Protein–DNA Interactions: The Story so Far and a New Method for Prediction

DOE PAGES

Jones, Susan; Thornton, Janet M.

2003-01-01

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. Inmore » this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.« less

Electron band structure of the high pressure cubic phase of AlH3

NASA Astrophysics Data System (ADS)

Shi, Hongliang; Zarifi, Niliffar; Yim, Wai-Leung; Tse, J. S.

2012-07-01

The electronic band structure of the cubic Pm3n phase of AlH3 stable above 100 GPa is examined with semi-local, Tran-Blaha modified Becke-Johnson local density approximation (TB-mBJLDA), screened hybrid density functionals and GW methods. The shift of the conduction band to higher energy with increasing pressure is predicted by all methods. However, there are significant differences in detail band structure. In the pressure range from 90 to160 GPa, semi-local, hybrid functional and TB-mBJLDA calculations predicted that AlH3 is a poor metal. In comparison, GW calculations show a gap opening at 160 GPa and AlH3 becomes a small gap semi-conductor. From the trends of the calculated band shifts, it can be concluded that the favourable conditions leading to the nesting of Fermi surfaces predicted by semi-local calculation have disappeared if the exchange term is included. The results highlight the importance of the correction to the exchange energy on the band structure of hydrogen dominant dense metal hydrides at high pressure hydrides and may help to rationalize the absence of superconductivity in AlH3 from experimental measurements.

Molecular structures of carotenoids as predicted by MNDO-AM1 molecular orbital calculations

NASA Astrophysics Data System (ADS)

Hashimoto, Hideki; Yoda, Takeshi; Kobayashi, Takayoshi; Young, Andrew J.

2002-02-01

Semi-empirical molecular orbital calculations using AM1 Hamiltonian (MNDO-AM1 method) were performed for a number of biologically important carotenoid molecules, namely all- trans-β-carotene, all- trans-zeaxanthin, and all- trans-violaxanthin (found in higher plants and algae) together with all- trans-canthaxanthin, all- trans-astaxanthin, and all- trans-tunaxanthin in order to predict their stable structures. The molecular structures of all- trans-β-carotene, all- trans-canthaxanthin, and all- trans-astaxanthin predicted based on molecular orbital calculations were compared with those determined by X-ray crystallography. Predicted bond lengths, bond angles, and dihedral angles showed an excellent agreement with those determined experimentally, a fact that validated the present theoretical calculations. Comparison of the bond lengths, bond angles and dihedral angles of the most stable conformer among all the carotenoid molecules showed that the displacements are localized around the substituent groups and hence around the cyclohexene rings. The most stable conformers of all- trans-zeaxanthin and all- trans-violaxanthin gave rise to a torsion angle around the C6-C7 bond to be ±48.7 and -84.8°, respectively. This difference is a key factor in relation to the biological function of these two carotenoids in plants and algae (the xanthophyll cycle). Further analyses by calculating the atomic charges and using enpartment calculations (division of bond energies between component atoms) were performed to ascribe the cause of the different observed torsion angles.

An economic prediction of the finer resolution level wavelet coefficients in electronic structure calculations.

PubMed

Nagy, Szilvia; Pipek, János

2015-12-21

In wavelet based electronic structure calculations, introducing a new, finer resolution level is usually an expensive task, this is why often a two-level approximation is used with very fine starting resolution level. This process results in large matrices to calculate with and a large number of coefficients to be stored. In our previous work we have developed an adaptively refined solution scheme that determines the indices, where the refined basis functions are to be included, and later a method for predicting the next, finer resolution coefficients in a very economic way. In the present contribution, we would like to determine whether the method can be applied for predicting not only the first, but also the other, higher resolution level coefficients. Also the energy expectation values of the predicted wave functions are studied, as well as the scaling behaviour of the coefficients in the fine resolution limit.

Ab-initio conformational epitope structure prediction using genetic algorithm and SVM for vaccine design.

PubMed

Moghram, Basem Ameen; Nabil, Emad; Badr, Amr

2018-01-01

T-cell epitope structure identification is a significant challenging immunoinformatic problem within epitope-based vaccine design. Epitopes or antigenic peptides are a set of amino acids that bind with the Major Histocompatibility Complex (MHC) molecules. The aim of this process is presented by Antigen Presenting Cells to be inspected by T-cells. MHC-molecule-binding epitopes are responsible for triggering the immune response to antigens. The epitope's three-dimensional (3D) molecular structure (i.e., tertiary structure) reflects its proper function. Therefore, the identification of MHC class-II epitopes structure is a significant step towards epitope-based vaccine design and understanding of the immune system. In this paper, we propose a new technique using a Genetic Algorithm for Predicting the Epitope Structure (GAPES), to predict the structure of MHC class-II epitopes based on their sequence. The proposed Elitist-based genetic algorithm for predicting the epitope's tertiary structure is based on Ab-Initio Empirical Conformational Energy Program for Peptides (ECEPP) Force Field Model. The developed secondary structure prediction technique relies on Ramachandran Plot. We used two alignment algorithms: the ROSS alignment and TM-Score alignment. We applied four different alignment approaches to calculate the similarity scores of the dataset under test. We utilized the support vector machine (SVM) classifier as an evaluation of the prediction performance. The prediction accuracy and the Area Under Receiver Operating Characteristic (ROC) Curve (AUC) were calculated as measures of performance. The calculations are performed on twelve similarity-reduced datasets of the Immune Epitope Data Base (IEDB) and a large dataset of peptide-binding affinities to HLA-DRB1*0101. The results showed that GAPES was reliable and very accurate. We achieved an average prediction accuracy of 93.50% and an average AUC of 0.974 in the IEDB dataset. Also, we achieved an accuracy of 95.125% and an AUC of 0.987 on the HLA-DRB1*0101 allele of the Wang benchmark dataset. The results indicate that the proposed prediction technique "GAPES" is a promising technique that will help researchers and scientists to predict the protein structure and it will assist them in the intelligent design of new epitope-based vaccines. Copyright © 2017 Elsevier B.V. All rights reserved.

Electronic Structure, Optical and Transport Properties of Double Perovskite La2NbMnO6: A Theoretical Understanding from DFT Calculations

NASA Astrophysics Data System (ADS)

Parrey, Khursheed Ahmad; Khandy, Shakeel Ahmad; Islam, Ishtihadah; Laref, Amel; Gupta, Dinesh C.; Niazi, Asad; Aziz, Anver; Ansari, S. G.; Khenata, R.; Rubab, Seemin

2018-03-01

Double perovskite La2NbMnO6 was systematically studied using the first-principles calculations. The structural, electronic, optical and transport properties of this compound were calculated. Spin resolved band structure predicted this material as a half-metal with an energy gap of 3.75 eV in spin down state. The optical coefficients including optical conductivity, reflectivity and electron energy loss are calculated for photon energy up to 30.00 eV to understand the optical response of this perovskite. The strong absorption of all the ultraviolet and infrared frequencies of the spectrum by this material may suggest the potential application of this material for the optoelectronic devices in ultraviolet and infra-red region. Also, the thermoelectric properties with a speculation from the half-metallic electronic structure are reported. Subsequently, the Seebeck coefficient, electrical and thermal conductivity coefficients are calculated to predict the thermoelectric figure of merit (zT), the maximum of which is found out to be 0.14 at 800 K.

Predicted phototoxicities of carbon nano-material by quantum mechanical calculations.

EPA Science Inventory

The basis of this research is obtaining the best quantum mechanical structure of carbon nanomaterials and is fundamental in determining their other properties. Therefore, their predictive phototoxicity is directly related to the materials’ structure. The results of this project w...

Fatigue-Crack-Growth Structural Analysis

NASA Technical Reports Server (NTRS)

Newman, J. C., Jr.

1986-01-01

Elastic and plastic deformations calculated under variety of loading conditions. Prediction of fatigue-crack-growth lives made with FatigueCrack-Growth Structural Analysis (FASTRAN) computer program. As cyclic loads are applied to initial crack configuration, FASTRAN predicts crack length and other parameters until complete break occurs. Loads are tensile or compressive and of variable or constant amplitude. FASTRAN incorporates linear-elastic fracture mechanics with modifications of load-interaction effects caused by crack closure. FASTRAN considered research tool, because of lengthy calculation times. FASTRAN written in FORTRAN IV for batch execution.

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

DOE PAGES

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng; ...

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements.

PubMed

Weck, Philippe F; Kim, Eunja; Wang, Yifeng; Kruichak, Jessica N; Mills, Melissa M; Matteo, Edward N; Pellenq, Roland J-M

2017-08-01

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematically compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.

Model representations of kerogen structures: An insight from density functional theory calculations and spectroscopic measurements

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

Weck, Philippe F.; Kim, Eunja; Wang, Yifeng

Molecular structures of kerogen control hydrocarbon production in unconventional reservoirs. Significant progress has been made in developing model representations of various kerogen structures. These models have been widely used for the prediction of gas adsorption and migration in shale matrix. However, using density functional perturbation theory (DFPT) calculations and vibrational spectroscopic measurements, we here show that a large gap may still remain between the existing model representations and actual kerogen structures, therefore calling for new model development. Using DFPT, we calculated Fourier transform infrared (FTIR) spectra for six most widely used kerogen structure models. The computed spectra were then systematicallymore » compared to the FTIR absorption spectra collected for kerogen samples isolated from Mancos, Woodford and Marcellus formations representing a wide range of kerogen origin and maturation conditions. Limited agreement between the model predictions and the measurements highlights that the existing kerogen models may still miss some key features in structural representation. A combination of DFPT calculations with spectroscopic measurements may provide a useful diagnostic tool for assessing the adequacy of a proposed structural model as well as for future model development. This approach may eventually help develop comprehensive infrared (IR)-fingerprints for tracing kerogen evolution.« less

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model.

PubMed

Diaz-Rodriguez, Sebastian; Bozada, Samantha M; Phifer, Jeremy R; Paluch, Andrew S

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of [Formula: see text] log units (ranking 15 out of 62 entries), the correlation coefficient (R) was [Formula: see text] (ranking 35), and [Formula: see text] of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

The effects of molecular structure on the electrical conductivity of polymers

NASA Technical Reports Server (NTRS)

Burke, Luke A.

1992-01-01

The role of Quantum Theoretical Methods is both predictive and supportive of experimental results in Chemistry. Present day methods are able to calculate vibrational spectra and stereochemical interactions for molecules of moderate size (up to 20 atoms). As for the predictive side, the electronic structure of molecules and polymers can be calculated in order to narrow down the field of many potential candidates, which would have the novel properties looked for. The following has been accomplished at the Rutgers Camden Chemistry Department as results of calculations on molecular and polymeric systems of interest to the Polymers Branch of the NASA Lewis Research Center, under Grant NAG3-956.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites.

PubMed

Konc, Janez; Miller, Benjamin T; Štular, Tanja; Lešnik, Samo; Woodcock, H Lee; Brooks, Bernard R; Janežič, Dušanka

2015-11-23

Proteins often exist only as apo structures (unligated) in the Protein Data Bank, with their corresponding holo structures (with ligands) unavailable. However, apoproteins may not represent the amino-acid residue arrangement upon ligand binding well, which is especially problematic for molecular docking. We developed the ProBiS-CHARMMing web interface by connecting the ProBiS ( http://probis.cmm.ki.si ) and CHARMMing ( http://www.charmming.org ) web servers into one functional unit that enables prediction of protein-ligand complexes and allows for their geometry optimization and interaction energy calculation. The ProBiS web server predicts ligands (small compounds, proteins, nucleic acids, and single-atom ligands) that may bind to a query protein. This is achieved by comparing its surface structure against a nonredundant database of protein structures and finding those that have binding sites similar to that of the query protein. Existing ligands found in the similar binding sites are then transposed to the query according to predictions from ProBiS. The CHARMMing web server enables, among other things, minimization and potential energy calculation for a wide variety of biomolecular systems, and it is used here to optimize the geometry of the predicted protein-ligand complex structures using the CHARMM force field and to calculate their interaction energies with the corresponding query proteins. We show how ProBiS-CHARMMing can be used to predict ligands and their poses for a particular binding site, and minimize the predicted protein-ligand complexes to obtain representations of holoproteins. The ProBiS-CHARMMing web interface is freely available for academic users at http://probis.nih.gov.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

PubMed Central

Reimers, Jeffrey R.; Panduwinata, Dwi; Visser, Johan; Chin, Yiing; Tang, Chunguang; Goerigk, Lars; Ford, Michael J.; Sintic, Maxine; Sum, Tze-Jing; Coenen, Michiel J. J.; Hendriksen, Bas L. M.; Elemans, Johannes A. A. W.; Hush, Noel S.; Crossley, Maxwell J.

2015-01-01

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate−molecule interactions (e.g., −100 kcal mol−1 to −150 kcal mol−1 for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70–110 kcal mol−1) and entropy effects (25–40 kcal mol−1 at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations. PMID:26512115

Conformational equilibria of alkanes in aqueous solution: relationship to water structure near hydrophobic solutes.

PubMed Central

Ashbaugh, H S; Garde, S; Hummer, G; Kaler, E W; Paulaitis, M E

1999-01-01

Conformational free energies of butane, pentane, and hexane in water are calculated from molecular simulations with explicit waters and from a simple molecular theory in which the local hydration structure is estimated based on a proximity approximation. This proximity approximation uses only the two nearest carbon atoms on the alkane to predict the local water density at a given point in space. Conformational free energies of hydration are subsequently calculated using a free energy perturbation method. Quantitative agreement is found between the free energies obtained from simulations and theory. Moreover, free energy calculations using this proximity approximation are approximately four orders of magnitude faster than those based on explicit water simulations. Our results demonstrate the accuracy and utility of the proximity approximation for predicting water structure as the basis for a quantitative description of n-alkane conformational equilibria in water. In addition, the proximity approximation provides a molecular foundation for extending predictions of water structure and hydration thermodynamic properties of simple hydrophobic solutes to larger clusters or assemblies of hydrophobic solutes. PMID:10423414

First-Principles Predictions of Near-Edge X-ray Absorption Fine Structure Spectra of Semiconducting Polymers

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

Su, Gregory M.; Patel, Shrayesh N.; Pemmaraju, C. D.

The electronic structure and molecular orientation of semiconducting polymers in thin films determine their ability to transport charge. Methods based on near-edge X-ray absorption fine structure (NEXAFS) spectroscopy can be used to probe both the electronic structure and microstructure of semiconducting polymers in both crystalline and amorphous films. However, it can be challenging to interpret NEXAFS spectra on the basis of experimental data alone, and accurate, predictive calculations are needed to complement experiments. Here, we show that first-principles density functional theory (DFT) can be used to model NEXAFS spectra of semiconducting polymers and to identify the nature of transitions inmore » complicated NEXAFS spectra. Core-level X-ray absorption spectra of a set of semiconducting polymers were calculated using the excited electron and core-hole (XCH) approach based on constrained-occupancy DFT. A comparison of calculations on model oligomers and periodic structures with experimental data revealed the requirements for accurate prediction of NEXAFS spectra of both conjugated homopolymers and donor–acceptor polymers. The NEXAFS spectra predicted by the XCH approach were applied to study molecular orientation in donor–acceptor polymers using experimental spectra and revealed the complexity of using carbon edge spectra in systems with large monomeric units. The XCH approach has sufficient accuracy in predicting experimental NEXAFS spectra of polymers that it should be considered for design and analysis of measurements using soft X-ray techniques, such as resonant soft X-ray scattering and scanning transmission X-ray microscopy.« less

Towards Accurate Ab Initio Predictions of the Spectrum of Methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Kwak, Dochan (Technical Monitor)

2001-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born- Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Theoretical prediction and direct observation of the 9R structure in Ag

NASA Astrophysics Data System (ADS)

Ernst, F.; Finnis, M. W.; Hofmann, D.; Muschik, T.; Schönberger, U.; Wolf, U.; Methfessel, M.

1992-07-01

Molecular-dynamics simulations of the Σ3<110>(211) twin boundary in Ag predict a thin (1 nm) boundary phase of the 9R (α-Sm) structure. High-resolution electron microscopy shows the presence of the predicted structure. We also calculate the energy ab initio for several hypothetical structures of Cu and Ag. Low energies of the 9R structure and other polytypes, low experimental stacking-fault energies, and the hcp-fcc energy difference are correlated and explained in terms of an effective nearest-neighbor Ising interaction.

Rtools: a web server for various secondary structural analyses on single RNA sequences.

PubMed

Hamada, Michiaki; Ono, Yukiteru; Kiryu, Hisanori; Sato, Kengo; Kato, Yuki; Fukunaga, Tsukasa; Mori, Ryota; Asai, Kiyoshi

2016-07-08

The secondary structures, as well as the nucleotide sequences, are the important features of RNA molecules to characterize their functions. According to the thermodynamic model, however, the probability of any secondary structure is very small. As a consequence, any tool to predict the secondary structures of RNAs has limited accuracy. On the other hand, there are a few tools to compensate the imperfect predictions by calculating and visualizing the secondary structural information from RNA sequences. It is desirable to obtain the rich information from those tools through a friendly interface. We implemented a web server of the tools to predict secondary structures and to calculate various structural features based on the energy models of secondary structures. By just giving an RNA sequence to the web server, the user can get the different types of solutions of the secondary structures, the marginal probabilities such as base-paring probabilities, loop probabilities and accessibilities of the local bases, the energy changes by arbitrary base mutations as well as the measures for validations of the predicted secondary structures. The web server is available at http://rtools.cbrc.jp, which integrates software tools, CentroidFold, CentroidHomfold, IPKnot, CapR, Raccess, Rchange and RintD. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Puzzle of magnetic moments of Ni clusters revisited using quantum Monte Carlo method.

PubMed

Lee, Hung-Wen; Chang, Chun-Ming; Hsing, Cheng-Rong

2017-02-28

The puzzle of the magnetic moments of small nickel clusters arises from the discrepancy between values predicted using density functional theory (DFT) and experimental measurements. Traditional DFT approaches underestimate the magnetic moments of nickel clusters. Two fundamental problems are associated with this puzzle, namely, calculating the exchange-correlation interaction accurately and determining the global minimum structures of the clusters. Theoretically, the two problems can be solved using quantum Monte Carlo (QMC) calculations and the ab initio random structure searching (AIRSS) method correspondingly. Therefore, we combined the fixed-moment AIRSS and QMC methods to investigate the magnetic properties of Ni n (n = 5-9) clusters. The spin moments of the diffusion Monte Carlo (DMC) ground states are higher than those of the Perdew-Burke-Ernzerhof ground states and, in the case of Ni 8-9 , two new ground-state structures have been discovered using the DMC calculations. The predicted results are closer to the experimental findings, unlike the results predicted in previous standard DFT studies.

First principles predictions of electronic and elastic properties of BaPb2As2 in the ThCr2Si2-type structure

NASA Astrophysics Data System (ADS)

Bourourou, Y.; Amari, S.; Yahiaoui, I. E.; Bouhafs, B.

2018-01-01

A first-principles approach is used to predicts the electronic and elastic properties of BaPb2As2 superconductor compound, using full-potential linearized augmented plane wave plus local orbitals (FP-L/APW+lo) scheme within the local density approximation LDA. The calculated equilibrium structural parameter a agree well with the experiment while the c/a ratio is far away from the experimental result. The band structure, density of states, together with the charge density and chemical bonding are discussed. The calculated elastic constants for our compound indicate that it is mechanically stable at ambient pressure. Polycrystalline elastic moduli (Young's, Bulk, shear Modulus and the Poisson's ratio) were calculated according to the Voigte-Reusse-Hill (VRH) average.

Structural Revisions of a Class of Natural Products: Scaffolds of Aglycon Analogues of Fusicoccins and Cotylenins Isolated from Fungi.

PubMed

Tang, Ying; Xue, Yongbo; Du, Guang; Wang, Jianping; Liu, Junjun; Sun, Bin; Li, Xiao-Nian; Yao, Guangmin; Luo, Zengwei; Zhang, Yonghui

2016-03-14

The reisolation and structural revision of brassicicene D is described, and inspired us to reassign the core skeletons of brassicicenes C-H, J and K, ranging from dicyclopenta[a,d]cyclooctane to tricyclo[9.2.1.0(3,7)]tetradecane using quantum-chemical predictions and experimental validation strategies. Three novel, highly modified fusicoccanes, brassicicenes L-N, were also isolated from the fungus Alternaria brassicicola, and their structures were unequivocally established by spectroscopic data, ECD calculations, and crystallography. The reassigned structures represent the first class of bridgehead double-bond-containing natural products with a bicyclo[6.2.1]undecane carbon skeleton. Furthermore, their stabilities were first predicted with olefin strain energy calculations. Collectively, these findings extend our view of the application of computational predictions and biosynthetic logic-based structure elucidation to address problems related to the structure and stability of natural products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High pressure phase transitions in tetrahedrally coordinated semiconducting compounds

NASA Technical Reports Server (NTRS)

Yu, S. C.; Spain, I. L.; Skelton, E. F.

1978-01-01

New experimental results are reported for structural transitions at high pressure in several III-V compounds and two II-VI compounds. These data, together with earlier results, are then compared with the predictions of model calculations of Van Vechten. Experimental transition pressures are often at variance with calculated values. However, his calculation assumes that the high pressure phase is metallic, with the beta-Sn structure. The present results show that several compounds assume an ionic NaCl structure at high pressure, while others have neither the beta-Sn nor NaCl structure.

Molecular Dynamic Simulation and Inhibitor Prediction of Cysteine Synthase Structured Model as a Potential Drug Target for Trichomoniasis

PubMed Central

Singh, Satendra; Singh, Atul Kumar; Gautam, Budhayash

2013-01-01

In our presented research, we made an attempt to predict the 3D model for cysteine synthase (A2GMG5_TRIVA) using homology-modeling approaches. To investigate deeper into the predicted structure, we further performed a molecular dynamics simulation for 10 ns and calculated several supporting analysis for structural properties such as RMSF, radius of gyration, and the total energy calculation to support the predicted structured model of cysteine synthase. The present findings led us to conclude that the proposed model is stereochemically stable. The overall PROCHECK G factor for the homology-modeled structure was −0.04. On the basis of the virtual screening for cysteine synthase against the NCI subset II molecule, we present the molecule 1-N, 4-N-bis [3-(1H-benzimidazol-2-yl) phenyl] benzene-1,4-dicarboxamide (ZINC01690699) having the minimum energy score (−13.0 Kcal/Mol) and a log P value of 6 as a potential inhibitory molecule used to inhibit the growth of T. vaginalis infection. PMID:24073401

Development of a ReaxFF reactive force field for ammonium nitrate and application to shock compression and thermal decomposition.

PubMed

Shan, Tzu-Ray; van Duin, Adri C T; Thompson, Aidan P

2014-02-27

We have developed a new ReaxFF reactive force field parametrization for ammonium nitrate. Starting with an existing nitramine/TATB ReaxFF parametrization, we optimized it to reproduce electronic structure calculations for dissociation barriers, heats of formation, and crystal structure properties of ammonium nitrate phases. We have used it to predict the isothermal pressure-volume curve and the unreacted principal Hugoniot states. The predicted isothermal pressure-volume curve for phase IV solid ammonium nitrate agreed with electronic structure calculations and experimental data within 10% error for the considered range of compression. The predicted unreacted principal Hugoniot states were approximately 17% stiffer than experimental measurements. We then simulated thermal decomposition during heating to 2500 K. Thermal decomposition pathways agreed with experimental findings.

Molecular structure and vibrational assignments of 2,4-dichlorophenoxyacetic acid herbicide

NASA Astrophysics Data System (ADS)

Badawi, Hassan M.

2010-09-01

The structural stability of 2,4-dichlorophenoxyacetic acid was investigated by the DFT-B3LYP and the ab initio MP2 calculations with the 6-311G** basis set. From the calculations at both levels of theory the Cgcpp structure was predicted to be the lowest energy minimum for the acid. The DFT and the MP2 levels disagreed about the nature of the second stable structure of 2,4-dichlorophenoxyacetic acid. At the DFT-B3LYP level of calculation the planar Tttp ( transoid O dbnd C sbnd O sbnd H) and the non-planar Tgcpp ( cisoid O dbnd C sbnd O sbnd H) forms were predicted to be 0.7 and 1.5 kcal/mol, respectively higher in energy than the Cgcpp conformation. At the MP2 level the two high energy Tttp and Tgcpp forms were predicted to be 2.7 and 1.4 kcal/mol, respectively higher in energy than the ground state Cgcpp structure. The Tgcpp form was adopted as the second possible structure of 2,4-dichlorophenoxyacetic acid on the basis of the fact that the Møller-Plesset calculations account better than the DFT ones for the non-bonding O⋯H interactions. The vibrational frequencies of the lowest energy Cgcpp conformer were computed at the B3LYP level of theory and tentative vibrational assignments were provided on the basis of normal coordinate analysis and experimental infrared and Raman data.

Towards accurate ab initio predictions of the vibrational spectrum of methane

NASA Technical Reports Server (NTRS)

Schwenke, David W.

2002-01-01

We have carried out extensive ab initio calculations of the electronic structure of methane, and these results are used to compute vibrational energy levels. We include basis set extrapolations, core-valence correlation, relativistic effects, and Born-Oppenheimer breakdown terms in our calculations. Our ab initio predictions of the lowest lying levels are superb.

Predicting relative binding affinities of non-peptide HIV protease inhibitors with free energy perturbation calculations

NASA Astrophysics Data System (ADS)

McCarrick, Margaret A.; Kollman, Peter A.

1999-03-01

The relative binding free energies in HIV protease of haloperidol thioketal (THK) and three of its derivatives were examined with free energy calculations. THK is a weak inhibitor (IC50 = 15 μM) for which two cocrystal structures with HIV type 1 proteases have been solved [Rutenber, E. et al., J. Biol. Chem., 268 (1993) 15343]. A THK derivative with a phenyl group on C2 of the piperidine ring was expected to be a poor inhibitor based on experiments with haloperidol ketal and its 2- phenyl derivative (Caldera, P., personal communication). Our calculations predict that a 5-phenyl THK derivative, suggested based on examination of the crystal structure, will bind significantly better than THK. Although there are large error bars as estimated from hysteresis, the calculations predict that the 5-phenyl substituent is clearly favored over the 2-phenyl derivative as well as the parent compound. The unfavorable free energies of solvation of both phenyl THK derivatives relative to the parent compound contributed to their predicted binding free energies. In a third simulation, the change in binding free energy for 5-benzyl THK relative to THK was calculated. Although this derivative has a lower free energy in the protein, its decreased free energy of solvation increases the predicted ΔΔG(bind) to the same range as that of the 2-phenyl derivative.

Rotational Parameters from Vibronic Eigenfunctions of Jahn-Teller Active Molecules

NASA Astrophysics Data System (ADS)

Garner, Scott M.; Miller, Terry A.

2017-06-01

The structure in rotational spectra of many free radical molecules is complicated by Jahn-Teller distortions. Understanding the magnitudes of these distortions is vital to determining the equilibrium geometric structure and details of potential energy surfaces predicted from electronic structure calculations. For example, in the recently studied {\\widetilde{A}^2E^{''} } state of the NO_3 radical, the magnitudes of distortions are yet to be well understood as results from experimental spectroscopic studies of its vibrational and rotational structure disagree with results from electronic structure calculations of the potential energy surface. By fitting either vibrationally resolved spectra or vibronic levels determined by a calculated potential energy surface, we obtain vibronic eigenfunctions for the system as linear combinations of basis functions from products of harmonic oscillators and the degenerate components of the electronic state. Using these vibronic eigenfunctions we are able to predict parameters in the rotational Hamiltonian such as the Watson Jahn-Teller distortion term, h_1, and compare with the results from the analysis of rotational experiments.

The pKa Cooperative: A Collaborative Effort to Advance Structure-Based Calculations of pKa values and Electrostatic Effects in Proteins

PubMed Central

Nielsen, Jens E.; Gunner, M. R.; Bertrand García-Moreno, E.

2012-01-01

The pKa Cooperative http://www.pkacoop.org was organized to advance development of accurate and useful computational methods for structure-based calculation of pKa values and electrostatic energy in proteins. The Cooperative brings together laboratories with expertise and interest in theoretical, computational and experimental studies of protein electrostatics. To improve structure-based energy calculations it is necessary to better understand the physical character and molecular determinants of electrostatic effects. The Cooperative thus intends to foment experimental research into fundamental aspects of proteins that depend on electrostatic interactions. It will maintain a depository for experimental data useful for critical assessment of methods for structure-based electrostatics calculations. To help guide the development of computational methods the Cooperative will organize blind prediction exercises. As a first step, computational laboratories were invited to reproduce an unpublished set of experimental pKa values of acidic and basic residues introduced in the interior of staphylococcal nuclease by site-directed mutagenesis. The pKa values of these groups are unique and challenging to simulate owing to the large magnitude of their shifts relative to normal pKa values in water. Many computational methods were tested in this 1st Blind Prediction Challenge and critical assessment exercise. A workshop was organized in the Telluride Science Research Center to assess objectively the performance of many computational methods tested on this one extensive dataset. This volume of PROTEINS: Structure, Function, and Bioinformatics introduces the pKa Cooperative, presents reports submitted by participants in the blind prediction challenge, and highlights some of the problems in structure-based calculations identified during this exercise. PMID:22002877

Post processing of protein-compound docking for fragment-based drug discovery (FBDD): in-silico structure-based drug screening and ligand-binding pose prediction.

PubMed

Fukunishi, Yoshifumi

2010-01-01

For fragment-based drug development, both hit (active) compound prediction and docking-pose (protein-ligand complex structure) prediction of the hit compound are important, since chemical modification (fragment linking, fragment evolution) subsequent to the hit discovery must be performed based on the protein-ligand complex structure. However, the naïve protein-compound docking calculation shows poor accuracy in terms of docking-pose prediction. Thus, post-processing of the protein-compound docking is necessary. Recently, several methods for the post-processing of protein-compound docking have been proposed. In FBDD, the compounds are smaller than those for conventional drug screening. This makes it difficult to perform the protein-compound docking calculation. A method to avoid this problem has been reported. Protein-ligand binding free energy estimation is useful to reduce the procedures involved in the chemical modification of the hit fragment. Several prediction methods have been proposed for high-accuracy estimation of protein-ligand binding free energy. This paper summarizes the various computational methods proposed for docking-pose prediction and their usefulness in FBDD.

Predicting the equilibrium solubility of solid polycyclic aromatic hydrocarbons and dibenzothiophene using a combination of MOSCED plus molecular simulation or electronic structure calculations

NASA Astrophysics Data System (ADS)

Phifer, Jeremy R.; Cox, Courtney E.; da Silva, Larissa Ferreira; Nogueira, Gabriel Gonçalves; Barbosa, Ana Karolyne Pereira; Ley, Ryan T.; Bozada, Samantha M.; O'Loughlin, Elizabeth J.; Paluch, Andrew S.

2017-06-01

Methods to predict the equilibrium solubility of non-electrolyte solids are important for the design of novel separation processes. Here we demonstrate how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here SMD or SM8, can be used to predict parameters for the MOdified Separation of Cohesive Energy Density (MOSCED) method. The method is applied to the solutes naphthalene, anthracene, phenanthrene, pyrene and dibenzothiophene, compounds of interested to the petroleum industry and for environmental remediation. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. Comparing to a total of 422 non-aqueous and 193 aqueous experimental solubilities, we find the proposed method is able to well correlate the data. The use of MOSCED is additionally advantageous as it is a solubility parameter-based method useful for intuitive solvent selection and formulation.

A statistical analysis of RNA folding algorithms through thermodynamic parameter perturbation.

PubMed

Layton, D M; Bundschuh, R

2005-01-01

Computational RNA secondary structure prediction is rather well established. However, such prediction algorithms always depend on a large number of experimentally measured parameters. Here, we study how sensitive structure prediction algorithms are to changes in these parameters. We found already that for changes corresponding to the actual experimental error to which these parameters have been determined, 30% of the structure are falsely predicted whereas the ground state structure is preserved under parameter perturbation in only 5% of all the cases. We establish that base-pairing probabilities calculated in a thermal ensemble are viable although not a perfect measure for the reliability of the prediction of individual structure elements. Here, a new measure of stability using parameter perturbation is proposed, and its limitations are discussed.

Intermolecular shielding contributions studied by modeling the 13C chemical-shift tensors of organic single crystals with plane waves

PubMed Central

Johnston, Jessica C.; Iuliucci, Robbie J.; Facelli, Julio C.; Fitzgerald, George; Mueller, Karl T.

2009-01-01

In order to predict accurately the chemical shift of NMR-active nuclei in solid phase systems, magnetic shielding calculations must be capable of considering the complete lattice structure. Here we assess the accuracy of the density functional theory gauge-including projector augmented wave method, which uses pseudopotentials to approximate the nodal structure of the core electrons, to determine the magnetic properties of crystals by predicting the full chemical-shift tensors of all 13C nuclides in 14 organic single crystals from which experimental tensors have previously been reported. Plane-wave methods use periodic boundary conditions to incorporate the lattice structure, providing a substantial improvement for modeling the chemical shifts in hydrogen-bonded systems. Principal tensor components can now be predicted to an accuracy that approaches the typical experimental uncertainty. Moreover, methods that include the full solid-phase structure enable geometry optimizations to be performed on the input structures prior to calculation of the shielding. Improvement after optimization is noted here even when neutron diffraction data are used for determining the initial structures. After geometry optimization, the isotropic shift can be predicted to within 1 ppm. PMID:19831448

Predicting the helix packing of globular proteins by self-correcting distance geometry.

PubMed

Mumenthaler, C; Braun, W

1995-05-01

A new self-correcting distance geometry method for predicting the three-dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 A to 3.1 A for the helical segments compared to the experimentally determined structures. For two proteins, the predicted constraints were not restrictive enough to yield a conclusive prediction. The method can be applied to all small globular proteins, provided the secondary structure is known from NMR analysis or can be predicted with high reliability.

Comparison of binding energies of SrcSH2-phosphotyrosyl peptides with structure-based prediction using surface area based empirical parameterization.

PubMed Central

Henriques, D. A.; Ladbury, J. E.; Jackson, R. M.

2000-01-01

The prediction of binding energies from the three-dimensional (3D) structure of a protein-ligand complex is an important goal of biophysics and structural biology. Here, we critically assess the use of empirical, solvent-accessible surface area-based calculations for the prediction of the binding of Src-SH2 domain with a series of tyrosyl phosphopeptides based on the high-affinity ligand from the hamster middle T antigen (hmT), where the residue in the pY+ 3 position has been changed. Two other peptides based on the C-terminal regulatory site of the Src protein and the platelet-derived growth factor receptor (PDGFR) are also investigated. Here, we take into account the effects of proton linkage on binding, and test five different surface area-based models that include different treatments for the contributions to conformational change and protein solvation. These differences relate to the treatment of conformational flexibility in the peptide ligand and the inclusion of proximal ordered solvent molecules in the surface area calculations. This allowed the calculation of a range of thermodynamic state functions (deltaCp, deltaS, deltaH, and deltaG) directly from structure. Comparison with the experimentally derived data shows little agreement for the interaction of SrcSH2 domain and the range of tyrosyl phosphopeptides. Furthermore, the adoption of the different models to treat conformational change and solvation has a dramatic effect on the calculated thermodynamic functions, making the predicted binding energies highly model dependent. While empirical, solvent-accessible surface area based calculations are becoming widely adopted to interpret thermodynamic data, this study highlights potential problems with application and interpretation of this type of approach. There is undoubtedly some agreement between predicted and experimentally determined thermodynamic parameters: however, the tolerance of this approach is not sufficient to make it ubiquitously applicable. PMID:11106171

How Structure Defines Affinity in Protein-Protein Interactions

PubMed Central

Erijman, Ariel; Rosenthal, Eran; Shifman, Julia M.

2014-01-01

Protein-protein interactions (PPI) in nature are conveyed by a multitude of binding modes involving various surfaces, secondary structure elements and intermolecular interactions. This diversity results in PPI binding affinities that span more than nine orders of magnitude. Several early studies attempted to correlate PPI binding affinities to various structure-derived features with limited success. The growing number of high-resolution structures, the appearance of more precise methods for measuring binding affinities and the development of new computational algorithms enable more thorough investigations in this direction. Here, we use a large dataset of PPI structures with the documented binding affinities to calculate a number of structure-based features that could potentially define binding energetics. We explore how well each calculated biophysical feature alone correlates with binding affinity and determine the features that could be used to distinguish between high-, medium- and low- affinity PPIs. Furthermore, we test how various combinations of features could be applied to predict binding affinity and observe a slow improvement in correlation as more features are incorporated into the equation. In addition, we observe a considerable improvement in predictions if we exclude from our analysis low-resolution and NMR structures, revealing the importance of capturing exact intermolecular interactions in our calculations. Our analysis should facilitate prediction of new interactions on the genome scale, better characterization of signaling networks and design of novel binding partners for various target proteins. PMID:25329579

First-principle calculations of structural, electronic, optical, elastic and thermal properties of MgXAs2 (X=Si, Ge) compounds

NASA Astrophysics Data System (ADS)

Cheddadi, S.; Boubendira, K.; Meradji, H.; Ghemid, S.; Hassan, F. El Haj; Lakel, S.; Khenata, R.

