Calculation of molecular free energies in classical potentials
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2016-02-01
Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations.
Calculating vibrational spectra using modified Shepard interpolated potential energy surfaces.
Evenhuis, Christian R; Manthe, Uwe
2008-07-14
A potential energy interpolation approach based on modified Shepard interpolation and specifically designed for calculation of vibrational states is presented. The importance of the choice of coordinates for the rate of convergence is demonstrated. Studying the vibrational states of the water molecule as a test case, a coordinate system comprised of inverse bond distances and trigonometric functions of the bond angle is found to be particularly efficient. Different sampling schemes used to locate the reference points in the modified Shepard interpolation are investigated. A final scheme is recommended, which allows the construction of potential energy surfaces to sub-wave-number accuracy.
Free energy calculations: an efficient adaptive biasing potential method.
Dickson, Bradley M; Legoll, Frédéric; Lelièvre, Tony; Stoltz, Gabriel; Fleurat-Lessard, Paul
2010-05-06
We develop an efficient sampling and free energy calculation technique within the adaptive biasing potential (ABP) framework. By mollifying the density of states we obtain an approximate free energy and an adaptive bias potential that is computed directly from the population along the coordinates of the free energy. Because of the mollifier, the bias potential is "nonlocal", and its gradient admits a simple analytic expression. A single observation of the reaction coordinate can thus be used to update the approximate free energy at every point within a neighborhood of the observation. This greatly reduces the equilibration time of the adaptive bias potential. This approximation introduces two parameters: strength of mollification and the zero of energy of the bias potential. While we observe that the approximate free energy is a very good estimate of the actual free energy for a large range of mollification strength, we demonstrate that the errors associated with the mollification may be removed via deconvolution. The zero of energy of the bias potential, which is easy to choose, influences the speed of convergence but not the limiting accuracy. This method is simple to apply to free energy or mean force computation in multiple dimensions and does not involve second derivatives of the reaction coordinates, matrix manipulations nor on-the-fly adaptation of parameters. For the alanine dipeptide test case, the new method is found to gain as much as a factor of 10 in efficiency as compared to two basic implementations of the adaptive biasing force methods, and it is shown to be as efficient as well-tempered metadynamics with the postprocess deconvolution giving a clear advantage to the mollified density of states method.
CO dimer: new potential energy surface and rovibrational calculations.
Dawes, Richard; Wang, Xiao-Gang; Carrington, Tucker
2013-08-15
The spectrum of CO dimer was investigated by solving the rovibrational Schrödinger equation on a new potential energy surface constructed from coupled-cluster ab initio points. The Schrödinger equation was solved with a Lanczos algorithm. Several 4D (rigid monomer) global ab initio potential energy surfaces (PESs) were made using a previously reported interpolating moving least-squares (IMLS) fitting procedure specialized to describe the interaction of two linear fragments. The potential has two nonpolar minima giving rise to a complicated set of energy level stacks, which are very sensitive to the shapes and relative depths of the two wells. Although the CO dimer has defied previous attempts at an accurate purely ab initio description our best surface yields results in good agreement with experiment. Root-mean-square (rms) fitting errors of less than 0.1 cm(-1) were obtained for each of the fits using 2226 ab initio data at different levels. This allowed direct assessment of the quality of various levels of ab initio theory for prediction of spectra. Our tests indicate that standard CCSD(T) is slow to converge the interaction energy even when sextuple zeta bases as large as ACV6Z are used. The explicitly correlated CCSD(T)-F12b method was found to recover significantly more correlation energy (from singles and doubles) at the CBS limit. Correlation of the core-electrons was found to be important for this system. The best PES was obtained by extrapolation of calculations at the CCSD(T)(AE)-F12b/CVnZ-F12 (n = 3,4) levels. The calculated energy levels were compared to 105 J ≤ 10 levels from experiment. The rms error for 68 levels with J ≤ 6 is only 0.29 cm(-1). The calculated energy levels were assigned stack labels using several tools. New stacks were found. One of them, stack y1, has an energy lower than many previously known stacks and may be observable.
Footprinting molecular electrostatic potential surfaces for calculation of solvation energies.
Calero, Christian Solis; Farwer, Jochen; Gardiner, Eleanor J; Hunter, Christopher A; Mackey, Mark; Scuderi, Serena; Thompson, Stuart; Vinter, Jeremy G
2013-11-07
A liquid is composed of an ensemble of molecules that populate a large number of different states, so calculation of the solvation energy of a molecule in solution requires a method for summing the interactions with the environment over all of these states. The surface site interaction model for the properties of liquids at equilibrium (SSIMPLE) simplifies the surface of a molecule to a discrete number of specific interaction sites (SSIPs). The thermodynamic properties of these interaction sites can be characterised experimentally, for example, through measurement of association constants for the formation of simple complexes that feature a single H-bonding interaction. Correlation of experimentally determined solution phase H-bond parameters with gas phase ab initio calculations of maxima and minima on molecular electrostatic potential surfaces (MEPS) provides a method for converting gas phase calculations on isolated molecules to parameters that can be used to estimate solution phase interaction free energies. This approach has been generalised using a footprinting technique that converts an MEPS into a discrete set of SSIPs (each described by a polar interaction parameter, εi). These SSIPs represent the molecular recognition properties of the entire surface of the molecule. For example, water is described by four SSIPs, two H-bond donor sites and two H-bond acceptor sites. A liquid mixture is described as an ensemble of SSIPs that represent the components of the mixture at appropriate concentrations. Individual SSIPs are assumed to be independent, so speciation of SSIP contacts can be calculated based on properties of the individual SSIP interactions, which are given by the sum of a polar (εiεj) and a non-polar (E(vdW)) interaction term. Results are presented for calculation the free energies of transfer of a range of organic molecules from the pure liquid into water, from the pure liquid into n-hexadecane, from n-hexadecane into water, from n-octanol into
New Soft-Core Potential Function for Molecular Dynamics Based Alchemical Free Energy Calculations.
Gapsys, Vytautas; Seeliger, Daniel; de Groot, Bert L
2012-07-10
The fields of rational drug design and protein engineering benefit from accurate free energy calculations based on molecular dynamics simulations. A thermodynamic integration scheme is often used to calculate changes in the free energy of a system by integrating the change of the system's Hamiltonian with respect to a coupling parameter. These methods exploit nonphysical pathways over thermodynamic cycles involving particle introduction and annihilation. Such alchemical transitions require the modification of the classical nonbonded potential energy terms by applying soft-core potential functions to avoid singularity points. In this work, we propose a novel formulation for a soft-core potential to be applied in nonequilibrium free energy calculations that alleviates singularities, numerical instabilities, and additional minima in the potential energy for all combinations of nonbonded interactions at all intermediate alchemical states. The method was validated by application to (a) the free energy calculations of a closed thermodynamic cycle, (b) the mutation influence on protein thermostability, (c) calculations of small ligand solvation free energies, and (d) the estimation of binding free energies of trypsin inhibitors. The results show that the novel soft-core function provides a robust and accurate general purpose solution to alchemical free energy calculations.
Sparta, Manuel; Hansen, Mikkel B; Matito, Eduard; Toffoli, Daniele; Christiansen, Ove
2010-10-12
The availability of an accurate representation of the potential energy surface (PES) is an essential prerequisite in an anharmonic vibrational calculation. At the same time, the high dimensionality of the fully coupled PES and the adverse scaling properties with respect to the molecular size make the construction of an accurate PES a computationally demanding task. In the past few years, our group tested and developed a series of tools and techniques aimed at defining computationally efficient, black-box protocols for the construction of PESs for use in vibrational calculations. This includes the definition of an adaptive density-guided approach (ADGA) for the construction of PESs from an automatically generated set of evaluation points. Another separate aspect has been the exploration of the use of derivative information through modified Shepard (MS) interpolation/extrapolation procedures. With this article, we present an assembled machinery where these methods are embedded in an efficient way to provide both a general machinery as well as concrete computational protocols. In this framework we introduce and discuss the accuracy and computational efficiency of two methods, called ADGA[2gx3M] and ADGA[2hx3M], where the ADGA recipe is used (with MS interpolation) to automatically define modest sized grids for up to two-mode couplings, while MS extrapolation based on, respectively, gradients only and gradients and Hessians from the ADGA determined points provides access to sufficiently accurate three-mode couplings. The performance of the resulting potentials is investigated in vibrational coupled cluster (VCC) calculations. Three molecular systems serve as benchmarks: a trisubstituted methane (CHFClBr), methanimine (CH2NH), and oxazole (C3H3NO). Furthermore, methanimine and oxazole are addressed in accurate calculations aiming to reproduce experimental results.
NASA Astrophysics Data System (ADS)
Bukowski, Robert; Szalewicz, Krzysztof; Groenenboom, Gerrit C.; van der Avoird, Ad
2008-03-01
A six-dimensional interaction potential for the water dimer has been fitted to ab initio interaction energies computed at 2510 dimer configurations. These energies were obtained by combining the supermolecular second-order energies extrapolated to the complete basis set limit from up to quadruple-zeta quality basis sets with the contribution from the coupled-cluster method including single, double, and noniterative triple excitations computed in a triple-zeta quality basis set. All basis sets were augmented by diffuse functions and supplemented by midbond functions. The energies have been fitted using an analytic form with the induction component represented by a polarizable term, making the potential directly transferable to clusters and the bulk phase. Geometries and energies of stationary points on the potential surface agree well with the results of high-level ab initio geometry optimizations.
CAS SCF/CI calculations of potential energy surfaces of He 3+ and He 2+
NASA Astrophysics Data System (ADS)
Balasubramanian, K.; Liao, M. Z.; Lin, S. H.
1987-12-01
Complete active space MC SCF (CAS SCF) calculations followed by second-order configuration interaction (SOCI) calculations are carried out on the potential energy surfaces (bending surface, linear surfaces) of the 2Σ g+ ground state of He 3+. The potential minimum for the 2Σ g+ state occurs at a linear geometry with HeHe bond length of 1.248 Å. The binding energy of He 3+ with respect to He + He + + He was calculated to be 2.47 eV at the SOCI level. The energy required to dissociate He 3+ ( 2Σ g+) into He 2+ ( 2Σ u+) and He( 1S) is calculated to be 0.14 eV. The same level of SOCI calculations of He 2+ yield a De value of 2.36 eV.
Quantum calculations of vibrational energies of H3O2- on an ab initio potential.
Huang, Xinchuan; Braams, Bastiaan J; Carter, Stuart; Bowman, Joel M
2004-04-28
We report a full-dimensional potential energy surface for H3O2-, based on fitting 66,965 ab initio electronic energies. A major feature of this potential is a barrier of roughly 200 cm-1 to internal rotation of the two hydroxyl groups about a line connecting the two oxygen atoms and the bridging hydrogen atom. The potential is used in calculations of vibrational energies, performed with the "Reaction Path" version of the code "MULTIMODE". The results are compared to recent infrared messenger experiments and are used to propose interpretations of the experimental results.
The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.
ERIC Educational Resources Information Center
Castano, F.; And Others
1983-01-01
The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)
The Calculation of Potential Energy Curves of Diatomic Molecules: The RKR Method.
ERIC Educational Resources Information Center
Castano, F.; And Others
1983-01-01
The RKR method for determining accurate potential energy curves is described. Advantages of using the method (compared to Morse procedure) and a TRS-80 computer program which calculates the classical turning points by an RKR method are also described. The computer program is available from the author upon request. (Author/JN)
Quantum scattering calculation for reaction Br + H2 on two potential energy surfaces
NASA Astrophysics Data System (ADS)
Quan, Wei-Long; Tang, Ping-Ying; Tang, Bi-Yu
Three-dimensional time-dependent quantum wave packet calculations have been carried out for Br + H2 on a new global ab initio and a semi-empirical extended London-Eyring-Polanyi-Sato potential energy surface. It is shown that on the ab initio surface, the threshold energy is much lower, and the reaction probabilities, cross sections, and rate constants are much larger. The effects of the initial rovibrational excitation have also been studied. Comparison of rate constants with experimental measurement implies that the ab initio surface is more suitable for quantum dynamic calculation. The possible reasons and mechanism for the dynamical difference on the two PES are analyzed and discussed.
NASA Astrophysics Data System (ADS)
Ahmed, A. A.; Julliard, M.; Chanon, F.; Chanon, M.; Gracian, F.; Pfister-Guillouzo, G.
1997-03-01
Experimental ionization potentials of quinoline 1 and substituted quinolines: 6-methylquinoline 2, 2,6-dimethylquinoline 3, 6-methoxyquinoline 4, 3-bromoquinoline 5, 2-chloro-4-methylquinoline 6, 4-hydroxyquinoline 7, 4-hydroxy-2-methylquinoline 8, 2-hydroxy-4-methylquinoline 9, 4-methoxyquinoline 10, 4- methoxy-2-methylquinoline 11, 2-methoxy-4-methylquinoline 12, were measured by photoelectron spectroscopy. Molecular orbital energies of the same derivatives were calculated by the Austin Method 1. The assignments of the bands of the photoelectron spectra were done with the aid of the theoretical calculations and on the basis of the substituent effects. For quinolines 1-6 a good agreement was found between the experimental ionization potentials and the calculated orbital energies.
Levitt, D G
1978-01-01
The electrostatic energy profile of one, two, or three ions in an aqueous channel through a lipid membrane is calculated. It is shown that the previous solution to this problem (based on the assumption that the channel is infinitely long) significantly overestimates the electrostatic energy barrier. For example, for a 3-A radius pore, the energy is 16 kT for the infinite channel and 6.7 kT for an ion in the center of a channel 25 A long. The energy as a function of the position of the ion is also determined. With this energy profile, the rate of crossing the membrane (using the Nernst-Planck equation) was estimated and found to be compatible with the maximum conductance observed for the gramicidin A channel. The total electrostatic energy (as a function of position) required to place two or three ions in the channel is also calculated. The electrostatic interaction is small for two ions at opposite ends of the channel and large for any positioning of the three ions. Finally, the gradient through the channel of an applied potential is calculated. The solution to these problems is based on solving an equivalent problem in which an appropriate surface charge is placed on the boundary between the lipid and aqueous regions. The magnitude of the surface charge is obtained from the numerical solution for a system of coupled integral equations. PMID:656542
NASA Astrophysics Data System (ADS)
Goldzak, Tamar; Gilary, Ido; Moiseyev, Nimrod
2012-05-01
We show here for a simple model system that the wavepacket dynamics in the interaction region can be described by a superposition of the non-Hermitian exponential divergent eigenfunctions of the physical Hamiltonian. We demonstrate how it is possible to obtain the complex eigenvalues and also the corresponding resonance eigenfunctions from the propagation of the wavepacket within the framework of the standard formalism of quantum mechanics. The general results demonstrated here for a simple model can lead to two different types of computational applications: (i) for systems where one can obtain the resonance energies and lifetimes as well as their corresponding eigenfunctions it is possible to study the evolution of the physical properties solely based on the initially populated resonance states without the need to propagate the wavepacket; (ii) for molecular systems where it is quite difficult to solve the non-Hermitian time-independent Schrödinger equation and obtain molecular resonance energies and functions. For this type of problem, the methods presented here enable one to evaluate the topology of complex potential energy surfaces from the wavepacket propagation and facilitate the study of the nuclear dynamics of ionizing molecular systems.
Meier, Patrick; Oschetzki, Dominik; Rauhut, Guntram; Berger, Robert
2014-05-14
A transformation of potential energy surfaces (PES) being represented by multi-mode expansions is introduced, which allows for the calculation of anharmonic vibrational spectra of any isotopologue from a single PES. This simplifies the analysis of infrared spectra due to significant CPU-time savings. An investigation of remaining deviations due to truncations and the so-called multi-level approximation is provided. The importance of vibrational-rotational couplings for small molecules is discussed in detail. In addition, an analysis is proposed, which provides information about the quality of the transformation prior to its execution. Benchmark calculations are provided for a set of small molecules.
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.
Potential energy surface and second virial coefficient of methane-water from ab initio calculations.
Akin-Ojo, Omololu; Szalewicz, Krzysztof
2005-10-01
Six-dimensional intermolecular potential energy surfaces (PESs) for the interaction of CH4 with H2O are presented, obtained from ab initio calculations using symmetry-adapted perturbation theory (SAPT) at two different levels of intramonomer correlation and the supermolecular approach at three different levels of electron correlation. Both CH4 and H2O are assumed to be rigid molecules with interatomic distances and angles fixed at the average values in the ground-state vibration. A physically motivated analytical expression for each PES has been developed as a sum of site-site functions. The PES of the CH4-H2O dimer has only two symmetry-distinct minima. From the SAPT calculations, the global minimum has an energy of -1.03 kcal/mol at a geometry where H2O is the proton donor, HO-H...CH4, with the O-H-C angle of 165 degrees, while the secondary minimum, with an energy of -0.72 kcal/mol, has CH4 in the role of the proton donor (H3C-H...OH2). We estimated the complete basis set limit of the SAPT interaction energy at the global minimum to be -1.06 kcal/mol. The classical cross second virial coefficient B12(T) has been calculated for the temperature range 298-653 K. Our best results agree well with some experiments, allowing an evaluation of the quality of experimental results.
Luiz Guilherme M. de Macedo; de Jong, Wibe A.
2008-01-24
The electronic structure and spectroscopic properties (R_{e}, ω_{e}x_{e}, β_{e}, T_{e} ) of the ground state and the 22 lowest excited states of chlorine molecule were studied within a four component relativistic framework using the MOLFDIR program package. The potential energy curves of all possible 23 covalent states were calculated using relativistic complete open shell configuration interaction (COSCI) approach. In addition, four component multi-reference configuration interaction with singles and doubles excitations (MRCISD) calculations were performed in order to infer the effects due to dynamical correlation in vertical excitations. The calculated properties are in good agreement with the available experimental data.
Buryak, Ilya; Vigasin, Andrey A.
2015-12-21
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
Buryak, Ilya; Vigasin, Andrey A
2015-12-21
The present paper aims at deriving classical expressions which permit calculation of the equilibrium constant for weakly interacting molecular pairs using a complete multidimensional potential energy surface. The latter is often available nowadays as a result of the more and more sophisticated and accurate ab initio calculations. The water dimer formation is considered as an example. It is shown that even in case of a rather strongly bound dimer the suggested expression permits obtaining quite reliable estimate for the equilibrium constant. The reliability of our obtained water dimer equilibrium constant is briefly discussed by comparison with the available data based on experimental observations, quantum calculations, and the use of RRHO approximation, provided the latter is restricted to formation of true bound states only.
Spectroscopic studies, potential energy surface and molecular orbital calculations of pramipexole
NASA Astrophysics Data System (ADS)
Muthu, S.; Uma Maheswari, J.; Srinivasan, S.; Isac paulraj, E.
2013-11-01
A systematic vibrational spectroscopic assignment and analysis of pramipexole [(S)-N6-propyl-4,5,6,7-tetrahydro-1,3-benzothiazole-2,6-diamine] has been carried out using FT-IR and FT-Raman spectral data. The vibrational analysis was aided by an electronic structure calculation based on the hybrid density functional method B3LYP using a 6-311G(d, p) and cc-pVTZ basis sets. Molecular equilibrium geometries, electronic energies, IR and Raman intensities, harmonic vibrational frequencies have been computed. The assignments are based on the experimental IR and Raman spectra, and a complete assignment of the observed spectra has been proposed. The UV-visible spectrum of the compound was recorded and the electronic properties, such as HOMO and LUMO energies and the maximum absorption λmax were determined by time-dependent DFT (TD-DFT) method. The geometrical parameters, vibrational frequencies and absorption wavelengths were compared with the experimental data. The complete vibrational assignments are performed on the basis of the potential energy distributions (PEDs) of the vibrational modes in terms of natural internal coordinates. The simulated FT-IR, FT-Raman, and UV spectra of the title compound have been constructed. In addition, the potential energy surface, HOMO and LUMO energies, the molecular electrostatic potential and the first-order hyperpolarizability have been computed. The magnitude of the first-order hyperpolarizability is 5 times larger than that of urea and the title compound may be a potential applicant for the development of NLO materials.
An analytical ab initio potential surface and the calculated tunneling energies for the HCl dimer
NASA Astrophysics Data System (ADS)
Bunker, P. R.; Epa, V. C.; Jensen, Per; Karpfen, Alfred
1991-03-01
The six-dimensional potential energy surface of the HCl dimer has been calculated ab initio at 1654 nuclear geometries [A. Karpfen, P. R. Bunker and P. Jensen, Chem. Phys., in press]. In the present paper we have fitted an analytical function to these points; the analytical function is similar to that used previously by us for the potential surface of the HF dimer. The fitted function has 38 adjustable parameters and the standard deviation of the weighted fit is 19.0 cm -1. We have determined the minimum energy path for the trans-bending tunneling motion on this surface, and have calculated the tunneling and K-rotation energies and wavefunctions. Around equilibrium the path is qualitatively similar to that for the HF dimer in that there are two equivalent hydrogen-bonded structures of Cs symmetry (which are approximately L-shaped with a "bound" and a "free" H-atom) that can tunnel through a C2 h saddle point (the "closed" C2 h saddle point). However, away from equilibrium the path is qualitatively different from that found for the HF dimer since the HCl dimer never becomes linear along the path; in fact it passes through a second C2 h saddle point (the "open" C2 h saddle point). As a result the A-rotational constant only varies slightly along the path, and this explains the experimental observation that the tunneling splitting varies little with K-type rotation for the HCl dimer, in contrast to the situation for the HF dimer. Quantitatively it is clear that errors in the ab initio calculation, errors in the fitting of an analytic function to the points, the correction to the path that is caused by the zero point motion in the other vibrations, and the coupling between the four low-frequency modes, will all be relatively more significant than they were for the HF dimer because the full six-dimensional potential is much flatter; the ab initio dissociation energy is only ˜600 cm -1, and the ab initio tunneling barrier is only ˜70 cm -1. Therefore, we modify the
CASSCF/CI calculations of low-lying states and potential energy surfaces of Au3
NASA Astrophysics Data System (ADS)
Balasubramanian, K.; Liao, M. Z.
1987-05-01
Complete active space MCSCF (CASSCF) and second-order configuration interaction (SOCI) calculations of low-lying electronic states [2B2,2A1] of Au3 as well as the 1Σ+g state of Au2 are carried out. The bending potential energy surfaces of 2A1 and 2B2 states are also presented. A barrier is found in the potential energy surface of the 2A1 state in moving from the linear to bent structure. Two nearly-degenerate structures are found for the ground state. The 2Σ+u state arising from the linear structure with an Au-Au bond length of 2.66 Å is only 3.2 kcal/mol below the 2A1 bent state. The equilibrium geometry of the 2A1 state is an isosceles triangle with an apex angle of 54°. The Au3 cluster is found to be more stable than the gold dimer. The effect of d correlation is studied on Au2 by carrying out MRSDCI (multireference singles and doubles CI) calculations on the 1Σ+g state of Au2 which include excitations from the d orbitals.
Calculation of smooth potential energy surfaces using local electron correlation methods
NASA Astrophysics Data System (ADS)
Mata, Ricardo A.; Werner, Hans-Joachim
2006-11-01
The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl- with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.
Calculation of smooth potential energy surfaces using local electron correlation methods
Mata, Ricardo A.; Werner, Hans-Joachim
2006-11-14
The geometry dependence of excitation domains in local correlation methods can lead to noncontinuous potential energy surfaces. We propose a simple domain merging procedure which eliminates this problem in many situations. The method is applied to heterolytic bond dissociations of ketene and propadienone, to SN2 reactions of Cl{sup -} with alkylchlorides, and in a quantum mechanical/molecular mechanical study of the chorismate mutase enzyme. It is demonstrated that smooth potentials are obtained in all cases. Furthermore, basis set superposition error effects are reduced in local calculations, and it is found that this leads to better basis set convergence when computing barrier heights or weak interactions. When the electronic structure strongly changes between reactants or products and the transition state, the domain merging procedure leads to a balanced description of all structures and accurate barrier heights.
Balanced Basis Sets in the Calculation of Potential Energy Curves for Diatomic Molecules.
NASA Astrophysics Data System (ADS)
Barclay, V. J.
"Balanced" basis sets, which describe the internuclear region as well as the nuclear region, are examined in the context of an ab initio selection-extrapolation configuration -interaction method (MRD-CI). The sets are balanced by adding bond functions (BF's), which are s, p and d-type orbitals at the bond mid-point, to atomic-centred molecular basis sets, which have double and triple sets of valence -shell orbitals (DZ and TZ) and one or two sets of polarization functions (PF's). Potential energy curves and spectroscopic constants were calculated for the ground states of the hydrides H _2, OH, NaH, MgH, MH, SiH, PH, SH, HCl, and for the ionized species OH^+ and OH^{++}, and for the A^3Sigma_{u}, w^3Delta_{u} and B^3Pi_{g} excited states of N_2. The basis sets containing bond functions gave curves and constants superior to the DZP and (where calculated) TZPP results, and of quality similar to large basis set calculations in the literature. The single and double ionization potentials of OH, and the term energies of the N_2 excited states had error at the atomic asymptotes for all basis sets. The dissociation energies of the ground states of ten first-row diatomics (C_2, N_2, O_2, F_2, CN, CO, CF, NO, NF, and FO) were studied using balanced basis sets. A correlation was found to exist between the actual bond order of a species, and the number and kinds of orbitals which comprise the optimum BF. For MRD-CI diatomic calculations, the following BF's should be added to a DZP basis set (sp) (for a bond order of 1); 2(sp) (B. O. 1.5); (spd) (B. O. 2); 3(sp) (B. O. 2.5); 2(spd) (B. O. 3). The prescribed BF basis method was tested on the 26 second-row congeners Si _2, P_2, S _2, Cl_2, SiP, SiS, SiCl, PS, PCl, and ClS, and mixed-row congeners SiN, SiO, SiF, PO, PF, SF, SiC, PN, SO, ClF, CP, CS, CCl, NS, NCl, and ClO. An average error of 6% and a maximum error of 10% relative to known experimental D_{e }'s was found: compared to an average error of 18% for TZPP calculations
Calculated ground state potential surface and excitation energies for the copper trimer
NASA Technical Reports Server (NTRS)
Walch, S. P.; Laskowski, B. C.
1986-01-01
In the context of their relevance to catalysis and to materials science problems, transition metals and transition metal (TM) compounds are currently of considerable interest, and studies have been conducted of the copper trimer, Cu3. The present investigation is concerned with a study of the ground state surface and several groups of excited states in order to improve the understanding of the spectroscopy of Cu3. Differences of the current study from previous investigations are related to an employment of larger basis sets and a more extensive electron correlation. This was done with the objective to obtain a more accurate definition of the ground state surface. Features of the bonding in the copper dimer are considered to obtain a basis for an understanding of the copper trimer. Attention is given to calculational details, the ground state surface, and calculated vertical excitation energies. The results of SCF/SDCI calculations are reported for portions of the ground surface, for two groups of excited states, and for the ionization potential of Cu3.
NASA Technical Reports Server (NTRS)
Koehler, T. L.
1986-01-01
An iterative technique that determines the reference atmosphere which incorporates the effects of uneven surface topography is presented. This method has been successfully applied in several available potential energy studies. An alternative method due to Taylor is also evaluated. While Taylor presented excellent continuous formulations of the available potential energy that include topography, his method for determining the reference atmosphere distributions failed to provide the accuracy needed to produce reliable available potential energy estimates. Since topography has a significant influence on the general circulation, it is important to employ techniques that incorporate its effects in the determination of available potential energy.
Redox potentials of protein disulfide bonds from free-energy calculations.
Li, Wenjin; Baldus, Ilona B; Gräter, Frauke
2015-04-30
Thiol/disulfide exchange in proteins is a vital process in all organisms. To ensure specificity, the involved thermodynamics and kinetics are believed to be tailored by the structure and dynamics of the protein hosting the thiol/disulfide pair. We here aim at predicting the thermodynamics of thiol/disulfide pairs in proteins. We devise a free-energy calculation scheme, which makes use of the Crooks Gaussian intersection method to estimate the redox potential of thiol/disulfide pairs in 12 proteins belonging to the thioredoxin superfamily, namely, thioredoxins, glutaredoxins, and thiol-disulfide oxidoreductases in disulfide bond formation systems. We obtained a satisfying correlation of computed with experimental redox potentials (varying by 160 mV), with a residual error of ∼40 mV (8 kJ/mol), which drastically reduces when considering a less diverse set of only thioredoxins. Our simple and transferrable approach provides a route toward estimating redox potentials of any disulfide-containing protein given that its (reduced or oxidized) structure is known and thereby represents a step toward a rational design of redox proteins.
An accurate potential energy curve for helium based on ab initio calculations
NASA Astrophysics Data System (ADS)
Janzen, A. R.; Aziz, R. A.
1997-07-01
Korona, Williams, Bukowski, Jeziorski, and Szalewicz [J. Chem. Phys. 106, 1 (1997)] constructed a completely ab initio potential for He2 by fitting their calculations using infinite order symmetry adapted perturbation theory at intermediate range, existing Green's function Monte Carlo calculations at short range and accurate dispersion coefficients at long range to a modified Tang-Toennies potential form. The potential with retardation added to the dipole-dipole dispersion is found to predict accurately a large set of microscopic and macroscopic experimental data. The potential with a significantly larger well depth than other recent potentials is judged to be the most accurate characterization of the helium interaction yet proposed.
Research for the calculation of the potential transfer energy on ±800kV DC Transmission Lines
NASA Astrophysics Data System (ADS)
Ren, Huisong; Wang, Hui; Gao, Liyuan; Li, Jinliang
2017-07-01
It would be hard to be repaired in the case of a power outage if the ±800kV ultra high voltage DC (UHVDC) transmission line was put into operation, so live working is the guarantee for its security and stability. It’s necessary to calculate potential transfer energy to ensure the safety of the live working personnel. The transfer energy can be calculated by establishing the equivalent model of the process of potential transfer. Potential differences and capacitance parameters can be calculated by the finite element method, thereby transfer energy in different transfer distances can be worked out. The results show that the transfer energy increases with the increase of the transfer distance and the transfer energy reaches to 1.0 J when the distance is 0.5 m. So the potential transfer rod is necessary for the security of the live working personnel on ±800kV DC transmission lines.
Potential energy curves of Li+2 from all-electron EA-EOM-CCSD calculations
NASA Astrophysics Data System (ADS)
Musiał, Monika; Medrek, Magdalena; Kucharski, Stanisław A.
2015-10-01
The electron attachment (EA) equation-of-motion coupled-cluster theory provides description of the states obtained by the attachment of an electron to the reference system. If the reference is assumed to be a doubly ionised cation, then the EA results relate to the singly ionised ion. In the current work, the above scheme is applied to the calculations of the potential energy curves (PECs) of the Li+2 cation adopting the doubly ionised Li2 +2 structure as the reference system. The advantage of such computational strategy relies on the fact that the closed-shell Li2 +2 reference dissociates into closed-shell fragments (Li2 +2 ⇒ Li+ + Li+), hence the RHF (restricted Hartree-Fock) function can be used as the reference in the whole range of interatomic distances. This scheme offers the first principle method without any model or effective potential parameters for the description of the bond-breaking processes. In this study, the PECs and selected spectroscopic constants for 18 electronic states of the Li+2 ion were computed and compared with experimental and other theoretical results. †In honour of Professor Sourav Pal on the occasion of an anniversary in his private and scientific life.
Verna, L.K.
1992-01-01
The covalent attachment of an aromatic amine to guanine C8 can produce a conformational change within the DNA molecule. This conformational change is likely to influence the altered DNA's biological capacity. The author used semi-empirical potential energy calculations to evaluate conformational patterns of DNA-aromatic amine adducts using the series: aniline, 4-aminobiphenyl, 2-aminofluorene and 1-aminopyrene. An exhaustive search was made of the conformational space for carcinogen modified two-base sequences. Information was incorporated into single stranded modified trimers. Modified strands were incorporated in duplex trimers. Nine-base modified duplexes were constructed and evaluated. This procedure produced distinctly different patterns for each aromatic amine investigated. It was apparent that the base sequence in which the carcinogen modification was found was crucial to the conformational change produced. At the dimer level, aniline allows both syn and anti guanine orientations at the carcinogen modification site. There were base-base and base-carcinogen stacked states, suggesting a flexible adduct easily able to assume many conformations. 4-Aminobiphenyl attachment resulted in low energy base-carcinogen stacked states, and a guanine torsion predominantly in a low syn orientation. The flexibility of this adduct was greatly reduced from that of the aniline adduct. 2-Aminofluorene adducts assumed more of a conformational mix. The major portion was base-base stacked with modified guanine anti, with a portion with base-carcinogen stacking and guanine syn or low syn. 1-Aminopyrene adducts were inflexible. The majority assumed a base-carcinogen stack with guanine syn. The conformational profiles of large modified pieces provided details of a unique low energy wedge conformation, in which aminofluorene, particularly, was able to fit into the minor groove with very little helix distortion.
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 CH2 (+) 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(+)(X(1)Σ(+))+H((2)S)→C(+)((2)P)+H2(X(1)Σg (+)) 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(+)/H containing systems.
NASA Astrophysics Data System (ADS)
Polyansky, Oleg L.; Ovsyannikov, Roman I.; Kyuberis, Aleksandra A.; Lodi, Lorenzo; Tennyson, Jonathan; Yachmenev, Andrey; Yurchenko, Sergei N.; Zobov, Nikolai F.
2016-09-01
An ab initio potential energy surface (PES) for gas-phase ammonia NH3 has been computed using the methodology pioneered for water (Polyansky et al., 2013). Multireference configuration interaction calculations are performed at about 50 000 points using the aug-cc-pCVQZ and aug-cc-pCV5Z basis sets and basis set extrapolation. Relativistic and adiabatic surfaces are also computed. The points are fitted to a suitable analytical form, producing the most accurate ab initio PES for this molecule available. The rotation-vibration energy levels are computed using nuclear motion program TROVE in both linearised and curvilinear coordinates. Better convergence is obtained using curvilinear coordinates. Our results are used to assign the visible spectrum of 14NH3 recorded by Coy and Lehmann (1986). Rotation-vibration energy levels for the isotopologues NH2D, NHD2, ND3 and 15NH3 are also given. An ab initio value for the dissociation energy D0 of 14NH3 is also presented.
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)
Coles, Phillip; Yurchenko, Sergei N.; Polyansky, Oleg; Kyuberis, Aleksandra; Ovsyannikov, Roman I.; Zobov, Nikolay Fedorovich; Tennyson, Jonathan
2017-06-01
We present a new spectroscopic potential energy surface (PES) for ^{14}NH_3, produced by refining a high accuracy ab initio PES to experimental energy levels taken predominantly from MARVEL. The PES reproduces 1722 matched J=0-8 experimental energies with a root-mean-square error of 0.035 cm-1 under 6000 cm^{-1} and 0.059 under 7200 cm^{-1}. In conjunction with a new DMS calculated using multi reference configuration interaction (MRCI) and H=aug-cc-pVQZ, N=aug-cc-pWCVQZ basis sets, an infrared (IR) line list has been computed which is suitable for use up to 2000 K. The line list is used to assign experimental lines in the 7500 - 10,500 cm^{-1} region and previously unassigned lines in HITRAN in the 6000-7000 cm^{-1} region. Oleg L. Polyansky, Roman I. Ovsyannikov, Aleksandra A. Kyuberis, Lorenzo Lodi, Jonathan Tennyson, Andrey Yachmenev, Sergei N. Yurchenko, Nikolai F. Zobov, J. Mol. Spec., 327 (2016) 21-30 Afaf R. Al Derzia, Tibor Furtenbacher, Jonathan Tennyson, Sergei N. Yurchenko, Attila G. Császár, J. Quant. Spectrosc. Rad. Trans., 161 (2015) 117-130
Spin-orbit configuration interaction calculation of the potential energy curves of iodine oxide
Roszak, S.; Krauss, M.; Alekseyev, A.B.; Liebermann, H.P.; Buenker, R.J.
2000-04-06
An ab initio configuration interaction (CI) study including spin-orbit coupling is carried out for the ground and excited states of the IO radical by employing relativistic effective core potentials. The computed spectroscopic constants are in good agreement with available experimental data, with some tendency to underestimate the strength of bonding. The first excited state, a{sup 4}{Sigma}{sup {minus}}, which has not yet been observed experimentally, is predicted to be bound by 30.1 kJ/mol and to have a significantly larger equilibrium distance than the ground state. It is split by spin-orbit interaction into 1/2 and 3/2 components, with the 1/2 component being the lower one with a calculated spin-orbit splitting of 210 cm{sup {minus}1}. The most interesting state in the low-energy IO spectrum, A{sub 1}{sup 2}{Pi}{sub 3/2}, is shown to be predissociated due to interaction with a number of repulsive electronic states. Predissociation of the A{sup 1}, {nu}{prime} = 0, 1 vibrational levels is attributed to a fairly weak spin-orbit coupling with the {sup 2}{Delta}{sub 3/2} state, while rotationally dependent predissociation of the {nu}{prime} = 2 level is explained by the coupling with the 1/2(III) state having mainly {sup 2}{Sigma}{sup {minus}} character. Strong predissociation of the {nu}{prime} {ge} 4 levels is attributed to interaction with the higher-lying {Omega} = 3/2 states, with predominantly {sup 4}{Sigma}{sup +} and {sup 4}{Delta} origin.
Microscopic calculation of interacting boson model parameters by potential-energy surface mapping
Bentley, I.; Frauendorf, S.
2011-06-15
A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.
New Method for Calculating the Potential Energy of Deformed Nuclei within the Liquid-Drop Model
Kurmanov, R.S.; Kosenko, G.I.
2004-11-01
The method that we previously developed for going over from double volume integrals to double surface integrals in calculating the Coulomb energy of nuclei that have a sharp surface is generalized to the case of nuclei where the range of nuclear forces is finite and where the nuclear surface is diffuse. New formulas for calculating the Coulomb and the nuclear energy of deformed nuclei are obtained within this approach. For a spherically symmetric nucleus, in which case there is an analytic solution to the problem in question, the results are compared with those that are quoted in the literature, and it is shown that the respective results coincide identically. A differential formulation of the method developed previously by Krappe, Nix, and Sierk for going over from double volume integrals to double surface integrals is proposed here on the basis of the present approach.
Monge-Palacios, M; Corchado, J C; Espinosa-Garcia, J
2013-06-07
To understand the reactivity and mechanism of the OH + NH3 → H2O + NH2 gas-phase reaction, which evolves through wells in the entrance and exit channels, a detailed dynamics study was carried out using quasi-classical trajectory calculations. The calculations were performed on an analytical potential energy surface (PES) recently developed by our group, PES-2012 [Monge-Palacios et al. J. Chem. Phys. 138, 084305 (2013)]. Most of the available energy appeared as H2O product vibrational energy (54%), reproducing the only experimental evidence, while only the 21% of this energy appeared as NH2 co-product vibrational energy. Both products appeared with cold and broad rotational distributions. The excitation function (constant collision energy in the range 1.0-14.0 kcal mol(-1)) increases smoothly with energy, contrasting with the only theoretical information (reduced-dimensional quantum scattering calculations based on a simplified PES), which presented a peak at low collision energies, related to quantized states. Analysis of the individual reactive trajectories showed that different mechanisms operate depending on the collision energy. Thus, while at high energies (E(coll) ≥ 6 kcal mol(-1)) all trajectories are direct, at low energies about 20%-30% of trajectories are indirect, i.e., with the mediation of a trapping complex, mainly in the product well. Finally, the effect of the zero-point energy constraint on the dynamics properties was analyzed.
NASA Astrophysics Data System (ADS)
Moszynski, Robert; Wormer, Paul E. S.; Jeziorski, Bogumil; van der Avoird, Ad
1994-08-01
Symmetry-adapted perturbation theory has been applied to compute the HeHF intermolecular potential energy surface for three internuclear distances in the HF subunit. The interaction energy is found to be dominated by the first-order exchange contribution and by the dispersion energy (including the intramonomer correlation effects). However, smaller corrections as the electrostatics, induction, and second-order exchange are found to be nonnegligible, and the final shape of the potential results from a delicate balance of attractive and repulsive contributions due to the four fundamental intermolecular interactions: electrostatics, exchange, induction, and dispersion. For a broad range of He-HF configurations the theoretical potential agrees very well with the empirical potential of Lovejoy and Nesbitt [C. M. Lovejoy and D. J. Nesbitt, J. Chem. Phys. 93, 5387 (1990)], which was adjusted to reproduce the near-infrared spectrum of the complex. Our potential has a global minimum of ɛm=-39.68 cm-1 for the linear He-HF geometry at Rm=6.16 bohr, and a secondary minimum of ɛm=-36.13 cm-1 for the linear He-FH geometry at Rm=5.59 bohr. These values are in very good agreement with the corresponding empirical results: ɛm=-39.20 cm-1 and Rm=6.17 bohr for the global minimum, and ɛm=-35.12 cm-1 and Rm=5.67 bohr for the secondary minimum.
NASA Astrophysics Data System (ADS)
Schipper, P. R. T.; Gritsenko, O. V.; van Gisbergen, S. J. A.; Baerends, E. J.
2000-01-01
An approximate Kohn-Sham exchange-correlation potential νxcSAOP is developed with the method of statistical averaging of (model) orbital potentials (SAOP) and is applied to the calculation of excitation energies as well as of static and frequency-dependent multipole polarizabilities and hyperpolarizabilities within time-dependent density functional theory (TDDFT). νxcSAOP provides high quality results for all calculated response properties and a substantial improvement upon the local density approximation (LDA) and the van Leeuwen-Baerends (LB) potentials for the prototype molecules CO, N2, CH2O, and C2H4. For the first three molecules and the lower excitations of the C2H4 the average error of the vertical excitation energies calculated with νxcSAOP approaches the benchmark accuracy of 0.1 eV for the electronic spectra.
Calculation of Potential Energy Surfaces for HCO and HNO Using Many-Body Methods.
1986-06-01
Additional copies of this report may be obtained from the National Technical Information Service, U. S. Department of Commerce , Springfield...ACCESSION N~ -C iCP ET TALG ME Technical Report BRL-TR-2737 )VA 6 C TITLE ’and Sttifl) e TYPE OF REPORT & PERIOD COVERED Final CALCULATION OF POTENTIAL...Report) 13 S’JPPMENTAR, NCTES *U1niversity of Connecticut Storrs, CT ’Q KEY WOR$ ), .’Cun’inue un over** side if rf. . e . r’ and identify 5, block nurmber
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.
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.
Mosyagin, Igor; Hellman, Olle; Olovsson, Weine; Simak, Sergei I; Abrikosov, Igor A
2016-11-03
Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation.
2016-01-01
Free energy calculations at finite temperature based on ab initio molecular dynamics (AIMD) simulations have become possible, but they are still highly computationally demanding. Besides, achieving simultaneously high accuracy of the calculated results and efficiency of the computational algorithm is still a challenge. In this work we describe an efficient algorithm to determine accurate free energies of solids in simulations using the recently proposed temperature-dependent effective potential method (TDEP). We provide a detailed analysis of numerical approximations employed in the TDEP algorithm. We show that for a model system considered in this work, hcp Fe, the obtained thermal equation of state at 2000 K is in excellent agreement with the results of standard calculations within the quasiharmonic approximation. PMID:27700093
Quantum calculations of vibrational energies of H3O2(-) and H5O2(+) with new ab initio potentials
NASA Astrophysics Data System (ADS)
Huang, Xinchuan; Braams, Bastiaan J.; Carter, Stuart; Bowman, Joel M.
2004-03-01
We have performed quantum mechanical studies of the vibrations of H3O2(-) and H5O2(+) in full dimensionality and with sufficient accuracy to resolve important features of the measured spectra. The computational procedure starts with extensive electronic structure calculations (several 10K configurations) at the CCSD(T) level of theory with augmented VTZ basis set using MOLPRO 2002. Then a global fit to the potential energy surface is constructed, based on a functional form that respects the spatial and permutational symmetries of the system. This PES fit is employed in a "Reaction Path Hamiltonian" MULTIMODE [1] calculation to obtain the vibrational spectrum. We provide comparisons with experimental data [2]. [1] MULTIMODE: A code to calculate rovibrational energies of polyatomic molecules, J. M. Bowman, S. Carter, and X.-C. Huang, Int. Rev. Phys. Chem. 22, 533 (2003). [2] Quantum calculations of vibrational energies of H3O2(-) with a new ab initio potential reveal large tunneling splittings. Manuscript in preparation, Dec 2003.
Calculating potential energy curves with fixed-node diffusion Monte Carlo: CO and N2
NASA Astrophysics Data System (ADS)
Powell, Andrew D.; Dawes, Richard
2016-12-01
This study reports on the prospect for the routine use of Quantum Monte Carlo (QMC) for the electronic structure problem, applying fixed-node Diffusion Monte Carlo (DMC) to generate highly accurate Born-Oppenheimer potential energy curves (PECs) for small molecular systems. The singlet ground electronic states of CO and N2 were used as test cases. The PECs obtained by DMC employing multiconfigurational trial wavefunctions were compared with those obtained by conventional high-accuracy electronic structure methods such as multireference configuration interaction and/or the best available empirical spectroscopic curves. The goal was to test whether a straightforward procedure using available QMC codes could be applied robustly and reliably. Results obtained with DMC codes were found to be in close agreement with the benchmark PECs, and the n3 scaling with the number of electrons (compared with n7 or worse for conventional high-accuracy quantum chemistry) could be advantageous depending on the system size. Due to a large pre-factor in the scaling, for the small systems tested here, it is currently still much more computationally intensive to compute PECs with QMC. Nevertheless, QMC algorithms are particularly well-suited to large-scale parallelization and are therefore likely to become more relevant for future massively parallel hardware architectures.
NASA Astrophysics Data System (ADS)
Tokmachev, A. M.; Robb, M. A.
The spin-Hamiltonian valence bond theory relies upon covalent configurations formed by singly occupied orbitals differing by their spin counterparts. This theory has been proven to be successful in studying potential energy surfaces of the ground and lowest excited states in organic molecules when used as a part of the hybrid molecular mechanics - valence bond method. The method allows one to consider systems with large active spaces formed by n electrons in n orbitals and relies upon a specially proposed graphical unitary group approach. At the same time, the restriction of the equality of the numbers of electrons and orbitals in the active space is too severe: it excludes from the consideration a lot of interesting applications. We can mention here carbocations and systems with heteroatoms. Moreover, the structure of the method makes it difficult to study charge-transfer excited states because they are formed by ionic configurations. In the present work we tackle these problems by significant extension of the spin-Hamiltonian approach. We consider (i) more general active space formed by n ± m electrons in n orbitals and (ii) states with the charge transfer. The main problem addressed is the generation of Hamiltonian matrices for these general cases. We propose a scheme combining operators of electron exchange and hopping, generating all nonzero matrix elements step-by-step. This scheme provides a very efficient way to generate the Hamiltonians, thus extending the applicability of spin-Hamiltonian valence bond theory.
NASA Technical Reports Server (NTRS)
Brewer, D. A.; Schug, J. C.; Phillips, D. H.
1980-01-01
Some potential energy curves for CF2O were calculated using projected-unrestricted Hartree-Fock (PUHF) theory. The calculations employed a contracted (4s 3p) Gaussian-type atomic orbital basis set. Bound states were found for the X-tilde 1A1 and 1,3A2 states while the 1,3B1 and 1,3B2 states were repulsive in the valence representation. The merits of the PUHF treatment for excited states are discussed. The results are discussed in terms of available experimental information and previous calculations with particular emphasis on the question of the photolysis channels open in the solar spectral region.
de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M
2014-12-26
We report reaction cross sections, energy disposal, and rate constants for the OH + HBr → Br + H2O and OH + DBr → Br + HDO reactions from quasiclassical trajectory calculations using an ab initio potential energy surface [ de Oliveira-Filho , A. G. S. ; Ornellas , F. R. ; Bowman , J. M. J. Phys. Chem. Lett. 2014 , 5 , 706 - 712 ]. Comparison with available experiments are made and generally show good agreement.
NASA Astrophysics Data System (ADS)
Kakizaki, Akira; Takayanagi, Toshiyuki; Shiga, Motoyuki
2007-11-01
Path integral molecular dynamics simulations for the H6+ and D6+ cluster cations have been carried out in order to understand the floppy nature of their molecular structure due to quantum-mechanical fluctuation. A full-dimensional analytical potential energy surface for the ground electronic state of H6+ has been developed on the basis of accurate ab initio electronic structure calculations at the CCSD(T)/cc-pVTZ level. It is found that the outer H 2(D 2) nuclei rotate almost freely and that the probability density distributions of the central H 2(D 2) nuclei show strong spatial delocalization.
NASA Astrophysics Data System (ADS)
Bender, Jason D.; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G.; Schwartzentruber, Thomas; Candler, Graham V.
2015-08-01
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30 000 K were considered for each of the two temperatures. Over 2.4 × 109 trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature Tv. The rate constant depends more strongly on T when Tv is low, and it depends more strongly on Tv when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = Tv and a nonequilibrium test set in which Tv < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as Tv decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability's dependence on v
Bender, Jason D; Valentini, Paolo; Nompelis, Ioannis; Paukku, Yuliya; Varga, Zoltan; Truhlar, Donald G; Schwartzentruber, Thomas; Candler, Graham V
2015-08-07
Accurate modeling of high-temperature hypersonic flows in the atmosphere requires consideration of collision-induced dissociation of molecular species and energy transfer between the translational and internal modes of the gas molecules. Here, we describe a study of the N2 + N2⟶N2 + 2N and N2 + N2⟶4N nitrogen dissociation reactions using the quasiclassical trajectory (QCT) method. The simulations used a new potential energy surface for the N4 system; the surface is an improved version of one that was presented previously. In the QCT calculations, initial conditions were determined based on a two-temperature model that approximately separates the translational-rotational temperature from the vibrational temperature of the N2 diatoms. Five values from 8000 K to 30,000 K were considered for each of the two temperatures. Over 2.4 × 10(9) trajectories were calculated. We present results for ensemble-averaged dissociation rate constants as functions of the translational-rotational temperature T and the vibrational temperature T(v). The rate constant depends more strongly on T when T(v) is low, and it depends more strongly on T(v) when T is low. Quasibound reactant states contribute significantly to the rate constants, as do exchange processes at higher temperatures. We discuss two sets of runs in detail: an equilibrium test set in which T = T(v) and a nonequilibrium test set in which T(v) < T. In the equilibrium test set, high-v and moderately-low-j molecules contribute most significantly to the overall dissociation rate, and this state specificity becomes stronger as the temperature decreases. Dissociating trajectories tend to result in a major loss of vibrational energy and a minor loss of rotational energy. In the nonequilibrium test set, as T(v) decreases while T is fixed, higher-j molecules contribute more significantly to the dissociation rate, dissociating trajectories tend to result in a greater rotational energy loss, and the dissociation probability
NASA Astrophysics Data System (ADS)
Battle, Keith; Alan Salter, E.; Wesley Edmunds, R.; Wierzbicki, Andrzej
2010-04-01
Antifreeze proteins (AFPs) are a unique class of proteins that inhibit ice growth without changing the melting point of ice. In this work, we study the detailed molecular mechanism of interactions between the hydrophobic side of the winter flounder (WF) AFP and two mutants, AAAA and SSSS, in which threonine residues are substituted by serines and alanines, respectively. Umbrella sampling molecular dynamics simulations of the separation of the proteins from the (2 0 1) surface in an explicit water box is carried out to calculate the potential of mean force free energies of adsorption using AMBER10i. We estimate wild-type WF's free energy of adsorption to ice to be about -12.0 kcal/mol. Gas-phase pseudopotential plane-wave calculations of methane adsorption onto select surfaces of ice are also carried out under periodic boundary conditions to address the possible enthalpic role of WF's methyl groups in binding. The contributions of hydrophobic residues to the free energy of adsorption are discussed.
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.
Dral, Pavlo O; Owens, Alec; Yurchenko, Sergei N; Thiel, Walter
2017-06-28
We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CH3Cl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g., 10% of the points) without any significant loss of accuracy. In ab initio rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KRR-based machine learning by up to 90%.
