Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field.

PubMed

Xu, Dong; Zhang, Yang

2012-07-01

Ab initio protein folding is one of the major unsolved problems in computational biology owing to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1-20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 nonhomologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in one-third cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction experiment, QUARK server outperformed the second and third best servers by 18 and 47% based on the cumulative Z-score of global distance test-total scores in the FM category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress toward the solution of the most important problem in the field. Copyright © 2012 Wiley Periodicals, Inc.

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions.

PubMed

Paton, Robert S; Goodman, Jonathan M

2009-04-01

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

Vibrational modes in thymine molecule from an ab initio MO calculation

NASA Astrophysics Data System (ADS)

Aida, Misako; Kaneko, Motohisa; Dupuis, Michel; Ueda, Toyotoshi; Ushizawa, Koichi; Ito, Gen; Kumakura, Akiko; Tsuboi, Masamichi

1997-03-01

Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations.

PubMed

Chaudret, Robin; Gresh, Nohad; Narth, Christophe; Lagardère, Louis; Darden, Thomas A; Cisneros, G Andrés; Piquemal, Jean-Philip

2014-09-04

We demonstrate as a proof of principle the capabilities of a novel hybrid MM'/MM polarizable force field to integrate short-range quantum effects in molecular mechanics (MM) through the use of Gaussian electrostatics. This lead to a further gain in accuracy in the representation of the first coordination shell of metal ions. It uses advanced electrostatics and couples two point dipole polarizable force fields, namely, the Gaussian electrostatic model (GEM), a model based on density fitting, which uses fitted electronic densities to evaluate nonbonded interactions, and SIBFA (sum of interactions between fragments ab initio computed), which resorts to distributed multipoles. To understand the benefits of the use of Gaussian electrostatics, we evaluate first the accuracy of GEM, which is a pure density-based Gaussian electrostatics model on a test Ca(II)-H2O complex. GEM is shown to further improve the agreement of MM polarization with ab initio reference results. Indeed, GEM introduces nonclassical effects by modeling the short-range quantum behavior of electric fields and therefore enables a straightforward (and selective) inclusion of the sole overlap-dependent exchange-polarization repulsive contribution by means of a Gaussian damping function acting on the GEM fields. The S/G-1 scheme is then introduced. Upon limiting the use of Gaussian electrostatics to metal centers only, it is shown to be able to capture the dominant quantum effects at play on the metal coordination sphere. S/G-1 is able to accurately reproduce ab initio total interaction energies within closed-shell metal complexes regarding each individual contribution including the separate contributions of induction, polarization, and charge-transfer. Applications of the method are provided for various systems including the HIV-1 NCp7-Zn(II) metalloprotein. S/G-1 is then extended to heavy metal complexes. Tested on Hg(II) water complexes, S/G-1 is shown to accurately model polarization up to quadrupolar response level. This opens up the possibility of embodying explicit scalar relativistic effects in molecular mechanics thanks to the direct transferability of ab initio pseudopotentials. Therefore, incorporating GEM-like electron density for a metal cation enable the introduction of nonambiguous short-range quantum effects within any point-dipole based polarizable force field without the need of an extensive parametrization.

Parametrization of an Orbital-Based Linear-Scaling Quantum Force Field for Noncovalent Interactions

PubMed Central

2015-01-01

We parametrize a linear-scaling quantum mechanical force field called mDC for the accurate reproduction of nonbonded interactions. We provide a new benchmark database of accurate ab initio interactions between sulfur-containing molecules. A variety of nonbond databases are used to compare the new mDC method with other semiempirical, molecular mechanical, ab initio, and combined semiempirical quantum mechanical/molecular mechanical methods. It is shown that the molecular mechanical force field significantly and consistently reproduces the benchmark results with greater accuracy than the semiempirical models and our mDC model produces errors twice as small as the molecular mechanical force field. The comparisons between the methods are extended to the docking of drug candidates to the Cyclin-Dependent Kinase 2 protein receptor. We correlate the protein–ligand binding energies to their experimental inhibition constants and find that the mDC produces the best correlation. Condensed phase simulation of mDC water is performed and shown to produce O–O radial distribution functions similar to TIP4P-EW. PMID:24803856

Ab Initio Protein Structure Assembly Using Continuous Structure Fragments and Optimized Knowledge-based Force Field

PubMed Central

Xu, Dong; Zhang, Yang

2012-01-01

Ab initio protein folding is one of the major unsolved problems in computational biology due to the difficulties in force field design and conformational search. We developed a novel program, QUARK, for template-free protein structure prediction. Query sequences are first broken into fragments of 1–20 residues where multiple fragment structures are retrieved at each position from unrelated experimental structures. Full-length structure models are then assembled from fragments using replica-exchange Monte Carlo simulations, which are guided by a composite knowledge-based force field. A number of novel energy terms and Monte Carlo movements are introduced and the particular contributions to enhancing the efficiency of both force field and search engine are analyzed in detail. QUARK prediction procedure is depicted and tested on the structure modeling of 145 non-homologous proteins. Although no global templates are used and all fragments from experimental structures with template modeling score (TM-score) >0.5 are excluded, QUARK can successfully construct 3D models of correct folds in 1/3 cases of short proteins up to 100 residues. In the ninth community-wide Critical Assessment of protein Structure Prediction (CASP9) experiment, QUARK server outperformed the second and third best servers by 18% and 47% based on the cumulative Z-score of global distance test-total (GDT-TS) scores in the free modeling (FM) category. Although ab initio protein folding remains a significant challenge, these data demonstrate new progress towards the solution of the most important problem in the field. PMID:22411565

A partition function-based weighting scheme in force field parameter development using ab initio calculation results in global configurational space.

PubMed

Wu, Yao; Dai, Xiaodong; Huang, Niu; Zhao, Lifeng

2013-06-05

In force field parameter development using ab initio potential energy surfaces (PES) as target data, an important but often neglected matter is the lack of a weighting scheme with optimal discrimination power to fit the target data. Here, we developed a novel partition function-based weighting scheme, which not only fits the target potential energies exponentially like the general Boltzmann weighting method, but also reduces the effect of fitting errors leading to overfitting. The van der Waals (vdW) parameters of benzene and propane were reparameterized by using the new weighting scheme to fit the high-level ab initio PESs probed by a water molecule in global configurational space. The molecular simulation results indicate that the newly derived parameters are capable of reproducing experimental properties in a broader range of temperatures, which supports the partition function-based weighting scheme. Our simulation results also suggest that structural properties are more sensitive to vdW parameters than partial atomic charge parameters in these systems although the electrostatic interactions are still important in energetic properties. As no prerequisite conditions are required, the partition function-based weighting method may be applied in developing any types of force field parameters. Copyright © 2013 Wiley Periodicals, Inc.

Comment on 'Parametrization of Stillinger-Weber potential based on a valence force field model: application to single-layer MoS2 and black phosphorus'.

PubMed

Midtvedt, Daniel; Croy, Alexander

2016-06-10

We compare the simplified valence-force model for single-layer black phosphorus with the original model and recent ab initio results. Using an analytic approach and numerical calculations we find that the simplified model yields Young's moduli that are smaller compared to the original model and are almost a factor of two smaller than ab initio results. Moreover, the Poisson ratios are an order of magnitude smaller than values found in the literature.

Phenolic Polymer Solvation in Water and Ethylene Glycol, II: Ab Initio Computations.

PubMed

Bauschlicher, Charles W; Bucholz, Eric W; Haskins, Justin B; Monk, Joshua D; Lawson, John W

2017-04-06

Ab initio techniques are used to study the interaction of ethylene glycol and water with a phenolic polymer. The water bonds more strongly with the phenolic OH than with the ring. The phenolic OH groups can form hydrogen bonds between themselves. For more than one water molecule, there is a competition between water-water and water-phenolic interactions. Ethylene glycol shows the same effects as those of water, but the potential energy surface is further complicated by CH 2 -phenolic interactions, different conformers of ethylene glycol, and two OH groups on each molecule. Thus, the ethylene glycol-phenolic potential is more complicated than the water-phenolic potential. The results of the ab initio calculations are compared to those obtained using a force field. These calibration studies show that the water system is easier to describe than the ethylene glycol system. The calibration studies confirm the reliability of force fields used in our companion molecular dynamics study of a phenolic polymer in water and ethylene solutions.

Organic ion association in aqueous phase and ab initio-based force fields: The case of carboxylate/ammonium salts

NASA Astrophysics Data System (ADS)

Houriez, Céline; Vallet, Valérie; Réal, Florent; Meot-Ner Mautner, Michael; Masella, Michel

2017-10-01

We performed molecular dynamics simulations of carboxylate/methylated ammonium ion pairs solvated in bulk water and of carboxylate/methylated ammonium salt solutions at ambient conditions using an ab initio-based polarizable force field whose parameters are assigned to reproduce only high end quantum computations, at the Møller-Plesset second-order perturbation theory/complete basis set limit level, regarding single ions and ion pairs as isolated and micro-hydrated in gas phase. Our results agree with the available experimental results regarding carboxylate/ammonium salt solutions. For instance, our force field approach predicts the percentage of acetate associated with ammonium ions in CH3 COO-/CH3 NH3+ solutions at the 0.2-0.8M concentration scale to range from 14% to 35%, in line with the estimates computed from the experimental ion association constant in liquid water. Moreover our simulations predict the number of water molecules released from the ion first hydration shell to the bulk upon ion association to be about 2.0 ± 0.6 molecules for acetate/protonated amine ion pairs, 3.1 ± 1.5 molecules for the HCOO-/NH4+ pair and 3.3 ± 1.2 molecules for the CH3COO-/(CH3)4N+ pair. For protonated amine-based ion pairs, these values are in line with experiment for alkali/halide pairs solvated in bulk water. All these results demonstrate the promising feature of ab initio-based force fields, i.e., their capacity in accurately modeling chemical systems that cannot be readily investigated using available experimental techniques.

Development of a Polarizable Force Field For Proteins via Ab Initio Quantum Chemistry: First Generation Model and Gas Phase Tests

PubMed Central

KAMINSKI, GEORGE A.; STERN, HARRY A.; BERNE, B. J.; FRIESNER, RICHARD A.; CAO, YIXIANG X.; MURPHY, ROBERT B.; ZHOU, RUHONG; HALGREN, THOMAS A.

2014-01-01

We present results of developing a methodology suitable for producing molecular mechanics force fields with explicit treatment of electrostatic polarization for proteins and other molecular system of biological interest. The technique allows simulation of realistic-size systems. Employing high-level ab initio data as a target for fitting allows us to avoid the problem of the lack of detailed experimental data. Using the fast and reliable quantum mechanical methods supplies robust fitting data for the resulting parameter sets. As a result, gas-phase many-body effects for dipeptides are captured within the average RMSD of 0.22 kcal/mol from their ab initio values, and conformational energies for the di- and tetrapeptides are reproduced within the average RMSD of 0.43 kcal/mol from their quantum mechanical counterparts. The latter is achieved in part because of application of a novel torsional fitting technique recently developed in our group, which has already been used to greatly improve accuracy of the peptide conformational equilibrium prediction with the OPLS-AA force field.1 Finally, we have employed the newly developed first-generation model in computing gas-phase conformations of real proteins, as well as in molecular dynamics studies of the systems. The results show that, although the overall accuracy is no better than what can be achieved with a fixed-charges model, the methodology produces robust results, permits reasonably low computational cost, and avoids other computational problems typical for polarizable force fields. It can be considered as a solid basis for building a more accurate and complete second-generation model. PMID:12395421

Beyond Born-Mayer: Improved models for short-range repulsion in ab initio force fields

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.; ...

2016-06-23

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethyl cyclopropene V. 3,3-Dimethyl-1-(trimethylgermyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2004-02-01

3,3-Dimethyl-1-(trimethylgermyl)cyclopropene ( I) was synthesised using a standard procedure. The IR and Raman spectra of I in the liquid phase were measured. The molecular geometry of I was optimised completely at the HF/6-31G* level. The HF/6-31G*//HF/6-31G* force field was calculated and scaled using the set of scale factors transferred from those determined previously for scaling the theoretical force fields of 3,3-dimethylbutene-1 and 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The assignments of the observed vibrational bands were performed using the theoretical frequencies calculated from the scaled HF/6-31G*//HF/6-31G* force field and the ab initio values of the IR intensities, Raman cross-sections and depolarisation ratios. The theoretical spectra are given. The completely optimised structural parameters of I and its vibrational frequencies are compared with corresponding data of related molecules.

Machine Learning Force Field Parameters from Ab Initio Data

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

Li, Ying; Li, Hui; Pickard, Frank C.

Machine learning (ML) techniques with the genetic algorithm (GA) have been applied to determine a polarizable force field parameters using only ab initio data from quantum mechanics (QM) calculations of molecular clusters at the MP2/6-31G(d,p), DFMP2(fc)/jul-cc-pVDZ, and DFMP2(fc)/jul-cc-pVTZ levels to predict experimental condensed phase properties (i.e., density and heat of vaporization). The performance of this ML/GA approach is demonstrated on 4943 dimer electrostatic potentials and 1250 cluster interaction energies for methanol. Excellent agreement between the training data set from QM calculations and the optimized force field model was achieved. The results were further improved by introducing an offset factor duringmore » the machine learning process to compensate for the discrepancy between the QM calculated energy and the energy reproduced by optimized force field, while maintaining the local “shape” of the QM energy surface. Throughout the machine learning process, experimental observables were not involved in the objective function, but were only used for model validation. The best model, optimized from the QM data at the DFMP2(fc)/jul-cc-pVTZ level, appears to perform even better than the original AMOEBA force field (amoeba09.prm), which was optimized empirically to match liquid properties. The present effort shows the possibility of using machine learning techniques to develop descriptive polarizable force field using only QM data. The ML/GA strategy to optimize force fields parameters described here could easily be extended to other molecular systems.« less

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Hydration and Ion Pairing in Aqueous Mg2+ and Zn2+ Solutions: Force-Field Description Aided by Neutron Scattering Experiments and Ab Initio Molecular Dynamics Simulations.

PubMed

Duboué-Dijon, Elise; Mason, Philip E; Fischer, Henry E; Jungwirth, Pavel

2018-04-05

Magnesium and zinc dications possess the same charge and have an almost identical size, yet they behave very differently in aqueous solutions and play distinct biological roles. It is thus crucial to identify the origins of such different behaviors and to assess to what extent they can be captured by force-field molecular dynamics simulations. In this work, we combine neutron scattering experiments in a specific mixture of H 2 O and D 2 O (the so-called null water) with ab initio molecular dynamics simulations to probe the difference in the hydration structure and ion-pairing properties of chloride solutions of the two cations. The obtained data are used as a benchmark to develop a scaled-charge force field for Mg 2+ that includes electronic polarization in a mean field way. We show that using this electronic continuum correction we can describe aqueous magnesium chloride solutions well. However, in aqueous zinc chloride specific interaction terms between the ions need to be introduced to capture ion pairing quantitatively.

Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

NASA Astrophysics Data System (ADS)

Ylikantola, A.; Linnanto, J.; Knuutinen, J.; Oravilahti, A.; Toivakka, M.

2013-07-01

The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree-Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree-Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree-Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

NASA Astrophysics Data System (ADS)

Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

2017-10-01

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

An Accurate ab initio Quartic Force Field and Vibrational Frequencies for CH4 and Isotopomers

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Martin, Jan M. L.; Taylor, Peter R.

1995-01-01

A very accurate ab initio quartic force field for CH4 and its isotopomers is presented. The quartic force field was determined with the singles and doubles coupled-cluster procedure that includes a quasiperturbative estimate of the effects of connected triple excitations, CCSD(T), using the correlation consistent polarized valence triple zeta, cc-pVTZ, basis set. Improved quadratic force constants were evaluated with the correlation consistent polarized valence quadruple zeta, cc-pVQZ, basis set. Fundamental vibrational frequencies are determined using second-order perturbation theory anharmonic analyses. All fundamentals of CH4 and isotopomers for which accurate experimental values exist and for which there is not a large Fermi resonance, are predicted to within +/- 6 cm(exp -1). It is thus concluded that our predictions for the harmonic frequencies and the anharmonic constants are the most accurate estimates available. It is also shown that using cubic and quartic force constants determined with the correlation consistent polarized double zeta, cc-pVDZ, basis set in conjunction with the cc-pVQZ quadratic force constants and equilibrium geometry leads to accurate predictions for the fundamental vibrational frequencies of methane, suggesting that this approach may be a viable alternative for larger molecules. Using CCSD(T), core correlation is found to reduce the CH4 r(e), by 0.0015 A. Our best estimate for r, is 1.0862 +/- 0.0005 A.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm(-1) studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations.

PubMed

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Pietropolli Charmet, Andrea; Gambi, Alberto

2012-06-07

Difluoromethane (CH(2)F(2), HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH(2)F(2), providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm(-1). Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm(-1) while intensities are predicted within few km mol(-1) from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν(1)>, |2ν(8)>, |2ν(2)> three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm(-1) region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH(2)F(2) as a prototype molecule to test ab initio calculations and theoretical models.

Anharmonic force field and vibrational dynamics of CH2F2 up to 5000 cm-1 studied by Fourier transform infrared spectroscopy and state-of-the-art ab initio calculations

NASA Astrophysics Data System (ADS)

Tasinato, Nicola; Regini, Giorgia; Stoppa, Paolo; Charmet, Andrea Pietropolli; Gambi, Alberto

2012-06-01

Difluoromethane (CH2F2, HFC-32) is a molecule used in refrigerant mixtures as a replacement of the more environmentally hazardous, ozone depleting, chlorofluorocarbons. On the other hand, presenting strong vibration-rotation bands in the 9 μm atmospheric window, it is a greenhouse gas which contributes to global warming. In the present work, the vibrational and ro-vibrational properties of CH2F2, providing basic data for its atmospheric modeling, are studied in detail by coupling medium resolution Fourier transform infrared spectroscopy to high-level electronic structure ab initio calculations. Experimentally a full quantum assignment and accurate integrated absorption cross sections are obtained up to 5000 cm-1. Ab initio calculations are carried out by using CCSD(T) theory and large basis sets of either the correlation consistent or atomic natural orbital hierarchies. By using vibrational perturbation theory to second order a complete set of vibrational and ro-vibrational parameters is derived from the ab initio quartic anharmonic force fields, which well compares with the spectroscopic constants retrieved experimentally. An excellent agreement between theory and experiment is achieved for vibrational energy levels and integrated absorption cross sections: transition frequencies up to four quanta of vibrational excitation are reproduced with a root mean square deviation (RMSD) of 7 cm-1 while intensities are predicted within few km mol-1 from the experiment. Basis set performances and core correlation effects are discussed throughout the paper. Particular attention is focused in the understanding of the anharmonic couplings which rule the vibrational dynamics of the |ν1⟩, |2ν8⟩, |2ν2⟩ three levels interacting system. The reliability of the potential energy and dipole moment surfaces in reproducing the vibrational eigenvalues and intensities as well as in modeling the vibrational and ro-vibrational mixings over the whole 400-5000 cm-1 region is also demonstrated by spectacular spectral simulations carried out by using the ro-vibrational Hamiltonian constants, and the relevant coupling terms, obtained from the perturbation treatment of the ab initio anharmonic force field. The present results suggest CH2F2 as a prototype molecule to test ab initio calculations and theoretical models.

Determination of Quantum Chemistry Based Force Fields for Molecular Dynamics Simulations of Aromatic Polymers

NASA Technical Reports Server (NTRS)

Jaffe, Richard; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

Ab initio quantum chemistry calculations for model molecules can be used to parameterize force fields for molecular dynamics simulations of polymers. Emphasis in our research group is on using quantum chemistry-based force fields for molecular dynamics simulations of organic polymers in the melt and glassy states, but the methodology is applicable to simulations of small molecules, multicomponent systems and solutions. Special attention is paid to deriving reliable descriptions of the non-bonded and electrostatic interactions. Several procedures have been developed for deriving and calibrating these parameters. Our force fields for aromatic polyimide simulations will be described. In this application, the intermolecular interactions are the critical factor in determining many properties of the polymer (including its color).

The accuracy of ab initio calculations without ab initio calculations for charged systems: Kriging predictions of atomistic properties for ions in aqueous solutions

NASA Astrophysics Data System (ADS)

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

2018-06-01

Using the machine learning method kriging, we predict the energies of atoms in ion-water clusters, consisting of either Cl- or Na+ surrounded by a number of water molecules (i.e., without Na+Cl- interaction). These atomic energies are calculated following the topological energy partitioning method called Interacting Quantum Atoms (IQAs). Kriging predicts atomic properties (in this case IQA energies) by a model that has been trained over a small set of geometries with known property values. The results presented here are part of the development of an advanced type of force field, called FFLUX, which offers quantum mechanical information to molecular dynamics simulations without the limiting computational cost of ab initio calculations. The results reported for the prediction of the IQA components of the energy in the test set exhibit an accuracy of a few kJ/mol, corresponding to an average error of less than 5%, even when a large cluster of water molecules surrounding an ion is considered. Ions represent an important chemical system and this work shows that they can be correctly taken into account in the framework of the FFLUX force field.

Theoretical and experimental studies of the structure and vibrational spectra of NTO

NASA Astrophysics Data System (ADS)

Sorescu, Dan C.; Sutton, Teressa R. L.; Thompson, Donald L.; Beardall, David; Wight, Charles A.

1996-10-01

The structure and vibrational spectra of the high explosive 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) have been determined by ab initio molecular orbital calculations at the Hartree-Fock and second-order Møller-Plesset levels and by density functional theory (B3LYP). Experimental frequencies for the molecule have been determined from infrared spectra of pure NTO films and NTO molecules isolated in an argon matrix at 21 K. A force field for gas phase NTO has been obtained based on calculated results at the MP2/6-311G∗∗ level. In addition, a force field for solid state NTO has been constructed using the experimental vibrational frequencies for NTO films and scaled ab initio vibrational frequencies. Differences between the solid state and gas phase results indicate that the environment and preparation procedure exert a marked influence on the spectral characteristics of the NTO molecule.

Cost-Effective Method for Free-Energy Minimization in Complex Systems with Elaborated Ab Initio Potentials.

PubMed

Bistafa, Carlos; Kitamura, Yukichi; Martins-Costa, Marilia T C; Nagaoka, Masataka; Ruiz-López, Manuel F

2018-06-12

We describe a method to locate stationary points in the free-energy hypersurface of complex molecular systems using high-level correlated ab initio potentials. In this work, we assume a combined QM/MM description of the system although generalization to full ab initio potentials or other theoretical schemes is straightforward. The free-energy gradient (FEG) is obtained as the mean force acting on relevant nuclei using a dual level strategy. First, a statistical simulation is carried out using an appropriate, low-level quantum mechanical force-field. Free-energy perturbation (FEP) theory is then used to obtain the free-energy derivatives for the target, high-level quantum mechanical force-field. We show that this composite FEG-FEP approach is able to reproduce the results of a standard free-energy minimization procedure with high accuracy, while simultaneously allowing for a drastic reduction of both computational and wall-clock time. The method has been applied to study the structure of the water molecule in liquid water at the QCISD/aug-cc-pVTZ level of theory, using the sampling from QM/MM molecular dynamics simulations at the B3LYP/6-311+G(d,p) level. The obtained values for the geometrical parameters and for the dipole moment of the water molecule are within the experimental error, and they also display an excellent agreement when compared to other theoretical estimations. The developed methodology represents therefore an important step toward the accurate determination of the mechanism, kinetics, and thermodynamic properties of processes in solution, in enzymes, and in other disordered chemical systems using state-of-the-art ab initio potentials.

Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field

PubMed Central

2016-01-01

Small metal ions play critical roles in numerous biological processes. Of particular interest is how metalloenzymes are allosterically regulated by the binding of specific ions. Understanding how ion binding affects these biological processes requires atomic models that accurately treat the microscopic interactions with the protein ligands. Theoretical approaches at different levels of sophistication can contribute to a deeper understanding of these systems, although computational models must strike a balance between accuracy and efficiency in order to enable long molecular dynamics simulations. In this study, we present a systematic effort to optimize the parameters of a polarizable force field based on classical Drude oscillators to accurately represent the interactions between ions (K+, Na+, Ca2+, and Cl–) and coordinating amino-acid residues for a set of 30 biologically important proteins. By combining ab initio calculations and experimental thermodynamic data, we derive a polarizable force field that is consistent with a wide range of properties, including the geometries and interaction energies of gas-phase ion/protein-like model compound clusters, and the experimental solvation free-energies of the cations in liquids. The resulting models display significant improvements relative to the fixed-atomic-charge additive CHARMM C36 force field, particularly in their ability to reproduce the many-body electrostatic nonadditivity effects estimated from ab initio calculations. The analysis clarifies the fundamental limitations of the pairwise additivity assumption inherent in classical fixed-charge force fields, and shows its dramatic failures in the case of Ca2+ binding sites. These optimized polarizable models, amenable to computationally efficient large-scale MD simulations, set a firm foundation and offer a powerful avenue to study the roles of the ions in soluble and membrane transport proteins. PMID:25578354

Investigation of base pairs containing oxidized guanine using ab initio method and ABEEMσπ polarizable force field.

PubMed

Liu, Cui; Wang, Yang; Zhao, Dongxia; Gong, Lidong; Yang, Zhongzhi

2014-02-01

The integrity of the genetic information is constantly threatened by oxidizing agents. Oxidized guanines have all been linked to different types of cancers. Theoretical approaches supplement the assorted experimental techniques, and bring new sight and opportunities to investigate the underlying microscopic mechanics. Unfortunately, there is no specific force field to DNA system including oxidized guanines. Taking high level ab initio calculations as benchmark, we developed the ABEEMσπ fluctuating charge force field, which uses multiple fluctuating charges per atom. And it was applied to study the energies, structures and mutations of base pairs containing oxidized guanines. The geometries were obtained in reference to other studies or using B3LYP/6-31+G* level optimization, which is more rational and timesaving among 24 quantum mechanical methods selected and tested by this work. The energies were determined at MP2/aug-cc-pVDZ level with BSSE corrections. Results show that the constructed potential function can accurately simulate the change of H-bond and the buckled angle formed by two base planes induced by oxidized guanine, and it provides reliable information of hydrogen bonding, stacking interaction and the mutation processes. The performance of ABEEMσπ polarizable force field in predicting the bond lengths, bond angles, dipole moments etc. is generally better than those of the common force fields. And the accuracy of ABEEMσπ PFF is close to that of the MP2 method. This shows that ABEEMσπ model is a reliable choice for further research of dynamics behavior of DNA fragment including oxidized guanine. Copyright © 2013 Elsevier Inc. All rights reserved.

Vibrational spectra and ab initio analysis of tert-butyl, trimethylsilyl, and trimethylgermyl derivatives of 3,3-dimethylcyclopropene III. 3,3-Dimethyl-1-(trimethylsilyl)cyclopropene

NASA Astrophysics Data System (ADS)

De Maré, G. R.; Panchenko, Yu. N.; Abramenkov, A. V.; Baird, M. S.; Tverezovsky, V. V.; Nizovtsev, A. V.; Bolesov, I. G.

2003-07-01

The experimental Raman and IR vibrational spectra of 3,3-dimethyl-1-(trimethylsilyl)cyclopropene in the liquid phase were recorded. Total geometry optimisation was carried out at the HF/6-31G* level and the HF/6-31G*//HF/6-31G* force field was computed. This force field was corrected by scale factors determined previously (using Pulay's method) for correction of the HF/6-31G*//HF/6-31G* force fields of 3,3-dimethylbutene-1, 1-methyl-, 1,2-dimethyl-, and 3,3-dimethylcyclopropene. The theoretical vibrational frequencies calculated from the scaled quantum mechanical force field and the theoretical intensities obtained from the quantum mechanical calculation were used to construct predicted spectra and to perform the vibrational analysis of the experimental spectra.

Ab initio calculation of harmonic force fields and vibrational spectra for the arsine oxides and sulfides R sub 3 AsY (R = H, F; Y = O, S) and related compounds

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

Schneider, W.; Thiel, W.; Komornicki, A.

1990-04-05

Ab initio self-consistent-field calculations using effective core potentials and polarized double-zeta basis sets are reported for the arsenic compounds H{sub 3}As, H{sub 3}AsO, H{sub 3}AsS, F{sub 3}As, F{sub 3}AsO, F{sub 3}AsS, cis- and trans-H{sub 2}AsOH, and HAsO. The calculated geometries, rotational constants, vibrational frequencies, Coriolis coupling constants, centrifugal distortion constants, infrared band intensities, and force fields are compared with the available experimental data. Good agreement is found in the case of the known molecules, especially H{sub 3}As and F{sub 3}As, so that the predictions for the unknown molecules are expected to be realistic. The theoretical results confirm a recent spectroscopicmore » identification of H{sub 3}AsO, H{sub 2}AsOH, and HAsO and suggest reassignment of several observed frequencies.« less

Modeling the hydration of mono-atomic anions from the gas phase to the bulk phase: the case of the halide ions F-, Cl-, and Br-.

PubMed

Trumm, Michael; Martínez, Yansel Omar Guerrero; Réal, Florent; Masella, Michel; Vallet, Valérie; Schimmelpfennig, Bernd

2012-01-28

In this work, we investigate the hydration of the halide ions fluoride, chloride, and bromide using classical molecular dynamics simulations at the 10 ns scale and based on a polarizable force-field approach, which treats explicitly the cooperative bond character of strong hydrogen bond networks. We have carried out a thorough analysis of the ab initio data at the MP2 or CCSD(T) level concerning anion/water clusters in gas phase to adjust the force-field parameters. In particular, we consider the anion static polarizabilities computed in gas phase using large atomic basis sets including additional diffuse functions. The information extracted from trajectories in solution shows well structured first hydration shells formed of 6.7, 7.0, and 7.6 water molecules at about 2.78 Å, 3.15 Å, and 3.36 Å for fluoride, chloride, and bromide, respectively. These results are in excellent agreement with the latest neutron- and x-ray diffraction studies. In addition, our model reproduces several other properties of halide ions in solution, such as diffusion coefficients, description of hydration processes, and exchange reactions. Moreover, it is also able to reproduce the electrostatic properties of the anions in solution (in terms of anion dipole moment) as reported by recent ab initio quantum simulations. All the results show the ability of the proposed model in predicting data, as well as the need of accounting explicitly for the cooperative character of strong hydrogen bonds to reproduce ab initio potential energy surfaces in a mean square sense and to build up a reliable force field. © 2012 American Institute of Physics

Molecular simulation of the thermophysical properties and phase behaviour of impure CO2 relevant to CCS.

PubMed

Cresswell, Alexander J; Wheatley, Richard J; Wilkinson, Richard D; Graham, Richard S

2016-10-20

Impurities from the CCS chain can greatly influence the physical properties of CO 2 . This has important design, safety and cost implications for the compression, transport and storage of CO 2 . There is an urgent need to understand and predict the properties of impure CO 2 to assist with CCS implementation. However, CCS presents demanding modelling requirements. A suitable model must both accurately and robustly predict CO 2 phase behaviour over a wide range of temperatures and pressures, and maintain that predictive power for CO 2 mixtures with numerous, mutually interacting chemical species. A promising technique to address this task is molecular simulation. It offers a molecular approach, with foundations in firmly established physical principles, along with the potential to predict the wide range of physical properties required for CCS. The quality of predictions from molecular simulation depends on accurate force-fields to describe the interactions between CO 2 and other molecules. Unfortunately, there is currently no universally applicable method to obtain force-fields suitable for molecular simulation. In this paper we present two methods of obtaining force-fields: the first being semi-empirical and the second using ab initio quantum-chemical calculations. In the first approach we optimise the impurity force-field against measurements of the phase and pressure-volume behaviour of CO 2 binary mixtures with N 2 , O 2 , Ar and H 2 . A gradient-free optimiser allows us to use the simulation itself as the underlying model. This leads to accurate and robust predictions under conditions relevant to CCS. In the second approach we use quantum-chemical calculations to produce ab initio evaluations of the interactions between CO 2 and relevant impurities, taking N 2 as an exemplar. We use a modest number of these calculations to train a machine-learning algorithm, known as a Gaussian process, to describe these data. The resulting model is then able to accurately predict a much broader set of ab initio force-field calculations at comparatively low numerical cost. Although our method is not yet ready to be implemented in a molecular simulation, we outline the necessary steps here. Such simulations have the potential to deliver first-principles simulation of the thermodynamic properties of impure CO 2 , without fitting to experimental data.

Developing force fields when experimental data is sparse: AMBER/GAFF-compatible parameters for inorganic and alkyl oxoanions.

PubMed

Kashefolgheta, Sadra; Vila Verde, Ana

2017-08-09

We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham. The parameters were developed primarily relying on experimental information - hydration free energies and solution activity derivatives at 0.5 m concentration - with ab initio, gas phase calculations being used for the cases where experimental information is missing. The ab initio parameterization scheme presented here is distinct from other approaches because it explicitly connects gas phase binding energies to intermolecular interactions in solution. We demonstrate that the original GAFF/AMBER parameters often overestimate anion-cation interactions, leading to an excessive number of contact ion pairs in solutions of carboxylate ions, and to aggregation in solutions of divalent ions. GAFF/AMBER parameters lead to excessive numbers of salt bridges in proteins and of contact ion pairs between sodium and acidic protein groups, issues that are resolved by using the optimized parameters presented here.

A comparison of force fields and calculation methods for vibration intervals of isotopic H3(+) molecules

NASA Astrophysics Data System (ADS)

Carney, G. D.; Adler-Golden, S. M.; Lesseski, D. C.

1986-04-01

This paper reports (1) improved values for low-lying vibration intervals of H3(+), H2D(+), D2H(+), and D3(+) calculated using the variational method and Simons-Parr-Finlan (1973) representations of the Carney-Porter (1976) and Dykstra-Swope (1979) ab initio H3(+) potential energy surfaces, (2) quartic normal coordinate force fields for isotopic H3(+) molecules, (3) comparisons of variational and second-order perturbation theory, and (4) convergence properties of the Lai-Hagstrom internal coordinate vibrational Hamiltonian. Standard deviations between experimental and ab initio fundamental vibration intervals of H3(+), H2D(+), D2H(+), and D3(+) for these potential surfaces are 6.9 (Carney-Porter) and 1.2/cm (Dykstra-Swope). The standard deviations between perturbation theory and exact variational fundamentals are 5 and 10/cm for the respective surfaces. The internal coordinate Hamiltonian is found to be less efficient than the previously employed 't' coordinate Hamiltonian for these molecules, except in the case of H2D(+).

Ab initio and density functional force field studies on the IR spectra and structure of diazonium dicyanomethylide (diazodicyanomethane)

NASA Astrophysics Data System (ADS)

Georgieva, Miglena K.

2004-03-01

The structure of diazonium dicyanomethylide (diazodicyanomethane) +N 2-C(CN) 2-↔N 2C(CN) 2 has been studied on the basis of ab initio HF, MP2 and DFT BLYP force field calculations, as well as of literature IR spectra and X-ray diffraction structural data. The results have been compared with those obtained for a series of chemical relatives of the title compound, i.e. molecules, push-pull molecules, anions and zwitterions, containing α-dicyano or diazo fragments, and especially substituted ammonium dicyanomethylides and diazomethane +N 2-CH 2-↔N 2CH 2. It has been found on the basis of spectral, bond length, bond order and electric charge analyses that the diazonium (or carbanionic, left) canonical form is much more important for the title zwitterion, than the corresponding one for diazomethane. So, the title compound can be named (and considered as) both diazonium dicyanomethylide and dicyanodiazomethane.

Development of a Scaled Quantum Mechanical Force Field for Peptides in Aqueous Solution

DTIC Science & Technology

1996-03-01

differ. Raman and IR techniques are complimentary which helps in assignment of observed vibrational modes. As described in beginning organic ...1588 I NH, .i.sor(98) 2076 2100 24 CH3 55(95) 2125 2207 82 CH3 as’ (56), CH3 as’ (43) 2235 2253 18 CH3 as’(55), CH3 as’(41) 2888 COff .(100) 3155 NH...Application of self- consistent-field ab initio calculations to organic molecules I. Equilibrium struc- ture and force constants of hydrocarbons

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

A new force field including charge directionality for TMAO in aqueous solution

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

Usui, Kota; Nagata, Yuki, E-mail: sulpizi@uni-mainz.de, E-mail: nagata@mpip-mainz.mpg.de; Hunger, Johannes

We propose a new force field for trimethylamine N-oxide (TMAO), which is designed to reproduce the long-lived and highly directional hydrogen bond between the TMAO oxygen (O{sub TMAO}) atom and surrounding water molecules. Based on the data obtained by ab initio molecular dynamics simulations, we introduce three dummy sites around O{sub TMAO} to mimic the O{sub TMAO} lone pairs and we migrate the negative charge on the O{sub TMAO} to the dummy sites. The force field model developed here improves both structural and dynamical properties of aqueous TMAO solutions. Moreover, it reproduces the experimentally observed dependence of viscosity upon increasingmore » TMAO concentration quantitatively. The simple procedure of the force field construction makes it easy to implement in molecular dynamics simulation packages and makes it compatible with the existing biomolecular force fields. This paves the path for further investigation of protein-TMAO interaction in aqueous solutions.« less

AN IN SILICO INVESTIGATION OF THE ENANTIOSELECTIVE METABOLISM RATES OF TRIAZOLE FUGICIDES

EPA Science Inventory

The objective of this work is to use in silico methods such as ab initio quantum and classical force-field methods to explore and develop an understanding for the enantioselective metabolism rates experimentally observed in the triazole fungicide bromuconazole. This directed stud...

Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

PubMed

Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

2016-03-05

The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Explicit polarization (X-Pol) potential using ab initio molecular orbital theory and density functional theory.

PubMed

Song, Lingchun; Han, Jaebeom; Lin, Yen-lin; Xie, Wangshen; Gao, Jiali

2009-10-29

The explicit polarization (X-Pol) method has been examined using ab initio molecular orbital theory and density functional theory. The X-Pol potential was designed to provide a novel theoretical framework for developing next-generation force fields for biomolecular simulations. Importantly, the X-Pol potential is a general method, which can be employed with any level of electronic structure theory. The present study illustrates the implementation of the X-Pol method using ab initio Hartree-Fock theory and hybrid density functional theory. The computational results are illustrated by considering a set of bimolecular complexes of small organic molecules and ions with water. The computed interaction energies and hydrogen bond geometries are in good accord with CCSD(T) calculations and B3LYP/aug-cc-pVDZ optimizations.

Ab initio description of continuum effects in A=11 exotic systems with chiral NN+3N forces

NASA Astrophysics Data System (ADS)

Calci, Angelo; Navratil, Petr; Roth, Robert; Dohet-Eraly, Jeremy; Quaglioni, Sofia; Hupin, Guillaume

2016-09-01

Based on the fundamental symmetries of QCD, chiral effective field theory (EFT) provides two- (NN), three- (3N) and many-nucleon interactions in a consistent and systematically improvable scheme. The rapid developments to construct divers families of chiral NN+3N interactions and the conceptual and technical improvements of ab initio many-body approaches pose a great opportunity for nuclear physics. By studying particular interesting phenomena in nuclear structure and reaction observables one can discriminate between different forces and study the predictive power of chiral EFT. The accurate description of the 11Be nucleus, in particular, the ground-state parity inversion and exceptionally strong E1 transition between its two bound states constitute an enormous challenge for the developments of nuclear forces and many-body approaches. We present a sensitivity analysis of structure and reaction observables to different NN+3N interactions in 11Be and n+10Be as well as the mirror p+10C scattering using the ab initio NCSM with continuum (NCSMC). Supported by the U.S. Department of Energy, Office of Science, Office of Nuclear Physics, under Work Proposal No. SCW1158. TRIUMF receives federal funding via a contribution agreement with the National Research Council of Canada.

Transferability of polarizable models for ion-water electrostatic interaction

NASA Astrophysics Data System (ADS)

Masia, Marco

2009-06-01

Studies of ion-water systems at condensed phase and at interfaces have pointed out that molecular and ionic polarization plays an important role for many phenomena ranging from hydrogen bond dynamics to water interfaces' structure. Classical and ab initio Molecular Dynamics simulations reveal that induced dipole moments at interfaces (e.g. air-water and water-protein) are usually high, hinting that polarizable models to be implemented in classical force fields should be very accurate in reproducing the electrostatic properties of the system. In this paper the electrostatic properties of three classical polarizable models for ion-water interaction are compared with ab initio results both at gas and condensed phase. For Li+- water and Cl--water dimers the reproducibility of total dipole moments obtained with high level quantum chemical calculations is studied; for the same ions in liquid water, Car-Parrinello Molecular Dynamics simulations are used to compute the time evolution of ionic and molecular dipole moments, which are compared with the classical models. The PD2-H2O model developed by the author and coworkers [Masia et al. J. Chem. Phys. 2004, 121, 7362] together with the gaussian intermolecular damping for ion-water interaction [Masia et al. J. Chem. Phys. 2005, 123, 164505] showed to be the fittest in reproducing the ab initio results from gas to condensed phase, allowing for force field transferability.

Accurate Vibrational-Rotational Parameters and Infrared Intensities of 1-Bromo-1-fluoroethene: A Joint Experimental Analysis and Ab Initio Study.

PubMed

Pietropolli Charmet, Andrea; Stoppa, Paolo; Giorgianni, Santi; Bloino, Julien; Tasinato, Nicola; Carnimeo, Ivan; Biczysko, Malgorzata; Puzzarini, Cristina

2017-05-04

The medium-resolution gas-phase infrared (IR) spectra of 1-bromo-1-fluoroethene (BrFC═CH 2 , 1,1-C 2 H 2 BrF) were investigated in the range 300-6500 cm -1 , and the vibrational analysis led to the assignment of all fundamentals as well as many overtone and combination bands up to three quanta, thus giving an accurate description of its vibrational structure. Integrated band intensity data were determined with high precision from the measurements of their corresponding absorption cross sections. The vibrational analysis was supported by high-level ab initio investigations. CCSD(T) computations accounting for extrapolation to the complete basis set and core correlation effects were employed to accurately determine the molecular structure and harmonic force field. The latter was then coupled to B2PLYP and MP2 computations in order to account for mechanical and electrical anharmonicities. Second-order perturbative vibrational theory was then applied to the thus obtained hybrid force fields to support the experimental assignment of the IR spectra.

Ab Initio Molecular Dynamics and Lattice Dynamics-Based Force Field for Modeling Hexagonal Boron Nitride in Mechanical and Interfacial Applications.

PubMed

Govind Rajan, Ananth; Strano, Michael S; Blankschtein, Daniel

2018-04-05

Hexagonal boron nitride (hBN) is an up-and-coming two-dimensional material, with applications in electronic devices, tribology, and separation membranes. Herein, we utilize density-functional-theory-based ab initio molecular dynamics (MD) simulations and lattice dynamics calculations to develop a classical force field (FF) for modeling hBN. The FF predicts the crystal structure, elastic constants, and phonon dispersion relation of hBN with good accuracy and exhibits remarkable agreement with the interlayer binding energy predicted by random phase approximation calculations. We demonstrate the importance of including Coulombic interactions but excluding 1-4 intrasheet interactions to obtain the correct phonon dispersion relation. We find that improper dihedrals do not modify the bulk mechanical properties and the extent of thermal vibrations in hBN, although they impact its flexural rigidity. Combining the FF with the accurate TIP4P/Ice water model yields excellent agreement with interaction energies predicted by quantum Monte Carlo calculations. Our FF should enable an accurate description of hBN interfaces in classical MD simulations.

Polarizable atomic multipole-based force field for DOPC and POPE membrane lipids

NASA Astrophysics Data System (ADS)

Chu, Huiying; Peng, Xiangda; Li, Yan; Zhang, Yuebin; Min, Hanyi; Li, Guohui

2018-04-01

A polarizable atomic multipole-based force field for the membrane bilayer models 1,2-dioleoyl-phosphocholine (DOPC) and 1-palmitoyl-2-oleoyl-phosphatidylethanolamine (POPE) has been developed. The force field adopts the same framework as the Atomic Multipole Optimized Energetics for Biomolecular Applications (AMOEBA) model, in which the charge distribution of each atom is represented by the permanent atomic monopole, dipole and quadrupole moments. Many-body polarization including the inter- and intra-molecular polarization is modelled in a consistent manner with distributed atomic polarizabilities. The van der Waals parameters were first transferred from existing AMOEBA parameters for small organic molecules and then optimised by fitting to ab initio intermolecular interaction energies between models and a water molecule. Molecular dynamics simulations of the two aqueous DOPC and POPE membrane bilayer systems, consisting of 72 model molecules, were then carried out to validate the force field parameters. Membrane width, area per lipid, volume per lipid, deuterium order parameters, electron density profile, etc. were consistent with experimental values.

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Origin of the anomalous long lifetime of ¹⁴C.

PubMed

Maris, P; Vary, J P; Navrátil, P; Ormand, W E; Nam, H; Dean, D J

2011-05-20

We report the microscopic origins of the anomalously suppressed beta decay of ¹⁴C to ¹⁴N using the ab initio no-core shell model with the Hamiltonian from the chiral effective field theory including three-nucleon force terms. The three-nucleon force induces unexpectedly large cancellations within the p shell between contributions to beta decay, which reduce the traditionally large contributions from the nucleon-nucleon interactions by an order of magnitude, leading to the long lifetime of ¹⁴C.

Evaluation of synthetic linear motor-molecule actuation energetics

PubMed Central

Brough, Branden; Northrop, Brian H.; Schmidt, Jacob J.; Tseng, Hsian-Rong; Houk, Kendall N.; Stoddart, J. Fraser; Ho, Chih-Ming

2006-01-01

By applying atomic force microscope (AFM)-based force spectroscopy together with computational modeling in the form of molecular force-field simulations, we have determined quantitatively the actuation energetics of a synthetic motor-molecule. This multidisciplinary approach was performed on specifically designed, bistable, redox-controllable [2]rotaxanes to probe the steric and electrostatic interactions that dictate their mechanical switching at the single-molecule level. The fusion of experimental force spectroscopy and theoretical computational modeling has revealed that the repulsive electrostatic interaction, which is responsible for the molecular actuation, is as high as 65 kcal·mol−1, a result that is supported by ab initio calculations. PMID:16735470

Improved atomistic simulation of diffusion and sorption in metal oxides

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

2001-01-01

Gas diffusion and sorption on the surface of metal oxides are investigated using atomistic simulations, that make use of two different force fields for the description of the intramolecular and intermolecular interactions. MD and MC computations are presented and estimates of the mean residence time, Henry's constant, and the heat of adsorption are provided for various common gases (CO, CO2, O2, CH4, Xe), and semiconducting substrates that hold promise for gas sensor applications (SnO2, BaTiO3). Comparison is made between the performance of a simple, first generation force field (Universal) and a more detailed, second generation field (COMPASS) under the same conditions and the same assumptions regarding the generation of the working configurations. It is found that the two force fields yield qualitatively similar results in all cases examined here. However, direct comparison with experimental data reveals that the accuracy of the COMPASS-based computations is not only higher than that of the first generation force field but exceeds even that of published specialized methods, based on ab initio computations.

Chiral EFT based nuclear forces: achievements and challenges

NASA Astrophysics Data System (ADS)

Machleidt, R.; Sammarruca, F.

2016-08-01

During the past two decades, chiral effective field theory has become a popular tool to derive nuclear forces from first principles. Two-nucleon interactions have been worked out up to sixth order of chiral perturbation theory and three-nucleon forces up to fifth order. Applications of some of these forces have been conducted in nuclear few- and many-body systems—with a certain degree of success. But in spite of these achievements, we are still faced with great challenges. Among them is the issue of a proper uncertainty quantification of predictions obtained when applying these forces in ab initio calculations of nuclear structure and reactions. A related problem is the order by order convergence of the chiral expansion. We start this review with a pedagogical introduction and then present the current status of the field of chiral nuclear forces. This is followed by a discussion of representative examples for the application of chiral two- and three-body forces in the nuclear many-body system including convergence issues.

A transferable force field for CdS-CdSe-PbS-PbSe solid systems

NASA Astrophysics Data System (ADS)

Fan, Zhaochuan; Koster, Rik S.; Wang, Shuaiwei; Fang, Changming; Yalcin, Anil O.; Tichelaar, Frans D.; Zandbergen, Henny W.; van Huis, Marijn A.; Vlugt, Thijs J. H.

2014-12-01

A transferable force field for the PbSe-CdSe solid system using the partially charged rigid ion model has been successfully developed and was used to study the cation exchange in PbSe-CdSe heteronanocrystals [A. O. Yalcin et al., "Atomic resolution monitoring of cation exchange in CdSe-PbSe heteronanocrystals during epitaxial solid-solid-vapor growth," Nano Lett. 14, 3661-3667 (2014)]. In this work, we extend this force field by including another two important binary semiconductors, PbS and CdS, and provide detailed information on the validation of this force field. The parameterization combines Bader charge analysis, empirical fitting, and ab initio energy surface fitting. When compared with experimental data and density functional theory calculations, it is shown that a wide range of physical properties of bulk PbS, PbSe, CdS, CdSe, and their mixed phases can be accurately reproduced using this force field. The choice of functional forms and parameterization strategy is demonstrated to be rational and effective. This transferable force field can be used in various studies on II-VI and IV-VI semiconductor materials consisting of CdS, CdSe, PbS, and PbSe. Here, we demonstrate the applicability of the force field model by molecular dynamics simulations whereby transformations are initiated by cation exchange.

An efficient and numerically stable procedure for generating sextic force fields in normal mode coordinates

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

Sibaev, M.; Crittenden, D. L., E-mail: deborah.crittenden@canterbury.ac.nz

In this paper, we outline a general, scalable, and black-box approach for calculating high-order strongly coupled force fields in rectilinear normal mode coordinates, based upon constructing low order expansions in curvilinear coordinates with naturally limited mode-mode coupling, and then transforming between coordinate sets analytically. The optimal balance between accuracy and efficiency is achieved by transforming from 3 mode representation quartic force fields in curvilinear normal mode coordinates to 4 mode representation sextic force fields in rectilinear normal modes. Using this reduced mode-representation strategy introduces an error of only 1 cm{sup −1} in fundamental frequencies, on average, across a sizable testmore » set of molecules. We demonstrate that if it is feasible to generate an initial semi-quartic force field in curvilinear normal mode coordinates from ab initio data, then the subsequent coordinate transformation procedure will be relatively fast with modest memory demands. This procedure facilitates solving the nuclear vibrational problem, as all required integrals can be evaluated analytically. Our coordinate transformation code is implemented within the extensible PyPES library program package, at http://sourceforge.net/projects/pypes-lib-ext/.« less

Transferable Force Field for Metal–Organic Frameworks from First-Principles: BTW-FF

PubMed Central

2014-01-01

We present an ab-initio derived force field to describe the structural and mechanical properties of metal–organic frameworks (or coordination polymers). The aim is a transferable interatomic potential that can be applied to MOFs regardless of metal or ligand identity. The initial parametrization set includes MOF-5, IRMOF-10, IRMOF-14, UiO-66, UiO-67, and HKUST-1. The force field describes the periodic crystal and considers effective atomic charges based on topological analysis of the Bloch states of the extended materials. Transferable potentials were developed for the four organic ligands comprising the test set and for the associated Cu, Zn, and Zr metal nodes. The predicted materials properties, including bulk moduli and vibrational frequencies, are in agreement with explicit density functional theory calculations. The modal heat capacity and lattice thermal expansion are also predicted. PMID:25574157

An Angular Overlap Model for Cu(II) Ion in the AMOEBA Polarizable Force Field

PubMed Central

Xiang, Jin Yu; Ponder, Jay W.

2014-01-01

An extensible polarizable force field for transition metal ion was developed based on AMOEBA and the angular overlap model (AOM) with consistent treatment of electrostatics for all atoms. Parameters were obtained by fitting molecular mechanics (MM) energies to various ab initio gas-phase calculations. The results of parameterization were presented for copper (II) ion ligated to water and model fragments of amino acid residues involved in the copper binding sites of type 1 copper proteins. Molecular dynamics (MD) simulations were performed on aqueous copper (II) ion at various temperatures, as well as plastocyanin (1AG6) and azurin (1DYZ). Results demonstrated that the AMOEBA-AOM significantly improves the accuracy of classical MM in a number of test cases when compared to ab initio calculations. The Jahn-Teller distortion for hexa-aqua copper (II) complex was handled automatically without specifically designating axial and in-plane ligands. Analyses of MD trajectories resulted in a 6-coordination first solvation shell for aqueous copper (II) ion and a 1.8ns average residence time of water molecules. The ensemble average geometries of 1AG6 and 1DYZ copper binding sites were in general agreement with X-ray and previous computational studies. PMID:25045338

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Ab initio conformational analysis of N-formyl ?-alanine amide including electron correlation

NASA Astrophysics Data System (ADS)

Yu, Ching-Hsing; Norman, Mya A.; Schäfer, Lothar; Ramek, Michael; Peeters, Anik; van Alsenoy, Christian

2001-06-01

The conformational properties of N-formyl L-alanine amide (ALA) were investigated using RMP2/6-311G∗∗ ab initio gradient geometry optimization. One hundred forty four structures of ALA were optimized at 30° grid points in its φ(N-C(α)), ψ(C(α)-C‧) conformational space. Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces, in φ,ψ-space, of bond lengths, bond angles, torsional sensitivity and electrostatic atomic charges. Analyses show that, in agreement with previous studies, the right-handed helical conformation, αR, is not a local energy minimum of the potential energy surface of ALA. Comparisons with protein crystallographic data show that the characteristic differences between geometrical trends in dipeptides and proteins, previously found for ab initio dipeptide structures obtained without electron correlation, are also found in the electron-correlated geometries. In contrast to generally accepted features of force fields used in empirical molecular modeling, partial atomic charges obtained by the CHELPG method are found to be not constant, but to vary significantly throughout the φ,ψ-space. By comparing RHF and MP2 structures, the effects of dispersion forces on ALA were studied, revealing molecular contractions for those conformations, in which small adjustments of torsional angles entail large changes in non-bonded distances.

A Combined Molecular Dynamics and Experimental Study of Doped Polypyrrole.

PubMed

Fonner, John M; Schmidt, Christine E; Ren, Pengyu

2010-10-01

Polypyrrole (PPy) is a biocompatible, electrically conductive polymer that has great potential for battery, sensor, and neural implant applications. Its amorphous structure and insolubility, however, limit the experimental techniques available to study its structure and properties at the atomic level. Previous theoretical studies of PPy in bulk are also scarce. Using ab initio calculations, we have constructed a molecular mechanics force field of chloride-doped PPy (PPyCl) and undoped PPy. This model has been designed to integrate into the OPLS force field, and parameters are available for the Gromacs and TINKER software packages. Molecular dynamics (MD) simulations of bulk PPy and PPyCl have been performed using this force field, and the effects of chain packing and electrostatic scaling on the bulk polymer density have been investigated. The density of flotation of PPyCl films has been measured experimentally. Amorphous X-ray diffraction of PPyCl was obtained and correlated with atomic structures sampled from MD simulations. The force field reported here is foundational for bridging the gap between experimental measurements and theoretical calculations for PPy based materials.

Thermodynamic properties for applications in chemical industry via classical force fields.

PubMed

Guevara-Carrion, Gabriela; Hasse, Hans; Vrabec, Jadran

2012-01-01

Thermodynamic properties of fluids are of key importance for the chemical industry. Presently, the fluid property models used in process design and optimization are mostly equations of state or G (E) models, which are parameterized using experimental data. Molecular modeling and simulation based on classical force fields is a promising alternative route, which in many cases reasonably complements the well established methods. This chapter gives an introduction to the state-of-the-art in this field regarding molecular models, simulation methods, and tools. Attention is given to the way modeling and simulation on the scale of molecular force fields interact with other scales, which is mainly by parameter inheritance. Parameters for molecular force fields are determined both bottom-up from quantum chemistry and top-down from experimental data. Commonly used functional forms for describing the intra- and intermolecular interactions are presented. Several approaches for ab initio to empirical force field parameterization are discussed. Some transferable force field families, which are frequently used in chemical engineering applications, are described. Furthermore, some examples of force fields that were parameterized for specific molecules are given. Molecular dynamics and Monte Carlo methods for the calculation of transport properties and vapor-liquid equilibria are introduced. Two case studies are presented. First, using liquid ammonia as an example, the capabilities of semi-empirical force fields, parameterized on the basis of quantum chemical information and experimental data, are discussed with respect to thermodynamic properties that are relevant for the chemical industry. Second, the ability of molecular simulation methods to describe accurately vapor-liquid equilibrium properties of binary mixtures containing CO(2) is shown.

Continuum and three-nucleon force effects on Be 9 energy levels

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

Langhammer, Joachim; Navrátil, Petr; Quaglioni, Sofia

2015-02-05

In this paper, we extend the recently proposed ab initio no-core shell model with continuum to include three-nucleon (3N) interactions beyond the few-body domain. The extended approach allows for the assessment of effects of continuum degrees of freedom as well as of the 3N force in ab initio calculations of structure and reaction observables of p- and lower-sd-shell nuclei. As a first application we concentrate on energy levels of the 9Be system for which all excited states lie above the n- 8Be threshold. For all energy levels, the inclusion of the continuum significantly improves the agreement with experiment, which wasmore » an issue in standard no-core shell model calculations. Furthermore, we find the proper treatment of the continuum indispensable for reliable statements about the quality of the adopted 3N interaction from chiral effective field theory. Finally, in particular, we find the 1/2 + resonance energy, which is of astrophysical interest, in good agreement with experiment.« less

Impact of Short-Range Forces on Defect Production from High-Energy Collisions

DOE PAGES

Stoller, R. E.; Tamm, A.; Béland, L. K.; ...

2016-04-25

Primary radiation damage formation in solid materials typically involves collisions between atoms that have up to a few hundred keV of kinetic energy. The distance between two colliding atoms can approach 0.05 nm during these collisions. At such small atomic separations, force fields fitted to equilibrium properties tend to significantly underestimate the potential energy of the colliding dimer. To enable molecular dynamics simulations of high-energy collisions, it is common practice to use a screened Coulomb force field to describe the interactions and to smoothly join this to the equilibrium force field at a suitable interatomic spacing. But, there is nomore » accepted standard method for choosing the parameters used in the joining process, and our results prove that defect production is sensitive to how the force fields are linked. A new procedure is presented that involves the use of ab initio calculations to determine the magnitude and spatial dependence of the pair interactions at intermediate distances, along with systematic criteria for choosing the joining parameters. Results are presented for the case of nickel, which demonstrate the use and validity of the procedure.« less

Salt permeation and exclusion in hydroxylated and functionalized silica pores.

PubMed

Leung, Kevin; Rempe, Susan B; Lorenz, Christian D

2006-03-10

We use combined ab initio molecular dynamics (AIMD), grand canonical Monte Carlo, and molecular dynamics techniques to study the effect of pore surface chemistry and confinement on the permeation of salt into silica nanopore arrays filled with water. AIMD shows that 11.6 A diameter hydroxylated silica pores are relatively stable in water, whereas amine groups on functionalized pore surfaces abstract silanol protons, turning into NH3+. Free energy calculations using an ab initio parametrized force field show that the hydroxylated pores strongly attract Na+ and repel Cl- ions. Pores lined with NH3+ have the reverse surface charge polarity. Finally, studies of ions in carbon nanotubes suggest that hydration of Cl- is more strongly frustrated by pure confinement effects than Na+.

