrate that (i) in complex materials, phantom modes may exhibit very slow decay (appearing as leading tunneling terms implying qualitative and huge quantitative errors), (ii) the phantom modes are spurious, (iii) unlike the pseudopotential ``ghost'' states, phantoms are an apparently unavoidable artifact of large numerical basis sets, (iv) a presumed increase in computational accuracy increases the number of phantoms, effectively corrupting the CBS results despite the higher accuracy achieved in resolving the true CBS modes and the real band structure, and (v) the phantom modes cannot be easily separated from the true CBS modes. We discuss implications for direct transport calculations. The strategy for dealing with the phantom states is discussed in the context of optimizing high-quality high- κ dielectric materials for decreased tunneling leakage.
NASA Technical Reports Server (NTRS)
Avrett, E. H.
1986-01-01
Calculated results based on two chromospheric flare models F1 and F2 of Machado, et al., (1980) are presented. Two additional models are included: F1*, which has enhanced temperatures relative to the weak-flare model F1 in the upper photosphere and low chromosphere, and F3 which has enhanced temperatures relative to the strong flare model F2 in the upper chromosphere. Each model is specified by means of a given variation of the temperature as a function of column mass. The corresponding variation of particle density and the geometrical height scale are determined by assuming hydrostatic equilibrium. The coupled equations of statistical equilibrium is solved as is radiative transfer for H, H-, He I-II, C I-IV, Si I-II, Mg I-II, Fe, Al, O I-II, Na, and Ca II. The overall absorption and emission of radiation by lines throughout the spectrum is determined by means of a reduced set of opacities sampled from a compilation of over 10 to the 7th power individual lines. That the white flight flare continuum may arise by extreme chromospheric overheating as well as by an enhancement of the minimum temperature region is also shown. The radiative cooling rate calculations for our brightest flare model suggest that chromospheric overheating provides enhanced radiation that could cause significant heating deep in the flare atmosphere.
NASA Technical Reports Server (NTRS)
Fernando, G. W.; Cooper, B. R.; Ramana, M. V.; Krakauer, H.; Ma, C. Q.
1986-01-01
An accurate and efficient film linearized muffin-tin orbital (FLMTO) technique for surface electronic-structure calculations is presented which uses only 60-70 basis functions, as opposed to the 300 functions used in the linear augmented plane-wave method. Calculations for three different (3d and 4d) transition-metal films resulted in high quality results for five-layer slabs of Cu(001), Fe(001), and Ru(001), in addition to good results for the work functions and projected density of states. By retaining the LMTO small basis size, computer time and memory are reduced, making practical the study of systems with a larger number of atoms in the two-dimensional unit cell.
Hoff, R.W.; Gardner, D.G.; Gardner, M.A.
1984-10-05
A technique for modeling quasiparticle excitation energies and rotational parameters in odd-odd deformed nuclei has been used to construct sets of discrete states with energy 0 to 1.5 MeV in /sup 176/Lu and /sup 236/Np. These data were used as part of the input for calculation of isomer production cross-section ratios in the /sup 175/Lu(n,..gamma..)/sup 176/Lu and /sup 237/Np(n,2n)/sup 236/Np reactions. In order to achieve agreement with experiment, it has been found necessary to include in the modeled set many rotational bands (35 to 95), which are comprised of hundreds of levels with their gamma-ray branching ratios. It is essential that enough bands be included to produce a representative selection of K quantum numbers in the de-excitation cascade. 20 refs., 3 figs., 3 tabs.
NASA Astrophysics Data System (ADS)
Jin, R. Y.; Sun, X. H.; Liu, Y. F.; Long, W.; Chen, B.; Shen, S. Q.; Ma, H. X.
2016-01-01
Series of isoxazole derivatives were synthesized by substituted chalcones and 2-chloro-6-fluorobenzene formaldehyde oxime with 1,3-dipolar cycloaddition. The target compounds were determined by melting point, IR, 1H NMR, elemental analyses and HRMS. The crystal structure of compound 3a was detected by X-ray diffraction and it crystallizes in the triclinic space group p2(1)/c with z = 4. The molecular geometry of compound 3a was optimized using density functional theory (DFT/B3LYP) method with the 6-31G+(d,p) basis set in the ground state. From the optimized geometry of the molecule, FT-IR, FT-Raman, HOMO-LUMO and natural bond orbital (NBO) were calculated at B3LYP/6-31G+(d,p) level. Finally, the antifungal activity of the synthetic compounds were evaluated against Pythium solani, Gibberella nicotiancola, Fusarium oxysporium f.sp. niveum and Gibberella saubinetii.
Jin, R Y; Sun, X H; Liu, Y F; Long, W; Chen, B; Shen, S Q; Ma, H X
2016-01-01
Series of isoxazole derivatives were synthesized by substituted chalcones and 2-chloro-6-fluorobenzene formaldehyde oxime with 1,3-dipolar cycloaddition. The target compounds were determined by melting point, IR, (1)H NMR, elemental analyses and HRMS. The crystal structure of compound 3a was detected by X-ray diffraction and it crystallizes in the triclinic space group p2(1)/c with z=4. The molecular geometry of compound 3a was optimized using density functional theory (DFT/B3LYP) method with the 6-31G+(d,p) basis set in the ground state. From the optimized geometry of the molecule, FT-IR, FT-Raman, HOMO-LUMO and natural bond orbital (NBO) were calculated at B3LYP/6-31G+(d,p) level. Finally, the antifungal activity of the synthetic compounds were evaluated against Pythium solani, Gibberella nicotiancola, Fusarium oxysporium f.sp. niveum and Gibberella saubinetii. PMID:26218917
Theoretical method for calculating relative joint geometry of assembled robot arms
NASA Technical Reports Server (NTRS)
Barker, L. K.; Moore, M. C.
1983-01-01
Equations are developed to extract the relative joint parameters of an assembled robot arm. Specifically, the Denavit-Hartenberg parameters, which completely characterize the relative joint geometry, are calculated. These parameters are needed to control the hand of the robot arm by resolved rate. As an example, the parameter extraction equations are used with perfect simulated data (no measurement noise) obtained from a mathematical model of a six-degree-of-freedom robot arm. For an actual application, measurement data needed to estimate the relative joint parameters can be generated by moving a robot arm to different positions, measuring the location of the hand (or other extension) in base coordinates, and recording the corresponding joint angles.
NASA Astrophysics Data System (ADS)
Jones, Jasmine; Zhang, Rui; Heins, David; Castle, Katherine
In postmastectomy radiotherapy, an increasing number of patients have tissue expanders inserted subpectorally when receiving immediate breast reconstruction. These tissue expanders are composed of silicone and are inflated with saline through an internal metallic port; this serves the purpose of stretching the muscle and skin tissue over time, in order to house a permanent implant. The issue with administering radiation therapy in the presence of a tissue expander is that the port's magnetic core can potentially perturb the dose delivered to the Planning Target Volume, causing significant artifacts in CT images. Several studies have explored this problem, and suggest that density corrections must be accounted for in treatment planning. However, very few studies accurately calibrated commercial TP systems for the high density material used in the port, and no studies employed fusion imaging to yield a more accurate contour of the port in treatment planning. We compared depth dose values in the water phantom between measurement and TPS calculations, and we were able to overcome some of the inhomogeneities presented by the image artifact by fusing the KVCT and MVCT images of the tissue expander together, resulting in a more precise comparison of dose calculations at discrete locations. We expect this method to be pivotal in the quantification of dose distribution in the PTV. Research funded by the LS-AMP Award.
Coello Pérez, Eduardo A.; Papenbrock, Thomas F.
2015-07-27
In this paper, we present a model-independent approach to electric quadrupole transitions of deformed nuclei. Based on an effective theory for axially symmetric systems, the leading interactions with electromagnetic fields enter as minimal couplings to gauge potentials, while subleading corrections employ gauge-invariant nonminimal couplings. This approach yields transition operators that are consistent with the Hamiltonian, and the power counting of the effective theory provides us with theoretical uncertainty estimates. We successfully test the effective theory in homonuclear molecules that exhibit a large separation of scales. For ground-state band transitions of rotational nuclei, the effective theory describes data well within theoretical uncertainties at leading order. To probe the theory at subleading order, data with higher precision would be valuable. For transitional nuclei, next-to-leading-order calculations and the high-precision data are consistent within the theoretical uncertainty estimates. In addition, we study the faint interband transitions within the effective theory and focus on the E2 transitions from the 0_{2}^{+} band (the “β band”) to the ground-state band. Here the predictions from the effective theory are consistent with data for several nuclei, thereby proposing a solution to a long-standing challenge.
Crystalline Ice as a Cryoprotectant: Theoretical Calculation of Cooling Speed in Capillary Tubes
Yakovlev, Sergey; Downing, Kenneth H.
2014-01-01
It is generally assumed that vitrification of both cells and the surrounding medium provides the best preservation of ultrastructure of biological material for study by electron microscopy. At the same time it is known that the cell cytoplasm may provide substantial cryoprotection for internal cell structure even when the medium crystallizes. Thus vitrification of the medium is not essential for good structural preservation. In contrast, a high cooling rate is an essential factor for good cryopreservation because it limits phase separation and movement of cellular components during freezing, thus preserving the native-like state. Here we present calculations of freezing rates that incorporate the effect of medium crystallization, using finite difference methods. We demonstrate that crystallization of the medium in capillary tubes may increase the cooling rate of suspended cells by a factor of 25-300 depending on the distance from the center. We conclude that crystallization of the medium, for example due to low cryoprotectant content, may actually improve cryopreservation of some samples in a near native state. PMID:21534954
Theoretical Calculations of Supersonic Wave Drag at Zero Lift for a Particular Store Arrangement
NASA Technical Reports Server (NTRS)
Margolis, Kenneth; Malvestuto, Frank S , Jr; Maxie, Peter J , Jr
1958-01-01
An analysis, based on the linearized thin-airfoil theory for supersonic speeds, of the wave drag at zero lift has been carried out for a simple two-body arrangement consisting of two wedgelike surfaces, each with a rhombic lateral cross section and emanating from a common apex. Such an arrangement could be used as two stores, either embedded within or mounted below a wing, or as auxiliary bodies wherein the upper halves could be used as stores and the lower halves for bomb or missile purposes. The complete range of supersonic Mach numbers has been considered and it was found that by orienting the axes of the bodies relative to each other a given volume may be redistributed in a manner which enables the wave drag to be reduced within the lower supersonic speed range (where the leading edge is substantially subsonic). At the higher Mach numbers, the wave drag is always increased. If, in addition to a constant volume, a given maximum thickness-chord ratio is imposed, then canting the two surfaces results in higher wave drag at all Mach numbers. For purposes of comparison, analogous drag calculations for the case of two parallel winglike bodies with the same cross-sectional shapes as the canted configuration have been included. Consideration is also given to the favorable (dragwise) interference pressures acting on the blunt bases of both arrangements.
Burns, R.M.; Hubbard, J.L.; McCullough, E.A. Jr.
1995-12-01
X-ray structural characterization of a series of CpRu(NE)LL` complexes (Cp = cyclopentadieny), C{sub 5}R{sub 5}; L, L` = ligand; E = O, S) reveals systematic trends in the coordination conformation of the cyclopentadienyl ligand. The thionitrosyl complex (C{sub 5}(CH{sub 3}){sub 5})Ru(NS)Cl{sub 2} exhibits a slipped (eta-3,eta-2 Cp ring, with the central C(skeletal)-CH{sub 3} bond of the more tightly bound eta-3 portion eclipsing the Ru-N-S vector. With NO derivatives, ring {open_quotes}slippage{close_quotes} is not significant, but ring orientation is variable depending upon the L and L` ligand set. NMR spectroscopy measurements show that the barriers to changes in ring conformation become very low in solution. For catalytic purposes, it is of interest to fix the Cp geometry with respect to rotation. Ab initio SCF and DFT calculations have been performed, using the NWChem suite of computer codes, developed at Pacific Northwest Laboratory, to explore three questions: By what mechanism does the choice of ligand affect the Cp orientation? What is the barrier to rotation of the Cp? By what mechanism does salvation affect the barriers to Cp rotation?
Theoretical investigation of lead vapor adsorption on kaolinite surfaces with DFT calculations.
Wang, Xinye; Huang, Yaji; Pan, Zhigang; Wang, Yongxing; Liu, Changqi
2015-09-15
Kaolinite can be used as the in-furnace sorbent/additive to adsorb lead (Pb) vapor at high temperature. In this paper, the adsorptions of Pb atom, PbO molecule and PbCl2 molecule on kaolinie surfaces were investigated by density functional theory (DFT) calculation. Si surface is inert to Pb vapor adsorption while Al surfaces with dehydroxylation are active for the unsaturated Al atoms and the O atoms losing H atoms. The adsorption energy of PbO is much higher than that of Pb atom and PbCl2. Considering the energy barriers, it is easy for PbO and PbCl2 to adsorb on Al surfaces but difficult to escape. The high energy barriers of de-HCl process cause the difficulties of PbCl2 to form PbO·Al2O3·2SiO2 with kaolinite. Considering the inertia of Si atoms and the activity of Al atoms after dehydroxylation, calcination, acid/alkali treatment and some other treatment aiming at amorphous silica producing and Al activity enhancement can be used as the modification measures to improve the performance of kaolinite as the in-furnace metal capture sorbent. PMID:25880048
Li, Y. Q.; Zhang, P. Y.; Han, K. L.
2015-03-28
A global many-body expansion potential energy surface is reported for the electronic ground state of CH{sub 2}{sup +} by fitting high level ab initio energies calculated at the multireference configuration interaction level with the aug-cc-pV6Z basis set. The topographical features of the new global potential energy surface are examined in detail and found to be in good agreement with those calculated directly from the raw ab initio energies, as well as previous calculations available in the literature. In turn, in order to validate the potential energy surface, a test theoretical study of the reaction CH{sup +}(X{sup 1}Σ{sup +})+H({sup 2}S)→C{sup +}({sup 2}P)+H{sub 2}(X{sup 1}Σ{sub g}{sup +}) has been carried out with the method of time dependent wavepacket on the title potential energy surface. The total integral cross sections and the rate coefficients have been calculated; the results determined that the new potential energy surface can both be recommended for dynamics studies of any type and as building blocks for constructing the potential energy surfaces of larger C{sup +}/H containing systems.
NASA Technical Reports Server (NTRS)
Stallcop, J. R.
1974-01-01
The theory for calculating the absorption of laser radiation by hydrogen is outlined for the temperatures and pressures of common laboratory plasmas. Nonhydrogenic corrections for determining the absorption by helium are also included. The coefficients for the absorption of He-Ne laser radiation at the wavelengths of 0.633, 1.15, and 3.39 microns in a H plasma is presented for temperatures in the range from 10,000 to 40,000 K and electron number densities in the range from 10 to the 15th power to 10 to the 18th power per cu cm. The total absorption of a H-He plasma calculated from this theory is compared with the measured absorption. The theoretical composition of the H-He absorption is analyzed with respect to the significant absorption processes, inverse bremsstrahlung, photoionization, resonance excitation, and photodetachment.
NASA Astrophysics Data System (ADS)
Yin, Caixia; Zhang, Jingjing; Huo, Fangjun
2013-11-01
The interaction between 1,4-dihydroxyanthraquinone (1,4-DHA) and metal ions was studied by UV-Visible and fluorescence spectroscopies in solution. Time-dependent density functional theory calculations confirmed complex structures. The investigation results showed 1,4-DHA can selectively respond some metal ions and can be monitored by UV-Vis, fluorescence spectra and naked-eye. So 1,4-DHA has a potential application in the design of metal ions probe. More, as typical metal ions, Hg2+ and Er3+, their reaction abilities for 1,4-DHA were studied in detailed. Experimental results showed they have better response for 1,4-DHA. And theoretical calculation concluded that Er3+ easily reacts with 1,4-DHA over Hg2+ attributed to the low reaction energy of Er3+-1,4-DHA than Hg2+-1,4-DHA.
Mintz, S.L. ); Pourkaviani, M. )
1989-12-01
Theoretical calculations are presented for the reaction {nu}{sub {ital e}}+{sup 12}C{r arrow}{sup 12}N{sub g.s.} +{ital e}{sup {minus}} for {ital E}{sub {nu}} from threshold to 135 MeV, for the reaction {nu}{sub {mu}}+{sup 12}C{r arrow}{sup 12}N{sub g.s.} +{mu}{sup {minus}}, and the corresponding antineutrino reaction for {ital E}{sub {nu}} from threshold to 160 MeV. Use is made of updated form factors based on more recent data for {ital e}{sup {minus}}+{sup 12}C{r arrow}{sup 12}C{sup *}+{ital e}{prime} {minus} and {gamma}+{sup 12}C{r arrow}{sup 12}C{sup *}. The recent neutrino reaction experiments are discussed in light of these calculations.
Novotny, O.; Hahn, M.; Lestinsky, M.; Savin, D. W.; Badnell, N. R.; Bernhardt, D.; Mueller, A.; Schippers, S.; Grieser, M.; Krantz, C.; Repnow, R.; Wolf, A.
2012-07-01
We have measured electron-ion recombination for Fe XII forming Fe XI using a merged-beam configuration at the heavy-ion storage ring TSR located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany. The measured merged-beam recombination rate coefficient (MBRRC) for collision energies from 0 to 1500 eV is presented. This work uses a new method for determining the absolute MBRRC based on a comparison of the ion beam decay rate with and without the electron beam on. For energies below 75 eV, the spectrum is dominated by dielectronic recombination (DR) resonances associated with 3s {yields} 3p and 3p {yields} 3d core excitations. At higher energies, we observe contributions from 3 {yields} N' and 2 {yields} N' core excitation DR. We compare our experimental results to state-of-the-art multi-configuration Breit-Pauli (MCBP) calculations and find significant differences, both in resonance energies and strengths. We have extracted the DR contributions from the measured MBRRC data and transformed them into a plasma recombination rate coefficient (PRRC) for temperatures in the range of 10{sup 3}-10{sup 7} K. We show that the previously recommended DR data for Fe XII significantly underestimate the PRRC at temperatures relevant for both photoionized plasmas (PPs) and collisionally ionized plasmas (CPs). This is contrasted with our MCBP PRRC results, which agree with the experiment to within 30% at PP temperatures and even better at CP temperatures. We find this agreement despite the disagreement shown by the detailed comparison between our MCBP and experimental MBRRC results. Last, we present a simple parameterized form of the experimentally derived PRRC for easy use in astrophysical modeling codes.
Microwave measurements and theoretical calculations on the structures of NNO-HCl complexes
NASA Astrophysics Data System (ADS)
Pauley, D. J.; Roehrig, M. A.; Adamowicz, L.; Shea, J. C.; Haubrich, S. T.; Kukolich, S. G.
1991-01-01
Pulsed-beam Fourier transform microwave spectroscopy was used to measure a and b dipole transitions for the N2O-H35Cl, N2O-H37Cl, N2O-D35Cl, and 15NNO-H35Cl van der Waals complexes. The observed transition frequencies were fit to determine the spectroscopic constants A-DK, B, C, DJ, DJK, eQqaa(Cl), and eQqbb(Cl). The structure of the complex appears to be a planar asymmetric top with a centers-of-mass separation Rc.m. ≊ 3.51 Å. The angle θ between Rc.m. and the HCl axis is approximately 110°. The angle φ between the N2O axis and Rc.m. is approximately 77°. The structure was fit using a weighted least squares fit to B and C isotopic rotational constants with Rc.m., θ, and φ as the adjustable parameters, and this procedure yielded three local minima with standard deviations less than 5 MHz. Principal axis coordinates for the Cl, H, and terminal N atoms in the complex were determined with single isotopic Kraitchman analysis to aid in the selection of the ``best'' structure. In a second structural analysis Rc.m. θ, and φ values were determined from the spectroscopic constants B, C, and eQqaa(Cl). The ``best fit'' structure parameters for N2O-HCl are Rc.m. =3.512(2) Å, θ =110(9)°, and φ = 77(2)°. Ab initio calculations of N2O-HCl structures using gaussian
Corzo, H H; Galano, Annia; Dolgounitcheva, O; Zakrzewski, V G; Ortiz, J V
2015-08-20
Two accurate and computationally efficient electron-propagator (EP) methods for calculating the valence, vertical ionization energies (VIEs) of closed-shell molecules have been identified through comparisons with related approximations. VIEs of a representative set of closed-shell molecules were calculated with EP methods using 10 basis sets. The most easily executed method, the diagonal, second-order (D2) EP approximation, produces results that steadily rise as basis sets are improved toward values based on extrapolated coupled-cluster singles and doubles plus perturbative triples calculations, but its mean errors remain unacceptably large. The outer valence Green function, partial third-order and renormalized partial third-order methods (P3+), which employ the diagonal self-energy approximation, produce markedly better results but have a greater tendency to overestimate VIEs with larger basis sets. The best combination of accuracy and efficiency with a diagonal self-energy matrix is the P3+ approximation, which exhibits the best trends with respect to basis-set saturation. Several renormalized methods with more flexible nondiagonal self-energies also have been examined: the two-particle, one-hole Tamm-Dancoff approximation (2ph-TDA), the third-order algebraic diagrammatic construction or ADC(3), the renormalized third-order (3+) method, and the nondiagonal second-order renormalized (NR2) approximation. Like D2, 2ph-TDA produces steady improvements with basis set augmentation, but its average errors are too large. Errors obtained with 3+ and ADC(3) are smaller on average than those of 2ph-TDA. These methods also have a greater tendency to overestimate VIEs with larger basis sets. The smallest average errors occur for the NR2 approximation; these errors decrease steadily with basis augmentations. As basis sets approach saturation, NR2 becomes the most accurate and efficient method with a nondiagonal self-energy. PMID:26226061
Theoretical calculation and experiment of microwave electromagnetic property of Ni(C) nanocapsules
NASA Astrophysics Data System (ADS)
Dan-Feng, Zhang; Zhi-Feng, Hao; Bi, Zeng; Yan-Nan, Qian; Ying-Xin, Huang; Zhen-Da, Yang
2016-04-01
With the combination of the dielectric loss of the carbon layer with the magnetic loss of the ferromagnetic metal core, carbon-coated nickel (Ni(C)) nanoparticles are expected to be the promising microwave absorbers. Microwave electromagnetic parameters and reflection loss in a frequency range of 2 GHz–18 GHz for paraffin-Ni(C) composites are investigated. The values of relative complex permittivity and permeability, the dielectric and magnetic loss tangent of paraffin-Ni(C) composites are measured, respectively, when the weight ratios of Ni(C) nanoparticles are equal to 10 wt%, 40 wt%, 50 wt%, 70 wt%, and 80 wt% in paraffin-Ni(C) composites. The results reveal that Ni(C) nanoparticles exhibit a peak of magnetic loss at about 13 GHz, suggesting that magnetic loss and a natural resonance could be found at that frequency. Based on the measured complex permittivity and permeability, the reflection losses of paraffin-Ni(C) composites with different weight ratios of Ni(C) nanoparticles and coating thickness values are simulated according to the transmission line theory. An excellent microwave absorption is obtained. To be proved by the experimental results, the reflection loss of composite with a coating thickness of 2 mm is measured by the Arch method. The results indicate that the maximum reflection loss reaches ‑26.73 dB at 12.7 GHz, and below ‑10 dB, the bandwidth is about 4 GHz. The fact that the measured absorption position is consistent with the calculated results suggests that a good electromagnetic match and a strong microwave absorption can be established in Ni(C) nanoparticles. The excellent Ni(C) microwave absorber is prepared by choosing an optimum layer number and the weight ratio of Ni(C) nanoparticles in paraffin-Ni(C) composites. Project supported by the Science and Technology Program of Guangdong Province, China (Grant Nos. 2014B010106005, 2013B051000077, and 2015A050502047) and the Science and Technology Program of Guangzhou City, China (Grant
Shieh, Minghuey; Chu, Yen-Yi; Hsu, Miao-Hsing; Ke, Wei-Ming; Lin, Chien-Nan
2011-01-17
The trichromium-lead complex [Pb{Cr(CO)5}3](2-) (1) was isolated from the reaction of PbCl2 and Cr(CO)6 in a KOH/MeOH solution, and the new mixed chromium-iron-lead complex [Pb{Cr(CO)5}{Fe(CO)4}2](2-) (3) was synthesized from the reaction of PbCl2 and Cr(CO)6 in a KOH/MeOH solution followed by the addition of Fe(CO)5. X-ray crystallography showed that 3 consisted of a central Pb atom bound in a trigonal-planar environment to two Fe(CO)4 and one Cr(CO)5 fragments. When complex 1 reacted with 1.5 equiv of Mn(CO)5Br, the Cr(CO)4-bridged dimeric lead-chromium carbonyl complex [Pb2Br2Cr4(CO)18](2-) (4) was produced. However, a similar reaction of 3 or the isostructural triiron-lead complex [Pb{Fe(CO)4}3](2-) (2) with Mn(CO)5Br in MeCN led to the formation of the Fe3Pb2-based trigonal-bipyramidal complexes [Fe3(CO)9{PbCr(CO)5}2](2-) (6) and [Fe3(CO)9{PbFe(CO)4}2](2-) (5), respectively. On the other hand, the Ru3Pb2-based trigonal-bipyramidal complex [Ru3(CO)9{PbCr(CO)5}2](2-) (7) was obtained directly from the reaction of PbCl2, Cr(CO)6, and Ru3(CO)12 in a KOH/MeOH solution. X-ray crystallography showed that 5 and 6 each had an Fe3Pb2 trigonal-bipyramidal core geometry, with three Fe(CO)3 groups occupying the equatorial positions and two PbFe(CO)4 or PbCr(CO)5 units in the axial positions, while 7 displayed a Ru3Pb2 trigonal-bipyramidal geometry with three equatorial Ru(CO)3 groups and two axial PbCr(CO)5 units. The complexes 3-7 were characterized spectroscopically, and their nature, formation, and electrochemistry were further examined by molecular orbital calculations at the B3LYP level of density functional theory. PMID:21142206
Jiang, He; Chen, Changshui
2015-04-23
Most material properties can be traced to electronic structures. Black silicon produced from SF6 or sulfur powder via irradiation with femtosecond laser pulses displays decreased infrared absorption after annealing, with almost no corresponding change in visible light absorption. The high-intensity laser pulses destroy the original crystal structure, and the doping element changes the material performance. In this work, the structural and electronic properties of several sulfur-doped silicon systems are investigated using first principle calculations. Depending on the sulfur concentration (level of doping) and the behavior of the sulfur atoms in the silicon lattice, different states or an absence of states are exhibited, compared with the undoped system. Moreover, the visible-infrared light absorption intensities are structure specific. The results of our theoretical calculations show that the conversion efficiency of sulfur-doped silicon solar cells depends on the sulfur concentrations. Additionally, two types of defect configurations exhibit light absorption characteristics that differ from the other configurations. These two structures produce a rapid increase in the theoretical photoelectric conversion efficiency in the range of the specific chemical potential studied. By controlling the positions of the atomic sulfur and the sulfur concentration in the preparation process, an efficient photovoltaic (PV) material may be obtainable. PMID:25798659
NASA Astrophysics Data System (ADS)
Egawa, Toru; Kameyama, Akiyo; Takeuchi, Hiroshi
2006-08-01
The molecular structures of vanillin (4-hydroxy-3-methoxybenzaldehyde), isovanillin (3-hydroxy-4-methoxybenzaldehyde) and ethylvanillin (3-ethoxy-4-hydroxybenzaldehyde) were determined by means of gas electron diffraction. Among them, vanillin and ethylvanillin have a vanilla odor but isovanillin smells differently. The nozzle temperatures were 125, 173 and 146 °C, for vanillin, isovanillin and ethylvanillin, respectively. The results of MP2 and B3LYP calculations with the 6-31G** basis set were used as supporting information. The MP2 calculations predicted that vanillin and isovanillin have two stable conformers and ethylvanillin has four stable conformers. The electron diffraction data were found to be consistent with these conformational compositions. The determined structural parameters ( rg and ∠ α) of vanillin are as follows: < r(C-C) ring>=1.397(4) Å; r(C 1-C aldehyde)=1.471(←) Å; r(C 3-O Me)=1.374(9) Å; r(C 4-O H)=1.361(←) Å; r(O-C Me)=1.428(←) Å; r(C dbnd6 O)=1.214(8) Å; < r(C-H)>=1.110(11) Å; r(O-H)=0.991(←) Å; ∠C 6-C 1-C 2=120.6(2)°; ∠C 1-C 2-C 3=118.8(←)°; ∠C 1-C 6-C 5=120.1(←)°; ∠C 2-C 1-C aldehyde=122.7(18)°; ∠C 1-C dbnd6 O=119.4(16)°; ∠C 4-C 3-O Me=112.2(12)°; ∠C 3-C 4-O H=119.1(←)°; ∠C 3-O-C=121.7(29)°. Those of isovanillin are as follows: < r(C-C) ring>=1.402(4) Å; r(C 1-C aldehyde)=1.479(←) Å; r(C 4-O Me)=1.369(9) Å; r(C 3-O H)=1.357(←) Å; r(O-C Me)=1.422(←) Å; r(C dbnd6 O)=1.221(9) Å; < r(C-H)>=1.114(14) Å; r(O-H)=0.995(←) Å; ∠C 6-C 1-C 2=120.2(3)°; ∠C 1-C 2-C 3=119.0(←)°; ∠C 1-C 6-C 5=119.9(←)°; ∠C 2-C 1-C aldehyde=124.6(25)°; ∠C 1-C dbnd6 O=121.3(24)°; ∠C 3-C 4-O Me=114.4(12)°; ∠C 4-C 3-O H=121.2(←)°; ∠C 4-O-C=123.8(26)°. Those of ethylvanillin are as follows: < r(C-C) ring>=1.397(6) Å; r(C 1-C aldehyde)=1.471(←) Å; r(C 3-O Et)=1.365(13) Å; r(C 4-O H)=1.352(←) Å; r(O-C Et)=1.427(←) Å; r(C-C Et)=1.494(21) Å; r(C dbnd6 O)=1.206(9) Å; < r
Punjabi, Alkesh; Ali, Halima
2011-02-15
Any canonical transformation of Hamiltonian equations is symplectic, and any area-preserving transformation in 2D is a symplectomorphism. Based on these, a discrete symplectic map and its continuous symplectic analog are derived for forward magnetic field line trajectories in natural canonical coordinates. The unperturbed axisymmetric Hamiltonian for magnetic field lines is constructed from the experimental data in the DIII-D [J. L. Luxon and L. E. Davis, Fusion Technol. 8, 441 (1985)]. The equilibrium Hamiltonian is a highly accurate, analytic, and realistic representation of the magnetic geometry of the DIII-D. These symplectic mathematical maps are used to calculate the magnetic footprint on the inboard collector plate in the DIII-D. Internal statistical topological noise and field errors are irreducible and ubiquitous in magnetic confinement schemes for fusion. It is important to know the stochasticity and magnetic footprint from noise and error fields. The estimates of the spectrum and mode amplitudes of the spatial topological noise and magnetic errors in the DIII-D are used as magnetic perturbation. The discrete and continuous symplectic maps are used to calculate the magnetic footprint on the inboard collector plate of the DIII-D by inverting the natural coordinates to physical coordinates. The combination of highly accurate equilibrium generating function, natural canonical coordinates, symplecticity, and small step-size together gives a very accurate calculation of magnetic footprint. Radial variation of magnetic perturbation and the response of plasma to perturbation are not included. The inboard footprint from noise and errors are dominated by m=3, n=1 mode. The footprint is in the form of a toroidally winding helical strip. The width of stochastic layer scales as (1/2) power of amplitude. The area of footprint scales as first power of amplitude. The physical parameters such as toroidal angle, length, and poloidal angle covered before striking, and the
NASA Astrophysics Data System (ADS)
Roehl, Jason L.
Diffusion of point defects on crystalline surfaces and in their bulk is an important and ubiquitous phenomenon affecting film quality, electronic properties and device functionality. A complete understanding of these diffusion processes enables one to predict and then control those processes. Such understanding includes knowledge of the structural, energetic and electronic properties of these native and non-native point defect diffusion processes. Direct experimental observation of the phenomenon is difficult and microscopic theories of diffusion mechanisms and pathways abound. Thus, knowing the nature of diffusion processes, of specific point defects in given materials, has been a challenging task for analytical theory as well as experiment. The recent advances in computing technology have been a catalyst for the rise of a third mode of investigation. The advent of tremendous computing power, breakthroughs in algorithmic development in computational applications of electronic density functional theory now enables direct computation of the diffusion process. This thesis demonstrates such a method applied to several different examples of point defect diffusion on the (001) surface of gallium arsenide (GaAs) and the bulk of cadmium telluride (CdTe) and cadmium sulfide (CdS). All results presented in this work are ab initio, total-energy pseudopotential calculations within the local density approximation to density-functional theory. Single particle wavefunctions were expanded in a plane-wave basis and reciprocal space k-point sampling was achieved by Monkhorst-Pack generated k-point grids. Both surface and bulk computations employed a supercell approach using periodic boundary conditions. Ga adatom adsorption and diffusion processes were studied on two reconstructions of the GaAs(001) surface including the c(4x4) and c(4x4)-heterodimer surface reconstructions. On the GaAs(001)- c(4x4) surface reconstruction, two distinct sets of minima and transition sites were
Hasnain, Sabeeha; McClendon, Christopher L; Hsu, Monica T; Jacobson, Matthew P; Bandyopadhyay, Pradipta
2014-01-01
A new coarse-grained model of the E. coli cytoplasm is developed by describing the proteins of the cytoplasm as flexible units consisting of one or more spheres that follow Brownian dynamics (BD), with hydrodynamic interactions (HI) accounted for by a mean-field approach. Extensive BD simulations were performed to calculate the diffusion coefficients of three different proteins in the cellular environment. The results are in close agreement with experimental or previously simulated values, where available. Control simulations without HI showed that use of HI is essential to obtain accurate diffusion coefficients. Anomalous diffusion inside the crowded cellular medium was investigated with Fractional Brownian motion analysis, and found to be present in this model. By running a series of control simulations in which various forces were removed systematically, it was found that repulsive interactions (volume exclusion) are the main cause for anomalous diffusion, with a secondary contribution from HI. PMID:25180859
Dong, Bing; Zhou, Xiao-Lin E-mail: lkworld@126.com; Chang, Jing; Liu, Ke E-mail: lkworld@126.com
2014-08-07
The structural and elastic properties of RuN{sub 2} were investigated through the first-principles calculation using generalized gradient approximation (GGA) and local density approximation (LDA) within the plane-wave pseudopotential density functional theory. The obtained equilibrium structure and mechanical properties are in excellent agreement with other theoretical results. Then we compared the elastic modulus of RuN{sub 2} with several other isomorphic noble metal nitrides. Results show that RuN{sub 2} can nearly rival with OsN{sub 2} and IrN{sub 2}, which indicate RuN{sub 2} is a potentially ultra-incompressible and hard material. By the elastic stability criteria, it is predicted that RuN{sub 2} is stable in our calculations (0–100 GPa). The calculated B/G ratios indicate that RuN{sub 2} possesses brittle nature at 0 GPa and when the pressure increases to 13.4 GPa (for LDA) or 20.8 GPa (for GGA), it begins to prone to ductility. Through the quasi-harmonic Debye model, we also investigated the thermodynamic properties of RuN{sub 2}.