2017-12-01

First-principle calculations on the structural, electronic, optical, elastic and thermal properties of the chalcopyrite MgXAs2 (X=Si, Ge) have been performed within the density functional theory (DFT) using the full-potential linearized augmented plane wave (FP-LAPW) method. The obtained equilibrium structural parameters are in good agreement with the available experimental data and theoretical results. The calculated band structures reveal a direct energy band gap for the interested compounds. The predicted band gaps using the modified Becke-Johnson (mBJ) exchange approximation are in fairly good agreement with the experimental data. The optical constants such as the dielectric function, refractive index, and the extinction coefficient are calculated and analysed. The independent elastic parameters namely, C_{11}, C_{12}, C_{13}, C_{33}, C_{44} and C_{66 } are evaluated. The effects of temperature and pressure on some macroscopic properties of MgSiAs2 and MgGeAs2 are predicted using the quasiharmonic Debye model in which the lattice vibrations are taken into account.

Dispersion Corrected Structural Properties and Quasiparticle Band Gaps of Several Organic Energetic Solids.

PubMed

Appalakondaiah, S; Vaitheeswaran, G; Lebègue, S

2015-06-18

We have performed ab initio calculations for a series of energetic solids to explore their structural and electronic properties. To evaluate the ground state volume of these molecular solids, different dispersion correction methods were accounted in DFT, namely the Tkatchenko-Scheffler method (with and without self-consistent screening), Grimme's methods (D2, D3(BJ)), and the vdW-DF method. Our results reveal that dispersion correction methods are essential in understanding these complex structures with van der Waals interactions and hydrogen bonding. The calculated ground state volumes and bulk moduli show that the performance of each method is not unique, and therefore a careful examination is mandatory for interpreting theoretical predictions. This work also emphasizes the importance of quasiparticle calculations in predicting the band gap, which is obtained here with the GW approximation. We find that the obtained band gaps are ranging from 4 to 7 eV for the different compounds, indicating their insulating nature. In addition, we show the essential role of quasiparticle band structure calculations to correlate the gap with the energetic properties.

Modeling the dynamic equilibrium between oligomers of (AlOCH3)n in methylaluminoxane (MAO). A theoretical study based on a combined quantum mechanical and statistical mechanical approach.

PubMed

Zurek, E; Woo, T K; Firman, T K; Ziegler, T

2001-01-15

Density functional theory (DFT) has been used to calculate the energies of 36 different methylaluminoxane (MAO) cage structures with the general formula (MeAlO)n, where n ranges from 4 to 16. A least-squares fit has been used to devise a formula which predicts the total energies of the MAO with different n's giving an rms deviation of 4.70 kcal/mol. These energies in conjunction with frequency calculations based on molecular mechanics have been used to estimate the finite temperature enthalpies, entropies, and free energies for these MAO structures. Furthermore, formulas have been devised which predict finite temperature enthalpies and entropies for MAO structures of any n for a temperature range of 198.15-598.15 K. Using these formulas, the free energies at different temperatures have been predicted for MAO structures where n ranges from 17 to 30. The free energy values were then used to predict the percentage of each n found at a given temperature. Our calculations give an average n value of 18.41, 17.23, 16.89, and 15.72 at 198.15, 298.15, 398.15, and 598.15 K, respectively. Topological arguments have also been used to show that the MAO cage structure contains a limited amount of square faces as compared to octagonal and hexagonal ones. It is also suggested that the limited number of square faces with their strained Al-O bonds explain the high molar Al:catalyst ratio required for activation. Moreover, in this study we outline a general methodology which may be used to calculate the percent abundance of an equilibrium mixture of oligomers with the general formula (X)n.

Predicting cyclohexane/water distribution coefficients for the SAMPL5 challenge using MOSCED and the SMD solvation model

NASA Astrophysics Data System (ADS)

Diaz-Rodriguez, Sebastian; Bozada, Samantha M.; Phifer, Jeremy R.; Paluch, Andrew S.

2016-11-01

We present blind predictions using the solubility parameter based method MOSCED submitted for the SAMPL5 challenge on calculating cyclohexane/water distribution coefficients at 298 K. Reference data to parameterize MOSCED was generated with knowledge only of chemical structure by performing solvation free energy calculations using electronic structure calculations in the SMD continuum solvent. To maintain simplicity and use only a single method, we approximate the distribution coefficient with the partition coefficient of the neutral species. Over the final SAMPL5 set of 53 compounds, we achieved an average unsigned error of 2.2± 0.2 log units (ranking 15 out of 62 entries), the correlation coefficient ( R) was 0.6± 0.1 (ranking 35), and 72± 6 % of the predictions had the correct sign (ranking 30). While used here to predict cyclohexane/water distribution coefficients at 298 K, MOSCED is broadly applicable, allowing one to predict temperature dependent infinite dilution activity coefficients in any solvent for which parameters exist, and provides a means by which an excess Gibbs free energy model may be parameterized to predict composition dependent phase-equilibrium.

Tight-Binding study of Boron structures

NASA Astrophysics Data System (ADS)

McGrady, Joseph W.; Papaconstantopoulos, Dimitrios A.; Mehl, Michael J.

2014-10-01

We have performed Linearized Augmented Plane Wave (LAPW) calculations for five crystal structures (alpha, dhcp, sc, fcc, bcc) of Boron which we then fitted to a non-orthogonal tight-binding model following the Naval Research Laboratory Tight-Binding (NRL-TB) method. The predictions of the NRL-TB approach for complicated Boron structures such as R105 (or β-rhombohedral) and T190 are in agreement with recent first-principles calculations. Fully utilizing the computational speed of the NRL-TB method we calculated the energy differences of various structures, including those containing vacancies using supercells with up to 5000 atoms.

Calculation of flight vibration levels of the AH-1G helicopter and correlation with existing flight vibration measurements

NASA Technical Reports Server (NTRS)

Sopher, R.; Twomey, W. J.

1990-01-01

NASA-Langley is sponsoring a rotorcraft structural dynamics program with the objective to establish in the U.S. a superior capability to utilize finite element analysis models for calculations to support industrial design of helicopter airframe structures. In the initial phase of the program, teams from the major U.S. manufacturers of helicopter airframes will apply extant finite element analysis methods to calculate loads and vibrations of helicopter airframes, and perform correlations between analysis and measurements. The aforementioned rotorcraft structural dynamics program was given the acronym DAMVIBS (Design Analysis Method for Vibrations). Sikorsky's RDYNE Rotorcraft Dynamics Analysis used for the correlation study, the specifics of the application of RDYNE to the AH-1G, and comparisons of the predictions of the method with flight data for loads and vibrations on the AH-1G are described. RDYNE was able to predict trends of variations of loads and vibrations with airspeed, but in some instances magnitudes differed from measured results by factors of two or three to one. Sensitivities were studied of predictions to rotor inflow modeling, effects of torsional modes, number of blade bending modes, fuselage structural damping, and hub modal content.

What can one learn about material structure given a single first-principles calculation?

NASA Astrophysics Data System (ADS)

Rajen, Nicholas; Coh, Sinisa

2018-05-01

We extract a variable X from electron orbitals Ψn k and energies En k in the parent high-symmetry structure of a wide range of complex oxides: perovskites, rutiles, pyrochlores, and cristobalites. Even though calculation was done only in the parent structure, with no distortions, we show that X dictates material's true ground-state structure. We propose using Wannier functions to extract concealed variables such as X both for material structure prediction and for high-throughput approaches.

MEGADOCK-Web: an integrated database of high-throughput structure-based protein-protein interaction predictions.

PubMed

Hayashi, Takanori; Matsuzaki, Yuri; Yanagisawa, Keisuke; Ohue, Masahito; Akiyama, Yutaka

2018-05-08

Protein-protein interactions (PPIs) play several roles in living cells, and computational PPI prediction is a major focus of many researchers. The three-dimensional (3D) structure and binding surface are important for the design of PPI inhibitors. Therefore, rigid body protein-protein docking calculations for two protein structures are expected to allow elucidation of PPIs different from known complexes in terms of 3D structures because known PPI information is not explicitly required. We have developed rapid PPI prediction software based on protein-protein docking, called MEGADOCK. In order to fully utilize the benefits of computational PPI predictions, it is necessary to construct a comprehensive database to gather prediction results and their predicted 3D complex structures and to make them easily accessible. Although several databases exist that provide predicted PPIs, the previous databases do not contain a sufficient number of entries for the purpose of discovering novel PPIs. In this study, we constructed an integrated database of MEGADOCK PPI predictions, named MEGADOCK-Web. MEGADOCK-Web provides more than 10 times the number of PPI predictions than previous databases and enables users to conduct PPI predictions that cannot be found in conventional PPI prediction databases. In MEGADOCK-Web, there are 7528 protein chains and 28,331,628 predicted PPIs from all possible combinations of those proteins. Each protein structure is annotated with PDB ID, chain ID, UniProt AC, related KEGG pathway IDs, and known PPI pairs. Additionally, MEGADOCK-Web provides four powerful functions: 1) searching precalculated PPI predictions, 2) providing annotations for each predicted protein pair with an experimentally known PPI, 3) visualizing candidates that may interact with the query protein on biochemical pathways, and 4) visualizing predicted complex structures through a 3D molecular viewer. MEGADOCK-Web provides a huge amount of comprehensive PPI predictions based on docking calculations with biochemical pathways and enables users to easily and quickly assess PPI feasibilities by archiving PPI predictions. MEGADOCK-Web also promotes the discovery of new PPIs and protein functions and is freely available for use at http://www.bi.cs.titech.ac.jp/megadock-web/ .

Improved Displacement Transfer Functions for Structure Deformed Shape Predictions Using Discretely Distributed Surface Strains

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2012-01-01

In the formulations of earlier Displacement Transfer Functions for structure shape predictions, the surface strain distributions, along a strain-sensing line, were represented with piecewise linear functions. To improve the shape-prediction accuracies, Improved Displacement Transfer Functions were formulated using piecewise nonlinear strain representations. Through discretization of an embedded beam (depth-wise cross section of a structure along a strain-sensing line) into multiple small domains, piecewise nonlinear functions were used to describe the surface strain distributions along the discretized embedded beam. Such piecewise approach enabled the piecewise integrations of the embedded beam curvature equations to yield slope and deflection equations in recursive forms. The resulting Improved Displacement Transfer Functions, written in summation forms, were expressed in terms of beam geometrical parameters and surface strains along the strain-sensing line. By feeding the surface strains into the Improved Displacement Transfer Functions, structural deflections could be calculated at multiple points for mapping out the overall structural deformed shapes for visual display. The shape-prediction accuracies of the Improved Displacement Transfer Functions were then examined in view of finite-element-calculated deflections using different tapered cantilever tubular beams. It was found that by using the piecewise nonlinear strain representations, the shape-prediction accuracies could be greatly improved, especially for highly-tapered cantilever tubular beams.

First-principles calculations of the structural, elastic and thermodynamic properties of mackinawite (FeS) and pyrite (FeS2)

NASA Astrophysics Data System (ADS)

Wen, Xiangli; Liang, Yuxuan; Bai, Pengpeng; Luo, Bingwei; Fang, Teng; Yue, Luo; An, Teng; Song, Weiyu; Zheng, Shuqi

2017-11-01

The thermodynamic properties of Fe-S compounds with different crystal structure are very different. In this study, the structural, elastic and thermodynamic properties of mackinawite (FeS) and pyrite (FeS2) were investigated by first-principles calculations. Examination of the electronic density of states shows that mackinawite (FeS) is metallic and that pyrite (FeS2) is a semiconductor with a band gap of Eg = 1.02 eV. Using the stress-strain method, the elastic properties including the bulk modulus and shear modulus were derived from the elastic Cij data. Density functional perturbation theory (DFPT) calculations within the quasi-harmonic approximation (QHA) were used to calculate the thermodynamic properties, and the two Fe-S compounds are found to be dynamically stable. The isothermal bulk modulus, thermal expansion coefficient, heat capacities, Gibbs free energy and entropy of the Fe-S compounds are obtained by first-principles phonon calculations. Furthermore, the temperature of the mackinawite (FeS) ⟶ pyrite (FeS2) phase transition at 0 GPa was predicted. Based on the calculation results, the model for prediction of Fe-S compounds in the Fe-H2S-H2O system was improved.

Density functional calculations on structural materials for nuclear energy applications and functional materials for photovoltaic energy applications (abstract only).

PubMed

Domain, C; Olsson, P; Becquart, C S; Legris, A; Guillemoles, J F

2008-02-13

Ab initio density functional theory calculations are carried out in order to predict the evolution of structural materials under aggressive working conditions such as cases with exposure to corrosion and irradiation, as well as to predict and investigate the properties of functional materials for photovoltaic energy applications. Structural metallic materials used in nuclear facilities are subjected to irradiation which induces the creation of large amounts of point defects. These defects interact with each other as well as with the different elements constituting the alloys, which leads to modifications of the microstructure and the mechanical properties. VASP (Vienna Ab initio Simulation Package) has been used to determine the properties of point defect clusters and also those of extended defects such as dislocations. The resulting quantities, such as interaction energies and migration energies, are used in larger scale simulation methods in order to build predictive tools. For photovoltaic energy applications, ab initio calculations are used in order to search for new semiconductors and possible element substitutions for existing ones in order to improve their efficiency.

Towards predictive many-body calculations of phonon-limited carrier mobilities in semiconductors

NASA Astrophysics Data System (ADS)

Poncé, Samuel; Margine, Elena R.; Giustino, Feliciano

2018-03-01

We probe the accuracy limit of ab initio calculations of carrier mobilities in semiconductors, within the framework of the Boltzmann transport equation. By focusing on the paradigmatic case of silicon, we show that fully predictive calculations of electron and hole mobilities require many-body quasiparticle corrections to band structures and electron-phonon matrix elements, the inclusion of spin-orbit coupling, and an extremely fine sampling of inelastic scattering processes in momentum space. By considering all these factors we obtain excellent agreement with experiment, and we identify the band effective masses as the most critical parameters to achieve predictive accuracy. Our findings set a blueprint for future calculations of carrier mobilities, and pave the way to engineering transport properties in semiconductors by design.

A New Superhard Phase and Physical Properties of ZrB₃ from First-Principles Calculations.

PubMed

Zhang, Gangtai; Bai, Tingting; Zhao, Yaru; Hu, Yanfei

2016-08-22

Using the first-principles particle swarm optimization algorithm for crystal structural prediction, we have predicted a novel monoclinic C 2/ m structure for ZrB₃, which is more energetically favorable than the previously proposed FeB₃-, TcP₃-, MoB₃-, WB₃-, and OsB₃-type structures in the considered pressure range. The new phase is mechanically and dynamically stable, as confirmed by the calculations of its elastic constants and phonon dispersion curve. The calculated large shear modulus (227 GPa) and high hardness (42.2 GPa) show that ZrB₃ within the monoclinic phase is a potentially superhard material. The analyses of the electronic density of states and chemical bonding reveal that the strong B-B and B-Zr covalent bonds are attributed to its high hardness. By the quasi-harmonic Debye model, the heat capacity, thermal expansion coefficient and Grüneisen parameter of ZrB₃ are also systemically investigated.

Stephan Lany | NREL

Science.gov Websites

scientist with a background in electronic structure calculations for semiconducting materials. He joined Program. Research Interests His research interests include prediction of band-structure, optical , electrical, and transport properties from electronic structure theory; photovoltaic and thermoelectric

Evaluation of dual flow thrust vectored nozzles with exhaust stream impingement. MS Thesis Final Technical Report, Oct. 1990 - Jul. 1991

NASA Technical Reports Server (NTRS)

Carpenter, Thomas W.

1991-01-01

The main objective of this project was to predict the expansion wave/oblique shock wave structure in an under-expanded jet expanding from a convergent nozzle. The shock structure was predicted by combining the calculated curvature of the free pressure boundary with principles and governing equations relating to oblique shock wave and expansion wave interaction. The procedure was then continued until the shock pattern repeated itself. A mathematical model was then formulated and written in FORTRAN to calculate the oblique shock/expansion wave structure within the jet. In order to study shock waves in expanding jets, Schlieren photography, a form of flow visualization, was employed. Thirty-six Schlieren photographs of jets from both a straight and 15 degree nozzle were taken. An iterative procedure was developed to calculate the shock structure within the jet and predict the non-dimensional values of Prandtl primary wavelength (w/rn), distance to Mach Disc (Ld) and Mach Disc radius (rd). These values were then compared to measurements taken from Schlieren photographs and experimental results. The results agreed closely to measurements from Schlieren photographs and previously obtained data. This method provides excellent results for pressure ratios below that at which a Mach Disc first forms. Calculated values of non-dimensional distance to the Mach Disc (Ld) agreed closely to values measured from Schlieren photographs and published data. The calculated values of non-dimensional Mach Disc radius (rd), however, deviated from published data by as much as 25 percent at certain pressure ratios.

Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery.

PubMed

Catana, Cornel; Stouten, Pieter F W

2007-01-01

The ability to accurately predict biological affinity on the basis of in silico docking to a protein target remains a challenging goal in the CADD arena. Typically, "standard" scoring functions have been employed that use the calculated docking result and a set of empirical parameters to calculate a predicted binding affinity. To improve on this, we are exploring novel strategies for rapidly developing and tuning "customized" scoring functions tailored to a specific need. In the present work, three such customized scoring functions were developed using a set of 129 high-resolution protein-ligand crystal structures with measured Ki values. The functions were parametrized using N-PLS (N-way partial least squares), a multivariate technique well-known in the 3D quantitative structure-activity relationship field. A modest correlation between observed and calculated pKi values using a standard scoring function (r2 = 0.5) could be improved to 0.8 when a customized scoring function was applied. To mimic a more realistic scenario, a second scoring function was developed, not based on crystal structures but exclusively on several binding poses generated with the Flo+ docking program. Finally, a validation study was conducted by generating a third scoring function with 99 randomly selected complexes from the 129 as a training set and predicting pKi values for a test set that comprised the remaining 30 complexes. Training and test set r2 values were 0.77 and 0.78, respectively. These results indicate that, even without direct structural information, predictive customized scoring functions can be developed using N-PLS, and this approach holds significant potential as a general procedure for predicting binding affinity on the basis of in silico docking.

Prediction of Ras-effector interactions using position energy matrices.

PubMed

Kiel, Christina; Serrano, Luis

2007-09-01

One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein-protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences. Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types. All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/). Supplementary data are available at Bioinformatics online.

Structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 phases from first-principles calculations

NASA Astrophysics Data System (ADS)

Li, X. D.; Li, K.; Wei, C. H.; Han, W. D.; Zhou, N. G.

2018-06-01

The structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 are systematically investigated by using first-principles calculations method based on density functional theory (DFT). The calculated formation enthalpies and cohesive energies show that CaSi2 possesses the greatest structural stability and CaSi has the strongest alloying ability. The structural stability of the three phases is compared according to electronic structures. Further analysis on electronic structures indicates that the bonding of these phases exhibits the combinations of metallic, covalent, and ionic bonds. The elastic constants are calculated, and the bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and anisotropy factor of polycrystalline materials are deduced. Additionally, the thermodynamic properties were theoretically predicted and discussed.

A Method to Predict the Structure and Stability of RNA/RNA Complexes.

PubMed

Xu, Xiaojun; Chen, Shi-Jie

2016-01-01

RNA/RNA interactions are essential for genomic RNA dimerization and regulation of gene expression. Intermolecular loop-loop base pairing is a widespread and functionally important tertiary structure motif in RNA machinery. However, computational prediction of intermolecular loop-loop base pairing is challenged by the entropy and free energy calculation due to the conformational constraint and the intermolecular interactions. In this chapter, we describe a recently developed statistical mechanics-based method for the prediction of RNA/RNA complex structures and stabilities. The method is based on the virtual bond RNA folding model (Vfold). The main emphasis in the method is placed on the evaluation of the entropy and free energy for the loops, especially tertiary kissing loops. The method also uses recursive partition function calculations and two-step screening algorithm for large, complicated structures of RNA/RNA complexes. As case studies, we use the HIV-1 Mal dimer and the siRNA/HIV-1 mutant (T4) to illustrate the method.

Numerical study of the electronic structure, elastic and optical properties of defect quaternary semiconductor CuGaSnSe4

NASA Astrophysics Data System (ADS)

Shen, Kesheng; Lu, Hai; Zhang, Xianzhou; Jiao, Zhaoyong

2018-06-01

The electronic structure, elastic and optical properties of the defect quaternary semiconductor CuGaSnSe4 in I 4 bar structure are systematically investigated using first-principles calculations. We summarize and discuss some of the studies on CuGaSnSe4 in partially ordered chalcopyrite structure and find that there are three atomic arrangements so far, but it is still uncertain which is the most stable. Through detailed simulation and comparison with the corresponding literature, we get three models and predict that M1 model should be the most stable. The band structure and optical properties of compound CuGaSnSe4, including dielectric constant, refractive index and absorption spectrum, are drawn for a more intuitive understanding. The elastic constants are also calculated, which not only prove that CuGaSnSe4 in I 4 bar structure is stable naturally but also help solve the problem of no data to accurately predict axial thermal expansion coefficients. The calculated values of the zero frequency dielectric constant and refractive index are comparable to those of the corresponding chalcopyrite structure but slightly larger.

Monte Carlo Simulations of Electron Energy-Loss Spectra with the Addition of Fine Structure from Density Functional Theory Calculations.

PubMed

Attarian Shandiz, Mohammad; Guinel, Maxime J-F; Ahmadi, Majid; Gauvin, Raynald

2016-02-01

A new approach is presented to introduce the fine structure of core-loss excitations into the electron energy-loss spectra of ionization edges by Monte Carlo simulations based on an optical oscillator model. The optical oscillator strength is refined using the calculated electron energy-loss near-edge structure by density functional theory calculations. This approach can predict the effects of multiple scattering and thickness on the fine structure of ionization edges. In addition, effects of the fitting range for background removal and the integration range under the ionization edge on signal-to-noise ratio are investigated.

Electrostrictive Mechanism of Nanostructure Formation at Solid Surfaces Irradiated by Femtosecond Laser Pulses.

PubMed

Pavlyniuk, Oleg R; Datsyuk, Vitaly V

2016-12-01

The significance of the mechanical pressure of light in creation of laser-induced periodic surface structures (LIPSSs) is investigated. Distributions of the electrically induced normal pressure and tangential stress at the illuminated solid surface, as well as the field of volume electrostrictive forces, are calculated taking into account surface plasmon polariton (SPP) excitation. Based on these calculations, we predict surface destruction and structure formation due to inelastic deformations during single femtosecond pulses. The calculated fields of the electromagnetic forces are found to agree well with the experimental ripple structures. We thus conclude that the electrostrictive forces can explain the origin of the periodic ripple structures.

Evaluation of a Progressive Failure Analysis Methodology for Laminated Composite Structures

NASA Technical Reports Server (NTRS)

Sleight, David W.; Knight, Norman F., Jr.; Wang, John T.

1997-01-01

A progressive failure analysis methodology has been developed for predicting the nonlinear response and failure of laminated composite structures. The progressive failure analysis uses C plate and shell elements based on classical lamination theory to calculate the in-plane stresses. Several failure criteria, including the maximum strain criterion, Hashin's criterion, and Christensen's criterion, are used to predict the failure mechanisms. The progressive failure analysis model is implemented into a general purpose finite element code and can predict the damage and response of laminated composite structures from initial loading to final failure.

Phase Transition and Physical Properties of InS

NASA Astrophysics Data System (ADS)

Wang, Hai-Yan; Li, Xiao-Feng; Xu, Lei; Li, Xu-Sheng; Hu, Qian-Ku

2018-02-01

Using the crystal structure prediction method based on particle swarm optimization algorithm, three phases (Pnnm, C2/m and Pm-3m) for InS are predicted. The new phase Pm-3m of InS under high pressure is firstly reported in the work. The structural features and electronic structure under high pressure of InS are fully investigated. We predicted the stable ground-state structure of InS was the Pnnm phase and phase transformation of InS from Pnnm phase to Pm-3m phase is firstly found at the pressure of about 29.5 GPa. According to the calculated enthalpies of InS with four structures in the pressure range from 20 GPa to 45 GPa, we find the C2/m phase is a metastable phase. The calculated band gap value of about 2.08 eV for InS with Pnnm structure at 0 GPa agrees well with the experimental value. Moreover, the electronic structure suggests that the C2/m and Pm-3m phase are metallic phases. Supported by the National Natural Science Foundation of China under Grant Nos. 11404099, 11304140, 11147167 and Funds of Outstanding Youth of Henan Polytechnic University, China under Grant No. J2014-05

Correlation of predicted and measured thermal stresses on an advanced aircraft structure with dissimilar materials. [hypersonic heating simulation

NASA Technical Reports Server (NTRS)

Jenkins, J. M.

1979-01-01

Additional information was added to a growing data base from which estimates of finite element model complexities can be made with respect to thermal stress analysis. The manner in which temperatures were smeared to the finite element grid points was examined from the point of view of the impact on thermal stress calculations. The general comparison of calculated and measured thermal stresses is guite good and there is little doubt that the finite element approach provided by NASTRAN results in correct thermal stress calculations. Discrepancies did exist between measured and calculated values in the skin and the skin/frame junctures. The problems with predicting skin thermal stress were attributed to inadequate temperature inputs to the structural model rather than modeling insufficiencies. The discrepancies occurring at the skin/frame juncture were most likely due to insufficient modeling elements rather than temperature problems.

Quantitative structure-retention relationships of flavonoids unraveled by immobilized artificial membrane chromatography.

PubMed

Santoro, Adriana Leandra; Carrilho, Emanuel; Lanças, Fernando Mauro; Montanari, Carlos Alberto

2016-06-10

The pharmacokinetic properties of flavonoids with differing degrees of lipophilicity were investigated using immobilized artificial membranes (IAMs) as the stationary phase in high performance liquid chromatography (HPLC). For each flavonoid compound, we investigated whether the type of column used affected the correlation between the retention factors and the calculated octanol/water partition (log Poct). Three-dimensional (3D) molecular descriptors were calculated from the molecular structure of each compound using i) VolSurf software, ii) the GRID method (computational procedure for determining energetically favorable binding sites in molecules of known structure using a probe for calculating the 3D molecular interaction fields, between the probe and the molecule), and iii) the relationship between partition and molecular structure, analyzed in terms of physicochemical descriptors. The VolSurf built-in Caco-2 model was used to estimate compound permeability. The extent to which the datasets obtained from different columns differ both from each other and from both the calculated log Poct and the predicted permeability in Caco-2 cells was examined by principal component analysis (PCA). The immobilized membrane partition coefficients (kIAM) were analyzed using molecular descriptors in partial least square regression (PLS) and a quantitative structure-retention relationship was generated for the chromatographic retention in the cholesterol column. The cholesterol column provided the best correlation with the permeability predicted by the Caco-2 cell model and a good fit model with great prediction power was obtained for its retention data (R(2)=0.96 and Q(2)=0.85 with four latent variables). Copyright © 2015 Elsevier B.V. All rights reserved.

Discriminating the structure of exo-2-aminonorbornane using nuclear quadrupole coupling interactions.

PubMed

Écija, Patricia; Cocinero, Emilio J; Lesarri, Alberto; Millán, Judith; Basterretxea, Francisco; Fernández, José A; Castaño, Fernando

2011-04-28

The intrinsic conformational and structural properties of the bicycle exo-2-aminonorbornane have been probed in a supersonic jet expansion using Fourier-transform microwave (FT-MW) spectroscopy and quantum chemical calculations. The rotational spectrum revealed two different conformers arising from the internal rotation of the amino group, exhibiting small (MHz) hyperfine patterns originated by the (14)N nuclear quadrupole coupling interaction. Complementary ab initio (MP2) and DFT (B3LYP and M05-2X) calculations provided comparative predictions for the structural properties, rotational and centrifugal distortion data, hyperfine parameters, and isomerization barriers. Due to the similarity of the rotational constants, the structural assignment of the observed rotamers and the calculation of the torsion angles of the amino group were based on the conformational dependence of the (14)N nuclear quadrupole coupling hyperfine tensor. In the most stable conformation (ss), the two amino N-H bonds are staggered with respect to the adjacent C-H bond. In the second conformer (st), only one of the N-H bonds is staggered and the other is trans. A third predicted conformer (ts) was not detected, consistent with a predicted conformational relaxation to conformer ss through a low barrier of 5.2 kJ mol(-1).

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

PubMed

Tang, Yat T; Marshall, Garland R

2011-02-28

Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable scoring function was an objective of this study, the main focus was evaluation of the use of high-resolution X-ray crystal structures with high-quality thermodynamic parameters from isothermal titration calorimetry for scoring function development. With the increasing application of structure-based methods in molecular design, this study suggests that using high-resolution crystal structures, separating enthalpy and entropy contributions to binding free energy, and including descriptors to better capture entropic contributions may prove to be effective strategies toward rapid and accurate calculation of binding affinity.

Modeling and measurements of XRD spectra of extended solids under high pressure

NASA Astrophysics Data System (ADS)

Batyrev, I. G.; Coleman, S. P.; Stavrou, E.; Zaug, J. M.; Ciezak-Jenkins, J. A.

2017-06-01

We present results of evolutionary simulations based on density functional calculations of various extended solids: N-Si and N-H using variable and fixed concentration methods of USPEX. Predicted from the evolutionary simulations structures were analyzed in terms of thermo-dynamical stability and agreement with experimental X-ray diffraction spectra. Stability of the predicted system was estimated from convex-hull plots. X-ray diffraction spectra were calculated using a virtual diffraction algorithm which computes kinematic diffraction intensity in three-dimensional reciprocal space before being reduced to a two-theta line profile. Calculations of thousands of XRD spectra were used to search for a structure of extended solids at certain pressures with best fits to experimental data according to experimental XRD peak position, peak intensity and theoretically calculated enthalpy. Comparison of Raman and IR spectra calculated for best fitted structures with available experimental data shows reasonable agreement for certain vibration modes. Part of this work was performed by LLNL, Contract DE-AC52-07NA27344. We thank the Joint DoD / DOE Munitions Technology Development Program, the HE C-II research program at LLNL and Advanced Light Source, supported by BES DOE, Contract No. DE-AC02-05CH112.

Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

PubMed

Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia

2015-01-01

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. Copyright © 2015 Elsevier B.V. All rights reserved.

A polymer dataset for accelerated property prediction and design.

PubMed

Huan, Tran Doan; Mannodi-Kanakkithodi, Arun; Kim, Chiho; Sharma, Vinit; Pilania, Ghanshyam; Ramprasad, Rampi

2016-03-01

Emerging computation- and data-driven approaches are particularly useful for rationally designing materials with targeted properties. Generally, these approaches rely on identifying structure-property relationships by learning from a dataset of sufficiently large number of relevant materials. The learned information can then be used to predict the properties of materials not already in the dataset, thus accelerating the materials design. Herein, we develop a dataset of 1,073 polymers and related materials and make it available at http://khazana.uconn.edu/. This dataset is uniformly prepared using first-principles calculations with structures obtained either from other sources or by using structure search methods. Because the immediate target of this work is to assist the design of high dielectric constant polymers, it is initially designed to include the optimized structures, atomization energies, band gaps, and dielectric constants. It will be progressively expanded by accumulating new materials and including additional properties calculated for the optimized structures provided.

A high-throughput exploration of magnetic materials by using structure predicting methods

NASA Astrophysics Data System (ADS)

Arapan, S.; Nieves, P.; Cuesta-López, S.

2018-02-01

We study the capability of a structure predicting method based on genetic/evolutionary algorithm for a high-throughput exploration of magnetic materials. We use the USPEX and VASP codes to predict stable and generate low-energy meta-stable structures for a set of representative magnetic structures comprising intermetallic alloys, oxides, interstitial compounds, and systems containing rare-earths elements, and for both types of ferromagnetic and antiferromagnetic ordering. We have modified the interface between USPEX and VASP codes to improve the performance of structural optimization as well as to perform calculations in a high-throughput manner. We show that exploring the structure phase space with a structure predicting technique reveals large sets of low-energy metastable structures, which not only improve currently exiting databases, but also may provide understanding and solutions to stabilize and synthesize magnetic materials suitable for permanent magnet applications.

An Ab Initio Study of CuCO

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.

1994-01-01

Modified coupled-pair functional (MCPF) calculations and coupled cluster singles and doubles calculations, which include a perturbational estimate of the connected triples [CCSD(T)], yield a bent structure for CuCO, thus, supporting the prediction of a nonlinear structure based on density functional (DF) calculations. Our best estimate for the binding energy is 4.9 +/- 1.4 kcal/mol; this is in better agreement with experiment (6.0 +/- 1.2 kcal/mol) than the DF approach which yields a value (19.6 kcal/mol) significantly larger than experiment.

Linear Scaling Density Functional Calculations with Gaussian Orbitals

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1999-01-01

Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.

Metastable Structural Phases of Metals in Columns IVB to Vib, and Rows 4 TO 6 OF the Periodic Table

NASA Astrophysics Data System (ADS)

Nnolim, Neme; Tyson, Trevor

2002-03-01

Total energy calculations as a function of strain along the <001> direction have been carried out for the bcc metals V, Nb, Ta, Cr, Mo and W, and the hcp metals Ti, Zr and Hf, all in the block of the periodic table defined by columns IVB to VIB, and rows 4 to 6. Since strain along the <001> direction corresponds to variation of the c lattice constant with respect to the a lattice constant, the total energy per unit cell has being calculated as a function of the c/a ratio. The highly accurate FP-LAPW (Full Potential Linearized Augmented Plane Wave) band structure method in the DFT (Density Functional Theory) formalism has been used for the calculations. In all cases except for the hcp column IVB elements, Zr, Hf and Ti, a metastable state was predicted from the calculations. Electronic properties are computed for all structures and are correlated with electrical and mechanical properties of metastable phases that have been observed experimentally. Properties of metastable phases, which were predicted in this work but which as of yet have not been observed experimentally, have also been predicted. Special attention is paid to the phases of tantalum and calculated transport properties are used to show that the observed high resistivity of the beta phase of tantalum relative to the alpha bcc phase cannot be explained solely by simple tetragonal distortions of the bcc phase.

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data.

PubMed

Durig, Douglas T; Durig, M S; Durig, James R

2005-05-01

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.

First-principles theory of cation and intercalation ordering in Li xCoO 2

NASA Astrophysics Data System (ADS)

Wolverton, C.; Zunger, Alex

Several types of cation- and vacancy-ordering are of interest in the Li xCoO 2 battery cathode material since they can have a profound effect on the battery voltage. We present a first-principles theoretical approach which can be used to calculate both cation- and vacancy-ordering patterns at both zero and finite temperatures. This theory also provides quantum-mechanical predictions (i.e., without the use of any experimental input) of battery voltages of both ordered and disordered Li xCoO 2/Li cells from the energetics of the Li intercalation reactions. Our calculations allow us to search the entire configurational space to predict the lowest-energy ground-state structures, search for large voltage cathodes, explore metastable low-energy states, and extend our calculations to finite temperatures, thereby searching for order-disorder transitions and states of partial disorder. We present the first prediction of the stable spinel structure LiCo 2O 4 for the 50% delithiated Li 0.5CoO 2.

Advances and trends in computational structural mechanics

NASA Technical Reports Server (NTRS)

Noor, A. K.

1986-01-01

Recent developments in computational structural mechanics are reviewed with reference to computational needs for future structures technology, advances in computational models for material behavior, discrete element technology, assessment and control of numerical simulations of structural response, hybrid analysis, and techniques for large-scale optimization. Research areas in computational structural mechanics which have high potential for meeting future technological needs are identified. These include prediction and analysis of the failure of structural components made of new materials, development of computational strategies and solution methodologies for large-scale structural calculations, and assessment of reliability and adaptive improvement of response predictions.

Geometric modeling of Plateau borders using the orthographic projection method for closed cell rigid polyurethane foam thermal conductivity prediction

NASA Astrophysics Data System (ADS)

Xu, Jie; Wu, Tao; Peng, Chuang; Adegbite, Stephen

2017-09-01

The geometric Plateau border model for closed cell polyurethane foam was developed based on volume integrations of approximated 3D four-cusp hypocycloid structure. The tetrahedral structure of convex struts was orthogonally projected into 2D three-cusp deltoid with three central cylinders. The idealized single unit strut was modeled by superposition. The volume of each component was calculated by geometric analyses. The strut solid fraction f s and foam porosity coefficient δ were calculated based on representative elementary volume of Kelvin and Weaire-Phelan structures. The specific surface area Sv derived respectively from packing structures and deltoid approximation model were put into contrast against strut dimensional ratio ɛ. The characteristic foam parameters obtained from this semi-empirical model were further employed to predict foam thermal conductivity.

Electronic structure Fermi liquid theory of high Tc superconductors: Comparison of predictions with experiments

NASA Technical Reports Server (NTRS)

Yu, Jaejun; Freeman, A. J.

1991-01-01

Predictions of local density functional (LDF) calculations of the electronic structure and transport properties of high T(sub c) superconductors are presented. As evidenced by the excellent agreement with both photoemission and positron annihilation experiments, a Fermi liquid nature of the 'normal' state of the high T(sub c) superconductors become clear for the metallic phase of these oxides. In addition, LDF predictions on the normal state transport properties are qualitatively in agreement with experiments on single crystals. It is emphasized that the signs of the Hall coefficients for the high T(sub c) superconductors are not consistent with the types of dopants (e.g., electron-doped or hole-doped) but are determined by the topology of the Fermi surfaces obtained from the LDF calculations.

Predicting the thermodynamic stability of double-perovskite halides from density functional theory

DOE PAGES

Han, Dan; Zhang, Tao; Huang, Menglin; ...