Applicability of effective fragment potential version 2 - Molecular dynamics (EFP2-MD) simulations for predicting excess properties of mixed solvents

NASA Astrophysics Data System (ADS)

Kuroki, Nahoko; Mori, Hirotoshi

2018-02-01

Effective fragment potential version 2 - molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations were applied to water-methanol binary mixture. Comparing EFP2s defined with (aug-)cc-pVXZ (X = D,T) basis sets, it was found that large sets are necessary to generate sufficiently accurate EFP2 for predicting mixture properties. It was shown that EFP2-MD could predict the excess molar volume. Since the computational cost of EFP2-MD are far less than ab initio MD, the results presented herein demonstrate that EFP2-MD is promising for predicting physicochemical properties of novel mixed solvents.

Design principles for high–pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures

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

Hölzl, Christoph; Horinek, Dominik, E-mail: dominik.horinek@ur.de; Kibies, Patrick

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures – while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatmentmore » of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute’s response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.« less

Design principles for high-pressure force fields: Aqueous TMAO solutions from ambient to kilobar pressures.

PubMed

Hölzl, Christoph; Kibies, Patrick; Imoto, Sho; Frach, Roland; Suladze, Saba; Winter, Roland; Marx, Dominik; Horinek, Dominik; Kast, Stefan M

2016-04-14

Accurate force fields are one of the major pillars on which successful molecular dynamics simulations of complex biomolecular processes rest. They have been optimized for ambient conditions, whereas high-pressure simulations become increasingly important in pressure perturbation studies, using pressure as an independent thermodynamic variable. Here, we explore the design of non-polarizable force fields tailored to work well in the realm of kilobar pressures--while avoiding complete reparameterization. Our key is to first compute the pressure-induced electronic and structural response of a solute by combining an integral equation approach to include pressure effects on solvent structure with a quantum-chemical treatment of the solute within the embedded cluster reference interaction site model (EC-RISM) framework. Next, the solute's response to compression is taken into account by introducing pressure-dependence into selected parameters of a well-established force field. In our proof-of-principle study, the full machinery is applied to N,N,N-trimethylamine-N-oxide (TMAO) in water being a potent osmolyte that counteracts pressure denaturation. EC-RISM theory is shown to describe well the charge redistribution upon compression of TMAO(aq) to 10 kbar, which is then embodied in force field molecular dynamics by pressure-dependent partial charges. The performance of the high pressure force field is assessed by comparing to experimental and ab initio molecular dynamics data. Beyond its broad usefulness for designing non-polarizable force fields for extreme thermodynamic conditions, a good description of the pressure-response of solutions is highly recommended when constructing and validating polarizable force fields.

On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

DTIC Science & Technology

2008-12-01

DE ABSTRACT A quantum-mechanically-based potential energy function that describes interactions of dimers of the explosive ...method is capable of producing force fields for interactions of the molecular crystalline explosive RDX, and appears to be suitable to enable reliable...Ridge, TN. Byrd, E.F.C., Scuseria, G.E., Chabalowski, C.F., 2004: “An ab initio study of solid nitromethane , HMX, RDX and CL20: Successes and

Neutron matter with Quantum Monte Carlo: chiral 3N forces and static response

DOE PAGES

Buraczynski, M.; Gandolfi, S.; Gezerlis, A.; ...

2016-03-14

Neutron matter is related to the physics of neutron stars and that of neutron-rich nuclei. Moreover, Quantum Monte Carlo (QMC) methods offer a unique way of solving the many-body problem non-perturbatively, providing feedback on features of nuclear interactions and addressing scenarios that are inaccessible to other approaches. Our contribution goes over two recent accomplishments in the theory of neutron matter: a) the fusing of QMC with chiral effective field theory interactions, focusing on local chiral 3N forces, and b) the first attempt to find an ab initio solution to the problem of static response.

Unified ab initio approaches to nuclear structure and reactions

DOE PAGES

Navratil, Petr; Quaglioni, Sofia; Hupin, Guillaume; ...

2016-04-13

The description of nuclei starting from the constituent nucleons and the realistic interactions among them has been a long-standing goal in nuclear physics. In addition to the complex nature of the nuclear forces, with two-, three- and possibly higher many-nucleon components, one faces the quantum-mechanical many-nucleon problem governed by an interplay between bound and continuum states. In recent years, significant progress has been made in ab initio nuclear structure and reaction calculations based on input from QCD-employing Hamiltonians constructed within chiral effective field theory. After a brief overview of the field, we focus on ab initio many-body approaches—built upon the no-core shell model—that are capable of simultaneously describing both bound and scattering nuclear states, and present results for resonances in light nuclei, reactions important for astrophysics and fusion research. In particular, we review recent calculations of resonances in the 6He halo nucleus, of five- and six-nucleon scattering, and an investigation of the role of chiral three-nucleon interactions in the structure of 9Be. Further, we discuss applications to the 7Bemore » $${({\\rm{p}},\\gamma )}^{8}{\\rm{B}}$$ radiative capture. Lastly, we highlight our efforts to describe transfer reactions including the 3H$${({\\rm{d}},{\\rm{n}})}^{4}$$He fusion.« less

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Wu, Chun; Wang, Zhi-Xiang; Zhou, Yaoqi; Duan, Yong

2008-06-01

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 μs) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A˚ Cα root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A˚ Cα RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Φ-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A˚ Cα RMSD away from the experimentally determined structure.

An ab-initio study of the relative stability of the ggg and the gtg conformer in hexane

NASA Astrophysics Data System (ADS)

Koglin, Eckhard; Meier, Robert J.

1999-10-01

Earlier ab-initio work suggested, on the basis of MP2 level calculations, that the hexane ggg conformer is more stable than the gtg conformer. Because this is unexpected and if true might have a significant impact on force field parametrisations, we have applied Hartree-Fock and post-HF methods to evaluate the relative stability of these conformers. We find that at levels higher than MP2 the gtg conformer is more stable than the ggg conformer, in agreement with the conventional idea that each additional gauche bond causes a further decrease in stability of the conformer. DFT methods were also applied, but although DFT methods including gradient corrections show correct qualitative behaviour, quantitatively the relative energies are far off compared to the post-HF results.

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

PubMed Central

2015-01-01

The charge distribution of halogen atoms on organochlorine compounds can be highly anisotropic and even display a so-called σ-hole, which leads to strong halogen bonds with electron donors. In this paper, we have systematically investigated a series of chloromethanes with one to four chloro substituents using a polarizable multipole-based molecular mechanics model. The atomic multipoles accurately reproduced the ab initio electrostatic potential around chloromethanes, including CCl4, which has a prominent σ-hole on the Cl atom. The van der Waals parameters for Cl were fitted to the experimental density and heat of vaporization. The calculated hydration free energy, solvent reaction fields, and interaction energies of several homo- and heterodimer of chloromethanes are in good agreement with experimental and ab initio data. This study suggests that sophisticated electrostatic models, such as polarizable atomic multipoles, are needed for accurate description of electrostatics in organochlorine compounds and halogen bonds, although further improvement is necessary for better transferability. PMID:24484473

Elastic dipoles of point defects from atomistic simulations

NASA Astrophysics Data System (ADS)

Varvenne, Céline; Clouet, Emmanuel

2017-12-01

The interaction of point defects with an external stress field or with other structural defects is usually well described within continuum elasticity by the elastic dipole approximation. Extraction of the elastic dipoles from atomistic simulations is therefore a fundamental step to connect an atomistic description of the defect with continuum models. This can be done either by a fitting of the point-defect displacement field, by a summation of the Kanzaki forces, or by a linking equation to the residual stress. We perform here a detailed comparison of these different available methods to extract elastic dipoles, and show that they all lead to the same values when the supercell of the atomistic simulations is large enough and when the anharmonic region around the point defect is correctly handled. But, for small simulation cells compatible with ab initio calculations, only the definition through the residual stress appears tractable. The approach is illustrated by considering various point defects (vacancy, self-interstitial, and hydrogen solute atom) in zirconium, using both empirical potentials and ab initio calculations.

Use of Molecular Modeling to Determine the Interaction and Competition of Gases within Coal for Carbon Dioxide Sequestration

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

Jeffrey D. Evanseck; Jeffry D. Madura

A 3-dimensional coal structural model for the Argonne Premium Coal Pocahontas No. 3 has been generated. The model was constructed based on the wealth of structural information available in the literature with the enhancement that the structural diversity within the structure was represented implicitly (for the first time) based on image analysis of HRTEM in combination with LDMS data. The complex and large structural model (>10,000 carbon atoms) will serve as a basis for examining the interaction of gases within this low volatile bituminous coal. Simulations are of interest to permit reasonable simulations of the host-guest interactions with regard tomore » carbon dioxide sequestration within coal and methane displacement from coal. The molecular structure will also prove useful in examining other coal related behavior such as solvent swelling, liquefaction and other properties. Molecular models of CO{sub 2} have been evaluated with water to analyze which classical molecular force-field parameters are the most reasonable to predict the interactions of CO{sub 2} with water. The comparison of the molecular force field models was for a single CO{sub 2}-H{sub 2}O complex and was compared against first principles quantum mechanical calculations. The interaction energies and the electrostatic interaction distances were used as criteria in the comparison. The ab initio calculations included Hartree-Fock, B3LYP, and Moeller-Plesset 2nd, 3rd, and 4th order perturbation theories with basis sets up to the aug-cc-pvtz basis set. The Steele model was the best literature model, when compared to the ab initio data, however, our new CO{sub 2} model reproduces the QM data significantly better than the Steele force-field model.« less

Spectroscopically determined force field for water dimer: physically enhanced treatment of hydrogen bonding in molecular mechanics energy functions.

PubMed

Mannfors, Berit; Palmo, Kim; Krimm, Samuel

2008-12-11

Our ab initio transformed spectroscopically determined force field (SDFF) methodology emphasizes, in addition to accurate structure and energy performance, comparable prediction of vibrational properties in order to improve reproduction of interaction forces. It is now applied to the determination of a molecular mechanics (MM) force field for the water monomer and dimer as an initial step in developing a more physically based treatment of the hydrogen bonding that not only underlies condensed-phase water but also must be important in molecular-level protein-water interactions. Essential electrical components of the SDFF for monomer water are found to be the following: an off-plane charge distribution, this distribution consisting of four off-atom charge sites in traditional lone pair (LP) but also in inverted lone pair (ILP) positions; allowance for a diffuse size to these off-atom sites; and the incorporation of charge fluxes (i.e., the change in charge with change in internal coordinate). Parametrization of such an LP/ILP model together with the SDFF analytically transformed valence force field results in essentially exact agreement with ab initio (in this case MP2/6-31++G(d,p)) structure, electrical, and vibrational properties. Although we demonstrate that the properties of this monomer electrical model together with its van der Waals and polarization interactions are transferable to the dimer, this is not sufficient in reproducing comparable dimer properties, most notably the huge increase in infrared intensity of a donor OH stretch mode. This deficiency, which can be eliminated by a large dipole-derivative-determined change in the effective charge flux of the donor hydrogen-bonded OH bond, is not accounted for by the charge flux change in this bond due to the induction effects of the acceptor electric field alone, and can only be fully removed by an added bond flux associated with the extent of overlap of the wave functions of the two molecules. We show that this overlap charge flux (OCF) emulates an actual O-H...LP-O intermolecular dipole flux, reflecting the unitary nature of the hydrogen-bonded system in the context of MM-separable molecules. The effectiveness of incorporating the OCF noncanonical character demonstrates that a distinctively QM-unique property can be substantively represented in MM energy functions.

Accurate ab initio quartic force fields for the ions HCO(+) and HOC(+)

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Taylor, Peter R.; Lee, Timothy J.

1993-01-01

The quartic force fields of HCO(+) and HOC(+) have been computed using augmented coupled cluster methods and basis sets of spdf and spdfg quality. Calculations on HCN, CO, and N2 have been performed to assist in calibrating the computed results. Going from an spdf to an spdfg basis shortens triple bonds by about 0.004 A, and increases the corresponding harmonic frequency by 10-20/cm, leaving bond distances about 0.003 A too long and triple bond stretching frequencies about 5/cm too low. Accurate estimates for the bond distances, fundamental frequencies, and thermochemical quantities are given. HOC(+) lies 37.8 +/- 0.5 kcal/mol (0 K) above HCO(+); the classical barrier height for proton exchange is 76.7 +/- 1.0 kcal/mol.

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

PubMed

He, Yi; Xiao, Yi; Liwo, Adam; Scheraga, Harold A

2009-10-01

We explored the energy-parameter space of our coarse-grained UNRES force field for large-scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual-bond-angle bending and side-chain-rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy-term weights were generated randomly, and good sets were selected by carrying out replica-exchange molecular dynamics simulations of two peptides with a minimal alpha-helical and a minimal beta-hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native-like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native-like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with alpha or alpha + beta structure and found to locate native-like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. Copyright 2009 Wiley Periodicals, Inc.

Thermal Conductivities in Solids from First Principles: Accurate Computations and Rapid Estimates

NASA Astrophysics Data System (ADS)

Carbogno, Christian; Scheffler, Matthias

In spite of significant research efforts, a first-principles determination of the thermal conductivity κ at high temperatures has remained elusive. Boltzmann transport techniques that account for anharmonicity perturbatively become inaccurate under such conditions. Ab initio molecular dynamics (MD) techniques using the Green-Kubo (GK) formalism capture the full anharmonicity, but can become prohibitively costly to converge in time and size. We developed a formalism that accelerates such GK simulations by several orders of magnitude and that thus enables its application within the limited time and length scales accessible in ab initio MD. For this purpose, we determine the effective harmonic potential occurring during the MD, the associated temperature-dependent phonon properties and lifetimes. Interpolation in reciprocal and frequency space then allows to extrapolate to the macroscopic scale. For both force-field and ab initio MD, we validate this approach by computing κ for Si and ZrO2, two materials known for their particularly harmonic and anharmonic character. Eventually, we demonstrate how these techniques facilitate reasonable estimates of κ from existing MD calculations at virtually no additional computational cost.

Equilibrium and Dynamics Properties of Poly(oxyethylene) Melts and Related Poly(alkylethers) from Simulations and Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Smith, Grant D.; Jaffe, R. L.; Yoon, D. Y.; Arnold, James O. (Technical Monitor)

1994-01-01

Molecular dynamics simulations of POE melts have been performed utilizing a potential force field parameterized to reproduce conformer energies and rotational energy barriers in dimethoxyethane as determined from ab initio electronic structure calculations. Chain conformations and dimensions of POE from the simulations were found to be in good agreement with predictions of a rotational isomeric state (RIS) model based upon the ab initio conformational. energies. The melt chains were found to be somewhat extended relative to chains at theta conditions. This effect will be discussed in light of neutron scattering experiments which indicate that POE chains are extended in the melt relative to theta solutions. The conformational characteristics of POE chains will also be compared with those of other poly (alkylethers), namely poly(oxymethylene), poly(oxytrimethylene) and poly(oxytetramethylene). Local conformational dynamics were found to be more rapid than in polymethylene. Calculated C-H vector correlation times were found to be in reasonable agreement with experimental values from C-13 NMR spin-lattice relaxation times. The influence of ionic salts on local conformations and dynamics will also be discussed.

Ab initio many-body calculations of nucleon- 4He scattering with three-nucleon forces

DOE PAGES

Hupin, Guillaume; Langhammer, Joachim; Navratil, Petr; ...

2013-11-27

We extend the ab initio no-core shell model/resonating-group method to include three-nucleon (3N) interactions for the description of nucleon-nucleus collisions. We outline the formalism, give algebraic expressions for the 3N-force integration kernels, and discuss computational aspects of two alternative implementations. The extended theoretical framework is then applied to nucleon- 4He elastic scattering using similarity-renormalization-group (SRG)-evolved nucleon-nucleon plus 3N potentials derived from chiral effective field theory. We analyze the convergence properties of the calculated phase shifts and explore their dependence upon the SRG evolution parameter. We include up to six excited states of the 4He target and find significant effects frommore » the inclusion of the chiral 3N force, e.g., it enhances the spin-orbit splitting between the 3/2 – and 1/2 – resonances and leads to an improved agreement with the phase shifts obtained from an accurate R-matrix analysis of the five-nucleon experimental data. As a result, we find remarkably good agreement with measured differential cross sections at various energies below the d+ 3H threshold, while analyzing powers manifest larger deviations from experiment for certain energies and angles.« less

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches.

PubMed

Antipov, Sergey V; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2017-11-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research "Molecular Ultrafast Science and Technology," are presented: These include Bohmian dynamics description of the collision of H with H 2 , local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase.

Ultrafast dynamics induced by the interaction of molecules with electromagnetic fields: Several quantum, semiclassical, and classical approaches

PubMed Central

Antipov, Sergey V.; Bhattacharyya, Swarnendu; El Hage, Krystel; Xu, Zhen-Hao; Meuwly, Markus; Rothlisberger, Ursula; Vaníček, Jiří

2018-01-01

Several strategies for simulating the ultrafast dynamics of molecules induced by interactions with electromagnetic fields are presented. After a brief overview of the theory of molecule-field interaction, we present several representative examples of quantum, semiclassical, and classical approaches to describe the ultrafast molecular dynamics, including the multiconfiguration time-dependent Hartree method, Bohmian dynamics, local control theory, semiclassical thawed Gaussian approximation, phase averaging, dephasing representation, molecular mechanics with proton transfer, and multipolar force fields. In addition to the general overview, some focus is given to the description of nuclear quantum effects and to the direct dynamics, in which the ab initio energies and forces acting on the nuclei are evaluated on the fly. Several practical applications, performed within the framework of the Swiss National Center of Competence in Research “Molecular Ultrafast Science and Technology,” are presented: These include Bohmian dynamics description of the collision of H with H2, local control theory applied to the photoinduced ultrafast intramolecular proton transfer, semiclassical evaluation of vibrationally resolved electronic absorption, emission, photoelectron, and time-resolved stimulated emission spectra, infrared spectroscopy of H-bonding systems, and multipolar force fields applications in the condensed phase. PMID:29376107

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

An extensive ab initio study of the structures, vibrational spectra, quadratic force fields, and relative energetics of three isomers of Cl2O2

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rohlfing, Celeste MCM.; Rice, Julia E.

1992-01-01

Quantum mechanical computational methods are employed for an ab initio investigation of: (1) the molecular properties of the lowest isomers of the ClO dimer; and (2) predicted molecular and thermochemical properties. Techniques employed include electron correlation and particularly singles and doubles coupled-cluster (CCSD) theory with or without perturbational estimates of the effects of connected triple excitations. The isomers ClOClO and ClClO2 are found to have higher energies than the ClOOCl isomer, and the theoretical vibrational frequencies of the isomers are well correlated with experimental data. Experimental values of the heat of formation for the isomers are also compared with calculations based on an isodesmic reaction with Cl2O, H2O, and HOOH.

Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

PubMed

Timko, Jeff; Kuyucak, Serdar

2012-11-28

Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

An accurate ab initio quartic force field for ammonia

NASA Technical Reports Server (NTRS)

Martin, J. M. L.; Lee, Timothy J.; Taylor, Peter R.

1992-01-01

The quartic force field of ammonia is computed using basis sets of spdf/spd and spdfg/spdf quality and an augmented coupled cluster method. After correcting for Fermi resonance, the computed fundamentals and nu 4 overtones agree on average to better than 3/cm with the experimental ones except for nu 2. The discrepancy for nu 2 is principally due to higher-order anharmonicity effects. The computed omega 1, omega 3, and omega 4 confirm the recent experimental determination by Lehmann and Coy (1988) but are associated with smaller error bars. The discrepancy between the computed and experimental omega 2 is far outside the expected error range, which is also attributed to higher-order anharmonicity effects not accounted for in the experimental determination. Spectroscopic constants are predicted for a number of symmetric and asymmetric top isotopomers of NH3.

Molecular Modeling of Water Interfaces: From Molecular Spectroscopy to Thermodynamics.

PubMed

Nagata, Yuki; Ohto, Tatsuhiko; Backus, Ellen H G; Bonn, Mischa

2016-04-28

Understanding aqueous interfaces at the molecular level is not only fundamentally important, but also highly relevant for a variety of disciplines. For instance, electrode-water interfaces are relevant for electrochemistry, as are mineral-water interfaces for geochemistry and air-water interfaces for environmental chemistry; water-lipid interfaces constitute the boundaries of the cell membrane, and are thus relevant for biochemistry. One of the major challenges in these fields is to link macroscopic properties such as interfacial reactivity, solubility, and permeability as well as macroscopic thermodynamic and spectroscopic observables to the structure, structural changes, and dynamics of molecules at these interfaces. Simulations, by themselves, or in conjunction with appropriate experiments, can provide such molecular-level insights into aqueous interfaces. In this contribution, we review the current state-of-the-art of three levels of molecular dynamics (MD) simulation: ab initio, force field, and coarse-grained. We discuss the advantages, the potential, and the limitations of each approach for studying aqueous interfaces, by assessing computations of the sum-frequency generation spectra and surface tension. The comparison of experimental and simulation data provides information on the challenges of future MD simulations, such as improving the force field models and the van der Waals corrections in ab initio MD simulations. Once good agreement between experimental observables and simulation can be established, the simulation can be used to provide insights into the processes at a level of detail that is generally inaccessible to experiments. As an example we discuss the mechanism of the evaporation of water. We finish by presenting an outlook outlining four future challenges for molecular dynamics simulations of aqueous interfacial systems.

The torsional energy profile of 1,2-diphenylethane: an ab initio study

NASA Astrophysics Data System (ADS)

Ivanov, Petko M.

1997-08-01

Ab initio molecular orbital calculations were carried out for the antiperiplanar (ap), the synclinal (sc), phenyl/phenyl eclipsed (syn barrier), and phenyl/H eclipsed (ap/sc barrier) conformations of 1,2-diphenylethane, and the energy ordering of conformations thus obtained was compared with the torsional energy profile estimated with the MM2 and MM3 molecular mechanics force fields. The basis set effect on the results was studied at the restricted Hartree-Fock (RHF) self-consistent field (SCF) level of theory, and the electron correlation energies were corrected by the second-order (MP2) Møller-Plesset perturbation treatment using the 6-31G * basis set. The performance of a DFT model (Becke-style three-parameter hybrid method using the correlation functional of Lee, Yang and Parr, B3LYP) was also tested to assess relative energies of the conformations using two basis sets, 6-31G * and 6-311G **. The RHF and B3LYP results are qualitatively the same, while the MP2 calculations produced significant differences in the geometries and reversed the order of preference for the antiperiplanar and the synclinal conformations.

Coupling of ab initio density functional theory and molecular dynamics for the multiscale modeling of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ng, T. Y.; Yeak, S. H.; Liew, K. M.

2008-02-01

A multiscale technique is developed that couples empirical molecular dynamics (MD) and ab initio density functional theory (DFT). An overlap handshaking region between the empirical MD and ab initio DFT regions is formulated and the interaction forces between the carbon atoms are calculated based on the second-generation reactive empirical bond order potential, the long-range Lennard-Jones potential as well as the quantum-mechanical DFT derived forces. A density of point algorithm is also developed to track all interatomic distances in the system, and to activate and establish the DFT and handshaking regions. Through parallel computing, this multiscale method is used here to study the dynamic behavior of single-walled carbon nanotubes (SWCNTs) under asymmetrical axial compression. The detection of sideways buckling due to the asymmetrical axial compression is reported and discussed. It is noted from this study on SWCNTs that the MD results may be stiffer compared to those with electron density considerations, i.e. first-principle ab initio methods.

The electromigration force in metallic bulk

NASA Astrophysics Data System (ADS)

Lodder, A.; Dekker, J. P.

1998-01-01

The voltage induced driving force on a migrating atom in a metallic system is discussed in the perspective of the Hellmann-Feynman force concept, local screening concepts and the linear-response approach. Since the force operator is well defined in quantum mechanics it appears to be only confusing to refer to the Hellmann-Feynman theorem in the context of electromigration. Local screening concepts are shown to be mainly of historical value. The physics involved is completely represented in ab initio local density treatments of dilute alloys and the implementation does not require additional precautions about screening, being typical for jellium treatments. The linear-response approach is shown to be a reliable guide in deciding about the two contributions to the driving force, the direct force and the wind force. Results are given for the wind valence for electromigration in a number of FCC and BCC metals, calculated using an ab initio KKR-Green's function description of a dilute alloy.

Cross-Linked Nanotube Materials with Variable Stiffness Tethers

NASA Technical Reports Server (NTRS)

Frankland, Sarah-Jane V.; Odegard, Gregory M.; Herzog, Matthew N.; Gates, Thomas S.; Fay, Catherine C.

2004-01-01

The constitutive properties of a cross-linked single-walled carbon nanotube material are predicted with a multi-scale model. The material is modeled as a transversely isotropic solid using concepts from equivalent-continuum modeling. The elastic constants are determined using molecular dynamics simulation. Some parameters of the molecular force field are determined specifically for the cross-linker from ab initio calculations. A demonstration of how the cross-linked nanotubes may affect the properties of a nanotube/polyimide composite is included using a micromechanical analysis.

Selenoglycosides in silico: ab initio-derived reparameterization of MM4, conformational analysis using histo-blood group ABH antigens and lectin docking as indication for potential of bioactivity

NASA Astrophysics Data System (ADS)

Strino, Francesco; Lii, Jenn-Huei; Koppisetty, Chaitanya A. K.; Nyholm, Per-Georg; Gabius, Hans-Joachim

2010-12-01

The identification of glycan epitopes such as the histo-blood group ABH determinants as docking sites for bacterial/viral infections and signals in growth regulation fuels the interest to develop non-hydrolysable mimetics for therapeutic applications. Inevitably, the required substitution of the linkage oxygen atom will alter the derivative's topology. Our study addresses the question of the impact of substitution of oxygen by selenium. In order to characterize spatial parameters and flexibility of selenoglycosides, we first performed ab initio calculations on model compounds to refine the MM4 force field. The following application of the resulting MM4R version appears to reduce the difference to ab initio data when compared to using the MM4 estimator. Systematic conformational searches on the derivatives of histo-blood group ABH antigens revealed increased flexibility with acquisition of additional low-energy conformer(s), akin to the behavior of S-glycosides. Docking analysis using the Glide program for eight test cases indicated potential for bioactivity, giving further experimental investigation a clear direction to testing Se-glycosides as lectin ligands.

Microwave spectra and molecular structures of (Z)-pent-2-en-4-ynenitrile and maleonitrile.

PubMed

Halter, R J; Fimmen, R L; McMahon, R J; Peebles, S A; Kuczkowski, R L; Stanton, J F

2001-12-12

Accurate equilibrium structures have been determined for (Z)-pent-2-en-4-ynenitrile (8) and maleonitrile (9) by combining microwave spectroscopy data and ab initio quantum chemistry calculations. The microwave spectra of 10 isotopomers of 8 and 5 isotopomers of 9 were obtained using a pulsed nozzle Fourier transform microwave spectrometer. The ground-state rotational constants were adjusted for vibration-rotation interaction effects calculated from force fields obtained from ab initio calculations. The resultant equilibrium rotational constants were used to determine structures that are in very good agreement with those obtained from high-level ab initio calculations (CCSD(T)/cc-pVTZ). The geometric parameters in 8 and 9 are very similar; they also do not differ significantly from the all-carbon analogue, (Z)-hex-3-ene-1,5-diyne (7), the parent molecule for the Bergman cyclization. A small deviation from linearity about the alkyne and cyano linkages is observed for 7-9 and several related species where accurate equilibrium parameters are available. The data on 7-9 should be of interest to radioastronomy and may provide insights on the formation and interstellar chemistry of unsaturated species such as the cyanopolyynes.

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 Calculation of Accurate Vibrational Frequencies for Molecules of Interest in Atmospheric Chemistry

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

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 +/- 8 cm(sup -1) on average, and molecular bond distances are accurate to within +/- 0.001-0.003 A, 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 rovibrational spectra from the interstellar medium. Some recent examples demonstrating this accuracy win 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.

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

Van Vleet, Mary J.; Misquitta, Alston J.; Stone, Anthony J.

Short-range repulsion within inter-molecular force fields is conventionally described by either Lennard-Jones or Born-Mayer forms. Despite their widespread use, these simple functional forms are often unable to describe the interaction energy accurately over a broad range of inter-molecular distances, thus creating challenges in the development of ab initio force fields and potentially leading to decreased accuracy and transferability. Herein, we derive a novel short-range functional form based on a simple Slater-like model of overlapping atomic densities and an iterated stockholder atom (ISA) partitioning of the molecular electron density. We demonstrate that this Slater-ISA methodology yields a more accurate, transferable, andmore » robust description of the short-range interactions at minimal additional computational cost compared to standard Lennard-Jones or Born-Mayer approaches. Lastly, we show how this methodology can be adapted to yield the standard Born-Mayer functional form while still retaining many of the advantages of the Slater-ISA approach.« less

Cheap but accurate calculation of chemical reaction rate constants from ab initio data, via system-specific, black-box force fields

NASA Astrophysics Data System (ADS)

Steffen, Julien; Hartke, Bernd

2017-10-01

Building on the recently published quantum-mechanically derived force field (QMDFF) and its empirical valence bond extension, EVB-QMDFF, it is now possible to generate a reliable potential energy surface for any given elementary reaction step in an essentially black box manner. This requires a limited and pre-defined set of reference data near the reaction path and generates an accurate approximation of the reference potential energy surface, on and off the reaction path. This intermediate representation can be used to generate reaction rate data, with far better accuracy and reliability than with traditional approaches based on transition state theory (TST) or variational extensions thereof (VTST), even if those include sophisticated tunneling corrections. However, the additional expense at the reference level remains very modest. We demonstrate all this for three arbitrarily chosen example reactions.

Vibrational Frequencies and Spectroscopic Constants for 1(sup 3)A' HNC and 1(sup 3)A' HOC+ from High-Accuracy Quartic Force Fields

NASA Technical Reports Server (NTRS)

Fortenberry, Ryan C.; Crawford, T. Daniel; Lee, Timothy J.

2014-01-01

The spectroscopic constants and vibrational frequencies for the 1(sup 3)A' states of HNC, DNC, HOC+, and DOC+ are computed and discussed in this work. The reliable CcCR quartic force field based on high-level coupled cluster ab initio quantum chemical computations is exclusively utilized to provide the anharmonic potential. Then, second order vibrational perturbation theory and vibrational configuration interaction methods are employed to treat the nuclear Schroedinger equation. Second-order perturbation theory is also employed to provide spectroscopic data for all molecules examined. The relationship between these molecules and the corresponding 1(sup 3)A' HCN and HCO+ isomers is further developed here. These data are applicable to laboratory studies involving formation of HNC and HOC+ as well as astronomical observations of chemically active astrophysical environments.

Scaling Atomic Partial Charges of Carbonate Solvents for Lithium Ion Solvation and Diffusion

DOE PAGES

Chaudhari, Mangesh I.; Nair, Jijeesh R.; Pratt, Lawrence R.; ...

2016-10-21

Lithium-ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) were studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to assess nonpolarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) was adapted to take advantage of fourfold occupancy of the near-neighbor solvation structure observed in simulations and used to calculate solvation free energies. The computed free energy for transfer of Li + to PC from water, based on electronicmore » structure calculations with cluster-QCT, agrees with the experimental value. The simulation-based direct-QCT results with scaled partial charges agree with the electronic structure-based QCT values. The computed Li +/PF 6 - transference numbers of 0.35/0.65 (EC) and 0.31/0.69 (PC) agree well with NMR experimental values of 0.31/0.69 (EC) and 0.34/0.66 (PC) and similar values obtained here with impedance spectroscopy. These combined results demonstrate that solvent partial charges can be scaled in systems dominated by strong electrostatic interactions to achieve trends in ion solvation and transport properties that are comparable to ab initio and experimental results. Thus, the results support the use of scaled partial charges in simple, nonpolarizable force fields in future studies of these electrolyte solutions.« less

Computing the Rotational Diffusion of Biomolecules via Molecular Dynamics Simulation and Quaternion Orientations.

PubMed

Chen, Po-Chia; Hologne, Maggy; Walker, Olivier

2017-03-02

Rotational diffusion (D rot ) is a fundamental property of biomolecules that contains information about molecular dimensions and solute-solvent interactions. While ab initio D rot prediction can be achieved by explicit all-atom molecular dynamics simulations, this is hindered by both computational expense and limitations in water models. We propose coarse-grained force fields as a complementary solution, and show that the MARTINI force field with elastic networks is sufficient to compute D rot in >10 proteins spanning 5-157 kDa. We also adopt a quaternion-based approach that computes D rot orientation directly from autocorrelations of best-fit rotations as used in, e.g., RMSD algorithms. Over 2 μs trajectories, isotropic MARTINI+EN tumbling replicates experimental values to within 10-20%, with convergence analyses suggesting a minimum sampling of >50 × τ theor to achieve sufficient precision. Transient fluctuations in anisotropic tumbling cause decreased precision in predictions of axisymmetric anisotropy and rhombicity, the latter of which cannot be precisely evaluated within 2000 × τ theor for GB3. Thus, we encourage reporting of axial decompositions D x , D y , D z to ease comparability between experiment and simulation. Where protein disorder is absent, we observe close replication of MARTINI+EN D rot orientations versus CHARMM22*/TIP3p and experimental data. This work anticipates the ab initio prediction of NMR-relaxation by combining coarse-grained global motions with all-atom local motions.

Toward ab initio molecular dynamics modeling for sum-frequency generation spectra; an efficient algorithm based on surface-specific velocity-velocity correlation function.

PubMed

Ohto, Tatsuhiko; Usui, Kota; Hasegawa, Taisuke; Bonn, Mischa; Nagata, Yuki

2015-09-28

Interfacial water structures have been studied intensively by probing the O-H stretch mode of water molecules using sum-frequency generation (SFG) spectroscopy. This surface-specific technique is finding increasingly widespread use, and accordingly, computational approaches to calculate SFG spectra using molecular dynamics (MD) trajectories of interfacial water molecules have been developed and employed to correlate specific spectral signatures with distinct interfacial water structures. Such simulations typically require relatively long (several nanoseconds) MD trajectories to allow reliable calculation of the SFG response functions through the dipole moment-polarizability time correlation function. These long trajectories limit the use of computationally expensive MD techniques such as ab initio MD and centroid MD simulations. Here, we present an efficient algorithm determining the SFG response from the surface-specific velocity-velocity correlation function (ssVVCF). This ssVVCF formalism allows us to calculate SFG spectra using a MD trajectory of only ∼100 ps, resulting in the substantial reduction of the computational costs, by almost an order of magnitude. We demonstrate that the O-H stretch SFG spectra at the water-air interface calculated by using the ssVVCF formalism well reproduce those calculated by using the dipole moment-polarizability time correlation function. Furthermore, we applied this ssVVCF technique for computing the SFG spectra from the ab initio MD trajectories with various density functionals. We report that the SFG responses computed from both ab initio MD simulations and MD simulations with an ab initio based force field model do not show a positive feature in its imaginary component at 3100 cm(-1).

Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate

PubMed Central

2015-01-01

Phosphate groups are commonly observed in biomolecules such as nucleic acids and lipids. Due to their highly charged and polarizable nature, modeling these compounds with classical force fields is challenging. Using quantum mechanical studies and liquid-phase simulations, the AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl phosphate (TMP) has been developed. On the basis of ab initio calculations, it was found that ion binding and the solution environment significantly impact both the molecular geometry and the energy differences between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ calculations of methyl phosphates at several conformations with their chemical environments taken into account. Many-body polarization is handled via a Thole-style induction model using distributed atomic polarizabilities. van der Waals parameters of phosphate and oxygen atoms are determined by fitting to the quantum mechanical interaction energy curves for water with DMP or TMP. Additional stretch-torsion and angle-torsion coupling terms were introduced in order to capture asymmetry in P–O bond lengths and angles due to the generalized anomeric effect. The resulting force field for DMP and TMP is able to accurately describe both the molecular structure and conformational energy surface, including bond and angle variations with conformation, as well as interaction of both species with water and metal ions. The force field was further validated for TMP in the condensed phase by computing hydration free energy, liquid density, and heat of vaporization. The polarization behavior between liquid TMP and TMP in water is drastically different. PMID:26574325

Force-field parametrization and molecular dynamics simulations of Congo red

NASA Astrophysics Data System (ADS)

Król, Marcin; Borowski, Tomasz; Roterman, Irena; Piekarska, Barbara; Stopa, Barbara; Rybarska, Joanna; Konieczny, Leszek

2004-01-01

Congo red, a diazo dye widely used in medical diagnosis, is known to form supramolecular systems in solution. Such a supramolecular system may interact with various proteins. In order to examine the nature of such complexes empirical force field parameters for the Congo red molecule were developed. The parametrization of bonding terms closely followed the methodology used in the development of the charmm22 force field, except for the calculation of charges. Point charges were calculated from a fit to a quantum mechanically derived electrostatic potential using the CHELP-BOW method. Obtained parameters were tested in a series of molecular dynamics simulations of both a single molecule and a micelle composed of Congo red molecules. It is shown that newly developed parameters define a stable minimum on the hypersurface of the potential energy and crystal and ab initio geometries and rotational barriers are well reproduced. Furthermore, rotations around C-N bonds are similar to torsional vibrations observed in crystals of diphenyl-diazene, which confirms that the flexibility of the molecule is correct. Comparison of results obtained from micelles molecular dynamics simulations with experimental data shows that the thermal dependence of micelle creation is well reproduced.

Sampling the potential energy surface of a DNA duplex damaged by a food carcinogen: Force field parameterization by ab initio quantum calculations and conformational searching using molecular mechanics computations

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-DNA orientations, compromising its ability to act as a faithful template during DNA replication.

i-PI: A Python interface for ab initio path integral molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Ceriotti, Michele; More, Joshua; Manolopoulos, David E.

2014-03-01

Recent developments in path integral methodology have significantly reduced the computational expense of including quantum mechanical effects in the nuclear motion in ab initio molecular dynamics simulations. However, the implementation of these developments requires a considerable programming effort, which has hindered their adoption. Here we describe i-PI, an interface written in Python that has been designed to minimise the effort required to bring state-of-the-art path integral techniques to an electronic structure program. While it is best suited to first principles calculations and path integral molecular dynamics, i-PI can also be used to perform classical molecular dynamics simulations, and can just as easily be interfaced with an empirical forcefield code. To give just one example of the many potential applications of the interface, we use it in conjunction with the CP2K electronic structure package to showcase the importance of nuclear quantum effects in high-pressure water. Catalogue identifier: AERN_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AERN_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 138626 No. of bytes in distributed program, including test data, etc.: 3128618 Distribution format: tar.gz Programming language: Python. Computer: Multiple architectures. Operating system: Linux, Mac OSX, Windows. RAM: Less than 256 Mb Classification: 7.7. External routines: NumPy Nature of problem: Bringing the latest developments in the modelling of nuclear quantum effects with path integral molecular dynamics to ab initio electronic structure programs with minimal implementational effort. Solution method: State-of-the-art path integral molecular dynamics techniques are implemented in a Python interface. Any electronic structure code can be patched to receive the atomic coordinates from the Python interface, and to return the forces and energy that are used to integrate the equations of motion. Restrictions: This code only deals with distinguishable particles. It does not include fermonic or bosonic exchanges between equivalent nuclei, which can become important at very low temperatures. Running time: Depends dramatically on the nature of the simulation being performed. A few minutes for short tests with empirical force fields, up to several weeks for production calculations with ab initio forces. The examples provided with the code run in less than an hour.

Building machine learning force fields for nanoclusters

NASA Astrophysics Data System (ADS)

Zeni, Claudio; Rossi, Kevin; Glielmo, Aldo; Fekete, Ádám; Gaston, Nicola; Baletto, Francesca; De Vita, Alessandro

2018-06-01

We assess Gaussian process (GP) regression as a technique to model interatomic forces in metal nanoclusters by analyzing the performance of 2-body, 3-body, and many-body kernel functions on a set of 19-atom Ni cluster structures. We find that 2-body GP kernels fail to provide faithful force estimates, despite succeeding in bulk Ni systems. However, both 3- and many-body kernels predict forces within an ˜0.1 eV/Å average error even for small training datasets and achieve high accuracy even on out-of-sample, high temperature structures. While training and testing on the same structure always provide satisfactory accuracy, cross-testing on dissimilar structures leads to higher prediction errors, posing an extrapolation problem. This can be cured using heterogeneous training on databases that contain more than one structure, which results in a good trade-off between versatility and overall accuracy. Starting from a 3-body kernel trained this way, we build an efficient non-parametric 3-body force field that allows accurate prediction of structural properties at finite temperatures, following a newly developed scheme [A. Glielmo et al., Phys. Rev. B 95, 214302 (2017)]. We use this to assess the thermal stability of Ni19 nanoclusters at a fractional cost of full ab initio calculations.

Conformational stability, r(0) structural parameters, vibrational assignments and ab initio calculations of ethyldichlorophosphine.

PubMed

Darkhalil, Ikhlas D; Paquet, Charles; Waqas, Mohammad; Gounev, Todor K; Durig, James R

2015-02-05

Variable temperature (-60 to -100 °C) studies of ethyldichlorophosphine, CH3CH2PCl2, of the infrared spectra (4000-400 cm(-1)) dissolved in liquid xenon have been carried out. From these data, the two conformers have been identified and the enthalpy difference has been determined between the more stable trans conformer and the less stable gauche form to be 88±9 cm(-1) (1.04±0.11 kJ/mol). The percentage of abundance of the gauche conformer is estimated to be 57% at ambient temperature. The conformational stabilities have been predicted from ab initio calculations by utilizing many different basis sets up to aug-cc-pVTZ for both MP2(full) and density functional theory calculations by the B3LYP method. Vibrational assignments have been provided for both conformers which have been predicted by MP2(full)/6-31G(d) ab initio calculations to predict harmonic force fields, wavenumbers of the fundamentals, infrared intensities, Raman activities and depolarization ratios for both conformers. Estimated r0 structural parameters have been obtained from adjusted MP2(full)/6-311+G(d,p) calculations. The results are discussed and compared to the corresponding properties of some related molecules. Copyright © 2014 Elsevier B.V. All rights reserved.

The AB Initio Mia Method: Theoretical Development and Practical Applications

NASA Astrophysics Data System (ADS)

Peeters, Anik

The bottleneck in conventional ab initio Hartree -Fock calculations is the storage of the electron repulsion integrals because their number increases with the fourth power of the number of basis functions. This problem can be solved by a combination of the multiplicative integral approximation (MIA) and the direct SCF method. The MIA approach was successfully applied in the geometry optimisation of some biologically interesting compounds like the neurolepticum Haloperidol and two TIBO derivatives, inactivators of HIV1. In this thesis the potency of the MIA-method is shown by the application of this method in the calculation of the forces on the nuclei. In addition, the MIA method enabled the development of a new model for performing crystal field studies: the supermolecule model. The results for this model are in better agreement with experimental data than the results for the point charge model. This is illustrated by the study of some small molecules in the solid state: 2,3-diketopiperazine, formamide oxime and two polymorphic forms of glycine, alpha-glycine and beta-glycine.

Ab initio predictions of the symmetry energy and recent constraints

NASA Astrophysics Data System (ADS)

Sammarruca, Francesca

2017-01-01

The symmetry energy plays a crucial role in the structure and the dynamics of neutron-rich systems, including the formation of neutron skins, the location of neutron drip lines, as well as intriguing correlations with the structure of compact stars. With experimental efforts in progress or being planned to shed light on the less known aspects of the nuclear chart, microscopic predictions based on ab initio approaches are very important. In recent years, chiral effective field theory has become popular because of its firm connection with quantum chromodynamics and its systematic approach to the development of nuclear forces. Predictions of the symmetry energy obtained from modern chiral interactions will be discussed in the light of recent empirical constraints extracted from heavy ion collisions at 400 MeV per nucleon at GSI. Applications of our equations of state to neutron-rich systems will also be discussed, with particular emphasis on neutron skins, which are sensitive to the density dependence of the symmetry energy.

All-atom ab initio native structure prediction of a mixed fold (1FME): A comparison of structural and folding characteristics of various ββα miniproteins

NASA Astrophysics Data System (ADS)

Kim, Eunae; Jang, Soonmin; Pak, Youngshang

2009-11-01

We performed an all-atom ab initio native structure prediction of 1FME, which is one of the computationally challenging mixed fold ββα miniproteins, by combining a novel conformational search algorithm (multiplexed Q-replica exchange molecular dynamics scheme) with a well-balanced all-atom force field employing a generalized Born implicit solvation model (param99MOD5/GBSA). The nativelike structure of 1FME was identified from the lowest free energy minimum state and in excellent agreement with the NMR structure. Based on the interpretation of the free energy landscape, the structural properties as well as the folding behaviors of 1FME were compared with other ββα miniproteins (1FSD, 1PSV, and BBA5) that we have previously studied with the same force field. Our simulation showed that the 28-residue ββα miniproteins (1FME, 1FSD, and 1PSV) share a common feature of the free energy topography and exhibit the three local minimum states on each computed free energy map, but the 23-residue miniprotein (BBA5) follows a downhill folding with a single minimum state. Also, the structure and stability changes resulting from the two point mutation (Gln1→Glu1 and Ile7→Tyr7) of 1FSD were investigated in details for direct comparison with the experiment. The comparison shows that upon mutation, the experimentally observed turn type switch from an irregular turn (1FSD) to type I' turn (1FME) was well reproduced with the present simulation.

Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains

PubMed Central

Han, Wei; Schulten, Klaus

2012-01-01

PACE, a hybrid force field which couples united-atom protein models with coarse-grained (CG) solvent, has been further optimized, aiming to improve itse ciency for folding simulations. Backbone hydration parameters have been re-optimized based on hydration free energies of polyalanyl peptides through atomistic simulations. Also, atomistic partial charges from all-atom force fields were combined with PACE in order to provide a more realistic description of interactions between charged groups. Using replica exchange molecular dynamics (REMD), ab initio folding using the new PACE has been achieved for seven small proteins (16 – 23 residues) with different structural motifs. Experimental data about folded states, such as their stability at room temperature, melting point and NMR NOE constraints, were also well reproduced. Moreover, a systematic comparison of folding kinetics at room temperature has been made with experiments, through standard MD simulations, showing that the new PACE may speed up the actual folding kinetics 5-10 times. Together with the computational speedup benefited from coarse-graining, the force field provides opportunities to study folding mechanisms. In particular, we used the new PACE to fold a 73-residue protein, 3D, in multiple 10 – 30 μs simulations, to its native states (Cα RMSD ~ 0.34 nm). Our results suggest the potential applicability of the new PACE for the study of folding and dynamics of proteins. PMID:23204949

The harmonic force field of benzene. A local density functional study

NASA Astrophysics Data System (ADS)

Bérces, Attila; Ziegler, Tom

1993-03-01

The harmonic force field of benzene has been calculated by a method based on local density functional theory (LDF). The calculations were carried out employing a triple zeta basis set with triple polarization on hydrogen and double polarization on carbon. The LDF force field was compared to the empirical field due to Ozkabak, Goodman, and Thakur [A. G. Ozkabak, L. Goodman, and S. N. Thakur, J. Phys. Chem. 95, 9044 (1991)], which has served as a benchmark for theoretical calculations as well as the theoretical field based on scaled Hartree-Fock ab initio calculation due to Pulay, Fogarasi, and Boggs [P. Pulay, G. Fogarasi, and J. E. Boggs, J. Chem. Phys. 74, 3999 (1981)]. The calculated LDF force field is in excellent qualitative and very good quantitative agreement with the theoretical field proposed by Pulay, Fogarasi, and Boggs as well as the empirical field due to Ozkabak, Goodman, and Thakur. The LDF field is closest to the values of Pulay and co-workers in those cases where the force constants due to Pulay, Fogarasi, and Boggs and to Ozkabak, Goodman, and Thakur differ in sign or magnitude. The accuracy of the LDF force field was investigated by evaluating a number of eigenvalue and eigenfunction dependent quantities from the the LDF force constants. The quantities under investigation include vibrational frequencies of seven isotopomers, isotopic shifts, as well as absorption intensities. The calculations were performed at both theoretical optimized and approximate equilibrium reference geometries. The predicted frequencies are usually within 1%-2% compared to the empirical harmonic frequencies. The least accurate frequency deviates by 5% from the experimental value. The average deviations from the empirical harmonic frequencies of C6H6 and C6D6 are 16.7 cm-1 (1.5%) and 15.2 cm-1 (1.7%), respectively, not including CH stretching frequencies, in the case where a theoretical reference geometry was used. The accuracy of the out-of-plane force field is especially remarkable; the average deviations for the C6H6 and C6D6 frequencies, based on the LDF force field, are 9.4 cm-1 (1.2%) and 7.3 cm-1 (1.2%), respectively. The absorption intensities were not predicted as accurately as it was expected based on the size of the basis set applied. An analysis is provided to ensure that the force constants are not significantly affected by numerical errors due to the numerical integration scheme employed.

Interaction and dynamics of ionic liquids based on choline and amino acid anions

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

Campetella, M.; Bodo, E., E-mail: enrico.bodo@uniroma1.it; Caminiti, R., E-mail: ruggero.caminiti@uniroma1.it

2015-06-21

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial inmore » establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.« less

Interaction and dynamics of ionic liquids based on choline and amino acid anions

NASA Astrophysics Data System (ADS)

Campetella, M.; Bodo, E.; Caminiti, R.; Martino, A.; D'Apuzzo, F.; Lupi, S.; Gontrani, L.

2015-06-01

The combination of amino acid anions with the choline cation gives origin to a new and potentially important class of organic ionic liquids that might represent a viable and bio-compatible alternative with respect to the traditional ones. We present here a detailed study of the bulk phase of the prototype system composed of the simplest amino acid (alanine) anion and the choline cation, based on ab initio and classical molecular dynamics. Theoretical findings have been validated by comparing with accurate experimental X-ray diffraction data and infrared spectra. We find that hydrogen bonding (HB) features in these systems are crucial in establishing their local geometric structure. We have also found that these HBs once formed are persistent and that the proton resides exclusively on the choline cation. In addition, we show that a classical force field description for this particular ionic liquid can be accurately performed by using a slightly modified version of the generalized AMBER force field.

Ab initio folding of proteins using all-atom discrete molecular dynamics

PubMed Central

Ding, Feng; Tsao, Douglas; Nie, Huifen; Dokholyan, Nikolay V.

2008-01-01

Summary Discrete molecular dynamics (DMD) is a rapid sampling method used in protein folding and aggregation studies. Until now, DMD was used to perform simulations of simplified protein models in conjunction with structure-based force fields. Here, we develop an all-atom protein model and a transferable force field featuring packing, solvation, and environment-dependent hydrogen bond interactions. Using the replica exchange method, we perform folding simulations of six small proteins (20–60 residues) with distinct native structures. In all cases, native or near-native states are reached in simulations. For three small proteins, multiple folding transitions are observed and the computationally-characterized thermodynamics are in quantitative agreement with experiments. The predictive power of all-atom DMD highlights the importance of environment-dependent hydrogen bond interactions in modeling protein folding. The developed approach can be used for accurate and rapid sampling of conformational spaces of proteins and protein-protein complexes, and applied to protein engineering and design of protein-protein interactions. PMID:18611374

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization.

PubMed

Mazack, Michael J M; Gao, Jiali

2014-05-28

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

An atomistic fingerprint algorithm for learning ab initio molecular force fields

NASA Astrophysics Data System (ADS)

Tang, Yu-Hang; Zhang, Dongkun; Karniadakis, George Em

2018-01-01

Molecular fingerprints, i.e., feature vectors describing atomistic neighborhood configurations, is an important abstraction and a key ingredient for data-driven modeling of potential energy surface and interatomic force. In this paper, we present the density-encoded canonically aligned fingerprint algorithm, which is robust and efficient, for fitting per-atom scalar and vector quantities. The fingerprint is essentially a continuous density field formed through the superimposition of smoothing kernels centered on the atoms. Rotational invariance of the fingerprint is achieved by aligning, for each fingerprint instance, the neighboring atoms onto a local canonical coordinate frame computed from a kernel minisum optimization procedure. We show that this approach is superior over principal components analysis-based methods especially when the atomistic neighborhood is sparse and/or contains symmetry. We propose that the "distance" between the density fields be measured using a volume integral of their pointwise difference. This can be efficiently computed using optimal quadrature rules, which only require discrete sampling at a small number of grid points. We also experiment on the choice of weight functions for constructing the density fields and characterize their performance for fitting interatomic potentials. The applicability of the fingerprint is demonstrated through a set of benchmark problems.

Operator evolution for ab initio electric dipole transitions of 4He

DOE PAGES

Schuster, Micah D.; Quaglioni, Sofia; Johnson, Calvin W.; ...

2015-07-24

A goal of nuclear theory is to make quantitative predictions of low-energy nuclear observables starting from accurate microscopic internucleon forces. A major element of such an effort is applying unitary transformations to soften the nuclear Hamiltonian and hence accelerate the convergence of ab initio calculations as a function of the model space size. The consistent simultaneous transformation of external operators, however, has been overlooked in applications of the theory, particularly for nonscalar transitions. We study the evolution of the electric dipole operator in the framework of the similarity renormalization group method and apply the renormalized matrix elements to the calculationmore » of the 4He total photoabsorption cross section and electric dipole polarizability. All observables are calculated within the ab initio no-core shell model. Furthermore, we find that, although seemingly small, the effects of evolved operators on the photoabsorption cross section are comparable in magnitude to the correction produced by including the chiral three-nucleon force and cannot be neglected.« less

Single-ion 4f element magnetism: an ab-initio look at Ln(COT)2(-).

PubMed

Gendron, Frédéric; Pritchard, Benjamin; Bolvin, Hélène; Autschbach, Jochen

2015-12-14

The electron densities associated with the Ln 4f shell, and spin and orbital magnetizations ('magnetic moment densities'), are investigated for the Ln(COT)2(-) series. The densities are obtained from ab-initio calculations including spin-orbit coupling. For Ln = Ce, Pr the magnetizations are also derived from crystal field models and shown to agree with the ab-initio results. Analysis of magnetizations from ab-initio calculations may be useful in assisting research on single molecule magnets.

Energetics of defects formation and oxygen migration in pyrochlore compounds from first principles calculations

NASA Astrophysics Data System (ADS)

Li, Yan; Kowalski, Piotr M.

2018-07-01

In order to get better understanding of the selective order-disorder transition in pyrochlore compounds, using ab initio methods we calculated the formation energies of coupled cation anti-site and anion Frenkel pair defects and the energy barriers for the oxygen migration for number of families of A2B2 O7 pyrochlore-type compounds. While these parameters have been previously computed with force field-based methods, the ab initio results provide more reliable values that can be confidently used in subsequent analysis. We found a fairly good correlation between the formation energies of the coupled defects and the stability field of pyrochlores. In line with previous studies, the compounds that crystallize in defect fluorite structure are found to have smaller values of coupled defect formation energies than those crystallizing in the pyrochlore phase, although the correlation is not that sharp as in the case of isolated anion Frenkel pair defect. The investigation of the energy barriers for the oxygen migration shows that it is not a good, sole indicator of the tendency of the order-disorder phase transition in pyrochlores. However, we found that the oxygen migration barrier is reduced in the presence of the cation antisite defect. This points at disordering-induced enhancement of oxygen diffusion in pyrochlore compounds.

Emergent properties of nuclei from ab initio coupled-cluster calculations

NASA Astrophysics Data System (ADS)

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; Papenbrock, T.

2016-06-01

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. This endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. This paper reviews some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLO{}{{sat}} is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon-nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. The coupling to the continuum impacts the energies of the {J}π =1/{2}-,3/{2}-,7/{2}-,3/{2}+ states in {}{17,23,25}O, and—contrary to naive shell-model expectations—the level ordering of the {J}π =3/{2}+,5/{2}+,9/{2}+ states in {}{53,55,61}Ca. ).

Fabricating Atom-Sized Gaps by Field-Aided Atom Migration in Nanoscale Junctions

NASA Astrophysics Data System (ADS)

Liu, Ran; Bi, Jun-Jie; Xie, Zhen; Yin, Kaikai; Wang, Dunyou; Zhang, Guang-Ping; Xiang, Dong; Wang, Chuan-Kui; Li, Zong-Liang

2018-05-01

The gap sizes between electrodes generated by typical methods are generally much larger than the dimension of a common molecule when fabricating a single-molecule junction, which dramatically suppresses the yield of single-molecule junctions. Based on the ab initio calculations, we develop a strategy named the field-aided method to accurately fabricate an atomic-sized gap between gold nanoelectrodes. To understand the mechanism of this strategy, configuration evolutions of gold nanojunction in stretching and compressing processes are calculated. The numerical results show that, in the stretching process, the gold atoms bridged between two electrodes are likely to form atomic chains. More significantly, lattice vacant positions can be easily generated in stretching and compressing processes, which make field-aided gap generation possible. In field-aided atom migration (FAAM), the external field can exert driving force, enhance the initial energy of the system, and decrease the barrier in the migration path, which makes the atom migration feasible. Conductance and stretching and compressing forces, as measurable variables in stretching and compressing processes, present very useful signals for determining the time to perform FAAM. Following this desirable strategy, we successfully fabricate gold nanogaps with a dimension of 0.38 ±0.05 nm in the experiment, as our calculation simulates.

Structure models: From shell model to ab initio methods. A brief introduction to microscopic theories for exotic nuclei

NASA Astrophysics Data System (ADS)

Bacca, Sonia

2016-04-01

A brief review of models to describe nuclear structure and reactions properties is presented, starting from the historical shell model picture and encompassing modern ab initio approaches. A selection of recent theoretical results on observables for exotic light and medium-mass nuclei is shown. Emphasis is given to the comparison with experiment and to what can be learned about three-body forces and continuum properties.

Unified description of ^{6}Li structure and deuterium-^{4}He dynamics with chiral two- and three-nucleon forces.

PubMed

Hupin, Guillaume; Quaglioni, Sofia; Navrátil, Petr

2015-05-29

We provide a unified ab initio description of the ^{6}Li ground state and elastic scattering of deuterium (d) on ^{4}He (α) using two- and three-nucleon forces from chiral effective field theory. We analyze the influence of the three-nucleon force and reveal the role of continuum degrees of freedom in shaping the low-lying spectrum of ^{6}Li. The calculation reproduces the empirical binding energy of ^{6}Li, yielding an asymptotic D- to S-state ratio of the ^{6}Li wave function in the d+α configuration of -0.027, in agreement with a determination from ^{6}Li-^{4}He elastic scattering, but overestimates the excitation energy of the 3^{+} state by 350 keV. The bulk of the computed differential cross section is in good agreement with data. These results endorse the application of the present approach to the evaluation of the ^{2}H(α,γ)^{6}Li radiative capture, responsible for the big-bang nucleosynthesis of ^{6}Li.

Study of hydrogen-molecule guests in type II clathrate hydrates using a force-matched potential model parameterised from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Burnham, Christian J.; Futera, Zdenek; English, Niall J.