NASA Astrophysics Data System (ADS)
Dral, Pavlo O.; Owens, Alec; Yurchenko, Sergei N.; Thiel, Walter
2017-06-01
We present an efficient approach for generating highly accurate molecular potential energy surfaces (PESs) using self-correcting, kernel ridge regression (KRR) based machine learning (ML). We introduce structure-based sampling to automatically assign nuclear configurations from a pre-defined grid to the training and prediction sets, respectively. Accurate high-level ab initio energies are required only for the points in the training set, while the energies for the remaining points are provided by the ML model with negligible computational cost. The proposed sampling procedure is shown to be superior to random sampling and also eliminates the need for training several ML models. Self-correcting machine learning has been implemented such that each additional layer corrects errors from the previous layer. The performance of our approach is demonstrated in a case study on a published high-level ab initio PES of methyl chloride with 44 819 points. The ML model is trained on sets of different sizes and then used to predict the energies for tens of thousands of nuclear configurations within seconds. The resulting datasets are utilized in variational calculations of the vibrational energy levels of CH3Cl. By using both structure-based sampling and self-correction, the size of the training set can be kept small (e.g., 10% of the points) without any significant loss of accuracy. In ab initio rovibrational spectroscopy, it is thus possible to reduce the number of computationally costly electronic structure calculations through structure-based sampling and self-correcting KRR-based machine learning by up to 90%.
NASA Astrophysics Data System (ADS)
Jaquet, Ralph; Staemmler, Volker
1982-07-01
Ab initio calculations including electron correlation effects (mainly on CEPA-PNO level) have been performed for the potential energy surface (PES) of the reaction of 2P carbon ions with molecular hydrogen. For the collinear abstraction reactions (C ∞v symmetry: 2σ +, 2Π-2) the minimum energy paths have been determined. The vertical insertion reaction (C 2v; 2A 1,B 1, 2B 2) has been investigated with particular emphasis (minimum energy path, barrier heights, intersystem crossing). The influence of the size of the orbital basis and of electron correlation has been studied in some detail. The interaction of the 2A 1, and 2B 2 surfaces has been analyzed, leading to the conclusion that close to C 2v symmetry a low energy path exists by which CH 2+( 2A 1)can be easily formed, with a barrier ( 2B 2 → 2A 1) ≈ 18 kcal/mol below the asymptote. The analysis of electron correlation effects reveals that it is compulsory to correlate the whole valence shell if one wants to obtain reliable surfaces. The influence of singly excited configurations for getting the correct behaviour of the PES is generally small.
Probing calculated O2+ potential-energy curves with an XUV-IR pump-probe experiment
NASA Astrophysics Data System (ADS)
Cörlin, Philipp; Fischer, Andreas; Schönwald, Michael; Sperl, Alexander; Mizuno, Tomoya; Thumm, Uwe; Pfeifer, Thomas; Moshammer, Robert
2015-04-01
We study dissociative photoionization of molecular oxygen in a kinematically complete XUV-IR pump-probe experiment. Detecting charged fragments and photoelectrons in coincidence using a reaction microscope, we observe a pump-probe delay-dependent yield of very low energetic O+ ions which oscillates with a period of 40 fs . This feature is caused by a time-dependent vibrational wave packet in the potential of the binding O2+(a Π4u) state, which is probed by resonant absorption of a single infrared photon to the weakly repulsive O2+(f Π4g) state. By quantitative comparison of the experimental kinetic-energy-release (KER) and quantum-beat (QB) spectra with the results of a coupled-channel simulation, we are able to discriminate between the calculated adiabatic O2+ potential-energy curves (PECs) of Marian et al. [Marian, Marian, Peyerimhoff, Hess, Buenker, and Seger, Mol. Phys. 46, 779 (1982), 10.1080/00268978200101591] and Magrakvelidze et al. [Magrakvelidze, Aikens, and Thumm, Phys. Rev. A 86, 023402 (2012), 10.1103/PhysRevA.86.023402]. In general, we find a good agreement between experimental and simulated KER and QB spectra. However, we could not reproduce all features of the experimental data with these PECs. In contrast, adjusting a Morse potential to the experimental data, most features of the experimental spectra are well reproduced by our simulation. By comparing this Morse potential to theoretically predicted PECs, we demonstrate the sensitivity of our experimental method to small changes in the shape of the binding potential.
NASA Astrophysics Data System (ADS)
Tarana, Michal; Čurík, Roman
2016-05-01
We introduce a computational method developed for study of long-range molecular Rydberg states of such systems that can be approximated by two electrons in a model potential of the atomic cores. The method is based on a two-electron R-matrix approach inside a sphere centered on one of the atoms. The wave function is then connected to a Coulomb region outside the sphere via a multichannel version of the Coulomb Green's function. This approach is applied to a study of Rydberg states of Rb2 for internuclear separations R from 40 to 320 bohrs and energies corresponding to n from 7 to 30. We report bound states associated with the low-lying 3Po resonance and with the virtual state of the rubidium atom that turn into ion-pair-like bound states in the Coulomb potential of the atomic Rydberg core. The results are compared with previous calculations based on single-electron models employing a zero-range contact-potential and short-range modele potential. Czech Science Foundation (Project No. P208/14-15989P).
NASA Technical Reports Server (NTRS)
Green, Sheldon; Defrees, D. J.; Mclean, A. D.
1991-01-01
Theoretical computations of broadening parameters are reported for three microwave lines of H2O in a bath of He atoms. The potential-energy surfaces employed are corrected for basis-set superposition error, and their reliability is checked by repeating the calculations with a different basis set for orbital expansion. The results are presented in extensive tables and discussed in detail. The corrections applied are shown to have a significant impact on the accuracy of the room-temperature broadenings determined: 8.9 sq A for the 22.2-GHz line, 11.8 sq A for the 183,3-GHz line, and 10.0 sq A for the 380.2-GHz line, in good agreement with published experimental data. The importance of collisional broadening for the atmospheric transmission of radiation and for remote-sensing applications is indicated.
NASA Technical Reports Server (NTRS)
Green, Sheldon; Defrees, D. J.; Mclean, A. D.
1991-01-01
Theoretical computations of broadening parameters are reported for three microwave lines of H2O in a bath of He atoms. The potential-energy surfaces employed are corrected for basis-set superposition error, and their reliability is checked by repeating the calculations with a different basis set for orbital expansion. The results are presented in extensive tables and discussed in detail. The corrections applied are shown to have a significant impact on the accuracy of the room-temperature broadenings determined: 8.9 sq A for the 22.2-GHz line, 11.8 sq A for the 183,3-GHz line, and 10.0 sq A for the 380.2-GHz line, in good agreement with published experimental data. The importance of collisional broadening for the atmospheric transmission of radiation and for remote-sensing applications is indicated.
Varela-Alvarez, Adrian; Sordo, Jose A.; Rayon, V. M.; Redondo, P.; Barrientos, C.
2009-10-14
The gas-phase reaction between calcium monocation and fluoromethane: Ca{sup +}+CH{sub 3}F{yields}CaF{sup +}+CH{sub 3} was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople's, Dunning's, Ahlrichs', and Stuttgart-Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K (7.2x10{sup -11}-5.9x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}) agrees reasonably well with the experimental value at the same temperature [(2.6{+-}0.8)x10{sup -10} cm{sup 3} molecule{sup -1} s{sup -1}]. Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.
Varela-Alvarez, Adrián; Rayón, V M; Redondo, P; Barrientos, C; Sordo, José A
2009-10-14
The gas-phase reaction between calcium monocation and fluoromethane: Ca(+)+CH(3)F-->CaF(+)+CH(3) was theoretically analyzed. The potential energy hypersurface was explored by using density functional theory methodology with different functionals and Pople's, Dunning's, Ahlrichs', and Stuttgart-Dresden basis sets. Kinetics calculations (energy and total angular momentum resolved microcanonical variational/conventional theory) were accomplished. The theoretically predicted range for the global kinetic rate constant values at 295 K (7.2x10(-11)-5.9x10(-10) cm(3) molecule(-1) s(-1)) agrees reasonably well with the experimental value at the same temperature [(2.6+/-0.8)x10(-10) cm(3) molecule(-1) s(-1)]. Explicit consideration of a two transition state model, where the formation of a weakly bounded prereactive complex is preceded by an outer transition state (entrance channel) and followed by an inner transition state connecting with a second intermediate that finally leads to products, is mandatory. Experimental observations on the correlation, or lack of correlation, between reaction rate constants and second ionization energies of the metal might well be rationalized in terms of this two transition state model.
Marinakis, Sarantos; Dean, Indigo Lily; Kłos, Jacek; Lique, François
2015-09-07
We present a new set of potential energy surfaces (PESs) for the CH(X(2)Π)-He van der Waals system. Ab initio calculations of the CH-He PES were carried out using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations [RCCSD(T)]. The augmented correlation-consistent polarized valence quadruple-zeta (aug-cc-pVQZ) basis set was employed augmented by mid-bond functions. Integral cross sections for the rotational excitation in CH-He collisions were calculated using the new PES and compared with available experimental results. The newly constructed PES reproduces the available experimental results for CH(X(2)Π, v = 0)-He collisions better than any previously available PES. Differential cross sections (DCS) are presented for the first time for this system and discussed within the context of rotational rainbows. Finally, our work provides the first rate thermal coefficients for this system that are crucially needed for astrochemical modelling and future anticipated experiments in CH(X(2)Π)-He collisions.
NASA Astrophysics Data System (ADS)
Mehring, Matthias; Klüner, Thorsten
2013-07-01
Being one of the most important catalytically active metal oxide surfaces, the aim of this study was the description of the laser-induced photodesorption of the CO adsorbate from a TiO2(110) surface. As a first step, this paper presents two-dimensional potential energy surfaces of a CO molecule on a rutile TiO2(110) surface. Focussing on the desorption mechanism taking place in this adsorbate-substrate system, the quantum chemical and quantum dynamical calculations regarding the desorption coordinate Z and the polar angle θ allowed a first insight into the mechanistic processes in the CO-TiO2(110) system which are relevant for laser-induced photodesorption. For the electronic ground state X1A1 the adsorption minimum was found for the polar angle θ = 0°, which corresponds to a linear coordination of the CO adsorbate with the carbon atom down to the substrate surface. This is in contrast to the electronically excited state A3B2, where the adsorption minimum was found for the polar angle θ = 180°, which describes a linear coordination with the oxygen atom of the CO molecule on top of the rutile TiO2(110) surface. Moreover, this paper shows exemplary quantum dynamical calculations which simulate the laser-induced photodesorption as a first step to understand the desorption process in detail. Hence, higher dimensional calculations regarding more than 2 degrees of freedom of the CO molecule on the substrate surface are needed to get a complete description of this complex adsorbate-substrate system.
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.
Landfill Gas Energy Benefits Calculator
This page contains the LFG Energy Benefits Calculator to estimate direct, avoided, and total greenhouse gas reductions, as well as environmental and energy benefits, for a landfill gas energy project.
Biogas - the calculable energy
NASA Astrophysics Data System (ADS)
Kith, Károly; Nagy, Orsolya; Balla, Zoltán; Tamás, András
2015-04-01
EU actions against climate change are rising energy prices, both have emphasized the use of renewable energy,increase investments and energy efficiency. A number of objectives formulated in the EC decree no. 29/2009 by 2020. This document is based on the share of renewable energies in energy consumption should be increased to 20% (EC, 2009). The EU average is 20% but the share of renewables vary from one member state to another. In Hungary in 2020, 14.65% renewable energy share is planned to be achieved. According to the latest Eurostat data, the share of renewable energy in energy consumption of the EU average was 14.1%, while in Hungary, this share was 9.6% in 2012. (EUROSTAT, 2014). The use of renewable energy plant level is influenced by several factors. The most important of these is the cost savings and efficiency gains. Hungarian investments in renewable energy production usually have high associated costs and the payback period is substantially more than five years, depending on the support rate. For example, the payback period is also influenced by the green electricity generated feed prices, which is one of the lowest in Hungary compared the Member States of the European Union. Consequently, it is important to increase the production of green energy. Nowadays, predictable biogas energy is an outstanding type of decentralized energy production. It follows directly that agricultural by-products can be used to produce energy and they also create jobs by the construction of a biogas plant. It is important to dispose of and destroy hazardous and noxious substances in energy production. It follows from this that the construction of biogas plants have a positive impact, in addition to green energy which is prepared to reduce the load on the environment. The production of biogas and green electricity is one of the most environment friendly forms of energy production. Biogas production also has other important ecological effects, such as the substitution of
NASA Astrophysics Data System (ADS)
Landry, Guillaume; Granton, Patrick V.; Reniers, Brigitte; Öllers, Michel C.; Beaulieu, Luc; Wildberger, Joachim E.; Verhaegen, Frank
2011-10-01
This work compares Monte Carlo (MC) dose calculations for 125I and 103Pd low-dose rate (LDR) brachytherapy sources performed in virtual phantoms containing a series of human soft tissues of interest for brachytherapy. The geometries are segmented (tissue type and density assignment) based on simulated single energy computed tomography (SECT) and dual energy (DECT) images, as well as the all-water TG-43 approach. Accuracy is evaluated by comparison to a reference MC dose calculation performed in the same phantoms, where each voxel's material properties are assigned with exactly known values. The objective is to assess potential dose calculation accuracy gains from DECT. A CT imaging simulation package, ImaSim, is used to generate CT images of calibration and dose calculation phantoms at 80, 120, and 140 kVp. From the high and low energy images electron density ρe and atomic number Z are obtained using a DECT algorithm. Following a correction derived from scans of the calibration phantom, accuracy on Z and ρe of ±1% is obtained for all soft tissues with atomic number Z in [6,8] except lung. GEANT4 MC dose calculations based on DECT segmentation agreed with the reference within ±4% for 103Pd, the most sensitive source to tissue misassignments. SECT segmentation with three tissue bins as well as the TG-43 approach showed inferior accuracy with errors of up to 20%. Using seven tissue bins in our SECT segmentation brought errors within ±10% for 103Pd. In general 125I dose calculations showed higher accuracy than 103Pd. Simulated image noise was found to decrease DECT accuracy by 3-4%. Our findings suggest that DECT-based segmentation yields improved accuracy when compared to SECT segmentation with seven tissue bins in LDR brachytherapy dose calculation for the specific case of our non-anthropomorphic phantom. The validity of our conclusions for clinical geometry as well as the importance of image noise in the tissue segmentation procedure deserves further
Landry, Guillaume; Granton, Patrick V; Reniers, Brigitte; Ollers, Michel C; Beaulieu, Luc; Wildberger, Joachim E; Verhaegen, Frank
2011-10-07
This work compares Monte Carlo (MC) dose calculations for (125)I and (103)Pd low-dose rate (LDR) brachytherapy sources performed in virtual phantoms containing a series of human soft tissues of interest for brachytherapy. The geometries are segmented (tissue type and density assignment) based on simulated single energy computed tomography (SECT) and dual energy (DECT) images, as well as the all-water TG-43 approach. Accuracy is evaluated by comparison to a reference MC dose calculation performed in the same phantoms, where each voxel's material properties are assigned with exactly known values. The objective is to assess potential dose calculation accuracy gains from DECT. A CT imaging simulation package, ImaSim, is used to generate CT images of calibration and dose calculation phantoms at 80, 120, and 140 kVp. From the high and low energy images electron density ρ(e) and atomic number Z are obtained using a DECT algorithm. Following a correction derived from scans of the calibration phantom, accuracy on Z and ρ(e) of ±1% is obtained for all soft tissues with atomic number Z ∊ [6,8] except lung. GEANT4 MC dose calculations based on DECT segmentation agreed with the reference within ±4% for (103)Pd, the most sensitive source to tissue misassignments. SECT segmentation with three tissue bins as well as the TG-43 approach showed inferior accuracy with errors of up to 20%. Using seven tissue bins in our SECT segmentation brought errors within ±10% for (103)Pd. In general (125)I dose calculations showed higher accuracy than (103)Pd. Simulated image noise was found to decrease DECT accuracy by 3-4%. Our findings suggest that DECT-based segmentation yields improved accuracy when compared to SECT segmentation with seven tissue bins in LDR brachytherapy dose calculation for the specific case of our non-anthropomorphic phantom. The validity of our conclusions for clinical geometry as well as the importance of image noise in the tissue segmentation procedure deserves
NASA Astrophysics Data System (ADS)
Lee, Teck-Ghee; Rochow, C.; Martin, R.; Clark, T. K.; Forrey, R. C.; Balakrishnan, N.; Stancil, P. C.; Schultz, D. R.; Dalgarno, A.; Ferland, Gary J.
2005-01-01
The two most recently published potential energy surfaces (PESs) for the HeH2 complex, the so-called MR (Muchnick and Russek) and BMP (Boothroyd, Martin, and Peterson) surfaces, are quantitatively evaluated and compared through the investigation of atom-diatom collision processes. The BMP surface is expected to be an improvement, approaching chemical accuracy, over all conformations of the PES compared to that of the MR surface. We found significant differences in inelastic rovibrational cross sections computed on the two surfaces for processes dominated by large changes in target rotational angular momentum. In particular, the H2(ν=1,j=0) total quenching cross section computed using the BMP potential was found to be a factor of 1000 larger than that obtained with the MR surface. A lesser discrepancy persists over a large range of energies from the ultracold to thermal and occurs for other low-lying initial rovibrational levels. The MR surface was used in previous calculations of the H2(ν=1,j=0) quenching rate coefficient and gave results in close agreement with the experimental data of Audibert et al. which were obtained for temperatures between 50 and 300 K. Examination of the rovibronic coupling matrix elements, which are obtained following a Legendre expansion of the PES, suggests that the magnitude of the anisotropy of the BMP potential is too large in the interaction region. However, cross sections for elastic and pure rotational processes obtained from the two PESs differ typically by less than a factor of 2. The small differences may be ascribed to the long-range and anharmonic components of the PESs. Exceptions occur for (ν=10,j=0) and (ν=11,j=1) where significant enhancements have been found for the low-energy quenching and elastic cross sections due to zero-energy resonances in the BMP PES which are not present in the MR potential.
Dham, Ashok K; McCourt, Frederick R W; Meath, William J
2009-06-28
Exchange-Coulomb model potential energy surfaces have been developed for the Ne-CO interaction. The initial model is a three-dimensional potential energy surface based upon computed Heitler-London interaction energies and literature results for the long-range induction and dispersion energies, all as functions of interspecies distance, the orientation of CO relative to the interspecies axis, and the bond length of the CO molecule. Both a rigid-rotor model potential energy surface, obtained by setting the CO bond length equal to its experimental spectroscopic equilibrium value, and a vibrationally averaged model potential energy surface, obtained by averaging the stretching dependence over the ground vibrational motion of the CO molecule, have been constructed from the full data set. Adjustable parameters in each model potential energy surface have been determined through fitting a selected subset of pure rotational transition frequencies calculated for the (20)Ne-(12)C(12)O isotopolog to precisely known experimental values. Both potential energy surfaces provide calculated results for a wide range of available experimental microwave, millimeter-wave, and midinfrared Ne-CO transition frequencies that are generally far superior to those obtained using the best current literature potential energy surfaces. The vibrationally averaged CO ground state potential energy surface, employed together with a potential energy surface obtained from it by replacing the ground vibrational state average of the CO stretching dependence of the potential energy surface by an average over the first excited CO vibrational state, has been found to be particularly useful for computing and/or interpreting mid-IR transition frequencies in the Ne-CO dimer.
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1991-01-01
Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1991-01-01
Extensive ab initio calculations on the ground state potential energy surface of H2 + H2O were performed using a large contracted Gaussian basis set and a high level of correlation treatment. An analytical representation of the potential energy surface was then obtained which reproduces the calculated energies with an overall root-mean-square error of only 0.64 mEh. The analytic representation explicitly includes all nine internal degrees of freedom and is also well behaved as the H2 dissociates; it thus can be used to study collision-induced dissociation or recombination of H2. The strategy used to minimize the number of energy calculations is discussed, as well as other advantages of the present method for determining the analytical representation.
Lu, Xiya; Cui, Qiang
2013-02-21
Free energy simulations using a finite sphere boundary condition rather than a periodic boundary condition (PBC) are attractive in the study of very large biomolecular systems. To understand the quantitative impact of various approximations in such simulations, we compare charging free energies in both solution and protein systems calculated in a linear response framework with the Generalized Solvent Boundary Potential (GSBP) and PBC simulations. For simple ions in solution, we find good agreements between GSBP and PBC charging free energies, once the relevant correction terms are taken into consideration. For PBC simulations with the particle-mesh-Ewald for long-range electrostatics, the contribution (ΔG(P-M)) due to the use of a particle rather than molecule based summation scheme in real space is found to be significant, as pointed out by Hünenberger and co-workers. For GSBP, when the inner region is close to be charge neutral, the key correction is the overpolarization of water molecules at the inner/outer dielectric boundary; the magnitude of the correction (ΔG(s-pol)), however, is relatively small. For charging (oxidation) free energy in proteins, the situation is more complex, although good agreement between GSBP and PBC can still be obtained when care is exercised. The smooth dielectric boundary approximation inherent to GSBP tends to make significant errors when the inner region is featured with a high net charge. However, the error can be corrected with Poisson-Boltzmann calculations using snapshots from GSBP simulations in a straightforward and robust manner. Because of the more complex charge and solvent distributions, the magnitudes of ΔG(P-M) and ΔG(s-pol) in protein simulations appear to be different from those derived for solution simulations, leading to uncertainty in directly comparing absolute charging free energies from PBC and GSBP simulations for protein systems. The relative charging/oxidation free energies, however, are robust. With the
Ma, Jianyi; Guo, Hua; Dawes, Richard
2012-09-21
The title reaction is thought to be responsible for the production of molecular nitrogen in interstellar clouds. In this work, we report quantum capture calculations on a new two-dimensional potential energy surface determined by interpolating high-level ab initio data. The low-temperature rate constant calculated using a capture model is quite large and has a positive temperature dependence, in agreement with a recent experiment. The origin of the aforementioned behaviors of the rate constant is analyzed.
Qu, Chen; Bowman, Joel M
2016-09-14
We report a full-dimensional, permutationally invariant potential energy surface (PES) for the cyclic formic acid dimer. This PES is a least-squares fit to 13475 CCSD(T)-F12a/haTZ (VTZ for H and aVTZ for C and O) energies. The energy-weighted, root-mean-square fitting error is 11 cm(-1) and the barrier for the double-proton transfer on the PES is 2848 cm(-1), in good agreement with the directly-calculated ab initio value of 2853 cm(-1). The zero-point vibrational energy of 15 337 ± 7 cm(-1) is obtained from diffusion Monte Carlo calculations. Energies of fundamentals of fifteen modes are calculated using the vibrational self-consistent field and virtual-state configuration interaction method. The ground-state tunneling splitting is computed using a reduced-dimensional Hamiltonian with relaxed potentials. The highest-level, four-mode coupled calculation gives a tunneling splitting of 0.037 cm(-1), which is roughly twice the experimental value. The tunneling splittings of (DCOOH)2 and (DCOOD)2 from one to three mode calculations are, as expected, smaller than that for (HCOOH)2 and consistent with experiment.
Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures
PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...
Abstract Title: Calculated molecular structures and potential energy functions of P AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures.
Abstract:
PAHs with methyl group substitution near a bay region represent a cl...
Calculated molecular structures and potential energy functions ofP AHs with methyl crowding in the bay region and their metabolites: Comparison to experimental structures
PAHs with methyl group substitution near a bay region represent a class of chemicals associated with ...
Hanni, Matti; Lantto, Perttu; Runeberg, Nino; Jokisaari, Jukka; Vaara, Juha
2004-09-22
Quantum chemical calculations of the nuclear shielding tensor, the nuclear quadrupole coupling tensor, and the spin-rotation tensor are reported for the Xe dimer using ab initio quantum chemical methods. The binary chemical shift delta, the anisotropy of the shielding tensor Delta sigma, the nuclear quadrupole coupling tensor component along the internuclear axis chi( parallel ), and the spin-rotation constant C( perpendicular ) are presented as a function of internuclear distance. The basis set superposition error is approximately corrected for by using the counterpoise correction (CP) method. Electron correlation effects are systematically studied via the Hartree-Fock, complete active space self-consistent field, second-order Møller-Plesset many-body perturbation, and coupled-cluster singles and doubles (CCSD) theories, the last one without and with noniterative triples, at the nonrelativistic all-electron level. We also report a high-quality theoretical interatomic potential for the Xe dimer, gained using the relativistic effective potential/core polarization potential scheme. These calculations used valence basis set of cc-pVQZ quality supplemented with a set of midbond functions. The second virial coefficient of Xe nuclear shielding, which is probably the experimentally best-characterized intermolecular interaction effect in nuclear magnetic resonance spectroscopy, is computed as a function of temperature, and compared to experiment and earlier theoretical results. The best results for the second virial coefficient, obtained using the CCSD(CP) binary chemical shift curve and either our best theoretical potential or the empirical potentials from the literature, are in good agreement with experiment. Zero-point vibrational corrections of delta, Delta sigma, chi (parallel), and C (perpendicular) in the nu=0, J=0 rovibrational ground state of the xenon dimer are also reported.
Jorfi, M; González-Lezana, T; Zanchet, A; Honvault, P; Bussery-Honvault, B
2013-03-07
We report quasiclassical trajectory dynamical calculations for the C((3)P) + OH(X(2)Π) → CO(a(3)Π) + H((2)S) using a recently developed ab initio potential energy surface for the first electronic state of HCO of 1(2)A″ symmetry. The dependence of integral cross sections on the collision energy was determined. Product energy and angular distributions have also been calculated. Integral cross sections show no energy threshold and decrease as the collision energy increases. The comparison with results obtained from a statistical quantum method seems to confirm that the reaction is mainly dominated by an indirect mechanism in which a long-lived intermediate complex is involved.
Calculation of Rydberg interaction potentials
NASA Astrophysics Data System (ADS)
Weber, Sebastian; Tresp, Christoph; Menke, Henri; Urvoy, Alban; Firstenberg, Ofer; Büchler, Hans Peter; Hofferberth, Sebastian
2017-07-01
The strong interaction between individual Rydberg atoms provides a powerful tool exploited in an ever-growing range of applications in quantum information science, quantum simulation and ultracold chemistry. One hallmark of the Rydberg interaction is that both its strength and angular dependence can be fine-tuned with great flexibility by choosing appropriate Rydberg states and applying external electric and magnetic fields. More and more experiments are probing this interaction at short atomic distances or with such high precision that perturbative calculations as well as restrictions to the leading dipole-dipole interaction term are no longer sufficient. In this tutorial, we review all relevant aspects of the full calculation of Rydberg interaction potentials. We discuss the derivation of the interaction Hamiltonian from the electrostatic multipole expansion, numerical and analytical methods for calculating the required electric multipole moments and the inclusion of electromagnetic fields with arbitrary direction. We focus specifically on symmetry arguments and selection rules, which greatly reduce the size of the Hamiltonian matrix, enabling the direct diagonalization of the Hamiltonian up to higher multipole orders on a desktop computer. Finally, we present example calculations showing the relevance of the full interaction calculation to current experiments. Our software for calculating Rydberg potentials including all features discussed in this tutorial is available as open source.
NASA Astrophysics Data System (ADS)
Gonzalez, Dayana; Mebel, Alexander
2016-03-01
It has been recently shown that Titan provides a unique perspective in our solar system: its atmosphere is comparable to a model of prebiotic Earth's. Provided the organic cationic and anionic molecular species identified by the Cassini spacecraft, this research characterizes reaction pathways for the reactions of methyl derivatives of the cyclopropenyl cation, the methyl cation with methyl- and dimethyl-acetylene, and reactions of resonance structures of protonated acrylonitrile with CH2NH. Isomerization and dissociation reactions involving methyl-cyclopropenyl cations, the perinaphthenyl cation and anion, and cations of pyrimidine and purine precursors of nucleobases will be examined to locate reaction pathways, intermediates, transition states, and products of the reactions. Gaussian '09 software is used for ab initio calculations to map out the PES. Geometry optimizations and vibrational frequency computations are preformed via the double-hybrid density functional B2PLYP-D3. Single-point energies are refined by use of the explicitly-correlated coupled-cluster CCSD(T)-F12 method. Rate constants are calculated using microcanonical RRKM theory, and pressure effects evaluated used the Master Equation approach; these allow for prediction of absolute rate constants and product branching ratios at different pressures and temperatures.
Bulut, Niyazi; Kłos, Jacek; Alexander, Millard H
2012-03-14
We present converged exact quantum wave packet calculations of reaction probabilities, integral cross sections, and thermal rate coefficients for the title reaction. Calculations have been carried out on the ground 1(2)A' global adiabatic potential energy surface of Deskevich et al. [J. Chem. Phys. 124, 224303 (2006)]. Converged wave packet reaction probabilities at selected values of the total angular momentum up to a partial wave of J = 140 with the HCl reagent initially selected in the v = 0, j = 0-16 rovibrational states have been obtained for the collision energy range from threshold up to 0.8 eV. The present calculations confirm an important enhancement of reactivity with rotational excitation of the HCl molecule. First, accurate integral cross sections and rate constants have been calculated and compared with the available experimental data.
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. Copyright © 2013 Wiley Periodicals, Inc..
NASA Astrophysics Data System (ADS)
Mancini, John S.; Bowman, Joel M.
2013-03-01
We report a global, full-dimensional, ab initio potential energy surface describing the HCl-H2O dimer. The potential is constructed from a permutationally invariant fit, using Morse-like variables, to over 44 000 CCSD(T)-F12b/aug-cc-pVTZ energies. The surface describes the complex and dissociated monomers with a total RMS fitting error of 24 cm-1. The normal modes of the minima, low-energy saddle point and separated monomers, the double minimum isomerization pathway and electronic dissociation energy are accurately described by the surface. Rigorous quantum mechanical diffusion Monte Carlo (DMC) calculations are performed to determine the zero-point energy and wavefunction of the complex and the separated fragments. The calculated zero-point energies together with a De value calculated from CCSD(T) with a complete basis set extrapolation gives a D0 value of 1348 ± 3 cm-1, in good agreement with the recent experimentally reported value of 1334 ± 10 cm-1 [B. E. Casterline, A. K. Mollner, L. C. Ch'ng, and H. Reisler, J. Phys. Chem. A 114, 9774 (2010), 10.1021/jp102532m]. Examination of the DMC wavefunction allows for confident characterization of the zero-point geometry to be dominant at the C2v double-well saddle point and not the Cs global minimum. Additional support for the delocalized zero-point geometry is given by numerical solutions to the 1D Schrödinger equation along the imaginary-frequency out-of-plane bending mode, where the zero-point energy is calculated to be 52 cm-1 above the isomerization barrier. The D0 of the fully deuterated isotopologue is calculated to be 1476 ± 3 cm-1, which we hope will stand as a benchmark for future experimental work.
Mancini, John S; Bowman, Joel M
2013-03-28
We report a global, full-dimensional, ab initio potential energy surface describing the HCl-H2O dimer. The potential is constructed from a permutationally invariant fit, using Morse-like variables, to over 44,000 CCSD(T)-F12b∕aug-cc-pVTZ energies. The surface describes the complex and dissociated monomers with a total RMS fitting error of 24 cm(-1). The normal modes of the minima, low-energy saddle point and separated monomers, the double minimum isomerization pathway and electronic dissociation energy are accurately described by the surface. Rigorous quantum mechanical diffusion Monte Carlo (DMC) calculations are performed to determine the zero-point energy and wavefunction of the complex and the separated fragments. The calculated zero-point energies together with a De value calculated from CCSD(T) with a complete basis set extrapolation gives a D0 value of 1348 ± 3 cm(-1), in good agreement with the recent experimentally reported value of 1334 ± 10 cm(-1) [B. E. Casterline, A. K. Mollner, L. C. Ch'ng, and H. Reisler, J. Phys. Chem. A 114, 9774 (2010)]. Examination of the DMC wavefunction allows for confident characterization of the zero-point geometry to be dominant at the C(2v) double-well saddle point and not the C(s) global minimum. Additional support for the delocalized zero-point geometry is given by numerical solutions to the 1D Schrödinger equation along the imaginary-frequency out-of-plane bending mode, where the zero-point energy is calculated to be 52 cm(-1) above the isomerization barrier. The D0 of the fully deuterated isotopologue is calculated to be 1476 ± 3 cm(-1), which we hope will stand as a benchmark for future experimental work.
Shimazaki, Tomomi; Nakajima, Takahito
2014-09-21
We previously reported a screened Hartree-Fock (HF) exchange potential for energy band structure calculations [T. Shimazaki and Y. Asai, J. Chem. Phys. 130, 164702 (2009); T. Shimazaki and Y. Asai, J. Chem. Phys. 132, 224105 (2010)]. In this paper, we discuss the Coulomb-hole (COH) interaction and screened Slater-formula and determine the energy band diagrams of several semiconductors, such as diamond, silicon, AlAs, AlP, GaAs, GaP, and InP, based on the screened HF exchange potential and Slater-formula with COH interaction, to demonstrate the adequacy of those theoretical concepts. The screened HF exchange potential and Slater-formula are derived from a simplified dielectric function and, therefore, include the dielectric constant in their expressions. We also present a self-consistent calculation technique to automatically determine the dielectric constant, which is incorporated into each self-consistent field step.
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.
Yu, Hua-Gen; Han, Huixian; Guo, Hua
2016-04-14
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. The low-lying vibrational levels of all isotopomers are assigned and the agreement with available experimental data is better than 1 cm(-1).
Vidal-Vidal, Ángel; Pérez-Rodríguez, Martín; Torré, Jean-Philippe; Piñeiro, Manuel M
2015-03-14
CO2 and CH4 clathrate hydrates of type I were studied by means of DFT and QTAIM, in order to better understand their properties at the molecular level. Sub-cells of type I hydrates were modeled as independent rigid cages, both empty and containing guest molecules. Interaction potentials of guest molecules inside each cage, and moving from a cell to the adjacent one, were calculated using the DFT approximation B3LYP/6-311+g(d,p), considering the cases with and without long range Coulombic corrections. The selected theory level was validated by comparison of the simulated Raman spectra with the experimental ones, for the case of type I lattice at full occupation of CO2 and CH4, respectively. For this comparison, Fermi resonances of CO2 were taken into account by transforming experimental bands to the corresponding theoretical non-mixed states. On the one hand, our results confirm the validity of the theory level selected for the model. We have shown the high anisotropy of the guest-cell interaction potential of the molecules analyzed, which has implications in the formulation and use of equations of state, and in the study of transport properties as well. On the other hand, our results suggest that the concentration of guest species inside type I hydrates could be computed from the comparison of experimental and predicted Raman spectra, although there are non-trivial experimental limitations to get over for that purpose.
Sellers, Michael S; Lísal, Martin; Brennan, John K
2016-03-21
We present an extension of various free-energy methodologies to determine the chemical potential of the solid and liquid phases of a fully-flexible molecule using classical simulation. The methods are applied to the Smith-Bharadwaj atomistic potential representation of cyclotrimethylene trinitramine (RDX), a well-studied energetic material, to accurately determine the solid and liquid phase Gibbs free energies, and the melting point (Tm). We outline an efficient technique to find the absolute chemical potential and melting point of a fully-flexible molecule using one set of simulations to compute the solid absolute chemical potential and one set of simulations to compute the solid-liquid free energy difference. With this combination, only a handful of simulations are needed, whereby the absolute quantities of the chemical potentials are obtained, for use in other property calculations, such as the characterization of crystal polymorphs or the determination of the entropy. Using the LAMMPS molecular simulator, the Frenkel and Ladd and pseudo-supercritical path techniques are adapted to generate 3rd order fits of the solid and liquid chemical potentials. Results yield the thermodynamic melting point Tm = 488.75 K at 1.0 atm. We also validate these calculations and compare this melting point to one obtained from a typical superheated simulation technique.
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1991-01-01
Additional calculations which characterize potential energy sources (PESs) for the excited 3A-double-prime state, for a bound 2(2A-prime) state, for HN2(+), and for the Rydberg states associated with HN2(+). It is anticipated that these excited state PESs will be important in interpreting and designing experiments to characterize the ground state HN2 species via neutralized ion beam techniques.
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1991-01-01
Additional calculations which characterize potential energy sources (PESs) for the excited 3A-double-prime state, for a bound 2(2A-prime) state, for HN2(+), and for the Rydberg states associated with HN2(+). It is anticipated that these excited state PESs will be important in interpreting and designing experiments to characterize the ground state HN2 species via neutralized ion beam techniques.
NASA Technical Reports Server (NTRS)
Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.
1993-01-01
A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.
NASA Technical Reports Server (NTRS)
Bowman, Joel M.; Gazdy, Bela; Bentley, Joseph A.; Lee, Timothy J.; Dateo, Christopher E.
1993-01-01
A potential energy surface for the HCN/HNC system which is a fit to extensive, high-quality ab initio, coupled-cluster calculations is presented. All HCN and HNC states with energies below the energy of the first delocalized state are reported and characterized. Vibrational transition energies are compared with all available experimental data on HCN and HNC, including high CH-overtone states up to 23,063/cm. A simulation of the (A-tilde)-(X-tilde) stimulated emission pumping (SEP) spectrum is also reported, and the results are compared to experiment. Franck-Condon factors are reported for odd bending states of HCN, with one quantum of vibrational angular momentum, in order to compare with the recent assignment by Jonas et al. (1992), on the basis of axis-switching arguments of a number of previously unassigned states in the SEP spectrum.
Morikami, Kenji; Itezono, Yoshiko; Nishimoto, Masahiro; Ohta, Masateru
2014-01-01
Compounds with a medium-sized flexible ring often show atropisomerism that is caused by the high-energy barriers between long-lived conformers that can be isolated and often have different biological properties to each other. In this study, the frequency of the transition between the two stable conformers, aS and aR, of thienotriazolodiazepine compounds with flexible 7-membered rings was estimated computationally by Monte Carlo (MC) simulations and validated experimentally by NMR experiments. To estimate the energy barriers for transitions as precisely as possible, the potential energy (PE) surfaces used in the MC simulations were calculated by molecular orbital (MO) methods. To accomplish the MC simulations with the MO-based PE surfaces in a practical central processing unit (CPU) time, the MO-based PE of each conformer was pre-calculated and stored before the MC simulations, and then only referred to during the MC simulations. The activation energies for transitions calculated by the MC simulations agreed well with the experimental ΔG determined by the NMR experiments. The analysis of the transition trajectories of the MC simulations revealed that the transition occurred not only through the transition states, but also through many different transition paths. Our computational methods gave us quantitative estimates of atropisomerism of the thienotriazolodiazepine compounds in a practical period of time, and the method could be applicable for other slow-dynamics phenomena that cannot be investigated by other atomistic simulations.
NASA Astrophysics Data System (ADS)
Schmatz, Stefan; Botschwina, Peter; Hauschildt, Jan; Schinke, Reinhard
2002-12-01
An effective two-dimensional potential energy surface has been constructed for the SN2 reaction Cl-+CH3Br→ClCH3+Br- from coupled-cluster calculations with a large basis set. In the quantum dynamics calculations Radau coordinates were employed to describe the Cl-C and C-Br stretching modes. Making use of the filter diagonalization method and an optical potential, bound states as well as resonance states up to energies far above the dissociation threshold have been calculated. The resonance widths fluctuate over several orders of magnitude. In addition to a majority of Feshbach-type resonances there are also exceedingly long-lived shape resonances, which can only decay by tunneling. Owing to a smaller width of the potential barrier and a larger density of states, tunneling through the barrier is more important for Cl-+CH3Br than for Cl-+CH3Cl despite the larger total mass of this system. Excitation of the C-Br stretching vibration enhances the tunneling probability of the entrance channel complex.
Cheng, Mary Hongying; Coalson, Rob D
2005-01-13
This paper presents empirical formulas for calculating the dielectric self-energy and ion-ion pair interactions in cylindrical ion channels. The proposed approach can be extended to more complex channel structures, for example, (i) a "straight" channel with variable radius and (ii) a "curved" channel with constant radius. For calibration purposes, we compare results obtained based on the approximate effective potentials developed herein to exact electrostatic calculations obtained via the algorithm of Graf et al.: the agreement is satisfactory. A dynamic lattice Monte Carlo (DLMC) technique is used to further assess the accuracy and efficiency of the proposed empirical potentials. The concentration profiles and current-voltage curves produced with our simple empirical energy formulas are in excellent agreement with numerical results obtained using the algorithm of Graf et al., which calculates all relevant electrostatic forces exactly. The use of effective ion-ion potentials greatly reduces the computer memory required to perform DLMC ion permeation simulations in dielectrically inhomogeneous environments, thus enabling treatment of larger systems than can be handled by numerically exact techniques.
Warehime, Michael; Johnson, Erin R.; Kłos, Jacek
2015-01-14
We report new potential energy surfaces for the ground state Ar–NO(X{sup 2}Π) van der Waals system calculated using the unrestricted Hartree-Fock (UHF) method with the addition of the Becke-Roussel correlation functional and exchange-hole dipole moment dispersion correction (XDM). We compare UHFBR-XDM surfaces and those previously reported by Alexander from coupled cluster CCSD(T) calculations [J. Chem. Phys. 111, 7426 (1999)]. The bound states of Ar–NO have been investigated with these new UHFBR-XDM surfaces, including relative energy-level spacing, adiabatic bender states and wave functions, and spectroscopic data. These results have been found to be in good agreement with calculations based on the CCSD(T) PESs. These new PESs are used to investigate the inelastic scattering of NO(X) by Ar. Full close-coupling integral cross sections at collision energies of 442 cm{sup −1}, 1774 cm{sup −1} and differential cross sections at collision energy of 530 cm{sup −1} were determined for transitions out of the lowest NO(X) rotational level (j = ω = 1/2,f). These cross sections are in good agreement with those calculated with CCSD(T) and accordingly in good agreement with the most recent initial and final state resolved experimental data. The UHFBR-XDM scheme yields high-quality potential surfaces with computational cost comparable to the Hartree-Fock method and our results may serve as a benchmark for application of this scheme to collisions between larger molecules.
NASA Astrophysics Data System (ADS)
Banerjee, Arup; Harbola, Manoj K.
1999-11-01
van Leeuwen and Baerends proposed a Becke-like nonlocal correction to the local-density-approximation (LDA) exchange-correlation potential so that its asymptotic structure becomes exact i.e., -1/r [Phys. Rev. A 49, 2421 (1994)]. They showed that it significantly improves the value of the highest occupied orbital eigenvalue of atoms and molecules. However, the correction is exchangelike in nature. With this in mind, in this paper we investigate how this correction affects the total energies and highest eigenvalues within the exchange-only approximation. We show that the potential also corrects the LDA errors substantially within this approximation, and leads to total energies and high eigenvalues which compare well with their Hartree-Fock counterparts. Improvement in the asymptotic behavior of the potential should also result in better values of the response properties of these systems. We show that with this correction one obtains better estimates, both within the exchange-only approximation and with correlation included, of the linear and nonlinear polarizabilities of inert gas atoms. This is quite significant, since the LDA is known to overestimate the nonlinear polarizabilities of these atoms by roughly 100%. On the other hand, for alkaline-earth atoms the values of polarizabilities obtained with this correction are not satisfactory. Nonetheless, hyperpolarizabilities show a marked improvement over the LDA results.
Tachikawa, Hiroto; Iyama, Tetsuji
2004-10-25
One-dimensional potential energy curves for the isomerization of protonated Schiff base of retinal (PSBR) in bacteriorhodopsin (bR), i.e., isomerization from all-trans- to 13-cis-forms, have been calculated by means of time-dependent density functional theory (TD-DFT) calculations, in order to elucidate the mechanism of initial step in photo-absorption. The transition state of the isomerization in the first excited state is located at theta(13-14)=58 degrees , where theta(13-14) means twist angle around the C(13)=C(14) double bond of PSBR The potential barrier is formed by the avoided crossing between S(1) (B(u)-like) and S(2) (A(g)-like) states. The mechanism of the isomerization was discussed on the basis of theoretical results.
Dodsworth, Jeremy A; McDonald, Austin I; Hedlund, Brian P
2012-08-01
To inform hypotheses regarding the relative importance of chemolithotrophic metabolisms in geothermal environments, we calculated free energy yields of 26 chemical reactions potentially supporting chemolithotrophy in two US Great Basin hot springs, taking into account the effects of changing reactant and product activities on the Gibbs free energy as each reaction progressed. Results ranged from 1.2 × 10(-5) to 3.6 J kg(-1) spring water, or 3.7 × 10(-5) to 11.5 J s(-1) based on measured flow rates, with aerobic oxidation of CH(4) or NH4 + giving the highest average yields. Energy yields calculated without constraining pH were similar to those at constant pH except for reactions where H(+) was consumed, which often had significantly lower yields when pH was unconstrained. In contrast to the commonly used normalization of reaction chemical affinities per mole of electrons transferred, reaction energy yields for a given oxidant varied by several orders of magnitude and were more sensitive to differences in the activities of products and reactants. The high energy yield of aerobic ammonia oxidation is consistent with previous observations of significant ammonia oxidation rates and abundant ammonia-oxidizing archaea in sediments of these springs. This approach offers an additional lens through which to view the thermodynamic landscape of geothermal springs. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
Ghosh, Debashree; Roy, Anirban; Seidel, Robert; Winter, Bernd; Bradforth, Stephen; Krylov, Anna I.
2012-01-01
The effect of hydration on the lowest vertical ionization energy (VIE) of phenol and phenolate solvated in bulk water was characterized using the equation-of-motion ionization potential coupled-cluster (EOM-IP-CCSD) and effective fragment potential (EFP) methods (referred to as EOM/EFP), and determined experimentally by valence photo-emission measurements using microjets and synchrotron radiation. The computed solvent-induced shifts in VIEs (ΔVIE) are −0.66 eV and +5.72 eV for phenol and phenolate, respectively. Our best estimates of the absolute values of VIEs (7.9 and 7.7 eV for phenol and phenolate) agree reasonably well with the respective experimental values (7.8±0.1 eV and 7.1±0.1 eV). The EOM/EFP scheme was benchmarked against full EOM-IP-CCSD using micro-solvated phenol and phenolate clusters. A protocol for calculating redox potentials with EOM/EFP was developed based on linear response approximation (LRA) of free energy determination. The oxidation potentials of phenol and phenolate calculated using LRA and EOM/EFP are 1.32 V and 0.89 V, respectively; they agree well with experimental values. PMID:22497288
NASA Astrophysics Data System (ADS)
Rossi, Ivan; Truhlar, Donald G.
1995-02-01
We used a genetic algorithm to fit a set of energy differences obtained by neglect-of-diatomic-differential-overlap (NDDO) molecular orbital theory to reference ab initio data, yielding a set of specific reaction parameters (SRP) for the reaction Cl + CH 4. Only a small number ab initio points along a distinguished-coordinate path were used as input, but the surface is well fit both on and off the reaction path over a range of energies three times wider than the input range. The resulting NDDO-SRP potential energy surface is almost four orders of magnitude less expensive to evaluate than the reference ab initio surface and is well suited for direct dynamics calculations.
Bouhafs, Nezha; Lique, François
2015-11-14
We present a new three-dimensional potential energy surface (PES) for the NH(X{sup 3}Σ{sup −})–Ne van der Waals system, which explicitly takes into account the NH vibrational motion. Ab initio calculations of the NH–Ne PES were carried out using the open-shell single- and double-excitation coupled cluster approach with non-iterative perturbational treatment of triple excitations [RCCSD(T)]. The augmented correlation-consistent quadruple zeta (aug-cc-pVQZ) basis set was employed. Mid-bond functions were also included in order to improve the accuracy in the van der Waals well. Using this new PES, we have studied the collisional excitation of NH(X{sup 3}Σ{sup −}) by Ne. Close-coupling calculations of the collisional excitation cross sections of the fine-structure levels of NH by Ne are performed for energies up to 3000 cm{sup −1}, which yield, after thermal average, rate coefficients up to 350 K. The propensity rules between fine-structure levels are reported, and it is found that F-conserving cross sections are larger than F-changing cross sections even if the propensity rules are not as strong as for the NH–He system. The calculated rate coefficients are compared with available experimental measurements at room temperature and a fairly good agreement is found between experimental and theoretical data, confirming the good quality of the scattering calculations and also the accuracy of the potential energy surface used in this work.
Lynch, G.C.; Truhlar, D.G. ); Brown, F.B.; Zhao, J.G. )
1995-01-05
We have carried out multireference configuration interaction calculations with a large basis set for the H[sub 2]Br system at 104 geometries preselected for convenient use in fitting an analytic potential energy surface for the reactions H + HBr [yields] H[sub 2]Br and H + H[prime]Br [yields] H[prime] + HBr. The external part of the correlation energy is scaled (SEC method) to yield a 101 geometry data set which is fitted using the extended London -Eyring-Polanyi-Sato method with bond-distance- and internal-angle-dependent Sato parameters plus a three-center term localized at the colinear H-Br-H saddle point. The unweighted root-mean-square error for 88 points corresponding to collinear and bent H-H-Br geometries and collinear H-Br-H geometries is 0.55 kcal/mol, with larger deviations for bent H-Br-H geometries. Rate constants were calculated by combining the new analytic potential energy surface with improved canonical variational transition state theory and the least-action semiclassical tunneling approximation. For the abstraction reaction, H + HBr [yields] H[sub 2] + Br, and four deuterium and muonium isotopic analogs, agreement with experiment is very good. 87 refs., 11 figs., 30 tabs.
Good Practices in Free-energy Calculations
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher
2013-01-01
As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.
NASA Astrophysics Data System (ADS)
Zhang, Yan; Lin, Hai
2009-05-01
Testosterone hydroxylation is a prototypical reaction of human cytochrome P450 3A4, which metabolizes about 50% of oral drugs on the market. Reaction dynamics calculations were carried out for the testosterone 6β-hydrogen abstraction and the 6β-d1-testosterone 6β-duterium abstraction employing a model that consists of the substrate and the active oxidant compound I. The calculations were performed at the level of canonical variational transition state theory with multidimensional tunneling and were based on a semiglobal full-dimensional potential energy surface generated by the multiconfiguration molecular mechanics technique. The tunneling coefficients were found to be around 3, indicating substantial contributions by quantum tunneling. However, the tunneling made only modest contributions to the kinetic isotope effects. The kinetic isotope effects were computed to be about 2 in the doublet spin state and about 5 in the quartet spin state.
Model potential calculations of lithium transitions.
NASA Technical Reports Server (NTRS)
Caves, T. C.; Dalgarno, A.
1972-01-01
Semi-empirical potentials are constructed that have eigenvalues close in magnitude to the binding energies of the valence electron in lithium. The potentials include the long range polarization force between the electron and the core. The corresponding eigenfunctions are used to calculate dynamic polarizabilities, discrete oscillator strengths, photoionization cross sections and radiative recombination coefficients. A consistent application of the theory imposes a modification on the transition operator, but its effects are small for lithium. The method presented can be regarded as a numerical generalization of the widely used Coulomb approximation.
González-Lavado, Eloisa; Corchado, Jose C.; Espinosa-Garcia, Joaquin
2014-02-14
Based exclusively on high-level ab initio calculations, a new full-dimensional analytical potential energy surface (PES-2014) for the gas-phase reaction of hydrogen abstraction from methane by an oxygen atom is developed. The ab initio information employed in the fit includes properties (equilibrium geometries, relative energies, and vibrational frequencies) of the reactants, products, saddle point, points on the reaction path, and points on the reaction swath, taking especial caution respecting the location and characterization of the intermediate complexes in the entrance and exit channels. By comparing with the reference results we show that the resulting PES-2014 reproduces reasonably well the whole set of ab initio data used in the fitting, obtained at the CCSD(T) = FULL/aug-cc-pVQZ//CCSD(T) = FC/cc-pVTZ single point level, which represents a severe test of the new surface. As a first application, on this analytical surface we perform an extensive dynamics study using quasi-classical trajectory calculations, comparing the results with recent experimental and theoretical data. The excitation function increases with energy (concave-up) reproducing experimental and theoretical information, although our values are somewhat larger. The OH rotovibrational distribution is cold in agreement with experiment. Finally, our results reproduce experimental backward scattering distribution, associated to a rebound mechanism. These results lend confidence to the accuracy of the new surface, which substantially improves the results obtained with our previous surface (PES-2000) for the same system.
NASA Astrophysics Data System (ADS)
Jaquet, Ralph; Staemmler, Volker
1981-08-01
Ab initio calculations including electron correlation effects (mainly on CEPA-PNO level) have been performed for the potential energy surface of the reaction of 3P oxygen atoms with molecular hydrogen. The collinear abstraction reaction (C ∞v symmetry) and the vertical insertion reaction (C 2v) have been investigated with particular emphasis.The influence of the orbital basis size and of electron correlation both on the reaction energy and on the barrier height and location for the abstraction reaction has been studied in some detail. Our extrapolated value for the barrier for this reaction is 13.4 ± 1.0 kcal/mol, in fair agreement with the experimental activation energy, while the insertion reaction has to pass over a barrier of =48 kcal/mol. The analysis of electron correlation effects reveals that it is compulsory to include all singly and doubly substituted configurations, to correct for unlinked cluster contributions and to use fairly large basis sets if one wants to get accurate ab initio potential surfaces for the reactions of triplet oxygen atoms.