2018-05-24

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less

Predicting the thermodynamic stability of double-perovskite halides from density functional theory

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

Han, Dan; Zhang, Tao; Huang, Menglin

Recently, a series of double-perovskite halide compounds such as Cs 2AgBiCl 6 and Cs 2AgBiBr 6 have attracted intensive interest as promising alternatives to the solar absorber material CH 3NH 3PbI 3 because they are Pb-free and may exhibit enhanced stability. The thermodynamic stability of a number of double-perovskite halides has been predicted based on density functional theory (DFT) calculations of compound formation energies. In this paper, we found that the stability prediction can be dependent on the approximations used for the exchange-correlation functionals, e.g., the DFT calculations using the widely used Perdew, Burke, Ernzerhof (PBE) functional predict that Csmore » 2AgBiBr 6 is thermodynamically unstable against phase-separation into the competing phases such as AgBr, Cs 2AgBr 3, Cs 3Bi 2Br 9, etc., obviously inconsistent with the good stability observed experimentally. The incorrect prediction by the PBE calculation results from its failure to predict the correct ground-state structures of AgBr, AgCl, and CsCl. By contrast, the DFT calculations based on local density approximation, optB86b-vdW, and optB88-vdW functionals predict the ground-state structures of these binary halides correctly. Furthermore, the optB88-vdW functional is found to give the most accurate description of the lattice constants of the double-perovskite halides and their competing phases. Given these two aspects, we suggest that the optB88-vdW functional should be used for predicting thermodynamic stability in the future high-throughput computational material design or the construction of the Materials Genome database for new double-perovskite halides. As a result, using different exchange-correlation functionals has little influence on the dispersion of the conduction and the valence bands near the electronic bandgap; however, the calculated bandgap can be affected indirectly by the optimized lattice constant, which varies for different functionals.« less

Structural prediction and analysis of VIH-related peptides from selected crustacean species.

PubMed

Nagaraju, Ganji Purna Chandra; Kumari, Nunna Siva; Prasad, Ganji Lakshmi Vara; Rajitha, Balney; Meenu, Madan; Rao, Manam Sreenivasa; Naik, Bannoth Reddya

2009-08-17

The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous extra technical aspects. As a result, no structural information is available for VIH peptide sequences registered in the Genbank. In this situation, it is not surprising that predictive methods have achieved great interest. Here, in this study the molt-inhibiting hormone (MIH) of the kuruma prawn (Marsupenaeus japonicus) is used, to predict the structure of four VIHrelated peptides in the crustacean species. The high similarity of the 3D-structures and the calculated physiochemical characteristics of these peptides suggest a common fold for the entire family.

A statistical learning approach to the modeling of chromatographic retention of oligonucleotides incorporating sequence and secondary structure data

PubMed Central

Sturm, Marc; Quinten, Sascha; Huber, Christian G.; Kohlbacher, Oliver

2007-01-01

We propose a new model for predicting the retention time of oligonucleotides. The model is based on ν support vector regression using features derived from base sequence and predicted secondary structure of oligonucleotides. Because of the secondary structure information, the model is applicable even at relatively low temperatures where the secondary structure is not suppressed by thermal denaturing. This makes the prediction of oligonucleotide retention time for arbitrary temperatures possible, provided that the target temperature lies within the temperature range of the training data. We describe different possibilities of feature calculation from base sequence and secondary structure, present the results and compare our model to existing models. PMID:17567619

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Developing hybrid approaches to predict pKa values of ionizable groups

PubMed Central

Witham, Shawn; Talley, Kemper; Wang, Lin; Zhang, Zhe; Sarkar, Subhra; Gao, Daquan; Yang, Wei

2011-01-01

Accurate predictions of pKa values of titratable groups require taking into account all relevant processes associated with the ionization/deionization. Frequently, however, the ionization does not involve significant structural changes and the dominating effects are purely electrostatic in origin allowing accurate predictions to be made based on the electrostatic energy difference between ionized and neutral forms alone using a static structure. On another hand, if the change of the charge state is accompanied by a structural reorganization of the target protein, then the relevant conformational changes have to be taken into account in the pKa calculations. Here we report a hybrid approach that first predicts the titratable groups, which ionization is expected to cause conformational changes, termed “problematic” residues, then applies a special protocol on them, while the rest of the pKa’s are predicted with rigid backbone approach as implemented in multi-conformation continuum electrostatics (MCCE) method. The backbone representative conformations for “problematic” groups are generated with either molecular dynamics simulations with charged and uncharged amino acid or with ab-initio local segment modeling. The corresponding ensembles are then used to calculate the pKa of the “problematic” residues and then the results are averaged. PMID:21744395

Report on the sixth blind test of organic crystal structure prediction methods

PubMed Central

Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.; Bhattacharya, Saswata; Boese, A. Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J.; Bylsma, Rita; Campbell, Josh E.; Car, Roberto; Case, David H.; Chadha, Renu; Cole, Jason C.; Cosburn, Katherine; Cuppen, Herma M.; Curtis, Farren; Day, Graeme M.; DiStasio Jr, Robert A.; Dzyabchenko, Alexander; van Eijck, Bouke P.; Elking, Dennis M.; van den Ende, Joost A.; Facelli, Julio C.; Ferraro, Marta B.; Fusti-Molnar, Laszlo; Gatsiou, Christina-Anna; Gee, Thomas S.; de Gelder, René; Ghiringhelli, Luca M.; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W. M.; Hoja, Johannes; Hylton, Rebecca K.; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T.; Kendrick, John; de Klerk, Niek J. J.; Ko, Hsin-Yu; Kuleshova, Liudmila N.; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J. J.; Lund, Albert M.; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E.; McCabe, Patrick; McMahon, David P.; Meekes, Hugo; Metz, Michael P.; Misquitta, Alston J.; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J.; Neumann, Marcus A.; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R.; Orendt, Anita M.; Pagola, Gabriel I.; Pantelides, Constantinos C.; Pickard, Chris J.; Podeszwa, Rafal; Price, Louise S.; Price, Sarah L.; Pulido, Angeles; Read, Murray G.; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P.; Singh, Pawanpreet; Sugden, Isaac J.; Szalewicz, Krzysztof; Taylor, Christopher R.; Tkatchenko, Alexandre; Tuckerman, Mark E.; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E.; de Wijs, Gilles A.; Yang, Jack; Zhu, Qiang; Groom, Colin R.

2016-01-01

The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

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.

Density functional theory calculations establish the experimental evidence of the DX center atomic structure in CdTe.

PubMed

Lany, Stephan; Wolf, Herbert; Wichert, Thomas

2004-06-04

The In DX center and the DX-like configuration of the Cd host atom in CdTe are investigated using density functional theory. The simultaneous calculation of the atomic structure and the electric field gradient (EFG) allows one to correlate the theoretically predicted structure of the DX center with an experimental observable, namely, the EFG obtained from radioactive 111In/111Cd probe atoms in In doped CdTe. In this way, the experimental identification of the DX center structure is established.

A first principles prediction of the crystal structure of C6Br2ClFH2

NASA Astrophysics Data System (ADS)

Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

2008-04-01

We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

Validation of Molecular Dynamics Simulations for Prediction of Three-Dimensional Structures of Small Proteins.

PubMed

Kato, Koichi; Nakayoshi, Tomoki; Fukuyoshi, Shuichi; Kurimoto, Eiji; Oda, Akifumi

2017-10-12

Although various higher-order protein structure prediction methods have been developed, almost all of them were developed based on the three-dimensional (3D) structure information of known proteins. Here we predicted the short protein structures by molecular dynamics (MD) simulations in which only Newton's equations of motion were used and 3D structural information of known proteins was not required. To evaluate the ability of MD simulationto predict protein structures, we calculated seven short test protein (10-46 residues) in the denatured state and compared their predicted and experimental structures. The predicted structure for Trp-cage (20 residues) was close to the experimental structure by 200-ns MD simulation. For proteins shorter or longer than Trp-cage, root-mean square deviation values were larger than those for Trp-cage. However, secondary structures could be reproduced by MD simulations for proteins with 10-34 residues. Simulations by replica exchange MD were performed, but the results were similar to those from normal MD simulations. These results suggest that normal MD simulations can roughly predict short protein structures and 200-ns simulations are frequently sufficient for estimating the secondary structures of protein (approximately 20 residues). Structural prediction method using only fundamental physical laws are useful for investigating non-natural proteins, such as primitive proteins and artificial proteins for peptide-based drug delivery systems.

Exploration of phase transition in ThS under pressure: An ab-initio investigation

NASA Astrophysics Data System (ADS)

Sahoo, B. D.; Mukherjee, D.; Joshi, K. D.; Kaushik, T. C.

2018-04-01

The ab-initio total energy calculations have been performed in thorium sulphide (ThS) to explore its high pressure phase stability. Our calculations predict a phase transformation from ambient rocksalt type structure (B1 phase) to a rhombohedral structure (R-3m phase) at ˜ 15 GPa and subsequently R-3m phase transforms to CsCl type structure (B2 phase) at ˜ 45 GPa. The first phase transition has been identified as second order type; whereas, the second transition is of first order type with volume discontinuity of 6.5%. The predicted high pressure R-3m phase is analogous to the experimentally observed hexagonal (distorted fcc) phase (Benedict et al., J. Less-Common Met., 1984) above 20 GPa. Further, using these calculations we have derived the equation of state which has been utilized to determine various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus at ambient conditions.

Investigation of structural stability and elastic properties of CrH and MnH: A first principles study

NASA Astrophysics Data System (ADS)

Kanagaprabha, S.; Rajeswarapalanichamy, R.; Sudhapriyanga, G.; Murugan, A.; Santhosh, M.; Iyakutti, K.

2015-06-01

The structural and mechanical properties of CrH and MnH are investigated using first principles calculation based on density functional theory as implemented in VASP code with generalized gradient approximation. The calculated ground state properties are in good agreement with previous experimental and other theoretical results. A structural phase transition from NaCl to NiAs phase at a pressure of 76 GPa is predicted for both CrH and MnH.

Crystal structure optimisation using an auxiliary equation of state

NASA Astrophysics Data System (ADS)

Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

2015-11-01

Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

Pressure-induced structural transformations and polymerization in ThC2

PubMed Central

Guo, Yongliang; Yu, Cun; Lin, Jun; Wang, Changying; Ren, Cuilan; Sun, Baoxing; Huai, Ping; Xie, Ruobing; Ke, Xuezhi; Zhu, Zhiyuan; Xu, Hongjie

2017-01-01

Thorium-carbon systems have been thought as promising nuclear fuel for Generation IV reactors which require high-burnup and safe nuclear fuel. Existing knowledge on thorium carbides under extreme condition remains insufficient and some is controversial due to limited studies. Here we systematically predict all stable structures of thorium dicarbide (ThC2) under the pressure ranging from ambient to 300 GPa by merging ab initio total energy calculations and unbiased structure searching method, which are in sequence of C2/c, C2/m, Cmmm, Immm and P6/mmm phases. Among these phases, the C2/m is successfully observed for the first time via in situ synchrotron XRD measurements, which exhibits an excellent structural correspondence to our theoretical predictions. The transition sequence and the critical pressures are predicted. The calculated results also reveal the polymerization behaviors of the carbon atoms and the corresponding characteristic C-C bonding under various pressures. Our work provides key information on the fundamental material behavior and insights into the underlying mechanisms that lay the foundation for further exploration and application of ThC2. PMID:28383571

Pressure-induced structural transformations and polymerization in ThC2

NASA Astrophysics Data System (ADS)

Guo, Yongliang; Yu, Cun; Lin, Jun; Wang, Changying; Ren, Cuilan; Sun, Baoxing; Huai, Ping; Xie, Ruobing; Ke, Xuezhi; Zhu, Zhiyuan; Xu, Hongjie

2017-04-01

Thorium-carbon systems have been thought as promising nuclear fuel for Generation IV reactors which require high-burnup and safe nuclear fuel. Existing knowledge on thorium carbides under extreme condition remains insufficient and some is controversial due to limited studies. Here we systematically predict all stable structures of thorium dicarbide (ThC2) under the pressure ranging from ambient to 300 GPa by merging ab initio total energy calculations and unbiased structure searching method, which are in sequence of C2/c, C2/m, Cmmm, Immm and P6/mmm phases. Among these phases, the C2/m is successfully observed for the first time via in situ synchrotron XRD measurements, which exhibits an excellent structural correspondence to our theoretical predictions. The transition sequence and the critical pressures are predicted. The calculated results also reveal the polymerization behaviors of the carbon atoms and the corresponding characteristic C-C bonding under various pressures. Our work provides key information on the fundamental material behavior and insights into the underlying mechanisms that lay the foundation for further exploration and application of ThC2.

Pressure-induced structural transformations and polymerization in ThC2.

PubMed

Guo, Yongliang; Yu, Cun; Lin, Jun; Wang, Changying; Ren, Cuilan; Sun, Baoxing; Huai, Ping; Xie, Ruobing; Ke, Xuezhi; Zhu, Zhiyuan; Xu, Hongjie

2017-04-06

Thorium-carbon systems have been thought as promising nuclear fuel for Generation IV reactors which require high-burnup and safe nuclear fuel. Existing knowledge on thorium carbides under extreme condition remains insufficient and some is controversial due to limited studies. Here we systematically predict all stable structures of thorium dicarbide (ThC 2 ) under the pressure ranging from ambient to 300 GPa by merging ab initio total energy calculations and unbiased structure searching method, which are in sequence of C2/c, C2/m, Cmmm, Immm and P6/mmm phases. Among these phases, the C2/m is successfully observed for the first time via in situ synchrotron XRD measurements, which exhibits an excellent structural correspondence to our theoretical predictions. The transition sequence and the critical pressures are predicted. The calculated results also reveal the polymerization behaviors of the carbon atoms and the corresponding characteristic C-C bonding under various pressures. Our work provides key information on the fundamental material behavior and insights into the underlying mechanisms that lay the foundation for further exploration and application of ThC 2 .

Ab Initio Prediction of the Structural, Electronic, Elastic, and Thermoelectric Properties of Half-Heusler Ternary Compounds TiIrX (X = As and Sb)

NASA Astrophysics Data System (ADS)

Chibani, S.; Arbouche, O.; Zemouli, M.; Amara, K.; Benallou, Y.; Azzaz, Y.; Belgoumène, B.; Bentayeb, A.; Ameri, M.

2018-01-01

The structural, electronic, elastic, and thermoelectric properties of TiIrX (X = As and Sb) half-Heusler compounds with 18 valence electrons were studied using density functional theory. The generalized gradient approximation of Perdew-Burke and Ernzerhof used for calculation of the structural parameters and elastic properties of TiIrAs and TiIrSb denotes that the computed lattice constants were in excellent agreement with the available experimental data and previous theoretical works. Furthermore, the calculated elastic constants for both compounds satisfy the Born criteria indicating their mechanical stabilities. The modified Becke-Johnson potential (TB-mBJ) was used to provide a better description of the electronic structures, which indicate that both compounds are narrow-gap semiconductors. Additionally, the investigations of thermoelectric performance were carried out using the results of ab initio band-structure calculations and the semi-classical Boltzmann theory within the constant relaxation time approximations. The predicted values of the figure of merit ZT e are close to unity at room temperature. This reveals that TiIrAs and TiIrSb compounds are excellent candidates for practical applications in the thermoelectric devices.

Creep Damage Analysis of a Lattice Truss Panel Structure

NASA Astrophysics Data System (ADS)

Jiang, Wenchun; Li, Shaohua; Luo, Yun; Xu, Shugen

2017-01-01

The creep failure for a lattice truss sandwich panel structure has been predicted by finite element method (FEM). The creep damage is calculated by three kinds of stresses: as-brazed residual stress, operating thermal stress and mechanical load. The creep damage at tensile and compressive loads have been calculated and compared. The creep rate calculated by FEM, Gibson-Ashby and Hodge-Dunand models have been compared. The results show that the creep failure is located at the fillet at both tensile and creep loads. The damage rate at the fillet at tensile load is 50 times as much as that at compressive load. The lattice truss panel structure has a better creep resistance to compressive load than tensile load, because the creep and stress triaxiality at the fillet has been decreased at compressive load. The maximum creep strain at the fillet and the equivalent creep strain of the panel structure increase with the increase of applied load. Compared with Gibson-Ashby model and Hodge-Dunand models, the modified Gibson-Ashby model has a good prediction result compared with FEM. However, a more accurate model considering the size effect of the structure still needs to be developed.

The direct field boundary impedance of two-dimensional periodic structures with application to high frequency vibration prediction.

PubMed

Langley, Robin S; Cotoni, Vincent

2010-04-01

Large sections of many types of engineering construction can be considered to constitute a two-dimensional periodic structure, with examples ranging from an orthogonally stiffened shell to a honeycomb sandwich panel. In this paper, a method is presented for computing the boundary (or edge) impedance of a semi-infinite two-dimensional periodic structure, a quantity which is referred to as the direct field boundary impedance matrix. This terminology arises from the fact that none of the waves generated at the boundary (the direct field) are reflected back to the boundary in a semi-infinite system. The direct field impedance matrix can be used to calculate elastic wave transmission coefficients, and also to calculate the coupling loss factors (CLFs), which are required by the statistical energy analysis (SEA) approach to predicting high frequency vibration levels in built-up systems. The calculation of the relevant CLFs enables a two-dimensional periodic region of a structure to be modeled very efficiently as a single subsystem within SEA, and also within related methods, such as a recently developed hybrid approach, which couples the finite element method with SEA. The analysis is illustrated by various numerical examples involving stiffened plate structures.

Ferromagnetism in half-metallic quaternary FeVTiAl Heusler compound

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

Bhat, Tahir Mohiuddin; Bhat, Idris Hamid; Yousuf, Saleem

The electronic structure and magnetic properties of FeVTiAl quaternary Heusler alloy have been investigated within the density functional theory framework. The material was found completely spin-polarized half-metallic Ferromagnet in the ground state with F-43m structure. The structural stability was further confirmed by calculating different elastic constants in the cubic phase. Present study predicts an energy band gap of 0.72 eV calculated in localized minority spin channel at an equilibrium lattice parameter of 6.0Å. The calculated total spin magnetic moment of 2 µ{sub B}/f.u. is in agreement with the Slater-Pauling rule for full Heusler alloys.

Comparison of the performance of different DFT methods in the calculations of the molecular structure and vibration spectra of serotonin (5-hydroxytryptamine, 5-HT)

NASA Astrophysics Data System (ADS)

Yang, Yue; Gao, Hongwei

2012-04-01

Serotonin (5-hydroxytryptamine, 5-HT) is a monoamine neurotransmitter which plays an important role in treating acute or clinical stress. The comparative performance of different density functional theory (DFT) methods at various basis sets in predicting the molecular structure and vibration spectra of serotonin was reported. The calculation results of different methods including mPW1PW91, HCTH, SVWN, PBEPBE, B3PW91 and B3LYP with various basis sets including LANL2DZ, SDD, LANL2MB, 6-31G, 6-311++G and 6-311+G* were compared with the experimental data. It is remarkable that the SVWN/6-311++G and SVWN/6-311+G* levels afford the best quality to predict the structure of serotonin. The results also indicate that PBEPBE/LANL2DZ level show better performance in the vibration spectra prediction of serotonin than other DFT methods.

Reaction between nickel or iron and xenon under high pressure

NASA Astrophysics Data System (ADS)

Dewaele, A.; Pépin, C. M.; Geneste, G.; Garbarino, G.

2017-04-01

Xe-Ni and Xe-Fe systems are studied in a pressure range relevant to the Earth's core (135-210 GPa) using laser-heated diamond anvil cells and synchrotron X-ray diffraction. The stability of several intermetallic compounds, including XeNi? and XeFe?, has been recently calculated using structural searches and density functional theory (DFT) above 155 and 190 GPa, respectively [Zhu L, Liu H, Pickard CJ, et al. Nat Chem. 2014;6:644-648]. We have synthesized XeNi? around 150 GPa, confirming the prediction; however, it has a cubic ?-Cu?Au structure, different from the predicted one for XeNi? but identical to the structure predicted for XeFe?. ?-XeNi? is calculated to be metastable with DFT. A disordered Ni?Xe? (?) alloy is observed to form prior to this compound. This alloy is interesting in the perspective of a possible storage of xenon in the Earth's core. We have not observed any reaction between Xe and Fe up to 210 GPa.

Resonance Scattering of Fe XVII X-ray and EUV Lines

NASA Technical Reports Server (NTRS)

Bhatia, A. K.; Saba, J. L. R.; Fisher, Richard R. (Technical Monitor)

2001-01-01

Over the years a number of calculations have been carried out to derive intensities of various X-ray and EUV lines in Fe XVII to compare with observed spectra. The predicted intensities have not agreed with solar observations, particularly for the line at 1.5.02 Angstroms; resonance scattering has been suggested as the source for much of the disagreement. The atomic data calculated earlier used seven configurations having n=3 orbitals and the scattering calculations were carried out only for incident energies above the threshold of the highest fine-structure level. These calculations have now been extended to thirteen configurations having n=4 orbitals and the scattering calculations are carried out below as well as above the threshold of the highest fine structure level. These improved calculations of Fe XVII change the intensity ratios compared to those obtained earlier, bringing the optically thin F(15.02)/F(16.78) ratio and several other ratios closer to the observed values. However, some disagreement with the solar observations still persists, even thought the agreement of the presently calculated optically thin F(15.02)/F(15.26) ratio with the experimental results of Brown et al. (1998) and Laming et al. (2000) has improved. Some of the remaining discrepancy is still thought to be the effect of opacity, which is consistent with expected physical conditions for solar sources. EUV intensity ratios are also calculated and compared with observations. Level populations and intensity ratios are calculated, as a function of column density of Fe XVII, in the slab and cylindrical geometries. As found previously, the predicted intensities for the resonance lines at 15.02 and 15.26 Angstroms exhibit initial increases in flux relative to the forbidden line at 17.10 Angstroms and the resonance line at 16.78 Angstroms as optical thickness increases. The same behavior is predicted for the lines at 12.262 and 12.122 Angstroms. Predicted intensities for some of the allowed EUV lines are also affected by opacity.

Oxysulfide LiAlSO: A Lithium Superionic Conductor from First Principles.

PubMed

Wang, Xuelong; Xiao, Ruijuan; Li, Hong; Chen, Liquan

2017-05-12

Through first-principles calculations and crystal structure prediction techniques, we identify a new layered oxysulfide LiAlSO in orthorhombic structure as a novel lithium superionic conductor. Two kinds of stacking sequences of layers of AlS_{2}O_{2} are found in different temperature ranges. Phonon and molecular dynamics simulations verify their dynamic stabilities, and wide band gaps up to 5.6 eV are found by electronic structure calculations. The lithium migration energy barrier simulations reveal the collective interstitial-host ion "kick-off" hopping mode with barriers lower than 50 meV as the dominating conduction mechanism for LiAlSO, indicating it to be a promising solid-state electrolyte in lithium secondary batteries with fast ionic conductivity and a wide electrochemical window. This is a first attempt in which the lithium superionic conductors are designed by the crystal structure prediction method and may help explore other mixed-anion battery materials.

Oxysulfide LiAlSO: A Lithium Superionic Conductor from First Principles

NASA Astrophysics Data System (ADS)

Wang, Xuelong; Xiao, Ruijuan; Li, Hong; Chen, Liquan

2017-05-01

Through first-principles calculations and crystal structure prediction techniques, we identify a new layered oxysulfide LiAlSO in orthorhombic structure as a novel lithium superionic conductor. Two kinds of stacking sequences of layers of AlS2O2 are found in different temperature ranges. Phonon and molecular dynamics simulations verify their dynamic stabilities, and wide band gaps up to 5.6 eV are found by electronic structure calculations. The lithium migration energy barrier simulations reveal the collective interstitial-host ion "kick-off" hopping mode with barriers lower than 50 meV as the dominating conduction mechanism for LiAlSO, indicating it to be a promising solid-state electrolyte in lithium secondary batteries with fast ionic conductivity and a wide electrochemical window. This is a first attempt in which the lithium superionic conductors are designed by the crystal structure prediction method and may help explore other mixed-anion battery materials.

Dislocation core structures of tungsten with dilute solute hydrogen

NASA Astrophysics Data System (ADS)

Wang, Yinan; Li, Qiulin; Li, Chengliang; Shu, Guogang; Xu, Ben; Liu, Wei

2017-12-01

In this paper, a combination of quantum mechanical and interatomic potential-based atomistic calculations are used to predict the core structures of screw and edge dislocations in tungsten in the presence of a particular concentration of hydrogen atoms. These configurations of the core structures are the results of two competing energies: the interaction between the partial dislocations and the corresponding generalized stacking fault energy in between the two partial dislocations, which are presented in this work. With this, we can precisely predict the configurations of the hydrogen-doped dislocation core structures.

Positron Annihilation Studies of the Electronic Structure of Selected High-Temperature Cuprate and Organic Superconductors.

NASA Astrophysics Data System (ADS)

Chan, Lie Ping

The understanding of the electronic structure of the high-T_{c} superconductors could be important for a full theoretical description of the mechanism behind superconductivity in these materials. In this thesis, we present our measurements of the positron -electron momentum distributions of the cuprate superconductors Bi_2Sr_2CaCu _2O_8, Tl _2Ba_2Ca _2Cu_3O_ {10}, and the organic superconductor kappa-(BEDT)_2Cu(NCS) _2. We use the positron Two-dimensional Angular Correlation of Annihilation Radiation technique to make the measurements on single crystals and compare our high-statistics data with band structure calculations to determine the existence and nature of the respective Fermi surfaces. The spectra from unannealed Bi _2Sr_2CaCu _2O_8 exhibit effects of the superlattice modulation in the BiO_2 layers, and a theoretical understanding of the modulation effects on the electronic band structure is required to interpret these spectra. Since the present theory does not consider the modulation, we have developed a technique to remove the modulation effects from our spectra, and the resultant data when compared with the positron -electron momentum distribution calculation, yield features consistent with the predicted CuO_2 and BiO_2 Fermi surfaces. In the data from unannealed Tl_2Ba _2Ca_2Cu_3 O_{10}, we only observe indications of the TlO Fermi surfaces, and attribute the absence of the predicted CuO_2 Fermi surfaces to the poor sample quality. In the absence of positron-electron momentum calculations for kappa-(BEDT)_2Cu(NCS) _2, we compare our data to electronic band structure calculations, and observed features suggestive of the predicted Fermi surface contributions from the BEDT cation layers. A complete positron-electron calculation for kappa-(BEDT)_2 Cu(NCS)_2 is required to understand the positron wavefunction effects in this material.

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Free molecular collision cross section calculation methods for nanoparticles and complex ions with energy accommodation

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

Larriba, Carlos, E-mail: clarriba@umn.edu; Hogan, Christopher J.

2013-10-15

The structures of nanoparticles, macromolecules, and molecular clusters in gas phase environments are often studied via measurement of collision cross sections. To directly compare structure models to measurements, it is hence necessary to have computational techniques available to calculate the collision cross sections of structural models under conditions matching measurements. However, presently available collision cross section methods contain the underlying assumption that collision between gas molecules and structures are completely elastic (gas molecule translational energy conserving) and specular, while experimental evidence suggests that in the most commonly used background gases for measurements, air and molecular nitrogen, gas molecule reemission ismore » largely inelastic (with exchange of energy between vibrational, rotational, and translational modes) and should be treated as diffuse in computations with fixed structural models. In this work, we describe computational techniques to predict the free molecular collision cross sections for fixed structural models of gas phase entities where inelastic and non-specular gas molecule reemission rules can be invoked, and the long range ion-induced dipole (polarization) potential between gas molecules and a charged entity can be considered. Specifically, two calculation procedures are described detail: a diffuse hard sphere scattering (DHSS) method, in which structures are modeled as hard spheres and collision cross sections are calculated for rectilinear trajectories of gas molecules, and a diffuse trajectory method (DTM), in which the assumption of rectilinear trajectories is relaxed and the ion-induced dipole potential is considered. Collision cross section calculations using the DHSS and DTM methods are performed on spheres, models of quasifractal aggregates of varying fractal dimension, and fullerene like structures. Techniques to accelerate DTM calculations by assessing the contribution of grazing gas molecule collisions (gas molecules with altered trajectories by the potential interaction) without tracking grazing trajectories are further discussed. The presented calculation techniques should enable more accurate collision cross section predictions under experimentally relevant conditions than pre-existing approaches, and should enhance the ability of collision cross section measurement schemes to discern the structures of gas phase entities.« less

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

PubMed

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Long-range empirical potential model: extension to hexagonal close-packed metals.

PubMed

Dai, Y; Li, J H; Liu, B X

2009-09-23

An n-body potential is developed and satisfactorily applied to hcp metals, Co, Hf, Mg, Re, Ti, and Zr, in the form of long-range empirical potential. The potential can well reproduce the lattice constants, c/a ratios, cohesive energies, and the bulk modulus for their stable structures (hcp) and metastable structures (bcc or fcc). Meanwhile, the potential can correctly predict the order of structural stability and distinguish the energy differences between their stable hcp structure and other structures. The energies and forces derived by the potential can smoothly go to zero at cutoff radius, thus completely avoiding the unphysical behaviors in the simulations. The developed potential is applied to study the vacancy, surface fault, stacking fault and self-interstitial atom in the hcp metals. The calculated formation energies of vacancy and divacancy and activation energies of self-diffusion by vacancies are in good agreement with the values in experiments and in other works. The calculated surface energies and stacking fault energies are also consistent with the experimental data and those obtained in other theoretical works. The calculated formation energies generally agree with the results in other works, although the stable configurations of self-interstitial atoms predicted in this work somewhat contrast with those predicted by other methods. The proposed potential is shown to be relevant for describing the interaction of bcc, fcc and hcp metal systems, bringing great convenience for researchers in constructing potentials for metal systems constituted by any combination of bcc, fcc and hcp metals.

Structural prediction and analysis of VIH-related peptides from selected crustacean species

PubMed Central

Nagaraju, Ganji Purna Chandra; Kumari, Nunna Siva; Prasad, Ganji Lakshmi Vara; Rajitha, Balney; Meenu, Madan; Rao, Manam Sreenivasa; Naik, Bannoth Reddya

2009-01-01

The tentative elucidation of the 3D-structure of vitellogenesis inhibiting hormone (VIH) peptides is conversely underprivileged by difficulties in gaining enough peptide or protein, diffracting crystals, and numerous extra technical aspects. As a result, no structural information is available for VIH peptide sequences registered in the Genbank. In this situation, it is not surprising that predictive methods have achieved great interest. Here, in this study the molt-inhibiting hormone (MIH) of the kuruma prawn (Marsupenaeus japonicus) is used, to predict the structure of four VIHrelated peptides in the crustacean species. The high similarity of the 3D-structures and the calculated physiochemical characteristics of these peptides suggest a common fold for the entire family. PMID:20011146

Planning, creating and documenting a NASTRAN finite element model of a modern helicopter

NASA Technical Reports Server (NTRS)

Gabal, R.; Reed, D.; Ricks, R.; Kesack, W.

1985-01-01

Mathematical models based on the finite element method of structural analysis as embodied in the NASTRAN computer code are widely used by the helicopter industry to calculate static internal loads and vibration of airframe structure. The internal loads are routinely used for sizing structural members. The vibration predictions are not yet relied on during design. NASA's Langley Research Center sponsored a program to conduct an application of the finite element method with emphasis on predicting structural vibration. The Army/Boeing CH-47D helicopter was used as the modeling subject. The objective was to engender the needed trust in vibration predictions using these models and establish a body of modeling guides which would enable confident future prediction of airframe vibration as part of the regular design process.

Decoupling effect and forecasting of economic growth and energy structure under the peak constraint of carbon emissions in China.

PubMed

Wang, Shijin; Li, Cunfang; Yang, Lizhu

2018-06-26

The decoupling effect between economic growth and energy structure was quantitatively analyzed from 1999 to 2014 across China. The results showed it existed weak decoupling effects in most regions. Based on the analysis of the influence of energy structure on carbon intensity, using scenario simulation methods and Markov chain modeling, the carbon intensity was predicted for China in 2020. The impact of energy structure adjustment on the carbon intensity to meet China's carbon target by 18 possible scenarios are calculated. Furthermore, the peak value of carbon emissions was also calculated in 2030. The results showed that the carbon intensity predicted for China in 2020 can be achieved regardless of whether the energy structure was adjusted or not when energy saving and carbon reduction policies maintained with economic growth at 6-7%. Moreover, given fixed energy structure growth, for each 1% of economic growth, the carbon intensity will decrease by about 3.5%. Given fixed economic growth, the decrease of energy intensity will be greater if the control of energy consumption is stronger. The effect of energy structure adjustment on the decreasing of carbon intensity will be 4% higher under constraints than without constraints. On average, the contribution of energy structure adjustment to achieving the carbon intensity target was calculated as 4% higher than that with constraints. In addition, given relatively fixed economic growth at 6-7%, the peak value of carbon emission in 2030 was calculated as 13.209 billion tons with constraints and 14.38 billion tons without constraints.

Prediction of B1 to B10 phase transition in LuN under pressure: An ab-initio investigation

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

Sahoo, B. D., E-mail: bdsahoo@barc.gov.in; Mukherjee, D.; Joshi, K. D.

2016-05-23

Ab-initio total energy calculations have been performed in lutetium nitride (LuN) as a function of hydrostatic compression to understand the high pressure behavior of this compound. Our calculations predict a phase transition from ambient rocksalt type structure (B1 phase) to a tetragonal structure (B10 phase) at ~ 240 GPa. The phase transition has been identified as first order in nature with volume discontinuity of ~ 6%. The predicted high pressure phase has been found to be stable up to at least 400 GPa, the maximum pressure up to which calculations have been performed.Further, to substantiate the results of static lattice calculations analysismore » of lattice dynamic stability of B1 and B10 phase has been carried out at different pressures. Apart from this, we have analyzed the lattice dynamic stability CsCl type (B2) phase around the 240 GPa, the pressure reported for B1 to B2 transition in previous all-electron calculations by Gupta et al. 2013. We find that the B2 structure is lattice dynamically unstable at this pressure and remains unstable up to ~ 400 GPa, ruling out the possibility of B1 to B2 phase transition at least up to ~ 400 GPa. Further, the theoretically determined equation of state has been utilized to derive various physical quantities such as zero pressure equilibrium volume, bulk modulus, and pressure derivative of bulk modulus of B1 phase at ambient conditions.« less

Valence-Band Electronic Structures of High-Pressure-Phase PdF2-type Platinum-Group Metal Dioxides MO2 (M = Ru, Rh, Ir, and Pt)

NASA Astrophysics Data System (ADS)

Soda, Kazuo; Kobayashi, Daichi; Mizui, Tatsuya; Kato, Masahiko; Shirako, Yuichi; Niwa, Ken; Hasegawa, Masashi; Akaogi, Masaki; Kojitani, Hiroshi; Ikenaga, Eiji; Muro, Takayuki

2018-04-01

The valence-band electronic structures of high-pressure-phase PdF2-type (HP-PdF2-type) platinum-group metal dioxides MO2 (M = Ru, Rh, Ir, and Pt) were studied by synchrotron radiation photoelectron spectroscopy and first-principles calculations. The obtained photoelectron spectra for HP-PdF2-type RuO2, RhO2, and IrO2 agree well with the calculated valence-band densities of states (DOSs) for these compounds, indicating their metallic properties, whereas the DOS of HP-PdF2-type PtO2 (calculated in the presence and absence of spin-orbit interactions) predicts that this material may be metallic or semimetallic, which is inconsistent with the electric conductivity reported to date and the charging effect observed in current photoelectron measurements. Compared with the calculated results, the valence-band spectrum of PtO2 appears to have shifted toward the high-binding-energy side and reveals a gradual intensity decrease toward the Fermi energy EF, implying a semiconductor-like electronic structure. Spin-dependent calculations predict a ferromagnetic ground state with a magnetization of 0.475 μB per formula unit for HP-PdF2-type RhO2.

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

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors.

PubMed

Nandi, Sisir; Monesi, Alessandro; Drgan, Viktor; Merzel, Franci; Novič, Marjana

2013-10-30

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Quantitative structure-property relationships for prediction of boiling point, vapor pressure, and melting point.

PubMed

Dearden, John C

2003-08-01

Boiling point, vapor pressure, and melting point are important physicochemical properties in the modeling of the distribution and fate of chemicals in the environment. However, such data often are not available, and therefore must be estimated. Over the years, many attempts have been made to calculate boiling points, vapor pressures, and melting points by using quantitative structure-property relationships, and this review examines and discusses the work published in this area, and concentrates particularly on recent studies. A number of software programs are commercially available for the calculation of boiling point, vapor pressure, and melting point, and these have been tested for their predictive ability with a test set of 100 organic chemicals.

Local and average structure of Mn- and La-substituted BiFeO3

NASA Astrophysics Data System (ADS)

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space group symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.

Local and average structure of Mn- and La-substituted BiFeO 3

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

Jiang, Bo; Selbach, Sverre M.

2017-06-01

The local and average structure of solid solutions of the multiferroic perovskite BiFeO 3 is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO 3. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions.« less

Information-theoretic indices usage for the prediction and calculation of octanol-water partition coefficient.

PubMed

Persona, Marek; Kutarov, Vladimir V; Kats, Boris M; Persona, Andrzej; Marczewska, Barbara

2007-01-01

The paper describes the new prediction method of octanol-water partition coefficient, which is based on molecular graph theory. The results obtained using the new method are well correlated with experimental values. These results were compared with the ones obtained by use of ten other structure correlated methods. The comparison shows that graph theory can be very useful in structure correlation research.

Annular tautomerism: experimental observations and quantum mechanics calculations.

PubMed

Cruz-Cabeza, Aurora J; Schreyer, Adrian; Pitt, William R

2010-06-01

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein-small molecule crystal structures.

Annular tautomerism: experimental observations and quantum mechanics calculations

NASA Astrophysics Data System (ADS)

Cruz-Cabeza, Aurora J.; Schreyer, Adrian; Pitt, William R.