2018-03-01

The force-matching method has been applied to parameterise an empirical potential model for water-water and water-hydrogen intermolecular interactions for use in clathrate-hydrate simulations containing hydrogen guest molecules. The underlying reference simulations constituted ab initio molecular dynamics (AIMD) of clathrate hydrates with various occupations of hydrogen-molecule guests. It is shown that the resultant model is able to reproduce AIMD-derived free-energy curves for the movement of a tagged hydrogen molecule between the water cages that make up the clathrate, thus giving us confidence in the model. Furthermore, with the aid of an umbrella-sampling algorithm, we calculate barrier heights for the force-matched model, yielding the free-energy barrier for a tagged molecule to move between cages. The barrier heights are reasonably large, being on the order of 30 kJ/mol, and are consistent with our previous studies with empirical models [C. J. Burnham and N. J. English, J. Phys. Chem. C 120, 16561 (2016) and C. J. Burnham et al., Phys. Chem. Chem. Phys. 19, 717 (2017)]. Our results are in opposition to the literature, which claims that this system may have very low barrier heights. We also compare results to that using the more ad hoc empirical model of Alavi et al. [J. Chem. Phys. 123, 024507 (2005)] and find that this model does very well when judged against the force-matched and ab initio simulation data.

Correction of erroneously packed protein's side chains in the NMR structure based on ab initio chemical shift calculations.

PubMed

Zhu, Tong; Zhang, John Z H; He, Xiao

2014-09-14

In this work, protein side chain (1)H chemical shifts are used as probes to detect and correct side-chain packing errors in protein's NMR structures through structural refinement. By applying the automated fragmentation quantum mechanics/molecular mechanics (AF-QM/MM) method for ab initio calculation of chemical shifts, incorrect side chain packing was detected in the NMR structures of the Pin1 WW domain. The NMR structure is then refined by using molecular dynamics simulation and the polarized protein-specific charge (PPC) model. The computationally refined structure of the Pin1 WW domain is in excellent agreement with the corresponding X-ray structure. In particular, the use of the PPC model yields a more accurate structure than that using the standard (nonpolarizable) force field. For comparison, some of the widely used empirical models for chemical shift calculations are unable to correctly describe the relationship between the particular proton chemical shift and protein structures. The AF-QM/MM method can be used as a powerful tool for protein NMR structure validation and structural flaw detection.

Amino acid anions in organic ionic compounds. An ab initio study of selected ion pairs.

PubMed

Benedetto, A; Bodo, E; Gontrani, L; Ballone, P; Caminiti, R

2014-03-06

The combination of amino acids in their deprotonated and thus anionic form with a choline cation gives origin to a new and potentially important class of organic ionic compounds. A series of such neutral ion pairs has been investigated by first principle methods. The results reveal intriguing structural motives as well as regular patterns in the charge distribution and predict a number of vibrational and optical properties that could guide the experimental investigation of these compounds. The replacement of choline with its phosphocholine analogue causes the spontaneous reciprocal neutralization of cations and anions, taking place through the transfer of a proton between the two ions. Systems of this kind, therefore, provide a wide and easily accessible playground to probe the ionic/polar transition in organic systems, while the easy transfer of H(+) among neutral and ionic species points to their potential application as proton conductors. The analysis of the ab initio data highlights similarities as well as discrepancies from the rigid-ions force-field picture and suggests directions for the improvement of empirical models.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling.

PubMed

Bonfanti, Matteo; Jackson, Bret; Hughes, Keith H; Burghardt, Irene; Martinazzo, Rocco

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

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

Bonfanti, Matteo, E-mail: matteo.bonfanti@unimi.it; Jackson, Bret; Hughes, Keith H.

2015-09-28

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theorymore » for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics.« less

Nano-scale investigations of electric-dipole-layer enhanced field and thermionic emission from high current density cathodes

NASA Astrophysics Data System (ADS)

Vlahos, Vasilios

Cesium iodide coated graphitic fibers and scandate cathodes are two important electron emission technologies. The coated fibers are utilized as field emitters for high power microwave sources. The scandate cathodes are promising thermionic cathode materials for pulsed power vacuum electron devices. This work attempts to understand the fundamental physical and chemical relationships between the atomic structure of the emitting cathode surfaces and the superior emission characteristics of these cathodes. Ab initio computational modeling in conjunction with experimental investigations was performed on coated fiber cathodes to understand the origin of their very low turn on electric field, which can be reduced by as much as ten-fold compared to uncoated fibers. Copious amounts of cesium and oxygen were found co-localized on the fiber, but no iodine was detected on the surface. Additional ab initio studies confirmed that cesium oxide dimers could lower the work function significantly. Surface cesium oxide dipoles are therefore proposed as the source of the observed reduction in the turn on electric field. It is also proposed that emission may be further enhanced by secondary electrons from cesium oxide during operation. Thermal conditioning of the coated cathode may be a mechanism by which surface cesium iodide is converted into cesium oxide, promoting the depletion of iodine by formation of volatile gas. Ab initio modeling was also utilized to investigate the stability and work functions of scandate structures. The work demonstrated that monolayer barium-scandium-oxygen surface structures on tungsten can dramatically lower the work function of the underlying tungsten substrate from 4.6 eV down to 1.16 eV, by the formation of multiple surface dipoles. On the basis of this work, we conclude that high temperature kinetics force conventional dispenser cathodes (barium-oxygen monolayers on tungsten) to operate in a non-equilibrium compositional steady state with higher than optimal work functions of ˜2 eV. We hypothesize that scandium enables the barium-oxygen surface monolayer kinetics to access a more thermodynamically stable phase with reported work functions as low as ˜1.3 eV.

Energy-free machine learning force field for aluminum.

PubMed

Kruglov, Ivan; Sergeev, Oleg; Yanilkin, Alexey; Oganov, Artem R

2017-08-17

We used the machine learning technique of Li et al. (PRL 114, 2015) for molecular dynamics simulations. Atomic configurations were described by feature matrix based on internal vectors, and linear regression was used as a learning technique. We implemented this approach in the LAMMPS code. The method was applied to crystalline and liquid aluminum and uranium at different temperatures and densities, and showed the highest accuracy among different published potentials. Phonon density of states, entropy and melting temperature of aluminum were calculated using this machine learning potential. The results are in excellent agreement with experimental data and results of full ab initio calculations.

Revisiting imidazolium based ionic liquids: Effect of the conformation bias of the [NTf2] anion studied by molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Neumann, Jan; Golub, Benjamin; Odebrecht, Lisa-Marie; Ludwig, Ralf; Paschek, Dietmar

2018-05-01

We study ionic liquids composed of 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([CnMIm][NTf2]) with varying chain-length n = 2, 4, 6, 8 by using molecular dynamics simulations. We show that a reparametrization of the dihedral potentials as well as charges of the [NTf2] anion leads to an improvement of the force field model introduced by Köddermann, Paschek, and Ludwig [ChemPhysChem 8, 2464 (2007)] (KPL-force field). A crucial advantage of the new parameter set is that the minimum energy conformations of the anion (trans and gauche), as deduced from ab initio calculations and Raman experiments, are now both well represented by our model. In addition, the results for [CnMIm][NTf2] show that this modification leads to an even better agreement between experiment and molecular dynamics simulation as demonstrated for densities, diffusion coefficients, vaporization enthalpies, reorientational correlation times, and viscosities. Even though we focused on a better representation of the anion conformation, also the alkyl chain-length dependence of the cation behaves closer to the experiment. We strongly encourage to use the new NGOLP (Neumann, Golub, Odebrecht, Ludwig, Paschek) force field for the [NTf2] anion instead of the earlier KPL parameter set for computer simulations aiming to describe the thermodynamics, dynamics, and also structure of imidazolium-based ionic liquids.

Static force fields simulations of reduced CeO2 (110) surface: Structure and adsorption of H2O molecule

NASA Astrophysics Data System (ADS)

Vives, Serge; Meunier, Cathy

2018-02-01

The CeO2(110) surface properties are largely involved in the catalysis, energy and biological phenomenon. The Static Force Fields simulations are able to describe large atomic systems surface even if no information on the electronic structure can be obtained. We employ those simulations to study the formation of the neutral 2 CeCe‧ VO•• cluster. We focus on seven different cluster configurations and find that the defect formation energy is the lower for the 1N-2N configurations. Two geometries are possible, as it is the case for the ab initio studies, the in plane and the more stable bridging one. We evidence the modifications of the surface energy and the Potential Energy Surface due to the presence of the 2 CeCe‧ VO•• defect. The physical adsorption of a water molecule is calculated and the geometry described for all the cluster configurations. The H2O molecule physisorption stabilizes the Ce(110) surface and the presence of the 2 CeCe‧ VO•• defect increases this effect.

Simulation Protocol for Prediction of a Solid-Electrolyte Interphase on the Silicon-based Anodes of a Lithium-Ion Battery: ReaxFF Reactive Force Field.

PubMed

Yun, Kang-Seop; Pai, Sung Jin; Yeo, Byung Chul; Lee, Kwang-Ryeol; Kim, Sun-Jae; Han, Sang Soo

2017-07-06

We propose the ReaxFF reactive force field as a simulation protocol for predicting the evolution of solid-electrolyte interphase (SEI) components such as gases (C 2 H 4 , CO, CO 2 , CH 4 , and C 2 H 6 ), and inorganic (Li 2 CO 3 , Li 2 O, and LiF) and organic (ROLi and ROCO 2 Li: R = -CH 3 or -C 2 H 5 ) products that are generated by the chemical reactions between the anodes and liquid electrolytes. ReaxFF was developed from ab initio results, and a molecular dynamics simulation with ReaxFF realized the prediction of SEI formation under real experimental conditions and with a reasonable computational cost. We report the effects on SEI formation of different kinds of Si anodes (pristine Si and SiO x ), of the different types and compositions of various carbonate electrolytes, and of the additives. From the results, we expect that ReaxFF will be very useful for the development of novel electrolytes or additives and for further advances in Li-ion battery technology.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores.

PubMed

Law, Y K; Hassanali, A A

2018-03-14

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

The importance of nuclear quantum effects in spectral line broadening of optical spectra and electrostatic properties in aromatic chromophores

NASA Astrophysics Data System (ADS)

Law, Y. K.; Hassanali, A. A.

2018-03-01

In this work, we examine the importance of nuclear quantum effects on capturing the line broadening and vibronic structure of optical spectra. We determine the absorption spectra of three aromatic molecules indole, pyridine, and benzene using time dependent density functional theory with several molecular dynamics sampling protocols: force-field based empirical potentials, ab initio simulations, and finally path-integrals for the inclusion of nuclear quantum effects. We show that the absorption spectrum for all these chromophores are similarly broadened in the presence of nuclear quantum effects regardless of the presence of hydrogen bond donor or acceptor groups. We also show that simulations incorporating nuclear quantum effects are able to reproduce the heterogeneous broadening of the absorption spectra even with empirical force fields. The spectral broadening associated with nuclear quantum effects can be accounted for by the broadened distribution of chromophore size as revealed by a particle in the box model. We also highlight the role that nuclear quantum effects have on the underlying electronic structure of aromatic molecules as probed by various electrostatic properties.

Ab initio molecular orbital studies of the positive muon and muonium in 4-arylmethyleneamino-TEMPO derivatives

NASA Astrophysics Data System (ADS)

Briere, T. M.; Jeong, J.; Das, T. P.; Ohira, S.; Nagamine, K.

2000-08-01

The muon and muonium bonding sites of the 4-arylmethyleneamino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical crystals with aryl groups consisting of biphenyl and 4-pyridyl were studied via ab initio Hartree-Fock theory. The hyperfine fields, including both intramolecular and intermolecular interactions, were calculated at the sites of interest and compared to zero field μSR results.

An unscaled quantum mechanical harmonic force field for p-benzoquinone

NASA Astrophysics Data System (ADS)

Nonella, Marco; Tavan, Paul

1995-10-01

Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of CO bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 and 1800 cm -1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.

Ab Initio Crystal Field for Lanthanides.

PubMed

Ungur, Liviu; Chibotaru, Liviu F

2017-03-13

An ab initio methodology for the first-principle derivation of crystal-field (CF) parameters for lanthanides is described. The methodology is applied to the analysis of CF parameters in [Tb(Pc) 2 ] - (Pc=phthalocyanine) and Dy 4 K 2 ([Dy 4 K 2 O(OtBu) 12 ]) complexes, and compared with often used approximate and model descriptions. It is found that the application of geometry symmetrization, and the use of electrostatic point-charge and phenomenological CF models, lead to unacceptably large deviations from predictions based on ab initio calculations for experimental geometry. It is shown how the predictions of standard CASSCF (Complete Active Space Self-Consistent Field) calculations (with 4f orbitals in the active space) can be systematically improved by including effects of dynamical electronic correlation (CASPT2 step) and by admixing electronic configurations of the 5d shell. This is exemplified for the well-studied Er-trensal complex (H 3 trensal=2,2',2"-tris(salicylideneimido)trimethylamine). The electrostatic contributions to CF parameters in this complex, calculated with true charge distributions in the ligands, yield less than half of the total CF splitting, thus pointing to the dominant role of covalent effects. This analysis allows the conclusion that ab initio crystal field is an essential tool for the decent description of lanthanides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

POTENTIOLOGY (noun): study focusing on the development of new interatomic pair potential forms; sometimes pursued in an obsessive compulsive manner [The New Yorel Dictionary (2002, unpublished)].} IN SPECTROSCOPY: IT MATTERS

NASA Astrophysics Data System (ADS)

Le Roy, Robert J.

2009-06-01

Spectroscopists have long attempted to summarize what they know about small molecules in terms of a knowledge of potential energy curves or surfaces. For most of the past century, this involved deducing polynomial-expansion force-field coefficients from energy level expressions fitted to experimental data, or for diatomic molecules, by generating tables of many-digit RKR turning points from such expressions. In recent years, however, it has become increasingly common either to use high-level ab initio calculations to compute the desired potentials, or to determine parametrized global analytic potential functions from direct fits to spectroscopic data. In the former case, this invoked a need for robust, flexible, compact, and `portable' analytic potentials for summarizing the information contained in the (sometimes very large numbers of) ab initio points, and making them `user friendly'. In the latter case, the same properties are required for potentials used in the least-squares fitting procedure. In both cases, there is also a cardinal need for potential function forms that extrapolate sensibly, beyond the range of the experimental data or ab initio points. This talk will describe some recent developments in this area, and make a case for what is arguably the `best' general-purpose analytic potential function form now available. Applications to both diatomic molecules and simple polyatomic molecules will be discussed. footnote

Emergent properties of nuclei from ab initio coupled-cluster calculations

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

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

Emergent properties of nuclei from ab initio coupled-cluster calculations

DOE PAGES

Hagen, G.; Hjorth-Jensen, M.; Jansen, G. R.; ...

2016-05-17

Emergent properties such as nuclear saturation and deformation, and the effects on shell structure due to the proximity of the scattering continuum and particle decay channels are fascinating phenomena in atomic nuclei. In recent years, ab initio approaches to nuclei have taken the first steps towards tackling the computational challenge of describing these phenomena from Hamiltonians with microscopic degrees of freedom. Our endeavor is now possible due to ideas from effective field theories, novel optimization strategies for nuclear interactions, ab initio methods exhibiting a soft scaling with mass number, and ever-increasing computational power. We review some of the recent accomplishments. We also present new results. The recently optimized chiral interaction NNLOmore » $${}_{{\\rm{sat}}}$$ is shown to provide an accurate description of both charge radii and binding energies in selected light- and medium-mass nuclei up to 56Ni. We derive an efficient scheme for including continuum effects in coupled-cluster computations of nuclei based on chiral nucleon–nucleon and three-nucleon forces, and present new results for unbound states in the neutron-rich isotopes of oxygen and calcium. Finally, the coupling to the continuum impacts the energies of the $${J}^{\\pi }=1/{2}^{-},3/{2}^{-},7/{2}^{-},3/{2}^{+}$$ states in $${}^{\\mathrm{17,23,25}}$$O, and—contrary to naive shell-model expectations—the level ordering of the $${J}^{\\pi }=3/{2}^{+},5/{2}^{+},9/{2}^{+}$$ states in $${}^{\\mathrm{53,55,61}}$$Ca.« less

Accurate schemes for calculation of thermodynamic properties of liquid mixtures from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Caro, Miguel A.; Laurila, Tomi; Lopez-Acevedo, Olga

2016-12-01

We explore different schemes for improved accuracy of entropy calculations in aqueous liquid mixtures from molecular dynamics (MD) simulations. We build upon the two-phase thermodynamic (2PT) model of Lin et al. [J. Chem. Phys. 119, 11792 (2003)] and explore new ways to obtain the partition between the gas-like and solid-like parts of the density of states, as well as the effect of the chosen ideal "combinatorial" entropy of mixing, both of which have a large impact on the results. We also propose a first-order correction to the issue of kinetic energy transfer between degrees of freedom (DoF). This problem arises when the effective temperatures of translational, rotational, and vibrational DoF are not equal, either due to poor equilibration or reduced system size/time sampling, which are typical problems for ab initio MD. The new scheme enables improved convergence of the results with respect to configurational sampling, by up to one order of magnitude, for short MD runs. To ensure a meaningful assessment, we perform MD simulations of liquid mixtures of water with several other molecules of varying sizes: methanol, acetonitrile, N, N-dimethylformamide, and n-butanol. Our analysis shows that results in excellent agreement with experiment can be obtained with little computational effort for some systems. However, the ability of the 2PT method to succeed in these calculations is strongly influenced by the choice of force field, the fluidicity (hard-sphere) formalism employed to obtain the solid/gas partition, and the assumed combinatorial entropy of mixing. We tested two popular force fields, GAFF and OPLS with SPC/E water. For the mixtures studied, the GAFF force field seems to perform as a slightly better "all-around" force field when compared to OPLS+SPC/E.

A coupled two-dimensional main chain torsional potential for protein dynamics: generation and implementation.

PubMed

Li, Yongxiu; Gao, Ya; Zhang, Xuqiang; Wang, Xingyu; Mou, Lirong; Duan, Lili; He, Xiao; Mei, Ye; Zhang, John Z H

2013-09-01

Main chain torsions of alanine dipeptide are parameterized into coupled 2-dimensional Fourier expansions based on quantum mechanical (QM) calculations at M06 2X/aug-cc-pvtz//HF/6-31G** level. Solvation effect is considered by employing polarizable continuum model. Utilization of the M06 2X functional leads to precise potential energy surface that is comparable to or even better than MP2 level, but with much less computational demand. Parameterization of the 2D expansions is against the full main chain torsion space instead of just a few low energy conformations. This procedure is similar to that for the development of AMBER03 force field, except unique weighting factor was assigned to all the grid points. To avoid inconsistency between quantum mechanical calculations and molecular modeling, the model peptide is further optimized at molecular mechanics level with main chain dihedral angles fixed before the calculation of the conformational energy on molecular mechanical level at each grid point, during which generalized Born model is employed. Difference in solvation models at quantum mechanics and molecular mechanics levels makes this parameterization procedure less straightforward. All force field parameters other than main chain torsions are taken from existing AMBER force field. With this new main chain torsion terms, we have studied the main chain dihedral distributions of ALA dipeptide and pentapeptide in aqueous solution. The results demonstrate that 2D main chain torsion is effective in delineating the energy variation associated with rotations along main chain dihedrals. This work is an implication for the necessity of more accurate description of main chain torsions in the future development of ab initio force field and it also raises a challenge to the development of quantum mechanical methods, especially the quantum mechanical solvation models.

Radii of neutron drops probed via the neutron skin thickness of nuclei

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

Zhao, P. W.; Gandolfi, S.

Multineutron systems are crucial to understanding the physics of neutron-rich nuclei and neutron stars. Neutron drops, neutrons confined in an external field, are investigated systematically in both nonrelativistic and relativistic density functional theories and with ab initio calculations. Here, we demonstrate a new strong linear correlation, which is universal in the realm of mean-field models, between the rms radii of neutron drops and the neutron skin thickness of 208 Pb and 48 Ca , i.e., the difference between the neutron and proton rms radii of a nucleus. This correlation can be used to deduce the radii of neutron drops frommore » the measured neutron skin thickness in a model-independent way, and the radii obtained for neutron drops can provide a useful constraint for realistic three-neutron forces, due to its high quality. Furthermore, we present a new correlation between the slope L of the symmetry energy and the radii of neutron drops, and provide the first validation of such a correlation by using density-functional models and ab initio calculations. These newly established correlations, together with more precise measurements of the neutron skin thicknesses of 208 Pb and 48 Ca and/or accurate determinations of L , will have an enduring impact on the understanding of multineutron interactions, neutron-rich nuclei, neutron stars, etc.« less

Radii of neutron drops probed via the neutron skin thickness of nuclei

DOE PAGES

Zhao, P. W.; Gandolfi, S.

2016-10-10

Multineutron systems are crucial to understanding the physics of neutron-rich nuclei and neutron stars. Neutron drops, neutrons confined in an external field, are investigated systematically in both nonrelativistic and relativistic density functional theories and with ab initio calculations. Here, we demonstrate a new strong linear correlation, which is universal in the realm of mean-field models, between the rms radii of neutron drops and the neutron skin thickness of 208 Pb and 48 Ca , i.e., the difference between the neutron and proton rms radii of a nucleus. This correlation can be used to deduce the radii of neutron drops frommore » the measured neutron skin thickness in a model-independent way, and the radii obtained for neutron drops can provide a useful constraint for realistic three-neutron forces, due to its high quality. Furthermore, we present a new correlation between the slope L of the symmetry energy and the radii of neutron drops, and provide the first validation of such a correlation by using density-functional models and ab initio calculations. These newly established correlations, together with more precise measurements of the neutron skin thicknesses of 208 Pb and 48 Ca and/or accurate determinations of L , will have an enduring impact on the understanding of multineutron interactions, neutron-rich nuclei, neutron stars, etc.« less

Curved-line search algorithm for ab initio atomic structure relaxation

NASA Astrophysics Data System (ADS)

Chen, Zhanghui; Li, Jingbo; Li, Shushen; Wang, Lin-Wang

2017-09-01

Ab initio atomic relaxations often take large numbers of steps and long times to converge, especially when the initial atomic configurations are far from the local minimum or there are curved and narrow valleys in the multidimensional potentials. An atomic relaxation method based on on-the-flight force learning and a corresponding curved-line search algorithm is presented to accelerate this process. Results demonstrate the superior performance of this method for metal and magnetic clusters when compared with the conventional conjugate-gradient method.

Accelerated path-integral simulations using ring-polymer interpolation

NASA Astrophysics Data System (ADS)

Buxton, Samuel J.; Habershon, Scott

2017-12-01

Imaginary-time path-integral (PI) molecular simulations can be used to calculate exact quantum statistical mechanical properties for complex systems containing many interacting atoms and molecules. The limiting computational factor in a PI simulation is typically the evaluation of the potential energy surface (PES) and forces at each ring-polymer "bead"; for an n-bead ring-polymer, a PI simulation is typically n times greater than the corresponding classical simulation. To address the increased computational effort of PI simulations, several approaches have been developed recently, most notably based on the idea of ring-polymer contraction which exploits either the separation of the PES into short-range and long-range contributions or the availability of a computationally inexpensive PES which can be incorporated to effectively smooth the ring-polymer PES; neither approach is satisfactory in applications to systems modeled by PESs given by on-the-fly ab initio calculations. In this article, we describe a new method, ring-polymer interpolation (RPI), which can be used to accelerate PI simulations without any prior assumptions about the PES. In simulations of liquid water modeled by an empirical PES (or force field) under ambient conditions, where quantum effects are known to play a subtle role in influencing experimental observables such as radial distribution functions, we find that RPI can accurately reproduce the results of fully-converged PI simulations, albeit with far fewer PES evaluations. This approach therefore opens the possibility of large-scale PI simulations using ab initio PESs evaluated on-the-fly without the drawbacks of current methods.

Atomistically determined phase-field modeling of dislocation dissociation, stacking fault formation, dislocation slip, and reactions in fcc systems

NASA Astrophysics Data System (ADS)

Rezaei Mianroodi, Jaber; Svendsen, Bob

2015-04-01

The purpose of the current work is the development of a phase field model for dislocation dissociation, slip and stacking fault formation in single crystals amenable to determination via atomistic or ab initio methods in the spirit of computational material design. The current approach is based in particular on periodic microelasticity (Wang and Jin, 2001; Bulatov and Cai, 2006; Wang and Li, 2010) to model the strongly non-local elastic interaction of dislocation lines via their (residual) strain fields. These strain fields depend in turn on phase fields which are used to parameterize the energy stored in dislocation lines and stacking faults. This energy storage is modeled here with the help of the "interface" energy concept and model of Cahn and Hilliard (1958) (see also Allen and Cahn, 1979; Wang and Li, 2010). In particular, the "homogeneous" part of this energy is related to the "rigid" (i.e., purely translational) part of the displacement of atoms across the slip plane, while the "gradient" part accounts for energy storage in those regions near the slip plane where atomic displacements deviate from being rigid, e.g., in the dislocation core. Via the attendant global energy scaling, the interface energy model facilitates an atomistic determination of the entire phase field energy as an optimal approximation of the (exact) atomistic energy; no adjustable parameters remain. For simplicity, an interatomic potential and molecular statics are employed for this purpose here; alternatively, ab initio (i.e., DFT-based) methods can be used. To illustrate the current approach, it is applied to determine the phase field free energy for fcc aluminum and copper. The identified models are then applied to modeling of dislocation dissociation, stacking fault formation, glide and dislocation reactions in these materials. As well, the tensile loading of a dislocation loop is considered. In the process, the current thermodynamic picture is compared with the classical mechanical one as based on the Peach-Köhler force.

Atomic Spectral Methods for Ab Initio Molecular Electronic Energy Surfaces: Transitioning From Small-Molecule to Biomolecular-Suitable Approaches.

PubMed

Mills, Jeffrey D; Ben-Nun, Michal; Rollin, Kyle; Bromley, Michael W J; Li, Jiabo; Hinde, Robert J; Winstead, Carl L; Sheehy, Jeffrey A; Boatz, Jerry A; Langhoff, Peter W

2016-08-25

Continuing attention has addressed incorportation of the electronically dynamical attributes of biomolecules in the largely static first-generation molecular-mechanical force fields commonly employed in molecular-dynamics simulations. We describe here a universal quantum-mechanical approach to calculations of the electronic energy surfaces of both small molecules and large aggregates on a common basis which can include such electronic attributes, and which also seems well-suited to adaptation in ab initio molecular-dynamics applications. In contrast to the more familiar orbital-product-based methodologies employed in traditional small-molecule computational quantum chemistry, the present approach is based on an "ex-post-facto" method in which Hamiltonian matrices are evaluated prior to wave function antisymmetrization, implemented here in the support of a Hilbert space of orthonormal products of many-electron atomic spectral eigenstates familiar from the van der Waals theory of long-range interactions. The general theory in its various forms incorporates the early semiempirical atoms- and diatomics-in-molecules approaches of Moffitt, Ellison, Tully, Kuntz, and others in a comprehensive mathematical setting, and generalizes the developments of Eisenschitz, London, Claverie, and others addressing electron permutation symmetry adaptation issues, completing these early attempts to treat van der Waals and chemical forces on a common basis. Exact expressions are obtained for molecular Hamiltonian matrices and for associated energy eigenvalues as sums of separate atomic and interaction-energy terms, similar in this respect to the forms of classical force fields. The latter representation is seen to also provide a long-missing general definition of the energies of individual atoms and of their interactions within molecules and matter free from subjective additional constraints. A computer code suite is described for calculations of the many-electron atomic eigenspectra and the pairwise-atomic Hamiltonian matrices required for practical applications. These matrices can be retained as functions of scalar atomic-pair separations and employed in assembling aggregate Hamiltonian matrices, with Wigner rotation matrices providing analytical representations of their angular degrees of freedom. In this way, ab initio potential energy surfaces are obtained in the complete absence of repeated evaluations and transformations of the one- and two-electron integrals at different molecular geometries required in most ab inito molecular calculations, with large Hamiltonian matrix assembly simplified and explicit diagonalizations avoided employing partitioning and Brillouin-Wigner or Rayleigh-Schrödinger perturbation theory. Illustrative applications of the important components of the formalism, selected aspects of the scaling of the approach, and aspects of "on-the-fly" interfaces with Monte Carlo and molecular-dynamics methods are described in anticipation of subsequent applications to biomolecules and other large aggregates.

Acceleration of saddle-point searches with machine learning.

PubMed

Peterson, Andrew A

2016-08-21

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the number of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.

Acceleration of saddle-point searches with machine learning

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

Peterson, Andrew A., E-mail: andrew-peterson@brown.edu

In atomistic simulations, the location of the saddle point on the potential-energy surface (PES) gives important information on transitions between local minima, for example, via transition-state theory. However, the search for saddle points often involves hundreds or thousands of ab initio force calls, which are typically all done at full accuracy. This results in the vast majority of the computational effort being spent calculating the electronic structure of states not important to the researcher, and very little time performing the calculation of the saddle point state itself. In this work, we describe how machine learning (ML) can reduce the numbermore » of intermediate ab initio calculations needed to locate saddle points. Since machine-learning models can learn from, and thus mimic, atomistic simulations, the saddle-point search can be conducted rapidly in the machine-learning representation. The saddle-point prediction can then be verified by an ab initio calculation; if it is incorrect, this strategically has identified regions of the PES where the machine-learning representation has insufficient training data. When these training data are used to improve the machine-learning model, the estimates greatly improve. This approach can be systematized, and in two simple example problems we demonstrate a dramatic reduction in the number of ab initio force calls. We expect that this approach and future refinements will greatly accelerate searches for saddle points, as well as other searches on the potential energy surface, as machine-learning methods see greater adoption by the atomistics community.« less

Complete 13C NMR chemical shifts assignment for cholesterol crystals by combined CP-MAS spectral editing and ab initio GIPAW calculations with dispersion forces.

PubMed

Küçükbenli, Emine; Sonkar, Kanchan; Sinha, Neeraj; de Gironcoli, Stefano

2012-04-12

We report here the first fully ab initio determination of (13)C NMR spectra for several crystal structures of cholesterol, observed in various biomaterials. We combine Gauge-Including Projector Augmented Waves (GIPAW) calculations at relaxed structures, fully including dispersion forces, with Magic Angle Spinning Solid State NMR experiments and spectral editing to achieve a detailed interpretation of the complex NMR spectra of cholesterol crystals. By introducing an environment-dependent secondary referencing scheme in our calculations, not only do we reproduce the characteristic spectral features of the different crystalline polymorphs, thus clearly discriminating among them, but also closely represent the spectrum in the region of several highly overlapping peaks. This, in combination with spectral editing, allows us to provide a complete peak assignment for monohydrate (ChM) and low-temperature anhydrous (ChAl) crystal polymorphs. Our results show that the synergy between ab initio calculations and refined experimental techniques can be exploited for an accurate and efficient NMR crystallography of complex systems of great interest for biomaterial studies. The method is general in nature and can be applied for studies of various complex biomaterials.

Ab initio molecular dynamics in a finite homogeneous electric field.

PubMed

Umari, P; Pasquarello, Alfredo

2002-10-07

We treat homogeneous electric fields within density functional calculations with periodic boundary conditions. A nonlocal energy functional depending on the applied field is used within an ab initio molecular dynamics scheme. The reliability of the method is demonstrated in the case of bulk MgO for the Born effective charges, and the high- and low-frequency dielectric constants. We evaluate the static dielectric constant by performing a damped molecular dynamics in an electric field and avoiding the calculation of the dynamical matrix. Application of this method to vitreous silica shows good agreement with experiment and illustrates its potential for systems of large size.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics.

PubMed

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Spectroscopic (FT-IR and FT-Raman) investigation, first order hyperpolarizability, NBO, HOMO-LUMO and MEP analysis of 6-nitrochromone by ab initio and density functional theory calculations

NASA Astrophysics Data System (ADS)

Senthil kumar, J.; Jeyavijayan, S.; Arivazhagan, M.

2015-02-01

The vibrational spectral analysis is carried out using FT-Raman and FT-IR spectroscopy in the range 3500-50 cm-1 and 4000-400 cm-1, respectively, for 6-nitrochromone (6NC). The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimization and normal coordinates force field calculation based on ab initio HF and DFT gradient calculations employing the HF/6-311++G(d,p) and B3LYP/6-311++G(d,p) basis set. Stability of the molecule has been analyzed using NBO analysis. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Thermodynamic properties like entropy, heat capacity, zero-point energy and Mulliken's charge analysis have been calculated for the 6NC. The complete assignments were performed on the basis of total energy distribution (TED) of the vibrational modes with scaled quantum mechanical (SQM) method. The MEP map shows the negative potential sites are on oxygen atoms as well as the positive potential sites are around the hydrogen atoms.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

NASA Astrophysics Data System (ADS)

Tanzi, Luana; Ramondo, Fabio; Caminiti, Ruggero; Campetella, Marco; Di Luca, Andrea; Gontrani, Lorenzo

2015-09-01

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations and anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.

Potential-Energy and Free-Energy Surfaces of Glycyl-Phenylalanyl-Alanine (GFA) Tripeptide. Experiment and Theory

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

Valdes, Haydee; Spiwok, Vojtech; Rezac, Jan

2008-04-17

The free-energy surface (FES) of glycyl-phenylalanyl-alanine (GFA) tripeptide was explored by molecular dynamics (MD) simulations in combination with high-level correlated ab initio quantum chemical calculations and metadynamics. Both the MD and metadynamics employed the tightbinding DFT-D method instead of the AMBER force field, which yielded inaccurate results. We classified the minima localised in the FESs as follows: a) the backbone-conformational arrangement; and b) the existence of a COOH---OC intramolecular H-bond (families CO₂Hfree and CO₂Hbonded). Comparison with experimental results showed that the most stable minima in the FES correspond to the experimentally observed structures. Remarkably, however, we did not observe experimentallymore » the CO₂Hbonded family (also predicted by metadynamics), although its stability is comparable to that of the CO₂Hfree structures. This fact was explained by the former’s short excited state lifetime. We also carried out ab initio calculations using DFT-D and the M06-2X functional. The importance of the dispersion energy in stabilizing peptide conformers is well reflected by our pioneer analysis using the DFT-SAPT method to explore the nature of the backbone/side-chain interactions.« less

Unified description of 6Li structure and deuterium- 4He dynamics with chiral two- and three-nucleon forces

DOE PAGES

Hupin, Guillaume; Quaglioni, Sofia; Navratil, Petr

2015-05-29

Here, we provide a unified ab initio description of the 6Li ground state and elastic scattering of deuterium (d) on 4He (α) using two- and three-nucleon forces from chiral effective field theory. We analyze the influence of the three-nucleon force and reveal the role of continuum degrees of freedom in shaping the low-lying spectrum of 6Li. The calculation reproduces the empirical binding energy of 6Li, yielding an asymptotic D- to S-state ratio of the 6Li wave function in the d+α configuration of –0.027, in agreement with a determination from 6Li– 4He elastic scattering, but overestimates the excitation energy of themore » 3 + state by 350 keV. The bulk of the computed differential cross section is in good agreement with data. These results endorse the application of the present approach to the evaluation of the 2H(α,γ) 6Li radiative capture, responsible for the big-bang nucleosynthesis of 6Li.« less

Revisiting the Electronic Structure of FeS Monomers Using ab Initio Ligand Field Theory and the Angular Overlap Model.

PubMed

Chilkuri, Vijay Gopal; DeBeer, Serena; Neese, Frank

2017-09-05

Iron-sulfur (FeS) proteins are universally found in nature with actives sites ranging in complexity from simple monomers to multinuclear sites from two up to eight iron atoms. These sites include mononuclear (rubredoxins), dinuclear (ferredoxins and Rieske proteins), trinuclear (e.g., hydrogenases), and tetranuclear (various ferredoxins and high-potential iron-sulfur proteins). The electronic structure of the higher-nuclearity clusters is inherently extremely complex. Hence, it is reasonable to take a bottom-up approach in which clusters of increasing nuclearity are analyzed in terms of the properties of their lower nuclearity constituents. In the present study, the first step is taken by an in-depth analysis of mononuclear FeS systems. Two different FeS molecules with phenylthiolate and methylthiolate as ligands are studied in their oxidized and reduced forms using modern wave function-based ab initio methods. The ab initio electronic spectra and wave function are presented and analyzed in detail. The very intricate electronic structure-geometry relationship in these systems is analyzed using ab initio ligand field theory (AILFT) in conjunction with the angular overlap model (AOM) parametrization scheme. The simple AOM model is used to explain the effect of geometric variations on the electronic structure. Through a comparison of the ab initio computed UV-vis absorption spectra and the available experimental spectra, the low-energy part of the many-particle spectrum is carefully analyzed. We show ab initio calculated magnetic circular dichroism spectra and present a comparison with the experimental spectrum. Finally, AILFT parameters and the ab initio spectra are compared with those obtained experimentally to understand the effect of the increased covalency of the thiolate ligands on the electronic structure of FeS monomers.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO reversible reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HNO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X double bond H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate (Delta)H(sub f, sup o) value for HNO using state-of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +/- 0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

The Heat of Formation of HNO

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Dateo, Christopher E.

1995-01-01

The HNO molecule is of interest in both combustion and atmospheric chemistry. For example, Guadagnini et al. have recently presented ab initio potential energy surfaces for the three lowest lying electronic states of HNO and then used these in examining several chemical reactions that take place in the combustion of nitrogen containing fuels and in the oxidation of atmospheric nitrogen. We have previously studied the ground state potential energy surface (i.e., stationary points along the HNO rev. reaction HON path), vibrational spectrum (using an accurate quartic force field), zero-point energy, and bonding of HNO using coupled-cluster ab initio methods. HNO is also very interesting because of the unique nature of its bonding characteristics. That is, the potential energy surface is very flat along the H-N bonding coordinate thereby giving unusual harmonic and fundamental vibrational frequencies, and the H-N bond energy is rather weak in comparison to other H-N bond energies. In fact, using experimental heats of formation for HO, H, and NO, the H- bond energy is computed to be only 49.9 kcal/ mol (298 K). However, ab initio calculations of isodesmic reaction energies involving HNO, FNO, ClNO, and several other molecules have shown that there is an inconsistency in the experimental heats of formation of the XNO (X=H, F, and Cl) species. Hence the motivation for this study was to determine a very accurate(DELTA)H(sup o)(sub f) value for HNO using state of-the-art ab initio methods. Based on many recent studies it is evident that the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T), in conjunction with large one-particle basis sets should be reliable to better than +0.8 kcal/mol for this quantity. The computational methodology is described in the next section followed by our results and discussion. Conclusions are presented in the final section.

Materials perspective on Casimir and van der Waals interactions

NASA Astrophysics Data System (ADS)

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.; Rodriguez-Lopez, P.; Rodriguez, A. W.; Podgornik, R.

2016-10-01

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. Such interactions are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insights into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. This review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. The outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.

Molecular polarizability of water from local dielectric response theory

DOE PAGES

Ge, Xiaochuan; Lu, Deyu

2017-08-08

Here, we propose a fully ab initio theory to compute the electron density response under the perturbation in the local field. This method is based on our recently developed local dielectric response theory [Phys. Rev. B 92, 241107(R), 2015], which provides a rigorous theoretical framework to treat local electronic excitations in both nite and extended systems beyond the commonly employed dipole approximation. We have applied this method to study the electronic part of the molecular polarizability of water in ice Ih and liquid water. Our results reveal that the crystal field of the hydrogen-bond network has strong anisotropic effects, whichmore » significantly enhance the out-of-plane component and suppress the in-plane component perpendicular to the bisector direction. The contribution from the charge transfer is equally important, which increases the isotropic molecular polarizability by 5-6%. Our study provides new insights into the dielectric properties of water, which form the basis to understand electronic excitations in water and to develop accurate polarizable force fields of water.« less

Accurate ab initio Quartic Force Fields of Cyclic and Bent HC2N Isomers

NASA Technical Reports Server (NTRS)

Inostroza, Natalia; Huang, Xinchuan; Lee, Timothy J.

2012-01-01

Highly correlated ab initio quartic force field (QFFs) are used to calculate the equilibrium structures and predict the spectroscopic parameters of three HC2N isomers. Specifically, the ground state quasilinear triplet and the lowest cyclic and bent singlet isomers are included in the present study. Extensive treatment of correlation effects were included using the singles and doubles coupled-cluster method that includes a perturbational estimate of the effects of connected triple excitations, denoted CCSD(T). Dunning s correlation-consistent basis sets cc-pVXZ, X=3,4,5, were used, and a three-point formula for extrapolation to the one-particle basis set limit was used. Core-correlation and scalar relativistic corrections were also included to yield highly accurate QFFs. The QFFs were used together with second-order perturbation theory (with proper treatment of Fermi resonances) and variational methods to solve the nuclear Schr dinger equation. The quasilinear nature of the triplet isomer is problematic, and it is concluded that a QFF is not adequate to describe properly all of the fundamental vibrational frequencies and spectroscopic constants (though some constants not dependent on the bending motion are well reproduced by perturbation theory). On the other hand, this procedure (a QFF together with either perturbation theory or variational methods) leads to highly accurate fundamental vibrational frequencies and spectroscopic constants for the cyclic and bent singlet isomers of HC2N. All three isomers possess significant dipole moments, 3.05D, 3.06D, and 1.71D, for the quasilinear triplet, the cyclic singlet, and the bent singlet isomers, respectively. It is concluded that the spectroscopic constants determined for the cyclic and bent singlet isomers are the most accurate available, and it is hoped that these will be useful in the interpretation of high-resolution astronomical observations or laboratory experiments.

TOUCHSTONE II: a new approach to ab initio protein structure prediction.

PubMed

Zhang, Yang; Kolinski, Andrzej; Skolnick, Jeffrey

2003-08-01

We have developed a new combined approach for ab initio protein structure prediction. The protein conformation is described as a lattice chain connecting C(alpha) atoms, with attached C(beta) atoms and side-chain centers of mass. The model force field includes various short-range and long-range knowledge-based potentials derived from a statistical analysis of the regularities of protein structures. The combination of these energy terms is optimized through the maximization of correlation for 30 x 60,000 decoys between the root mean square deviation (RMSD) to native and energies, as well as the energy gap between native and the decoy ensemble. To accelerate the conformational search, a newly developed parallel hyperbolic sampling algorithm with a composite movement set is used in the Monte Carlo simulation processes. We exploit this strategy to successfully fold 41/100 small proteins (36 approximately 120 residues) with predicted structures having a RMSD from native below 6.5 A in the top five cluster centroids. To fold larger-size proteins as well as to improve the folding yield of small proteins, we incorporate into the basic force field side-chain contact predictions from our threading program PROSPECTOR where homologous proteins were excluded from the data base. With these threading-based restraints, the program can fold 83/125 test proteins (36 approximately 174 residues) with structures having a RMSD to native below 6.5 A in the top five cluster centroids. This shows the significant improvement of folding by using predicted tertiary restraints, especially when the accuracy of side-chain contact prediction is >20%. For native fold selection, we introduce quantities dependent on the cluster density and the combination of energy and free energy, which show a higher discriminative power to select the native structure than the previously used cluster energy or cluster size, and which can be used in native structure identification in blind simulations. These procedures are readily automated and are being implemented on a genomic scale.

The Anharmonic Force Field of Ethylene, C2H4, by Means of Accurate Ab Initio Calculations

NASA Technical Reports Server (NTRS)

Martin, Jan M. L.; Lee, Timothy J.; Taylor, Peter R.; Francois, Jean-Pierre; Langhoff, Stephen R. (Technical Monitor)

1995-01-01

The quartic force field of ethylene, C2H4, has been calculated ab initio using augmented coupled cluster, CCSD(T), methods and correlation consistent basis sets of spdf quality. For the C-12 isotopomers C2H4, C2H3D, H2CCD2, cis-C2H2D2, trans-C2H2D2, C2HD3, and C2D4, all fundamentals could be reproduced to better than 10 per centimeter, except for three cases of severe Fermi type 1 resonance. The problem with these three bands is identified as a systematic overestimate of the Kiij Fermi resonance constants by a factor of two or more; if this is corrected for, the predicted fundamentals come into excellent agreement with experiment. No such systematic overestimate is seen for Fermi type 2 resonances. Our computed harmonic frequencies suggest a thorough revision of the accepted experimentally derived values. Our computed and empirically corrected re geometry differs substantially from experimentally derived values: both the predicted rz geometry and the ground-state rotational constants are, however, in excellent agreement with experiment, suggesting revision of the older values. Anharmonicity constants agree well with experiment for stretches, but differ substantially for stretch-bend interaction constants, due to equality constraints in the experimental analysis that do not hold. Improved criteria for detecting Fermi and Coriolis resonances are proposed and found to work well, contrary to the established method based on harmonic frequency differences that fails to detect several important resonances for C2H4 and its isotopomers. Surprisingly good results are obtained with a small spd basis at the CCSD(T) level. The well-documented strong basis set effect on the v8 out-of-plane motion is present to a much lesser extent when correlation-optimized polarization functions are used. Complete sets of anharmonic, rovibrational coupling, and centrifugal distortion constants for the isotopomers are available as supplementary material to the paper.

Potentials of Mean Force With Ab Initio Mixed Hamiltonian Models of Solvation

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

Dupuis, Michel; Schenter, Gregory K.; Garrett, Bruce C.

2003-08-01

We give an account of a computationally tractable and efficient procedure for the calculation of potentials of mean force using mixed Hamiltonian models of electronic structure where quantum subsystems are described with computationally intensive ab initio wavefunctions. The mixed Hamiltonian is mapped into an all-classical Hamiltonian that is amenable to a thermodynamic perturbation treatment for the calculation of free energies. A small number of statistically uncorrelated (solute-solvent) configurations are selected from the Monte Carlo random walk generated with the all-classical Hamiltonian approximation. Those are used in the averaging of the free energy using the mixed quantum/classical Hamiltonian. The methodology ismore » illustrated for the micro-solvated SN2 substitution reaction of methyl chloride by hydroxide. We also compare the potential of mean force calculated with the above protocol with an approximate formalism, one in which the potential of mean force calculated with the all-classical Hamiltonian is simply added to the energy of the isolated (non-solvated) solute along the reaction path. Interestingly the latter approach is found to be in semi-quantitative agreement with the full mixed Hamiltonian approximation.« less

29 CFR 4.190 - Contract cancellation.

Code of Federal Regulations, 2010 CFR

2010-07-01

... in paragraph (a). Such contract is without warrant of law and has no force and effect and is void ab initio, 33 Comp Gen. 63; Decision of the Comptroller General, B-115051, August 6, 1953. Furthermore, any...

29 CFR 4.190 - Contract cancellation.

Code of Federal Regulations, 2012 CFR

2012-07-01

... in paragraph (a). Such contract is without warrant of law and has no force and effect and is void ab initio, 33 Comp Gen. 63; Decision of the Comptroller General, B-115051, August 6, 1953. Furthermore, any...

29 CFR 4.190 - Contract cancellation.

Code of Federal Regulations, 2013 CFR

2013-07-01

... in paragraph (a). Such contract is without warrant of law and has no force and effect and is void ab initio, 33 Comp Gen. 63; Decision of the Comptroller General, B-115051, August 6, 1953. Furthermore, any...

29 CFR 4.190 - Contract cancellation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... in paragraph (a). Such contract is without warrant of law and has no force and effect and is void ab initio, 33 Comp Gen. 63; Decision of the Comptroller General, B-115051, August 6, 1953. Furthermore, any...

29 CFR 4.190 - Contract cancellation.

Code of Federal Regulations, 2014 CFR

2014-07-01

... in paragraph (a). Such contract is without warrant of law and has no force and effect and is void ab initio, 33 Comp Gen. 63; Decision of the Comptroller General, B-115051, August 6, 1953. Furthermore, any...

AMOEBA 2.0: A physics-first approach to biomolecular simulations

NASA Astrophysics Data System (ADS)

Rackers, Joshua; Ponder, Jay

The goal of the AMOEBA force field project is to use classical physics to understand and predict the nature of interactions between biological molecules. While making significant advances over the past decade, the ultimate goal of predicting binding energies with ``chemical accuracy'' remains elusive. The primary source of this inaccuracy comes from the physics of how molecules interact at short range. For example, despite AMOEBA's advanced treatment of electrostatics, the force field dramatically overpredicts the electrostatic energy of DNA stacking interactions. AMOEBA 2.0 works to correct these errors by including simple, first principles physics-based terms to account for the quantum mechanical nature of these short-range molecular interactions. We have added a charge penetration term that considerably improves the description of electrostatic interactions at short range. We are reformulating the polarization term of AMOEBA in terms of basic physics assertions. And we are reevaluating the van der Waals term to match ab initio energy decompositions. These additions and changes promise to make AMOEBA more predictive. By including more physical detail of the important short-range interactions of biological molecules, we hope to move closer to the ultimate goal of true predictive power.

High-Accuracy Quartic Force Field Calculations for the Spectroscopic Constants and Vibrational Frequencies of 1(exp 1)A' l-C3H(-): A Possible Link to Lines Observed in the Horsehead Nebula PDR

NASA Technical Reports Server (NTRS)

Fortenberry, Ryan C.; Huang, Xinchuan; Crawford, T. Daniel; Lee, Timothy J.

2013-01-01

It has been shown that rotational lines observed in the Horsehead nebula photon-dominated-region (PDR) are probably not caused by l-C3H+, as was originally suggested. In the search for viable alternative candidate carriers, quartic force fields are employed here to provide highly accurate rotational constants, as well as fundamental vibrational frequencies, for another candidate carrier: 1 (sup 1)A' C3H(-). The ab initio computed spectroscopic constants provided in this work are, compared to those necessary to define the observed lines, as accurate as the computed spectroscopic constants for many of the known interstellar anions. Additionally, the computed D-eff for C3H(-) is three times closer to the D deduced from the observed Horsehead nebula lines relative to l-C3H(+). As a result, 1 (sup 1)A' C3H(-). is a more viable candidate for these observed rotational transitions and would be the seventh confirmed interstellar anion detected within the past decade and the first C(sub n)H(-) molecular anion with an odd n.

Scalable improvement of SPME multipolar electrostatics in anisotropic polarizable molecular mechanics using a general short-range penetration correction up to quadrupoles.

PubMed

Narth, Christophe; Lagardère, Louis; Polack, Étienne; Gresh, Nohad; Wang, Qiantao; Bell, David R; Rackers, Joshua A; Ponder, Jay W; Ren, Pengyu Y; Piquemal, Jean-Philip

2016-02-15

We propose a general coupling of the Smooth Particle Mesh Ewald SPME approach for distributed multipoles to a short-range charge penetration correction modifying the charge-charge, charge-dipole and charge-quadrupole energies. Such an approach significantly improves electrostatics when compared to ab initio values and has been calibrated on Symmetry-Adapted Perturbation Theory reference data. Various neutral molecular dimers have been tested and results on the complexes of mono- and divalent cations with a water ligand are also provided. Transferability of the correction is adressed in the context of the implementation of the AMOEBA and SIBFA polarizable force fields in the TINKER-HP software. As the choices of the multipolar distribution are discussed, conclusions are drawn for the future penetration-corrected polarizable force fields highlighting the mandatory need of non-spurious procedures for the obtention of well balanced and physically meaningful distributed moments. Finally, scalability and parallelism of the short-range corrected SPME approach are addressed, demonstrating that the damping function is computationally affordable and accurate for molecular dynamics simulations of complex bio- or bioinorganic systems in periodic boundary conditions. Copyright © 2016 Wiley Periodicals, Inc.

Potential interstellar noble gas molecules: ArOH+ and NeOH+ rovibrational analysis from quantum chemical quartic force fields

NASA Astrophysics Data System (ADS)

Theis, Riley A.; Fortenberry, Ryan C.

2016-03-01

The discovery of ArH+ in the interstellar medium has shown that noble gas chemistry may be of more chemical significance than previously believed. The present work extends the known chemistry of small noble gas molecules to NeOH+ and ArOH+. Besides their respective neonium and argonium diatomic cation cousins, these hydroxyl cation molecules are the most stable small noble gas molecules analyzed of late. ArOH+ is once again more stable than the neon cation, but both are well-behaved enough for a complete quartic force field analysis of their rovibrational properties. The Ar-O bond in ArOH+ , for instance, is roughly three-quarters of the strength of the Ar-H bond in ArH+ highlighting the rigidity of this system. The rotational constants, geometries, and vibrational frequencies for both molecules and their various isotopologues are computed from ab initio quantum chemical theory at high-level, and it is shown that these cations may form in regions where peroxy or weakly-bound alcohols may be present. The resulting data should be of significant assistance for the laboratory or observational analysis of these potential interstellar molecules.

Analysis of fcc metals fracture behaviour: Fracture behaviour of fcc metals: brittle/ductile behaviour criteria : with ab-initio, embedded atom and pseudopotential parameterization for Au, Ir and Al. analysis for Au, Ir and Al.

NASA Astrophysics Data System (ADS)

Gornostyrev, Yu. N.; Katsnelson, M. I.; Mryasov, Oleg N.; Freeman, A. J.; Trefilov, M. V.

1998-03-01

Theoretical analysis of the fracture behaviour of fcc Au, Ir and Al have been performed within various brittle/ductile criteria (BDC) with ab-initio, embedded atom (EAM), and pseudopotential parameterizations. We systematically examined several important aspects of the fracture behaviour: (i) dislocation structure, (ii) energetics of the cleavage decohesion and (iii) character of the interatomic interactions. Unit dislocation structures were analyzed within a two dimensional generalization of the Peierls-Nabarro model with restoring forces determined from ab-initio total energy calculations and found to be split with well defined highly mobile partials for all considered metals. We find from ab-initio and pseudopotential that in contrast with most of fcc metals, cleavage decohesion curve for Al appreciably differs from UBER relation. Finally, using ab-initio, EAM and pseudopotential parameterizations, we demonstrate that (i) Au (as a typical example of a ductile metal) is well described within existing BDC's, (ii) anomalous cleavage-like crack propagation of Ir is driven predominantly by it's high elastic modulus and (iii) Al is not described within BDC due to it's long-range interatomic interactions (and hence requires adjustments of the brittle/ductile criteria).

Comparative study of generalized born models: Born radii and peptide folding.

PubMed

Zhu, Jiang; Alexov, Emil; Honig, Barry

2005-02-24

In this study, we have implemented four analytical generalized Born (GB) models and investigated their performance in conjunction with the GROMOS96 force field. The four models include that of Still and co-workers, the HCT model of Cramer, Truhlar, and co-workers, a modified form of the AGB model of Levy and co-workers, and the GBMV2 model of Brooks and co-workers. The models were coded independently and implemented in the GROMOS software package and in TINKER. They were compared in terms of their ability to reproduce the results of Poisson-Boltzmann (PB) calculations and in their performance in the ab initio peptide folding of two peptides, one that forms a beta-hairpin in solution and one that forms an alpha-helix. In agreement with previous work, the GBMV2 model is most successful in reproducing PB results while the other models tend to underestimate the effective Born radii of buried atoms. In contrast, stochastic dynamics simulations on the folding of the two peptides, the C-terminus beta-hairpin of the B1 domain of protein G and the alanine-based alpha-helical peptide 3K(I), suggest that the simpler GB models are more effective in sampling conformational space. Indeed, the Still model used in conjunction with the GROMOS96 force field is able to fold the hairpin peptide to a native-like structure without the benefit of enhanced sampling techniques. This is due in part to the properties of the united-atom GROMOS96 force field which appears to be more flexible, and hence to sample more efficiently, than force fields such as OPLSAA. Our results suggest a general strategy which involves using different combinations of force fields and solvent models in different applications, for example, using GROMOS96 and a simple GB model in sampling and OPLSAA and a more accurate GB model in refinement. The fact that various methods have been implemented in a unified way should facilitate the testing and subsequent use of different methods to evaluate conformational free energies in different applications. Our results also bear on some general issues involved in peptide folding and structure prediction which are addressed in the Discussion.

Towards ab initio Calculations with the Dynamical Vertex Approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Kaufmann, Josef; Gunacker, Patrik; Pickem, Matthias; Thunström, Patrik; Tomczak, Jan M.; Held, Karsten

2018-04-01

While key effects of the many-body problem — such as Kondo and Mott physics — can be understood in terms of on-site correlations, non-local fluctuations of charge, spin, and pairing amplitudes are at the heart of the most fascinating and unresolved phenomena in condensed matter physics. Here, we review recent progress in diagrammatic extensions to dynamical mean-field theory for ab initio materials calculations. We first recapitulate the quantum field theoretical background behind the two-particle vertex. Next we discuss latest algorithmic advances in quantum Monte Carlo simulations for calculating such two-particle quantities using worm sampling and vertex asymptotics, before giving an introduction to the ab initio dynamical vertex approximation (AbinitioDΓA). Finally, we highlight the potential of AbinitioDΓA by detailing results for the prototypical correlated metal SrVO3.

Ab initio parameterization of a charge optimized many-body forcefield for Si-SiO2: Validation and thermal transport in nanostructures.

PubMed

France-Lanord, Arthur; Soukiassian, Patrick; Glattli, Christian; Wimmer, Erich

2016-03-14

In an effort to extend the reach of current ab initio calculations to simulations requiring millions of configurations for complex systems such as heterostructures, we have parameterized the third-generation Charge Optimized Many-Body (COMB3) potential using solely ab initio total energies, forces, and stress tensors as input. The quality and the predictive power of the new forcefield are assessed by computing properties including the cohesive energy and density of SiO2 polymorphs, surface energies of alpha-quartz, and phonon densities of states of crystalline and amorphous phases of SiO2. Comparison with data from experiments, ab initio calculations, and molecular dynamics simulations using published forcefields including BKS (van Beest, Kramer, and van Santen), ReaxFF, and COMB2 demonstrates an overall improvement of the new parameterization. The computed temperature dependence of the thermal conductivity of crystalline alpha-quartz and the Kapitza resistance of the interface between crystalline Si(001) and amorphous silica is in excellent agreement with experiment, setting the stage for simulations of complex nanoscale heterostructures.

Ab initio molecular orbital calculations on the associated complexes of lithium cyanide with ammonia

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

Mohandas, P.; Shivaglal, M.C.; Chandrasekhar, J.

Ab initio molecular orbital (MO) calculations with the 3-21G and 6-31G basis sets are carried out on a series of complexes of NH{sub 3} with Li{sup +}, C{triple_bond}N{sup -}, LiCN, and its isomer LiNC. The BSSE-corrected interaction energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies are evaluated for 15 species. Complexes with trifurcated (C{sub 3v}) structures are calculated to be saddle points on the potential energy surfaces and have one imaginary frequency each. Calculated energies, geometrical parameters, internal force constants, and harmonic vibrational frequencies of the various species considered are discussed in terms of the nature of associationmore » of LiCN with ammonia. The vibrational frequencies of the relevant complexed species are compared with the experimental frequencies reported earlier for solutions of lithium cyanide in liquid ammonia. 40 refs., 1 fig., 4 tabs.« less

Relativistic Brueckner-Hartree-Fock theory for neutron drops

NASA Astrophysics Data System (ADS)

Shen, Shihang; Liang, Haozhao; Meng, Jie; Ring, Peter; Zhang, Shuangquan

2018-05-01

Neutron drops confined in an external field are studied in the framework of relativistic Brueckner-Hartree-Fock theory using the bare nucleon-nucleon interaction. The ground-state energies and radii of neutron drops with even numbers from N =4 to N =50 are calculated and compared with results obtained from other nonrelativistic ab initio calculations and from relativistic density functional theory. Special attention has been paid to the magic numbers and to the subshell closures. The single-particle energies are investigated and the monopole effect of the tensor force on the evolutions of the spin-orbit and the pseudospin-orbit splittings is discussed. The results provide interesting insights into neutron-rich systems and can form an important guide for future density functionals.