NASA Astrophysics Data System (ADS)
Sethi, Arun; Bhatia, Akriti; Bhatia, Gitika; Shrivastava, Atul; Prakash, Rohit
2013-11-01
One pot allylic oxidation of 3β-acetoxypregna-5,16-diene-20-one (2) and nucleophilic addition at C-16 position of 3β-hydroxypregna-5,16-diene-20-one (3) yielded 3β-acetoxypregna-5,16-diene-7,20-dione (4) and 3β-hydroxy-16α-(5'-hydroxypentyloxy)-pregn-5-ene-20-one (5) respectively in high yield. A detailed theoretical study supported by X-ray analysis of compounds 4 and 5 has been carried out. Conformational analysis of compounds 4 and 5 was done with the help of crystal structure, which crystallize out in orthorhombic form having P212121 space group. Structural characterization of compounds 4 and 5 was done with the aid of 1H, 13C NMR, IR, UV, ESI-MS and ESI-HRMS. The molecular geometries and vibrational frequencies for compounds 4 and 5 in the ground state were calculated using the Density functional theory (DFT) with 6-31G(d,p) basis set and compared with experimental data. 1H and 13C nuclear magnetic resonance magnetic shifts of 4 and 5 were calculated using GIAO method and compared with the experimental data. UV-Vis spectra of both the compounds were recorded and electronic properties such as HOMO-LUMO energies were calculated by time dependent TD-DFT approach. The compounds were screened for their anti-hyperlipidemic and anti-oxidant activity.
NASA Astrophysics Data System (ADS)
Gaur, A.; Shrivastava, B. D.
2014-09-01
The terms X-ray absorption near edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) refer, respectively, to the structure in the X-ray absorption spectrum at low and high energies relative to the absorption edge. Routine analysis of EXAFS experiments generally makes use of simplified models and several many-body parameters, e.g. mean free paths, many-body amplitude factors, and Debye-Waller factors, as incorporated in EXAFS analysis software packages like IFEFFIT which includes Artemis. Similar considerations apply to XANES, where the agreement between theory and experiment is often less satisfactory. The recently available computer code FEFF9 uses the real-space Green's function (RSGF) approach to calculate dielectric response over a broad spectrum including the dominant low-energy region. This code includes improved treatments of many-body effects such as inelastic losses, core-hole effects, vibrational amplitudes, and the extension to full spectrum calculations of optical constants including solid state effects. In the present work, using FEFF9, we have calculated the X-ray absorption spectrum at the K-edge of copper in a complex, viz., aqua (diethylenetriamine) (isonicotinato) copper(II), the crystal structure of which is unknown. The theoretical spectrum has been compared with the experimental spectrum, recorded by us at the XAFS beamline 11.1 at ELETTRA synchrotron source, Italy, in both XANES and EXAFS regions.
NASA Astrophysics Data System (ADS)
Kajiya, Daisuke; Saitow, Ken-ichi
2013-08-01
Carbonyl compounds are solutes that are highly soluble in supercritical CO2 (scCO2). Their solubility governs the efficiency of chemical reactions, and is significantly increased by changing a chromophore. To effectively use scCO2 as solvent, it is crucial to understand the high solubility of carbonyl compounds, the solvation structure, and the solute-solvent intermolecular interactions. We report Raman spectroscopic data, for three prototypical ketones dissolved in scCO2, and four theoretical analyses. The vibrational Raman spectra of the C=O stretching modes of ketones (acetone, acetophenone, and benzophenone) were measured in scCO2 along the reduced temperature Tr = T/Tc = 1.02 isotherm as a function of the reduced density ρr = ρ/ρc in the range 0.05-1.5. The peak frequencies of the C=O stretching modes shifted toward lower energies as the fluid density increased. The density dependence was analyzed by using perturbed hard-sphere theory, and the shift was decomposed into attractive and repulsive energy components. The attractive energy between the ketones and CO2 was up to nine times higher than the repulsive energy, and its magnitude increased in the following order: acetone < acetophenone < benzophenone. The Mulliken charges of the three solutes and CO2 molecules obtained by using quantum chemistry calculations described the order of the magnitude of the attractive energy and optimized the relative configuration between each solute and CO2. According to theoretical calculations for the dispersion energy, the dipole-induced-dipole interaction energy, and the frequency shift due to their interactions, the experimentally determined attractive energy differences in the three solutes were attributed to the dispersion energies that depended on a chromophore attached to the carbonyl groups. It was found that the major intermolecular interaction with the attractive shift varied from dipole-induced dipole to dispersion depending on the chromophore in the ketones in
Coello Pérez, Eduardo A.; Papenbrock, Thomas F.
2015-07-27
In this paper, we present a model-independent approach to electric quadrupole transitions of deformed nuclei. Based on an effective theory for axially symmetric systems, the leading interactions with electromagnetic fields enter as minimal couplings to gauge potentials, while subleading corrections employ gauge-invariant nonminimal couplings. This approach yields transition operators that are consistent with the Hamiltonian, and the power counting of the effective theory provides us with theoretical uncertainty estimates. We successfully test the effective theory in homonuclear molecules that exhibit a large separation of scales. For ground-state band transitions of rotational nuclei, the effective theory describes data well within theoreticalmore » uncertainties at leading order. To probe the theory at subleading order, data with higher precision would be valuable. For transitional nuclei, next-to-leading-order calculations and the high-precision data are consistent within the theoretical uncertainty estimates. In addition, we study the faint interband transitions within the effective theory and focus on the E2 transitions from the 02+ band (the “β band”) to the ground-state band. Here the predictions from the effective theory are consistent with data for several nuclei, thereby proposing a solution to a long-standing challenge.« less
Hahn, M.; Novotný, O.; Savin, D. W.; Badnell, N. R.; Grieser, M.; Krantz, C.; Repnow, R.; Wolf, A.; Lestinsky, M.; Müller, A.; Schippers, S.
2014-06-10
We have measured dielectronic recombination (DR) for Fe{sup 12+} forming Fe{sup 11+} using the heavy ion storage ring TSR located at the Max Planck Institute for Nuclear Physics in Heidelberg, Germany. Using our results, we have calculated a plasma rate coefficient from these data that can be used for modeling astrophysical and laboratory plasmas. For the low temperatures characteristic of photoionized plasmas, the experimentally derived rate coefficient is orders of magnitude larger than the previously recommended atomic data. The existing atomic data were also about 40% smaller than our measurements at temperatures relevant for collisionally ionized plasmas. Recent state-of-the-art theory has difficulty reproducing the detailed energy dependence of the DR spectrum. However, for the Maxwellian plasma rate coefficient, recent theoretical results agree with our measurements to within about 30% for both photoionized and collisionally ionized plasmas.
NASA Technical Reports Server (NTRS)
Dickerson, R. R.; Stedman, D. H.; Chameides, W. L.; Crutzen, P. J.; Fishman, J.
1979-01-01
The paper presents an experimental technique which measures j/O3-O(1-D)/, the rate of solar photolysis of ozone to singlet oxygen atoms. It is shown that a flow actinometer carries dilute O3 in N2O into direct sunlight where the O(1D) formed reacts with N2O to form NO which chemiluminescence detects, with a time resolution of about one minute. Measurements indicate a photolysis rate of 1.2 (+ or - .2) x 10 to the -5/s for a cloudless sky, 45 deg zenith angle, 0.345 cm ozone column and zero albedo. Finally, ground level results compare with theoretical calculations based on the UV actinic flux as a function of ozone column and solar zenith angle.
NASA Astrophysics Data System (ADS)
Loued, W.; Wéry, J.; Dorlando, A.; Alimi, K.
2015-02-01
In this paper, the significance of annealing, in two different atmospheres (air and vacuum), on the surface characteristics of poly (lactic acid) (PLA) films was investigated. X-ray diffraction (XRD) measurements correlated to atomic force microscopy (AFM) observations of the cast PLA films show that thermal treatment under air atmosphere is responsible for a significant increase of crystallinity with the increase of temperature. However, band gap energy of the title compound is slightly affected by annealing at different temperatures. As for the untreated PLA, the molecular geometry was optimized using density functional theory (DFT/B3LYP) method with 6-31g (d) basis set in ground state. From the optimized geometry, HOMO and LUMO energies and quantum chemical parameters were performed at B3LYP/6-31g (d). The theoretical results, applied to simulated optical spectra of the compound, were compared to the observed ones. On the basis of theoretical vibrational analyses, the thermodynamic properties were calculated at different temperatures, revealing the correlation between internal energy (U), enthalpy (H), entropy (S), Free energy (G) and temperatures.
NASA Astrophysics Data System (ADS)
Egawa, Toru; Kachi, Yukari; Takeshima, Tsuguhide; Takeuchi, Hiroshi; Konaka, Shigehiro
2003-10-01
The molecular structure and conformation of carvone, a compound with a minty odor, were investigated by means of gas electron diffraction supported by theoretical calculations. Electron diffraction patterns were recorded by heating the nozzle up to 128 °C to obtain enough scattering intensity. The infrared spectrum was also measured by using an absorption cell with a path length of 10 m. The obtained molecular scattering intensities were analyzed with the aid of theoretical calculations and infrared spectroscopy. It was revealed that the experimental data are well reproduced by assuming that carvone consists of a mixture of three conformers that have the isopropenyl group in the equatorial position and mutually differ in the torsional angle around the single bond connecting the ring and the isopropenyl group. It was also found that the puckering amplitude of the ring of carvone is close to those of menthol and isomenthol, a minty compound and its nonminty isomer. The determined structural parameters ( rg and ∠ α) of the most abundant conformer of carvone are as follows: < r(C-C)>=1.520(3) Å; < r(CC)>=1.360(5) Å; r(CO)=1.225(5) Å; < r(C-H)>=1.104(4)Å; <∠CC-C>=121.1(5)°; <∠C-C-C>=110.4(5)°; ∠C-CO-C=117.1(14)°; <∠C-C-H>=111.1(13)°. Angle brackets denote average values and parenthesized values are the estimated limits of error (3 σ) referring to the last significant digit.
Aarset, Kirsten; Page, Elizabeth M; Rice, David A
2006-07-20
The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+G(d,p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol(-1) lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond. PMID:16836466
NASA Astrophysics Data System (ADS)
Piedra, Patricio G.
Despite considerable efforts by many atmospheric scientists, the identification and classification of aerosols remain a big challenge. On the atmospheric scale, large surveys of aerosols rely heavily on light scattering. The degree of linear polarization (DLP) is sensitive to the size and index of refraction of the aerosol particles and may provide an accurate method for discriminating aerosol types. In this thesis, Mie scattering was implemented to yield both the parallel and perpendicular components of the scattered electric field. In a first set of results, the calculated DLP was used to reproduce measurements of DLP along a principal plane for several sites taken by the robotic network of sun-photometers, AERONET. The agreement of theory and experiment is excellent. Having verified this agreement, we calculated the DLP of the particle size distributions from four sites whose aerosols belong to four different types: urban-industrial, biomass, dust and mixed aerosol. The DLP of these types of aerosols was obtained and might constitute a basis for discrimination between aerosols. However, we did not find significant distinctions in the polarization curves of these sites, suggesting it would be difficult to discriminate aerosol types by polarization measurements alone. As a final analysis, we explored the sensitivity of the DLP to changes in the volume concentration distribution and the index of refraction.
Ionizing Collisions of Electrons with Radical Species OH, H2 O2 and HO2; Theoretical Calculations
NASA Astrophysics Data System (ADS)
Joshipura, K. N.; Pandya, S. H.; Vaishnav, B. G.; Patel, U. R.
2016-05-01
In this paper we present our calculated total ionization cross sections (TICS) of electron impact on radical targets OH, H2 O2 and HO2 at energies from threshold to 2000 eV. Reactive species such as these pose difficulties in measurements of electron scattering cross sections. No measured data have been reported in this regard except an isolated TICS measurement on OH radical, and hence the present work on the title radicals hold significance. These radical species are present in an environment in which water molecules undergo dissociation (neutral or ionic) in interactions with photons or electrons. The embedding environments could be quite diverse, ranging from our atmosphere to membranes of living cells. Ionization of OH, H2 O2 or HO2 can give rise to further chemistry in the relevant bulk medium. Therefore, it is appropriate and meaningful to examine electron impact ionization of these radicals in comparison with that of water molecules, for which accurate da are available. For the OH target single-centre scattering calculations are performed by starting with a 4-term complex potential, that describes simultaneous elastic plus inelastic scattering. TICS are obtained from the total inelastic cross sections in the complex scattering potential - ionization contribution formalism , a well established method. For H2 O2 and HO2 targets, we employ the additivity rule with overlap or screening corrections. Detailed results will be presented in the Conference.
Zhu, Zunlue; Yu, Wei; Wang, Shuai; Sun, Jinfeng; Shi, Deheng
2014-10-15
The spectroscopic properties of 23 Ω states generated from the 13 Λ-S states of BO radical are studied for the first time for internuclear separations from about 0.07 to 1.0nm. Of the 13 Λ-S states, each of the F(2)Π, 1(2)Φ and 1(2)Δ states is found to possess the double well. Each of the 1(4)Π, C(2)Π, 1(2)Σ(-) and 2(2)Σ(-) states possesses one well with one barrier. The A(2)Π, 1(4)Π and F(2)Π are the inverted states with the spin-orbit coupling effect taken into account. All the states possess the deep well except for the 1(2)Φ. The potential energy curves (PECs) are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are included into the calculations. The PECs are extrapolated to the complete basis set limit. The spin-orbit coupling effect is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The spectroscopic parameters are evaluated, and compared with the available measurements and other theoretical results. The Franck-Condon factors and radiative lifetimes of the transitions from the B(2)Σ(+), C(2)Π, D(2)Σ(+), 1(2)Σ(-) and 1(4)Π Λ-S states to the ground state are calculated for several low vibrational levels, and some necessary discussion is made. Analyses show that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. PMID:24820321
Vasiltsova, Tatiana; Heintz, Andreas
2007-12-21
A recently developed statistical mechanical model for calculating Kirkwood correlation factors gK in self associating liquids and liquid mixtures has been applied for the simultaneous description of gK, the molar enthalpy of mixing HEM and the infrared absorption of monomer alcoholic species as function of the composition in alkanol + hexane and alkanol + pentane mixtures (alkanol: butan-1-ol, pentan-1-ol, hexan-1-ol, heptan-1-ol, sec-butanol, tert-butanol). The majority of parameters involved into the theory are obtained by independent quantum mechanical ab initio calculations of molecular clusters consisting of up to four alcohol molecules. As a consequence only two parameters have to be adjusted freely to each binary system, a third parameter responsible for the non specific intermolecular dispersion interaction has been adjusted within a limited range of possible values given by physical arguments. Excellent agreement between theory and experimental data of gK, HEM and IR absorbance is obtained covering the whole range of concentration including the temperature dependence of these properties without adjusting further parameters. The Kirkwood correlation factor gK turns out to be a sensitive response to peculiarities of the molecular structure of hydrogen bonded systems in the condensed liquid state. The successful application of the theoretical model opens a new way of a deeper and more reliable understanding of such liquid structures. PMID:18046469
NASA Astrophysics Data System (ADS)
Yurchenko, Sergei N.; Thiel, Walter; Jensen, Per
2007-10-01
We present a new computational method with associated computer program TROVE (Theoretical ROVibrational Energies) to perform variational calculations of rovibrational energies for general polyatomic molecules of arbitrary structure in isolated electronic states. The (approximate) nuclear kinetic energy operator is represented as an expansion in terms of internal coordinates. The main feature of the computational scheme is a numerical construction of the kinetic energy operator, which is an integral part of the computation process. Thus the scheme is self-contained, i.e., it requires no analytical pre-derivation of the kinetic energy operator. It is also general, since it can be used in connection with any internal coordinates. The method represents an extension of our model for pyramidal XY 3 molecules reported previously [S.N. Yurchenko, M. Carvajal, P. Jensen, H. Lin, J.J. Zheng, W. Thiel, Mol. Phys. 103 (2005) 359]. Non-rigid molecules are treated in the Hougen-Bunker-Johns approach [J.T. Hougen, P.R. Bunker, J.W.C. Johns, J. Mol. Spectrosc. 34 (1970) 136]. In this case, the variational calculations employ a numerical finite basis representation for the large-amplitude motion using basis functions that are generated by Numerov-Cooley integration of the appropriate one-dimensional Schrödinger equation.
NASA Astrophysics Data System (ADS)
Seo, Dong-Hwa; Urban, Alexander; Ceder, Gerbrand
2015-09-01
Transition-metal (TM) oxides play an increasingly important role in technology today, including applications such as catalysis, solar energy harvesting, and energy storage. In many of these applications, the details of their electronic structure near the Fermi level are critically important for their properties. We propose a first-principles-based computational methodology for the accurate prediction of oxygen charge transfer in TM oxides and lithium TM (Li-TM) oxides. To obtain accurate electronic structures, the Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional is adopted, and the amount of exact Hartree-Fock exchange (mixing parameter) is adjusted to reproduce reference band gaps. We show that the HSE06 functional with optimal mixing parameter yields not only improved electronic densities of states, but also better energetics (Li-intercalation voltages) for LiCo O2 and LiNi O2 as compared to the generalized gradient approximation (GGA), Hubbard U corrected GGA (GGA +U ), and standard HSE06. We find that the optimal mixing parameters for TM oxides are system specific and correlate with the covalency (ionicity) of the TM species. The strong covalent (ionic) nature of TM-O bonding leads to lower (higher) optimal mixing parameters. We find that optimized HSE06 functionals predict stronger hybridization of the Co 3 d and O 2 p orbitals as compared to GGA, resulting in a greater contribution from oxygen states to charge compensation upon delithiation in LiCo O2 . We also find that the band gaps of Li-TM oxides increase linearly with the mixing parameter, enabling the straightforward determination of optimal mixing parameters based on GGA (α =0.0 ) and HSE06 (α =0.25 ) calculations. Our results also show that G0W0@GGA +U band gaps of TM oxides (M O ,M =Mn ,Co ,Ni ) and LiCo O2 agree well with experimental references, suggesting that G0W0 calculations can be used as a reference for the calibration of the mixing parameter in cases when no experimental band gap has been
Friesner, Richard A.; Baik, Mu-Hyun; Gherman, Benjamin F.; Guallar, Victor; Wirstam, Maria E.; Murphy, Robert B.; Lippard, Stephen J.
2003-03-01
Over the past several years, rapid advances in computational hardware, quantum chemical methods, and mixed quantum mechanics/molecular mechanics (QM/MM) techniques have made it possible to model accurately the interaction of ligands with metal-containing proteins at an atomic level of detail. In this paper, we describe the application of our computational methodology, based on density functional (DFT) quantum chemical methods, to two diiron-containing proteins that interact with dioxygen: methane monooxygenase (MMO) and hemerythrin (Hr). Although the active sites are structurally related, the biological function differs substantially. MMO is an enzyme found in methanotrophic bacteria and hydroxylates aliphatic C-H bonds, whereas Hr is a carrier protein for dioxygen used by a number of marine invertebrates. Quantitative descriptions of the structures and energetics of key intermediates and transition states involved in the reaction with dioxygen are provided, allowing their mechanisms to be compared and contrasted in detail. An in-depth understanding of how the chemical identity of the first ligand coordination shell, structural features, electrostatic and van der Waals interactions of more distant shells control ligand binding and reactive chemistry is provided, affording a systematic analysis of how iron-containing proteins process dioxygen. Extensive contact with experiment is made in both systems, and a remarkable degree of accuracy and robustness of the calculations is obtained from both a qualitative and quantitative perspective.
NASA Astrophysics Data System (ADS)
Olivier, Thomas; Billard, Franck; Akhouayri, Hassan
2004-06-01
Self-focusing is one of the dramatic phenomena that may occur during the propagation of a high power laser beam in a nonlinear material. This phenomenon leads to a degradation of the wave front and may also lead to a photoinduced damage of the material. Realistic simulations of the propagation of high power laser beams require an accurate knowledge of the nonlinear refractive index γ. In the particular case of fused silica and in the nanosecond regime, it seems that electronic mechanisms as well as electrostriction and thermal effects can lead to a significant refractive index variation. Compared to the different methods used to measure this parmeter, the Z-scan method is simple, offers a good sensitivity and may give absolute measurements if the incident beam is accurately studied. However, this method requires a very good knowledge of the incident beam and of its propagation inside a nonlinear sample. We used a split-step propagation algorithm to simlate Z-scan curves for arbitrary beam shape, sample thickness and nonlinear phase shift. According to our simulations and a rigorous analysis of the Z-scan measured signal, it appears that some abusive approximations lead to very important errors. Thus, by reducing possible errors on the interpretation of Z-scan experimental studies, we performed accurate measurements of the nonlinear refractive index of fused silica that show the significant contribution of nanosecond mechanisms.
NASA Astrophysics Data System (ADS)
Kaneta, Yasunori; Ishino, Shiori; Chen, Ying; Iwata, Shuichi; Iwase, Akihiro
2011-10-01
To clarify the relationship between a magnetic property and a defect structure in FeRh inter-metallic compound theoretically, energy band calculations are performed based on the density functional theory. Under the assumption that the majority of defect structure is a type of site-exchanged one between Fe and Rh atoms, total energy for various magnetic structures is evaluated within a super-cell of 2×2×2 cubic cells. Due to the site-exchange defect pair of nearest neighbor Fe and Rh atoms in 12.5%/f.u. (f.u.: formula unit) density, the total energy increases by 1.91 eV/pair in the anti-ferromagnetic structure and 0.88 eV/pair in the ferromagnetic structure. Although the anti-ferromagnetic structure is the stable state at low temperatures in defect-free FeRh, it becomes unstable with an amount of the site-exchange defect density. Threshold defect density to stabilize ferromagnetic state is estimated to be 0.8%/f.u. This phenomenon is expected in ion irradiated FeRh.
NASA Astrophysics Data System (ADS)
Shlyaptseva, Alla; Mancini, Roberto
1998-05-01
We study theoretically the polarization properties of X-ray spectra of Be-like Fe ions excited through resonant capture by an electron beam with different electron densities. Our previous work in this area was related to the study of polarization of dielectronic satellite lines of Fe ions excited by a low-density electron beam. (A.S. Shlyaptseva, R.C. Mancini, P. Neill, P. Beiersdorfer, J.R. Crespo López-Urrutia, and K. Widmann, Phys. Rev. A, 57), 888 (1998) Here we extend our work to the case of higher-density electron beams. As the density of the electron beam increases, new channels of electron capture appear. Thus the atomic and polarization characteristics of the satellite lines change. Moreover, additional X-ray satellite lines will appear. Using the density matrix formalism, we calculate the polarization characteristics and polarization-dependent spectra of dielectronic satellite lines of Be-like Fe produced at different energies and densities of the electron beam. We compare the results of the present work with our previous ones for low-density electron beams. These results are relevant to the identification of X-ray polarization-dependent spectral features and for X-ray line polarization spectroscopy.
NASA Astrophysics Data System (ADS)
Rittner, Roberto; Ducati, Lucas C.; Tormena, Cláudio F.; Cormanich, Rodrigo A.; Fiorin, Barbara C.; Braga, Carolyne B.; Abraham, Raymond J.
2013-02-01
The s-cis-trans isomerism of two furan derivatives [2-acetyl- (AF) and 2-acetyl-5-methylfuran, (AMF)] was analyzed, using data from the deconvolution of their carbonyl absorption band in two solvents (CH2Cl2 and CH3CN). These infrared data showed that the O,O-trans conformers predominate in the less polar solvent (CH2Cl2), but these equilibria change in a more polar solvent (CH3CN) leading to a slight predominance of the O,O-cis conformers, in agreement with the theoretical calculations. The later results were obtained using B3LYP-IEFPCM/6-31++g(3df,3p) level of theory, which taking into account the solvent effects at IEFPCM (Integral Equation Formalism Polarizable Continuum Model). Low temperature 13C NMR spectra in CD2Cl2 (ca. -75 °C) showed pairs of signals for each carbon, due to the known high energy barrier for the cis-trans interconversion leading to a large predominance of the trans isomers, which decreases in acetone-d6. This was confirmed by their 1H NMR spectra at the same temperatures. Moreover, despite the larger hyperconjugative interactions for the O,O-cis isomers, obtained from NBO data, these isomers are destabilized by the their Lewis energy.
Zou, Yidong; Wang, Xiangxue; Ai, Yuejie; Liu, Yunhai; Li, Jiaxing; Ji, Yongfei; Wang, Xiangke
2016-04-01
Graphene oxide (GO) has attracted considerable attention because of its remarkable enhanced adsorption and multifunctional properties. However, the toxic properties of GO nanosheets released into the environment could lead to the instability of biological system. In aqueous phase, GO may interact with fine mineral particles, such as chloridion intercalated nanocrystallined Mg/Al layered double hydroxides (LDH-Cl) and nanocrystallined Mg/Al LDHs (LDH-CO3), which are considered as coagulant molecules for the coagulation and removal of GO from aqueous solutions. Herein the coagulation of GO on LDHs were studied as a function of solution pH, ionic strength, contact time, temperature and coagulant concentration. The presence of LDH-Cl and LDH-CO3 improved the coagulation of GO in solution efficiently, which was mainly attributed to the surface oxygen-containing functional groups of LDH-Cl and LDH-CO3 occupying the binding sites of GO. The coagulation of GO by LDH-Cl and LDH-CO3 was strongly dependent on pH and ionic strength. Results of theoretical DFT calculations indicated that the coagulation of GO on LDHs was energetically favored by electrostatic interactions and hydrogen bonds, which was further evidenced by FTIR and XPS analysis. By integrating the experimental results, it was clear that LDH-Cl could be potentially used as a cost-effective coagulant for the elimination of GO from aqueous solutions, which could efficiently decrease the potential toxicity of GO in the natural environment. PMID:26978487
NASA Astrophysics Data System (ADS)
Qu, Y. D.; Zhang, W. J.; Kong, X. Q.; Zhao, X.
2016-03-01
The heat-transfer behavior of the interface of Flyer plate (or Base Plate) has great influence on the microcosmic structures, stress distributions, and interface distortion of the welded interface of composite plates by explosive welding. In this paper, the temperature distributions in the combing zone are studied for the case of Cu/Fe composite plate jointed by explosive welding near the lower limit of explosive welding. The results show that Flyer plate (Cu plate) and Base Plate (Fe plate) firstly almost have the same melting rate in the explosive welding process. Then, the melting rate of Cu plate becomes higher than that of Fe plate. Finally, the melt thicknesses of Cu plate and Fe plate trend to be different constants, respectively. Meanwhile, the melting layer of Cu plate is thicker than that of Fe plate. The research could supply some theoretical foundations for calculating the temperature distribution and optimizing the explosive welding parameters of Cu/Fe composite plate to some extent.
Radoń, Mariusz; Gąssowska, Katarzyna; Szklarzewicz, Janusz; Broclawik, Ewa
2016-04-12
Aqua complexes of transition metals are useful models for understanding the electronic structure of metal-oxide species relevant in photocatalytic water splitting. Moreover, spin-forbidden d-d transitions of aqua complexes provide valuable experimental data of spin-state energetics, which can be used for benchmarking of computational methods. Here, low-energy spin states of Fe(III) and Ru(III) aqua complexes are studied with an array of DFT and high-level wave function methods (CASPT2, RASPT2, NEVPT2, CCSD(T)-F12, and other coupled cluster methods up to full CCSDT). The results from single-reference and multireference methods are cross-checked, and the amount of multireference character for both considered spin states of [Fe(H2O)6](3+) is carefully analyzed. In addition to small [M(H2O)6](3+) clusters (M = Fe, Ru), we also employ larger models [M(H2O)6·(H2O)12](3+), with explicit water molecules in the second coordination sphere, to describe the situation in aqueous solution. By comparing the results for both types of models, our calculations evidence large and systematic solvation effects on the spin-state energetics. It is found that, due to the interaction with hydrogen-bonded water molecules in the second coordination sphere, the first coordination sphere undergoes a noticeable contraction and deformation. In consequence, the presence of solvation shell affects the relative energies of spin states by as much as 3-4 × 10(3) cm(-1) (∼10 kcal/mol). Once this solvation effect is accounted for, the spin-state energetics from CCSD(T) and NEVPT2 calculations turn out to be in an excellent agreement with the experimental estimates, which was not the case for isolated [M(H2O)6](3+) species is gas phase. We thus postulate that significant discrepancies between theory and experimental data for [Fe(H2O)6](3+) that were previously reported in the literature may be plausibly resolved and attributed to the neglect of explicit solvation effects and also, to some extent, to
NASA Astrophysics Data System (ADS)
Gambuzzi, Elisa; Pedone, Alfonso; Menziani, Maria Cristina; Angeli, Frédéric; Caurant, Daniel; Charpentier, Thibault
2014-01-01
Silicon and aluminium chemical environments in silicate and aluminosilicate glasses with compositions 60SiO2·20Na2O·20CaO (CSN), 60SiO2·20Al2O3·20CaO (CAS), 78SiO2·11Al2O3·11Na2O (NAS) and 60SiO2·10Al2O3·10Na2O·20CaO (CASN) have been investigated by 27Al and 29Si solid state magic angle spinning (MAS) and multiple quantum MAS (MQMAS) nuclear magnetic resonance (NMR) experiments. To interpret the NMR data, first-principles calculations using density functional theory were performed on structural models of these glasses. These models were generated by Shell-model molecular dynamics (MD) simulations. The theoretical NMR parameters and spectra were computed using the gauge including projected augmented wave (GIPAW) method and spin-effective Hamiltonians, respectively. This synergetic computational-experimental approach offers a clear structural characterization of these glasses, particularly in terms of network polymerization, chemical disorder (i.e. Si and Al distribution in second coordination sphere) and modifier cation distributions. The relationships between the local structural environments and the 29Si and 27Al NMR parameters are highlighted, and show that: (i) the isotropic chemical shift of both 29Si and 27Al increases of about +5 ppm for each Al added in the second sphere and (ii) both the 27Al and 29Si isotropic chemical shifts linearly decrease with the reduction of the average Si/Al-O-T bond angle. Conversely, 27Al and 29Si NMR parameters are much less sensitive to the connectivity with triple bridging oxygen atoms, precluding their indirect detection from 27Al and 29Si NMR.
Huang, Xinchuan; Valeev, Edward F; Lee, Timothy J
2010-12-28
One-particle basis set extrapolation is compared with one of the new R12 methods for computing highly accurate quartic force fields (QFFs) and spectroscopic data, including molecular structures, rotational constants, and vibrational frequencies for the H(2)O, N(2)H(+), NO(2)(+), and C(2)H(2) molecules. In general, agreement between the spectroscopic data computed from the best R12 and basis set extrapolation methods is very good with the exception of a few parameters for N(2)H(+) where it is concluded that basis set extrapolation is still preferred. The differences for H(2)O and NO(2)(+) are small and it is concluded that the QFFs from both approaches are more or less equivalent in accuracy. For C(2)H(2), however, a known one-particle basis set deficiency for C-C multiple bonds significantly degrades the quality of results obtained from basis set extrapolation and in this case the R12 approach is clearly preferred over one-particle basis set extrapolation. The R12 approach used in the present study was modified in order to obtain high precision electronic energies, which are needed when computing a QFF. We also investigated including core-correlation explicitly in the R12 calculations, but conclude that current approaches are lacking. Hence core-correlation is computed as a correction using conventional methods. Considering the results for all four molecules, it is concluded that R12 methods will soon replace basis set extrapolation approaches for high accuracy electronic structure applications such as computing QFFs and spectroscopic data for comparison to high-resolution laboratory or astronomical observations, provided one uses a robust R12 method as we have done here. The specific R12 method used in the present study, CCSD(T)(R12), incorporated a reformulation of one intermediate matrix in order to attain machine precision in the electronic energies. Final QFFs for N(2)H(+) and NO(2)(+) were computed, including basis set extrapolation, core-correlation, scalar
Liu, Hui; Shi, Deheng; Sun, Jinfeng; Zhu, Zunlue; Shulin, Zhang
2014-04-24
The potential energy curves (PECs) of 54 spin-orbit states generated from the 22 electronic states of O2 molecule are investigated for the first time for internuclear separations from about 0.1 to 1.0nm. Of the 22 electronic states, the X(3)Σg(-), A(')(3)Δu, A(3)Σu(+), B(3)Σu(-), C(3)Πg, a(1)Δg, b(1)Σg(+), c(1)Σu(-), d(1)Πg, f(1)Σu(+), 1(5)Πg, 1(3)Πu, 2(3)Σg(-), 1(5)Σu(-), 2(1)Σu(-) and 2(1)Δg are found to be bound, whereas the 1(5)Σg(+), 2(5)Σg(+), 1(1)Πu, 1(5)Δg, 1(5)Πu and 2(1)Πu are found to be repulsive ones. The B(3)Σu(-) and d(1)Πg states possess the double well. And the 1(3)Πu, C(3)Πg, A'(3)Δu, 1(5)Δg and 2(5)Σg(+) states are the inverted ones when the spin-orbit coupling is included. The PEC calculations are done by the complete active space self-consistent field (CASSCF) method, which is followed by the internally contracted multireference configuration interaction (icMRCI) approach with the Davidson correction. Core-valence correlation and scalar relativistic corrections are taken into account. The convergence of present calculations is evaluated with respect to the basis set and level of theory. The vibrational properties are discussed for the 1(5)Πg, 1(3)Πu, d(1)Πg and 1(5)Σu(-) states and for the second well of the B(3)Σu(-) state. The spin-orbit coupling effect is accounted for by the state interaction method with the Breit-Pauli Hamiltonian. The PECs of all the electronic states and spin-orbit states are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and compared with available experimental and other theoretical results. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is obtained that the effect of spin-orbit coupling on the spectroscopic parameters are small almost for all the electronic states involved in this paper except for the 1(5)Σu(-), 1(5)Πg and 1(3)Πu. PMID:24486866
Payne, Walter A.; Harding, Lawrence B.; Stief, Louis J.; Parker, James F. , 1925-; Klippenstein, Stephen J.; Nesbitt, Fred L.; Cody, Regina J.