2010-06-01

The use of MP2 level quantum mechanical (QM) calculations on isolated heteroaromatic ring systems for the prediction of the tautomeric propensities of whole molecules in a crystalline environment was examined. A Polarisable Continuum Model was used in the calculations to account for environment effects on the tautomeric relative stabilities. The calculated relative energies of tautomers were compared to relative abundances within the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB). The work was focussed on 84 annular tautomeric forms of 34 common ring systems. Good agreement was found between the calculations and the experimental data even if the quantity of these data was limited in many cases. The QM results were compared to those produced by much faster semiempirical calculations. In a search for other sources of the useful experimental data, the relative numbers of known compounds in which prototropic positions were often substituted by heavy atoms were also analysed. A scheme which groups all annular tautomeric transformations into 10 classes was developed. The scheme was designed to encompass a comprehensive set of known and theoretically possible tautomeric ring systems generated as part of a previous study. General trends across analogous ring systems were detected as a result. The calculations and statistics collected on crystallographic data as well as the general trends observed should be useful for the better modelling of annular tautomerism in the applications such as computer-aided drug design, small molecule crystal structure prediction, the naming of compounds and the interpretation of protein—small molecule crystal structures.

Predicting Welding Distortion in a Panel Structure with Longitudinal Stiffeners Using Inherent Deformations Obtained by Inverse Analysis Method

PubMed Central

Liang, Wei; Murakawa, Hidekazu

2014-01-01

Welding-induced deformation not only negatively affects dimension accuracy but also degrades the performance of product. If welding deformation can be accurately predicted beforehand, the predictions will be helpful for finding effective methods to improve manufacturing accuracy. Till now, there are two kinds of finite element method (FEM) which can be used to simulate welding deformation. One is the thermal elastic plastic FEM and the other is elastic FEM based on inherent strain theory. The former only can be used to calculate welding deformation for small or medium scale welded structures due to the limitation of computing speed. On the other hand, the latter is an effective method to estimate the total welding distortion for large and complex welded structures even though it neglects the detailed welding process. When the elastic FEM is used to calculate the welding-induced deformation for a large structure, the inherent deformations in each typical joint should be obtained beforehand. In this paper, a new method based on inverse analysis was proposed to obtain the inherent deformations for weld joints. Through introducing the inherent deformations obtained by the proposed method into the elastic FEM based on inherent strain theory, we predicted the welding deformation of a panel structure with two longitudinal stiffeners. In addition, experiments were carried out to verify the simulation results. PMID:25276856

Predicting welding distortion in a panel structure with longitudinal stiffeners using inherent deformations obtained by inverse analysis method.

PubMed

Liang, Wei; Murakawa, Hidekazu

2014-01-01

Welding-induced deformation not only negatively affects dimension accuracy but also degrades the performance of product. If welding deformation can be accurately predicted beforehand, the predictions will be helpful for finding effective methods to improve manufacturing accuracy. Till now, there are two kinds of finite element method (FEM) which can be used to simulate welding deformation. One is the thermal elastic plastic FEM and the other is elastic FEM based on inherent strain theory. The former only can be used to calculate welding deformation for small or medium scale welded structures due to the limitation of computing speed. On the other hand, the latter is an effective method to estimate the total welding distortion for large and complex welded structures even though it neglects the detailed welding process. When the elastic FEM is used to calculate the welding-induced deformation for a large structure, the inherent deformations in each typical joint should be obtained beforehand. In this paper, a new method based on inverse analysis was proposed to obtain the inherent deformations for weld joints. Through introducing the inherent deformations obtained by the proposed method into the elastic FEM based on inherent strain theory, we predicted the welding deformation of a panel structure with two longitudinal stiffeners. In addition, experiments were carried out to verify the simulation results.

Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure-Function Relationships.

PubMed

Huang, Yandong; Yue, Zhi; Tsai, Cheng-Chieh; Henderson, Jack A; Shen, Jana

2018-03-15

Despite the relevance of understanding structure-function relationships, robust prediction of proton donors and nucleophiles in enzyme active sites remains challenging. Here we tested three types of state-of-the-art computational methods to calculate the p K a 's of the buried and hydrogen bonded catalytic dyads in five enzymes. We asked the question what determines the p K a order, i.e., what makes a residue proton donor vs a nucleophile. The continuous constant pH molecular dynamics simulations captured the experimental p K a orders and revealed that the negative nucleophile is stabilized by increased hydrogen bonding and solvent exposure as compared to the proton donor. Surprisingly, this simple trend is not apparent from crystal structures and the static structure-based calculations. While the generality of the findings awaits further testing via a larger set of data, they underscore the role of dynamics in bridging enzyme structures and functions.

A polymer dataset for accelerated property prediction and design

DOE PAGES

Huan, Tran Doan; Mannodi-Kanakkithodi, Arun; Kim, Chiho; ...

2016-03-01

Emerging computation- and data-driven approaches are particularly useful for rationally designing materials with targeted properties. Generally, these approaches rely on identifying structure-property relationships by learning from a dataset of sufficiently large number of relevant materials. The learned information can then be used to predict the properties of materials not already in the dataset, thus accelerating the materials design. Herein, we develop a dataset of 1,073 polymers and related materials and make it available at http://khazana.uconn.edu/. This dataset is uniformly prepared using first-principles calculations with structures obtained either from other sources or by using structure search methods. Because the immediate targetmore » of this work is to assist the design of high dielectric constant polymers, it is initially designed to include the optimized structures, atomization energies, band gaps, and dielectric constants. As a result, it will be progressively expanded by accumulating new materials and including additional properties calculated for the optimized structures provided.« less

First principles calculation of material properties of group IV elements and III-V compounds

NASA Astrophysics Data System (ADS)

Malone, Brad Dean

This thesis presents first principles calculations on the properties of group IV elements and group III-V compounds. It includes investigations into what structure a material is likely to form in, and given that structure, what are its electronic, optical, and lattice dynamical properties as well as what are the properties of defects that might be introduced into the sample. The thesis is divided as follows: • Chapter 1 contains some of the conceptual foundations used in the present work. These involve the major approximations which allow us to approach the problem of systems with huge numbers of interacting electrons and atomic cores. • Then, in Chapter 2, we discuss one of the major limitations to the DFT formalism introduced in Chapter 1, namely its inability to predict the quasiparticle spectra of materials and in particular the band gap of a semiconductor. We introduce a Green's function approach to the electron self-energy Sigma known as the GW approximation and use it to compute the quasiparticle band structures of a number of group IV and III-V semiconductors. • In Chapter 3 we present a first-principles study of a number of high-pressure metastable phases of Si with tetrahedral bonding. The phases studied include all experimentally determined phases that result from decompression from the metallic beta-Sn phase, specifically the BC8 (Si-III), hexagonal diamond (Si-IV), and R8 (Si-XII). In addition to these, we also study the hypothetical ST12 structure found upon decompression from beta-Sn in germanium. • Our attention is then turned to the first principles calculations of optical properties in Chapter 4. The Bethe-Salpeter equation is then solved to obtain the optical spectrum of this material including electron-hole interactions. The calculated optical spectrum is compared with experimental data for other forms of silicon commonly used in photovoltaic devices, namely the cubic, polycrystalline, and amorphous forms. • In Chapter 5 we present first principles calculations of the quasiparticle and optical excitation spectra of recently predicted silicon and germanium polytypes in the body-centered-tetragonal (bct) structure. The quasiparticle spectra calculated within the GW approximation predict that both silicon and germanium in the bct structure are small band gap materials. The optical spectra are then evaluated by solving the Bethe-Salpeter equation taking into account. • We examine the low-pressure phases of Ge in Chapter 6 by performing first principles calculations of the electronic structure and lattice dynamics of the R8, BC8, ST12, and hexagonal diamond structures of Ge. To aid future experimental investigation, we include predictions of the Raman-active frequencies of these phases as well as present the full phonon dispersion throughout the zone. • In Chapter 7 we demonstrate how first principles calculations can be used to predict new structures. In a study aimed at finding new useful forms of silicon, we use an ab initio random structure searching (AIRSS) method to identify a new phase of silicon in the Ibamstructure. The Ibam phase is found to be semimetallic within density functional theory with a small band overlap, and it is expected that quasiparticle corrections using the GW approximation would yield a semiconducting state with a small band gap. • We present a first-principles study of boron and phosphorus substitutional defects in Si-XII in Chapter 8. Recent result from nanoindentation experiments reveal that the Si-XII phase is semiconducting and has the interesting property that it can be doped n- and p-type at room temperature without an annealing step. Using the hybrid functional of Heyd, Scuseria, and Ernzerhof (HSE), we examine the formation energies of the B and P defects at the two distinct atomic sites in Si-XII to find on which site the substitutional defects are more easily accommodated. We also estimate the thermodynamic transition levels of each defect in its relevant charge states. (Abstract shortened by UMI.).

First principles calculation of the structural, electronic, and magnetic properties of Au-Pd atomic chains

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

Dave, Mudra R., E-mail: mdave-phy@yahoo.co.in; Sharma, A. C.

2015-06-24

The structural, electronic and magnetic properties of free standing Au-Pd bimetallic atomic chain is studied using ab-initio method. It is found that electronic and magnetic properties of chains depend on position of atoms and number of atoms. Spin polarization factor for different atomic configuration of atomic chain is calculated predicting a half metallic behavior. It suggests a total spin polarised transport in these chains.

Casimir Pressure in Mds-Structures

NASA Astrophysics Data System (ADS)

Yurova, V. A.; Bukina, M. N.; Churkin, Yu. V.; Fedortsov, A. B.; Klimchitskaya, G. L.

2012-07-01

The Casimir pressure on the dielectric layer in metal-dielectric-semiconductor (MDS) structures is calculated in the framework of the Lifshitz theory at nonzero temperature. In this calculation the standard parameters of semiconductor devices with a thin dielectric layer are used. We consider the thickness of a layer decreasing from 40 to 1 nm. At the shortest thickness the Casimir pressure achieves 8 MPa. At small thicknesses the results are compared with the predictions of nonrelativistic theory.

Ab Initio Predictions of Hexagonal Zr(B,C,N) Polymorphs for Coherent Interface Design

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

Hu, Chongze; Huang, Jingsong; Sumpter, Bobby G.

2017-10-27

Density functional theory calculations are used to explore hexagonal (HX) NiAs-like polymorphs of Zr(B,C,N) and compare with corresponding Zr(B,C,N) Hagg-like face-centered cubic rocksalt (B1) phases. While all predicted compounds are mechanically stable according to the Born-Huang criteria, only HX Zr(C,N) are found dynamically stable from ab initio molecular dynamics simulations and lattice dynamics calculations. HX ZrN emerges as a candidate structure with ground state energy, elastic constants, and extrinsic mechanical parameters comparable with those of B1 ZrN. Ab initio band structure and semi-classical Boltzmann transport calculations predict a metallic character and a monotonic increase in electrical conductivity with the numbermore » of valence electrons. Electronic structure calculations indicate that the HX phases gain their stability and mechanical attributes by Zr d- non-metal p hybridization and by broadening of Zr d bands. Furthermore, it is shown that the HX ZrN phase provides a low-energy coherent interface model for connecting B1 ZrN domains, with significant energetic advantage over an atomistic interface model derived from high resolution transmission electron microscopy images. The ab initio characterizations provided herein should aid the experimental identification of non-Hagg-like hard phases. Furthermore, the results can also enrich the variety of crystalline phases potentially available for designing coherent interfaces in superhard nanostructured materials and in materials with multilayer characteristics.« less

The prospect of modern thermomechanics in structural integrity calculations of large-scale pressure vessels

NASA Astrophysics Data System (ADS)

Fekete, Tamás

2018-05-01

Structural integrity calculations play a crucial role in designing large-scale pressure vessels. Used in the electric power generation industry, these kinds of vessels undergo extensive safety analyses and certification procedures before deemed feasible for future long-term operation. The calculations are nowadays directed and supported by international standards and guides based on state-of-the-art results of applied research and technical development. However, their ability to predict a vessel's behavior under accidental circumstances after long-term operation is largely limited by the strong dependence of the analysis methodology on empirical models that are correlated to the behavior of structural materials and their changes during material aging. Recently a new scientific engineering paradigm, structural integrity has been developing that is essentially a synergistic collaboration between a number of scientific and engineering disciplines, modeling, experiments and numerics. Although the application of the structural integrity paradigm highly contributed to improving the accuracy of safety evaluations of large-scale pressure vessels, the predictive power of the analysis methodology has not yet improved significantly. This is due to the fact that already existing structural integrity calculation methodologies are based on the widespread and commonly accepted 'traditional' engineering thermal stress approach, which is essentially based on the weakly coupled model of thermomechanics and fracture mechanics. Recently, a research has been initiated in MTA EK with the aim to review and evaluate current methodologies and models applied in structural integrity calculations, including their scope of validity. The research intends to come to a better understanding of the physical problems that are inherently present in the pool of structural integrity problems of reactor pressure vessels, and to ultimately find a theoretical framework that could serve as a well-grounded theoretical foundation for a new modeling framework of structural integrity. This paper presents the first findings of the research project.

Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of D-amino acid oxidase inhibitors.

PubMed

Orgován, Zoltán; Ferenczy, György G; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M

2018-02-01

Optimization of fragment size D-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

Validation of tautomeric and protomeric binding modes by free energy calculations. A case study for the structure based optimization of d-amino acid oxidase inhibitors

NASA Astrophysics Data System (ADS)

Orgován, Zoltán; Ferenczy, György G.; Steinbrecher, Thomas; Szilágyi, Bence; Bajusz, Dávid; Keserű, György M.

2018-02-01

Optimization of fragment size d-amino acid oxidase (DAAO) inhibitors was investigated using a combination of computational and experimental methods. Retrospective free energy perturbation (FEP) calculations were performed for benzo[d]isoxazole derivatives, a series of known inhibitors with two potential binding modes derived from X-ray structures of other DAAO inhibitors. The good agreement between experimental and computed binding free energies in only one of the hypothesized binding modes strongly support this bioactive conformation. Then, a series of 1-H-indazol-3-ol derivatives formerly not described as DAAO inhibitors was investigated. Binding geometries could be reliably identified by structural similarity to benzo[d]isoxazole and other well characterized series and FEP calculations were performed for several tautomers of the deprotonated and protonated compounds since all these forms are potentially present owing to the experimental pKa values of representative compounds in the series. Deprotonated compounds are proposed to be the most important bound species owing to the significantly better agreement between their calculated and measured affinities compared to the protonated forms. FEP calculations were also used for the prediction of the affinities of compounds not previously tested as DAAO inhibitors and for a comparative structure-activity relationship study of the benzo[d]isoxazole and indazole series. Selected indazole derivatives were synthesized and their measured binding affinity towards DAAO was in good agreement with FEP predictions.

Ko Displacement Theory for Structural Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.

2010-01-01

The development of the Ko displacement theory for predictions of structure deformed shapes was motivated in 2003 by the Helios flying wing, which had a 247-ft (75-m) wing span with wingtip deflections reaching 40 ft (12 m). The Helios flying wing failed in midair in June 2003, creating the need to develop new technology to predict in-flight deformed shapes of unmanned aircraft wings for visual display before the ground-based pilots. Any types of strain sensors installed on a structure can only sense the surface strains, but are incapable to sense the overall deformed shapes of structures. After the invention of the Ko displacement theory, predictions of structure deformed shapes could be achieved by feeding the measured surface strains into the Ko displacement transfer functions for the calculations of out-of-plane deflections and cross sectional rotations at multiple locations for mapping out overall deformed shapes of the structures. The new Ko displacement theory combined with a strain-sensing system thus created a revolutionary new structure- shape-sensing technology.

New determination of the fine structure constant from the electron value and QED.

PubMed

Gabrielse, G; Hanneke, D; Kinoshita, T; Nio, M; Odom, B

2006-07-21

Quantum electrodynamics (QED) predicts a relationship between the dimensionless magnetic moment of the electron (g) and the fine structure constant (alpha). A new measurement of g using a one-electron quantum cyclotron, together with a QED calculation involving 891 eighth-order Feynman diagrams, determine alpha(-1)=137.035 999 710 (96) [0.70 ppb]. The uncertainties are 10 times smaller than those of nearest rival methods that include atom-recoil measurements. Comparisons of measured and calculated g test QED most stringently, and set a limit on internal electron structure.

Potential high-Tc superconducting lanthanum and yttrium hydrides at high pressure

PubMed Central

Liu, Hanyu; Naumov, Ivan I.; Hoffmann, Roald; Ashcroft, N. W.; Hemley, Russell J.

2017-01-01

A systematic structure search in the La–H and Y–H systems under pressure reveals some hydrogen-rich structures with intriguing electronic properties. For example, LaH10 is found to adopt a sodalite-like face-centered cubic (fcc) structure, stable above 200 GPa, and LaH8 a C2/m space group structure. Phonon calculations indicate both are dynamically stable; electron phonon calculations coupled to Bardeen–Cooper–Schrieffer (BCS) arguments indicate they might be high-Tc superconductors. In particular, the superconducting transition temperature Tc calculated for LaH10 is 274–286 K at 210 GPa. Similar calculations for the Y–H system predict stability of the sodalite-like fcc YH10 and a Tc above room temperature, reaching 305–326 K at 250 GPa. The study suggests that dense hydrides consisting of these and related hydrogen polyhedral networks may represent new classes of potential very high-temperature superconductors. PMID:28630301

Phonon vibrational frequencies of all single-wall carbon nanotubes at the lambda point: reduced matrix calculations.

PubMed

Wang, Yufang; Wu, Yanzhao; Feng, Min; Wang, Hui; Jin, Qinghua; Ding, Datong; Cao, Xuewei

2008-12-01

With a simple method-the reduced matrix method, we simplified the calculation of the phonon vibrational frequencies according to SWNTs structure and their phonon symmetric property and got the dispersion properties of all SWNTs at Gamma point in Brillouin zone, whose diameters lie between 0.6 and 2.5 nm. The calculating time is shrunk about 2-4 orders. A series of the dependent relationships between the diameters of SWNTs and the frequencies of Raman and IR active modes are given. Several fine structures including "glazed tile" structures in omega approximately d figures are found, which might predict a certain macro-quantum phenomenon of the phonons in SWNTs.

Prediction and Analysis of CO2 Emission in Chongqing for the Protection of Environment and Public Health

PubMed Central

Yang, Shuai; Wang, Yu; Ao, Wengang; Bai, Yun; Li, Chuan

2018-01-01

Based on the consumption of fossil energy, the CO2 emissions of Chongqing are calculated and analyzed from 1997 to 2015 in this paper. Based on the calculation results, the consumption of fossil fuels and the corresponding CO2 emissions of Chongqing in 2020 are predicted, and the supporting data and corresponding policies are provided for the government of Chongqing to reach its goal as the economic unit of low-carbon emission in the ‘13th Five-Year Plan’. The results of the analysis show that there is a rapid decreasing trend of CO2 emissions in Chongqing during the ‘12th Five-Year Plan’, which are caused by the adjustment policy of the energy structure in Chongqing. Therefore, the analysis and prediction are primarily based on the adjustment of Chongqing’s coal energy consumption in this paper. At the initial stage, support vector regression (SVR) method is applied to predict the other fossil energy consumption and the corresponding CO2 emissions of Chongqing in 2020. Then, with the energy intensity of 2015 and the official target of CO2 intensity in 2020, the total fossil energy consumption and CO2 emissions of Chongqing in 2020 are predicted respectively. By the above results of calculation, the coal consumption and its corresponding CO2 emissions of Chongqing in 2020 are determined. To achieve the goal of CO2 emissions of Chongqing in 2020, the coal consumption level and energy intensity of Chongqing are calculated, and the adjustment strategies for energy consumption structure in Chongqing are proposed. PMID:29547505

Quantitative 1D diffraction signatures during dual detector scatter VOI breast CBCT

NASA Astrophysics Data System (ADS)

LeClair, Robert J.

2017-03-01

Dual detector VOI scatter CBCT is similar to dual detector VOI CBCT except that during the high resolution scan, the low resolution flat panel detector is also used to capture the scattered photons. Simulations show a potential use of scatter to diagnose suspicious VOIs. Energy integrated signals due to scatter (EISs) were computed for a specific imaging task involving a malignant lesion and was labelled as a hypothetical experiment (expt) result. The signal was compared to predictions (pred) using benign and malignant lesions. The ΔEISs=EISs|expt - EISs|pred displayed eye catching diffraction structure when the prediction calculation used a benign lesion. The structure occurred even when the phantom compositions were different for prediction and experiment calculations. Since the diffraction structure has a circularly symmetric behaviour because the tissues are amorphous in nature, the 2D ΔEISs patterns were transformed to 1D signals. The 1D signals were obtained by calculating the mean ΔEISs signals in rings. The mean pixel values were a function of the momentum transfer argument q = 4π sin(θ/2)/λ which ranged from 12 to 46 nm-1. The 1D signals correlated well with the 2D profiles. Of particular interest were scatter signatures between q = 20 and 30 nm-1 where malignant tissue is predicted to scatter more than benign fibroglandular tissue. The 1D diffraction signatures could allow a better method to diagnose a suspicious lesion during dual detector scatter VOI CBCT.

A model of rotationally-sampled wind turbulence for predicting fatigue loads in wind turbines

NASA Technical Reports Server (NTRS)

Spera, David A.

1995-01-01

Empirical equations are presented with which to model rotationally-sampled (R-S) turbulence for input to structural-dynamic computer codes and the calculation of wind turbine fatigue loads. These equations are derived from R-S turbulence data which were measured at the vertical-plane array in Clayton, New Mexico. For validation, the equations are applied to the calculation of cyclic flapwise blade loads for the NASA/DOE Mod-2 2.5-MW experimental HAWT's (horizontal-axis wind turbines), and the results compared to measured cyclic loads. Good correlation is achieved, indicating that the R-S turbulence model developed in this study contains the characteristics of the wind which produce many of the fatigue loads sustained by wind turbines. Empirical factors are included which permit the prediction of load levels at specified percentiles of occurrence, which is required for the generation of fatigue load spectra and the prediction of the fatigue lifetime of structures.

A novel method for structure-based prediction of ion channel conductance properties.

PubMed Central

Smart, O S; Breed, J; Smith, G R; Sansom, M S

1997-01-01

A rapid and easy-to-use method of predicting the conductance of an ion channel from its three-dimensional structure is presented. The method combines the pore dimensions of the channel as measured in the HOLE program with an Ohmic model of conductance. An empirically based correction factor is then applied. The method yielded good results for six experimental channel structures (none of which were included in the training set) with predictions accurate to within an average factor of 1.62 to the true values. The predictive r2 was equal to 0.90, which is indicative of a good predictive ability. The procedure is used to validate model structures of alamethicin and phospholamban. Two genuine predictions for the conductance of channels with known structure but without reported conductances are given. A modification of the procedure that calculates the expected results for the effect of the addition of nonelectrolyte polymers on conductance is set out. Results for a cholera toxin B-subunit crystal structure agree well with the measured values. The difficulty in interpreting such studies is discussed, with the conclusion that measurements on channels of known structure are required. Images FIGURE 1 FIGURE 3 FIGURE 4 FIGURE 6 FIGURE 10 PMID:9138559

Structures of undecagold clusters: Ligand effect

NASA Astrophysics Data System (ADS)

Spivey, Kasi; Williams, Joseph I.; Wang, Lichang

2006-12-01

The most stable structure of undecagold, or Au 11, clusters was predicted from our DFT calculations to be planar [L. Xiao, L. Wang, Chem. Phys. Lett. 392 (2004) 452; L. Xiao, B. Tollberg, X. Hu, L. Wang, J. Chem. Phys. 124 (2005) 114309.]. The structures of ligand protected undecagold clusters were shown to be three-dimensional experimentally. In this work, we used DFT calculations to study the ligand effect on the structures of Au 11 clusters. Our results show that the most stable structure of Au 11 is in fact three-dimensional when SCH 3 ligands are attached. This indicates that the structures of small gold clusters are altered substantially in the presence of ligands.

Calculating the dermal flux of chemicals with OELs based on their molecular structure: An attempt to assign the skin notation.

PubMed

Kupczewska-Dobecka, Małgorzata; Jakubowski, Marek; Czerczak, Sławomir

2010-09-01

Our objectives included calculating the permeability coefficient and dermal penetration rates (flux value) for 112 chemicals with occupational exposure limits (OELs) according to the LFER (linear free-energy relationship) model developed using published methods. We also attempted to assign skin notations based on each chemical's molecular structure. There are many studies available where formulae for coefficients of permeability from saturated aqueous solutions (K(p)) have been related to physicochemical characteristics of chemicals. The LFER model is based on the solvation equation, which contains five main descriptors predicted from chemical structure: solute excess molar refractivity, dipolarity/polarisability, summation hydrogen bond acidity and basicity, and the McGowan characteristic volume. Descriptor values, available for about 5000 compounds in the Pharma Algorithms Database were used to calculate permeability coefficients. Dermal penetration rate was estimated as a ratio of permeability coefficient and concentration of chemical in saturated aqueous solution. Finally, estimated dermal penetration rates were used to assign the skin notation to chemicals. Defined critical fluxes defined from the literature were recommended as reference values for skin notation. The application of Abraham descriptors predicted from chemical structure and LFER analysis in calculation of permeability coefficients and flux values for chemicals with OELs was successful. Comparison of calculated K(p) values with data obtained earlier from other models showed that LFER predictions were comparable to those obtained by some previously published models, but the differences were much more significant for others. It seems reasonable to conclude that skin should not be characterised as a simple lipophilic barrier alone. Both lipophilic and polar pathways of permeation exist across the stratum corneum. It is feasible to predict skin notation on the basis of the LFER and other published models; from among 112 chemicals 94 (84%) should have the skin notation in the OEL list based on the LFER calculations. The skin notation had been estimated by other published models for almost 94% of the chemicals. Twenty-nine (25.8%) chemicals were identified to have significant absorption and 65 (58%) the potential for dermal toxicity. We found major differences between alternative published analytical models and their ability to determine whether particular chemicals were potentially dermotoxic. Copyright © 2010 Elsevier B.V. All rights reserved.

π-Stacking, C-H/π, and halogen bonding interactions in bromobenzene and mixed bromobenzene-benzene clusters.

PubMed

Reid, Scott A; Nyambo, Silver; Muzangwa, Lloyd; Uhler, Brandon

2013-12-19

Noncovalent interactions play an important role in many chemical and biochemical processes. Building upon our recent study of the homoclusters of chlorobenzene, where π-π stacking and CH/π interactions were identified as the most important binding motifs, in this work we present a study of bromobenzene (PhBr) and mixed bromobenzene-benzene clusters. Electronic spectra in the region of the PhBr monomer S0-S1 (ππ*) transition were obtained using resonant two-photon ionization (R2PI) methods combined with time-of-flight mass analysis. As previously found for related systems, the PhBr cluster spectra show a broad feature whose center is red-shifted from the monomer absorption, and electronic structure calculations indicate the presence of multiple isomers and Franck-Condon activity in low-frequency intermolecular modes. Calculations at the M06-2X/aug-cc-pVDZ level find in total eight minimum energy structures for the PhBr dimer: four π-stacked structures differing in the relative orientation of the Br atoms (denoted D1-D4), one T-shaped structure (D5), and three halogen bonded structures (D6-D8). The calculated binding energies of these complexes, corrected for basis set superposition error (BSSE) and zero-point energy (ZPE), are in the range of -6 to -24 kJ/mol. Time-dependent density functional theory (TDDFT) calculations predict that these isomers absorb over a range that is roughly consistent with the breadth of the experimental spectrum. To examine the influence of dipole-dipole interaction, R2PI spectra were also obtained for the mixed PhBr···benzene dimer, where the spectral congestion is reduced and clear vibrational structure is observed. This structure is well-simulated by Franck-Condon calculations that incorporate the lowest frequency intermolecular modes. Calculations find four minimum energy structures for the mixed dimer and predict that the binding energy of the global minimum is reduced by ~30% relative to the global minimum PhBr dimer structure.

First-principles study on the phase transitions, crystal stabilities and thermodynamic properties of TiN under high pressure

NASA Astrophysics Data System (ADS)

Sun, Xinjun; Liu, Changdong; Guo, Yongliang; Sun, Deyan; Ke, Xuezhi

2018-03-01

The structural and thermodynamic properties of titanium nitride (TiN) have been investigated by merging first-principles calculations and particle-swarm algorithm. The three phases are identified for TiN, including the B1, the P63 / mmc, and the B2 phases. A new phase of anti-TiP structure with the space group P63 / mmc has been predicted. The calculated phase transition from the B1 to the P63 / mmc occurs at 270 GPa. The vibrational, elastic, and thermodynamic properties for the three phases have been calculated and discussed.

D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions

NASA Astrophysics Data System (ADS)

Gathiaka, Symon; Liu, Shuai; Chiu, Michael; Yang, Huanwang; Stuckey, Jeanne A.; Kang, You Na; Delproposto, Jim; Kubish, Ginger; Dunbar, James B.; Carlson, Heather A.; Burley, Stephen K.; Walters, W. Patrick; Amaro, Rommie E.; Feher, Victoria A.; Gilson, Michael K.

2016-09-01

The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.

D3R Grand Challenge 2015: Evaluation of Protein-Ligand Pose and Affinity Predictions

PubMed Central

Gathiaka, Symon; Liu, Shuai; Chiu, Michael; Yang, Huanwang; Stuckey, Jeanne A; Kang, You Na; Delproposto, Jim; Kubish, Ginger; Dunbar, James B.; Carlson, Heather A.; Burley, Stephen K.; Walters, W. Patrick; Amaro, Rommie E.; Feher, Victoria A.; Gilson, Michael K.

2017-01-01

The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (i) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (ii) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor. PMID:27696240

Grain growth prediction based on data assimilation by implementing 4DVar on multi-phase-field model

NASA Astrophysics Data System (ADS)

Ito, Shin-ichi; Nagao, Hiromichi; Kasuya, Tadashi; Inoue, Junya

2017-12-01

We propose a method to predict grain growth based on data assimilation by using a four-dimensional variational method (4DVar). When implemented on a multi-phase-field model, the proposed method allows us to calculate the predicted grain structures and uncertainties in them that depend on the quality and quantity of the observational data. We confirm through numerical tests involving synthetic data that the proposed method correctly reproduces the true phase-field assumed in advance. Furthermore, it successfully quantifies uncertainties in the predicted grain structures, where such uncertainty quantifications provide valuable information to optimize the experimental design.

CALCULATING PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FOR ENVIRONMENTAL MODELING FROM MOLECULAR STRUCTURE

EPA Science Inventory

Mathematical models for predicting the transport and fate of pollutants in the environment require reactivity parameter values-- that is value of the physical and chemical constants that govern reactivity. Although empirical structure activity relationships have been developed t...

Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method

NASA Astrophysics Data System (ADS)

Mariappan, G.; Sundaraganesan, N.

2014-01-01

A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations.

An ab initio study of the structure and atomic transport in bulk liquid Ag and its liquid-vapor interface

NASA Astrophysics Data System (ADS)

del Rio, Beatriz G.; González, David J.; González, Luis E.

2016-10-01

Several static and dynamic properties of bulk liquid Ag at a thermodynamic state near its triple point have been calculated by means of ab initio molecular dynamics simulations. The calculated static structure shows a very good agreement with the available experimental data. The dynamical structure reveals propagating excitations whose dispersion at long wavelengths is compatible with the experimental sound velocity. Results are also reported for other transport coefficients. Additional simulations have also been performed so as to study the structure of the free liquid surface. The calculated longitudinal ionic density profile shows an oscillatory behaviour, whose properties are analyzed through macroscopic and microscopic methods. The intrinsic X-ray reflectivity of the surface is predicted to show a layering peak associated to the interlayer distance.

Crystal field analysis of the energy level structure of Cs2NaAlF6:Cr3+

NASA Astrophysics Data System (ADS)

Rudowicz, C.; Brik, M. G.; Avram, N. M.; Yeung, Y. Y.; Gnutek, P.

2006-06-01

An analysis of the energy level structure of Cr3+ ions in Cs2NaAlF6 crystal is performed using the exchange charge model (ECM) together with the crystal field analysis/microscopic spin Hamiltonian (CFA/MSH) computer package. Utilizing the crystal structure data, our approach enables modelling of the crystal field parameters (CFPs) and thus the energy level structure for Cr3+ ions at the two crystallographically inequivalent sites in Cs2NaAlF6. Using the ECM initial adjustment procedure, the CFPs are calculated in the crystallographic axis system centred at the Cr3+ ion at each site. Additionally the CFPs are also calculated using the superposition model (SPM). The ECM and SPM predicted CFP values match very well. Consideration of the symmetry aspects for the so-obtained CFP datasets reveals that the latter axis system matches the symmetry-adapted axis system related directly to the six Cr-F bonds well. Using the ECM predicted CFPs as an input for the CFA/MSH package, the complete energy level schemes are calculated for Cr3+ ions at the two sites. Comparison of the theoretical results with the experimental spectroscopic data yields satisfactory agreement. Our results confirm that the actual symmetry at both impurity sites I and II in the Cs2NaAlF6:Cr3+ system is trigonal D3d. The ECM predicted CFPs may be used as the initial (starting) parameters for simulations and fittings of the energy levels for Cr3+ ions in structurally similar hosts.

First-principles prediction of low-energy structures for AlH3

NASA Astrophysics Data System (ADS)

Sun, Shoutian; Ke, Xuezhi; Chen, Changfeng; Tanaka, Isao

2009-01-01

We report density-functional calculations that predict ten different low-energy structures for aluminum hydride AlH3 with space groups Pnma , P6/mmm , I4/mcm , P4/mbm , P4/nmm , Pm3¯m , P21/m , P21/c , Pbcm , and P4/n . Phonon calculations within harmonic approximation reveal unstable modes in the P6/mmm , I4/mcm , P4/mbm , P4/nmm , Pm3¯m , P21/m , and P21/c structures, indicating that they are unstable at low temperatures. The calculations show that the thermodynamic stabilities for AlH3 with space groups Pnma , Pbcm , and P4/n are overall close to the existing α - and γ-AlH3 . From x-ray powder-diffraction patterns, the simulated main-peak positions for AlH3 (P4/n) are in good agreement with experimental δ-AlH3 . A full Rietveld analysis reveals that the fitting space groups R3¯c , Pbcm , and Pnma to the experimental x-ray powder-diffraction pattern of α-AlH3 gives almost the same satisfactory result.

Comparison of measured temperatures, thermal stresses and creep residues with predictions on a built-up titanium structure

NASA Technical Reports Server (NTRS)

Jenkins, Jerald M.

1987-01-01

Temperature, thermal stresses, and residual creep stresses were studied by comparing laboratory values measured on a built-up titanium structure with values calculated from finite-element models. Several such models were used to examine the relationship between computational thermal stresses and thermal stresses measured on a built-up structure. Element suitability, element density, and computational temperature discrepancies were studied to determine their impact on measured and calculated thermal stress. The optimum number of elements is established from a balance between element density and suitable safety margins, such that the answer is acceptably safe yet is economical from a computational viewpoint. It is noted that situations exist where relatively small excursions of calculated temperatures from measured values result in far more than proportional increases in thermal stress values. Measured residual stresses due to creep significantly exceeded the values computed by the piecewise linear elastic strain analogy approach. The most important element in the computation is the correct definition of the creep law. Computational methodology advances in predicting residual stresses due to creep require significantly more viscoelastic material characterization.

Monte Carlo approach in assessing damage in higher order structures of DNA

NASA Technical Reports Server (NTRS)

Chatterjee, A.; Schmidt, J. B.; Holley, W. R.

1994-01-01

We have developed a computer monitor of nuclear DNA in the form of chromatin fibre. The fibres are modeled as a ideal solenoid consisting of twenty helical turns with six nucleosomes per turn. The chromatin model, in combination with are Monte Carlo theory of radiation damage induces by charged particles, based on general features of tack structure and stopping power theory, has been used to evaluate the influence of DNA structure on initial damage. An interesting has emerged from our calculations. Our calculated results predict the existence of strong spatial correlations in damage sites associated with the symmetries in the solenoidal model. We have calculated spectra of short fragments of double stranded DNA produced by multiple double strand breaks induced by both high and low LET radiation. The spectra exhibit peaks at multiples of approximately 85 base pairs (the nucleosome periodicity), and approximately 1000 base pairs (solenoid periodicity). Preliminary experiments to investigate the fragment distributions from irradiated DNA, made by B. Rydberg at Lawrence Berkeley Laboratory, confirm the existence of short DNA fragments and are in substantial agreement with the predictions of our theory.

Molecular Simulation-Based Structural Prediction of Protein Complexes in Mass Spectrometry: The Human Insulin Dimer

PubMed Central

Li, Jinyu; Rossetti, Giulia; Dreyer, Jens; Raugei, Simone; Ippoliti, Emiliano; Lüscher, Bernhard; Carloni, Paolo

2014-01-01

Protein electrospray ionization (ESI) mass spectrometry (MS)-based techniques are widely used to provide insight into structural proteomics under the assumption that non-covalent protein complexes being transferred into the gas phase preserve basically the same intermolecular interactions as in solution. Here we investigate the applicability of this assumption by extending our previous structural prediction protocol for single proteins in ESI-MS to protein complexes. We apply our protocol to the human insulin dimer (hIns2) as a test case. Our calculations reproduce the main charge and the collision cross section (CCS) measured in ESI-MS experiments. Molecular dynamics simulations for 0.075 ms show that the complex maximizes intermolecular non-bonded interactions relative to the structure in water, without affecting the cross section. The overall gas-phase structure of hIns2 does exhibit differences with the one in aqueous solution, not inferable from a comparison with calculated CCS. Hence, care should be exerted when interpreting ESI-MS proteomics data based solely on NMR and/or X-ray structural information. PMID:25210764

Finite element modeling as a tool for predicting the fracture behavior of robocast scaffolds.