An atomic charge model for graphene oxide for exploring its bioadhesive properties in explicit water.

PubMed

Stauffer, D; Dragneva, N; Floriano, W B; Mawhinney, R C; Fanchini, G; French, S; Rubel, O

2014-07-28

Graphene Oxide (GO) has been shown to exhibit properties that are useful in applications such as biomedical imaging, biological sensors, and drug delivery. The binding properties of biomolecules at the surface of GO can provide insight into the potential biocompatibility of GO. Here we assess the intrinsic affinity of amino acids to GO by simulating their adsorption onto a GO surface. The simulation is done using Amber03 force-field molecular dynamics in explicit water. The emphasis is placed on developing an atomic charge model for GO. The adsorption energies are computed using atomic charges obtained from an ab initio electrostatic potential based method. The charges reported here are suitable for simulating peptide adsorption to GO.

Ab Initio Ligand Field Molecular Mechanics and the Nature of Metal-Ligand π-Bonding in Fe(II) 2,6-di(pyrazol-1-yl)pyridine Spin Crossover Complexes.

PubMed

Deeth, Robert J; Halcrow, Malcolm A; Kershaw Cook, Laurence J; Raithby, Paul R

2018-04-06

A ligand field molecular mechanics (LFMM) force field has been constructed for the spin states of [Fe(bpp) 2 ] 2+ (bpp=2,6-di(pyrazol-1-yl)pyridine) and related complexes. A new charge scheme is employed which interpolates between partial charges for neutral bpp and protonated [H 3 bpp] 3+ to achieve a target metal charge. The LFMM angular overlap model (AOM) parameters are fitted to fully ab initio d orbital energies. However, several AOM parameter sets are possible. The ambiguity is resolved by calculating the Jahn-Teller distortion mode for high spin, which indicates that in [Fe(bpp) 2 ] 2+ pyridine is a π-acceptor and pyrazole a weak π-donor. The alternative fit, assumed previously, where both ligands act as π-donors leads to an inconsistent distortion. LFMM optimisations in the presence of [BF 4 ] - or [PF 6 ] - anions are in good agreement with experiment and the model also correctly predicts the spin state energetics for 3-pyrazolyl substituents where the interactions are mainly steric. However, for 4-pyridyl or 4-pyrazolyl substituents, LFMM only treats the electrostatic contribution which, for the pyridyl substituents, generates a fair correlation with the spin crossover transition temperatures, T 1/2 , but in the reverse sense to the dominant electronic effect. Thus, LFMM generates its smallest spin state energy difference for the substituent with the highest T 1/2 . One parameter set for all substituted bpp ligands is insufficient and further LFMM development will be required. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Single functional group interactions with individual carbon nanotubes

NASA Astrophysics Data System (ADS)

Friddle, Raymond W.; Lemieux, Melburne C.; Cicero, Giancarlo; Artyukhin, Alexander B.; Tsukruk, Vladimir V.; Grossman, Jeffrey C.; Galli, Giulia; Noy, Aleksandr

2007-11-01

Carbon nanotubes display a consummate blend of materials properties that affect applications ranging from nanoelectronic circuits and biosensors to field emitters and membranes. These applications use the non-covalent interactions between the nanotubes and chemical functionalities, often involving a few molecules at a time. Despite their wide use, we still lack a fundamental understanding and molecular-level control of these interactions. We have used chemical force microscopy to measure the strength of the interactions of single chemical functional groups with the sidewalls of vapour-grown individual single-walled carbon nanotubes. Surprisingly, the interaction strength does not follow conventional trends of increasing polarity or hydrophobicity, and instead reflects the complex electronic interactions between the nanotube and the functional group. Ab initio calculations confirm the observed trends and predict binding force distributions for a single molecular contact that match the experimental results. Our analysis also reveals the important role of molecular linkage dynamics in determining interaction strength at the single functional group level.

Ab initio multiple spawning on laser-dressed states: a study of 1,3-cyclohexadiene photoisomerization via light-induced conical intersections

NASA Astrophysics Data System (ADS)

Kim, Jaehee; Tao, Hongli; Martinez, Todd J.; Bucksbaum, Phil

2015-08-01

We extend the ab initio multiple spawning method to include both field-free and field-induced nonadiabatic transitions. We apply this method to describe ultrafast pump-probe experiments of the photoinduced ring-opening of gas phase 1,3-cyclohexadiene. In the absence of a control field, nonadiabatic transitions mediated by a conical intersection (CoIn) lead to rapid ground state recovery with both 1,3-cyclohexadiene and ring-opened hexatriene products. However, application of a control field within the first 200 fs after photoexcitation results in suppression of the hexatriene product. We demonstrate that this is a consequence of population dumping prior to reaching the CoIn and further interpret this in terms of light-induced CoIns created by the control field.

All-Atom MD Simulation of DNA Condensation Using Ab Initio Derived Force Field Parameters of Cobalt(III)-Hexammine.

PubMed

Sun, Tiedong; Mirzoev, Alexander; Korolev, Nikolay; Lyubartsev, Alexander P; Nordenskiöld, Lars

2017-08-24

It is well established that the presence of the trivalent cobalt(III)-hexammine cation (CoHex 3+ ) at submillimolar concentrations leads to bundling (condensation) of double-stranded DNA molecules, which is caused by DNA-DNA attraction induced by the multivalent counterions. However, the detailed mechanism of this process is still not fully understood. Furthermore, in all-atom molecular dynamics (MD) simulations, spontaneous aggregation of several DNA oligonucleotides in the presence of CoHex 3+ has previously not been demonstrated. In order to obtain a rigorous description of CoHex 3+ -nucleic acid interactions and CoHex 3+ -induced DNA condensation to be used in MD simulations, we have derived optimized force field parameters of the CoHex 3+ ion. They were obtained from Car-Parrinello molecular dynamics simulation of a single CoHex 3+ ion in the presence of 125 water molecules. The new set of force field parameters reproduces the experimentally known transition of DNA from B- to A-form, and qualitatively describes changes of DNA and RNA persistence lengths. We then carried out a 2 μs long atomistic simulation of four DNA oligomers each consisting of 36 base pairs in the presence of CoHex 3+ . We demonstrate that, in this system, DNA molecules display attractive interactions and aggregate into bundle-like structures. This behavior depends critically on the details of the CoHex 3+ interaction with DNA. A control simulation with a similar setup but in the presence of Mg 2+ does not induce DNA-DNA attraction, which is also in agreement with experiment.

Communication: Influence of external static and alternating electric fields on water from long-time non-equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Futera, Zdenek; English, Niall J.

2017-07-01

The response of water to externally applied electric fields is of central relevance in the modern world, where many extraneous electric fields are ubiquitous. Historically, the application of external fields in non-equilibrium molecular dynamics has been restricted, by and large, to relatively inexpensive, more or less sophisticated, empirical models. Here, we report long-time non-equilibrium ab initio molecular dynamics in both static and oscillating (time-dependent) external electric fields, therefore opening up a new vista in rigorous studies of electric-field effects on dynamical systems with the full arsenal of electronic-structure methods. In so doing, we apply this to liquid water with state-of-the-art non-local treatment of dispersion, and we compute a range of field effects on structural and dynamical properties, such as diffusivities and hydrogen-bond kinetics.

Ab initio implementation of quantum trajectory mean-field approach and dynamical simulation of the N{sub 2}CO photodissociation

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

Xie, Binbin; Liu, Lihong; Cui, Ganglong

2015-11-21

In this work, the recently introduced quantum trajectory mean-field (QTMF) approach is implemented and employed to explore photodissociation dynamics of diazirinone (N{sub 2}CO), which are based on the high-level ab initio calculation. For comparison, the photodissociation process has been simulated as well with the fewest-switches surface hopping (FSSH) and the ab initio multiple spawning (AIMS) methods. Overall, the dynamical behavior predicted by the three methods is consistent. The N{sub 2}CO photodissociation at λ > 335 nm is an ultrafast process and the two C—N bonds are broken in a stepwise way, giving birth to CO and N{sub 2} as themore » final products in the ground state. Meanwhile, some noticeable differences were found in the QTMF, FSSH, and AIMS simulated time constants for fission of the C—N bonds, excited-state lifetime, and nonadiabatic transition ratios in different intersection regions. These have been discussed in detail. The present study provides a clear evidence that direct ab initio QTMF approach is one of the reliable tools for simulating nonadiabatic dynamics processes.« less

Approximate Quantum Dynamics using Ab Initio Classical Separable Potentials: Spectroscopic Applications.

PubMed

Hirshberg, Barak; Sagiv, Lior; Gerber, R Benny

2017-03-14

Algorithms for quantum molecular dynamics simulations that directly use ab initio methods have many potential applications. In this article, the ab initio classical separable potentials (AICSP) method is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wave function of the nuclei and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics simulations. The nuclear wave function can thus be propagated in time using the effective potentials generated "on the fly". As a test of the method for realistic systems, calculations of the stationary anharmonic frequencies of hydrogen stretching modes were carried out for several polyatomic systems, including three amino acids and the guanine-cytosine pair of nucleobases. Good agreement with experiments was found. The method scales very favorably with the number of vibrational modes and should be applicable for very large molecules, e.g., peptides. The method should also be applicable for properties such as vibrational line widths and line shapes. Work in these directions is underway.

Ab initio calculation of the electronic absorption spectrum of liquid water

NASA Astrophysics Data System (ADS)

Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa

2014-04-01

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

Structural studies on choline-carboxylate bio-ionic liquids by x-ray scattering and molecular dynamics

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

Tanzi, Luana; Ramondo, Fabio, E-mail: fabio.ramondo@univaq.it; Caminiti, Ruggero

2015-09-21

We report a X-ray diffraction and molecular dynamics study on three choline-based bio-ionic liquids, choline formate, [Ch] [For], choline propanoate, [Ch][Pro], and choline butanoate, [Ch][But]. For the first time, this class of ionic liquids has been investigated by X-ray diffraction. Experimental and theoretical structure factors have been compared for each term of the series. Local structural organization has been obtained from ab initio calculations through static models of isolated ion pairs and dynamic simulations of small portions of liquids through twelve, ten, and nine ion pairs for [Ch][For], [Ch][Pro], and [Ch][But], respectively. All the theoretical models indicate that cations andmore » anions are connected by strong hydrogen bonding and form stable ion pairs in the liquid that are reminiscent of the static ab initio ion pairs. Different structural aspects may affect the radial distribution function, like the local structure of ion pairs and the conformation of choline. When small portions of liquids have been simulated by dynamic quantum chemical methods, some key structural features of the X-ray radial distribution function were well reproduced whereas the classical force fields here applied did not entirely reproduce all the observed structural features.« less

Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations.

PubMed

Lei, Hongxing; Wu, Chun; Liu, Haiguang; Duan, Yong

2007-03-20

High-accuracy ab initio folding has remained an elusive objective despite decades of effort. To explore the folding landscape of villin headpiece subdomain HP35, we conducted two sets of replica exchange molecular dynamics for 200 ns each and three sets of conventional microsecond-long molecular dynamics simulations, using AMBER FF03 force field and a generalized-Born solvation model. The protein folded consistently to the native state; the lowest C(alpha)-rmsd from the x-ray structure was 0.46 A, and the C(alpha)- rmsd of the center of the most populated cluster was 1.78 A at 300 K. ab initio simulations have previously not reached this level. The folding landscape of HP35 can be partitioned into the native, denatured, and two intermediate-state regions. The native state is separated from the major folding intermediate state by a small barrier, whereas a large barrier exists between the major folding intermediate and the denatured states. The melting temperature T(m) = 339 K extracted from the heat-capacity profile was in close agreement with the experimentally derived T(m) = 342 K. A comprehensive picture of the kinetics and thermodynamics of HP35 folding emerges when the results from replica exchange and conventional molecular dynamics simulations are combined.

Materials perspective on Casimir and van der Waals interactions

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

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. In such interactions these are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insightsmore » into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. Our review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. Finally, the outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.« less

Materials perspective on Casimir and van der Waals interactions

DOE PAGES

Woods, L. M.; Dalvit, D. A. R.; Tkatchenko, A.; ...

2016-11-02

Interactions induced by electromagnetic fluctuations, such as van der Waals and Casimir forces, are of universal nature present at any length scale between any types of systems. In such interactions these are important not only for the fundamental science of materials behavior, but also for the design and improvement of micro- and nanostructured devices. In the past decade, many new materials have become available, which has stimulated the need for understanding their dispersive interactions. The field of van der Waals and Casimir forces has experienced an impetus in terms of developing novel theoretical and computational methods to provide new insightsmore » into related phenomena. The understanding of such forces has far reaching consequences as it bridges concepts in materials, atomic and molecular physics, condensed-matter physics, high-energy physics, chemistry, and biology. Our review summarizes major breakthroughs and emphasizes the common origin of van der Waals and Casimir interactions. Progress related to novel ab initio modeling approaches and their application in various systems, interactions in materials with Dirac-like spectra, force manipulations through nontrivial boundary conditions, and applications of van der Waals forces in organic and biological matter are examined. Finally, the outlook of the review is to give the scientific community a materials perspective of van der Waals and Casimir phenomena and stimulate the development of experimental techniques and applications.« less

The TensorMol-0.1 model chemistry: a neural network augmented with long-range physics.

PubMed

Yao, Kun; Herr, John E; Toth, David W; Mckintyre, Ryker; Parkhill, John

2018-02-28

Traditional force fields cannot model chemical reactivity, and suffer from low generality without re-fitting. Neural network potentials promise to address these problems, offering energies and forces with near ab initio accuracy at low cost. However a data-driven approach is naturally inefficient for long-range interatomic forces that have simple physical formulas. In this manuscript we construct a hybrid model chemistry consisting of a nearsighted neural network potential with screened long-range electrostatic and van der Waals physics. This trained potential, simply dubbed "TensorMol-0.1", is offered in an open-source Python package capable of many of the simulation types commonly used to study chemistry: geometry optimizations, harmonic spectra, open or periodic molecular dynamics, Monte Carlo, and nudged elastic band calculations. We describe the robustness and speed of the package, demonstrating its millihartree accuracy and scalability to tens-of-thousands of atoms on ordinary laptops. We demonstrate the performance of the model by reproducing vibrational spectra, and simulating the molecular dynamics of a protein. Our comparisons with electronic structure theory and experimental data demonstrate that neural network molecular dynamics is poised to become an important tool for molecular simulation, lowering the resource barrier to simulating chemistry.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit

NASA Astrophysics Data System (ADS)

Lee, Hee-Seung; Tuckerman, Mark E.

2007-04-01

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30ps) preceded a 60ps long production run. The temperature drift during the entire 60ps trajectory was found to be minimal. The diffusion coefficient [0.055Å2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

Dynamical properties of liquid water from ab initio molecular dynamics performed in the complete basis set limit.

PubMed

Lee, Hee-Seung; Tuckerman, Mark E

2007-04-28

Dynamical properties of liquid water were studied using Car-Parrinello [Phys. Rev. Lett. 55, 2471 (1985)] ab initio molecular dynamics (AIMD) simulations within the Kohn-Sham (KS) density functional theory employing the Becke-Lee-Yang-Parr exchange-correlation functional for the electronic structure. The KS orbitals were expanded in a discrete variable representation basis set, wherein the complete basis set limit can be easily reached and which, therefore, provides complete convergence of ionic forces. In order to minimize possible nonergodic behavior of the simulated water system in a constant energy (NVE) ensemble, a long equilibration run (30 ps) preceded a 60 ps long production run. The temperature drift during the entire 60 ps trajectory was found to be minimal. The diffusion coefficient [0.055 A2/ps] obtained from the present work for 32 D2O molecules is a factor of 4 smaller than the most up to date experimental value, but significantly larger than those of other recent AIMD studies. Adjusting the experimental result so as to match the finite-sized system used in the present study brings the comparison between theory and experiment to within a factor of 3. More importantly, the system is not observed to become "glassy" as has been reported in previous AIMD studies. The computed infrared spectrum is in good agreement with experimental data, especially in the low frequency regime where the translational and librational motions of water are manifested. The long simulation length also made it possible to perform detailed studies of hydrogen bond dynamics. The relaxation dynamics of hydrogen bonds observed in the present AIMD simulation is slower than those of popular force fields, such as the TIP4P potential, but comparable to that of the TIP5P potential.

Optical absorption spectra and g factor of MgO: Mn2+explored by ab initio and semi empirical methods

NASA Astrophysics Data System (ADS)

Andreici Eftimie, E.-L.; Avram, C. N.; Brik, M. G.; Avram, N. M.

2018-02-01

In this paper we present a methodology for calculations of the optical absorption spectra, ligand field parameters and g factor for the Mn2+ (3d5) ions doped in MgO host crystal. The proposed technique combines two methods: the ab initio multireference (MR) and the semi empirical ligand field (LF) in the framework of the exchange charge model (ECM) respectively. Both methods of calculations are applied to the [MnO6]10-cluster embedded in an extended point charge field of host matrix ligands based on Gellé-Lepetit procedure. The first step of such investigations was the full optimization of the cubic structure of perfect MgO crystal, followed by the structural optimization of the doped of MgO:Mn2+ system, using periodic density functional theory (DFT). The ab initio MR wave functions approaches, such as complete active space self-consistent field (CASSCF), N-electron valence second order perturbation theory (NEVPT2) and spectroscopy oriented configuration interaction (SORCI), are used for the calculations. The scalar relativistic effects have also been taken into account through the second order Douglas-Kroll-Hess (DKH2) procedure. Ab initio ligand field theory (AILFT) allows to extract all LF parameters and spin-orbit coupling constant from such calculations. In addition, the ECM of ligand field theory (LFT) has been used for modelling theoptical absorption spectra. The perturbation theory (PT) was employed for the g factor calculation in the semi empirical LFT. The results of each of the aforementioned types of calculations are discussed and the comparisons between the results obtained and the experimental results show a reasonable agreement, which justifies this new methodology based on the simultaneous use of both methods. This study establishes fundamental principles for the further modelling of larger embedded cluster models of doped metal oxides.

Simulating contrast inversion in atomic force microscopy imaging with real-space pseudopotentials

NASA Astrophysics Data System (ADS)

Lee, Alex J.; Sakai, Yuki; Chelikowsky, James R.

2017-02-01

Atomic force microscopy (AFM) measurements have reported contrast inversions for systems such as Cu2N and graphene that can hamper image interpretation and characterization. Here, we apply a simulation method based on ab initio real-space pseudopotentials to gain an understanding of the tip-sample interactions that influence the inversion. We find that chemically reactive tips induce an attractive binding force that results in the contrast inversion. We find that the inversion is tip height dependent and not observed when using less reactive CO-functionalized tips.

Weak interactions in Graphane/BN systems under static electric fields—A periodic ab-initio study.

PubMed

Steinkasserer, Lukas Eugen Marsoner; Gaston, Nicola; Paulus, Beate

2015-04-21

Ab-initio calculations via periodic Hartree-Fock (HF) and local second-order Møller-Plesset perturbation theory (LMP2) are used to investigate the adsorption properties of combined Graphane/boron nitride systems and their response to static electric fields. It is shown how the latter can be used to alter both structural as well as electronic properties of these systems.

Prediction of the thermophysical properties of molten salt fast reactor fuel from first-principles

NASA Astrophysics Data System (ADS)

Gheribi, A. E.; Corradini, D.; Dewan, L.; Chartrand, P.; Simon, C.; Madden, P. A.; Salanne, M.

2014-05-01

Molten fluorides are known to show favourable thermophysical properties which make them good candidate coolants for nuclear fission reactors. Here we investigate the special case of mixtures of lithium fluoride and thorium fluoride, which act both as coolant and as fuel in the molten salt fast reactor concept. By using ab initio parameterised polarisable force fields, we show that it is possible to calculate the whole set of properties (density, thermal expansion, heat capacity, viscosity and thermal conductivity) which are necessary for assessing the heat transfer performance of the melt over the whole range of compositions and temperatures. We then deduce from our calculations several figures of merit which are important in helping the optimisation of the design of molten salt fast reactors.

New DMFT capabilities in CASTEP

NASA Astrophysics Data System (ADS)

Plekhanov, Evgeny; Sacksteder, Vincent; Hasnip, Phil; Probert, Matt; Clark, Stewart; Weber, Cedric; Refson, Keith

We present the first implementation of Dynamical Mean-Field Theory in UK's major ab-initio code CASTEP. This implementation: i) is modular; ii) allows great flexibility in choosing local basis set for downfolding/upfolding of self-energy; iii) permits wide choice of impurity solvers (including external solver libraries); and iv) gives the user a possibility to use several self-consistency schemes and calculate total energy and forces. We explain in details the theoretical framework used. We benchmark our implementation on several strongly-correlated insulating systems with d- and f-shells: γ-Ce and Ce2O3 by using Hubbard I and CTHYB-QMC solvers. Our results appear to be in excellent agreement with the reference data published previously in the literature. EPSRC-funded project ''Strong Correlation meets Materials Modelling: DMFT and GW in CASTEP''.

A hybrid method for solutes in complex solvents: Density functional theory combined with empirical force fields

NASA Astrophysics Data System (ADS)

Eichinger, M.; Tavan, P.; Hutter, J.; Parrinello, M.

1999-06-01

We present a hybrid method for molecular dynamics simulations of solutes in complex solvents as represented, for example, by substrates within enzymes. The method combines a quantum mechanical (QM) description of the solute with a molecular mechanics (MM) approach for the solvent. The QM fragment of a simulation system is treated by ab initio density functional theory (DFT) based on plane-wave expansions. Long-range Coulomb interactions within the MM fragment and between the QM and the MM fragment are treated by a computationally efficient fast multipole method. For the description of covalent bonds between the two fragments, we introduce the scaled position link atom method (SPLAM), which removes the shortcomings of related procedures. The various aspects of the hybrid method are scrutinized through test calculations on liquid water, the water dimer, ethane and a small molecule related to the retinal Schiff base. In particular, the extent to which vibrational spectra obtained by DFT for the solute can be spoiled by the lower quality force field of the solvent is checked, including cases in which the two fragments are covalently joined. The results demonstrate that our QM/MM hybrid method is especially well suited for the vibrational analysis of molecules in condensed phase.

Molecular dynamics study of some non-hydrogen-bonding base pair DNA strands

NASA Astrophysics Data System (ADS)

Tiwari, Rakesh K.; Ojha, Rajendra P.; Tiwari, Gargi; Pandey, Vishnudatt; Mall, Vijaysree

2018-05-01

In order to elucidate the structural activity of hydrophobic modified DNA, the DMMO2-D5SICS, base pair is introduced as a constituent in different set of 12-mer and 14-mer DNA sequences for the molecular dynamics (MD) simulation in explicit water solvent. AMBER 14 force field was employed for each set of duplex during the 200ns production-dynamics simulation in orthogonal-box-water solvent by the Particle-Mesh-Ewald (PME) method in infinite periodic boundary conditions (PBC) to determine conformational parameters of the complex. The force-field parameters of modified base-pair were calculated by Gaussian-code using Hartree-Fock /ab-initio methodology. RMSD Results reveal that the conformation of the duplex is sequence dependent and the binding energy of the complex depends on the position of the modified base-pair in the nucleic acid strand. We found that non-bonding energy had a significant contribution to stabilising such type of duplex in comparison to electrostatic energy. The distortion produced within strands by such type of base-pair was local and destabilised the duplex integrity near to substitution, moreover the binding energy of duplex depends on the position of substitution of hydrophobic base-pair and the DNA sequence and strongly supports the corresponding experimental study.

Designing Free Energy Surfaces That Match Experimental Data with Metadynamics

DOE PAGES

White, Andrew D.; Dama, James F.; Voth, Gregory A.

2015-04-30

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. Previously we introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. We also introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psimore » angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. Finally, the example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.« less

Quantum mechanical force fields for condensed phase molecular simulations

NASA Astrophysics Data System (ADS)

Giese, Timothy J.; York, Darrin M.

2017-09-01

Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.

Analysis of the Free-Energy Surface of Proteins from Reversible Folding Simulations

PubMed Central

Allen, Lucy R.; Krivov, Sergei V.; Paci, Emanuele

2009-01-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical λ-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins. PMID:19593364

Designing free energy surfaces that match experimental data with metadynamics.

PubMed

White, Andrew D; Dama, James F; Voth, Gregory A

2015-06-09

Creating models that are consistent with experimental data is essential in molecular modeling. This is often done by iteratively tuning the molecular force field of a simulation to match experimental data. An alternative method is to bias a simulation, leading to a hybrid model composed of the original force field and biasing terms. We previously introduced such a method called experiment directed simulation (EDS). EDS minimally biases simulations to match average values. In this work, we introduce a new method called experiment directed metadynamics (EDM) that creates minimal biases for matching entire free energy surfaces such as radial distribution functions and phi/psi angle free energies. It is also possible with EDM to create a tunable mixture of the experimental data and free energy of the unbiased ensemble with explicit ratios. EDM can be proven to be convergent, and we also present proof, via a maximum entropy argument, that the final bias is minimal and unique. Examples of its use are given in the construction of ensembles that follow a desired free energy. The example systems studied include a Lennard-Jones fluid made to match a radial distribution function, an atomistic model augmented with bioinformatics data, and a three-component electrolyte solution where ab initio simulation data is used to improve a classical empirical model.

Analysis of the free-energy surface of proteins from reversible folding simulations.

PubMed

Allen, Lucy R; Krivov, Sergei V; Paci, Emanuele

2009-07-01

Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

Realistic Modeling of Multi-Scale MHD Dynamics of the Solar Atmosphere

NASA Technical Reports Server (NTRS)

Kitiashvili, Irina; Mansour, Nagi N.; Wray, Alan; Couvidat, Sebastian; Yoon, Seokkwan; Kosovichev, Alexander

2014-01-01

Realistic 3D radiative MHD simulations open new perspectives for understanding the turbulent dynamics of the solar surface, its coupling to the atmosphere, and the physical mechanisms of generation and transport of non-thermal energy. Traditionally, plasma eruptions and wave phenomena in the solar atmosphere are modeled by prescribing artificial driving mechanisms using magnetic or gas pressure forces that might arise from magnetic field emergence or reconnection instabilities. In contrast, our 'ab initio' simulations provide a realistic description of solar dynamics naturally driven by solar energy flow. By simulating the upper convection zone and the solar atmosphere, we can investigate in detail the physical processes of turbulent magnetoconvection, generation and amplification of magnetic fields, excitation of MHD waves, and plasma eruptions. We present recent simulation results of the multi-scale dynamics of quiet-Sun regions, and energetic effects in the atmosphere and compare with observations. For the comparisons we calculate synthetic spectro-polarimetric data to model observational data of SDO, Hinode, and New Solar Telescope.

Density functional theory and molecular dynamics study of the uranyl ion (UO₂)²⁺.

PubMed

Rodríguez-Jeangros, Nicolás; Seminario, Jorge M

2014-03-01

The detection of uranium is very important, especially in water and, more importantly, in the form of uranyl ion (UO₂)²⁺, which is one of its most abundant moieties. Here, we report analyses and simulations of uranyl in water using ab initio modified force fields for water with improved parameters and charges of uranyl. We use a TIP4P model, which allows us to obtain accurate water properties such as the boiling point and the second and third shells of water molecules in the radial distribution function thanks to a fictitious charge that corrects the 3-point models by reproducing the exact dipole moment of the water molecule. We also introduced non-bonded interaction parameters for the water-uranyl intermolecular force field. Special care was taken in testing the effect of a range of uranyl charges on the structure of uranyl-water complexes. Atomic charges of the solvated ion in water were obtained using density functional theory (DFT) calculations taking into account the presence of nitrate ions in the solution, forming a neutral ensemble. DFT-based force fields were calculated in such a way that water properties, such as the boiling point or the pair distribution function stand. Finally, molecular dynamics simulations of a water box containing uranyl cations and nitrate anions are performed at room temperature. The three peaks in the oxygen-oxygen radial distribution function for water were found to be kept in the presence of uranyl thanks to the improvement of interaction parameters and charges. Also, we found three shells of water molecules surrounding the uranyl ion instead of two as was previously thought.

Ab Initio Classical Dynamics Simulations of CO_2 Line-Mixing Effects in Infrared Bands

NASA Astrophysics Data System (ADS)

Lamouroux, Julien; Hartmann, Jean-Michel; Tran, Ha; Snels, Marcel; Stefani, Stefania; Piccioni, Giuseppe

2013-06-01

Ab initio calculations of line-mixing effects in CO_2 infrared bands are presented and compared with experiments. The predictions were carried using requantized Classical Dynamics Molecular Simulations (rCDMS) based on an approach previously developed and successfully tested for CO_2 isolated line shapes. Using classical dynamics equations, the force and torque applied to each molecule by the surrounding molecules (described by an ab initio intermolecular potential) are computed at each time step. This enables, using a requantization procedure, to predict dipole and isotropic polarizability auto-correlation functions whose Fourier-Laplace transforms yield the spectra. The quality of the rCDMS calculations is demonstrated by comparisons with measured spectra in the spectral regions of the 3ν_3 and 2ν_1+2ν_2+ν_3 Infrared bands. J.-M. Hartmann, H. Tran, N. H. Ngo, et al., Phys. Rev. Lett. A {87} (2013), 013403. H. Tran, C. Boulet, M. Snels, S. Stefani, J. Quant. Spectrosc. Radiat. Transfer {112} (2011), 925-936.

Simulation of charge transfer and orbital rehybridization in molecular and condensed matter systems

NASA Astrophysics Data System (ADS)

Nistor, Razvan A.

The mixing and shifting of electronic orbitals in molecules, or between atoms in bulk systems, is crucially important to the overall structure and physical properties of materials. Understanding and accurately modeling these orbital interactions is of both scientific and industrial relevance. Electronic orbitals can be perturbed in several ways. Doping, adding or removing electrons from systems, can change the bond-order and the physical properties of certain materials. Orbital rehybridization, driven by either thermal or pressure excitation, alters the short-range structure of materials and changes their long-range transport properties. Macroscopically, during bond formation, the shifting of electronic orbitals can be interpreted as a charge transfer phenomenon, as electron density may pile up around, and hence, alter the effective charge of, a given atom in the changing chemical environment. Several levels of theory exist to elucidate the mechanisms behind these orbital interactions. Electronic structure calculations solve the time-independent Schrodinger equation to high chemical accuracy, but are computationally expensive and limited to small system sizes and simulation times. Less fundamental atomistic calculations use simpler parameterized functional expressions called force-fields to model atomic interactions. Atomistic simulations can describe systems and time-scales larger and longer than electronic-structure methods, but at the cost of chemical accuracy. In this thesis, both first-principles and phenomenological methods are addressed in the study of several encompassing problems dealing with charge transfer and orbital rehybridization. Firstly, a new charge-equilibration method is developed that improves upon existing models to allow next-generation force-fields to describe the electrostatics of changing chemical environments. Secondly, electronic structure calculations are used to investigate the doping dependent energy landscapes of several high-temperature superconducting materials in order to parameterize the apparently large nonlinear electron-phonon coupling. Thirdly, ab initio simulations are used to investigate the role of pressure-driven structural re-organization in the crystalline-to-amorphous (or, metallic-to-insulating) transition of a common binary phase-change material composed of Ge and Sb. Practical applications of each topic will be discussed. Keywords. Charge-equilibration methods, molecular dynamics, electronic structure calculations, ab initio simulations, high-temperature superconductors, phase-change materials.

Anharmonic Rovibrational Calculations of Singlet Cyclic C4 Using a New Ab Initio Potential and a Quartic Force

NASA Technical Reports Server (NTRS)

Wang, Xiaohong; Huang, Xinchuan; Bowman, Joel M.; Lee, Timothy J.

2013-01-01

We report a CCSD(T)/cc-pCV5Z quartic force field (QFF) and a semi-global CCSD(T)-F12b/aug-cc-pVTZ potential energy surface (PES) for singlet, cyclic C4. Vibrational fundamentals, combinations and overtones are obtained using vibrational second-order perturbation theory (VPT2) and the vibrational configurationinteraction (VCI) approach. Agreement is within 10 cm(exp -1) between the VCI calculated fundamentals on the QFF and PES using the MULTIMODE (MM) program, and VPT2 and VCI results agree for the fundamentals. The agreement between VPT2- QFF and MM-QFF results is also good for the C4 combinations and overtones. The J = 1 and J = 2 rovibrational energies are reported from both VCI (MM) on the PES and VPT2 on the QFF calculations. The spectroscopic constants of (12)C4 and two C(sub 2v)-symmetry, single (13)C-substituted isotopologues are presented, which may help identification of cyclic C4 in future experimental analyses or astronomical observations.

Ab initio investigation of the first hydration shell of protonated glycine

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

Wei, Zhichao; Chen, Dong, E-mail: dongchen@henu.edu.cn, E-mail: boliu@henu.edu.cn; Zhao, Huiling

2014-02-28

The first hydration shell of the protonated glycine is built up using Monte Carlo multiple minimum conformational search analysis with the MMFFs force field. The potential energy surfaces of the protonated glycine and its hydration complexes with up to eight water molecules have been scanned and the energy-minimized structures are predicted using the ab initio calculations. First, three favorable structures of protonated glycine were determined, and the micro-hydration processes showed that water can significantly stabilize the unstable conformers, and then their first hydration shells were established. Finally, we found that seven water molecules are required to fully hydrate the firstmore » hydration shell for the most stable conformer of protonated glycine. In order to analyse the hydration process, the dominant hydration sites located around the ammonium and carboxyl groups are studied carefully and systemically. The results indicate that, water molecules hydrate the protonated glycine in an alternative dynamic hydration process which is driven by the competition between different hydration sites. The first three water molecules are strongly attached by the ammonium group, while only the fourth water molecule is attached by the carboxyl group in the ultimate first hydration shell of the protonated glycine. In addition, the first hydration shell model has predicted most identical structures and a reasonable accord in hydration energy and vibrational frequencies of the most stable conformer with the conductor-like polarizable continuum model.« less

Ab initio calculation of the electronic absorption spectrum of liquid water

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

Martiniano, Hugo F. M. C.; Galamba, Nuno; Cabral, Benedito J. Costa, E-mail: ben@cii.fc.ul.pt

2014-04-28

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are inmore » good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.« less

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride.

PubMed

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-14

To understand the initial hydration processes of CaCl 2 , we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl 2 (H 2 O) n - (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl-Ca ion pair is investigated in CaCl 2 (H 2 O) n - anions, where the first Ca-Cl ionic bond required 4 water molecules, and both Ca-Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl 2 (H 2 O) n clusters, breaking of the first Ca-Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl 2 (H 2 O) n requires fewer water molecules than those for MgCl 2 (H 2 O) n . Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Molecular dynamics simulation, ab initio calculation, and size-selected anion photoelectron spectroscopy study of initial hydration processes of calcium chloride

NASA Astrophysics Data System (ADS)

He, Zhili; Feng, Gang; Yang, Bin; Yang, Lijiang; Liu, Cheng-Wen; Xu, Hong-Guang; Xu, Xi-Ling; Zheng, Wei-Jun; Gao, Yi Qin

2018-06-01

To understand the initial hydration processes of CaCl2, we performed molecular simulations employing the force field based on the theory of electronic continuum correction with rescaling. Integrated tempering sampling molecular dynamics were combined with ab initio calculations to overcome the sampling challenge in cluster structure search and refinement. The calculated vertical detachment energies of CaCl2(H2O)n- (n = 0-8) were compared with the values obtained from photoelectron spectra, and consistency was found between the experiment and computation. Separation of the Cl—Ca ion pair is investigated in CaCl2(H2O)n- anions, where the first Ca—Cl ionic bond required 4 water molecules, and both Ca—Cl bonds are broken when the number of water molecules is larger than 7. For neutral CaCl2(H2O)n clusters, breaking of the first Ca—Cl bond starts at n = 5, and 8 water molecules are not enough to separate the two ion pairs. Comparing with the observations on magnesium chloride, it shows that separating one ion pair in CaCl2(H2O)n requires fewer water molecules than those for MgCl2(H2O)n. Coincidentally, the solubility of calcium chloride is higher than that of magnesium chloride in bulk solutions.

Role of Quantum Vibrations on the Structural, Electronic, and Optical Properties of 9-Methylguanine.

PubMed

Law, Yu Kay; Hassanali, Ali A

2015-11-05

In this work, we report theoretical predictions of the UV-absorption spectra of 9-methylguanine using time dependent density functional theory (TDDFT). Molecular dynamics simulations of the hydrated DNA base are peformed using an empirical force field, Born-Oppenheimer ab initio molecular dynamics (AIMD), and finally path-integral AIMD to understand the role of the underlying electronic potential, solvation, and nuclear quantum vibrations on the absorption spectra. It is shown that the conformational distributions, including hydrogen bonding interactions, are perturbed by the inclusion of nuclear quantum effects, leading to significant changes in the total charge and dipole fluctuations of the DNA base. The calculated absorption spectra using the different sampling protocols shows that the inclusion of nuclear quantum effects causes a significant broadening and red shift of the spectra bringing it into closer agreement with experiments.

How does the trans-cis photoisomerization of azobenzene take place in organic solvents?

PubMed

Tiberio, Giustiniano; Muccioli, Luca; Berardi, Roberto; Zannoni, Claudio

2010-04-06

The trans-cis photoisomerization of azobenzene-containing materials is key to a number of photomechanical applications, but the actual conversion mechanism in condensed phases is still largely unknown. Herein, we study the n, pi* isomerization in a vacuum and in various solvents via a modified molecular dynamics simulation adopting an ab initio torsion-inversion force field in the ground and excited states, while allowing for electronic transitions and a stochastic decay to the fundamental state. We determine the trans-cis photoisomerization quantum yield and decay times in various solvents (n-hexane, anisole, toluene, ethanol, and ethylene glycol), and obtain results comparable with experimental ones where available. A profound difference between the isomerization mechanism in vacuum and in solution is found, with the often neglected mixed torsional-inversion pathway being the most important in solvents.

FT-IR, FT-Raman, NMR studies and ab initio-HF, DFT-B3LYP vibrational analysis of 4-chloro-2-fluoroaniline

NASA Astrophysics Data System (ADS)

Arivazhagan, M.; Anitha Rexalin, D.

2012-10-01

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 4-chloro-2-fluoroaniline (CFA) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of ab initio and density functional theory (DFT) methods. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The 1H and 13C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the Gauge including atomic orbital (GIAO) method. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of CFA are calculated using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) methods on the finite-field approach. The calculated results also show that the CFA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The result confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The HOMO-LUMO energies UV-vis spectral analysis and MEP are performed by B3LYP/6-311++G(d,p) approach. A detailed interpretation of the infrared and Raman spectra of CFA is also reported based on total energy distribution (TED). The difference between the observed and scaled wave number values of the most of the fundamentals is very small.

FT-IR, FT-Raman, NMR studies and ab initio-HF, DFT-B3LYP vibrational analysis of 4-chloro-2-fluoroaniline.

PubMed

Arivazhagan, M; Anitha Rexalin, D

2012-10-01

The Fourier transform infrared (FT-IR) and Fourier transform Raman (FT-Raman) spectra of 4-chloro-2-fluoroaniline (CFA) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of ab initio and density functional theory (DFT) methods. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule are calculated by the Gauge including atomic orbital (GIAO) method. The first order hyperpolarizability (β(0)) of this novel molecular system and related properties (β, α(0) and Δα) of CFA are calculated using B3LYP/6-311++G(d,p) and HF/6-311++G(d,p) methods on the finite-field approach. The calculated results also show that the CFA molecule might have microscopic nonlinear optical (NLO) behavior with non-zero values. Stability of the molecule arising from hyper conjugative interactions, charge delocalization has been analyzed using natural bond orbital (NBO) analysis. The result confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The HOMO-LUMO energies UV-vis spectral analysis and MEP are performed by B3LYP/6-311++G(d,p) approach. A detailed interpretation of the infrared and Raman spectra of CFA is also reported based on total energy distribution (TED). The difference between the observed and scaled wave number values of the most of the fundamentals is very small. Copyright © 2012 Elsevier B.V. All rights reserved.

Magnetic Excitations in Polyoxotungstate-Supported Lanthanoid Single-Molecule Magnets: An Inelastic Neutron Scattering and ab Initio Study.

PubMed

Vonci, Michele; Giansiracusa, Marcus J; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2017-01-03

Inelastic neutron scattering (INS) has been used to investigate the crystal field (CF) magnetic excitations of the analogs of the most representative lanthanoid-polyoxometalate single-molecule magnet family: Na 9 [Ln(W 5 O 18 ) 2 ] (Ln = Nd, Tb, Ho, Er). Ab initio complete active space self-consistent field/restricted active space state interaction calculations, extended also to the Dy analog, show good agreement with the experimentally determined low-lying CF levels, with accuracy better in most cases than that reported for approaches based only on simultaneous fitting to CF models of magnetic or spectroscopic data for isostructural Ln families. In this work we demonstrate the power of a combined spectroscopic and computational approach. Inelastic neutron scattering has provided direct access to CF levels, which together with the magnetometry data, were employed to benchmark the ab initio results. The ab initio determined wave functions corresponding to the CF levels were in turn employed to assign the INS transitions allowed by selection rules and interpret the observed relative intensities of the INS peaks. Ultimately, we have been able to establish the relationship between the wave function composition of the CF split Ln III ground multiplets and the experimentally measured magnetic and spectroscopic properties for the various analogs of the Na 9 [Ln(W 5 O 18 ) 2 ] family.

Electron–Positron Pair Flow and Current Composition in the Pulsar Magnetosphere

NASA Astrophysics Data System (ADS)

Brambilla, Gabriele; Kalapotharakos, Constantinos; Timokhin, Andrey N.; Harding, Alice K.; Kazanas, Demosthenes

2018-05-01

We perform ab initio particle-in-cell (PIC) simulations of a pulsar magnetosphere with electron–positron plasma produced only in the regions close to the neutron star surface. We study how the magnetosphere transitions from the vacuum to a nearly force-free configuration. We compare the resulting force-free-like configuration with those obtained in a PIC simulation where particles are injected everywhere as well as with macroscopic force-free simulations. We find that, although both PIC solutions have similar structure of electromagnetic fields and current density distributions, they have different particle density distributions. In fact, in the injection from the surface solution, electrons and positrons counterstream only along parts of the return current regions and most of the particles leave the magnetosphere without returning to the star. We also find that pair production in the outer magnetosphere is not critical for filling the whole magnetosphere with plasma. We study how the current density distribution supporting the global electromagnetic configuration is formed by analyzing particle trajectories. We find that electrons precipitate to the return current layer inside the light cylinder and positrons precipitate to the current sheet outside the light cylinder by crossing magnetic field lines, contributing to the charge density distribution required by the global electrodynamics. Moreover, there is a population of electrons trapped in the region close to the Y-point. On the other hand, the most energetic positrons are accelerated close to the Y-point. These processes can have observational signatures that, with further modeling effort, would help to distinguish this particular magnetosphere configuration from others.

Communication: XFAIMS—eXternal Field Ab Initio Multiple Spawning for electron-nuclear dynamics triggered by short laser pulses

DOE PAGES

Mignolet, Benoit; Curchod, Basile F. E.; Martinez, Todd J.

2016-11-17

Attoscience is an emerging field where attosecond pulses or few cycle IR pulses are used to pump and probe the correlated electron-nuclear motion of molecules. We present the trajectory-guided eXternal Field Ab Initio Multiple Spawning (XFAIMS) method that models such experiments “on-the-fly,” from laser pulse excitation to fragmentation or nonadiabatic relaxation to the ground electronic state. For the photoexcitation of the LiH molecule, we show that XFAIMS gives results in close agreement with numerically exact quantum dynamics simulations, both for atto- and femtosecond laser pulses. As a result, we then show the ability of XFAIMS to model the dynamics inmore » polyatomic molecules by studying the effect of nuclear motion on the photoexcitation of a sulfine (H 2CSO).« less

Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials.

PubMed

Olsen, Jógvan Magnus Haugaard; List, Nanna Holmgaard; Kristensen, Kasper; Kongsted, Jacob

2015-04-14

Quantum-mechanical embedding methods have in recent years gained significant interest and may now be applied to predict a wide range of molecular properties calculated at different levels of theory. To reach a high level of accuracy in embedding methods, both the electronic structure model of the active region and the embedding potential need to be of sufficiently high quality. In fact, failures in quantum mechanics/molecular mechanics (QM/MM)-based embedding methods have often been associated with the QM/MM methodology itself; however, in many cases the reason for such failures is due to the use of an inaccurate embedding potential. In this paper, we investigate in detail the quality of the electronic component of embedding potentials designed for calculations on protein biostructures. We show that very accurate explicitly polarizable embedding potentials may be efficiently designed using fragmentation strategies combined with single-fragment ab initio calculations. In fact, due to the self-interaction error in Kohn-Sham density functional theory (KS-DFT), use of large full-structure quantum-mechanical calculations based on conventional (hybrid) functionals leads to less accurate embedding potentials than fragment-based approaches. We also find that standard protein force fields yield poor embedding potentials, and it is therefore not advisable to use such force fields in general QM/MM-type calculations of molecular properties other than energies and structures.

Relativistic force field: parametric computations of proton-proton coupling constants in (1)H NMR spectra.

PubMed

Kutateladze, Andrei G; Mukhina, Olga A

2014-09-05

Spin-spin coupling constants in (1)H NMR carry a wealth of structural information and offer a powerful tool for deciphering molecular structures. However, accurate ab initio or DFT calculations of spin-spin coupling constants have been very challenging and expensive. Scaling of (easy) Fermi contacts, fc, especially in the context of recent findings by Bally and Rablen (Bally, T.; Rablen, P. R. J. Org. Chem. 2011, 76, 4818), offers a framework for achieving practical evaluation of spin-spin coupling constants. We report a faster and more precise parametrization approach utilizing a new basis set for hydrogen atoms optimized in conjunction with (i) inexpensive B3LYP/6-31G(d) molecular geometries, (ii) inexpensive 4-31G basis set for carbon atoms in fc calculations, and (iii) individual parametrization for different atom types/hybridizations, not unlike a force field in molecular mechanics, but designed for the fc's. With the training set of 608 experimental constants we achieved rmsd <0.19 Hz. The methodology performs very well as we illustrate with a set of complex organic natural products, including strychnine (rmsd 0.19 Hz), morphine (rmsd 0.24 Hz), etc. This precision is achieved with much shorter computational times: accurate spin-spin coupling constants for the two conformers of strychnine were computed in parallel on two 16-core nodes of a Linux cluster within 10 min.

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface

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

Lisal, Martin; Department of Physics, Faculty of Science, J. E. Purkinje University, 400 96 Usti n. Lab.; Izak, Pavel

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf{sub 2}N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 {mu}mol/m{sup 2} at 300 K. For [bmim][Tf{sub 2}N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are {+-}0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and itsmore » value decreases with increase of the n-hexane surface density. The [bmim][Tf{sub 2}N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.« less

Molecular dynamics simulations of n-hexane at 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide interface.

PubMed

Lísal, Martin; Izák, Pavel

2013-07-07

Molecular dynamics simulations of n-hexane adsorbed onto the interface of 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl) imide ([bmim][Tf2N]) are performed at three n-hexane surface densities, ranged from 0.7 to 2.3 μmol/m(2) at 300 K. For [bmim][Tf2N] room-temperature ionic liquid, we use a non-polarizable all-atom force field with the partial atomic charges based on ab initio calculations for the isolated ion pair. The net charges of the ions are ±0.89e, which mimics the anion to cation charge transfer and polarization effects. The OPLS-AA force field is employed for modeling of n-hexane. The surface tension is computed using the mechanical route and its value decreases with increase of the n-hexane surface density. The [bmim][Tf2N]/n-hexane interface is analyzed using the intrinsic method, and the structural and dynamic properties of the interfacial, sub-interfacial, and central layers are computed. We determine the surface roughness, global and intrinsic density profiles, and orientation ordering of the molecules to describe the structure of the interface. We further compute the survival probability, normal and lateral self-diffusion coefficients, and re-orientation correlation functions to elucidate the effects of n-hexane on dynamics of the cations and anions in the layers.

Atomistic Simulation of Initiation in Hexanitrostilbene

NASA Astrophysics Data System (ADS)

Shan, Tzu-Ray; Wixom, Ryan; Yarrington, Cole; Thompson, Aidan

2015-06-01

We report on the effect of cylindrical voids on hot spot formation, growth and chemical reaction initiation in hexanitrostilbene (HNS) crystals subjected to shock. Large-scale, reactive molecular dynamics simulations are performed using the reactive force field (ReaxFF) as implemented in the LAMMPS software. The ReaxFF force field description for HNS has been validated previously by comparing the isothermal equation of state to available diamond anvil cell (DAC) measurements and density function theory (DFT) calculations and by comparing the primary dissociation pathway to ab initio calculations. Micron-scale molecular dynamics simulations of a supported shockwave propagating through the HNS crystal along the [010] orientation are performed with an impact velocity (or particle velocity) of 1.25 km/s, resulting in shockwave propagation at 4.0 km/s in the bulk material and a bulk shock pressure of ~ 11GPa. The effect of cylindrical void sizes varying from 0.02 to 0.1 μm on hot spot formation and growth rate has been studied. Interaction between multiple voids in the HNS crystal and its effect on hot spot formation will also be addressed. Results from the micron-scale atomistic simulations are compared with hydrodynamics simulations. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE National Nuclear Security Administration under Contract DE-AC04-94AL85000.

DFT energy optimization of a large carbohydrate: cyclomaltohexaicosaose (CA-26)

USDA-ARS?s Scientific Manuscript database

CA-26 is the largest cyclodextrin (546 atoms) for which refined X-ray structural data is available. Because of its size, 26 D-glucose residues, it is beyond the scope of study of most ab initio or density functional methods, and to date has only been computationally examined using empirical force fi...

Development of glue type potentials for the Al-Pb system: computer simulation of Pb/Al interfaces and phase diagram calculation

NASA Astrophysics Data System (ADS)

Landa, Alex; Wynblatt, Paul; Siegel, Donald; Adams, Jim; Johnson, Erik; Dahmen, Uli

2000-03-01

Empirical many-body potentials have been constructed for the Al-Pb system using the ``force matching" method. The potentials have been fitted to a set of the ground state physical quantities calculated within ab initio approach and a massive quantum mechanical forces database for samples of bulk Al-Pb liquid alloys generated using ab initio molecular dynamics program VASP. Monte Carlo simulations using these potentials have been employed to compute an Al-Pb phase diagram, which is in fair agreement with experimental data, and to model the structure of (111) and (100) Pb/Al interfaces. The calculated free energy ratios for the Pb/Al 100 and 111 interfaces are in good agreement with recent high-resolution transmission electron microscopy measurements. The constructed glue potentials correctly reflects the large change in anisotropy which is observed experimentally between isolated Pb crystals and Pb crystals embedded in Al. Support by the DOE under grants DE-FG02-99ER45773 and DE-AC03-76SF00098, the NSF under grant DMR9619353 and the Danish Natural Sciences Research Council.

A tungsten-rhenium interatomic potential for point defect studies

DOE PAGES

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-28

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

A tungsten-rhenium interatomic potential for point defect studies

NASA Astrophysics Data System (ADS)

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

2018-05-01

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures in the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancies and self-interstitial defects sufficiently accurately and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).

A tungsten-rhenium interatomic potential for point defect studies

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

Setyawan, Wahyu; Gao, Ning; Kurtz, Richard J.

A tungsten-rhenium (W-Re) classical interatomic potential is developed within the embedded atom method (EAM) interaction framework. A force-matching method is employed to fit the potential to ab initio forces, energies, and stresses. Simulated annealing is combined with the conjugate gradient technique to search for an optimum potential from over 1000 initial trial sets. The potential is designed for studying point defects in W-Re systems. It gives good predictions of the formation energies of Re defects in W and the binding energies of W self-interstitial clusters with Re. The potential is further evaluated for describing the formation energy of structures inmore » the σ and χ intermetallic phases. The predicted convex-hulls of formation energy are in excellent agreement with ab initio data. In pure Re, the potential can reproduce the formation energies of vacancy and self-interstitial defects sufficiently accurately, and gives the correct ground state self-interstitial configuration. Furthermore, by including liquid structures in the fit, the potential yields a Re melting temperature (3130 K) that is close to the experimental value (3459 K).« less

Ab-initio adsorption study of chitosan on functionalized graphene: critical role of van der Waals interactions.

PubMed

Rahman, R; Mazumdar, D

2012-03-01

We investigate the adsorption process of an organic biomolecule (chitosan) on epoxy-functionalized graphene using ab-initio density functional methods incorporating van-der-waals (vdW) interactions. The role of London dispersion force on the cohesive energy and conformal preference of the molecule is quantitatively elucidated. Functionalizing graphene with epoxy leads to weak hydrogen-bond interactions with chitosan. Binding energy values increase by over an order of magnitude after including vdW corrections, implying that dispersive interactions dominate the physisorption process. Conformal study show binding upto 30 kcal/mol when the molecule is oriented with the hydroxyl group approaching the functionalized graphene. Our study advances the promise of functionalized graphene for a variety of applications.

Determination of the electronic energy levels of colloidal nanocrystals using field-effect transistors and Ab-initio calculations.

PubMed

Bisri, Satria Zulkarnaen; Degoli, Elena; Spallanzani, Nicola; Krishnan, Gopi; Kooi, Bart Jan; Ghica, Corneliu; Yarema, Maksym; Heiss, Wolfgang; Pulci, Olivia; Ossicini, Stefano; Loi, Maria Antonietta

2014-08-27

Colloidal nanocrystals electronic energy levels are determined by strong size-dependent quantum confinement. Understanding the configuration of the energy levels of nanocrystal superlattices is vital in order to use them in heterostructures with other materials. A powerful method is reported to determine the energy levels of PbS nanocrystal assemblies by combining the utilization of electric-double-layer-gated transistors and advanced ab-initio theory. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The study of molecular spectroscopy by ab initio methods

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1991-01-01

This review illustrates the potential of theory for solving spectroscopic problems. The accuracy of approximate techniques for including electron correlation have been calibrated by comparison with full configuration-interaction calculations. Examples of the application of ab initio calculations to vibrational, rotational, and electronic spectroscopy are given. It is shown that the state-averaged, complete active space self-consistent field, multireference configuration-interaction procedure provides a good approach for treating several electronic states accurately in a common molecular orbital basis.

Ab Initio Protein Structure Prediction Using Chunk-TASSER

PubMed Central

Zhou, Hongyi; Skolnick, Jeffrey

2007-01-01

We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models are built and refined by the TASSER methodology, which searches conformational space via parallel hyperbolic Monte Carlo. We employ an optimized reduced force field that includes knowledge-based statistical potentials and restraints derived from the chunks as well as threading templates. The method is tested on a dataset of 425 hard target proteins ≤250 amino acids in length. The average TM-scores of the best of top five models per target are 0.266, 0.336, and 0.362 by the threading algorithm SP3, original TASSER and chunk-TASSER, respectively. For a subset of 80 proteins with predicted α-helix content ≥50%, these averages are 0.284, 0.356, and 0.403, respectively. The percentages of proteins with the best of top five models having TM-score ≥0.4 (a statistically significant threshold for structural similarity) are 3.76, 20.94, and 28.94% by SP3, TASSER, and chunk-TASSER, respectively, overall, while for the subset of 80 predominantly helical proteins, these percentages are 2.50, 23.75, and 41.25%. Thus, chunk-TASSER shows a significant improvement over TASSER for modeling hard targets where no good template can be identified. We also tested chunk-TASSER on 21 medium/hard targets <200 amino-acids-long from CASP7. Chunk-TASSER is ∼11% (10%) better than TASSER for the total TM-score of the first (best of top five) models. Chunk-TASSER is fully automated and can be used in proteome scale protein structure prediction. PMID:17496016

Accelerating ab initio path integral molecular dynamics with multilevel sampling of potential surface

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

Geng, Hua Y., E-mail: huay.geng@gmail.com; Department of Chemistry and Chemical Biology, Cornell University, Baker Laboratory, Ithaca, NY 14853

A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics (AI-PIMD) simulation, without compromising the overall accuracy. To validate the method, the internal energy and free energy of an Einstein crystal are calculated and compared with the analytical solutions. As a preliminary application, we assess the performance of the method in a realistic model—the FCC phase of dense atomic hydrogen, in which the calculated result shows that the acceleration rate ismore » about 3 to 4-fold for a two-level implementation, and can be increased up to 10 times if extrapolation is used. With only 16 beads used for the ab initio potential sampling, this method gives a well converged internal energy. The residual error in pressure is just about 3 GPa, whereas it is about 20 GPa for a plain AI-PIMD calculation with the same number of beads. The vibrational free energy of the FCC phase of dense hydrogen at 300 K is also calculated with an AI-PIMD thermodynamic integration method, which gives a result of about 0.51 eV/proton at a density of r{sub s}=0.912.« less

Analysis of a Li-Ion Nanobattery with Graphite Anode Using Molecular Dynamics Simulations

DOE PAGES

Ponce, Victor; Galvez-Aranda, Diego E.; Seminario, Jorge M.

2017-05-19

In this work, molecular dynamics simulations were performed of the initial charging of a Li-ion nanobattery with a graphite anode and lithium hexaflourphosphate (LiPF 6) salt dissolved in ethylene carbonate (CO 3C 2H 4) solvent as the electrolyte solution. The charging was achieved through the application of external electric fields simulating voltage sources. A variety of force fields were combined to simulate the materials of the nanobattery, including the solid electrolyte interphase, metal collectors, and insulator cover. Some of the force field parameters were estimated using ab initio methods and others were taken from the literature. We studied the behaviormore » of Li-ions traveling from cathode to anode through electrolyte solutions of concentrations 1.15 and 3.36 M. Time-dependent variables such as energy, temperature, volume, polarization, and mean square displacement are reported; a few of these variables, as well as others such as current, resistance, current density, conductivity, and resistivity are reported as a function of the external field and charging voltage. A solid electrolyte interphase (SEI) layer was also added to the model to study the mechanism behind the diffusion of the Li-ions through the SEI. As the battery is charged, the depletion of Li atoms in the cathode and their accumulation in the anode follow a linear increase of the polarizability in the solvent, until reaching a saturation point after which the charging of the battery stops, i.e., the energy provided by the external source decays to very low levels. Lastly, the nanobattery model containing the most common materials of a commercial lithium-ion battery is very useful to determine atomistic information that is difficult or too expensive to obtain experimentally; available data shows consistency with our results.« less

Analytic Interatomic Forces in the Random Phase Approximation

NASA Astrophysics Data System (ADS)

Ramberger, Benjamin; Schäfer, Tobias; Kresse, Georg

2017-03-01

We discuss that in the random phase approximation (RPA) the first derivative of the energy with respect to the Green's function is the self-energy in the G W approximation. This relationship allows us to derive compact equations for the RPA interatomic forces. We also show that position dependent overlap operators are elegantly incorporated in the present framework. The RPA force equations have been implemented in the projector augmented wave formalism, and we present illustrative applications, including ab initio molecular dynamics simulations, the calculation of phonon dispersion relations for diamond and graphite, as well as structural relaxations for water on boron nitride. The present derivation establishes a concise framework for forces within perturbative approaches and is also applicable to more involved approximations for the correlation energy.

Relaxation of structural parameters and potential coefficients of nonrigid molecules. General symmetry properties and application to ab initio study of 1,2-difluoroethane

NASA Astrophysics Data System (ADS)

Ha, T.-K.; Günthard, H. H.