Locating gravitational potential energy
NASA Astrophysics Data System (ADS)
Keeports, David
2017-01-01
Where does gravitational potential energy reside when a ball is in the air? The perfectly correct answer is that it is located in the ball-Earth system. Still, mechanical energy conservation problems are routinely solved by assigning a potential energy to the ball alone. Provided here is a proof that such an assignment introduces only an entirely undetectable error.
Preller, M; Grunenberg, J; Bulychev, V P; Bulanin, M O
2011-05-07
We report the structure and spectroscopic characteristics for the Xe:HI van der Waals binary isomers determined from variational solutions of two-dimensional and three-dimensional (3D) vibrational Schrödinger equations. The solutions are based on a potential energy surface computed at the coupled-cluster level of theory including single and double excitations and a non-iterative perturbation treatment of triple excitations [CCSD(T)]. The dipole moment surface was calculated using quadratic configuration interaction (QCISD). The global potential minimum is shown to be located at the anti-hydrogen-bonded Xe-IH isomer, 21 cm(-1) below the secondary local minimum associated with the hydrogen-bonded Xe-HI isomeric form. The dissociation energy from the global minimum is 245.9 cm(-1). 3D Schrödinger equations are solved for the rotational quantum numbers J = k = 0, 1, and 2, without invoking an adiabatic separation of high- and low-frequency degrees of freedom. The vibrational ground state resides in the Xe-HI potential well, while the first excited state, 8.59 cm(-1) above the ground, occupies the Xe-IH well. We find that intra-complex dynamics exhibits a sudden transformation upon increase of the r(HI) bond length, accompanied by abrupt changes in the geometric and dipole parameters. A similar chaotic behavior is predicted to occur for Xe:DI at a shorter r(DI) bond length, which implies stronger coupling between low- and high-frequency motions in the heavier complex. Our calculations confirm a strong enhancement for the r(HI) stretch fundamental and a significant weakening for the first overtone vibrational transitions in Xe:HI, as compared to those in the free HI molecule. A qualitative explanation of this, earlier experimentally detected effect is suggested.
Honvault, P; Bussery-Honvault, B; Launay, J-M; Aoiz, F J; Bañares, L
2006-04-21
Time-independent quantum mechanical (QM) and quasiclassical trajectory (QCT) scattering calculations have been carried out for the C(1D) + H2 --> CH + H reaction at a collision energy of 80 meV on a newly developed ab initio potential energy surface [B. Bussery-Honvault et al., Phys. Chem. Chem. Phys. 7, 1476 (2005)] of 1 1A" symmetry, corresponding to the second singlet state 1 1B1 of CH2. A general good agreement has been found between the QM and QCT rotational distributions and differential cross sections (DCSs). In both cases, DCSs are strongly peaked in the forward direction with a small contribution in the backward direction in contrast with those obtained on the 1 1A' surface, which are nearly symmetric. Rotational distributions obtained on the 1 1A" surface are somewhat colder than those calculated on the 1 1A' surface. The specific dynamics and the contribution of the 1 1A" surface to the overall reactivity of this system are discussed.
Wang, Xiaohong; Bowman, Joel M
2013-02-12
We calculate the probabilities for the association reactions H+HCN→H2CN* and cis/trans-HCNH*, using quasiclassical trajectory (QCT) and classical trajectory (CT) calculations, on a new global ab initio potential energy surface (PES) for H2CN including the reaction channels. The surface is a linear least-squares fit of roughly 60 000 CCSD(T)-F12b/aug-cc-pVDZ electronic energies, using a permutationally invariant basis with Morse-type variables. The reaction probabilities are obtained at a variety of collision energies and impact parameters. Large differences in the threshold energies in the two types of dynamics calculations are traced to the absence of zero-point energy in the CT calculations. We argue that the QCT threshold energy is the realistic one. In addition, trajectories find a direct pathway to trans-HCNH, even though there is no obvious transition state (TS) for this pathway. Instead the saddle point (SP) for the addition to cis-HCNH is evidently also the TS for direct formation of trans-HCNH.
Purwanto, Wirawan; Zhang, Shiwei; Krakauer, Henry
2009-03-07
We show that the recently developed phaseless auxiliary-field quantum Monte Carlo (AFQMC) method can be used to study excited states, providing an alternative to standard quantum chemistry methods. The phaseless AFQMC approach, whose computational cost scales as M(3)-M(4) with system size M, has been shown to be among the most accurate many-body methods in ground state calculations. For excited states, prevention of collapse into the ground state and control of the Fermion sign/phase problem are accomplished by the approximate phaseless constraint with a trial wave function. Using the challenging C(2) molecule as a test case, we calculate the potential energy curves of the ground and two low-lying singlet excited states. The trial wave function is obtained by truncating complete active space wave functions, with no further optimization. The phaseless AFQMC results using a small basis set are in good agreement with exact full configuration-interaction calculations, while those using large basis sets are in good agreement with experimental spectroscopic constants.
NASA Astrophysics Data System (ADS)
Abel, Martin; Frommhold, Lothar; Wang, Fei; Gustafsson, Magnus; Li, Xiaoping; Hunt, Katharine L. C.
2010-10-01
Absorption by pairs of H2 molecules is an important opacity source in the atmospheres of the outer planets, and thus of special astronomical interest. The emission spectra of cool white dwarf stars differ significantly from the expected blackbody spectra, amongst other reasons due to absorption by H2-H2, H2-He, and H2-H collisional complexes in the stellar atmospheres. To model the radiative processes in these atmospheres, which have temperatures of several thousand kelvin, one needs accurate knowledge of the induced dipole (ID) and potential energy surfaces (PES) of such collisional complexes. These come from quantum-chemical calculations with the H2 bonds stretched or compressed far from equilibrium. Laboratory measurements of collision-induced (CI) absorption exist only at much lower temperature. For H2 pairs at room temperature, the calculated spectra of the rototranslational band, the fundamental band, and the first overtone match the experimental data very well. In addition, with the newly obtained IDS it became possible to reproduce the measurements in the far blue wing of the rototranslational spectrum of H2 at 77.5 K, as well as at 300 K. Similarly good agreement between theory and measurement is seen in the fundamental band of molecular deuterium at room temperature. Furthermore, we also show the calculated absorption spectra of H2-He at 600 K and of H2-H2 at 2,000 K, for which there are no experimental data for comparison.
On calculating the potential vorticity flux
Hsu, Pei-Chun; Diamond, P. H.
2015-03-15
We discuss and compare different approaches to calculating the dynamics of anisotropic flow structure formation in quasi two-dimensional turbulence based on potential vorticity (PV) transport in real space. The general structure of the PV flux in the relaxation processes is deduced non-perturbatively. The transport coefficients of the PV flux are then systematically calculated using perturbation theory. We develop two non-perturbative relaxation models: the first is a mean field theory for the dynamics of minimum enstrophy relaxation based on the requirement that the mean flux of PV dissipates total potential enstrophy but conserves total fluid kinetic energy. The results show that the structure of PV flux has the form of a sum of a positive definite hyper-viscous and a negative or positive viscous flux of PV. Turbulence spreading is shown to be related to PV mixing via the link of turbulence energy flux to PV flux. In the relaxed state, the ratio of the PV gradient to zonal flow velocity is homogenized. This homogenized quantity sets a constraint on the amplitudes of PV and zonal flow in the relaxed state. The second relaxation model is derived from symmetry principles alone. The form of PV flux contains a nonlinear convective term in addition to viscous and hyper-viscous terms. For both cases, the transport coefficients are calculated using perturbation theory. For a broad turbulence spectrum, a modulational calculation of the PV flux gives both a negative viscosity and a positive hyper-viscosity. For a narrow turbulence spectrum, the result of a parametric instability analysis shows that PV transport is also convective. In both relaxation and perturbative analyses, it is shown that turbulent PV transport is sensitive to flow structure, and the transport coefficients are nonlinear functions of flow shear.
Moulds, Rebecca J; Buntine, Mark A; Lawrance, Warren D
2004-09-08
The potential energy surfaces of the van der Waals complexes benzene-Ar and p-difluorobenzene-Ar have been investigated at the second-order Møller-Plesset (MP2) level of theory with the aug-cc-pVDZ basis set. Calculations were performed with unconstrained geometry optimization for all stationary points. This study has been performed to elucidate the nature of a conflict between experimental results from dispersed fluorescence and velocity map imaging (VMI). The inconsistency is that spectra for levels of p-difluorobenzene-Ar and -Kr below the dissociation thresholds determined by VMI show bands where free p-difluorobenzene emits, suggesting that dissociation is occurring. We proposed that the bands observed in the dispersed fluorescence spectra are due to emission from states in which the rare gas atom orbits the aromatic chromophore; these states are populated by intramolecular vibrational redistribution from the initially excited level [S. M. Bellm, R. J. Moulds, and W. D. Lawrance, J. Chem. Phys. 115, 10709 (2001)]. To test this proposition, stationary points have been located on both the benzene-Ar and p-difluorobenzene-Ar potential energy surfaces (PESs) to determine the barriers to this orbiting motion. Comparison with previous single point CCSD(T) calculations of the benzene-Ar PES has been used to determine the amount by which the barriers are overestimated at the MP2 level. As there is little difference in the comparable regions of the benzene-Ar and p-difluorobenzene-Ar PESs, the overestimation is expected to be similar for p-difluorobenzene-Ar. Allowing for this overestimation gives the barrier to movement of the Ar atom around the pDFB ring via the valley between the H atoms as < or = 204 cm(-1) in S0 (including zero point energy). From the estimated change upon electronic excitation, the corresponding barrier in S1 is estimated to be < or = 225 cm(-1). This barrier is less than the 240 cm(-1) energy of 30(2), the vibrational level for which the
NASA Astrophysics Data System (ADS)
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 (X2Π, 14Π, 16Π, 12Σ+, 14Σ+, 16Σ+, 14Σ-, 24Π and 14Δ) 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(4Su) + Se(3Pg) and N(4Su) + Se(3Dg), of NSe radical. Of these Λ-S states, the 16Σ+, 14Σ+, 16Π, 24Π and 14Δ are found to be rather weakly bound states. The 12Σ+ is found to be unstable and has double wells. And the 16Σ+, 14Σ+, 14Π and 16Π 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 X2Π 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 also in fair agreement with available measurements. It
NASA Astrophysics Data System (ADS)
Shi, Deheng; Niu, Xianghong; Sun, Jinfeng; Zhu, Zunlue
2014-01-01
The potential energy curves (PECs) of X1Σ+, a3Π, 13Σ+, 13Δ, 11Δ, 11Σ-, 13Σ-, 11Π, 21Σ+, 23Π, 21Π and 23Σ+ Λ-S states of CBr+ cation and corresponding 23 Ω states are calculated for the first time using the CASSCF method, which is followed by the internally contracted MRCI approach with the aug-cc-pVQZ basis set. All the Λ-S states involved are found to be bound and dissociate into the first dissociation limit of CBr+ cation. Of these Λ-S states, only the 13Σ+ and 13Σ- are inverted ones. The spin-orbit (SO) coupling is accounted for by the state interaction approach with the Breit-Pauli Hamiltonian. Core-valence correlation is included by a cc-pCVTZ basis set. Relativistic correction is calculated with the third-order Douglas-Kroll Hamiltonian approximation at the level of cc-pVQZ basis set. To obtain more reliable results, the PECs obtained by the MRCI calculations are corrected for size-extensivity errors by means of the Davidson modification. The PEC crossings of different Λ-S states are studied. With these PECs, the spectroscopic parameters of all the Λ-S and Ω states involved are obtained by fitting the first ten vibrational levels whenever available, which are calculated by solving the rovibrational Schrödinger equation using the Numerov's method. The spectroscopic parameters are compared with those reported in the literature. Excellent agreement is found between the present results and available measurements. In particular, the energy separation of 352.26 cm-1 between the a3Π0+ and the a3Π1 Ω states agrees well with the measurements of 369±8 cm-1, and the ωe results of 907.45 and 907.08 cm-1 for the a3Π0+ and a3Π1 Ω states are in excellent agreement with the measurements of 906±2 and 903±6 cm-1, respectively. These show that the spectroscopic parameters obtained in the present paper can be expected to be reliable predicted ones.
Li, Quan-Song; Zhang, Feng; Fang, Wei-Hai; Yu, Jian-Guo
2006-02-07
In the present work, the wavelength-dependent mechanistic photochemistry of glyoxal in the gas phase has been explored by ab initio calculations of potential-energy surfaces, surface crossing points, and adiabatic and nonadiabatic rates. The CHOCHO molecules in S1 by photoexcitation at 393-440 nm mainly decay to the ground state via internal conversion, which is followed by molecular eliminations to form CO, H2CO,H2, and HCOH. Upon photodissociation of CHOCHO at 350-390 nm, intersystem crossing to T1 followed by the C-C bond cleavage is the dominant process in this wavelength range, which is responsible for the formation of the CHO radicals. The C-C and C-H bond cleavages along the S1 pathway are energetically accessible upon photodissociation of CHOCHO at 290-310 nm, which can compete with the S1-->T1 intersystem crossing process. The present study predicts that the C-H bond cleavage on the S1 surface is probably a new photolysis pathway at high excitation energy, which has not been observed experimentally. In addition, the trans-cis isomerization is predicted to occur more easily in the ground state than in the excited states.
NASA Astrophysics Data System (ADS)
Barragán, Patricia; Pérez de Tudela, Ricardo; Qu, Chen; Prosmiti, Rita; Bowman, Joel M.
2013-07-01
Diffusion Monte Carlo (DMC) and path-integral Monte Carlo computations of the vibrational ground state and 10 K equilibrium state properties of the H_7^+/D_7^+ cations are presented, using an ab initio full-dimensional potential energy surface. The DMC zero-point energies of dissociated fragments H_5^+(D_5^+)+H2(D2) are also calculated and from these results and the electronic dissociation energy, dissociation energies, D0, of 752 ± 15 and 980 ± 14 cm-1 are reported for H_7^+ and D_7^+, respectively. Due to the known error in the electronic dissociation energy of the potential surface, these quantities are underestimated by roughly 65 cm-1. These values are rigorously determined for first time, and compared with previous theoretical estimates from electronic structure calculations using standard harmonic analysis, and available experimental measurements. Probability density distributions are also computed for the ground vibrational and 10 K state of H_7^+ and D_7^+. These are qualitatively described as a central H_3^+/D_3^+ core surrounded by "solvent" H2/D2 molecules that nearly freely rotate.
Barragán, Patricia; Pérez de Tudela, Ricardo; Qu, Chen; Prosmiti, Rita; Bowman, Joel M
2013-07-14
Diffusion Monte Carlo (DMC) and path-integral Monte Carlo computations of the vibrational ground state and 10 K equilibrium state properties of the H7 (+)/D7 (+) cations are presented, using an ab initio full-dimensional potential energy surface. The DMC zero-point energies of dissociated fragments H5 (+)(D5 (+))+H2(D2) are also calculated and from these results and the electronic dissociation energy, dissociation energies, D0, of 752 ± 15 and 980 ± 14 cm(-1) are reported for H7 (+) and D7 (+), respectively. Due to the known error in the electronic dissociation energy of the potential surface, these quantities are underestimated by roughly 65 cm(-1). These values are rigorously determined for first time, and compared with previous theoretical estimates from electronic structure calculations using standard harmonic analysis, and available experimental measurements. Probability density distributions are also computed for the ground vibrational and 10 K state of H7 (+) and D7 (+). These are qualitatively described as a central H3 (+)/D3 (+) core surrounded by "solvent" H2/D2 molecules that nearly freely rotate.
Majerz, I; Olovsson, I
2007-10-01
In the crystal structure of potassium hydrogen dichloromaleate there are two short hydrogen bonds of 2.44 A. The 'heavy-atom' structure is centrosymmetric (space group P1) with centers of symmetry in the middle of the O-O bonds, suggesting centered hydrogen bonds. However, earlier unconventional types of refinements of the extensive neutron data taken at 30, 90, 135, 170 and 295 K demonstrated that the H atoms are actually non-centered in the hydrogen bonds, although the environment is centrosymmetric. Traditionally it has been assumed that the hydrogen distribution adopts the same symmetry as the environment. Reviewing these unusual results it was considered of great interest to verify that the non-centered locations of the H atoms are reasonable from an energy point of view. Quantum mechanical calculations have now been carried out for the potential-energy surfaces (PES) for both the centered and non-centered locations of the H atoms. In all cases the non-centered positions are closer to the energy minima in the PES than the centered positions, and this result confirms that the structure is best described with non-centered H atoms. There is virtually perfect agreement between the quantum-mechanically derived reaction coordinates (QMRC) and the bond-order reaction coordinates (BORC) derived using Pauling's bond-order concept together with the principle of conservation of bond order. [Part I: Olovsson et al. (2001). Acta Cryst. B57, 311-316; Part II: Olovsson et al. (2002). Acta Cryst. B58, 627-631.].
Analysis of Potential Energy Surfaces.
ERIC Educational Resources Information Center
Fernandez, G. M.; And Others
1988-01-01
Introduces different methodological strategies in analyzing potential energy surfaces (PES) used in chemical reactivity studies. Discusses the theory of PES and gives examples to be used for student work. Provides procedures for calculating normal coordinates and vibrational properties of an activated complex. (ML)
Analysis of Potential Energy Surfaces.
ERIC Educational Resources Information Center
Fernandez, G. M.; And Others
1988-01-01
Introduces different methodological strategies in analyzing potential energy surfaces (PES) used in chemical reactivity studies. Discusses the theory of PES and gives examples to be used for student work. Provides procedures for calculating normal coordinates and vibrational properties of an activated complex. (ML)
CALCULATION OF POTENTIAL DEPRESSION IN KLYSTRON GAPS,
A calculation in cylindrical geometry for the potential depression in klystron gaps is pre sented. The results of this calculation, which takes into...account the mutual effect of depressed potential and increased charge density, is in the form of a series involving Bessel functions of imaginary
Using Bayes' theorem for free energy calculations
NASA Astrophysics Data System (ADS)
Rogers, David M.
Statistical mechanics is fundamentally based on calculating the probabilities of molecular-scale events. Although Bayes' theorem has generally been recognized as providing key guiding principals for setup and analysis of statistical experiments [83], classical frequentist models still predominate in the world of computational experimentation. As a starting point for widespread application of Bayesian methods in statistical mechanics, we investigate the central quantity of free energies from this perspective. This dissertation thus reviews the basics of Bayes' view of probability theory, and the maximum entropy formulation of statistical mechanics before providing examples of its application to several advanced research areas. We first apply Bayes' theorem to a multinomial counting problem in order to determine inner shell and hard sphere solvation free energy components of Quasi-Chemical Theory [140]. We proceed to consider the general problem of free energy calculations from samples of interaction energy distributions. From there, we turn to spline-based estimation of the potential of mean force [142], and empirical modeling of observed dynamics using integrator matching. The results of this research are expected to advance the state of the art in coarse-graining methods, as they allow a systematic connection from high-resolution (atomic) to low-resolution (coarse) structure and dynamics. In total, our work on these problems constitutes a critical starting point for further application of Bayes' theorem in all areas of statistical mechanics. It is hoped that the understanding so gained will allow for improvements in comparisons between theory and experiment.
NASA Astrophysics Data System (ADS)
Grubbs, G. S. Grubbs, Ii; Cooke, S. A.; Novick, Stewart E.
2012-06-01
Claisen rearrangement ethers are a fundamental organic, pericyclic rearrangement reaction reagent. In the mechanism of a Claisen rearrangement, a vinyl allyl ether is needed to provide the necessary Lewis acid/base sites on the molecule for the rearrangement and are simply heated. This rearrangement was first discovered by heating up the title molecule, allyl phenyl ether. However, much like the Diels-Alder, Cope, and other pericyclic reactions, conformation and coordination of chemical groups is key to the Claisen mechanism. In this study, the authors present some structural characteristics of allyl phenyl ether from an analysis of the microwave spectra in the 8-14 GHz region using a CP-FTMW spectrometer. This is, to the authors knowledge, the first known microwave region study of the title molecule. Three conformers have been observed and assigned to date and will be discussed. Along with the rotational spectra, geometry calculations and potential energy surfaces performed at the MP2/6-311G++(3d,2p) level will be discussed and compared to the experimental results. Modeling the Claisen aromatic rearrangement mechanism using CP-FTMW spectroscopy will also be discussed. L. Claisen Chemische Berichte 45, 3157, October 1912.
Sala, Matthieu; Kirkby, Oliver M; Guérin, Stéphane; Fielding, Helen H
2014-02-21
There have been a number of recent experimental investigations of the nonadiabatic relaxation dynamics of aniline following excitation to the first three singlet excited states, 1(1)ππ*, 1(1)π3s/πσ* and 2(1)ππ*. Motivated by differences between the interpretations of experimental observations, we have employed CASSCF and XMCQDPT2 calculations to explore the potential energy landscape and relaxation pathways of photoexcited aniline. We find a new prefulvene-like MECI connecting the 1(1)ππ* state with the GS in which the carbon-atom carrying the amino group is distorted out-of-plane. This suggests that excitation above the 1(1)π3s/πσ* vertical excitation energy could be followed by electronic relaxation from the 1(1)ππ* state to the ground-electronic state through this MECI. We find a MECI connecting the 1(1)π3s/πσ* and 1(1)ππ* states close to the local minimum on 1(1)π3s/πσ* which suggests that photoexcitation to the 1(1)π3s/πσ* state could be followed by relaxation to the 1(1)ππ* state and to the dissociative component of the 1(1)π3s/πσ* state. We also find evidence for a new pathway from the 2(1)ππ* state to the ground electronic state that is likely to pass through a three-state conical intersection involving the 2(1)ππ*, 1(1)π3s/πσ* and 1(1)ππ* states.
Rowley, Christopher N; Roux, Benoît
2013-10-01
Electrophysiological studies have established that the permeation of Ba(2+) ions through the KcsA K(+)-channel is impeded by the presence of K(+) ions in the external solution, while no effect is observed for external Na(+) ions. This Ba(2+) "lock-in" effect suggests that at least one of the external binding sites of the KcsA channel is thermodynamically selective for K(+). We used molecular dynamics simulations to interpret these lock-in experiments in the context of the crystallographic structure of KcsA. Assuming that the Ba(2+) is bound in site S(2) in the dominant blocked state, we examine the conditions that could impede its translocation and cause the observed "lock-in" effect. Although the binding of a K(+) ion to site S(1) when site S(2) is occupied by Ba(2+) is prohibitively high in energy (>10 kcal/mol), binding to site S0 appears to be more plausible (ΔG > 4 kcal/mol). The 2D potential of mean force (PMF) for the simultaneous translocation of Ba(2+) from site S(2) to site S(1) and of a K(+) ion on the extracellular side shows a barrier that is consistent with the concept of external lock-in. The barrier opposing the movement of Ba(2+) is very high when a cation is in site S(0), and considerably smaller when the site is unoccupied. Furthermore, free energy perturbation calculations show that site S(0) is selective for K(+) by 1.8 kcal/mol when S(2) is occupied by Ba(2+). However, the same site S(0) is nonselective when site S(2) is occupied by K(+), which shows that the presence of Ba(2+) affects the selectivity of the pore. A theoretical framework within classical rate theory is presented to incorporate the concentration dependence of the external ions on the lock-in effect.
Wolf, D.
1984-01-01
A new computer code is described which permits the investigation of the energy and structure of coincident-site lattice (CSL) grain boundaries in metals. As an improvement over computer programs used by other workers, the full second-derivative (force-constant) matrix associated with a given interatomic potential is applied for the iterative energy minimization. Using this extremely efficient and reliable procedure the effect of the form of the interatomic potential and its truncation radius on the predicted grain-boundary energy and structure is investigated. Six different potentials for aluminum, ranging from a Morse potential to a pseudopotential, are applied to the simulation of the energy and structure (100) CSL twist boundaries with values of ..sigma.., the inverse density of CSL sites, ranging between ..sigma.. = 5 and ..sigma.. = 73. It is found that not only do both the energy and structure of a given boundary vary greatly from one potential to another, but also that the relative energies of different boundaries, i.e. the boundary-energy vs misfit-angle curves, depend on the potential. In contrast to recent claims of Brokman and Balluffi, no cusps in these curves are found for potentials which ignore the charge-density oscillations. The two basic assumptions of the Brokman-Balluffi cusp model are found to be valid only for extremely simple potentials with very short cutoff radii. It is suggested that (1) charge-density oscillations may be important for predicting grain-boundary properties, and (2) no obvious relationship exists between grain-boundary geometry (..sigma..) and the energy. 39 references, 18 figures, 1 table.
NASA Astrophysics Data System (ADS)
Uniyal, Shweta; Chand, Manesh; Joshi, Subodh; Semalty, P. D.
2016-05-01
The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.
Uniyal, Shweta Chand, Manesh Joshi, Subodh Semalty, P. D.
2016-05-06
The modified embedded atom method (MEAM) potential parameters have been employed to calculate the unrelaxed divacancy formation energy, binding energy and surface energies for low index planes in bcc transition metals. The calculated results of divacancy binding energy and vacancy formation energy compare well with experimental and other available calculated results.
Density functional calculation of intermolecular potentials.
Nyeland, Carl
2011-06-30
Calculations of intermolecular potentials following the density functional theory (DFT) turn out to be very complicated without using some appropriate approximations. Most often the following three approximations have been considered. In one approximation the disturbed charge distributions during collisions are reduced to sums of undisturbed charge distributions from the colliding species. In another approximation, the so-called local density approximation (LDA), one neglects the fact that the intermolecular potentials that depend on charge densities also depend on gradients in the densities. In a third approximation one assumes that the intermolecular potential can be considered as a sum of two terms: a term for the long-range geometry and a term for the short-range geometry. In this Article the three approximations mentioned will be discussed for numerical accuracy for calculations of potentials between inert gas atoms and for calculations of potentials between surfaces and inert gas atoms. In the discussion a few other approximations will be mentioned too.
NASA Astrophysics Data System (ADS)
Bogdanchikov, G. A.; Baklanov, A. V.; Parker, D. H.
2004-02-01
The new class of substitution reactions with oxygen molecule as an agent has been studied by combination of quantum chemistry calculation and transition state theory (TST). The 'inversion substitution' processes RH + O 2 → RO 2 + H (R=CH 3 and SiH 3) have been investigated. The energy for the stationary points (reagents, products and transition states) on the reaction coordinate has been calculated by G2M(CC,MP2) method and rate constants have been calculated within TST approach. The results show that in methane case the reaction considered (CH 4 + O 2 → CH 3O 2 + H) does not compete with generally accepted mechanism (CH 4 + O 2 → CH 3 + HO 2), but it does at elevated temperature in silane case.
Tests of MULTIMODE calculations of rovibrational energies of CH 4
NASA Astrophysics Data System (ADS)
Wu, Jiayan; Huang, Xinchuan; Carter, Stuart; Bowman, Joel M.
2006-08-01
We report variational calculations of rovibrational energies of CH 4 using the code MULTIMODE and an ab initio force field of Schwenke and Partridge. The systematic convergence of the energies with respect to the level of mode coupling is presented. Converged vibrational energies calculated using the five-mode representation of the potential for zero total angular momentum are compared with previous, benchmark calculations based on Radau coordinates using this force field for zero total angular momentum and for J = 1. Very good agreement with the previous benchmark calculations is found.
Perturbation theory calculations of model pair potential systems
Gong, Jianwu
2016-01-01
Helmholtz free energy is one of the most important thermodynamic properties for condensed matter systems. It is closely related to other thermodynamic properties such as chemical potential and compressibility. It is also the starting point for studies of interfacial properties and phase coexistence if free energies of different phases can be obtained. In this thesis, we will use an approach based on the Weeks-Chandler-Anderson (WCA) perturbation theory to calculate the free energy of both solid and liquid phases of Lennard-Jones pair potential systems and the free energy of liquid states of Yukawa pair potentials. Our results indicate that the perturbation theory provides an accurate approach to the free energy calculations of liquid and solid phases based upon comparisons with results from molecular dynamics (MD) and Monte Carlo (MC) simulations.
NASA Astrophysics Data System (ADS)
Lee, Soono; Dakkouri, Marwan; Choo, Jaebum; Laane, Jaan
2000-03-01
The electronic absorption spectra of cyclobutanone, cyclopentanone, bicyclo[3.1.0]hexan-3-one, and tetrahydrofuran-3-one were recorded and analyzed in the 28,000 - 44,000 cm-1 region. Several dozen absorption bands were assigned for each molecule. These arise from combinations of the ring vibrations and the C=O wagging vibrations. Assigned bands were compared with previously recorded jet-cooled fluorescence excitation spectra. Additional C=O out-of-plane wagging bands were found for cyclopentanone and tetrahydrofuran-3-one, and the potential energy functions for this vibration in these molecules were recalculated. These potential energy functions have barriers to inversion reflecting the fact that the carbonyl group is bent out of the ring plane in the S1(n, π*) excited electronic state.
Mourik, Van Tonja; Wilson, Angela K.; Dunning, Thomas H.
1999-02-20
The potential energy curves of the rare gas dimers He2, Ne2, and Ar2 have been computed using correlation consistent basis sets ranging from singly augmented aug-cc-pVDZ sets through triply augmented t-aug-cc-pV6Z sets, with the augmented sextuple basis sets being reported herein. Several methods for including electron correlation were investigated, namely Moller Plesset perturbation theory (MP2, MP3 and MP4) and coupled cluster theory [CCSD and CCSD(T)].
Carter, Stuart; Wang, Yimin; Bowman, Joel M
2017-02-17
The code MULTIMODE is used in its reaction path version, along with ab initio potential energy and dipole moment surfaces introduced earlier, to predict the infrared spectra of both trans and cis forms of HOCO at temperatures 296 and 15 K. All six fundamentals are isolated for each isomer and temperature, and their main features examined, paying particular attention to the OH stretch fundamental, whose spectrum has been reported experimentally for trans-HOCO. The current spectra for cis-HOCO, while not of "spectroscopic" accuracy, should be sufficient to aid in new experimental efforts to record the spectrum of this isomer.
Energy and mass balance calculations for incinerators
Lee, C.C.; Huffman, G.L.
1998-01-01
Calculation of energy and mass balance within an incinerator is a very important part of designing and/or evaluating the incineration process. This article describes a simple computer model used to calculate an energy and mass balance for a rotary kiln incinerator. The main purpose of the model is to assist US Environmental Protection Agency (EPA) permit writers in evaluating the adequacy of the data submitted by applicants seeking incinerator permits. The calculation is based on the assumption that a thermodynamic equilibrium condition exits within the combustion chamber. Key parameters that the model can calculate include theoretical combustion air, excess air needed for actual combustion cases, flue gas flow rate, and exit temperature.
Calculation of Rydberg energy levels for the francium atom
NASA Astrophysics Data System (ADS)
Huang, Shi-Zhong; Chu, Jin-Min
2010-06-01
Based on the weakest bound electron potential model theory, the Rydberg energy levels and quantum defects of the np2Po1/2 (n = 7-50) and np2Po3/2 (n = 7-50) spectrum series for the francium atom are calculated. The calculated results are in excellent agreement with the 48 measured levels, and 40 energy levels for highly excited states are predicted.
Calculating Standard Reduction Potentials of [4Fe–4S] Proteins
Perrin, Bradley S.; Niu, Shuqiang; Ichiye, Toshiko
2013-03-15
The oxidation–reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combinatio of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.
NASA Astrophysics Data System (ADS)
Jiang, Hao; Xu, Minzhong; Hutson, Jeremy M.; Bačić, Zlatko
2005-08-01
The ground-state energies and HF vibrational frequency shifts of ArnHF clusters have been calculated on the nonadditive potential-energy surfaces (PESs) for n =2-7 and on the pairwise-additive PESs for the clusters with n =1-12, using the diffusion Monte Carlo (DMC) method. For n >3, the calculations have been performed for the lowest-energy isomer and several higher-lying isomers which are the closest in energy. They provide information about the isomer dependence of the HF redshift, and enable direct comparison with the experimental data recently obtained in helium nanodroplets. The agreement between theory and experiment is excellent, in particular, for the nonadditive DMC redshifts. The relative, incremental redshifts are reproduced accurately even at the lower level of theory, i.e., the DMC and quantum five-dimensional (rigid Arn) calculations on the pairwise-additive PESs. The nonadditive interactions make a significant contribution to the frequency shift, on the order of 10%-12%, and have to be included in the PESs in order for the theory to yield accurate magnitude of the HF redshift. The energy gaps between the DMC ground states of the cluster isomers are very different from the energy separation of their respective minima on the PES, due to the considerable variations in the intermolecular zero-point energy of different ArnHF isomers.
Free-Energy Calculations. A Mathematical Perspective
NASA Technical Reports Server (NTRS)
Pohorille, Andrzej
2015-01-01
conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.
NASA Astrophysics Data System (ADS)
Bronshtein, Michael D.; Nazmutdinov, Renat R.; Schmickler, Wolfgang
2004-12-01
An effective computational scheme to construct the adiabatic potential energy surfaces (APES) along the reaction coordinates for an electron transfer reaction occurring by two steps at a metal electrode is considered in the framework of the Anderson-Newns model. Two Theorems have been proved which predict the existence of all possible solutions of the Anderson-Newns equations at arbitrary values of the key parameters and point out the region for each solution. Asymptotic formulas for solutions near multiple roots have been derived and combined in an effective way with numerical routines. The analysis of some important properties of the APES, which can be of interest for modelling the electrochemical electron transfer processes, is presented as well. The APES describing the reduction of Zn(II) and In(III) aqua-complexes at a mercury electrode have been built and discussed.
Mai, Binh Khanh; Kim, Yongho
2016-10-03
Protonolysis by platinum or palladium complexes has been extensively studied because it is the microscopic reverse of the C-H bond activation reaction. The protonolysis of (COD)Pt(II)Me2, which exhibits abnormally large kinetic isotope effects (KIEs), is proposed to occur via a concerted pathway (SE2 mechanism) with large tunneling. However, further investigation of KIEs for the protonolysis of ZnMe2 and others led to a conclusion that there is no noticeable correlation between the mechanism and magnitude of KIE. In this study, we demonstrated that variational transition state theory including multidimensional tunneling (VTST/MT) could accurately predict KIEs and Arrhenius parameters of the protonolysis of alkylmetal complexes based on the potential energy surfaces generated by density functional theory. The predicted KIEs, Ea(D) - Ea(H) values, and AH/AD ratios for the protonolysis of (COD)Pt(II)Me2 and Zn(II)Me2 by TFA agreed very well with experimental values. The protonolysis of ZnMe2 with the concerted pathway has a very flat potential energy surface, which produces a very small tunneling effect and therefore a small KIE. The predicted KIE for the stepwise protonolysis (SE(ox) mechanism) of (COD)Pt(II)Me2 was much smaller than that of the concerted pathway, but greater than the KIE of the concerted protonolysis of ZnMe2. A large KIE, which entails a significant tunneling effect, could be used as an experimental probe of the concerted pathway. However, a normal or small KIE should not be used as an indicator of the stepwise mechanism, and the interplay between experiments and reliable theory including tunneling would be essential to uncover the mechanism correctly.
Calculation of astrophysical S factor at low energy levels
NASA Astrophysics Data System (ADS)
Andic, Halil Ibrahim; Ozer, Okan
2017-02-01
Nuclear reactions are very important for the structure, evolution, nucleosynthesis and various observational manifestations of main-sequence stars, white dwarfs and neutron stars. For astrophysical applications, one needs to know value of S-factor for many reactions at low energies. The experimental measurements of cross-sections at such low energies are essentially not easily available since the Coulomb barrier. Theoretical calculations are model dependent, so that nuclear physics uncertainties of calculated S-factor can be substantial. Using the supersymmetric quantum mechanics one can obtain the supersymmetric partner potential that can vary by several orders of magnitude in the energy range of a given reaction in the calculation of S factor. Since the determination of reaction rates requires accurate values of cross sections at very low energies, then in order to eliminate the main part of the energy dependence of these cross sections one makes use of the astrophysical S-factor in Taylor Expansion series about zero-energy.
Alaska's renewable energy potential.
Not Available
2009-02-01
This paper delivers a brief survey of renewable energy technologies applicable to Alaska's climate, latitude, geography, and geology. We first identify Alaska's natural renewable energy resources and which renewable energy technologies would be most productive. e survey the current state of renewable energy technologies and research efforts within the U.S. and, where appropriate, internationally. We also present information on the current state of Alaska's renewable energy assets, incentives, and commercial enterprises. Finally, we escribe places where research efforts at Sandia National Laboratories could assist the state of Alaska with its renewable energy technology investment efforts.
Monte Carlo algorithm for free energy calculation.
Bi, Sheng; Tong, Ning-Hua
2015-07-01
We propose a Monte Carlo algorithm for the free energy calculation based on configuration space sampling. An upward or downward temperature scan can be used to produce F(T). We implement this algorithm for the Ising model on a square lattice and triangular lattice. Comparison with the exact free energy shows an excellent agreement. We analyze the properties of this algorithm and compare it with the Wang-Landau algorithm, which samples in energy space. This method is applicable to general classical statistical models. The possibility of extending it to quantum systems is discussed.
Calculating Free Energies Using Average Force
NASA Technical Reports Server (NTRS)
Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)
2001-01-01
A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.
Wave Energy Potential in the Latvian EEZ
NASA Astrophysics Data System (ADS)
Beriņš, J.; Beriņš, J.; Kalnačs, J.; Kalnačs, A.
2016-06-01
The present article deals with one of the alternative forms of energy - sea wave energy potential in the Latvian Exclusice Economic Zone (EEZ). Results have been achieved using a new method - VEVPP. Calculations have been performed using the data on wave parameters over the past five years (2010-2014). We have also considered wave energy potential in the Gulf of Riga. The conclusions have been drawn on the recommended methodology for the sea wave potential and power calculations for wave-power plant pre-design stage.
Calculating the potential to emit particulate matter
Vaart, D.R. van der
1996-09-01
As the implementation of the 1990 amendments to the Clean Air Act, and Title V in particular, continues, questions regarding the calculation of a facility`s potential to emit continue to surface. The US Environmental Protection Agency (EPA) has provided limited guidance decisions, although many are still being made during Title V implementation. This paper discusses what is meant by PM-10 and the validity of using sieve analysis in estimating particulate emissions. Title V of the Clean Air Amendments of 1990, and the accompanying regulations in 40 CFR Part 70, defines a major source subject to Title V by calculating its potential emissions of all regulated pollutants, both criteria and hazardous air pollutants. For PM, the threshold emission rate is 100 tons per year (tpy) for applicability to Title V. Much discussion has ensued regarding a definition of PM for the purpose of determining a facility`s potential to emit. Recently, EPA provided guidance which indicated that only PM-10 should be considered for making this determination although many states regulate larger particles through their state implementation plan (SIP) as a surrogate for PM-10.
Large scale self energy calculations for ion-surface interactions
NASA Astrophysics Data System (ADS)
Kürpick, P.; Thumm, U.
1996-03-01
We present large scale non-perturbative self energy calculations for the interaction of an ion with a metal surface. Using both the simple jellium potential and more sophisticated ab initio potentials(P. J. Jennings, R. O. Jones and M. Weinert, Phys. Rev. B, 37), 6113 (1988)., we study the complex self energy matrix for various n-manifolds allowing for the calculation of diabatic and adiabatic non-perturbative level shifts and widths, and hybrid orbitals(P. Kürpick and U.Thumm, to be published.). Besides this self energy calculations a new adiabatic close--coupling calculation is being developed that will be applied to the interaction of ions in various charge states with metal surfaces.
Singularity embedding method in potential flow calculations
NASA Technical Reports Server (NTRS)
Jou, W. H.; Huynh, H.
1982-01-01
The so-called H-type mesh is used in a finite-element (or finite-volume) calculation of the potential flow past an airfoil. Due to coordinate singularity at the leading edge, a special singular trial function is used for the elements neighboring the leading edge. The results using the special singular elements are compared to those using the regular elements. It is found that the unreasonable pressure distribution obtained by the latter is removed by the embedding of the singular element. Suggestions to extend the present method to transonic cases are given.
NASA Astrophysics Data System (ADS)
Tanaka, Hideki; Nakanishi, Koichiro; Touhara, Hidekazu
1984-11-01
Molecular dynamics (MD) calculation has been carried out for a dilute aqueous solution of tert-butyl alcohol (TBA) at 298.15 K and with experimental density value by the use of constant temperature technique developed previously. The total number of molecule is 216, seven of which are TBA. The mole fraction of TBA is thus 0.032. For water-water and TBA-water interactions, the MCY (Matsuoka-Clementi-Yoshimine) potential and previously reported potential determined by MO calculation are used. A new potential for TBA-TBA is determined by ab initio LCAO SCF calculations for more than 500 different configurations with an STO-3G basis set and subsequent multiparameter fitting of the MO data to a 12-6-3-1 type potential energy function. The MD calculation is extended up to 84 000 time steps (26 ps) and final 60 000 time steps are used to calculate both static and dynamic properties of the system. Both hydrophobic hydration and interaction due to TBA molecules are proved to be stronger than those of methanol studied previously. Structural promotion of water is clearly observed in radial distribution functions and trajectories of each molecule. The configuration and trajectory of all the molecules in solution indicate clearly the association of TBA molecules. It is also found from pair interaction distribution functions that no hydrogen bonding interaction occurs between two TBA molecules. The self-diffusion coefficient of water in the solution is appreciably smaller than that in pure water.
Predicting proteinase specificities from free energy calculations.
Mekonnen, Seble Merid; Olufsen, Magne; Smalås, Arne O; Brandsdal, Bjørn O
2006-10-01
The role of the primary binding residue (P1) in complexes between three different subtilases (subtilisin Carlsberg, thermitase and proteinase K) and their canonical protein inhibitor eglin c have been studied by free energy calculations. Based on the crystal structures of eglin c in complex with subtilisin Carlsberg and thermitase, and a homology model of the eglin c-proteinase K complex, a total of 57 mutants have been constructed and docked into their host proteins. The binding free energy was then calculated using molecular dynamics (MD) simulations combined with the linear interaction energy (LIE) method for all complexes differing only in the nature of the amino acid at the P1 position. LIE calculations for 19 different complexes for each subtilase were thus carried out excluding proline. The effects of substitutions at the P1 position on the binding free energies are found to be very large, and positively charged residues (Arg, Lys and His) are particularly deleterious for all three enzymes. The charged variants of the acidic side chains are found to bind more favorably as compared to their protonated states in all three subtilases. Furthermore, hydrophobic amino acids are accommodated most favorably at the S1-site in all three enzymes. Comparison of the three series of binding free energies shows only minor differences in the 19 computed relative binding free energies among these subtilases. This is further reflected in the correlation coefficient between the 23 relative binding free energies obtained, including the possible protonation states of ionizable side chains, but excluding the P1 Pro, for subtilisin Carlsberg versus thermitase (0.95), subtilisin versus proteinase K (0.94) and thermitase versus proteinase K (0.96).
Bond-Energy and Surface-Energy Calculations in Metals
ERIC Educational Resources Information Center
Eberhart, James G.; Horner, Steve
2010-01-01
A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…
Bond-Energy and Surface-Energy Calculations in Metals
ERIC Educational Resources Information Center
Eberhart, James G.; Horner, Steve
2010-01-01
A simple technique appropriate for introductory materials science courses is outlined for the calculation of bond energies in metals from lattice energies. The approach is applied to body-centered cubic (bcc), face-centered cubic (fcc), and hexagonal-closest-packed (hcp) metals. The strength of these bonds is tabulated for a variety metals and is…
Protein Thermostability Calculations Using Alchemical Free Energy Simulations
Seeliger, Daniel; de Groot, Bert L.
2010-01-01
Abstract Thermal stability of proteins is crucial for both biotechnological and therapeutic applications. Rational protein engineering therefore frequently aims at increasing thermal stability by introducing stabilizing mutations. The accurate prediction of the thermodynamic consequences caused by mutations, however, is highly challenging as thermal stability changes are caused by alterations in the free energy of folding. Growing computational power, however, increasingly allows us to use alchemical free energy simulations, such as free energy perturbation or thermodynamic integration, to calculate free energy differences with relatively high accuracy. In this article, we present an automated protocol for setting up alchemical free energy calculations for mutations of naturally occurring amino acids (except for proline) that allows an unprecedented, automated screening of large mutant libraries. To validate the developed protocol, we calculated thermodynamic stability differences for 109 mutations in the microbial Ribonuclease Barnase. The obtained quantitative agreement with experimental data illustrates the potential of the approach in protein engineering and design. PMID:20483340
Energy Band Calculations for Maximally Even Superlattices
NASA Astrophysics Data System (ADS)
Krantz, Richard; Byrd, Jason
2007-03-01
Superlattices are multiple-well, semiconductor heterostructures that can be described by one-dimensional potential wells separated by potential barriers. We refer to a distribution of wells and barriers based on the theory of maximally even sets as a maximally even superlattice. The prototypical example of a maximally even set is the distribution of white and black keys on a piano keyboard. Black keys may represent wells and the white keys represent barriers. As the number of wells and barriers increase, efficient and stable methods of calculation are necessary to study these structures. We have implemented a finite-element method using the discrete variable representation (FE-DVR) to calculate E versus k for these superlattices. Use of the FE-DVR method greatly reduces the amount of calculation necessary for the eigenvalue problem.
First Principles Structure Calculations Using the General Potential Lapw Method
NASA Astrophysics Data System (ADS)
Wei, Su-Huai
We have developed a completely general first principles self-consistent full-potential linearized-augmented-plane -wave (LAPW) method program within the density functional formalism to calculate electronic band structure, total energy, pressure and other quantities. No symmetry assumptions are used for the crystal structure. Shape unrestricted charge densities and potentials are calculated inside muffin -tin (MT) spheres as well as in the interstitial regions. All contributions to the Hamiltonian matrix elements are completely taken into account. The core states are treated fully relativistically using the spherical part of the potential only. Scalar relativistic effects are included for the band-states, and spin-orbit coupling is included using a second variation procedure. Both core states and valence states are treated self-consistently, the frozen core approximation is not required. The fast Fourier transformation method is used wherever it is applicable, and this greatly improves the efficiency. This state-of-the-art program has been tested extensively to check the accuracy and convergence properties by comparing calculated electronic band structures, ground state properties, equations of state and cohesive energies for bulk W and GaAs with other theoretical calculations and experimental results. It has been successfully applied to calculate and predict structural and metal-insulator phase transitions for close-packed crystal BaSe and BaTe and the geometric structure of the d-band metal W(001) surface. The results are in generally good agreement with experiment.
Kusuda, T
1980-10-31
The TC 4.7 simplified energy calculation method is a bin method used by the REAP procedure of the Carrier Corporation, except for the load estimating calculations. The simplified procedure was compared with hourly simulation procedures for an office building in Washington, DC. The comparison studied the extent as well as the reasons for agreement and discrepancies due to these two different types of annual energy analysis (bin method and hourly simulation methods). Results of the parallel calculations are discussed and the major reasons of discrepancies between the hourly simulation technique and the simplified TC 4.7 method are identified. Data resulting from the calculation methods are tabulated. (MCW)
de Oliveira-Filho, Antonio G S; Ornellas, Fernando R; Bowman, Joel M
2014-02-20
We report a permutationally invariant, ab initio potential energy surface (PES) for the OH + HBr → Br + H2O reaction. The PES is a fit to roughly 26 000 spin-free UCCSD(T)/cc-pVDZ-F12a energies and has no classical barrier to reaction. It is used in quasiclassical trajectory calculations with a focus on the thermal rate constant, k(T), over the temperature range 5 to 500 K. Comparisons with available experimental data over the temperature range 23 to 416 K are made using three approaches to treat the OH rotational and associated electronic partition function. All display an inverse temperature dependence of k(T) below roughly 160 K and a nearly constant temperature dependence above 160 K, in agreement with experiment. The calculated rate constant with no treatment of spin-orbit coupling is overall in the best agreement with experiment, being (probably fortuitously) within 20% of it.
Perturbation energy as an alternative to the total energy calculations
NASA Astrophysics Data System (ADS)
Kutepov, Andrey; Antropov, Vladimir; van Schilfgaarde, Mark; Antonov, Victor
2014-03-01
We analyze different approaches to determine the energy from a perturbation using modern electronic structure methods. We compare the energy of perturbation from standard perturbation theory with what is obtained directly in self consistent band structure methods. The method is applied for studies such perturbations as internal magnetic field and spin orbital coupling in solids. This method is further compared with integration over the coupling constant. Numerical tests have been performed for magnetic Fe and Gd systems using the local density approximation. The main advantage of present scheme is its usefulness in methods for strongly correlated electronic systems studies where total energy calculations are not always possible. Specific calculations are performed using self consistent quasiparticle GW and LDA+U calculations for MnBi where the right value of magnetic moment and sign/value of magnetic anisotropy as a function of temperature have been obtained. This research is supported in part by the Critical Materials Institute, an Energy Innovation Hub funded by the U.S. Department of Energy, Office of Energy Efficiency and Renewable Energy through the Ames Laboraory.
Theoretical studies of potential energy surfaces
Harding, L.B.
1995-07-01
MRCI (configuration interaction) calculations were used to examine possible pathways for the O{sub 2} + CCH reaction. The H{sub 2} + CN potential surface was examined. An initial survey was made of the HCl + CN potential energy surface at a low level of theory.
Hua -Gen Yu; Han, Huixian; Guo, Hua
2016-03-29
Vibrational energy levels of the ammonium cation (NH_{4}^{+}) 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 NH_{4}^{+} and ND_{4}^{+} exhibit a polyad structure, characterized by a collective quantum number P = 2(v_{1} + v_{3}) + v_{2} + v_{4}. 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}.
Zero energy scattering calculation in Euclidean space
NASA Astrophysics Data System (ADS)
Carbonell, J.; Karmanov, V. A.
2016-03-01
We show that the Bethe-Salpeter equation for the scattering amplitude in the limit of zero incident energy can be transformed into a purely Euclidean form, as it is the case for the bound states. The decoupling between Euclidean and Minkowski amplitudes is only possible for zero energy scattering observables and allows determining the scattering length from the Euclidean Bethe-Salpeter amplitude. Such a possibility strongly simplifies the numerical solution of the Bethe-Salpeter equation and suggests an alternative way to compute the scattering length in Lattice Euclidean calculations without using the Luscher formalism. The derivations contained in this work were performed for scalar particles and one-boson exchange kernel. They can be generalized to the fermion case and more involved interactions.
NASA Astrophysics Data System (ADS)
Zhou, Shiqi; Solana, J. R.
2013-06-01
The first four perturbation coefficients in the expansion of the Helmholtz free energy in power series of the inverse of the reduced temperature for a number of potential models with hard-sphere cores plus core-softened and discontinuous tails are obtained from Monte Carlo simulations. The potential models considered include square-well, double square-well, and square-shoulder plus square-well, with different potential parameters. These simulation data are used to evaluate the performance of a traditional macroscopic compressibility approximation (MCA) for the second order coefficient and a recent coupling parameter series expansion (CPSE) for the first four coefficients. Comprehensive comparison indicates the incapability of the MCA for the second order coefficient in most non-stringent situations, and significance of the CPSE in accurately calculating these four coefficients.
The theoretical shape of sucrose crystals from energy calculations
NASA Astrophysics Data System (ADS)
Saska, Michael; Myerson, Allan S.
1983-05-01
The surface energies of individual crystallographic faces of crystalline sucrose were calculated using two forms of the 6-exp (Buckingham) potential. Hydrogen bond energies were calculated as a sum of O-H, O…H and O…O interactions where the Lippincott-Schroeder short-range potential was used for O-H and O…H pairs and the 6-exp potential for the non-bonded O…O interactions. Assuming that the surface energy equals half of the cohesive energy of the crystal, the attachment and surface energies of most of the faces found on as sucrose crystal were calculated. A computer program was written to draw the theoretical shape of crystals given the positions (central distances) of its faces. The resulting sucrose shapes are elongated along the c-axis. It is argued that the c-axis elongated habit is an intrinsic shape for vapor grown sucrose crystals (if realizable) and it is suggested that the usual shapes of solution grown sucrose crystals can be explained in terms of solvent (water) adsorption.
NASA Astrophysics Data System (ADS)
Dothe, H.; Braunstein, M.; Duff, J. W.; Sharma, R. D.