2004-10-01
The rate coefficient has been measured under pseudo-first-order conditions for the Cl + CH{sub 3} association reaction at T = 202, 250, and 298 K and P = 0.3-2.0 Torr helium using the technique of discharge-flow mass spectrometry with low-energy (12-eV) electron-impact ionization and collision-free sampling. Cl and CH{sub 3} were generated rapidly and simultaneously by reaction of F with HCl and CH{sub 4}, respectively. Fluorine atoms were produced by microwave discharge in an approximately 1% mixture of F{sub 2} in He. The decay of CH{sub 3} was monitored under pseudo-first-order conditions with the Cl-atom concentration in large excess over the CH{sub 3} concentration ([Cl]{sub 0}/[CH{sub 3}]{sub 0} = 9-67). Small corrections were made for both axial and radial diffusion and minor secondary chemistry. The rate coefficient was found to be in the falloff regime over the range of pressures studied. For example, at T = 202 K, the rate coefficient increases from 8.4 x 10{sup -12} at P = 0.30 Torr He to 1.8 x 10{sup -11} at P = 2.00 Torr He, both in units of cm{sup 3} molecule{sup -1} s{sup -1}. A combination of ab initio quantum chemistry, variational transition-state theory, and master-equation simulations was employed in developing a theoretical model for the temperature and pressure dependence of the rate coefficient. Reasonable empirical representations of energy transfer and of the effect of spin-orbit interactions yield a temperature- and pressure-dependent rate coefficient that is in excellent agreement with the present experimental results. The high-pressure limiting rate coefficient from the RRKM calculations is k{sub 2} = 6.0 x 10{sup -11} cm{sup 3} molecule{sup -1} s{sup -1}, independent of temperature in the range from 200 to 300 K.
Yoshikawa, T.; Iwasaki, T.; Wada, K.; Suyama, K.
2006-07-01
To examine the procedures of the reprocessing, the vitrification and the geologic disposal, precise burn-up calculation for high burn-up and MOX fuels has been performed for not only PWR but also BWR by using SWAT and SWAT2 codes which are the integrated bum-up calculation code systems combined with the bum-up calculation code, ORIGEN2, and the transport calculation code, SRAC (the collision probability method) or MVP (the continuous energy Monte Carlo method), respectively. The calculation results shows that all of the evaluated items (heat generation and concentrations of Mo and Pt) largely increase and those significantly effect to the current procedures of the vitrification and the geologic disposal. The calculation result by SWAT2 confirms that the bundle calculation is required for BWR to be discussed about those effects in details, especially for the MOX fuel. (authors)
NASA Astrophysics Data System (ADS)
Troncoso Romero, David E.; Meyer-Baese, Uwe; Dolecek, Gordana Jovanovic
2014-12-01
This paper presents an extension to the theoretical lower bounds for the number of adders and for the adder depth in multiplierless single constant multiplications (SCM). It is shown that the number of prime factors of the constants is key information to extend the current lower bounds in certain cases that have not yet been exposed. Additionally, the hidden theoretical lower bound for the number of adders required to preserve the minimum adder depth is revealed.
NASA Astrophysics Data System (ADS)
Yamashita, Takefumi; Fujitani, Hideaki
2014-08-01
We study several free energy calculation methods in the dissociation process of lysozyme and its antibody. We introduce the multi-step targeted molecular dynamics (mTMD) method to determine the dissociation pathway. The dissociation free energy calculated along the mTMD dissociation pathway is significantly lower than that along the dissociation pathway determined by the steered molecular dynamics (SMD) method. This indicates that SMD leads to a meta-stable dissociation state. While the SMD restrains the distance between the two proteins, the mTMD restrains the internal structures additionally. We discuss the effect of fragility of the protein structures on the free energy calculations.
Deridder, Sander; Desmet, Gert
2012-02-01
Using computational fluid dynamics (CFD), the effective B-term diffusion constant γ(eff) has been calculated for four different random sphere packings with different particle size distributions and packing geometries. Both fully porous and porous-shell sphere packings are considered. The obtained γ(eff)-values have subsequently been used to determine the value of the three-point geometrical constant (ζ₂) appearing in the 2nd-order accurate effective medium theory expression for γ(eff). It was found that, whereas the 1st-order accurate effective medium theory expression is accurate to within 5% over most part of the retention factor range, the 2nd-order accurate expression is accurate to within 1% when calculated with the best-fit ζ₂-value. Depending on the exact microscopic geometry, the best-fit ζ₂-values typically lie in the range of 0.20-0.30, holding over the entire range of intra-particle diffusion coefficients typically encountered for small molecules (0.1 ≤ D(pz)/D(m) ≤ 0.5). These values are in agreement with the ζ₂-value proposed by Thovert et al. for the random packing they considered. PMID:22236565
Homayoon, Zahra
2014-09-28
A new, full (nine)-dimensional potential energy surface and dipole moment surface to describe the NO{sup +}(H{sub 2}O) cluster is reported. The PES is based on fitting of roughly 32 000 CCSD(T)-F12/aug-cc-pVTZ electronic energies. The surface is a linear least-squares fit using a permutationally invariant basis with Morse-type variables. The PES is used in a Diffusion Monte Carlo study of the zero-point energy and wavefunction of the NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) complexes. Using the calculated ZPE the dissociation energies of the clusters are reported. Vibrational configuration interaction calculations of NO{sup +}(H{sub 2}O) and NO{sup +}(D{sub 2}O) using the MULTIMODE program are performed. The fundamental, a number of overtone, and combination states of the clusters are reported. The IR spectrum of the NO{sup +}(H{sub 2}O) cluster is calculated using 4, 5, 7, and 8 modes VSCF/CI calculations. The anharmonic, coupled vibrational calculations, and IR spectrum show very good agreement with experiment. Mode coupling of the water “antisymmetric” stretching mode with the low-frequency intermolecular modes results in intensity borrowing.
NASA Astrophysics Data System (ADS)
Jönsson, P.; Radžiūtė, L.; Gaigalas, G.; Godefroid, M. R.; Marques, J. P.; Brage, T.; Froese Fischer, C.; Grant, I. P.
2016-01-01
Multiconfiguration Dirac-Hartree-Fock (MCDHF) calculations and relativistic configuration interaction (RCI) calculations are performed for states of the 3s23p2, 3s3p3 and 3s23p3d configurations in the Si-like ions Ti IX - Ge XIX, Sr XXV, Zr XXVII and Mo XXIX. Valence and core-valence electron correlation effects are accounted for through large configuration state function expansions. Calculated energy levels are compared with data from other calculations and with experimental data from the reference databases. Lifetime and transition rates along with uncertainty estimations are given for all ions. Energies from the calculations are in excellent agreement with observations and computed wavelength are almost of spectroscopic accuracy, aiding line identification in spectra. Full Tables 2, 3, and 5 are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/585/A26
NASA Astrophysics Data System (ADS)
Roberts, Ralph
2001-09-01
The accuracy of a CT-based dose calculation on a treatment planning system (TPS) for a radiotherapy patient with a metallic prosthesis has not previously been reported. In this study, the accuracy of the CT-based inhomogeneity correction on a pencil beam TPS (Helax TMS) was determined in a phantom containing a metallic prosthesis. A steel prosthesis phantom and a titanium prosthesis phantom were investigated. The phantoms were CT-scanned and dose plans produced on the TPS, using the CT images to provide density information for the inhomogeneity corrections. Verification measurements were performed on a linear accelerator for 6 and 15 MV x-rays. Measured dose profiles at three different depths were compared to the calculations of the TPS. For the titanium prosthesis and for 6 MV x-rays, the TPS overestimated the beam attenuation by approximately 20% at 15 and 20 cm depths in the phantom. This is due to a limitation in the density allocation of this TPS: any Hounsfield number (HN) above a certain threshold is allocated the density of steel. For the steel prosthesis, the TPS performed the correct mapping of HN to mass density. The dose calculation was within 6% for 6 MV x-rays at 15 and 20 cm depths. However, the accuracy of dose calculation varied with beam energy and depth, with large errors in the region close to the prosthesis. The TPS overestimated the dose by 11% for 6 MV and 15% for 15 MV x-rays at 11 cm depth, 2.5 cm beyond the steel prosthesis. These results highlight the limitations in the density allocation of this TPS and demonstrate shortcomings in the pencil beam dose calculation.
NASA Astrophysics Data System (ADS)
Zhou, Chang-Xin; Mo, Jian-Xia; Wang, Xue-Yao; Zhang, Jian; Gan, Li-She
2011-03-01
Using DFT at the B3LYP/6-31+G (d) level, DFT-D at the wb97xd/tzvpp level and TD-DFT at the B3LYP/aug-cc-pVDZ level, computational analysis of the first examples of naturally occurring dimeric indolizidine alkaloids, flueggenines A and B, accomplished the simulation and interpretation of their IR, UV and ECD spectra. Compared with the experimental ones, the calculated IR and UV spectra allowed the reinforcement of the carbon skeletons and functional groups. Calculation of the ECD spectra assured the formerly assigned absolute configurations for flueggenines A and B.
NASA Astrophysics Data System (ADS)
Karton, Amir; Martin, Jan M. L.
2012-10-01
Accurate isomerization energies are obtained for a set of 45 C8H8 isomers by means of the high-level, ab initio W1-F12 thermochemical protocol. The 45 isomers involve a range of hydrocarbon functional groups, including (linear and cyclic) polyacetylene, polyyne, and cumulene moieties, as well as aromatic, anti-aromatic, and highly-strained rings. Performance of a variety of DFT functionals for the isomerization energies is evaluated. This proves to be a challenging test: only six of the 56 tested functionals attain root mean square deviations (RMSDs) below 3 kcal mol-1 (the performance of MP2), namely: 2.9 (B972-D), 2.8 (PW6B95), 2.7 (B3PW91-D), 2.2 (PWPB95-D3), 2.1 (ωB97X-D), and 1.2 (DSD-PBEP86) kcal mol-1. Isomers involving highly-strained fused rings or long cumulenic chains provide a 'torture test' for most functionals. Finally, we evaluate the performance of composite procedures (e.g. G4, G4(MP2), CBS-QB3, and CBS-APNO), as well as that of standard ab initio procedures (e.g. MP2, SCS-MP2, MP4, CCSD, and SCS-CCSD). Both connected triples and post-MP4 singles and doubles are important for accurate results. SCS-MP2 actually outperforms MP4(SDQ) for this problem, while SCS-MP3 yields similar performance as CCSD and slightly bests MP4. All the tested empirical composite procedures show excellent performance with RMSDs below 1 kcal mol-1.
Li, Y.; Krieger, J.B. ); Norman, M.R. ); Iafrate, G.J. )
1991-11-15
The optimized-effective-potential (OEP) method and a method developed recently by Krieger, Li, and Iafrate (KLI) are applied to the band-structure calculations of noble-gas and alkali halide solids employing the self-interaction-corrected (SIC) local-spin-density (LSD) approximation for the exchange-correlation energy functional. The resulting band gaps from both calculations are found to be in fair agreement with the experimental values. The discrepancies are typically within a few percent with results that are nearly the same as those of previously published orbital-dependent multipotential SIC calculations, whereas the LSD results underestimate the band gaps by as much as 40%. As in the LSD---and it is believed to be the case even for the exact Kohn-Sham potential---both the OEP and KLI predict valence-band widths which are narrower than those of experiment. In all cases, the KLI method yields essentially the same results as the OEP.
NASA Astrophysics Data System (ADS)
Vogt, Natalja; Khaikin, Leonid S.; Grikina, Olga E.; Rykov, Anatolii N.
2013-10-01
The equilibrium structure of uracil, one of the nucleobases, which build nucleic acids, has been determined for the first time by the gas-phase electron diffraction (GED) method. The necessary rovibrational corrections to the experimental internuclear distances have been calculated with quadratic and cubic force constants in the MP2(all)/cc-pVTZ approximation. For the first time, the equilibrium structure has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-zeta basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ). The optimized structural parameters have been corrected for the diffuse-function effects and extrapolated to the higher basis set (cc-pwCVQZ) using results of MP2 computations (named as best ab initio structure). The GED equilibrium structure remarkably agrees with the best ab initio one as well as with that one derived from microwave (MW) rotational constants by Puzzarini and Barone. Thus, it has been revealed that the precise experiment and coupled-cluster calculations yield the same results when accurate vibrational corrections (including anharmonic ones) are considered in the experimental structural analysis. Moreover, it has been shown that the equilibrium structure derived from the GED data, being in general of one order less accurate than that determined from the MW rotational constants, is still reliable and accurate.
Rice, Betsy M; Byrd, Edward F C
2016-03-01
Quantum and classical molecular dynamics simulations are used to explore whether chemical reactivity of shocked formic acid occurs at pressures greater than 15 GPa, a question arising from results of different shock compression experiments. The classical molecular dynamics simulations were performed using a quantum-based nonreactive pair additive interaction potential whereas the full resolution quantum mechanical molecular dynamics simulations allow chemical reactions. Although the shock Hugoniot curve calculated using nonreactive classical MD for formic acid is in reasonable agreement with one set of experimental results, shock Hugoniot points calculated using Born-Oppenheimer MD at 30 GPa are in agreement with the set of experimental data that suggests chemical reactivity at these elevated temperatures and pressures. Examination of atomic positions throughout the Born-Oppenheimer MD trajectories clearly indicates extensive and complex chemical reaction, chiefly involving hydrogen-atom transfer and intermolecular complexation. PMID:26654191
NASA Astrophysics Data System (ADS)
Boopalachandran, Praveenkumar; Sheu, Hong-Li; Laane, Jaan
2012-09-01
The infrared and Raman spectra of 2-chloropyridine, 3-chloropyridine, 2-bromopyridine, and 3-bromopyridine have been recorded and assigned. Density functional theory calculations (B3LYP with 6-311++G(d,p) basis set) produce excellent agreement with the experimental values. Ab initio calculations (MP2 with the cc-pVTZ basis set) were utilized to compute the molecular structures, which were compared to those of pyridine and the corresponding fluoropyridines. All of the 2-halopyridines show a shortening of the N-C(2) bond resulting from the halogen substitution on the C(2) carbon atom. All of the other ring bond distances for the 2-halopyridines and 3-halopyridines are little different from pyridine itself.
Hua -Gen Yu; Han, Huixian; Guo, Hua
2016-03-29
Vibrational energy levels of the ammonium cation (NH4+) and its deuterated isotopomers are calculated using a numerically exact kinetic energy operator on a recently developed nine-dimensional permutation invariant semiglobal potential energy surface fitted to a large number of high-level ab initio points. Like CH4, the vibrational levels of NH4+ and ND4+ exhibit a polyad structure, characterized by a collective quantum number P = 2(v1 + v3) + v2 + v4. As a result, the low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm–1.
Rodríguez, Juan I; Ayers, Paul W; Götz, Andreas W; Castillo-Alvarado, F L
2009-07-14
A new approach for computing the atom-in-molecule [quantum theory of atoms in molecule (QTAIM)] energies in Kohn-Sham density-functional theory is presented and tested by computing QTAIM energies for a set of representative molecules. In the new approach, the contribution for the correlation-kinetic energy (T(c)) is computed using the density-functional theory virial relation. Based on our calculations, it is shown that the conventional approach where atomic energies are computed using only the noninteracting part of the kinetic energy might be in error by hundreds of kJ/mol. PMID:19603962
Shi, Deheng; Li, Peiling; Sun, Jinfeng; Zhu, Zunlue
2014-01-01
The potential energy curves (PECs) of 28 Ω states generated from 9 Λ-S states (X(2)Π, 1(4)Π, 1(6)Π, 1(2)Σ(+), 1(4)Σ(+), 1(6)Σ(+), 1(4)Σ(-), 2(4)Π and 1(4)Δ) are studied for the first time using an ab initio quantum chemical method. All the 9 Λ-S states correlate to the first two dissociation limits, N((4)Su)+Se((3)Pg) and N((4)Su)+Se((3)Dg), of NSe radical. Of these Λ-S states, the 1(6)Σ(+), 1(4)Σ(+), 1(6)Π, 2(4)Π and 1(4)Δ are found to be rather weakly bound states. The 1(2)Σ(+) is found to be unstable and has double wells. And the 1(6)Σ(+), 1(4)Σ(+), 1(4)Π and 1(6)Π are found to be the inverted ones with the SO coupling included. The PEC calculations are made by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson modification. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. The convergence of the present calculations is discussed with respect to the basis set and the level of theory. Core-valence correlation corrections are included with a cc-pCVTZ basis set. Scalar relativistic corrections are calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of spin-orbit coupling constants is discussed in brief for some Λ-S states with one shallow well on each PEC. The spectroscopic parameters of 9 Λ-S and 28 Ω states are determined by fitting the first ten vibrational levels whenever available, which are calculated by solving the rovibrational Schrödinger equation with Numerov's method. The splitting energy in the X(2)Π Λ-S state is determined to be about 864.92 cm(-1), which agrees favorably with the measurements of 891.80 cm(-1). Moreover, other spectroscopic parameters of Λ-S and Ω states involved here are
Xu, T.; Barich, D.H.; Torres, P.D.; Haw, J.F.
1997-01-15
The benzenium, toluenium, and ethylbenzenium ions were synthesized on aluminium bromide by coadsorption of the precursors with either HBr or alkyl bromide. Principal components of the {sup 13}C chemical shift tensors for the ring carbons of these species were measured from magic angle spinning spectra. The benzenium ion was static at 77 K but underwent both proton scrambling and anisotropic rotation at 298 K as well as oligomerization at higher loadings. The para form of the toluenium ion was the dominant isomer at 77 K, but a temperature-dependent equilibrium between the para and ortho isomers was observed at 273 K. The energy calculations at MP4(fc,sdq)/ 6-311+G{sup *}//MP2/6-311+G{sup *} with thermal corrections resulted in good agreement between calculated and measured proton affinities for benzene, toluene, and ethylbenzene. For toluenium ion, the energies of the ortho and meta isomers were 1.2 and 5.4 kcal/mol, respectively, above the para isomer, consistent with the temperature-dependent {sup 13}C NMR spectra in the solid state. {sup 13}C chemical shift tensors calculated at the GIAO-MP2/tzp/dz//MP2/ 6-311+G{sup *} and GIAO-MP2/tzp/dz//B3LYP/6-311+G{sup *} levels of theory were in very close agreement with each other and generally in satisfactory agreement with experimental principal components. 64 refs., 8 figs., 4 tabs.
NASA Astrophysics Data System (ADS)
Dolmella, A.; Gatto, S.; Girardi, E.; Bandoli, G.
1999-12-01
Coumatetralyl and chlorophacinone, two substances related to 4-hydroxycoumarin (HC) and to 1,3-indandione (ID), respectively, show activity as anticoagulant rodenticides. In the present study we have investigated the solid-state structures of coumatetralyl and chlorophacinone by means of X-ray single-crystal and powder diffraction, along with thermal analysis. The crystal structures of the two compounds have been used as input geometries for a series of computational chemistry efforts, involving other anticoagulant derivatives as well. Thus, ab initio, semiempirical molecular orbital, molecular mechanics and molecular dynamics/simulated annealing calculations have been performed on thirteen anticoagulant rodenticides. In particular, the annealing calculations have been made to assess the conformational freedom of the compounds under scrutiny. All the generated conformers have been classified into families. The classification has first been made empirically, and then validated by means of a cluster analysis. A number of structural and physico-chemical parameters derived from the calculations has been used in turn for structure-activity relationships (SARs) investigations. In the latter, we have assessed how the selected parameters affect toxicity. The results seem to be consistent with a three-dimensional biophore model, in which higher toxicity is predicted for the more voluminous rodenticides. We suggest that these compounds better fit the active site of the target enzyme vitamin K 2,3-epoxide reductase (KO-reductase).
NASA Astrophysics Data System (ADS)
Shi, De-Heng; Liu, Qionglan; Yu, Wei; Sun, Jinfeng; Zhu, Zunlue
2014-05-01
The potential energy curves (PECs) of 23 Ω states generated from the 12 electronic states (X1 Σ +, 21 Σ +, 11 Σ -, 11 Π, 21 Π, 11 Δ, 13 Σ +, 23 Σ +, 13 Σ -, a3 Π, 23 Π and 13 Δ) are studied for the first time. All the states correlate to the first dissociation channel of the SiBr+ cation. Of these electronic states, the 23 Σ + is the repulsive one without the spin-orbit coupling, whereas it becomes the bound one with the spin-orbit coupling added. On the one hand, without the spin-orbit coupling, the 11 Π, 21 Π and 23 Π are the rather weakly bound states, and only the 11 Π state possesses the double well; on the other hand, with the spin-orbit coupling included, the a3 Π and 11 Π states possess the double well, and the 13 Σ + and 13 Σ - are the inverted states. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with the Davidson modification. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation with a cc-pVTZ-DK basis set. Core-valence correlation correction is included with a cc-pCVTZ basis set. The spin-orbit coupling is accounted for by the state interaction method with the Breit-Pauli Hamiltonian using the all-electron aug-cc-pCVTZ basis set. All the PECs are extrapolated to the complete basis set limit. The variation with internuclear separation of the spin-orbit coupling constant is discussed in brief. The spectroscopic parameters are evaluated for the 11 bound electronic states and the 23 bound Ω states, and are compared with available measurements. Excellent agreement has been found between the present results and the experimental data. It demonstrates that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The Franck-Condon factors and radiative lifetimes of the transitions from the a3 Π 0 + and a3 Π 1 states to the X1 Σ + 0+ state are calculated for several low vibrational levels, and
Shi, Deheng; Liu, Qionglan; Sun, Jinfeng; Zhu, Zunlue
2014-03-25
The potential energy curves (PECs) of 28 Ω states generated from the 12 states (X(4)Σ(-), 1(2)Π, 1(2)Σ(-), 1(2)Δ, 1(2)Σ(+), 2(2)Π, A(4)Π, B(4)Σ(-), 3(2)Π, 1(6)Σ(-), 2(2)Σ(-) and 1(6)Π) of the BN(+) cation are studied for the first time for internuclear separations from about 0.1 to 1.0 nm using an ab initio quantum chemical method. All the Λ-S states correlate to the first four dissociation channels. The 1(6)Σ(-), 3(2)Π and A(4)Π states are found to be the inverted ones. The 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are found to possess the double well. The PECs are calculated by the complete active space self-consistent field method, which is followed by the internally contracted multireference configuration interaction approach with the Davidson correction. Core-valence correlation correction is included by a cc-pCV5Z basis set. Scalar relativistic correction is calculated by the third-order Douglas-Kroll Hamiltonian approximation at the level of a cc-pV5Z basis set. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian using the all-electron cc-pCV5Z basis set. All the PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are obtained, and the vibrational properties of 1(2)Σ(+), 2(2)Π, 3(2)Π and 2(2)Σ(-) states are evaluated. Analyses demonstrate that the spectroscopic parameters reported here can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters are not obvious almost for all the Λ-S states involved in the present paper. PMID:24334021
Baker, Christopher M.; Lopes, Pedro E. M.; Zhu, Xiao; Roux, Benoît; MacKerell, Alexander D.
2010-01-01
Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce accurately pure liquid phase thermodynamic properties as well as additional target data. While the polarizable force field resulting from this optimization procedure has been shown to satisfactorily reproduce a wide range of experimental reference data across numerous series of small molecules, a slight but systematic overestimate of the hydration free energies has also been noted. Here, the reproduction of experimental hydration free energies is greatly improved by the introduction of pair-specific LJ parameters between solute heavy atoms and water oxygen atoms that override the standard LJ parameters obtained from combining rules. The changes are small and a systematic protocol is developed for the optimization of pair-specific LJ parameters and applied to the development of pair-specific LJ parameters for alkanes, alcohols and ethers. The resulting parameters not only yield hydration free energies in good agreement with experimental values, but also provide a framework upon which other pair-specific LJ parameters can be added as new compounds are parametrized within the CHARMM Drude polarizable force field. Detailed analysis of the contributions to the hydration free energies reveals that the dispersion interaction is the main source of the systematic errors in the hydration free energies. This information suggests that the systematic error may result from problems with the LJ combining rules and is combined with analysis of the pair-specific LJ parameters obtained in this work to identify a preliminary improved combining rule. PMID:20401166
NASA Astrophysics Data System (ADS)
Meehan, Timothy Erickson
1992-01-01
Unrestricted Hartree-Fock calculations were performed on Fe_{x}CO clusters to model the CO(alpha_1), CO(alpha_2), and CO( alpha_3) adsorptions on the Fe(100) surface. Clusters of FeCO(C_{4v}) and a multiplicity of 5, Fe_2 CO(C_{2v}) and a multiplicity of 7, and Fe_2CO(C _{s}) and a multiplicity of 7, were constructed to model, respectively, the adsorption for the on top site, bridging site, and tilted CO structure at the 4-fold site. The CO position was optimized with respect to the Fe bulk distances using gradient techniques and the partial geometry optimization. CO stretching frequencies were calculated for each optimized geometry, and we find no evidence supporting CO adsorption in the bridging site. Using a full basis set the calculated CO stretching frequencies for the FeCO(C_{4v}), Fe_2CO(C_ {2v}), and the Fe_2 CO(C_{s}) clusters are 1992, 1767, and 771 cm^{ -1}, respectively. The CSOV analysis was executed to analyze the major orbital interactions between the CO and Fe_{x} clusters. For both Fe_2CO clusters, the CO pi^* perpendicular to the Fe _2 axis had a more significant contribution involving the pi backdonation from the Fe_2 clusters. Furthermore, the spin minority d electrons are mainly responsible for the pi backdonation. Due to problems with SCF convergence incurred during the Fe_{x}CO studies, we were forced to investigate a number of different techniques to achieve SCF convergence. Therefore, techniques that generate starting guesses of the eigenvectors for the SCF procedure and techniques used to accelerate SCF convergence are reviewed. The standard guesses of H _{core} and charge build -up are examined, and we introduce a new incremental cluster method for generating starting guesses for large clusters. The standard techniques of extrapolation, DIIS, damping, level shifting, restrict, and symmetry blocking are examined, and we also developed the hacker method and partial geometry optimization as new techniques to achieve SCF convergence. Results
Nixha, Arleta Rifati; Arslan, Mustafa; Atalay, Yusuf; Gençer, Nahit; Ergün, Adem; Arslan, Oktay
2013-08-01
Synthesis of carbazole substituted chalcone urea derivatives and their polyphenol oxidase enzyme activity effects on the diphenolase activity of banana tyrosinase were evaluated. Tyrosinase has been purified from banana on an affinity gel comprised of Sepharose 4B-L-tyrosine-p-aminobenzoic acid. The results showed that most of the compounds (3,4,5a,5d-h) inhibited and some of them (5c,5i-l) activated the tyrosinase enzyme activity. The molecular calculations were performed using Gaussian software for the synthesized compounds to explain the experimental results. PMID:22803668
Talaczyńska, Alicja; Lewandowska, Kornelia; Jelińska, Anna; Garbacki, Piotr; Podborska, Agnieszka; Zalewski, Przemysław; Oszczapowicz, Irena; Sikora, Adam; Kozak, Maciej; Cielecka-Piontek, Judyta
2015-01-01
FT-IR and Raman scattering spectra of cefuroxime axetil were proposed for identification studies of its crystalline and amorphous forms. An analysis of experimental spectra was supported by quantum-chemical calculations performed with the use of B3LYP functional and 6-31G(d,p) as a basis set. The geometric structure of a cefuroxime axetil molecule, HOMO and LUMO orbitals, and molecular electrostatic potential were also determined by using DFT (density functional theory). The benefits of applying FT-IR and Raman scattering spectroscopy for characterization of drug subjected to degradation were discussed. PMID:25654137
Lewandowska, Kornelia; Jelińska, Anna; Zalewski, Przemysław; Oszczapowicz, Irena; Sikora, Adam; Kozak, Maciej
2015-01-01
FT-IR and Raman scattering spectra of cefuroxime axetil were proposed for identification studies of its crystalline and amorphous forms. An analysis of experimental spectra was supported by quantum-chemical calculations performed with the use of B3LYP functional and 6-31G(d,p) as a basis set. The geometric structure of a cefuroxime axetil molecule, HOMO and LUMO orbitals, and molecular electrostatic potential were also determined by using DFT (density functional theory). The benefits of applying FT-IR and Raman scattering spectroscopy for characterization of drug subjected to degradation were discussed. PMID:25654137
Bachollet, Sylvestre P J T; Volz, Daniel; Fiser, Béla; Münch, Stephan; Rönicke, Franziska; Carrillo, Jokin; Adams, Harry; Schepers, Ute; Gómez-Bengoa, Enrique; Bräse, Stefan; Harrity, Joseph P A
2016-08-22
Ten borylated bipyridines (BOBIPYs) have been synthesized and selected structural modifications have been made that allow useful structure-optical property relationships to be gathered. These systems have been further investigated using DFT calculations and spectroscopic measurements, showing blue to green fluorescence with quantum yields up to 41 %. They allow full mapping of the structure to determine where selected functionalities can be implemented, to tune the optical properties or to incorporate linking groups. The best derivative was thus functionalised with an alkyne linker, which would enable further applications through click chemistry and in this optic, the stability of the fluorophores has been evaluated. PMID:27465819
Malenda, R. F.; Price, T. J.; Stevens, J.; Uppalapati, S. L.; Fragale, A.; Weiser, P. M.; Kuczala, A.; Hickman, A. P.; Talbi, D.
2015-06-14
We have performed extensive calculations to investigate thermal energy, rotationally inelastic collisions of NaK (A{sup 1}Σ{sup +}) with He. We determined a potential energy surface using a multi-reference configuration interaction wave function as implemented by the GAMESS electronic structure code, and we have performed coupled channel scattering calculations using the Arthurs and Dalgarno formalism. We also calculate the Grawert coefficients B{sub λ}(j, j′) for each j → j′ transition. These coefficients are used to determine the probability that orientation and alignment are preserved in collisions taking place in a cell environment. The calculations include all rotational levels with j or j′ between 0 and 50, and total (translational and rotational) energies in the range 0.0002–0.0025 a.u. (∼44–550 cm{sup −1}). The calculated cross sections for transitions with even values of Δj tend to be larger than those for transitions with odd Δj, in agreement with the recent experiments of Wolfe et al. (J. Chem. Phys. 134, 174301 (2011)). The calculations of the energy dependence of the cross sections and the calculations of the fraction of orientation and alignment preserved in collisions also exhibit distinctly different behaviors for odd and even values of Δj. The calculations also indicate that the average fraction of orientation or alignment preserved in a transition becomes larger as j increases. We interpret this behavior using the semiclassical model of Derouard, which also leads to a simple way of visualizing the distribution of the angles between the initial and final angular momentum vectors j and j′. Finally, we compare the exact quantum results for j → j′ transitions with results based on the simpler, energy sudden approximation. That approximation is shown to be quite accurate.
NASA Astrophysics Data System (ADS)
Shi, Deheng; Liu, Qionglan; Wang, Shuai; Sun, Jinfeng; Zhu, Zunlue
2015-01-01
The potential energy curves (PECs) of 59 Ω states generated from the 17 Λ-S states (X1Σ+, a3Σ+, 15Σ+, b3Δ, c3Π, 15Π, 25Σ+, 23Δ, 23Π, 33Σ+, A1Π, 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π) of AsP molecule are studied for the first time for internuclear separations from about 0.10 to 1.10 nm. All the Λ-S states are contributed to the first three dissociation channels of AsP molecule except for the A1Π. The 23Σ+, 35Σ+, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the repulsive states. The a3Σ+, 15Π, b3Δ, 17Σ+, 15Δ, 25Δ, and 25Π are found to be the inverted states. Each of the 33Σ+, c3Π, 23Π, 15Π, and 15Σ+ states has one potential barrier. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with Davidson correction. Core-valence correlation and scalar relativistic corrections are included. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling effect is accounted for. All these PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the bound states involved, and are compared with available measurements. Excellent agreement has been found between the present results and the measurements. It shows that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters is not obvious for all the Λ-S bound states except for few ones such as 15Σ+ and c3Π.
Yang, Linlin; Guo, Lianshun; Chen, Qianqian; Sun, Huafei; Yan, Hui; Zeng, Qinghua; Zhang, Xianxi; Pan, Xu; Dai, Songyuan
2012-09-01
A series of unsymmetrical phthalocyanine sensitizer candidates with different donor and acceptor substituents, namely ZnPcBPh, ZnPcBOPh, ZnPcBtBu, ZnPcBN(Ph)₂, ZnPcBNHPh, ZnPcBNH₂, ZnPcBNHCH₃ and ZnPcBN(CH₃)₂, were designed and calculated using density functional theory (DFT) and time-dependent DFT calculations. The molecular orbital energy levels, the molecular orbital spatial distributions and the electronic absorption spectra of the ZnPcB series molecules were compared with those of TT7 and TT8 to reveal the substituent effects of different donor and acceptor groups on the phthalocyanine compounds and select good sesitizer candidates. The results show that some of these compounds have considerably smaller orbital energy gaps, red-shifted absorption bands and better charge-separated states, causing them to absorb photons in the lower energy region. Several new absorption bands emerge in the 400-600 nm region, which makes it possible for them to become panchromatic sensitizers. This characteristic is superior to the phthalocyanine sensitizers reported previously, including the current record holder, PcS6. The sensitizer candidates screened in the current work are very promising for providing good performance and might even challenge the photon-to-electricity conversion efficiency record of 4.6% for phthalocyanine sensitizers. PMID:23085158
NASA Astrophysics Data System (ADS)
Jamróz, Marta K.; Bąk, Joanna; Gliński, Jan A.; Koczorowska, Agnieszka; Wawer, Iwona
2009-09-01
Actein is a prominent triterpene glycoside occurring in Actaea racemosa. The triterpene glycosides are believed to be responsible for the estrogenic activity of an extract prepared from this herb. We determined in the crystal structure of actein by X-ray crystallography to be monoclinic P2(1) chiral space group. Refining the disorder, we determined 70% and 30% of contributions of ( S)- and ( R)-actein, respectively. The IR and Raman spectra suggest that actein forms at least four different types of hydrogen bonds. The 13C NMR spectra of actein were recorded both in solution and solid state. The 13C CPMAS spectrum of actein displays multiplet signals, in agreement with the crystallographic data. The NMR shielding constants were calculated for actein using GIAO approach and a variety of basis sets: 6-31G**, 6-311G**, 6-31+G**, cc-pVDZ, cc-pVDZ-su1 and 6-31G**-su1, as well as IGLO approach combined with the IGLO II basis set. The best results (RMSD of 1.6 ppm and maximum error of 3.4 ppm) were obtained with the 6-31G**-su1 basis set. The calculations of the shielding constants are helpful in the interpretation of the 13C CPMAS NMR spectra of actein and actein's analogues.