1989-07-01

Structural parameters like bond length, bond angles, etc. and harmonic and anharmonic potential coefficients of molecules with internal rotation, inversion or puckering modes are generally assumed to vary with the large amplitude internal coordinates in a concerted manner (relaxation). Taking the coordinate vectors of the nuclear configuration of semirigid molecules with relaxation (SRMRs) as functions of relaxing structural parameters and finite amplitude internal coordinate, the isometric group of SRMRs is discussed and the irreducible representations of the latter are shown to classify into engendered and nonengendered ones. On this basis a concept of equivalent sets of nuclei SRMRs is introduced and an analytical expression is derived which defines the most general functional form of relaxation increments of all common types of structural parameters compatible with isometric symmetry. This formula is shown to be a close analog of an analytical expression defining the transformations induced by the isometric group of infinitesimal internal coordinates associated with typical structural parameters. Furthermore analogous formulae are given for the most general form of the relaxation of harmonic potential coefficients as a function of finite internal coordinates. The general relations are illustrated by ab initio calculations for 1,2-difluoroethane at the MP4/DZP//HF/4-31G* level for twelve values of the dihedral angle including complete structure optimization. The potential to internal rotation is found to be in essential agreement with experimentally derived data. For a complete set of ab initio structural parameters the associated relaxation increments are represented as Fourier series, which are shown to confirm the form predicted by the general formula and the isometric group of 1,2-difluoroethane. Depending on type of the structural parameters (bond length, bond angles, etc.), the associated relaxation increments appear to follow some simple rules. Similarly a complete set of harmonic potential coefficients derived from the ab initio calculations will be analyzed in terms of Fourier series and shown to conform to the symmetry requirements of the symmetry group. Relaxation of potential coefficients is found to amount to up to ≈5% for some types of diagonal and nondiagonal terms and to reflect certain "topological" rules similar to regularities of harmonic potential constants of quasi-rigid molecules found in empirical determinations of valence force fields.

Surface chemical analysis and ab initio investigations of CsI coated C fiber cathodes for high power microwave sources

NASA Astrophysics Data System (ADS)

Vlahos, Vasilios; Morgan, Dane; LaCour, Matthew; Golby, Ken; Shiffler, Don; Booske, John H.

2010-02-01

CsI coated C fiber cathodes are promising electron emitters utilized in field emission applications. Ab initio calculations, in conjunction with experimental investigations on CsI-spray coated C fiber cathodes, were performed in order to better understand the origin of the low turn-on E-field obtained, as compared to uncoated C fibers. One possible mechanism for lowering the turn-on E-field is surface dipole layers reducing the work function. Ab initio modeling revealed that surface monolayers of Cs, CsI, Cs2O, and CsO are all capable of producing low work function C fiber cathodes (1 eV<Φ<1.5 eV), yielding a reduction in the turn-on E-field by as much as ten times, when compared to the bare fiber. Although a CsI-containing aqueous solution is spray deposited on the C fiber surface, energy dispersive x-ray spectroscopy and scanning auger microscopy measurements show coabsorption of Cs and I into the fiber interior and Cs and O on the fiber surface, with no surface I. It is therefore proposed that a cesium oxide (CsxOy) surface coating is responsible, at least in part, for the low turn E-field and superior emission characteristics of this type of fiber cathode. This CsxOy layer could be formed during preconditioning heating. CsxOy surface layers cannot only lower the fiber work function by the formation of surface dipoles (if they are thin enough) but may also enhance surface emission through their ability to emit secondary electrons due to a process of grazing electron impact. These multiple electron emission processes may explain the reported 10-100 fold reduction in the turn-on E-field of coated C fibers.

Open sd-shell nuclei from first principles

DOE PAGES

Jansen, Gustav R.; Signoracci, Angelo J.; Hagen, Gaute; ...

2016-07-05

We extend the ab initio coupled-cluster effective interaction (CCEI) method to open-shell nuclei with protons and neutrons in the valence space, and compute binding energies and excited states of isotopes of neon and magnesium. We employ a nucleon-nucleon and three-nucleon interaction from chiral effective field theory evolved to a lower cutoff via a similarity renormalization group transformation. We find good agreement with experiment for binding energies and spectra, while charge radii of neon isotopes are underestimated. For the deformed nuclei 20Ne and 24Mg we reproduce rotational bands and electric quadrupole transitions within uncertainties estimated from an effective field theory formore » deformed nuclei, thereby demonstrating that collective phenomena in sd-shell nuclei emerge from complex ab initio calculations.« less

Open sd-shell nuclei from first principles

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

Jansen, Gustav R.; Signoracci, Angelo J.; Hagen, Gaute

We extend the ab initio coupled-cluster effective interaction (CCEI) method to open-shell nuclei with protons and neutrons in the valence space, and compute binding energies and excited states of isotopes of neon and magnesium. We employ a nucleon-nucleon and three-nucleon interaction from chiral effective field theory evolved to a lower cutoff via a similarity renormalization group transformation. We find good agreement with experiment for binding energies and spectra, while charge radii of neon isotopes are underestimated. For the deformed nuclei 20Ne and 24Mg we reproduce rotational bands and electric quadrupole transitions within uncertainties estimated from an effective field theory formore » deformed nuclei, thereby demonstrating that collective phenomena in sd-shell nuclei emerge from complex ab initio calculations.« less

Perspective: Quantum mechanical methods in biochemistry and biophysics.

PubMed

Cui, Qiang

2016-10-14

In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

Benchmarking polarizable molecular dynamics simulations of aqueous sodium hydroxide by diffraction measurements.

PubMed

Vácha, Robert; Megyes, Tunde; Bakó, Imre; Pusztai, László; Jungwirth, Pavel

2009-04-23

Results from molecular dynamics simulations of aqueous hydroxide of varying concentrations have been compared with experimental structural data. First, the polarizable POL3 model was verified against neutron scattering using a reverse Monte Carlo fitting procedure. It was found to be competitive with other simple water models and well suited for combining with hydroxide ions. Second, a set of four polarizable models of OH- were developed by fitting against accurate ab initio calculations for small hydroxide-water clusters. All of these models were found to provide similar results that robustly agree with structural data from X-ray scattering. The present force field thus represents a significant improvement over previously tested nonpolarizable potentials. Although it cannot in principle capture proton hopping and can only approximately describe the charge delocalization within the immediate solvent shell around OH-, it provides structural data that are almost entirely consistent with data obtained from scattering experiments.

Nuclear spin relaxation due to chemical shift anisotropy of gas-phase 129Xe.

PubMed

Hanni, Matti; Lantto, Perttu; Vaara, Juha

2011-08-14

Nuclear spin relaxation provides detailed dynamical information on molecular systems and materials. Here, first-principles modeling of the chemical shift anisotropy (CSA) relaxation time for the prototypic monoatomic (129)Xe gas is carried out, both complementing and predicting the results of NMR measurements. Our approach is based on molecular dynamics simulations combined with pre-parametrized ab initio binary nuclear shielding tensors, an "NMR force field". By using the Redfield relaxation formalism, the simulated CSA time correlation functions lead to spectral density functions that, for the first time, quantitatively determine the experimental spin-lattice relaxation times T(1). The quality requirements on both the Xe-Xe interaction potential and binary shielding tensor are investigated in the context of CSA T(1). Persistent dimers Xe(2) are found to be responsible for the CSA relaxation mechanism in the low-density limit of the gas, completely in line with the earlier experimental findings.

DFT-derived reactive potentials for the simulation of activated processes: the case of CdTe and CdTe:S.

PubMed

Hu, Xiao Liang; Ciaglia, Riccardo; Pietrucci, Fabio; Gallet, Grégoire A; Andreoni, Wanda

2014-06-19

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.

A single molecule rectifier with strong push-pull coupling

NASA Astrophysics Data System (ADS)

Saraiva-Souza, Aldilene; Macedo de Souza, Fabricio; Aleixo, Vicente F. P.; Girão, Eduardo Costa; Filho, Josué Mendes; Meunier, Vincent; Sumpter, Bobby G.; Souza Filho, Antônio Gomes; Del Nero, Jordan

2008-11-01

We theoretically investigate the electronic charge transport in a molecular system composed of a donor group (dinitrobenzene) coupled to an acceptor group (dihydrophenazine) via a polyenic chain (unsaturated carbon bridge). Ab initio calculations based on the Hartree-Fock approximations are performed to investigate the distribution of electron states over the molecule in the presence of an external electric field. For small bridge lengths (n =0-3) we find a homogeneous distribution of the frontier molecular orbitals, while for n >3 a strong localization of the lowest unoccupied molecular orbital is found. The localized orbitals in between the donor and acceptor groups act as conduction channels when an external electric field is applied. We also calculate the rectification behavior of this system by evaluating the charge accumulated in the donor and acceptor groups as a function of the external electric field. Finally, we propose a phenomenological model based on nonequilibrium Green's function to rationalize the ab initio findings.

Ab Initio Calculation of Photoionization and Inelastic Photon Scattering Spectra of He below the N=2 Threshold in a dc Electric Field

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

Mihelic, Andrej; Zitnik, Matjaz

2007-06-15

We study the Stark effect on doubly excited states of the helium atom below N=2. We present the ab initio photoionization and total inelastic photon scattering cross sections calculated with the method of complex scaling for field strengths F{<=}100 kV/cm. The calculations are compared to the measurements of the ion [Phys. Rev. Lett. 90, 133002 (2003)] and vacuum ultraviolet fluorescence yields [Phys. Rev. Lett. 96, 093001 (2006)]. For the case of photoionization and for incident photons with polarization vector P parallel to the electric field F, we confirm the propensity rule proposed by Tong and Lin [Phys. Rev. Lett. 92,more » 223003 (2004)]. Furthermore, the rule is also shown to apply for F perpendicular P and for the case of the inelastic scattering in both experimental geometries.« less

Electric field gradient in FeTiO3 by nuclear magnetic resonance and ab initio calculations.

PubMed

Procházka, V; Stěpánková, H; Chlan, V; Tuček, J; Cuda, J; Kouřil, K; Filip, J; Zbořil, R

2011-05-25

Temperature dependence of nuclear magnetic resonance (NMR) spectra of (47)Ti and (49)Ti in polycrystalline ilmenite FeTiO(3) was measured in the range from 5 to 300 K under an external magnetic field of 9.401 T. NMR spectra collected between 300 and 77 K exhibit a resolved quadrupole splitting. The electric field gradient (EFG) tensor was evaluated for Ti nuclei and the ratio of (47)Ti and (49)Ti nuclear quadrupole moments was refined during the fitting procedure. Below 77 K, the fine structure of quadrupole splitting disappears due to the enormous increase of anisotropy. As a counterpart, ab initio calculations were performed using full potential augmented plane waves + local orbitals. The calculated EFG tensors for Ti and Fe were compared to the experimental ones evaluated from NMR and the Mössbauer spectroscopy experiments.

Real-time ab initio simulations of excited-state dynamics in nanostructures

NASA Astrophysics Data System (ADS)

Tomanek, David

2007-03-01

Combining time-dependent ab initio density functional calculations for electrons with molecular dynamics simulations for ions, we investigate the effect of excited-state dynamics in nanostructures. In carbon nanotubes, we find electronic excitations to last for a large fraction of a picosecond. The de-excitation process is dominated by coupling to other electronic degrees of freedom during the first few hundred femtoseconds. Later, the de-excitation process becomes dominated by coupling to ionic motion. The onset point and damping rate in that regime change with initial ion velocities, a manifestation of temperature dependent electron-phonon coupling. Considering the fact that the force field in the electronically excited state differs significantly from the ground state, as reflected in the Franck-Condon effect, atomic bonds can easily be broken or restored during the relatively long lifetime of electronic excitations. This effect can be utilized in a ``photo-surgery" of nanotubes, causing structural self-healing at vacancy sites or selective de-oxidation processes induced by photo-absorption. Also, electronic excitations are a key ingredient for the understanding of sputtering processes in nanostructures, induced by energetic collisions with ions. Yoshiyuki Miyamoto, Angel Rubio, and David Tomanek, Phys. Rev. Lett. 97, 126104 (2006). Yoshiyuki Miyamoto, Savas Berber, Mina Yoon, Angel Rubio, and David Tomanek, Chem. Phys. Lett. 392, 209 (2004). Yoshiyuki Miyamoto, Noboru Jinbo, Hisashi Nakamura, Angel Rubio, and David Tomanek, Phys. Rev. B 70, 233408 (2004). Yoshiyuki Miyamoto, Arkady Krasheninnikov, and David Tomanek (in preparation).

Importance of dispersion and electron correlation in ab initio protein folding.

PubMed

He, Xiao; Fusti-Molnar, Laszlo; Cui, Guanglei; Merz, Kenneth M

2009-04-16

Dispersion is well-known to be important in biological systems, but the effect of electron correlation in such systems remains unclear. In order to assess the relationship between the structure of a protein and its electron correlation energy, we employed both full system Hartree-Fock (HF) and second-order Møller-Plesset perturbation (MP2) calculations in conjunction with the Polarizable Continuum Model (PCM) on the native structures of two proteins and their corresponding computer-generated decoy sets. Because of the expense of the MP2 calculation, we have utilized the fragment molecular orbital method (FMO) in this study. We show that the sum of the Hartree-Fock (HF) energy and force field (LJ6)-derived dispersion energy (HF + LJ6) is well correlated with the energies obtained using second-order Møller-Plesset perturbation (MP2) theory. In one of the two examples studied, the correlation energy as well as the empirical dispersive energy term was able to discriminate between native and decoy structures. On the other hand, for the second protein we studied, neither the correlation energy nor dispersion energy showed discrimination capabilities; however, the ab initio MP2 energy and the HF+LJ6 both ranked the native structure correctly. Furthermore, when we randomly scrambled the Lennard-Jones parameters, the correlation between the MP2 energy and the sum of the HF energy and dispersive energy (HF+LJ6) significantly drops, which indicates that the choice of Lennard-Jones parameters is important.

Anything Can Happen out There: A Holistic Approach to Field Trips

ERIC Educational Resources Information Center

Plutino, Alessia

2016-01-01

This paper looks back at an academic-led language field trip project, now in its third year, involving ab-initio students of Italian at the University of Southampton. It considers the role of academic-led field trips in Modern Languages (ML) and it explores the underlying pedagogical approaches that were adopted to enhance students' engagement,…

Determination of structure and properties of molecular crystals from first principles.

PubMed

Szalewicz, Krzysztof

2014-11-18

CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.

Spectroscopic determination of the water pair potential

NASA Astrophysics Data System (ADS)

Fellers, Raymond Scott, II

This thesis details the first experimental determination of a water pair potential via nonlinear least squares fit of high precision microwave and far-IR vibration- rotation-tunneling (VRT) data. Provided is a review of the theory of intermolecular forces, methods of determining these forces by ab initio theory, and a survey of analytical forms that are parameterized to model such forces. Also reviewed are important features of water dimer VRT spectra, in particular the characteristic tunneling splittings due to hydrogen bond rearrangements, and how these features are related to the anisotropy of the water dimer potential energy surface (PES). Comparisons are made between high level ab initio calculations of the water dimer PES and a number of well known water pair potentials. The importance of the intramolecular degrees of freedom in the parameterization of a new PES is studied through a systematic series of ab initio calculations. These results suggest that a reasonably accurate pair potential can be constructed with the constraint of rigid monomers. ÅThe computation of the VRT states of the water dimer in a fully-coupled six-dimensional Hamiltonian by the split Wigner pseudospectral (SWPS) method is presented. Discussed in detail is the performance of the code and recent improvements of the algorithm which significantly decrease the execution time over an earlier implementation. The VRT states of several potentials are calculated and compared to experiment. It is shown that none of these potentials can reproduce the water dimer tunneling splittings with quantitative accuracy. The SWPS code is embedded in a non-linear least squares fitting routine and is used to fit a potential to 22 microwave and far-IR transitions. The resulting PES, VRT- 1(R,P), is derived from the ab initio/semiempirical ASPW (Anisotropic Site Potential for Water) potential which includes multipole expansions for the electrostatic, dispersion, exchange- repulsion, and induction terms. Induction is iterated to first-order. VRT-1(R,P) reproduces VRT spectra and temperature dependent second virial coefficients to high accuracy. The dimer equilibrium and zero-point binding energies (De and D0) are 4.91 kcal mol and 3.46 kcal/mol, respectively, which are in agreement with the best theoretical estimates. The dimer equilibrium structure [ROO = 2.924 Å, θ a = 48.5°, and θd = 50.2°] agrees with large basis set MP2 calculations. Additionally, the trimer equilibrium structure [ROO = 2.756 Å and D e=15.6 kcal/mol] and tetramer equilibrium structure [R OO = 2.783 Å and De = 25.9 kcal/mol] are also very close to second-order Möller-Plesset (MP2) calculations. The hydrogen bond rearrangement pathways of the dimer PES are determined by the eigenvector following method. The two lowest energy rearrangement barriers, corresponding to the acceptor switching and interchange motions, are 157 cm-1 and 207 cm-1, respectively, which is in excellent agreement with ab initio predictions of 158 cm -1 and 199 cm-1, respectively

Manipulating Si(100) at 5 K using qPlus frequency modulated atomic force microscopy: Role of defects and dynamics in the mechanical switching of atoms

NASA Astrophysics Data System (ADS)

Sweetman, A.; Jarvis, S.; Danza, R.; Bamidele, J.; Kantorovich, L.; Moriarty, P.

2011-08-01

We use small-amplitude qPlus frequency modulated atomic force microscopy (FM-AFM), at 5 K, to investigate the atomic-scale mechanical stability of the Si(100) surface. By operating at zero applied bias the effect of tunneling electrons is eliminated, demonstrating that surface manipulation can be performed by solely mechanical means. Striking differences in surface response are observed between different regions of the surface, most likely due to variations in strain associated with the presence of surface defects. We investigate the variation in local energy surface by ab initio simulation, and comment on the dynamics observed during force spectroscopy.

Simulating contrast inversion in atomic force microscopy imaging with real-space pseudopotentials

NASA Astrophysics Data System (ADS)

Lee, Alex; Sakai, Yuki; Chelikowsky, James

Atomic force microscopy measurements have reported contrast inversions for systems such as Cu2N and graphene that can hamper image interpretation and characterization. Here, we apply a simulation method based on ab initio real-space pseudopotentials to gain an understanding of the tip-sample interactions that influence the inversion. We find that chemically reactive tips induce an attractive binding force that results in the contrast inversion. The inversion is tip height dependent and not observed when using less reactive CO-functionalized tips. Work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Assessment of Simple Models for Molecular Simulation of Ethylene Carbonate and Propylene Carbonate as Solvents for Electrolyte Solutions.

PubMed

Chaudhari, Mangesh I; Muralidharan, Ajay; Pratt, Lawrence R; Rempe, Susan B

2018-02-12

Progress in understanding liquid ethylene carbonate (EC) and propylene carbonate (PC) on the basis of molecular simulation, emphasizing simple models of interatomic forces, is reviewed. Results on the bulk liquids are examined from the perspective of anticipated applications to materials for electrical energy storage devices. Preliminary results on electrochemical double-layer capacitors based on carbon nanotube forests and on model solid-electrolyte interphase (SEI) layers of lithium ion batteries are considered as examples. The basic results discussed suggest that an empirically parameterized, non-polarizable force field can reproduce experimental structural, thermodynamic, and dielectric properties of EC and PC liquids with acceptable accuracy. More sophisticated force fields might include molecular polarizability and Buckingham-model description of inter-atomic overlap repulsions as extensions to Lennard-Jones models of van der Waals interactions. Simple approaches should be similarly successful also for applications to organic molecular ions in EC/PC solutions, but the important case of Li[Formula: see text] deserves special attention because of the particularly strong interactions of that small ion with neighboring solvent molecules. To treat the Li[Formula: see text] ions in liquid EC/PC solutions, we identify interaction models defined by empirically scaled partial charges for ion-solvent interactions. The empirical adjustments use more basic inputs, electronic structure calculations and ab initio molecular dynamics simulations, and also experimental results on Li[Formula: see text] thermodynamics and transport in EC/PC solutions. Application of such models to the mechanism of Li[Formula: see text] transport in glassy SEI models emphasizes the advantage of long time-scale molecular dynamics studies of these non-equilibrium materials.

An ab initio CASSCF study of zero field splitting fluctuations in the octet ground state of aqueous [Gd(iii)(HPDO3A)(H2O)

NASA Astrophysics Data System (ADS)

Khan, Shehryar; Pollet, Rodolphe; Vuilleumier, Rodolphe; Kowalewski, Jozef; Odelius, Michael

2017-12-01

In this work, we present ab initio calculations of the zero-field splitting (ZFS) of a gadolinium complex [Gd(iii)(HPDO3A)(H2O)] sampled from an ab initio molecular dynamics (AIMD) simulation. We perform both post-Hartree-Fock (complete active space self-consistent field—CASSCF) and density functional theory (DFT) calculations of the ZFS and compare and contrast the methods with experimental data. Two different density functional approximations (TPSS and LC-BLYP) were investigated. The magnitude of the ZFS from the CASSCF calculations is in good agreement with experiment, whereas the DFT results in varying degrees overestimate the magnitude of the ZFS for both functionals and exhibit a strong functional dependence. It was found in the sampling over the AIMD trajectory that the fluctuations in the transient ZFS tensor derived from DFT are not correlated with those of CASSCF nor does the magnitude of the ZFS from CASSCF and DFT correlate. From the fluctuations in the ZFS tensor, we extract a correlation time of the transient ZFS which is on the sub-picosecond time scale, showing a faster decay than experimental estimates.

Consistent force field modeling of matrix isolated molecules. V. Minimum energy path potential to the conformer conversion of 1,2-difluoroethane: Ar 364, ab initio calculation of electric multipole moments and electric polarization contribution to the conversion barrier

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 shifts will be discussed.

Structural, dynamical, and transport properties of the hydrated halides: How do At{sup −} bulk properties compare with those of the other halides, from F{sup −} to I{sup −}?

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

Réal, Florent, E-mail: florent.real@univ-lille1.fr; Severo Pereira Gomes, André; Guerrero Martínez, Yansel Omar

2016-03-28

The properties of halides from the lightest, fluoride (F{sup −}), to the heaviest, astatide (At{sup −}), have been studied in water using a polarizable force-field approach based on molecular dynamics (MD) simulations at the 10 ns scale. The selected force-field explicitly treats the cooperativity within the halide-water hydrogen bond networks. The force-field parameters have been adjusted to ab initio data on anion/water clusters computed at the relativistic Möller-Plesset second-order perturbation theory level of theory. The anion static polarizabilities of the two heaviest halides, I{sup −} and At{sup −}, were computed in the gas phase using large and diffuse atomic basis sets,more » and taking into account both electron correlation and spin-orbit coupling within a four-component framework. Our MD simulation results show the solvation properties of I{sup −} and At{sup −} in aqueous phase to be very close. For instance, their first hydration shells are structured and encompass 9.2 and 9.1 water molecules at about 3.70 ± 0.05 Å, respectively. These values have to be compared to the F{sup −}, Cl{sup −}, and Br{sup −} ones, i.e., 6.3, 8.4, and 9.0 water molecules at 2.74, 3.38, and 3.55 Å, respectively. Moreover our computations predict the solvation free energy of At{sup −} in liquid water at ambient conditions to be 68 kcal mol{sup −1}, a value also close the I{sup −} one, about 70 kcal mol{sup −1}. In all, our simulation results for I{sup −} are in excellent agreement with the latest neutron- and X-ray diffraction studies. Those for the At{sup −} ion are predictive, as no theoretical or experimental data are available to date.« less

Dielectric Response and Born Dynamic Charge of BN Nanotubes from Ab Initio Finite Electric Field Calculations

NASA Astrophysics Data System (ADS)

Guo, Guang-Yu; Ishibashi, Shoji; Tamura, Tomoyuki; Terakura, Kiyoyuki

2007-03-01

Since the discovery of carbon nanotubes (CNTs) in 1991 by Iijima, carbon and other nanotubes have attracted considerable interest worldwide because of their unusual properties and also great potentials for technological applications. Though CNTs continue to attract great interest, other nanotubes such as BN nanotubes (BN-NTs) may offer different opportunities that CNTs cannot provide. In this contribution, we present the results of our recent systematic ab initio calculations of the static dielectric constant, electric polarizability, Born dynamical charge, electrostriction coefficient and piezoelectric constant of BN-NTs using the latest crystalline finite electric field theory [1]. [1] I. Souza, J. Iniguez, and D. Vanderbilt, Phys. Rev. Lett. 89, 117602 (2002); P. Umari and A. Pasquarello, Phys. Rev. Lett. 89, 157602 (2002).

Electromagnetic forces in negative-refractive-index metamaterials: A first-principles study

NASA Astrophysics Data System (ADS)

Yannopapas, Vassilios; Galiatsatos, Pavlos G.

2008-04-01

According to the theory of Veselago, when a particle immersed within a metamaterial with negative refractive index is illuminated by plane wave, it experiences a reversed radiation force due to the antiparallel directions of the phase velocity and energy flow. By employing an ab initio method, we show that, in the limit of zero losses, the effect of reversed radiation pressure is generally true only for the specular beam. Waves generated by diffraction of the incident light at the surface of the slab of the metamaterial can produce a total force which is parallel to the radiation flow. However, when the actual losses of the materials are taken into account, the phenomenon of reversed radiation force is evident within the whole range of a negative refractive index band.

Ab initio velocity-field curves in monoclinic β-Ga2O3

NASA Astrophysics Data System (ADS)

Ghosh, Krishnendu; Singisetti, Uttam

2017-07-01

We investigate the high-field transport in monoclinic β-Ga2O3 using a combination of ab initio calculations and full band Monte Carlo (FBMC) simulation. Scattering rate calculation and the final state selection in the FBMC simulation use complete wave-vector (both electron and phonon) and crystal direction dependent electron phonon interaction (EPI) elements. We propose and implement a semi-coarse version of the Wannier-Fourier interpolation method [Giustino et al., Phys. Rev. B 76, 165108 (2007)] for short-range non-polar optical phonon (EPI) elements in order to ease the computational requirement in FBMC simulation. During the interpolation of the EPI, the inverse Fourier sum over the real-space electronic grids is done on a coarse mesh while the unitary rotations are done on a fine mesh. This paper reports the high field transport in monoclinic β-Ga2O3 with deep insight into the contribution of electron-phonon interactions and velocity-field characteristics for electric fields ranging up to 450 kV/cm in different crystal directions. A peak velocity of 2 × 107 cm/s is estimated at an electric field of 200 kV/cm.

The electronegativity equalization method and the split charge equilibration applied to organic systems: parametrization, validation, and comparison.

PubMed

Verstraelen, Toon; Van Speybroeck, Veronique; Waroquier, Michel

2009-07-28

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500,000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM.

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

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

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Numerical Optimization of Density Functional Tight Binding Models: Application to Molecules Containing Carbon, Hydrogen, Nitrogen, and Oxygen

DOE PAGES

Krishnapriyan, A.; Yang, P.; Niklasson, A. M. N.; ...

2017-10-17

New parametrizations for semiempirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater- Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions. The adjustable parameters in these functions were optimized by simulated annealing and steepest descent algorithms to minimize the value ofmore » an objective function that quantifies the error between the DFTB model and ab initio calculated data. The accuracy and transferability of the resulting DFTB models for the C, H, N, and O system were assessed by comparing the predicted atomization energies and equilibrium molecular geometries of small molecules that were not included in the training data from DFTB to ab initio data. The DFTB models provide accurate predictions of the properties of hydrocarbons and more complex molecules containing C, H, N, and O.« less

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

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

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Temperature dependent effective potential method for accurate free energy calculations of solids

NASA Astrophysics Data System (ADS)

Hellman, Olle; Steneteg, Peter; Abrikosov, I. A.; Simak, S. I.

2013-03-01

We have developed a thorough and accurate method of determining anharmonic free energies, the temperature dependent effective potential technique (TDEP). It is based on ab initio molecular dynamics followed by a mapping onto a model Hamiltonian that describes the lattice dynamics. The formalism and the numerical aspects of the technique are described in detail. A number of practical examples are given, and results are presented, which confirm the usefulness of TDEP within ab initio and classical molecular dynamics frameworks. In particular, we examine from first principles the behavior of force constants upon the dynamical stabilization of the body centered phase of Zr, and show that they become more localized. We also calculate the phase diagram for 4He modeled with the Aziz potential and obtain results which are in favorable agreement both with respect to experiment and established techniques.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

DOE PAGES

Huang, Jing; Mei, Ye; König, Gerhard; ...

2017-01-24

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

PubMed

Huang, Jing; Mei, Ye; König, Gerhard; Simmonett, Andrew C; Pickard, Frank C; Wu, Qin; Wang, Lee-Ping; MacKerell, Alexander D; Brooks, Bernard R; Shao, Yihan

2017-02-14

In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other 11 solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. This suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

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

Huang, Jing; Mei, Ye; König, Gerhard

Here in this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PADmore » energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R 2 value of 0.71 for aniline (in 10,000 TIP3P water configurations) and 0.87 or higher for other eleven solute molecules, while the PAD model has a much better performance with R 2 values of 0.98 or higher. The PAC model reproduces reference QM/MM hydration free energies for 12 solute molecules with a RMSD of 0.59 kcal/mol. The PAD model is even more accurate, with a much smaller RMSD of 0.12 kcal/mol, with respect to the reference. Lastly, this suggests that polarization effects, including both local charge distortion and intramolecular charge transfer, can be well captured by induced dipole type models with proper parametrization.« less

From tunneling to point contact: Correlation between forces and current

NASA Astrophysics Data System (ADS)

Sun, Yan; Mortensen, Henrik; Schär, Sacha; Lucier, Anne-Sophie; Miyahara, Yoichi; Grütter, Peter; Hofer, Werner

2005-05-01

We used a combined ultrahigh vacuum scanning tunneling and atomic force microscope (STM/AFM) to study W tip-Au(111) sample interactions in the regimes from weak coupling to strong interaction and simultaneously measure current changes from picoamperes to microamperes. Close correlation between conductance and interaction forces in a STM configuration was observed. In particular, the electrical and mechanical points of contact are determined based on the observed barrier collapse and adhesive bond formation, respectively. These points of contact, as defined by force and current measurements, coincide within measurement error. Ab initio calculations of the current as a function of distance in the tunneling regime is in quantitative agreement with experimental results. The obtained results are discussed in the context of dissipation in noncontact AFM as well as electrical contact formation in molecular electronics.

CERES: An ab initio code dedicated to the calculation of the electronic structure and magnetic properties of lanthanide complexes.

PubMed

Calvello, Simone; Piccardo, Matteo; Rao, Shashank Vittal; Soncini, Alessandro

2018-03-05

We have developed and implemented a new ab initio code, Ceres (Computational Emulator of Rare Earth Systems), completely written in C++11, which is dedicated to the efficient calculation of the electronic structure and magnetic properties of the crystal field states arising from the splitting of the ground state spin-orbit multiplet in lanthanide complexes. The new code gains efficiency via an optimized implementation of a direct configurational averaged Hartree-Fock (CAHF) algorithm for the determination of 4f quasi-atomic active orbitals common to all multi-electron spin manifolds contributing to the ground spin-orbit multiplet of the lanthanide ion. The new CAHF implementation is based on quasi-Newton convergence acceleration techniques coupled to an efficient library for the direct evaluation of molecular integrals, and problem-specific density matrix guess strategies. After describing the main features of the new code, we compare its efficiency with the current state-of-the-art ab initio strategy to determine crystal field levels and properties, and show that our methodology, as implemented in Ceres, represents a more time-efficient computational strategy for the evaluation of the magnetic properties of lanthanide complexes, also allowing a full representation of non-perturbative spin-orbit coupling effects. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab-initio Studies of Zero-Field Splittings

DOE PAGES

Stavretis, Shelby E.; Atanasov, Mihail; Podlesnyak, Andrey A.; ...

2015-10-02

Zero-field splitting (ZFS) parameters of nondeuterated metalloporphyrins [Fe(TPP)X] (X = F, Br, I; H 2TPP = tetraphenylporphyrin) are determined by inelastic neutron scattering (INS). The ZFS values are D = 4.49(9) cm –1 for tetragonal polycrystalline [Fe(TPP)F], and D = 8.8(2) cm –1, E = 0.1(2) cm –1 and D = 13.4(6) cm –1, E = 0.3(6) cm –1 for monoclinic polycrystalline [Fe(TPP)Br] and [Fe(TPP)I], respectively. Along with our recent report of the ZFS value of D = 6.33(8) cm –1 for tetragonal polycrystalline [Fe(TPP)Cl], these data provide a rare, complete determination of ZFS parameters in a metalloporphyrin halide series.more » The electronic structure of [Fe(TPP)X] (X = F, Cl, Br, I) has been studied by multireference ab initio methods: the complete active space self-consistent field (CASSCF) and the N-electron valence perturbation theory (NEVPT2) with the aim of exploring the origin of the large and positive zero-field splitting D of the 6A 1 ground state. D was calculated from wave functions of the electronic multiplets spanned by the d 5 configuration of Fe(III) along with spin–orbit coupling accounted for by quasi degenerate perturbation theory. Results reproduce trends of D from inelastic neutron scattering data increasing in the order from F, Cl, Br, to I. A mapping of energy eigenvalues and eigenfunctions of the S = 3/2 excited states on ligand field theory was used to characterize the σ- and π-antibonding effects decreasing from F to I. This is in agreement with similar results deduced from ab initio calculations on CrX 6 3- complexes and also with the spectrochemical series showing a decrease of the ligand field in the same directions. A correlation is found between the increase of D and decrease of the π- and σ-antibonding energies e λ X (λ = σ, π) in the series from X = F to I. Analysis of this correlation using second-order perturbation theory expressions in terms of angular overlap parameters rationalizes the experimentally deduced trend. Furthermore, D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed.« less

Magnetic Transitions in Iron Porphyrin Halides by Inelastic Neutron Scattering and Ab Initio Studies of Zero-Field Splittings.

PubMed

Stavretis, Shelby E; Atanasov, Mihail; Podlesnyak, Andrey A; Hunter, Seth C; Neese, Frank; Xue, Zi-Ling

2015-10-19

Zero-field splitting (ZFS) parameters of nondeuterated metalloporphyrins [Fe(TPP)X] (X = F, Br, I; H₂TPP = tetraphenylporphyrin) have been directly determined by inelastic neutron scattering (INS). The ZFS values are D = 4.49(9) cm⁻¹ for tetragonal polycrystalline [Fe(TPP)F], and D = 8.8(2) cm⁻¹, E = 0.1(2) cm⁻¹ and D = 13.4(6) cm⁻¹, E = 0.3(6) cm⁻¹ for monoclinic polycrystalline [Fe(TPP)Br] and [Fe(TPP)I], respectively. Along with our recent report of the ZFS value of D = 6.33(8) cm⁻¹ for tetragonal polycrystalline [Fe(TPP)Cl], these data provide a rare, complete determination of ZFS parameters in a metalloporphyrin halide series. The electronic structure of [Fe(TPP)X] (X = F, Cl, Br, I) has been studied by multireference ab initio methods: the complete active space self-consistent field (CASSCF) and the N-electron valence perturbation theory (NEVPT2) with the aim of exploring the origin of the large and positive zero-field splitting D of the ⁶A₁ ground state. D was calculated from wave functions of the electronic multiplets spanned by the d⁵ configuration of Fe(III) along with spin–orbit coupling accounted for by quasi degenerate perturbation theory. Results reproduce trends of D from inelastic neutron scattering data increasing in the order from F, Cl, Br, to I. A mapping of energy eigenvalues and eigenfunctions of the S = 3/2 excited states on ligand field theory was used to characterize the σ- and π-antibonding effects decreasing from F to I. This is in agreement with similar results deduced from ab initio calculations on CrX₆³⁻ complexes and also with the spectrochemical series showing a decrease of the ligand field in the same directions. A correlation is found between the increase of D and decrease of the π- and σ-antibonding energies e(λ)(X) (λ = σ, π) in the series from X = F to I. Analysis of this correlation using second-order perturbation theory expressions in terms of angular overlap parameters rationalizes the experimentally deduced trend. D parameters from CASSCF and NEVPT2 results have been calibrated against those from the INS data, yielding a predictive power of these approaches. Methods to improve the quantitative agreement between ab initio calculated and experimental D and spectroscopic transitions for high-spin Fe(III) complexes are proposed.

2D-HB-Network at the air-water interface: A structural and dynamical characterization by means of ab initio and classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Pezzotti, Simone; Serva, Alessandra; Gaigeot, Marie-Pierre

2018-05-01

Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ˜90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

Effect of Heteroatoms on Field-Induced Slow Magnetic Relaxation of Mononuclear FeIII ( S = 5/2) Ions within Polyoxometalates.

PubMed

Minato, Takuo; Aravena, Daniel; Ruiz, Eliseo; Yamaguchi, Kazuya; Mizuno, Noritaka; Suzuki, Kosuke

2018-06-01

In this paper, the synthesis and magnetic properties of mononuclear Fe III -containing polyoxometalates (POMs) with different types of heteroatoms, TBA 7 H 10 [(A-α-XW 9 O 34 ) 2 Fe] (II X , X = Ge, Si; TBA = tetra- n-butylammonium), are reported. In these POMs, mononuclear highly distorted six-coordinate octahedral [FeO 6 ] 9- units are sandwiched by two trivacant lacunary units [A-α-XW 9 O 34 ] 10- (X = Ge, Si). These POMs exhibit field-induced slow magnetic relaxation based on the single high-spin Fe III magnetic center ( S = 5/2). Combining experiment and ab initio calculations, we investigated the effect of heteroatoms of the lacunary units on the field-induced slow magnetic relaxation of these POMs. By changing the heteroatoms from Si (II Si ) to Ge (II Ge ), the coordination geometry around the Fe III ion is mildly changed. Concretely, the axial Fe-O bond length in II Ge is shortened compared with that in II Si , and consequently the distortion of the [FeO 6 ] 9- unit in II Ge from the ideal octahedral coordination geometry becomes larger than that in II Si . The effective demagnetization barrier of II Ge (11.4 K) is slightly larger than that of II Si (9.2 K). Multireference ab initio calculations predict zero-field splitting parameters in good agreement with experiment. Although the differences in the coordination geometries and magnetic properties of II Ge and II Si are quite small, ab initio calculations indicate subtle changes in the magnetic anisotropy which are in line with the observed magnetic relaxation properties.

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

DOE PAGES

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr; ...

2016-05-10

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Deuteron-induced nucleon transfer reactions within an ab initio framework: First application to p -shell nuclei

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

Raimondi, Francesco; Hupin, Guillaume; Navratil, Petr

Low-energy transfer reactions in which a proton is stripped from a deuteron projectile and dropped into a target play a crucial role in the formation of nuclei in both primordial and stellar nucleosynthesis, as well as in the study of exotic nuclei using radioactive beam facilities and inverse kinematics. Here, ab initio approaches have been successfully applied to describe the 3H(d,n) 4He and 3He(d,p) 4He fusion processes. An ab initio treatment of transfer reactions would also be desirable for heavier targets. In this work, we extend the ab initio description of (d,p) reactions to processes with light p-shell nuclei. Asmore » a first application, we study the elastic scattering of deuterium on 7Li and the 7Li(d,p) 8Li transfer reaction based on a two-body Hamiltonian. We use the no-core shell model to compute the wave functions of the nuclei involved in the reaction, and describe the dynamics between targets and projectiles with the help of microscopic-cluster states in the spirit of the resonating group method. The shapes of the excitation functions for deuterons impinging on 7Li are qualitatively reproduced up to the deuteron breakup energy. The interplay between d– 7Li and p– 8Li particle-decay channels determines some features of the 9Be spectrum above the d+ 7Li threshold. Our prediction for the parity of the 17.298 MeV resonance is at odds with the experimental assignment. Deuteron stripping reactions with p-shell targets can now be computed ab initio, but calculations are very demanding. Finally, a quantitative description of the 7Li(d,p) 8Li reaction will require further work to include the effect of three-nucleon forces and additional decay channels and to improve the convergence rate of our calculations.« less

Structural properties and FTIR-Raman spectra of the anti-hypertensive clonidine hydrochloride agent and their dimeric species

NASA Astrophysics Data System (ADS)

Romano, Elida; Davies, Lilian; Brandán, Silvia Antonia

2017-04-01

The structural and vibrational properties of the α-adrenergic agonist clonidine hydrochloride agent and their anionic and dimeric species were studied combining the experimental FT-IR and Raman spectra in solid phase with ab-initio calculations based on the density functional theory (DFT). All the calculations were performed by using the hybrid B3LYP with the 6-31G* and 6-311++G** basis sets. The structural properties for those species were studied employing the Natural Bond Orbital (NBO), Atoms in Molecules theory (AIM) and frontier orbitals calculations. The complete assignments of the FTIR and Raman spectra were performed combining the DFT calculations with the Pulay's Scaled Quantum Mechanics Force Field (SQMFF) methodology. Very good concordances between the theoretical and experimental spectra were found. In addition, the force constants for those three species were computed and compared with the values reported for similar antihypertensive agents. The ionic nature of the H→Cl bond and the high value of the LP(1)N4 → LP*(1)H18 charge transfer could explain the high reactivity of clonidine hydrochloride in relation to other antihypertensive agent and the strong shifthing of the band assigned to the Nsbnd H stretching mode linked to the Hsbnd Cl bond toward lower wavenumbers.

Ab Initio Effective Rovibrational Hamiltonians for Non-Rigid Molecules via Curvilinear VMP2

NASA Astrophysics Data System (ADS)

Changala, Bryan; Baraban, Joshua H.

2017-06-01

Accurate predictions of spectroscopic constants for non-rigid molecules are particularly challenging for ab initio theory. For all but the smallest systems, ``brute force'' diagonalization of the full rovibrational Hamiltonian is computationally prohibitive, leaving us at the mercy of perturbative approaches. However, standard perturbative techniques, such as second order vibrational perturbation theory (VPT2), are based on the approximation that a molecule makes small amplitude vibrations about a well defined equilibrium structure. Such assumptions are physically inappropriate for non-rigid systems. In this talk, we will describe extensions to curvilinear vibrational Møller-Plesset perturbation theory (VMP2) that account for rotational and rovibrational effects in the molecular Hamiltonian. Through several examples, we will show that this approach provides predictions to nearly microwave accuracy of molecular constants including rotational and centrifugal distortion parameters, Coriolis coupling constants, and anharmonic vibrational and tunneling frequencies.

Excited states of 4He

NASA Astrophysics Data System (ADS)

Aoyama, Shigeyoshi

2013-04-01

The study of the 4He nucleus is important because it is the most basic sub-unit (cluster) in nuclei. We have investigated the structures and the reaction mechanisms in 4He by using the correlated Gaussian basis function with the global vector representation. In order to treat the boundary condition for the ab-initio calculation of the four nucleons, we employ the Microscopic R-matrix Method (MRM) and the Complex Scaling Method (CSM) . Elastic-scattering phase shifts for four-nucleon systems are studied in an ab-initio type cluster model with MRM in order to clarify the role of the tensor force and to investigate cluster distortions in low energy d+d and t+p scattering. For 1S0, the calculated phase shifts show that the t+p and h+n channels are strongly coupled to the d+d channel for the case of the realistic interaction.

The mechanism of addition to a CN triple bond. An ab initio study of the first stages of the Stephen, Gatterman and Houben-Hoesch reactions

NASA Astrophysics Data System (ADS)

Alagona, Giuliano; Tomasi, Jacopo

The mechanism of addition of HCl to the triple bond of RCN (R=H, CH,) is studied by means of ab initio SCF and CI calculations. Geometries and energies of minima (initial H-bonded complexes, products) and saddle points (transition state) are completed by a determination of the intrinsic reaction coordinate and of a relatively large portion of the energy hypersurface. The evolution of the electronic structure along the reaction coordinate is interpreted using localized orbitals. Particular attention is paid to the effect of chemical substitution, for which a new test, based on the electrostatic forces acting on nuclei along the reaction coordinate, has been employed. CI calculations performed over canonical and localized orbitals are compared to determine whether the latter formulation is more convenient for non-equilibrium geometries.

Strong π-π interaction of porphyrins on (6,5) carbon nanotubes with full surface coverage: Ab-initio calculations

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

Orellana, Walter, E-mail: worellana@unab.cl

2014-07-14

The stability, electronic, and optical properties of (6,5) single-walled carbon nanotubes (CNTs) functionalized with free-base tetraphenylporphyrin (TPP) molecules through π-stacking interactions are studied by ab-initio calculations. The stability and optical response of the CNT-TPP compounds for increasing CNT-surface coverage are investigated. Our results show that four TPP molecules forming a ring around the CNT is the most stable configuration, showing strong binding energies of about 2.5 eV/TPP. However, this binding energy can increase even more after additional molecules assemble side by side along the CNT, favoring the formation of a full single layer of TPP, as experimentally suggested. The strong π-πmore » attractive forces induce molecular distortions that move the TPP higher-occupied molecular orbital levels inside the CNT bandgap, changing the optical response of the TPP molecules stacked on the CNT.« less

A molecular dynamics and ab initio analysis of the electronic structure of single-walled carbon nanotubes adhered to a substrate

NASA Astrophysics Data System (ADS)

Van Der Geest, A. G.; Lu, Z.; Lusk, M. T.; Dunn, M. L.

2011-04-01

Single-wall nanotubes can adhere to planar surfaces via van der Waals forces, and this causes the tubes to deform. We use classical molecular dynamics to estimate this deformation and density functional theory to quantify its impact on electronic band structure. For (n,0) tubes, adhesion causes the maximum bandgap to rise more rapidly with diameter, but the value of the maximum is not affected. The influence of adhesion forces on bandgap was found to correlate with that associated with lateral, uniaxial compression for moderate values of adhesion energy and compressive distortion.

Transport model of controlled molecular rectifier showing unusual negative differential resistance effect.

PubMed

Granhen, Ewerton Ramos; Reis, Marcos Allan Leite; Souza, Fabrício M; Del Nero, Jordan

2010-12-01

We investigate theoretically the charge accumulated Q in a three-terminal molecular device in the presence of an external electric field. Our approach is based on ab initio Hartree-Fock and density functional theory methodology contained in Gaussian package. Our main finding is a negative differential resistance (NDR) in the charge Q as a function of an external electric field. To explain this NDR effect we apply a phenomenological capacitive model based on a quite general system composed of many localized levels (that can be LUMOs of a molecule) coupled to source and drain. The capacitance accounts for charging effects that can result in Coulomb blockade (CB) in the transport. We show that this CB effect gives rise to a NDR for a suitable set of phenomenological parameters, like tunneling rates and charging energies. The NDR profile obtained in both ab initio and phenomenological methodologies are in close agreement.

Modeling molecule-plasmon interactions using quantized radiation fields within time-dependent electronic structure theory

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

Nascimento, Daniel R.; DePrince, A. Eugene, E-mail: deprince@chem.fsu.edu

2015-12-07

We present a combined cavity quantum electrodynamics/ab initio electronic structure approach for simulating plasmon-molecule interactions in the time domain. The simple Jaynes-Cummings-type model Hamiltonian typically utilized in such simulations is replaced with one in which the molecular component of the coupled system is treated in a fully ab initio way, resulting in a computationally efficient description of general plasmon-molecule interactions. Mutual polarization effects are easily incorporated within a standard ground-state Hartree-Fock computation, and time-dependent simulations carry the same formal computational scaling as real-time time-dependent Hartree-Fock theory. As a proof of principle, we apply this generalized method to the emergence ofmore » a Fano-like resonance in coupled molecule-plasmon systems; this feature is quite sensitive to the nanoparticle-molecule separation and the orientation of the molecule relative to the polarization of the external electric field.« less

Optical, Fluorescence with quantum analysis of hydrazine (1, 3- Dinitro Phenyl) by DFT and Ab initio approach

NASA Astrophysics Data System (ADS)

Cecily Mary Glory, D.; Sambathkumar, K.; Madivanane, R.; Velmurugan, G.; Gayathri, R.; Nithiyanantham, S.; Venkatachalapathy, M.; Rajkamal, N.

2018-07-01

Experimental and computational study of molecular structure, vibrational and UV-spectral analysis of Hydrazine (1, 3- Dinitrophenyl) (HDP) derivatives. The crystal was grown by slow cooling method and the crystalline perfection of single crystals was evaluated by high resolution X-ray diffractometry (HRXRD) using a multicrystal X-ray diffractometer. Fluorescence, FT-IR and FT-Raman spectra of HDP crystal were recorded. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) followed by scaled quantum force field methodology (SQMFF). NMR studies have confirmed respectively the crystal structure and functional groups of the grown crystal. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) result complements the experimental findings. The calculated MESP, UV, HOMO-LUMO energies show that charge transfer done within the molecule. And various thermodynamic parameters are studied. Fukui determines the local reactive site of electrophilic, nucleophilic, descriptor.

Induced Hyperon-Nucleon-Nucleon Interactions and the Hyperon Puzzle.

PubMed

Wirth, Roland; Roth, Robert

2016-10-28

We present the first ab initio calculations for p-shell hypernuclei including hyperon-nucleon-nucleon (YNN) contributions induced by a similarity renormalization group transformation of the initial hyperon-nucleon interaction. The transformation including the YNN terms conserves the spectrum of the Hamiltonian while drastically improving model-space convergence of the importance-truncated no-core model, allowing a precise extraction of binding and excitation energies. Results using a hyperon-nucleon interaction at leading order in chiral effective field theory for lower- to mid-p-shell hypernuclei show a good reproduction of experimental excitation energies while hyperon separation energies are typically overestimated. The induced YNN contributions are strongly repulsive and we show that they are related to a decoupling of the Σ hyperons from the hypernuclear system, i.e., a suppression of the Λ-Σ conversion terms in the Hamiltonian. This is linked to the so-called hyperon puzzle in neutron-star physics and provides a basic mechanism for the explanation of strong ΛNN three-baryon forces.

Structure, stability, and properties of the trans peroxo nitrate radical: the importance of nondynamic correlation.

PubMed

Dutta, Achintya Kumar; Dar, Manzoor; Vaval, Nayana; Pal, Sourav

2014-02-27

We report a comparative single-reference and multireference coupled-cluster investigation on the structure, potential energy surface, and IR spectroscopic properties of the trans peroxo nitrate radical, one of the key intermediates in stratospheric NOX chemistry. The previous single-reference ab initio studies predicted an unbound structure for the trans peroxo nitrate radical. However, our Fock space multireference coupled-cluster calculation confirms a bound structure for the trans peroxo nitrate radical, in accordance with the experimental results reported earlier. Further, the analysis of the potential energy surface in FSMRCC method indicates a well-behaved minima, contrary to the shallow minima predicted by the single-reference coupled-cluster method. The harmonic force field analysis, of various possible isomers of peroxo nitrate also reveals that only the trans structure leads to the experimentally observed IR peak at 1840 cm(-1). The present study highlights the critical importance of nondynamic correlation in predicting the structure and properties of high-energy stratospheric NOx radicals.

A Simplified Model of Local Structure in Aqueous Proline Amino Acid Revealed by First-Principles Molecular Dynamics Simulations

PubMed Central

Troitzsch, Raphael Z.; Tulip, Paul R.; Crain, Jason; Martyna, Glenn J.

2008-01-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data. PMID:18790850

SchNet - A deep learning architecture for molecules and materials

NASA Astrophysics Data System (ADS)

Schütt, K. T.; Sauceda, H. E.; Kindermans, P.-J.; Tkatchenko, A.; Müller, K.-R.

2018-06-01

Deep learning has led to a paradigm shift in artificial intelligence, including web, text, and image search, speech recognition, as well as bioinformatics, with growing impact in chemical physics. Machine learning, in general, and deep learning, in particular, are ideally suitable for representing quantum-mechanical interactions, enabling us to model nonlinear potential-energy surfaces or enhancing the exploration of chemical compound space. Here we present the deep learning architecture SchNet that is specifically designed to model atomistic systems by making use of continuous-filter convolutional layers. We demonstrate the capabilities of SchNet by accurately predicting a range of properties across chemical space for molecules and materials, where our model learns chemically plausible embeddings of atom types across the periodic table. Finally, we employ SchNet to predict potential-energy surfaces and energy-conserving force fields for molecular dynamics simulations of small molecules and perform an exemplary study on the quantum-mechanical properties of C20-fullerene that would have been infeasible with regular ab initio molecular dynamics.

Three-Dimensional Mapping of Microenvironmental Control of Methyl Rotational Barriers

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

Hembree, William I; Baudry, Jerome Y

2011-01-01

Sterical (van der Waals-induced) rotational barriers of methyl groups are investigated theoretically, using ab initio and empirical force field calculations, for various three-dimensional microenvironmental conditions around the methyl group rotator of a model neopentane molecule. The destabilization (reducing methyl rotational barriers) or stabilization (increasing methyl rotational barriers) of the staggered conformation of the methyl rotator depends on a combination of microenvironmental contributions from (i) the number of atoms around the rotator, (ii) the distance between the rotator and the microenvironmental atoms, and (iii) the dihedral angle between the stator, rotator, and molecular environment around the rotator. These geometrical criteria combinemore » their respective effects in a linearly additive fashion, with no apparent cooperative effects, and their combination in space around a rotator may increase, decrease, or leave the rotator s rotational barrier unmodified. This is exemplified in a geometrical analysis of the alanine dipeptide crystal where microenvironmental effects on methyl rotators barrier of rotation fit the geometrical mapping described in the neopentane model.« less

A simplified model of local structure in aqueous proline amino acid revealed by first-principles molecular dynamics simulations.

PubMed

Troitzsch, Raphael Z; Tulip, Paul R; Crain, Jason; Martyna, Glenn J

2008-12-01

Aqueous proline solutions are deceptively simple as they can take on complex roles such as protein chaperones, cryoprotectants, and hydrotropic agents in biological processes. Here, a molecular level picture of proline/water mixtures is developed. Car-Parrinello ab initio molecular dynamics (CPAIMD) simulations of aqueous proline amino acid at the B-LYP level of theory, performed using IBM's Blue Gene/L supercomputer and massively parallel software, reveal hydrogen-bonding propensities that are at odds with the predictions of the CHARMM22 empirical force field but are in better agreement with results of recent neutron diffraction experiments. In general, the CPAIMD (B-LYP) simulations predict a simplified structural model of proline/water mixtures consisting of fewer distinct local motifs. Comparisons of simulation results to experiment are made by direct evaluation of the neutron static structure factor S(Q) from CPAIMD (B-LYP) trajectories as well as to the results of the empirical potential structure refinement reverse Monte Carlo procedure applied to the neutron data.

Dynamic NMR study of trans-cyclodecene

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

Pawar, D.M.; Noe, E.A.

1996-12-18

The slow-exchange {sup 13}C spectrum of trans-cyclodecene at -154.9{degree}C shows eight peaks of the olefinic carbons, and these are interpreted in terms of five conformations. Three of the conformations are of C{sub 1} symmetry, and two are of C{sub 2} symmetry. Further evidence for the number of conformations and their symmetries came from a proton NMR spectrum of the olefinic hydrogens taken at -154.9{degree}C with decoupling the allylic hydrogens. Populations ranged from 3.0% to 37.6% with the least-populated conformation having a free energy of 0.59 kcal/mol, relative to the most stable conformer. The conformations studied by Saunders and Jimenez-Vazquez usingmore » Allinger`s MM3 force field are described, and the calculated strain energies and populations are discussed. Energies for six conformations were also obtained from ab initio calculations at the HF/6-311G{sup *} level. 22 refs., 4 figs., 3 tabs.« less

Relating Ab Initio Mechanical Behavior of Intergranular Glassy Films in Γ-Si3N4 to Continuum Scales

NASA Astrophysics Data System (ADS)

Ouyang, L.; Chen, J.; Ching, W.; Misra, A.

2006-05-01

Nanometer thin intergranular glassy films (IGFs) form in polycrystalline ceramics during sintering at high temperatures. The structure and properties of these IGFs are significantly changed by doping with rare earth elements. We have performed highly accurate large-scale ab initio calculations of the mechanical properties of both undoped and Yittria doped (Y-IGF) model by theoretical uniaxial tensile experiments. Uniaxial strain was applied by incrementally stretching the super cell in one direction, while the other two dimensions were kept constant. At each strain, all atoms in the model were fully relaxed using Vienna Ab initio Simulation Package VASP. The relaxed model at a given strain serves as the starting position for the next increment of strain. This process is carried on until the total energy (TE) and stress data show that the "sample" is fully fractured. Interesting differences are seen between the stress-strain response of undoped and Y-doped models. For the undoped model, the stress-strain behavior indicates that the initial atomic structure of the IGF is such that there is negligible coupling between the x- and the y-z directions. However, once the behavior becomes non- linear the lateral stresses increase, indicating that the atomic structure evolves with loading [1]. To relate the ab initio calculations to the continuum scales we analyze the atomic-scale deformation field under this uniaxial loading [1]. The applied strain in the x-direction is mostly accommodated by the IGF part of the model and the crystalline part experiences almost negligible strain. As the overall strain on the sample is incrementally increased, the local strain field evolves such that locations proximal to the softer spots attract higher strains. As the load progresses, the strain concentration spots coalesce and eventually form persistent strain localization zone across the IGF. The deformation pattern obtained through ab initio calculations indicates that it is possible to construct discrete grain-scale models that may be used to bridge these calculations to the continuum scale for finite element analysis. Reference: 1. J. Chen, L. Ouyang, P. Rulis, A. Misra, W. Y. Ching, Phys. Rev. Lett. 95, 256103 (2005)

Isotope shifts in the 7 s →8 s transition of francium: Measurements and comparison to ab initio theory

NASA Astrophysics Data System (ADS)

Kalita, M. R.; Behr, J. A.; Gorelov, A.; Pearson, M. R.; DeHart, A. C.; Gwinner, G.; Kossin, M. J.; Orozco, L. A.; Aubin, S.; Gomez, E.; Safronova, M. S.; Dzuba, V. A.; Flambaum, V. V.

2018-04-01

We observe the electric-dipole forbidden 7 s →8 s transition in the francium isotopes Fr-211208 and 213Fr using a two-photon excitation scheme. We collect the atoms online from an accelerator and confine them in a magneto-optical trap for the measurements. In combination with previous measurements of the 7 s →7 p1 /2 transition we perform a King plot analysis. We compare the thus-determined ratio of the field shift constants (1.228 ± 0.019) to results obtained from new ab initio calculations (1.234 ± 0.010).

Ab initio quantum chemistry: methodology and applications.

PubMed

Friesner, Richard A

2005-05-10

This Perspective provides an overview of state-of-the-art ab initio quantum chemical methodology and applications. The methods that are discussed include coupled cluster theory, localized second-order Moller-Plesset perturbation theory, multireference perturbation approaches, and density functional theory. The accuracy of each approach for key chemical properties is summarized, and the computational performance is analyzed, emphasizing significant advances in algorithms and implementation over the past decade. Incorporation of a condensed-phase environment by means of mixed quantum mechanical/molecular mechanics or self-consistent reaction field techniques, is presented. A wide range of illustrative applications, focusing on materials science and biology, are discussed briefly.

Interaction between benzenedithiolate and gold: Classical force field for chemical bonding

NASA Astrophysics Data System (ADS)

Leng, Yongsheng; Krstić, Predrag S.; Wells, Jack C.; Cummings, Peter T.; Dean, David J.