PubMed

Miranda, Pedro; Pajares, Antonia; Guiberteau, Fernando

2008-11-01

The use of finite element modeling to calculate the stress fields in complex scaffold structures and thus predict their mechanical behavior during service (e.g., as load-bearing bone implants) is evaluated. The method is applied to identifying the fracture modes and estimating the strength of robocast hydroxyapatite and beta-tricalcium phosphate scaffolds, consisting of a three-dimensional lattice of interpenetrating rods. The calculations are performed for three testing configurations: compression, tension and shear. Different testing orientations relative to the calcium phosphate rods are considered for each configuration. The predictions for the compressive configurations are compared to experimental data from uniaxial compression tests.

NASA Langley developments in response calculations needed for failure and life prediction

NASA Technical Reports Server (NTRS)

Housner, Jerrold M.

1993-01-01

NASA Langley developments in response calculations needed for failure and life predictions are discussed. Topics covered include: structural failure analysis in concurrent engineering; accuracy of independent regional modeling demonstrated on classical example; functional interface method accurately joins incompatible finite element models; interface method for insertion of local detail modeling extended to curve pressurized fuselage window panel; interface concept for joining structural regions; motivation for coupled 2D-3D analysis; compression panel with discontinuous stiffener coupled 2D-3D model and axial surface strains at the middle of the hat stiffener; use of adaptive refinement with multiple methods; adaptive mesh refinement; and studies on quantity effect of bow-type initial imperfections on reliability of stiffened panels.

Computational predictions of the new Gallium nitride nanoporous structures

NASA Astrophysics Data System (ADS)

Lien, Le Thi Hong; Tuoc, Vu Ngoc; Duong, Do Thi; Thu Huyen, Nguyen

2018-05-01

Nanoporous structural prediction is emerging area of research because of their advantages for a wide range of materials science and technology applications in opto-electronics, environment, sensors, shape-selective and bio-catalysis, to name just a few. We propose a computationally and technically feasible approach for predicting Gallium nitride nanoporous structures with hollows at the nano scale. The designed porous structures are studied with computations using the density functional tight binding (DFTB) and conventional density functional theory methods, revealing a variety of promising mechanical and electronic properties, which can potentially find future realistic applications. Their stability is discussed by means of the free energy computed within the lattice-dynamics approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with their parent’s bulk stable phase. The electronic band structures of these nanoporous structures are finally examined in detail.

The electronic structure, elastic and optical properties of Cu2ZnGe(SexS1 - x)4 alloys: density functional calculations

NASA Astrophysics Data System (ADS)

Shen, Kesheng; Jia, Guangrui; Zhang, Xianzhou; Jiao, Zhaoyong

2016-10-01

The electronic structure, elastic and optical properties of Cu2ZnGe(SexS1 - x)4 alloys are systematically analysed using first-principles calculations. The lattice parameters agree well with the theoretical and experimental values which are searched as complete as possible indicating our calculations are reliable. The elastic properties are investigated first and are compared with the similar compounds CZTS and CZTSe due to the unavailable experimental data currently. The variation of the optical properties caused by the increase of Se/S ratio is discussed. The static optical constants are calculated and the corrected values are also predicted according to the available experimental data.

A novel prediction method about single components of analog circuits based on complex field modeling.

PubMed

Zhou, Jingyu; Tian, Shulin; Yang, Chenglin

2014-01-01

Few researches pay attention to prediction about analog circuits. The few methods lack the correlation with circuit analysis during extracting and calculating features so that FI (fault indicator) calculation often lack rationality, thus affecting prognostic performance. To solve the above problem, this paper proposes a novel prediction method about single components of analog circuits based on complex field modeling. Aiming at the feature that faults of single components hold the largest number in analog circuits, the method starts with circuit structure, analyzes transfer function of circuits, and implements complex field modeling. Then, by an established parameter scanning model related to complex field, it analyzes the relationship between parameter variation and degeneration of single components in the model in order to obtain a more reasonable FI feature set via calculation. According to the obtained FI feature set, it establishes a novel model about degeneration trend of analog circuits' single components. At last, it uses particle filter (PF) to update parameters for the model and predicts remaining useful performance (RUP) of analog circuits' single components. Since calculation about the FI feature set is more reasonable, accuracy of prediction is improved to some extent. Finally, the foregoing conclusions are verified by experiments.

A theoretical analysis of deformation behavior of auxetic plied yarn structure

NASA Astrophysics Data System (ADS)

Zeng, Jifang; Hu, Hong

2018-07-01

This paper presents a theoretical analysis of the auxetic plied yarn (APY) structure formed with two types of single yarns having different diameter and modulus. A model which can be used to predict its deformation behavior under axial extension is developed based on the theoretical analysis. The developed model is first compared with the experimental data obtained in the previous study, and then used to predict the effects of different structural and material parameters on the auxetic behavior of the APY. The calculation results show that the developed model can correctly predict the variation trend of the auxetic behavior of the APY, which first increases and then decrease with the increase of the axial strain. The calculation results also indicate that the auxetic behavior of the APY simultaneously depends on the diameter ratio of the soft yarn and stiff yarn as well as the ratio between the pitch length and stiff yarn diameter. The study provides a way to design and fabricate APYs with the same auxetic behavior by using different soft and stiff yarns as long as these two ratios are kept unchanged.

Ternary Bismuthide SrPtBi 2: Computation and Experiment in Synergism to Explore Solid-State Materials

DOE PAGES

Gui, Xin; Zhao, Xin; Sobczak, Zuzanna; ...

2018-02-14

A combination of theoretical calculation and the experimental synthesis to explore the new ternary compound is demonstrated in the Sr–Pt–Bi system. Because Pt–Bi is considered as a new critical charge-transfer pair for superconductivity, it inspired us to investigate the Sr–Pt–Bi system. With a thorough calculation of all the known stable/metastable compounds in the Sr–Pt–Bi system and crystal structure predictions, the thermodynamic stability of hypothetical stoichiometry, SrPtBi2, is determined. Following the high-temperature synthesis and crystallographic analysis, the first ternary bismuthide in Sr–Pt–Bi, SrPtBi2 was prepared, and the stoichiometry was confirmed experimentally. SrPtBi 2 crystallizes in the space group Pnma (S.G. 62,more » Pearson Symbol oP48), which matches well with theoretical prediction using an adaptive genetic algorithm. Using first-principles calculations, we demonstrate that the orthorhombic structure has lower formation energies than other 112 structure types, such as tetragonal BaMnBi 2 (CuSmP 2) and LaAuBi 2 (CuHfSi 2) structure types. The bonding analysis indicates that the Pt–Bi interactions play a critical role in structural stability. The physical property measurements show the metallic properties at the low temperature, which agrees with the electronic structure assessment.« less

Quantum-gravity predictions for the fine-structure constant

NASA Astrophysics Data System (ADS)

Eichhorn, Astrid; Held, Aaron; Wetterich, Christof

2018-07-01

Asymptotically safe quantum fluctuations of gravity can uniquely determine the value of the gauge coupling for a large class of grand unified models. In turn, this makes the electromagnetic fine-structure constant calculable. The balance of gravity and matter fluctuations results in a fixed point for the running of the gauge coupling. It is approached as the momentum scale is lowered in the transplanckian regime, leading to a uniquely predicted value of the gauge coupling at the Planck scale. The precise value of the predicted fine-structure constant depends on the matter content of the grand unified model. It is proportional to the gravitational fluctuation effects for which computational uncertainties remain to be settled.

Pseudoracemic amino acid complexes: blind predictions for flexible two-component crystals.

PubMed

Görbitz, Carl Henrik; Dalhus, Bjørn; Day, Graeme M

2010-08-14

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.

Shaping up the protein folding funnel by local interaction: lesson from a structure prediction study.

PubMed

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-02-28

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of "chimera proteins." In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape.

Shaping up the protein folding funnel by local interaction: Lesson from a structure prediction study

PubMed Central

Chikenji, George; Fujitsuka, Yoshimi; Takada, Shoji

2006-01-01

Predicting protein tertiary structure by folding-like simulations is one of the most stringent tests of how much we understand the principle of protein folding. Currently, the most successful method for folding-based structure prediction is the fragment assembly (FA) method. Here, we address why the FA method is so successful and its lesson for the folding problem. To do so, using the FA method, we designed a structure prediction test of “chimera proteins.” In the chimera proteins, local structural preference is specific to the target sequences, whereas nonlocal interactions are only sequence-independent compaction forces. We find that these chimera proteins can find the native folds of the intact sequences with high probability indicating dominant roles of the local interactions. We further explore roles of local structural preference by exact calculation of the HP lattice model of proteins. From these results, we suggest principles of protein folding: For small proteins, compact structures that are fully compatible with local structural preference are few, one of which is the native fold. These local biases shape up the funnel-like energy landscape. PMID:16488978

First-principles theory of iron up to earth-core pressures: Structural, vibrational, and elastic properties

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

Soederlind, P.; Moriarty, J.A.; Wills, J.M.

1996-06-01

{ital Ab} {ital initio} electronic-structure calculations, based on density-functional theory and a full-potential linear-muffin-tin-orbital method, have been used to predict crystal-structure phase stabilities, elastic constants, and Brillouin-zone-boundary phonons for iron under compression. Total energies for five crystal structures, bcc, fcc, bct, hcp, and dhcp, have been calculated over a wide volume range. In agreement with experiment and previous theoretical calculations, a magnetic bcc ground state is obtained at ambient pressure and a nonmagnetic hcp ground state is found at high pressure, with a predicted bcc {r_arrow} hcp phase transition at about 10 GPa. Also in agreement with very recent diamond-anvil-cellmore » experiments, a metastable dhcp phase is found at high pressure, which remains magnetic and consequently accessible at high temperature up to about 50 GPa. In addition, the bcc structure becomes mechanically unstable at pressures above 2 Mbar (200 GPa) and a metastable, but still magnetic, bct phase ({ital c}/{ital a} {approx_equal} 0.875) develops. For high-pressure nonmagnetic iron, fcc and hcp elastic constants and fcc phonon frequencies have been calculated to above 4 Mbar. These quantities rise smoothly with pressure, but an increasing tendency towards elastic anisotropy as a function of compression is observed, and this has important implications for the solid inner-core of the earth. The fcc elastic-constant and phonon data have also been used in combination with generalized pseudopotential theory to develop many-body interatomic potentials, from which high-temperature thermodynamic properties and melting can be obtained. In this paper, these potentials have been used to calculate full fcc and hcp phonon spectra and corresponding Debye temperatures as a function of compression. {copyright} {ital 1996 The American Physical Society.}« less

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

PubMed

Hirsh, Layla; Paladin, Lisanna; Piovesan, Damiano; Tosatto, Silvio C E

2018-05-09

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

NASA Astrophysics Data System (ADS)

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.

PubMed

Misini Ignjatović, Majda; Caldararu, Octav; Dong, Geng; Muñoz-Gutierrez, Camila; Adasme-Carreño, Francisco; Ryde, Ulf

2016-09-01

We have estimated the binding affinity of three sets of ligands of the heat-shock protein 90 in the D3R grand challenge blind test competition. We have employed four different methods, based on five different crystal structures: first, we docked the ligands to the proteins with induced-fit docking with the Glide software and calculated binding affinities with three energy functions. Second, the docked structures were minimised in a continuum solvent and binding affinities were calculated with the MM/GBSA method (molecular mechanics combined with generalised Born and solvent-accessible surface area solvation). Third, the docked structures were re-optimised by combined quantum mechanics and molecular mechanics (QM/MM) calculations. Then, interaction energies were calculated with quantum mechanical calculations employing 970-1160 atoms in a continuum solvent, combined with energy corrections for dispersion, zero-point energy and entropy, ligand distortion, ligand solvation, and an increase of the basis set to quadruple-zeta quality. Fourth, relative binding affinities were estimated by free-energy simulations, using the multi-state Bennett acceptance-ratio approach. Unfortunately, the results were varying and rather poor, with only one calculation giving a correlation to the experimental affinities larger than 0.7, and with no consistent difference in the quality of the predictions from the various methods. For one set of ligands, the results could be strongly improved (after experimental data were revealed) if it was recognised that one of the ligands displaced one or two water molecules. For the other two sets, the problem is probably that the ligands bind in different modes than in the crystal structures employed or that the conformation of the ligand-binding site or the whole protein changes.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection

NASA Astrophysics Data System (ADS)

Cox, Courtney E.; Phifer, Jeremy R.; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T.; O'Loughlin, Elizabeth J.; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T.; Paluch, Andrew S.

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

Combining MOSCED with molecular simulation free energy calculations or electronic structure calculations to develop an efficient tool for solvent formulation and selection.

PubMed

Cox, Courtney E; Phifer, Jeremy R; Ferreira da Silva, Larissa; Gonçalves Nogueira, Gabriel; Ley, Ryan T; O'Loughlin, Elizabeth J; Pereira Barbosa, Ana Karolyne; Rygelski, Brett T; Paluch, Andrew S

2017-02-01

Solubility parameter based methods have long been a valuable tool for solvent formulation and selection. Of these methods, the MOdified Separation of Cohesive Energy Density (MOSCED) has recently been shown to correlate well the equilibrium solubility of multifunctional non-electrolyte solids. However, before it can be applied to a novel solute, a limited amount of reference solubility data is required to regress the necessary MOSCED parameters. Here we demonstrate for the solutes methylparaben, ethylparaben, propylparaben, butylparaben, lidocaine and ephedrine how conventional molecular simulation free energy calculations or electronic structure calculations in a continuum solvent, here the SMD or SM8 solvation model, can instead be used to generate the necessary reference data, resulting in a predictive flavor of MOSCED. Adopting the melting point temperature and enthalpy of fusion of these compounds from experiment, we are able to predict equilibrium solubilities. We find the method is able to well correlate the (mole fraction) equilibrium solubility in non-aqueous solvents over four orders of magnitude with good quantitative agreement.

First principles calculation of thermo-mechanical properties of thoria using Quantum ESPRESSO

NASA Astrophysics Data System (ADS)

Malakkal, Linu; Szpunar, Barbara; Zuniga, Juan Carlos; Siripurapu, Ravi Kiran; Szpunar, Jerzy A.

2016-05-01

In this work, we have used Quantum ESPRESSO (QE), an open source first principles code, based on density-functional theory, plane waves, and pseudopotentials, along with quasi-harmonic approximation (QHA) to calculate the thermo-mechanical properties of thorium dioxide (ThO2). Using Python programming language, our group developed qe-nipy-advanced, an interface to QE, which can evaluate the structural and thermo-mechanical properties of materials. We predicted the phonon contribution to thermal conductivity (kL) using the Slack model. We performed the calculations within local density approximation (LDA) and generalized gradient approximation (GGA) with the recently proposed version for solids (PBEsol). We employed a Monkhorst-Pack 5 × 5 × 5 k-points mesh in reciprocal space with a plane wave cut-off energy of 150 Ry to obtain the convergence of the structure. We calculated the dynamical matrices of the lattice on a 4 × 4 × 4 mesh. We have predicted the heat capacity, thermal expansion and the phonon contribution to thermal conductivity, as a function of temperature up to 1400K, and compared them with the previous work and known experimental results.

Crystal structure prediction supported by incomplete experimental data

NASA Astrophysics Data System (ADS)

Tsujimoto, Naoto; Adachi, Daiki; Akashi, Ryosuke; Todo, Synge; Tsuneyuki, Shinji

2018-05-01

We propose an efficient theoretical scheme for structure prediction on the basis of the idea of combining methods, which optimize theoretical calculation and experimental data simultaneously. In this scheme, we formulate a cost function based on a weighted sum of interatomic potential energies and a penalty function which is defined with partial experimental data totally insufficient for conventional structure analysis. In particular, we define the cost function using "crystallinity" formulated with only peak positions within the small range of the x-ray-diffraction pattern. We apply this method to well-known polymorphs of SiO2 and C with up to 108 atoms in the simulation cell and show that it reproduces the correct structures efficiently with very limited information of diffraction peaks. This scheme opens a new avenue for determining and predicting structures that are difficult to determine by conventional methods.

Theoretical prediction of low-density hexagonal ZnO hollow structures

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

Tuoc, Vu Ngoc, E-mail: tuoc.vungoc@hust.edu.vn; Huan, Tran Doan; Thao, Nguyen Thi

2016-10-14

Along with wurtzite and zinc blende, zinc oxide (ZnO) has been found in a large number of polymorphs with substantially different properties and, hence, applications. Therefore, predicting and synthesizing new classes of ZnO polymorphs are of great significance and have been gaining considerable interest. Herein, we perform a density functional theory based tight-binding study, predicting several new series of ZnO hollow structures using the bottom-up approach. The geometry of the building blocks allows for obtaining a variety of hexagonal, low-density nanoporous, and flexible ZnO hollow structures. Their stability is discussed by means of the free energy computed within the lattice-dynamicsmore » approach. Our calculations also indicate that all the reported hollow structures are wide band gap semiconductors in the same fashion with bulk ZnO. The electronic band structures of the ZnO hollow structures are finally examined in detail.« less

Theoretical investigation of the structural, elastic, electronic and optical properties of the ternary indium sulfide layered structures AInS2 (A = K, Rb and Cs)

NASA Astrophysics Data System (ADS)

Bouchenafa, M.; Sidoumou, M.; Halit, M.; Benmakhlouf, A.; Bouhemadou, A.; Maabed, S.; Bentabet, A.; Bin-Omran, S.

2018-02-01

Ab initio calculations were performed to investigate the structural, elastic, electronic and optical properties of the ternary layered systems AInS2 (A = K, Rb and Cs). The calculated structural parameters are in good agreement with the existing experimental data. Analysis of the electronic band structure shows that the three studied materials are direct band-gap semiconductors. Density of states, charge transfers and charge density distribution maps were computed and analyzed. Numerical estimations of the elastic moduli and their related properties for single-crystal and polycrystalline aggregates were predicted. The optical properties were calculated for incident radiation polarized along the [100], [010] and [001] crystallographic directions. The studied materials exhibit a noticeable anisotropic behaviour in the elastic and optical properties, which is expected due to the symmetry and the layered nature of these compounds.

Photoelectron spectroscopy of nitromethane anion clusters

NASA Astrophysics Data System (ADS)

Pruitt, Carrie Jo M.; Albury, Rachael M.; Goebbert, Daniel J.

2016-08-01

Nitromethane anion and nitromethane dimer, trimer, and hydrated cluster anions were studied by photoelectron spectroscopy. Vertical detachment energies, estimated electron affinities, and solvation energies were obtained from the photoelectron spectra. Cluster structures were investigated using theoretical calculations. Predicted detachment energies agreed with experiment. Calculations show water binds to nitromethane anion through two hydrogen bonds. The dimer has a non-linear structure with a single ionic Csbnd H⋯O hydrogen bond. The trimer has two different solvent interactions, but both involve the weak Csbnd H⋯O hydrogen bond.

Ab-initio study of pressure evolution of structural, mechanical and magnetic properties of cementite (Fe3C) phase

NASA Astrophysics Data System (ADS)

Gorai, S.; Ghosh, P. S.; Bhattacharya, C.; Arya, A.

2018-04-01

The pressure evolution of phase stability, structural and mechanical properties of Fe3C in ferro-magnetic (FM) and high pressure non magnetic (NM) phase is investigated from first principle calculations. The 2nd order FM to NM phase transition of Fe3C is identified around 60 GPa. Pressure (or density) variation of sound velocities from our ab-initio calculated single crystal elastic constants are determined to predict these parameters at Earth's outer core pressure.

Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

NASA Astrophysics Data System (ADS)

Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien

2018-01-01

The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.

An approximate methods approach to probabilistic structural analysis

NASA Technical Reports Server (NTRS)

Mcclung, R. C.; Millwater, H. R.; Wu, Y.-T.; Thacker, B. H.; Burnside, O. H.

1989-01-01

A major research and technology program in Probabilistic Structural Analysis Methods (PSAM) is currently being sponsored by the NASA Lewis Research Center with Southwest Research Institute as the prime contractor. This program is motivated by the need to accurately predict structural response in an environment where the loadings, the material properties, and even the structure may be considered random. The heart of PSAM is a software package which combines advanced structural analysis codes with a fast probability integration (FPI) algorithm for the efficient calculation of stochastic structural response. The basic idea of PAAM is simple: make an approximate calculation of system response, including calculation of the associated probabilities, with minimal computation time and cost, based on a simplified representation of the geometry, loads, and material. The deterministic solution resulting should give a reasonable and realistic description of performance-limiting system responses, although some error will be inevitable. If the simple model has correctly captured the basic mechanics of the system, however, including the proper functional dependence of stress, frequency, etc. on design parameters, then the response sensitivities calculated may be of significantly higher accuracy.

Investigating the Energetic Ordering of Stable and Metastable TiO 2 Polymorphs Using DFT+ U and Hybrid Functionals

DOE PAGES

Curnan, Matthew T.; Kitchin, John R.

2015-08-12

Prediction of transition metal oxide BO 2 (B = Ti, V, etc.) polymorph energetic properties is critical to tunable material design and identifying thermodynamically accessible structures. Determining procedures capable of synthesizing particular polymorphs minimally requires prior knowledge of their relative energetic favorability. Information concerning TiO 2 polymorph relative energetic favorability has been ascertained from experimental research. In this study, the consistency of first-principles predictions and experimental results involving the relative energetic ordering of stable (rutile), metastable (anatase and brookite), and unstable (columbite) TiO 2 polymorphs is assessed via density functional theory (DFT). Considering the issues involving electron–electron interaction and chargemore » delocalization in TiO 2 calculations, relative energetic ordering predictions are evaluated over trends varying Ti Hubbard U 3d or exact exchange fraction parameter values. Energetic trends formed from varying U 3d predict experimentally consistent energetic ordering over U 3d intervals when using GGA-based functionals, regardless of pseudopotential selection. Given pertinent linear response calculated Hubbard U values, these results enable TiO 2 polymorph energetic ordering prediction. Here, the hybrid functional calculations involving rutile–anatase relative energetics, though demonstrating experimentally consistent energetic ordering over exact exchange fraction ranges, are not accompanied by predicted fractions, for a first-principles methodology capable of calculating exact exchange fractions precisely predicting TiO 2 polymorph energetic ordering is not available.« less

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

Range and stability of structural colors generated by Morpho-inspired color reflectors.

PubMed

Chung, Kyungjae; Shin, Jung H

2013-05-01

The range and stability of structural colors generated by Morpho-inspired color reflectors are investigated. We find that despite the internal randomness of such structures that gives rise to their Morpho-like angle-independent iridescence, their colors under ambient lighting condition can be predicted by simple transfer-matrix calculations of corresponding planar multilayer structures. By calculating the possible range of colors generated by multilayers of different structures and material combinations using such transfer-matrix methods, we find that low-refractive index multilayers with intrastructure absorption, such as the melanin-containing chitin/air multilayer structure from the Morpho butterflies, can provide not only the most pure structural colors with the largest color gamut, but also the highest stability of color against variations in multilayer structure.

Finite Element Based HWB Centerbody Structural Optimization and Weight Prediction

NASA Technical Reports Server (NTRS)

Gern, Frank H.

2012-01-01

This paper describes a scalable structural model suitable for Hybrid Wing Body (HWB) centerbody analysis and optimization. The geometry of the centerbody and primary wing structure is based on a Vehicle Sketch Pad (VSP) surface model of the aircraft and a FLOPS compatible parameterization of the centerbody. Structural analysis, optimization, and weight calculation are based on a Nastran finite element model of the primary HWB structural components, featuring centerbody, mid section, and outboard wing. Different centerbody designs like single bay or multi-bay options are analyzed and weight calculations are compared to current FLOPS results. For proper structural sizing and weight estimation, internal pressure and maneuver flight loads are applied. Results are presented for aerodynamic loads, deformations, and centerbody weight.

Image Texture Predicts Avian Density and Species Richness

PubMed Central

Wood, Eric M.; Pidgeon, Anna M.; Radeloff, Volker C.; Keuler, Nicholas S.

2013-01-01

For decades, ecologists have measured habitat attributes in the field to understand and predict patterns of animal distribution and abundance. However, the scale of inference possible from field measured data is typically limited because large-scale data collection is rarely feasible. This is problematic given that conservation and management typical require data that are fine grained yet broad in extent. Recent advances in remote sensing methodology offer alternative tools for efficiently characterizing wildlife habitat across broad areas. We explored the use of remotely sensed image texture, which is a surrogate for vegetation structure, calculated from both an air photo and from a Landsat TM satellite image, compared with field-measured vegetation structure, characterized by foliage-height diversity and horizontal vegetation structure, to predict avian density and species richness within grassland, savanna, and woodland habitats at Fort McCoy Military Installation, Wisconsin, USA. Image texture calculated from the air photo best predicted density of a grassland associated species, grasshopper sparrow (Ammodramus savannarum), within grassland habitat (R2 = 0.52, p-value <0.001), and avian species richness among habitats (R2 = 0.54, p-value <0.001). Density of field sparrow (Spizella pusilla), a savanna associated species, was not particularly well captured by either field-measured or remotely sensed vegetation structure variables, but was best predicted by air photo image texture (R2 = 0.13, p-value = 0.002). Density of ovenbird (Seiurus aurocapillus), a woodland associated species, was best predicted by pixel-level satellite data (mean NDVI, R2 = 0.54, p-value <0.001). Surprisingly and interestingly, remotely sensed vegetation structure measures (i.e., image texture) were often better predictors of avian density and species richness than field-measured vegetation structure, and thus show promise as a valuable tool for mapping habitat quality and characterizing biodiversity across broad areas. PMID:23675463

Electro-mechanical Properties of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Anantram, M. P.; Yang, Liu; Han, Jie; Liu, J. P.; Saubum Subhash (Technical Monitor)

1998-01-01

We present a simple picture to understand the bandgap variation of carbon nanotubes with small tensile and torsional strains, independent of chirality. Using this picture, we are able to predict a simple dependence of d(Bandoap)$/$d(strain) on the value of $(N_x-N_y)*mod 3$, for semiconducting tubes. We also predict a novel change in sign of d(Bandgap)$/$d(strain) as a function of tensile strain arising from a change in the value of $q$ corresponding to the minimum bandgap. These calculations are complemented by calculations of the change in bandgap using energy minimized structures, and some important differences are discussed. The calculations are based on the $i$ electron approximation.

Computed Energetics of Nucleotides in Spatial Ribozyme Structures: An Accurate Identification of Functional Regions from Structure

PubMed Central

Torshin, Ivan Y.

2004-01-01

Ribozymes are functionally diverse RNA molecules with intrinsic catalytic activity. Multiple structural and biochemical studies are required to establish which nucleotide bases are involved in the catalysis. The relative energetic properties of the nucleotide bases have been analyzed in a set of the known ribozyme structures. It was found that many of the known catalytic nucleotides can be identified using only the structure without any additional biochemical data. The results of the calculations compare well with the available biochemical data on RNA stability. Extensive in silico mutagenesis suggests that most of the nucleotides in ribozymes stabilize the RNA. The calculations show that relative contribution of the catalytic bases to RNA stability observably differs from contributions of the noncatalytic bases. Distinction between the concepts of “relative stability” and “mutational stability” is suggested. As results of prediction for several models of ribozymes appear to be in agreement with the published data on the potential active site regions, the method can potentially be used for prediction of functional nucleotides from nucleic sequence. PMID:15105962

Stabilizing the hexagonal close packed structure of hard spheres with polymers: Phase diagram, structure, and dynamics

NASA Astrophysics Data System (ADS)

Edison, John R.; Dasgupta, Tonnishtha; Dijkstra, Marjolein

2016-08-01

We study the phase behaviour of a binary mixture of colloidal hard spheres and freely jointed chains of beads using Monte Carlo simulations. Recently Panagiotopoulos and co-workers predicted [Nat. Commun. 5, 4472 (2014)] that the hexagonal close packed (HCP) structure of hard spheres can be stabilized in such a mixture due to the interplay between polymer and the void structure in the crystal phase. Their predictions were based on estimates of the free-energy penalty for adding a single hard polymer chain in the HCP and the competing face centered cubic (FCC) phase. Here we calculate the phase diagram using free-energy calculations of the full binary mixture and find a broad fluid-solid coexistence region and a metastable gas-liquid coexistence region. For the colloid-monomer size ratio considered in this work, we find that the HCP phase is only stable in a small window at relatively high polymer reservoir packing fractions, where the coexisting HCP phase is nearly close packed. Additionally we investigate the structure and dynamic behaviour of these mixtures.

Comparative Protein Structure Modeling Using MODELLER

PubMed Central

Webb, Benjamin; Sali, Andrej

2016-01-01

Comparative protein structure modeling predicts the three-dimensional structure of a given protein sequence (target) based primarily on its alignment to one or more proteins of known structure (templates). The prediction process consists of fold assignment, target-template alignment, model building, and model evaluation. This unit describes how to calculate comparative models using the program MODELLER and how to use the ModBase database of such models, and discusses all four steps of comparative modeling, frequently observed errors, and some applications. Modeling lactate dehydrogenase from Trichomonas vaginalis (TvLDH) is described as an example. The download and installation of the MODELLER software is also described. PMID:27322406

Quasiparticle semiconductor band structures including spin-orbit interactions.

PubMed

Malone, Brad D; Cohen, Marvin L

2013-03-13

We present first-principles calculations of the quasiparticle band structure of the group IV materials Si and Ge and the group III-V compound semiconductors AlP, AlAs, AlSb, InP, InAs, InSb, GaP, GaAs and GaSb. Calculations are performed using the plane wave pseudopotential method and the 'one-shot' GW method, i.e. G(0)W(0). Quasiparticle band structures, augmented with the effects of spin-orbit, are obtained via a Wannier interpolation of the obtained quasiparticle energies and calculated spin-orbit matrix. Our calculations explicitly treat the shallow semicore states of In and Ga, which are known to be important in the description of the electronic properties, as valence states in the quasiparticle calculation. Our calculated quasiparticle energies, combining both the ab initio evaluation of the electron self-energy and the vector part of the pseudopotential representing the spin-orbit effects, are in generally very good agreement with experimental values. These calculations illustrate the predictive power of the methodology as applied to group IV and III-V semiconductors.

Interlayer interactions in graphites.

PubMed

Chen, Xiaobin; Tian, Fuyang; Persson, Clas; Duan, Wenhui; Chen, Nan-xian

2013-11-06

Based on ab initio calculations of both the ABC- and AB-stacked graphites, interlayer potentials (i.e., graphene-graphene interaction) are obtained as a function of the interlayer spacing using a modified Möbius inversion method, and are used to calculate basic physical properties of graphite. Excellent consistency is observed between the calculated and experimental phonon dispersions of AB-stacked graphite, showing the validity of the interlayer potentials. More importantly, layer-related properties for nonideal structures (e.g., the exfoliation energy, cleave energy, stacking fault energy, surface energy, etc.) can be easily predicted from the interlayer potentials, which promise to be extremely efficient and helpful in studying van der Waals structures.

Recent advances in statistical energy analysis

NASA Technical Reports Server (NTRS)

Heron, K. H.

1992-01-01

Statistical Energy Analysis (SEA) has traditionally been developed using modal summation and averaging approach, and has led to the need for many restrictive SEA assumptions. The assumption of 'weak coupling' is particularly unacceptable when attempts are made to apply SEA to structural coupling. It is now believed that this assumption is more a function of the modal formulation rather than a necessary formulation of SEA. The present analysis ignores this restriction and describes a wave approach to the calculation of plate-plate coupling loss factors. Predictions based on this method are compared with results obtained from experiments using point excitation on one side of an irregular six-sided box structure. Conclusions show that the use and calculation of infinite transmission coefficients is the way forward for the development of a purely predictive SEA code.

Pole structure of the Λ ( 1405 ) in a recent QCD simulation

DOE PAGES

Molina, R.; Doring, M.

2016-09-27

The Λ(1405) baryon is difficult to detect in experiment, absent in many quark model calculations, and supposedly manifested through a two-pole structure. Its uncommon properties made it subject to numerous experimental and theoretical studies in recent years. Lattice-QCD eigenvalues for different quark masses were recently reported by the Adelaide group. We compare these eigenvalues to predictions of a model based on Unitary Chiral Perturbation Theory. The UχPT calculation predicts the quark mass dependence remarkably well. It also explains the overlap pattern with different meson-baryon components, mainly πΣ and K¯N, at different quark masses. As a result, more accurate lattice QCDmore » data are required to draw definite conclusions on the nature of the Λ(1405).« less

Progress in the prediction of pKa values in proteins

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

Alexov, Emil; Mehler, Ernest L.; Baker, Nathan A.

2011-12-15

The pKa-cooperative aims to provide a forum for experimental and theoretical researchers interested in protein pKa values and protein electrostatics in general. The first round of the pKa -cooperative, which challenged computational labs to carry out blind predictions against pKas experimentally determined in the laboratory of Bertrand Garcia-Moreno, was completed and results discussed at the Telluride meeting (July 6-10, 2009). This paper serves as an introduction to the reports submitted by the blind prediction participants that will be published in a special issue of PROTEINS: Structure, Function and Bioinformatics. Here we briefly outline existing approaches for pKa calculations, emphasizing methodsmore » that were used by the participants in calculating the blind pKa values in the first round of the cooperative. We then point out some of the difficulties encountered by the participating groups in making their blind predictions, and finally try to provide some insights for future developments aimed at improving the accuracy of pKa calculations.« less

Prediction of betavoltaic battery output parameters based on SEM measurements and Monte Carlo simulation.

PubMed

Yakimov, Eugene B

2016-06-01

An approach for a prediction of (63)Ni-based betavoltaic battery output parameters is described. It consists of multilayer Monte Carlo simulation to obtain the depth dependence of excess carrier generation rate inside the semiconductor converter, a determination of collection probability based on the electron beam induced current measurements, a calculation of current induced in the semiconductor converter by beta-radiation, and SEM measurements of output parameters using the calculated induced current value. Such approach allows to predict the betavoltaic battery parameters and optimize the converter design for any real semiconductor structure and any thickness and specific activity of beta-radiation source. Copyright © 2016 Elsevier Ltd. All rights reserved.

Predicting growth of graphene nanostructures using high-fidelity atomistic simulations

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

McCarty, Keven F.; Zhou, Xiaowang; Ward, Donald K.

2015-09-01

In this project we developed t he atomistic models needed to predict how graphene grows when carbon is deposited on metal and semiconductor surfaces. We first calculated energies of many carbon configurations using first principles electronic structure calculations and then used these energies to construct an empirical bond order potentials that enable s comprehensive molecular dynamics simulation of growth. We validated our approach by comparing our predictions to experiments of graphene growth on Ir, Cu and Ge. The robustness of ou r understanding of graphene growth will enable high quality graphene to be grown on novel substrates which will expandmore » the number of potential types of graphene electronic devices.« less

Prediction study of structural, elastic and electronic properties of FeMP (M = Ti, Zr, Hf) compounds

NASA Astrophysics Data System (ADS)

Tanto, A.; Chihi, T.; Ghebouli, M. A.; Reffas, M.; Fatmi, M.; Ghebouli, B.

2018-06-01

First principles calculations are applied in the study of FeMP (M = Ti, Zr, Hf) compounds. We investigate the structural, elastic, mechanical and electronic properties by combining first-principles calculations with the CASTEP approach. For ideal polycrystalline FeMP (M = Ti, Zr, Hf) the shear modulus, Young's modulus, Poisson's ratio, elastic anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature are also calculated from the single crystal elastic constants. The shear anisotropic factors and anisotropy are obtained from the single crystal elastic constants. The Debye temperature is calculated from the average elastic wave velocity obtained from shear and bulk modulus as well as the integration of elastic wave velocities in different directions of the single crystal.

Studying the properties of a predicted tetragonal silicon by first principles

NASA Astrophysics Data System (ADS)

Xue, Han-Yu; Zhang, Can; Pang, Dong-Dong; Huang, Xue-Qian; Lv, Zhen-Long; Duan, Man-Yi

2018-03-01

Silicon is a very important material in many technological fields. It also has a complicated phase diagram of scientific interest. Here we reported a new allotrope of silicon obtained from crystal structure prediction. We studied its electronic, vibrational, dielectric, elastic and hardness properties by first-principles calculations. The results indicate that it is an indirect narrow-band-gap semiconductor. It is dynamically stable with a doubly degenerate infrared-active mode at its Brillouin zone center. Born effective charges of the constituent element are very small, resulting in a negligible ionic dielectric contribution. Calculated elasticity-related quantities imply that it is mechanically stable but anisotropic. There exist slowly increasing stages in the stress-strain curves of this crystal, which make it difficult to estimate the hardness of the crystal by calculating its ideal strengths. Taking advantage of the hardness model proposed by Šimůnek, we obtained a value of 12.0 GPa as its hardness. This value is lower than that of the cubic diamond-structural Si by about 5.5%.

4-Methyl-1H-Indazole-5-Boronic acid: Crystal structure, vibrational spectra and DFT simulations

NASA Astrophysics Data System (ADS)

Dikmen, Gökhan

2017-12-01

Molecular structure, conformer forms, geometric parameters and vibrational assignments and properties of 4-Methyl-1H-Indazole-5-Boronic Acid (4M1HI5BA) were theoretically and experimentally studied using Raman, FT-IR, XRD spectroscopic methods and quantum chemical calculations. Raman and FT-IR spectra were examined range from 4000 to 400 cm-1. Moreover, single crystals of 4M1HI5BA were prepared in order to use in XRD experiments. Vibrational assignments were carried out using total energy distribution (TED) values. Furthermore, HOMO and LUMO were calculated for 4M1HI5BA. Four different conformations of 4M1HI5BA were calculated in only gas phase. The theoretical and experimental results show that in order to predict vibrational wavenumbers B3LYP/6-311++G(d,p) may provide acceptable results and the most stable conformer of 4M1HI5BA is predicted to be envelope conformer.