2001-12-01
The daytime observation of 5.3 μ m thermospheric emission from the NO fundamental vibration-rotation band by the interferometer aboard the cryogenic infrared radiance instrumentation for shuttle (CIRRIS 1A) has provided important insight into the phenomenology of NO formation. The four major mechanisms to the 5.3 μ m emission considered by previous modeling are solar pumping, inelastic collisions of O with NO(v=0), the reactions of N(2D) with O2, and the reactions of N(4S) with O2. It has previously been shown that the reaction of N(4S) with O2 is consistent with rotationally nonthermal 5.3 μ m emission, while the N(2D)+O2 reaction has been assumed to contribute to rotationally thermal emission. The assumption of a thermal rotational distribution from the N(2D)+O2 reaction cannot be confirmed by the CIRRIS 1A data. The existence of a significant fraction of nonthermal atoms in the tail of the N(2D) energy distribution function (EDF) in the daylit thermosphere was demonstrated earlier (AGU Spring 2001). Therefore the investigation of possible nonthermal behavior in NO formation via the N(2D)+O2 reaction in the daylit and aurorally dosed thermosphere requires energy dependent cross sections for the reaction between N(2D) and O2. To calculate the N(2D)+O2 cross sections, potential energy surfaces (PES) of the NO2 system are required. The output of these calculations include the energy dependent cross sections and the vibrational and rotational distribution of the nascent NO needed for accurate calculation of the cooling rates due to 5.3 μ m emission. This work concentrates on the first step towards the calculation of such cross sections, the ab initio calculations of the NO2 PES. Previous existing PES, using different basis sets and electron correlation levels, have shown disagreements in the magnitude of the barriers for the lowest lying doublet surfaces in the reaction entrance channel. Comparative results from our calculations are presented here, showing PES
Potential Energy Curves of Hydrogen Fluoride
NASA Technical Reports Server (NTRS)
Fallon, Robert J.; Vanderslice, Joseph T.; Mason, Edward A.
1960-01-01
Potential energy curves for the X(sup 1)sigma+ and V(sup 1)sigma+ states of HF and DF have been calculated by the Rydberg-Klein-Rees method. The results calculated from the different sets of data for HF and DF are found to be in very good agreement. The theoretical results of Karo are compared to the experimental results obtained here.
Lead Optimization Mapper: Automating free energy calculations for lead optimization
Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.
2013-01-01
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce Lead Optimization Mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license. PMID:24072356
Lead optimization mapper: automating free energy calculations for lead optimization
NASA Astrophysics Data System (ADS)
Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P.; Summa, Christopher M.; Jaber, Vivian R.; Lim, Nathan M.; Mobley, David L.
2013-09-01
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license.
Lead optimization mapper: automating free energy calculations for lead optimization.
Liu, Shuai; Wu, Yujie; Lin, Teng; Abel, Robert; Redmann, Jonathan P; Summa, Christopher M; Jaber, Vivian R; Lim, Nathan M; Mobley, David L
2013-09-01
Alchemical free energy calculations hold increasing promise as an aid to drug discovery efforts. However, applications of these techniques in discovery projects have been relatively few, partly because of the difficulty of planning and setting up calculations. Here, we introduce lead optimization mapper, LOMAP, an automated algorithm to plan efficient relative free energy calculations between potential ligands within a substantial library of perhaps hundreds of compounds. In this approach, ligands are first grouped by structural similarity primarily based on the size of a (loosely defined) maximal common substructure, and then calculations are planned within and between sets of structurally related compounds. An emphasis is placed on ensuring that relative free energies can be obtained between any pair of compounds without combining the results of too many different relative free energy calculations (to avoid accumulation of error) and by providing some redundancy to allow for the possibility of error and consistency checking and provide some insight into when results can be expected to be unreliable. The algorithm is discussed in detail and a Python implementation, based on both Schrödinger's and OpenEye's APIs, has been made available freely under the BSD license.
A comparison of internal energy calculation methods for diatomic molecules
NASA Technical Reports Server (NTRS)
Liu, Yen; Shakib, Farzin; Vinokur, Marcel
1990-01-01
Various methods of calculating the internal energy of diatomic molecules are studied. An accurate and efficient method for computing the eigenvalues of the vibrational Schroedinger equation for an arbitrary potential is developed. The method is based on a finite-element discretization using the cubic Lobatto element. A combination of spectrum slicing and the Laguerre algorithm is used to solve for the eigenvalues. A simple method to compute the quasi-bound states is presented. For N2 molecules, all vibrational-rotational states of eleven available electronic potentials are computed, and summed to obtain the exact internal energy function with temperature. The total computation required 314 seconds of CPU-time on NASA's Cray 2 computer. Various approximate models are discussed and compared with the exact numerical simulation. It is shown that the splitting of the macroscopic internal energy into separate electronic, rotational, and vibrational energies is not justified at high temperatures.
A comparison of internal energy calculation methods for diatomic molecules
NASA Technical Reports Server (NTRS)
Liu, Yen; Shakib, Farzin; Vinokur, Marcel
1990-01-01
Various methods of calculating the internal energy of diatomic molecules are studied. An accurate and efficient method for computing the eigenvalues of the vibrational Schroedinger equation for an arbitrary potential is developed. The method is based on a finite-element discretization using the cubic Lobatto element. A combination of spectrum slicing and the Laguerre algorithm is used to solve for the eigenvalues. A simple method to compute the quasi-bound states is presented. For N2 molecules, all vibrational-rotational states of eleven available electronic potentials are computed, and summed to obtain the exact internal energy function with temperature. The total computation required 314 seconds of CPU-time on NASA's Cray 2 computer. Various approximate models are discussed and compared with the exact numerical simulation. It is shown that the splitting of the macroscopic internal energy into separate electronic, rotational, and vibrational energies is not justified at high temperatures.
Dirac Calculations for Proton Inelastic Scattering at Intermediate Energies
NASA Astrophysics Data System (ADS)
El-Nohy, N. A.; El-Hammamy, M. N.; Aly, N. E.; Abdel-Moneim, A. M.; Hamza, A. F.
2016-12-01
Relativistic proton inelastic scattering from different targets (16O, 24Mg, 28Si, 40Ca, 54Fe, 58Ni, 90Zr, 154Sm, 176Yb, and 208Pb) at intermediate energies is analyzed in the framework of phenomenological optical potentials based on the Dirac formalism. Parameters of the Dirac phenomenological potential with Woods Saxon (WS) shape are obtained. The first order vibrational collective model with one phonon is used to calculate the transition optical potentials to the first low-lying excited state (2+) of the investigated target nuclei. Also, the variation of deformation length ( δ) with energy and mass number is studied. It is noticed that the deformation length increases slightly with energy at intermediate range.
LHC Physics Potential versus Energy
Quigg, Chris; /Fermilab
2009-08-01
Parton luminosities are convenient for estimating how the physics potential of Large Hadron Collider experiments depends on the energy of the proton beams. I present parton luminosities, ratios of parton luminosities, and contours of fixed parton luminosity for gg, u{bar d}, and qq interactions over the energy range relevant to the Large Hadron Collider, along with example analyses for specific processes.
Deskevich, Michael P.; Hayes, Michael Y.; Takahashi, Kaito; Skodje, Rex T.; Nesbitt, David J.
2006-06-14
This paper presents a new ground state (1 {sup 2}A{sup '}) electronic potential energy surface for the F({sup 2}P)+HCl{yields}HF+Cl({sup 2}P) reaction. The ab initio calculations are done at the multireference configuration interaction+Davidson correction (MRCI+Q) level of theory by complete basis set extrapolation of the aug-cc-pVnZ (n=2,3,4) energies. Due to low-lying charge transfer states in the transition state region, the molecular orbitals are obtained by six-state dynamically weighted multichannel self-consistent field methods. Additional perturbative refinement of the energies is achieved by implementing simple one-parameter correlation energy scaling to reproduce the experimental exothermicity ({delta}E=-33.06 kcal/mol) for the reaction. Ab initio points are fitted to an analytical function based on sum of two- and three-body contributions, yielding a rms deviation of <0.3 kcal/mol for all geometries below 10 kcal/mol above the barrier. Of particular relevance to nonadiabatic dynamics, the calculations show significant multireference character in the transition state region, which is located 3.8 kcal/mol with respect to F+HCl reactants and features a strongly bent F-H-Cl transition state geometry ({theta}{approx_equal}123.5 deg. ). Finally, the surface also exhibits two conical intersection seams that are energetically accessible at low collision energies. These seams arise naturally from allowed crossings in the C{sub {infinity}}{sub v} linear configuration that become avoided in C{sub s} bent configurations of both the reactant and product, and should be a hallmark of all X-H-Y atom transfer reaction dynamics between ({sup 2}P) halogen atoms.
Kamimura, Sunao; Obukuro, Yuki; Matsushima, Shigenori; Nakamura, Hiroyuki; Arai, Masao; Xu, Chao-Nan
2015-12-15
The electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is evaluated by the scalar-relativistic full potential linearized augmented plane wave (FLAPW+lo) method using the modified Becke–Johnson potential (Tran–Blaha potential) combined with the local density approximation correlation (MBJ–LDA). The fundamental gap between the valence band (VB) and conduction band (CB) is estimated to be 3.96 eV, which is close to the experimental value. Sn 5s states and Sr 4d states are predominant in the lower and upper CB, respectively. On the other hand, the lower VB is mainly composed of Sn 5s, 5p, and O 2p states, while the upper VB mainly consists of O 2p states. These features of the DOS are well reflected by the optical transition between the upper VB and lower CB, as seen in the energy dependence of the dielectric function. Furthermore, the absorption coefficient estimated from the MBJ–LDA is similar to the experimental result. - Graphical abstract: Calculated energy band structure along the symmetry lines of the first BZ of Sr{sub 3}Sn{sub 2}O{sub 7} crystal obtained using the MBJ potential. - Highlights: • Electronic structure of Sr{sub 3}Sn{sub 2}O{sub 7} is calculated on the basis of MBJ–LDA method for the first time. • Band gap of Sr{sub 3}Sn{sub 2}O{sub 7} is determined accurately on the basis of MBJ–LDA method. • The experimental absorption spectrum of Sr{sub 3}Sn{sub 2}O{sub 7} produced by MBJ–LDA is more accurate than that obtained by GGA method.
Atomistic calculations of dislocation core energy in aluminium
Zhou, X. W.; Sills, R. B.; Ward, D. K.; ...
2017-02-16
A robust molecular dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: it does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield highly converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and Burgers vector. These calculations show that, for the face-centred-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elasticmore » energy: Ec = A·sin2β + B·cos2β, and this dependence is independent of temperature between 100 and 300 K. By further analysing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and radius of a perfect versus extended dislocation. With our methodology, the dislocation core energy can be accurately accounted for in models of plastic deformation.« less
Atomistic calculations of dislocation core energy in aluminium
NASA Astrophysics Data System (ADS)
Zhou, X. W.; Sills, R. B.; Ward, D. K.; Karnesky, R. A.
2017-02-01
A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy: Ec=A sin2β +B cos2β , and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. With our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.
Atomistic calculations of dislocation core energy in aluminium
Zhou, Xiaowang W.; Sills, Ryan B.; Ward, Donald K.; ...
2017-02-16
A robust molecular-dynamics simulation method for calculating dislocation core energies has been developed. This method has unique advantages: It does not require artificial boundary conditions, is applicable for mixed dislocations, and can yield converged results regardless of the atomistic system size. Utilizing a high-fidelity bond order potential, we have applied this method in aluminium to calculate the dislocation core energy as a function of the angle β between the dislocation line and the Burgers vector. These calculations show that, for the face-centered-cubic aluminium explored, the dislocation core energy follows the same functional dependence on β as the dislocation elastic energy:more » Ec = Asin2β + Bcos2β, and this dependence is independent of temperature between 100 and 300 K. By further analyzing the energetics of an extended dislocation core, we elucidate the relationship between the core energy and the core radius of a perfect versus an extended dislocation. As a result, with our methodology, the dislocation core energy can accurately be accounted for in models of dislocation-mediated plasticity.« less
Ásgeirsson, Vilhjálmur; Bauer, Christoph A.
2017-01-01
We introduce a fully stand-alone version of the Quantum Chemistry Electron Ionization Mass Spectra (QCEIMS) program [S. Grimme, Angew. Chem. Int. Ed., 2013, 52, 6306] allowing efficient simulations for molecules composed of elements with atomic numbers up to Z = 86. The recently developed extended tight-binding semi-empirical method GFN-xTB has been combined with QCEIMS, thereby eliminating dependencies on third-party electronic structure software. Furthermore, for reasonable calculations of ionization potentials, as required by the method, a second tight-binding variant, IPEA-xTB, is introduced here. This novel combination of methods allows the automatic, fast and reasonably accurate computation of electron ionization mass spectra for structurally different molecules across the periodic table. In order to validate and inspect the transferability of the method, we perform large-scale simulations for some representative organic, organometallic, and main-group inorganic systems. Theoretical spectra for 23 molecules are compared directly to experimental data taken from standard databases. For the first time, realistic quantum chemistry based EI-MS for organometallic systems like ferrocene or copper(ii)acetylacetonate are presented. Compared to previously used semiempirical methods, GFN-xTB is faster, more robust, and yields overall higher quality spectra. The partially analysed theoretical reaction and fragmentation mechanisms are chemically reasonable and reveal in unprecedented detail the extreme complexity of high energy gas phase ion chemistry including complicated rearrangement reactions prior to dissociation. PMID:28959412
Energy potential of geothermal energy in Germany
Kayser, M.; Kaltschmitt, M.
2000-06-01
The use of terrestrial heat could fulfill certain energy demands. For the evaluation of the possibilities in the energy system of Germany, the available potentials are one of the most important criteria. Within this context, in the past only the available resources and the reserves have been discussed. But these data have hardly practical relevance for the energy-political and energy-economic discussions, since they do not consider the conditions in the corresponding energy system. In this article, therefore, explanations additional to the overall existing amount of heat in underground portions are shown, which could be used also from a technical point of view. In addition, the demand-side restrictions are considered and the share of the available heat is pointed out which can be used within the energy system of Germany. The explanations show that consideration of the demand side is necessary to make relevant statements. The investigations also make clear that terrestrial heat will never be able to cover more than just a part of the energy demand for warmth in Germany.
Fanourgakis, George S; Aprà, Edoardo; Xantheas, Sotiris S
2004-08-08
We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest-lying isomers within each of the four major families of minima of (H(2)O)(20). These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CPS estimates are -200.1 (dodecahedron, 30 hydrogen bonds), -212.6 (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds), and -217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). The energetic ordering of the various (H(2)O)(20) isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA, and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within <1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3% to 5%.
Fanourgakis, Georgios S.; Apra, Edoardo; Xantheas, Sotiris S.
2004-08-08
We report estimates of complete basis set (CBS) limits at the second-order Møller-Plesset perturbation level of theory (MP2) for the binding energies of the lowest lying isomers within each of the four major families of minima of (H2O)20. These were obtained by performing MP2 calculations with the family of correlation-consistent basis sets up to quadruple zeta quality, augmented with additional diffuse functions (aug-cc-pVnZ, n=D, T, Q). The MP2/CBS estimates are: -200.1 kcal/mol (dodecahedron, 30 hydrogen bonds), -212.6 kcal/mol (fused cubes, 36 hydrogen bonds), -215.0 (face-sharing pentagonal prisms, 35 hydrogen bonds) and –217.9 kcal/mol (edge-sharing pentagonal prisms, 34 hydrogen bonds). The energetic ordering of the various (H2O)20 isomers does not follow monotonically the number of hydrogen bonds as in the case of smaller clusters such as the different isomers of the water hexamer. The dodecahedron lies ca. 18 kcal/mol higher in energy than the most stable edge-sharing pentagonal prism isomer. The TIP4P, ASP-W4, TTM2-R, AMOEBA and TTM2-F empirical potentials also predict the energetic stabilization of the edge-sharing pentagonal prisms with respect to the dodecahedron, albeit they universally underestimate the cluster binding energies with respect to the MP2/CBS result. Among them, the TTM2-F potential was found to predict the absolute cluster binding energies to within < 1% from the corresponding MP2/CBS values, whereas the error for the rest of the potentials considered in this study ranges from 3-5%.
NASA Astrophysics Data System (ADS)
Gunde, R.; Ha, T.-K.; Günthard, H. H.
1990-08-01
In this paper results of consistent force field modeling (CFF) of the potential function to conversion of the gauche (g) to the trans (t) conformer of 1,2-difluoroethane (DFE) isolated in an argon matrix will be reported. Starting point are locally stable configurations gDFE:Ar 364 (defect GH1) and tDFE:Ar 364 (TH1) obtained in previous work from CFF modeling of a cube shaped Ar 364 fragment containing one DFE molecule in its center. Using the dihedral angle of DFE as an independent parameter the minimum energy path of the conversion process gDFE:Ar 364→tDFE:Ar 364 will be determined by CFF energy minimization. Determination of the minimum energy path is found to require large numbers of energy minimization steps and to lead to a rather complicated motion of the molecule with respect to the crystal fragment. Surprisingly the molecule-matrix interactions lead to a reduction of the g-t barrier by ≈500 cal/mol and to a stabilization of the trans species by ≈500 cal/mol. This finding is a consequence of a delicate interplay of matrix-molecule and matrix-matrix interactions. Calculation of the electric polarization energy (induced dipole-first-order polarization approximation) is based on extended ab initio calculations of dipole and quadrupole moments and a bond polarizability estimate of the first-order polarizability of DFE as a function of the internal rotation angle, on Fourier expansion of multipole components and use of symmetry for reduction of the order of the linear system defining the (self-consistent) induced dipole moments of all Ar atoms. Electric polarization is found to alter the potential function of the conversion process in a profound way: the g-t barrier and the t-g energy difference are increased to ≈3000 cal/mol and to ≈1500 cal/mol respectively (≈2500 and ≈530 cal/mol respectively for free DFE). Further applications of the technique developed in this work to related problems of matrix isolated molecules, e.g., vibrational matrix
Proliferation Potential of Accelerator-Drive Systems: Feasibility Calculations
Riendeau, C.D.; Moses, D.L.; Olson, A.P.
1998-11-01
Accelerator-driven systems for fissile materials production have been proposed and studied since the early 1950s. Recent advances in beam power levels for small accelerators have raised the possibility that such use could be feasible for a potential proliferator. The objective of this study is to review the state of technology development for accelerator-driven spallation neutron sources and subcritical reactors. Energy and power requirements were calculated for a proton accelerator-driven neutron spallation source and subcritical reactors to produce a significant amount of fissile material--plutonium.
Relativity, potential energy, and mass
NASA Astrophysics Data System (ADS)
Hecht, Eugene
2016-11-01
This paper is an exploration of the concept of energy, illuminated by the transformative insights of the special theory of relativity. Focusing on potential energy (PE), it will be shown that PE as presently defined is in conflict with the tenets of special relativity. Even though PE remains an indispensable theoretical device its actual physicality is questionable. Moreover its ontological status is quite different from that of both kinetic energy and mass, a significant point that is not widely appreciated. We will establish that PE is a theoretical concept as opposed to an empirical one; it is a descriptor of mass-energy without a detectable physical presence of its own. PE is a measure of energy stored, it is not the energy stored.
CHP Energy and Emissions Savings Calculator
Download the CHP Emissions Calculator, a tool that calculates the difference between the anticipated carbon dioxide, methane, nitrous oxide, sulfur dioxide, and nitrogen oxide emissions from a CHP system to those of a separate heat and power system.
Wu, Dong-lan; Tan, Bin; Qin, Jiu-ying; Wan, Hui-jun; Xie, An-dong; Yan, Bing; Ding, Da-jun
2015-11-05
Ab initio calculations on potential energy curves (PECs), spectroscopic constants, transition dipole moments, radiative transition probabilities and lifetimes for the ground state (X(2)Σ(+)) and the first excited state (A(2)Π) of MgX (X=F, Cl, Br, I) molecules are determined by high-level internally contracted multi-reference configuration interaction (ic-MRCI) method. In order to improve the calculation, the Davidson modification (+Q) and scalar relativistic correction are included. The present results show that most of spectroscopic constants are in accordance with the measurements, the equilibrium internuclear distance Re increases while the other spectroscopic constants reduce along with the increasing of the atomic number of the halogen from F to I. Diagonal vibrational transitions are found to be dominant for the A(2)Π→X(2)Σ(+) system of MgX molecules. The corresponding radiative lifetimes of ν'=0 are computed to be 7.24, 9.98, 18.94 and 22.72 ns for MgF, MgCl, MgBr, and MgI, respectively. The calculated result of MgF molecule is in good agreement with the recent theoretical result of 7.16 ns, with a small relative error percent of 1.11%.
Espinosa-Garcia, J; Rangel, C; Corchado, J C
2016-06-22
We report an analytical full-dimensional potential energy surface for the GeH4 + OH → GeH3 + H2O reaction based on ab initio calculations. It is a practically barrierless reaction with very high exothermicity and the presence of intermediate complexes in the entrance and exit channels, reproducing the experimental evidence. Using this surface, thermal rate constants for the GeH4 + OH/OD isotopic reactions were calculated using two approaches: variational transition state theory (VTST) and quasi-classical trajectory (QCT) calculations, in the temperature range 200-1000 K, and results were compared with the only experimental data at 298 K. Both methods showed similar values over the whole temperature range, with differences less than 30%; and the experimental data was reproduced at 298 K, with negative temperature dependence below 300 K, which is associated with the presence of an intermediate complex in the entrance channel. However, while the QCT approach reproduced the experimental kinetic isotope effect, the VTST approach underestimated it. We suggest that this difference is associated with the harmonic approximation used in the treatment of vibrational frequencies.
Potential energy function for the hydroperoxyl radical
Lemon, W.J.; Hase, W.L.
1987-03-12
A switching function formalism is used to derive an analytic potential energy surface for the O + OH in equilibrium HO/sub 2/ in equilibrium H + O/sub 2/ reactive system. Both experimental and ab initio data are used to derive parameters for the potential energy surface. Trajectory calculations for highly excited HO/sub 2/ are performed on this surface. From these trajectories quasi-periodic eigentrajectories are found for vibrational levels near the HO/sub 2/ dissociation threshold with small amounts of quanta in the OH stretch mode and large amounts of quanta in the OO stretch mode.
Potential energy surfaces for cluster emitting nuclei
Poenaru, Dorin N.; Gherghescu, Radu A.; Greiner, Walter
2006-01-15
Potential energy surfaces are calculated by use of the most advanced asymmetric two-center shell model that allows us to obtain shell-and-pairing corrections that are added to the Yukawa-plus-exponential model deformation energy. Shell effects are of crucial importance for the experimental observation of spontaneous disintegration by heavy-ion emission. Results for {sup 222}Ra, {sup 232}U, {sup 236}Pu, and {sup 242}Cm illustrate the main ideas and show for the first time, for a cluster emitter, a potential barrier obtained by use of the macroscopic-microscopic method.
Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations
Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.
2011-01-01
The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530
Optimization of energetic electron energy degradation calculations
NASA Astrophysics Data System (ADS)
Swartz, W. E.
1985-07-01
It is pointed out that, in the past two decades, much progress has been made in the theoretical computation of energetic electron transport and thermalization in the ionosphere. The present investigation is concerned with an optimized scheme which uses the same discrete formalism at all energies, and guarantees numerical energy conservation independently of the energy grid size or configuration. The considered method was employed by Kelley et al. (1977) and by Swartz et al. (1979). Attention is given to energy degradation and reapportionment with energy conservation following inelastic collisions, energy reapportionment with energy conservation of emergent primaries following ionizing collisions, the establishment of consistent sources for numerical comparisons, and an example of an energy grid with the minimum number of cells.
Microscopic calculations of {lambda} single-particle energies.
Usmani, Q. N.
1998-02-12
{Lambda} binding energy data for total baryon number A {le} 208 and for {Lambda} angular momenta {ell}{sub {Lambda}} {le} 3 are analyzed in terms of phenomenological (but generally consistent with meson-exchange) {Lambda}N and {Lambda}NN potentials. The Fermi-Hypernetted-Chain technique is used to calculate the expectation values for the {Lambda} binding to nuclear matter. Accurate effective {Lambda}N and {Lambda}NN potentials are obtained which are folded with the core nucleus nucleon densities to calculate the {Lambda} single particle potential U{sub {Lambda}}(r). We use a dispersive {Lambda}NN potential but also include an explicit {rho} dependence to allow for reduced repulsion in the surface, and the best fits have a large {rho} dependence giving consistency with the variational Monte Carlo calculations for {sub {Lambda}}{sup 5}He. The exchange fraction of the {Lambda}N space-exchange potential is found to be 0.2-0.3 corresponding to m{sub {Lambda}}* {approx_equal} (0.74-0.82)m{sub {Lambda}}. Charge symmetry breaking is found to be significant for heavy hypernuclei with a large neutron excess, with a strength consistent with that obtained from the A = 4 hypernuclei.
Assessment of Triton Potential Energy
NASA Astrophysics Data System (ADS)
Friar, J. L.; Payne, G. L.
1995-12-01
An assessment is made of the dominant features contributing to the triton potential energy, with the objective of understanding qualitatively their origins and sensitivities. Relativistic effects, short-range repulsion, and OPEP dominance are discussed. A determination of the importance of various regions of nucleon-nucleon separation is made numerically.
Energies of Screened Coulomb Potentials.
ERIC Educational Resources Information Center
Lai, C. S.
1979-01-01
This article shows that, by applying the Hellman-Feynman theorem alone to screened Coulomb potentials, the first four coefficients in the energy series in powers of the perturbation parameter can be obtained from the unperturbed Coulomb system. (Author/HM)
Potential energy savings from aquifer thermal energy storage
Anderson, M.R.; Weijo, R.O.
1988-07-01
Pacific Northwest Laboratory researchers developed an aggregate-level model to estimate the short- and long-term potential energy savings from using aquifer thermal storage (ATES) in the United States. The objectives of this effort were to (1) develop a basis from which to recommend whether heat or chill ATES should receive future research focus and (2) determine which market sector (residential, commercial, or industrial) offers the largest potential energy savings from ATES. Information was collected on the proportion of US land area suitable for ATES applications. The economic feasibility of ATES applications was then evaluated. The potential energy savings from ATES applications was calculated. Characteristic energy use in the residential, commercial, and industrial sectors was examined, as was the relationship between waste heat production and consumption by industrial end-users. These analyses provided the basis for two main conclusions: heat ATES applications offer higher potential for energy savings than do chill ATES applications; and the industrial sector can achieve the highest potential energy savings for the large consumption markets. Based on these findings, it is recommended that future ATES research and development efforts be directed toward heat ATES applications in the industrial sector. 11 refs., 6 figs., 9 tabs.
An inversion technique for the calculation of embedding potentials
NASA Astrophysics Data System (ADS)
Roncero, O.; de Lara-Castells, M. P.; Villarreal, P.; Flores, F.; Ortega, J.; Paniagua, M.; Aguado, A.
2008-11-01
A new embedding method to include local correlation in large systems is proposed. In this method the density of the whole system, calculated via density functional theory approaches, is partitioned in two pieces, one corresponding to the subsystem of interest and the rest to the environment. In the second step, an embedding potential is obtained iteratively using as a driving force the self-repulsion due to the density difference, in a similar form as proposed by Zhao et al. [Phys. Rev. A 50, 2138 (1994)], to obtain the "exact" exchange-correlation functional. Such potential is added to the Fock equation to build the localized molecular orbitals which are further used to include the local electronic correlation in the subsystem of interest. This method is an alternative to the previous DFT-based embedding methods first proposed by Wesolowski and Washell [J. Phys. Chem. 97, 8050 (1993)] and after enhanced by Govind et al. [J. Chem. Phys. 110, 7677 (1999)] and adapted to metal extended systems, which use density functionals to describe the kinetic energy contribution to the embedding potential, whose precise form has been largely treated in the literature and its crucial role is discussed here. The method is applied to hydrogen chains and its van der Waals interaction with H2. The results obtained are in very good agreement with exact calculations performed on the whole system, which demonstrates that the method proposed is a very promising route to introduce correlation in large systems.
Improved initial guess for minimum energy path calculations
Smidstrup, Søren; Pedersen, Andreas; Stokbro, Kurt
2014-06-07
A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.
California Industrial Energy Efficiency Potential
Coito, Fred; Worrell, Ernst; Price, Lynn; Masanet, Eric; RafaelFriedmann; Rufo, Mike
2005-06-01
This paper presents an overview of the modeling approach andhighlights key findings of a California industrial energy efficiencypotential study. In addition to providing estimates of technical andeconomic potential, the study examines achievable program potential undervarious program-funding scenarios. The focus is on electricity andnatural gas savings for manufacturing in the service territories ofCalifornia's investor-owned utilities (IOUs). The assessment is conductedby industry type and by end use. Both crosscutting technologies andindustry-specific process measures are examined. Measure penetration intothe marketplace is modeled as a function of customer awareness, measurecost effectiveness, and perceived market barriers. Data for the studycomes from a variety of sources, including: utility billing records, theEnergy Information Association (EIA) Manufacturing Energy ConsumptionSurvey (MECS), state-sponsored avoided cost studies, energy efficiencyprogram filings, and technology savings and cost data developed throughLawrence Berkeley National Laboratory (LBNL). The study identifies 1,706GWh and 47 Mth (million therms) per year of achievable potential over thenext twelve years under recent levels of program expenditures, accountingfor 5.2 percent of industrial electricity consumption and 1.3 percent ofindustrial natural gas consumption. These estimates grow to 2,748 GWh and192 Mth per year if all cost-effective and achievable opportunities arepursued. Key industrial electricity end uses, in terms of energy savingspotential, include compressed air and pumping systems that combine toaccount for about half of the total achievable potential estimates. Fornatural gas, savings are concentrated in the boiler and process heatingend uses, accounting for over 99 percent to total achievablepotential.
NASA Astrophysics Data System (ADS)
Tan, Rui Shan; Zhai, Huan Chen; Yan, Wei; Gao, Feng; Lin, Shi Ying
2017-04-01
A new ab initio potential energy surface (PES) for the ground state of Li + HCl reactive system has been constructed by three-dimensional cubic spline interpolation of 36 654 ab initio points computed at the MRCI+Q/aug-cc-pV5Z level of theory. The title reaction is found to be exothermic by 5.63 kcal/mol (9 kcal/mol with zero point energy corrections), which is very close to the experimental data. The barrier height, which is 2.99 kcal/mol (0.93 kcal/mol for the vibrationally adiabatic barrier height), and the depth of van der Waals minimum located near the entrance channel are also in excellent agreement with the experimental findings. This study also identified two more van der Waals minima. The integral cross sections, rate constants, and their dependence on initial rotational states are calculated using an exact quantum wave packet method on the new PES. They are also in excellent agreement with the experimental measurements.
Quantum Monte Carlo calculations of the dimerization energy of borane.
Fracchia, Francesco; Bressanini, Dario; Morosi, Gabriele
2011-09-07
Accurate thermodynamic data are required to improve the performance of chemical hydrides that are potential hydrogen storage materials. Boron compounds are among the most interesting candidates. However, different experimental measurements of the borane dimerization energy resulted in a rather wide range (-34.3 to -39.1) ± 2 kcal/mol. Diffusion Monte Carlo (DMC) simulations usually recover more than 95% of the correlation energy, so energy differences rely less on error cancellation than other methods. DMC energies of BH(3), B(2)H(6), BH(3)CO, CO, and BH(2)(+) allowed us to predict the borane dimerization energy, both via the direct process and indirect processes such as the dissociation of BH(3)CO. Our D(e) = -43.12(8) kcal/mol, corrected for the zero point energy evaluated by considering the anharmonic contributions, results in a borane dimerization energy of -36.59(8) kcal/mol. The process via the dissociation of BH(3)CO gives -34.5(2) kcal/mol. Overall, our values suggest a slightly less D(e) than the most recent W4 estimate D(e) = -44.47 kcal/mol [A. Karton and J. M. L. Martin, J. Phys. Chem. A 111, 5936 (2007)]. Our results show that reliable thermochemical data for boranes can be predicted by fixed node (FN)-DMC calculations.
Theoretical studies of potential energy surfaces
Harding, L.B.
1993-12-01
The goal of this program is to calculate accurate potential energy surfaces (PES) for both reactive and nonreactive systems. To do this the electronic Schrodinger equation must be solved. Our approach to this problem starts with multiconfiguration self-consistent field (MCSCF) reference wavefunctions. These reference wavefunctions are designed to be sufficiently flexible to accurately describe changes in electronic structure over a broad range of geometries. Electron correlation effects are included via multireference, singles and doubles configuration interaction (MRSDCI) calculations. With this approach, the authors are able to provide useful predictions of the energetics for a broad range of systems.
Examining the Potential of Renewable Energy
Not Available
2006-09-01
This outreach document goes to potential partners for NREL's Renewable Energy Potential Initiative, which will explore the long-term potential of Renewable Energy to meet a substantial share of U.S. energy needs.
Potential Energy Surfaces and Dynamics of High Energy Species
2009-04-13
such calculations with dynamics and condensed phase models, and (b) apply these methods to design and evaluate potentially new high energy species. The...IBM SP2 at the Maui High Performance Computation Center, the heat of formation for 1 is predicted to be 456.8 kcallmol. This translates to an l sp...which numerical derivatives become trivially parallel in a coarse-grained sense by having each function evaluation performed on a different node. If
Calculating free energies of organic molecules on insulating substrates.
Gaberle, Julian; Gao, David Z; Shluger, Alexander L
2017-01-01
The challenges and limitations in calculating free energies and entropies of adsorption and interaction of organic molecules on an insulating substrate are discussed. The adhesion of 1,3,5-tri(4'-cyano-[1,1'-biphenyl]-4-yl)benzene (TCB) and 1,4-bis(4-cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules to step edges on the KCl(001) surface and the formation of molecular dimers were studied using classical molecular dynamics. Both molecules contain the same anchoring groups and benzene ring structures, yet differ in their flexibility. Therefore, the entropic contributions to their free energy differ, which affects surface processes. Using potential of mean force and thermodynamic integration techniques, free energy profiles and entropy changes were calculated for step adhesion and dimer formation of these molecules. However, converging these calculations is nontrivial and comes at large computational cost. We illustrate the difficulties as well as the possibilities of applying these methods towards understanding dynamic processes of organic molecules on insulating substrates.
Non-Equilibrium Properties from Equilibrium Free Energy Calculations
NASA Technical Reports Server (NTRS)
Pohorille, Andrew; Wilson, Michael A.
2012-01-01
Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.
The potential of renewable energy
Not Available
1990-03-01
On June 27 and 28, 1989, the US Department of Energy (DOE) national laboratories were convened to discuss plans for the development of a National Energy Strategy (NES) and, in particular, the analytic needs in support of NES that could be addressed by the laboratories. As a result of that meeting, interlaboratory teams were formed to produce analytic white papers on key topics, and a lead laboratory was designated for each core laboratory team. The broad-ranging renewables assignment is summarized by the following issue statement from the Office of Policy, Planning and Analysis: to what extent can renewable energy technologies contribute to diversifying sources of energy supply What are the major barriers to greater renewable energy use and what is the potential timing of widespread commercialization for various categories of applications This report presents the results of the intensive activity initiated by the June 1989 meeting to produce a white paper on renewable energy. Scores of scientists, analysts, and engineers in the five core laboratories gave generously of their time over the past eight months to produce this document. Their generous, constructive efforts are hereby gratefully acknowledged. 126 refs., 44 figs., 32 tabs.
Calculating Free Energy Changes in Continuum Solvation Models
Ho, Junming; Ertem, Mehmed Z.
2016-02-27
We recently showed for a large dataset of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pKa calculations,more » as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol-1 and 25 kJ mol-1 respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.« less
Calculating Free Energy Changes in Continuum Solvation Models
Ho, Junming; Ertem, Mehmed Z.
2016-02-27
We recently showed for a large dataset of pK_{a}s and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents (Phys. Chem. Chem. Phys. 2015, 17, 2859). In this paper, we significantly expand the scope of our study to examine the suitability of this approach for the calculation of general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMDM062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems and reaction types. This includes cluster-continuum schemes for pK_{a} calculations, as well as various neutral, radical and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and bimolecular SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar – the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 kJ mol^{-1} and 25 kJ mol^{-1} respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment. The results indicate that when appropriate combinations of electronic structure methods are employed, the direct approach provides a reliable alternative to the thermodynamic cycle calculations of solution phase kinetics and thermodynamics across a broad range of organic reactions.
Jia, Xiangyu; Wang, Meiting; Shao, Yihan; König, Gerhard; Brooks, Bernard R; Zhang, John Z H; Mei, Ye
2016-02-09
In this work, the solvation free energies of 20 organic molecules from the 4th Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL4) have been calculated. The sampling of phase space is carried out at a molecular mechanical level, and the associated free energy changes are estimated using the Bennett Acceptance Ratio (BAR). Then the quantum mechanical (QM) corrections are computed through the indirect Non-Boltzmann Bennett's acceptance ratio (NBB) or the thermodynamics perturbation (TP) method. We show that BAR+TP gives a minimum analytic variance for the calculated solvation free energy at the Gaussian limit and performs slightly better than NBB in practice. Furthermore, the expense of the QM calculations in TP is only half of that in NBB. We also show that defining the biasing potential as the difference of the solute-solvent interaction energy, instead of the total energy, can converge the calculated solvation free energies much faster but possibly to different values. Based on the experimental solvation free energies which have been published before, it is discovered in this study that BLYP yields better results than MP2 and some other later functionals such as B3LYP, M06-2X, and ωB97X-D.
Computer programs for calculating potential flow in propulsion system inlets
NASA Technical Reports Server (NTRS)
Stockman, N. O.; Button, S. L.
1975-01-01
Calculational procedure evolved in process of designing inlets. Douglas axisymmetric potential flow program called EOD calculates incompressible potential flow about arbitrary bodies. Program SCIRCL generates input for EOD from inlet components. Program COMBYN takes basic solutions output by EOD and combines them into solutions of interest and applied compressibility correction.
Edge energies : atomistic calculations of a continuum quantity.
Hamilton, John C.
2005-06-01
Controlling the properties of self-assembled nanostructures requires controlling their shape. Size-dependent shape transitions, frequently observed at nanolength scales, are commonly attributed to edge energy effects. To rigorously test such theories against experiment, quantitative atomistic calculations of edge energies are essential, yet none exist. I describe a fundamental ambiguity in the atomistic definition of edge energies, propose a definition based on equimolar dividing surfaces, and present an atomistic calculation of edge energies for Pd clusters.
Computed potential energy surfaces for chemical reactions
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1988-01-01
The minimum energy path for the addition of a hydrogen atom to N2 is characterized in CASSCF/CCI calculations using the (4s3p2d1f/3s2p1d) basis set, with additional single point calculations at the stationary points of the potential energy surface using the (5s4p3d2f/4s3p2d) basis set. These calculations represent the most extensive set of ab initio calculations completed to date, yielding a zero point corrected barrier for HN2 dissociation of approx. 8.5 kcal mol/1. The lifetime of the HN2 species is estimated from the calculated geometries and energetics using both conventional Transition State Theory and a method which utilizes an Eckart barrier to compute one dimensional quantum mechanical tunneling effects. It is concluded that the lifetime of the HN2 species is very short, greatly limiting its role in both termolecular recombination reactions and combustion processes.
Diuretic potential of energy drinks.
Riesenhuber, A; Boehm, M; Posch, M; Aufricht, C
2006-07-01
Recent literature suggests that both caffeine and taurine can induce diuresis and natriuresis in rat and man. Although they act via different cellular mechanisms, their diuretic actions might be additive. This is of considerable interest, as several commercially available energy drinks contain both substances. In this study we examined the possible diuretic effects of caffeine and taurine in a cross-over-design in which 12 healthy male volunteers received each of 4 different test drinks (750 ml of energy drink containing 240 mg caffeine and 3 g taurine, the three other test drinks either lacked caffeine, taurine or both) after restraining from fluids for 12 h. Mixed model analyses demonstrated that urinary output and natriuresis were significantly increased by caffeine (mean differences 243 ml and 27 mmol; both p < 0.001) and that there were no such effects of taurine (mean differences 59 ml and -4 mmol). Additionally, urinary osmolarity at baseline was significantly related to the urinary output (p < 0.001). Urine osmolarity values at baseline and in the 6 h urine collection did not differ significantly between treatments. Taken together, our study demonstrates that diuretic and natriuretic effects of the tested energy drink were largely mediated by caffeine. Taurine played no significant role in the fluid balance in moderately dehydrated healthy young consumers. Consequently, the diuretic potential of energy drinks will not differ significantly from other caffeine containing beverages.
Zhou, Yong; Zhang, Dong H.
2014-11-21
Eight-dimensional (8D) transition-state wave packet simulations have been performed on two latest potential energy surfaces (PES), the Zhou-Fu-Wang-Collins-Zhang (ZFWCZ) PES [Y. Zhou, B. Fu, C. Wang, M. A. Collins, and D. H. Zhang, J. Chem. Phys. 134, 064323 (2011)] and the Xu-Chen-Zhang (XCZ)-neural networks (NN) PES [X. Xu, J. Chen, and D. H. Zhang, Chin. J. Chem. Phys. 27, 373 (2014)]. Reaction rate constants for both the H+CH{sub 4} reaction and the H{sub 2}+CH{sub 3} reaction are calculated. Simulations of the H+CH{sub 4} reaction based on the XCZ-NN PES show that the ZFWCZ PES predicts rate constants with reasonable high accuracy for low temperatures while leads to slightly lower results for high temperatures, in line with the distribution of interpolation error associated with the ZFWCZ PES. The 8D H+CH{sub 4} rate constants derived on the ZFWCZ PES compare well with full-dimensional 12D results based on the equivalent m-ZFWCZ PES, with a maximum relative difference of no more than 20%. Additionally, very good agreement is shown by comparing the 8D XCZ-NN rate constants with the 12D results obtained on the ZFWCZ-WM PES, after considering the difference in static barrier height between these two PESs. The reaction rate constants calculated for the H{sub 2}+CH{sub 3} reaction are found to be in good consistency with experimental observations.
Gimondi, Ilaria; Cavallotti, Carlo; Vanuzzo, Gianmarco; Balucani, Nadia; Casavecchia, Piergiorgio
2016-07-14
The mechanism of the O((3)P) + CH3CCH reaction was investigated using a combined experimental/theoretical approach. Experimentally the reaction dynamics was studied using crossed molecular beams (CMB) with mass-spectrometric detection and time-of-flight analysis at 9.2 kcal/mol collision energy. Theoretically master equation (ME) simulations were performed on a potential energy surface (PES) determined using high-level ab initio electronic structure calculations. In this paper (II) the theoretical results are described and compared with experiments, while in paper (I) are reported and discussed the results of the experimental study. The PES was investigated by determining structures and vibrational frequencies of wells and transition states at the CASPT2/aug-cc-pVTZ level using a minimal active space. Energies were then determined at the CASPT2 level increasing systematically the active space and at the CCSD(T) level extrapolating to the complete basis set limit. Two separate portions of the triplet PES were investigated, as O((3)P) can add either on the terminal or the central carbon of the unsaturated propyne bond. Minimum energy crossing points (MECPs) between the triplet and singlet PESs were searched at the CASPT2 level. The calculated spin-orbit coupling constants between the T1 and S0 electronic surfaces were ∼25 cm(-1) for both PESs. The portions of the singlet PES that can be accessed from the MECPs were investigated at the same level of theory. The system reactivity was predicted integrating stochastically the one-dimensional ME using Rice-Ramsperger-Kassel-Marcus theory to determine rate constants on the full T1/S0 PESs, accounting explicitly for intersystem crossing (ISC) using the Landau-Zener model. The computational results are compared both with the branching ratios (BRs) determined experimentally in the companion paper (I) and with those estimated in a recent kinetic study at 298 K. The ME results allow to interpret the main system reactivity: CH
Spectral element discontinuous Galerkin simulations for wake potential calculations : NEKCEM.
Min, M.; Fischer, P. F.; Chae, Y.-C.
2008-01-01
In this paper we present high-order spectral element discontinuous Galerkin simulations for wake field and wake potential calculations. Numerical discretizations are based on body-conforming hexagonal meshes on Gauss-Lobatto-Legendre grids. We demonstrate wake potential profiles for cylindrically symmetric cavity structures in 3D, including the cases for linear and quadratic transitions between two cross sections. Wake potential calculations are carried out on 2D surfaces for various bunch sizes.
Ab initio calculation of the potential bubble nucleus 34Si
NASA Astrophysics Data System (ADS)
Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.
2017-03-01
Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to
Calculation of energy deposition distributions for simple geometries
NASA Technical Reports Server (NTRS)
Watts, J. W., Jr.
1973-01-01
When high-energy charged particles pass through a thin detector, the ionization energy loss in that detector is subject to fluctuations or straggling which must be considered in interpreting the data. Under many conditions, which depend upon the charge and energy of the incident particle and the detector geometry, the ionization energy lost by the particle is significantly different from the energy deposited in the detector. This problem divides naturally into a calculation of the energy loss that results in excitation and low-energy secondary electrons which do not travel far from their production points, and a calculation of energy loss that results in high-energy secondary electrons which can escape from the detector. The first calculation is performed using a modification of the Vavilov energy loss distribution. A cutoff energy is introduced above which all electrons are ignored and energy transferred to low energy particles is assumed to be equivalent to the energy deposited by them. For the second calculation, the trajectory of the primary particle is considered as a source of secondary high-energy electrons. The electrons from this source are transported using Monte Carlo techniques and multiple scattering theory, and the energy deposited by them in the detector is calculated. The results of the two calculations are then combined to predict the energy deposition distribution. The results of these calculations are used to predict the charge resolution of parallel-plate pulse ionization chambers that are being designed to measure the charge spectrum of heavy nuclei in the galactic cosmic-ray flux.
NASA Astrophysics Data System (ADS)
Bird, Rebecca A.; Read, Mark S. D.
2017-02-01
A new potential has been derived for ceria and used to calculate its lattice and defect properties. The Ce4+ ⋯O2- potential is obtained via a combination of empirical fitting to crystal structural data and parametric fitting to additional physical properties, while the O2- ⋯O2- potential is transferred from earlier publications on UO2 and PuO2 . The overall potential is subsequently verified and validated by calculation of elastic and dielectric constants, whose values agree favourably with those measured experimentally. The potential is then employed to calculate intrinsic defect formation energies and predict the most favourable type of intrinsic disorder.
Potential energy surface of cyclooctatetraene
NASA Astrophysics Data System (ADS)
Andrés, José L.; Castaño, Obis; Morreale, Antonio; Palmeiro, Raul; Gomperts, Roberto
1998-01-01
We present a theoretical study of the cyclooctatetraene (COT) molecule. Seven COT structures are located on the singlet ground state potential energy surface. Four of them, which present D2d (tub), Cs (bicyclo[4.2.0]octa-2,4,7-triene or BOT), C2h (chair) and D4 (crown) symmetries are stable species, and the other three are transition state structures showing Cs, D4h, and D8h symmetry. We discuss the symmetry of wave functions for these stationary points. Geometries, energies, and harmonic vibrational frequencies of these structures, and energy gaps between singlet-triplet states and low-lying singlets are presented. For the planar D4h and D8h structures, Jahn-Teller and tunneling effects have also been discussed. Ring inversion, bond shifting and valence isomerization reactive channels from the tub COT conformer are discussed from the point of view of the corresponding transition state structures. Where possible, in order to lend support to this theoretical information comparisons with recent transition state spectroscopy data are made.
Computed potential energy surfaces for chemical reactions
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1994-01-01
Quantum mechanical methods have been used to compute potential energy surfaces for chemical reactions. The reactions studied were among those believed to be important to the NASP and HSR programs and included the recombination of two H atoms with several different third bodies; the reactions in the thermal Zeldovich mechanism; the reactions of H atom with O2, N2, and NO; reactions involved in the thermal De-NO(x) process; and the reaction of CH(squared Pi) with N2 (leading to 'prompt NO'). These potential energy surfaces have been used to compute reaction rate constants and rates of unimolecular decomposition. An additional application was the calculation of transport properties of gases using a semiclassical approximation (and in the case of interactions involving hydrogen inclusion of quantum mechanical effects).
Density functional theory for comprehensive orbital energy calculations
NASA Astrophysics Data System (ADS)
Nakata, Ayako; Tsuneda, Takao
2013-08-01
This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.
Density functional theory for comprehensive orbital energy calculations.
Nakata, Ayako; Tsuneda, Takao
2013-08-14
This study reveals the reason core 1s orbital energies and the highest occupied molecular orbital (HOMO) energies of hydrogen and rare gas atoms are underestimated by long-range corrected (LC) density functional theory (DFT), which quantitatively reproduces the HOMO energies of other systems and the lowest unoccupied molecular orbital (LUMO) energies. Applying the pseudospectral regional (PR) self-interaction correction (SIC) drastically improved the underestimated orbital energies in LC-DFT calculations, while maintaining or improving the accuracies in the calculated valence HOMO and LUMO energies. This indicates that the self-interaction error in exchange functionals causes the underestimations of core 1s orbital energies and the HOMO energies of hydrogen and rare gas atoms in LC-DFT calculations. To clarify the reason for the improvement, the fractional occupation dependences of total electronic energies and orbital energies were examined. The calculated results clearly showed that the LC-PR functional gives almost linear dependences of total electronic energies for a slight decrease in the occupation number of core 1s orbitals, although this linear dependence disappears for significant decrease due to the shrinking of exchange self-interaction regions. It was also clarified that the PRSIC hardly affects the occupation number dependences of the total electronic energies and orbital energies for the fractional occupations of HOMOs and LUMOs. As a result, it was concluded that core orbital energies are obtained accurately by combining LC-DFT with PRSIC.
Potential energy surfaces of Polonium isotopes
NASA Astrophysics Data System (ADS)
Nerlo-Pomorska, B.; Pomorski, K.; Schmitt, C.; Bartel, J.
2015-11-01
The evolution of the potential energy landscape is analysed in detail for ten even-even polonium isotopes in the mass range 188\\lt A\\lt 220 as obtained within the macroscopic-microscopic approach, relying on the Lublin-Strasbourg drop model and the Yukawa-folded single-particle energies for calculating the microscopic shell and pairing corrections. A variant of the modified Funny-Hills nuclear shape parametrization is used to efficiently map possible fission paths. The approach explains the main features of the fragment partition as measured in low-energy fission along the polonium chain. The latter lies in a transitional region of the nuclear chart, and will be essential to consistently understand the evolution of fission properties from neutron-deficient mercury to heavy actinides. The ability of our method to predict fission observables over such an extended region looks promising.
Calculation of the energy levels of lithium-like ions
NASA Astrophysics Data System (ADS)
Nadykto, B. A.
An attempt is made to develop a straightforward and sufficiently accurate method for calculating the energies of complex ion states. The method is based on Bohr's computational model and Sommerfeld's model in relativistic form (for circular orbits only). The method proposed here makes it possible to calculate excited ion states having different atomic and quantum numbers. A similar method can be used for calculating the energies of ion states with the number of electrons exceeding three.
Investigation of Multipole Electrostatics in Hydration Free Energy Calculations
Shi, Yue; Wu, Chuanjie; Ponder, Jay W.; Ren, Pengyu
2010-01-01
Hydration free energy (HFE) is generally used for evaluating molecular solubility, which is an important property for pharmaceutical and chemical engineering processes. Accurately predicting HFE is also recognized as one fundamental capability of molecular mechanics force field. Here we present a systematic investigation on HFE calculations with AMOEBA polarizable force field at various parameterization and simulation conditions. The HFEs of seven small organic molecules have been obtained alchemically using the Bennett Acceptance Ratio (BAR) method. We have compared two approaches to derive the atomic multipoles from quantum mechanical (QM) calculations: one directly from the new distributed multipole analysis (DMA) and the other involving fitting to the electrostatic potential around the molecules. Wave functions solved at the MP2 level with four basis sets (6-311G*, 6-311++G(2d,2p), cc-pVTZ, and aug-cc-pVTZ) are used to derive the atomic multipoles. HFEs from all four basis sets show a reasonable agreement with experimental data (root mean square error 0.63 kcal/mol for aug-ccpVTZ). We conclude that aug-cc-pVTZ gives the best performance when used with AMOEBA, and 6-311++G(2d,2p) is comparable but more efficient for larger systems. The results suggest that the inclusion of diffuse basis functions is important for capturing intermolecular interactions. The effect of long-range correction to van der Waals interaction on the hydration free energies is about 0.1 kcal/mol when the cutoff is 12Å, and increases linearly with the number of atoms in the solute/ligand. In addition, we also discussed the results from a hybrid approach that combines polarizable solute with fixed-charge water in the hydration free energy calculation. PMID:20925089
Calculation of relativistic nucleon-nucleon potentials in three dimensions
NASA Astrophysics Data System (ADS)
Hadizadeh, M. R.; Radin, M.