2005-06-01

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as ˜100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Interaction between benzenedithiolate and gold: classical force field for chemical bonding.

PubMed

Leng, Yongsheng; Krstić, Predrag S; Wells, Jack C; Cummings, Peter T; Dean, David J

2005-06-22

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.

Ab initio calculations of the concentration dependent band gap reduction in dilute nitrides

NASA Astrophysics Data System (ADS)

Rosenow, Phil; Bannow, Lars C.; Fischer, Eric W.; Stolz, Wolfgang; Volz, Kerstin; Koch, Stephan W.; Tonner, Ralf

2018-02-01

While being of persistent interest for the integration of lattice-matched laser devices with silicon circuits, the electronic structure of dilute nitride III/V-semiconductors has presented a challenge to ab initio computational approaches. The origin of the computational problems is the strong distortion exerted by the N atoms on most host materials. Here, these issues are resolved by combining density functional theory calculations based on the meta-GGA functional presented by Tran and Blaha (TB09) with a supercell approach for the dilute nitride Ga(NAs). Exploring the requirements posed to supercells, it is shown that the distortion field of a single N atom must be allowed to decrease so far that it does not overlap with its periodic images. This also prevents spurious electronic interactions between translational symmetric atoms, allowing us to compute band gaps in very good agreement with experimentally derived reference values. In addition to existing approaches, these results offer a promising ab initio avenue to the electronic structure of dilute nitride semiconductor compounds.

Ab initio simulations of iron-nickel alloys at Earth's core conditions

NASA Astrophysics Data System (ADS)

Côté, Alexander S.; Vočadlo, Lidunka; Brodholt, John P.

2012-09-01

We report ab initio density functional theory calculations on iron-nickel (FeNi) alloys at conditions representative of the Earth's inner core. We test different concentrations of Ni, up to ∼39 wt% using ab initio lattice dynamics, and investigate the thermodynamic and vibrational stability of the three candidate crystal structures (bcc, hcp and fcc). First of all, at inner core pressures, we find that pure Fe transforms from the hcp to the fcc phase at around 6000 K. Secondly, in agreement with low pressure experiments on Fe-Ni alloys, we find the fcc structure is stabilised by the incorporation of Ni under core pressures and temperatures. Our results show that the fcc structure may, therefore, be stable under core conditions depending on the temperature in the inner core and the Ni content. Lastly, we find that within the quasi-harmonic approximation, there is no stability field for FeNi alloys in the bcc structure under core conditions.

Towards an ab-initio treatment of nonlocal electronic correlations with dynamical vertex approximation

NASA Astrophysics Data System (ADS)

Galler, Anna; Gunacker, Patrik; Tomczak, Jan; Thunström, Patrik; Held, Karsten

Recently, approaches such as the dynamical vertex approximation (D ΓA) or the dual-fermion method have been developed. These diagrammatic approaches are going beyond dynamical mean field theory (DMFT) by including nonlocal electronic correlations on all length scales as well as the local DMFT correlations. Here we present our efforts to extend the D ΓA methodology to ab-initio materials calculations (ab-initio D ΓA). Our approach is a unifying framework which includes both GW and DMFT-type of diagrams, but also important nonlocal correlations beyond, e.g. nonlocal spin fluctuations. In our multi-band implementation we are using a worm sampling technique within continuous-time quantum Monte Carlo in the hybridization expansion to obtain the DMFT vertex, from which we construct the reducible vertex function using the two particle-hole ladders. As a first application we show results for transition metal oxides. Support by the ERC project AbinitioDGA (306447) is acknowledged.

Morse-Smale Analysis of Ion Diffusion in Ab Initio Battery Materials Simulations

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

Gyulassy, Attila; Knoll, Aaron; Lau, Kah Chun

Ab initio molecular dynamics (AIMD) simulations are increasingly useful in modeling, optimizing and synthesizing materials in energy sciences. In solving Schrödinger’s equation, they generate the electronic structure of the simulated atoms as a scalar field. However, methods for analyzing these volume data are not yet common in molecular visualization. The Morse-Smale complex is a proven, versatile tool for topological analysis of scalar fields. In this paper, we apply the discrete Morse-Smale complex to analysis of first-principles battery materials simulations. We consider a carbon nanosphere structure used in battery materials research, and employ Morse-Smale decomposition to determine the possible lithium ionmore » diffusion paths within that structure. Our approach is novel in that it uses the wavefunction itself as opposed distance fields, and that we analyze the 1-skeleton of the Morse-Smale complex to reconstruct our diffusion paths. Furthermore, it is the first application where specific motifs in the graph structure of the complete 1-skeleton define features, namely carbon rings with specific valence. We compare our analysis of DFT data with that of a distance field approximation, and discuss implications on larger classical molecular dynamics simulations.« less

Hyperfine field and electronic structure of magnetite below the Verwey transition

NASA Astrophysics Data System (ADS)

Řezníček, R.; Chlan, V.; Štěpánková, H.; Novák, P.

2015-03-01

Magnetite represents a prototype compound with a mixed valence of iron cations. Its structure and electron ordering below the Verwey transition have been studied for decades. A recently published precise crystallographic structure [Senn et al., Nature (London) 481, 173 (2012), 10.1038/nature10704] accompanied by a suggestion of a "trimeron" model has given a new impulse to magnetite research. Here we investigate hyperfine field anisotropy in the C c phase of magnetite by quantitative reanalysis of published measurements of the dependences of the 57Fe nuclear magnetic resonance frequencies on the external magnetic field direction. Further, ab initio density-functional-theory-based calculations of hyperfine field depending on the magnetization direction using the recently reported crystal structure are carried out, and analogous hyperfine anisotropy data linked to particular crystallographic sites are determined. These two sets of data are compared, and mutually matching groups of the iron B sites in the 8:5:3 ratio are found. Moreover, information on electronic structure is obtained from the ab initio calculations. Our results are compared with the trimeron model and with an alternative analysis [Patterson, Phys. Rev. B 90, 075134 (2014), 10.1103/PhysRevB.90.075134] as well.

Efficient calculation of the energy of a molecule in an arbitrary electric field

NASA Astrophysics Data System (ADS)

Pulay, Peter; Janowski, Tomasz

In thermodynamic (e.g., Monte Carlo) simulations with electronic embedding, the energy of the active site or solute must be calculated for millions of configurations of the environment (solvent or protein matrix) to obtain reliable statistics. This precludes the use of accurate but expensive ab initio and density functional techniques. Except for the immediate neighbors, the effect of the environment is electrostatic. We show that the energy of a molecule in the irregular field of the environment can be determined very efficiently by expanding the electric potential in known functions, and precalculating the first and second order response of the molecule to the components of the potential. These generalized multipole moments and polarizabilities allow the calculation of the energy of the system without further ab initio calculations. Several expansion functions were explored: polynomials, distributed inverse powers, and sine functions. The latter provide the numerically most stable fit but require new types of integrals. Distributed inverse powers can be simulated using dummy atoms, and energies calculated this way provide a very good approximation to the actual energies in the field of the environment.

An ab-initio coupled mode theory for near field radiative thermal transfer.

PubMed

Chalabi, Hamidreza; Hasman, Erez; Brongersma, Mark L

2014-12-01

We investigate the thermal transfer between finite-thickness planar slabs which support surface phonon polariton modes (SPhPs). The thickness-dependent dispersion of SPhPs in such layered materials provides a unique opportunity to manipulate and enhance the near field thermal transfer. The key accomplishment of this paper is the development of an ab-initio coupled mode theory that accurately describes all of its thermal transfer properties. We illustrate how the coupled mode parameters can be obtained in a direct fashion from the dispersion relation of the relevant modes of the system. This is illustrated for the specific case of a semi-infinite SiC substrate placed in close proximity to a thin slab of SiC. This is a system that exhibits rich physics in terms of its thermal transfer properties, despite the seemingly simple geometry. This includes a universal scaling behavior of the thermal conductance with the slab thickness and spacing. The work highlights and further increases the value of coupled mode theories in rapidly calculating and intuitively understanding near-field transfer.

Three-Nucleon Forces and Triplet Pairing in Neutron Matter

NASA Astrophysics Data System (ADS)

Papakonstantinou, P.; Clark, J. W.

2017-12-01

The existence of superfluidity of the neutron component in the core of a neutron star, associated specifically with triplet P-wave pairing, is currently an open question that is central to interpretation of the observed cooling curves and other neutron-star observables. Ab initio theoretical calculations aimed at resolving this issue face unique challenges in the relevant high-density domain, which reaches beyond the saturation density of symmetrical nuclear matter. These issues include uncertainties in the three-nucleon (3N) interaction and in the effects of strong short-range correlations—and more generally of in-medium modification of nucleonic self-energies and interactions. A survey of existing solutions of the gap equations in the triplet channel demonstrates that the net impact on the gap magnitude of 3N forces, coupled channels, and mass renormalization shows extreme variation dependent on specific theoretical inputs, in some cases even pointing to the absence of a triplet gap, thus motivating a detailed analysis of competing effects within a well-controlled model. In the present study, we track the effects of the 3N force and in-medium modifications in the representative case of the ^3P_2 channel, based on the Argonne v_{18} two-nucleon (2N) interaction supplemented by 3N interactions of the Urbana IX family. Sensitivity of the results to the input interaction is clearly demonstrated. We point out consistency issues with respect to the simultaneous treatment of 3N forces and in-medium effects, which warrant further investigation. We consider this pilot study as the first step toward a systematic and comprehensive exploration of coupled-channel ^3P F_2 pairing using a broad range of 2N and 3N interactions from the current generation of refined semi-phenomenological models and models derived from chiral effective field theory.

Effective Forces Between Colloidal Particles

NASA Technical Reports Server (NTRS)

Tehver, Riina; Banavar, Jayanth R.; Koplik, Joel

1999-01-01

Colloidal suspensions have proven to be excellent model systems for the study of condensed matter and its phase behavior. Many of the properties of colloidal suspensions can be investigated with a systematic variation of the characteristics of the systems and, in addition, the energy, length and time scales associated with them allow for experimental probing of otherwise inaccessible regimes. The latter property also makes colloidal systems vulnerable to external influences such as gravity. Experiments performed in micro-ravity by Chaikin and Russell have been invaluable in extracting the true behavior of the systems without an external field. Weitz and Pusey intend to use mixtures of colloidal particles with additives such as polymers to induce aggregation and form weak, tenuous, highly disordered fractal structures that would be stable in the absence of gravitational forces. When dispersed in a polarizable medium, colloidal particles can ionize, emitting counterions into the solution. The standard interaction potential in these charged colloidal suspensions was first obtained by Derjaguin, Landau, Verwey and Overbeek. The DLVO potential is obtained in the mean-field linearized Poisson-Boltzmann approximation and thus has limited applicability. For more precise calculations, we have used ab initio density functional theory. In our model, colloidal particles are charged hard spheres, the counterions are described by a continuum density field and the solvent is treated as a homogeneous medium with a specified dielectric constant. We calculate the effective forces between charged colloidal particles by integrating over the solvent and counterion degrees of freedom, taking into account the direct interactions between the particles as well as particle-counterion, counterion-counterion Coulomb, counterion entropic and correlation contributions. We obtain the effective interaction potential between charged colloidal particles in different configurations. We evaluate two- and three-body forces in the bulk as well as study the influence of soft walls. We qualitatively explain the effects of the walls on the forces and demonstrate that many-body effects are negligible in our system. With adjustments in the parameters, the DLVO pair-potential can describe the results quantitatively. Besides electrostatic interactions, entropic depletion effects that arise from (hard-core) exclusion play an important role in determining the behavior of multi-component colloidal suspensions. A standard theory for depletion forces is due to Asakura and Oosawa and is based on the ideal gas approximation. To go beyond this approximation, we have studied entropic forces in molecular dynamics simulations of systems of hard spheres (the effects of the solvent have been ignored). The effective depletion forces for these systems can be found either from equilibrium distribution functions or from direct momentum transfer calculations. Our results obtained by either method show qualitative differences from the Asakura-Oosawa forces, indicating a longer range, higher value at contact and most importantly a more complicated structure, comprising of several maxima and minima. Our calculations include the determination of effective forces between two spheres, a hard sphere and a wall, and the behavior of a hard sphere near a step-edge and a corner. We also demonstrate that such entropic forces do not necessarily satisfy pairwise additivity.

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

Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.

We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCEmore » allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.« less

On the R-Dependence of the Spin-Orbit Coupling Constant: Potential Energy Functions of Xe2+ by High-Resolution Photoelectron Spectroscopy and ab initio Quantum Chemistry

DTIC Science & Technology

2008-01-01

ORGANIZATION NAME(S) AND ADDRESS(ES) 8. PERFORMING ORGANIZATION REPORT NUMBER Air Force Research Laboratory /RVBXR AFRL-RV-HA-TR-2008-1053 29 Randolph...the umn 2 in Table I) features a very similiar behavior of a(R) g states so that the asymptotic value of a(R) exactly coffe - although these a(R) curves

Light focusing through a multiple scattering medium: ab initio computer simulation

NASA Astrophysics Data System (ADS)

Danko, Oleksandr; Danko, Volodymyr; Kovalenko, Andrey

2018-01-01

The present study considers ab initio computer simulation of the light focusing through a complex scattering medium. The focusing is performed by shaping the incident light beam in order to obtain a small focused spot on the opposite side of the scattering layer. MSTM software (Auburn University) is used to simulate the propagation of an arbitrary monochromatic Gaussian beam and obtain 2D distribution of the optical field in the selected plane of the investigated volume. Based on the set of incident and scattered fields, the pair of right and left eigen bases and corresponding singular values were calculated. The pair of right and left eigen modes together with the corresponding singular value constitute the transmittance eigen channel of the disordered media. Thus, the scattering process is described in three steps: 1) initial field decomposition in the right eigen basis; 2) scaling of decomposition coefficients for the corresponding singular values; 3) assembling of the scattered field as the composition of the weighted left eigen modes. Basis fields are represented as a linear combination of the original Gaussian beams and scattered fields. It was demonstrated that 60 independent control channels provide focusing the light into a spot with the minimal radius of approximately 0.4 μm at half maximum. The intensity enhancement in the focal plane was equal to 68 that coincided with theoretical prediction.

Adaptive switching of interaction potentials in the time domain: an extended Lagrangian approach tailored to transmute force field to QM/MM simulations and back.

PubMed

Böckmann, Marcus; Doltsinis, Nikos L; Marx, Dominik

2015-06-09

An extended Lagrangian formalism that allows for a smooth transition between two different descriptions of interactions during a molecular dynamics simulation is presented. This time-adaptive method is particularly useful in the context of multiscale simulation as it provides a sound recipe to switch on demand between different hierarchical levels of theory, for instance between ab initio ("QM") and force field ("MM") descriptions of a given (sub)system in the course of a molecular dynamics simulation. The equations of motion can be integrated straightforwardly using the usual propagators, such as the Verlet algorithm. First test cases include a bath of harmonic oscillators, of which a subset is switched to a different force constant and/or equilibrium position, as well as an all-MM to QM/MM transition in a hydrogen-bonded water dimer. The method is then applied to a smectic 8AB8 liquid crystal and is shown to be able to switch dynamically a preselected 8AB8 molecule from an all-MM to a QM/MM description which involves partition boundaries through covalent bonds. These examples show that the extended Lagrangian approach is not only easy to implement into existing code but that it is also efficient and robust. The technique moreover provides easy access to a conserved energy quantity, also in cases when Nosé-Hoover chain thermostatting is used throughout dynamical switching. A simple quadratic driving potential proves to be sufficient to guarantee a smooth transition whose time scale can be easily tuned by varying the fictitious mass parameter associated with the auxiliary variable used to extend the Lagrangian. The method is general and can be applied to time-adaptive switching on demand between two different levels of theory within the framework of hybrid scale-bridging simulations.

Quantitative verification of ab initio self-consistent laser theory.

PubMed

Ge, Li; Tandy, Robert J; Stone, A D; Türeci, Hakan E

2008-10-13

We generalize and test the recent "ab initio" self-consistent (AISC) time-independent semiclassical laser theory. This self-consistent formalism generates all the stationary lasing properties in the multimode regime (frequencies, thresholds, internal and external fields, output power and emission pattern) from simple inputs: the dielectric function of the passive cavity, the atomic transition frequency, and the transverse relaxation time of the lasing transition.We find that the theory gives excellent quantitative agreement with full time-dependent simulations of the Maxwell-Bloch equations after it has been generalized to drop the slowly-varying envelope approximation. The theory is infinite order in the non-linear hole-burning interaction; the widely used third order approximation is shown to fail badly.

Mapping energetics of atom probe evaporation events through first principles calculations.

PubMed

Peralta, Joaquín; Broderick, Scott R; Rajan, Krishna

2013-09-01

The purpose of this work is to use atomistic modeling to determine accurate inputs into the atom probe tomography (APT) reconstruction process. One of these inputs is evaporation field; however, a challenge occurs because single ions and dimers have different evaporation fields. We have calculated the evaporation field of Al and Sc ions and Al-Al and Al-Sc dimers from an L1₂-Al₃Sc surface using ab initio calculations and with a high electric field applied to the surface. The evaporation field is defined as the electric field at which the energy barrier size is calculated as zero, corresponding to the minimum field that atoms from the surface can break their bonds and evaporate from the surface. The evaporation field of the surface atoms are ranked from least to greatest as: Al-Al dimer, Al ion, Sc ion, and Al-Sc dimer. The first principles results were compared with experimental data in the form of an ion evaporation map, which maps multi-ion evaporations. From the ion evaporation map of L1₂-Al₃Sc, we extract relative evaporation fields and identify that an Al-Al dimer has a lower evaporation field than an Al-Sc dimer. Additionally, comparatively an Al-Al surface dimer is more likely to evaporate as a dimer, while an Al-Sc surface dimer is more likely to evaporate as single ions. These conclusions from the experiment agree with the ab initio calculations, validating the use of this approach for modeling APT energetics. Copyright © 2013 Elsevier B.V. All rights reserved.

Ab initio phonon point defect scattering and thermal transport in graphene

NASA Astrophysics Data System (ADS)

Polanco, Carlos A.; Lindsay, Lucas

2018-01-01

We study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitude smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (˜ω0 ) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. This work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.

Interpolating moving least-squares methods for fitting potential energy surfaces: using classical trajectories to explore configuration space.

PubMed

Dawes, Richard; Passalacqua, Alessio; Wagner, Albert F; Sewell, Thomas D; Minkoff, Michael; Thompson, Donald L

2009-04-14

We develop two approaches for growing a fitted potential energy surface (PES) by the interpolating moving least-squares (IMLS) technique using classical trajectories. We illustrate both approaches by calculating nitrous acid (HONO) cis-->trans isomerization trajectories under the control of ab initio forces from low-level HF/cc-pVDZ electronic structure calculations. In this illustrative example, as few as 300 ab initio energy/gradient calculations are required to converge the isomerization rate constant at a fixed energy to approximately 10%. Neither approach requires any preliminary electronic structure calculations or initial approximate representation of the PES (beyond information required for trajectory initial conditions). Hessians are not required. Both approaches rely on the fitting error estimation properties of IMLS fits. The first approach, called IMLS-accelerated direct dynamics, propagates individual trajectories directly with no preliminary exploratory trajectories. The PES is grown "on the fly" with the computation of new ab initio data only when a fitting error estimate exceeds a prescribed tight tolerance. The second approach, called dynamics-driven IMLS fitting, uses relatively inexpensive exploratory trajectories to both determine and fit the dynamically accessible configuration space. Once exploratory trajectories no longer find configurations with fitting error estimates higher than the designated accuracy, the IMLS fit is considered to be complete and usable in classical trajectory calculations or other applications.

Covariant density functional theory: predictive power and first attempts of a microscopic derivation

NASA Astrophysics Data System (ADS)

Ring, Peter

2018-05-01

We discuss systematic global investigations with modern covariant density functionals. The number of their phenomenological parameters can be reduced considerable by using microscopic input from ab-initio calculations in nuclear matter. The size of the tensor force is still an open problem. Therefore we use the first full relativistic Brueckner-Hartree-Fock calculations in finite nuclear systems in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

Gordon Research Conference on High Temperature Chemistry (1982), Tilton School, Tilton, New Hampshire, July 26-30, 1982.

DTIC Science & Technology

1982-08-01

Session on Recent Advances in High Temperature Chemistry’ Thursday. July 29 Ab Initio Calculations of Molecular W. Weltner, Discussion Leader Structure...atomic fluorescence 13 R. Schoonmaker, Oberlin College: "Scattering of molecular beams from surfaces, dynamics of gas-surface interactions and the...Air Force Geophys. Lab., Ianscom, AFB ,iA Group V1310, lela Park, Cleveland, OH 44112 01731 Saboungi, Marie-Louise off campus Myers, Clifford and

Progress on first-principles-based materials design for hydrogen storage.

PubMed

Park, Noejung; Choi, Keunsu; Hwang, Jeongwoon; Kim, Dong Wook; Kim, Dong Ok; Ihm, Jisoon

2012-12-04

This article briefly summarizes the research activities in the field of hydrogen storage in sorbent materials and reports our recent works and future directions for the design of such materials. Distinct features of sorption-based hydrogen storage methods are described compared with metal hydrides and complex chemical hydrides. We classify the studies of hydrogen sorbent materials in terms of two key technical issues: (i) constructing stable framework structures with high porosity, and (ii) increasing the binding affinity of hydrogen molecules to surfaces beyond the usual van der Waals interaction. The recent development of reticular chemistry is summarized as a means for addressing the first issue. Theoretical studies focus mainly on the second issue and can be grouped into three classes according to the underlying interaction mechanism: electrostatic interactions based on alkaline cations, Kubas interactions with open transition metals, and orbital interactions involving Ca and other nontransitional metals. Hierarchical computational methods to enable the theoretical predictions are explained, from ab initio studies to molecular dynamics simulations using force field parameters. We also discuss the actual delivery amount of stored hydrogen, which depends on the charging and discharging conditions. The usefulness and practical significance of the hydrogen spillover mechanism in increasing the storage capacity are presented as well.

Highly Surface-Active Ca(OH)2 Monolayer as a CO2 Capture Material.

PubMed

Özçelik, V Ongun; Gong, Kai; White, Claire E

2018-03-14

Greenhouse gas emissions originating from fossil fuel combustion contribute significantly to global warming, and therefore the design of novel materials that efficiently capture CO 2 can play a crucial role in solving this challenge. Here, we show that reducing the dimensionality of bulk crystalline portlandite results in a stable monolayer material, named portlandene, that is highly effective at capturing CO 2 . On the basis of theoretical analysis comprised of ab initio quantum mechanical calculations and force-field molecular dynamics simulations, we show that this single-layer phase is robust and maintains its stability even at high temperatures. The chemical activity of portlandene is seen to further increase upon defect engineering of its surface using vacancy sites. Defect-containing portlandene is capable of separating CO and CO 2 from a syngas (CO/CO 2 /H 2 ) stream, yet is inert to water vapor. This selective behavior and the associated mechanisms have been elucidated by examining the electronic structure, local charge distribution, and bonding orbitals of portlandene. Additionally, unlike conventional CO 2 capturing technologies, the regeneration process of portlandene does not require high temperature heat treatment because it can release the captured CO 2 by application of a mild external electric field, making portlandene an ideal CO 2 capturing material for both pre- and postcombustion processes.

Progress on first-principles-based materials design for hydrogen storage

PubMed Central

Park, Noejung; Choi, Keunsu; Hwang, Jeongwoon; Kim, Dong Wook; Kim, Dong Ok; Ihm, Jisoon

2012-01-01

This article briefly summarizes the research activities in the field of hydrogen storage in sorbent materials and reports our recent works and future directions for the design of such materials. Distinct features of sorption-based hydrogen storage methods are described compared with metal hydrides and complex chemical hydrides. We classify the studies of hydrogen sorbent materials in terms of two key technical issues: (i) constructing stable framework structures with high porosity, and (ii) increasing the binding affinity of hydrogen molecules to surfaces beyond the usual van der Waals interaction. The recent development of reticular chemistry is summarized as a means for addressing the first issue. Theoretical studies focus mainly on the second issue and can be grouped into three classes according to the underlying interaction mechanism: electrostatic interactions based on alkaline cations, Kubas interactions with open transition metals, and orbital interactions involving Ca and other nontransitional metals. Hierarchical computational methods to enable the theoretical predictions are explained, from ab initio studies to molecular dynamics simulations using force field parameters. We also discuss the actual delivery amount of stored hydrogen, which depends on the charging and discharging conditions. The usefulness and practical significance of the hydrogen spillover mechanism in increasing the storage capacity are presented as well. PMID:23161910

Effect of electron-to-ion mass ratio on radial electric field generation in tokamak

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

Li, Zhenqian; Dong, Jiaqi; Sheng, Zhengmao

Generation of coherent radial electric fields in plasma by drift-wave turbulence driven by plasma inhomogeneities is ab initio studied using gyro-kinetic particle simulation for conditions of operational tokamaks. In particular, the effect of the electron-to-ion mass ratio epsilon on the entire evolution of the plasma is considered. In conclusion, it is found that the electric field can be increased, and the turbulence-induced particle transport reduced, by making epsilon smaller, in agreement with many existing experimental observations.

Effect of electron-to-ion mass ratio on radial electric field generation in tokamak

DOE PAGES

Li, Zhenqian; Dong, Jiaqi; Sheng, Zhengmao; ...

2017-11-21

Generation of coherent radial electric fields in plasma by drift-wave turbulence driven by plasma inhomogeneities is ab initio studied using gyro-kinetic particle simulation for conditions of operational tokamaks. In particular, the effect of the electron-to-ion mass ratio epsilon on the entire evolution of the plasma is considered. In conclusion, it is found that the electric field can be increased, and the turbulence-induced particle transport reduced, by making epsilon smaller, in agreement with many existing experimental observations.

10 μm High-resolution spectrum of trans -acrolein: Rotational analysis of the ν 11 , ν 16 , ν 14 and ν 16 + ν 18 - ν 18 bands

NASA Astrophysics Data System (ADS)

Xu, Li-Hong; Jiang, Xingjie; Shi, Hongyu; Lees, R. M.; McKellar, A. R. W.; Tokaryk, D. W.; Appadoo, D. R. T.

2011-07-01

High-resolution Fourier transform spectra of trans-acrolein, H 2C dbnd C(H) sbnd C(H) dbnd O, have been recorded in the 10 μm region at both room and cooled temperatures on the modified Bomem DA3.002 at the National Research Council of Canada and the Bruker IFS 125HR spectrometer at the far infrared beam line of the Canadian Light Source in Saskatoon. Vibrational fundamentals analyzed so far include the ν11, ν16 and ν14 bands centered at 911.3, 958.7 and 992.7 cm -1 corresponding respectively to the A' in-plane dbnd CH 2-rocking mode, the A″ out-of-plane dbnd CH 2-wagging mode, and the A″ wagging mode highly mixed between the ⩾C sbnd H vinyl and ⩾C sbnd H formyl groups [Vibrational mode descriptions are based on Y.N. Panchenko, P. Pulay, F. Török, J. Mol. Spectrosc. 34 (1976) 283-289.] As well, the ν16 + ν18 - ν18 hot band centred at 957.6 cm -1 has been analyzed, where ν18 is the low-frequency (157.9 cm -1) A″ ⩾C sbnd C ⪕ torsional mode. The ν11 band is a/ b type while the ν16, ν14 and ν16 + ν18 - ν18 bands are c-type. The assigned transitions of each band have been fitted to a Watson asymmetric rotor Hamiltonian, with ground state parameters fixed to values obtained from rotational analyses in the literature. As well, a combined 3-state fit for ν11, ν16 and ν14 was carried out including Coriolis and Z1 constants which account for J and Δ K interactions. Transition dipole moments have been calculated for each of the fundamentals using the ab initio B3LYP method and 6-311++G ∗∗ basis set. For the A' vibrational modes, we have also evaluated transition dipole a- and b-components in the principal axis system from vibrational displacements and dipole moment derivatives. Our ab initio results predict that the ν11 in-plane dbnd CH 2 rocking mode has an a-type transition strength about three times greater than the b-type, which is consistent with our observations. Our ab initio force field analysis gives vibrational mode descriptions consistent with previously published work for all 13 A' modes. However, for the five A″ vibrational modes, our ab initio results disagree with two of the descriptions of Panchenko et al. and three of the descriptions of Hamada et al. [Y. Hamada, Y. Nishimura, M. Tsuboi, Chem. Phys. 100 (1985) 365-375].

Determination of nuclear quadrupole moments – An example of the synergy of ab initio calculations and microwave spectroscopy

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

Kellö, Vladimir

Highly correlated scalar relativistic calculations of electric field gradients at nuclei in diatomic molecules in combination with accurate nuclear quadrupole coupling constants obtained from microwave spectroscopy are used for determination of nuclear quadrupole moments.

Theory-restricted resonant x-ray reflectometry of quantum materials

NASA Astrophysics Data System (ADS)

Fürsich, Katrin; Zabolotnyy, Volodymyr B.; Schierle, Enrico; Dudy, Lenart; Kirilmaz, Ozan; Sing, Michael; Claessen, Ralph; Green, Robert J.; Haverkort, Maurits W.; Hinkov, Vladimir

2018-04-01

The delicate interplay of competing phases in quantum materials is dominated by parameters such as the crystal field potential, the spin-orbit coupling, and, in particular, the electronic correlation strength. Whereas small quantitative variations of the parameter values can thus qualitatively change the material, these values can hitherto hardly be obtained with reasonable precision, be it theoretically or experimentally. Here we propose a solution combining resonant x-ray reflectivity (RXR) with multiplet ligand field theory (MLFT). We first perform ab initio DFT calculations within the MLFT framework to get initial parameter values, which we then use in a fit of the theoretical model to RXR. To validate our method, we apply it to NiO and SrTiO3 and obtain parameter values, which are amended by as much as 20 % compared to the ab initio results. Our approach is particularly useful to investigate topologically trivial and nontrivial correlated insulators, staggered moments in magnetically or orbitally ordered materials, and reconstructed interfaces.

Weak-field few-femtosecond VUV photodissociation dynamics of water isotopologues

NASA Astrophysics Data System (ADS)

Baumann, Arne; Bazzi, Sophia; Rompotis, Dimitrios; Schepp, Oliver; Azima, Armin; Wieland, Marek; Popova-Gorelova, Daria; Vendrell, Oriol; Santra, Robin; Drescher, Markus

2017-07-01

We present a joint experimental and theoretical study of the VUV-induced dynamics of H2O and its deuterated isotopologues in the first excited state (A ˜1B1 ) utilizing a VUV-pump VUV-probe scheme combined with a b initio classical trajectory calculations. 16-fs VUV pulses centered at 161 nm created by fifth-order harmonic generation are employed for single-shot pump-probe measurements. Combined with a precise determination of the VUV pulses' temporal profile, they provide the necessary temporal resolution to elucidate sub-10-fs dissociation dynamics in the 1+1 photon ionization time window. Ionization with a single VUV photon complements established strong-field ionization schemes by disclosing the molecular dynamics under perturbative conditions. Kinetic isotope effects derived from the pump-probe experiment are found to be in agreement with our by ab initio classical trajectory calculations, taking into account photoionization cross sections for the ground and first excited state of the water cation.

The ab initio Calculation of Electric Field Gradient at the Site of P Impurity in α-Al3O2

NASA Astrophysics Data System (ADS)

Zhang, Qiao-Li; Yuan, Da-Qing; Zhang, Huan-Qiao; Fan, Ping; Zuo, Yi; Zheng, Yong-Nan; Masuta, K.; Fukuda, M.; Mihara, M.; Minamisono, T.; Kitagawa, A.; Zhu, Sheng-Yun

2012-09-01

An ab initio calculation of the electric-field gradient (EFG) at the site of a phosphorous impurity substituting an Al atom in α-Al2O3 is carried out using the WIEN2k code with the full-potential linearized augmented plane wave plus local orbital method (LAPW+lo) in the frame of density functional theory. The atomic lattice relaxations caused by the implanted impurities were calculated for two different charged states to well describe the electronic structure of the doped system. The EFG at the site of the phosphorous impurity in the charged supercell calculated with the exchange-correlation potential of the Wu-Cohen generalized gradient approximation (WC-GGA) is 0.573 × 1021 V/m2. Then, the nuclear quadrupole moment of the I = 3 state in 28P is deduced to be 137 mb from the quadrupole interaction frequency of 190 kHz measured recently by the β-NQR method.

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

Trevisanutto, Paolo E.; Vignale, Giovanni, E-mail: vignaleg@missouri.edu

Ab initio electronic structure calculations of two-dimensional layered structures are typically performed using codes that were developed for three-dimensional structures, which are periodic in all three directions. The introduction of a periodicity in the third direction (perpendicular to the layer) is completely artificial and may lead in some cases to spurious results and to difficulties in treating the action of external fields. In this paper we develop a new approach, which is “native” to quasi-2D materials, making use of basis function that are periodic in the plane, but atomic-like in the perpendicular direction. We show how some of the basicmore » tools of ab initio electronic structure theory — density functional theory, GW approximation and Bethe-Salpeter equation — are implemented in the new basis. We argue that the new approach will be preferable to the conventional one in treating the peculiarities of layered materials, including the long range of the unscreened Coulomb interaction in insulators, and the effects of strain, corrugations, and external fields.« less

Proton affinity of the histidine-tryptophan cluster motif from the influenza A virus from ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Bankura, Arindam; Klein, Michael L.; Carnevale, Vincenzo

2013-08-01

Ab initio molecular dynamics calculations have been used to compare and contrast the deprotonation reaction of a histidine residue in aqueous solution with the situation arising in a histidine-tryptophan cluster. The latter is used as a model of the proton storage unit present in the pore of the M2 proton conducting ion channel. We compute potentials of mean force for the dissociation of a proton from the Nδ and Nɛ positions of the imidazole group to estimate the pKas. Anticipating our results, we will see that the estimated pKa for the first protonation event of the M2 channel is in good agreement with experimental estimates. Surprisingly, despite the fact that the histidine is partially desolvated in the M2 channel, the affinity for protons is similar to that of a histidine in aqueous solution. Importantly, the electrostatic environment provided by the indoles is responsible for the stabilization of the charged imidazolium.

Nonequilibrium ab initio molecular dynamics determination of Ti monovacancy migration rates in B 1 TiN

NASA Astrophysics Data System (ADS)

Gambino, D.; Sangiovanni, D. G.; Alling, B.; Abrikosov, I. A.

2017-09-01

We use the color diffusion (CD) algorithm in nonequilibrium (accelerated) ab initio molecular dynamics simulations to determine Ti monovacancy jump frequencies in NaCl-structure titanium nitride (TiN), at temperatures ranging from 2200 to 3000 K. Our results show that the CD method extended beyond the linear-fitting rate-versus-force regime [Sangiovanni et al., Phys. Rev. B 93, 094305 (2016), 10.1103/PhysRevB.93.094305] can efficiently determine metal vacancy migration rates in TiN, despite the low mobilities of lattice defects in this type of ceramic compound. We propose a computational method based on gamma-distribution statistics, which provides unambiguous definition of nonequilibrium and equilibrium (extrapolated) vacancy jump rates with corresponding statistical uncertainties. The acceleration-factor achieved in our implementation of nonequilibrium molecular dynamics increases dramatically for decreasing temperatures from 500 for T close to the melting point Tm, up to 33 000 for T ≈0.7 Tm .

Electronic structure, dielectric response, and surface charge distribution of RGD (1FUV) peptide.

PubMed

Adhikari, Puja; Wen, Amy M; French, Roger H; Parsegian, V Adrian; Steinmetz, Nicole F; Podgornik, Rudolf; Ching, Wai-Yim

2014-07-08

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor.

Ab initio prediction of the vibration-rotation-tunneling spectrum of HCl-(H2O)2

NASA Astrophysics Data System (ADS)

Wormer, P. E. S.; Groenenboom, G. C.; van der Avoird, A.

2001-08-01

Quantum calculations of the vibration-rotation-tunneling (VRT) levels of the trimer HCl-(H2O)2 are presented. Two internal degrees of freedom are considered—the rotation angles of the two nonhydrogen-bonded (flipping) hydrogens in the complex—together with the overall rotation of the trimer in space. The kinetic energy expression of van der Avoird et al. [J. Chem. Phys. 105, 8034 (1996)] is used in a slightly modified form. The experimental microwave geometry of Kisiel et al. [J. Chem. Phys. 112, 5767 (2000)] served as input in the generation of a planar reference structure. The two-dimensional potential energy surface is generated ab initio by the iterative coupled-cluster method based on singly and doubly excited states with triply excited states included noniteratively [CCSD(T)]. Frequencies of vibrations and tunnel splittings are predicted for two isotopomers. The effect of the nonadditive three-body forces is considered and found to be important.

Automated combinatorial method for fast and robust prediction of lattice thermal conductivity

NASA Astrophysics Data System (ADS)

Plata, Jose J.; Nath, Pinku; Usanmaz, Demet; Toher, Cormac; Fornari, Marco; Buongiorno Nardelli, Marco; Curtarolo, Stefano

The lack of computationally inexpensive and accurate ab-initio based methodologies to predict lattice thermal conductivity, κl, without computing the anharmonic force constants or performing time-consuming ab-initio molecular dynamics, is one of the obstacles preventing the accelerated discovery of new high or low thermal conductivity materials. The Slack equation is the best alternative to other more expensive methodologies but is highly dependent on two variables: the acoustic Debye temperature, θa, and the Grüneisen parameter, γ. Furthermore, different definitions can be used for these two quantities depending on the model or approximation. Here, we present a combinatorial approach based on the quasi-harmonic approximation to elucidate which definitions of both variables produce the best predictions of κl. A set of 42 compounds was used to test accuracy and robustness of all possible combinations. This approach is ideal for obtaining more accurate values than fast screening models based on the Debye model, while being significantly less expensive than methodologies that solve the Boltzmann transport equation.

Electron transport in extended carbon-nanotube/metal contacts: Ab initio based Green function method

NASA Astrophysics Data System (ADS)

Fediai, Artem; Ryndyk, Dmitry A.; Cuniberti, Gianaurelio

2015-04-01

We have developed a new method that is able to predict the electrical properties of the source and drain contacts in realistic carbon nanotube field effect transistors (CNTFETs). It is based on large-scale ab initio calculations combined with a Green function approach. For the first time, both internal and external parts of a realistic CNT-metal contact are taken into account at the ab initio level. We have developed the procedure allowing direct calculation of the self-energy for an extended contact. Within the method, it is possible to calculate the transmission coefficient through a contact of both finite and infinite length; the local density of states can be determined in both free and embedded CNT segments. We found perfect agreement with the experimental data for Pd and Al contacts. We have explained why CNTFETs with Pd electrodes are p -type FETs with ohmic contacts, which can carry current close to the ballistic limit (provided contact length is large enough), whereas in CNT-Al contacts transmission is suppressed to a significant extent, especially for holes.

Alkyl hydrogen atom abstraction reactions of the CN radical with ethanol

NASA Astrophysics Data System (ADS)

Athokpam, Bijyalaxmi; Ramesh, Sai G.

2018-04-01

We present a study of the abstraction of alkyl hydrogen atoms from the β and α positions of ethanol by the CN radical in solution using the Empirical Valence Bond (EVB) method. We have built separate 2 × 2 EVB models for the Hβ and Hα reactions, where the atom transfer is parameterized using ab initio calculations. The intra- and intermolecular potentials of the reactant and product molecules were modelled with the General AMBER Force Field, with some modifications. We have carried out the dynamics in water and chloroform, which are solvents of contrasting polarity. We have computed the potential of mean force for both abstractions in each of the solvents. They are found to have a small and early barrier along the reaction coordinate with a large energy release. Analyzing the solvent structure around the reaction system, we have found two solvents to have little effect on either reaction. Simulating the dynamics from the transition state, we also study the fate of the energies in the HCN vibrational modes. The HCN molecule is born vibrationally hot in the CH stretch in both reactions and additionally in the HCN bends for the Hα abstraction reaction. In the early stage of the dynamics, we find that the CN stretch mode gains energy at the expense of the energy in CH stretch mode.

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions.

PubMed

Danecek, Petr; Kapitán, Josef; Baumruk, Vladimír; Bednárová, Lucie; Kopecký, Vladimír; Bour, Petr

2007-06-14

The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800 cm(-1)) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third and fourth energy derivatives), except for a few weak combination bands which were dominated by the anharmonic tensor contributions.

Anharmonic effects in IR, Raman, and Raman optical activity spectra of alanine and proline zwitterions

NASA Astrophysics Data System (ADS)

Daněček, Petr; Kapitán, Josef; Baumruk, Vladimír; Bednárová, Lucie; Kopecký, Vladimír; Bouř, Petr

2007-06-01

The difference spectroscopy of the Raman optical activity (ROA) provides extended information about molecular structure. However, interpretation of the spectra is based on complex and often inaccurate simulations. Previously, the authors attempted to make the calculations more robust by including the solvent and exploring the role of molecular flexibility for alanine and proline zwitterions. In the current study, they analyze the IR, Raman, and ROA spectra of these molecules with the emphasis on the force field modeling. Vibrational harmonic frequencies obtained with 25 ab initio methods are compared to experimental band positions. The role of anharmonic terms in the potential and intensity tensors is also systematically explored using the vibrational self-consistent field, vibrational configuration interaction (VCI), and degeneracy-corrected perturbation calculations. The harmonic approach appeared satisfactory for most of the lower-wavelength (200-1800cm-1) vibrations. Modern generalized gradient approximation and hybrid density functionals, such as the common B3LYP method, provided a very good statistical agreement with the experiment. Although the inclusion of the anharmonic corrections still did not lead to complete agreement between the simulations and the experiment, occasional enhancements were achieved across the entire region of wave numbers. Not only the transitional frequencies of the C-H stretching modes were significantly improved but also Raman and ROA spectral profiles including N-H and C-H lower-frequency bending modes were more realistic after application of the VCI correction. A limited Boltzmann averaging for the lowest-frequency modes that could not be included directly in the anharmonic calculus provided a realistic inhomogeneous band broadening. The anharmonic parts of the intensity tensors (second dipole and polarizability derivatives) were found less important for the entire spectral profiles than the force field anharmonicities (third and fourth energy derivatives), except for a few weak combination bands which were dominated by the anharmonic tensor contributions.

Structural, electronic and magnetic properties of LaCr2Si2C: Ab initio calculation, mean field approximation and Monte-Carlo simulation

NASA Astrophysics Data System (ADS)

Endichi, A.; Zaari, H.; Benyoussef, A.; El Kenz, A.

2018-06-01

The magnetic behavior of LaCr2Si2C compound is investigated in this work, using first principle methods, Monte Carlo simulation (MCS) and mean field approximation (MFA). The structural, electronic and magnetic properties are described using ab initio method in the framework of the Generalized Gradient Approximation (GGA), and the Full Potential-Linearized Augmented Plane Wave (FP-LAPW) method implemented in the WIEN2K packages. We have also computed the coupling terms between magnetic atoms which are used in Hamiltonian model. A theoretical study realized by mean field approximation and Monte Carlo Simulation within the Ising model is used to more understand the magnetic properties of this compound. Thereby, our results showed a ferromagnetic ordering of the Cr magnetic moments below the Curie temperature of 30 K (Tc < 30 K) in LaCr2Si2C. Other parameters are also computed as: the magnetization, the energy, the specific heat and the susceptibility. This material shows the small sign of supra-conductivity; and future researches could be focused to enhance the transport and magnetic properties of this system.

Enhanced angular overlap model for nonmetallic f -electron systems

NASA Astrophysics Data System (ADS)

Gajek, Z.

2005-07-01

An efficient method of interpretation of the crystal field effect in nonmetallic f -electron systems, the enhanced angular overlap model (EAOM), is presented. The method is established on the ground of perturbation expansion of the effective Hamiltonian for localized electrons and first-principles calculations related to available experimental data. The series of actinide compounds AO2 , oxychalcogenides AOX , and dichalcogenides UX2 where X=S ,Se,Te and A=U ,Np serve as probes of the effectiveness of the proposed method. An idea is to enhance the usual angular overlap model with ab initio calculations of those contributions to the crystal field potential, which cannot be represented by the usual angular overlap model (AOM). The enhancement leads to an improved fitting and makes the approach intrinsically coherent. In addition, the ab initio calculations of the main, AOM-consistent part of the crystal field potential allows one to fix the material-specific relations for the EAOM parameters in the effective Hamiltonian. Consequently, the electronic structure interpretation based on EAOM can be extended to systems of the lowest point symmetries or/and deficient experimental data. Several examples illustrating the promising capabilities of EAOM are given.

Magnetization, resistivity, specific heat and ab initio calculations of Gd₅Sb₃.

PubMed

Samatham, S Shanmukharao; Patel, Akhilesh Kumar; Lukoyanov, Alexey V; Suresh, K G

2018-06-07

We report on the combined results of structural, magnetic, transport and calorimetric properties of Mn₅Si₃-type hexagonal Gd₅Sb₃, together with <i>ab-initio</i> calculations. It exhibits a ferromagnetic (FM)-like transition at 265 K, antiferromagnetic (AFM) Néel transition at 95.5 K followed by a spin-orientation transition at 62 K. The system is found to be in AFM state down to 2 K in a field of 70 kOe. The FM-AFM phase coexistence is not noticeable despite large positive Curie-Weiss temperature (θ_CW = 223.5 ± 0.2 K). Instead, low-temperature AFM and high-temperature FM-like phases are separated in large temperatures. Temperature-magnetic field (<i>H</i>-<i>T</i>) phase diagram reveals field-driven complex magnetic phases. Within the AFM phase, the system is observed to undergo field-driven spin-orientation transitions. Field-induced tricritical and quantum critical points appear to be absent due to strong AFM nature and by the intervention of FM-like state between paramagnetic and AFM states, respectively. The metallic behavior of the compound is inferred from resistivity along with large Sommerfeld parameter. However, no sign of strong electron-correlations is reasoned from the Kadowaki-Wood's ratio <i>A</i>/γ² ∼ 1.9×10^-6 μΩ.cm.(mol.K)²(mJ)^-2, despite heavy γ. Essentially, <i>ab initio</i> calculations accounting for electronic correlations confirm AFM nature of low-temperature magnetic state in Gd₅Sb₃ and attainable FM ordering in agreement with experimental data. © 2018 IOP Publishing Ltd.

Ab initio simulations of subatomic resolution images in noncontact atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-03-01

Direct imaging of polycyclic aromatic molecules with a subatomic resolution has recently been achieved with noncontact atomic force microscopy (nc-AFM). Specifically, nc-AFM employing a CO functionalized tip has provided details of the chemical bond in aromatic molecules, including the discrimination of bond order. However, the underlying physics of such high resolution imaging remains problematic. By employing new, efficient algorithms based on real space pseudopotentials, we calculate the forces between the nc-AFM tip and specimen. We simulate images of planar organic molecules with two different approaches: 1) with a chemically inert tip and 2) with a CO functionalized tip. We find dramatic differences in the resulting images, which are consistent with recent experimental work. Our work is supported by the DOE under DOE/DE-FG02-06ER46286 and by the Welch Foundation under Grant F-1837. Computational resources were provided by NERSC and XSEDE.

Ab initio potential energy and dipole moment surfaces of the F(-)(H2O) complex.

PubMed

Kamarchik, Eugene; Toffoli, Daniele; Christiansen, Ove; Bowman, Joel M

2014-02-05

We present full-dimensional, ab initio potential energy and dipole moment surfaces for the F(-)(H2O) complex. The potential surface is a permutationally invariant fit to 16,114 coupled-cluster single double (triple)/aVTZ energies, while the dipole surface is a covariant fit to 11,395 CCSD(T)/aVTZ dipole moments. Vibrational self-consistent field/vibrational configuration interaction (VSCF/VCI) calculations of energies and the IR-spectrum are presented both for F(-)(H2O) and for the deuterated analog, F(-)(D2O). A one-dimensional calculation of the splitting of the ground state, due to equivalent double-well global minima, is also reported. Copyright © 2013 Elsevier B.V. All rights reserved.

Static electric polarizabilities and first hyperpolarizabilities of molecular ions RgH + (Rg = He, Ne, Ar, Kr, Xe): ab initio study

NASA Astrophysics Data System (ADS)

Cukras, Janusz; Antušek, Andrej; Holka, Filip; Sadlej, Joanna

2009-06-01

Extensive ab initio calculations of static electric properties of molecular ions of general formula RgH + (Rg = He, Ne, Ar, Kr, Xe) involving the finite field method and coupled cluster CCSD(T) approach have been done. The relativistic effects were taken into account by Douglas-Kroll-Hess approximation. The numerical stability and reliability of calculated values have been tested using the systematic sequence of Dunning's cc-pVXZ-DK and ANO-RCC-VQZP basis sets. The influence of ZPE and pure vibrational contribution has been discussed. The component αzz has increasing trend in RgH + while the relativistic effect on αzz leads to a small increase of this molecular parameter.

Magnetic properties of vanadium doped CdTe: Ab initio calculations

NASA Astrophysics Data System (ADS)

Goumrhar, F.; Bahmad, L.; Mounkachi, O.; Benyoussef, A.

2017-04-01

In this paper, we are applying the ab initio calculations to study the magnetic properties of vanadium doped CdTe. This study is based on the Korringa-Kohn-Rostoker method (KKR) combined with the coherent potential approximation (CPA), within the local density approximation (LDA). This method is called KKR-CPA-LDA. We have calculated and plotted the density of states (DOS) in the energy diagram for different concentrations of dopants. We have also investigated the magnetic and half-metallic properties of this compound and shown the mechanism of exchange interaction. Moreover, we have estimated the Curie temperature Tc for different concentrations. Finally, we have shown how the crystal field and the exchange splittings vary as a function of the concentrations.

Ab initio molecular orbital and infrared spectroscopic study of the conformation of secondary amides: derivatives of formanilide, acetanilide and benzylamides

NASA Astrophysics Data System (ADS)

Ilieva, S.; Hadjieva, B.; Galabov, B.

1999-09-01

Ab initio molecular orbital calculations at HF/4-31G level and infrared spectroscopic data for the frequencies are applied to analyse the grouping in a series model aromatic secondary amides: formanilide; acetanilide; o-methylacetanilide; 2,6-dimethylformanilide, 2,6-dimethylacetanilide; N-benzylacetamide and N-benzylformamide. The theoretical and experimental data obtained show that the conformational state of the molecules studied is determined by the fine balance of several intramolecular factors: resonance effect between the amide group and the aromatic ring, steric interaction between various substituents around the -NH-CO- grouping in the aromatic ring, conjugation between the carbonyl bond and the nitrogen lone pair as well as direct field influences inside the amide group.

The fragmentation of ethanol cation under an electric field: An ab initio/RRKM study

NASA Astrophysics Data System (ADS)

Lu, Hsiu-Feng; Li, F.-Y.; Lin, Chun-Chin; Nagaya, K.; Chao, Ito; Lin, S. H.

2007-08-01

We present a theoretical study of ethanol cation under an electric field due to the existence of laser field in order to understand the influence of electric field on the mass spectrum of ethanol. The electric field was applied to the four major reaction channels of an ethanol cation, such as the conversion between C 2H 5OH + and c-C 2H 5OH +, CH 3-elimination and two α-H-eliminations, respectively. The correlation between product distribution and field strength is quite complex due to the different responses of the reactants and transition states toward the external electric field. This makes the product distribution change as field strength varies.

Direct Simulation Monte Carlo Application of the Three Dimensional Forced Harmonic Oscillator Model

DTIC Science & Technology

2017-12-07

quasi -classical scattering theory [3,4] or trajectory [5] calculations, semiclassical, as well as close-coupled [6,7] or full [8] quantum mechanical...the quasi -classical trajectory (QCT) calculations approach for ab initio modeling of collision processes. The DMS method builds on an earlier work...nu ar y 30 , 2 01 8 | h ttp :// ar c. ai aa .o rg | D O I: 1 0. 25 14 /1 .T 52 28 to directly use quasi -classical or quantum mechanic

Proton Distribution Radii of 12-19C Illuminate Features of Neutron Halos

DOE PAGES

Kanungo, R.; Horiuchi, W.; Hagen, Gaute; ...

2016-09-02

We report proton radii of 12-19C densities derived from first accurate charge changing cross section measurements at 900A MeV with a carbon target. A thick neutron surface evolves from ~0.5 fm in 15C to ~1 fm in 19C. Also, the halo radius in 19C is found to be 6.4±0.7 fm as large as 11Li. Ab initio calculations based on chiral nucleon-nucleon and three-nucleon forces reproduce the radii well.

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Repulsive tip tilting as the dominant mechanism for hydrogen bond-like features in atomic force microscopy imaging

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

Lee, Alex J.; Sakai, Yuki; Kim, Minjung

2016-05-09

Experimental atomic force microscopy (AFM) studies have reported distinct features in regions with little electron density for various organic systems. These unexpected features have been proposed to be a direct visualization of intermolecular hydrogen bonding. Here, we apply a computational method using ab initio real-space pseudopotentials along with a scheme to account for tip tilting to simulate AFM images of the 8-hydroxyquinoline dimer and related systems to develop an understanding of the imaging mechanism for hydrogen bonds. We find that contrast for the observed “hydrogen bond” feature comes not from the electrostatic character of the bonds themselves but rather frommore » repulsive tip tilting induced by neighboring electron-rich atoms.« less

Structural and configurational properties of nanoconfined monolayer ice from first principles

PubMed Central

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations. PMID:26728125

Structural and configurational properties of nanoconfined monolayer ice from first principles

NASA Astrophysics Data System (ADS)

Corsetti, Fabiano; Matthews, Paul; Artacho, Emilio

2016-01-01

Understanding the structural tendencies of nanoconfined water is of great interest for nanoscience and biology, where nano/micro-sized objects may be separated by very few layers of water. Here we investigate the properties of ice confined to a quasi-2D monolayer by a featureless, chemically neutral potential, in order to characterize its intrinsic behaviour. We use density-functional theory simulations with a non-local van der Waals density functional. An ab initio random structure search reveals all the energetically competitive monolayer configurations to belong to only two of the previously-identified families, characterized by a square or honeycomb hydrogen-bonding network, respectively. We discuss the modified ice rules needed for each network, and propose a simple point dipole 2D lattice model that successfully explains the energetics of the square configurations. All identified stable phases for both networks are found to be non-polar (but with a topologically non-trivial texture for the square) and, hence, non-ferroelectric, in contrast to previous predictions from a five-site empirical force-field model. Our results are in good agreement with very recently reported experimental observations.

Proline-based chiral stationary phases: a molecular dynamics study of the interfacial structure.

PubMed

Ashtari, M; Cann, N M

2011-09-16

Proline chains have generated considerable interest as a possible basis for new selectors in chiral chromatography. In this article, we employ molecular dynamics simulations to examine the interfacial structure of two diproline chiral selectors, one with a terminal trimethylacetyl group and one with a terminal t-butyl carbamate group. The solvents consist of a relatively apolar n-hexane/2-propanol and a polar water/methanol mixture. We begin with electronic structure calculations for the two chiral selectors to assess the energetics of conformational changes, particularly along the backbone where the amide bonds can alternate between cis and trans conformations. Force fields have been developed for the two selectors, based on these ab initio calculations. Molecular dynamics simulations of the selective interfaces are performed to examine the preferred backbone conformations, as a function of end-group and solvent. The full chiral surface includes the diproline selectors, trimethylsilyl end-caps, and silanol groups. Connection is made with selectivity measurements on these interfaces, where significant differences are observed between these two very similar selectors. Copyright © 2011 Elsevier B.V. All rights reserved.

Low Energy Nuclear Structure Modeling: Can It Be Improved?

NASA Astrophysics Data System (ADS)

Stone, Jirina R.

Since the discovery of the atomic nucleus in 1911 generations of physicists have devoted enormous effort to understand low energy nuclear structure. Properties of nuclei in their ground state, including mass, binding energy and shape, provide vital input to many areas of sub-atomic physics as well as astrophysics and cosmology. Low energy excited states are equally important for understanding nuclear dynamics. Yet, no consensus exists as to what is the best path to a theory which would not only consistently reproduce a wide variety of experimental data but also have enough predictive power to yield credible predictions in areas where data are still missing. In this contribution some of the main obstacles preventing building such a theory are discussed. These include modification of the free nucleon-nucleon force in the nuclear environment and effects of the sub-nucleon (quark) structure of the nucleon. Selected classes of nuclear models, mean-field, shell and ab-initio models are briefly outlined. Finally, suggestions are made for, at least partial, progress that can be achieved with the quark-meson coupling model, as reported in recent publication [1].

Molecular dynamics simulations of aqueous solutions of ethanolamines.

PubMed

López-Rendón, Roberto; Mora, Marco A; Alejandre, José; Tuckerman, Mark E

2006-08-03

We report on molecular dynamics simulations performed at constant temperature and pressure to study ethanolamines as pure components and in aqueous solutions. A new geometric integration algorithm that preserves the correct phase space volume is employed to study molecules having up to three ethanol chains. The most stable geometry, rotational barriers, and atomic charges were obtained by ab initio calculations in the gas phase. The calculated dipole moments agree well with available experimental data. The most stable conformation, due to intramolecular hydrogen bonding interactions, has a ringlike structure in one of the ethanol chains, leading to high molecular stability. All molecular dynamics simulations were performed in the liquid phase. The interaction parameters are the same for the atoms in the ethanol chains, reducing the number of variables in the potential model. Intermolecular hydrogen bonding is also analyzed, and it is shown that water associates at low water mole fractions. The force field reproduced (within 1%) the experimental liquid densities at different temperatures of pure components and aqueous solutions at 313 K. The excess and partial molar volumes are analyzed as a function of ethanolamine concentration.

Simulation of gas diffusion and sorption in nanoceramic semiconductors

NASA Astrophysics Data System (ADS)

Skouras, E. D.; Burganos, V. N.; Payatakes, A. C.

1999-05-01

Gas diffusion and sorption in nanoceramic semiconductors are studied using atomistic simulation techniques and numerical results are presented for a variety of sorbate-sorbent systems. SnO2, BaTiO3, CuO, and MgO substrates are built on the computer using lattice constants and atomic parameters that have been either measured or computed by ab initio methods. The Universal force field is employed here for the description of both intramolecular and nonbonded interactions for various gas sorbates, including CH4, CO, CO2, and O2, pure and in binary mixtures. Mean residence times are determined by molecular dynamics computations, whereas the Henry constant and the isosteric heat of adsorption are estimated by a Monte Carlo technique. The effects of surface hydroxylation on the diffusion and sorption characteristics are quantified and discussed in view of their significance in practical gas sensing applications. The importance of fast diffusion on the response time of the sensitive layer and of the sorption efficiency on the overall sensitivity as well as the potential synergy of the two phenomena are discussed.

Vibrational spectra and structure of benzil and its 18O- and d 10-labelled derivatives: a quantum chemical and experimental study

NASA Astrophysics Data System (ADS)

Kolev, Tsonko M.; Stamboliyska, Bistra A.