BAC-MP4 predictions of thermochemistry for the gas-phase tin compounds in the Sn-H-C-Cl system.

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

Allendorf, Mark D.; Melius, Carl F.

2004-09-01

In this work, the BAC-MP4 method is extended for the first time to compounds in the fourth row of the periodic table, resulting in a self-consistent set of thermochemical data for 56 tin-containing molecules in the Sn-H-C-Cl system. The BAC-MP4 method combines ab initio electronic structure calculations with empirical corrections to obtain accurate heats of formation. To obtain electronic energies for tin-containing species, the standard 6-31G(d,p) basis set used in BAC-MP4 calculations is augmented with a relativistic effective core potential to describe the electronic structure of the tin atom. Both stable compounds and radical species are included in this study.more » Trends within homologous series and calculated bond dissociation energies are consistent with previous BAC-MP4 predictions for group 14 compounds and the limited data available from the literature, indicating that the method is performing well for these compounds.« less

A high-throughput approach to profile RNA structure.

PubMed

Delli Ponti, Riccardo; Marti, Stefanie; Armaos, Alexandros; Tartaglia, Gian Gaetano

2017-03-17

Here we introduce the Computational Recognition of Secondary Structure (CROSS) method to calculate the structural profile of an RNA sequence (single- or double-stranded state) at single-nucleotide resolution and without sequence length restrictions. We trained CROSS using data from high-throughput experiments such as Selective 2΄-Hydroxyl Acylation analyzed by Primer Extension (SHAPE; Mouse and HIV transcriptomes) and Parallel Analysis of RNA Structure (PARS; Human and Yeast transcriptomes) as well as high-quality NMR/X-ray structures (PDB database). The algorithm uses primary structure information alone to predict experimental structural profiles with >80% accuracy, showing high performances on large RNAs such as Xist (17 900 nucleotides; Area Under the ROC Curve AUC of 0.75 on dimethyl sulfate (DMS) experiments). We integrated CROSS in thermodynamics-based methods to predict secondary structure and observed an increase in their predictive power by up to 30%. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Structural, electronic, and thermodynamic properties of curium dioxide: Density functional theory calculations

NASA Astrophysics Data System (ADS)

Hou, Ling; Li, Wei-Dong; Wang, Fangwei; Eriksson, Olle; Wang, Bao-Tian

2017-12-01

We present a systematic investigation of the structural, magnetic, electronic, mechanical, and thermodynamic properties of CmO2 with the local density approximation (LDA)+U and the generalized gradient approximation (GGA)+U approaches. The strong Coulomb repulsion and the spin-orbit coupling (SOC) effects on the lattice structures, electronic density of states, and band gaps are carefully studied, and compared with other A O2 (A =U , Np, Pu, and Am). The ferromagnetic configuration with half-metallic character is predicted to be energetically stable while a charge-transfer semiconductor is predicted for the antiferromagnetic configuration. The elastic constants and phonon spectra show that the fluorite structure is mechanically and dynamically stable. Based on the first-principles phonon density of states, the lattice vibrational energy is calculated using the quasiharmonic approximation. Then, the Gibbs free energy, thermal expansion coefficient, specific heat, and entropy are obtained and compared with experimental data. The mode Grüneisen parameters are presented to analyze the anharmonic properties. The Slack relation is applied to obtain the lattice thermal conductivity in temperature range of 300-1600 K. The phonon group velocities are also calculated to investigate the heat transfer. For all these properties, if available, we compare the results of CmO2 with other A O2 .

Spectral and structural studies of the anti-cancer drug Flutamide by density functional theoretical method.

PubMed

Mariappan, G; Sundaraganesan, N

2014-01-03

A comprehensive screening of the more recent DFT theoretical approach to structural analysis is presented in this section of theoretical structural analysis. The chemical name of 2-methyl-N-[4-nitro-3-(trifluoromethyl)phenyl]-propanamide is usually called as Flutamide (In the present study it is abbreviated as FLT) and is an important and efficacious drug in the treatment of anti-cancer resistant. The molecular geometry, vibrational spectra, electronic and NMR spectral interpretation of Flutamide have been studied with the aid of density functional theory method (DFT). The vibrational assignments of the normal modes were performed on the basis of the PED calculations using the VEDA 4 program. Comparison of computational results with X-ray diffraction results of Flutamide allowed the evaluation of structure predictions and confirmed B3LYP/6-31G(d,p) as accurate for structure determination. Application of scaling factors for IR and Raman frequency predictions showed good agreement with experimental values. This is supported the assignment of the major contributors of the vibration modes of the title compound. Stability of the molecule arising from hyperconjugative interactions leading to its bioactivity, charge delocalization have been analyzed using natural bond orbital (NBO) analysis. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The comparison of measured FTIR, FT-Raman, and UV-Visible data to calculated values allowed assignment of major spectral features of the title molecule. Besides, Frontier molecular orbital analyze was also investigated using theoretical calculations. Copyright © 2013 Elsevier B.V. All rights reserved.

Vibrational spectroscopic and structural investigations on fullerene: A DFT approach

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

Christy, P. Anto; Premkumar, S.; Asath, R. Mohamed

2016-05-06

The molecular structure of fullerene (C{sub 60}) molecule was optimized by the DFT/B3LYP method with 6-31G and 6-31G(d,p) basis sets using Gaussian 09 program. The vibrational frequencies were calculated for the optimized molecular structure of the molecule. The calculated vibrational frequencies confirm that the molecular structure of the molecule was located at the minimum energy potential energy surface. The calculated vibrational frequencies were assigned on the basis of functional group analysis and also confirmed using the GaussView 05 software. The frontier molecular orbitals analysis was carried out. The FMOs related molecular properties were predicted. The higher ionization potential, higher electronmore » affinity, higher softness, lower band gap energy and lower hardness values were obtained, which confirm that the fullerene molecule has a higher molecular reactivity. The Mulliken atomic charge distribution of the molecule was also calculated. Hence, these results play an important role due to its potential applications as drug delivery devices.« less

Prediction on the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase based on gene expression programming.

PubMed

Li, Yuqin; You, Guirong; Jia, Baoxiu; Si, Hongzong; Yao, Xiaojun

2014-01-01

Quantitative structure-activity relationships (QSAR) were developed to predict the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase via heuristic method (HM) and gene expression programming (GEP). The descriptors of 33 pyrrolidine derivatives were calculated by the software CODESSA, which can calculate quantum chemical, topological, geometrical, constitutional, and electrostatic descriptors. HM was also used for the preselection of 5 appropriate molecular descriptors. Linear and nonlinear QSAR models were developed based on the HM and GEP separately and two prediction models lead to a good correlation coefficient (R (2)) of 0.93 and 0.94. The two QSAR models are useful in predicting the inhibition ratio of pyrrolidine derivatives on matrix metalloproteinase during the discovery of new anticancer drugs and providing theory information for studying the new drugs.

Assessment and Validation of Machine Learning Methods for Predicting Molecular Atomization Energies.

PubMed

Hansen, Katja; Montavon, Grégoire; Biegler, Franziska; Fazli, Siamac; Rupp, Matthias; Scheffler, Matthias; von Lilienfeld, O Anatole; Tkatchenko, Alexandre; Müller, Klaus-Robert

2013-08-13

The accurate and reliable prediction of properties of molecules typically requires computationally intensive quantum-chemical calculations. Recently, machine learning techniques applied to ab initio calculations have been proposed as an efficient approach for describing the energies of molecules in their given ground-state structure throughout chemical compound space (Rupp et al. Phys. Rev. Lett. 2012, 108, 058301). In this paper we outline a number of established machine learning techniques and investigate the influence of the molecular representation on the methods performance. The best methods achieve prediction errors of 3 kcal/mol for the atomization energies of a wide variety of molecules. Rationales for this performance improvement are given together with pitfalls and challenges when applying machine learning approaches to the prediction of quantum-mechanical observables.

Structure-Based Predictions of Activity Cliffs

PubMed Central

Husby, Jarmila; Bottegoni, Giovanni; Kufareva, Irina; Abagyan, Ruben; Cavalli, Andrea

2015-01-01

In drug discovery, it is generally accepted that neighboring molecules in a given descriptors' space display similar activities. However, even in regions that provide strong predictability, structurally similar molecules can occasionally display large differences in potency. In QSAR jargon, these discontinuities in the activity landscape are known as ‘activity cliffs’. In this study, we assessed the reliability of ligand docking and virtual ligand screening schemes in predicting activity cliffs. We performed our calculations on a diverse, independently collected database of cliff-forming co-crystals. Starting from ideal situations, which allowed us to establish our baseline, we progressively moved toward simulating more realistic scenarios. Ensemble- and template-docking achieved a significant level of accuracy, suggesting that, despite the well-known limitations of empirical scoring schemes, activity cliffs can be accurately predicted by advanced structure-based methods. PMID:25918827

Simple extrapolation method to predict the electronic structure of conjugated polymers from calculations on oligomers

DOE PAGES

Larsen, Ross E.

2016-04-12

In this study, we introduce two simple tight-binding models, which we call fragment frontier orbital extrapolations (FFOE), to extrapolate important electronic properties to the polymer limit using electronic structure calculations on only a few small oligomers. In particular, we demonstrate by comparison to explicit density functional theory calculations that for long oligomers the energies of the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO), and of the first electronic excited state are accurately described as a function of number of repeat units by a simple effective Hamiltonian parameterized from electronic structure calculations on monomers, dimers and, optionally,more » tetramers. For the alternating copolymer materials that currently comprise some of the most efficient polymer organic photovoltaic devices one can use these simple but rigorous models to extrapolate computed properties to the polymer limit based on calculations on a small number of low-molecular-weight oligomers.« less

Predicting gaseous reaction rates of short chain chlorinated paraffins with ·OH: overcoming the difficulty in experimental determination.

PubMed

Li, Chao; Xie, Hong-Bin; Chen, Jingwen; Yang, Xianhai; Zhang, Yifei; Qiao, Xianliang

2014-12-02

Short chain chlorinated paraffins (SCCPs) are under evaluation for inclusion in the Stockholm Convention on persistent organic pollutants. However, information on their reaction rate constants with gaseous ·OH (kOH) is unavailable, limiting the evaluation of their persistence in the atmosphere. Experimental determination of kOH is confined by the unavailability of authentic chemical standards for some SCCP congeners. In this study, we evaluated and selected density functional theory (DFT) methods to predict kOH of SCCPs, by comparing the experimental kOH values of six polychlorinated alkanes (PCAs) with those calculated by the different theoretical methods. We found that the M06-2X/6-311+G(3df,2pd)//B3LYP/6-311 +G(d,p) method is time-effective and can be used to predict kOH of PCAs. Moreover, based on the calculated kOH of nine SCCPs and available experimental kOH values of 22 PCAs with low carbon chain, a quantitative structure-activity relationship (QSAR) model was developed. The molecular structural characteristics determining the ·OH reaction rate were discussed. logkOH was found to negatively correlate with the percentage of chlorine substitutions (Cl%). The DFT calculation method and the QSAR model are important alternatives to the conventional experimental determination of kOH for SCCPs, and are prospective in predicting their persistence in the atmosphere.

Intramolecular BSSE and dispersion affect the structure of a dipeptide conformer

NASA Astrophysics Data System (ADS)

Hameed, Rabia; Khan, Afsar; van Mourik, Tanja

2018-05-01

B3LYP and MP2 calculations with the commonly-used 6-31+G(d) basis set predict qualitatively different structures for the Tyr-Gly conformer book1, which is the most stable conformer identified in a previous study. The structures differ mainly in the ψtyr Ramachandran angle (138° in the B3LYP structure and 120° in the MP2 structure). The causes for the discrepant structures are attributed to missing dispersion in the B3LYP calculations and large intramolecular BSSE in the MP2 calculations. The correct ψtyr value is estimated to be 130°. The MP2/6-31+G(d) profile identified an additional conformer, not present on the B3LYP surface, with a ψtyr value of 96° and a more folded structure. This minimum is, however, likely an artefact of large intramolecular BSSE values. We recommend the use of basis sets of at least quadruple-zeta quality in density functional theory (DFT), DFTaugmented with an empirical dispersion term (DFT-D) and second-order Møller-Plesset perturbation theory (MP2 ) calculations in cases where intramolecular BSSE is expected to be large.

Progressive Failure Analysis Methodology for Laminated Composite Structures

NASA Technical Reports Server (NTRS)

Sleight, David W.

1999-01-01

A progressive failure analysis method has been developed for predicting the failure of laminated composite structures under geometrically nonlinear deformations. The progressive failure analysis uses C(exp 1) shell elements based on classical lamination theory to calculate the in-plane stresses. Several failure criteria, including the maximum strain criterion, Hashin's criterion, and Christensen's criterion, are used to predict the failure mechanisms and several options are available to degrade the material properties after failures. The progressive failure analysis method is implemented in the COMET finite element analysis code and can predict the damage and response of laminated composite structures from initial loading to final failure. The different failure criteria and material degradation methods are compared and assessed by performing analyses of several laminated composite structures. Results from the progressive failure method indicate good correlation with the existing test data except in structural applications where interlaminar stresses are important which may cause failure mechanisms such as debonding or delaminations.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

Atomic-scale properties of Ni-based FCC ternary, and quaternary alloys

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

Tamm, Artur; Aabloo, Alvo; Klintenberg, Mattias

2015-08-26

The aim of our study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. The salient features for the ternary alloy are a negative SRO parameter between Ni Cr and a positive between Cr Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni Cr and Ni Fe pairs and positive formore » Cr Cr and Fe Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. Finally, the predicted SRO has an impact on point-defect energetics, electron phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys.« less

BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP.

PubMed

Schneider, Markus; Rosam, Mathias; Glaser, Manuel; Patronov, Atanas; Shah, Harpreet; Back, Katrin Christiane; Daake, Marina Angelika; Buchner, Johannes; Antes, Iris

2016-10-01

Substrate binding to Hsp70 chaperones is involved in many biological processes, and the identification of potential substrates is important for a comprehensive understanding of these events. We present a multi-scale pipeline for an accurate, yet efficient prediction of peptides binding to the Hsp70 chaperone BiP by combining sequence-based prediction with molecular docking and MMPBSA calculations. First, we measured the binding of 15mer peptides from known substrate proteins of BiP by peptide array (PA) experiments and performed an accuracy assessment of the PA data by fluorescence anisotropy studies. Several sequence-based prediction models were fitted using this and other peptide binding data. A structure-based position-specific scoring matrix (SB-PSSM) derived solely from structural modeling data forms the core of all models. The matrix elements are based on a combination of binding energy estimations, molecular dynamics simulations, and analysis of the BiP binding site, which led to new insights into the peptide binding specificities of the chaperone. Using this SB-PSSM, peptide binders could be predicted with high selectivity even without training of the model on experimental data. Additional training further increased the prediction accuracies. Subsequent molecular docking (DynaDock) and MMGBSA/MMPBSA-based binding affinity estimations for predicted binders allowed the identification of the correct binding mode of the peptides as well as the calculation of nearly quantitative binding affinities. The general concept behind the developed multi-scale pipeline can readily be applied to other protein-peptide complexes with linearly bound peptides, for which sufficient experimental binding data for the training of classical sequence-based prediction models is not available. Proteins 2016; 84:1390-1407. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Optimizing finite element predictions of local subchondral bone structural stiffness using neural network-derived density-modulus relationships for proximal tibial subchondral cortical and trabecular bone.

PubMed

Nazemi, S Majid; Amini, Morteza; Kontulainen, Saija A; Milner, Jaques S; Holdsworth, David W; Masri, Bassam A; Wilson, David R; Johnston, James D

2017-01-01

Quantitative computed tomography based subject-specific finite element modeling has potential to clarify the role of subchondral bone alterations in knee osteoarthritis initiation, progression, and pain. However, it is unclear what density-modulus equation(s) should be applied with subchondral cortical and subchondral trabecular bone when constructing finite element models of the tibia. Using a novel approach applying neural networks, optimization, and back-calculation against in situ experimental testing results, the objective of this study was to identify subchondral-specific equations that optimized finite element predictions of local structural stiffness at the proximal tibial subchondral surface. Thirteen proximal tibial compartments were imaged via quantitative computed tomography. Imaged bone mineral density was converted to elastic moduli using multiple density-modulus equations (93 total variations) then mapped to corresponding finite element models. For each variation, root mean squared error was calculated between finite element prediction and in situ measured stiffness at 47 indentation sites. Resulting errors were used to train an artificial neural network, which provided an unlimited number of model variations, with corresponding error, for predicting stiffness at the subchondral bone surface. Nelder-Mead optimization was used to identify optimum density-modulus equations for predicting stiffness. Finite element modeling predicted 81% of experimental stiffness variance (with 10.5% error) using optimized equations for subchondral cortical and trabecular bone differentiated with a 0.5g/cm 3 density. In comparison with published density-modulus relationships, optimized equations offered improved predictions of local subchondral structural stiffness. Further research is needed with anisotropy inclusion, a smaller voxel size and de-blurring algorithms to improve predictions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structure of supersonic jet flow and its radiated sound

NASA Technical Reports Server (NTRS)

Mankbadi, Reda R.; Hayer, M. Ehtesham; Povinelli, Louis A.

1994-01-01

The present paper explores the use of large-eddy simulations as a tool for predicting noise from first principles. A high-order numerical scheme is used to perform large-eddy simulations of a supersonic jet flow with emphasis on capturing the time-dependent flow structure representating the sound source. The wavelike nature of this structure under random inflow disturbances is demonstrated. This wavelike structure is then enhanced by taking the inflow disturbances to be purely harmonic. Application of Lighthill's theory to calculate the far-field noise, with the sound source obtained from the calculated time-dependent near field, is demonstrated. Alternative approaches to coupling the near-field sound source to the far-field sound are discussed.

Lone pair effect, structural distortions, and potential for superconductivity in Tl perovskites.

PubMed

Schoop, Leslie M; Müchler, Lukas; Felser, Claudia; Cava, R J

2013-05-06

Drawing the analogy to BaBiO3, we investigate via ab initio electronic structure calculations potential new superconductors of the type ATlX3 with A = Rb and Cs and X = F, Cl, and Br, with a particular emphasis on RbTlCl3. On the basis of chemical reasoning, supported by the calculations, we show that Tl-based perovskites have structural and charge instabilities driven by the lone pair effect, similar to the case of BaBiO3, effectively becoming A2Tl(+)Tl(3+)X6. We find that upon hole doping of RbTlCl3, structures without Tl(+) and Tl(3+) charge disproportionation become more stable, although the ideal cubic perovskite, often viewed as the best host for superconductivity, should not be the most stable phase in the system. The known superconductor (Sr,K)BiO3 and hole doped RbTlCl3, predicted to be most stable in the same tetragonal structure, display highly analogous calculated electronic band structures.

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

A Novel Prediction Method about Single Components of Analog Circuits Based on Complex Field Modeling

PubMed Central

Tian, Shulin; Yang, Chenglin

2014-01-01

Few researches pay attention to prediction about analog circuits. The few methods lack the correlation with circuit analysis during extracting and calculating features so that FI (fault indicator) calculation often lack rationality, thus affecting prognostic performance. To solve the above problem, this paper proposes a novel prediction method about single components of analog circuits based on complex field modeling. Aiming at the feature that faults of single components hold the largest number in analog circuits, the method starts with circuit structure, analyzes transfer function of circuits, and implements complex field modeling. Then, by an established parameter scanning model related to complex field, it analyzes the relationship between parameter variation and degeneration of single components in the model in order to obtain a more reasonable FI feature set via calculation. According to the obtained FI feature set, it establishes a novel model about degeneration trend of analog circuits' single components. At last, it uses particle filter (PF) to update parameters for the model and predicts remaining useful performance (RUP) of analog circuits' single components. Since calculation about the FI feature set is more reasonable, accuracy of prediction is improved to some extent. Finally, the foregoing conclusions are verified by experiments. PMID:25147853

Calculations vs. measurements of remnant dose rates for SNS spent structures

NASA Astrophysics Data System (ADS)

Popova, I. I.; Gallmeier, F. X.; Trotter, S.; Dayton, M.

2018-06-01

Residual dose rate measurements were conducted on target vessel #13 and proton beam window #5 after extraction from their service locations. These measurements were used to verify calculation methods of radionuclide inventory assessment that are typically performed for nuclear waste characterization and transportation of these structures. Neutronics analyses for predicting residual dose rates were carried out using the transport code MCNPX and the transmutation code CINDER90. For transport analyses complex and rigorous geometry model of the structures and their surrounding are applied. The neutronics analyses were carried out using Bertini and CEM high energy physics models for simulating particles interaction. Obtained preliminary calculational results were analysed and compared to the measured dose rates and overall are showing good agreement with in 40% in average.

Calculations vs. measurements of remnant dose rates for SNS spent structures

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

Popova, Irina I.; Gallmeier, Franz X.; Trotter, Steven M.

Residual dose rate measurements were conducted on target vessel #13 and proton beam window #5 after extraction from their service locations. These measurements were used to verify calculation methods of radionuclide inventory assessment that are typically performed for nuclear waste characterization and transportation of these structures. Neutronics analyses for predicting residual dose rates were carried out using the transport code MCNPX and the transmutation code CINDER90. For transport analyses complex and rigorous geometry model of the structures and their surrounding are applied. The neutronics analyses were carried out using Bertini and CEM high energy physics models for simulating particles interaction.more » Obtained preliminary calculational results were analysed and compared to the measured dose rates and overall are showing good agreement with in 40% in average.« less

Computational flow field in energy efficient engine (EEE)

NASA Astrophysics Data System (ADS)

Miki, Kenji; Moder, Jeff; Liou, Meng-Sing

2016-11-01

In this paper, preliminary results for the recently-updated Open National Combustor Code (Open NCC) as applied to the EEE are presented. The comparison between two different numerical schemes, the standard Jameson-Schmidt-Turkel (JST) scheme and the advection upstream splitting method (AUSM), is performed for the cold flow and the reacting flow calculations using the RANS. In the cold flow calculation, the AUSM scheme predicts a much stronger reverse flow in the central recirculation zone. In the reacting flow calculation, we test two cases: gaseous fuel injection and liquid spray injection. In the gaseous fuel injection case, the overall flame structures of the two schemes are similar to one another, in the sense that the flame is attached to the main nozzle, but is detached from the pilot nozzle. However, in the exit temperature profile, the AUSM scheme shows a more uniform profile than that of the JST scheme, which is close to the experimental data. In the liquid spray injection case, we expect different flame structures in this scenario. We will give a brief discussion on how two numerical schemes predict the flame structures inside the Eusing different ways to introduce the fuel injection. Supported by NASA's Transformational Tools and Technologies project.

Computational Flow Field in Energy Efficient Engine (EEE)

NASA Technical Reports Server (NTRS)

Miki, Kenji; Moder, Jeff; Liou, Meng-Sing

2016-01-01

In this paper, preliminary results for the recently-updated Open National Combustion Code (Open NCC) as applied to the EEE are presented. The comparison between two different numerical schemes, the standard Jameson-Schmidt-Turkel (JST) scheme and the advection upstream splitting method (AUSM), is performed for the cold flow and the reacting flow calculations using the RANS. In the cold flow calculation, the AUSM scheme predicts a much stronger reverse flow in the central recirculation zone. In the reacting flow calculation, we test two cases: gaseous fuel injection and liquid spray injection. In the gaseous fuel injection case, the overall flame structures of the two schemes are similar to one another, in the sense that the flame is attached to the main nozzle, but is detached from the pilot nozzle. However, in the exit temperature profile, the AUSM scheme shows a more uniform profile than that of the JST scheme, which is close to the experimental data. In the liquid spray injection case, we expect different flame structures in this scenario. We will give a brief discussion on how two numerical schemes predict the flame structures inside the EEE using different ways to introduce the fuel injection.

Modeling Fission Product Sorption in Graphite Structures

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

Szlufarska, Izabela; Morgan, Dane; Allen, Todd

2013-04-08

The goal of this project is to determine changes in adsorption and desorption of fission products to/from nuclear-grade graphite in response to a changing chemical environment. First, the project team will employ principle calculations and thermodynamic analysis to predict stability of fission products on graphite in the presence of structural defects commonly observed in very high- temperature reactor (VHTR) graphites. Desorption rates will be determined as a function of partial pressure of oxygen and iodine, relative humidity, and temperature. They will then carry out experimental characterization to determine the statistical distribution of structural features. This structural information will yield distributionsmore » of binding sites to be used as an input for a sorption model. Sorption isotherms calculated under this project will contribute to understanding of the physical bases of the source terms that are used in higher-level codes that model fission product transport and retention in graphite. The project will include the following tasks: Perform structural characterization of the VHTR graphite to determine crystallographic phases, defect structures and their distribution, volume fraction of coke, and amount of sp2 versus sp3 bonding. This information will be used as guidance for ab initio modeling and as input for sorptivity models; Perform ab initio calculations of binding energies to determine stability of fission products on the different sorption sites present in nuclear graphite microstructures. The project will use density functional theory (DFT) methods to calculate binding energies in vacuum and in oxidizing environments. The team will also calculate stability of iodine complexes with fission products on graphite sorption sites; Model graphite sorption isotherms to quantify concentration of fission products in graphite. The binding energies will be combined with a Langmuir isotherm statistical model to predict the sorbed concentration of fission products on each type of graphite site. The model will include multiple simultaneous adsorbing species, which will allow for competitive adsorption effects between different fission product species and O and OH (for modeling accident conditions).« less

Predicting the Highly Nonlinear Mechanical Properties of Polymeric Materials

NASA Astrophysics Data System (ADS)

Porter, David

2009-06-01

Over the past few years, we have developed models that calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular and morphological structure. A review of these models is presented here, with emphasis on combining the fundamental aspects of molecular physics that dictate these properties and the pragmatic need to make realistic predictions for our customers; the designer of new materials and the engineers who use these materials. The models calculate the highly nonlinear mechanical properties of polymers as a function of temperature, strain and strain rate from their molecular structure. The model is based upon the premise that mechanical properties are a direct consequence of energy stored and energy dissipated during deformation of a material. This premise is transformed into a consistent set of structure-property relations for the equation of state, EoS, and the engineering constitutive relations in a polymer by quantifying energy storage and loss at the molecular level of interactions between characteristic groups of atoms in a polymer. These relations are derived from a simple volumetric mean field Lennard-Jones potential function for the potential energy of intermolecular interactions in a polymer. First, properties such as temperature-volume relations and glass transition temperature are calculated directly from the potential function. Then, the `shock' EoS is derived simply by differentiating the potential function with respect to volume, assuming that the molecules cannot relax in the time scales of the deformation. The energy components are then used to predict the dynamic mechanical spectrum of a polymer in terms of temperature and rate. This can be transformed directly into the highly nonlinear stress-strain relations through yield. The constitutive relations are formulated as a set of analytical equations that predict properties directly in terms of a small set of structural parameters that can be calculated directly and independently from the chemical composition and morphology of a polymer. A number of examples are given to illustrate the model and also to show that the method can be applied, with appropriate modifications, to other materials.

Band structure and thermoelectric properties of half-Heusler semiconductors from many-body perturbation theory

NASA Astrophysics Data System (ADS)

Zahedifar, Maedeh; Kratzer, Peter

2018-01-01

Various ab initio approaches to the band structure of A NiSn and A CoSb half-Heusler compounds (A = Ti, Zr, Hf) are compared and their consequences for the prediction of thermoelectric properties are explored. Density functional theory with the generalized-gradient approximation (GGA), as well as the hybrid density functional HSE06 and ab initio many-body perturbation theory in the form of the G W0 approach, are employed. The G W0 calculations confirm the trend of a smaller band gap (0.75 to 1.05 eV) in A NiSn compared to the A CoSb compounds (1.13 to 1.44 eV) already expected from the GGA calculations. While in A NiSn materials the G W0 band gap is 20% to 50% larger than in HSE06, the fundamental gap of A CoSb materials is smaller in G W0 compared to HSE06. This is because G W0 , similar to PBE, locates the valence band maximum at the L point of the Brillouin zone, whereas it is at the Γ point in the HSE06 calculations. The differences are attributed to the observation that the relative positions of the d levels of the transition metal atoms vary among the different methods. Using the calculated band structures and scattering rates taking into account the band effective masses at the extrema, the Seebeck coefficients, thermoelectric power factors, and figures of merit Z T are predicted for all six half-Heusler compounds. Comparable performance is predicted for the n -type A NiSn materials, whereas clear differences are found for the p -type A CoSb materials. Using the most reliable G W0 electronic structure, ZrCoSb is predicted to be the most efficient material with a power factor of up to 0.07 W/(K2 m) at a temperature of 600 K. We find strong variations among the different ab initio methods not only in the prediction of the maximum power factor and Z T value of a given material, but also in comparing different materials to each other, in particular in the p -type thermoelectric materials. Thus we conclude that the most elaborate, but also most costly G W0 method is required to perform a reliable computational search for the optimum material.

Applications of Displacement Transfer Functions to Deformed Shape Predictions of the GIII Swept-Wing Structure

NASA Technical Reports Server (NTRS)

Lung, Shun-Fat; Ko, William L.

2016-01-01

The displacement transfer functions (DTFs) were applied to the GIII swept wing for the deformed shape prediction. The calculated deformed shapes are very close to the correlated finite element results as well as the measured data. The convergence study showed that using 17 strain stations, the wing-tip displacement prediction error was 1.6 percent, and that there is no need to use a large number of strain stations for G-III wing shape predictions.

Multi-fidelity machine learning models for accurate bandgap predictions of solids

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

Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

Multi-fidelity machine learning models for accurate bandgap predictions of solids

DOE PAGES

Pilania, Ghanshyam; Gubernatis, James E.; Lookman, Turab

2016-12-28

Here, we present a multi-fidelity co-kriging statistical learning framework that combines variable-fidelity quantum mechanical calculations of bandgaps to generate a machine-learned model that enables low-cost accurate predictions of the bandgaps at the highest fidelity level. Additionally, the adopted Gaussian process regression formulation allows us to predict the underlying uncertainties as a measure of our confidence in the predictions. In using a set of 600 elpasolite compounds as an example dataset and using semi-local and hybrid exchange correlation functionals within density functional theory as two levels of fidelities, we demonstrate the excellent learning performance of the method against actual high fidelitymore » quantum mechanical calculations of the bandgaps. The presented statistical learning method is not restricted to bandgaps or electronic structure methods and extends the utility of high throughput property predictions in a significant way.« less

Attenuation of radiation from distributed gamma sources as a function of wall thickness of a concrete blockhouse

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

Schmoke, M. A.; Rexroad, R. E.; Tiller, H. J.

1963-06-15

The experiment described constitutes part of the shielding program conducted by Army Nuclear Defense Laboratory and was designed to experimentally verify theoretical calculations used to predict the amount of radiation protection afforded by above-ground structures in a fallout radiation field. This method requires the knowledge of some physical parameters of a structure such as mass thickness of the walls and the geometric orientation of the detectors within the structure. From this information, a reduction factor for any given structure may be calculated. This Laboratory's experimental program was initially begun by measuring the attenuation of a simple structure with no complicatingmore » internal or external geometries and will proceed to more complex structures with basements, interior partitions, and upper floors. (auth)« less

Theoretical Prediction of Magnetism in C-doped TlBr

NASA Astrophysics Data System (ADS)

Zhou, Yuzhi; Haller, E. E.; Chrzan, D. C.

2014-05-01

We predict that C, N, and O dopants in TlBr can display large, localized magnetic moments. Density functional theory based electronic structure calculations show that the moments arise from partial filling of the crystal-field-split localized p states of the dopant atoms. A simple model is introduced to explain the magnitude of the moments.

Ab initio predictions of structural and elastic properties of struvite: contribution to urinary stone research.

PubMed

Piechota, Jacek; Prywer, Jolanta; Torzewska, Agnieszka

2012-01-01

In the present work, we carried out density functional calculations of struvite--the main component of the so-called infectious urinary stones--to study its structural and elastic properties. Using a local density approximation and a generalised gradient approximation, we calculated the equilibrium structural parameters and elastic constants C(ijkl). At present, there is no experimental data for these elastic constants C (ijkl) for comparison. Besides the elastic constants, we also present the calculated macroscopic mechanical parameters, namely the bulk modulus (K), the shear modulus (G) and Young's modulus (E). The values of these moduli are found to be in good agreement with available experimental data. Our results imply that the mechanical stability of struvite is limited by the shear modulus, G. The study also explores the energy-band structure to understand the obtained values of the elastic constants.

Structures, molecular orbitals and UV-vis spectra investigations on methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate: a computational study.

PubMed

Wang, Tsang-Hsiu; Chu, Hsing-Yu; Wang, I-Teng

2014-10-15

The methyl 1-benzyl-1H-1,2,3-triazole-4-carboxylate (C11H11N3O2) has been studied by theoretically methods. The structure of this compound is optimized by density functional theory (DFT), the second-order Møller-Plesset perturbation theory (MP2) and G3 theory (G3(MP2)) levels. Our calculation results are in very good agreement with experimental values. Compared to a perfect pentagonal structure, the geometrical structures of C11H11N3O2 show a little distortion of 1,2,3-triazole ring due to the highly electronegativity of substitution groups. In addition, dipole moment and frontier molecular orbitals (FMOs) of the C11H11N3O2 are calculated as well. Because of solvent effect, the HOMO-LUMO energy gap in methanol is predicted to be smaller than in gas phase by 0.367eV. The simulated UV-vis spectra are investigated by time-dependent density functional theory (TD-DFT), and two obviously absorption features have been predicted. These two absorption features are located between 170nm and 210nm, which is in ultraviolet C range. Moreover, the UV absorption features in methanol are predicted to be more intense than in gas phase; besides, the red shift is predicted in methanol as well. Copyright © 2014 Elsevier B.V. All rights reserved.

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

PubMed Central

2011-01-01

Background The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. Results We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. Conclusions Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone. PMID:21219630

Topological ring currents in the "empty" ring of benzo-annelated perylenes.

PubMed

Dickens, Timothy K; Mallion, Roger B

2011-01-27

Cyclic conjugation in benzo-annelated perylenes is examined by means of the topological π-electron ring currents calculated for each of their constituent rings, in a study that is an exact analogy of a recent investigation by Gutman et al. based on energy-effect values for the corresponding rings in each of these structures. "Classical" approaches, such as Kekulé structures, Clar "sextet" formulas, and circuits of conjugation, predict that the central ring in perylene is "empty" and thus contributes negligibly to cyclic conjugation. However, conclusions from the present calculations of topological ring currents agree remarkably with those arising from the earlier study involving energy-effect values in that, contrary to what would be predicted from the classical approaches, rings annelated in an angular fashion relative to the central ring of these perylene structures materially increase the extent of that ring's involvement in cyclic conjugation. It is suggested that such close quantitative agreement between the predictions of these two superficially very different indices (energy effect and topological ring current) might be due to the fact that, ultimately, both depend, albeit in ostensibly quite different ways, only on an adjacency matrix that contains information about the carbon-carbon connectivity of the conjugated system in question.

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

PubMed Central

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID:24748752

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling.

PubMed

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.

Asymmetrical reverse vortex flow due to induced-charge electro-osmosis around carbon stacking structures.

PubMed

Sugioka, Hideyuki

2011-05-01

Broken symmetry of vortices due to induced-charge electro-osmosis (ICEO) around stacking structures is important for the generation of a large net flow in a microchannel. Following theoretical predictions in our previous study, we herein report experimental observations of asymmetrical reverse vortex flows around stacking structures of carbon posts with a large height (~110 μm) in water, prepared by the pyrolysis of a photoresist film in a reducing gas. Further, by the use of a coupled calculation method that considers boundary effects precisely, the experimental results, except for the problem of anomalous flow reversal, are successfully explained. That is, unlike previous predictions, the precise calculations here show that stacking structures accelerate a reverse flow rather than suppressing it for a microfluidic channel because of the deformation of electric fields near the stacking portions; these structures can also generate a large net flow theoretically in the direction opposite that of a previous prediction for a standard vortex flow. Furthermore, by solving the one-dimensional Poisson-Nernst-Plank (PNP) equations in the presence of ac electric fields, we find that the anomalous flow reversal occurs by the phase retardation between the induced diffuse charge and the tangential electric field. In addition, we successfully explain the nonlinearity of the flow velocity on the applied voltage by the PNP analysis. In the future, we expect to improve the pumping performance significantly by using stacking structures of conductive posts along with a low-cost process. © 2011 American Physical Society

Blinded evaluation of farnesoid X receptor (FXR) ligands binding using molecular docking and free energy calculations

NASA Astrophysics Data System (ADS)

Selwa, Edithe; Elisée, Eddy; Zavala, Agustin; Iorga, Bogdan I.

2018-01-01

Our participation to the D3R Grand Challenge 2 involved a protocol in two steps, with an initial analysis of the available structural data from the PDB allowing the selection of the most appropriate combination of docking software and scoring function. Subsequent docking calculations showed that the pose prediction can be carried out with a certain precision, but this is dependent on the specific nature of the ligands. The correct ranking of docking poses is still a problem and cannot be successful in the absence of good pose predictions. Our free energy calculations on two different subsets provided contrasted results, which might have the origin in non-optimal force field parameters associated with the sulfonamide chemical moiety.