Woldegebriel, Michael
2015-11-17
In toxicology screening (forensic, food-safety), due to several analytical errors (e.g., retention time shift, lack of repeatability in m/z scans, etc.), the ability to confidently identify/confirm a compound remains a challenge. Due to these uncertainties, a probabilistic approach is currently preferred. However, if a probabilistic approach is followed, the only statistical method that is capable of estimating the probability of whether the compound of interest (COI) is present/absent in a given sample is Bayesian statistics. Bayes' theorem can combine prior information (prior probability) with data (likelihood) to give an optimal probability (posterior probability) reflecting the presence/absence of the COI. In this work, a novel method for calculating an informative prior probability for a Bayesian model in targeted toxicology screening is introduced. In contrast to earlier proposals making use of literature citation rates and the prior knowledge of the analyst, this method presents a thorough and nonsubjective approach. The formulation approaches the probability calculation as a clustering and random draw problem that incorporates few analytical method parameters meticulously estimated to reflect sensitivity and specificity of the system. The practicality of the method has been demonstrated and validated using real data and simulated analytical techniques. PMID:26482700
Theoretical calculation of the dehydrogenation of ethanol on a Rh/CeO2(111) surface.
Chen, Hui-Lung; Liu, Shih-Hung; Ho, Jia-Jen
2006-08-01
We applied periodic density-functional theory (DFT) to investigate the dehydrogenation of ethanol on a Rh/CeO2 (111) surface. Ethanol is calculated to have the greatest energy of adsorption when the oxygen atom of the molecule is adsorbed onto a Ce atom in the surface, relative to other surface atoms (Rh or O). Before forming a six-membered ring of an oxametallacyclic compound (Rh-CH2CH2O-Ce(a)), two hydrogen atoms from ethanol are first eliminated; the barriers for dissociation of the O-H and the beta-carbon (CH2-H) hydrogens are calculated to be 12.00 and 28.57 kcal/mol, respectively. The dehydrogenated H atom has the greatest adsorption energy (E(ads) = 101.59 kcal/mol) when it is adsorbed onto an oxygen atom of the surface. The dehydrogenation continues with the loss of two hydrogens from the alpha-carbon, forming an intermediate species Rh-CH2CO-Ce(a), for which the successive barriers are 34.26 and 40.84 kcal/mol. Scission of the C-C bond occurs at this stage with a dissociation barrier Ea = 49.54 kcal/mol, to form Rh-CH(2(a)) + 4H(a) + CO(g). At high temperatures, these adsorbates desorb to yield the final products CH(4(g)), H(2(g)), and CO(g). PMID:16869591
Given, P.H.; Weldon, D.; Zoeller, J.H.
1984-03-01
The various formulae for calculating calorific values for coals from ultimate analyses depend essentially on a propositon due to Dulong, that the heat of combustion of an organic compound is nearly equal to the heats of combustion of the elements in it, multiplied by their percentage content in the compound in question. This proposition assumes that the enthalpy of decomposition is negligible compared with the heat of combustion. The various published formulae, such as that due to Mott and Spooner, include empirical adjustments to allow for the fact that the enthalpy of formation or decomposition of no organic compound is zero (except rarely by chance). A new equation is proposed, which excludes empirical correction terms but includes a term explicitly related to the enthalpy of decomposition. As expected from the behavior of known compounds, this enthalpy varies with rank, but it also varies at the same level of rank with the geological history of the sample: rank is not the only source of variance in coal properties. The new equation is at least as effective in predicting calorific values for a set of 992 coals as equivalent equations derived for 6 subsets of the coals. On the whole, the distributions of differences between observed and calculated calorific values are skewed to only a small extent. About 86% of the differences lie between -300 and +300 Btu/lb (+- 700 kJ/kg). 10 references, 7 figures, 4 tables.
NASA Astrophysics Data System (ADS)
Li, L. H.; Hu, L.; Yang, S. J.; Wang, W. L.; Wei, B.
2016-01-01
The thermodynamic properties, including the density, volume expansion coefficient, ratio of specific heat to emissivity of intermetallic Ni7Zr2 alloy, have been measured using the non-contact electrostatic levitation technique. These properties vary linearly with temperature at solid and liquid states, even down to the obtained maximum undercooling of 317 K. The enthalpy, glass transition, diffusion coefficient, shear viscosity, and surface tension were obtained by using molecular dynamics simulations. Ni7Zr2 has a relatively poor glass forming ability, and the glass transition temperature is determined as 1026 K. The inter-diffusivity of Ni7Zr2 alloy fitted by Vogel-Fulcher-Tammann law yields a fragility parameter of 8.49, which indicates the fragile nature of this alloy. Due to the competition of increased thermodynamic driving force and decreased atomic diffusion, the dendrite growth velocity of Ni7Zr2 compound exhibits double-exponential relationship to the undercooling. The maximum growth velocity is predicted to be 0.45 m s-1 at the undercooling of 335 K. Theoretical analysis reveals that the dendrite growth is a diffusion-controlled process and the atomic diffusion speed is only 2.0 m s-1.
Shi, Deheng; Liu, Qionglan; Wang, Shuai; Sun, Jinfeng; Zhu, Zunlue
2015-01-25
The potential energy curves (PECs) of 59 Ω states generated from the 17 Λ-S states (X(1)Σ(+), a(3)Σ(+), 1(5)Σ(+), b(3)Δ, c(3)Π, 1(5)Π, 2(5)Σ(+), 2(3)Δ, 2(3)Π, 3(3)Σ(+), A(1)Π, 2(3)Σ(+), 3(5)Σ(+), 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π) of AsP molecule are studied for the first time for internuclear separations from about 0.10 to 1.10nm. All the Λ-S states are contributed to the first three dissociation channels of AsP molecule except for the A(1)Π. The 2(3)Σ(+), 3(5)Σ(+), 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π are found to be the repulsive states. The a(3)Σ(+), 1(5)Π, b(3)Δ, 1(7)Σ(+), 1(5)Δ, 2(5)Δ, and 2(5)Π are found to be the inverted states. Each of the 3(3)Σ(+), c(3)Π, 2(3)Π, 1(5)Π, and 1(5)Σ(+) states has one potential barrier. The PECs are calculated by the CASSCF method, which is followed by the internally contracted MRCI approach with Davidson correction. Core-valence correlation and scalar relativistic corrections are included. The convergent behavior of present calculations is discussed with respect to the basis set and level of theory. The spin-orbit coupling effect is accounted for. All these PECs are extrapolated to the complete basis set limit. The spectroscopic parameters are evaluated for the bound states involved, and are compared with available measurements. Excellent agreement has been found between the present results and the measurements. It shows that the spectroscopic parameters reported in this paper can be expected to be reliably predicted ones. The conclusion is gained that the effect of spin-orbit coupling on the spectroscopic parameters is not obvious for all the Λ-S bound states except for few ones such as 1(5)Σ(+) and c(3)Π. PMID:25145917
NASA Astrophysics Data System (ADS)
Jiang, Teng; Wang, Long; Zhang, Sui; Sun, Ping-Chuan; Ding, Chuan-Fan; Chu, Yan-Qiu; Zhou, Ping
2011-10-01
Curcumin has been recognized as a potential natural drug to treat the Alzheimer's disease (AD) by chelating baleful metal ions, scavenging radicals and preventing the amyloid β (Aβ) peptides from the aggregation. In this paper, Al(III)-curcumin complexes with Al(III) were synthesized and characterized by liquid-state 1H, 13C and 27Al nuclear magnetic resonance (NMR), mass spectroscopy (MS), ultraviolet spectroscopy (UV) and generalized 2D UV-UV correlation spectroscopy. In addition, the density functional theory (DFT)-based UV and chemical shift calculations were also performed to view insight into the structures and properties of curcumin and its complexes. It was revealed that curcumin could interact strongly with Al(III) ion, and form three types of complexes under different molar ratios of [Al(III)]/[curcumin], which would restrain the interaction of Al(III) with the Aβ peptide, reducing the toxicity effect of Al(III) on the peptide.
Levitt, M
1978-01-01
Calculations on a 20-base pair segment of DNA double helix using empirical energy functions show that DNA can be bent smoothly and uniformly into a superhelix with a small enough radius (45 A) to fit the dimensions of chromatin. The variation of energy with the twist of the base pairs about the helix axis shows the straight DNA free in solution is most stable with about 10 1/2 base pairs per turn rather than 10 as observed in the solid state, whereas superhelical DNA in chromatin is most stable with about 10 base pairs per turn. This result, which has a simple physical interpretation, explains the pattern of nuclease cuts and the linkage number changes observed for DNA arranged in chromatin. PMID:273227
NASA Astrophysics Data System (ADS)
Churakov, S. V.; Parrinello, M.
2003-04-01
The carbonation of brucite (Mg(OH)2) has been considered as a potential technology for cleaning industrial carbon dioxide waste. The kinetics of the reaction Mg(OH)2 + CO2 -> MgCO3 + H2O have been studied experimentally at 573°C by Bearat at al. [1]. Their experiments suggest that the carbonation of magnesium hydroxide proceeds by the reaction Mg(OH)2 -> MgO + H2O followed by the adsorption of CO2 molecules on the dehydrated brucite surface. Due to the large difference in volumes between Mg(OH)2 and MgO, dehydration causes the formation of dislocations and cracks, allowing water molecules to leave the brucite surface and facilitating the advance of the carbonation front in the bulk solid. The detailed mechanism of this process is however unknown. We used the Car-Parrinello ab initio molecular dynamics method to study the structure and dynamics of the (0001), (1-100) and (11-20) surfaces of brucit and calculated the enthalpy and activation barrier of H2O nucleation and dehydration on different surfaces. The results obtained are in agreement with previous studies of brucite dehydration by Masini and Bernasconi [2]. The reactive Car-Parrinello molecular dynamics method [3] has been applied to investigate the detailed mechanism of the dehydration-carbonation reaction at the (1-100) interface of brucite with the gas phase. Based on the results of our MD simulations and the calculated enthalpy of CO2 adsorption on the dehydrated brucite surfaces we propose a mechanism for the dehydration/carbonation reaction. [1] Bearat H, McKelvy MJ, Chizmeshya AVG, Sharma R, Carpenter RW (2002) J. Amer. Ceram. Soc. 85(4):742 [2] Masini P and Bernasconi M (2001) J. Phys. Cond. Mat. 13: 1-12 [3] Iannuzzi M, Laio A and Parrinello M (2003) Phys. Rev. Lett. (submitted)
NASA Astrophysics Data System (ADS)
Seo, Jaemyeong Mango; Ganbat, Gantuya; Han, Ji-Young; Baik, Jong-Jin
2015-11-01
Many big cities around the world are located near mountains. In city-mountain regions, thermally and topographically forced local winds are produced and they affect the transport of pollutants emitted into the urban atmosphere. A better understanding of the dynamics of thermally and topographically forced local winds is necessary to improve the prediction of local winds and to cope with environmental problems. In this study, we theoretically examine the interactions of urban breezes with mountain slope winds in the presence of basic-state wind within the context of the response of a stably stratified atmosphere to prescribed thermal and mechanical forcing. The interactions between urban breezes and mountain slope winds are viewed through the linear superposition of individual analytical solutions for urban thermal forcing, mountain thermal forcing, and mountain mechanical forcing. A setting is considered in which a city is located downwind of a mountain. In the nighttime, in the mountain-side urban area, surface/near-surface horizontal flows induced by mountain cooling and mountain mechanical forcing cooperatively interact with urban breezes, resulting in strengthened winds. In the daytime, in the urban area, surface/near-surface horizontal flows induced by mountain heating are opposed to urban breezes, giving rise to weakened winds. It is shown that the degree of interactions between urban breezes and mountain slope winds is sensitive to mountain height and basic-state wind speed. Particularly, a change in basic-state wind speed affects not only the strength of thermally and mechanically induced flows (internal gravity waves) but also their vertical wavelength and decaying rate. The examination of a case in a setting in which a city is located upwind of a mountain reveals that basic-state wind direction is an important factor that significantly affects the interactions of urban breezes with mountain slope winds.
Bubin, Sergiy; Adamowicz, Ludwik
2011-12-01
In this article we report accurate nonrelativistic variational calculations of the ground and two excited states of C(+) ion. We employ extended and well optimized basis sets of all-electron explicitly correlated Gaussians to represent the wave functions of the states. The optimization of the basis functions is performed with a procedure employing the analytic gradient of the energy with respect to the nonlinear parameters of the Gaussians. The calculations explicitly include the effects due to the finite nuclear mass. The calculated transition energies between the three states are compared to the experimentally derived values. Finally, we present expectation values of some small positive and negative powers of the interparticle distances and contact densities. PMID:22149776
NASA Astrophysics Data System (ADS)
Fähnle, Manfred; Drautz, Ralf; Lechermann, Frank; Singer, Reinhard; Diaz-Ortiz, Alejandro; Dosch, Helmut
2005-05-01
The cover picture from the Feature Article [1] depicts the calculated landscape of lowest formation energies for the ternary compound system Ni-Fe-Al. The figure shows for each composition the difference in the formation energy (in meV/atom) for the respective homogeneous configuration with lowest energy on the bcc and the fcc parent lattice. The phases on the fcc lattice dominate the Ni- and Al-rich regions of the Gibbs triangle.The first author Manfred Fähnle is Professor at the University of Stuttgart and member of the theory group of the department of Prof. Schütz at the Max-Planck-Institut für Metallforschung in Stuttgart. In 1980 he was awarded with the Otto-Hahn medal of the Max-Planck Society and in 1985 he received the Academy Award for Physics of the University of Göttingen. His present research interests are the static and dynamic properties of bulk and nanostructured magnetic systems, as well as the ab-initio statistical mechanics of alloys.
Lin, Chun Che; Xiao, Zhi Ren; Guo, Guang-Yu; Chan, Ting-Shan; Liu, Ru-Shi
2010-03-10
The orthophosphate host family, A(I)B(II)PO(4) (A(I) = monovalent cation, B(II) = divalent cation), has recently been made available as phosphors that combine with near-UV lighting chips for use in solid-state white light-emitting diodes (LEDs). This study elucidates the crystalline structure and lattice parameters of the products via a solid-state reaction, using powder X-ray diffraction (XRD) and GSAS refinement. The versatility of the phosphor host A(I)B(II)PO(4) is established by examining isovalent substitutions of four cations in the structure-Li or K for A(I), Sr or Ba for B(II)-and three doped activators, RE = Eu(2+), Tb(3+), and Sm(3+). The luminescence properties, decay time, and Commission Internationale de l'Eclairage (CIE) chromaticity index are determined for various concentrations of these activators and metal constituents of the host. The thermal stabilities of all of these compounds are determined for the first time from the crystal structure and the coordination environment of the rare-earth metal. The morphology, composition, and particle size were measured in detail. Finally, density functional calculations were performed using the generalized gradient approximation plus an on-site Coulombic interaction correction (GGA+U) scheme to investigate the electronic structures of the KSrPO(4) system. A concise model was proposed to explain the luminescence mechanism. PMID:20155924
NASA Astrophysics Data System (ADS)
Cai, Yufei; Zhang, Jianhui; Zhu, Chunling; Huang, Jun; Jiang, Feng
2016-05-01
The atomizer with micro cone apertures has advantages of ultra-fine atomized droplets, low power consumption and low temperature rise. The current research of this kind of atomizer mainly focuses on the performance and its application while there is less research of the principle of the atomization. Under the analysis of the dispenser and its micro-tapered aperture's deformation, the volume changes during the deformation and vibration of the micro-tapered aperture on the dispenser are calculated by coordinate transformation. Based on the characters of the flow resistance in a cone aperture, it is found that the dynamic cone angle results from periodical changes of the volume of the micro-tapered aperture of the atomizer and this change drives one-way flows. Besides, an experimental atomization platform is established to measure the atomization rates with different resonance frequencies of the cone aperture atomizer. The atomization performances of cone aperture and straight aperture atomizers are also measured. The experimental results show the existence of the pumping effect of the dynamic tapered angle. This effect is usually observed in industries that require low dispersion and micro- and nanoscale grain sizes, such as during production of high-pressure nozzles and inhalation therapy. Strategies to minimize the pumping effect of the dynamic cone angle or improve future designs are important concerns. This research proposes that dynamic micro-tapered angle is an important cause of atomization of the atomizer with micro cone apertures.
Yang, Huaiyu; Gao, Zhaobing; Li, Ping; Yu, Kunqian; Yu, Ye; Xu, Tian-Le; Li, Min; Jiang, Hualiang
2012-01-01
Voltage sensing confers conversion of a change in membrane potential to signaling activities underlying the physiological processes. For an ion channel, voltage sensitivity is usually experimentally measured by fitting electrophysiological data to Boltzmann distributions. In our study, a two-state model of the ion channel and equilibrium statistical mechanics principle were used to test the hypothesis of empirically calculating the overall voltage sensitivity of an ion channel on the basis of its closed and open conformations, and determine the contribution of individual residues to the voltage sensing. We examined the theoretical paradigm by performing experimental measurements with Kv1.2 channel and a series of mutants. The correlation between the calculated values and the experimental values is at respective level, R2 = 0.73. Our report therefore provides in silico prediction of key conformations and has identified additional residues critical for voltage sensing. PMID:22768937
NASA Astrophysics Data System (ADS)
Alvarez, R. M. S.; Cutin, E. H.; Mack, H.-G.; Sala, O.; Della Védova, C. O.
1994-12-01
The FTIR spectrum for vapour and the Raman spectrum for the liquid of difluorosulphenilimine cyanide (F2S(O)NCN) are presented. CS symmetry is suggested for the main conformer in the liquid phase. Vibrational assignments are made for all but the torsional fundamental mode. The symmetry force constants were calculated using an approximate value for the torsion. The study was complemented by theoretical calculations at various levels of sophistication. According to the ab initio methods (HF/3-21G*, HF/6-31G*, MP2/6-31G*) two stable conformations of the compound exist in the gas phase. The main form possesses CS symmetry (δ(OSNC) = 180°, trans), whilst for the less stable rotamer C1 symmetry (δ(OSNC) = 4 to 26°, near-cis) is predicted.
NASA Astrophysics Data System (ADS)
Wang, Xiaoyan; Zhang, Luo; Zhang, Zhongju; Wang, Xin
2016-05-01
The morphologies of the materials have strong effects on their performance in particular applications. In our experiment, we synthesized LaPO4 successfully by the typical hydrothermal method in acidic conditions. The morphologies, preferred orientation and crystal facets are characterized by scanning electron microscopy, selected-area electron diffraction and high-resolution transmission electron microscopy. Combining the experimental findings, the surface energies of two major surfaces, (110) and (031) planes, were calculated using density functional theory methods. The theoretical calculations on the slabs surface energies were performed to simulate the shape of nanoparticles by the Wulff construction. The experimental results indicate that LaPO4 prepared in this work shows rodlike structure. The equilibrium shape of clava with large length-diameter ratio is achieved. With increasing hydrogen ion concentration in solutions, the morphologies present as sticks and their length-diameter ratios tend bigger, which is consistent with experimental results to a great extent.
NASA Astrophysics Data System (ADS)
Bogdanova, Yu. A.; Gubin, S. A.; Victorov, S. B.; Anikeev, A. A.
2016-06-01
An improved version of the equation of state model for two-component fluid mixtures whose molecules interact with the Exp-6 type potential has been proposed in previous works. The thermodynamic parameters of N2, O2, and CO2 shock-wave compression are calculated using the equation of state model for two-component fluid mixtures based on perturbation theory. Products of compression of these substances are two-component mixtures. Analogous calculations are also performed using an effective one-fluid model. A comparison of the results obtained with the available experimental data and results of Monte Carlo simulation allows us to conclude that the proposed theoretical equation of state model is superior to effective one-fluid model in accuracy and reliably describes the thermodynamic properties of two-component fluid mixtures in a wide pressure and temperature ranges.
NASA Astrophysics Data System (ADS)
Lim, Sara N.; Pradhan, Anil K.; Nahar, Sultana N.
2013-06-01
When used with X-ray radiotherapy, heavy elements (high atomic number Z or HZ) such as gold(Au) and platinum(Pt) have the potential to greatly sensitize and enhance the damage to tumor tissues. While HZ radiosensitization has been shown to be higly effective in reducing tumor sizes, much work still needs to be done to determine the ideal X-ray energy/energy spectrum. The likelihood of photoelectric absorption of X-rays that result in the production of cell-killing Auger electrons relative to the photon scatter in an HZ sensitized tumor has to be determined for treatments using X-rays from various sources and energies to assess their efficacy. In this report, we present computations that outline the dependence of photoelectric absorption on X-ray energy. The relative X-ray absorption by a radiosensitized tumor was calculated to contrast the efficacy of different X-ray sources in Auger electron production at different tumor depths. Enhanced photoabsorption of low-energy X-rays from broadband sources in the keV range is shown to be much higher than from those in the MeV range. In addition, with the use of the Monte Carlo code package Geant4, we present the total X-ray energy deposited into a radiosensitized tumor located at different depths in a phantom. The enhancement in radiation dose deposition will also be analysed at the microscopic cellular level to determine the HZ radiosensitizer concentration required. Potential use of monochromatic X-rays for more precise HZ radiosensitization will also be described.
Wasson, I. R.; Ramsbottom, C. A.; Scott, M. P.
2011-10-01
In this paper, we present electron-impact excitation collision strengths and Maxwellian averaged effective collision strengths for the complicated iron-peak ion Cr II. We consider specifically the allowed lines for transitions from the 3d {sup 5} and 3d {sup 4}4s even parity configuration states to the 3d {sup 4}4p odd parity configuration levels. The parallel suite of R-Matrix packages, RMATRX II, which have recently been extended to allow for the inclusion of relativistic effects, were used to compute the collision cross sections. A total of 108 LS{pi}/280 J{pi} levels from the basis configurations 3d {sup 5}, 3d {sup 4}4s, and 3d {sup 4}4p were included in the wavefunction representation of the target including all doublet, quartet, and sextet terms. Configuration interaction and correlation effects were carefully considered by the inclusion of seven more configurations and a pseudo-corrector 4d-bar type orbital. The 10 configurations incorporated into the Cr II model thus listed are 3d {sup 5}, 3d {sup 4}4s, 3d {sup 4}4p, 3d {sup 3}4s {sup 2}, 3d {sup 3}4p {sup 2}, 3d {sup 3}4s4p, 3d{sup 4}4d-bar, 3d{sup 3}4s4d-bar, 3d{sup 3}4p4d-bar, and 3d{sup 3}4d-bar{sup 2}, constituting the largest Cr II target model considered to date in a scattering calculation. The Maxwellian averaged effective collision strengths are computed for a wide range of electron temperatures 2000-100,000 K which are astrophysically significant. Care has been taken to ensure that the partial wave contributions to the collision strengths for these allowed lines have converged with 'top-up' from the Burgess-Tully sum rule incorporated. Comparisons are made with the results of Bautista et al. and significant differences are found for some of the optically allowed lines considered.
NASA Astrophysics Data System (ADS)
Sarkar, Sougata; Chowdhury, Joydeep; Dutta, Soumen; Pal, Tarasankar
2016-12-01
calculations for these prescribed model systems were also carried out to have a plausible understanding of their equilibrium geometries and the vibrational wavenumbers. An idea about the molecular orientation of the adsorbate over nanocolloidal gold substrate is also documented.
Cappelletti, David; Aquilanti, Vincenzo; Bartocci, Alessio; Nunzi, Francesca; Tarantelli, Francesco; Belpassi, Leonardo; Pirani, Fernando
2016-07-14
Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique by measuring both the integral cross section value, Q, and its dependence on the collision velocity, v. The adopted experimental conditions have been appropriate to resolve the oscillating "glory" pattern, a quantum interference effect controlled by the features of the intermolecular interaction, for all the three case studies. The analysis of the Q(v) data, performed by adopting a suitable representation of the intermolecular potential function, provided the basic features of the anisotropic potential energy surfaces at intermediate and large separation distances and information on the relative role of the physically relevant types of contributions to the global interaction. The present work demonstrates that while O2-CH4 and O2-CF4 are basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreaciable intermolecular bond stabilization by charge transfer is operative in O2-CCl4. Ab initio calculations of the strength of the interaction, coupled with detailed analysis of electronic charge displacement promoted by the formation of the dimer, fully rationalizes the experimental findings. This investigation indicates that the interactions of O2, when averaged over its relative orientations, are similar to that of a noble gas (Ng), specifically Ar. We also show that the binding energy in the basic configurations of the prototypical Ng-CF4,CCl4 systems [ Cappelletti , D. ; Chem. Eur. J. 2015 , 21 , 6234 - 6240 ] can be reconstructed by using the interactions in Ng-F and Ng-Cl systems, previously characterized by molecular beam scattering experiments of state-selected halogen atom beams. This information is fundamental to approach the modeling of the weak intermolecular halogen bond. On the basis of the electronic polarizability, this also confirms [ Aquilanti , V. ; Angew. Chem., Int. Ed. 2005 , 44 , 2356 - 2360 ] that O2
Sarkar, Sougata; Chowdhury, Joydeep; Dutta, Soumen; Pal, Tarasankar
2016-12-01
A pH dependent normal Raman scattering (NRS) and surface enhanced Raman scattering (SERS) spectral patterns of citrazinic acid (CZA), a biologically important molecule, have been investigated. The acid, with different pKa values (~4 and ~11) for the two different functional groups (-COOH and -OH groups), shows interesting range of color changes (yellow at pH~14 and brown at pH~2) with the variation in solution pH. Thus, depending upon the pH of the medium, CZA molecule can exist in various protonated and/or deprotonated forms. Here we have prescribed the existence different possible forms of CZA at different pH (Forms "C", "H" and "Dprot" at pH~14 and Forms "A", "D", and "P" at pH~2 respectively). The NRS spectra of these solutions and their respective SERS spectra over gold nanoparticles were recorded. The spectra clearly differ in their spectral profiles. For example the SERS spectra recorded with the CZA solution at pH~2 shows blue shift for different bands compared to its NRS window e.g. 406 to 450cm(-1), 616 to 632cm(-1), 1332 to 1343cm(-1) etc. Again, the most enhanced peak at ~1548cm(-1) in NRS while in the SERS window this appears at ~1580cm(-1). Similar observation was also made for CZA at pH~14. For example, the 423cm(-1) band in the NRS profile experience a blue shift and appears at ~447cm(-1) in the SERS spectrum as well as other bands at ~850, ~1067 and ~1214cm(-1) in the SERS window are markedly enhanced. It is also worth noting that the SERS spectra at the different pH also differ from each other. These spectral differences indicate the existence of various adsorptive forms of the CZA molecule depending upon the pH of the solution. Therefore based on the experimental findings we propose different possible molecular forms of CZA at different pH (acidic and alkaline) conditions. For example forms 'A', 'D' and 'P' existing in acidic pH (pH~2) and three other deprotonated forms 'C', 'H' and 'Dprot' in alkaline pH (pH~14). The DFT calculations for these
Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard
2016-01-01
Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy3+ and Y3+on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke’s model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases. PMID:26888438
NASA Astrophysics Data System (ADS)
Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard
2016-02-01
Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy3+ and Y3+on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke’s model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases.
Qu, Liu; Choy, Kwang-Leong; Wheatley, Richard
2016-01-01
Ceramic oxides that have high-temperature capabilities can be deposited on the superalloy components in aero engines and diesel engines to advance engine efficiency and reduce fuel consumption. This paper aims to study doping effects of Dy(3+) and Y(3+)on the thermodynamic properties of ZrO2 synthesized via a sol-gel route for a better control of the stoichiometry, combined with molecular dynamics (MD) simulation for the calculation of theoretical properties. The thermal conductivity is investigated by the MD simulation and Clarke's model. This can improve the understanding of the microstructure and thermodynamic properties of (DyY)Zr2O7 (DYZ) at the atomistic level. The phonon-defect scattering and phonon-phonon scattering processes are investigated via the theoretical calculation, which provides an effective way to study thermal transport properties of ionic oxides. The measured and predicted thermal conductivity of DYZ is lower than that of 4 mol % Y2O3 stabilized ZrO2 (4YSZ). It is discovered that DYZ is thermochemically compatible with Al2O3 at 1300 °C, whereas at 1350 °C DYZ reacts with Al2O3 forming a small amount of new phases. PMID:26888438
NASA Astrophysics Data System (ADS)
Mikhailov, S. V.; Pimikov, A. V.; Stefanis, N. G.
2016-06-01
We consider the calculation of the pion-photon transition form factor Fγ*γπ0(Q2) within light-cone sum rules focusing attention to the low-mid region of momenta. The central aim is to estimate the theoretical uncertainties which originate from a wide variety of sources related to (i) the relevance of next-to-next-to-leading order radiative corrections (ii) the influence of the twist-four and the twist-six term (iii) the sensitivity of the results on auxiliary parameters, like the Borel scale M2, (iv) the role of the phenomenological description of resonances, and (v) the significance of a small but finite virtuality of the quasireal photon. Predictions for Fγ*γπ0(Q2) are presented which include all these uncertainties and found to comply within the margin of experimental error with the existing data in the Q2 range between 1 and 5 GeV2 , thus justifying the reliability of the applied calculational scheme. This provides a solid basis for confronting theoretical predictions with forthcoming data bearing small statistical errors.
Calculation of Temperature Rise in Calorimetry.
ERIC Educational Resources Information Center
Canagaratna, Sebastian G.; Witt, Jerry
1988-01-01
Gives a simple but fuller account of the basis for accurately calculating temperature rise in calorimetry. Points out some misconceptions regarding these calculations. Describes two basic methods, the extrapolation to zero time and the equal area method. Discusses the theoretical basis of each and their underlying assumptions. (CW)
Huang, B-T; Lu, J-Y
2015-06-15
Purpose: We introduce a new method combined with the deformable image registration (DIR) and regions-of-interest mapping (ROIM) technique to accurately calculate dose on daily CBCT for esophageal cancer. Methods: Patients suffered from esophageal cancer were enrolled in the study. Prescription was set to 66 Gy/30 F and 54 Gy/30 F to the primary tumor (PTV66) and subclinical disease (PTV54) . Planning CT (pCT) were segmented into 8 substructures in terms of their differences in physical density, such as gross target volume (GTV), venae cava superior (SVC), aorta, heart, spinal cord, lung, muscle and bones. The pCT and its substructures were transferred to the MIM software to readout their mean HU values. Afterwards, a deformable planning CT to daily KV-CBCT image registration method was then utilized to acquire a new structure set on CBCT. The newly generated structures on CBCT were then transferred back to the treatment planning system (TPS) and its HU information were overridden manually with mean HU values obtained from pCT. Finally, the treatment plan was projected onto the CBCT images with the same beam arrangements and monitor units (MUs) to accomplish dose calculation. Planning target volume (PTV) and organs at risk (OARs) from both of the pCT and CBCT were compared to evaluate the dose calculation accuracy. Results: It was found that the dose distribution in the CBCT showed little differences compared to the pCT, regardless of whether PTV or OARs were concerned. Specifically, dose variation in GTV, PTV54, PTV66, SVC, lung and heart were within 0.1%. The maximum dose variation was presented in the spinal cord, which was up to 2.7% dose difference. Conclusion: The proposed method combined with DIR and ROIM technique to accurately calculate dose distribution on CBCT for esophageal cancer is feasible.
Acher, Eléonor; Hacene Cherkaski, Yanis; Dumas, Thomas; Tamain, Christelle; Guillaumont, Dominique; Boubals, Nathalie; Javierre, Guilhem; Hennig, Christoph; Solari, Pier Lorenzo; Charbonnel, Marie-Christine
2016-06-01
The structures of plutonium(IV) and uranium(VI) ions with a series of N,N-dialkyl amides ligands with linear and branched alkyl chains were elucidated from single-crystal X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS), and theoretical calculations. In the field of nuclear fuel reprocessing, N,N-dialkyl amides are alternative organic ligands to achieve the separation of uranium(VI) and plutonium(IV) from highly concentrated nitric acid solution. EXAFS analysis combined with XRD shows that the coordination structure of U(VI) is identical in the solution and in the solid state and is independent of the alkyl chain: two amide ligands and four bidentate nitrate ions coordinate the uranyl ion. With linear alkyl chain amides, Pu(IV) also adopt identical structures in the solid state and in solution with two amides and four bidentate nitrate ions. With branched alkyl chain amides, the coordination structure of Pu(IV) was more difficult to establish unambiguously from EXAFS. Density functional theory (DFT) calculations were consequently performed on a series of structures with different coordination modes. Structural parameters and Debye-Waller factors derived from the DFT calculations were used to compute EXAFS spectra without using fitting parameters. By using this methodology, it was possible to show that the branched alkyl chain amides form partly outer-sphere complexes with protonated ligands hydrogen bonded to nitrate ions. PMID:27171842
NASA Astrophysics Data System (ADS)
Garrett, Bruce C.; Truhlar, Donald G.
1980-03-01
Rate constants are calculated for the reactions D+H2→DH+H and H+D2→HD+D and compared to measured values. An accurate potential energy surface, based on the ab initio calculations of Liu and Siegbahn, was used. Rates were calculated using both conventional transition state theory and canonical variational theory. In the former, the generalized transition state dividing surface is located at the saddle point; in the latter it is located to maximize the generalized free energy of activation. We show that, in the absence of tunneling corrections, locating the generalized-transition-state dividing surface variationally has an important quantitative effect on the predicted rate constants for these systems and that, when tunneling is included, most of the effect of using a better dividing surface can be included in conventional transition state theory for these systems by using a consistent transmission coefficient for quantal scattering by the vibrationally adiabatic potential energy curve. Tunneling effects are important for these reactions even for temperatures larger than 400 K. We show how to separate classical recrossing effects from quantal corrections on reaction-coordinate motion in both the transmission coefficients and the kinetic isotope effects. Our most complete calculations are in excellent agreement with most of the measured rate constants and kinetic isotope effects.
NASA Astrophysics Data System (ADS)
Koyama, Yuka; Ueno-Noto, Kaori; Takano, Keiko
2013-07-01
In HIV-1 infection, human antibody 2G12 is capable of recognizing the high-mannose glycans on the HIV-1 surface glycoprotein, gp120. To investigate the ligand binding mechanisms of antibody 2G12 with glycans aiming for the contribution to the medications, we carried out classical molecular dynamics (MD) simulations and ab initio fragment molecular orbital (FMO) calculations on the antibody 2G12 complex with its high-mannose ligand. We found that Mannose D1 of the ligand had the largest binding affinity with the antibody, which was well consistent with experimental reports. Furthermore, significant roles of Mannose 4 and 4‧ in the ligand binding were theoretically indicated.
Reeves, Kyle G.; Kanai, Yosuke
2014-07-14
Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.
NASA Astrophysics Data System (ADS)
Reeves, Kyle G.; Kanai, Yosuke
2014-07-01
Oxidation state is a powerful concept that is widely used in chemistry and materials physics, although the concept itself is arguably ill-defined quantum mechanically. In this work, we present impartial comparison of four, well-recognized theoretical approaches based on Lowdin atomic orbital projection, Bader decomposition, maximally localized Wannier function, and occupation matrix diagonalization, for assessing how well transition metal oxidation states can be characterized. Here, we study a representative molecular complex, tris(bipyridine)ruthenium. We also consider the influence of water solvation through first-principles molecular dynamics as well as the improved electronic structure description for strongly correlated d-electrons by including Hubbard correction in density functional theory calculations.