2002-12-01

Geometry and vibrational spectroscopic data of benzil-d 0 benzil-d 10 and benzil- 18O calculated at various levels of theory (RHF/6-31G*, B3LYP/6-31G*, BLYP/6-31G*) are reported. The theoretical results are discussed mainly in terms of the comparisons with infrared (4000-100 cm -1) and Raman (4000-50 cm -1) spectral data. The calculated isotopic frequency shifts, induced by the 18O- and d 10-labeling, are in a good agreement with the measured values. A complete vibrational assignment was made with the help of ab initio force field calculations. The data thus obtained were used for reassigning some vibrational frequencies. The results of the optimized molecular structure obtained on the basis of RHF and the DFT calculations are presented and compared with the experimental X-ray diffraction for the benzil-d 0 single crystal. It turns out that the best structural parameters are predicted by the B3LYP/6-31G* method.

Vibrational spectra and structure of benzil and its 18O- and d10-labelled derivatives: a quantum chemical and experimental study.

PubMed

Kolev, Tsonko M; Stamboliyska, Bistra A

2002-12-01

Geometry and vibrational spectroscopic data of benzil-d0 benzil-d10 and benzil-18O calculated at various levels of theory (RHF/6-31G*, B3LYP/6-31G*, BLYP/6-31G*) are reported. The theoretical results are discussed mainly in terms of the comparisons with infrared (4000-100 cm(-1)) and Raman (4000-50 cm(-1)) spectral data. The calculated isotopic frequency shifts, induced by the 18O- and d10-labeling, are in a good agreement with the measured values. A complete vibrational assignment was made with the help of ab initio force field calculations. The data thus obtained were used for reassigning some vibrational frequencies. The results of the optimized molecular structure obtained on the basis of RHF and the DFT calculations are presented and compared with the experimental X-ray diffraction for the benzil-d0 single crystal. It turns out that the best structural parameters are predicted by the B3LYP/6-31G* method.

Understanding the Origins of Dipolar Couplings and Correlated Motion in the Vibrational Spectrum of Water.

PubMed

Heyden, Matthias; Sun, Jian; Forbert, Harald; Mathias, Gerald; Havenith, Martina; Marx, Dominik

2012-08-16

The combination of vibrational spectroscopy and molecular dynamics simulations provides a powerful tool to obtain insights into the molecular details of water structure and dynamics in the bulk and in aqueous solutions. Applying newly developed approaches to analyze correlations of charge currents, molecular dipole fluctuations, and vibrational motion in real and k-space, we compare results from nonpolarizable water models, widely used in biomolecular modeling, to ab initio molecular dynamics. For the first time, we unfold the infrared response of bulk water into contributions from correlated fluctuations in the three-dimensional, anisotropic environment of an average water molecule, from the OH-stretching region down to the THz regime. Our findings show that the absence of electronic polarizability in the force field model not only results in differences in dipolar couplings and infrared absorption but also induces artifacts into the correlated vibrational motion between hydrogen-bonded water molecules, specifically at the intramolecular bending frequency. Consequently, vibrational motion is partially ill-described with implications for the accuracy of non-self-consistent, a posteriori methods to add polarizability.

A six-coordinate ytterbium complex exhibiting easy-plane anisotropy and field-induced single-ion magnet behavior.

PubMed

Liu, Jun-Liang; Yuan, Kang; Leng, Ji-Dong; Ungur, Liviu; Wernsdorfer, Wolfgang; Guo, Fu-Sheng; Chibotaru, Liviu F; Tong, Ming-Liang

2012-08-06

The field-induced blockage of magnetization behavior was first observed in an Yb(III)-based molecule with a trigonally distorted octahedral coordination environment. Ab initio calculations and micro-SQUID measurements were performed to demonstrate the exhibition of easy-plane anisotropy, suggesting the investigated complex is the first pure lanthanide field-induced single-ion magnet (field-induced SIM) of this type. Furthermore, we found the relaxation time obeys a power law instead of an exponential law, indicating that the relaxation process should be involved a direct process rather than an Orbach process.

AB INITIO PULSAR MAGNETOSPHERE: THREE-DIMENSIONAL PARTICLE-IN-CELL SIMULATIONS OF OBLIQUE PULSARS

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

Philippov, Alexander A.; Spitkovsky, Anatoly; Cerutti, Benoit, E-mail: sashaph@princeton.edu

2015-03-01

We present “first-principles” relativistic particle-in-cell simulations of the oblique pulsar magnetosphere with pair formation. The magnetosphere starts to form with particles extracted from the surface of the neutron star. These particles are accelerated by surface electric fields and emit photons capable of producing electron–positron pairs. We inject secondary pairs at the locations of primary energetic particles whose energy exceeds the threshold for pair formation. We find solutions that are close to the ideal force-free magnetosphere with the Y-point and current sheet. Solutions with obliquities ≤40° do not show pair production in the open field line region because the local currentmore » density along the magnetic field is below the Goldreich–Julian value. The bulk outflow in these solutions is charge-separated, and pair formation happens in the current sheet and return current layer only. Solutions with higher inclinations show pair production in the open field line region, with high multiplicity of the bulk flow and the size of the pair-producing region increasing with inclination. We observe the spin-down of the star to be comparable to MHD model predictions. The magnetic dissipation in the current sheet ranges between 20% for the aligned rotator and 3% for the orthogonal rotator. Our results suggest that for low obliquity neutron stars with suppressed pair formation at the light cylinder, the presence of phenomena related to pair activity in the bulk of the polar region, e.g., radio emission, may crucially depend on the physics beyond our simplified model, such as the effects of curved spacetime or multipolar surface fields.« less

Ab initio phonon point defect scattering and thermal transport in graphene

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

Polanco, Carlos A.; Lindsay, Lucas R.

Here, we study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitudemore » smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (~ω 0) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. In conclusion, this work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.« less

Car and Parrinello meet Green and Kubo: simulating atomic heat transport from equilibrium ab initio molecular dynamics

NASA Astrophysics Data System (ADS)

Baroni, Stefano

Modern simulation methods based on electronic-structure theory have long been deemed unfit to compute heat transport coefficients within the Green-Kubo formalism. This is so because the quantum-mechanical energy density from which the heat flux is derived is inherently ill defined, thus allegedly hampering the use of the Green-Kubo formula. While this objection would actually apply to classical systems as well, I will demonstrate that the thermal conductivity is indeed independent of the specific microscopic expression for the energy density and current from which it is derived. This fact results from a kind of gauge invariance stemming from energy conservation and extensivity, which I will illustrate numerically for a classical Lennard-Jones fluid. I will then introduce an expression for the adiabatic energy flux, derived within density-functional theory, that allows simulating atomic heat transport using equilibrium ab initio molecular dynamics. The resulting methodology is demonstrated by comparing results from ab-initio and classical molecular-dynamics simulations of a model liquid-Argon system, for which accurate inter-atomic potentials are derived by the force-matching method, and applied to compute the thermal conductivity of heavy water at ambient conditions. The problem of evaluating transport coefficients along with their accuracy from relatively short trajectories is finally addressed and discussed with a few representative examples. Partially funded by the European Union through the MaX Centre of Excellence (Grant No. 676598).

Ab initio phonon point defect scattering and thermal transport in graphene

DOE PAGES

Polanco, Carlos A.; Lindsay, Lucas R.

2018-01-04

Here, we study the scattering of phonons from point defects and their effect on lattice thermal conductivity κ using a parameter-free ab initio Green's function methodology. Specifically, we focus on the scattering of phonons by boron (B), nitrogen (N), and phosphorus substitutions as well as single- and double-carbon vacancies in graphene. We show that changes of the atomic structure and harmonic interatomic force constants locally near defects govern the strength and frequency trends of the scattering of out-of-plane acoustic (ZA) phonons, the dominant heat carriers in graphene. ZA scattering rates due to N substitutions are nearly an order of magnitudemore » smaller than those for B defects despite having similar mass perturbations. Furthermore, ZA phonon scattering rates from N defects decrease with increasing frequency in the lower-frequency spectrum in stark contrast to expected trends from simple models. ZA phonon-vacancy scattering rates are found to have a significantly softer frequency dependence (~ω 0) in graphene than typically employed in phenomenological models. The rigorous Green's function calculations demonstrate that typical mass-defect models do not adequately describe ZA phonon-defect scattering rates. Our ab initio calculations capture well the trend of κ vs vacancy density from experiments, though not the magnitudes. In conclusion, this work elucidates important insights into phonon-defect scattering and thermal transport in graphene, and demonstrates the applicability of first-principles methods toward describing these properties in imperfect materials.« less

Conformational and Structural Studies of Isopropylamine from Temperature Dependent Raman Spectra of Xenon Solutions and {AB INITIO} Calculations

NASA Astrophysics Data System (ADS)

Klaassen, Joshua J.; Darkhalil, Ikhlas D.; Durig, James R.

2012-06-01

The Raman and infrared spectra (4000 to 50 cm-1) of the gas, liquid or solution, and solid have been recorded of isopropylamine, (CH3)2CHNH2. Variable temperature (-50 to -100oC) studies of the Raman spectra (3500 to 100 cm-1) dissolved in liquid xenon have been carried out. From these data, both the {trans} and {gauche} conformers have been identified and their relative stability obtained. The enthalpy difference has been determined from 20 band pairs at 6 temperatures to be 113 +/- 11 cm-1 (1.35 +/- 0.13 kJ mol-1) with the {trans} conformer the more stable form. The percentage of the {gauche} conformer is estimated to be 54 +/- 1 percent at ambient temperature. The conformational stabilities have been predicted from {ab initio} calculations utilizing several different basis sets up to aug-cc-pVTZ from both MP2(full) and density functional theory calculations by the B3LYP method. By utilizing previously reported microwave rotational constants along with {ab initio} MP2(full)/6-311+G(d,p) predicted structural values, adjusted r0 parameters have been obtained for the {trans} conformer. The determined heavy atom and NH2 distances in angstroms are C-C = 1.530(3), C-N = 1.465(3), N-H = 1.019(3) and angles in degrees NCC = 108.9(5), CCC = 111.0(5), HNC = 110.3(5). The structural parameters for the {gauche} conformer were estimated by using the same adjustment differences to the {gauche} form as those obtained for the corresponding {trans} parameters. Vibrational assignments have been provided for the observed bands for both conformers which are supported by MP2(full)/6-31G(d) {ab initio} calculations to predict harmonic force constants, wavenumbers, infrared intensities, Raman activities and depolarization ratios for both conformers. The results are discussed and compared to the corresponding properties of some related molecules.

A new parameter-free soft-core potential for silica and its application to simulation of silica anomalies

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

Izvekov, Sergei, E-mail: sergiy.izvyekov.civ@mail.mil; Rice, Betsy M.

2015-12-28

A core-softening of the effective interaction between oxygen atoms in water and silica systems and its role in developing anomalous thermodynamic, transport, and structural properties have been extensively debated. For silica, the progress with addressing these issues has been hampered by a lack of effective interaction models with explicit core-softening. In this work, we present an extension of a two-body soft-core interatomic force field for silica recently reported by us [S. Izvekov and B. M. Rice, J. Chem. Phys. 136(13), 134508 (2012)] to include three-body forces. Similar to two-body interaction terms, the three-body terms are derived using parameter-free force-matching ofmore » the interactions from ab initio MD simulations of liquid silica. The derived shape of the O–Si–O three-body potential term affirms the existence of repulsion softening between oxygen atoms at short separations. The new model shows a good performance in simulating liquid, amorphous, and crystalline silica. By comparing the soft-core model and a similar model with the soft-core suppressed, we demonstrate that the topology reorganization within the local tetrahedral network and the O–O core-softening are two competitive mechanisms responsible for anomalous thermodynamic and kinetic behaviors observed in liquid and amorphous silica. The studied anomalies include the temperature of density maximum locus and anomalous diffusivity in liquid silica, and irreversible densification of amorphous silica. We show that the O–O core-softened interaction enhances the observed anomalies primarily through two mechanisms: facilitating the defect driven structural rearrangements of the silica tetrahedral network and modifying the tetrahedral ordering induced interactions toward multiple characteristic scales, the feature which underlies the thermodynamic anomalies.« less

Ab initio atomic recombination reaction energetics on model heat shield surfaces

NASA Technical Reports Server (NTRS)

Senese, Fredrick; Ake, Robert

1992-01-01

Ab initio quantum mechanical calculations on small hydration complexes involving the nitrate anion are reported. The self-consistent field method with accurate basis sets has been applied to compute completely optimized equilibrium geometries, vibrational frequencies, thermochemical parameters, and stable site labilities of complexes involving 1, 2, and 3 waters. The most stable geometries in the first hydration shell involve in-plane waters bridging pairs of nitrate oxygens with two equal and bent hydrogen bonds. A second extremely labile local minimum involves out-of-plane waters with a single hydrogen bond and lies about 2 kcal/mol higher. The potential in the region of the second minimum is extremely flat and qualitatively sensitive to changes in the basis set; it does not correspond to a true equilibrium structure.

Ab-initio calculations of the Ruddlesden Popper phases CaMnO3, CaO(CaMnO3) and CaO(CaMnO3)2

NASA Astrophysics Data System (ADS)

Cardoso, C.; Borges, R. P.; Gasche, T.; Godinho, M.

2008-01-01

The present work reports ab-initio density functional theory calculations for the Ruddlesden-Popper phase CaO(CaMnO3)n compounds. In order to study the evolution of the properties with the number of perovskite layers, a detailed analysis of the densities of states calculated for each compound and for several magnetic configurations was performed. The effect of distortions of the crystal structure on the magnetic ground state is also analysed and the exchange constants and transition temperatures are calculated for the three compounds using a mean field model. The calculated magnetic ground state structures and magnetic moments are in good agreement with experimental results and previous calculations.

Distinguishing between relaxation pathways by combining dissociative ionization pump probe spectroscopy and ab initio calculations: a case study of cytosine.

PubMed

Kotur, Marija; Weinacht, Thomas C; Zhou, Congyi; Kistler, Kurt A; Matsika, Spiridoula

2011-05-14

We present a general method for tracking molecular relaxation along different pathways from an excited state down to the ground state. We follow the excited state dynamics of cytosine pumped near the S(0)-S(1) resonance using ultrafast laser pulses in the deep ultraviolet and probed with strong field near infrared pulses which ionize and dissociate the molecules. The fragment ions are detected via time of flight mass spectroscopy as a function of pump probe delay and probe pulse intensity. Our measurements reveal that different molecular fragments show different timescales, indicating that there are multiple relaxation pathways down to the ground state. We interpret our measurements with the help of ab initio electronic structure calculations of both the neutral molecule and the molecular cation for different conformations en route to relaxation back down to the ground state. Our measurements and calculations show passage through two seams of conical intersections between ground and excited states and demonstrate the ability of dissociative ionization pump probe measurements in conjunction with ab initio electronic structure calculations to track molecular relaxation through multiple pathways.

CO ADSORPTION AS A PROBE OF THE ELECTRIC FIELD IN ALKALINE-EARTH EXCHANGED ZEOLITE BETA USING FTIR AND AB INITIO QUANTUM CALCULATIONS. (R825304)

EPA Science Inventory

The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

Electronic, magnetic properties and phase diagrams of system with Fe4N compound: An ab initio calculations and Monte Carlo study

NASA Astrophysics Data System (ADS)

Masrour, R.; Jabar, A.; Hlil, E. K.

2018-05-01

Self-consistent ab initio calculations, based on Density Functional Theory (DFT) approach and using Full potential Linear Augmented Plane Wave (FLAPW) method, are performed to investigate the electronic and magnetic properties of the Fe4N compound. Polarized spin and spin-orbit coupling are included in calculations within the framework of the ferromagnetic state between Fe(I) and Fe(II) in Fe4N compound. We have used the obtained data from abinitio calculations as an input in Monte Carlo simulation to calculate the magnetic properties of this compounds such as the ground state phase diagrams, total and partial magnetization of Fe(I) and Fe(II) as well as the transition temperatures are computed. The variation of magnetization with the crystal field are also studied. The magnetic hysteresis cycle of the same Fe4N compound are determined for different values of temperatures and crystal field values. The two-step hysteresis loop are evidenced, which is typical for Fe4N structure. The ferromagnetic and superparamagnetic phase is observed as well.

On the Reduction of Molecular Degrees of Freedom in Computer Simulations

NASA Astrophysics Data System (ADS)

Lyubartsev, Alexander P.; Laaksonen, Aatto

Molecular simulations, based on atomistic force fields are a standard theoretical tool in materials, polymers and biosciences. While various methods, with quantum chemistry incorporated, have been developed for condensed phase simulations during the last decade, there is another line of development with the purpose to bridge the time and length scales based on coarse-graining. This is expected to lead to some very interesting breakthroughs in the near future. In this lecture we will first give some background to common atomistic force fields. After that, we review a few common simple techniques for reducing the number of motional degrees of freedom to speed up the simulations. Finally, we present a powerful method for reducing uninteresting degrees of freedom. This is done by solving the Inverse Problem to obtain the interaction potentials. More precisely, we make use of the radial distribution functions, and by using the method of Inverse Monte Carlo [Lyubartsev & Laaksonen, Phys. Rev. E. 52, 3730 (1995)], we can construct effective potentials which are consistent with the original RDFs. This makes it possible to simulate much larger system than would have been possible by using atomistic force fields. We present many examples: How to simulate aqueous electrolyte solutions without any water molecules but still having the hydration structure around the ions - at the speed of a primitive electrolyte model calculation. We demonstrate how a coarse-grained model can be constructed for a double-helix DNA and how it can be used. It is accurate enough to reproduce the experimental results for ion condensation around DNA for several different counterions. We also show how we can construct site-site potentials for large-scale atomistic classical simulations of arbitrary liquids from smaller scale ab initio simulations. This methodology allows us to start from a simulation with the electrons and atomic nuclei, to construct a set of atomistic effective interaction potentials, and to use them in classical simulations. As a next step we can construct a new set of potentials beyond the atomistic description and carry out mesoscopic simulations, for example by using Dissipative Particle Dynamics. In this way we can tie together three different levels of description. The Dissipative Particle Dynamics method appears as a very promising tool to use with our coarse-grained potentials.

First principles molecular dynamics of molten NaCl

NASA Astrophysics Data System (ADS)

Galamba, N.; Costa Cabral, B. J.

2007-03-01

First principles Hellmann-Feynman molecular dynamics (HFMD) results for molten NaCl at a single state point are reported. The effect of induction forces on the structure and dynamics of the system is studied by comparison of the partial radial distribution functions and the velocity and force autocorrelation functions with those calculated from classical MD based on rigid-ion and shell-model potentials. The first principles results reproduce the main structural features of the molten salt observed experimentally, whereas they are incorrectly described by both rigid-ion and shell-model potentials. Moreover, HFMD Green-Kubo self-diffusion coefficients are in closer agreement with experimental data than those predicted by classical MD. A comprehensive discussion of MD results for molten NaCl based on different ab initio parametrized polarizable interionic potentials is also given.

Ab Initio Study of KCl and AgCl Clusters.

NASA Astrophysics Data System (ADS)

McKeough, James; Hira, Ajit; Cathey, Tommy; Valdez, Alexandra

This paper presents a theoretical study of molecular clusters that examines the chemical and physical properties of small KnCln and AgnCln clusters (n = 2 - 24). Due to combinations of attractive and repulsive long-range forces, such clusters exhibit structural and dynamical behavior different from that of homogeneous clusters. The potentially important role of these molecular species in biochemical and medicinal processes is widely known. This work applies the hybrid ab initio methods to derive the different alkali-halide (MnHn) geometries. Of particular interest is the competition between hexagonal ring geometries and rock salt structures. Electronic energies, rotational constants, dipole moments, and vibrational frequencies for these geometries are calculated. Magic numbers for cluster stability are identified and are related to the property of cluster compactness. Mapping of the singlet, triplet, and quintet, potential energy surfaces is performed. Calculations were performed to examine the interactions of these clusters with some atoms and molecules of biological interest, including O, O2, and Fe. Potential design of new medicinal drugs is explored. We will also investigate model and material dependence of the results. AMP program of the National Science Foundation.

Electronic and magnetic properties of iron doped zirconia: Theory and experiment

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

Debernardi, A., E-mail: alberto.debernardi@mdm.imm.cnr.it; Sangalli, D.; Lamperti, A.

We systematically investigated, both theoretically and experimentally, Zr{sub 1−x}Fe{sub x}O{sub 2−y} ranging from diluted (x ≈ 0.05) up to large (x ≈ 0.25) Fe concentration. By atomic layer deposition, we grew thin films of high-κ zirconia in cubic phase with Fe uniformly distributed in the film, as proven by time of flight secondary ion mass spectrometry and transmission electron microscopy measurements. Iron is in Fe{sup 3+} oxidation state suggesting the formation of oxygen vacancies with y concentration close to x/2. By ab-initio simulations, we studied the phase diagram relating the stability of monoclinic vs. tetragonal phase as a function of Fe doping and filmmore » thickness: the critical thickness at which the pure zirconia is stabilized in the tetragonal phase is estimated ranging from 2 to 6 nm according to film morphology. Preliminary results by X-ray magnetic circular dichroism and alternating gradient force magnetometry are discussed in comparison to ab initio data enlightening the role of oxygen vacancies in the magnetic properties of the system.« less

A new potential energy surface for vibration-vibration coupling in HF-HF collisions. Formulation and quantal scattering calculations

NASA Astrophysics Data System (ADS)

Schwenke, David W.; Truhlar, Donald G.

1988-04-01

We present new ab initio calculations of the HF-HF interaction potential for the case where both molecules are simultaneously displaced from their equilibrium internuclear distance. These and previous ab initio calculations are then fit to a new analytic representation which is designed to be efficient to evaluate and to provide an especially faithful account of the forces along the vibrational coordinates. We use the new potential for two sets of quantal scattering calculations for collisions in three dimensions with total angular momentum zero. First we test that the angular harmonic representation of the anisotropy is adequate by comparing quantal rigid rotator calculations to those carried out for potentials involving higher angular harmonics and for which the expansion in angular harmonics is systematically increased to convergence. Then we carry out large-scale quantal calculations of vibration-vibration energy transfer including the coupling of both sets of vibrational and rotational coordinates. These calculations indicate that significant rotational energy transfer accompanies the vibration-to-vibration energy transfer process.

Strong influence of coadsorbate interaction on CO desorption dynamics on Ru(0001) probed by ultrafast x-ray spectroscopy and ab initio simulations

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

Xin, H.; LaRue, J.; Oberg, H.

2015-04-16

We show that coadsorbed oxygen atoms have a dramatic influence on the CO desorption dynamics from Ru(0001). In contrast to the precursor-mediated desorption mechanism on Ru(0001), the presence of surface oxygen modifies the electronic structure of Ru atoms such that CO desorption occurs predominantly via the direct pathway. This phenomenon is directly observed in an ultrafast pump-probe experiment using a soft x-ray free-electron laser to monitor the dynamic evolution of the valence electronic structure of the surface species. This is supported with the potential of mean force along the CO desorption path obtained from density-functional theory calculations. Charge density distributionmore » and frozen-orbital analysis suggest that the oxygen-induced reduction of the Pauli repulsion, and consequent increase of the dative interaction between the CO 5σ and the charged Ru atom, is the electronic origin of the distinct desorption dynamics. Ab initio molecular dynamics simulations of CO desorption from Ru(0001) and oxygen-coadsorbed Ru(0001) provide further insights into the surface bond-breaking process.« less

Electronic Structure, Dielectric Response, and Surface Charge Distribution of RGD (1FUV) Peptide

PubMed Central

Adhikari, Puja; Wen, Amy M.; French, Roger H.; Parsegian, V. Adrian; Steinmetz, Nicole F.; Podgornik, Rudolf; Ching, Wai-Yim

2014-01-01

Long and short range molecular interactions govern molecular recognition and self-assembly of biological macromolecules. Microscopic parameters in the theories of these molecular interactions are either phenomenological or need to be calculated within a microscopic theory. We report a unified methodology for the ab initio quantum mechanical (QM) calculation that yields all the microscopic parameters, namely the partial charges as well as the frequency-dependent dielectric response function, that can then be taken as input for macroscopic theories of electrostatic, polar, and van der Waals-London dispersion intermolecular forces. We apply this methodology to obtain the electronic structure of the cyclic tripeptide RGD-4C (1FUV). This ab initio unified methodology yields the relevant parameters entering the long range interactions of biological macromolecules, providing accurate data for the partial charge distribution and the frequency-dependent dielectric response function of this peptide. These microscopic parameters determine the range and strength of the intricate intermolecular interactions between potential docking sites of the RGD-4C ligand and its integrin receptor. PMID:25001596

An ab initio study of Fe(CO)n, n = 1,5, and Cr(CO)6

NASA Technical Reports Server (NTRS)

Barnes, Leslie A.; Rosi, Marzio; Bauschlicher, Charles W., Jr.

1991-01-01

Ab initio calculations have been performed for Cr(CO)6 and Fe(CO)n, n = 1,5. Basis sets of better than double zeta quality are used, and correlation is included using the modified coupler-pair functional method. The computed geometries and force constants are in reasonable agreement with experiment. The sequential bond dissociation energies of CO from Fe(CO)5 are estimated to be: 39, 31, 25, 22, and greater than 5 kcal/mol. It is noted that the first bond dissociation energy is relative to the singlet ground state of Fe(CO)5 and the lowest singlet state of Fe(CO)4, whereas the second is relative to the ground triplet states of Fe(CO)4 and Fe(CO)3. In addition, the binding energy for Fe-CO would be modified to 18 kcal/mol if dissociation occurred to the Fe(5F) excited state asymptote. The CO binding energies for Fe and Cr are found to be in poorer agreement with experiment than those found in a previous study on Ni(CO)4. The origins of this difference are discussed.

Universal tight binding model for chemical reactions in solution and at surfaces. II. Water.

PubMed

Lozovoi, A Y; Sheppard, T J; Pashov, D L; Kohanoff, J J; Paxton, A T

2014-07-28

A revised water model intended for use in condensed phase simulations in the framework of the self consistent polarizable ion tight binding theory is constructed. The model is applied to water monomer, dimer, hexamers, ice, and liquid, where it demonstrates good agreement with theoretical results obtained by more accurate methods, such as DFT and CCSD(T), and with experiment. In particular, the temperature dependence of the self diffusion coefficient in liquid water predicted by the model, closely reproduces experimental curves in the temperature interval between 230 K and 350 K. In addition, and in contrast to standard DFT, the model properly orders the relative densities of liquid water and ice. A notable, but inevitable, shortcoming of the model is underestimation of the static dielectric constant by a factor of two. We demonstrate that the description of inter and intramolecular forces embodied in the tight binding approximation in quantum mechanics leads to a number of valuable insights which can be missing from ab initio quantum chemistry and classical force fields. These include a discussion of the origin of the enhanced molecular electric dipole moment in the condensed phases, and a detailed explanation for the increase of coordination number in liquid water as a function of temperature and compared with ice--leading to insights into the anomalous expansion on freezing. The theory holds out the prospect of an understanding of the currently unexplained density maximum of water near the freezing point.

Divalent Ion Parameterization Strongly Affects Conformation and Interactions of an Anionic Biomimetic Polymer.

PubMed

Daily, Michael D; Baer, Marcel D; Mundy, Christopher J

2016-03-10

The description of peptides and the use of molecular dynamics simulations to refine structures and investigate the dynamics on an atomistic scale are well developed. Through a consensus in this community over multiple decades, parameters were developed for molecular interactions that only require the sequence of amino-acids and an initial guess for the three-dimensional structure. The recent discovery of peptoids will require a retooling of the currently available interaction potentials in order to have the same level of confidence in the predicted structures and pathways as there is presently in the peptide counterparts. Here we present modeling of peptoids using a combination of ab initio molecular dynamics (AIMD) and atomistic resolution classical force field (FF) to span the relevant time and length scales. To properly account for the dominant forces that stabilize ordered structures of peptoids, namely steric-, electrostatic, and hydrophobic interactions mediated through side chain-side chain interactions in the FF model, those have to be first mapped out using high fidelity atomistic representations. A key feature here is not only to use gas phase quantum chemistry tools, but also account for solvation effects in the condensed phase through AIMD. One major challenge is to elucidate ion binding to charged or polar regions of the peptoid and its concomitant role in the creation of local order. Here, similar to proteins, a specific ion effect is observed suggesting that both the net charge and the precise chemical nature of the ion will need to be described.

Band Structure and Contact Resistance of Carbon Nanotubes Deformed by a Metal Contact.

PubMed

Hafizi, Roohollah; Tersoff, Jerry; Perebeinos, Vasili

2017-11-17

Capillary and van der Waals forces cause nanotubes to deform or even collapse under metal contacts. Using ab initio band structure calculations, we find that these deformations reduce the band gap by as much as 30%, while fully collapsed nanotubes become metallic. Moreover, degeneracy lifting due to the broken axial symmetry, and wave functions mismatch between the fully collapsed and the round portions of a CNT, lead to a 3 times higher contact resistance. The latter we demonstrate by contact resistance calculations within the tight-binding approach.

Pulling monatomic gold wires with single molecules: an Ab initio simulation.

PubMed

Krüger, Daniel; Fuchs, Harald; Rousseau, Roger; Marx, Dominik; Parrinello, Michele

2002-10-28

Car-Parrinello molecular dynamics simulations demonstrate that pulling a single thiolate molecule anchored on a stepped gold surface does not preferentially break the sulfur-gold chemical bond. Instead, it is found that this process leads to the formation of a monoatomic gold nanowire, followed by breaking a gold-gold bond with a rupture force of about 1.2 nN. The simulations also indicate that previous single-molecule thiolate-gold and gold-gold rupture experiments both probe the same phenomenon, namely, the breaking of a gold-gold bond within a gold nanowire.

Role of orbital overlap in atomic manipulation

NASA Astrophysics Data System (ADS)

Jarvis, Sam; Sweetman, Adam; Bamidele, Joseph; Kantorovich, Lev; Moriarty, Philip

2012-06-01

We conduct ab initio simulations illustrating that the ability to achieve atomic manipulation using a dynamic force microscope depends on the precise orientation of the dangling bond(s) at the tip apex and their charge density with respect to those of surface atoms. Using the Si(100)-c(4×2) surface as a prototype, we demonstrate that it is possible to select tip apices capable of performing atomic manipulation tasks which are unachievable using another choice of apex. Specific tip apices can be identified via examination of F(z) curves taken at different lateral positions.

Evidence for prevalent Z = 6 magic number in neutron-rich carbon isotopes.

PubMed

Tran, D T; Ong, H J; Hagen, G; Morris, T D; Aoi, N; Suzuki, T; Kanada-En'yo, Y; Geng, L S; Terashima, S; Tanihata, I; Nguyen, T T; Ayyad, Y; Chan, P Y; Fukuda, M; Geissel, H; Harakeh, M N; Hashimoto, T; Hoang, T H; Ideguchi, E; Inoue, A; Jansen, G R; Kanungo, R; Kawabata, T; Khiem, L H; Lin, W P; Matsuta, K; Mihara, M; Momota, S; Nagae, D; Nguyen, N D; Nishimura, D; Otsuka, T; Ozawa, A; Ren, P P; Sakaguchi, H; Scheidenberger, C; Tanaka, J; Takechi, M; Wada, R; Yamamoto, T

2018-04-23

The nuclear shell structure, which originates in the nearly independent motion of nucleons in an average potential, provides an important guide for our understanding of nuclear structure and the underlying nuclear forces. Its most remarkable fingerprint is the existence of the so-called magic numbers of protons and neutrons associated with extra stability. Although the introduction of a phenomenological spin-orbit (SO) coupling force in 1949 helped in explaining the magic numbers, its origins are still open questions. Here, we present experimental evidence for the smallest SO-originated magic number (subshell closure) at the proton number six in 13-20 C obtained from systematic analysis of point-proton distribution radii, electromagnetic transition rates and atomic masses of light nuclei. Performing ab initio calculations on 14,15 C, we show that the observed proton distribution radii and subshell closure can be explained by the state-of-the-art nuclear theory with chiral nucleon-nucleon and three-nucleon forces, which are rooted in the quantum chromodynamics.

Relevance of 4f-3d exchange to finite-temperature magnetism of rare-earth permanent magnets: An ab-initio-based spin model approach for NdFe{sub 12}N

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

Matsumoto, Munehisa; Akai, Hisazumi; Doi, Shotaro

2016-06-07

A classical spin model derived ab initio for rare-earth-based permanent magnet compounds is presented. Our target compound, NdFe{sub 12}N, is a material that goes beyond today's champion magnet compound Nd{sub 2}Fe{sub 14}B in its intrinsic magnetic properties with a simpler crystal structure. Calculated temperature dependence of the magnetization and the anisotropy field agrees with the latest experimental results in the leading order. Having put the realistic observables under our numerical control, we propose that engineering 5d-electron-mediated indirect exchange coupling between 4f-electrons in Nd and 3d-electrons from Fe would most critically help enhance the material's utility over the operation-temperature range.

Ab initio quantum chemical calculation of electron transfer matrix elements for large molecules

NASA Astrophysics Data System (ADS)

Zhang, Linda Yu; Friesner, Richard A.; Murphy, Robert B.

1997-07-01

Using a diabatic state formalism and pseudospectral numerical methods, we have developed an efficient ab initio quantum chemical approach to the calculation of electron transfer matrix elements for large molecules. The theory is developed at the Hartree-Fock level and validated by comparison with results in the literature for small systems. As an example of the power of the method, we calculate the electronic coupling between two bacteriochlorophyll molecules in various intermolecular geometries. Only a single self-consistent field (SCF) calculation on each of the monomers is needed to generate coupling matrix elements for all of the molecular pairs. The largest calculations performed, utilizing 1778 basis functions, required ˜14 h on an IBM 390 workstation. This is considerably less cpu time than would be necessitated with a supermolecule adiabatic state calculation and a conventional electronic structure code.

Coherent band excitations in CePd 3: A comparison of neutron scattering and ab initio theory

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

Goremychkin, Eugene A.; Park, Hyowon; Osborn, Raymond

In common with many strongly correlated electron systems, intermediate valence compounds are believed to display a crossover from a high-temperature regime of incoherently fluctuating local moments to a low-temperature regime of coherent hybridized bands. In this work, we show that inelastic neutron scattering measurements of the dynamic magnetic susceptibility of CePd 3 provides a benchmark for ab initio calculations based on dynamical mean field theory. The magnetic response is strongly momentum dependent thanks to the formation of coherent f-electron bands at low temperature, with an amplitude that is strongly enhanced by local particle-hole interactions. Finally, the agreement between experiment andmore » theory shows that we have a robust first-principles understanding of the temperature dependence of f-electron coherence.« less

Comparative studies of the spectroscopy of CuCl2: DFT versus standard ab initio approaches

NASA Astrophysics Data System (ADS)

Ramírez-Solís, A.; Poteau, R.; Vela, A.; Daudey, J. P.

2005-04-01

The XΠg2-Σg +2, XΠg2-Δg2, XΠg2-Σu +2, XΠg2-Πu2 transitions on CuCl2 have been studied using several exchange-correlation functionals from the various types of density functional theory (DFT) approaches like local density approximation (LDA), generalized gradient approximation (GGA), hybrid and meta-GGA. The results are compared with the experience and with those coming from the most sophisticated nondynamic and dynamic electronic correlation treatments using the same relativistic effective core potentials and especially developed basis sets to study the electronic structure of the five lowest states and the corresponding vertical and adiabatic transition energies. The calculated transition energies for three of the hybrid functionals (B3LYP, B97-2, and PBE0) are in very good agreement with the benchmark ab initio results and experimental figures. All of the other functionals largely overestimate the XΠg2-Σg +2 and XΠg2-Δg2 transition energies, many of them even placing the Δg2 ligand field state above the charge transfer Πu2 and Σu +2 states. The relative weight of the Hartree-Fock exchange in the definition of the functional used appears to play a key role in the accurate description of the ΛSΣ density defined by the orientation of the 3d hole (σ, π, or δ) on Cu in the field of both chlorine atoms, but no simple connection of this weight with the quality of the spectra has been found. Mulliken charges and spin densities are carefully analyzed; a possible link between the extent of spin density on the metal for the XΠg2 state and the performance of the various functionals was observed, suggesting that those that lead to the largest values (close to 0.65) are the ones that best reproduce these four transitions. Most functionals lead to a remarkably low ionicity for the three ligand field states even for the best performing functionals, compared to the complete active space (SCF) (21, 14) ab initio values. These findings show that not only large variational ab initio calculations can produce reliable spectroscopic results for extremely complex systems where delicate electronic correlation effects have to be carefully dealt with. However, those functionals that were recently shown to perform best for a series of molecular properties [J. Chem. Phys. 121 3405 (2004)] are not the ones that produce the best transition energies for this complex case.

Coherent Raman Spectra of the nu(1) Mode of 10BF3 and 11BF3

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

Kirkpatrick, Robynne; Masiello, Tony; Weber, Alfons

2006-05-01

High resolution (0.001cm-1) coherent anti-Stokes Raman spectroscopy (CARS) was used to directly examine the v1 symmetric stretching mode of the planar symmetric D3h molecules 10BF3 and 11BF3. Simulations of the spectra were done using v1 rovibrational parameters deduced from published infrared hot-band and difference-band studies and the close similarity to the observed CARS spectra confirms the validity of the infrared constants. No significant perturbations by Fermi resonance or Coriolis interactions with nearby states are observed, in marked contrast to the case of sulfur trioxide, a similar D3h molecule recently studied. In the harmonic approximation, the 10BF3 and 11BF3 v1 Q-more » branches would be identical since the isotopic substitution is at the center of mass but, interestingly, the v1 stretching frequency for 11BF3 is found to be 0.198 cm-1 higher than for the lighter 10BF3 isotopomer. This counterintuitive result is reproduced almost exactly (0.200 cm -1) by ab initio calculations (B3LYP/cc-pVTZ) that included evaluation of cubic and quartic forced constants and xij anharmonicity constants. The ab initio computations also predict to within 1% the ?B, ?C changes in the rotational constants in going from the ground state to the v1=1 vibrational level. The results illustrate nicely the complementary interplay of modern infrared, Raman, and ab initio methods in obtaining and analyzing rovibrational spectra.« less

14N NQR lineshape in nanocrystals: An ab initio investigation of urea

PubMed Central

Gregorovič, Alan

2017-01-01

14N nuclear quadrupole resonance (NQR) lineshapes mostly contain information of low interest, although in nanocrystals they may display some unexpected behaviour. In this work, we present an ab initio computational study of the 14N NQR lineshapes in urea nanocrystals as a function of the nanocrystal size and geometry, focusing on the surface induced broadening of the lineshapes. The lineshapes were obtained through a calculation of the electric field gradient for each nitrogen site in the nanocrystal separately, taking into account the individual crystal field by embedding the molecule of interest in a suitable lattice of point multipoles representing other urea molecules in the nanocrystal. The small influence of distant molecules is found with a series expansion, using the in-crystal Sternheimer shieldings which we also calculated ab initio. We have considered nanocrystals with two geometries: a sphere and a cube, with characteristic sizes between 5 and 100 nm. Our calculations suggest that there is a dramatic difference between the linewidths for the two geometries. For spheres, we find a steep drop in linewidths at ∼10 nm; at 5 nm the linewidth is ∼11 kHz, whereas for sizes above 20 nm the linewidth is practically negligible (<100 Hz). For cubes, on the other hand, we find a steady 1/size decrease, from 12 kHz at 10 nm to 1.2 kHz at 100 nm. This analysis is important for 14N NQR spectroscopy of crystalline pharmaceuticals, where nanoparticles are increasingly more often embedded in some sort of matrix. Although this is only a theoretical analysis, we believe that this work can serve as a guidance for the forthcoming experimental analysis. PMID:28527464

Improvement of the ab initio embedded cluster method for luminescence properties of doped materials by taking into account impurity induced distortions: the example of Y2O3:Bi(3+).

PubMed

Réal, Florent; Ordejón, Belén; Vallet, Valérie; Flament, Jean-Pierre; Schamps, Joël

2009-11-21

New ab initio embedded-cluster calculations devoted to simulating the electronic spectroscopy of Bi(3+) impurities in Y(2)O(3) sesquioxide for substitutions in either S(6) or C(2) cationic sites have been carried out taking special care of the quality of the environment. A considerable quantitative improvement with respect to previous studies [F. Real et al. J. Chem. Phys. 125, 174709 (2006); F. Real et al. J. Chem. Phys. 127, 104705 (2007)] is brought by using environments of the impurities obtained via supercell techniques that allow the whole (pseudo) crystal to relax (WCR geometries) instead of environments obtained from local relaxation of the first coordination shell only (FSR geometries) within the embedded cluster approach, as was done previously. In particular the uniform 0.4 eV discrepancy of absorption energies found previously with FSR environments disappears completely when the new WCR environments of the impurities are employed. Moreover emission energies and hence Stokes shifts are in much better agreement with experiment. These decisive improvements are mainly due to a lowering of the local point-group symmetry (S(6)-->C(3) and C(2)-->C(1)) when relaxing the geometry of the emitting (lowest) triplet state. This symmetry lowering was not observed in FSR embedded cluster relaxations because the crystal field of the embedding frozen at the genuine pure crystal positions seems to be a more important driving force than the interactions within the cluster, thus constraining the overall symmetry of the system. Variations of the doping rate are found to have negligible influence on the spectra. In conclusion, the use of WCR environments may be crucial to render the structural distortions occurring in a doped crystal and it may help to significantly improve the embedded-cluster methodology to reach the quantitative accuracy necessary to interpret and predict luminescence properties of doped materials of this type.

Can Ab Initio Theory Explain the Phenomenon of Parity Inversion in Be 11 ?

DOE PAGES

Calci, Angelo; Navratil, Petr; Roth, Robert; ...

2016-12-09

The weakly bound exotic 11Be nucleus, famous for its ground-state parity inversion and distinct n + 10Be halo structure, is investigated from first principles using chiral two- and three-nucleon forces. An explicit treatment of continuum effects is found to be indispensable. We study the sensitivity of the 11Be spectrum to the details of the three-nucleon force and demonstrate that only certain chiral interactions are capable of reproducing the parity inversion. With such interactions, the extremely large E1 transition between the bound states is reproduced. We compare our photodisintegration calculations to conflicting experimental data and predict a distinct dip around themore » 3/2 – 1 resonance energy. Finally, we predict low-lying 3/2 + and 9/2 + resonances that are not or not sufficiently measured in experiments.« less

Ab initio calculation of the rotational spectrum of methane vibrational ground state

NASA Astrophysics Data System (ADS)

Cassam-Chenaï, P.; Liévin, J.

2012-05-01

In a previous article we have introduced an alternative perturbation scheme to the traditional one starting from the harmonic oscillator, rigid rotator Hamiltonian, to find approximate solutions of the spectral problem for rotation-vibration molecular Hamiltonians. The convergence of our method for the methane vibrational ground state rotational energy levels was quicker than that of the traditional method, as expected, and our predictions were quantitative. In this second article, we study the convergence of the ab initio calculation of effective dipole moments for methane within the same theoretical frame. The first order of perturbation when applied to the electric dipole moment operator of a spherical top gives the expression used in previous spectroscopic studies. Higher orders of perturbation give corrections corresponding to higher centrifugal distortion contributions and are calculated accurately for the first time. Two potential energy surfaces of the literature have been used for solving the anharmonic vibrational problem by means of the vibrational mean field configuration interaction approach. Two corresponding dipole moment surfaces were calculated in this work at a high level of theory. The predicted intensities agree better with recent experimental values than their empirical fit. This suggests that our ab initio dipole moment surface and effective dipole moment operator are both highly accurate.

Unified theory of quantized electrons, phonons, and photons out of equilibrium: A simplified ab initio approach based on the generalized Baym-Kadanoff ansatz

NASA Astrophysics Data System (ADS)

de Melo, Pedro Miguel M. C.; Marini, Andrea

2016-04-01

We present a full ab initio description of the coupled out-of-equilibrium dynamics of photons, phonons, and electrons. In the present approach, the quantized nature of the electromagnetic field as well as of the nuclear oscillations is fully taken into account. The result is a set of integrodifferential equations, written on the Keldysh contour, for the Green's functions of electrons, phonons, and photons where the different kinds of interactions are merged together. We then concentrate on the electronic dynamics in order to reduce the problem to a computationally feasible approach. By using the generalized Baym-Kadanoff ansatz and the completed collision approximation, we introduce a series of efficient but controllable approximations. In this way, we reduce all equations to a set of decoupled equations for the density matrix that describe all kinds of static and dynamical correlations. The final result is a coherent, general, and inclusive scheme to calculate several physical quantities: carrier dynamics, transient photoabsorption, and light emission, all of which include, at the same time, electron-electron, electron-phonon, and electron-photon interactions. We further discuss how all these observables can be easily calculated within the present scheme using a fully atomistic ab initio approach.

An ab initio chemical reaction model for the direct simulation Monte Carlo study of non-equilibrium nitrogen flows.

PubMed

Mankodi, T K; Bhandarkar, U V; Puranik, B P

2017-08-28

A new ab initio based chemical model for a Direct Simulation Monte Carlo (DSMC) study suitable for simulating rarefied flows with a high degree of non-equilibrium is presented. To this end, Collision Induced Dissociation (CID) cross sections for N 2 +N 2 →N 2 +2N are calculated and published using a global complete active space self-consistent field-complete active space second order perturbation theory N 4 potential energy surface and quasi-classical trajectory algorithm for high energy collisions (up to 30 eV). CID cross sections are calculated for only a selected set of ro-vibrational combinations of the two nitrogen molecules, and a fitting scheme based on spectroscopic weights is presented to interpolate the CID cross section for all possible ro-vibrational combinations. The new chemical model is validated by calculating equilibrium reaction rate coefficients that can be compared well with existing shock tube and computational results. High-enthalpy hypersonic nitrogen flows around a cylinder in the transition flow regime are simulated using DSMC to compare the predictions of the current ab initio based chemical model with the prevailing phenomenological model (the total collision energy model). The differences in the predictions are discussed.

Semiclassical initial value representation for the quantum propagator in the Heisenberg interaction representation

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

Petersen, Jakob; Pollak, Eli, E-mail: eli.pollak@weizmann.ac.il

2015-12-14

One of the challenges facing on-the-fly ab initio semiclassical time evolution is the large expense needed to converge the computation. In this paper, we suggest that a significant saving in computational effort may be achieved by employing a semiclassical initial value representation (SCIVR) of the quantum propagator based on the Heisenberg interaction representation. We formulate and test numerically a modification and simplification of the previous semiclassical interaction representation of Shao and Makri [J. Chem. Phys. 113, 3681 (2000)]. The formulation is based on the wavefunction form of the semiclassical propagation instead of the operator form, and so is simpler andmore » cheaper to implement. The semiclassical interaction representation has the advantage that the phase and prefactor vary relatively slowly as compared to the “standard” SCIVR methods. This improves its convergence properties significantly. Using a one-dimensional model system, the approximation is compared with Herman-Kluk’s frozen Gaussian and Heller’s thawed Gaussian approximations. The convergence properties of the interaction representation approach are shown to be favorable and indicate that the interaction representation is a viable way of incorporating on-the-fly force field information within a semiclassical framework.« less

Insights into unbound-bound states of GPR142 receptor in a membrane-aqueous system using molecular dynamics simulations.

PubMed

Kaushik, Aman Chandra; Sahi, Shakti

2018-05-01

G protein coupled receptors (GPCRs) are source machinery in signal transduction pathways and being one of the major therapeutic targets play a significant in drug discovery. GPR142, an orphan GPCR, has been implicated in the regulation of insulin, thereby having a crucial role in Type II diabetes management. Deciphering of the structures of orphan, GPCRs (O-GPCRs) offer better prospects for advancements in research in ion translocation and transduction of extracellular signals. As the crystallographic structure of GPR142 is not available in PDB, therefore, threading and ab initio-based approaches were used for 3D modeling of GPR142. Molecular dynamic simulations (900 ns) were performed on the 3D model of GPR142 and complexes of GPR142 with top five hits, obtained through virtual screening, embedded in lipid bilayer with aqueous system using OPLS force field. Compound 1, 3, and 4 may act as scaffolds for designing potential lead agonists for GPR142. The finding of GPR142 MD simulation study provides more comprehensive representation of the functional properties. The concern for Type II diabetes is increasing worldwide and successful treatment of this disease demands novel drugs with better efficacy.

Mode-selective chemistry on metal surfaces: The dissociative chemisorption of CH 4 on Pt(111)

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

Guo, Han; Jackson, Bret

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore CH 4 dissociation on Pt(111). Computed sticking probabilities for molecules in the ground, 1v 3 and 2v 3, states are in very good agreement with the available experimental data, reproducing the variation in reactivity with collision energy and vibrational state. As was found in similar studies on Ni(100) and Ni(111), exciting the 1v 1 symmetric stretch of CH 4 is more effective at promoting the dissociative chemisorption of CH 4 than exciting the 1v 3 antisymmetric stretch. This behavior is explained in terms of symmetry,more » mode-softening, and nonadiabatic transitions between vibrationally adiabatic states. We find that the efficacies of the bending modes for promoting reaction are reasonably large, and similar to the 1v 3 state. The vibrational efficacies for promoting reaction on Ni(111) are larger than for reaction on Pt(111), due to the larger nonadiabatic couplings. As a result, our computed sticking probabilities are in good agreement with results from recent ab initio molecular dynamics and reactive force field studies.« less

Mode-selective chemistry on metal surfaces: The dissociative chemisorption of CH{sub 4} on Pt(111)

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

Guo, Han; Jackson, Bret, E-mail: jackson@chem.umass.edu

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore CH{sub 4} dissociation on Pt(111). Computed sticking probabilities for molecules in the ground, 1v{sub 3} and 2v{sub 3}, states are in very good agreement with the available experimental data, reproducing the variation in reactivity with collision energy and vibrational state. As was found in similar studies on Ni(100) and Ni(111), exciting the 1v{sub 1} symmetric stretch of CH{sub 4} is more effective at promoting the dissociative chemisorption of CH{sub 4} than exciting the 1v{sub 3} antisymmetric stretch. This behavior is explained in terms of symmetry,more » mode-softening, and nonadiabatic transitions between vibrationally adiabatic states. We find that the efficacies of the bending modes for promoting reaction are reasonably large, and similar to the 1v{sub 3} state. The vibrational efficacies for promoting reaction on Ni(111) are larger than for reaction on Pt(111), due to the larger nonadiabatic couplings. Our computed sticking probabilities are in good agreement with results from recent ab initio molecular dynamics and reactive force field studies.« less

Mode-selective chemistry on metal surfaces: The dissociative chemisorption of CH 4 on Pt(111)

DOE PAGES

Guo, Han; Jackson, Bret

2016-05-13

A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore CH 4 dissociation on Pt(111). Computed sticking probabilities for molecules in the ground, 1v 3 and 2v 3, states are in very good agreement with the available experimental data, reproducing the variation in reactivity with collision energy and vibrational state. As was found in similar studies on Ni(100) and Ni(111), exciting the 1v 1 symmetric stretch of CH 4 is more effective at promoting the dissociative chemisorption of CH 4 than exciting the 1v 3 antisymmetric stretch. This behavior is explained in terms of symmetry,more » mode-softening, and nonadiabatic transitions between vibrationally adiabatic states. We find that the efficacies of the bending modes for promoting reaction are reasonably large, and similar to the 1v 3 state. The vibrational efficacies for promoting reaction on Ni(111) are larger than for reaction on Pt(111), due to the larger nonadiabatic couplings. As a result, our computed sticking probabilities are in good agreement with results from recent ab initio molecular dynamics and reactive force field studies.« less

Colour centres and nanostructures on the surface of laser crystals

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

Kulagin, N A

2012-11-30

This paper presents a study of structural and radiationinduced colour centres in the bulk and ordered nanostructures on the surface of doped laser crystals: sapphire, yttrium aluminium garnet and strontium titanate. The influence of thermal annealing, ionising radiation and plasma exposure on the spectroscopic properties of high-purity materials and crystals containing Ti, V and Cr impurities is examined. Colour centres resulting from changes in the electronic state of impurities and plasma-induced surface modification of the crystals are studied by optical, EPR and X-ray spectroscopies, scanning electron microscopy and atomic force microscopy. X-ray line valence shift measurements are used to assessmore » changes in the electronic state of some impurity and host ions in the bulk and on the surface of oxide crystals. Conditions are examined for the formation of one- and two-level arrays of ordered crystallites 10{sup -10} to 10{sup -7} m in size on the surface of crystals doped with irongroup and lanthanoid ions. The spectroscopic properties of the crystals are analysed using ab initio self-consistent field calculations for Me{sup n+} : [O{sup 2-}]{sub k} clusters. (interaction of laser radiation with matter. laser plasma)« less

Poly-proline-based chiral stationary phases: a molecular dynamics study of triproline, tetraproline, pentaproline and hexaproline interfaces.

PubMed

Ashtari, M; Cann, N M

2012-11-23

Poly-proline chains and derivatives have been recently examined as the basis for new chiral stationary phases in high performance liquid chromatography. The selectivity of poly-proline has been measured for peptides with up to ten proline units. In this article, we employ molecular dynamics simulations to examine the interfacial structure and solvation of surface-bound poly-proline chiral selectors. Specifically, we study the interfacial structure of trimethylacetyl-terminated poly-proline chains with three-to-six prolines. The surface includes silanol groups and end-caps, to better capture the characteristics of the stationary phase, and the solvent is either a polar water/methanol or a relatively apolar n-hexane/2-propanol mixture. We begin with a comprehensive ab initio study of the conformers, their energies, and an assessment of conformer flexibility. Force fields have been developed for each poly-proline selector. Molecular dynamics simulations are employed to study the preferred backbone conformations and solvent hydrogen bonding for different poly-proline/solvent interfaces. For triproline, the effect of two different terminal groups, trimethylacetyl and t-butyl carbamate are compared. Copyright © 2012 Elsevier B.V. All rights reserved.

Thin film lubrication of hexadecane confined by iron and iron oxide surfaces: A crucial role of surface structure

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

Ta, D. T.; Tieu, A. K.; Zhu, H. T., E-mail: hongtao@uow.edu.au

2015-10-28

A comparative analysis of thin film lubrication of hexadecane between different iron and its oxide surfaces has been carried out using classical molecular dynamic simulation. An ab initio force-field, COMPASS, was applied for n-hexadecane using explicit atom model. An effective potential derived from density functional theory calculation was utilized for the interfacial interaction between hexadecane and the tribo-surfaces. A quantitative surface parameterization was introduced to investigate the influence of surface properties on the structure, rheological properties, and tribological performance of the lubricant. The results show that although the wall-fluid attraction of hexadecane on pure iron surfaces is significantly stronger thanmore » its oxides, there is a considerable reduction of shear stress of confined n-hexadecane film between Fe(100) and Fe(110) surfaces compared with FeO(110), FeO(111), Fe{sub 2}O{sub 3}(001), and Fe{sub 2}O{sub 3}(012). It was found that, in thin film lubrication of hexadecane between smooth iron and iron oxide surfaces, the surface corrugation plays a role more important than the wall-fluid adhesion strength.« less

Unraveling the formation mechanism of graphitic nitrogen-doping in thermally treated graphene with ammonia

NASA Astrophysics Data System (ADS)

Li, Xiao-Fei; Lian, Ke-Yan; Liu, Lingling; Wu, Yingchao; Qiu, Qi; Jiang, Jun; Deng, Mingsen; Luo, Yi

2016-03-01

Nitrogen-doped graphene (N-graphene) has attractive properties that has been widely studied over the years. However, its possible formation process still remains unclear. Here, we propose a highly feasible formation mechanism of the graphitic-N doing in thermally treated graphene with ammonia by performing ab initio molecular dynamic simulations at experimental conditions. Results show that among the commonly native point defects in graphene, only the single vacancy 5-9 and divacancy 555-777 have the desirable electronic structures to trap N-containing groups and to mediate the subsequent dehydrogenation processes. The local structure of the defective graphene in combining with the thermodynamic and kinetic effect plays a crucial role in dominating the complex atomic rearrangement to form graphitic-N which heals the corresponding defect perfectly. The importance of the symmetry, the localized force field, the interaction of multiple trapped N-containing groups, as well as the catalytic effect of the temporarily formed bridge-N are emphasized, and the predicted doping configuration agrees well with the experimental observation. Hence, the revealed mechanism will be helpful for realizing the targeted synthesis of N-graphene with reduced defects and desired properties.

Dielectric Study of Alcohols Using Broadband Terahertz Time Domain Spectroscopy (THz-TDS).

NASA Astrophysics Data System (ADS)

Sarkar, Sohini; Saha, Debasis; Banerjee, Sneha; Mukherjee, Arnab; Mandal, Pankaj

2016-06-01

Broadband Terahertz-Time Domain Spectroscopy (THz-TDS) (1-10 THz) has been utilized to study the complex dielectric properties of methanol, ethanol, 1-propanol, 2-propanol, 1-butanol, and 1-octanol. Previous reports on dielectric study of alcohols were limited to 5 THz. At THz (1 THz = 33.33 wn = 4 meV) frequency range (0.1 to 15 THz), the molecular reorientation and several intermolecular vibrations (local oscillation of dipoles) may coexist and contribute to the overall liquid dynamics. We find that the Debye type relaxations barely contribute beyond 1 THz, rather three harmonic oscillators dominate the entire spectral range. To get insights on the modes responsible for the observed absorption in THz frequency range, we performed all atom molecular dynamics (MD) using OPLS force field and ab initio quantum calculations. Combined experimental and theoretical study reveal that the complex dielectric functions of alcohols have contribution from a) alkyl group oscillation within H-bonded network ( 1 THz), b) intermolecular H-bond stretching ( 5 THz) , and c) librational motions in alcohols. The present work, therefore, complements all previous studies on alcohols at lower frequencies and provides a clear picture on them in a broad spectral range from microwave to 10 THz.

Computer Simulations of Polytetrafluoroethylene in the Solid State

NASA Astrophysics Data System (ADS)

Holt, D. B.; Farmer, B. L.; Eby, R. K.; Macturk, K. S.

1996-03-01

Force field parameters (Set I) for fluoropolymers were previously derived from MOPAC AM1 semiempirical data on model molecules. A second set (Set II) was derived from the AM1 results augmented by ab initio calculations. Both sets yield reasonable helical and phase II packing structures for polytetrafluoroethylene (PTFE) chains. However, Set I and Set II differ in the strength of van der Waals interactions, with Set II having deeper potential wells (order of magnitude). To differentiate which parameter set provides a better description of PTFE behavior, molecular dynamics simulations have been performed with Biosym Discover on clusters of PTFE chains which begin in a phase II packing environment. Added to the model are artificial constraints which allow the simulation of thermal expansion without having to define periodic boundary conditions for each specific temperature of interest. The preliminary dynamics simulations indicate that the intra- and intermolecular interactions provided by Set I are too weak. The degree of helical disorder and chain motion are high even at temperatures well below the phase II-phase IV transition temperature (19 C). Set II appears to yield a better description of PTFE in the solid state.