2017-02-01
In this paper, we have applied a three-dimensional approach for the calculation of the relativistic nucleon-nucleon potential. The quadratic operator relation between the non-relativistic and the relativistic nucleon-nucleon interactions is formulated as a function of relative two-nucleon momentum vectors, which leads to a three-dimensional integral equation. The integral equation is solved by the iteration method, and the matrix elements of the relativistic potential are calculated from non-relativistic ones. The spin-independent Malfliet-Tjon potential is employed in the numerical calculations, and the numerical tests indicate that the two-nucleon observables calculated by the relativistic potential are preserved with high accuracy.
The Calculation of the Electrostatic Potential of Infinite Charge Distributions
ERIC Educational Resources Information Center
Redzic, Dragan V.
2012-01-01
We discuss some interesting aspects in the calculation of the electrostatic potential of charge distributions extending to infinity. The presentation is suitable for the advanced undergraduate level. (Contains 3 footnotes.)
The Calculation of the Electrostatic Potential of Infinite Charge Distributions
ERIC Educational Resources Information Center
Redzic, Dragan V.
2012-01-01
We discuss some interesting aspects in the calculation of the electrostatic potential of charge distributions extending to infinity. The presentation is suitable for the advanced undergraduate level. (Contains 3 footnotes.)
Energy deposition calculated by PHITS code in Pb spallation target
NASA Astrophysics Data System (ADS)
Yu, Quanzhi
2016-01-01
Energy deposition in a Pb spallation target irradiated by high energetic protons was calculated by PHITS2.52 code. The validation of the energy deposition and neutron production calculated by PHITS code was performed. Results show good agreements between the simulation results and the experimental data. Detailed comparison shows that for the total energy deposition, PHITS simulation result was about 15% overestimation than that of the experimental data. For the energy deposition along the length of the Pb target, the discrepancy mainly presented at the front part of the Pb target. Calculation indicates that most of the energy deposition comes from the ionizations of the primary protons and the produced secondary particles. With the event generator mode of PHITS, the deposit energy distribution for the particles and the light nulclei is presented for the first time. It indicates that the primary protons with energy more than 100 MeV are the most contributors to the total energy deposition. The energy depositions peaking at 10 MeV and 0.1 MeV, are mainly caused by the electrons, pions, d, t, 3He and also α particles during the cascade process and the evaporation process, respectively. The energy deposition density caused by different proton beam profiles are also calculated and compared. Such calculation and analyses are much helpful for better understanding the physical mechanism of energy deposition in the spallation target, and greatly useful for the thermal hydraulic design of the spallation target.
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2013 CFR
2013-04-01
... 18 Conservation of Power and Water Resources 1 2013-04-01 2013-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2014 CFR
2014-04-01
... 18 Conservation of Power and Water Resources 1 2014-04-01 2014-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2010 CFR
2010-04-01
... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2011 CFR
2011-04-01
... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
18 CFR 11.13 - Energy gains calculations.
Code of Federal Regulations, 2012 CFR
2012-04-01
... 18 Conservation of Power and Water Resources 1 2012-04-01 2012-04-01 false Energy gains calculations. 11.13 Section 11.13 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY COMMISSION, DEPARTMENT OF ENERGY REGULATIONS UNDER THE FEDERAL POWER ACT ANNUAL CHARGES UNDER PART I OF...
Semiclassical energy levels and the corresponding potentials in nonhydrogenic ions
NASA Astrophysics Data System (ADS)
Pankratov, P.; Meyer-Ter-Vehn, J.
1992-11-01
A semiclassical expression is derived for the potential seen by an nl-shell electron in a nonhydrogenic ion. Corresponding energies Enl are compared with experimental values and with results of self-consistent-field calculations.
Convective Available Potential Energy of World Ocean
NASA Astrophysics Data System (ADS)
Su, Z.; Ingersoll, A. P.; Thompson, A. F.
2012-12-01
Here, for the first time, we propose the concept of Ocean Convective Available Potential Energy (OCAPE), which is the maximum kinetic energy (KE) per unit seawater mass achievable by ocean convection. OCAPE occurs through a different mechanism from atmospheric CAPE, and involves the interplay of temperature and salinity on the equation of state of seawater. The thermobaric effect, which arises because the thermal coefficient of expansion increases with depth, is an important ingredient of OCAPE. We develop an accurate algorithm to calculate the OCAPE for a given temperature and salinity profile. We then validate our calculation of OCAPE by comparing it with the conversion of OCAPE to KE in a 2-D numerical model. We propose that OCAPE is an important energy source of ocean deep convection and contributes to deep water formation. OCAPE, like Atmospheric CAPE, can help predict deep convection and may also provide a useful constraint for modelling deep convection in ocean GCMs. We plot the global distribution of OCAPE using data from the World Ocean Atlas 2009 (WOA09) and see many important features. These include large values of OCAPE in the Labrador, Greenland, Weddell and Mediterranean Seas, which are consistent with our present observations and understanding, but also identify some new features like the OCAPE pattern in the Antarctic Circumpolar Current (ACC). We propose that the diagnosis of OCAPE can improve our understanding of global patterns of ocean convection and deep water formation as well as ocean stratification, the meridional overturning circulation and mixed layer processes. The background of this work is briefly introduced as below. Open-ocean deep convection can significantly modify water properties both at the ocean surface and throughout the water column (Gordon 1982). Open-ocean convection is also an important mechanism for Ocean Deep Water formation and the transport of heat, freshwater and nutrient (Marshall and Schott 1999). Open
Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton
2013-08-15
Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.
Guidelines for the analysis of free energy calculations
NASA Astrophysics Data System (ADS)
Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
2015-05-01
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, http://arxiv.org/abs/alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.
Guidelines for the analysis of free energy calculations.
Klimovich, Pavel V; Shirts, Michael R; Mobley, David L
2015-05-01
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.
Guidelines for the analysis of free energy calculations
Klimovich, Pavel V.; Shirts, Michael R.; Mobley, David L.
2015-01-01
Free energy calculations based on molecular dynamics (MD) simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical–analysis.py, freely available on GitHub at https://github.com/choderalab/pymbar–examples, that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope these tools and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations. PMID:25808134
Advancing Drug Discovery through Enhanced Free Energy Calculations.
Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A
2017-07-18
, is potentially transformative in enabling hard to drug targets to be attacked, and in facilitating the development of superior compounds, in various dimensions, for a wide range of targets. More effective integration of FEP+ calculations into the drug discovery process will ensure that the results are deployed in an optimal fashion for yielding the best possible compounds entering the clinic; this is where the greatest payoff is in the exploitation of computer driven design capabilities. A key conclusion from the work described is the surprisingly robust and accurate results that are attainable within the conventional classical simulation, fixed charge paradigm. No doubt there are individual cases that would benefit from a more sophisticated energy model or dynamical treatment, and properties other than protein-ligand binding energies may be more sensitive to these approximations. We conclude that an inflection point in the ability of MD simulations to impact drug discovery has now been attained, due to the confluence of hardware and software development along with the formulation of "good enough" theoretical methods and models.
Wadt, W.R.; Hay, P.J.
1985-01-01
A consistent set of ab initio effective core potentials (ECP) has been generated for the main group elements from Na to Bi using the procedure originally developed by Kahn. The ECP's are derived from all-electron numerical Hartree--Fock atomic wave functions and fit to analytical representations for use in molecular calculations. For Rb to Bi the ECP's are generated from the relativistic Hartree--Fock atomic wave functions of Cowan which incorporate the Darwin and mass--velocity terms. Energy-optimized valence basis sets of (3s3p) primitive Gaussians are presented for use with the ECP's. Comparisons between all-electron and valence-electron ECP calculations are presented for NaF, NaCl, Cl/sub 2/, Cl/sub 2//sup -/, Br/sub 2/, Br/sub 2//sup -/, and Xe/sub 2//sup +/. The results show that the average errors introduced by the ECP's are generally only a few percent.
Calculation of electron binding energies of {Na}_{55}^- clusters
NASA Astrophysics Data System (ADS)
Melikyan, Armen; Minassian, Hayk; Grigoryan, Valeri G.; Springborg, Michael
2016-07-01
Within the frame of the one-electron approximation, we calculate the electron binding energies of the {Na}_{55}^- cluster which allows for the identification of the icosahedral structure of the cluster through comparison with experimental photoelectron spectroscopy data. The surface of the icosahedral cluster is represented as a slightly deformed spherical surface, and the corresponding splitting of the energy levels caused by this symmetry reduction is calculated. Subsequently, we demonstrate that the calculated energies of photoelectrons agree very well with the experimental values. This gives an unambiguous demonstration of the role of the cluster structure in photoelectron spectra, whereas electronic shell filling effects are less important.
Sensitivity of methods for calculating energy expenditure by use of doubly labeled water
Seale, J.; Miles, C.; Bodwell, C.E.
1989-02-01
Attempts to estimate human energy expenditure by use of doubly labeled water have produced three methods currently used for calculating carbon dioxide production from isotope disappearance data: (1) the two-point method, (2) the regression method, and (3) the integration method. An ideal data set was used to determine the error produced in the calculated energy expenditure for each method when specific variables were perturbed. The analysis indicates that some of the calculation methods are more susceptible to perturbations in certain variables than others. Results from an experiment on one adult human subject are used to illustrate the potential for error in actual data. Samples of second void urine, 24-h urine, and breath collected every other day for 21 days are used to calculate the average daily energy expenditure by three calculation methods. The difference between calculated energy expenditure and metabolizable energy on a weight-maintenance diet is used to estimate the error associated with the doubly labeled water method.
NASA Astrophysics Data System (ADS)
McCoy, Rhonda Patrice
4,5-Diazafluoren-9-one (DAFO) is an aromatic ketone synthesized by oxidizing 1,10-phenanthroline with potassium permanganate. In this present study, the Raman spectra of DAFO in the solid and solution states were recorded in the 100-2000 cm-1 spectral region using 1064, 633, 532, and 514 nm excitation sources. A normal mode analysis of DAFO was performed using density functional theory; the BLYP and B3LYP functionals, each with the 6-31G(d) and 6-311(d) basis sets were employed. The fundamental modes on the Raman spectrum of DAFO were assigned with the appropriate symmetry element using the BLYP functional and 6-31G(d) basis set. The vibrational modes were described and quantified by potential energy distribution calculations. The Raman frequencies for the solid and solution spectra were compared; the observed frequency shifts are attributed to hydrogen bonding or dipole-dipole interactions occurring between the solvent and DAFO ligand. To further assess solute-solvent interactions the UV-vis spectra of DAFO was obtained in hydrogen bonding, polar aprotic, and non-polar solvents. The fine structure of the band observed at lambda max becomes more resolved as solvent polarity decreases, therefore confirming solute-solvent interactions in polar solvents. A silver complex of DAFO was synthesized with the intent of understanding how coordination affected the Raman frequencies. The bands assigned to pyridine ring bending, nu(C=N), and nu(C=O) were shifted because of coordination. These shifts have been attributed to the molecule being perturbed because of coordination. Therefore, the Ag-DAFO complex was analyzed by X-Ray diffraction and the molecular geometries of the free and coordinated ligand were compared. The resolved crystalline structure revealed the silver ion coordinated DAFO using the lone pairs of electrons from the nitrogens in the pyridine ring. Analysis of the molecular geometry revealed the C=O bond increases in double bond character and the C5-C14 bond
Nonintuitive Diabatic Potential Energy Surfaces for Thioanisole.
Li, Shaohong L; Xu, Xuefei; Hoyer, Chad E; Truhlar, Donald G
2015-09-03
Diabatization of potential energy surfaces is a technique that enables convenient molecular dynamics simulations of electronically nonadiabatic processes, but diabatization itself is nonunique and can be inconvenient; the best methods to achieve diabatization are still under study. Here, we present the diabatization of two electronic states of thioanisole in the S-CH3 bond stretching and C-C-S-C torsion two-dimensional nuclear coordinate space containing a conical intersection. We use two systematic methods: the (orbital-dependent) 4-fold way and the (orbital-free) Boys localization diabatization method. These very different methods yield strikingly similar diabatic potential energy surfaces that cross at geometries where the adiabatic surfaces are well separated and do not exhibit avoided crossings, and the contours of the diabatic gap and diabatic coupling are similar for the two methods. The validity of the diabatization is supported by comparing the nonadiabatic couplings calculated from the diabatic matrix elements to those calculated by direct differentiation of the adiabatic states.
Calculating potential fields using microchannel spatial light modulators
NASA Technical Reports Server (NTRS)
Reid, Max B.
1993-01-01
We describe and present experimental results of the optical calculation of potential field maps suitable for mobile robot navigation. The optical computation employs two write modes of a microchannel spatial light modulator (MSLM). In one mode, written patterns expand spatially, and this characteristic is used to create an extended two dimensional function representing the influence of the goal in a robot's workspace. Distinct obstacle patterns are written in a second, non-expanding, mode. A model of the mechanisms determining MSLM write mode characteristics is developed and used to derive the optical calculation time for full potential field maps. Field calculations at a few hertz are possible with current technology, and calculation time vs. map size scales favorably in comparison to digital electronic computation.
Geothermal Energy: Tapping the Potential
ERIC Educational Resources Information Center
Johnson, Bill
2008-01-01
Ground source geothermal energy enables one to tap into the earth's stored renewable energy for heating and cooling facilities. Proper application of ground-source geothermal technology can have a dramatic impact on the efficiency and financial performance of building energy utilization (30%+). At the same time, using this alternative energy…
Algorithms of the Potential Field Calculation in a Three-Dimensional Box
NASA Astrophysics Data System (ADS)
Rudenko, G. V.; Anfinogentov, S. A.
2017-08-01
The potential field inside a three-dimensional box with the normal magnetic field component given on all boundaries needs to be calculated to estimate important quantities related to the magnetic field, such as free energy and relative helicity. In this work we present an analysis of three methods for calculating the potential field inside a three-dimensional box. The accuracy and performance of the methods are tested on artificial models with a priori known solutions.
Computer programs for calculating potential flow in propulsion system inlets
NASA Technical Reports Server (NTRS)
Stockman, N. O.; Button, S. L.
1973-01-01
In the course of designing inlets, particularly for VTOL and STOL propulsion systems, a calculational procedure utilizing three computer programs evolved. The chief program is the Douglas axisymmetric potential flow program called EOD which calculates the incompressible potential flow about arbitrary axisymmetric bodies. The other two programs, original with Lewis, are called SCIRCL AND COMBYN. Program SCIRCL generates input for EOD from various specified analytic shapes for the inlet components. Program COMBYN takes basic solutions output by EOD and combines them into solutions of interest, and applies a compressibility correction.
Chemical potential calculations in dense liquids using metadynamics
NASA Astrophysics Data System (ADS)
Perego, C.; Giberti, F.; Parrinello, M.
2016-10-01
The calculation of chemical potential has traditionally been a challenge in atomistic simulations. One of the most used approaches is Widom's insertion method in which the chemical potential is calculated by periodically attempting to insert an extra particle in the system. In dense systems this method fails since the insertion probability is very low. In this paper we show that in a homogeneous fluid the insertion probability can be increased using metadynamics. We test our method on a supercooled high density binary Lennard-Jones fluid. We find that we can obtain efficiently converged results even when Widom's method fails.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Ab initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Partridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- (mu)E(sub h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(sub 0) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
The Wind Energy Potential of Iceland
NASA Astrophysics Data System (ADS)
Nawri, Nikolai; Nína Petersen, Guðrún; Bjornsson, Halldór; Hahmann, Andrea N.; Jónasson, Kristján; Bay Hasager, Charlotte; Clausen, Niels-Erik
2014-05-01
infrastructure and the power grid, as well as due to the harsh winter climate. However, even in easily accessible regions, wind energy potential in Iceland, as measured by annual average power density, is among the highest in Western Europe. Based on these results, 14 test sites were selected for more detailed analyses using the Wind Atlas Analysis and Application Program (WAsP). These calculations show that a modest wind farm of ten medium size turbines would produce more energy throughout the year than a small hydro power plant, making wind energy a viable additional option.
Green Function Calculation for Full-potential Multiple Scattering Methods
NASA Astrophysics Data System (ADS)
Wang, Yang; Stocks, G. Malcolm; Nicholson, Don
2001-03-01
The Green function in the multiple scattering theory of Korringa(J.Korringa, Physica) 13, 392 (1947)., Kohn and Rostoker(W.Kohn and N.Rostoker, Phys. Rev.) 94, 1111 (1954). provides a very convenient approach to the electronic structure calculation for solids. The Green function was originally developed for muffin-tin potentials(J.S. Faulkner and G.M. Stocks, Phys. Rev.) B 21, 3222 (1980)., but can be generalized to the full potential case in which the one-electron potential associated with each atom is of arbitrary geometric shape. In this talk, we present our numerical techniques for Green function calculation in our newly developed full potential multiple scattering method code. We test the calculated Green function against the analytical expression for the case of three dimensional space filling simple analytic potentials. We show how the surface integral technique is used for the calculation of the single site scattering matrices and irregular solutions. We also discuss the L-convergence properties of the Green function.
Energy restriction and potential energy restriction mimetics.
Nikolai, Sibylle; Pallauf, Kathrin; Huebbe, Patricia; Rimbach, Gerald
2015-12-01
Energy restriction (ER; also known as caloric restriction) is the only nutritional intervention that has repeatedly been shown to increase lifespan in model organisms and may delay ageing in humans. In the present review we discuss current scientific literature on ER and its molecular, metabolic and hormonal effects. Moreover, criteria for the classification of substances that might induce positive ER-like changes without having to reduce energy intake are summarised. Additionally, the putative ER mimetics (ERM) 2-deoxy-d-glucose, metformin, rapamycin, resveratrol, spermidine and lipoic acid and their suggested molecular targets are discussed. While there are reports on these ERM candidates that describe lifespan extension in model organisms, data on longevity-inducing effects in higher organisms such as mice remain controversial or are missing. Furthermore, some of these candidates produce detrimental side effects such as immunosuppression or lactic acidosis, or have not been tested for safety in long-term studies. Up to now, there are no known ERM that could be recommended without limitations for use in humans.
A novel lattice energy calculation technique for simple inorganic crystals
NASA Astrophysics Data System (ADS)
Kaya, Cemal; Kaya, Savaş; Banerjee, Priyabrata
2017-01-01
In this pure theoretical study, a hitherto unexplored equation based on Shannon radii of the ions forming that crystal and chemical hardness of any crystal to calculate the lattice energies of simple inorganic ionic crystals has been presented. To prove the credibility of this equation, the results of the equation have been compared with experimental outcome obtained from Born-Fajans-Haber- cycle which is fundamentally enthalpy-based thermochemical cycle and prevalent theoretical approaches proposed for the calculation of lattice energies of ionic compounds. The results obtained and the comparisons made have demonstrated that the new equation is more useful compared to other theoretical approaches and allows to exceptionally accurate calculation of lattice energies of inorganic ionic crystals without doing any complex calculations.
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.
Calculation of interaction-induced spectra using complex absorbing potentials
Gustafsson, Magnus; Antipov, Sergey V.
2010-10-29
A complex absorbing potential method is implemented for calculation of collision-induced spectra. The scheme provides a way to avoid the integration of the Schroedinger equation to very large separations of the collisional pair. The method is tested by reproducing a previously computed absorption spectrum for H-He at two different temperatures.
On the calculation of absolute macromolecular binding free energies
Luo, Hengbin; Sharp, Kim
2002-01-01
The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B → AB with an association constant KAB is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of KAB is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior. PMID:12149474
Nonperturbative calculation of the London-van der Waals interaction potential
NASA Astrophysics Data System (ADS)
Berman, P. R.; Ford, G. W.; Milonni, P. W.
2014-02-01
The so-called remarkable formula [G. W. Ford, J. T. Lewis, and R. F. O'Connell, Phys. Rev. Lett. 55, 2273 (1985), 10.1103/PhysRevLett.55.2273] for the Helmholtz free energy is applied to the problem of determining the interaction potential to all orders in the coupling strength of a pair of oscillator dipoles interacting through the familiar dipole-dipole interaction of electrodynamics. Simple, straightforward calculations lead to expressions for (1) the London short-range potential, (2) the Casimir-Polder long-range potential, and (3) the potential at high temperature. Explicit results are shown for both the temperature dependence of the interaction potential and its deviation from the weak-coupling limit. It is stressed that the interaction potential is a change in free energy, not the energy; in particular, in the high temperature case, the change of energy is zero.
Performance calculation and simulation system of high energy laser weapon
NASA Astrophysics Data System (ADS)
Wang, Pei; Liu, Min; Su, Yu; Zhang, Ke
2014-12-01
High energy laser weapons are ready for some of today's most challenging military applications. Based on the analysis of the main tactical/technical index and combating process of high energy laser weapon, a performance calculation and simulation system of high energy laser weapon was established. Firstly, the index decomposition and workflow of high energy laser weapon was proposed. The entire system was composed of six parts, including classical target, platform of laser weapon, detect sensor, tracking and pointing control, laser atmosphere propagation and damage assessment module. Then, the index calculation modules were designed. Finally, anti-missile interception simulation was performed. The system can provide reference and basis for the analysis and evaluation of high energy laser weapon efficiency.
Potential of renewable and alternative energy sources
NASA Astrophysics Data System (ADS)
Konovalov, V.; Pogharnitskaya, O.; Rostovshchikova, A.; Matveenko, I.
2015-11-01
The article deals with application potential of clean alternative renewable energy sources. By means of system analysis the forecast for consumption of electrical energy in Tomsk Oblast as well as main energy sources of existing energy system have been studied up to 2018. Engineering potential of renewable and alternative energy sources is evaluated. Besides, ranking in the order of their efficiency descending is performed. It is concluded that Tomsk Oblast has high potential of alternative and renewable energy sources, among which the most promising development perspective is implementation of gasification stations to save fuel consumed by diesel power stations as well as building wind-power plants.
2016-12-01
DECISION SUPPORT TOOL FOR WASTE-TO- ENERGY CALCULATIONS USING ENERGY RETURN ON INVESTMENT by Adam C. Haag December 2016 Thesis Advisor...SUPPORT TOOL FOR WASTE-TO- ENERGY CALCULATIONS USING ENERGY RETURN ON INVESTMENT 5. FUNDING NUMBERS 6. AUTHOR(S) Adam C. Haag 7. PERFORMING...economic viability of sites for waste-to- energy technologies, mirroring the current tool’s capabilities and expanding its use. This tool returns
Towards a standardized setup for surface energy calculations
NASA Astrophysics Data System (ADS)
Kaminski, Jakub W.; Kratzer, Peter; Ratsch, Christian
2017-02-01
High-throughput design of new materials with desired electronic properties, based on screening of large collections of crystal structures organized in the from of libraries or databases require fast, widely applicable, consistent and unsupervised methods to calculate the property of interest. In this work we present an approach for the calculation of surface energies of two-dimensional periodic crystal lattices which meets all these requirements. For materials slabs which are terminated with two identical surfaces, the task of calculating the surface energy is trivial. More problematic are the cases where both terminating surfaces are different, as there is no single established method allowing for equal treatment of a wide range of surface morphologies and orientations. Our proposed approach addresses this problem. It relies on appropriately chosen capping atoms, whose bonding energy contributions are used to approximate the total energy of the surface. The choice of the capping atoms is governed by a set of simple guidelines that are applicable for surfaces with different terminations. We present the results for different semiconductor materials and show that our approach leads to surface energies with errors that are below 10%, and that are as low as 2% in many cases. We show that hydrogen is not always the best choice for a capping atom if accurate surface energies are the target of the calculations.
Triton Binding Energy of Kharkov Potential
NASA Astrophysics Data System (ADS)
Kamada, H.; Shebeko, O.; Arslanaliev, A.
2017-03-01
The Kharkov potential is a recent field theoretical model of nucleon-nucleon (NN) interaction that has been built up in the framework of the instant form of relativistic dynamics starting with the total Hamiltonian of interacting meson and nucleon fields and using the method of unitary clothing transformations. The latter connect the representation of "bare" particles and the representation of "clothed" particles, i.e., the particles with physical properties. Unlike many available NN potentials each of which is the kernel of the corresponding nonrelativistic Lippmann-Schwinger (LS) equation this potential being dependent in momentum space on the Feynman-like propagators and covariant cutoff factors at the meson-nucleon vertices is the kernel of relativistic integral equations for the NN bound and scattering states. Therefore we do not need to invent any transform of a given nonrelativistic potential to its relativistic counterpart. As a feasible study, we have started with the so-called 5ch Faddeev calculation for three-nucleon bound state (triton) and obtained a reasonable value of its binding energy (-7.42 MeV).
Theoretical characterization of the potential energy surface for NH + NO
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1993-01-01
The potential energy surface for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculation to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics.
MCSCF potential energy surface for photodissociation of formaldehyde
NASA Technical Reports Server (NTRS)
Jaffe, R. L.; Morokuma, K.
1976-01-01
The ground state potential energy surface for the dissociation of formaldehyde (H2CO to H2 and CO) is calculated with the ab initio MCSCF method with an extended (4-31G) basis set. The location, barrier height, and force constants of the transition state are determined, and the normal coordinate analysis is carried out. The calculated barrier height is 4.5 eV. Based on the calculated quantities, the detailed mechanism of the photochemical dissociation is discussed.
Theoretical characterization of the potential energy surface for NH + NO
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1993-01-01
The potential energy surface for NH + NO was characterized using complete active space self-consistent field (CASSCF) gradient calculation to determine the stationary point geometries and frequencies followed by CASSCF/internally contracted configuration interaction calculations to refine the energetics. The present results are in qualitative accord with the BAC-MP4 calculations, but there are differences as large as 8 kcal/mol in the detailed energetics.
MCSCF potential energy surface for photodissociation of formaldehyde
NASA Technical Reports Server (NTRS)
Jaffe, R. L.; Morokuma, K.
1976-01-01
The ground state potential energy surface for the dissociation of formaldehyde (H2CO to H2 and CO) is calculated with the ab initio MCSCF method with an extended (4-31G) basis set. The location, barrier height, and force constants of the transition state are determined, and the normal coordinate analysis is carried out. The calculated barrier height is 4.5 eV. Based on the calculated quantities, the detailed mechanism of the photochemical dissociation is discussed.
Calculating fusion neutron energy spectra from arbitrary reactant distributions
NASA Astrophysics Data System (ADS)
Eriksson, J.; Conroy, S.; Andersson Sundén, E.; Hellesen, C.
2016-02-01
The Directional Relativistic Spectrum Simulator (DRESS) code can perform Monte-Carlo calculations of reaction product spectra from arbitrary reactant distributions, using fully relativistic kinematics. The code is set up to calculate energy spectra from neutrons and alpha particles produced in the D(d, n)3He and T(d, n)4He fusion reactions, but any two-body reaction can be simulated by including the corresponding cross section. The code has been thoroughly tested. The kinematics calculations have been benchmarked against the kinematics module of the ROOT Data Analysis Framework. Calculated neutron energy spectra have been validated against tabulated fusion reactivities and against an exact analytical expression for the thermonuclear fusion neutron spectrum, with good agreement. The DRESS code will be used as the core of a detailed synthetic diagnostic framework for neutron measurements at the JET and MAST tokamaks.
NASA Astrophysics Data System (ADS)
Kiyohara, Shin; Mizoguchi, Teruyasu
2016-08-01
Segregation of silver at copper grain boundaries was investigated using theoretical calculations. Empirical potentials for copper-silver alloys were generated to systematically investigate the segregation. The segregation energies of the [001]-axis symmetric tilt Σ5 (210) and Σ25 (430) grain boundaries were calculated, and the most stable segregation sites for silver at these copper grain boundaries were determined. The generated empirical potential was validated by comparing it with that obtained from the first principles calculation. The segregation of silver at copper grain boundaries strongly depends on the open space at the segregation site.
Intermolecular potential energy surface for CS2 dimer.
Farrokhpour, Hossein; Mombeini, Zainab; Namazian, Mansoor; Coote, Michelle L
2011-04-15
A new four-dimensional intermolecular potential energy surface for CS(2) dimer is obtained by ab initio calculation of the interaction energies for a range of configurations and center-of-mass separation distances for the first time. The calculations were performed using the supermolecular approach at the Møller-Plesset second-order perturbation (MP2) level of theory with the augmented correlation consistent basis sets (aug-cc-pVxZ, x = D, T) and corrected for the basis-set superposition error using the full counterpoise correction method. A two-point extrapolation method was used to extrapolate the calculated energy points to the complete basis set limit. The effect of using the higher levels of theory, quadratic configuration interaction containing single, double, and perturbative triple excitations QCISD(T) and coupled cluster singles, doubles and perturbative triples excitations CCSD(T), on the shape of potential energy surface was investigated. It is shown that the MP2 level of theory apparently performs extremely poorly for describing the intermolecular potential energy surface, overestimating the total energy by a factor of nearly 1.73 in comparison with the QCISD(T) and CCSD(T) values. The value of isotropic dipole-dipole dispersion coefficient (C(6) ) of CS(2) fluid was obtained from the extrapolated MP2 potential energy surface. The MP2 extrapolated energy points were fitted to well-known analytical potential functions using two different methods to represent the potential energy surface analytically. The most stable configuration of the dimer was determined at R = 6.23 au, α = 90°, β = 90°, and γ = 90°, with a well depth of 3.980 kcal mol(-1) at the MP2 level of theory. Finally, the calculated second virial coefficients were compared with experimental values to test the quality of the presented potential energy surface. Copyright © 2010 Wiley Periodicals, Inc.
Guide for Conducting Energy Efficiency Potential Studies
The Guide for Conducting Energy Efficiency Potential Studies is provided to assist state officials, regulators, legislators, and others in implementing the recommendations of the National Action Plan for Energy Efficiency.
Assessment of wind energy potential in Poland
NASA Astrophysics Data System (ADS)
Starosta, Katarzyna; Linkowska, Joanna; Mazur, Andrzej
2014-05-01
The aim of the presentation is to show the suitability of using numerical model wind speed forecasts for the wind power industry applications in Poland. In accordance with the guidelines of the European Union, the consumption of wind energy in Poland is rapidly increasing. According to the report of Energy Regulatory Office from 30 March 2013, the installed capacity of wind power in Poland was 2807MW from 765 wind power stations. Wind energy is strongly dependent on the meteorological conditions. Based on the climatological wind speed data, potential energy zones within the area of Poland have been developed (H. Lorenc). They are the first criterion for assessing the location of the wind farm. However, for exact monitoring of a given wind farm location the prognostic data from numerical model forecasts are necessary. For the practical interpretation and further post-processing, the verification of the model data is very important. Polish Institute Meteorology and Water Management - National Research Institute (IMWM-NRI) runs an operational model COSMO (Consortium for Small-scale Modelling, version 4.8) using two nested domains at horizontal resolutions of 7 km and 2.8 km. The model produces 36 hour and 78 hour forecasts from 00 UTC, for 2.8 km and 7 km domain resolutions respectively. Numerical forecasts were compared with the observation of 60 SYNOP and 3 TEMP stations in Poland, using VERSUS2 (Unified System Verification Survey 2) and R package. For every zone the set of statistical indices (ME, MAE, RMSE) was calculated. Forecast errors for aerological profiles are shown for Polish TEMP stations at Wrocław, Legionowo and Łeba. The current studies are connected with a topic of the COST ES1002 WIRE-Weather Intelligence for Renewable Energies.
Thermal conductivity calculations of crystalline quartz from the BKS potential
NASA Astrophysics Data System (ADS)
Yoon, Young-Gui; Car, Roberto; Srolovitz, David J.; Scandolo, Sandro
2003-03-01
We present thermal conductivity calculations from the classical BKS potential[1]. Following a velocity rescaling method for a constant heat flux proposed by P. Jund and R. Jullien[2], thermal conductivity as a heat flux to temperature gradient ratio is directly calculated in periodic simulation cells. Our calculations in a wide temperature range at which crystalline quartz exists are consistent with the experimental trend[3]. The conductivity decreases with temperature in the alpha-quartz regime, and increases after the phase transition to beta-quartz. The temperature dependence is rather small in the beta-quartz regime. [1] B. W. H. van Beest, G. J. Kramer, and R. A. van Santen, Phy. Rev. Lett. 64, 1995 (1990). [2] P. Jund, and R. Jullien, Phy. Rev. B 59, 13707 (1999). [3] H. Kanamori, N. Fujii, and H. Mizutani, J. Geophys. Res. 73, 595 (1968).
Calculation of exchange energies using algebraic perturbation theory
Burrows, B. L.; Dalgarno, A.; Cohen, M.
2010-04-15
An algebraic perturbation theory is presented for efficient calculations of localized states and hence of exchange energies, which are the differences between low-lying states of the valence electron of a molecule, formed by the collision of an ion Y{sup +} with an atom X. For the case of a homonuclear molecule these are the gerade and ungerade states and the exchange energy is an exponentially decreasing function of the internuclear distance. For such homonuclear systems the theory is used in conjunction with the Herring-Holstein technique to give accurate exchange energies for a range of intermolecular separations R. Since the perturbation parameter is essentially 1/R, this method is suitable for large R. In particular, exchange energies are calculated for X{sub 2}{sup +} systems, where X is H, Li, Na, K, Rb, or Cs.
Removing the barrier to the calculation of activation energies
Mesele, Oluwaseun O.; Thompson, Ward H.
2016-10-06
Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.
Removing the barrier to the calculation of activation energies
Mesele, Oluwaseun O.; Thompson, Ward H.
2016-10-06
Approaches for directly calculating the activation energy for a chemical reaction from a simulation at a single temperature are explored with applications to both classical and quantum systems. The activation energy is obtained from a time correlation function that can be evaluated from the same molecular dynamics trajectories or quantum dynamics used to evaluate the rate constant itself and thus requires essentially no extra computational work.
Representing Global Reactive Potential Energy Surfaces Using Gaussian Processes.
Kolb, Brian; Marshall, Paul; Zhao, Bin; Jiang, Bin; Guo, Hua
2017-04-06
Representation of multidimensional global potential energy surfaces suitable for spectral and dynamical calculations from high-level ab initio calculations remains a challenge. Here, we present a detailed study on constructing potential energy surfaces using a machine learning method, namely, Gaussian process regression. Tests for the (3)A″ state of SH2, which facilitates the SH + H ↔ S((3)P) + H2 abstraction reaction and the SH + H' ↔ SH' + H exchange reaction, suggest that the Gaussian process is capable of providing a reasonable potential energy surface with a small number (∼1 × 10(2)) of ab initio points, but it needs substantially more points (∼1 × 10(3)) to converge reaction probabilities. The implications of these observations for construction of potential energy surfaces are discussed.
Perspective: Alchemical free energy calculations for drug discovery
Mobley, David L.; Klimovich, Pavel V.
2012-01-01
Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery. PMID:23267463
The calculation of band gap energy in zinc oxide films
NASA Astrophysics Data System (ADS)
Arif, Ali; Belahssen, Okba; Gareh, Salim; Benramache, Said
2015-01-01
We investigated the optical properties of undoped zinc oxide thin films as the n-type semiconductor; the thin films were deposited at different precursor molarities by ultrasonic spray and spray pyrolysis techniques. The thin films were deposited at different substrate temperatures ranging between 200 and 500 °C. In this paper, we present a new approach to control the optical gap energy of ZnO thin films by concentration of the ZnO solution and substrate temperatures from experimental data, which were published in international journals. The model proposed to calculate the band gap energy with the Urbach energy was investigated. The relation between the experimental data and theoretical calculation suggests that the band gap energies are predominantly estimated by the Urbach energies, film transparency, and concentration of the ZnO solution and substrate temperatures. The measurements by these proposal models are in qualitative agreements with the experimental data; the correlation coefficient values were varied in the range 0.96-0.99999, indicating high quality representation of data based on Equation (2), so that the relative errors of all calculation are smaller than 4%. Thus, one can suppose that the undoped ZnO thin films are chemically purer and have many fewer defects and less disorder owing to an almost complete chemical decomposition and contained higher optical band gap energy.
Perspective: Alchemical free energy calculations for drug discovery
NASA Astrophysics Data System (ADS)
Mobley, David L.; Klimovich, Pavel V.
2012-12-01
Computational techniques see widespread use in pharmaceutical drug discovery, but typically prove unreliable in predicting trends in protein-ligand binding. Alchemical free energy calculations seek to change that by providing rigorous binding free energies from molecular simulations. Given adequate sampling and an accurate enough force field, these techniques yield accurate free energy estimates. Recent innovations in alchemical techniques have sparked a resurgence of interest in these calculations. Still, many obstacles stand in the way of their routine application in a drug discovery context, including the one we focus on here, sampling. Sampling of binding modes poses a particular challenge as binding modes are often separated by large energy barriers, leading to slow transitions. Binding modes are difficult to predict, and in some cases multiple binding modes may contribute to binding. In view of these hurdles, we present a framework for dealing carefully with uncertainty in binding mode or conformation in the context of free energy calculations. With careful sampling, free energy techniques show considerable promise for aiding drug discovery.
NASA Astrophysics Data System (ADS)
Li, Zhijie; Kenmotsu, Takahiro; Kawamura, Takaichi; Ono, Tadayoshi; Yamamura, Yasunori
1999-06-01
In order to test the availabilities of the theoretical screening lengths with the shell effect and the new local electronic-energy-loss model proposed by Yamamura et al., the sputtering yields due to various ion impacts on monatomic materials were calculated with the ACAT code. It is found that the sputtering yields calculated by the Molière potential with the present theoretical screening lengths are in reasonable good agreement with experimental data and Yamamura's empirical sputtering formula without free parameters.
Effect of composition on antiphase boundary energy in Ni3Al based alloys: Ab initio calculations
NASA Astrophysics Data System (ADS)
Gorbatov, O. I.; Lomaev, I. L.; Gornostyrev, Yu. N.; Ruban, A. V.; Furrer, D.; Venkatesh, V.; Novikov, D. L.; Burlatsky, S. F.
2016-06-01
The effect of composition on the antiphase boundary (APB) energy of Ni-based L 12-ordered alloys is investigated by ab initio calculations employing the coherent potential approximation. The calculated APB energies for the {111} and {001} planes reproduce experimental values of the APB energy. The APB energies for the nonstoichiometric γ' phase increase with Al concentration and are in line with the experiment. The magnitude of the alloying effect on the APB energy correlates with the variation of the ordering energy of the alloy according to the alloying element's position in the 3 d row. The elements from the left side of the 3 d row increase the APB energy of the Ni-based L 12-ordered alloys, while the elements from the right side slightly affect it except Ni. The way to predict the effect of an addition on the {111} APB energy in a multicomponent alloy is discussed.
Desjarlais, Michael Paul; Muller, Richard Partain
2006-02-01
The optimized effective potential (OEP) method allows orbital-dependent functionals to be used in density functional theory (DFT), which, in particular, allows exact exchange formulations of the exchange energy to be used in DFT calculations. Because the exact exchange is inherently self-interaction correcting, the resulting OEP calculations have been found to yield superior band-gaps for condensed-phase systems. Here we apply these methods to the isolated atoms He and Be, and compare to high quality experiments and calculations to demonstrate that the orbital energies accurately reproduce the excited state spectrum for these species. These results suggest that coupling the exchange-only OEP calculations with proper (orbital-dependent or other) correlation functions might allow quantitative accuracy from DFT calculations.
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.
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.
General method for calculating derivatives of the lattice electrostatic energy.
NASA Technical Reports Server (NTRS)
Macdonald, D. E.; Eftis, J.; Arkilic, G. M.
1972-01-01
A method for calculating the derivatives of lattice electrostatic strain energy is proposed. It offers a computation procedure that is more general, concise, and systematic than any of the procedures previously used by Fuchs (1936), Cousins (1967), and Suzuki et al. (1968). The method can also easily be extended to fourth- and higher-order derivatives without undue difficulty.
RKRV potential energy curves and dissociation energies of NH and PH
NASA Astrophysics Data System (ADS)
Reddy, R. R.; Viswanath, R.
1989-05-01
The turning points of the potential energy curves for the ground states of NH and PH molecules were calculated using the approach of Rydberg-Klein-Rees modified by Vanderslice et al. (1960), together with the energy values obtained from the Lippincott potential function. These values were compared with those obtained by Jarmain (1960). The values of the dissociation energies of the NH and PH were estimated to be about 3.45 and 3.16, respectively.
Energy potential of modern landfills
Bogner, J.E.
1990-01-01
Methane produced by refuse decomposition in a sanitary landfill can be recovered for commercial use. Landfill methane is currently under-utilized, with commercial recovery at only a small percentage of US landfills. New federal regulations mandating control of landfill gas migration and atmospheric emissions are providing impetus to methane recovery schemes as a means of recovering costs for increased environmental control. The benefits of landfill methane recovery include utilization of an inexpensive renewable energy resource, removal of explosive gas mixtures from the subsurface, and mitigation of observed historic increases in atmospheric methane. Increased commercial interest in landfill methane recovery is dependent on the final form of Clean Air Act amendments pertaining to gaseous emissions from landfills; market shifts in natural gas prices; financial incentives for development of renewable energy resources; and support for applied research and development to develop techniques for increased control of the gas generation process in situ. This paper will discuss the controls on methane generation in landfills. In addition, it will address how landfill regulations affect landfill design and site management practices which, in turn, influence decomposition rates. Finally, future trends in landfilling, and their relationship to gas production, will be examined. 19 refs., 2 figs., 3 tabs.
Effects of internal gain assumptions in building energy calculations
NASA Astrophysics Data System (ADS)
Christensen, C.; Perkins, R.
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations. Heating and cooling loads from simulations using the Department of Energy 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
Three dimensional calculation of flux of low energy atmospheric neutrinos
NASA Technical Reports Server (NTRS)
Lee, H.; Bludman, S. A.
1985-01-01
Results of three-dimensional Monte Carlo calculation of low energy flux of atmospheric neutrinos are presented and compared with earlier one-dimensional calculations 1,2 valid at higher neutrino energies. These low energy neutrinos are the atmospheric background in searching for neutrinos from astrophysical sources. Primary cosmic rays produce the neutrino flux peaking at near E sub=40 MeV and neutrino intensity peaking near E sub v=100 MeV. Because such neutrinos typically deviate by 20 approximately 30 from the primary cosmic ray direction, three-dimensional effects are important for the search of atmospheric neutrinos. Nevertheless, the background of these atmospheric neutrinos is negligible for the detection of solar and supernova neutrinos.
Calculation of potential flow past airship bodies in yaw
NASA Technical Reports Server (NTRS)
Lotz, I
1932-01-01
An outline of Von Karman's method of computing the potential flow of airships in yaw by means of partially constant dipolar superposition on the axis of the body is followed by several considerations for beginning and end of the superposition. Then this method is improved by postulating a continuous, in part linearly variable dipolar superposition on the axis. The second main part of the report brings the calculation of the potential flow by means of sources and sinks, arranged on the surface of the airship body. The integral equation which must satisfy this surface superposition is posed, and the core reduced to functions developed from whole elliptical normal integrals. The functions are shown diagrammatically. The integration is resolvable by iteration. The consequence of the method is good. The formulas for computing the velocity on the surface and of the potential for any point conclude the report.
Calculations of specific cellular doses for low-energy electrons
NASA Astrophysics Data System (ADS)
Liu, C. S.; Tung, C.-J.; Hu, Y. H.; Chou, C. M.; Chao, T. C.; Lee, C. C.
2009-05-01
The objectives of this work were to calculate the cellular doses and the lineal energies of low-energy electrons in liquid water for different source-target geometry in a cell. Calculated specific cellular doses and their variations were analyzed for the dependences on electron energy, source-target geometry, elastic interaction, and type of energy depositions, i.e. starter, stopper, insider and crosser. Two approaches, i.e. the probabilistic method and the mixed method, were applied. In the probabilistic method, the Monte Carlo Penelope code was used. In the mixed method, the range-energy relation and the sampling of electron paths were applied. It was found that for N ← Cy elastic interactions led to a change of the specific cellular dose by about 30% for electron energies below 10 keV. Here N ← Cy denotes electrons emitted from the source region, Cy (cytoplasm), to deposit energy in the target region, N (cell nucleus). The variation of specific cellular dose was found greater (more than 10%) for N ← Cy than N ← N, C ← C and C ← CS, where C and CS denote the cell and cell surface, respectively. The lineal energy distribution varied substantially with electron energy, source-target geometry, and target size. The maximum values of the relative dose-mean lineal energy for 1, 5 and 10 keV electrons, relative to 36 keV reference electrons used to define the relative biological effectiveness, occurred at target radii of several tens, hundreds and thousands nanometers, respectively.
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Ab Initio Potential Energy Surface for H-H2
NASA Technical Reports Server (NTRS)
Patridge, Harry; Bauschlicher, Charles W., Jr.; Stallcop, James R.; Levin, Eugene
1993-01-01
Ab initio calculations employing large basis sets are performed to determine an accurate potential energy surface for H-H2 interactions for a broad range of separation distances. At large distances, the spherically averaged potential determined from the calculated energies agrees well with the corresponding results determined from dispersion coefficients; the van der Waals well depth is predicted to be 75 +/- 3 micro E(h). Large basis sets have also been applied to reexamine the accuracy of theoretical repulsive potential energy surfaces (25-70 kcal/mol above the H-H2 asymptote) at small interatomic separations; the Boothroyd, Keogh, Martin, and Peterson (BKMP) potential energy surface is found to agree with results of the present calculations within the expected uncertainty (+/- 1 kcal/mol) of the fit. Multipolar expansions of the computed H-H2 potential energy surface are reported for four internuclear separation distances (1.2, 1.401, 1.449, and 1.7a(0)) of the hydrogen molecule. The differential elastic scattering cross section calculated from the present results is compared with the measurements from a crossed beam experiment.
Potential Water and Energy Savings from Showerheads
Biermayer, Peter J.
2005-09-28
This paper estimates the benefits and costs of six water reduction scenarios. Benefits and costs of showerhead scenarios are ranked in this paper by an estimated water reduction percentage. To prioritize potential water and energy saving scenarios regarding showerheads, six scenarios were analyzed for their potential water and energy savings and the associated dollar savings to the consumer.
Geothermal Energy Potential in Western United States
ERIC Educational Resources Information Center
Pryde, Philip R.
1977-01-01
Reviews types of geothermal energy sources in the western states, including hot brine systems and dry steam systems. Conversion to electrical energy is a major potential use of geothermal energy, although it creates environmental disruptions such as noise, corrosion, and scaling of equipment. (AV)
Geothermal Energy Potential in Western United States
ERIC Educational Resources Information Center
Pryde, Philip R.
1977-01-01
Reviews types of geothermal energy sources in the western states, including hot brine systems and dry steam systems. Conversion to electrical energy is a major potential use of geothermal energy, although it creates environmental disruptions such as noise, corrosion, and scaling of equipment. (AV)
Ultrasonic energy in liposome production: process modelling and size calculation.
Barba, A A; Bochicchio, S; Lamberti, G; Dalmoro, A
2014-04-21
The use of liposomes in several fields of biotechnology, as well as in pharmaceutical and food sciences is continuously increasing. Liposomes can be used as carriers for drugs and other active molecules. Among other characteristics, one of the main features relevant to their target applications is the liposome size. The size of liposomes, which is determined during the production process, decreases due to the addition of energy. The energy is used to break the lipid bilayer into smaller pieces, then these pieces close themselves in spherical structures. In this work, the mechanisms of rupture of the lipid bilayer and the formation of spheres were modelled, accounting for how the energy, supplied by ultrasonic radiation, is stored within the layers, as the elastic energy due to the curvature and as the tension energy due to the edge, and to account for the kinetics of the bending phenomenon. An algorithm to solve the model equations was designed and the relative calculation code was written. A dedicated preparation protocol, which involves active periods during which the energy is supplied and passive periods during which the energy supply is set to zero, was defined and applied. The model predictions compare well with the experimental results, by using the energy supply rate and the time constant as fitting parameters. Working with liposomes of different sizes as the starting point of the experiments, the key parameter is the ratio between the energy supply rate and the initial surface area.
Potential function and dissociation energy of alkali halide
NASA Astrophysics Data System (ADS)
Srivastava, Abhay P.; Pandey, Anjani K.; Pandey, Brijesh K.
2016-05-01
Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L5 potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.
Potential function and dissociation energy of alkali halide
Srivastava, Abhay P.; Pandey, Brijesh K.; Pandey, Anjani K.
2016-05-06
Dissociation energy of some alkali halides have been calculated by using different interaction potential function such as Born-Mayer, Varshani-Shukla and L{sub 5} potential model. The theoretical calculation is compared with experimental values. The Result shows that the values of dissociation energy as calculated by using different potential models have an equal amount of deviation with experimental values. The above said deviation with experimental values can be explained by consideration of rotational-vibrational coupling between the constituents of molecules in the limelight of molecular spectroscopy. Findings of present work suggest that the existing potential model need to be reviewed in view of the correction factors solely depending on the rotational, vibrational and electronic coupling between the constituents of molecules.
Efficient free energy calculations of quantum systems through computer simulations
NASA Astrophysics Data System (ADS)
Antonelli, Alex; Ramirez, Rafael; Herrero, Carlos; Hernandez, Eduardo
2009-03-01
In general, the classical limit is assumed in computer simulation calculations of free energy. This approximation, however, is not justifiable for a class of systems in which quantum contributions for the free energy cannot be neglected. The inclusion of quantum effects is important for the determination of reliable phase diagrams of these systems. In this work, we present a new methodology to compute the free energy of many-body quantum systems [1]. This methodology results from the combination of the path integral formulation of statistical mechanics and efficient non-equilibrium methods to estimate free energy, namely, the adiabatic switching and reversible scaling methods. A quantum Einstein crystal is used as a model to show the accuracy and reliability the methodology. This new method is applied to the calculation of solid-liquid coexistence properties of neon. Our findings indicate that quantum contributions to properties such as, melting point, latent heat of fusion, entropy of fusion, and slope of melting line can be up to 10% of the calculated values using the classical approximation. [1] R. M. Ramirez, C. P. Herrero, A. Antonelli, and E. R. Hernández, Journal of Chemical Physics 129, 064110 (2008)
Calculated stacking-fault energies of elemental metals
NASA Astrophysics Data System (ADS)
Rosengaard, N. M.; Skriver, H. L.
1993-05-01
We have performed ab initio calculations of twin, intrinsic, and extrinsic face-centered-cubic stacking faults for all the 3d, 4d, and 5d transition metals by means of a Green's-function technique, based on the linear-muffin-tin-orbitals method within the tight-binding and atomic-sphere approximations. The results are in excellent agreement with recent layer Korringa-Kohn-Rostoker Green's-function calculations where stacking-fault energies for Ni, Cu, Rh, Pd, Ag, Ir, and Au were found by means of the so-called force theorem. We find that the self-consistent fault energies for all the metals in the three transition series vary with atomic number essentially as the calculated structural energy differences between the face-centered-cubic and the hexagonal-close-packed phases. In addition we find that the simple relations between the different types of fault energies predicted by models based on the local atomic coordination are obeyed to a high degree of accuracy.
Surface energy balance calculations for small northern lakes
NASA Astrophysics Data System (ADS)
Binyamin, J.; Rouse, W. R.; Davies, J. A.; Oswald, C. J.; Schertzer, W. M.
2006-12-01
An energy balance model is used to determine diurnal surface energy balance components for three different sized high-latitude Canadian lakes in the Mackenzie River Basin (MRB) during the open water seasons of 2000, 2001, and 2002. Surface net radiation is derived from the component fluxes of the radiation balance. Turbulent heat fluxes are calculated using the aerodynamic method with input from local meteorological stations and experimentally derived drag coefficients. Lake heat storage, determined as a residual of the surface energy balance, is used together with measured water temperature profiles to calculate the daily mixing layer depth. The model uses readily available meteorological inputs for radiation calculations.Verification results for surface energy balance components show mean bias error (MBE) generally less than 5% of the mean measured daily fluxes and root mean square error (RMSE) less than 38%, which decreases to less than 16% for 10-day averaging periods. The model tends to overestimate net radiation by 7% and latent and sensible heat fluxes by about 4% and 1%, respectively, on average. Inferred slab layer depths indicate that the shallowest lake was isothermal while the deeper lakes showed temporal variations as expected.
Binding Energy Calculations for Novel Ternary Ionic Lattices
NASA Astrophysics Data System (ADS)
Rodríguez-Mijangos, Ricardo; Vazquez-Polo, Gustavo
2002-03-01
Theoretical calculations for the binding energy between metalic ions and negative ions on a novel ternary ionic lattice is carried out for several solid solutions prepared with different concentrations and characterized recently (1). The ternary lattices that reach a good miscibility are: KCl(x)KBr(y)RbCl(z) in three different concentrations: (x=y=z=0.33), (x=0.5, y=0.25, z=0.25) and (x=0.33, y=0.07, z=0.60). The binding energy for these novel structures is calculated from the lattice constants obtained by X ray diffractometry analysis performed on the samples and the Vegard law (2). For the repulsive force exponent m, an average of the m values was considered. The energy values obtained by the Born´expression are compared with corresponding energy values from the lattice with more complex expressions, such as the Born Mayer, Born-Van der Walls. There is a good aggreement between all these calculations. (1)R. R. Mijangos, A. Cordero-Borboa, E. Alvarez, M. Cervantes, Physics Letters A 282 (2001) 195-200. (2) G. Vazquez-Polo, R. R. Mijangos et al. Revista Mexicana de Fisica, 47, Diciembre 2001. In Press.