NASA Astrophysics Data System (ADS)
Ducati, Lucas C.; Braga, Carolyne B.; Rittner, Roberto; Tormena, Cláudio F.
2013-12-01
Literature data are controversial regarding the conformational equilibria of 2-acetylpyrrole (AP) and its N-methyl derivative (AMP). Now, a detailed study through infrared spectroscopy and theoretical calculations has shown that previous data were erroneously interpreted, since only a N,O-cis conformer is present in solution and that it is the stable conformer in the isolated state (ΔEtrans-cis = 5.05 kcal mol-1, for AP; ΔEtrans-cis = 7.14 kcal mol-1, for AMP). Carbonyl and Nsbnd H absorption data in different solvents, supported by theoretical results taking into account the solvent effects [at IEFPCM-B3LYP/6-311++G(3df,3p) level of theory] clearly demonstrated that only the N,O-cis conformer is present in solution. However, a doublet was observed for AP, in CCl4, which can be attributed to this conformer and the lowest wavenumber component to the cis dimer form, stabilized through intermolecular hydrogen bonds (NH⋯Odbnd C). The overall preference for the N,O-cis conformer, in AP and AMP, as interpreted by the NBO analysis, indicated that the hyperconjugative effect is the main contribution to stabilize this rotamer, overcoming the possible steric repulsion. 13C NMR experiments at low temperature in two different solvents (CS2/CDCl2 and acetone-d6) confirmed the occurrence of a single conformer since no separated signals were observed.
NASA Astrophysics Data System (ADS)
Hamdad, N.; Bouhafs, B.
2010-11-01
An electron is a magnetic solid that can perturb local moment via exchange interactions between spin and those of the ions. In our paper, we explore the fundamental physics behind the scarcity of ferromagnetic coexistence on the calcium manganese perovskite oxide CaMnO 3, and examine the structural, electronic and magnetic properties of some known magnetically ordered systems. Various magnetic structures are studied using the first-principles calculation based on density functional theory DFT, using different approximations such as local density approximation (LDA), generalized gradient approximation (GGA), LSDA+U, and GGA+U, which motivated our obtained results. We described in our paper the ground states of different magnetic phases: ferromagnetic (Ferro), A-type anti-ferromagnetic (A-AFM), and G-type anti-ferromagnetic (G-AFM), and the non-spin polarized (NSP) configuration for the ideal cubic perovskite structure. We investigated also a detailed study on the four-layered 4H-hexagonal structure of the compound. We have shown the band structure, density of states and the charge density of all configurations considered in our examination. The magnetic moment and the effect of the U-Hubbard term on our calculation are discussed. Our results are in excellent agreement with available theoretical works and experimental data.
Shin, Hee Won; Ocola, Esther J.; Laane, Jaan; Kim, Sunghwan
2014-01-21
The fluorescence excitation spectra of jet-cooled benzocyclobutane have been recorded and together with its ultraviolet absorption spectra have been used to assign the vibrational frequencies for this molecule in its S{sub 1}(π,π{sup *}) electronic excited state. Theoretical calculations at the CASSCF(6,6)/aug-cc-pVTZ level of theory were carried out to compute the structure of the molecule in its excited state. The calculated structure was compared to that of the molecule in its electronic ground state as well as to the structures of related molecules in their S{sub 0} and S{sub 1}(π,π{sup *}) electronic states. In each case the decreased π bonding in the electronic excited states results in longer carbon-carbon bonds in the benzene ring. The skeletal vibrational frequencies in the electronic excited state were readily assigned and these were compared to the ground state and to the frequencies of five similar molecules. The vibrational levels in both S{sub 0} and S{sub 1}(π,π{sup *}) states were remarkably harmonic in contrast to the other bicyclic molecules. The decreases in the frequencies of the out-of-plane skeletal modes reflect the increased floppiness of these bicyclic molecules in their S{sub 1}(π,π{sup *}) excited state.
NASA Astrophysics Data System (ADS)
Tanaka, Isao; Mizoguchi, Teruyasu; Yamamoto, Tomoyuki
2009-03-01
Both electron energy loss near edge structure (ELNES) spectroscopy and x-ray absorption near edge structure (XANES) spectroscopy provide information on the local structural and chemical environments of selected elements of interest. Recent technological progress in scanning transmission electron microscopy has enabled ELNES measurements with atomic column spatial resolution. Very dilute concentrations (nanograms per milliliter or ppb level) of dopants can be observed using third-generation synchrotron facilities when x-ray fluorescence is measured with highly efficient detectors. With such technical developments, ELNES and XANES have become established as essential tools in a large number of fields of natural science, including condensed matter physics, chemistry, mineralogy and materials science. In addition to these developments in experimental methodology, notable progress in reproducing spectra using theoretical methods has recently been made. Using first-principles methods, one can analyze and interpret spectra without reference to experiment. This is quite important since we are often interested in the analysis of exotic materials or specific atoms located at lattice discontinuities such as surfaces and interfaces, where appropriate experimental data are difficult to obtain. Using the structures predicted by reliable first-principles calculations, one can calculate theoretical ELNES and XANES spectra without too much difficulty even in such cases. Despite the fact that ELNES and XANES probe the same phenomenon—essentially the electric dipole transition from a core orbital to an unoccupied band—there have not been many opportunities for researchers in the two areas to meet and discuss. Theoretical calculations of ELNES spectra have been mainly confined to the electron microscopy community. On the other hand, the theory of XANES has been developed principally by researchers in the x-ray community. Publications describing the methods have been written more
Theoretical approaches to metal chemistry
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W.; Langhoff, Stephen R.; Partridge, Harry; Halicioglu, Timur; Taylor, Peter R.
1987-01-01
Theoretical calculations on metals ranging from very accurate ab initio studies of diatomic and triatomic systems to model studies of larger clusters are presented. Recent improvements in the representation of one-particle and n-particle spaces have made possible the prediction that Al2 has a 3Pi(u) ground state, even though the 3Sigma(-)g state lies within 200/cm. Results suggest that cluster geometry varies dramatically with cluster size, and that rather large clusters are required before the bulk structure becomes optimal. Al cluster studies show that three-body terms are needed for quantitative agreement with ab initio calculations.
NASA Astrophysics Data System (ADS)
Biswas, Nandita; Thomas, Susy; Kapoor, Sudhir; Mishra, Amaresh; Wategaonkar, Sanjay; Mukherjee, Tulsi
2008-11-01
Structural and vibrational properties of mono- and multichromophoric hemicyanine (HC) dyes in solution and adsorbed on silver-coated films have been investigated using optical absorption and resonance Raman scattering techniques, with interpretations aided by theoretical calculations. This is the first report on the Raman spectroscopic studies of multichromophoric HC derivatives. The structure of the monomer, N-propyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC3), and its charged and neutral silver complexes (HC3-Ag) in the ground electronic (S0) state were optimized using density functional calculations with the B3LYP method using the 6-31G* and LANL2DZ basis sets. The ground state structure of N-hexyl-4-(p-N,N-dimethylamino styryl)pyridinium bromide (HC6) and multichromophoric HC dyes were computed using the HF /6-31G* method. The negligible shift or broadening observed in the electronic absorption and resonance Raman spectra in solution with increasing size of the HC chromophore suggests that the excitations are localized within individual monomer units in bis and tetra chromophores. However, in the tris chromophore, considerable redshift and broadening were observed, indicating a significant electronic interaction between the nonbonded electrons of the N atom and the aromatic π-system that is supported by the calculated excitation energies using the time-dependent density functional theory method. The effect of HC dye concentration on the electronic absorption spectra of the silver-coated film showed significant broadening, which was attributed to the formation of H- and J-aggregates in addition to the formation of a metal-molecule complex. A considerable redshift along various vibrations observed in the surface-enhanced resonance Raman scattering (SERRS) spectra of the HC derivatives indicates that adsorption on the silver surface leads to a considerable interaction of the electron rich moiety of HC derivatives with the silver surface. The
Farrokhpour, H; Karachi, S; Chermahini, A Najafi
2016-09-01
In the present work, the chirality recognition of the enantiomers of a chiral molecule (1-phenyl-1-propanol) interacting with a nanotubular cyclic peptide (E-type cyclic decapeptide) was investigated by their ionization in the gas phase, theoretically. The absolute energy difference between the interaction of the S- and R-enantiomer with the cyclic peptide, calculated at the M06-2X/6-311++G(d, p) level of theory, was 4.70 kcal·mol(-1). Two different schemes of "Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)" method such as (quantum mechanics (QM):molecular mechanics (MM)) and (QM:QM) were employed to study the effect of the interaction on the gas-phase ionization energies of the enantiomers and cyclic peptide, separately. The symmetry-adapted cluster/configuration interaction (SAC-CI) methodology was used for the calculation of the ionization energies. It was found that the difference between the interactions of R- and S-enantiomer with the cyclic peptide caused different changes in the photoelectron spectrum of each enantiomer so that these changes could be used for the chirality discrimination of the enantiomers in the gas phase. Similarly, the photoelectron spectrum of the cyclic peptide interacting with the R and S-enantiomer were calculated, separately, and it was observed that the difference in the interaction with the R- and S-enantiomer created different changes in the spectrum of cyclic peptide. Finally, it was shown that the difference in the interaction of cyclic peptide with the enantiomers of a chiral molecule in the gas phase can be used for the identification of enantiomers in the gas phase by the direct ionization. PMID:27500312
Aldeghi, Matteo; Heifetz, Alexander; Bodkin, Michael J.; Knapp, Stefan
2016-01-01
Accurate prediction of binding affinities has been a central goal of computational chemistry for decades, yet remains elusive. Despite good progress, the required accuracy for use in a drug-discovery context has not been consistently achieved for drug-like molecules. Here, we perform absolute free energy calculations based on a thermodynamic cycle for a set of diverse inhibitors binding to bromodomain-containing protein 4 (BRD4) and demonstrate that a mean absolute error of 0.6 kcal mol–1 can be achieved. We also show a similar level of accuracy (1.0 kcal mol–1) can be achieved in pseudo prospective approach. Bromodomains are epigenetic mark readers that recognize acetylation motifs and regulate gene transcription, and are currently being investigated as therapeutic targets for cancer and inflammation. The unprecedented accuracy offers the exciting prospect that the binding free energy of drug-like compounds can be predicted for pharmacologically relevant targets. PMID:26798447
Woon, D.E. )
1994-02-15
Dimer interactions of helium, neon, and argon have been studied using the augmented correlation consistent basis sets of Dunning and co-workers. Two correlation methods have been employed throughout; Moller--Plesset perturbation theory through fourth-order (MP4) and single and double excitation coupled-cluster theory with perturbative treatment of triple excitations [CCSD(T)]. Full configuration interaction (FCI) calculations were performed on He[sub 2] for some basis sets. In general, only valence electrons were correlated, although some calculations which also correlated the [ital n]=2 shell of Ar[sub 2] were performed. Dimer potential energy curves were determined using the supermolecule method with and without the counterpoise correction. A series of additional basis sets beyond the augmented correlation consistent sets were explored in which the diffuse region of the radial function space has been systematically saturated. In combination with the systematic expansion across angular function space which is inherent to the correlation consistent prescription, this approach guarantees very accurate atomic polarizabilities and hyperpolarizabilities and should lead to an accurate description of dispersion forces. The best counterpoise-corrected MP4 values for the well depths of the three dimers are (in microhartrees, empirical values in parentheses) He[sub 2], 31.9 (34.6); Ne[sub 2], 123 (134); and Ar[sub 2], 430 (454). The corresponding CCSD(T) values are He[sub 2], 33.1; Ne[sub 2], 128; and Ar[sub 2], 417. Although these values are very good, the nearly exponential convergence of well depth as a function of basis quality afforded by using the various series of correlation consistent basis sets allows estimation of complete basis set (CBS) limiting values. The MP4 estimated CBS limits are He[sub 2], 32.2; Ne[sub 2], 126; and Ar[sub 2], 447.
Hostaš, Jiří; Jakubec, Dávid; Laskowski, Roman A; Gnanasekaran, Ramachandran; Řezáč, Jan; Vondrášek, Jiří; Hobza, Pavel
2015-09-01
Representative pairs of amino acid side chains and nucleic acid bases extracted from available high-quality structures of protein-DNA complexes were analyzed using a range of computational methods. CCSD(T)/CBS interaction energies were calculated for the chosen 272 pairs. These reference interaction energies were used to test the MP2.5/CBS, MP2.X/CBS, MP2-F12, DFT-D3, PM6, and Amber force field methods. Method MP2.5 provided excellent agreement with reference data (root-mean-square error (RMSE) of 0.11 kcal/mol), which is more than 1 order of magnitude faster than the CCSD(T) method. When MP2-F12 and MP2.5 were combined, the results were within reasonable accuracy (0.20 kcal/mol), with a computational savings of almost 2 orders of magnitude. Therefore, this method is a promising tool for accurate calculations of interaction energies in protein-DNA motifs of up to ∼100 atoms, for which CCSD(T)/CBS benchmark calculations are not feasible. B3-LYP-D3 calculated with def2-TZVPP and def2-QZVP basis sets yielded sufficiently good results with a reasonably small RMSE. This method provided better results for neutral systems, whereas positively charged species exhibited the worst agreement with the benchmark data. The Amber force field yielded unbalanced results-performing well for systems containing nonpolar amino acids but severely underestimating interaction energies for charged complexes. The semiempirical PM6 method with corrections for hydrogen bonding and dispersion energy (PM6-D3H4) exhibited considerably smaller error than the Amber force field, which makes it an effective tool for modeling extended protein-ligand complexes (of up to 10,000 atoms). PMID:26575904
NASA Astrophysics Data System (ADS)
Lestinsky, M.; Badnell, N. R.; Bernhardt, D.; Grieser, M.; Hoffmann, J.; Lukić, D.; Müller, A.; Orlov, D. A.; Repnow, R.; Savin, D. W.; Schmidt, E. W.; Schnell, M.; Schippers, S.; Wolf, A.; Yu, D.
2009-06-01
We have measured electron-ion recombination for Fe9+ forming Fe8+ and for Fe10+ forming Fe9+ using a merged beams arrangement at the TSR heavy-ion storage ring in Heidelberg, Germany. The measured merged beams recombination rate coefficients (MBRRC) for relative energies from 0 to 75 eV are presented, covering all dielectronic recombination (DR) resonances associated with 3s → 3p and 3p → 3d core transitions in the spectroscopic species Fe X and Fe XI, respectively. We compare our experimental results to state-of-the-art multiconfiguration Breit-Pauli (MCBP) calculations and find significant differences. Poor agreement between the measured and theoretical resonance structure is seen for collision energies below 48 eV for Fe X and below 35 eV for Fe XI. The integrated resonance strengths, though, are in reasonable agreement. At higher energies, good agreement is seen for the resonance structure but for the resonance strengths theory is significantly larger than experiment by a factor of ≈ 1.5 (2) for Fe X (Fe XI). From the measured MBRRC, we have extracted the DR contributions and transform them into plasma recombination rate coefficients (PRRCs) for astrophysical plasmas with temperatures in the range of 102-107 K. This range spans across the regimes where each ion forms in photoionized or in collisionally ionized plasmas. For both temperature regimes, the experimental uncertainties are 25% at a 90% confidence level. As expected based on predictions from active galactic nucleus observations as well as our previous laboratory and theoretical work on M-shell iron, the formerly recommended DR data severely underestimated the rate coefficient at temperatures relevant for photoionized gas. At these temperatures relevant for photoionized gas, we find agreement between our experimental results and MCBP theory. This is somewhat surprising given the poor agreement in MBRRC resonance structure. At the higher temperatures relevant for collisionally ionized gas, the MCBP
Garten, C.T. Jr.; Lomax, R.D.
1987-06-01
This report describes data obtained during a preliminary characterization of /sup 90/Sr levels in browse vegetation from the vicinity of seeps adjacent to ORNL solid waste storage areas (SWSA) where deer (Odocoileus virginianus) were suspected to accumulate /sup 90/Sr through the food chain. The highest strontium concentrations in plant samples were found at seeps associated with SWSA-5. Strontium-90 concentrations in honeysuckle and/or blackberry shoots from two seeps in SWSA-5 averaged 39 and 19 nCi/g dry weight (DW), respectively. The maximum concentration observed was 90 nCi/g DW. Strontium-90 concentrations in honeysuckle and blackberry shoots averaged 7.4 nCi/g DW in a study area south of SWSA-4, and averaged 1.0 nCi/g DW in fescue grass from a seepage area located on SWSA-4. A simple model (based on metabolic data for mule deer) has been used to describe the theoretical accumulation of /sup 90/Sr in bone of whitetail deer following ingestion of contaminated vegetation. These model calculations suggest that if 30 pCi /sup 90/Sr/g deer bone is to be the accepted screening level for retaining deer killed on the reservation, then 5-pCi /sup 90/Sr/g DW vegetation should be considered as a possible action level in making decisions about the need for remedial measures, because unrestricted access and full utilization of vegetation contaminated with <5 pCi/g DW results in calculated steady-state (maximum) /sup 90/Sr bone concentrations of <30 pCi/g in a 45-kg buck.
Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward
2015-02-01
The vibrational and reorientational motions of NH3 ligands and ClO4(-) anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385cm(-1), associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR≈10(-12)-10(-13)s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5kJmol(-1), in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TC(c)=137.6K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6](2+) cation and ClO4(-) anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models. PMID:25459713
NASA Astrophysics Data System (ADS)
Hetmańczyk, Joanna; Hetmańczyk, Łukasz; Migdał-Mikuli, Anna; Mikuli, Edward
2015-02-01
The vibrational and reorientational motions of NH3 ligands and ClO4- anions were investigated by Fourier transform middle-infrared spectroscopy (FT-IR) in the high- and low-temperature phases of [Mn(NH3)6](ClO4)2. The temperature dependencies of full width at half maximum (FWHM) of the infrared bands at: 591 and 3385 cm-1, associated with: ρr(NH3) and νas(N-H) modes, respectively, indicate that there exist fast (correlation times τR ≈ 10-12-10-13 s) reorientational motions of NH3 ligands, with a mean values of activation energies: 7.8 and 4.5 kJ mol-1, in the phase I and II, respectively. These reorientational motions of NH3 ligands are only slightly disturbed in the phase transition region and do not significantly contribute to the phase transition mechanism. Fourier transform far-infrared and middle-infrared spectra with decreasing of temperature indicated characteristic changes at the vicinity of PT at TCc = 137.6 K (on cooling), which suggested lowering of the crystal structure symmetry. Infrared spectra of [Mn(NH3)6](ClO4)2 were recorded and interpreted by comparison with respective theoretical spectra calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311 + G(d,p) basis set (on H, N, Cl, O atoms) for the isolated equilibrium two models (Model 1 - separate isolated [Mn(NH3)6]2+ cation and ClO4- anion and Model 2 - [Mn(NH3)6(ClO4)2] complex system). Calculated optical spectra show a good agreement with the experimental infrared spectra (FT-FIR and FT-MIR) for the both models.
Hartzell, S.; Guatteri, Mariagiovanna; Mai, P.M.; Liu, P.-C.; Fisk, M. R.
2005-01-01
In the evolution of methods for calculating synthetic time histories of ground motion for postulated earthquakes, kinematic source models have dominated to date because of their ease of application. Dynamic models, however, which incorporate a physical relationship between important faulting parameters of stress drop, slip, rupture velocity, and rise time, are becoming more accessible. This article compares a class of kinematic models based on the summation of a fractal distribution of subevent sizes with a dynamic model based on the slip-weakening friction law. Kinematic modeling is done for the frequency band 0.2 to 10.0. Hz, dynamic models are calculated from 0.2 to 2.0. Hz. The strong motion data set for the 1994 Northridge earthquake is used to evaluate and compare the synthetic time histories. Source models are propagated to the far field by convolution with 1D and 3D theoretical Green’s functions. In addition, the kinematic model is used to evaluate the importance of propagation path effects: velocity structure, scattering, and nonlinearity. At present, the kinematic model gives a better broadband fit to the Northridge ground motion than the simple slip-weakening dynamic model. In general, the dynamic model overpredicts rise times and produces insufficient shorter-period energy. Within the context of the slip-weakening model, the Northridge ground motion requires a short slip-weakening distance, on the order of 0.15 m or less. A more complex dynamic model including rate weakening or one that allows shorter rise times near the hypocenter may fit the data better.
Chen, Hui-Fen; Yang, Wen-Bin; Lin, Lang; Guo, Xiang-Guang; Dui, Xue-jing; Wu, Xiao-Yuan; Lu, Can-Zhong; Zhang, Cui-Juan
2013-05-01
Two μ₂-tetrazolyl bridged metal complexes, ([CdI(PTZ)(H₂O)]·H₂O)ₙ1 and ([Cu(PTZ)₂]·H₂O)ₙ2 (HPTZ=5-(pyrazinyl) tetrazolate), were hydrothermally synthesized and fully characterized by X-ray crystallography, elemental analyses and spectrum techniques. In 1, cadmium ions are bridged by tridentate μ₂-κ²N2,N5:κ¹N1 chelating PTZ⁻ ligand and halide linkers into an infinite 1D chain, while in 2 copper ions are connected by tridentate μ₂-κ²N7,N12:κ¹N8 and bidentate μ₂-κ¹N1:κ¹N2 chelating-bridging PTZ⁻ ligands to form a 1D castellated chain structure. Compound 1 displays phosphorescence with a lifetime of ~7.74 ms in the visible region, and the origin of the luminescent emission is primary assigned to the combination of ligand-centered emission, metal-to-ligand charge transfer and ligand-to-ligand charge transfer, which has been probed by the density of states (DOS) calculations. Magnetic measurement reveals that compound 2 displays an anti-ferromagnetic ordering. - Graphical abstract: Two new complexes based on 5-(pyrazinyl) tertrazolate, namely ([CdI(PTZ)(H2O)]·H2O)n and ([Cu(PTZ)2]·H2O)n have been synthesized and characterized. Compound 1 exhibits interesting green luminescence. Compound 2 displays an anti-ferromagnetic ordering. Highlights: • We report two novel 1D μ₂-tetrazolyl bridged Cd(II) and Cu(II) compounds. • The cadmium(II) compound exhibits a green luminescence. • Theoretical calculations were conducted to elucidate the green luminescence. • The Cu(II) compound exhibits an anti-ferromagnetic ordering.
Dai, Zuyang; Sun, Wei; Wang, Jia; Mo, Yuxiang
2015-08-01
The spin-vibronic energy levels of the cyanoacetylene cation have been measured using the one-photon zero-kinetic energy (ZEKE) photoelectron spectroscopic method. All three degenerate vibrational modes showing vibronic coupling, i.e., Renner-Teller (RT) effect, have been observed. All the splitting spin-vibronic energy levels of the fundamental H-C≡C bending vibration (v5) have been determined. The spin-vibronic energy levels of the degenerate vibrational modes have also been calculated using a diabatic model in which the harmonic terms as well as all the second-order vibronic coupling terms are used. The theoretical predictions are in good agreement with the experimental data and are used to assign the ZEKE spectrum. It is found that the RT effects for the H-(CC)-CN bending (v7) and the C-C≡N bending (v6) vibrations are weak, whereas they are strong for the H-C≡C bending (v5) vibration. The cross-mode RT couplings between any of the two degenerate vibrations are strong. The spin-orbit resolved fundamental vibrational energy levels of the C≡N stretching (v2) and C-H stretching (v1) vibrations have also been observed. The spin-orbit energy splitting of the ground state has been determined for the first time as 43 ± 2 cm(-1), and the ionization energy of HCCCN is found to be 93 903.5 ± 2 cm(-1). PMID:26254647
NASA Astrophysics Data System (ADS)
Chernin, Artur D.
1994-08-01
In a paper published in 1953, i.e., more than a decade before the observational discovery of the cosmic microwave background radiation, George Gamow predicted theoretically the temperature of this radiation. He estimated it to be 7 K, which is very close to the subsequently measured value of about 3 K. Gamow found the present temperature of the background radiation on the basis of general formulas of cosmological dynamics. This prediction was in no way related to primordial nucleosynthesis.This circumstance has and is still causing misunderstanding in those cases in which the authors have raised doubts about Gamow's results, although an actual error has never been demonstrated. A detailed analysis makes it possible to understand how Gamow's calculation is possible. The problem lies in the fact that Gamow makes a certain additional implicit assumption which allows him to dispense with information on nucleosynthesis. This assumption is discussed in the context of the state of cosmology in the period from the fifties to the seventies, and of the current status of this branch of science.
NASA Astrophysics Data System (ADS)
Dai, Zuyang; Sun, Wei; Wang, Jia; Mo, Yuxiang
2015-08-01
The spin-vibronic energy levels of the cyanoacetylene cation have been measured using the one-photon zero-kinetic energy (ZEKE) photoelectron spectroscopic method. All three degenerate vibrational modes showing vibronic coupling, i.e., Renner-Teller (RT) effect, have been observed. All the splitting spin-vibronic energy levels of the fundamental H—C≡C bending vibration (v5) have been determined. The spin-vibronic energy levels of the degenerate vibrational modes have also been calculated using a diabatic model in which the harmonic terms as well as all the second-order vibronic coupling terms are used. The theoretical predictions are in good agreement with the experimental data and are used to assign the ZEKE spectrum. It is found that the RT effects for the H—(CC)—CN bending (v7) and the C—C≡N bending (v6) vibrations are weak, whereas they are strong for the H—C≡C bending (v5) vibration. The cross-mode RT couplings between any of the two degenerate vibrations are strong. The spin-orbit resolved fundamental vibrational energy levels of the C≡N stretching (v2) and C—H stretching (v1) vibrations have also been observed. The spin-orbit energy splitting of the ground state has been determined for the first time as 43 ± 2 cm-1, and the ionization energy of HCCCN is found to be 93 903.5 ± 2 cm-1.
Paglia, Gianluca; Rohl, Andrew L.; Gale, Julian D.; Buckley, Craig E.
2005-06-01
We have performed an extensive computational study of {gamma}-Al{sub 2}O{sub 3}, beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. This suggests that cations of {gamma}-Al{sub 2}O{sub 3} are not exclusively held in spinel positions, that the spinel model of {gamma}-Al{sub 2}O{sub 3} does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of {gamma}-Al{sub 2}O{sub 3}. The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of {gamma}-Al{sub 2}O{sub 3} than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other
NASA Astrophysics Data System (ADS)
Paglia, Gianluca; Rohl, Andrew L.; Buckley, Craig E.; Gale, Julian D.
2005-06-01
We have performed an extensive computational study of γ-Al2O3 , beginning with the geometric analysis of approximately 1.47 billion spinel-based structural candidates, followed by derivative method energy minimization calculations of approximately 122 000 structures. Optimization of the spinel-based structural models demonstrated that structures exhibiting nonspinel site occupancy after simulation were more energetically favorable, as suggested in other computational studies. More importantly, none of the spinel structures exhibited simulated diffraction patterns that were characteristic of γ-Al2O3 . This suggests that cations of γ-Al2O3 are not exclusively held in spinel positions, that the spinel model of γ-Al2O3 does not accurately reflect its structure, and that a representative structure cannot be achieved from molecular modeling when the spinel representation is used as the starting structure. The latter two of these three findings are extremely important when trying to accurately model the structure. A second set of starting models were generated with a large number of cations occupying c symmetry positions, based on the findings from recent experiments. Optimization of the new c symmetry-based structural models resulted in simulated diffraction patterns that were characteristic of γ-Al2O3 . The modeling, conducted using supercells, yields a more accurate and complete determination of the defect structure of γ-Al2O3 than can be achieved with current experimental techniques. The results show that on average over 40% of the cations in the structure occupy nonspinel positions, and approximately two-thirds of these occupy c symmetry positions. The structures exhibit variable occupancy in the site positions that follow local symmetry exclusion rules. This variation was predominantly represented by a migration of cations away from a symmetry positions to other tetrahedral site positions during optimization which were found not to affect the diffraction
Accurate Evaluation of Quantum Integrals
NASA Technical Reports Server (NTRS)
Galant, David C.; Goorvitch, D.
1994-01-01
Combining an appropriate finite difference method with Richardson's extrapolation results in a simple, highly accurate numerical method for solving a Schr\\"{o}dinger's equation. Important results are that error estimates are provided, and that one can extrapolate expectation values rather than the wavefunctions to obtain highly accurate expectation values. We discuss the eigenvalues, the error growth in repeated Richardson's extrapolation, and show that the expectation values calculated on a crude mesh can be extrapolated to obtain expectation values of high accuracy.
Marc Vanderhaeghen
2007-04-01
The theoretical issues in the interpretation of the precision measurements of the nucleon-to-Delta transition by means of electromagnetic probes are highlighted. The results of these measurements are confronted with the state-of-the-art calculations based on chiral effective-field theories (EFT), lattice QCD, large-Nc relations, perturbative QCD, and QCD-inspired models. The link of the nucleon-to-Delta form factors to generalized parton distributions (GPDs) is also discussed.
NNLOPS accurate associated HW production
NASA Astrophysics Data System (ADS)
Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia
2016-06-01
We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.
Parker, James K; Payne, Walter A; Cody, Regina J; Nesbitt, Fred L; Stief, Louis J; Klippenstein, Stephen J; Harding, Lawrence B
2007-02-15
The rate coefficient has been measured under pseudo-first-order conditions for the Cl+CH3 association reaction at T=202, 250, and 298 K and P=0.3-2.0 Torr helium using the technique of discharge-flow mass spectrometry with low-energy (12-eV) electron-impact ionization and collision-free sampling. Cl and CH3 were generated rapidly and simultaneously by reaction of F with HCl and CH4, respectively. Fluorine atoms were produced by microwave discharge in an approximately 1% mixture of F2 in He. The decay of CH3 was monitored under pseudo-first-order conditions with the Cl-atom concentration in large excess over the CH3 concentration ([Cl]0/[CH3]0=9-67). Small corrections were made for both axial and radial diffusion and minor secondary chemistry. The rate coefficient was found to be in the falloff regime over the range of pressures studied. For example, at T=202 K, the rate coefficient increases from 8.4x10(-12) at P=0.30 Torr He to 1.8x10(-11) at P=2.00 Torr He, both in units of cm3 molecule-1 s-1. A combination of ab initio quantum chemistry, variational transition-state theory, and master-equation simulations was employed in developing a theoretical model for the temperature and pressure dependence of the rate coefficient. Reasonable empirical representations of energy transfer and of the effect of spin-orbit interactions yield a temperature- and pressure-dependent rate coefficient that is in excellent agreement with the present experimental results. The high-pressure limiting rate coefficient from the RRKM calculations is k2=6.0x10(-11) cm3 molecule-1 s-1, independent of temperature in the range from 200 to 300 K. PMID:17253663
Monari, Antonio; Rivail, Jean-Louis; Assfeld, Xavier
2013-02-19
Molecular mechanics methods can efficiently compute the macroscopic properties of a large molecular system but cannot represent the electronic changes that occur during a chemical reaction or an electronic transition. Quantum mechanical methods can accurately simulate these processes, but they require considerably greater computational resources. Because electronic changes typically occur in a limited part of the system, such as the solute in a molecular solution or the substrate within the active site of enzymatic reactions, researchers can limit the quantum computation to this part of the system. Researchers take into account the influence of the surroundings by embedding this quantum computation into a calculation of the whole system described at the molecular mechanical level, a strategy known as the mixed quantum mechanics/molecular mechanics (QM/MM) approach. The accuracy of this embedding varies according to the types of interactions included, whether they are purely mechanical or classically electrostatic. This embedding can also introduce the induced polarization of the surroundings. The difficulty in QM/MM calculations comes from the splitting of the system into two parts, which requires severing the chemical bonds that link the quantum mechanical subsystem to the classical subsystem. Typically, researchers replace the quantoclassical atoms, those at the boundary between the subsystems, with a monovalent link atom. For example, researchers might add a hydrogen atom when a C-C bond is cut. This Account describes another approach, the Local Self Consistent Field (LSCF), which was developed in our laboratory. LSCF links the quantum mechanical portion of the molecule to the classical portion using a strictly localized bond orbital extracted from a small model molecule for each bond. In this scenario, the quantoclassical atom has an apparent nuclear charge of +1. To achieve correct bond lengths and force constants, we must take into account the inner shell of
Gutowski, Keith E; Rogers, Robin D; Dixon, David A
2007-03-01
The research described in this product was performed in part in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the Department of Energy's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory. A computational approach to the prediction of the heats of formation (ΔHf°’s) of solid-state energetic salts from electronic structure and volume-based thermodynamics (VBT) calculations is described. The method uses as its starting point reliable ΔHf°’s for energetic precursor molecules and ions. The ΔHf°’s of more complex energetics species such as substituted imidazole, 1,2,4-triazole, and tetrazole molecules and ions containing amino, azido, and nitro (including methyl) substituents are calculated using an isodesmic approach at the MP2/complete basis set level. On the basis of comparisons to experimental data for neutral analogues, this isodesmic approach is accurate to <3 kcal/mol for the predicted cation and anion ΔHf°’s. The ΔHf°’s of the energetic salts in the solid state are derived from lattice energy (UL) calculations using a VBT approach. Improved values for the ∝ and β parameters of 19.9 (kcal nm)/mol and 37.6 kcal/mol for the UL equation were obtained on the basis of comparisons to experimental UL’s for a series of 23 salts containing ammonium, alkylammonium, and hydrazinium cations. The total volumes are adjusted to account for differences between predicted and experimental total volumes due to different shapes of the ions (flat vs spherical). The predicted ΔHf°’s of the energetic salts are estimated to have error bars of 6-7 kcal/mol, on the basis of comparisons to established experimental ΔHf°’s of a subset of the salts studied. Energetic salts with the highest positive ΔHf°’s are predicted for azido-containing cations, coupled with heterocyclic anions containing nitro substituents. The substitution of functional groups on
Al-Jaroudi, Said S; Altaf, Muhammad; Al-Saadi, Abdulaziz A; Kawde, Abdel-Nasser; Altuwaijri, Saleh; Ahmad, Saeed; Isab, Anvarhusein A
2015-10-01
The gold(III) complexes of the type (1,2-diaminocyclohexane)(1,3-diaminopropane)gold(III) chloride, [(DACH)Au(pn)]Cl3, [where DACH = cis-, trans-1,2- and S,S-1,2-diaminocyclohexane and pn = 1,3-diaminopropane] have been synthesized and characterized using various spectroscopic and analytical techniques including elemental analysis, UV-Vis and FTIR spectroscopy; solution as well as solid-state NMR measurements. The solid-state (13)C NMR shows that 1,2-diaminocyclohexane (1,2-DACH) and 1,3-diaminopropane (pn) are strongly bound to the gold(III) center via N donor atoms. The stability of the mixed diamine ligand gold(III) was checked by UV-Vis spectroscopy and NMR measurements. The molecular structure of compound 1 (containing cis-1,2-DACH) was determined by X-ray diffraction analysis. The structure of 1 consists of [(cis-DACH)Au(pn)](3+) complex ion and chloride counter ions. Each gold atom in the complex ion adopts a distorted square-planar geometry. The structural details and relative stabilities of the four possible isomers of the complexes were also estimated at the B3LYP/LANL2DZ level of theoretical calculations. The computational study demonstrates that trans- conformations are slightly more stable than the cis- conformations. The antiproliferative effects and cytotoxic properties of the mixed ligand gold(III) complexes were evaluated in vitro on human gastric SGC7901 and prostate PC3 cancer cells using MTT assay. The antiproliferative study of the gold(III) complexes on PC3 and SGC7901 cells indicate that complex 3 (containing 1S,2S-(+)-1,2-(DACH)) is the most effective antiproliferative agent. The IC50 data reveal that the in vitro cytotoxicity of complex 3 against SGC7901 cancer cells manifested similar and very pronounced cytotoxic effects with respect to cisplatin. Moreover, the electrochemical behavior, and the interaction of complex 3 with two well-known model proteins, namely, hen egg white lysozyme and bovine serum albumin is also reported. PMID
Zhang, Lijuan; Liu, Sheng; Cheng, Min; Du, Yikui; Zhu, Qihe
2016-01-14
The mass-analyzed threshold ionization spectra of jet-cooled cis- and trans-3-fluoro-N-methylaniline (3FNMA) were recorded by ionizing via the vibrationless 0(0) and various vibrational levels of the S1 state. The adiabatic ionization energies of cis- and trans-3FNMA are determined to be 61,742 ± 5 and 61,602 ± 5 cm(-1), respectively. In the 0-1800 cm(-1) region, most of the observed vibrations in the D0 state result from the in-plane ring deformation and substituent-sensitive modes. For the high-frequency vibration region, the infrared-ultraviolet double-resonance and autoionization-detected infrared spectroscopies were applied to investigate the N-H and C-H stretching vibrations of bare 3FNMA in the S0 and D0 states. The C-H stretching vibrational information, which we failed to obtain for the bare 3FNMA cation, is complemented by recording the infrared-photodissociation spectra of its Ar cluster cation. It is revealed that a red-shifted frequency and an enhanced intensity are observed for the N-H stretch, while blue-shifted frequencies and greatly decreased intensities are found for both aromatic and the methyl C-H stretches. The blue shift of the C-H stretches is first explained by the balance of two factors, namely, the hyperconjugative interaction and the rehybridization effect. Analysis of the vibrational frequencies reveals a correlation between the relative stability of two rotamers in different electronic states and the relative rigidity of aromatic ring, indicating a mechanism of the long-range interactions "through bond" between the substituents. The density functional theory calculations can well reproduce the vibrational spectra in both S0 and D0 states. With the experimental and theoretical data, the substitution and conformation effects on the properties of 3FNMA in the S0 and D0 states, including the molecular structures, the reactive sites of electrophilic attack, and the vibrational behaviors, were discussed in detail. PMID:26669268
NASA Technical Reports Server (NTRS)
Predoi-Cross, A.; Hambrook, Kyle; Brawley-Tremblay, Marco; Bouanich, J. P.; Smith, Mary Ann H.