The Application of Some Hartree-Fock Model Calculation to the Analysis of Atomic and Free-Ion Optical Spectra

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

Hayhurst, Thomas Laine

1980-08-06

Techniques for applying ab-initio calculations to the is of atomic spectra are investigated, along with the relationship between the semi-empirical and ab-initio forms of Slater-Condon theory. Slater-Condon theory is reviewed with a focus on the essential features that lead to the effective Hamiltonians associated with the semi-empirical form of the theory. Ab-initio spectroscopic parameters are calculated from wavefunctions obtained via self-consistent field methods, while multi-configuration Hamiltonian matrices are constructed and diagonalized with computer codes written by Robert Cowan of Los Alamos Scientific Laboratory. Group theoretical analysis demonstrates that wavefunctions more general than Slater determinants (i.e. wavefunctions with radial correlations betweenmore » electrons) lead to essentially the same parameterization of effective Hamiltonians. In the spirit of this analysis, a strategy is developed for adjusting ab-initio values of the spectroscopic parameters, reproducing parameters obtained by fitting the corresponding effective Hamiltonian. Secondary parameters are used to "screen" the calculated (primary) spectroscopic parameters, their values determined by least squares. Extrapolations of the secondary parameters determined from analyzed spectra are attempted to correct calculations of atoms and ions without experimental levels. The adjustment strategy and extrapolations are tested on the K I sequence from K 0+ through Fe 7+, fitting to experimental levels for V 4+, and Cr 5+; unobserved levels and spectra are predicted for several members of the sequence. A related problem is also discussed: Energy levels of the Uranium hexahalide complexes, (UX 6) 2- for X= F, Cl, Br, and I, are fit to an effective Hamiltonian (the f 2 configuration in O h symmetry) with corrections proposed by Brian Judd.« less

Rhenium Complex with Noninnocent Dioxolene Ligand: Combined Experimental and ab Initio Study of [(3,5-di-tert-Bu2C6H2O2)ReCl3(OPPh3)].

PubMed

Abramov, Pavel A; Gritsan, Nina P; Suturina, Elizaveta A; Bogomyakov, Artem S; Sokolov, Maxim N

2015-07-20

Reaction of [ReOCl3(PPh3)2] with 3,5-di-tert-butyl-1,2-benzoquinone (3,5-DTBQ) in hot toluene produces a new complex [(3,5-di-tert-Bu2C6H2O2)Re(OPPh3)Cl3] (1), which was isolated and characterized by elemental analysis, IR, UV-vis spectroscopy, and cyclic voltammetry. In order to clarify the charge state of rhenium and the coordinated dioxolene ligand, X-ray experiments at 150 and 290 K were carried out. The C-O, C-C, and Re-O bond distances at both 150 and 290 K fall between those for semiquinolate (3,5-DTBSQ) and catecholate (3,5-DTBCat) forms; an empirical "metrical oxidation state" of the dioxolene ligand was estimated to be -1.5. High-level ab initio calculations (SOC-CASSCF/NEVPT2) revealed a mixed valence nature of the triplet ground state of complex 1 corresponding to a superposition of the Re(IV)-SQ and Re(V)-cat forms. In agreement with the high-level ab initio and DFT calculations, the temperature dependence of the magnetic susceptibility (5-300 K) is well described in the assumption of the triplet ground state, with the anomalously large zero-field splitting (ZFS) arising from the spin-orbit coupling. According to the ab initio calculations, all absorption bands in the visible region of the electronic absorptions spectrum are assigned to the LMCT bands, with significant contribution of the intraligand transition in the most intense band at 555 nm.

Electronic and magnetic structures of Fe3O4 ferrimagnetic investigated by first principle, mean field and series expansions calculations

NASA Astrophysics Data System (ADS)

Masrour, R.; Hlil, E. K.; Hamedoun, M.; Benyoussef, A.; Mounkachi, O.; El Moussaoui, H.

2015-03-01

Self-consistent ab initio calculations, based on density functional theory (DFT) approach and using a full potential linear augmented plane wave (FLAPW) method, are performed to investigate both electronic and magnetic properties of the Fe3O4. Polarized spin and spin-orbit coupling are included in calculations within the framework of the antiferromagnetic state between two adjacent Fe plans. Magnetic moment considered to lie along (010) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters. The exchange interactions between the magnetic atoms Fe-Fe in Fe3O4 are given using the mean field theory. The high temperature series expansions (HTSEs) of the magnetic susceptibility of with the magnetic moments, mFe in Fe3O4 is given up to seventh order series in (1/kBT). The Néel temperature TN is obtained by HTSEs of the magnetic susceptibility series combined with the Padé approximant method. The critical exponent γ associated with the magnetic susceptibility is deduced as well.

Ab initio calculation of electron–phonon coupling in monoclinic β-Ga{sub 2}O{sub 3} crystal

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

Ghosh, Krishnendu, E-mail: kghosh3@buffalo.edu; Singisetti, Uttam, E-mail: uttamsin@buffalo.edu

2016-08-15

The interaction between electrons and vibrational modes in monoclinic β-Ga{sub 2}O{sub 3} is theoretically investigated using ab-initio calculations. The large primitive cell of β-Ga{sub 2}O{sub 3} gives rise to 30 phonon modes all of which are taken into account in transport calculation. The electron-phonon interaction is calculated under density functional perturbation theory and then interpolated using Wannier–Fourier interpolation. The long-range interaction elements between electrons and polar optical phonon (POP) modes are calculated separately using the Born effective charge tensor. The direction dependence of the long-range POP coupling in a monoclinic crystal is explored and is included in the transport calculations.more » Scattering rate calculations are done using the Fermi golden rule followed by solving the Boltzmann transport equation using the Rode's method to estimate low field mobility. A room temperature mobility of 115 cm{sup 2}/V s is observed. Comparison with recent experimentally reported mobility is done for a wide range of temperatures (30 K–650 K). It is also found that the POP interaction dominates the electron mobility under low electric field conditions. The relative contribution of the different POP modes is analyzed and the mode 21 meV POP is found to have the highest impact on low field electron mobility at room temperature.« less

Surface Segregation Energies of BCC Binaries from Ab Initio and Quantum Approximate Calculations

NASA Technical Reports Server (NTRS)

Good, Brian S.

2003-01-01

We compare dilute-limit segregation energies for selected BCC transition metal binaries computed using ab initio and quantum approximate energy method. Ab initio calculations are carried out using the CASTEP plane-wave pseudopotential computer code, while quantum approximate results are computed using the Bozzolo-Ferrante-Smith (BFS) method with the most recent parameterization. Quantum approximate segregation energies are computed with and without atomistic relaxation. The ab initio calculations are performed without relaxation for the most part, but predicted relaxations from quantum approximate calculations are used in selected cases to compute approximate relaxed ab initio segregation energies. Results are discussed within the context of segregation models driven by strain and bond-breaking effects. We compare our results with other quantum approximate and ab initio theoretical work, and available experimental results.

Molecular hyperfine fields in organic magnetoresistance devices

NASA Astrophysics Data System (ADS)

Giro, Ronaldo; Rosselli, Flávia P.; dos Santos Carvalho, Rafael; Capaz, Rodrigo B.; Cremona, Marco; Achete, Carlos A.

2013-03-01

We calculate molecular hyperfine fields in organic magnetoresistance (OMAR) devices using ab initio calculations. To do so, we establish a protocol for the accurate determination of the average hyperfine field Bhf and apply it to selected molecular ions: NPB, TPD, and Alq3. Then, we make devices with precisely the same molecules and perform measurements of the OMAR effect, in order to address the role of hole-transport layer in the characteristic magnetic field B0 of OMAR. Contrary to common belief, we find that molecular hyperfine fields are not only caused by hydrogen nuclei. We also find that dipolar contributions to the hyperfine fields can be comparable to the Fermi contact contributions. However, such contributions are restricted to nuclei located in the same molecular ion as the charge carrier (intramolecular), as extramolecular contributions are negligible.

Dynamical correlation effects on photoisomerization: Ab initio multiple spawning dynamics with MS-CASPT2 for a model trans-protonated Schiff base

DOE PAGES

Liu, Lihong; Liu, Jian; Martinez, Todd J.

2015-12-17

Here, we investigate the photoisomerization of a model retinal protonated Schiff base (trans-PSB3) using ab initio multiple spawning (AIMS) based on multi-state second order perturbation theory (MSPT2). Discrepancies between the photodynamical mechanism computed with three-root state-averaged complete active space self-consistent field (SA-3-CASSCF, which does not include dynamic electron correlation effects) and MSPT2 show that dynamic correlation is critical in this photoisomerization reaction. Furthermore, we show that the photodynamics of trans-PSB3 is not well described by predictions based on minimum energy conical intersections (MECIs) or minimum energy conical intersection (CI) seam paths. Instead, most of the CIs involved in the photoisomerizationmore » are far from MECIs and minimum energy CI seam paths. Thus, both dynamical nuclear effects and dynamic electron correlation are critical to understanding the photochemical mechanism.« less

Correlation of electronic structure and magnetic moment in Ga1-xMnxN : First-principles, mean field and high temperature series expansions calculations

NASA Astrophysics Data System (ADS)

Masrour, R.; Hlil, E. K.

2016-08-01

Self-consistent ab initio calculations based on density-functional theory and using both full potential linearized augmented plane wave and Korring-Kohn-Rostoker-coherent potential approximation methods, are performed to investigate both electronic and magnetic properties of the Ga1-xMnxN system. Magnetic moments considered to lie along (001) axes are computed. Obtained data from ab initio calculations are used as input for the high temperature series expansions (HTSEs) calculations to compute other magnetic parameters such as the magnetic phase diagram and the critical exponent. The increasing of the dilution x in this system has allowed to verify a series of HTSEs predictions on the possibility of ferromagnetism in dilute magnetic insulators and to demonstrate that the interaction changes from antiferromagnetic to ferromagnetic passing through the spins glace phase.

Ab initio study of the molecular structure and vibrational spectrum of nitric acid and its protonated forms

NASA Technical Reports Server (NTRS)

Lee, Timothy J.; Rice, Julia E.

1992-01-01

The equilibrium structures, harmonic vibrational frequencies, IR intensities, and relative energetics of HNO3 and its protonated form H2NO3+ were investigated using double-zeta plus polarization and triple-zeta plus polarization basis sets in conjunction with high-level ab initio methods. The latter include second-order Moller-Plesset perturbation theory, the single and double excitation coupled cluster (CCSD) methods, a perturbational estimate of the effects of connected triple excitations (CCSD(T)), and the self-consistent field. To determine accurate energy differences CCSD(T) energies were computed using large atomic natural orbital basis sets. Four different isomers of H2NO3+ were considered. The lowest energy form of protonated nitric acid was found to correspond to a complex between H2O and NO2+, which is consistent with earlier theoretical and experimental studies.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids

NASA Astrophysics Data System (ADS)

Kim, Jeongnim; Baczewski, Andrew D.; Beaudet, Todd D.; Benali, Anouar; Chandler Bennett, M.; Berrill, Mark A.; Blunt, Nick S.; Josué Landinez Borda, Edgar; Casula, Michele; Ceperley, David M.; Chiesa, Simone; Clark, Bryan K.; Clay, Raymond C., III; Delaney, Kris T.; Dewing, Mark; Esler, Kenneth P.; Hao, Hongxia; Heinonen, Olle; Kent, Paul R. C.; Krogel, Jaron T.; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M. Graham; Luo, Ye; Malone, Fionn D.; Martin, Richard M.; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A.; Mitas, Lubos; Morales, Miguel A.; Neuscamman, Eric; Parker, William D.; Pineda Flores, Sergio D.; Romero, Nichols A.; Rubenstein, Brenda M.; Shea, Jacqueline A. R.; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F.; Townsend, Joshua P.; Tubman, Norm M.; Van Der Goetz, Brett; Vincent, Jordan E.; ChangMo Yang, D.; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-01

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater–Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program’s capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Berry curvature dipole in Weyl semimetal materials: An ab initio study

NASA Astrophysics Data System (ADS)

Zhang, Yang; Sun, Yan; Yan, Binghai

2018-01-01

Noncentrosymmetric metals are anticipated to exhibit a dc photocurrent in the nonlinear optical response caused by the Berry curvature dipole in momentum space. Weyl semimetals (WSMs) are expected to be excellent candidates for observing these nonlinear effects because they carry a large Berry curvature concentrated in small regions, i.e., near the Weyl points. We have implemented the semiclassical Berry curvature dipole formalism into an ab initio scheme and investigated the second-order nonlinear response for two representative groups of materials: the TaAs-family type-I WSMs and the MoTe2-family type-II WSMs. Both types of WSMs exhibited a Berry curvature dipole in which type-II Weyl points are usually superior to the type-I WSM because of the strong tilt. Corresponding nonlinear susceptibilities in several materials promise a nonlinear Hall effect in the dc field limit, which is within the experimentally detectable range.

QMCPACK: an open source ab initio quantum Monte Carlo package for the electronic structure of atoms, molecules and solids.

PubMed

Kim, Jeongnim; Baczewski, Andrew T; Beaudet, Todd D; Benali, Anouar; Bennett, M Chandler; Berrill, Mark A; Blunt, Nick S; Borda, Edgar Josué Landinez; Casula, Michele; Ceperley, David M; Chiesa, Simone; Clark, Bryan K; Clay, Raymond C; Delaney, Kris T; Dewing, Mark; Esler, Kenneth P; Hao, Hongxia; Heinonen, Olle; Kent, Paul R C; Krogel, Jaron T; Kylänpää, Ilkka; Li, Ying Wai; Lopez, M Graham; Luo, Ye; Malone, Fionn D; Martin, Richard M; Mathuriya, Amrita; McMinis, Jeremy; Melton, Cody A; Mitas, Lubos; Morales, Miguel A; Neuscamman, Eric; Parker, William D; Pineda Flores, Sergio D; Romero, Nichols A; Rubenstein, Brenda M; Shea, Jacqueline A R; Shin, Hyeondeok; Shulenburger, Luke; Tillack, Andreas F; Townsend, Joshua P; Tubman, Norm M; Van Der Goetz, Brett; Vincent, Jordan E; Yang, D ChangMo; Yang, Yubo; Zhang, Shuai; Zhao, Luning

2018-05-16

QMCPACK is an open source quantum Monte Carlo package for ab initio electronic structure calculations. It supports calculations of metallic and insulating solids, molecules, atoms, and some model Hamiltonians. Implemented real space quantum Monte Carlo algorithms include variational, diffusion, and reptation Monte Carlo. QMCPACK uses Slater-Jastrow type trial wavefunctions in conjunction with a sophisticated optimizer capable of optimizing tens of thousands of parameters. The orbital space auxiliary-field quantum Monte Carlo method is also implemented, enabling cross validation between different highly accurate methods. The code is specifically optimized for calculations with large numbers of electrons on the latest high performance computing architectures, including multicore central processing unit and graphical processing unit systems. We detail the program's capabilities, outline its structure, and give examples of its use in current research calculations. The package is available at http://qmcpack.org.

Magneto-optical spectroscopy of Co{sub 2}FeSi Heusler compound

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

Veis, M., E-mail: veis@karlov.mff.cuni.cz; Beran, L.; Antos, R.

2014-05-07

Magneto-optical and electronic properties of the Co{sub 2}FeSi Heusler compound were studied by polar Kerr magneto-optical spectroscopy and ab-initio calculations. The thin-film samples were grown by dc/rf magnetron co-sputtering on MgO(100) substrates. A Cr seed layer was deposited prior to the Co{sub 2}FeSi layer to achieve its epitaxial growth. The magneto-optical spectroscopy was carried out using generalized magneto-optical ellipsometry with rotating analyzer in the photon energy range from 1.4 to 5.5 eV with an applied magnetic field of up to 1.2 T. The polar Kerr spectra showed a smooth spectral behavior up to 5.5 eV indicating nearly free charge carriers. Experimental data weremore » compared with ab-initio calculations based on density functional theory employing the full-potential linearized augmented plane wave method.« less

Carbonate-Bridged Lanthanoid Triangles: Single-Molecule Magnet Behavior, Inelastic Neutron Scattering, and Ab Initio Studies.

PubMed

Giansiracusa, Marcus J; Vonci, Michele; Van den Heuvel, Willem; Gable, Robert W; Moubaraki, Boujemaa; Murray, Keith S; Yu, Dehong; Mole, Richard A; Soncini, Alessandro; Boskovic, Colette

2016-06-06

Optimization of literature synthetic procedures has afforded, in moderate yield, homogeneous and crystalline samples of the five analogues Na11[{RE(OH2)}3CO3(PW9O34)2] (1-RE; RE = Y, Tb, Dy, Ho, and Er). Phase-transfer methods have allowed isolation of the mixed salts (Et4N)9Na2[{RE(OH2)}3CO3(PW9O34)2] (2-RE; RE = Y and Er). The isostructural polyanions in these compounds are comprised of a triangular arrangement of trivalent rare-earth ions bridged by a μ3-carbonate ligand and sandwiched between two trilacunary Keggin {PW9O34} polyoxometalate ligands. Alternating-current (ac) magnetic susceptibility studies of 1-Dy, 1-Er, and 2-Er reveal the onset of frequency dependence for the out-of-phase susceptibility in the presence of an applied magnetic field at the lowest measured temperatures. Inelastic neutron scattering (INS) spectra of 1-Ho and 1-Er exhibit transitions between the lowest-lying crystal-field (CF) split states of the respective J = 8 and (15)/2 ground-state spin-orbit multiplets of the Ho(III) and Er(III) ions. Complementary ab initio calculations performed for these two analogues allow excellent reproduction of the experimental magnetic susceptibility and low-temperature magnetization data and are in reasonable agreement with the experimental INS data. The ab initio calculations reveal that the slight difference in coordination environments of the three Ln(III) ions in each complex gives rise to differences in the CF splitting that are not insignificant. This theoretical result is consistent with the observation of multiple relaxation processes by ac magnetic susceptibility and the broadness of the measured INS peaks. The ab initio calculations also indicate substantial mixing of the MJ contributions to the CF split energy levels of each Ln(III) ion. Calculations indicate that the CF ground states of the Ho(III) centers in 1-Ho are predominantly comprised of contributions from small MJ, while those of the Er(III) centers in 1-Er are predominantly comprised of contributions from large MJ, giving rise to slow magnetic relaxation. Although no direct evidence for intramolecular RE···RE magnetic coupling is observed in either magnetic or INS studies, on the basis of the ab initio calculations, we find noncollinear magnetic axes in 1-Er that are coplanar with the erbium triangle and radially arranged with respect to the triangle's centroid; thus, we argue that the absence of magnetic coupling in this system arises from dipolar and antiferromagnetic superexchange interactions that cancel each other out.

Helium Nanodroplet Isolation of the Cyclobutyl, 1-Methylallyl, and Allylcarbinyl Radicals: Infrared Spectroscopy and Ab Initio Computations

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

Brown, Alaina R.; Franke, Peter R.; Douberly, Gary E.

Gas-phase cyclobutyl radical (*C 4H 7) is produced via pyrolysis of cyclobutylmethyl nitrite (C 4H 7(CH 2)ONO). Other (C 4H 7)-C-center dot radicals, such as 1-methylallyl and allylcarbinyl, are similarly produced from nitrite precursors. Nascent radicals are promptly solvated in liquid He droplets, allowing for the acquisition of infrared spectra in the CH stretching region. For the cyclobutyl and 1-methylallyl radicals, anharmonic frequencies are predicted by VPT2+K simulations based upon a hybrid CCSD(T) force field with quadratic (cubic and quartic) force constants computed using the ANO1 (ANO0) basis set. A density functional theoretical method is used to compute the forcemore » field for the allylcarbinyl radical. For all *C 4H 7 radicals, resonance polyads in the 2800-3000 cm -1 region appear as a result of anharmonic coupling between the CH stretching fundamentals and CH, bend overtones and combinations. Upon pyrolysis of the cyclobutylmethyl nitrite precursor to produce the cyclobutyl radical, an approximately 2-fold increase in the source temperature leads to the appearance of spectral signatures that can be assigned to 1-methylallyl and 1,3-butadiene. On the basis of a previously reported *C 4H 7 potential energy surface, this result is interpreted as evidence for the unimolecular decomposition of the cyclobutyl radical via ring opening, prior to it being captured by helium droplets. On the *C 4H 7 potential surface, 1,3-butadiene is formed from cyclobutyl ring opening and H atom loss, and the 1-methylallyl radical is the most energetically stable intermediate along the decomposition pathway. Here, the allylcarbinyl radical is a higher-energy (C 4H 7)-C-center dot intermediate along the ring-opening path, and the spectral signatures of this radical are not observed under the same conditions that produce 1-methylallyl and 1,3-butadiene from the unimolecular decomposition of cyclobutyl.« less

Helium Nanodroplet Isolation of the Cyclobutyl, 1-Methylallyl, and Allylcarbinyl Radicals: Infrared Spectroscopy and Ab Initio Computations

DOE PAGES

Brown, Alaina R.; Franke, Peter R.; Douberly, Gary E.

2017-09-22

Gas-phase cyclobutyl radical (*C 4H 7) is produced via pyrolysis of cyclobutylmethyl nitrite (C 4H 7(CH 2)ONO). Other (C 4H 7)-C-center dot radicals, such as 1-methylallyl and allylcarbinyl, are similarly produced from nitrite precursors. Nascent radicals are promptly solvated in liquid He droplets, allowing for the acquisition of infrared spectra in the CH stretching region. For the cyclobutyl and 1-methylallyl radicals, anharmonic frequencies are predicted by VPT2+K simulations based upon a hybrid CCSD(T) force field with quadratic (cubic and quartic) force constants computed using the ANO1 (ANO0) basis set. A density functional theoretical method is used to compute the forcemore » field for the allylcarbinyl radical. For all *C 4H 7 radicals, resonance polyads in the 2800-3000 cm -1 region appear as a result of anharmonic coupling between the CH stretching fundamentals and CH, bend overtones and combinations. Upon pyrolysis of the cyclobutylmethyl nitrite precursor to produce the cyclobutyl radical, an approximately 2-fold increase in the source temperature leads to the appearance of spectral signatures that can be assigned to 1-methylallyl and 1,3-butadiene. On the basis of a previously reported *C 4H 7 potential energy surface, this result is interpreted as evidence for the unimolecular decomposition of the cyclobutyl radical via ring opening, prior to it being captured by helium droplets. On the *C 4H 7 potential surface, 1,3-butadiene is formed from cyclobutyl ring opening and H atom loss, and the 1-methylallyl radical is the most energetically stable intermediate along the decomposition pathway. Here, the allylcarbinyl radical is a higher-energy (C 4H 7)-C-center dot intermediate along the ring-opening path, and the spectral signatures of this radical are not observed under the same conditions that produce 1-methylallyl and 1,3-butadiene from the unimolecular decomposition of cyclobutyl.« less

Ab Initio-Based Predictions of Hydrocarbon Combustion Chemistry

DTIC Science & Technology

2015-07-15

There are two prime objectives of the research. One is to develop and apply efficient methods for using ab initio potential energy surfaces (PESs...31-Mar-2015 Approved for Public Release; Distribution Unlimited Final Report: Ab Initio -Based Predictions of Hydrocarbon Combustion Chemistry The...Office P.O. Box 12211 Research Triangle Park, NC 27709-2211 hydrocarbon combustion, ab initio quantum chemistry, potential energy surfaces, chemical

On the way to a microscopic derivation of covariant density functionals in nuclei

NASA Astrophysics Data System (ADS)

Ring, Peter

2018-02-01

Several methods are discussed to derive covariant density functionals from the microscopic input of bare nuclear forces. In a first step there are semi-microscopic functionals, which are fitted to ab-initio calculations of nuclear matter and depend in addition on very few phenomenological parameters. They are able to describe nuclear properties with the same precision as fully phenomenological functionals. In a second step we present first relativistic Brueckner-Hartree-Fock calculations in finite nuclei in order to study properties of such functionals, which cannot be obtained from nuclear matter calculations.

Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model.

PubMed

Laury, Marie L; Wang, Lee-Ping; Pande, Vijay S; Head-Gordon, Teresa; Ponder, Jay W

2015-07-23

A set of improved parameters for the AMOEBA polarizable atomic multipole water model is developed. An automated procedure, ForceBalance, is used to adjust model parameters to enforce agreement with ab initio-derived results for water clusters and experimental data for a variety of liquid phase properties across a broad temperature range. The values reported here for the new AMOEBA14 water model represent a substantial improvement over the previous AMOEBA03 model. The AMOEBA14 model accurately predicts the temperature of maximum density and qualitatively matches the experimental density curve across temperatures from 249 to 373 K. Excellent agreement is observed for the AMOEBA14 model in comparison to experimental properties as a function of temperature, including the second virial coefficient, enthalpy of vaporization, isothermal compressibility, thermal expansion coefficient, and dielectric constant. The viscosity, self-diffusion constant, and surface tension are also well reproduced. In comparison to high-level ab initio results for clusters of 2-20 water molecules, the AMOEBA14 model yields results similar to AMOEBA03 and the direct polarization iAMOEBA models. With advances in computing power, calibration data, and optimization techniques, we recommend the use of the AMOEBA14 water model for future studies employing a polarizable water model.

FTIR spectroscopy and thermodynamics of hydrogen adsorbed in a cross-linked polymer.

PubMed

Spoto, Giuseppe; Vitillo, Jenny G; Cocina, Donato; Damin, Alessandro; Bonino, Francesca; Zecchina, Adriano

2007-09-28

The adsorption of H(2) in a cross-linked poly(styrene-co-divinylbenzene) (St-DVB) microporous polymer (BET surface area 920 m(2) g(-1)) is studied by volumetric and gravimetric methods, FTIR spectroscopy at variable temperature (300-14 K) and ab initio calculations. At 77 K the polymer reversibly stores up to 1.3 mass% H(2) at a pressure of 1 bar and 1.8 mass% at 10 bar. The adsorption process involves the specific interaction of H(2) with the structural phenyl rings through weak dispersive forces. The interacting molecules become IR active and give rise to vibrational and rotational-vibrational manifestations which are affected by the temperature, the contact time and the H(2) equilibrium pressure. The spectra of the H(2)/St-DVB system reported here represent the first IR evidence of the adsorption of hydrogen on unsaturated molecules. The adsorption enthalpy is evaluated by the VTIR (variable temperature IR spectroscopy) method (C. Otero Areán et al., Phys. Chem. Chem. Phys., 2007, DOI: 10.1039/b615535a) and compared with the results of ab initio calculations for the H(2)/benzene interaction and with literature data.

Quantum state preparation of homonuclear molecular ions enabled via a cold buffer gas: An ab initio study for the H2+ and the D2+ case

NASA Astrophysics Data System (ADS)

Schiller, S.; Kortunov, I.; Hernández Vera, M.; Gianturco, F.; da Silva, H.

2017-04-01

Precision vibrational spectroscopy of the molecular hydrogen ions is of significant interest for determining fundamental constants, for searching for new forces, and for testing quantum electrodynamics calculations. Future experiments can profit from the ability of preparing molecular hydrogen ions at ultralow kinetic energy and in preselected internal states, with respect to vibration, rotation, and spin degrees of freedom. For the homonuclear ions (H2+ , D2+ ), direct laser cooling of the rotational degree of freedom is not feasible. We show by quantum calculations that rotational cooling by cold He buffer gas is an effective approach. For this purpose we have computed the energy-dependent cross sections for rotationally elastic and inelastic collisions, h2+ (v =0 ,N ) +He → h2+ (v =0 ,N') +He (where h =H ,D ) , using ab initio coupled-channel calculations. We find that rotational cooling to the lowest rotational state is possible within tens of seconds under experimentally realistic conditions. We furthermore describe possible protocols for the preparation of a single quantum state, where also the spin state is well defined.

Structural characterization of tellurite glasses doped with transition metal oxides using Raman spectra and ab initio calculations.

PubMed

Mohamed, Tarek A; Shaltout, I; Al Yahyaei, K M

2006-05-01

Systems of iron tellurite glasses were prepared by melt quenching with compositions of [85%TeO2+5%Fe2O3+10%TMO], where transition metal oxides (TMO) are TiO2, V2O5, MnO, CoO, NiO and CuO. Furthermore, the main structural units of these samples have been characterized by means of Raman spectra (150-1200 cm(-1)) as well as wavenumber predictions by means of Gaussian 98 ab initio calculations for the proposed site symmetries of TeO4(4-) triagonal bipyramid (C2v) and Te2O7(6-) bridged tetrahedra (Cs and C1). Aided by normal coordinate analysis, calculated vibrational frequencies, Raman scattering activities, force constants in internal coordinates and potential energy distributions (PEDs), revised vibrational assignments for the fundamental modes have been proposed. The main structural features are correlated to the dominant units of triagonal bipyramid (tbp) or bridged tetrahedral (TeO3+1 binds to TeO3 through TeOTe bridge; corner sharing). Moreover, the Raman spectra of the investigated tellurites reflect a structural change from tbp (coordination number is four) to triagonal pyramidal (coordination number is three).

Accurate classical short-range forces for the study of collision cascades in Fe–Ni–Cr

DOE PAGES

Béland, Laurent Karim; Tamm, Artur; Mu, Sai; ...

2017-05-10

The predictive power of a classical molecular dynamics simulation is largely determined by the physical validity of its underlying empirical potential. In the case of high-energy collision cascades, it was recently shown that correctly modeling interactions at short distances is necessary to accurately predict primary damage production. An ab initio based framework is introduced for modifying an existing embedded-atom method FeNiCr potential to handle these short-range interactions. Density functional theory is used to calculate the energetics of two atoms approaching each other, embedded in the alloy, and to calculate the equation of state of the alloy as it is compressed.more » The pairwise terms and the embedding terms of the potential are modi ed in accordance with the ab initio results. Using this reparametrized potential, collision cascades are performed in Ni 50Fe 50, Ni 80Cr 20 and Ni 33Fe 33Cr 33. The simulations reveal that alloying Ni and NiCr to Fe reduces primary damage production, in agreement with some previous calculations. Alloying Ni and NiFe to Cr does not reduce primary damage production, in contradiction with previous calculations.« less

Diffusion Monte Carlo calculations of Xenon and Krypton at High Pressure

NASA Astrophysics Data System (ADS)

Shulenburger, Luke; Mattsson, Thomas R.

2011-06-01

Ab initio calculations based on density functional theory (DFT) have proven a valuable tool in understanding the properties of materials at extreme conditions. However, there are entire classes of materials where the current limitations of DFT cast doubt upon the predictive power of the method. These include so called strongly correlated systems and materials where van der Waals forces are important. Diffusion Monte Carlo (DMC) can treat materials with a different class of approximations that have generally proven to be more accurate. The use of DMC together with DFT may therefore improve the predictive capability of the ab initio calculation of materials at extreme conditions. We present two examples of this approach. In the first we use DMC total energies to address the discrepancy between DFT and diamond anvil cell melt curves of Xe. In the second, DMC is used to address the choice of density functional used in calculations of the Kr hugoniot. Sandia National Laboratories is a multiprogram laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy's National Nuclear Security Administration under Contract No. DE-AC04-94AL85000. Belonoshko et al. PRB 74, 054114 (2006).

Current Status of Protein Force Fields for Molecular Dynamics

PubMed Central

Lopes, Pedro E.M.; Guvench, Olgun

2015-01-01

Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

Protein Folding and Structure Prediction from the Ground Up: The Atomistic Associative Memory, Water Mediated, Structure and Energy Model.

PubMed

Chen, Mingchen; Lin, Xingcheng; Zheng, Weihua; Onuchic, José N; Wolynes, Peter G

2016-08-25

The associative memory, water mediated, structure and energy model (AWSEM) is a coarse-grained force field with transferable tertiary interactions that incorporates local in sequence energetic biases using bioinformatically derived structural information about peptide fragments with locally similar sequences that we call memories. The memory information from the protein data bank (PDB) database guides proper protein folding. The structural information about available sequences in the database varies in quality and can sometimes lead to frustrated free energy landscapes locally. One way out of this difficulty is to construct the input fragment memory information from all-atom simulations of portions of the complete polypeptide chain. In this paper, we investigate this approach first put forward by Kwac and Wolynes in a more complete way by studying the structure prediction capabilities of this approach for six α-helical proteins. This scheme which we call the atomistic associative memory, water mediated, structure and energy model (AAWSEM) amounts to an ab initio protein structure prediction method that starts from the ground up without using bioinformatic input. The free energy profiles from AAWSEM show that atomistic fragment memories are sufficient to guide the correct folding when tertiary forces are included. AAWSEM combines the efficiency of coarse-grained simulations on the full protein level with the local structural accuracy achievable from all-atom simulations of only parts of a large protein. The results suggest that a hybrid use of atomistic fragment memory and database memory in structural predictions may well be optimal for many practical applications.

Modeling the interaction Between Ethylene Diamine and Water Films on the Surface of a Carbon Nanotube

NASA Technical Reports Server (NTRS)

Jaffe, Richard L.; Walther, Jens H.; Zimmerli, Urs; Koumoutsakos, Petros

2004-01-01

It has been observed that a carbon nanotube (CNT) AFM tip coated with ethylene diamine (EDA) penetrates the liquid water-air interface more easily than an uncoated nanotube tip. The EDA coating remains intact through repeated cycles of dipping and removal. In order to understand the physical basis for this observation, we use ab initio quantum chemistry calculations to study the EDA-CNT-water interaction and to parameterize a force field describing this system. Molecular dynamics (MD) simulations are carried out for EDA-water mixtures and an EDA-coated carbon nanotube immmed in water. These simulations are similar to our earlier MD study that characterized the CNT-water interface. The attractive CNT-EDA and CNT-water interactions arise primarily from van der Waals forces, and the EDA-EDA, EDA-water and water-water interactions are mainly due to hydrogen bond formation. The binding energ of single EDA molecule to the nanotube is nearly three times larger than the corresponding value found for water (4.3 versus 1.5 kcal mol, respectively). The EDA molecules readily stick to and diffuse along the CNT surface. As a resulf mixing of the EDA and water films does not occur on the timescale of the MD simulations. The EDA film reduces the hydrophobicity of the nanotube surface and acts like a prototypical surfactant in stabilizing the suspension of carbon nanotubes in water. For this presentation, we use the MD simulations to determine how the presence of the carbon nanotube surface perturbs the properties of EDA-water mixtures.

Unified field theory from the classical wave equation: Preliminary application to atomic and nuclear structure

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

Múnera, Héctor A., E-mail: hmunera@hotmail.com; Retired professor, Department of Physics, Universidad Nacional de Colombia, Bogotá, Colombia, South America

2016-07-07

It is postulated that there exists a fundamental energy-like fluid, which occupies the flat three-dimensional Euclidean space that contains our universe, and obeys the two basic laws of classical physics: conservation of linear momentum, and conservation of total energy; the fluid is described by the classical wave equation (CWE), which was Schrödinger’s first candidate to develop his quantum theory. Novel solutions for the CWE discovered twenty years ago are nonharmonic, inherently quantized, and universal in the sense of scale invariance, thus leading to quantization at all scales of the universe, from galactic clusters to the sub-quark world, and yielding amore » unified Lorentz-invariant quantum theory ab initio. Quingal solutions are isomorphic under both neo-Galilean and Lorentz transformations, and exhibit nother remarkable property: intrinsic unstability for large values of ℓ (a quantum number), thus limiting the size of each system at a given scale. Unstability and scale-invariance together lead to nested structures observed in our solar system; unstability may explain the small number of rows in the chemical periodic table, and nuclear unstability of nuclides beyond lead and bismuth. Quingal functions lend mathematical basis for Boscovich’s unified force (which is compatible with many pieces of evidence collected over the past century), and also yield a simple geometrical solution for the classical three-body problem, which is a useful model for electronic orbits in simple diatomic molecules. A testable prediction for the helicoidal-type force is suggested.« less

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

40 CFR 89.126 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... certificate void ab initio. (d) When the Administrator denies, suspends, revokes, or voids ab initio a... such fraud or other misconduct that makes the certification invalid ab initio. [59 FR 31335, June 17...

FT-IR and Raman spectra, DFT and SQMFF calculations for geometrical interpretation and vibrational analysis of 3-nitro-p-toluic acid

NASA Astrophysics Data System (ADS)

Nataraj, A.; Balachandran, V.; Karthick, T.

2012-08-01

The Fourier transform infrared (FT-IR) and FT-Raman of 3-nitro-p-toluic acid (NTA) have been recorded and analyzed. The equilibrium geometry, bonding features and harmonic vibrational frequencies have been investigated with the help of ab initio and density functional theory (DFT) methods. The assignments of the vibrational spectra have been carried out with the help of normal coordinate analysis (NCA) following the scaled quantum mechanical force field methodology (SQMFF). The optimized geometric bond lengths and bond angles obtained by computation show good agreement with experimental data of the relative compound. The computed dimer parameters also show good agreement with experimental data. The first hyperpolarizability (β0) of this noval molecular system and related properties (β, α0, and Δα) of NTA are calculated using B3LYP/6-311++G(d,p) method on the finite-field approach. Stability of the molecule arising from hyperconjugative interactions, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. The results show that charge in electron density (ED) in the σ* and π* antibonding orbital and second order delocalization energies E(2) confirms the occurrence of intramolecular charge transfer (ICT) within the molecule. The calculated HOMO and LUMO energies also show that charge transfer occurs within the molecule. Finally the calculations results were applied to simulated infrared and Raman spectra of the title compound which show good agreement with observed spectra.

Structural predictions for Correlated Electron Materials Using the Functional Dynamical Mean Field Theory Approach

NASA Astrophysics Data System (ADS)

Haule, Kristjan

2018-04-01

The Dynamical Mean Field Theory (DMFT) in combination with the band structure methods has been able to address reach physics of correlated materials, such as the fluctuating local moments, spin and orbital fluctuations, atomic multiplet physics and band formation on equal footing. Recently it is getting increasingly recognized that more predictive ab-initio theory of correlated systems needs to also address the feedback effect of the correlated electronic structure on the ionic positions, as the metal-insulator transition is almost always accompanied with considerable structural distortions. We will review recently developed extension of merger between the Density Functional Theory (DFT) and DMFT method, dubbed DFT+ embedded DMFT (DFT+eDMFT), whichsuccessfully addresses this challenge. It is based on the stationary Luttinger-Ward functional to minimize the numerical error, it subtracts the exact double-counting of DFT and DMFT, and implements self-consistent forces on all atoms in the unit cell. In a few examples, we will also show how the method elucidated the important feedback effect of correlations on crystal structure in rare earth nickelates to explain the mechanism of the metal-insulator transition. The method showed that such feedback effect is also essential to understand the dynamic stability of the high-temperature body-centered cubic phase of elemental iron, and in particular it predicted strong enhancement of the electron-phonon coupling over DFT values in FeSe, which was very recently verified by pioneering time-domain experiment.

Molecular structure, vibrational spectroscopic (FT-IR, FT-Raman), UV-vis spectra, first order hyperpolarizability, NBO analysis, HOMO and LUMO analysis, thermodynamic properties of benzophenone 2,4-dicarboxylic acid by ab initio HF and density functional method

NASA Astrophysics Data System (ADS)

Chaitanya, K.

2012-02-01

The FT-IR (4000-450 cm -1) and FT-Raman spectra (3500-100 cm -1) of benzophenone 2,4-dicarboxylic acid (2,4-BDA) have been recorded in the condensed state. Density functional theory calculation with B3LYP/6-31G(d,p) basis set have been used to determine ground state molecular geometries (bond lengths and bond angles), harmonic vibrational frequencies, infrared intensities, Raman activities and bonding features of the title compounds. The assignments of the vibrational spectra have been carried out with the help of normal co-ordinate analysis (NCA) following the scaled quantum mechanical force field (SQMFF) methodology. The first order hyperpolarizability ( β0) and related properties ( β, α0 and Δ α) of 2,4-BDA is calculated using HF/6-31G(d,p) method on the finite-field approach. The stability of molecule has been analyzed by using NBO analysis. The calculated first hyperpolarizability shows that the molecule is an attractive molecule for future applications in non-linear optics. The calculated HOMO and LUMO energies show that charge transfer occurs within these molecules. Mulliken population analysis on atomic charges is also calculated. Because of vibrational analyses, the thermodynamic properties of the title compound at different temperatures have been calculated. Finally, the UV-vis spectra and electronic absorption properties were explained and illustrated from the frontier molecular orbitals.

Ab initio study of Fe(+)-benzyne

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1993-01-01

The interaction of Fe(+) with benzyne is studied using the self-consistent-field (SCF), complete active space SCF, and modified-coupled-pair functional levels of theory. The most stable structure is planar, where the Fe(+) has inserted into the in-plane pi bond, although the C-C bond distance suggests that some in-plane pi bonding remains. This system is compared with Sc(+) bonding to benzyne and other ligands.

Ab Initio Investigation of Frictional Properties of Graphene on SiC Surfaces

NASA Astrophysics Data System (ADS)

Sayin, Ceren; Gülseren, Oğuz

The exact origin and nature of various nanotribological observations on graphene such as dependence of friction on layer thickness, direction and surface morphology are yet to be fully understood. In this talk, we report on the frictional properties of graphene on 4H-SiC{0001} surfaces obtained from first principles calculations. We investigate sliding of graphene layers of various thickness along different directions on both the Si- and C-terminated faces including van-der Waals interactions. We observe that upon sliding under certain conditions, the interaction between the surface and graphene layers alternates between van-der Waals and covalent forces which dramatically affects friction. We examine the relation of frictional force to applied normal load, small out-of-plane geometric deformations of graphene and electronic structure of the systems. This work is supported by TUBITAK Project No:114F162.

Magneto-Structural Correlations in Pseudotetrahedral Forms of the [Co(SPh)4]2- Complex Probed by Magnetometry, MCD Spectroscopy, Advanced EPR Techniques, and ab Initio Electronic Structure Calculations.

PubMed

Suturina, Elizaveta A; Nehrkorn, Joscha; Zadrozny, Joseph M; Liu, Junjie; Atanasov, Mihail; Weyhermüller, Thomas; Maganas, Dimitrios; Hill, Stephen; Schnegg, Alexander; Bill, Eckhard; Long, Jeffrey R; Neese, Frank

2017-03-06

The magnetic properties of pseudotetrahedral Co(II) complexes spawned intense interest after (PPh 4 ) 2 [Co(SPh) 4 ] was shown to be the first mononuclear transition-metal complex displaying slow relaxation of the magnetization in the absence of a direct current magnetic field. However, there are differing reports on its fundamental magnetic spin Hamiltonian (SH) parameters, which arise from inherent experimental challenges in detecting large zero-field splittings. There are also remarkable changes in the SH parameters of [Co(SPh) 4 ] 2- upon structural variations, depending on the counterion and crystallization conditions. In this work, four complementary experimental techniques are utilized to unambiguously determine the SH parameters for two different salts of [Co(SPh) 4 ] 2- : (PPh 4 ) 2 [Co(SPh) 4 ] (1) and (NEt 4 ) 2 [Co(SPh) 4 ] (2). The characterization methods employed include multifield SQUID magnetometry, high-field/high-frequency electron paramagnetic resonance (HF-EPR), variable-field variable-temperature magnetic circular dichroism (VTVH-MCD), and frequency domain Fourier transform THz-EPR (FD-FT THz-EPR). Notably, the paramagnetic Co(II) complex [Co(SPh) 4 ] 2- shows strong axial magnetic anisotropy in 1, with D = -55(1) cm -1 and E/D = 0.00(3), but rhombic anisotropy is seen for 2, with D = +11(1) cm -1 and E/D = 0.18(3). Multireference ab initio CASSCF/NEVPT2 calculations enable interpretation of the remarkable variation of D and its dependence on the electronic structure and geometry.

Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes

PubMed Central

Hu, Hao; Yang, Weitao

2013-01-01

Determining the free energies and mechanisms of chemical reactions in solution and enzymes is a major challenge. For such complex reaction processes, combined quantum mechanics/molecular mechanics (QM/MM) method is the most effective simulation method to provide an accurate and efficient theoretical description of the molecular system. The computational costs of ab initio QM methods, however, have limited the application of ab initio QM/MM methods. Recent advances in ab initio QM/MM methods allowed the accurate simulation of the free energies for reactions in solution and in enzymes and thus paved the way for broader application of the ab initio QM/MM methods. We review here the theoretical developments and applications of the ab initio QM/MM methods, focusing on the determination of reaction path and the free energies of the reaction processes in solution and enzymes. PMID:24146439

Simulation of field-induced molecular dissociation in atom-probe tomography: Identification of a neutral emission channel

NASA Astrophysics Data System (ADS)

Zanuttini, David; Blum, Ivan; Rigutti, Lorenzo; Vurpillot, François; Douady, Julie; Jacquet, Emmanuelle; Anglade, Pierre-Matthieu; Gervais, Benoit

2017-06-01

We investigate the dynamics of dicationic metal-oxide molecules under large electric-field conditions, on the basis of ab initio calculations coupled to molecular dynamics. Applied to the case of ZnO2 + in the field of atom probe tomography (APT), our simulation reveals the dissociation into three distinct exit channels. The proportions of these channels depend critically on the field strength and on the initial molecular orientation with respect to the field. For typical field strength used in APT experiments, an efficient dissociation channel leads to emission of neutral oxygen atoms, which escape detection. The calculated composition biases and their dependence on the field strength show remarkable consistency with recent APT experiments on ZnO crystals. Our work shows that bond breaking in strong static fields may lead to significant neutral atom production, and therefore to severe elemental composition biases in measurements.

Proportional Counter Calibration and Analysis for 12C + p Resonance Scattering

NASA Astrophysics Data System (ADS)

Nelson, Austin; Rogachev, Grigory; Uberseder, Ethan; Hooker, Josh; Koshchiy, Yevgen

2014-09-01

Light exotic nuclei provide a unique opportunity to test the predictions of modern ab initio theoretical calculations near the drip line. In ab initio approaches, nuclear structure is described starting from bare nucleon-nucleon and three-nucleon interactions. Calculations are very heavy and can only be performed for the lightest nuclei (A < 16). Experimental information on the structure of light exotic nuclei is crucial to determine the validity of these calculations and to fix the parameters for the three-nucleon forces. Resonance scattering with rare isotope beams is a very effective tool to study spectroscopy of nuclei near the drip line. A new setup was developed at the Cyclotron Institute for effective resonance scattering measurements. The setup includes ionization chamber, silicon array, and an array of proportional counters. The proportional counter array, consisting of 8 anode wires arranged in a parallel cellular grid, is used for particle identification and to track the positioning of light recoils. The main objective of this project was to test the performance and perform position calibration of this proportional counter array. The test was done using 12C beam. The excitation function for 12C + p elastic scattering was measured and calibration of the proportional counter was performed using known resonances in 13N. The method of calibration, including solid angle calculations, normalization corrections, and position calibration will be presented. Light exotic nuclei provide a unique opportunity to test the predictions of modern ab initio theoretical calculations near the drip line. In ab initio approaches, nuclear structure is described starting from bare nucleon-nucleon and three-nucleon interactions. Calculations are very heavy and can only be performed for the lightest nuclei (A < 16). Experimental information on the structure of light exotic nuclei is crucial to determine the validity of these calculations and to fix the parameters for the three-nucleon forces. Resonance scattering with rare isotope beams is a very effective tool to study spectroscopy of nuclei near the drip line. A new setup was developed at the Cyclotron Institute for effective resonance scattering measurements. The setup includes ionization chamber, silicon array, and an array of proportional counters. The proportional counter array, consisting of 8 anode wires arranged in a parallel cellular grid, is used for particle identification and to track the positioning of light recoils. The main objective of this project was to test the performance and perform position calibration of this proportional counter array. The test was done using 12C beam. The excitation function for 12C + p elastic scattering was measured and calibration of the proportional counter was performed using known resonances in 13N. The method of calibration, including solid angle calculations, normalization corrections, and position calibration will be presented. Funded by DOE and NSF-REU Program; Grant No. PHY-1263281.

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

PubMed Central

2014-01-01

Background The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks. Success of structure based drug discovery severely hinges on the availability of structures. Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is continually widening. Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing medium to high sequence similarities. With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem. Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with advancing drug design attempts as one of the goals. Results Bhageerath-H web-server was validated on 75 CASP10 targets which showed TM-scores ≥0.5 in 91% of the cases and Cα RMSDs ≤5Å from the native in 58% of the targets, which is well above the CASP10 water mark. Comparison with some leading servers demonstrated the uniqueness of the hybrid methodology in effectively sampling conformational space, scoring best decoys and refining low resolution models to high and medium resolution. Conclusion Bhageerath-H methodology is web enabled for the scientific community as a freely accessible web server. The methodology is fielded in the on-going CASP11 experiment. PMID:25521245

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment.

PubMed

Liu, Hanchao; Wang, Yimin; Bowman, Joel M

2015-05-21

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm(-1) is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Quantum calculations of the IR spectrum of liquid water using ab initio and model potential and dipole moment surfaces and comparison with experiment

NASA Astrophysics Data System (ADS)

Liu, Hanchao; Wang, Yimin; Bowman, Joel M.

2015-05-01

The calculation and characterization of the IR spectrum of liquid water have remained a challenge for theory. In this paper, we address this challenge using a combination of ab initio approaches, namely, a quantum treatment of IR spectrum using the ab initio WHBB water potential energy surface and a refined ab initio dipole moment surface. The quantum treatment is based on the embedded local monomer method, in which the three intramolecular modes of each embedded H2O monomer are fully coupled and also coupled singly to each of six intermolecular modes. The new dipole moment surface consists of a previous spectroscopically accurate 1-body dipole moment surface and a newly fitted ab initio intrinsic 2-body dipole moment. A detailed analysis of the new dipole moment surface in terms of the coordinate dependence of the effective atomic charges is done along with tests of it for the water dimer and prism hexamer double-harmonic spectra against direct ab initio calculations. The liquid configurations are taken from previous molecular dynamics calculations of Skinner and co-workers, using the TIP4P plus E3B rigid monomer water potential. The IR spectrum of water at 300 K in the range of 0-4000 cm-1 is calculated and compared with experiment, using the ab initio WHBB potential and new ab initio dipole moment, the q-TIP4P/F potential, which has a fixed-charged description of the dipole moment, and the TTM3-F potential and dipole moment surfaces. The newly calculated ab initio spectrum is in very good agreement with experiment throughout the above spectral range, both in band positions and intensities. This contrasts to results with the other potentials and dipole moments, especially the fixed-charge q-TIP4P/F model, which gives unrealistic intensities. The calculated ab initio spectrum is analyzed by examining the contribution of various transitions to each band.

Levitation forces of a bulk YBCO superconductor in gradient varying magnetic fields

NASA Astrophysics Data System (ADS)

Jiang, J.; Gong, Y. M.; Wang, G.; Zhou, D. J.; Zhao, L. F.; Zhang, Y.; Zhao, Y.

2015-09-01

The levitation forces of a bulk YBCO superconductor in gradient varying high and low magnetic fields generated from a superconducting magnet were investigated. The magnetic field intensity of the superconducting magnet was measured when the exciting current was 90 A. The magnetic field gradient and magnetic force field were both calculated. The YBCO bulk was cooled by liquid nitrogen in field-cooling (FC) and zero-field-cooling (ZFC) condition. The results showed that the levitation forces increased with increasing the magnetic field intensity. Moreover, the levitation forces were more dependent on magnetic field gradient and magnetic force field than magnetic field intensity.

Anisotropic mechanoresponse of energetic crystallites: a quantum molecular dynamics study of nano-collision

NASA Astrophysics Data System (ADS)

Li, Ying; Kalia, Rajiv K.; Misawa, Masaaki; Nakano, Aiichiro; Nomura, Ken-Ichi; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-05-01

At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials.At the nanoscale, chemistry can happen quite differently due to mechanical forces selectively breaking the chemical bonds of materials. The interaction between chemistry and mechanical forces can be classified as mechanochemistry. An example of archetypal mechanochemistry occurs at the nanoscale in anisotropic detonating of a broad class of layered energetic molecular crystals bonded by inter-layer van der Waals (vdW) interactions. Here, we introduce an ab initio study of the collision, in which quantum molecular dynamic simulations of binary collisions between energetic vdW crystallites, TATB molecules, reveal atomistic mechanisms of anisotropic shock sensitivity. The highly sensitive lateral collision was found to originate from the twisting and bending to breaking of nitro-groups mediated by strong intra-layer hydrogen bonds. This causes the closing of the electronic energy gap due to an inverse Jahn-Teller effect. On the other hand, the insensitive collisions normal to multilayers are accomplished by more delocalized molecular deformations mediated by inter-layer interactions. Our nano-collision studies provide a much needed atomistic understanding for the rational design of insensitive energetic nanomaterials and the detonation synthesis of novel nanomaterials. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr08769d

Self-consistent-field perturbation theory for the Schröautdinger equation

NASA Astrophysics Data System (ADS)

Goodson, David Z.

1997-06-01

A method is developed for using large-order perturbation theory to solve the systems of coupled differential equations that result from the variational solution of the Schröautdinger equation with wave functions of product form. This is a noniterative, computationally efficient way to solve self-consistent-field (SCF) equations. Possible applications include electronic structure calculations using products of functions of collective coordinates that include electron correlation, vibrational SCF calculations for coupled anharmonic oscillators with selective coupling of normal modes, and ab initio calculations of molecular vibration spectra without the Born-Oppenheimer approximation.

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2010 CFR

2010-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2012 CFR

2012-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2013 CFR

2013-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

40 CFR 91.123 - Denial, revocation of certificate of conformity.

Code of Federal Regulations, 2014 CFR

2014-07-01

....203(f), 91.206(d), 91.208(c) or 91.209(g), the Administrator may void such certificate ab initio. (d) When the Administrator denies, revokes, or voids ab initio a certificate of conformity, the engine... makes the certificate void ab initio. ...

40 CFR 86.1850-01 - Denial, suspension or revocation of certificate of conformity.

Code of Federal Regulations, 2011 CFR

2011-07-01

... conditions specified in § 86.1843-01, the Administrator may deem such certificate void ab initio. (e) When the Administrator denies, suspends, revokes, or voids ab initio a certificate, EPA will provide the... that makes the certification void ab initio. ...

Ab initio calculation of proton-coupled electron transfer rates using the external-potential representation: A ubiquinol complex in solution

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

Yamamoto, Takeshi; Kato, Shigeki

2007-06-14

In quantum-mechanical/molecular-mechanical (QM/MM) treatment of chemical reactions in condensed phases, one solves the electronic Schroedinger equation for the solute (or an active site) under the electrostatic field from the environment. This Schroedinger equation depends parametrically on the solute nuclear coordinates R and the external electrostatic potential V. This fact suggests that one may use R and V as natural collective coordinates for describing the entire system, where V plays the role of collective solvent variables. In this paper such an (R,V) representation of the QM/MM canonical ensemble is described, with particular focus on how to treat charge transfer processes inmore » this representation. As an example, the above method is applied to the proton-coupled electron transfer of a ubiquinol analog with phenoxyl radical in acetonitrile solvent. Ab initio free-energy surfaces are calculated as functions of R and V using the reference interaction site model self-consistent field method, the equilibrium points and the minimum free-energy crossing point are located in the (R,V) space, and then the kinetic isotope effects (KIEs) are evaluated approximately. The results suggest that a stiffer proton potential at the transition state may be responsible for unusual KIEs observed experimentally for related systems.« less

Observation of high-spin mixed oxidation state of cobalt in ceramic Co3TeO6

NASA Astrophysics Data System (ADS)

Singh, Harishchandra; Ghosh, Haranath; Chandrasekhar Rao, T. V.; Sinha, A. K.; Rajput, Parasmani

2014-12-01

We report coexistence of high spin Co3+ and Co2+ in ceramic Co3TeO6 using X-ray Absorption Near Edge Structure (XANES), DC magnetization, and first principles ab-initio calculations. The main absorption line of cobalt Co K-edge XANES spectra, along with a linear combination fit, led us to estimate relative concentration of Co2+ and Co3+as 60:40. The pre edge feature of XANES spectrum shows crystal field splitting of ˜1.26 eV between eg and t2g states, suggesting a mixture of high spin states of both Co2+ and Co3+. Temperature dependent high field DC magnetization measurements reveal dominant antiferromagnetic order with two Neel temperatures (TN1 ˜ 29 K and TN2 ˜ 18 K), consistent with single crystal study. A larger effective magnetic moment is observed in comparison to that reported for single crystal (which contains only Co2+), supports our inference that Co3+ exists in high spin state. Furthermore, we show that both Co2+ and Co3+ being in high spin states constitute a favorable ground state through first principles ab-initio calculations, where Rietveld refined synchrotron X-ray diffraction data are used as input.

A systematic benchmark of the ab initio Bethe-Salpeter equation approach for low-lying optical excitations of small organic molecules

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

Bruneval, Fabien; Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720; Department of Physics, University of California, Berkeley, California 94720

2015-06-28

The predictive power of the ab initio Bethe-Salpeter equation (BSE) approach, rigorously based on many-body Green’s function theory but incorporating information from density functional theory, has already been demonstrated for the optical gaps and spectra of solid-state systems. Interest in photoactive hybrid organic/inorganic systems has recently increased and so has the use of the BSE for computing neutral excitations of organic molecules. However, no systematic benchmarks of the BSE for neutral electronic excitations of organic molecules exist. Here, we study the performance of the BSE for the 28 small molecules in Thiel’s widely used time-dependent density functional theory benchmark setmore » [Schreiber et al., J. Chem. Phys. 128, 134110 (2008)]. We observe that the BSE produces results that depend critically on the mean-field starting point employed in the perturbative approach. We find that this starting point dependence is mainly introduced through the quasiparticle energies obtained at the intermediate GW step and that with a judicious choice of starting mean-field, singlet excitation energies obtained from BSE are in excellent quantitative agreement with higher-level wavefunction methods. The quality of the triplet excitations is slightly less satisfactory.« less

ON ESTIMATING FORCE-FREENESS BASED ON OBSERVED MAGNETOGRAMS

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

Zhang, X. M.; Zhang, M.; Su, J. T., E-mail: xmzhang@nao.cas.cn

It is a common practice in the solar physics community to test whether or not measured photospheric or chromospheric vector magnetograms are force-free, using the Maxwell stress as a measure. Some previous studies have suggested that magnetic fields of active regions in the solar chromosphere are close to being force-free whereas there is no consistency among previous studies on whether magnetic fields of active regions in the solar photosphere are force-free or not. Here we use three kinds of representative magnetic fields (analytical force-free solutions, modeled solar-like force-free fields, and observed non-force-free fields) to discuss how measurement issues such asmore » limited field of view (FOV), instrument sensitivity, and measurement error could affect the estimation of force-freeness based on observed magnetograms. Unlike previous studies that focus on discussing the effect of limited FOV or instrument sensitivity, our calculation shows that just measurement error alone can significantly influence the results of estimates of force-freeness, due to the fact that measurement errors in horizontal magnetic fields are usually ten times larger than those in vertical fields. This property of measurement errors, interacting with the particular form of a formula for estimating force-freeness, would result in wrong judgments of the force-freeness: a truly force-free field may be mistakenly estimated as being non-force-free and a truly non-force-free field may be estimated as being force-free. Our analysis calls for caution when interpreting estimates of force-freeness based on measured magnetograms, and also suggests that the true photospheric magnetic field may be further away from being force-free than it currently appears to be.« less

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

NASA Astrophysics Data System (ADS)

Hicks, Stephen D.; Henley, C. L.

2010-03-01

Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a consistency check for the simulation, and we can also find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.

The effective molarity (EM)--a computational approach.

PubMed

Karaman, Rafik

2010-08-01

The effective molarity (EM) for 12 intramolecular S(N)2 processes involving the formation of substituted aziridines and substituted epoxides were computed using ab initio and DFT calculation methods. Strong correlation was found between the calculated effective molarity and the experimentally determined values. This result could open a door for obtaining EM values for intramolecular processes that are difficult to be experimentally provided. Furthermore, the calculation results reveal that the driving forces for ring-closing reactions in the two different systems are proximity orientation of the nucleophile to the electrophile and the ground strain energies of the products and the reactants. Copyright 2010 Elsevier Inc. All rights reserved.