Bonn potential and shell-model calculations for N=126 isotones
Coraggio, L.; Covello, A.; Gargano, A.; Itaco, N.; Kuo, T. T. S.
1999-12-01
We have performed shell-model calculations for the N=126 isotones {sup 210}Po, {sup 211}At, and {sup 212}Rn using a realistic effective interaction derived from the Bonn-A nucleon-nucleon potential by means of a G-matrix folded-diagram method. The calculated binding energies, energy spectra, and electromagnetic properties show remarkably good agreement with the experimental data. The results of this paper complement those of our previous study on neutron hole Pb isotopes, confirming that realistic effective interactions are now able to reproduce with quantitative accuracy the spectroscopic properties of complex nuclei. (c) 1999 The American Physical Society.
PDB ligand conformational energies calculated quantum-mechanically.
Sitzmann, Markus; Weidlich, Iwona E; Filippov, Igor V; Liao, Chenzhong; Peach, Megan L; Ihlenfeldt, Wolf-Dietrich; Karki, Rajeshri G; Borodina, Yulia V; Cachau, Raul E; Nicklaus, Marc C
2012-03-26
We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient
Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
Jorgensen, William L.; Thomas, Laura L.
2009-01-01
An overview is provided on the computation of free energy changes in solution using perturbation theory, overlap sampling, and related approximate methods. As a specific application, extensive results are provided for free energies of hydration of substituted benzenes using the OPLS-AA force field in explicit TIP4P water. For a similar amount of computer time, the double-wide sampling and overlap sampling methods yield very similar results in the free-energy perturbation calculations. With standard protocols, the average statistical uncertainty in computed differences in free energies of hydration is 0.1 – 0.2 kcal/mol. Application of the power-series expansion in the Peierls equation was also tested. Use of the first-order term is generally reliable, while inclusion of the slowly-convergent, second-order fluctuation term causes deterioration in the results for strongly hydrogen-bonded solutes. PMID:19936324
Low energy dipole strength from large scale shell model calculations
NASA Astrophysics Data System (ADS)
Sieja, Kamila
2017-09-01
Low energy enhancement of radiative strength functions has been deduced from experiments in several mass regions of nuclei. Such an enhancement is believed to impact the calculated neutron capture rates which are crucial input for reaction rates of astrophysical interest. Recently, shell model calculations have been performed to explain the upbend of the γ-strength as due to the M1 transitions between close-lying states in the quasi-continuum in Fe and Mo nuclei. Beyond mean-↓eld calculations in Mo suggested, however, a non-negligible role of electric dipole in the low energy enhancement. So far, no calculations of both dipole components within the same theoretical framework have been presented in this context. In this work we present newly developed large scale shell model appraoch that allows to treat on the same footing natural and non-natural parity states. The calculations are performed in a large sd - pf - gds model space, allowing for 1p{1h excitations on the top of the full pf-shell con↓guration mixing. We restrict the discussion to the magnetic part of the dipole strength, however, we calculate for the ↓rst time the magnetic dipole strength between states built of excitations going beyond the classical shell model spaces. Our results corroborate previous ↓ndings for the M1 enhancement for the natural parity states while we observe no enhancement for the 1p{1h contributions. We also discuss in more detail the e↑ects of con↓guration mixing limitations on the enhancement coming out from shell model calculations.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
NASA Technical Reports Server (NTRS)
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
NASA Technical Reports Server (NTRS)
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Ab Initio Calculations for the Surface Energy of Silver Nanoclusters
NASA Astrophysics Data System (ADS)
Medasani, Bharat; Vasiliev, Igor; Park, Young Ho
2007-03-01
We apply first principles computational methods to study the surface energy and the surface stress of silver nanoparticles. The structures, energies and lattice contractions of spherical Ag nanoclusters are calculated in the framework of density functional theory combined with the generalized gradient approximation. Our calculations predict the surface energies of Ag nanoclusters to be in the range of 1-2 J/m^2. These values are close to the bulk surface energy of silver, but are significantly lower than the recently reported value of 7.2 J/m^2 derived from the Kelvin equation for free Ag nanoparticles. From the lattice contraction and the nearest neighbor interatomic distance, we estimate the surface stress of the silver nanoclusters to be in the the range of 1-1.45 N/m. This result suggests that a liquid droplet model can be employed to evaluate the surface energy and the surface stress of Ag nanoparticles. K. K. Nanda et al., Phys. Rev. Lett. 91, 106102 (2003).
Expected Energy Method for Electro-Optical SNR Calculations.
1984-02-02
r’AD-Ri39 984 EXPECTED ENERGY METHOD FOR ELECTPO-OPTICRL SNR i/i CALCULRTIONS(U) MASSRCHUSETTS INST OF TECH LEXINGTON LINCOLN LAB G J MAYER 82 FEB 84...ENERGY METHOD FOR ELECTRO-OPTICAL SNR CALCULATIONS * Ci. MA YER Group 9 TECHNICAL REPORT 634 2 FEBRUARY 1984 Approved for public release; distribution...analysis of image and sensor element configuration. This method allows the optimal pixel size to be selected to maximize the expected SNR for any point
Calculated thermochemistry of aminonitroacetylene: a new high-energy material?
Mathews, Kelly Y; Ball, David W
2009-04-30
As part of an increased interest in amino- and nitro-substituted high-energy-density materials (as exemplified by FOX-7, 1,1-diamino-2,2-dinitroethylene), here we present calculated properties of aminonitroacetylene, NH(2)-CC-NO(2). Our results indicate that while the specific enthalpy of combustion is less than that of acetylene, its specific enthalpy of decomposition is greater than that of TNT, and its predicted density is large enough to predict substantial high-energy-density properties for this substance.
Variational calculation of highly excited rovibrational energy levels of H2O2.
Polyansky, Oleg L; Kozin, Igor N; Ovsyannikov, Roman I; Małyszek, Paweł; Koput, Jacek; Tennyson, Jonathan; Yurchenko, Sergei N
2013-08-15
Results are presented for highly accurate ab initio variational calculation of the rotation-vibration energy levels of H2O2 in its electronic ground state. These results use a recently computed potential energy surface and the variational nuclear-motion programs WARV4, which uses an exact kinetic energy operator, and TROVE, which uses a numerical expansion for the kinetic energy. The TROVE calculations are performed for levels with high values of rotational excitation, J up to 35. The purely ab initio calculations of the rovibrational energy levels reproduce the observed levels with a standard deviation of about 1 cm(-1), similar to that of the J = 0 calculation, because the discrepancy between theory and experiment for rotational energies within a given vibrational state is substantially determined by the error in the vibrational band origin. Minor adjustments are made to the ab initio equilibrium geometry and to the height of the torsional barrier. Using these and correcting the band origins using the error in J = 0 states lowers the standard deviation of the observed-calculated energies to only 0.002 cm(-1) for levels up to J = 10 and 0.02 cm(-1) for all experimentally known energy levels, which extend up to J = 35.
The Yukawa potential: ground state energy and critical screening
NASA Astrophysics Data System (ADS)
Edwards, James P.; Gerber, Urs; Schubert, Christian; Trejo, Maria A.; Weber, Axel
2017-08-01
We study the ground state energy and the critical screening parameter of the Yukawa potential in nonrelativistic quantum mechanics. After a short review of the existing literature on these quantities, we apply fifth-order perturbation theory to the calculation of the ground state energy, using the exact solutions of the Coulomb potential together with a cutoff on the principal number summations. We also perform a variational calculation of the ground state energy using a Coulomb-like radial wave function and the exact solution of the corresponding minimization condition. For not too large values of the screening parameter, close agreement is found between the perturbative and variational results. For the critical screening parameter, we devise a novel method that permits us to determine it to 10 digits. This is the most precise calculation of this quantity to date, and allows us to resolve some discrepancies between previous results.
Effects of internal gain assumptions in building energy calculations
NASA Astrophysics Data System (ADS)
Christensen, C.; Perkins, R.
1981-01-01
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multifamily-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
Effects of internal gain assumptions in building energy calculations
Christensen, C.; Perkins, R.
1981-01-01
The utilization of direct solar gains in buildings can be affected by operating profiles, such as schedules for internal gains, thermostat controls, and ventilation rates. Building energy analysis methods use various assumptions about these profiles. The effects of typical internal gain assumptions in energy calculations are described. Heating and cooling loads from simulations using the DOE 2.1 computer code are compared for various internal-gain inputs: typical hourly profiles, constant average profiles, and zero gain profiles. Prototype single-family-detached and multi-family-attached residential units are studied with various levels of insulation and infiltration. Small detached commercial buildings and attached zones in large commercial buildings are studied with various levels of internal gains. The results of this study indicate that calculations of annual heating and cooling loads are sensitive to internal gains, but in most cases are relatively insensitive to hourly variations in internal gains.
Complex energy approaches for calculating isobaric analogue states
Betan, R. Id; Kruppa, A. T.; Vertse, T.
2008-10-15
Parameters of isobaric analog resonance (IAR) are calculated in the framework of the Lane model using different methods. In the standard method, the direct numerical solution of the coupled channel (CC) Lane equations served as a reference for checking two complex energy methods, namely the complex energy shell model (CXSM) and the complex scaling (CS) approaches. The IAR parameters calculated by the CXSM and the CS methods agree with that of the CC results within 1 keV for all partial waves considered. Although the CXSM and the CS methods have similarities, an important difference is that only the CXSM method offers a direct way for studying the configurations of the IAR wave function.
NASA Astrophysics Data System (ADS)
Wu, Xiangyang
1999-07-01
The heterocyclic amine 2-amino-3-methylimidazo (4, 5-f) quinoline (IQ) is one of a number of carcinogens found in barbecued meat and fish. It induces tumors in mammals and is probably involved in human carcinogenesis, because of great exposure to such food carcinogens. IQ is biochemically activated to a derivative which reacts with DNA to form a covalent adduct. This adduct may deform the DNA and consequently cause a mutation. which may initiate carcinogenesis. To understand this cancer initiating event, it is necessary to obtain atomic resolution structures of the damaged DNA. No such structures are available experimentally due to synthesis difficulties. Therefore, we employ extensive molecular mechanics and dynamics calculations for this purpose. The major IQ-DNA adduct in the specific DNA sequence d(5'G1G2C G3CCA3') - d(5'TGGCGCC3') with IQ modified at G3 is studied. The d(5'G1G2C G3CC3') sequence has recently been shown to be a hot-spot for mutations when IQ modification is at G3. Although this sequence is prone to -2 deletions via a ``slippage mechanism'' even when unmodified, a key question is why IQ increases the mutation frequency of the unmodified DNA by about 104 fold. Is there a structural feature imposed by IQ that is responsible? The molecular mechanics and dynamics program AMBER for nucleic acids with the latest force field was chosen for this work. This force field has been demonstrated to reproduce well the B-DNA structure. However, some parameters, the partial charges, bond lengths and angles, dihedral parameters of the modified residue, are not available in the AMBER database. We parameterized the force field using high level ab initio quantum calculations. We created 800 starting conformations which uniformly sampled in combination at 18° intervals three torsion angles that govern the IQ-DNA orientations, and energy minimized them. The most important structures are abnormal; the IQ damaged guanine is rotated out of its standard B
Basic ingredients of free energy calculations: a review.
Christ, Clara D; Mark, Alan E; van Gunsteren, Wilfred F
2010-06-01
Methods to compute free energy differences between different states of a molecular system are reviewed with the aim of identifying their basic ingredients and their utility when applied in practice to biomolecular systems. A free energy calculation is comprised of three basic components: (i) a suitable model or Hamiltonian, (ii) a sampling protocol with which one can generate a representative ensemble of molecular configurations, and (iii) an estimator of the free energy difference itself. Alternative sampling protocols can be distinguished according to whether one or more states are to be sampled. In cases where only a single state is considered, six alternative techniques could be distinguished: (i) changing the dynamics, (ii) deforming the energy surface, (iii) extending the dimensionality, (iv) perturbing the forces, (v) reducing the number of degrees of freedom, and (vi) multi-copy approaches. In cases where multiple states are to be sampled, the three primary techniques are staging, importance sampling, and adiabatic decoupling. Estimators of the free energy can be classified as global methods that either count the number of times a given state is sampled or use energy differences. Or, they can be classified as local methods that either make use of the force or are based on transition probabilities. Finally, this overview of the available techniques and how they can be best used in a practical context is aimed at helping the reader choose the most appropriate combination of approaches for the biomolecular system, Hamiltonian and free energy difference of interest.
Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations
2016-01-01
Binding selectivity is a requirement for the development of a safe drug, and it is a critical property for chemical probes used in preclinical target validation. Engineering selectivity adds considerable complexity to the rational design of new drugs, as it involves the optimization of multiple binding affinities. Computationally, the prediction of binding selectivity is a challenge, and generally applicable methodologies are still not available to the computational and medicinal chemistry communities. Absolute binding free energy calculations based on alchemical pathways provide a rigorous framework for affinity predictions and could thus offer a general approach to the problem. We evaluated the performance of free energy calculations based on molecular dynamics for the prediction of selectivity by estimating the affinity profile of three bromodomain inhibitors across multiple bromodomain families, and by comparing the results to isothermal titration calorimetry data. Two case studies were considered. In the first one, the affinities of two similar ligands for seven bromodomains were calculated and returned excellent agreement with experiment (mean unsigned error of 0.81 kcal/mol and Pearson correlation of 0.75). In this test case, we also show how the preferred binding orientation of a ligand for different proteins can be estimated via free energy calculations. In the second case, the affinities of a broad-spectrum inhibitor for 22 bromodomains were calculated and returned a more modest accuracy (mean unsigned error of 1.76 kcal/mol and Pearson correlation of 0.48); however, the reparametrization of a sulfonamide moiety improved the agreement with experiment. PMID:28009512
Energy difference space random walk to achieve fast free energy calculations.
Min, Donghong; Yang, Wei
2008-05-21
A method is proposed to efficiently obtain free energy differences. In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states overlap.
Relative Binding Free Energy Calculations Applied to Protein Homology Models.
Cappel, Daniel; Hall, Michelle Lynn; Lenselink, Eelke B; Beuming, Thijs; Qi, Jun; Bradner, James; Sherman, Woody
2016-12-27
A significant challenge and potential high-value application of computer-aided drug design is the accurate prediction of protein-ligand binding affinities. Free energy perturbation (FEP) using molecular dynamics (MD) sampling is among the most suitable approaches to achieve accurate binding free energy predictions, due to the rigorous statistical framework of the methodology, correct representation of the energetics, and thorough treatment of the important degrees of freedom in the system (including explicit waters). Recent advances in sampling methods and force fields coupled with vast increases in computational resources have made FEP a viable technology to drive hit-to-lead and lead optimization, allowing for more efficient cycles of medicinal chemistry and the possibility to explore much larger chemical spaces. However, previous FEP applications have focused on systems with high-resolution crystal structures of the target as starting points-something that is not always available in drug discovery projects. As such, the ability to apply FEP on homology models would greatly expand the domain of applicability of FEP in drug discovery. In this work we apply a particular implementation of FEP, called FEP+, on congeneric ligand series binding to four diverse targets: a kinase (Tyk2), an epigenetic bromodomain (BRD4), a transmembrane GPCR (A2A), and a protein-protein interaction interface (BCL-2 family protein MCL-1). We apply FEP+ using both crystal structures and homology models as starting points and find that the performance using homology models is generally on a par with the results when using crystal structures. The robustness of the calculations to structural variations in the input models can likely be attributed to the conformational sampling in the molecular dynamics simulations, which allows the modeled receptor to adapt to the "real" conformation for each ligand in the series. This work exemplifies the advantages of using all-atom simulation methods with
Calculations of {sup 8}He+p elastic cross sections using a microscopic optical potential
Lukyanov, V. K.; Zemlyanaya, E. V.; Lukyanov, K. V.; Kadrev, D. N.; Antonov, A. N.; Gaidarov, M. K.; Massen, S. E.
2009-08-15
An approach to calculate microscopic optical potential with the real part obtained by a folding procedure and with the imaginary part inherent in the high-energy approximation is applied to study the {sup 8}He+p elastic-scattering data at energies of tens of MeV/nucleon. The neutron and proton density distributions obtained in different models for {sup 8}He are used in the calculations of the differential cross sections. The role of the spin-orbit potential is studied. Comparison of the calculations with the available experimental data on the elastic-scattering differential cross sections at beam energies of 15.7, 26.25, 32, 66, and 73 MeV/nucleon is performed. The problem of the ambiguities of the depths of each component of the optical potential is considered by means of the imposed physical criterion related to the known behavior of the volume integrals as functions of the incident energy. It is shown also that the role of the surface absorption is rather important, in particular for the lowest incident energies (e.g., 15.7 and 26.25 MeV/nucleon)
Self-consistent calculations of rare-gas-transition-metal interaction potentials
NASA Astrophysics Data System (ADS)
Drakova, D.; Doyen, G.; v. Trentini, F.
1985-11-01
A model Hamiltonian is used to calculate potential-energy surfaces for He and Ne on the (110) faces of Ni, Cu, Pd, and Ag. The calculations are nonperturbative, self-consistent, and contain no parameters which are fittable with respect to the gas-solid interaction. Static image-force effects are included. The theory represents the first quantum-mechanical approach to rare-gas-transition-metal potentials which includes the interaction of the rare-gas orbitals with the d electrons in a consistent way. Corrugation is found to be approximately proportional to the d-electron charge density. The sp band is represented by a Sommerfeld model with hybridization gap, which does not contribute to the corrugation. Part of the potential arises through the hybridization of the rare-gas orbitals with the unoccupied metal states. This interference energy is roughly a factor of 2 larger for neon than for helium, leading to larger corrugations of the neon potentials as compared with the helium potentials. This is in agreement with recent experiments, but in contrast to earlier theoretical predictions. The theoretically calculated corrugations and well depths compare reasonably to the experimental data where available. The computed values of corrugation for He increase in the order Ni, Cu, Ag, and Pd. This agrees with experiments where soft potentials have been fitted to the scattering data, although the predicted He/Ni(110) corrugation is overly large by more than a factor of 2. With increasing energy, the He corrugation increases slightly in the calculations. The dependence is nearly constant for Ni and strongest for Pd. For Ne/Ni(110) and Ne/Pd(110) corrugation decreases with energy. Image-force effects are found to be important for the corrugation and softness of the neon potentials.
Free energy perturbation calculations on glucosidase-inhibitor complexes.
Ruiza, F M; Grigera, J Raúl
2005-09-01
Free energy perturbation studies have been performed on Glucoamylase II (471) from Aspergillus awamori var. X100 complexed with three different inhibitors: (+)lentiginosine, (+)(1S,2S,7R,8aS) 1,2,7-trihydroxyindolizidine, (+)(1S,2S,7S,8aS) 1,2,7-trihydroxyindolizidine and the inactive compound (+)(1S,7R,8aS)-1,7-dihydroxyindolizidine. Molecular dynamic simulations were carried out using a recently developed procedure for fast Free Energy Perturbation calculations. In this procedure only a sphere of 1.8 nm around the central atom of the inhibitor is considered in the calculations. Crystallographic restraints are applied over this reduced system using a generated electron density map. The obtained values for the free energy differences agree with experimental data showing the importance of fast calculations in drug design even when the crystallographic structure of the complex is not available. As the method uses only the crystallographic structure of the receptor, it is possible to test the possible efficiency of even still not synthesised ligands, making the pre-selection of compounds much easy and faster.
Potential infrared relaxation channels calculated for CO2 clathrate hydrates
NASA Astrophysics Data System (ADS)
Lakhlifi, Azzedine; Dahoo, Pierre Richard; Chassefière, Eric
2017-01-01
The infrared bar-spectrum of a single carbon dioxide molecule encapsulated in nano-cage clathrate hydrate is determined using the LD (Lakhlifi-Dahoo) extended site inclusion model successfully applied to analyze the spectra of CO2 isotopologues isolated in rare gas matrices. Trapping is energetically more favorable in clathrate structure of type sI than sII. CO2 exhibits hindered orientational motions (librational motions) around its equilibrium configurations in the small and large nano-cages. The orientation transitions are weak, and the spectra are purely vibrational. In the static field inside the cage, the doubly degenerate bending mode ν2 is blue shifted and split. From the scheme of the calculated energy levels for the different degrees of freedom, which is comparable to that of CO2 in rare gas matrices, it is conjectured that infrared excited CO2 will rather relax radiatively. Non-radiative channels can be analyzed by binary collision model.
2017-01-01
Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke–Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke–Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps. PMID:28402113
Tran, Fabien; Blaha, Peter
2017-05-04
Recently, exchange-correlation potentials in density functional theory were developed with the goal of providing improved band gaps in solids. Among them, the semilocal potentials are particularly interesting for large systems since they lead to calculations that are much faster than with hybrid functionals or methods like GW. We present an exhaustive comparison of semilocal exchange-correlation potentials for band gap calculations on a large test set of solids, and particular attention is paid to the potential HLE16 proposed by Verma and Truhlar. It is shown that the most accurate potential is the modified Becke-Johnson potential, which, most noticeably, is much more accurate than all other semilocal potentials for strongly correlated systems. This can be attributed to its additional dependence on the kinetic energy density. It is also shown that the modified Becke-Johnson potential is at least as accurate as the hybrid functionals and more reliable for solids with large band gaps.
Saint Paul Energy Park: the potential for district heating
Lee, C.; Kron, R.; Davis, H.
1980-03-01
The results of ANL's study of the energy and economic aspects of using district heating in the St. Paul Energy Park are summarized. The Energy Park is a 6 million ft/sup 2/ residential, commercial office, and light industrial complex to be built in the midway area of St. Paul, Minnesota. Space heating and cooling design loads for the park were calculated assuming that the ASHRAE's 90-75 energy-conserving construction standards would be used in constructing the park's buildings. Based in part on this assumption, ANL estimated the costs and energy use characteristics of six possible energy system options for supplying Energy Park's space heating, space cooling, and domestic hot water heating needs. The results indicate that in today's economy, a central heating and cooling plant with natural gas boilers and electrically driven centrifugal chillers with thermal storage has good potential for energy and economic savings and clearly merits further consideration.
Collisionless Plasma Modeling in an Arbitrary Potential Energy Distribution
NASA Technical Reports Server (NTRS)
Liemohn, M. W.; Khazanov, G. V.
1997-01-01
A new technique for calculating a collisionless plasma along a field line is presented. The primary feature of the new model is that it can handle an arbitrary (including nonmonotonic) potential energy distribution. This was one of the limiting constraints on the existing models in this class, and these constraints are generalized for an arbitrary potential energy composition. The formulation for relating current density to the field-aligned potential as well as formulas for density, temperature and energy flux calculations are presented for several distribution functions, ranging from a bi-Lorentzian with a loss cone to an isotropic Maxwellian. A comparison of these results with previous models shows that the formulation reduces.to the earlier models under similar assumptions.
Collisionless Plasma Modeling in an Arbitrary Potential Energy Distribution
NASA Technical Reports Server (NTRS)
Liemohn, M. W.; Khazanov, G. V.
1997-01-01
A new technique for calculating a collisionless plasma along a field line is presented. The primary feature of the new model is that it can handle an arbitrary (including nonmonotonic) potential energy distribution. This was one of the limiting constraints on the existing models in this class, and these constraints are generalized for an arbitrary potential energy composition. The formulation for relating current density to the field-aligned potential as well as formulas for density, temperature and energy flux calculations are presented for several distribution functions, ranging from a bi-Lorentzian with a loss cone to an isotropic Maxwellian. A comparison of these results with previous models shows that the formulation reduces.to the earlier models under similar assumptions.
Potential energy stored by planets and grand minima events
NASA Astrophysics Data System (ADS)
Cionco, Rodolfo G.
2012-07-01
Recently, Wolff & Patrone (2010), have developed a simple but very interesting model by which the movement of the Sun around the barycentre of the Solar system could create potential energy that could be released by flows pre-existing inside the Sun. The authors claim that it is the first mechanism showing how planetary movements can modify internal structure in the Sun that can be related to solar cycle. In this work we point out limitations of mentioned mechanism (which is based on interchange arguments), which could be inapplicable to a real star. Then, we calculate the temporal evolution of potential energy stored in zones of Sun's interior in which the potential energy could be most efficiently stored taking into account detailed barycentric Sun dynamics. We show strong variations of potential energy related to Maunder Minimum, Dalton Minimum and the maximum of Cycle 22, around 1990. We discuss briefly possible implications of this putative mechanism to solar cycle specially Grand Minima events.
Variational Approach to Enhanced Sampling and Free Energy Calculations
NASA Astrophysics Data System (ADS)
Valsson, Omar; Parrinello, Michele
2014-08-01
The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.
Wind energy in China: Estimating the potential
NASA Astrophysics Data System (ADS)
Yuan, Jiahai
2016-07-01
Persistent and significant curtailment has cast concern over the prospects of wind power in China. A comprehensive assessment of the production of energy from wind has identified grid-integrated wind generation potential at 11.9-14% of China's projected energy demand by 2030.
Electronic structure calculations toward new potentially AChE inhibitors
NASA Astrophysics Data System (ADS)
de Paula, A. A. N.; Martins, J. B. L.; Gargano, R.; dos Santos, M. L.; Romeiro, L. A. S.
2007-10-01
The main purpose of this study was the use of natural non-isoprenoid phenolic lipid of cashew nut shell liquid from Anacardium occidentale as lead material for generating new potentially candidates of acetylcholinesterase inhibitors. Therefore, we studied the electronic structure of 15 molecules derivatives from the cardanol using the following groups: methyl, acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, N, N-diethylamine, piperidine, pyrrolidine, and N-benzylamine. The calculations were performed at RHF level using 6-31G, 6-31G(d), 6-31+G(d) and 6-311G(d,p) basis functions. Among the proposed compounds we found that the structures with substitution by acetyl, N, N-dimethylcarbamoyl, N, N-dimethylamine, and pyrrolidine groups were better correlated to rivastigmine indicating possible activity.
Calculating solar photovoltaic potential on residential rooftops in Kailua Kona, Hawaii
NASA Astrophysics Data System (ADS)
Carl, Caroline
As carbon based fossil fuels become increasingly scarce, renewable energy sources are coming to the forefront of policy discussions around the globe. As a result, the State of Hawaii has implemented aggressive goals to achieve energy independence by 2030. Renewable electricity generation using solar photovoltaic technologies plays an important role in these efforts. This study utilizes geographic information systems (GIS) and Light Detection and Ranging (LiDAR) data with statistical analysis to identify how much solar photovoltaic potential exists for residential rooftops in the town of Kailua Kona on Hawaii Island. This study helps to quantify the magnitude of possible solar photovoltaic (PV) potential for Solar World SW260 monocrystalline panels on residential rooftops within the study area. Three main areas were addressed in the execution of this research: (1) modeling solar radiation, (2) estimating available rooftop area, and (3) calculating PV potential from incoming solar radiation. High resolution LiDAR data and Esri's solar modeling tools and were utilized to calculate incoming solar radiation on a sample set of digitized rooftops. Photovoltaic potential for the sample set was then calculated with the equations developed by Suri et al. (2005). Sample set rooftops were analyzed using a statistical model to identify the correlation between rooftop area and lot size. Least squares multiple linear regression analysis was performed to identify the influence of slope, elevation, rooftop area, and lot size on the modeled PV potential values. The equations built from these statistical analyses of the sample set were applied to the entire study region to calculate total rooftop area and PV potential. The total study area statistical analysis findings estimate photovoltaic electric energy generation potential for rooftops is approximately 190,000,000 kWh annually. This is approximately 17 percent of the total electricity the utility provided to the entire island in
NASA Astrophysics Data System (ADS)
Harbola, Manoj; Myneni, Hemanadhan; Shamim, Md.
2014-03-01
The modified local spin density functional and the related local potential for excited-states are tested by employing the ionization potential theorem. The functional is constructed by splitting k-space. Since its functional derivative cannot be obtained easily, the corresponding potential is given by analogy to its ground-state counterpart. Further, to calculate the highest occupied orbital energy ɛmax accurately, the potential is corrected for its asymptotic behavior by employing the van Leeuwen-Barends correction to it. The highest occupied orbital energy ɛmax thus obtained is then compared with the ΔSCF ionization energy calculated using the excited-state functional. It is shown that the two match quite accurately, demonstrating thereby that our approach of constructing excited-state functional is on sound footing.
NASA Astrophysics Data System (ADS)
Negri, Matthias; Recanatini, Maurizio; Hartmann, Rolf W.
2011-09-01
17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) catalyzes the last step of the estrogen biosynthesis, namely the reduction of estrone to the biologically potent estradiol. As such it is a potentially attractive drug target for the treatment of estrogen-dependent diseases like breast cancer and endometriosis. 17β-HSD1 belongs to the bisubstrate enzymes and exists as an ensemble of conformations. These principally differ in the region of the βFαG'-loop, suggesting a prominent role in substrate and inhibitor binding. Although several classes of potent non-steroidal 17β-HSD1 inhibitors currently exist, their binding mode is still unclear. We aimed to elucidate the binding mode of bis(hydroxyphenyl)arenes, a highly potent class of 17β-HSD1 inhibitors, and to rank these compounds correctly with respect to their inhibitory potency, two essential aspects in drug design. Ensemble docking experiments resulted in a steroidal binding mode for the closed enzyme conformations and in an alternative mode for the opened and occluded conformers with the inhibitors placed below the NADPH interacting with it synergically via π-π stacking and H-bond formation. Both binding modes were investigated by MD simulations and MM-PBSA binding free energy estimations using as representative member for this class compound 1 (50 nM). Notably, only the alternative binding mode proved stable and was energetically more favorable, while when simulated in the steroidal binding mode compound 1 was displaced from the active site. In parallel, ab initio studies of small NADPH-inhibitor complexes were performed, which supported the importance of the synergistic interaction between inhibitors and cofactor.
Economic Energy Savings Potential in Federal Buildings
Brown, Daryl R.; Dirks, James A.; Hunt, Diane M.
2000-09-04
The primary objective of this study was to estimate the current life-cycle cost-effective (i.e., economic) energy savings potential in Federal buildings and the corresponding capital investment required to achieve these savings, with Federal financing. Estimates were developed for major categories of energy efficiency measures such as building envelope, heating system, cooling system, and lighting. The analysis was based on conditions (building stock and characteristics, retrofit technologies, interest rates, energy prices, etc.) existing in the late 1990s. The potential impact of changes to any of these factors in the future was not considered.
An ab initio potential energy surface and vibrational energy levels of ZnH2.
Huang, Zheng Guo; Yu, Lei; Dai, Yu Mei
2010-04-15
A three-dimensional potential energy surface of the electronic ground state of ZnH(2) (X1 Sigma(g)+) molecule is constructed from more than 7500 ab initio points calculated at the internally contracted multireference configuration interaction with the Davidson correction (icMRCI+Q) level employing large basis sets. The calculated relative energies of various dissociation reactions are in good agreement with the previous theoretical/experimental values. Low-lying vibrational energy levels of ZnH(2), ZnD(2), and HZnD are calculated on the three-dimensional potential energy surface using the Lanczos algorithm, and found to be in good agreement with the available experimental band origins and the previous theoretical values. 2009 Wiley Periodicals, Inc.
SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M.; Rearden, Bradley T.; Martin, William R.
2016-02-25
Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the development of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.
SCALE Continuous-Energy Eigenvalue Sensitivity Coefficient Calculations
Perfetti, Christopher M.; Rearden, Bradley T.; Martin, William R.
2016-02-25
Sensitivity coefficients describe the fractional change in a system response that is induced by changes to system parameters and nuclear data. The Tools for Sensitivity and UNcertainty Analysis Methodology Implementation (TSUNAMI) code within the SCALE code system makes use of eigenvalue sensitivity coefficients for an extensive number of criticality safety applications, including quantifying the data-induced uncertainty in the eigenvalue of critical systems, assessing the neutronic similarity between different critical systems, and guiding nuclear data adjustment studies. The need to model geometrically complex systems with improved fidelity and the desire to extend TSUNAMI analysis to advanced applications has motivated the developmentmore » of a methodology for calculating sensitivity coefficients in continuous-energy (CE) Monte Carlo applications. The Contributon-Linked eigenvalue sensitivity/Uncertainty estimation via Tracklength importance CHaracterization (CLUTCH) and Iterated Fission Probability (IFP) eigenvalue sensitivity methods were recently implemented in the CE-KENO framework of the SCALE code system to enable TSUNAMI-3D to perform eigenvalue sensitivity calculations using continuous-energy Monte Carlo methods. This work provides a detailed description of the theory behind the CLUTCH method and describes in detail its implementation. This work explores the improvements in eigenvalue sensitivity coefficient accuracy that can be gained through the use of continuous-energy sensitivity methods and also compares several sensitivity methods in terms of computational efficiency and memory requirements.« less
Free energy calculation from umbrella sampling using Bayesian inference
NASA Astrophysics Data System (ADS)
Bernstein, Noam; Stecher, Thomas; Csányi, Gábor
2013-03-01
Using simulations to obtain information about the free energy of a system far from its free energy minima requires biased sampling, for example using a series of harmonic umbrella confining potentials to scan over a range of collective variable values. One fundamental distinction between existing methods that use this approach is in what quantities are measured and how they are used: histograms of the system's probability distribution in WHAM, or gradients of the potential of mean force for umbrella integration (UI) and the single-sweep radial basis function (RBF) approach. Here we present a method that reconstructs the free energy from umbrella sampling data using Bayesian inference that effectively uses all available information from multiple umbrella windows. We show that for a single collective variable, our method can use histograms, gradients, or both, to match or outperform WHAM and UI in the accuracy of free energy for a given amount of total simulation time. In higher dimensions, our method can effectively use gradient information to reconstruct the multidimensional free energy surface. We test our method for the alanine polypeptide model system, and show that it is more accurate than a RBF reconstruction for sparse data, and more stable for abundant data.
Transported Geothermal Energy Technoeconomic Screening Tool - Calculation Engine
Liu, Xiaobing
2016-09-21
This calculation engine estimates technoeconomic feasibility for transported geothermal energy projects. The TGE screening tool (geotool.exe) takes input from input file (input.txt), and list results into output file (output.txt). Both the input and ouput files are in the same folder as the geotool.exe. To use the tool, the input file containing adequate information of the case should be prepared in the format explained below, and the input file should be put into the same folder as geotool.exe. Then the geotool.exe can be executed, which will generate a output.txt file in the same folder containing all key calculation results. The format and content of the output file is explained below as well.
Parquet decomposition calculations of the electronic self-energy
NASA Astrophysics Data System (ADS)
Gunnarsson, O.; Schäfer, T.; LeBlanc, J. P. F.; Merino, J.; Sangiovanni, G.; Rohringer, G.; Toschi, A.
2016-06-01
The parquet decomposition of the self-energy into classes of diagrams, those associated with specific scattering processes, can be exploited for different scopes. In this work, the parquet decomposition is used to unravel the underlying physics of nonperturbative numerical calculations. We show the specific example of dynamical mean field theory and its cluster extensions [dynamical cluster approximation (DCA)] applied to the Hubbard model at half-filling and with hole doping: These techniques allow for a simultaneous determination of two-particle vertex functions and self-energies and, hence, for an essentially "exact" parquet decomposition at the single-site or at the cluster level. Our calculations show that the self-energies in the underdoped regime are dominated by spin-scattering processes, consistent with the conclusions obtained by means of the fluctuation diagnostics approach [O. Gunnarsson et al., Phys. Rev. Lett. 114, 236402 (2015), 10.1103/PhysRevLett.114.236402]. However, differently from the latter approach, the parquet procedure displays important changes with increasing interaction: Even for relatively moderate couplings, well before the Mott transition, singularities appear in different terms, with the notable exception of the predominant spin channel. We explain precisely how these singularities, which partly limit the utility of the parquet decomposition and, more generally, of parquet-based algorithms, are never found in the fluctuation diagnostics procedure. Finally, by a more refined analysis, we link the occurrence of the parquet singularities in our calculations to a progressive suppression of charge fluctuations and the formation of a resonance valence bond state, which are typical hallmarks of a pseudogap state in DCA.
NASA Astrophysics Data System (ADS)
Baudin, Pablo; Kristensen, Kasper
2017-06-01
We present a new framework for calculating coupled cluster (CC) excitation energies at a reduced computational cost. It relies on correlated natural transition orbitals (NTOs), denoted CIS(D')-NTOs, which are obtained by diagonalizing generalized hole and particle density matrices determined from configuration interaction singles (CIS) information and additional terms that represent correlation effects. A transition-specific reduced orbital space is determined based on the eigenvalues of the CIS(D')-NTOs, and a standard CC excitation energy calculation is then performed in that reduced orbital space. The new method is denoted CorNFLEx (Correlated Natural transition orbital Framework for Low-scaling Excitation energy calculations). We calculate second-order approximate CC singles and doubles (CC2) excitation energies for a test set of organic molecules and demonstrate that CorNFLEx yields excitation energies of CC2 quality at a significantly reduced computational cost, even for relatively small systems and delocalized electronic transitions. In order to illustrate the potential of the method for large molecules, we also apply CorNFLEx to calculate CC2 excitation energies for a series of solvated formamide clusters (up to 4836 basis functions).
Applying supersymmetry to energy dependent potentials
Yekken, R.; Lassaut, M.; Lombard, R.J.
2013-11-15
We investigate the supersymmetry properties of energy dependent potentials in the D=1 dimensional space. We show the main aspects of supersymmetry to be preserved, namely the factorization of the Hamiltonian, the connections between eigenvalues and wave functions of the partner Hamiltonians. Two methods are proposed. The first one requires the extension of the usual rules via the concept of local equivalent potential. In this case, the superpotential becomes depending on the state. The second method, applicable when the potential depends linearly on the energy, is similar to what has been already achieved by means of the Darboux transform. -- Highlights: •Supersymmetry extended to energy dependent potentials. •Generalization of the concept of superpotential. •An alternative method used for linear E-dependence leads to the same results as Darboux transform.
Investigating energy-saving potentials in the cloud.
Lee, Da-Sheng
2014-02-20
Collecting webpage messages can serve as a sensor for investigating the energy-saving potential of buildings. Focusing on stores, a cloud sensor system is developed to collect data and determine their energy-saving potential. The owner of a store under investigation must register online, report the store address, area, and the customer ID number on the electric meter. The cloud sensor system automatically surveys the energy usage records by connecting to the power company website and calculating the energy use index (EUI) of the store. Other data includes the chain store check, company capital, location price, and the influence of weather conditions on the store; even the exposure frequency of store under investigation may impact the energy usage collected online. After collecting data from numerous stores, a multi-dimensional data array is constructed to determine energy-saving potential by identifying stores with similarity conditions. Similarity conditions refer to analyzed results that indicate that two stores have similar capital, business scale, weather conditions, and exposure frequency on web. Calculating the EUI difference or pure technical efficiency of stores, the energy-saving potential is determined. In this study, a real case study is performed. An 8-dimensional (8D) data array is constructed by surveying web data related to 67 stores. Then, this study investigated the savings potential of the 33 stores, using a site visit, and employed the cloud sensor system to determine the saving potential. The case study results show good agreement between the data obtained by the site visit and the cloud investigation, with errors within 4.17%. Among 33 the samples, eight stores have low saving potentials of less than 5%. The developed sensor on the cloud successfully identifies them as having low saving potential and avoids wasting money on the site visit.
Investigating Energy-Saving Potentials in the Cloud
Lee, Da-Sheng
2014-01-01
Collecting webpage messages can serve as a sensor for investigating the energy-saving potential of buildings. Focusing on stores, a cloud sensor system is developed to collect data and determine their energy-saving potential. The owner of a store under investigation must register online, report the store address, area, and the customer ID number on the electric meter. The cloud sensor system automatically surveys the energy usage records by connecting to the power company website and calculating the energy use index (EUI) of the store. Other data includes the chain store check, company capital, location price, and the influence of weather conditions on the store; even the exposure frequency of store under investigation may impact the energy usage collected online. After collecting data from numerous stores, a multi-dimensional data array is constructed to determine energy-saving potential by identifying stores with similarity conditions. Similarity conditions refer to analyzed results that indicate that two stores have similar capital, business scale, weather conditions, and exposure frequency on web. Calculating the EUI difference or pure technical efficiency of stores, the energy-saving potential is determined. In this study, a real case study is performed. An 8-dimensional (8D) data array is constructed by surveying web data related to 67 stores. Then, this study investigated the savings potential of the 33 stores, using a site visit, and employed the cloud sensor system to determine the saving potential. The case study results show good agreement between the data obtained by the site visit and the cloud investigation, with errors within 4.17%. Among 33 the samples, eight stores have low saving potentials of less than 5%. The developed sensor on the cloud successfully identifies them as having low saving potential and avoids wasting money on the site visit. PMID:24561405
NASA Astrophysics Data System (ADS)
Yang, Xue; Hassanein, Ahmed
2014-02-01
Tungsten surface binding energy is calculated using classical molecular dynamic simulations with three many-body potentials. We present the consistency in tungsten sputtering yield by beryllium bombardment between molecular dynamic LAMMPS code and binary collision approximation ITMC code using the new surface binding energy (11.75 eV). The commonly used heat of sublimation value (8.68 eV) could lead to overestimated sputtering yield results. The analysis of the sputtered tungsten angular distributions show that molecular dynamic accurately reproduced the [1 1 1] most prominent preferential ejection directions in bcc tungsten, while the distinct shapes by typical MC codes such as ITMC code is caused by the treatment of amorphous target. The ITMC calculated emitted tungsten energy profile matches the Thompson energy spectrum, while the molecular dynamic results generally follow the Falcone energy spectrum.
Potential of pin-by-pin SPN calculations as an industrial reference
Fliscounakis, M.; Girardi, E.; Courau, T.; Couyras, D.
2012-07-01
This paper aims at analysing the potential of pin-by-pin SP{sub n} calculations to compute the neutronic flux in PWR cores as an alternative to the diffusion approximation. As far as pin-by-pin calculations are concerned, a SPH equivalence is used to preserve the reactions rates. The use of SPH equivalence is a common practice in core diffusion calculations. In this paper, a methodology to generalize the equivalence procedure in the SP{sub n} equations context is presented. In order to verify and validate the equivalence procedure, SP{sub n} calculations are compared to 2D transport reference results obtained with the APOLL02 code. The validation cases consist in 3x3 analytical assembly color sets involving burn-up heterogeneities, UOX/MOX interfaces, and control rods. Considering various energy discretizations (up to 26 groups) and flux development orders (up to 7) for the SP{sub n} equations, results show that 26-group SP{sub 3} calculations are very close to the transport reference (with pin production rates discrepancies < 1%). This proves the high interest of pin-by-pin SP{sub n} calculations as an industrial reference when relying on 26 energy groups combined with SP{sub 3} flux development order. Additionally, the SP{sub n} results are compared to diffusion pin-by-pin calculations, in order to evaluate the potential benefit of using a SP{sub n} solver as an alternative to diffusion. Discrepancies on pin-production rates are less than 1.6% for 6-group SP{sub 3} calculations against 3.2% for 2-group diffusion calculations. This shows that SP{sub n} solvers may be considered as an alternative to multigroup diffusion. (authors)
Ionization potential of {sup 9}Be calculated including nuclear motion and relativistic corrections
Stanke, Monika; Kedziera, Dariusz; Bubin, Sergiy; Adamowicz, Ludwik
2007-05-15
Variational calculations employing explicitly correlated Gaussian functions have been performed for the ground states of {sup 9}Be and {sup 9}Be{sup +} including the nuclear motion [i.e., without assuming the Born-Oppenheimer (BO) approximation]. An approach based on the analytical energy gradient calculated with respect to the Gaussian exponential parameters was employed, leading to energies of the two systems noticeably improved over those found in the recent paper of Pachucki and Komasa [Phys. Rev. A 73, 052502 (2006)]. The non-BO wave functions were used to calculate the {alpha}{sup 2} relativistic corrections ({alpha}=e{sup 2}/({Dirac_h}/2{pi})c). With those corrections and the {alpha}{sup 3} and {alpha}{sup 4} corrections taken from Pachucki and Komasa, a new value of the ionization potential (IP) of {sup 9}Be was determined. It agrees very well with the most recent experimental IP.
Multiple scattering calculations of relativistic electron energy loss spectra
NASA Astrophysics Data System (ADS)
Jorissen, K.; Rehr, J. J.; Verbeeck, J.
2010-04-01
A generalization of the real-space Green’s-function approach is presented for ab initio calculations of relativistic electron energy loss spectra (EELS) which are particularly important in anisotropic materials. The approach incorporates relativistic effects in terms of the transition tensor within the dipole-selection rule. In particular, the method accounts for relativistic corrections to the magic angle in orientation resolved EELS experiments. The approach is validated by a study of the graphite CK edge, for which we present an accurate magic angle measurement consistent with the predicted value.
Empirically corrected HEAT method for calculating atomization energies
Brand, Holmann V
2008-01-01
We describe how to increase the accuracy ofthe most recent variants ofthe HEAT method for calculating atomization energies of molecules by means ofextremely simple empirical corrections that depend on stoichiometry and the number ofunpaired electrons in the molecule. Our corrections reduce the deviation from experiment for all the HEAT variants. In particular, our corrections reduce the average absolute deviation and the root-mean-square deviation ofthe 456-QP variant to 0.18 and 0.23 kJoule/mol (i.e., 0.04 and 0.05 kcallmol), respectively.
Potential energy surface and rovibrational energy levels of the H2-CS van der Waals complex.
Denis-Alpizar, Otoniel; Stoecklin, Thierry; Halvick, Philippe; Dubernet, Marie-Lise; Marinakis, Sarantos
2012-12-21
Owing to its large dipole, astrophysicists use carbon monosulfide (CS) as a tracer of molecular gas in the interstellar medium, often in regions where H(2) is the most abundant collider. Predictions of the rovibrational energy levels of the weakly bound complex CS-H(2) (not yet observed) and also of rate coefficients for rotational transitions of CS in collision with H(2) should help to interpret the observed spectra. This paper deals with the first goal, i.e., the calculation of the rovibrational energy levels. A new four-dimensional intermolecular potential energy surface for the H(2)-CS complex is presented. Ab initio potential energy calculations were carried out at the coupled-cluster level with single and double excitations and a perturbative treatment of triple excitations, using a quadruple-zeta basis set and midbond functions. The potential energy surface was obtained by an analytic fit of the ab initio data. The equilibrium structure of the H(2)-CS complex is found to be linear with the carbon pointing toward H(2) at the intermolecular separation of 8.6 a(o). The corresponding well depth is -173 cm(-1). The potential was used to calculate the rovibrational energy levels of the para-H(2)-CS and ortho-H(2)-CS complexes. The present work provides the first theoretical predictions of these levels. The calculated dissociation energies are found to be 35.9 cm(-1) and 49.9 cm(-1), respectively, for the para and ortho complexes. The second virial coefficient for the H(2)-CS pair has also been calculated for a large range of temperature. These results could be used to assign future experimental spectra and to check the accuracy of the potential energy surface.
High-Level Calculations on Nitrosooxyalanes: Possible New High-Energy Materials?
NASA Astrophysics Data System (ADS)
Stouffer, Michael L.; Ball, David W.
2010-06-01
As part of our survey of new potential high-energy materials, we have calculated the structures, vibrational frequencies and spectra, and various enthalpies of reaction for nitrosooxy-, dinitrosooxy-, and trinitrosooxyalane. Although the initial intent was to determine the properties of nitroalanes, in all cases the bonding to the central aluminum atom was through an oxygen atom of the NO2 group. All molecules optimized to a near planar structure. Calculations of their reaction energies showed that the higher the nitrosooxy content, the more negative the enthalpies of formation, with enthalpies of combustion or decomposition falling precipitously.
A Variational Approach to Enhanced Sampling and Free Energy Calculations
NASA Astrophysics Data System (ADS)
Parrinello, Michele
2015-03-01
The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.
Three-dimensional potential energy surface of Ar-CO.
Sumiyoshi, Yoshihiro; Endo, Yasuki
2015-01-14
A three-dimensional intermolecular potential energy surface of the Ar-CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.
Three-dimensional potential energy surface of Ar–CO
Sumiyoshi, Yoshihiro; Endo, Yasuki
2015-01-14
A three-dimensional intermolecular potential energy surface of the Ar–CO complex has been determined by fitting most of the previously reported spectroscopic data, where observed transition frequencies by microwave, millimeter-wave, submillimeter-wave, and infrared spectroscopy were reproduced simultaneously within their experimental accuracies. A free rotor model Hamiltonian considering all the freedom of motions for an atom-diatom system was applied to calculate vibration-rotation energies. A three-dimensional potential energy surface obtained by ab initio calculations at the CCSD(T)-F12b/aug-cc-pV5Z level of theory was parameterized by a model function consisting of 46 parameters. They were used as initial values for the least-squares analysis of the experimental data. A total of 20 parameters were optimized to reproduce all the spectroscopic data.
N2(+) bound quartet and sextet state potential energy curves
NASA Technical Reports Server (NTRS)
Partridge, H.; Bauschlicher, C. W., Jr.; Stallcop, J. R.
1985-01-01
The N2(+) potential energies have been determined from a complete active space self-consistent field calculation with active 2s and 2p electrons. A (6s 4p 3d 1f) Gaussian basis set was used together with additional higher angular momentum and diffuse functions. The calculated potential energy curves for the states 4Sigma(mu)(+), 4Pi(g), and 6Sigma(g)(+), for which there are no spectroscopic observations, are presented. The corresponding spectroscopic constants have been determined from a polynomial curve fit to the computed energies near the well minima and are shown. The 6Sigma(g)(+) state is found to be significantly bound, with a minimum at 1.72 A.
Low-energy K- optical potentials: deep or shallow?
NASA Astrophysics Data System (ADS)
Cieplý, A.; Friedman, E.; Gal, A.; Mareš, J.
2001-12-01
The K- optical potential in the nuclear medium is evaluated self consistently from a free-space K-Nt matrix constructed within a coupled-channel chiral approach. The fit of model parameters gives a good description of the low-energy data plus the available K- atomic data. The resulting optical potential is relatively `shallow' in contradiction to the potentials obtained from phenomenological analysis. The calculated (Kstop-,π) hypernuclear production rates are very sensitive to the details of kaonic bound state wave function. The (Kstop-,π) reaction could thus serve as a suitable tool to distinguish between shallow and deep K- optical potentials.
Pseudospectral Gaussian quantum dynamics: Efficient sampling of potential energy surfaces.
Heaps, Charles W; Mazziotti, David A
2016-04-28
Trajectory-based Gaussian basis sets have been tremendously successful in describing high-dimensional quantum molecular dynamics. In this paper, we introduce a pseudospectral Gaussian-based method that achieves accurate quantum dynamics using efficient, real-space sampling of the time-dependent basis set. As in other Gaussian basis methods, we begin with a basis set expansion using time-dependent Gaussian basis functions guided by classical mechanics. Unlike other Gaussian methods but characteristic of the pseudospectral and collocation methods, the basis set is tested with N Dirac delta functions, where N is the number of basis functions, rather than using the basis function as test functions. As a result, the integration for matrix elements is reduced to function evaluation. Pseudospectral Gaussian dynamics only requires O(N) potential energy calculations, in contrast to O(N(2)) evaluations in a variational calculation. The classical trajectories allow small basis sets to sample high-dimensional potentials. Applications are made to diatomic oscillations in a Morse potential and a generalized version of the Henon-Heiles potential in two, four, and six dimensions. Comparisons are drawn to full analytical evaluation of potential energy integrals (variational) and the bra-ket averaged Taylor (BAT) expansion, an O(N) approximation used in Gaussian-based dynamics. In all cases, the pseudospectral Gaussian method is competitive with full variational calculations that require a global, analytical, and integrable potential energy surface. Additionally, the BAT breaks down when quantum mechanical coherence is particularly strong (i.e., barrier reflection in the Morse oscillator). The ability to obtain variational accuracy using only the potential energy at discrete points makes the pseudospectral Gaussian method a promising avenue for on-the-fly dynamics, where electronic structure calculations become computationally significant.