An improved synthesis, spectroscopic (FT-IR, NMR) study and DFT computational analysis (IR, NMR, UV-Vis, MEP diagrams, NBO, NLO, FMO) of the 1,5-methanoazocino[4,3-b]indole core structure

NASA Astrophysics Data System (ADS)

Uludağ, Nesimi; Serdaroğlu, Goncagül

2018-03-01

This study examines the synthesis of azocino[4,3-b]indole structure, which constitutes the tetracyclic framework of uleine, dasycarpidoneand tubifolidineas well as ABDE substructure of the strychnosalkaloid family. It has been synthesized by Fischer indolization of 2 and through the cylization of 4 by 2,3-dichlor-5-6-dicyanobenzoquinone (DDQ). 1H and 1C NMR chemical shifts have been predicted with GIAO approach and the calculated chemical shifts show very good agreement with observed shifts. FT-IR spectroscopy is important for the analysis of functional groups of synthesized compounds and we also supported FT-IR vibrational analysis with computational IR analysis. The vibrational spectral analysis was performed at B3LYP level of the theory in both the gas and the water phases and it was compared with the observed IR values for the important functional groups. The DFT calculations have been conducted to determine the most stable structure of the 1,2,3,4,5,6,7-Hexahydro-1,5-methanoazocino [4,3-b] indole (5). The Frontier Molecular Orbital Analysis, quantum chemical parameters, physicochemical properties have been predicted by using the same theory of level in both gas phase and the water phase, at 631 + g** and 6311++g** basis sets. TD- DFT calculations have been performed to predict the UV- Vis spectral analysis for this synthesized molecule. The Natural Bond Orbital (NBO) analysis have been performed at B3LYP level of theory to elucidate the intra-molecular interactions such as electron delocalization and conjugative interactions. NLO calculations were conducted to obtain the electric dipole moment and polarizability of the title compound.

Structures of Mo2Oy- and Mo2Oy (y=2, 3, and 4) studied by anion photoelectron spectroscopy and density functional theory calculations.

PubMed

Yoder, Bruce L; Maze, Joshua T; Raghavachari, Krishnan; Jarrold, Caroline Chick

2005-03-01

The competitive structural isomers of the Mo(2)O(y) (-)Mo(2)O(y) (y=2, 3, and 4) clusters are investigated using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. The PE spectrum and calculations for MoO(3) (-)MoO(3) are also presented to show the level of agreement to be expected between the spectra and calculations. For MoO(3) (-) and MoO(3), the calculations predict symmetric C(3v) structures, an adiabatic electron affinity of 3.34 eV, which is above the observed value 3.17(2) eV. However, there is good agreement between observed and calculated vibrational frequencies and band profiles. The PE spectra of Mo(2)O(2) (-) and Mo(2)O(3) (-) are broad and congested, with partially resolved vibrational structure on the lowest energy bands observed in the spectra. The electron affinities (EA(a)s) of the corresponding clusters are 2.24(2) and 2.33(7) eV, respectively. Based on the calculations, the most stable structure of Mo(2)O(2) (-) is Y shaped, with the two Mo atoms directly bonded. Assignment of the Mo(2)O(3) (-) spectrum is less definitive, but a O-Mo-O-Mo-O structure is more consistent with overall electronic structure observed in the spectrum. The PE spectrum of Mo(2)O(4) (-) shows cleanly resolved vibrational structure and electronic bands, and the EA of the corresponding Mo(2)O(4) is determined to be 2.13(4) eV. The structure most consistent with the observed spectrum has two oxygen bridge bonds between the Mo atoms.

Evaluation of structure-reactivity descriptors and biological activity spectra of 4-(6-methoxy-2-naphthyl)-2-butanone using spectroscopic techniques

NASA Astrophysics Data System (ADS)

Agrawal, Megha; Deval, Vipin; Gupta, Archana; Sangala, Bagvanth Reddy; Prabhu, S. S.

2016-10-01

The structure and several spectroscopic features along with reactivity parameters of the compound 4-(6-methoxy-2-naphthyl)-2-butanone (Nabumetone) have been studied using experimental techniques and tools derived from quantum chemical calculations. Structure optimization is followed by force field calculations based on density functional theory (DFT) at the B3LYP/6-311++G(d,p) level of theory. The vibrational spectra have been interpreted with the aid of normal coordinate analysis. UV-visible spectrum and the effect of solvent have been discussed. The electronic properties such as HOMO and LUMO energies have been determined by TD-DFT approach. In order to understand various aspects of pharmacological sciences several new chemical reactivity descriptors - chemical potential, global hardness and electrophilicity have been evaluated. Local reactivity descriptors - Fukui functions and local softnesses have also been calculated to find out the reactive sites within molecule. Aqueous solubility and lipophilicity have been calculated which are crucial for estimating transport properties of organic molecules in drug development. Estimation of biological effects, toxic/side effects has been made on the basis of prediction of activity spectra for substances (PASS) prediction results and their analysis by Pharma Expert software. Using the THz-TDS technique, the frequency-dependent absorptions of NBM have been measured in the frequency range up to 3 THz.

Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets.

PubMed

Feinstein, Wei P; Brylinski, Michal

2015-01-01

Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come with a default protocol for calculating the box size, however, many of these procedures have not been systematically evaluated. In this study, we investigate how the docking accuracy of AutoDock Vina is affected by the selection of a search space. We propose a new procedure for calculating the optimal docking box size that maximizes the accuracy of binding pose prediction against a non-redundant and representative dataset of 3,659 protein-ligand complexes selected from the Protein Data Bank. Subsequently, we use the Directory of Useful Decoys, Enhanced to demonstrate that the optimized docking box size also yields an improved ranking in virtual screening. Binding pockets in both datasets are derived from the experimental complex structures and, additionally, predicted by eFindSite. A systematic analysis of ligand binding poses generated by AutoDock Vina shows that the highest accuracy is achieved when the dimensions of the search space are 2.9 times larger than the radius of gyration of a docking compound. Subsequent virtual screening benchmarks demonstrate that this optimized docking box size also improves compound ranking. For instance, using predicted ligand binding sites, the average enrichment factor calculated for the top 1 % (10 %) of the screening library is 8.20 (3.28) for the optimized protocol, compared to 7.67 (3.19) for the default procedure. Depending on the evaluation metric, the optimal docking box size gives better ranking in virtual screening for about two-thirds of target proteins. This fully automated procedure can be used to optimize docking protocols in order to improve the ranking accuracy in production virtual screening simulations. Importantly, the optimized search space systematically yields better results than the default method not only for experimental pockets, but also for those predicted from protein structures. A script for calculating the optimal docking box size is freely available at www.brylinski.org/content/docking-box-size. Graphical AbstractWe developed a procedure to optimize the box size in molecular docking calculations. Left panel shows the predicted binding pose of NADP (green sticks) compared to the experimental complex structure of human aldose reductase (blue sticks) using a default protocol. Right panel shows the docking accuracy using an optimized box size.

Modeling and control of flexible space structures

NASA Technical Reports Server (NTRS)

Wie, B.; Bryson, A. E., Jr.

1981-01-01

The effects of actuator and sensor locations on transfer function zeros are investigated, using uniform bars and beams as generic models of flexible space structures. It is shown how finite element codes may be used directly to calculate transfer function zeros. The impulse response predicted by finite-dimensional models is compared with the exact impulse response predicted by the infinite dimensional models. It is shown that some flexible structures behave as if there were a direct transmission between actuator and sensor (equal numbers of zeros and poles in the transfer function). Finally, natural damping models for a vibrating beam are investigated since natural damping has a strong influence on the appropriate active control logic for a flexible structure.

Conformational stability, structural parameters and vibrational assignment from variable temperature infrared spectra of krypton solutions and ab initio calculations of ethylisothiocyanate.

PubMed

Durig, James R; Zheng, Chao

2007-11-01

Variable temperature (-105 to -150 degrees C) studies of the infrared spectra (3500-400 cm(-1)) of ethylisothiocyanate, CH(3)CH(2)NCS, dissolved in liquid krypton have been recorded. Additionally the infrared spectra of the gas and solid have been re-investigated. These spectroscopic data indicate a single conformer in all physical states with a large number of molecules in the gas phase at ambient temperature in excited states of the CN torsional mode which has a very low barrier to conformational interchange. To aid in the analyses of the vibrational and rotational spectra, ab initio calculations have been carried out by the perturbation method to the second order (MP2) with valence and core electron correlation using a variety of basis sets up to 6-311+G(2df,2pd). With the smaller basis sets up to 6-311+G(d,p) and cc-PVDZ, the cis conformer is indicated as a transition state with all larger basis sets the cis conformer is the only stable form. The predicted energy difference from these calculations between the cis form and the higher energy trans conformer is about 125 cm(-1) which represents essentially the barrier to internal rotation of the NCS group (rotation around NC axis). Density functional theory calculation by the B3LYP method with the same basis sets predicts this barrier to be about 25 cm(-1). By utilizing the previously reported microwave rotational constants with the structural parameters predicted by the ab initio MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the cis form. The determined heavy atom parameters are: r(NC)=1.196(5), r(CS)=1.579(5), r(CN)=1.439(5), r(CC)=1.519(5)A for the distances and angles of angleCCN=112.1(5), angleCNC=146.2(5), angleNCS=174.0(5) degrees . The centrifugal distortion constants, dipole moments, conformational stability, vibrational frequencies, infrared intensities and Raman activities have been predicted from ab initio calculations and compared to experimental quantities when available. These results are compared to the corresponding quantities of some similar molecules.

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

PubMed

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

2012-08-01

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

Experimental and Theoretical Research on the Compression Performance of CFRP Sheet Confined GFRP Short Pipe

PubMed Central

Zhao, Qilin; Chen, Li; Shao, Guojian

2014-01-01

The axial compressive strength of unidirectional FRP made by pultrusion is generally quite lower than its axial tensile strength. This fact decreases the advantages of FRP as main load bearing member in engineering structure. A theoretical iterative calculation approach was suggested to predict the ultimate axial compressive stress of the combined structure and analyze the influences of geometrical parameters on the ultimate axial compressive stress of the combined structure. In this paper, the experimental and theoretical research on the CFRP sheet confined GFRP short pole was extended to the CFRP sheet confined GFRP short pipe, namely, a hollow section pole. Experiment shows that the bearing capacity of the GFRP short pipe can also be heightened obviously by confining CFRP sheet. The theoretical iterative calculation approach in the previous paper is amended to predict the ultimate axial compressive stress of the CFRP sheet confined GFRP short pipe, of which the results agree with the experiment. Lastly the influences of geometrical parameters on the new combined structure are analyzed. PMID:24672288

Prediction of nanofluids properties: the density and the heat capacity

NASA Astrophysics Data System (ADS)

Zhelezny, V. P.; Motovoy, I. V.; Ustyuzhanin, E. E.

2017-11-01

The results given in this report show that the additives of Al2O3 nanoparticles lead to increase the density and decrease the heat capacity of isopropanol. Based on the experimental data the excess molar volume and the excess molar heat capacity were calculated. The report suggests new method for predicting the molar volume and molar heat capacity of nanofluids. It is established that the values of the excess thermodynamic functions are determined by the properties and the volume of the structurally oriented layers of the base fluid molecules near the surface of nanoparticles. The heat capacity of the structurally oriented layers of the base fluid is less than the heat capacity of the base fluid for given parameters due to the greater regulation of its structure. It is shown that information on the geometric dimensions of the structured layers of the base fluid near nanoparticles can be obtained from data on the nanofluids density and at ambient temperature - by the dynamic light scattering method. For calculations of the nanofluids heat capacity over a wide range of temperatures a new correlation based on the extended scaling is proposed.

DFT calculations on spectroscopic and structural properties of a NLO chromophore

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avci, Davut; Tamer, Ömer; Atalay, Yusuf

2016-03-01

The molecular geometry optimization, vibrational frequencies and gauge including atomic orbital (GIAO) 1H and 13C NMR chemical shift values of 2-(1'-(4'''-Methoxyphenyl)-5'-(thien-2″-yl)pyrrol-2'-yl)-1,3-benzothiazole as potential nonlinear optical (NLO) material were calculated using density functional theory (DFT) HSEh1PBE method with 6-311G(d,p) basis set. The best of our knowledge, this study have not been reported to date. Additionally, a detailed vibrational study was performed on the basis of potential energy distribution (PED) using VEDA program. It is noteworthy that NMR chemical shifts are quite useful for understanding the relationship between the molecular structure and electronic properties of molecules. The computed IR and NMR spectra were used to determine the types of the experimental bands observed. Predicted values of structural and spectroscopic parameters of the chromophore were compared with each other so as to display the effects of the different substituents on the spectroscopic and structural properties. Obtained data showed that there is an agreement between the predicted and experimental data.

Benchmarking density functional theory predictions of framework structures and properties in a chemically diverse test set of metal-organic frameworks

DOE PAGES

Nazarian, Dalar; Ganesh, P.; Sholl, David S.

2015-09-30

We compiled a test set of chemically and topologically diverse Metal–Organic Frameworks (MOFs) with high accuracy experimentally derived crystallographic structure data. The test set was used to benchmark the performance of Density Functional Theory (DFT) functionals (M06L, PBE, PW91, PBE-D2, PBE-D3, and vdW-DF2) for predicting lattice parameters, unit cell volume, bonded parameters and pore descriptors. On average PBE-D2, PBE-D3, and vdW-DF2 predict more accurate structures, but all functionals predicted pore diameters within 0.5 Å of the experimental diameter for every MOF in the test set. The test set was also used to assess the variance in performance of DFT functionalsmore » for elastic properties and atomic partial charges. The DFT predicted elastic properties such as minimum shear modulus and Young's modulus can differ by an average of 3 and 9 GPa for rigid MOFs such as those in the test set. Moreover, we calculated the partial charges by vdW-DF2 deviate the most from other functionals while there is no significant difference between the partial charges calculated by M06L, PBE, PW91, PBE-D2 and PBE-D3 for the MOFs in the test set. We find that while there are differences in the magnitude of the properties predicted by the various functionals, these discrepancies are small compared to the accuracy necessary for most practical applications.« less

Modeling Alkyl p-Methoxy Cinnamate (APMC) as UV absorber based on electronic transition using semiempirical quantum mechanics ZINDO/s calculation

NASA Astrophysics Data System (ADS)

Salmahaminati; Azis, Muhlas Abdul; Purwiandono, Gani; Arsyik Kurniawan, Muhammad; Rubiyanto, Dwiarso; Darmawan, Arif

2017-11-01

In this research, modeling several alkyl p-methoxy cinnamate (APMC) based on electronic transition by using semiempirical mechanical quantum ZINDO/s calculation is performed. Alkyl cinnamates of C1 (methyl) up to C7 (heptyl) homolog with 1-5 example structures of each homolog are used as materials. Quantum chemistry-package software Hyperchem 8.0 is used to simulate the drawing of the structure, geometry optimization by a semiempirical Austin Model 1 algorithm and single point calculation employing a semiempirical ZINDO/s technique. ZINDO/s calculations use a defined criteria that singly excited -Configuration Interaction (CI) where a gap of HOMO-LUMO energy transition and maximum degeneracy level are 7 and 2, respectively. Moreover, analysis of the theoretical spectra is focused on the UV-B (290-320 nm) and UV-C (200-290 nm) area. The results show that modeling of the compound can be used to predict the type of UV protection activity depends on the electronic transition in the UV area. Modification of the alkyl homolog relatively does not change the value of wavelength absorption to indicate the UV protection activity. Alkyl cinnamate compounds are predicted as UV-B and UV-C sunscreen.

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

Callear, Samantha K.; Imberti, Silvia; Johnston, Andrew

The aqueous solution of dopamine hydrochloride has been investigated using neutron and X-ray total scattering data together with Monte-Carlo based modelling using Empirical Potential Structure Refinement. The conformation of the protonated dopamine molecule is presented and the results compared to the conformations found in crystal structures, dopamine-complexed protein crystal structures and predicted from theoretical calculations and pharmacophoric models. It is found that protonated dopamine adopts a range of conformations in solution, highlighting the low rotational energy barrier between different conformations, with the preferred conformation being trans-perpendicular. The interactions between each of the species present (protonated dopamine molecules, water molecules, andmore » chloride anions) have been determined and are discussed with reference to interactions observed in similar systems both in the liquid and crystalline state, and predicted from theoretical calculations. The expected strong hydrogen bonds between the strong hydrogen bond donors and acceptors are observed, together with evidence of weaker CH hydrogen bonds and π interactions also playing a significant role in determining the arrangement of adjacent molecules.« less

Prediction of Material Properties of Nanostructured Polymer Composites Using Atomistic Simulations

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Clancy, T.C.; Frankland, S.J.V.

2009-01-01

Atomistic models of epoxy polymers were built in order to assess the effect of structure at the nanometer scale on the resulting bulk properties such as elastic modulus and thermal conductivity. Atomistic models of both bulk polymer and carbon nanotube polymer composites were built. For the bulk models, the effect of moisture content and temperature on the resulting elastic constants was calculated. A relatively consistent decrease in modulus was seen with increasing temperature. The dependence of modulus on moisture content was less consistent. This behavior was seen for two different epoxy systems, one containing a difunctional epoxy molecule and the other a tetrafunctional epoxy molecule. Both epoxy structures were crosslinked with diamine curing agents. Multifunctional properties were calculated with the nanocomposite models. Molecular dynamics simulation was used to estimate the interfacial thermal (Kapitza) resistance between the carbon nanotube and the surrounding epoxy matrix. These estimated values were used in a multiscale model in order to predict the thermal conductivity of a nanocomposite as a function of the nanometer scaled molecular structure.

Structures in solutions from joint experimental-computational analysis: applications to cyclic molecules and studies of noncovalent interactions.

PubMed

Aliev, Abil E; Mia, Zakirin A; Khaneja, Harmeet S; King, Frank D

2012-01-26

The potential of an approach combining nuclear magnetic resonance (NMR) spectroscopy, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations for full structural characterizations in solution is assessed using cyclic organic compounds, namely, benzazocinone derivatives 1-3 with fused five- and eight-membered aliphatic rings, camphoric anhydride 4, and bullvalene 5. Various MD simulations were considered, using force field and semiempirical QM treatments, implicit and explicit solvation, and high-temperature MD calculations for selecting plausible molecular geometries for subsequent QM geometry optimizations using mainly B3LYP, M062X, and MP2 methods. The QM-predicted values of NMR parameters were compared to their experimental values for verification of the final structures derived from the MD/QM analysis. From these comparisons, initial estimates of quality thresholds (calculated as rms deviations) were 0.7-0.9 Hz for (3)J(HH) couplings, 0.07-0.11 Å for interproton distances, 0.05-0.08 ppm for (1)H chemical shifts, and 1.0-2.1 ppm for (13)C chemical shifts. The obtained results suggest that the accuracy of the MD analysis in predicting geometries and relative conformational energies is not critical and that the final geometry refinements of the structures selected from the MD simulations using QM methods are sufficient for correcting for the expected inaccuracy of the MD analysis. A unique example of C(sp(3))-H···N(sp(3)) intramolecular noncovalent interaction is also identified using the NMR/MD/QM and the natural bond orbital analyses. As the NMR/MD/QM approach relies on the final QM geometry optimization, comparisons of geometric characteristics predicted by different QM methods and those from X-ray and neutron diffraction measurements were undertaken using rigid and flexible cyclic systems. The joint analysis shows that intermolecular noncovalent interactions present in the solid state alter molecular geometries significantly compared to the geometries of isolated molecules from QM calculations.

High-pressure phase transitions of nitinol NiTi to a semiconductor with an unusual topological structure

NASA Astrophysics Data System (ADS)

Liu, Guangtao; Liu, Hanyu; Feng, Xiaolei; Redfern, Simon A. T.

2018-04-01

Systematic ab initio structure simulations have been used to explore the high-pressure behavior of nitinol (NiTi) at zero temperature. Our crystal structure prediction and first-principles calculations reveal that the known B 19 phase is dynamically unstable, and an orthorhombic structure (Pbcm) and a face-centered-cubic B 32 structure (F d 3 ¯m ) become stable above ˜4 and 29 GPa, respectively. The predicted, highest-pressure, B 32 phase is composed of two interpenetrating diamond structures, with a structural topology that is quite distinct from that of the other phases of NiTi. Interestingly, the B 32 phase shows an unusual semiconducting characteristic as a result of its unique band structure and the nature of 3 d orbitals localization, whose expected synthesis pressure is accessible to current experimental techniques.

Calculation of Electronic Structure and Field Induced Magnetic Collapse in Ferroic Materials

NASA Astrophysics Data System (ADS)

Entel, Peter; Arróyave, Raymundo; Singh, Navdeep; Sokolovskiy, Vladimir V.; Buchelnikov, Vasiliy D.

We have performed ab inito electronic structure calculations and Monte Carlo simulations of FeRh, Mn3GaC and Heusler intermetallics alloys such as Ni-Co-Cr-Mn-(Ga, In, Sn) which are of interest for solid refrigeration and energy systems, an emerging technology involving such solid-solid systems. The calculations reveal that the important magnetic phase diagrams of these alloys which show the magnetic collapse and allow predictions of the related magnetocaloric effect (MCE) which they exhibit at finite temperatures, can be obtained by ab inito and Monte Carlo computations in qualitatively good agreement with experimental data. This is a one-step procedure from theory to alloy design of ferroic functional devices.

A simple nonlocal damage model for predicting failure of notched laminates

NASA Technical Reports Server (NTRS)

Kennedy, T. C.; Nahan, M. F.

1995-01-01

The ability to predict failure loads in notched composite laminates is a requirement in a variety of structural design circumstances. A complicating factor is the development of a zone of damaged material around the notch tip. The objective of this study was to develop a computational technique that simulates progressive damage growth around a notch in a manner that allows the prediction of failure over a wide range of notch sizes. This was accomplished through the use of a relatively simple, nonlocal damage model that incorporates strain-softening. This model was implemented in a two-dimensional finite element program. Calculations were performed for two different laminates with various notch sizes under tensile loading, and the calculations were found to correlate well with experimental results.

4f fine-structure levels as the dominant error in the electronic structures of binary lanthanide oxides.

PubMed

Huang, Bolong

2016-04-05

The ground-state 4f fine-structure levels in the intrinsic optical transition gaps between the 2p and 5d orbitals of lanthanide sesquioxides (Ln2 O3 , Ln = La…Lu) were calculated by a two-way crossover search for the U parameters for DFT + U calculations. The original 4f-shell potential perturbation in the linear response method were reformulated within the constraint volume of the given solids. The band structures were also calculated. This method yields nearly constant optical transition gaps between Ln-5d and O-2p orbitals, with magnitudes of 5.3 to 5.5 eV. This result verifies that the error in the band structure calculations for Ln2 O3 is dominated by the inaccuracies in the predicted 4f levels in the 2p-5d transition gaps, which strongly and non-linearly depend on the on-site Hubbard U. The relationship between the 4f occupancies and Hubbard U is non-monotonic and is entirely different from that for materials with 3d or 4d orbitals, such as transition metal oxides. This new linear response DFT + U method can provide a simpler understanding of the electronic structure of Ln2 O3 and enables a quick examination of the electronic structures of lanthanide solids before hybrid functional or GW calculations. © 2015 Wiley Periodicals, Inc.

Structures of cage, prism, and book isomers of water hexamer from broadband rotational spectroscopy.

PubMed

Pérez, Cristóbal; Muckle, Matt T; Zaleski, Daniel P; Seifert, Nathan A; Temelso, Berhane; Shields, George C; Kisiel, Zbigniew; Pate, Brooks H

2012-05-18

Theory predicts the water hexamer to be the smallest water cluster with a three-dimensional hydrogen-bonding network as its minimum energy structure. There are several possible low-energy isomers, and calculations with different methods and basis sets assign them different relative stabilities. Previous experimental work has provided evidence for the cage, book, and cyclic isomers, but no experiment has identified multiple coexisting structures. Here, we report that broadband rotational spectroscopy in a pulsed supersonic expansion unambiguously identifies all three isomers; we determined their oxygen framework structures by means of oxygen-18-substituted water (H(2)(18)O). Relative isomer populations at different expansion conditions establish that the cage isomer is the minimum energy structure. Rotational spectra consistent with predicted heptamer and nonamer structures have also been identified.

Theoretical prediction of a new stable structure of Au28(SR)20 cluster

NASA Astrophysics Data System (ADS)

Sun, Xiangxiang; Wang, Pu; Xiong, Lin; Pei, Yong

2018-07-01

A new stable structure of Au28(SR)20 cluster is predicted, which has the same gold core as two known structures but different Au-S framework. The new Au28(SR)20 cluster is proposed to be a key link in the evolution of Au22(SR)18, Au34(SR)22 and Au40(SR)24 clusters. The four clusters belong to a homogenous Au16+6N(SR)16+2N series (N = 1-4). The relative stabilities of the new Au28 isomer structure were confirmed by density functional theory calculations including dispersion corrections (DFT-D). It is found that upon protection of certain SR ligands, the new isomer structure has lower or comparable energies to two known cluster structures.

Exploring phase stability, electronic and mechanical properties of Ce–Pb intermetallic compounds using first-principles calculations

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

Tao, Xiaoma; Computational Alloy Design Group, IMDEA Materials Institute, Getafe, Madrid 28906; Wang, Ziru

2016-05-15

The phase stability, electronic and mechanical properties of Ce–Pb intermetallics have been investigated by using first-principles calculations. Five stable and four metastable phases of Ce–Pb intermetallics were verified. Among them, CePb{sub 2} has been confirmed as HfGa{sub 2}-type structure. For Ce{sub 5}Pb{sub 3}, the high pressure phase transformation from D8{sub m} to D8{sub 8} with trivalent Ce has been predicted to occur at P=1.2 GPa and a high temperature phase transformation has been predicted from D8{sub m} to D8{sub 8} with tetravalent Ce at 531.5 K. The calculated lattice constants of the five stable phases are in good agreement withmore » experimental values. The electronic density of states, charge density and electron localization function of Ce{sub 3}Pb have been calculated, which indicated that the Ce and Pb show ionic behavior. The polycrystalline bulk modulus, shear modulus, Young's modulus, and Poisson's ratio are also estimated from the calculated single crystalline elastic constants. All of the calculated elastic constants satisfy mechanical stability criteria. The microhardness and mechanical anisotropy are predicted. The anisotropic nature of the Ce–Pb intermetallic compounds are demonstrated by the three-dimensional orientation dependent surfaces of Young's moduli and linear compressibility are also demonstrated. The longitudinal, transverse and average sound velocities and the Debye temperatures are also obtained in this work. The Ce{sub 3}Pb has the largest Debye temperature of 192.6 K, which means the Ce{sub 3}Pb has a highest melting point and high thermal conductivity than other compounds. - Graphical abstract: The convex hull plots of the enthalpies of formation for Ce–Pb binary systems calculated at 0 K. - Highlights: • The five stable and four metastable phases in the Ce–Pb binary system were predicted. • The crystal structure of CePb{sub 2} has been confirmed as HfGa{sub 2}-type.« less

Predicting Salt Permeability Coefficients in Highly Swollen, Highly Charged Ion Exchange Membranes.

PubMed

Kamcev, Jovan; Paul, Donald R; Manning, Gerald S; Freeman, Benny D

2017-02-01

This study presents a framework for predicting salt permeability coefficients in ion exchange membranes in contact with an aqueous salt solution. The model, based on the solution-diffusion mechanism, was tested using experimental salt permeability data for a series of commercial ion exchange membranes. Equilibrium salt partition coefficients were calculated using a thermodynamic framework (i.e., Donnan theory), incorporating Manning's counterion condensation theory to calculate ion activity coefficients in the membrane phase and the Pitzer model to calculate ion activity coefficients in the solution phase. The model predicted NaCl partition coefficients in a cation exchange membrane and two anion exchange membranes, as well as MgCl 2 partition coefficients in a cation exchange membrane, remarkably well at higher external salt concentrations (>0.1 M) and reasonably well at lower external salt concentrations (<0.1 M) with no adjustable parameters. Membrane ion diffusion coefficients were calculated using a combination of the Mackie and Meares model, which assumes ion diffusion in water-swollen polymers is affected by a tortuosity factor, and a model developed by Manning to account for electrostatic effects. Agreement between experimental and predicted salt diffusion coefficients was good with no adjustable parameters. Calculated salt partition and diffusion coefficients were combined within the framework of the solution-diffusion model to predict salt permeability coefficients. Agreement between model and experimental data was remarkably good. Additionally, a simplified version of the model was used to elucidate connections between membrane structure (e.g., fixed charge group concentration) and salt transport properties.

EcoSmart Fire as structure ignition model in wildland urban interface: predictions and validations

Treesearch

Mark A. Dietenberger; Charles R. Boardman

2016-01-01

EcoSmartFire is a Windows program that models heat damage and piloted ignition of structures from radiant exposure to discrete landscaped tree fires. It calculates the radiant heat transfer from cylindrical shaped fires to the walls and roof of the structure while accounting for radiation shadowing, attenuation, and ground reflections. Tests of litter burn, a 0.6 m...

A shielding theory for upward lightning

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

Shindo, Takatoshi; Aihara, Yoshinori

1993-01-01

A new shielding theory is proposed based on the assumption that the occurrence of lightning strokes on the Japan Sea coast in winter is due to the inception of upward leaders from tall structures. Ratios of the numbers of lightning strokes to high structures observed there in winter show reasonable agreement with values calculated by this theory. Shielding characteristics of a high structure in various conditions are predicted.

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Breit–Pauli atomic structure calculations for Fe XI

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

Aggarwal, Sunny, E-mail: sunny.du87@gmail.com; Singh, Jagjit; Mohan, Man

Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many ofmore » the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.« less

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.

Quantitative Structure-Antifungal Activity Relationships for cinnamate derivatives.

PubMed

Saavedra, Laura M; Ruiz, Diego; Romanelli, Gustavo P; Duchowicz, Pablo R

2015-12-01

Quantitative Structure-Activity Relationships (QSAR) are established with the aim of analyzing the fungicidal activities of a set of 27 active cinnamate derivatives. The exploration of more than a thousand of constitutional, topological, geometrical and electronic molecular descriptors, which are calculated with Dragon software, leads to predictions of the growth inhibition on Pythium sp and Corticium rolfsii fungi species, in close agreement to the experimental values extracted from the literature. A set containing 21 new structurally related cinnamate compounds is prepared. The developed QSAR models are applied to predict the unknown fungicidal activity of this set, showing that cinnamates like 38, 28 and 42 are expected to be highly active for Pythium sp, while this is also predicted for 28 and 34 in C. rolfsii. Copyright © 2015 Elsevier Inc. All rights reserved.

Binding site and affinity prediction of general anesthetics to protein targets using docking.

PubMed

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G

2012-05-01

The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explored whether a computational method, AutoDock, could serve as such a tool. High-resolution crystal data of water-soluble proteins (cytochrome C, apoferritin, and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus [GLIC]) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (http://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants were compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent cocrystallization data. Docking calculations for 6 general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known 50% effective concentration (EC(50)) values were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC(50) values and octanol/water partition coefficients for the 6 general anesthetics. All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (P = 0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site located in the extracellular domain of GLIC. The predicted affinities correlated significantly with the known EC(50) values for the 6 frequently used anesthetics in GLIC for the site identified in the experimental crystal data (P = 0.006). However, predicted affinities in apoferritin, human serum albumin, and cytochrome C did not correlate with these 6 anesthetics' known experimental EC(50) values. A weak correlation between the predicted affinities and the octanol/water partition coefficients was observed for the sites in GLIC. We demonstrated that anesthetic binding sites and relative affinities can be predicted using docking calculations in an automatic docking server (AutoDock) for both water-soluble and membrane proteins. Correlation of predicted affinity and EC(50) for 6 frequently used general anesthetics was only observed in GLIC, a member of a protein family relevant to anesthetic mechanism.

Binding Site and Affinity Prediction of General Anesthetics to Protein Targets Using Docking

PubMed Central

Liu, Renyu; Perez-Aguilar, Jose Manuel; Liang, David; Saven, Jeffery G.

2012-01-01

Background The protein targets for general anesthetics remain unclear. A tool to predict anesthetic binding for potential binding targets is needed. In this study, we explore whether a computational method, AutoDock, could serve as such a tool. Methods High-resolution crystal data of water soluble proteins (cytochrome C, apoferritin and human serum albumin), and a membrane protein (a pentameric ligand-gated ion channel from Gloeobacter violaceus, GLIC) were used. Isothermal titration calorimetry (ITC) experiments were performed to determine anesthetic affinity in solution conditions for apoferritin. Docking calculations were performed using DockingServer with the Lamarckian genetic algorithm and the Solis and Wets local search method (https://www.dockingserver.com/web). Twenty general anesthetics were docked into apoferritin. The predicted binding constants are compared with those obtained from ITC experiments for potential correlations. In the case of apoferritin, details of the binding site and their interactions were compared with recent co-crystallization data. Docking calculations for six general anesthetics currently used in clinical settings (isoflurane, sevoflurane, desflurane, halothane, propofol, and etomidate) with known EC50 were also performed in all tested proteins. The binding constants derived from docking experiments were compared with known EC50s and octanol/water partition coefficients for the six general anesthetics. Results All 20 general anesthetics docked unambiguously into the anesthetic binding site identified in the crystal structure of apoferritin. The binding constants for 20 anesthetics obtained from the docking calculations correlate significantly with those obtained from ITC experiments (p=0.04). In the case of GLIC, the identified anesthetic binding sites in the crystal structure are among the docking predicted binding sites, but not the top ranked site. Docking calculations suggest a most probable binding site located in the extracellular domain of GLIC. The predicted affinities correlated significantly with the known EC50s for the six commonly used anesthetics in GLIC for the site identified in the experimental crystal data (p=0.006). However, predicted affinities in apoferritin, human serum albumin, and cytochrome C did not correlate with these six anesthetics’ known experimental EC50s. A weak correlation between the predicted affinities and the octanol/water partition coefficients was observed for the sites in GLIC. Conclusion We demonstrated that anesthetic binding sites and relative affinities can be predicted using docking calculations in an automatic docking server (Autodock) for both water soluble and membrane proteins. Correlation of predicted affinity and EC50 for six commonly used general anesthetics was only observed in GLIC, a member of a protein family relevant to anesthetic mechanism. PMID:22392968

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein-RNA complexes.

PubMed

Chen, Fu; Sun, Huiyong; Wang, Junmei; Zhu, Feng; Liu, Hui; Wang, Zhe; Lei, Tailong; Li, Youyong; Hou, Tingjun

2018-06-21

Molecular docking provides a computationally efficient way to predict the atomic structural details of protein-RNA interactions (PRI), but accurate prediction of the three-dimensional structures and binding affinities for PRI is still notoriously difficult, partly due to the unreliability of the existing scoring functions for PRI. MM/PBSA and MM/GBSA are more theoretically rigorous than most scoring functions for protein-RNA docking, but their prediction performance for protein-RNA systems remains unclear. Here, we systemically evaluated the capability of MM/PBSA and MM/GBSA to predict the binding affinities and recognize the near-native binding structures for protein-RNA systems with different solvent models and interior dielectric constants (ϵ in ). For predicting the binding affinities, the predictions given by MM/GBSA based on the minimized structures in explicit solvent and the GBGBn1 model with ϵ in = 2 yielded the highest correlation with the experimental data. Moreover, the MM/GBSA calculations based on the minimized structures in implicit solvent and the GBGBn1 model distinguished the near-native binding structures within the top 10 decoys for 118 out of the 149 protein-RNA systems (79.2%). This performance is better than all docking scoring functions studied here. Therefore, the MM/GBSA rescoring is an efficient way to improve the prediction capability of scoring functions for protein-RNA systems. Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Theoretical prediction of novel ultrafine nanowires formed by Si12C12 cage-like clusters

NASA Astrophysics Data System (ADS)

Yong, Yongliang; Song, Bin; He, Pimo

2014-02-01

Using density functional theory calculations, we predict that novel SiC ultrafine nanowires can be produced via the coalescence of stable Si12C12 clusters. For the isolated Si12C12 clusters, we find that the cage-like structure with a distinct segregation between Si and C atoms is energetically more favourable than the fullerene-like structure with alternating Si-C bonds. Via the coalescence of Si12C12 clusters, three novel stable nanowires have been characterised. The band structure reveals that these nanowires are semiconductors with narrow gap, indicating that they may be used as infrared detectors and thermoelectrics.

Integrated modeling and analysis of a space-truss article

NASA Technical Reports Server (NTRS)

Stockwell, Alan E.; Perez, Sharon E.; Pappa, Richard S.

1990-01-01

MSC/NASTRAN is being used in the Controls-Structures Interaction (CSI) program at NASA Langley Research Center as a key analytical tool for structural analysis as well as the basis for control law development, closed-loop performance evaluation, and system safety checks. Guest investigators from academia and industry are performing dynamics and control experiments on a flight-like deployable space truss called Mini-Mast to determine the effectiveness of various active-vibration control laws. MSC/NASTRAN was used to calculate natural frequencies and mode shapes below 100 Hz to describe the dynamics of the 20-meter-long lightweight Mini-Mast structure. Gravitational effects contribute significantly to structural stiffness and are accounted for through a two-phase solution in which the differential stiffness matrix is calculated and then used in the eigensolution. Reduced modal models are extracted for control law design and evaluation of closed-loop system performance. Predicted actuator forces from controls simulations are then applied to the extended model to predict member loads and stresses. These pre-test analyses reduce risks associated with the structural integrity of the test article, which is a major concern in closed-loop control experiments due to potential instabilities.

Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

PubMed

Hartman, Joshua D; Beran, Gregory J O

2014-11-11

First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations.

Head losses prediction and analysis in a bulb turbine draft tube under different operating conditions using unsteady simulations

NASA Astrophysics Data System (ADS)

Wilhelm, S.; Balarac, G.; Métais, O.; Ségoufin, C.