2006-01-01
In this paper, we report measured Lorentz N2-broadening and N2-induced pressure-shift coefficients of CH3D in the v2 fundamental band using a multispectrum fitting technique. These measurements were made by analyzing 11 laboratory absorption spectra recorded at 0.0056 cm(exp -1) resolution using the McMath-Pierce Fourier transform spectrometer located at the National Solar Observatory on Kitt Peak, Arizona. The spectra were obtained using two absorption cells with path lengths of 10.2 and 25 cm. The total sample pressures ranged from 0.98 to 402.25 Torr with CH3D volume mixing ratios of 0.01 in nitrogen. We have been able to determine the N2 pressure- broadening coefficients of 368 v2 transitions with quantum numbers as high as J"= 20 and K = 16, where K" = K' equivalent to K (for a parallel band). The measured N2-broadening coefficients range from 0.0248 to 0.0742 cm(exp -1) atm(exp -1) at 296 K. All the measured pressure-shifts are negative. The reported N2-induced pressure-shift coefficients vary from about 0.0003 to 0.0094 cm(exp -1) atm(exp -1). We have examined the dependence of the measured broadening and shift parameters on the J", and K quantum numbers and also developed empirical expressions to describe the broadening coefficients in terms of m (m = -J", J", and J" + 1 in the (sup Q)P-, (sup Q)Q-, and (sup Q)R-branch, respectively) and K. On average, the empirical expressions reproduce the measured broadening coefficients to within 4.7%. The N2-broadening and pressureshift coefficients were calculated on the basis of a semiclassical model of interacting linear molecules performed by considering in addition to the electrostatic contributions the atom atom Lennard-Jones potential. The theoretical results of the broadening coefficients are in good overall agreement with the experimental data (8.7%). The N2-pressure shifts whose vibrational contribution is derived from parameters fitted in the (sup Q)Q-branch of self-induced shifts of CH3D, are also in
Golibrzuch, Kai; Shirhatti, Pranav R.; Kandratsenka, Alexander; Wodtke, Alec M.; Bartels, Christof; Max Planck Institute for Biophysical Chemistry, Göttingen 37077 ; Rahinov, Igor; Auerbach, Daniel J.; Max Planck Institute for Biophysical Chemistry, Göttingen 37077; Department of Chemistry and Biochemistry, University of California Santa Barbara, Santa Barbara, California 93106
2014-01-28
We present a combined experimental and theoretical study of NO(v = 3 → 3, 2, 1) scattering from a Au(111) surface at incidence translational energies ranging from 0.1 to 1.2 eV. Experimentally, molecular beam–surface scattering is combined with vibrational overtone pumping and quantum-state selective detection of the recoiling molecules. Theoretically, we employ a recently developed first-principles approach, which employs an Independent Electron Surface Hopping (IESH) algorithm to model the nonadiabatic dynamics on a Newns-Anderson Hamiltonian derived from density functional theory. This approach has been successful when compared to previously reported NO/Au scattering data. The experiments presented here show that vibrational relaxation probabilities increase with incidence energy of translation. The theoretical simulations incorrectly predict high relaxation probabilities at low incidence translational energy. We show that this behavior originates from trajectories exhibiting multiple bounces at the surface, associated with deeper penetration and favored (N-down) molecular orientation, resulting in a higher average number of electronic hops and thus stronger vibrational relaxation. The experimentally observed narrow angular distributions suggest that mainly single-bounce collisions are important. Restricting the simulations by selecting only single-bounce trajectories improves agreement with experiment. The multiple bounce artifacts discovered in this work are also present in simulations employing electronic friction and even for electronically adiabatic simulations, meaning they are not a direct result of the IESH algorithm. This work demonstrates how even subtle errors in the adiabatic interaction potential, especially those that influence the interaction time of the molecule with the surface, can lead to an incorrect description of electronically nonadiabatic vibrational energy transfer in molecule-surface collisions.
NASA Astrophysics Data System (ADS)
Liu, Gang; Mei, Yang; Zhang, Xin-Xin; Zheng, Wen-Chen
2015-05-01
The high-order perturbation formulas based on a two-mechanism model (where in addition to the contributions from the crystal-field (CF) mechanism in the usually-applied CF theory, those from the generally-neglected charge-transfer (CT) mechanism are also contained) are employed to calculate the spin-Hamiltonian parameters (g factors g//, g⊥ and the hyperfine structure constants A//, A⊥) of the square planar CuCl4 2 - clusters in Cs2ZrCl6 crystal. The needed CF energy levels in the calculations are obtained from the observed optical spectra. The calculated results show reasonable agreement with the experimented values. The negative sign of A// and positive sign of A⊥ are proposed from the calculations. The calculations also suggest that one should take account of the contributions due to both the CF and CT mechanisms for the exact and rational calculations of spin-Hamiltonian parameters of Cu2+-Cl- combination in crystals.
Theoretical dissociation energies for ionic molecules
NASA Technical Reports Server (NTRS)
Langhoff, S. R.; Bauschlicher, C. W., Jr.; Partridge, H.
1986-01-01
Ab initio calculations at the self-consistent-field and singles plus doubles configuration-interaction level are used to determine accurate spectroscopic parameters for most of the alkali and alkaline-earth fluorides, chlorides, oxides, sulfides, hydroxides, and isocyanides. Numerical Hartree-Fock (NHF) calculations are performed on selected systems to ensure that the extended Slater basis sets employed for the diatomic systems are near the Hartree-Fock limit. Extended Gaussian basis sets of at least triple-zeta plus double polarization equality are employed for the triatomic system. With this model, correlation effects are relatively small, but invariably increase the theoretical dissociation energies. The importance of correlating the electrons on both the anion and the metal is discussed. The theoretical dissociation energies are critically compared with the literature to rule out disparate experimental values. Theoretical (sup 2)Pi - (sup 2)Sigma (sup +) energy separations are presented for the alkali oxides and sulfides.
NASA Astrophysics Data System (ADS)
M, Shakil; Muhammad, Zafar; Shabbir, Ahmed; Muhammad Raza-ur-rehman, Hashmi; M, A. Choudhary; T, Iqbal
2016-07-01
The plane wave pseudo-potential method was used to investigate the structural, electronic, and elastic properties of CdSe1‑x Te x in the zinc blende phase. It is observed that the electronic properties are improved considerably by using LDA+U as compared to the LDA approach. The calculated lattice constants and bulk moduli are also comparable to the experimental results. The cohesive energies for pure CdSe and CdTe binary and their mixed alloys are calculated. The second-order elastic constants are also calculated by the Lagrangian theory of elasticity. The elastic properties show that the studied material has a ductile nature.
NASA Astrophysics Data System (ADS)
Ceylan, Ümit; Hacıyusufoğlu, Mehmet Emin; Yalçınc, Şerife Pınar; Sönmez, Mehmet; Aygün, Muhittin
2016-04-01
A new Schiff base compound, (E)-1-((2-hydroxynaphthalen-1-yl) methyleneamino)-5-(4-methoxybenzoyl)-4-(4-methoxyphenyl) pyrimidine-2(1H)-one, formula sum is given by C30H23N3O5, was synthesized and characterized by experimentally and theoretically. Optimized molecular structure was obtained using X-ray diffraction in the ground state. FT-IR, NMR and UV-Vis frequencies have been measured and compared with theoretically obtained data by using by DFT/B3LYP method with 6-31G(d) and 6-311++G(d,p) basis set. In addition, molecular electrostatic potential (MEP), dipole moments, NBO analysis, atomic charges, HOMO-LUMO and molecular electrostatic potential were computed. The calculated results show that the optimized geometry can well reproduce the crystal structure parameters, and the theoretical vibrational frequencies, 1H and 13C NMR chemical shifts show good agreement with experimental values.
NASA Astrophysics Data System (ADS)
İnkaya, Ersin; Dinçer, Muharrem; Şahan, Emine; Yıldırım, İsmail
2013-10-01
In this paper, we will report a combined experimental and theoretical investigation of the molecular structure and spectroscopic parameters (FT-IR, 1H NMR, 13C NMR) of 5-benzoyl-4-phenyl-2-methylthio-1H-pyrimidine. The compound crystallizes in the triclinic space group P-1 with Z = 2. The molecular geometry was also optimized using density functional theory (DFT/B3LYP) method with the 6-311G(d,p) and 6-311++G(d,p) basis sets in ground state and compared with the experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecules has been obtained by mapping electron density isosurface with electrostatic potential (ESP). Also, non-linear optical properties of the title compound were performed at B3LYP/6-311++G(d,p) level. The theoretical results showed an excellent agreement with the experimental values.
NASA Astrophysics Data System (ADS)
Peng, Xian; Cui, Guang-hua; Li, De-jie; Liu, Tong-fei
2010-04-01
A mononuclear copper(II) complex, [Cu(PIM) 2(PhCOO) 2] ( 1) [where PIM = 2-propylimidazole] has been synthesized and characterized by elemental analysis, IR, UV-Vis, TGA, and single crystal X-ray diffraction. The structural analysis indicated that Cu(II) atom in the complex is six-coordinated in a distorted octahedral geometry by two N atoms from two 2-propylimidazole and four O atoms from two benzoate ligands. In addition, based on crystal structural data, quantum chemistry calculation in DFT/B3LYP level has been used to reoptimize and explore the electronic structure of the compound 1; time-dependent DFT (TD-DFT) calculations have also been performed in order to elucidate its spectroscopic properties. All parameters from the calculations are in well accordance with our experimental result.
Afaneh, Akef T; Schreckenbach, Georg; Wang, Feiyue
2014-09-25
The structures and harmonic vibrational frequencies of water clusters (H2O)n, n = 1-10, have been computed using the M06-L/, B3LYP/, and CAM-BLYP/cc-pVTZ levels of theories. On the basis of the literature and our results, we use three hexamer structures of the water molecules to calculate an estimated "experimental" average solvation free energy of [Hg(H2O)6](2+). Aqueous formation constants (log K) for Hg(2+) complexes, [Hg(L)m(H2O)n](2-mq), L = Cl(-), HO(-), HS(-), and S(2-), are calculated using a combination of experimental (solvation free energies of ligands and Hg(2+)) and calculated gas- and liquid-phase free energies. A combined approach has been used that involves attaching n explicit water molecules to the Hg(2+) complexes such that the first coordination sphere is complete, then surrounding the resulting (Hg(2+)-Lm)-(OH2)n cluster by a dielectric continuum, and using suitable thermodynamic cycles. This procedure significantly improves the agreement between the calculated log K values and experiment. Thus, for some neutral and anionic Hg(II) complexes, particularly Hg(II) metal ion surrounded with homo- or heteroatoms, augmenting implicit solvent calculations with sufficient explicit water molecules to complete the first coordination sphere is required-and adequate-to account for strong short-range hydrogen bonding interactions between the anion and the solvent. Calculated values for formation constants of Hg(2+) complexes with S(2-) and SH(-) are proposed. Experimental measurements of these log K values have been lacking or controversial. PMID:25076413
Accurate thermoelastic tensor and acoustic velocities of NaCl
NASA Astrophysics Data System (ADS)
Marcondes, Michel L.; Shukla, Gaurav; da Silveira, Pedro; Wentzcovitch, Renata M.
2015-12-01
Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.
Accurate thermoelastic tensor and acoustic velocities of NaCl
Marcondes, Michel L.; Shukla, Gaurav; Silveira, Pedro da; Wentzcovitch, Renata M.
2015-12-15
Despite the importance of thermoelastic properties of minerals in geology and geophysics, their measurement at high pressures and temperatures are still challenging. Thus, ab initio calculations are an essential tool for predicting these properties at extreme conditions. Owing to the approximate description of the exchange-correlation energy, approximations used in calculations of vibrational effects, and numerical/methodological approximations, these methods produce systematic deviations. Hybrid schemes combining experimental data and theoretical results have emerged as a way to reconcile available information and offer more reliable predictions at experimentally inaccessible thermodynamics conditions. Here we introduce a method to improve the calculated thermoelastic tensor by using highly accurate thermal equation of state (EoS). The corrective scheme is general, applicable to crystalline solids with any symmetry, and can produce accurate results at conditions where experimental data may not exist. We apply it to rock-salt-type NaCl, a material whose structural properties have been challenging to describe accurately by standard ab initio methods and whose acoustic/seismic properties are important for the gas and oil industry.
NASA Technical Reports Server (NTRS)
Guiot, R.; Wunnenberg, H.
1980-01-01
The methods by which aerodynamic coefficients are determined and discussed. These include: calculations, wind tunnel experiments and experiments in flight for various prototypes of the Alpha Jet. A comparison of obtained results shows good correlation between expectations and in-flight test results.
NASA Astrophysics Data System (ADS)
Camargo, A. J.; Oliveira, J. H. H. L.; Trsic, M.; Berlinck, R. G. S.
2001-01-01
A detailed computational study was performed for compounds granulatimide, isogranulatimide, and didemnimides A, D, and E, using the semiempirical Austin model 1 quantum chemical method. The electronic features and structural parameters were confronted with the inhibition of the G2 cell cycle checkpoint of mammalian cancer cells. All compounds were submitted to a rigorous conformational analysis using the Tripos 5.2 force field implemented in the Spartan 5.01 program. The electronic density in specific regions of the molecules appears to play a pivotal role towards activity. The molecular planarity creates a broad negative electrostatic potential on the two sides of the active compounds (granulatimide and isogralulatimide) and a positive potential in their central core, while the non-planar compounds (didemnimides A, D, and E, which are inactive) present an asymmetric potential scattered over the molecules. These electrostatic potential features are likely to be the modulator of hydrophobicity or lipophilicity of the compounds, which appear correlated with activity. The hydrogen attached to the N atom of the pyrrole moiety of indole is more positive for active compounds than for the inactive molecules. The theoretical electronic spectra were obtained for all compounds using the configuration interaction method, with the AM1 routine. All transitions present π→π ∗ nature. The theoretical results are in good agreement with experimental values.
NASA Astrophysics Data System (ADS)
Predoi-Cross, Adriana; Bouanich, J. P.; Benner, D. Chris; May, A. D.; Drummond, J. R.
2000-07-01
We have measured the room temperature, widths, pressure shifts, and line asymmetry coefficients for many transitions of the first overtone band of CO and CO perturbed by N2. The broadening coefficients were obtained with an accuracy of about 1%. The pure CO profiles have been fitted by a Voigt profile while the CO-N2 spectral profiles have been fitted with a Lorentz and an empirical line shape model (HCv) that blends together a hard collision model and a speed-dependent Lorentz profile. In addition to the Voigt, Lorentz, and HCv models, we have added a dispersion profile to account for weak line mixing. The line broadening and shift coefficients are compared to semiclassical calculations employing a variety of intermolecular interactions. The line asymmetry results are compared to line mixing calculations based on the energy corrected sudden (ECS) model. The results indicate that effects other than line mixing also contribute to the measured line asymmetry.
Maffeo, Davide; Lampropoulou, Maria; Fardis, Michael; Lazarou, Yannis G; Mavridis, Irene M; Mavridou, Despoina A I; Urso, Elena; Pratsinis, Harris; Kletsas, Dimitris; Yannakopoulou, Konstantina
2010-04-21
Novel -type cyclodextrin (CD) derivatives, , and , bearing 6, 7 and 8 bis(carboxymethyl)amino (iminodiacetic acid) groups, respectively, were prepared, and their complexation with Eu(iii), Tb(iii) and Gd(iii) ions was studied. Luminescence titrations and mass spectrometry showed formation of multimetal complexes ( 2 to 3, mainly 3 and exactly 4 metal ions), whereas luminescence lifetime measurements revealed the presence of exchangeable water molecules. Semiempirical quantum mechanical calculations, performed by the PM3 method and assessed by DFT calculations on model ligands, indicated efficient multi-metal complexation, in agreement with the experiment. The structures showed coordination of the metal ions in the outer primary side of the CDs via 4 carboxylate O atoms, 2 N atoms and a glucopyranose O atom per metal ion. Coordination of water molecules was also predicted, in accordance with experimental results. Calculated bond lengths and angles were in agreement with literature experimental values of lanthanide complexes. Calculated energies showed that complex stability decreases in the order > > . (1)H NMR molecular relaxivity measurements for the Gd(iii) complexes of , or in water afforded values 4 to 10 times higher than the relaxivity of a commercial contrast agent at 12 MHz, and 6 to 20 times higher at 100 MHz. Solutions of and Gd(iii) complexes in human blood plasma displayed relaxivity values at 100 MHz 7 and 12 times, respectively, higher than the commercial agent. MTT tests of the Gd(iii) complexes using human skin fibroblasts did not show toxicity. Attempts to supramolecularly sensitize the luminescence of the lanthanide complexes using various aromatic CD guests were ineffective, evidently due to large guest-metal distances and inefficient inclusion. The described lanthanide complexes, could be useful as contrast agents in MRI. PMID:20449498
Bodo, E; Mangialardo, S; Ramondo, F; Ceccacci, F; Postorino, P
2012-11-29
We present an analysis of gas-phase structures of small clusters of n-alkylammonium nitrates (ethyl, propyl, and butyl) together with vibrational Raman spectroscopy of their respective liquid phases. The assignment and interpretation of the resonant frequencies have been performed by comparison with high-quality ab initio (DFT) computations. The theoretical spectra are in excellent agreement with the measured ones and allow the interpretation and assignment of almost all the spectral features. A careful analysis of the vibrational frequencies and of the electronic structure of the compounds has provided additional information on various structural features and on the rather complex hydrogen bonding network that exists in such compounds. A geometric structure of the short-range local arrangement in the bulk phases is also proposed. PMID:22973943
Fowe, Emmanuel Penka; Belser, Peter; Daul, Claude; Chermette, Henry
2005-04-21
In the present work, the ZORA spin-orbit Hamiltonian, in conjunction with the gauge including orbital (GIAO) method based on DFT theory has been used to calculate 195Pt chemical shift of 195PtClxBr(6-x)(2-) complexes. Excellent agreement with experiments has been obtained for calculations bearing on optimized geometries and all electrons triple zeta + polarization (TZP) STO basis sets: the relative error with respect to experiment amounts to <1.5%. It is found that the Pt chemical shift is dominated by the paramagnetic and the spin orbit contribution, whereas the diamagnetic term remains negligible. The influence of the quality of the basis sets has been studied and found to be small, provided a basis set like TZP is used. Several calculations have been performed in order to establish the sensitivity of the chemical shift to a variation in the bond lengths. A strong dependence has been found, with an increase of the chemical shift amounting to 150 ppm pm(-1) for a distance decrease. Large sensitivity to the solvation, leading to changes in the structure, is then expected. Different tests using conductor-like screening models have been performed in order to establish the sensitivity of the chemical shift to solvation. It has been observed that the changes in the geometry are more important than charge transfers. Finally, the sensitivity of the system to the exchange-correlation functional is found rather weak, at least among the GGA functionals. PMID:19787932
NASA Technical Reports Server (NTRS)
Zehe, Michael J.; Jaffe, Richard L.
2010-01-01
High-level ab initio calculations have been performed on the exo and endo isomers of gas-phase tetrahydrodicyclopentadiene (THDCPD), a principal component of the jet fuel JP10, using the Gaussian Gx and Gx(MPx) composite methods, as well as the CBS-QB3 method, and using a variety of isodesmic and homodesmotic reaction schemes. The impetus for this work is to help resolve large discrepancies existing between literature measurements of the formation enthalpy Delta (sub f)H deg (298) for exo-THDCPD. We find that use of the isodesmic bond separation reaction C10H16 + 14CH4 yields 12C2H6 yields results for the exo isomer (JP10) in between the two experimentally accepted values, for the composite methods G3(MP2), G3(MP2)//B3LYP, and CBS-QB3. Application of this same isodesmic bond separation scheme to gas-phase adamantane yields a value for Delta (sub f)H deg (298) within 5 kJ/mol of experiment. Isodesmic bond separation calculations for the endo isomer give a heat of formation in excellent agreement with the experimental measurement. Combining our calculated values for the gas-phase heat of formation with recent measurements of the heat of vaporization yields recommended values for Delta (sub f)H deg (298)liq of -126.4 and -114.7 kJ/mol for the exo and endo isomers, respectively.
NASA Astrophysics Data System (ADS)
Samsonowicz, M.; Kowczyk-Sadowy, M.; Piekut, J.; Regulska, E.; Lewandowski, W.
2016-04-01
The structural and vibrational properties of lithium, sodium, potassium, rubidium and cesium homovanillates were investigated in this paper. Supplementary molecular spectroscopic methods such as: FT-IR, FT-Raman in the solid phase, UV and NMR were applied. The geometrical parameters and energies were obtained from density functional theory (DFT) B3LYP method with 6-311++G** basis set calculations. The geometry of the molecule was fully optimized, vibrational spectra were calculated and fundamental vibrations were assigned. Geometric and magnetic aromaticity indices, atomic charges, dipole moments, HOMO and LUMO energies were also calculated. The microbial activity of investigated compounds was tested against Bacillus subtilis (BS), Pseudomonas aeruginosa (PA), Escherichia coli (EC), Staphylococcus aureus (SA) and Candida albicans (CA). The relationship between the molecular structure of tested compounds and their antimicrobial activity was studied. The principal component analysis (PCA) was applied in order to attempt to distinguish the biological activities of these compounds according to selected band wavenumbers. Obtained data show that the FT-IR spectra can be a rapid and reliable analytical tool and a good source of information for the quantitative analysis of the relationship between the molecular structure of the compound and its biological activity.
NASA Astrophysics Data System (ADS)
Karthikeyan, N.; Joseph Prince, J.; Ramalingam, S.; Periandy, S.
2015-05-01
In the present research work, the FT-IR, FT-Raman and 13C and 1H NMR spectra of the α-Methylstyrene were recorded. The observed fundamental frequencies in finger print as well as functional group regions were assigned according to their uniqueness region. The Gaussian computational calculations are carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The impact of the presence of vinyl group in phenyl structure of the compound is investigated. The modified vibrational pattern of the molecule associated vinyl group was analyzed. Moreover, 13C NMR and 1H NMR were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP methods and the 6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A study on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed.
Cao, Jun
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π(*) transition induces a cleavage of the C-N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π(*) excitation of the imine chromophore results in a cleavage of the C-C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N-O bond cleavages on both S1((1)ππ(*)) and S2((1)nNπ(*)) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles. PMID:26133423
NASA Astrophysics Data System (ADS)
Li, Qiang; Xu, Juping; Liu, Jiandang; Ye, Bangjiao
2016-05-01
We observed clear ferromagnetic ordering in 6H–SiC crystal bombarded with zinc ions, and presented a detailed investigation of magnetic properties in this sample. The magnetization of Zn-implanted 6H–SiC fell and rose with annealing temperature from 500 °C to 1100 °C. Meanwhile, amount of oxygen penetrated lattices and combined with Si-bonds after 1100 °C annealing. Using ab initio calculations based on density functional theory, we confirm that Zn ions play a role in the origin of ferromagnetism, while the localized moment is mainly comes from C2p electrons surrounding the foreign particle (which is Zn in this work). Silicon vacancies can provide localized moment about 2.0 μB/VSi and form stable ferromagnetic interaction at room temperature. Oxygen may facilitate this coupling and no need of VC-mediation any more. The calculations are consistent with experimental results. We concluded that the dangling C2p bonds are fundamental cause of magnetic ordering in whatever microstructures in 6H–SiC crystal. The type of foreign impurities is not crucial factor for the magnetic origin in such carbon-based materials.
Kostko, Oleg; Zhou, Jia; Sun, Bian Jian; Lie, Jie Shiuan; Chang, Agnes H.H.; Kaiser, Ralf I.; Ahmed, Musahid
2010-03-02
Results from single photon vacuum ultraviolet photoionization of astrophysically relevant CnN clusters, n = 4 - 12, in the photon energy range of 8.0 eV to 12.8 eV are presented. The experimental photoionization efficiency curves, combined with electronic structure calculations, provide improved ionization energies of the CnN species. A search through numerous nitrogen-terminated CnN isomers for n=4-9 indicates that the linear isomer has the lowest energy, and therefore should be the most abundant isomer in the molecular beam. Comparison with calculated results also shed light on the energetics of the linear CnN clusters, particularly in the trends of the even-carbon and the odd-carbon series. These results can help guide the search of potential astronomical observations of these neutral molecules together with their cations in highly ionized regions or regions with a high UV/VUV photon flux (ranging from the visible to VUV with flux maxima in the Lyman-a region) in the interstellar medium.
Kostko, Oleg; Zhou, Jia; Sun, Bian Jian; Lie, Jie Shiuan; Chang, Agnes H.H.; Kaiser, Ralf I.; Ahmed, Musahid
2010-06-10
Results from single photon vacuum ultraviolet photoionization of astrophysically relevant CnN clusters, n = 4 - 12, in the photon energy range of 8.0 eV to 12.8 eV are presented. The experimental photoionization efficiency curves, combined with electronic structure calculations, provide improved ionization energies of the CnN species. A search through numerous nitrogen-terminated CnN isomers for n=4-9 indicates that the linear isomer has the lowest energy, and therefore should be the most abundant isomer in the molecular beam. Comparison with calculated results also shed light on the energetics of the linear CnN clusters, particularly in the trends of the even-carbon and the odd-carbon series. These results can help guide the search of potential astronomical observations of these neutral molecules together with their cations in highly ionized regions or regions with a high UV/VUV photon flux (ranging from the visible to VUV with flux maxima in the Lyman- region) in the interstellar medium.
Kuyper, L.F.; Hunter, R.N. ); Ashton, D. ); Merz, K.M. Jr.; Kollman, P.A. )
1991-08-22
The authors have carried out experimental determinations of the free energy of solvation of anisole, 1,2-dimethoxybenzene (DMB), and 1,2,3-trimethoxybenzene (TMB) in water and perturbation free energy calculations on the relative aqueous solvation free energies of benzene, anisole, and TMB. The measured differences between the relative experimental free energies of solvation of benzene, anisole, DMB, and TMB support the concept of near additivity of aromatic methoxy group contributions to such gas phase to water transfer free energies. Calculated differences in solvation free energies were shown to be sensitive to the choice of electrostatic charge distribution model. Quantum mechanical electrostatic potential fit charge models from STO-3G, 4-31G, and 6-31G* basis sets were compared for their ability to reproduce the relative free energies of solvation found experimentally. The 6-31G* basis sets were compared for their ability to reproduce the relative free energies of solvation found experimentally. The 6-31G* charge model was the best in this regard and the STO-3G model was next in quality, but the 4-31G model significantly overestimated the effect of O-CH{sub 3} substitution on solvation free energies. Models based on scaled 4-31G charges also produced reasonable results.
Oh, Won Sup; Chon, Sung-Bin
2016-05-01
Fluid resuscitation, hemostasis, and transfusion is essential in care of hemorrhagic shock. Although estimation of the residual blood volume is crucial, the standard measuring methods are impractical or unsafe. Vital signs, central venous or pulmonary artery pressures are inaccurate. We hypothesized that the residual blood volume for acute, non-ongoing hemorrhage was calculable using serial hematocrit measurements and the volume of isotonic solution infused. Blood volume is the sum of volumes of red blood cells and plasma. For acute, non-ongoing hemorrhage, red blood cell volume would not change. A certain portion of the isotonic fluid would increase plasma volume. Mathematically, we suggest that the residual blood volume after acute, non-ongoing hemorrhage might be calculated as 0·25N/[(Hct1/Hct2)-1], where Hct1 and Hct2 are the initial and subsequent hematocrits, respectively, and N is the volume of isotonic solution infused. In vivo validation and modification is needed before clinical application of this model. PMID:27134507
2016-01-01
Fluid resuscitation, hemostasis, and transfusion is essential in care of hemorrhagic shock. Although estimation of the residual blood volume is crucial, the standard measuring methods are impractical or unsafe. Vital signs, central venous or pulmonary artery pressures are inaccurate. We hypothesized that the residual blood volume for acute, non-ongoing hemorrhage was calculable using serial hematocrit measurements and the volume of isotonic solution infused. Blood volume is the sum of volumes of red blood cells and plasma. For acute, non-ongoing hemorrhage, red blood cell volume would not change. A certain portion of the isotonic fluid would increase plasma volume. Mathematically, we suggest that the residual blood volume after acute, non-ongoing hemorrhage might be calculated as 0·25N/[(Hct1/Hct2)–1], where Hct1 and Hct2 are the initial and subsequent hematocrits, respectively, and N is the volume of isotonic solution infused. In vivo validation and modification is needed before clinical application of this model. PMID:27134507
Cao, Jun
2015-06-28
In the present work, the combined electronic structure calculations and dynamics simulations have been performed to explore photocleavages of 2-formyl-2H-azirine and isoxazole in the gas phase and the subsequent rearrangement reactions. The carbonyl n → π{sup *} transition induces a cleavage of the C—N single bond of 2-formyl-2H-azirine to yield β-formylvinylnitrene in open-shell singlet state. However, the n → π{sup *} excitation of the imine chromophore results in a cleavage of the C—C single bond, producing a nitrile ylide intermediate through an internal conversion to the ground state. β-formylvinylnitrene and nitrile ylide with the carbonyl group are easily transformed into 2-formyl-2H-azirine and oxazole, respectively. The N—O bond cleavages on both S{sub 1}({sup 1}ππ{sup *}) and S{sub 2}({sup 1}n{sub N}π{sup *}) of isoxazole are ultrafast processes, and they give products of 2-formyl-2H-azirine, 3-formylketenimine, HCN + CHCHO, and HCO + CHCHN. Both 2H-azirines and ketenimines were suggested to be formed from the triplet vinylnitrenes by intersystem crossing in the previous studies. However, our calculations show that the singlet β-formylvinylnitrene is responsible for the formation of 2-formyl-2H-azirine and 3-formylketenimine, and the singlet vinylnitrenes can play a key role in the photoinduced reactions of both 2H-azirines and isoxazoles.
Structure and spectra of HOCl(H{sub 2}O){sub n} clusters, n = 1--4: A theoretical calculation
Ortiz-Repiso, M.; Escribano, R.; Gomez, P.C.
2000-01-27
The geometrical structure, binding energy, and vibrational spectra of small clusters of HOCl and water molecules, HOCl(H{sub 2}O){sub n}, n = 1--4, have been investigated at the MP2 level of theory, using triple-Z, 6-311++G(d,p), basis sets. The ab initio results predict for the clusters an almost planar ring skeleton, made up of the o atoms and one H atom from each molecule, linked by hydrogen bonding to the next oxygen. The species with one water unit presents two almost equally stable conformers, syn and anti, in agreement with previous calculations. Two stable structures have also been found for clusters with three and four molecules of water, one where the H atom of the HOCl molecule makes part of the ring, and another one in which the Cl atom is in the ring. The more stable in either case is found to be the H-in molecule, with a difference of 35.6 kJ/mol in optimized energy. The predicted spectra for these two species are very different. As the number of water units increases, the corresponding clusters become more stable, and a number of physical effects is predicted. The more important one is the increase in the intramolecular O-H bond length, which is responsible for a large reduction in the wavenumber of the corresponding O-H vibration. The results indicate the formation of hydrogen bonds and a partial proton transfer from HOCl to the water ring structure. In a parallel calculation, water clusters, (H{sub 2}O){sub n}, n = 1--5, have also been investigated. The results agree well with those of previous authors.