Isotope Separation and Decay Energy Calculation for LISA Commissioning Experiment
NASA Astrophysics Data System (ADS)
Taylor, Nathaniel; Barker, Alyson; Garrett, Sierra; Rogers, Warren F.; MoNA Collaboration
2013-10-01
The commissioning experiment for the Large multi-Institutional Scintillator Array (LISA) was designed to investigate properties of neutron-unstable excited states of the 24O. The array is located at the NSCL, MSU and is used in conjunction with the Modular Neutron Array (MoNA) and the Sweeper Magnet. Oxygen fragments produced by the 26F secondary beam incident on a Be target are directed through the Sweeper Chamber which includes two tracking CRDC detectors, an ion chamber, and a thin and thick scintillator. Plotting the fragment's trajectory position vs. angle vs. time of flight allows for separation of the individual 22 , 23 , and 24 O isotopes, necessary for the calculation of the decay properties of individual states. Anomalous features in the fragments' emittance distribution, believed to result from little understood issues with the tracking detectors, required that we adopt a slightly different approach than that developed recently by the collaboration. Once the isotopes are successfully separated, decay energies are calculated by applying mass-invariant decay spectroscopy by associating the fragment's precise trajectory (determined by inverse-tracking through the Sweeper Magnet) and energy with those of the emitted neutron. Work supported by NSF grant PHY-1101745.
Valence calculations of binding energies of mid-row lanthanides
NASA Astrophysics Data System (ADS)
O'Malley, Steven M.; Beck, Donald R.
2008-05-01
Binding energies of mid-row lanthanides have been calculated by taking advantage of the >90% LS purity of the 4f^n subgroups of their neutral ground states ootnotetextAtomic Energy Levels -- The Rare-Earth Elements, edited by W. C. Martin, R. Zalubas, and L. Hagan, Natl. Bur. Stand. Ref. Data Ser. Natl. Bur. Stand. (U.S.) Circ. No. 60 (U.S. GPO, Washington, D.C., 1978).. As described in our recent work on Nd^- ootnotetextS. M. O'Malley and D. R. Beck, Phy. Rev. A 77, 012505 (2008)., the 4f^n electrons were treated as core-like and restricted to a single LS term throughout all Dirac-Fock and correlation configurations, resulting in manageable relativistic configuration-interaction calculations for these computationally complex systems. Several weakly bound 6p attachments (<200 meV) were found for each negative ion, and these were carefully analyzed with respect to approximate LS total configuration as well as the j's of the the 4f^n subgroup and 6p electron.
Hay, P.J.; Wadt, W.R.
1985-01-01
Ab initio effective core potentials (ECP's) have been generated to replace the Coulomb, exchange, and core-orthogonality effects of the chemically inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series relative ECP's have been generated which also incorporate the mass--velocity and Darwin relativistic effects into the potential. The ab initio ECP's should facilitate valence electron calculations on molecules containing transition-metal atoms with accuracies approaching all-electron calculations at a fraction of the computational cost. Analytic fits to the potentials are presented for use in multicenter integral evaluation. Gaussian orbital valence basis sets are developed for the (3d,4s,4p), (4d,5s,5p), and (5d,6s,6p) orbitals of the first, second, and third transition series atoms, respectively. All-electron and valence-electron atomic excitation energies are also compared for the low-lying states of Sc--Hg, and the valence-electron calculations are found to reproduce the all-electron excitation energies (typically within a few tenths of an eV).
Theoretical method for full ab initio calculation of DNA/RNA-ligand interaction energy
NASA Astrophysics Data System (ADS)
Chen, Xi H.; Zhang, John Z. H.
2004-06-01
In this paper, we further develop the molecular fractionation with conjugate caps (MFCC) scheme for quantum mechanical computation of DNA-ligand interaction energy. We study three oligonuclear acid interaction systems: dinucleotide dCG/water, trinucleotide dCGT/water, and a Watson-Crick paired DNA segment, dCGT/dGCA. Using the basic MFCC approach, the nucleotide chains are cut at each phosphate group and a pair of conjugate caps (concaps) are inserted. Five cap molecules have been tested among which the dimethyl phosphate anion is proposed to be the standard concap for application. For each system, one-dimensional interaction potential curves are computed using the MFCC method and the calculated interaction energies are found to be in excellent agreement with corresponding results obtained from the full system ab initio calculations. The current study extends the application of the MFCC method to ab initio calculations for DNA- or RNA-ligand interaction energies.
Intermolecular potential energy surface and thermophysical properties of propane
NASA Astrophysics Data System (ADS)
Hellmann, Robert
2017-03-01
A six-dimensional potential energy surface (PES) for the interaction of two rigid propane molecules was determined from supermolecular ab initio calculations up to the coupled cluster with single, double, and perturbative triple excitations level of theory for 9452 configurations. An analytical site-site potential function with 14 sites per molecule was fitted to the calculated interaction energies. To validate the analytical PES, the second virial coefficient and the dilute gas shear viscosity and thermal conductivity of propane were computed. The dispersion part of the potential function was slightly adjusted such that quantitative agreement with the most accurate experimental data for the second virial coefficient at room temperature was achieved. The adjusted PES yields values for the three properties that are in very good agreement with the best experimental data at all temperatures.
Biomass resource potential using energy crops
Wright, L.L.; Cushman, J.H.; Martin, S.A.
1993-09-01
Biomass energy crops can provide a significant and environmentally beneficial source of renewable energy feedstocks for the future. They can revitalize the agricultural sector of the US economy by providing profitable uses for marginal cropland. Energy crops include fast-growing trees, perennial grasses, and annual grasses, all capable of collecting solar energy and storing it as cellulosic compounds for several months to several years. Once solar energy is thus captured, it can be converted by means of currently available technologies to a wide variety of energy products such as electricity, heat, liquid transportation fuels, and gases. Experimental results from field trials have generated optimism that selected and improved energy crops, established on cropland with moderate limitations for crop production, have the potential for producing high yields. Both trees and grasses, under very good growing conditions, have produced average annual yields of 20 to 40 dry Mg ha{sup {minus}1} year{sup {minus}1}. Sorghum has shown especially high yields in the Midwest. Hybrids between sugar cane and its wild relatives, called energy cane, have yielded as much as 50 dry Mg ha{sup {minus}1} year{sup {minus}1} in Florida. These experimental results demonstrate that some species have the genetic potential for very rapid growth rates. New wood energy crop systems developed by the Department of Energy`s Biofuels Feedstock Development Program offer, at a minimum, a 100% increase in biomass production rates over the 2 to 4 Mg ha{sup {minus}1} year{sup {minus}1} of dry leafless woody biomass produced by most natural forest systems. Experimental data indicate that short rotation wood crops established on cropland with moderate limitations are capable of producing biomass yields of 8--20 dry Mg ha{sup {minus}1} year{sup {minus}1} with a present average about 11 dry Mg ha{sup {minus}1} year{sup {minus}1} on typical cropland sites.
Energy savings potential in air conditioners and chiller systems
Kaya, Durmus; Alidrisi, Hisham
2014-01-22
In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment cost and pay back periods were calculated.
Energy savings potential in air conditioners and chiller systems
Kaya, Durmus; Alidrisi, Hisham
2014-01-22
In the current paper we quantified and evaluated the energy saving potential in air conditioners and chiller systems. Here, we also showed how to reduce the cost of air conditioners and chiller systems in existing facilities on the basis of payback periods. Among the measures investigated were: (1) installing higher efficiency air conditioners, (2) installing higher efficiency chillers, (3) duty cycling air conditioning units, and (4) utilizing existing economizers on air conditioning units. For each method, examples were provided from Arizona, USA. In these examples, the amount of saved energy, the financial evaluation of this energy, and the investment costmore » and pay back periods were calculated.« less
Velaga, Srinath C; Anderson, Brian J
2014-01-16
Gas hydrate deposits are receiving increased attention as potential locations for CO2 sequestration, with CO2 replacing the methane that is recovered as an energy source. In this scenario, it is very important to correctly characterize the cage occupancies of CO2 to correctly assess the sequestration potential as well as the methane recoverability. In order to predict accurate cage occupancies, the guest–host interaction potential must be represented properly. Earlier, these potential parameters were obtained by fitting to experimental equilibrium data and these fitted parameters do not match with those obtained by second virial coefficient or gas viscosity data. Ab initio quantum mechanical calculations provide an independent means to directly obtain accurate intermolecular potentials. A potential energy surface (PES) between H2O and CO2 was computed at the MP2/aug-cc-pVTZ level and corrected for basis set superposition error (BSSE), an error caused due to the lower basis set, by using the half counterpoise method. Intermolecular potentials were obtained by fitting Exponential-6 and Lennard-Jones 6-12 models to the ab initio PES, correcting for many-body interactions. We denoted this model as the “VAS” model. Reference parameters for structure I carbon dioxide hydrate were calculated using the VAS model (site–site ab initio intermolecular potentials) as Δμ(w)(0) = 1206 ± 2 J/mol and ΔH(w)(0) = 1260 ± 12 J/mol. With these reference parameters and the VAS model, pure CO2 hydrate equilibrium pressure was predicted with an average absolute deviation of less than 3.2% from the experimental data. Predictions of the small cage occupancy ranged from 32 to 51%, and the large cage is more than 98% occupied. The intermolecular potentials were also tested by calculating the pure CO2 density and diffusion of CO2 in water using molecular dynamics simulations.
Potential reduction of DSN uplink energy cost
NASA Technical Reports Server (NTRS)
Dolinsky, S.; Degroot, N. F.
1982-01-01
DSN Earth stations typically transmit more power than that required to meet minimum specifications for uplink performance. Energy and cost savings that could result from matching the uplink power to the amount required for specified performance are studied. The Galileo mission was selected as a case study. Although substantial reduction in transmitted energy is possible, potential savings in source energy (oil or electricity) savings are much less. This is because of the rising inefficiency in power conversion and radio frequency power generation that accompanies reduced power output.
Potential reduction of DSN uplink energy cost
NASA Technical Reports Server (NTRS)
Dolinsky, S.; Degroot, N. F.
1982-01-01
DSN Earth stations typically transmit more power than that required to meet minimum specifications for uplink performance. Energy and cost savings that could result from matching the uplink power to the amount required for specified performance are studied. The Galileo mission was selected as a case study. Although substantial reduction in transmitted energy is possible, potential savings in source energy (oil or electricity) savings are much less. This is because of the rising inefficiency in power conversion and radio frequency power generation that accompanies reduced power output.
First-principles study of terpyrrole as a potential hydrogen cyanide sensor: DFT calculations.
Shokuhi Rad, Ali; Zardoost, Mohammad Reza; Abedini, Ehsan
2015-10-01
The sensitivity of terpyrrole (TPy; used as a polypyrrole model) to toxic hydrogen cyanide (HCN) adsorption was studied by using DFT to perform geometry optimization and to calculate the adsorption energy of HCN on TPy as well as orbital properties. The interaction of terpyrrole with HCN was studied for different relative orientations of the molecules. The adsorption energy, charge analysis, and the density of states were used to evaluate the ability of TPy to sense HCN in these different relative orientations. The adsorption energy was calculated to be -3.9 and -3.1 kcal mol(-1) for two possible relative orientations. Frontier molecular orbitals and energies indicated that some hybridization occurs during the adsorption of HCN on TPy when the molecules have appropriate relative orientations, resulting in an increase in conductivity. Considering the changes in the HOMO-LUMO energy gap that were calculated to occur during HCN adsorption, it is clear that TPy is sensitive to HCN adsorption, suggesting that TPy has the potential to act as an HCN sensor. Graphical abstract HCN adsorption on TPy.
Many-Body Potentials for Aqueous Be(2+) Derived from ab Initio Calculations.
Winter, Nicolas D
2016-12-08
An effective three-body potential for the aqueous Be(2+) ion has been constructed from a large number of high-level ab initio cluster calculations. The new potential was validated in subsequent molecular dynamics simulations of both gas phase ion-water clusters and bulk liquid. The structures of the first and second solvation shells were studied using radial distribution functions and angular distribution functions. The vibrational spectrum of Be(2+) and first shell waters was examined by computing power spectra from the molecular dynamics simulations. The observed bands showed reasonable agreement with experimental spectroscopic frequencies. The potential of mean force for water exchange between the first and second solvation shells was calculated and the energy barrier for exchange was found to have improved agreement with experiment relative to two-body force fields. Examination of the solvation structure near the transition state yielded results consistent with an associative mechanism.
Defect Properties in GaN: Ab Initio and Empirical Potential Calculations
Gao, Fei; Bylaska, Eric J.; Weber, William J.
2005-01-03
The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, eventually relax into a N+-N<11-20 > split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the Ga+-Ga<11-20 > split interstitial can bridge the gap between non-bounded Ga atoms. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials.
Potential energy sputtering of EUVL materials
Pomeroy, J M; Ratliff, L P; Gillaspy, J D; Bajt, S
2004-07-02
Of the many candidates employed for understanding the erosion of critical Extreme Ultraviolet Lithography (EUVL) components, potential energy damage remains relatively uninvestigated. Unlike the familiar kinetic energy sputtering, which is a consequence of the momentum transferred by an ion to atoms in the target, potential energy sputtering occurs when an ion rapidly collects charge from the target as it neutralizes. Since the neutralization energy of a singly charged ion is typically on the order of 10 eV, potential energy effects are generally neglected for low charge state ions, and hence the bulk of the sputtering literature. As an ion's charge state is increased, the potential energy (PE) increases rapidly, e.g. PE(Xe{sup 1+})= 11 eV, PE(Xe{sup 10+}) = 810 eV, PE(Xe{sup 20+}) = 4.6 keV, etc. By comparison, the binding energy of a single atom on a surface is typically about 5 eV, so even relatively inefficient energy transfer mechanisms can lead to large quantities of material being removed, e.g. 25% efficiency for Xe{sup 10+} corresponds to {approx} 40 atoms/ion. By comparison, singly charged xenon ions with {approx} 20 keV of kinetic energy sputter only about 5 atoms/ion at normal incidence, and less than 1 atom/ion at typical EUV source energies. EUV light sources are optimized for producing approximately 10{sup 16} xenon ions per shot with an average charge state of q=10 in the core plasma. At operational rates of {approx}10 kHz, the number of ions produced per second becomes a whopping 10{sup 20}. Even if only one in a billion ions reaches the collector, erosion rates could reach {approx}10{sup 12} atoms per second, severely reducing the collector lifetime (for an average yield of 10 atoms/ion). In addition, efforts to reduce contamination effects may contribute to reduced neutralization and even larger potential energy damages rates (discussed further below). In order to provide accurate estimates for collector lifetimes and to develop mitigation schemes
Ab initio molecular dynamics calculations of ion hydration free energies.
Leung, Kevin; Rempe, Susan B; von Lilienfeld, O Anatole
2009-05-28
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li(+), Cl(-), and Ag(+) ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (phi) contributions, we obtain absolute AIMD hydration free energies (DeltaG(hyd)) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model phi predictions. The sums of Li(+)/Cl(-) and Ag(+)/Cl(-) AIMD DeltaG(hyd), which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag(+)+Ni(+)-->Ag+Ni(2+) in water. The predictions for this reaction suggest that existing estimates of DeltaG(hyd) for unstable radiolysis intermediates such as Ni(+) may need to be extensively revised.
Calculated self-energy contributions for an ns valence electron using the multiple-commutator method
NASA Astrophysics Data System (ADS)
Labzowsky, Leonti; Goidenko, Igor; Tokman, Maria; Pyykkö, Pekka
1999-04-01
The self-energy (SE) correction is evaluated for a single valence ns electron of heavy and superheavy atoms with n up to 8 and the nuclear charge Z up to 119. The recently developed approach based on the commutator expansion is employed. Various Dirac-Slater one-electron local potentials with extended nuclei are used. The Lamb shifts were calculated by adding the average values of the Uehling potential to the SE contributions. The results confirm the earlier estimates for the quantum electrodynamical effects on the valence energies of heavy and superheavy atoms.
Quantum Calculations on Salt Bridges with Water: Potentials, Structure, and Properties
Liao, Sing; Green, Michael E.
2011-01-01
Salt bridges are electrostatic links between acidic and basic amino acids in a protein; quantum calculations are used here to determine the energetics and other properties of one form of these species, in the presence of water molecules. The acidic groups are carboxylic acids (aspartic and glutamic acids); proteins have two bases with pK above physiological pH: one, arginine, with a guanidinium basic group, the other lysine, which is a primary amine. Only arginine is modeled here, by ethyl guanidinium, while propionic acid is used as a model for either carboxylic acid. The salt bridges are accompanied by 0-12 water molecules; for each of the 13 systems, the energy-bond distance relation, natural bond orbitals (NBO), frequency calculations allowing thermodynamic corrections to room temperature, and dielectric constant dependence, were all calculated. The water molecules were found to arrange themselves in hydrogen bonded rings anchored to the oxygens of the salt bridge components. This was not surprising in itself, but it was found that the rings lead to a periodicity in the energy, and to a 'water addition' rule. The latter shows that the initial rings, with four oxygen atoms, become five member rings when an additional water molecule becomes available, with the additional water filling in at the bond with the lowest Wiberg index, as calculated using NBO. The dielectric constant dependence is the expected hyperbola, and the fit of the energy to the inverse dielectric constant is determined. There is an energy periodicity related to ring formation upon addition of water molecules. When 10 water molecules have been added, all spaces near the salt bridge are filled, completing the first hydration shell, and a second shell starts to form. The potentials associated with salt bridges depend on their hydration, and potentials assigned without regard to local hydration are likely to cause errors as large as or larger than kBT, thus suggesting a serious problem if these
NASA Astrophysics Data System (ADS)
Dapprich, S.; Pidun, U.; Ehlers, A. W.; Frenking, G.
1995-08-01
The metal-ligand bond dissociation energies (CO) nM-L are theoretically predicted at the HF, MP2 and CCSD(T) levels of theory using effective core potentials for the metals for M = Cr, Mo, W, Ni, Pd, Pt and for L = CO, NO +, CN -, NC -, CS, SiO, N 2. The bond energies at the HF level are too low and the MP2 values are too high, while the CCSD(T) results are in good agreement with experimental data. The bond energies at MP2 show the same trend as the CCSD(T) values and may therefore be used for the prediction of relative bond dissociation energies. The absolute values for the bond energies calculated at MP2 are significantly improved when they are corrected using the energies of isostructural reactions M(CO) n + L → M(CO) n-1 L + CO.
Free-energy calculation of structure-H hydrates
NASA Astrophysics Data System (ADS)
Okano, Yamato; Yasuoka, Kenji
2006-01-01
A molecular-dynamics (MD) simulation of structure-H hydrates was performed under constant pressure and temperature with 6120 TIP4P water molecules, 900 OPLS-UA methane molecules, and 180 large molecular guest substance (LMGS) molecules. The LMGS molecules were represented in the form of a one-site Lennard-Jones (LJ) model using the LJ parameters σ and ɛ. In order to clarify the thermodynamic stability of structure-H hydrates, we calculated the free-energy difference, changing on the σ and ɛ only of the LMGS molecules. In this simulation, stable crystals of structure-H hydrates and a minimum value of ΔG were obtained at σ ˜6.2Å and large values of ɛ. All simulations were performed using the special-purpose computer hardware MDGRAPE-2.
Communication: Fitting potential energy surfaces with fundamental invariant neural network
NASA Astrophysics Data System (ADS)
Shao, Kejie; Chen, Jun; Zhao, Zhiqiang; Zhang, Dong H.
2016-08-01
A more flexible neural network (NN) method using the fundamental invariants (FIs) as the input vector is proposed in the construction of potential energy surfaces for molecular systems involving identical atoms. Mathematically, FIs finitely generate the permutation invariant polynomial (PIP) ring. In combination with NN, fundamental invariant neural network (FI-NN) can approximate any function to arbitrary accuracy. Because FI-NN minimizes the size of input permutation invariant polynomials, it can efficiently reduce the evaluation time of potential energy, in particular for polyatomic systems. In this work, we provide the FIs for all possible molecular systems up to five atoms. Potential energy surfaces for OH3 and CH4 were constructed with FI-NN, with the accuracy confirmed by full-dimensional quantum dynamic scattering and bound state calculations.
Separable representation of energy-dependent optical potentials
NASA Astrophysics Data System (ADS)
Hlophe, L.; Elster, Ch.
2016-03-01
Background: One important ingredient for many applications of nuclear physics to astrophysics, nuclear energy, and stockpile stewardship are cross sections for reactions of neutrons with rare isotopes. Since direct measurements are often not feasible, indirect methods, e.g., (d ,p ) reactions, should be used. Those (d ,p ) reactions may be viewed as three-body reactions and described with Faddeev techniques. Purpose: Faddeev equations in momentum space have a long tradition of utilizing separable interactions in order to arrive at sets of coupled integral equations in one variable. Optical potentials representing the effective interactions in the neutron (proton) nucleus subsystem are usually non-Hermitian as well as energy dependent. Potential matrix elements as well as transition matrix elements calculated with them must fulfill the reciprocity theorem. The purpose of this paper is to introduce a separable, energy-dependent representation of complex, energy-dependent optical potentials that fulfill reciprocity exactly. Methods: Momentum space Lippmann-Schwinger integral equations are solved with standard techniques to obtain the form factors for the separable representation. Results: Starting from a separable, energy-independent representation of global optical potentials based on a generalization of the Ernst-Shakin-Thaler (EST) scheme, a further generalization is needed to take into account the energy dependence. Applications to n +48Ca ,n +208Pb , and p +208Pb are investigated for energies from 0 to 50 MeV with special emphasis on fulfilling reciprocity. Conclusions: We find that the energy-dependent separable representation of complex, energy-dependent phenomenological optical potentials fulfills reciprocity exactly. In addition, taking into account the explicit energy dependence slightly improves the description of the S matrix elements.
Tsuzuki, Seiji; Tanabe, Kazutoshi )
1991-03-21
Intermolecular interaction energies of methane dimer were calculated by using several basis sets up to 6-311G(3d,4p) with electron correlation energy correction by the Moeller-Plesset perturbation method and basis set superposition error (BSSE) correction by the counterpoise method to evaluate the basis set effect. The calculated interaction energies depended on the basis set considerably. Whereas the interaction energies of repulsive component calculated at HF level were not affected by the change of basis set, the dispersion energy component dependent greatly on the basis set used. The dispersion energies calculated with the Moeller-Plesset second- and third-order perturbation by using 6-311G(2d,2p) basis set were 0-10% and 4-6% smaller than those obtained with the fourth-order (MP4(SDTQ)) perturbation, respectively. The BSSE's calculated by the counterpoise method were still about 30% of the calculated intermolecular interaction energies for the conformers of energy minima event at the MP4(SDTQ)/6-311G(2d,2p) level. The calculated interaction potentials of dimers at the MP4(SDTQ)/6-311G(2d,2p) level were considerably shallower than those obtained by MM2 force fields but were close to the potentials given by the Williams potential and by the recently reported MM3 force field.
A novel method for calculating relative free energy of similar molecules in two environments
NASA Astrophysics Data System (ADS)
Farhi, Asaf; Singh, Bipin
2017-03-01
Calculating relative free energies is a topic of substantial interest and has many applications including solvation and binding free energies, which are used in computational drug discovery. However, there remain the challenges of accuracy, simple implementation, robustness and efficiency, which prevent the calculations from being automated and limit their use. Here we present an exact and complete decoupling analysis in which the partition functions of the compared systems decompose into the partition functions of the common and different subsystems. This decoupling analysis is applicable to submolecules with coupled degrees of freedom such as the methyl group and to any potential function (including the typical dihedral potentials), enabling to remove less terms in the transformation which results in a more efficient calculation. Then we show mathematically, in the context of partition function decoupling, that the two compared systems can be simulated separately, eliminating the need to design a composite system. We demonstrate the decoupling analysis and the separate transformations in a relative free energy calculation using MD simulations for a general force field and compare to another calculation and to experimental results. We present a unified soft-core technique that ensures the monotonicity of the numerically integrated function (analytical proof) which is important for the selection of intermediates. We show mathematically that in this soft-core technique the numerically integrated function can be non-steep only when we transform the systems separately, which can simplify the numerical integration. Finally, we show that when the systems have rugged energy landscape they can be equilibrated without introducing another sampling dimension which can also enable to use the simulation results for other free energy calculations.
Parallel Calculation of CCSDT and Mk-MRCCSDT Energies.
Prochnow, Eric; Harding, Michael E; Gauss, Jürgen
2010-08-10
A scheme for the parallel calculation of energies at the coupled-cluster singles, doubles, and triples (CCSDT) level of theory, several approximate iterative CCSDT schemes (CCSDT-1a, CCSDT-1b, CCSDT-2, CCSDT-3, and CC3), and for the state-specific multireference coupled-cluster ansatz suggested by Mukherjee with a full treatment of triple excitations (Mk-MRCCSDT) is presented. The proposed scheme is based on the adaptation of a highly efficient serial coupled-cluster code leading to a communication-minimized implementation by parallelizing the time-determining steps. The parallel algorithm is tailored for affordable cluster architectures connected by standard communication networks such as Gigabit Ethernet. In this way, CCSDT and Mk-MRCCSDT computations become feasible even for larger molecular systems and basis sets. An analysis of the time-determining steps for CCSDT and Mk-MRCCSDT, namely the computation of the triple-excitation amplitudes and their individual contributions, is carried out. Benchmark calculations are presented for the N2O, ozone, and benzene molecules, proving that the parallelization of these steps is sufficient to obtain an efficient parallel scheme. A first application to the case of 2,6-pyridyne using a triple-ζ quality basis (222 basis functions) is presented demonstrating the efficiency of the current implementation.
Spectroscopic properties and potential energy surfaces of GeH
NASA Astrophysics Data System (ADS)
Balasubramanian, K.; Li, Junqing
1988-04-01
MCSCF (complete active space SCF) followed by configuration interaction calculations are carried out on 12 electronic states of GeH. Relativistic configuration interaction calculations are carried out with the objective of computing the spin-orbit corrections for the low-lying states. These calculations reveal the existence of 10 bound electronic states of GeH for which spectroscopic properties are computed. The three experimentally observed bands ( a- X, A- X, B- X) are assigned and the uncertainties in the experimental Te and ωe values of these states are corrected. In addition, the spectroscopic properties of 8 states are calculated which are yet to be observed. The spin-orbit coupling constant for the ground state X( 2Π) is calculated to be 869 cm -1. An accurate dissociation energy of 2.81 eV was obtained using {MCSCF}/{SOCI} calculation which employed a large Gaussian basis set questioning the experimental De of ˜3.3 eV obtained from the predissociation in the A2Δ state. It is shown that the intersection of the repulsive 4Π curve which dissociates into the ground state atoms causes predissociation in the A( 2Δ) , B( 2Σ +) , 2Σ +(III), and 2Π(II) states. The potential energy surfaces of a few excited states contain barriers. The calculated ground state dipole moment of 0.098 D is in disagreement with an experimental value of 1.24 D, questioning the experimental dipole moment.
The Potential for Energy Efficiency and Renewable Energy in North Carolina
Hadley, SW
2003-08-06
As many states have restructured their electric power industry, they have established a ''systems benefit charge'' to help fund those activities that will no longer be funded by utilities in the new structure. Examples include weatherization of low-income housing, efficiency programs, and renewable energy development. Varying amounts have been collected and allocated depending on state needs and abilities. One question that arises is what are the potential results of funding the different types of programs. What is the potential for energy efficiency or for renewable power, and what would be accomplished given the amount of funding that the system benefit charge may provide? The purpose of this project is to provide an initial estimate of the potential for energy efficiency and renewable energy in North Carolina. This potential could be funded by a public benefits fund resulting from a green power program being considered in the state. It concentrates on electric energy savings and production. Savings in buildings can include improvements to space conditioning as well as improvements to lighting or other appliances. Distributed power potential, through use of combined heat and power and renewables such as photovoltaic, wind, and biomass were examined. The goal is to provide information to decision makers who are developing a green power program in North Carolina. It will not be a complete and detailed study of all efficiency potentials but is more of a scoping exercise to determine the relative impacts and begin the process for a more definitive study at a later date. Statewide energy savings potential cannot be directly measured but must be calculated. First, the word ''potential'' means that the savings have not occurred yet. Second, the savings are often only indirectly measured by estimating what energy use there would have been without the changes in technology or behavior. Calculations through sampling and statistical analysis or by simulation are a necessary
Calculations supporting evaluation of potential environmental standards for Yucca Mountain
Duguid, J.O.; Andrews, R.W.; Brandstetter, E.; Dale, T.F.; Reeves, M.
1994-04-01
The Energy Policy Act of 1992, Section 801 (US Congress, 1992) provides for the US Environmental Protection Agency (EPA) to contract the National Academy of Sciences (NAS) to conduct a study and provide findings and recommendations on reasonable standards for the disposal of high-level wastes at the Yucca Mountain site. The NAS study is to provide findings and recommendations which include, among other things, whether a health-based standard based on dose to individual members of the public from releases to the accessible environment will provide a reasonable standard for the protection of the health and safety of the public. The EPA, based upon and consistent with the findings and recommendations of the NAS, is required to promulgate standards for protection of the public from releases from radioactive materials stored or disposed of in a repository at the Yucca Mountain site. This document presents a number of different ``simple`` analyses of undisturbed repository performance that are intended to provide input to those responsible for setting appropriate environmental standards for a potential repository at the Yucca Mountain site in Nevada. Each of the processes included in the analyses has been simplified to capture the primary significance of that process in containing or isolating the waste from the biosphere. In these simplified analyses, the complex waste package interactions were approximated by a simple waste package ``failure`` distribution which is defined by the initiation and rate of waste package ``failures``. Similarly, releases from the waste package and the engineered barrier system are controlled by the very near field environment and the presence and rate of advective and diffusive release processes. Release was approximated by either a simple alteration-controlled release for the high solubility radionuclides and either a diffusive or advective-controlled release for the solubility-limited radionuclides.
Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid.
Saouane, Sofiane; Buth, Gernot; Fabbiani, Francesca P A
2013-11-01
The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure, PIXEL lattice energy calculations confirm the predominance of the Coulombic term (-379.1 kJ mol(-1)) ahead of the polarization (-141.4 kJ mol(-1)), dispersion (-133.7 kJ mol(-1)) and repulsion (266.3 kJ mol(-1)) contributions.
Effects of energy spectrum on dose distribution calculations for high energy electron beams.
Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik
2009-01-01
In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities.
Effects of energy spectrum on dose distribution calculations for high energy electron beams
Toutaoui, Abdelkader; Khelassi-Toutaoui, Nadia; Brahimi, Zakia; Chami, Ahmed Chafik
2009-01-01
In an early work we have demonstrated the possibility of using Monte Carlo generated pencil beams for 3D electron beam dose calculations. However, in this model the electron beam was considered as monoenergetic and the effects of the energy spectrum were taken into account by correction factors, derived from measuring central-axis depth dose curves. In the present model, the electron beam is considered as polyenergetic and the pencil beam distribution of a clinical electron beam, of a given nominal energy, is represented as a linear combination of Monte Carlo monoenergetic pencil beams. The coefficients of the linear combination describe the energy spectrum of the clinical electron beam, and are chosen to provide the best-fit between the calculated and measured central axis depth dose, in water. The energy spectrum is determined by the constrained least square method. The angular distribution of the clinical electron beam is determined by in-air penumbra measurements. The predictions of this algorithm agree very well with the measurements in the region near the surface, and the discrepancies between the measured and calculated dose distributions, behind 3D heterogeneities, are reduced to less than 10%. We have demonstrated a new algorithm for 3D electron beam dose calculations, which takes into account the energy spectra. Results indicate that the use of this algorithm leads to a better modeling of dose distributions downstream, from complex heterogeneities. PMID:20126560
Research on energy transmission calculation problem on laser detecting submarine
NASA Astrophysics Data System (ADS)
Fu, Qiang; Li, Yingchao; Zhang, Lizhong; Wang, Chao; An, Yan
2014-12-01
The laser detection and identification is based on the method of using laser as the source of signal to scan the surface of ocean. If the laser detection equipment finds out the target, it will immediately reflect the returning signal, and then through receiving and disposing the returning signal by the receiving system, to realize the function of detection and identification. Two mediums channels should be though in the process of laser detection transmission, which are the atmosphere and the seawater. The energy loss in the process of water transport, mainly considering the surface reflection and scattering attenuation and internal attenuation factors such as seawater. The energy consumption though atmospheric transmission, mainly considering the absorption of atmospheric and the attenuation causing by scattering, the energy consumption though seawater transmission, mainly considering the element such as surface reflection, the attenuation of scattering and internal attenuation of seawater. On the basis of the analysis and research, through the mode of establishment of atmospheric scattering, the model of sea surface reflection and the model of internal attenuation of seawater, determine the power dissipation of emitting lasers system, calculates the signal strength that reaches the receiver. Under certain conditions, the total attenuation of -98.92 dB by calculation, and put forward the related experiment scheme by the use of Atmospheric analog channel, seawater analog channel. In the experiment of the theory, we use the simulation pool of the atmosphere and the sea to replace the real environment where the laser detection system works in this kind of situation. To start with, we need to put the target in the simulating seawater pool of 10 meters large and then control the depth of the target in the sea level. We, putting the laser detection system in position where it is 2 kilometers far from one side, secondly use the equipment to aim at the target in some
The molecular potential energy surface and vibrational energy levels of methyl fluoride. Part II.
Manson, Steven A; Law, Mark M; Atkinson, Ian A; Thomson, Grant A
2006-06-28
New analytical bending and stretching, ground electronic state, potential energy surfaces for CH(3)F are reported. The surfaces are expressed in bond-length, bond-angle internal coordinates. The four-dimensional stretching surface is an accurate, least squares fit to over 2000 symmetrically unique ab initio points calculated at the CCSD(T) level. Similarly, the five-dimensional bending surface is a fit to over 1200 symmetrically unique ab initio points. This is an important first stage towards a full nine-dimensional potential energy surface for the prototype CH(3)F molecule. Using these surfaces, highly excited stretching and (separately) bending vibrational energy levels of CH(3)F are calculated variationally using a finite basis representation method. The method uses the exact vibrational kinetic energy operator derived for XY(3)Z systems by Manson and Law (preceding paper, Part I, Phys. Chem. Chem. Phys., 2006, 8, DOI: 10.1039/b603106d). We use the full C(3v) symmetry and the computer codes are designed to use an arbitrary potential energy function. Ultimately, these results will be used to design a compact basis for fully coupled stretch-bend calculations of the vibrational energy levels of the CH(3)F system.
Nikitin, A V; Rey, M; Tyuterev, Vl G
2015-03-07
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB4 molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q)(-2) type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH4 molecule is demonstrated.
Nikitin, A. V.; Rey, M.; Tyuterev, Vl. G.
2015-03-07
A simultaneous use of the full molecular symmetry and of an exact kinetic energy operator (KEO) is of key importance for accurate predictions of vibrational levels at a high energy range from a potential energy surface (PES). An efficient method that permits a fast convergence of variational calculations would allow iterative optimization of the PES parameters using experimental data. In this work, we propose such a method applied to tetrahedral AB{sub 4} molecules for which a use of high symmetry is crucial for vibrational calculations. A symmetry-adapted contracted angular basis set for six redundant angles is introduced. Simple formulas using this basis set for explicit calculation of the angular matrix elements of KEO and PES are reported. The symmetric form (six redundant angles) of vibrational KEO without the sin(q){sup −2} type singularity is derived. The efficient recursive algorithm based on the tensorial formalism is used for the calculation of vibrational matrix elements. A good basis set convergence for the calculations of vibrational levels of the CH{sub 4} molecule is demonstrated.
Hong, Tianzhen; Buhl, Fred; Haves, Philip
2008-03-28
California has been using DOE-2 as the main building energy analysis tool in the development of building energy efficiency standards (Title 24) and the code compliance calculations. However, DOE-2.1E is a mature program that is no longer supported by LBNL on contract to the USDOE, or by any other public or private entity. With no more significant updates in the modeling capabilities of DOE-2.1E during recent years, DOE-2.1E lacks the ability to model, with the necessary accuracy, a number of building technologies that have the potential to reduce significantly the energy consumption of buildings in California. DOE-2's legacy software code makes it difficult and time consuming to add new or enhance existing modeling features in DOE-2. Therefore the USDOE proposed to develop a new tool, EnergyPlus, which is intended to replace DOE-2 as the next generation building simulation tool. EnergyPlus inherited most of the useful features from DOE-2 and BLAST, and more significantly added new modeling capabilities far beyond DOE-2, BLAST, and other simulations tools currently available. With California's net zero energy goals for new residential buildings in 2020 and for new commercial buildings in 2030, California needs to evaluate and promote currently available best practice and emerging technologies to significantly reduce energy use of buildings for space cooling and heating, ventilating, refrigerating, lighting, and water heating. The California Energy Commission (CEC) needs to adopt a new building energy simulation program for developing and maintaining future versions of Title 24. Therefore, EnergyPlus became a good candidate to CEC for its use in developing and complying with future Title 24 upgrades. In 2004, the Pacific Gas and Electric Company contracted with ArchitecturalEnergy Corporation (AEC), Taylor Engineering, and GARD Analytics to evaluate EnergyPlus in its ability to model those energy efficiency measures specified in both the residential and
Potential Energy Cost Savings from Increased Commercial Energy Code Compliance
Rosenberg, Michael I.; Hart, Philip R.; Athalye, Rahul A.; Zhang, Jian; Cohan, David F.
2016-08-22
An important question for commercial energy code compliance is: “How much energy cost savings can better compliance achieve?” This question is in sharp contrast to prior efforts that used a checklist of code requirements, each of which was graded pass or fail. Percent compliance for any given building was simply the percent of individual requirements that passed. A field investigation method is being developed that goes beyond the binary approach to determine how much energy cost savings is not realized. Prototype building simulations were used to estimate the energy cost impact of varying levels of non-compliance for newly constructed office buildings in climate zone 4C. Field data collected from actual buildings on specific conditions relative to code requirements was then applied to the simulation results to find the potential lost energy savings for a single building or for a sample of buildings. This new methodology was tested on nine office buildings in climate zone 4C. The amount of additional energy cost savings they could have achieved had they complied fully with the 2012 International Energy Conservation Code is determined. This paper will present the results of the test, lessons learned, describe follow-on research that is needed to verify that the methodology is both accurate and practical, and discuss the benefits that might accrue if the method were widely adopted.
NASA Astrophysics Data System (ADS)
Wu, Xiao-Zhi; Wang, Rui; Wang, Shao-Feng; Wei, Qun-Yi
2010-08-01
The ab initio calculations have been used to study the generalized-stacking-fault energy (GSFE) surfaces and surface energies for the closed-packed (1 1 1) plane in FCC metals Cu, Ag, Au, Ni, Al, Rh, Ir, Pd, Pt, and Pb. The GSFE curves along <112> (1 1 1) direction and <110> (1 1 1) direction, and surface energies have been calculated from first principles. Based on the translational symmetry of the GSFE surfaces, the fitted expressions have been obtained from the Fourier series. Our results of the GSFEs and surface energies agree better with experimental results. The metals Al, Pd, and Pt have low γ/γI value, so full dislocation will be observed easily; while Cu, Ag, Au, and Ni have large γ/γI value, so it is preferred to create partial dislocation. From the calculations of surface energies, it is confirmed that the VIII column elements Ni, Rh, Ir, Pd, and Pt have higher surface energies than other metals.
The metabolic energy cost of action potential velocity
NASA Astrophysics Data System (ADS)
Crotty, Patrick; Sangrey, Thomas; Levy, William
2006-03-01
Voltage changes in neurons and other active cells are caused by the passage of ions across the cell membrane. These ionic currents depend on the transmembrane ion concentration gradients, which in unmyelinated axons are maintained during rest and restored after electrical activity by an ATPase sodium-potassium exchanger in the membrane. The amount of ATP consumed by this exchanger can be taken as the metabolic energy cost of any electrical activity in the axon. We use this measure, along with biophysical models of voltage-gated sodium and potassium ion channels, to quantify the energy cost of action potentials propagating in squid giant axons. We find that the energy of an action potential can be naturally divided into three separate components associated with different aspects of the action potential. We calculate these energy components as functions of the ion channel densities and axon diameters and find that the component associated with the rising phase and velocity of the action potential achieves a minimum near the biological values of these parameters. This result, which is robust with respect to other parameters such as temperature, suggests that evolution has optimized the axon for the energy of the action potential wavefront.
Potential energy hypersurface and molecular flexibility
NASA Astrophysics Data System (ADS)
Koča, Jaroslav
1993-02-01
The molecular flexibility phenomenon is discussed from the conformational potential energy(hyper) surface (PES) point of view. Flexibility is considered as a product of three terms: thermodynamic, kinetic and geometrical. Several expressions characterizing absolute and relative molecular flexibility are introduced, depending on a subspace studied of the entire conformational space, energy level E of PES as well as absolute temperature. Results obtained by programs DAISY, CICADA and PANIC in conjunction with molecular mechanics program MMX for flexibility analysis of isopentane, 2,2-dimethylpentane and isohexane molecules are introduced.
Zhang, Yong; Voth, Gregory A.
2011-01-01
Free energy calculations are one of the most useful methods for the study of ion transport mechanisms through confined spaces such as protein ion channels. Their reliability depends on a correctly defined reaction coordinate (RC). A straight line is usually not a proper RC for such complicated processes so in this work a combined metadynamics/umbrella sampling (MTD/US) method is proposed. In the combined method, the ion transport pathway is first identified by the MTD method and then the free energy profile or potential of mean force (PMF) along the path is calculated using umbrella sampling. This combined method avoids the discontinuity problem often associated with normal umbrella sampling calculations that assume a straight line RC and it provides a more physically accurate PMF for such processes. The method is demonstrated for the proton transport process through the protein channel of aquaporin-1. PMID:25100923
NASA Astrophysics Data System (ADS)
Zhang, Bo; Peng, Bo; Huang, Jingfang; Pitsianis, Nikos P.; Sun, Xiaobai; Lu, Benzhuo
2015-05-01
We present PAFMPB, an updated and parallel version of the AFMPB software package for fast calculation of molecular solvation-free energy. The new version has the following new features: (1) The adaptive fast multipole method and the boundary element methods are parallelized; (2) A tool is embedded for automatic molecular VDW/SAS surface mesh generation, leaving the requirement for a mesh file at input optional; (3) The package provides fast calculation of the total solvation-free energy, including the PB electrostatic and nonpolar interaction contributions. PAFMPB is implemented in C and Fortran programming languages, with the Cilk Plus extension to harness the computing power of both multicore and vector processing. Computational experiments demonstrate the successful application of PAFMPB to the calculation of the PB potential on a dengue virus system with more than one million atoms and a mesh with approximately 20 million triangles.
NASA Astrophysics Data System (ADS)
Hu, Ching-Han; Chong, Delano P.
1996-11-01
Our recent procedure of the unrestricted generalized transition state (uGTS) model for density functional calculations of core-electron binding energies has been applied to seven carbonyl and nitrosyl inorganic complexes: Fe(CO) 5, Ni(CO) 4, Mn(CO) 4NO, Co(CO) 3NO, Fe(CO) 2(NO) 2, Mn(NO) 3CO and Cr(NO) 4. The exchange-correlation potential is based on a combined functional of Becke's exchange (B88) and Perdew's correlation (P86). The cc-pVTZ basis set was used for the calculation of neutral molecules, while for the partial cation created in the uGTS approach we scaled the cc-pVTZ basis set using a procedure based on Clementi and Raimondi's rules for atomic screening. The average absolute deviation of the calculated core-electron binding energy from experiment is 0.28 eV.
Calculation of action potential propagation in nerve fiber.
Bogatov, N M; Grigoryan, L R; Ponetaeva, E G; Sinisyn, A S
2014-05-01
This article introduces generalization of the action potential spreading model which considers generation of the action potential in each segment of the nerve fiber. Behavior of the impulse signal waveform during the propagation process was analyzed. A mechanism of distributed generation of the charge in nerve fiber results in decrease of phase velocity of signal spreading rate. Amplitude of the action potential decreases and pulse width increases in the action potential propagation process. Copyright © 2014 Elsevier Ltd. All rights reserved.
Dong, Jichen; Wang, Huan; Peng, Hailin; Liu, Zhongfan
2017-01-01
The formation of grain boundaries (GBs) in graphene films is both fundamentally interesting and practically important for many applications. A GB in graphene is known as a linear defect and is formed during the coalescence of two single crystalline graphene domains. The covalent binding between domains is broadly known as the mechanism of GB formation during graphene chemical vapor deposition (CVD) growth. Here, we demonstrate another GB formation mechanism, where two graphene domains are connected by weak van der Waals interactions between overlapping graphene layers. The formation mechanism of the overlapping GBs (OLGBs) is systematically explored theoretically and the proposed conditions for forming OLGBs are validated by experimental observations. This discovery leads to a deep understanding of the mechanism of graphene CVD growth and reveals potential means for graphene quality control in CVD synthesis. PMID:28507676
Romańczyk, Piotr P; Rotko, Grzegorz; Kurek, Stefan S
2016-08-10
Formal potentials of the first reduction leading to dechlorination in dimethylformamide were obtained from convolution analysis of voltammetric data and confirmed by quantum chemical calculations for a series of polychlorinated benzenes: hexachlorobenzene (-2.02 V vs. Fc(+)/Fc), pentachloroanisole (-2.14 V), and 2,4-dichlorophenoxy- and 2,4,5-trichlorophenoxyacetic acids (-2.35 V and -2.34 V, respectively). The key parameters required to calculate the reduction potential, electron affinity and/or C-Cl bond dissociation energy, were computed at both DFT-D and CCSD(T)-F12 levels. Comparison of the obtained gas-phase energies and redox potentials with experiment enabled us to verify the relative energetics and the performance of various implicit solvent models. Good agreement with the experiment was achieved for redox potentials computed at the DFT-D level, but only for the stepwise mechanism owing to the error compensation. For the concerted electron transfer/C-Cl bond cleavage process, the application of a high level coupled cluster method is required. Quantum chemical calculations have also demonstrated the significant role of the π*ring and σ*C-Cl orbital mixing. It brings about the stabilisation of the non-planar, C2v-symmetric C6Cl6˙(-) radical anion, explains the experimentally observed low energy barrier and the transfer coefficient close to 0.5 for C6Cl5OCH3 in an electron transfer process followed by immediate C-Cl bond cleavage in solution, and an increase in the probability of dechlorination of di- and trichlorophenoxyacetic acids due to substantial population of the vibrational excited states corresponding to the out-of-plane C-Cl bending at ambient temperatures.
Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics
NASA Astrophysics Data System (ADS)
Hošek, Petr; Spiwok, Vojtěch
2016-01-01
Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.
NASA Astrophysics Data System (ADS)
Bhatta, Ram S.; Perry, David S.
2010-06-01
The inter-ring torsional potentials of poly (3-methyl thiophene) (P3MT) oligomers are investigated by means of electronic structure calculations. Single layer and ONIOM calculations were performed at B3LYP level with 6-31++G(d,p) basis on the partially optimized geometries of dimer, tetramer and hexamer of P3MT oligomers. Potential energy surfaces are computed as a function of the multiple inter-ring torsional angles involved. The following conclusions are reached: (i) A mixture of cis and trans geometries can be expected in a disordered polymer. (ii) The cis-trans barrier is low enough to allow cis-trans conversion at room temperature. (iii) In the dimer, the potential energy minima are about 30^0 from the cis and trans planar geometries, but planar geometries are stabilized as the chain length increases. (iv) The extended conjugation causes the torsional potential about one inter-ring bond to be coupled to other torsions along the oligomer chain.
Computed potential energy surfaces for chemical reactions
NASA Technical Reports Server (NTRS)
Walch, Stephen P.
1990-01-01
The objective was to obtain accurate potential energy surfaces (PES's) for a number of reactions which are important in the H/N/O combustion process. The interest in this is centered around the design of the SCRAM jet engine for the National Aerospace Plane (NASP), which was envisioned as an air-breathing hydrogen-burning vehicle capable of reaching velocities as large as Mach 25. Preliminary studies indicated that the supersonic flow in the combustor region of the scram jet engine required accurate reaction rate data for reactions in the H/N/O system, some of which was not readily available from experiment. The most important class of combustion reactions from the standpoint of the NASP project are radical recombinaton reactions, since these reactions result in most of the heat release in the combustion process. Theoretical characterizations of the potential energy surfaces for these reactions are presented and discussed.
The H 2O ++ Ground State Potential Energy Surface
NASA Astrophysics Data System (ADS)
Bunker, P. R.; Bludsky, Ota; Jensen, Per; Wesolowski, S. S.; Van Huis, T. J.; Yamaguchi, Y.; Schaefer, H. F.
1999-12-01
At the correlation-consistent polarized-valence quadruple-zeta complete active space self-consistent field second-order configuration interaction level of ab initio theory (cc-pVQZ CASSCF-SOCI), we calculated 129 points on the ground electronic state potential energy surface of the water dication H2O++; this calculation includes the energy of X3Σ- OH+ at equilibrium and the energy of the triplet oxygen atom. We determined the parameters in an analytical function that represents this surface out to the (OH+ + H+) and (O + 2H+) dissociation limits, for bending angles from 70 to 180°. There is a metastable minimum in this surface, at an energy of 43 600 cm-1 above the H+ + OH+ dissociation energy, and the geometry at this minimum is linear (D∞h), with an OH bond length of 1.195 Å. On the path to dissociation to H+ + OH+, there is a saddle point at an energy of 530 cm-1 above the minimum, and the geometry at the saddle point is linear (C∞ Kv) with OH bond lengths of 1.121 and 1.489 Å. Using the stabilization method, we calculated the lowest resonance on this surface. Relative to the metastable local minimum on the potential energy surface, the position of the lowest resonance for H2O++, D2O++, and T2O++ is 1977(85), 1473(25), and 1249(10) cm-1, respectively, where the width of each resonance (in cm-1) is given in parentheses.
Grid-based steered thermodynamic integration accelerates the calculation of binding free energies.
Fowler, Philip W; Jha, Shantenu; Coveney, Peter V
2005-08-15
The calculation of binding free energies is important in many condensed matter problems. Although formally exact computational methods have the potential to complement, add to, and even compete with experimental approaches, they are difficult to use and extremely time consuming. We describe a Grid-based approach for the calculation of relative binding free energies, which we call Steered Thermodynamic Integration calculations using Molecular Dynamics (STIMD), and its application to Src homology 2 (SH2) protein cell signalling domains. We show that the time taken to compute free energy differences using thermodynamic integration can be significantly reduced: potentially from weeks or months to days of wall-clock time. To be able to perform such accelerated calculations requires the ability to both run concurrently and control in realtime several parallel simulations on a computational Grid. We describe how the RealityGrid computational steering system, in conjunction with a scalable classical MD code, can be used to dramatically reduce the time to achieve a result. This is necessary to improve the adoption of this technique and further allows more detailed investigations into the accuracy and precision of thermodynamic integration. Initial results for the Src SH2 system are presented and compared to a reported experimental value. Finally, we discuss the significance of our approach.
Energy Savings Potential of Radiative Cooling Technologies
Fernandez, Nicholas; Wang, Weimin; Alvine, Kyle J.; Katipamula, Srinivas
2015-11-30
Pacific Northwest National Laboratory (PNNL), with funding from the U.S. Department of Energy’s (DOE’s) Building Technologies Program (BTP), conducted a study to estimate, through simulation, the potential cooling energy savings that could be achieved through novel approaches to capturing free radiative cooling in buildings, particularly photonic ‘selective emittance’ materials. This report documents the results of that study.
Potential energy landscapes of tetragonal pyramid molecules
NASA Astrophysics Data System (ADS)
Yoshida, Yuichiro; Sato, Hirofumi; Morgan, John W. R.; Wales, David J.
2016-11-01
Hiraoka et al. have developed a self-assembling system referred to as a nanocube (Hiraoka et al., 2008). In the present contribution a coarse-grained model for this system is analysed, focusing on how the potential energy landscape for self-assembly is related to the geometry of the building blocks. We find that six molecules assemble to form various clusters, with cubic and sheet structures the most stable. The relative stability is determined by the geometry of the building blocks.
Hydriding and dehydriding energies of PuHx from ab initio calculations
NASA Astrophysics Data System (ADS)
Yang, Yu; Zhang, Ping
2015-08-01
Based on ab initio calculations within the density-functional theory (DFT) + U theoretical formalism, we systematically study the electronic properties of different PuHx compounds. We successfully obtain the antiferromagnetic ground state for PuH2 and the ferromagnetic ground state for PuH3. In combination with chemical potential calculations, we obtain the hydriding and dehydriding energies for PuHx compounds at different temperatures, which accord well with available experimental results. The equilibrium hydrogen pressure along the hydriding and dehydriding processes is presented and carefully analyzed.