NASA Astrophysics Data System (ADS)
Chen, Wenwen; Cao, Fengjing; Zheng, Wenshu; Tian, Yue; Xianyu, Yunlei; Xu, Peng; Zhang, Wei; Wang, Zhuo; Deng, Ke; Jiang, Xingyu
2015-01-01
We report a method for rapid, effective detection of both Cr(iii) and Cr(vi) (in the form of Cr3+ and Cr2O72-, the main species of chromium in the natural environment) by making use of meso-2,3-dimercaptosuccinic acid (DMSA)-functionalized gold nanoparticles (Au NPs). The limit of detection (LOD) is 10 nM with the naked eye and the assay can be applied in detecting chromium in polluted soil from Yun-Nan Province in Southwest China. We use density functional theory to calculate the change of the Gibbs free energy (ΔG) of the interactions between the DMSA-Au NP system and various metal ions, which shows that DMSA-Au NPs have high specificity for both Cr3+ and Cr2O72-.We report a method for rapid, effective detection of both Cr(iii) and Cr(vi) (in the form of Cr3+ and Cr2O72-, the main species of chromium in the natural environment) by making use of meso-2,3-dimercaptosuccinic acid (DMSA)-functionalized gold nanoparticles (Au NPs). The limit of detection (LOD) is 10 nM with the naked eye and the assay can be applied in detecting chromium in polluted soil from Yun-Nan Province in Southwest China. We use density functional theory to calculate the change of the Gibbs free energy (ΔG) of the interactions between the DMSA-Au NP system and various metal ions, which shows that DMSA-Au NPs have high specificity for both Cr3+ and Cr2O72-. Electronic supplementary information (ESI) available: ΔG of the interactions between the DMSA-AuNPs and various metal ions, models of the metal ions (Mn+) and six water molecules, DLS results for DMSA-Au NPs before and after adding Cr3+, Cr2O72-, Cr3+ and Cr2O72- mixtures, comparison of the performance of different sensors. See DOI: 10.1039/c4nr06726f
Drahoš, Bohuslav; Herchel, Radovan; Trávníček, Zdeněk
2015-04-01
A series of first-row transition metal complexes with 15-membered pyridine-based macrocycle (3,12,18-triaza-6,9-dioxabicyclo[12.3.1]octadeca-1(18),14,16-triene = L) was prepared ([M(II)(L)Cl2], where M = Mn, Co, Ni, Zn (1, 3, 4, 6); [Fe(III)(L)Cl2]Cl (2), [Cu(II)(L)Cl]Cl (5)) and thoroughly characterized. Depending on the complexated metal atom, the coordination number varies from 7 (Mn, Fe, Co), through 5 + 2 for Ni and 4 + 1 for Cu, to 5 for Zn accompanied by changes in the coordination geometry from the pentagonal bipyramid (1-4) to the square pyramid (5 and 6). Along the series, the metal-oxygen distances were prolonged in such manner that their bonding character was investigated, apart from X-ray structural analysis, also by ab initio calculations (Mayer's bond order, electron localization function), which confirmed that, in 4 and 5, two and one oxygen donor atoms are semicoordinated, respectively, and one and two oxygen atoms are uncoordinated in 5, and 6, respectively. On the basis of the temperature variable magnetic susceptibility measurements, 1 and 2 behave as expected for 3d(5) high-spin configuration with negligible zero-field splitting (ZFS). On the other hand, a large axial ZFS (D(Co) ≈ 40 cm(-1), D(Ni) ≈ -6.0 cm(-1)) was found for 3 and 4, and rhombic ZFS (E/D ≈ 0.15) for 4. Antiferromagnetic exchange coupling was observed for 4 and 5 (J(Ni) = -0.48 cm(-1), and J(Cu) = -2.43 cm(-1), respectively). The obtained results correlate well with ab initio calculations of ZFS parameters as well as J-values, which indicate that the antiferromagnetic exchange is mediated by hydrogen bonds. The complexes were also investigated by cyclic voltammetry in water or acetonitrile. A quasi-reversible couple Mn(II)/Mn(III) at 1.13/0.97 V, an almost reversible couple Fe(II)/Fe(III) at 0.51/0.25 V, and a one-step/multistep reduction/oxidation of Cu(II) complex 5 at -0.33 V/0.06-0.61 V were detected. PMID:25761063
NASA Astrophysics Data System (ADS)
Dolmella, A.; Bandoli, G.; Cavallin, M.
2000-08-01
LU 25-109 ( II) and WAL 2014 (talsaclidine, III) are two M1 muscarinic agonists chemically related to the natural substance arecoline ( I). All these compounds have beneficial effects on memory and cognition in animals and humans, and they have been proposed in the treatment of Alzheimer's disease, but only III will likely find a place in therapy. In this work we have investigated the solid state structures of II and III, and the X-ray structures of the two molecules and of the parent compound I have been used to input a series of computational chemistry efforts. In particular, the X-ray geometries have been manipulated to model 20 molecular structures ( 1- 20) which have been submitted to ab initio, semiempirical quantum mechanics and molecular mechanics calculations. The conformational space accessible to the 20 structures has been assessed by means of potential energy maps. The reactivities of 1- 20 have been estimated by examining at the graphics terminal the composition and the extension of the frontier orbitals (HOMOs and LUMOs) and of the molecular electrostatic potential. The information obtained has been interpreted to explain the different degrees of activity shown by I- III. Our data indicate that III has better in vivo activity for its intermediate size, less polar surface, conformational rigidity and orientation of reactive domains.
NASA Technical Reports Server (NTRS)
Lucas, J. N.; Deng, W.; Oram, S. W.; Hill, F. S.; Durante, M.; George, K.; Wu, H.; Owens, C. L.; Yang, T.
1999-01-01
In the present study, F ratios for both stable chromosome aberrations, i.e. ratios of translocations to pericentric inversions, and unstable aberrations, i.e. dicentrics and centric rings, were measured using fluorescence in situ hybridization. F ratios for stable aberrations measured after exposure to low (2.89 Gy 60Co gamma rays) and high-LET (0.25 Gy 56Fe ions; 1.25 Gy 56Fe ions; 3.0 Gy 12C ions) radiation were 6.5 +/- 1.5, 4.7 +/- 1.6, 9.3 +/- 2.5 and 10.4 +/- 3.0, respectively. F ratios for unstable aberrations measured after low (2.89 Gy 60Co gamma rays) and high-LET (0.25 Gy 56Fe ions; 3.0 Gy 12C ions) radiations were 6.5 +/- 1.6, 6.3 +/- 2.3 and 11.1 +/- 3.7, respectively. No significant difference between the F ratios for low- and high-LET radiation was found. Further tests on the models for calculation of the F ratio proposed by Brenner and Sachs (Radiat. Res. 140, 134-142, 1994) showed that the F ratio may not be straightforward as a practical fingerprint for densely ionizing radiation.
NASA Astrophysics Data System (ADS)
Sadaf, Haseeba; Isab, Anvarhusein A.; Ahmad, Saeed; Espinosa, Arturo; Mas-Montoya, Míriam; Khan, Islam Ullah; Ejaz; Rehman, Seerat-ur; Ali, Muhammad Akhtar Javed; Saleem, Muhammad; Ruiz, José; Janiak, Christoph
2015-04-01
A new platinum(II) complex, [Pt(Tmtu)4][Pt(CN)4]·4H2O (1) was synthesized by reaction of K2[PtCl4], KCN and tetramethylthiourea (Tmtu). Its structure was determined by X-ray crystallography. The [Pt(CN)4]2- anion shows regular square planar geometry at platinum, while in the [Pt(Tmtu)4]2+ cation the geometry at platinum is somewhat distorted. Hydrogen bonding between water molecules and the cyanide nitrogen of [Pt(CN)4]2- ions stabilizes the structure and leads to a supramolecular 2D network. DFT calculations support the experimentally found dinuclear (homocoordinated) ion-pair structure 1 as the most stable in comparison to noncovalent dimer [Pt(CN)2(Tmtu)2]222 that could, in turn, be involved in the formation sequence of 1. Antimicrobial activities of the complex were evaluated by minimum inhibitory concentration and the results showed that the complex exhibited moderate activities against gram-negative bacteria (Escherichiacoli, Pseudomonas aeruginosa) and molds (Aspergillus niger,Penicilliumcitrinum).
NASA Astrophysics Data System (ADS)
Agirbas, Hikmet; Sagdinc, Seda; Kandemirli, Fatma; Kemal, Berat
2008-12-01
Salicylaldehyde (1) was reacted with aniline to afford 2-[( E)-(phenylimino)methyl]phenol (2). The reduction of (2) by NaBH 4 gave 2-((phenylamino)methyl)phenol ( 3) which was reacted with chloroacetyl chloride to give 2-chloro- N-(2-hydroxybenzyl)- N-phenylacetamide ( 4). Compound ( 4) was cyclized to 4-phenyl-4,5-dihydrobenzo[ f][1,4]oxazepin-3( 2H)-one (5) by NaOH in ethanol solution. The treatment of compound (5) with P 2S 5 gave corresponding 4-phenyl-4,5-dihydrobenzo[ f][1,4]oxazepin-3( 2H)-thione (6). The structures of (5) and (6) were determined by 1H NMR and IR spectra. The optimized structural parameters and vibrational frequencies of (5) and (6) were calculated by DFT with 6-31G(d,p) basis set. The mechanism of the cyclization reaction was studied by RHF with the standard 3-21G basis set.
Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.
2013-01-01
The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol−1) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non-periodic PB
Rocklin, Gabriel J.; Mobley, David L.; Dill, Ken A.; Hünenberger, Philippe H.
2013-11-14
The calculation of a protein-ligand binding free energy based on molecular dynamics (MD) simulations generally relies on a thermodynamic cycle in which the ligand is alchemically inserted into the system, both in the solvated protein and free in solution. The corresponding ligand-insertion free energies are typically calculated in nanoscale computational boxes simulated under periodic boundary conditions and considering electrostatic interactions defined by a periodic lattice-sum. This is distinct from the ideal bulk situation of a system of macroscopic size simulated under non-periodic boundary conditions with Coulombic electrostatic interactions. This discrepancy results in finite-size effects, which affect primarily the charging component of the insertion free energy, are dependent on the box size, and can be large when the ligand bears a net charge, especially if the protein is charged as well. This article investigates finite-size effects on calculated charging free energies using as a test case the binding of the ligand 2-amino-5-methylthiazole (net charge +1 e) to a mutant form of yeast cytochrome c peroxidase in water. Considering different charge isoforms of the protein (net charges −5, 0, +3, or +9 e), either in the absence or the presence of neutralizing counter-ions, and sizes of the cubic computational box (edges ranging from 7.42 to 11.02 nm), the potentially large magnitude of finite-size effects on the raw charging free energies (up to 17.1 kJ mol{sup −1}) is demonstrated. Two correction schemes are then proposed to eliminate these effects, a numerical and an analytical one. Both schemes are based on a continuum-electrostatics analysis and require performing Poisson-Boltzmann (PB) calculations on the protein-ligand system. While the numerical scheme requires PB calculations under both non-periodic and periodic boundary conditions, the latter at the box size considered in the MD simulations, the analytical scheme only requires three non
Accurate adiabatic correction in the hydrogen molecule
Pachucki, Krzysztof; Komasa, Jacek
2014-12-14
A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10{sup −12} at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H{sub 2}, HD, HT, D{sub 2}, DT, and T{sub 2} has been determined. For the ground state of H{sub 2} the estimated precision is 3 × 10{sup −7} cm{sup −1}, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.
Accurate adiabatic correction in the hydrogen molecule
NASA Astrophysics Data System (ADS)
Pachucki, Krzysztof; Komasa, Jacek
2014-12-01
A new formalism for the accurate treatment of adiabatic effects in the hydrogen molecule is presented, in which the electronic wave function is expanded in the James-Coolidge basis functions. Systematic increase in the size of the basis set permits estimation of the accuracy. Numerical results for the adiabatic correction to the Born-Oppenheimer interaction energy reveal a relative precision of 10-12 at an arbitrary internuclear distance. Such calculations have been performed for 88 internuclear distances in the range of 0 < R ⩽ 12 bohrs to construct the adiabatic correction potential and to solve the nuclear Schrödinger equation. Finally, the adiabatic correction to the dissociation energies of all rovibrational levels in H2, HD, HT, D2, DT, and T2 has been determined. For the ground state of H2 the estimated precision is 3 × 10-7 cm-1, which is almost three orders of magnitude higher than that of the best previous result. The achieved accuracy removes the adiabatic contribution from the overall error budget of the present day theoretical predictions for the rovibrational levels.
Wang, Xiangxue; Yang, Shubin; Shi, Weiqun; Li, Jiaxing; Hayat, Tasawar; Wang, Xiangke
2015-10-01
Herein the sorption of Eu(III) and (243)Am(III) on multiwalled carbon nanotubes (CNTs) are studied, and the results show that Eu(III) and (243)Am(III) could form strong inner-sphere surface complexes on CNT surfaces. However, the sorption of Eu(III) on CNTs is stronger than that of (243)Am(III) on CNTs, suggesting the difference in the interaction mechanisms or properties of Eu(III) and (243)Am(III) with CNTs, which is quite different from the results of Eu(III) and (243)Am(III) interaction on natural clay minerals and oxides. On the basis of the results of density functional theory calculations, the binding energies of Eu(III) on CNTs are much higher than those of (243)Am(III) on CNTs, indicating that Eu(III) could form stronger complexes with the oxygen-containing functional groups of CNTs than (243)Am(III), which is in good agreement with the experimental results of higher sorption capacity of CNTs for Eu(III). The oxygen-containing functional groups contribute significantly to the uptake of Eu(III) and (243)Am(III), and the binding affinity increases in the order of ≡S-OH < ≡S-COOH < ≡S-COO(-). This paper highlights the interaction mechanism of Eu(III) and (243)Am(III) with different oxygen-containing functional groups of CNTs, which plays an important role for the potential application of CNTs in the preconcentration, removal, and separation of trivalent lanthanides and actinides in environmental pollution cleanup. PMID:26371690
Zuo, Linzi; Guo, Yong; Li, Xiao; Fu, Heyun; Qu, Xiaolei; Zheng, Shourong; Gu, Cheng; Zhu, Dongqiang; Alvarez, Pedro J J
2016-01-19
A large effort is being made to develop nanosorbents with tunable surface chemistry for enhanced adsorption affinity and selectivity toward target organic contaminants. Heteroatom N-doped multiwall carbon nanotubes (N-MCNT) were synthesized by chemical vapor deposition of pyridine and were further investigated for the adsorptive removal of several aromatic chemicals varying in electronic donor and acceptor ability from aqueous solutions using a batch technique. Compared with commercial nondoped multiwall carbon nanotubes (MCNT), N-MCNT had similar specific surface area, morphology, and pore-size distribution but more hydrophilic surfaces and more surface defects due to the doping of graphitic and pyridinic N atoms. N-MCNT exhibited enhanced adsorption (2-10 folds) for the π-donor chemicals (2-naphthol and 1-naphthalmine) at pH ∼6 but similar adsorption for the weak π-donor chemical (naphthalene) and even lower adsorption (up to a 2-fold change) for the π-acceptor chemical (1,3-dinitrobenzene). The enhanced adsorption of 2-naphthol and 1-naphthalmine to N-MCNT was mainly attributed to the favored π-π electron-donor-acceptor (EDA) interaction between the π-donor adsorbate molecule and the polarized N-heterocyclic aromatic ring (π-acceptor) on N-MCNT. The proposed adsorption enhancement mechanisms were further tested through the pH effects on adsorption and the density function theory (DFT) calculation. The results show for the first time that the adsorptive interaction of π-donor aromatic compounds with carbon nanomaterials can be facilitated by N-doping. PMID:26669961
ERIC Educational Resources Information Center
Rom, Mark Carl
2011-01-01
Grades matter. College grading systems, however, are often ad hoc and prone to mistakes. This essay focuses on one factor that contributes to high-quality grading systems: grading accuracy (or "efficiency"). I proceed in several steps. First, I discuss the elements of "efficient" (i.e., accurate) grading. Next, I present analytical results…
ERIC Educational Resources Information Center
LoPresto, Michael C.
2014-01-01
What follows is a description of a theoretical model designed to calculate the playing frequencies of the musical pitches produced by a trombone. The model is based on quantitative treatments that demonstrate the effects of the flaring bell and cup-shaped mouthpiece sections on these frequencies and can be used to calculate frequencies that…
Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang
2014-10-14
The torsional energy levels of CH{sub 3}OH{sup +}, CH{sub 3}OD{sup +}, and CD{sub 3}OD{sup +} have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH{sub 3}OH, CH{sub 3}OD, and CD{sub 3}OD are determined as 10.8396, 10.8455, and 10.8732 eV with uncertainties of 0.0005 eV, respectively. Theoretical calculations have also been performed to obtain the torsional energy levels for the three isotopologues using a one-dimensional model with approximate zero-point energy corrections of the torsional potential energy curves. The calculated values are in good agreement with the experimental data. The barrier height of the torsional potential energy without zero-point energy correction was calculated as 157 cm{sup −1}, which is about half of that of the neutral (340 cm{sup −1}). The calculations showed that the cation has eclipsed conformation at the energy minimum and staggered one at the saddle point, which is the opposite of what is observed in the neutral molecule. The fundamental C–O stretch vibrational energy level for CD{sub 3}OD{sup +} has also been determined. The energy levels for the combinational excitation of the torsional vibration and the fundamental C–O stretch vibration indicate a strong torsion-vibration coupling.
Accurate Cross Sections for Microanalysis
Rez, Peter
2002-01-01
To calculate the intensity of x-ray emission in electron beam microanalysis requires a knowledge of the energy distribution of the electrons in the solid, the energy variation of the ionization cross section of the relevant subshell, the fraction of ionizations events producing x rays of interest and the absorption coefficient of the x rays on the path to the detector. The theoretical predictions and experimental data available for ionization cross sections are limited mainly to K shells of a few elements. Results of systematic plane wave Born approximation calculations with exchange for K, L, and M shell ionization cross sections over the range of electron energies used in microanalysis are presented. Comparisons are made with experimental measurement for selected K shells and it is shown that the plane wave theory is not appropriate for overvoltages less than 2.5 V. PMID:27446747
Park, J; Lee, J; Kim, H; Kim, I; Ye, S
2015-06-15
Purpose: To evaluate the effect of a tungsten eye-shield on the dose distribution of a patient. Methods: A 3D scanner was used to extract the dimension and shape of a tungsten eye-shield in the STL format. Scanned data was transferred into a 3D printer. A dummy eye shield was then produced using bio-resin (3D systems, VisiJet M3 Proplast). For a patient with mucinous carcinoma, the planning CT was obtained with the dummy eye-shield placed on the patient’s right eye. Field shaping of 6 MeV was performed using a patient-specific cerrobend block on the 15 x 15 cm{sup 2} applicator. The gantry angle was 330° to cover the planning target volume near by the lens. EGS4/BEAMnrc was commissioned from our measurement data from a Varian 21EX. For the CT-based dose calculation using EGS4/DOSXYZnrc, the CT images were converted to a phantom file through the ctcreate program. The phantom file had the same resolution as the planning CT images. By assigning the CT numbers of the dummy eye-shield region to 17000, the real dose distributions below the tungsten eye-shield were calculated in EGS4/DOSXYZnrc. In the TPS, the CT number of the dummy eye-shield region was assigned to the maximum allowable CT number (3000). Results: As compared to the maximum dose, the MC dose on the right lens or below the eye shield area was less than 2%, while the corresponding RTP calculated dose was an unrealistic value of approximately 50%. Conclusion: Utilizing a 3D scanner and a 3D printer, a dummy eye-shield for electron treatment can be easily produced. The artifact-free CT images were successfully incorporated into the CT-based Monte Carlo simulations. The developed method was useful in predicting the realistic dose distributions around the lens blocked with the tungsten shield.
Accurate monotone cubic interpolation
NASA Technical Reports Server (NTRS)
Huynh, Hung T.
1991-01-01
Monotone piecewise cubic interpolants are simple and effective. They are generally third-order accurate, except near strict local extrema where accuracy degenerates to second-order due to the monotonicity constraint. Algorithms for piecewise cubic interpolants, which preserve monotonicity as well as uniform third and fourth-order accuracy are presented. The gain of accuracy is obtained by relaxing the monotonicity constraint in a geometric framework in which the median function plays a crucial role.
Accurate Finite Difference Algorithms
NASA Technical Reports Server (NTRS)
Goodrich, John W.
1996-01-01
Two families of finite difference algorithms for computational aeroacoustics are presented and compared. All of the algorithms are single step explicit methods, they have the same order of accuracy in both space and time, with examples up to eleventh order, and they have multidimensional extensions. One of the algorithm families has spectral like high resolution. Propagation with high order and high resolution algorithms can produce accurate results after O(10(exp 6)) periods of propagation with eight grid points per wavelength.
Theoretical challenges in Double Beta Decay
NASA Astrophysics Data System (ADS)
Stoica, Sabin
2016-05-01
The study of the double beta decay (DBD), particularly the neutrino less decay mode, is of great interest for testing the lepton number conservation (LNC) and getting information about neutrino properties, as the neutrinos character (Dirac or Majorana particles?), their absolute mass and hierarchy, etc. [1]-[2]. To make predictions of the DBD lifetimes and put constraints on the neutrino parameters, one needs accurate calculations of the nuclear matrix elements (NME) and phase space factors (PSF) entering the DBD lifetime expressions. In this paper I present recent calculations of these quantities, performed with approaches developed by our group. Then, I compare the theoretical predictions for the two-neutrino (2v) DBD lifetimes, for the most experimentally interesting nuclei, with the experimental ones, and comment on the reliability of the neutrinoless (0v) DBD calculations.
An Accurate Temperature Correction Model for Thermocouple Hygrometers 1
Savage, Michael J.; Cass, Alfred; de Jager, James M.
1982-01-01
Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques. In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38°C). The model based on calibration at two temperatures is superior to that based on only one calibration. The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25°C, if the calibration slopes are corrected for temperature. PMID:16662241
An accurate temperature correction model for thermocouple hygrometers.
Savage, M J; Cass, A; de Jager, J M
1982-02-01
Numerous water relation studies have used thermocouple hygrometers routinely. However, the accurate temperature correction of hygrometer calibration curve slopes seems to have been largely neglected in both psychrometric and dewpoint techniques.In the case of thermocouple psychrometers, two temperature correction models are proposed, each based on measurement of the thermojunction radius and calculation of the theoretical voltage sensitivity to changes in water potential. The first model relies on calibration at a single temperature and the second at two temperatures. Both these models were more accurate than the temperature correction models currently in use for four psychrometers calibrated over a range of temperatures (15-38 degrees C). The model based on calibration at two temperatures is superior to that based on only one calibration.The model proposed for dewpoint hygrometers is similar to that for psychrometers. It is based on the theoretical voltage sensitivity to changes in water potential. Comparison with empirical data from three dewpoint hygrometers calibrated at four different temperatures indicates that these instruments need only be calibrated at, e.g. 25 degrees C, if the calibration slopes are corrected for temperature. PMID:16662241
NASA Astrophysics Data System (ADS)
Somerville, W. R. C.; Auguié, B.; Le Ru, E. C.
2016-03-01
SMARTIES calculates the optical properties of oblate and prolate spheroidal particles, with comparable capabilities and ease-of-use as Mie theory for spheres. This suite of MATLAB codes provides a fully documented implementation of an improved T-matrix algorithm for the theoretical modelling of electromagnetic scattering by particles of spheroidal shape. Included are scripts that cover a range of scattering problems relevant to nanophotonics and plasmonics, including calculation of far-field scattering and absorption cross-sections for fixed incidence orientation, orientation-averaged cross-sections and scattering matrix, surface-field calculations as well as near-fields, wavelength-dependent near-field and far-field properties, and access to lower-level functions implementing the T-matrix calculations, including the T-matrix elements which may be calculated more accurately than with competing codes.
Predict amine solution properties accurately
Cheng, S.; Meisen, A.; Chakma, A.
1996-02-01
Improved process design begins with using accurate physical property data. Especially in the preliminary design stage, physical property data such as density viscosity, thermal conductivity and specific heat can affect the overall performance of absorbers, heat exchangers, reboilers and pump. These properties can also influence temperature profiles in heat transfer equipment and thus control or affect the rate of amine breakdown. Aqueous-amine solution physical property data are available in graphical form. However, it is not convenient to use with computer-based calculations. Developed equations allow improved correlations of derived physical property estimates with published data. Expressions are given which can be used to estimate physical properties of methyldiethanolamine (MDEA), monoethanolamine (MEA) and diglycolamine (DGA) solutions.
NASA Astrophysics Data System (ADS)
Itano, Wayne M.; Ramsey, Norman F.
1993-07-01
The paper discusses current methods for accurate measurements of time by conventional atomic clocks, with particular attention given to the principles of operation of atomic-beam frequency standards, atomic hydrogen masers, and atomic fountain and to the potential use of strings of trapped mercury ions as a time device more stable than conventional atomic clocks. The areas of application of the ultraprecise and ultrastable time-measuring devices that tax the capacity of modern atomic clocks include radio astronomy and tests of relativity. The paper also discusses practical applications of ultraprecise clocks, such as navigation of space vehicles and pinpointing the exact position of ships and other objects on earth using the GPS.
NASA Astrophysics Data System (ADS)
Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna
2015-06-01
The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5c = 222.9 K on cooling and at TC5h = 225.4 K on heating) the CH3 groups perform fast (τR ≈ 10-12-10-13 s) reorientational motions. These motions start to slow down below TC5c Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6]2+ cation and ClO4- anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made.
Szostak, Elżbieta; Hetmańczyk, Joanna; Migdał-Mikuli, Anna
2015-06-15
The vibrational and reorientational dynamics of CH3 groups from (CH3)2SO ligands in the high- and low-temperature phases of [Mn(OS(CH3)2)6](ClO4)2 were investigated by quasielastic and inelastic incoherent neutron scattering (QENS and IINS) methods. The results show that above the phase transition temperature (detected earlier by differential scanning calorimetry (DSC) at TC5(c)=222.9K on cooling and at TC5(h)=225.4K on heating) the CH3 groups perform fast (τR≈10(-12)-10(-13)s) reorientational motions. These motions start to slow down below TC5(c) Neutron powder diffraction (NPD) measurements, performed simultaneously with QENS and IINS, indicated that this phase transition is associated with a change of the crystal structure, too. Theoretical infrared absorption, Raman and inelastic incoherent neutron scattering spectra were calculated using DFT method (B3LYP functional, LANL2DZ ECP basis set (on Mn atom) and 6-311+G(d,p) basis set (on C, H, S, O atoms) for the isolated equilibrium model (isolated [Mn(DMSO)6](2+) cation and ClO4(-) anion). Calculated spectra show a good agreement with the experimental spectra (FT-IR, RS and IINS). The comparison of the results obtained by these complementary methods was made. PMID:25795611
Accurate ab Initio Spin Densities
2012-01-01
We present an approach for the calculation of spin density distributions for molecules that require very large active spaces for a qualitatively correct description of their electronic structure. Our approach is based on the density-matrix renormalization group (DMRG) algorithm to calculate the spin density matrix elements as a basic quantity for the spatially resolved spin density distribution. The spin density matrix elements are directly determined from the second-quantized elementary operators optimized by the DMRG algorithm. As an analytic convergence criterion for the spin density distribution, we employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.2011, 134, 224101] to build an accurate complete-active-space configuration-interaction (CASCI) wave function from the optimized matrix product states. The spin density matrix elements can then also be determined as an expectation value employing the reconstructed wave function expansion. Furthermore, the explicit reconstruction of a CASCI-type wave function provides insight into chemically interesting features of the molecule under study such as the distribution of α and β electrons in terms of Slater determinants, CI coefficients, and natural orbitals. The methodology is applied to an iron nitrosyl complex which we have identified as a challenging system for standard approaches [J. Chem. Theory Comput.2011, 7, 2740]. PMID:22707921
NASA Astrophysics Data System (ADS)
LoPresto, Michael C.
2014-09-01
What follows is a description of a theoretical model designed to calculate the playing frequencies of the musical pitches produced by a trombone. The model is based on quantitative treatments that demonstrate the effects of the flaring bell and cup-shaped mouthpiece sections on these frequencies and can be used to calculate frequencies that compare well to both the desired frequencies of the musical pitches and those actually played on a real trombone.
Fleming, Donald G; Arseneau, Donald J; Sukhorukov, Oleksandr; Brewer, Jess H; Mielke, Steven L; Truhlar, Donald G; Schatz, George C; Garrett, Bruce C; Peterson, Kirk A
2011-11-14
The neutral muonic helium atom (4)Heμ, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation (μSR) measurements of the chemical reaction rate constant of (4)Heμ with molecular hydrogen, (4)Heμ + H(2) → (4)HeμH + H, at temperatures of 295.5, 405, and 500 K, as well as a μSR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, k(Heμ), are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for k(Heμ) are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for k(Heμ) on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H(2) and Mu + H(2) reactions in a novel study of kinetic isotope effects for the H + H(2) reactions over a factor of 36.1 in isotopic mass of the atomic reactant. PMID:22088068
Accurate and fast DFT calculations with the AM05 functional
NASA Astrophysics Data System (ADS)
Mattsson, Ann E.
2008-03-01
The AM05 functional [1] has the same excellent performance for solids as the hybrid density functionals tested in Paier et. al. (J. Chem. Phys 124, 154709 (2006); ibid 125, 249901 (2006)). This confirms the original finding that AM05 performs exceptionally well for solids and surfaces. While hybrid functionals are computationally expensive, preveting them from being used in large systems and/or long molecular dynamics simulations, the AM05 functional is on a regular semi-local GGA form with corresponding computational cost. The performance of AM05 is even superior to an `informed choice' between LDA and PBE. By comparing data from different electronic-structure codes we have determined that the numerical errors in this study are equal to or smaller than corresponding experimental uncertainties. Results for other systems will also be presented. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000. [1] R. Armiento and A. E. Mattsson, Phys. Rev. B 72, 085108 (2005).
Time-accurate Navier-Stokes calculations with multigrid acceleration
NASA Technical Reports Server (NTRS)
Melson, N. Duane; Atkins, Harold L.; Sanetrik, Mark D.
1993-01-01
A numerical scheme to solve the unsteady Navier-Stokes equations is described. The scheme is implemented by modifying the multigrid-multiblock version of the steady Navier-Stokes equations solver, TLNS3D. The scheme is fully implicit in time and uses TLNS3D to iteratively invert the equations at each physical time step. The design objective of the scheme is unconditional stability (at least for first- and second-order discretizations of the physical time derivatives). With unconditional stability, the choice of the time step is based on the physical phenomena to be resolved rather than limited by numerical stability which is especially important for high Reynolds number viscous flows, where the spatial variation of grid cell size can be as much as six orders of magnitude. An analysis of the iterative procedure and the implementation of this procedure in TLNS3D are discussed. Numerical results are presented to show both the capabilities of the scheme and its speed up relative to the use of global minimum time stepping. Reductions in computational times of an order of magnitude are demonstrated.
Using BRDFs for accurate albedo calculations and adjacency effect corrections
Borel, C.C.; Gerstl, S.A.W.
1996-09-01
In this paper the authors discuss two uses of BRDFs in remote sensing: (1) in determining the clear sky top of the atmosphere (TOA) albedo, (2) in quantifying the effect of the BRDF on the adjacency point-spread function and on atmospheric corrections. The TOA spectral albedo is an important parameter retrieved by the Multi-angle Imaging Spectro-Radiometer (MISR). Its accuracy depends mainly on how well one can model the surface BRDF for many different situations. The authors present results from an algorithm which matches several semi-empirical functions to the nine MISR measured BRFs that are then numerically integrated to yield the clear sky TOA spectral albedo in four spectral channels. They show that absolute accuracies in the albedo of better than 1% are possible for the visible and better than 2% in the near infrared channels. Using a simplified extensive radiosity model, the authors show that the shape of the adjacency point-spread function (PSF) depends on the underlying surface BRDFs. The adjacency point-spread function at a given offset (x,y) from the center pixel is given by the integral of transmission-weighted products of BRDF and scattering phase function along the line of sight.
Calculation of the Isotope Cluster for Polypeptides by Probability Grouping
Olson, Matthew T.; Yergey, Alfred L.
2014-01-01
This paper presents a novel theoretical basis for accurately calculating the isotope cluster of polypeptides. In contrast to previous approaches to this problem, which consider exhaustive or near exhaustive combinations of isotopic species, the program, Neutron Cluster, groups probabilities to yield highly accurate information without elucidating any fine structure within a nominal mass unit. This is a fundamental difference from any previously described algorithm for calculating the isotope cluster. As a result of this difference, the accurate isotope clusters for high molecular weight polypeptides can be calculated rapidly without any pruning. When applied to isotope enriched polypeptides, the algorithm introduces “grouping error”, which is described, quantified, and avoided by using probability partitioning. PMID:19026561
Calculation of the isotope cluster for polypeptides by probability grouping.
Olson, Matthew T; Yergey, Alfred L
2009-02-01
This paper presents a novel theoretical basis for accurately calculating the isotope cluster of polypeptides. In contrast to previous approaches to this problem, which consider exhaustive or near exhaustive combinations of isotopic species, the program, Neutron Cluster, groups probabilities to yield highly accurate information without elucidating any fine structure within a nominal mass unit. This is a fundamental difference from any previously described algorithm for calculating the isotope cluster. As a result of this difference, the accurate isotope clusters for high molecular weight polypeptides can be calculated rapidly without any pruning. When applied to isotope enriched polypeptides, the algorithm introduces "grouping error", which is described, quantified, and avoided by using probability partitioning. PMID:19026561
Theoretical prediction of optical absorption maxima for photosensory receptor mutants
NASA Astrophysics Data System (ADS)
Kawaguchi, Kazutomo; Yamato, Takahisa
2006-10-01
We found a linear correlation between the theoretically predicted shifts and experimentally observed absorption spectra for various mutants of photoactive yellow protein, a photosensory receptor. Excitation energies of mutants were evaluated by the combination of the high level ab initio calculation for the chromophore inside and the low level ab initio calculation for the surrounding protein environment. Importantly, the electronic states of these two regions were treated both as variables and they are solved consistently to each other. The protein-chromophore interaction has been accurately reproduced by this method.
Theoretical studies of molecular processes
NASA Astrophysics Data System (ADS)
Cui, Qiang
1997-09-01
The current thesis concerns with theoretical studies of molecular processes and consists of two parts. The first part includes theoretical studies of dynamics of unimolecular and bimolecular reactions, in particular those involving non-adiabatic processes. In chapter 2 and 3, we have presented our studies of detailed mechanisms for the photodissociation of C2H2 and C2H, and the ion-molecule reactions of C2H2+ + CH4 or NH3, respectively. In chapter 4, we have presented our study that extends TST to non-adiabatic reactions, and an application of the theory of the spin-forbidden reaction of CH(2/Pi)+N2. In chapter 5, we have included our analyses on the photodissociation of triplet ketene, where an extensive seam has been found all along the reaction coordinate. Finally, in Chapter 6, we have presented our study on the photodissociation of O3/sp-, which includes qualitative electronic structure calculations and construction of global potential energy functions for coupled electronic states. The second part of the thesis deals with theoretical studies of organometallic reactions, metal clusters, and gas-surface interactions. With theoretical calculations, one can study the reactivities of transition metal compounds systematically, which allows one to understand the key parameters that control the reactivities of those compounds. In chapter 2, we have presented our implementation of analytical hessian for effective core potential, which makes normal mode analysis possible for large organometallic systems and has proven to be very useful in the study of systems containing transition metals. In chapter 3-5, we have included our studies on the detailed mechanisms of several interesting reactions including platinum/palladium(0) catalyzed diboration and thioboration reactions of acetylene and olefin, and H- H/C-H bond activation on small metal clusters Pt/Pdn(n = 1[-]3). For truly large systems such as surfaces or proteins, full quantum mechanical treatments are
Bouanich, J P.; Boulet, C; Predoi-Cross, A; Sharpe, Steven W.; Sams, Robert L.; Smith, Mary A.; Rinsland, Curtis P.; Benner, D C.; Devi, V M.
2005-04-07
A semiclassical theory based upon the Robert-Bonamy formalism has been developed in order to explain the experimental measurements of self-broadening, self-induced pressure shift coefficients in the v1, v2, 2v2 bands of H12C14N and the 2v1 band of H13C14N as well as the temperature dependences of these parameters with special emphasis on the v2 band. Our calculations include only electrostatic interactions and neglect the vibrational dependence of the isotropic part of the intermolecular potential, which probably has a weak contribution to the HCN self-shifts for the bands investigated in this study. The agreement between theory and measurements is good in the cases of self-broadening coefficients and their variation with temperature, as well as the self-shift coefficients determined at room temperature. However, the observed temperature dependence of self-shift coefficients in the v2 band is different from that derived theoretically.
Small portable speed calculator
NASA Technical Reports Server (NTRS)
Burch, J. L.; Billions, J. C.
1973-01-01
Calculator is adapted stopwatch calibrated for fast accurate measurement of speeds. Single assembled unit is rugged, self-contained, and relatively inexpensive to manufacture. Potential market includes automobile-speed enforcement, railroads, and field-test facilities.
Fleming, Donald G.; Arseneau, Donald J.; Sukhorukov, Oleksandr; Brewer, Jess H.; Mielke, Steven L.; Truhlar, Donald G.; Schatz, George C.; Garrett, Bruce C.; Peterson, Kirk A.
2011-11-14
The neutral muonic helium atom {sup 4}He{mu}, in which one of the electrons of He is replaced by a negative muon, may be effectively regarded as the heaviest isotope of the hydrogen atom, with a mass of 4.115 amu. We report details of the first muon spin rotation ({mu}SR) measurements of the chemical reaction rate constant of {sup 4}He{mu} with molecular hydrogen, {sup 4}He{mu} + H{sub 2} {yields} {sup 4}He{mu}H + H, at temperatures of 295.5, 405, and 500 K, as well as a {mu}SR measurement of the hyperfine coupling constant of muonic He at high pressures. The experimental rate constants, k{sub He{mu}}, are compared with the predictions of accurate quantum mechanical (QM) dynamics calculations carried out on a well converged Born-Huang (BH) potential energy surface, based on complete configuration interaction calculations and including a Born-Oppenheimer diagonal correction. At the two highest measured temperatures the agreement between the quantum theory and experiment is good to excellent, well within experimental uncertainties that include an estimate of possible systematic error, but at 295.5 K the quantum calculations for k{sub He{mu}} are below the experimental value by 2.1 times the experimental uncertainty estimates. Possible reasons for this discrepancy are discussed. Variational transition state theory calculations with multidimensional tunneling have also been carried out for k{sub He{mu}} on the BH surface, and they agree with the accurate QM rate constants to within 30% over a wider temperature range of 200-1000 K. Comparisons between theory and experiment are also presented for the rate constants for both the D + H{sub 2} and Mu + H{sub 2} reactions in a novel study of kinetic isotope effects for the H + H{sub 2} reactions over a factor of 36.1 in isotopic mass of the atomic reactant.
Roy, Subhadip; Oyarzabal, Itziar; Vallejo, Julia; Cano, Joan; Colacio, Enrique; Bauza, Antonio; Frontera, Antonio; Kirillov, Alexander M; Drew, Michael G B; Das, Subrata
2016-09-01
A mononuclear cobalt(II) complex [Co(3,5-dnb)2(py)2(H2O)2] {3,5-Hdnb = 3,5-dinitrobenzoic acid; py = pyridine} was isolated in two polymorphs, in space groups C2/c (1) and P21/c (2). Single-crystal X-ray diffraction analyses reveal that 1 and 2 are not isostructural in spite of having equal formulas and ligand connectivity. In both structures, the Co(II) centers adopt octahedral {CoN2O4} geometries filled by pairs of mutually trans terminal 3,5-dnb, py, and water ligands. However, the structures of 1 and 2 disclose distinct packing patterns driven by strong intermolecular O-H···O hydrogen bonds, leading to their 0D→2D (1) or 0D→1D (2) extension. The resulting two-dimensional layers and one-dimensional chains were topologically classified as the sql and 2C1 underlying nets, respectively. By means of DFT theoretical calculations, the energy variations between the polymorphs were estimated, and the binding energies associated with the noncovalent interactions observed in the crystal structures were also evaluated. The study of the direct-current magnetic properties, as well as ab initio calculations, reveal that both 1 and 2 present a strong easy-plane magnetic anisotropy (D > 0), which is larger for the latter polymorph (D is found to exhibit values between +58 and 117 cm(-1) depending on the method). Alternating current dynamic susceptibility measurements show that these polymorphs exhibit field-induced slow relaxation of the magnetization with Ueff values of 19.5 and 21.1 cm(-1) for 1 and 2, respectively. The analysis of the whole magnetic data allows the conclusion that the magnetization relaxation in these polymorphs mainly takes place through a virtual excited state (Raman process). It is worth noting that despite the notable difference between the supramolecular networks of 1 and 2, they exhibit almost identical magnetization dynamics. This fact suggests that the relaxation process is intramolecular in nature and that the virtual state involved in the
Ghosh, Soumavo; Biswas, Saptarshi; Bauzá, Antonio; Barceló-Oliver, Miquel; Frontera, Antonio; Ghosh, Ashutosh
2013-07-01
Five heterobimetallic copper(II)-uranium(VI) complexes [(CuL(1))UO2(NO3)2] (1), [{CuL(1)(CH3CN)}UO2(NO3)2] (2), [{CuL(1)(CH3COCH3)}UO2(NO3)2] (3), [{CuL(2)(CH3CN)}UO2(NO3)2](4), and [{CuL(2)(CH3COCH3)}UO2(NO3)2][{CuL(2)}UO2(NO3)2] (5) have been synthesized by reacting the Cu(II)-derived metalloligands [CuL(1)] and [CuL(2)] (where, H2L(1) = N,N'-bis(α-methylsalicylidene)-1,3-propanediamine and H2L(2) = N,N'-bis(salicylidene)-1,3-propanediamine) with UO2(NO3)2·6H2O in 1:1 ratio by varying the reaction temperature and solvents. Absorption and fluorescence quenching experiments (steady-state and time-resolved) indicate the formation of 1:1 ground-state charge transfer copper(II)-uranium(VI) complexes in solution. X-ray single-crystal structure reveals that each complex contains diphenoxido bridged Cu(II)-U(VI) dinuclear core with two chelated nitrato coligands. The complexes are solvated (acetonitrile or acetone) in the axial position of the Cu(II) in different manner or desolvated. The supramolecular interactions that depend upon the co-ordinating metalloligands seem to control the solvation. In complexes 2 and 3 a rare NO3(-)···NO3(-) weak interaction plays an important role in forming supramolecular network whereas an uncommon U═O···NO3(-) weak interaction helps to self-assemble heterobinuclear units in complex 5. The significance of the noncovalent interactions in terms of energies and geometries has been analyzed using theoretical calculations. PMID:23786416
NASA Astrophysics Data System (ADS)
Mikeš, Daniel
2010-05-01
Theoretical geology Present day geology is mostly empirical of nature. I claim that geology is by nature complex and that the empirical approach is bound to fail. Let's consider the input to be the set of ambient conditions and the output to be the sedimentary rock record. I claim that the output can only be deduced from the input if the relation from input to output be known. The fundamental question is therefore the following: Can one predict the output from the input or can one predict the behaviour of a sedimentary system? If one can, than the empirical/deductive method has changes, if one can't than that method is bound to fail. The fundamental problem to solve is therefore the following: How to predict the behaviour of a sedimentary system? It is interesting to observe that this question is never asked and many a study is conducted by the empirical/deductive method; it seems that the empirical method has been accepted as being appropriate without question. It is, however, easy to argument that a sedimentary system is by nature complex and that several input parameters vary at the same time and that they can create similar output in the rock record. It follows trivially from these first principles that in such a case the deductive solution cannot be unique. At the same time several geological methods depart precisely from the assumption, that one particular variable is the dictator/driver and that the others are constant, even though the data do not support such an assumption. The method of "sequence stratigraphy" is a typical example of such a dogma. It can be easily argued that all the interpretation resulting from a method that is built on uncertain or wrong assumptions is erroneous. Still, this method has survived for many years, nonwithstanding all the critics it has received. This is just one example of the present day geological world and is not unique. Even the alternative methods criticising sequence stratigraphy actually depart from the same
Are Kohn-Sham conductances accurate?
Mera, H; Niquet, Y M
2010-11-19
We use Fermi-liquid relations to address the accuracy of conductances calculated from the single-particle states of exact Kohn-Sham (KS) density functional theory. We demonstrate a systematic failure of this procedure for the calculation of the conductance, and show how it originates from the lack of renormalization in the KS spectral function. In certain limits this failure can lead to a large overestimation of the true conductance. We also show, however, that the KS conductances can be accurate for single-channel molecular junctions and systems where direct Coulomb interactions are strongly dominant. PMID:21231333
Calculation of multiphoton ionization processes
NASA Technical Reports Server (NTRS)
Chang, T. N.; Poe, R. T.
1976-01-01
We propose an accurate and efficient procedure in the calculation of multiphoton ionization processes. In addition to the calculational advantage, this procedure also enables us to study the relative contributions of the resonant and nonresonant intermediate states.
Accurate ab initio vibrational energies of methyl chloride
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH{sub 3}{sup 35}Cl and CH{sub 3}{sup 37}Cl. The respective PESs, CBS-35{sup HL}, and CBS-37{sup HL}, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY {sub 3}Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35{sup HL} and CBS-37{sup HL} PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm{sup −1}, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH{sub 3}Cl without empirical refinement of the respective PESs.
Accurate ab initio vibrational energies of methyl chloride.
Owens, Alec; Yurchenko, Sergei N; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-28
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH3 (35)Cl and CH3 (37)Cl. The respective PESs, CBS-35( HL), and CBS-37( HL), are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35( HL) and CBS-37( HL) PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm(-1), respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs. PMID:26133427
Accurate ab initio vibrational energies of methyl chloride
NASA Astrophysics Data System (ADS)
Owens, Alec; Yurchenko, Sergei N.; Yachmenev, Andrey; Tennyson, Jonathan; Thiel, Walter
2015-06-01
Two new nine-dimensional potential energy surfaces (PESs) have been generated using high-level ab initio theory for the two main isotopologues of methyl chloride, CH335Cl and CH337Cl. The respective PESs, CBS-35 HL, and CBS-37 HL, are based on explicitly correlated coupled cluster calculations with extrapolation to the complete basis set (CBS) limit, and incorporate a range of higher-level (HL) additive energy corrections to account for core-valence electron correlation, higher-order coupled cluster terms, scalar relativistic effects, and diagonal Born-Oppenheimer corrections. Variational calculations of the vibrational energy levels were performed using the computer program TROVE, whose functionality has been extended to handle molecules of the form XY 3Z. Fully converged energies were obtained by means of a complete vibrational basis set extrapolation. The CBS-35 HL and CBS-37 HL PESs reproduce the fundamental term values with root-mean-square errors of 0.75 and 1.00 cm-1, respectively. An analysis of the combined effect of the HL corrections and CBS extrapolation on the vibrational wavenumbers indicates that both are needed to compute accurate theoretical results for methyl chloride. We believe that it would be extremely challenging to go beyond the accuracy currently achieved for CH3Cl without empirical refinement of the respective PESs.
NASA Astrophysics Data System (ADS)
Stöltzner, Michael
Answering to the double-faced influence of string theory on mathematical practice and rigour, the mathematical physicists Arthur Jaffe and Frank Quinn have contemplated the idea that there exists a `theoretical' mathematics (alongside `theoretical' physics) whose basic structures and results still require independent corroboration by mathematical proof. In this paper, I shall take the Jaffe-Quinn debate mainly as a problem of mathematical ontology and analyse it against the backdrop of two philosophical views that are appreciative towards informal mathematical development and conjectural results: Lakatos's methodology of proofs and refutations and John von Neumann's opportunistic reading of Hilbert's axiomatic method. The comparison of both approaches shows that mitigating Lakatos's falsificationism makes his insights about mathematical quasi-ontology more relevant to 20th century mathematics in which new structures are introduced by axiomatisation and not necessarily motivated by informal ancestors. The final section discusses the consequences of string theorists' claim to finality for the theory's mathematical make-up. I argue that ontological reductionism as advocated by particle physicists and the quest for mathematically deeper axioms do not necessarily lead to identical results.
NASA Technical Reports Server (NTRS)
Oliver, B. M.; Gower, J. F. R.
1977-01-01
A data acquisition system using a Litton LTN-51 inertial navigation unit (INU) was tested and used for aircraft track recovery and for location and tracking from the air of targets at sea. The characteristic position drift of the INU is compensated for by sighting landmarks of accurately known position at discrete time intervals using a visual sighting system in the transparent nose of the Beechcraft 18 aircraft used. For an aircraft altitude of about 300 m, theoretical and experimental tests indicate that calculated aircraft and/or target positions obtained from the interpolated INU drift curve will be accurate to within 10 m for landmarks spaced approximately every 15 minutes in time. For applications in coastal oceanography, such as surface current mapping by tracking artificial targets, the system allows a broad area to be covered without use of high altitude photography and its attendant needs for large targets and clear weather.
Accurate band-to-band registration of AOTF imaging spectrometer using motion detection technology
NASA Astrophysics Data System (ADS)
Zhou, Pengwei; Zhao, Huijie; Jin, Shangzhong; Li, Ningchuan
2016-05-01
This paper concerns the problem of platform vibration induced band-to-band misregistration with acousto-optic imaging spectrometer in spaceborne application. Registrating images of different bands formed at different time or different position is difficult, especially for hyperspectral images form acousto-optic tunable filter (AOTF) imaging spectrometer. In this study, a motion detection method is presented using the polychromatic undiffracted beam of AOTF. The factors affecting motion detect accuracy are analyzed theoretically, and calculations show that optical distortion is an easily overlooked factor to achieve accurate band-to-band registration. Hence, a reflective dual-path optical system has been proposed for the first time, with reduction of distortion and chromatic aberration, indicating the potential of higher registration accuracy. Consequently, a spectra restoration experiment using additional motion detect channel is presented for the first time, which shows the accurate spectral image registration capability of this technique.
Theoretical approximations and experimental extinction coefficients of biopharmaceuticals.
Miranda-Hernández, Mariana P; Valle-González, Elba R; Ferreira-Gómez, David; Pérez, Néstor O; Flores-Ortiz, Luis F; Medina-Rivero, Emilio
2016-02-01
UV spectrophotometric measurement is a widely accepted and standardized routine analysis for quantitation of highly purified proteins; however, the reliability of the results strictly depends on the accuracy of the employed extinction coefficients. In this work, an experimental estimation of the differential refractive index (dn/dc), based on dry weight measurements, was performed in order to determine accurate extinction coefficients for four biotherapeutic proteins and one synthetic copolymer after separation in a size-exclusion ultra-performance liquid chromatograph coupled to an ultraviolet, multiangle light scattering and refractive index (SE-UPLC-UV-MALS-RI) multidetection system. The results showed small deviations with respect to theoretical values, calculated from the specific amino acid sequences, for all the studied immunoglobulins. Nevertheless, for proteins like etanercept and glatiramer acetate, several considerations, such as glycan content, partial specific volume, polarizability, and higher order structure, should be considered to properly calculate theoretical extinction coefficient values. Herein, these values were assessed with simple approximations. The precision of the experimentally obtained extinction coefficients, and its convergence towards the theoretical values, makes them useful for characterization and comparability exercises. Also, these values provide insight into the absorbance and scattering properties of the evaluated proteins. Overall, this methodology is capable of providing accurate extinction coefficients useful for development studies. PMID:26715251
Lestinsky, M.; Hahn, M.; Novotny, O.; Savin, D. W.; Badnell, N. R.; Bernhardt, D.; Mueller, A.; Schippers, S.; Bing, D.; Grieser, M.; Hoffmann, J.; Jordon-Thaden, B.; Krantz, C.; Orlov, D. A.; Repnow, R.; Shornikov, A.; Wolf, A.
2012-10-10
We have measured electron-ion recombination for C-like Mg{sup 6+} forming Mg{sup 5+}, and for B-like Mg{sup 7+} forming Mg{sup 6+}. These studies were performed using a merged electron-ion beam arrangement at the TSR heavy ion storage ring located in Heidelberg, Germany. Both primary ions have metastable levels with significant lifetimes. Using a simple cascade model we estimate the population fractions in these metastable levels. For the Mg{sup 6+} results, we find that the majority of the stored ions are in a metastable level, while for Mg{sup 7+} the metastable fraction is insignificant. We present the Mg{sup 6+} merged beams recombination rate coefficient for DR via N = 2 {yields} N' = 2 core electron excitations ({Delta}N = 0 DR) and for Mg{sup 7+} via 2 {yields} 2 and 2 {yields} 3 core excitations. Taking the estimated metastable populations into account, we compare our results to state-of-the-art multiconfiguration Breit-Pauli theoretical calculations. Significant differences are found at low energies where theory is known to be unreliable. Moreover, for both ions we observe a discrepancy between experiment and theory for {Delta}N = 0 DR involving capture into high-n Rydberg levels and where the stabilization is primarily due to a radiative transition of the excited core electron. This is consistent with previous DR experiments on M-shell iron ions which were performed at TSR. The large metastable content of the Mg{sup 6+} ion beam precludes generating a plasma recombination rate coefficient (PRRC). However, this is not an issue for Mg{sup 7+} and we present an experimentally derived Mg{sup 7+} PRRC for plasma temperatures from 400 K to 10{sup 7} K with an estimated uncertainty of less than 27% at a 90% confidence level. We also provide a fit to our experimentally derived PRRC for use in plasma modeling codes.
NASA Astrophysics Data System (ADS)
Vaisburd, D. I.; Kharitonova, S. V.
1997-11-01
present article gives the results of theoretical calculations of the spectra and other characteristics of intraband electron and interband hole luminescence which are compared with the experimental data.
Theoretical study of the dipole moment function of the X2Sigma(+) state of CN. [in comets
NASA Technical Reports Server (NTRS)
Langhoff, Stephen R.; Bauschlicher, Charles W., Jr.
1989-01-01
The X2Sigma(+) state dipole moment function of CN is determined from accurate ab initio calculations. The calculated Einstein coefficient of 13.0 /s for the fundamental 1-0 vibrational band is in excellent agreement with the value measured by Treffers (1975) using a King furnace. The theoretical vibrational band strengths should be valuable in interpreting the fluorescence spectrum of CN in comets.
NASA Astrophysics Data System (ADS)
Borkowski, Andrzej; Kosek, Wiesław
2015-12-01
The paper presents a summary of research activities concerning theoretical geodesy performed in Poland in the period of 2011-2014. It contains the results of research on new methods of the parameter estimation, a study on robustness properties of the M-estimation, control network and deformation analysis, and geodetic time series analysis. The main achievements in the geodetic parameter estimation involve a new model of the M-estimation with probabilistic models of geodetic observations, a new Shift-Msplit estimation, which allows to estimate a vector of parameter differences and the Shift-Msplit(+) that is a generalisation of Shift-Msplit estimation if the design matrix A of a functional model has not a full column rank. The new algorithms of the coordinates conversion between the Cartesian and geodetic coordinates, both on the rotational and triaxial ellipsoid can be mentioned as a highlights of the research of the last four years. New parameter estimation models developed have been adopted and successfully applied to the control network and deformation analysis. New algorithms based on the wavelet, Fourier and Hilbert transforms were applied to find time-frequency characteristics of geodetic and geophysical time series as well as time-frequency relations between them. Statistical properties of these time series are also presented using different statistical tests as well as 2nd, 3rd and 4th moments about the mean. The new forecasts methods are presented which enable prediction of the considered time series in different frequency bands.
NASA Astrophysics Data System (ADS)
Császár, Attila G.
1989-10-01
Optimized geometries and complete, scaled quadratic force fields of HCOCN and HCSCN have been determined at different theoretical levels (HF/4-21, HF/6-31G **; geometries also at MP2/6-31G ** and MP2/6-311G **). Frequencies calculated from the force fields confirm, with one exception, the assignment of the vibrational spectrum of HCOCN. The vibrational fundamentals calculated for HCSCN (accurate within about 50 cm -1) could direct a spectroscopy study aimed at determining them. Calculated rotational and quartic centrifugal distortion (QCD) constants are in good agreement with the experimental data for both molecules, but QCD constants only after scaling of the force fields.
Accurate measurements of the collision stopping powers for 5 to 30 MeV electrons
NASA Astrophysics Data System (ADS)
MacPherson, Miller Shawn
Accurate knowledge of electron stopping powers is crucial for accurate radiation dosimetry and radiation transport calculations. Current values for stopping powers are based on a theoretical model, with estimated uncertainties of 0.5-1% (1σ) for electron energies greater than 100 keV. This work presents the first measurements of electron collision stopping powers capable of testing the theoretical values within these stated uncertainties. A large NaI spectrometer was used to measure the change in electron energy when an absorbing disk of known thickness was placed in an electron beam. Monte Carlo simulations of the experiment were performed to account for the effects of surrounding materials. Energy differences between the calculated and measured spectra were used to determine corrections to the soft collision component of the theoretical stopping powers employed by the Monte Carlo simulations. Four different elemental materials were studied: Be, Al, Cu, and Ta. This provided a wide range of atomic numbers and densities over which to test the theory. In addition, stopping powers were measured for graphite (both standard and pyrolytic), A-150 tissue equivalent plastic, C-552 air equivalent plastic, and water. The incident electron energies ranged from 5 to 30 MeV. Generally, the measured stopping powers agree with the theoretical values within the experimental uncertainties, which range from 0.4% to 0.7% (1σ). Aluminum, however, exhibits a 0.7% discrepancy at higher electron energies. Furthermore, these measurements have established that the grain density stopping power is appropriate for graphite, contrary to the recommendations of ICRU Report 37. This removes a 0.2% uncertainty in air kerma calibrations, and impacts on dosimetric quantities determined via graphite calorimetry, such as ɛG for Fricke dosimetry and (W/ e)air for ion chamber measurements.
How to accurately bypass damage
Broyde, Suse; Patel, Dinshaw J.
2016-01-01
Ultraviolet radiation can cause cancer through DNA damage — specifically, by linking adjacent thymine bases. Crystal structures show how the enzyme DNA polymerase η accurately bypasses such lesions, offering protection. PMID:20577203
Quantum Monte Carlo calculation of the binding energy of the beryllium dimer
NASA Astrophysics Data System (ADS)
Deible, Michael J.; Kessler, Melody; Gasperich, Kevin E.; Jordan, Kenneth D.
2015-08-01
The accurate calculation of the binding energy of the beryllium dimer is a challenging theoretical problem. In this study, the binding energy of Be2 is calculated using the diffusion Monte Carlo (DMC) method, using single Slater determinant and multiconfigurational trial functions. DMC calculations using single-determinant trial wave functions of orbitals obtained from density functional theory calculations overestimate the binding energy, while DMC calculations using Hartree-Fock or CAS(4,8), complete active space trial functions significantly underestimate the binding energy. In order to obtain an accurate value of the binding energy of Be2 from DMC calculations, it is necessary to employ trial functions that include excitations outside the valence space. Our best estimate DMC result for the binding energy of Be2, obtained by using configuration interaction trial functions and extrapolating in the threshold for the configurations retained in the trial function, is 908 cm-1, only slightly below the 935 cm-1 value derived from experiment.
Accurate Molecular Polarizabilities Based on Continuum Electrostatics
Truchon, Jean-François; Nicholls, Anthony; Iftimie, Radu I.; Roux, Benoît; Bayly, Christopher I.
2013-01-01
A novel approach for representing the intramolecular polarizability as a continuum dielectric is introduced to account for molecular electronic polarization. It is shown, using a finite-difference solution to the Poisson equation, that the Electronic Polarization from Internal Continuum (EPIC) model yields accurate gas-phase molecular polarizability tensors for a test set of 98 challenging molecules composed of heteroaromatics, alkanes and diatomics. The electronic polarization originates from a high intramolecular dielectric that produces polarizabilities consistent with B3LYP/aug-cc-pVTZ and experimental values when surrounded by vacuum dielectric. In contrast to other approaches to model electronic polarization, this simple model avoids the polarizability catastrophe and accurately calculates molecular anisotropy with the use of very few fitted parameters and without resorting to auxiliary sites or anisotropic atomic centers. On average, the unsigned error in the average polarizability and anisotropy compared to B3LYP are 2% and 5%, respectively. The correlation between the polarizability components from B3LYP and this approach lead to a R2 of 0.990 and a slope of 0.999. Even the F2 anisotropy, shown to be a difficult case for existing polarizability models, can be reproduced within 2% error. In addition to providing new parameters for a rapid method directly applicable to the calculation of polarizabilities, this work extends the widely used Poisson equation to areas where accurate molecular polarizabilities matter. PMID:23646034
Accurate phase-shift velocimetry in rock.
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R; Holmes, William M
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models. PMID:27111139
Accurate phase-shift velocimetry in rock
NASA Astrophysics Data System (ADS)
Shukla, Matsyendra Nath; Vallatos, Antoine; Phoenix, Vernon R.; Holmes, William M.
2016-06-01
Spatially resolved Pulsed Field Gradient (PFG) velocimetry techniques can provide precious information concerning flow through opaque systems, including rocks. This velocimetry data is used to enhance flow models in a wide range of systems, from oil behaviour in reservoir rocks to contaminant transport in aquifers. Phase-shift velocimetry is the fastest way to produce velocity maps but critical issues have been reported when studying flow through rocks and porous media, leading to inaccurate results. Combining PFG measurements for flow through Bentheimer sandstone with simulations, we demonstrate that asymmetries in the molecular displacement distributions within each voxel are the main source of phase-shift velocimetry errors. We show that when flow-related average molecular displacements are negligible compared to self-diffusion ones, symmetric displacement distributions can be obtained while phase measurement noise is minimised. We elaborate a complete method for the production of accurate phase-shift velocimetry maps in rocks and low porosity media and demonstrate its validity for a range of flow rates. This development of accurate phase-shift velocimetry now enables more rapid and accurate velocity analysis, potentially helping to inform both industrial applications and theoretical models.
Accurate Collisional Cross-Sections: Important Non-Lte Input Data
NASA Astrophysics Data System (ADS)
Mashonkina, L.
2010-11-01
Non-LTE modelling for a particular atom requires accurate collisional excitation and ionization cross-sections for the entire system of transitions in the atom. This review concerns with inelastic collisions with electrons and neutral hydrogen atoms. For the selected atoms, H i and Ca ii, comparisons are made between electron impact excitation rates from ab initio calculations and various theoretical approximations. The effect of the use of modern data on non-LTE modelling is shown. For most transitions and most atoms, hydrogen collisional rates are calculated using a semi-empirical modification of the classical Thomson formula for ionization by electrons. Approaches used to estimate empirically the efficiency of hydrogenic collisions in the statistical equilibrium of atoms are reviewed. This research was supported by the Deutsche Forschungsgemeinschaft with grant 436 RUS 17/13/07.
Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao
2015-01-01
Getting a land vehicle’s accurate position, azimuth and attitude rapidly is significant for vehicle based weapons’ combat effectiveness. In this paper, a new approach to acquire vehicle’s accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle’s accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm’s iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system’s working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249
Li, Kui; Wang, Lei; Lv, Yanhong; Gao, Pengyu; Song, Tianxiao
2015-01-01
Getting a land vehicle's accurate position, azimuth and attitude rapidly is significant for vehicle based weapons' combat effectiveness. In this paper, a new approach to acquire vehicle's accurate position and orientation is proposed. It uses biaxial optical detection platform (BODP) to aim at and lock in no less than three pre-set cooperative targets, whose accurate positions are measured beforehand. Then, it calculates the vehicle's accurate position, azimuth and attitudes by the rough position and orientation provided by vehicle based navigation systems and no less than three couples of azimuth and pitch angles measured by BODP. The proposed approach does not depend on Global Navigation Satellite System (GNSS), thus it is autonomous and difficult to interfere. Meanwhile, it only needs a rough position and orientation as algorithm's iterative initial value, consequently, it does not have high performance requirement for Inertial Navigation System (INS), odometer and other vehicle based navigation systems, even in high precise applications. This paper described the system's working procedure, presented theoretical deviation of the algorithm, and then verified its effectiveness through simulation and vehicle experiments. The simulation and experimental results indicate that the proposed approach can achieve positioning and orientation accuracy of 0.2 m and 20″ respectively in less than 3 min. PMID:26492249
NASA Astrophysics Data System (ADS)
Hmiel, A.; Winey, J. M.; Gupta, Y. M.; Desjarlais, M. P.
2016-05-01
Accurate theoretical calculations of the nonlinear elastic response of strong solids (e.g., diamond) constitute a fundamental and important scientific need for understanding the response of such materials and for exploring the potential synthesis and design of novel solids. However, without corresponding experimental data, it is difficult to select between predictions from different theoretical methods. Recently the complete set of third-order elastic constants (TOECs) for diamond was determined experimentally, and the validity of various theoretical approaches to calculate the same may now be assessed. We report on the use of density functional theory (DFT) methods to calculate the six third-order elastic constants of diamond. Two different approaches based on homogeneous deformations were used: (1) an energy-strain fitting approach using a prescribed set of deformations, and (2) a longitudinal stress-strain fitting approach using uniaxial compressive strains along the [100], [110], and [111] directions, together with calculated pressure derivatives of the second-order elastic constants. The latter approach provides a direct comparison to the experimental results. The TOECs calculated using the energy-strain approach differ significantly from the measured TOECs. In contrast, calculations using the longitudinal stress-uniaxial strain approach show good agreement with the measured TOECs and match the experimental values significantly better than the TOECs reported in previous theoretical studies. Our results on diamond have demonstrated that, with proper analysis procedures, first-principles calculations can indeed be used to accurately calculate the TOECs of strong solids.
Accurate Prediction of Binding Thermodynamics for DNA on Surfaces
Vainrub, Arnold; Pettitt, B. Montgomery
2011-01-01
For DNA mounted on surfaces for microarrays, microbeads and nanoparticles, the nature of the random attachment of oligonucleotide probes to an amorphous surface gives rise to a locally inhomogeneous probe density. These fluctuations of the probe surface density are inherent to all common surface or bead platforms, regardless if they exploit either an attachment of pre-synthesized probes or probes synthesized in situ on the surface. Here, we demonstrate for the first time the crucial role of the probe surface density fluctuations in performance of DNA arrays. We account for the density fluctuations with a disordered two-dimensional surface model and derive the corresponding array hybridization isotherm that includes a counter-ion screened electrostatic repulsion between the assayed DNA and probe array. The calculated melting curves are in excellent agreement with published experimental results for arrays with both pre-synthesized and in-situ synthesized oligonucleotide probes. The approach developed allows one to accurately predict the melting curves of DNA arrays using only the known sequence dependent hybridization enthalpy and entropy in solution and the experimental macroscopic surface density of probes. This opens the way to high precision theoretical design and optimization of probes and primers in widely used DNA array-based high-throughput technologies for gene expression, genotyping, next-generation sequencing, and surface polymerase extension. PMID:21972932
Theoretical Chemical Dynamics Studies of Elementary Combustion Reactions
Donald L. Thompson
2006-04-27
The purpose of this research was the development and application of theoretical/computational methods for accurate predictions of the rates of reactions in many-atom systems. The specific aim was to improve computational methods for studying the chemical dynamics of large, complex systems and to obtain a better understanding of the chemical reactions involving large polyatomic molecules and radicals. The focus was on the development an automatic potential energy surface generation algorithm that takes advantage of high-performance computing environments; e.g., software for rate calculations that direct quantum chemistry codes to produce ab initio predictions of reaction rates and related dynamics quantities. Specifically, we developed interpolative moving least-squares (IMLS) methods for accurately fitting ab initio energies to provide global PESs and for use in direct dynamics simulations.
Accurate spectral modeling for infrared radiation
NASA Technical Reports Server (NTRS)
Tiwari, S. N.; Gupta, S. K.
1977-01-01
Direct line-by-line integration and quasi-random band model techniques are employed to calculate the spectral transmittance and total band absorptance of 4.7 micron CO, 4.3 micron CO2, 15 micron CO2, and 5.35 micron NO bands. Results are obtained for different pressures, temperatures, and path lengths. These are compared with available theoretical and experimental investigations. For each gas, extensive tabulations of results are presented for comparative purposes. In almost all cases, line-by-line results are found to be in excellent agreement with the experimental values. The range of validity of other models and correlations are discussed.
The thermodynamic cost of accurate sensory adaptation
NASA Astrophysics Data System (ADS)
Tu, Yuhai
2015-03-01
Living organisms need to obtain and process environment information accurately in order to make decisions critical for their survival. Much progress have been made in identifying key components responsible for various biological functions, however, major challenges remain to understand system-level behaviors from the molecular-level knowledge of biology and to unravel possible physical principles for the underlying biochemical circuits. In this talk, we will present some recent works in understanding the chemical sensory system of E. coli by combining theoretical approaches with quantitative experiments. We focus on addressing the questions on how cells process chemical information and adapt to varying environment, and what are the thermodynamic limits of key regulatory functions, such as adaptation.
NASA Technical Reports Server (NTRS)
Bauschlicher, Charles W.; Arnold, James O. (Technical Monitor)
1997-01-01
The current methods of quantum chemical calculations will be reviewed. The accent will be on the accuracy that can be achieved with these methods. The basis set requirements and computer resources for the various methods will be discussed. The utility of the methods will be illustrated with some examples, which include the calculation of accurate bond energies for SiF$_n$ and SiF$_n^+$ and the modeling of chemical data storage.
Accurate basis set truncation for wavefunction embedding
NASA Astrophysics Data System (ADS)
Barnes, Taylor A.; Goodpaster, Jason D.; Manby, Frederick R.; Miller, Thomas F.
2013-07-01
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)], 10.1021/ct300544e to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.