Multireference coupled-cluster calculation of the dissociation energy profile of triplet ketene
NASA Astrophysics Data System (ADS)
Ogihara, Yusuke; Yamamoto, Takeshi; Kato, Shigeki
2011-07-01
Triplet ketene exhibits a steplike structure in the experimentally observed photodissociation rates, but its mechanism is still unknown despite many theoretical efforts. Here we revisit this problem by calculating the potential energy profile of triplet ketene with the Adamowicz and Mukherjee multireference coupled-cluster (MRCC) theories. At the MRCCSD level, the imaginary frequency of the dissociation barrier is calculated to be about 300i cm-1, which is slightly smaller than the previous estimates but is still much greater than the expected maximum value for reproducing the observed steps (100i cm-1). This implies that other types of mechanisms (including nonadiabatic ones) may be more plausible for the observed steps.
Caveat Emptor: Calculating All the Costs of Energy.
ERIC Educational Resources Information Center
Zinberg, Dorothy S.
This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…
Caveat Emptor: Calculating All the Costs of Energy.
ERIC Educational Resources Information Center
Zinberg, Dorothy S.
This paper examines the energy problem. Specific topics discussed include the recent history of oil and gas consumption in the United States, conservation, coal, solar energy, and nuclear energy. While solutions to the energy problem differ, there is an urgent need for broad, public debate. Ultimately, the decisions made regarding energy will be…
Enzymatic minimum free energy path calculations using swarms of trajectories.
Sanchez-Martinez, Melchor; Field, Martin; Crehuet, Ramon
2015-01-22
The development of approaches for simulating rare events in complex molecular systems is a central concern in chemical physics. In recent work, Roux and co-workers proposed a novel, swarms of trajectories (SoT) method for determining the transition paths of such events. It consists of the dynamical refinement on the system's free energy surface of a putative transition path that is parametrized in terms of a set of collective variables (CVs) that are identified as being important for the transition. In this work, we have implemented the SoT method and used it to investigate the catalytic mechanisms of two enzymatic reactions using hybrid QM/MM potentials. Our aim has been to test the performance of SoT for enzyme systems and to devise robust simulation protocols that can be employed in future studies of this type. We identify the conditions under which converged results can be obtained using inertial and Brownian dynamical evolutions of the CVs, show that the inclusion of several CVs can give significant additional insight into the mechanisms of the reactions, and show that the use of minimum energy paths as starting guesses can greatly accelerate path refinement.
Accuracy and precision of free-energy calculations via molecular simulation
NASA Astrophysics Data System (ADS)
Lu, Nandou
A quantitative characterization of the methodologies of free-energy perturbation (FEP) calculations is presented, and optimal implementation of the methods for reliable and efficient calculation is addressed. Some common misunderstandings in the FEP calculations are corrected. The two opposite directions of FEP calculations are uniquely defined as generalized insertion and generalized deletion, according to the entropy change along the perturbation direction. These two calculations are not symmetric; they produce free-energy results differing systematically due to the different capability of each to sample the important phase-space in a finite-length simulation. The FEP calculation errors are quantified by characterizing the simulation sampling process with the help of probability density functions for the potential energy change. While the random error in the FEP calculation is analyzed with a probabilistic approach, the systematic error is characterized as the most-likely inaccuracy, which is modeled considering the poor sampling of low-probability energy distribution tails. Our analysis shows that the entropy difference between the perturbation systems plays a key role in determining the reliability of FEP results, and the perturbation should be carried out in the insertion direction in order to ensure a good sampling and thus a reliable calculation. Easy-to-use heuristics are developed to estimate the simulation errors, as well as the simulation length that ensures a certain accuracy level of the calculation. The fundamental understanding obtained is then applied to tackle the problem of multistage FEP optimization. We provide the first principle of optimal staging: For each substage FEP calculation, the higher entropy system should be used as the reference to govern the sampling, i.e., the calculation should be conducted in the generalized insertion direction for each stage of perturbation. To minimize the simulation error, intermediate states should be
NASA Technical Reports Server (NTRS)
Rosen, A.; Ellis, D. E.; Adachi, H.; Averill, F. W.
1976-01-01
A numerical-variational method for performing self-consistent molecular calculations in the Hartree-Fock-Slater (HFS) model is presented. Molecular wavefunctions are expanded in terms of basis sets constructed from numerical HFS solutions of selected one-center atomlike problems. Binding energies and wavefunctions for the molecules are generated using a discrete variational method for a given molecular potential. In the self-consistent-charge (SCC) approximation to the complete self-consistent-field (SCF) method, results of a Mulliken population analysis of the molecular eigenfunctions are used in each iteration to produce 'atomic' occupation numbers. The simplest SCC potential is then obtained from overlapping spherical atomlike charge distributions. Molecular ionization energies are calculated using the transition-state procedure; results are given for CO, H2O, H2S, AlCl, InCl, and the Ni5O surface complex. Agreement between experimental and theoretical ionization energies for the free-molecule valence levels is generally within 1 eV. The simple SCC procedure gives a reasonably good approximation to the molecular potential, as shown by comparison with experiment, and with complete SCF calculations for CO, H2O, and H2S.
Calculating activation energies for temperature compensation in circadian rhythms
NASA Astrophysics Data System (ADS)
Bodenstein, C.; Heiland, I.; Schuster, S.
2011-10-01
Many biological species possess a circadian clock, which helps them anticipate daily variations in the environment. In the absence of external stimuli, the rhythm persists autonomously with a period of approximately 24 h. However, single pulses of light, nutrients, chemicals or temperature can shift the clock phase. In the case of light- and temperature-cycles, this allows entrainment of the clock to cycles of exactly 24 h. Circadian clocks have the remarkable property of temperature compensation, that is, the period of the circadian rhythm remains relatively constant within a physiological range of temperatures. For several organisms, temperature-regulated processes within the circadian clock have been identified in recent years. However, how these processes contribute to temperature compensation is not fully understood. Here, we theoretically investigate temperature compensation in general oscillatory systems. It is known that every oscillator can be locally temperature compensated around a reference temperature, if reactions are appropriately balanced. A balancing is always possible if the control coefficient with respect to the oscillation period of at least one reaction in the oscillator network is positive. However, for global temperature compensation, the whole physiological temperature range is relevant. Here, we use an approach which leads to an optimization problem subject to the local balancing principle. We use this approach to analyse different circadian clock models proposed in the literature and calculate activation energies that lead to temperature compensation.
Path-breaking schemes for nonequilibrium free energy calculations
NASA Astrophysics Data System (ADS)
Chelli, Riccardo; Gellini, Cristina; Pietraperzia, Giangaetano; Giovannelli, Edoardo; Cardini, Gianni
2013-06-01
We propose a path-breaking route to the enhancement of unidirectional nonequilibrium simulations for the calculation of free energy differences via Jarzynski's equality [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)], 10.1103/PhysRevLett.78.2690. One of the most important limitations of unidirectional nonequilibrium simulations is the amount of realizations necessary to reach suitable convergence of the work exponential average featuring the Jarzynski's relationship. In this respect, a significant improvement of the performances could be obtained by finding a way of stopping trajectories with negligible contribution to the work exponential average, before their normal end. This is achieved using path-breaking schemes which are essentially based on periodic checks of the work dissipated during the pulling trajectories. Such schemes can be based either on breaking trajectories whose dissipated work exceeds a given threshold or on breaking trajectories with a probability increasing with the dissipated work. In both cases, the computer time needed to carry out a series of nonequilibrium trajectories is reduced up to a factor ranging from 2 to more than 10, at least for the processes under consideration in the present study. The efficiency depends on several aspects, such as the type of process, the number of check-points along the pathway and the pulling rate as well. The method is illustrated through radically different processes, i.e., the helix-coil transition of deca-alanine and the pulling of the distance between two methane molecules in water solution.
Calculation of chemical potentials of chain molecules by the incremental gauge cell method.
Rasmussen, Christopher J; Vishnyakov, Aleksey; Neimark, Alexander V
2011-12-07
The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.
Calculation of chemical potentials of chain molecules by the incremental gauge cell method
NASA Astrophysics Data System (ADS)
Rasmussen, Christopher J.; Vishnyakov, Aleksey; Neimark, Alexander V.
2011-12-01
The gauge cell Monte Carlo method is extended to calculations of the incremental chemical potentials and free energies of linear chain molecules. The method was applied to chains of Lennard-Jones beads with stiff harmonic bonds up to 500 monomers in length. We show that the suggested method quantitatively reproduces the modified Widom particle insertion method of Kumar et al. [S. K. Kumar, I. Szleifer, and A. Z. Panagiotopoulos, Phys. Rev. Lett. 66(22), 2935 (1991)], 10.1103/PhysRevLett.66.2935, and is by an order of magnitude more efficient for long chains in terms of the computational time required for the same accuracy of chemical potential calculations. The chain increment ansatz, which suggests that the incremental chemical potential is independent of the chain length, was tested at different temperatures. We confirmed that the ansatz holds only for coils above the θ temperature. Special attention is paid to the effects of the magnitude of adsorption potential and temperature on the behavior of single chains in confinements that are comparable in size with the free chain radius of gyration. At sufficiently low temperatures, the dependence of the incremental chemical potential on the chain length in wetting pores is superficially similar to a capillary condensation isotherm, reflecting monolayer formation following by pore volume filling, as the chain length increases. We find that the incremental gauge cell method is an accurate and efficient technique for calculations of the free energies of chain molecules in bulk systems and nanoconfinements alike. The suggested method may find practical applications, such as modeling polymer partitioning on porous substrates and dynamics of chain translocation into nanopores.
Generalized Potential Energy Finite Elements for Modeling Molecular Nanostructures.
Chatzieleftheriou, Stavros; Adendorff, Matthew R; Lagaros, Nikos D
2016-10-24
The potential energy of molecules and nanostructures is commonly calculated in the molecular mechanics formalism by superimposing bonded and nonbonded atomic energy terms, i.e. bonds between two atoms, bond angles involving three atoms, dihedral angles involving four atoms, nonbonded terms expressing the Coulomb and Lennard-Jones interactions, etc. In this work a new, generalized numerical simulation is presented for studying the mechanical behavior of three-dimensional nanostructures at the atomic scale. The energy gradient and Hessian matrix of such assemblies are usually computed numerically; a potential energy finite element model is proposed herein where these two components are expressed analytically. In particular, generalized finite elements are developed that express the interactions among atoms in a manner equivalent to that invoked in simulations performed based on the molecular dynamics method. Thus, the global tangent stiffness matrix for any nanostructure is formed as an assembly of the generalized finite elements and is directly equivalent to the Hessian matrix of the potential energy. The advantages of the proposed model are identified in terms of both accuracy and computational efficiency. In the case of popular force fields (e.g., CHARMM), the computation of the Hessian matrix by implementing the proposed method is of the same order as that of the gradient. This analysis can be used to minimize the potential energy of molecular systems under nodal loads in order to derive constitutive laws for molecular systems where the entropy and solvent effects are neglected and can be approximated as solids, such as double stranded DNA nanostructures. In this context, the sequence dependent stretch modulus for some typical base pairs step is calculated.
Extraction of potential energy in charge asymmetry coordinate from experimental fission data
NASA Astrophysics Data System (ADS)
Paşca, H.; Andreev, A. V.; Adamian, G. G.; Antonenko, N. V.
2016-12-01
For fissioning isotopes of Ra, Ac, Th, Pa, and U, the potential energies as a function of the charge asymmetry coordinate are extracted from the experimental charge distributions of the fission fragment and compared with the calculated scission-point driving potentials. The role of the potential energy surfaces in the description of the fission charge distribution is discussed.
Novel mixture model for the representation of potential energy surfaces
NASA Astrophysics Data System (ADS)
Pham, Tien Lam; Kino, Hiori; Terakura, Kiyoyuki; Miyake, Takashi; Dam, Hieu Chi
2016-10-01
We demonstrate that knowledge of chemical physics on a materials system can be automatically extracted from first-principles calculations using a data mining technique; this information can then be utilized to construct a simple empirical atomic potential model. By using unsupervised learning of the generative Gaussian mixture model, physically meaningful patterns of atomic local chemical environments can be detected automatically. Based on the obtained information regarding these atomic patterns, we propose a chemical-structure-dependent linear mixture model for estimating the atomic potential energy. Our experiments show that the proposed mixture model significantly improves the accuracy of the prediction of the potential energy surface for complex systems that possess a large diversity in their local structures.
A global potential energy surface for ArH2
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1993-01-01
We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.
A global potential energy surface for ArH2
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1992-01-01
We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.
A global potential energy surface for ArH2
NASA Technical Reports Server (NTRS)
Schwenke, David W.; Walch, Stephen P.; Taylor, Peter R.
1993-01-01
We describe a simple analytic representation of the ArH2 potential energy surface which well reproduces the results of extensive ab initio electronic structure calculations. The analytic representation smoothly interpolates between the dissociated H2 and strong bonding limits. In the fitting process, emphasis is made on accurately reproducing regions of the potential expected to be important for high temperature (ca. 3000 K) collision processes. Overall, the anisotropy and H2 bond length dependence of the analytic representation well reproduce the input data.
Bytautas, Laimutis; Ruedenberg, Klaus
2008-06-07
A close approximation to the empirical potential energy curve of the neon dimer is obtained by coupled-cluster singles plus doubles plus noniterative triples calculations by using nonaugmented correlation-consistent basis sets without counterpoise corrections and complementing them by three-term extrapolations to the complete basis set limit. The potential energy is resolved into a self-consistent-field Hartree-Fock contribution and a correlation contribution. The latter is shown to decay in the long-range region in accordance with the empirical dispersion expansion.
NASA Astrophysics Data System (ADS)
Franz, Jan
2017-02-01
We present correlation-polarization potentials for the calculation of scattering cross sections of positrons with atoms and molecules. The potentials are constructed from a short-range correlation term and a long-range polarization term. For the short-range correlation term we present four different potentials that are derived from multi-component density functionals. For the long-range polarization term we employ a multi-term expansion. Quantum scattering calculations are presented for low energy collisions of positrons with two atomic targets (argon and krypton) and two molecular targets (nitrogen and methane). For collision energies below the threshold for Positronium formation our calculations of scattering cross sections are in good agreement with recent data sets from experiments and theory. Contribution to the Topical Issue "Low-Energy Interactions related to Atmospheric and Extreme Conditions", edited by S. Ptasinska, M. Smialek-Telega, A. Milosavljevic and B. Sivaraman.
Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.
Boulougouris, Georgios C
2014-05-15
The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be
The Potential For Energy Efficiency In The State of Iowa
Hadley, SW
2001-12-05
The purpose of this study was to do an initial estimate of the potential for energy savings in the state of Iowa. Several methods for determining savings were examined, including existing programs, surveys, savings calculators, and economic simulation. Each method has advantages and disadvantages, trading off between detail of information, accuracy of results, and scope. This paper concentrated on using economic simulation (the NEMS model (EIA 2000a)) to determine market potential for energy savings for the residential and commercial sectors. The results of surveys were used to calculate the economic potential for savings in the industrial sector. The NEMS model is used by the Energy Information Administration to calculate twenty-year projections of energy use for every region of the country. The results of the Annual Energy Outlook 2000 were used as the Base case (EIA 1999a). Two alternative cases were created to simulate energy savings policies. Voluntary, market-related programs were simulated by lowering the effective discount rates that end-users use when making decisions on equipment purchases. Standards programs in the residential sector were simulated by eliminating the availability of low efficiency equipment in future years. The parameters for these programs were based on the Moderate scenario from the DOE Clean Energy Futures study (Interlaboratory Working Group 2000), which assumed increased concern by society on energy efficiency but not to the point of fiscal policies such as taxes or direct subsidies. The study only considered a subset of the various programs, policies, and technologies that could reduce energy use. The major end-uses in the residential sector affected by the policies were space cooling (20% savings by 2020) and water heating (14% savings by 2020.) Figure S-1 shows the space cooling savings when voluntary programs and minimum efficiency standards were implemented. Refrigerators, freezers, and clothes dryers saw slight improvements
Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao
2009-04-28
A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.
Mondal, Abhisek; Datta, Saumen
2017-06-01
Hydrogen bond plays a unique role in governing macromolecular interactions with exquisite specificity. These interactions govern the fundamental biological processes like protein folding, enzymatic catalysis, molecular recognition. Despite extensive research work, till date there is no proper report available about the hydrogen bond's energy surface with respect to its geometric parameters, directly derived from proteins. Herein, we have deciphered the potential energy landscape of hydrogen bond directly from the macromolecular coordinates obtained from Protein Data Bank using quantum mechanical electronic structure calculations. The findings unravel the hydrogen bonding energies of proteins in parametric space. These data can be used to understand the energies of such directional interactions involved in biological molecules. Quantitative characterization has also been performed using Shannon entropic calculations for atoms participating in hydrogen bond. Collectively, our results constitute an improved way of understanding hydrogen bond energies in case of proteins and complement the knowledge-based potential. Proteins 2017; 85:1046-1055. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.
Nudged elastic band calculation of the binding potential for liquids at interfaces.
Buller, Oleg; Tewes, Walter; Archer, Andrew J; Heuer, Andreas; Thiele, Uwe; Gurevich, Svetlana V
2017-07-14
The wetting behavior of a liquid on solid substrates is governed by the nature of the effective interaction between the liquid-gas and the solid-liquid interfaces, which is described by the binding or wetting potential g(h) which is an excess free energy per unit area that depends on the liquid film height h. Given a microscopic theory for the liquid, to determine g(h), one must calculate the free energy for liquid films of any given value of h, i.e., one needs to create and analyze out-of-equilibrium states, since at equilibrium there is a unique value of h, specified by the temperature and chemical potential of the surrounding gas. Here we introduce a Nudged Elastic Band (NEB) approach to calculate g(h) and illustrate the method by applying it in conjunction with a microscopic lattice density functional theory for the liquid. We also show that the NEB results are identical to those obtained with an established method based on using a fictitious additional potential to stabilize the non-equilibrium states. The advantages of the NEB approach are discussed.
Nudged elastic band calculation of the binding potential for liquids at interfaces
NASA Astrophysics Data System (ADS)
Buller, Oleg; Tewes, Walter; Archer, Andrew J.; Heuer, Andreas; Thiele, Uwe; Gurevich, Svetlana V.
2017-07-01
The wetting behavior of a liquid on solid substrates is governed by the nature of the effective interaction between the liquid-gas and the solid-liquid interfaces, which is described by the binding or wetting potential g(h) which is an excess free energy per unit area that depends on the liquid film height h. Given a microscopic theory for the liquid, to determine g(h), one must calculate the free energy for liquid films of any given value of h, i.e., one needs to create and analyze out-of-equilibrium states, since at equilibrium there is a unique value of h, specified by the temperature and chemical potential of the surrounding gas. Here we introduce a Nudged Elastic Band (NEB) approach to calculate g(h) and illustrate the method by applying it in conjunction with a microscopic lattice density functional theory for the liquid. We also show that the NEB results are identical to those obtained with an established method based on using a fictitious additional potential to stabilize the non-equilibrium states. The advantages of the NEB approach are discussed.
NASA Astrophysics Data System (ADS)
Le Roy, Robert J.
2013-06-01
In recent years it has become increasingly common to analyse spectroscopic data by using ``direct potential fits" of simulated data generated from analytic potential energy functions to experiment to optimize the parameters defining that potential energy function. This has the advantages of circumventing use of the semiclassical approximations associated with traditional methodologies, and of directly yielding a closed-form expression that is the most compact and comprehensive way to summarize what we know about a molecule. A question which then arises is: What are the uncertainties in properties computed using this potential? It turns out that this question is very closely related to the question of how to apply this simulation/fitting method efficiently to the analysis of bound to continuum intensity data. Both depend upon being able to answer the question: What are the partial derivatives of a wavefunction with respect to the parameters defining the potential energy function from which it is generated? It will be shown that such partial derivatives may be obtained readily as the `particular' solutions of linear inhomogeneous differential equations of a type that is routinely solved in another context for calculating the centrifugal distortion constants of diatomic molecules. Applications of this technique have been incorporated into the publicly available bound-state data analysis and simulation program DPotFit and the distributed bound to continuum simulation/fitting program BCONT. J.M. Hutson, J. Phys. B (At. Mol. Phys) {14}, 851 (1981). J. Tellinghuisen, J. Mol. Spectrosc. {122}, 455 (1987). See http://leroy.uwaterloo.ca/programs/
Collapsed cone convolution of radiant energy for photon dose calculation in heterogeneous media.
Ahnesjö, A
1989-01-01
A method for photon beam dose calculations is described. The primary photon beam is raytraced through the patient, and the distribution of total radiant energy released into the patient is calculated. Polyenergetic energy deposition kernels are calculated from the spectrum of the beam, using a database of monoenergetic kernels. It is shown that the polyenergetic kernels can be analytically described with high precision by (A exp( -ar) + B exp( -br)/r2, where A, a, B, and b depend on the angle with respect to the impinging photons and the accelerating potential, and r is the radial distance. Numerical values of A, a, B, and b are derived and used to convolve energy deposition kernels with the total energy released per unit mass (TERMA) to yield dose distributions. The convolution is facilitated by the introduction of the collapsed cone approximation. In this approximation, all energy released into coaxial cones of equal solid angle, from volume elements on the cone axis, is rectilinearly transported, attenuated, and deposited in elements on the axis. Scaling of the kernels is implicitly done during the convolution procedure to fully account for inhomogeneities present in the irradiated volume. The number of computational operations needed to compute the dose with the method is proportional to the number of calculation points. The method is tested for five accelerating potentials; 4, 6, 10, 15, and 24 MV, and applied to two geometries; one is a stack of slabs of tissue media, and the other is a mediastinum-like phantom of cork and water. In these geometries, the EGS4 Monte Carlo system has been used to generate reference dose distributions with which the dose computed with the collapsed cone convolution method is compared. Generally, the agreement between the methods is excellent. Deviations are observed in situations of lateral charged particle disequilibrium in low density media, however, but the result is superior compared to that of the generalized Batho method.
Calculation of the Helmholtz potential of an elastic strand in an external electric field.
Khaliullin, Renat N; Schieber, Jay D
2011-02-14
We derive from statistical mechanics the Gibbs free energy of an elastic random-walk chain affected by the presence of an external electric field. Intrachain charge interactions are ignored. In addition, we find two approximations of the Helmholtz potential for this system analogous to the gaussian and Cohen-Padé approximations for an elastic strand without the presence of an electric field. Our expressions agree well with exact numerical calculations of the potential in a wide range of conditions. Our analog of the gaussian approximation exhibits distortion of the monomer density due to the presence of the electric field, and our analog of the Cohen-Padé approximation additionally includes finite chain extensibility effects. The Helmholtz potential may be used in modeling the dynamics of electrophoresis experiments.
Native Defect Properties in Beta-SiC: Ab Initio and Empirical Potential Calculations
Gao, Fei; Bylaska, Eric J.; Weber, William J.; Corrales, Louis R.
2001-06-25
There is considerable ambiguity about the formation of native defects and their clusters in SiC, since different empirical potential gives different results, particular related to the stability of interstitial configurations. Ab intio pseudopotential methods are used to study the formation and properties of native defects in beta-SiC. The results are compared with those calculated by molecular dynamics (MD) using a Tersoff potential, where the various cut-off distances found in the literature are employed. The formation energy of vacancies and antisite defects obtained by ab initio calculations are in good agreement with those given by the Tersoff potential, regardless of the cut-off distances, but there is a disparity for interstitials between the two methods, depending on the cut-off distances used in the Tersoff potential. The present results, however, provide guidelines for evaluating the quality and fit of empirical potentials for large-scale simulations of irradiation damage (displacement cascades) and point defect migration (recombination or annealing) in SiC.
California's biomass and its energy potential
Lucarelli, F.B. Jr.
1980-04-01
The potentials for using California's biomass for energy have been assessed. The study relies on the recent work of Amory Lovins and Lawrence Berkeley Laboratory's (LBL) Distributed Energy System's Project to specify an energy future for Californians. These works identify transportation fuels as the most valuable energy conversion for biomass. Within this context, the extent of five categories of terrestial biomass is estimated, in addition to the environmental impacts and monetary cost of collecting and transporting each biomass category. Estimates of the costs of transforming biomass into different fuels as well as a survey of government's role in a biomass energy program are presented. The major findings are summarized below. (1) California's existing biomass resources are sufficient to provide only 20 percent of its future liquid fuel requirements. (2) Meeting the full transportation demand with biomass derived fuels will require the development of exotic biomass sources such as kelp farms and significant reductions in automobile travel in the State. (3) Under assumptions of moderate increases in gasoline prices and without major new government incentives, the cost of transforming biomass into transport fuels will be competitive with the price of gasoline on a Btu basis by the year 1990. (4) The environmental impacts of collecting most forms of biomass are beneficial and should reduce air pollution from agricultural burning and water pollution from feedlot and dairy farm runoff. Moreover, the collection of logging residues should improve timber stand productivity and the harvest of chaparral should reduce the risk of wildfire in the State. (5) The institutional context for implementing biomass energy projects is complex and fragmented.
Variational Monte Carlo calculations for the binding energy of sub. Lambda. Lambda. sup 31 Si
Ahsan, M.H. ); Kaykobad, M. ); Ali, S. )
1991-01-01
The binding energy of the {Lambda}{Lambda} hypernucleus {sub {Lambda}{Lambda}}{sup 31}Si has been calculated variationally with a {sup 28}Si+{ital n}+{Lambda}+{Lambda} four-body model. The integrations have been carried out with the help of a Monte Carlo technique. Three different types of {Lambda}-{Lambda} and {Lambda}-{ital N} potentials have been used. {ital n}-{sup 28}Si and {Lambda}-{sup 28}Si potentials have been generated by folding the {ital N}-{ital N} and {Lambda}-{ital N} potentials into the harmonic-oscillator shell-model density distribution of {sup 28}Si. The calculated values of the binding energy for the three different potentials are 40.19, 46.30, and 39.90 MeV. These values are compared with the reported experimental value of 38.2{plus minus}6.3 MeV. The dependence of the binding energy on the depth of the {Lambda}-{Lambda} interaction has also been investigated.
Momentum-space optical potential SND elastic scattering calculations
NASA Astrophysics Data System (ADS)
Wolfe, D. H.; Hynes, M. V.; Picklesimer, A.; Tandy, P. C.; Thaler, R. M.
1983-03-01
Initial results are presented for proton-nucleus elastic scattering observables calculated with a newly developed microscopic momentum-space code. This is the first phase of a program to treat elastic and inelastic scatterig consistently via an integral equation approach. A number of microscopic features which are often approximated or ignored are quite amenable to exact treatment within this approach, e.g. non-local effectss in elastic scattering, and inelastic effects which are non-linear in the NN t-matrix and target densities but nevertheless confined to one participating nucleon.
Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.
Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A
2015-10-26
Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange.
NASA Astrophysics Data System (ADS)
Larriba, Carlos; Hogan, Christopher J.
2013-10-01
The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas
Larriba, Carlos Hogan, Christopher J.
2013-10-15
The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission is largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas
A calculation of the diffusion energies for adatoms on surfaces of F.C.C. metals
NASA Technical Reports Server (NTRS)
Halicioglu, T.; Pound, G. M.
1979-01-01
The activation energies for diffusion were determined for gold, platinum and iridium adatoms on plane and plane PT surfaces and were found to be in good agreement with the measurements reported by Bassett and Webber. The Lennard-Jones pair potentials were used to model the interatomic forces, and relaxation of the substrate atoms in near proximity to the adatom was considered in detail. The present calculations clarify the mechanism of the observed two-dimensional diffusion of platinum and iridium atoms on a plane PT surface. The results are compared with those obtained using Morse potential functions and different relaxation techniques.
A calculation of the diffusion energies for adatoms on surfaces of F.C.C. metals
NASA Technical Reports Server (NTRS)
Halicioglu, T.; Pound, G. M.
1979-01-01
The activation energies for diffusion were determined for gold, platinum and iridium adatoms on plane and plane PT surfaces and were found to be in good agreement with the measurements reported by Bassett and Webber. The Lennard-Jones pair potentials were used to model the interatomic forces, and relaxation of the substrate atoms in near proximity to the adatom was considered in detail. The present calculations clarify the mechanism of the observed two-dimensional diffusion of platinum and iridium atoms on a plane PT surface. The results are compared with those obtained using Morse potential functions and different relaxation techniques.
Potential energy surfaces of quintet and singlet O4.
Paukku, Yuliya; Yang, Ke R; Varga, Zoltan; Song, Guoliang; Bender, Jason D; Truhlar, Donald G
2017-07-21
We present global ground-state potential energy surfaces for the quintet and singlet spin states of the O4 system that are suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in electronically adiabatic, spin-conserving O2-O2 collisions. The surfaces are based on MS-CASPT2/maug-cc-pVTZ electronic structure calculations with scaled external correlation. The active space has 16 electrons in 12 orbitals. The calculations cover nine kinds of geometrical arrangements corresponding to dissociative diatom-diatom collisions of O2, geometries corresponding to O3-O, geometries identified by running trajectories, and geometries along linear synchronous transit paths. The global ground-state potential energy surfaces were obtained by a many-body approach with an accurate O-O pairwise interaction and a fit of the many-body interaction to 12 684 electronic structure data points for the singlet and 10 543 electronic structure data points for the quintet. The many-body fit is based on permutationally invariant polynomials in terms of bond-order functions of the six interatomic distances; the bond-order functions are mixed exponential-Gaussian functions.
Potential energy surfaces of quintet and singlet O4
NASA Astrophysics Data System (ADS)
Paukku, Yuliya; Yang, Ke R.; Varga, Zoltan; Song, Guoliang; Bender, Jason D.; Truhlar, Donald G.
2017-07-01
We present global ground-state potential energy surfaces for the quintet and singlet spin states of the O4 system that are suitable for treating high-energy vibrational-rotational energy transfer and collision-induced dissociation in electronically adiabatic, spin-conserving O2-O2 collisions. The surfaces are based on MS-CASPT2/maug-cc-pVTZ electronic structure calculations with scaled external correlation. The active space has 16 electrons in 12 orbitals. The calculations cover nine kinds of geometrical arrangements corresponding to dissociative diatom-diatom collisions of O2, geometries corresponding to O3-O, geometries identified by running trajectories, and geometries along linear synchronous transit paths. The global ground-state potential energy surfaces were obtained by a many-body approach with an accurate O-O pairwise interaction and a fit of the many-body interaction to 12 684 electronic structure data points for the singlet and 10 543 electronic structure data points for the quintet. The many-body fit is based on permutationally invariant polynomials in terms of bond-order functions of the six interatomic distances; the bond-order functions are mixed exponential-Gaussian functions.
Pham, Tri T; Shirts, Michael R
2011-07-21
Improving the efficiency of free energy calculations is important for many biological and materials design applications, such as protein-ligand binding affinities in drug design, partitioning between immiscible liquids, and determining molecular association in soft materials. We show that for any pair potential, moderately accurate estimation of the radial distribution function for a solute molecule is sufficient to accurately estimate the statistical variance of a sampling along a free energy pathway. This allows inexpensive analytical identification of low statistical error free energy pathways. We employ a variety of methods to estimate the radial distribution function (RDF) and find that the computationally cheap two-body "dilute gas" limit performs as well or better than 3D-RISM theory and other approximations for identifying low variance free energy pathways. With a RDF estimate in hand, we can search for pairwise interaction potentials that produce low variance. We give an example of a search minimizing statistical variance of solvation free energy over the entire parameter space of a generalized "soft core" potential. The free energy pathway arising from this optimization procedure has lower curvature in the variance and reduces the total variance by at least 50% compared to the traditional soft core solvation pathway. We also demonstrate that this optimized pathway allows free energies to be estimated with fewer intermediate states due to its low curvature. This free energy variance optimization technique is generalizable to solvation in any homogeneous fluid and for any type of pairwise potential and can be performed in minutes to hours, depending on the method used to estimate g(r).
Excitation energies from frozen-density embedding with accurate embedding potentials.
Artiukhin, Denis G; Jacob, Christoph R; Neugebauer, Johannes
2015-06-21
We present calculations of excitation energies within the time-dependent density functional theory (TDDFT) extension of frozen-density embedding (FDE) using reconstructed accurate embedding potentials. Previous applications of FDE showed significant deviations from supermolecular calculations; our current approach eliminates one potential error source and yields excitation energies of generally much better agreement with Kohn-Sham-TDDFT. Our results demonstrate that the embedding potentials represent the main error source in FDE-TDDFT calculations using standard approximate kinetic-energy functionals for excitations localized within one subsystem.
Excitation energies from frozen-density embedding with accurate embedding potentials
NASA Astrophysics Data System (ADS)
Artiukhin, Denis G.; Jacob, Christoph R.; Neugebauer, Johannes
2015-06-01
We present calculations of excitation energies within the time-dependent density functional theory (TDDFT) extension of frozen-density embedding (FDE) using reconstructed accurate embedding potentials. Previous applications of FDE showed significant deviations from supermolecular calculations; our current approach eliminates one potential error source and yields excitation energies of generally much better agreement with Kohn-Sham-TDDFT. Our results demonstrate that the embedding potentials represent the main error source in FDE-TDDFT calculations using standard approximate kinetic-energy functionals for excitations localized within one subsystem.
Computed potential energy surfaces for chemical reactions
NASA Technical Reports Server (NTRS)
Walch, Stephen P.; Levin, Eugene
1993-01-01
A new global potential energy surface (PES) is being generated for O(P-3) + H2 yields OH + H. This surface is being fit using the rotated Morse oscillator method, which was used to fit the previous POL-CI surface. The new surface is expected to be more accurate and also includes a much more complete sampling of bent geometries. A new study has been undertaken of the reaction N + O2 yields NO + O. The new studies have focused on the region of the surface near a possible minimum corresponding to the peroxy form of NOO. A large portion of the PES for this second reaction has been mapped out. Since state to state cross sections for the reaction are important in the chemistry of high temperature air, these studies will probably be extended to permit generation of a new global potential for reaction.
Dai, Zuyang; Gao, Shuming; Wang, Jia; Mo, Yuxiang
2014-10-14
The torsional energy levels of CH3OH(+), CH3OD(+), and CD3OD(+) have been determined for the first time using one-photon zero kinetic energy photoelectron spectroscopy. The adiabatic ionization energies for CH3OH, CH3OD, and CD3OD 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(-1), which is about half of that of the neutral (340 cm(-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 CD3OD(+) 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.
Potential energy surfaces and reaction dynamics of polyatomic molecules
Chang, Yan-Tyng
1991-11-01
A simple empirical valence bond (EVB) model approach is suggested for constructing global potential energy surfaces for reactions of polyatomic molecular systems. This approach produces smooth and continuous potential surfaces which can be directly utilized in a dynamical study. Two types of reactions are of special interest, the unimolecular dissociation and the unimolecular isomerization. For the first type, the molecular dissociation dynamics of formaldehyde on the ground electronic surface is investigated through classical trajectory calculations on EVB surfaces. The product state distributions and vector correlations obtained from this study suggest very similar behaviors seen in the experiments. The intramolecular hydrogen atom transfer in the formic acid dimer is an example of the isomerization reaction. High level ab initio quantum chemistry calculations are performed to obtain optimized equilibrium and transition state dimer geometries and also the harmonic frequencies.
Global Expression for Representing Diatomic Potential-Energy Curves
NASA Technical Reports Server (NTRS)
Ferrante, John; Schlosser, Herbert; Smith, John R.
1991-01-01
A three-parameter expression that gives an accurate fit to diatomic potential curves over the entire range of separation for charge transfers between 0 and 1. It is based on a generalization of the universal binding-energy relation of Smith et al. (1989) with a modification that describes the crossover from a partially ionic state to the neutral state at large separations. The expression is tested by comparison with first-principles calculations of the potential curves ranging from covalently bonded to ionically bonded. The expression is also used to calculate spectroscopic constants form a curve fit to the first-principles curves. A comparison is made with experimental values of the spectroscopic constants.
Global Expression for Representing Diatomic Potential-Energy Curves
NASA Technical Reports Server (NTRS)
Ferrante, John; Schlosser, Herbert; Smith, John R.
1991-01-01
A three-parameter expression that gives an accurate fit to diatomic potential curves over the entire range of separation for charge transfers between 0 and 1. It is based on a generalization of the universal binding-energy relation of Smith et al. (1989) with a modification that describes the crossover from a partially ionic state to the neutral state at large separations. The expression is tested by comparison with first-principles calculations of the potential curves ranging from covalently bonded to ionically bonded. The expression is also used to calculate spectroscopic constants form a curve fit to the first-principles curves. A comparison is made with experimental values of the spectroscopic constants.
Migani, Annapaola; Neyman, Konstantin M; Illas, Francesc; Bromley, Stefan T
2009-08-14
The performance of atomistic calculations using interionic potentials has been examined in detail with respect to the structures and energetic stabilities of ten configurational isomers (i.e., distinct Ce3+/Ce4+ cationic orderings) of a low energy octahedral ceria nanoparticle Ce19O32. The outcome of these calculations is compared with the results of corresponding density-functional (DF) calculations employing local and gradient corrected functionals with an additional corrective onsite Coulombic interaction applied to the f-electrons (i.e., LDA+U and GGA+U, respectively). Strikingly similar relative energy ordering of the isomers and atomic scale structural trends (e.g., cation-cation distances) are obtained in both the DF and interionic-potential calculations. The surprisingly good agreement between the DF electronic structure calculations and the relatively simple classical potentials is not found to be due to a single dominant interaction type but is due to a sensitive balance between long range electrostatics and local bonding contributions to the energy. Considering the relatively high computational cost and technical difficulty involved in obtaining charge-localized electronic solutions for reduced ceria using DF calculations, the use of interionic potentials for rapid and reliable preselection of the most stable Ce3+/Ce4+ cationic orderings is of considerable benefit.
S-matrix Calculations of Energy Levels of the Lithium Isoelectronic Sequence
sapirstein, J; Cheng, K T
2010-11-02
A QED approach to the calculation of the spectra of the lithium isoelectronic sequence is implemented. A modified Furry representation based on the Kohn-Sham potential is used to evaluate all one- and two-photon diagrams with the exception of the two-loop Lamb shift. Three-photon diagrams are estimated with Hamiltonian methods. After incorporating recent calculations of the two-loop Lamb shift and recoil corrections a comprehensive tabulation of the 2s, 2p{sub 1/2} and 2p{sub 3/2} energy levels as well as the 2s - 2p{sub 1/2} and 2s - 2p{sub 3/2} transition energies for Z = 10 - 100 is presented.
NASA Astrophysics Data System (ADS)
de Jong, Maarten; Qi, Liang; Olmsted, David L.; van de Walle, Axel; Asta, Mark
2016-03-01
A method is described for calculating the energetics of planar defects in alloys based on the special-quasirandom-structure (SQS) approach. We examine the accuracy of the approach employing atomistic calculations based on a classical embedded-atom-method (EAM) interatomic potential for hexagonal close packed (hcp) alloys, for which benchmark results can be obtained by direct configurational averaging. The results of these calculations demonstrate that the SQS-based approach can be employed to derive the concentration dependence of the energies of twin boundaries, unstable stacking faults, and surfaces to within an accuracy of approximately 10%. The SQS considered in this study contain up to 72 atoms and hence are small enough to be considered in first-principles density-functional-theory (DFT) based calculations. The application of the SQS-based approach in direct DFT-based calculations is demonstrated in a study of the concentration dependence of interfacial energies for {11 2 ¯1 } twins in hcp Ti-Al alloys.
CC2 oscillator strengths within the local framework for calculating excitation energies (LoFEx)
NASA Astrophysics Data System (ADS)
Baudin, Pablo; Kjærgaard, Thomas; Kristensen, Kasper
2017-04-01
In a recent work [P. Baudin and K. Kristensen, J. Chem. Phys. 144, 224106 (2016)], we introduced a local framework for calculating excitation energies (LoFEx), based on second-order approximated coupled cluster (CC2) linear-response theory. LoFEx is a black-box method in which a reduced excitation orbital space (XOS) is optimized to provide coupled cluster (CC) excitation energies at a reduced computational cost. In this article, we present an extension of the LoFEx algorithm to the calculation of CC2 oscillator strengths. Two different strategies are suggested, in which the size of the XOS is determined based on the excitation energy or the oscillator strength of the targeted transitions. The two strategies are applied to a set of medium-sized organic molecules in order to assess both the accuracy and the computational cost of the methods. The results show that CC2 excitation energies and oscillator strengths can be calculated at a reduced computational cost, provided that the targeted transitions are local compared to the size of the molecule. To illustrate the potential of LoFEx for large molecules, both strategies have been successfully applied to the lowest transition of the bivalirudin molecule (4255 basis functions) and compared with time-dependent density functional theory.
Mielke, Steven L; Truhlar, Donald G
2015-01-28
We present an improved version of our "path-by-path" enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P(-6)) to O(P(-12)), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational-rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan-Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300-3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
Mielke, Steven L. E-mail: truhlar@umn.edu; Truhlar, Donald G. E-mail: truhlar@umn.edu
2015-01-28
We present an improved version of our “path-by-path” enhanced same path extrapolation scheme for Feynman path integral (FPI) calculations that permits rapid convergence with discretization errors ranging from O(P{sup −6}) to O(P{sup −12}), where P is the number of path discretization points. We also present two extensions of our importance sampling and stratified sampling schemes for calculating vibrational–rotational partition functions by the FPI method. The first is the use of importance functions for dihedral angles between sets of generalized Jacobi coordinate vectors. The second is an extension of our stratification scheme to allow some strata to be defined based only on coordinate information while other strata are defined based on both the geometry and the energy of the centroid of the Feynman path. These enhanced methods are applied to calculate converged partition functions by FPI methods, and these results are compared to ones obtained earlier by vibrational configuration interaction (VCI) calculations, both calculations being for the Jordan–Gilbert potential energy surface. The earlier VCI calculations are found to agree well (within ∼1.5%) with the new benchmarks. The FPI partition functions presented here are estimated to be converged to within a 2σ statistical uncertainty of between 0.04% and 0.07% for the given potential energy surface for temperatures in the range 300–3000 K and are the most accurately converged partition functions for a given potential energy surface for any molecule with five or more atoms. We also tabulate free energies, enthalpies, entropies, and heat capacities.
NASA Astrophysics Data System (ADS)
Topping, David; Alibay, Irfan; Bane, Michael
2017-04-01
To predict the evolving concentration, chemical composition and ability of aerosol particles to act as cloud droplets, we rely on numerical modeling. Mechanistic models attempt to account for the movement of compounds between the gaseous and condensed phases at a molecular level. This 'bottom up' approach is designed to increase our fundamental understanding. However, such models rely on predicting the properties of molecules and subsequent mixtures. For partitioning between the gaseous and condensed phases this includes: saturation vapour pressures; Henrys law coefficients; activity coefficients; diffusion coefficients and reaction rates. Current gas phase chemical mechanisms predict the existence of potentially millions of individual species. Within a dynamic ensemble model, this can often be used as justification for neglecting computationally expensive process descriptions. Indeed, on whether we can quantify the true sensitivity to uncertainties in molecular properties, even at the single aerosol particle level it has been impossible to embed fully coupled representations of process level knowledge with all possible compounds, typically relying on heavily parameterised descriptions. Relying on emerging numerical frameworks, and designed for the changing landscape of high-performance computing (HPC), in this study we focus specifically on the ability to capture activity coefficients in liquid solutions using the UNIFAC method. Activity coefficients are often neglected with the largely untested hypothesis that they are simply too computationally expensive to include in dynamic frameworks. We present results demonstrating increased computational efficiency for a range of typical scenarios, including a profiling of the energy use resulting from reliance on such computations. As the landscape of HPC changes, the latter aspect is important to consider in future applications.
Potential energy surfaces of superheavy nuclei
Bender, M.; Rutz, K.; Maruhn, J.A.; Greiner, W.; Reinhard, P.-G. Rutz, K.; Maruhn, J.A.; Greiner, W.
1998-10-01
We investigate the structure of the potential energy surfaces of the superheavy nuclei {sub 158}{sup 258}Fm{sub 100}, {sub 156}{sup 264}Hs{sub 108}, {sub 166}{sup 278}112, {sub 184}{sup 298}114, and {sub 172}{sup 292}120 within the framework of self-consistent nuclear models, i.e., the Skyrme-Hartree-Fock approach and the relativistic mean-field model. We compare results obtained with one representative parametrization of each model which is successful in describing superheavy nuclei. We find systematic changes as compared to the potential energy surfaces of heavy nuclei in the uranium region: there is no sufficiently stable fission isomer any more, the importance of triaxial configurations to lower the first barrier fades away, and asymmetric fission paths compete down to rather small deformation. Comparing the two models, it turns out that the relativistic mean-field model gives generally smaller fission barriers. {copyright} {ital 1998} {ital The American Physical Society}
NASA Astrophysics Data System (ADS)
Artem'ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.
2016-01-01
We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2-5 nm and for neutron energies 3 × 10-7-10-3 eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.
Artem’ev, V. A.; Nezvanov, A. Yu.; Nesvizhevsky, V. V.
2016-01-15
We discuss properties of the interaction of slow neutrons with nano-dispersed media and their application for neutron reflectors. In order to increase the accuracy of model simulation of the interaction of neutrons with nanopowders, we perform precise quantum mechanical calculation of potential scattering of neutrons on single nanoparticles using the method of phase functions. We compare results of precise calculations with those performed within first Born approximation for nanodiamonds with the radius of 2–5 nm and for neutron energies 3 × 10{sup -7}–10{sup -3} eV. Born approximation overestimates the probability of scattering to large angles, while the accuracy of evaluation of integral characteristics (cross sections, albedo) is acceptable. Using Monte-Carlo method, we calculate albedo of neutrons from different layers of piled up diamond nanopowder.
Slavícek, Petr; Winter, Bernd; Faubel, Manfred; Bradforth, Stephen E; Jungwirth, Pavel
2009-05-13
Vertical ionization energies of the nucleosides cytidine and deoxythymidine in water, the lowest ones amounting in both cases to 8.3 eV, are obtained from photoelectron spectroscopy measurements in aqueous microjets. Ab initio calculations employing a nonequilibrium polarizable continuum model quantitatively reproduce the experimental spectra and provide molecular interpretation of the individual peaks of the photoelectron spectrum, showing also that lowest ionization originates from the base. Comparison of calculated vertical ionization potentials of pyrimidine bases, nucleosides, and nucleotides in water and in the gas phase underlines the dramatic effect of bulk hydration on the electronic structure. In the gas phase, the presence of sugar and, in particular, of phosphate has a strong effect on the energetics of ionization of the base. Upon bulk hydration, the ionization potential of the base in contrast becomes rather insensitive to the presence of the sugar and phosphate, which indicates a remarkable screening ability of the aqueous solvent. Accurate aqueous-phase vertical ionization potentials provide a significant improvement to the corrected gas-phase values used in the literature and represent important information in assessing the threshold energies for photooxidation and oxidation free energies of solvent-exposed DNA components. Likewise, such energetic data should allow improved assessment of delocalization and charge-hopping mechanisms in DNA ionized by radiation.
Horn, Paul R; Head-Gordon, Martin
2016-02-28
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.
NASA Astrophysics Data System (ADS)
Horn, Paul R.; Head-Gordon, Martin
2016-02-01
In energy decomposition analysis (EDA) of intermolecular interactions calculated via density functional theory, the initial supersystem wavefunction defines the so-called "frozen energy" including contributions such as permanent electrostatics, steric repulsions, and dispersion. This work explores the consequences of the choices that must be made to define the frozen energy. The critical choice is whether the energy should be minimized subject to the constraint of fixed density. Numerical results for Ne2, (H2O)2, BH3-NH3, and ethane dissociation show that there can be a large energy lowering associated with constant density orbital relaxation. By far the most important contribution is constant density inter-fragment relaxation, corresponding to charge transfer (CT). This is unwanted in an EDA that attempts to separate CT effects, but it may be useful in other contexts such as force field development. An algorithm is presented for minimizing single determinant energies at constant density both with and without CT by employing a penalty function that approximately enforces the density constraint.
Geothermal Energy Potential of Turkey: Inferred from the Aeromagnetic data
NASA Astrophysics Data System (ADS)
Ates, Abdullah; Bilim, Funda; Buyuksarac, Aydin; Bektas, Ozcan
2010-05-01
Geothermal energy potential of Turkey is well known. There are lots of hot springs with over 30° C water temperatures. However, the significance of these geothermal energy potential of Turkey is not adequately understood. We believe that the main reason for this; is the lack of exploration methods and tools in a wide area as large as Turkey. We exploited a well known physical property of rocks to estimate the geothermal energy potential. Physically, substances lose their magnetization above a temperature known as the Curie that is the 580° C for magnetite. Properties of the Curie temperature have been exploited to observe the bottom depth of the magnetization. That is the depth where the heat reaches to 580° C. In another word, there is no magnetization below this depth. In normal crust this depth is about 22-24 km. Thus, investigation of the bottom depth of magnetization by using aeromagnetic anomalies can lead to information that if there are any anomalous regions well above the normal crust. The aeromagnetic anomalies of whole of Turkey were surveyed by the Mineral Research and Exploration (MTA) of Turkey. The survey was completed during late 1980's. Five kilometers grid data were available and used for regional exploration purposes. Exploration of the geothermal energy potential of Turkey was done from west to east in the similar way to search for shallow high temperature regions. These are from west to east; i.) Western Turkey: Two major shallow depth regions were determined at the west of Kutahya and the north-east of Denizli. The Curie Point Depths (CPDs) were calculated as about 7 km and about 9 km in Kutahya and Denizli, respectively. Also, high heat flow values and crustal thinning (about 32 km from gravity anomalies of western Turkey) were calculated for western Turkey. ii.) Central Turkey: A CPD depth of 8 km was calculated. This gives us a temperature gradient of 0.073° C/m. Geothermal energy potential was studied using water chemistry and isotopic
Enhanced Ligand Sampling for Relative Protein–Ligand Binding Free Energy Calculations
2016-01-01
Free energy calculations are used to study how strongly potential drug molecules interact with their target receptors. The accuracy of these calculations depends on the accuracy of the molecular dynamics (MD) force field as well as proper sampling of the major conformations of each molecule. However, proper sampling of ligand conformations can be difficult when there are large barriers separating the major ligand conformations. An example of this is for ligands with an asymmetrically substituted phenyl ring, where the presence of protein loops hinders the proper sampling of the different ring conformations. These ring conformations become more difficult to sample when the size of the functional groups attached to the ring increases. The Adaptive Integration Method (AIM) has been developed, which adaptively changes the alchemical coupling parameter λ during the MD simulation so that conformations sampled at one λ can aid sampling at the other λ values. The Accelerated Adaptive Integration Method (AcclAIM) builds on AIM by lowering potential barriers for specific degrees of freedom at intermediate λ values. However, these methods may not work when there are very large barriers separating the major ligand conformations. In this work, we describe a modification to AIM that improves sampling of the different ring conformations, even when there is a very large barrier between them. This method combines AIM with conformational Monte Carlo sampling, giving improved convergence of ring populations and the resulting free energy. This method, called AIM/MC, is applied to study the relative binding free energy for a pair of ligands that bind to thrombin and a different pair of ligands that bind to aspartyl protease β-APP cleaving enzyme 1 (BACE1). These protein–ligand binding free energy calculations illustrate the improvements in conformational sampling and the convergence of the free energy compared to both AIM and AcclAIM. PMID:25906170
Spectroscopic constants and potential energy curves of yttrium carbide (YC).
Suo, Bingbing; Balasubramanian, Krishnan
2007-06-14
The potential energy curves of the low-lying electronic states of yttrium carbide (YC) and its cation are calculated at the complete active space self-consistent field and the multireference single and double excitation configuration interaction (MRSDCI) levels of theory. Fifteen low-lying electronic states of YC with different spin and spatial symmetries were identified. The X (4)Sigma- state prevails as the ground state of YC, and a low-lying excited A (4)Pi state is found to be 1661 cm(-1) higher at the MRSDCI level. The computations of the authors support the assignment of the observed spectra to a B (4)Delta(Omega=72)<--A (4)Pi(Omega=52) transition with a reinterpretation that the A (4)Pi state is appreciably populated under the experimental conditions as it is less than 2000 cm(-1) of the X (4)Sigma- ground state, and the previously suggested (4)Pi ground state is reassigned to the first low-lying excited state of YC. The potential energy curves of YC+ confirm a previous prediction by Seivers et al. [J. Chem. Phys. 105, 6322 (1996)] that the ground state of YC+ is formed through a second pathway at higher energies. The calculated ionization energy of YC is 6.00 eV, while the adiabatic electron affinity is 0.95 eV at the MRSDCI level. The computed ionization energy of YC and dissociation energy of YC+ confirm the revised experimental estimates provided by Seivers et al. although direct experimental measurements yielded results with greater errors due to uncertainty in collisional cross sections for YC+ formation.