2016-11-01

Flow prediction in a bulb turbine draft tube is conducted for two operating points using Unsteady RANS (URANS) simulations and Large Eddy Simulations (LES). The inlet boundary condition of the draft tube calculation is a rotating two dimensional velocity profile exported from a RANS guide vane- runner calculation. Numerical results are compared with experimental data in order to validate the flow field and head losses prediction. Velocity profiles prediction is improved with LES in the center of the draft tube compared to URANS results. Moreover, more complex flow structures are obtained with LES. A local analysis of the predicted flow field using the energy balance in the draft tube is then introduced in order to detect the hydrodynamic instabilities responsible for head losses in the draft tube. In particular, the production of turbulent kinetic energy next to the draft tube wall and in the central vortex structure is found to be responsible for a large part of the mean kinetic energy dissipation in the draft tube and thus for head losses. This analysis is used in order to understand the differences in head losses for different operating points. The numerical methodology could then be improved thanks to an in-depth understanding of the local flow topology.

Conformational energy calculations on polypeptides and proteins: use of a statistical mechanical procedure for evaluating structure and properties.

PubMed

Scheraga, H A; Paine, G H

1986-01-01

We are using a variety of theoretical and computational techniques to study protein structure, protein folding, and higher-order structures. Our earlier work involved treatments of liquid water and aqueous solutions of nonpolar and polar solutes, computations of the stabilities of the fundamental structures of proteins and their packing arrangements, conformations of small cyclic and open-chain peptides, structures of fibrous proteins (collagen), structures of homologous globular proteins, introduction of special procedures as constraints during energy minimization of globular proteins, and structures of enzyme-substrate complexes. Recently, we presented a new methodology for predicting polypeptide structure (described here); the method is based on the calculation of the probable and average conformation of a polypeptide chain by the application of equilibrium statistical mechanics in conjunction with an adaptive, importance sampling Monte Carlo algorithm. As a test, it was applied to Met-enkephalin.

Optical properties of extended-chain polymers under stress

NASA Astrophysics Data System (ADS)

Ramirez, Rafael G.; Eby, R. K.

1995-09-01

Birefringence and x-ray diffraction experiments have been carried out on Kevlar 49(superscript R) fibers under tensile stress to monitor structure changes under the stress field. The origin of the observed birefringence is discussed in some detail. Results from theoretical calculations using semi-empirical molecular orbital techniques are presented and contrasted to the experimental observations. The calculations involved the estimation of chain polarizability and were performed under simulated stress conditions using the AM1 Hamiltonian in MOPAC. Polarizability is then used to calculate the birefringence as a function of tensile stress, by using existing internal field theory. This theoretical approach is applied to predict the optical properties of highly oriented extended-chain polyethylene, as well as those for poly(p' phenylene therephtalamide); the latter being the base polymer in Kevlar fibers. Results reveal reasonable birefringence predictions when compared to available experimental results in the literature. Also, it is found that the contribution from orienting crystallites under the stress field, to the measured birefringence in Kevlar fibers, is only a small fraction of the total. However, the calculations predict a significant contribution from deformation (extension) at the molecular level.

Combined EXAFS Spectroscopic and Quantum Chemical Study on the Complex Formation of Am(III) with Formate.

PubMed

Fröhlich, Daniel R; Kremleva, Alena; Rossberg, André; Skerencak-Frech, Andrej; Koke, Carsten; Krüger, Sven; Rösch, Notker; Panak, Petra J

2017-06-19

The complexation of Am(III) with formate in aqueous solution is studied as a function of the pH value using a combination of extended X-ray absorption fine structure (EXAFS) spectroscopy, iterative transformation factor analysis (ITFA), and quantum chemical calculations. The Am L III -edge EXAFS spectra are analyzed to determine the molecular structure (coordination numbers; Am-O and Am-C distances) of the formed Am(III)-formate species and to track the shift of the Am(III) speciation with increasing pH. The experimental data are compared to predictions from density functional calculations. The results indicate that formate binds to Am(III) in a monodentate fashion, in agreement with crystal structures of lanthanide formates. Furthermore, the investigations are complemented by thermodynamic speciation calculations to verify further the results obtained.

Thermal Cycling Life Prediction of Sn-3.0Ag-0.5Cu Solder Joint Using Type-I Censored Data

PubMed Central

Mi, Jinhua; Yang, Yuan-Jian; Huang, Hong-Zhong

2014-01-01

Because solder joint interconnections are the weaknesses of microelectronic packaging, their reliability has great influence on the reliability of the entire packaging structure. Based on an accelerated life test the reliability assessment and life prediction of lead-free solder joints using Weibull distribution are investigated. The type-I interval censored lifetime data were collected from a thermal cycling test, which was implemented on microelectronic packaging with lead-free ball grid array (BGA) and fine-pitch ball grid array (FBGA) interconnection structures. The number of cycles to failure of lead-free solder joints is predicted by using a modified Engelmaier fatigue life model and a type-I censored data processing method. Then, the Pan model is employed to calculate the acceleration factor of this test. A comparison of life predictions between the proposed method and the ones calculated directly by Matlab and Minitab is conducted to demonstrate the practicability and effectiveness of the proposed method. At last, failure analysis and microstructure evolution of lead-free solders are carried out to provide useful guidance for the regular maintenance, replacement of substructure, and subsequent processing of electronic products. PMID:25121138

Embedded-atom-method interatomic potentials from lattice inversion.

PubMed

Yuan, Xiao-Jian; Chen, Nan-Xian; Shen, Jiang; Hu, Wangyu

2010-09-22

The present work develops a physically reliable procedure for building the embedded-atom-method (EAM) interatomic potentials for the metals with fcc, bcc and hcp structures. This is mainly based on Chen-Möbius lattice inversion (Chen et al 1997 Phys. Rev. E 55 R5) and first-principles calculations. Following Baskes (Baskes et al 2007 Phys. Rev. B 75 094113), this new version of the EAM eliminates all of the prior arbitrary choices in the determination of the atomic electron density and pair potential functions. Parameterizing the universal form deduced from the calculations within the density-functional scheme for homogeneous electron gas as the embedding function, the new-type EAM potentials for Cu, Fe and Ti metals have successfully been constructed by considering interatomic interactions up to the fifth neighbor, the third neighbor and the seventh neighbor, respectively. The predictions of elastic constants, structural energy difference, vacancy formation energy and migration energy, activation energy of vacancy diffusion, latent heat of melting and relative volume change on melting all satisfactorily agree with the experimental results available or first-principles calculations. The predicted surface energies for low-index crystal faces and the melting point are in agreement with the experimental data to the same extent as those calculated by other EAM-type potentials such as the FBD-EAM, 2NN MEAM and MS-EAM. In addition, the order among the predicted low-index surface energies is also consistent with the experimental information.

Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

PubMed

Brandenburg, Jan Gerit; Grimme, Stefan

2014-01-01

We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

Electronic band structures and excitonic properties of delafossites: A GW-BSE study

NASA Astrophysics Data System (ADS)

Wang, Xiaoming; Meng, Weiwei; Yan, Yanfa

2017-08-01

We report the band structures and excitonic properties of delafossites CuMO2 (M=Al, Ga, In, Sc, Y, Cr) calculated using the state-of-the-art GW-BSE approach. We evaluate different levels of self-consistency of the GW approximations, namely G0W0, GW0, GW, and QSGW, on the band structures and find that GW0, in general, predicts the band gaps in better agreement with experiments considering the electron-hole effect. For CuCrO2, the HSE wave function is used as the starting point for the perturbative GW0 calculations, since it corrects the band orders wrongly predicted by PBE. The discrepancy about the valence band characters of CuCrO2 is classified based on both HSE and QSGW calculations. The PBE wave functions, already good, are used for other delafossites. All the delafossites are shown to be indirect band gap semiconductors with large exciton binding energies, varying from 0.24 to 0.44 eV, in consistent with experimental findings. The excitation mechanisms are explained by examining the exciton amplitude projections on the band structures. Discrepancies compared with experiments are also addressed. The lowest and strongest exciton, mainly contributed from either Cu 3d → Cu 3p (Al, Ga, In) or Cu 3d → M 3d (M = Sc, Y, Cr) transitions, is always located at the L point of the rhombohedral Brillouin zone.

Polymorphism in Strontium Tungstate SrWO4 under Quasi-Hydrostatic Compression.

PubMed

Santamaria-Perez, David; Errandonea, Daniel; Rodriguez-Hernandez, Placida; Muñoz, Alfonso; Lacomba-Perales, Raul; Polian, Alain; Meng, Yue

2016-10-03

The structural and vibrational properties of SrWO 4 have been studied experimentally up to 27 and 46 GPa, respectively, by angle-dispersive synchrotron X-ray diffraction and Raman spectroscopy measurements as well as using ab initio calculations. The existence of four polymorphs upon quasi-hydrostatic compression is reported. The three phase transitions were found at 11.5, 19.0, and 39.5 GPa. The ambient-pressure SrWO 4 tetragonal scheelite-type structure (S.G. I4 1 /a) undergoes a transition to a monoclinic fergusonite-type structure (S.G. I2/a) at 11.5 GPa with a 1.5% volume decrease. Subsequently, at 19.0 GPa, another structural transformation takes place. Our calculations indicate two possible post-fergusonite phases, one monoclinic and the other orthorhombic. In the diffraction experiments, we observed the theoretically predicted monoclinic LaTaO 4 -type phase coexisting with the fergusonite-type phase up to 27 GPa. The coexistence of the two phases and the large volume collapse at the transition confirm a kinetic hindrance typical of first-order phase transitions. Significant changes in Raman spectra suggest a third pressure-induced transition at 39.5 GPa. The conclusions extracted from the experiments are complemented and supported by ab initio calculations. Our data provides insight into the structural mechanism of the first transition, with the formation of two additional W-O contacts. The fergusonite-type phase can be therefore considered as a structural bridge between the scheelite structure, composed of [WO 4 ] tetrahedra, and the new higher pressure phases, which contain [WO 6 ] octahedra. All the observed phases are compatible with the high-pressure structural systematics predicted for ABO 4 compounds using crystal-chemistry arguments such as the diagram proposed by Bastide.

Predicting the Structure of the Solar Corona for the Total Solar Eclipse of March 29,2006

NASA Technical Reports Server (NTRS)

Mikic, Z.; Linker, J. a.; Lionello, R.; Riley, P.; TItov, V.

2007-01-01

We describe the use of a three-dimensional MHD model to predict the s tructure of the corona prior to the total solar eclipse of March 29, 2006. The calculation uses the observed photospheric radial magnetic f ield as a boundary condition. We use a new version of our model that has an improved description of energy transport in the corona. The mo del allows us to predict the emission of X-ray and EUV radiation in t he corona. We compare the predicted polarization brightness in the co rona with four observations of the eclipse from Greece, Egypt, and Li bya, and we demonstrate that the model accurately predicts the largescale structure of the corona. We also compare X-ray emission from the model with GOES/SXI images.

Ab initio calculation of the potential bubble nucleus 34Si

NASA Astrophysics Data System (ADS)

Duguet, T.; Somà, V.; Lecluse, S.; Barbieri, C.; Navrátil, P.

2017-03-01

Background: The possibility that an unconventional depletion (referred to as a "bubble") occurs in the center of the charge density distribution of certain nuclei due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. Based on a mean-field rationale, a correlation between the occurrence of such a semibubble and an anomalously weak splitting between low angular-momentum spin-orbit partners has been further conjectured. Energy density functional and valence-space shell model calculations have been performed to identify and characterize the best candidates, among which 34Si appears as a particularly interesting case. While the experimental determination of the charge density distribution of the unstable 34Si is currently out of reach, (d ,p ) experiments on this nucleus have been performed recently to test the correlation between the presence of a bubble and an anomalously weak 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Purpose: We study the potential bubble structure of 34Si on the basis of the state-of-the-art ab initio self-consistent Green's function many-body method. Methods: We perform the first ab initio calculations of 34Si and 36S. In addition to binding energies, the first observables of interest are the charge density distribution and the charge root-mean-square radius for which experimental data exist in 36S. The next observable of interest is the low-lying spectroscopy of 35Si and 37S obtained from (d ,p ) experiments along with the spectroscopy of 33Al and 35P obtained from knock-out experiments. The interpretation in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input internucleon interactions. The convergence of the results with respect to the truncation of the many-body expansion, i.e., with respect to the many-body correlations included in the calculation, is studied in detail. We eventually compare our predictions to state-of-the-art multireference energy density functional and shell model calculations. Results: The prediction regarding the (non)existence of the bubble structure in 34Si varies significantly with the nuclear Hamiltonian used. However, demanding that the experimental charge density distribution and the root-mean-square radius of 36S be well reproduced, along with 34Si and 36S binding energies, only leaves the NNLOsat Hamiltonian as a serious candidate to perform this prediction. In this context, a bubble structure, whose fingerprint should be visible in an electron scattering experiment of 34Si, is predicted. Furthermore, a clear correlation is established between the occurrence of the bubble structure and the weakening of the 1 /2--3 /2- splitting in the spectrum of 35Si as compared to 37S. Conclusions: The occurrence of a bubble structure in the charge distribution of 34Si is convincingly established on the basis of state-of-the-art ab initio calculations. This prediction will have to be reexamined in the future when improved chiral nuclear Hamiltonians are constructed. On the experimental side, present results act as a strong motivation to measure the charge density distribution of 34Si in future electron scattering experiments on unstable nuclei. In the meantime, it is of interest to perform one-neutron removal on 34Si and 36S in order to further test our theoretical spectral strength distributions over a wide energy range.

Sensitivity analysis of tall buildings in Semarang, Indonesia due to fault earthquakes with maximum 7 Mw

NASA Astrophysics Data System (ADS)

Partono, Windu; Pardoyo, Bambang; Atmanto, Indrastono Dwi; Azizah, Lisa; Chintami, Rouli Dian

2017-11-01

Fault is one of the dangerous earthquake sources that can cause building failure. A lot of buildings were collapsed caused by Yogyakarta (2006) and Pidie (2016) fault source earthquakes with maximum magnitude 6.4 Mw. Following the research conducted by Team for Revision of Seismic Hazard Maps of Indonesia 2010 and 2016, Lasem, Demak and Semarang faults are three closest earthquake sources surrounding Semarang. The ground motion from those three earthquake sources should be taken into account for structural design and evaluation. Most of tall buildings, with minimum 40 meter high, in Semarang were designed and constructed following the 2002 and 2012 Indonesian Seismic Code. This paper presents the result of sensitivity analysis research with emphasis on the prediction of deformation and inter-story drift of existing tall building within the city against fault earthquakes. The analysis was performed by conducting dynamic structural analysis of 8 (eight) tall buildings using modified acceleration time histories. The modified acceleration time histories were calculated for three fault earthquakes with magnitude from 6 Mw to 7 Mw. The modified acceleration time histories were implemented due to inadequate time histories data caused by those three fault earthquakes. Sensitivity analysis of building against earthquake can be predicted by evaluating surface response spectra calculated using seismic code and surface response spectra calculated from acceleration time histories from a specific earthquake event. If surface response spectra calculated using seismic code is greater than surface response spectra calculated from acceleration time histories the structure will stable enough to resist the earthquake force.

Effect of spin-orbit interactions on the structural stability, thermodynamic properties, and transport properties of lead under pressure

NASA Astrophysics Data System (ADS)

Smirnov, N. A.

2018-03-01

The paper investigates the role of spin-orbit interaction in the prediction of structural stability, lattice dynamics, elasticity, thermodynamic and transport properties (electrical resistivity and thermal conductivity) of lead under pressure with the FP-LMTO (full-potential linear-muffin-tin orbital) method for the first-principles band structure calculations. Our calculations were carried out for three polymorphous lead modifications (fcc, hcp, and bcc) in generalized gradient approximation with the exchange-correlation functional PBEsol. They suggest that compared to the scalar-relativistic calculation, the account for the SO effects insignificantly influences the compressibility of Pb. At the same time, in the calculation of phonon spectra and transport properties, the role of SO interaction is important, at least, for P ≲150 GPa. At higher pressures, the contribution from SO interaction reduces but not vanishes. As for the relative structural stability, our studies show that SO effects influence weakly the pressure of the fcc →hcp transition and much higher the pressure of the hcp →bcc transition.

A strategy to improve the identification reliability of the chemical constituents by high-resolution mass spectrometry-based isomer structure prediction combined with a quantitative structure retention relationship analysis: Phthalide compounds in Chuanxiong as a test case.

PubMed

Zhang, Qingqing; Huo, Mengqi; Zhang, Yanling; Qiao, Yanjiang; Gao, Xiaoyan

2018-06-01

High-resolution mass spectrometry (HRMS) provides a powerful tool for the rapid analysis and identification of compounds in herbs. However, the diversity and large differences in the content of the chemical constituents in herbal medicines, especially isomerisms, are a great challenge for mass spectrometry-based structural identification. In the current study, a new strategy for the structural characterization of potential new phthalide compounds was proposed by isomer structure predictions combined with a quantitative structure-retention relationship (QSRR) analysis using phthalide compounds in Chuanxiong as an example. This strategy consists of three steps. First, the structures of phthalide compounds were reasonably predicted on the basis of the structure features and MS/MS fragmentation patterns: (1) the collected raw HRMS data were preliminarily screened by an in-house database; (2) the MS/MS fragmentation patterns of the analogous compounds were summarized; (3) the reported phthalide compounds were identified, and the structures of the isomers were reasonably predicted. Second, the QSRR model was established and verified using representative phthalide compound standards. Finally, the retention times of the predicted isomers were calculated by the QSRR model, and the structures of these peaks were rationally characterized by matching retention times of the detected chromatographic peaks and the predicted isomers. A multiple linear regression QSRR model in which 6 physicochemical variables were screened was built using 23 phthalide standards. The retention times of the phthalide isomers in Chuanxiong were well predicted by the QSRR model combined with reasonable structure predictions (R 2 =0.955). A total of 81 peaks were detected from Chuanxiong and assigned to reasonable structures, and 26 potential new phthalide compounds were structurally characterized. This strategy can improve the identification efficiency and reliability of homologues in complex materials. Copyright © 2018 Elsevier B.V. All rights reserved.

Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

NASA Astrophysics Data System (ADS)

Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

2018-01-01

Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of sufficiently high quality are available.

Tautomerism and spectroscopic properties of the immunosuppressant azathioprine.

PubMed

Makhyoun, Mohamed A; Massoud, Raghdaa A; Soliman, Saied M

2013-10-01

The molecular structure and the relative stabilities of the four possible tautomers of the immunosuppressant azathioprine (AZA) are calculated by DFT/B3LYP method using different basis sets. The results of the energy analysis and thermodynamic treatment of the obtained data are used to predict the relative stabilities of the AZA tautomers. The effect of solvents such as DMSO and water on the stability of the AZA tautomers was studied using the polarized continuum method (PCM) at the same level of theory. The calculation predicted that, the total energies of all tautomers are decreased indicating that all tautomers are more or less stabilized by the solvent effect. The vibrational spectra of AZA are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation is obtained between the experimental and calculated vibrational frequencies (R(2)=0.997). The electronic spectra of AZA in gas phase and in methanol as solvent are calculated using the TD-DFT method. The calculations predicted bathochromic shift in all the spectral bands in presence of solvent compared to the gas phase. Also the NMR spectra of all tautomers are calculated and the results are correlated with the experimental NMR chemical shifts where the most stable tautomer gives the best correlation coefficient (R(2)=0.996). Copyright © 2013 Elsevier B.V. All rights reserved.

VizieR Online Data Catalog: Brussels nuclear reaction rate library (Aikawa+, 2005)

NASA Astrophysics Data System (ADS)

Aikawa, M.; Arnould, M.; Goriely, S.; Jorissen, A.; Takahashi, K.

2005-07-01

The present data is part of the Brussels nuclear reaction rate library (BRUSLIB) for astrophysics applications and concerns nuclear reaction rate predictions calculated within the statistical Hauser-Feshbach approximation and making use of global and coherent microscopic nuclear models for the quantities (nuclear masses, nuclear structure properties, nuclear level densities, gamma-ray strength functions, optical potentials) entering the rate calculations. (4 data files).

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

DOE PAGES

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

2016-04-12

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. Furthermore, this observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn 3N 4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

NASA Astrophysics Data System (ADS)

Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

2016-04-01

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

PubMed

Caskey, Christopher M; Holder, Aaron; Shulda, Sarah; Christensen, Steven T; Diercks, David; Schwartz, Craig P; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S; Tumas, William; Perkins, John D; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M; Zakutayev, Andriy

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

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

Caskey, Christopher M.; Colorado School of Mines, Golden, Colorado 80401; Larix Chemical Science, Golden, Colorado 80401

2016-04-14

Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experimentsmore » indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn{sub 3}N{sub 4} spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

Predicting the activity of drugs for a group of imidazopyridine anticoccidial compounds.

PubMed

Si, Hongzong; Lian, Ning; Yuan, Shuping; Fu, Aiping; Duan, Yun-Bo; Zhang, Kejun; Yao, Xiaojun

2009-10-01

Gene expression programming (GEP) is a novel machine learning technique. The GEP is used to build nonlinear quantitative structure-activity relationship model for the prediction of the IC(50) for the imidazopyridine anticoccidial compounds. This model is based on descriptors which are calculated from the molecular structure. Four descriptors are selected from the descriptors' pool by heuristic method (HM) to build multivariable linear model. The GEP method produced a nonlinear quantitative model with a correlation coefficient and a mean error of 0.96 and 0.24 for the training set, 0.91 and 0.52 for the test set, respectively. It is shown that the GEP predicted results are in good agreement with experimental ones.

Ensemble-based docking: From hit discovery to metabolism and toxicity predictions.

PubMed

Evangelista, Wilfredo; Weir, Rebecca L; Ellingson, Sally R; Harris, Jason B; Kapoor, Karan; Smith, Jeremy C; Baudry, Jerome

2016-10-15

This paper describes and illustrates the use of ensemble-based docking, i.e., using a collection of protein structures in docking calculations for hit discovery, the exploration of biochemical pathways and toxicity prediction of drug candidates. We describe the computational engineering work necessary to enable large ensemble docking campaigns on supercomputers. We show examples where ensemble-based docking has significantly increased the number and the diversity of validated drug candidates. Finally, we illustrate how ensemble-based docking can be extended beyond hit discovery and toward providing a structural basis for the prediction of metabolism and off-target binding relevant to pre-clinical and clinical trials. Copyright © 2016 Elsevier Ltd. All rights reserved.

Strength design of Zr(x)Ti(x)Hf(x)Nb(x)Mo(x) alloys based on empirical electron theory of solids and molecules

NASA Astrophysics Data System (ADS)

Li, Y. K.; Chen, Y. W.; Cheng, X. W.; Wu, C.; Cheng, B.

2018-05-01

In this paper, the valence electron structure parameters of Zr(x)Ti(x)Hf(x)Nb(x)Mo(x) alloys were calculated based on the empirical electron theory of solids and molecules (EET), and their performance through these parameters were predicted. Subsequently, the alloys with special valence electron structure parameters were prepared byarc melting. The hardness and high-temperature mechanical properties were analyzed to verify the prediction. Research shows that the influence of shared electron number nA on the strongest bond determines the strength of these alloys and the experiments are consistent with the theoretical prediction.

Xanthine oxidase inhibitors beyond allopurinol and febuxostat; an overview and selection of potential leads based on in silico calculated physico-chemical properties, predicted pharmacokinetics and toxicity.

PubMed

Šmelcerović, Andrija; Tomović, Katarina; Šmelcerović, Žaklina; Petronijević, Živomir; Kocić, Gordana; Tomašič, Tihomir; Jakopin, Žiga; Anderluh, Marko

2017-07-28

Xanthine oxidase (XO), a versatile metalloflavoprotein enzyme, catalyzes the oxidative hydroxylation of hypoxanthine and xanthine to uric acid in purine catabolism while simultaneously producing reactive oxygen species. Both lead to the gout-causing hyperuricemia and oxidative damage of the tissues where overactivity of XO is present. Over the past years, significant progress and efforts towards the discovery and development of new XO inhibitors have been made and we believe that not only experts in the field, but also general readership would benefit from a review that addresses this topic. Accordingly, the aim of this article was to overview and select the most potent recently reported XO inhibitors and to compare their structures, mechanisms of action, potency and effectiveness of their inhibitory activity, in silico calculated physico-chemical properties as well as predicted pharmacokinetics and toxicity. Derivatives of imidazole, 1,3-thiazole and pyrimidine proved to be more potent than febuxostat while also displaying/possessing favorable predicted physico-chemical, pharmacokinetic and toxicological properties. Although being structurally similar to febuxostat, these optimized inhibitors bear some structural freshness and could be adopted as hits for hit-to-lead development and further evaluation by in vivo studies towards novel drug candidates, and represent valuable model structures for design of novel XO inhibitors. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Spectroscopic and DFT studies of bis-3-hydroxypyridinium and bis-3-hydroxymethylpyridinium dibromides with tetramethylene linker

NASA Astrophysics Data System (ADS)

Komasa, Anna

2018-01-01

Experimental and theoretical IR, Raman, UV-Vis, 1H and 13C NMR spectra of 1,4-di(3-hydroxypyridinium)butane dibromide and 1,4-di(3-hydroxymethylpyridinium)butane dibromide were obtained and analyzed. Optimized geometrical structures of the studied compounds were calculated by B3LYP method using 6-311++G(d,p) basis set and employed to determine the theoretical wavenumbers and intensities of IR and Raman spectra. The frequency assignments were supported by the potential energy distribution (PED) analysis. The significant role of the intermolecular interactions and the hydrogen bond was revealed on the basis of IR spectra. The calculated GIAO/B3LYP/6-311++G(d,p) isotropic magnetic shielding constants were used to predict the 1H and 13C chemical shifts for the optimized structures. Accuracy of the prediction of 1H and 13C chemical shifts was significantly improved by a simulation of the solvent in calculations. On the basis of UV-Vis spectra the acid-base equilibrium in the water solution of 1,4-di(3-hydroxypyridinium)butane dibromide was found.

Exact calculation of distributions on integers, with application to sequence alignment.

PubMed

Newberg, Lee A; Lawrence, Charles E

2009-01-01

Computational biology is replete with high-dimensional discrete prediction and inference problems. Dynamic programming recursions can be applied to several of the most important of these, including sequence alignment, RNA secondary-structure prediction, phylogenetic inference, and motif finding. In these problems, attention is frequently focused on some scalar quantity of interest, a score, such as an alignment score or the free energy of an RNA secondary structure. In many cases, score is naturally defined on integers, such as a count of the number of pairing differences between two sequence alignments, or else an integer score has been adopted for computational reasons, such as in the test of significance of motif scores. The probability distribution of the score under an appropriate probabilistic model is of interest, such as in tests of significance of motif scores, or in calculation of Bayesian confidence limits around an alignment. Here we present three algorithms for calculating the exact distribution of a score of this type; then, in the context of pairwise local sequence alignments, we apply the approach so as to find the alignment score distribution and Bayesian confidence limits.

Fast modeling of flux trapping cascaded explosively driven magnetic flux compression generators.

PubMed

Wang, Yuwei; Zhang, Jiande; Chen, Dongqun; Cao, Shengguang; Li, Da; Liu, Chebo

2013-01-01

To predict the performance of flux trapping cascaded flux compression generators, a calculation model based on an equivalent circuit is investigated. The system circuit is analyzed according to its operation characteristics in different steps. Flux conservation coefficients are added to the driving terms of circuit differential equations to account for intrinsic flux losses. To calculate the currents in the circuit by solving the circuit equations, a simple zero-dimensional model is used to calculate the time-varying inductance and dc resistance of the generator. Then a fast computer code is programmed based on this calculation model. As an example, a two-staged flux trapping generator is simulated by using this computer code. Good agreements are achieved by comparing the simulation results with the measurements. Furthermore, it is obvious that this fast calculation model can be easily applied to predict performances of other flux trapping cascaded flux compression generators with complex structures such as conical stator or conical armature sections and so on for design purpose.

Thermal, electronic and ductile properties of lead-chalcogenides under pressure.

PubMed

Gupta, Dinesh C; Bhat, Idris Hamid

2013-09-01

Fully relativistic pseudo-potential ab-initio calculations have been performed to investigate the high pressure phase transition, elastic and electronic properties of lead-chalcogenides including the less known lead polonium. The calculated ground state parameters, for the rock-salt structure show good agreement with the experimental data. PbS, PbSe, PbTe and PbPo undergo a first-order phase transition from rock-salt to CsCl structure at 19.4, 15.5, 11.5 and 7.3 GPa, respectively. The elastic properties have also been calculated. The calculations successfully predicted the location of the band gap at L-point of Brillouin zone and the band gap for each material at ambient pressure. It is observed that unlike other lead-chalcogenides, PbPo is semi-metal at ambient pressure. The pressure variation of the energy gap indicates that these materials metalize under pressure. The electronic structures of these materials have been computed in parent as well as in high pressure B2 phase.

Flutter calculations in three degrees of freedom

NASA Technical Reports Server (NTRS)

Theodorsen, Theodore; Garrick, I E

1942-01-01

The present paper is a continuation of the general study of flutter published in NACA reports nos. 496 and 685. The paper is mainly devoted to flutter in three degrees of freedom (bending, torsion, and aileron) for which a number of selected cases have been calculated and presented in graphical form. The results are analyzed and discussed with regard to the effects of structural damping, of fractional-span ailerons, and of mass-balancing. The analysis shows that more emphasis should be put on the effect of structural damping and less on mass-balancing. The conclusion is drawn that a definite minimum amount of structural damping, which is usually found to be present, is essential in the calculations for an adequate description of the flutter case. Theoretical flutter predictions are thus brought into closer agreement with the facts of experience. A brief discussion is included of a particular biplane that had experienced flutter at about 200 miles per hour. Some simplifications have been achieved in the method of calculation. (author)

Theoretical modeling of the electronic structure and exchange interactions in Cu(II)Pc

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.; Wang, Hai; Wu, Zhenlin; Gardener, Jules; Heutz, Sandrine; Jones, Tim; Aeppli, Gabriel

2012-12-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine (Cu(II)Pc) crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green's function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α- and β-phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Theoretical modeling of the electronic structure and exchange interactions in a Cu(II)Pc one-dimensional chain

NASA Astrophysics Data System (ADS)

Wu, Wei; Fisher, A. J.; Harrison, N. M.

2011-07-01

We calculate the electronic structure and exchange interactions in a copper(II)phthalocyanine [Cu(II)Pc] crystal as a one-dimensional molecular chain using hybrid exchange density functional theory (DFT). In addition, the intermolecular exchange interactions are also calculated in a molecular dimer using Green’s function perturbation theory (GFPT) to illustrate the underlying physics. We find that the exchange interactions depend strongly on the stacking angle, but weakly on the sliding angle (defined in the text). The hybrid DFT calculations also provide an insight into the electronic structure of the Cu(II)Pc molecular chain and demonstrate that on-site electron correlations have a significant effect on the nature of the ground state, the band gap, and magnetic excitations. The exchange interactions predicted by our DFT calculations and GFPT calculations agree qualitatively with the recent experimental results on newly found η-Cu(II)Pc and the previous results for the α and β phases. This work provides a reliable theoretical basis for the further application of Cu(II)Pc to molecular spintronics and organic-based quantum information processing.

Personalized Prediction of Psychosis: External validation of the NAPLS2 Psychosis Risk Calculator with the EDIPPP project

PubMed Central

Carrión, Ricardo E.; Cornblatt, Barbara A.; Burton, Cynthia Z.; Tso, Ivy F; Auther, Andrea; Adelsheim, Steven; Calkins, Roderick; Carter, Cameron S.; Niendam, Tara; Taylor, Stephan F.; McFarlane, William R.

2016-01-01

Objective In the current issue, Cannon and colleagues, as part of the second phase of the North American Prodrome Longitudinal Study (NAPLS2), report on a risk calculator for the individualized prediction of developing a psychotic disorder in a 2-year period. The present study represents an external validation of the NAPLS2 psychosis risk calculator using an independent sample of subjects at clinical high risk for psychosis collected as part of the Early Detection, Intervention, and Prevention of Psychosis Program (EDIPPP). Methods 176 subjects with follow-up (from the total EDIPPP sample of 210) rated as clinical high-risk (CHR) based on the Structured Interview for Prodromal Syndromes were used to construct a new prediction model with the 6 significant predictor variables in the NAPLS2 psychosis risk calculator (unusual thoughts, suspiciousness, Symbol Coding, verbal learning, social functioning decline, baseline age, and family history). Discrimination performance was assessed with the area under the receiver operating curve (AUC). The NAPLS2 risk calculator was then used to generate a psychosis risk estimate for each case in the external validation sample. Results The external validation model showed good discrimination, with an AUC of 79% (95% CI 0.644–0.937). In addition, the personalized risk generated by the NAPLS calculator provided a solid estimation of the actual conversion outcome in the validation sample. Conclusions In the companion papers in this issue, two independent samples of CHR subjects converge to validate the NAPLS2 psychosis risk calculator. This prediction calculator represents a meaningful step towards early intervention and personalized treatment of psychotic disorders. PMID:27363511

Statistical time-dependent model for the interstellar gas

NASA Technical Reports Server (NTRS)

Gerola, H.; Kafatos, M.; Mccray, R.

1974-01-01

We present models for temperature and ionization structure of low, uniform-density (approximately 0.3 per cu cm) interstellar gas in a galactic disk which is exposed to soft X rays from supernova outbursts occurring randomly in space and time. The structure was calculated by computing the time record of temperature and ionization at a given point by Monte Carlo simulation. The calculation yields probability distribution functions for ionized fraction, temperature, and their various observable moments. These time-dependent models predict a bimodal temperature distribution of the gas that agrees with various observations. Cold regions in the low-density gas may have the appearance of clouds in 21-cm absorption. The time-dependent model, in contrast to the steady-state model, predicts large fluctuations in ionization rate and the existence of cold (approximately 30 K), ionized (ionized fraction equal to about 0.1) regions.

Solvatochromism and prototropic reactions of 2-quinoxalinone

NASA Astrophysics Data System (ADS)

Santra, Swadeshmukul; Dogra, Sneh K.

1996-06-01

Spectral characteristics of 2-quinoxalinone (QNH) in twelve different solvents and those of N-methyl-2-quinoxalinone (QNM) and 2-methoxyquinoxaline (QOM) in five solvents have been studied. Spectral data, along with prototropic reactions have confirmed that QNH possesses a cyclic amide structure. Charge density and electrostatic potential energy mapping calculations carried out using semi-empirical quantum mechanical methods predict that the monocations of QNH and QNM are formed by protonating carbonyl O-11, whereas that of QOM, by protonating, N-1. Dications of all the molecules are formed by protonating N-4. Deprotonation of QNH takes place after QNH reorganizing to enol form, whereas CNDO/S-CI calculations predict that monoanion formed by deprotonation has a structure where charge density is delocalized over C-2, N-1 and O-11. p Ka and pK a∗ values for the various prototropic reactions have been measured and discussed.

Design Principles for Covalent Organic Frameworks as Efficient Electrocatalysts in Clean Energy Conversion and Green Oxidizer Production.

PubMed

Lin, Chun-Yu; Zhang, Lipeng; Zhao, Zhenghang; Xia, Zhenhai

2017-05-01

Covalent organic frameworks (COFs), an emerging class of framework materials linked by covalent bonds, hold potential for various applications such as efficient electrocatalysts, photovoltaics, and sensors. To rationally design COF-based electrocatalysts for oxygen reduction and evolution reactions in fuel cells and metal-air batteries, activity descriptors, derived from orbital energy and bonding structures, are identified with the first-principle calculations for the COFs, which correlate COF structures with their catalytic activities. The calculations also predict that alkaline-earth metal-porphyrin COFs could catalyze the direct production of H 2 O 2 , a green oxidizer and an energy carrier. These predictions are supported by experimental data, and the design principles derived from the descriptors provide an approach for rational design of new electrocatalysts for both clean energy conversion and green oxidizer production. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Raman and infrared spectra and theoretical calculations of dipicolinic acid, dinicotinic acid, and their dianions

NASA Astrophysics Data System (ADS)

McCann, Kathleen; Laane, Jaan

2008-11-01

The Raman and infrared spectra of dipicolinic acid (DPA) and dinicotinic acid (DNic) and their salts (CaDPA, Na 2DPA, and CaDNic) have been recorded and the spectra have been assigned. Ab initio and DFT calculations were carried out to predict the structures and vibrational spectra and were compared to the experimental results. Because of extensive intermolecular hydrogen bonding in the crystals of these molecules, the calculated structures and spectra for the individual molecules agree only moderately well with the experimental values. Theoretical calculations were also carried out for DPA dimers and DPA·2H 2O to better understand the intermolecular interactions. The spectra do show that DPA and its calcium salt, which are present in anthrax spores, can be distinguished from the very similar DNic and CaDNic.

Comparison of predicted binders in Rhipicephalus (Boophilus) microplus intestine protein variants Bm86 Campo Grande strain, Bm86 and Bm95.

PubMed

Andreotti, Renato; Pedroso, Marisela S; Caetano, Alexandre R; Martins, Natália F

2008-01-01

This paper reports the sequence analysis of Bm86 Campo Grande strain comparing it with Bm86 and Bm95 antigens from the preparations TickGardPLUS and Gavac, respectively. The PCR product was cloned into pMOSBlue and sequenced. The secondary structure prediction tool PSIPRED was used to calculate alpha helices and beta strand contents of the predicted polypeptide. The hydrophobicity profile was calculated using the algorithms from the Hopp and Woods method, in addition to identification of potential MHC class-I binding regions in the antigens. Pair-wise alignment revealed that the similarity between Bm86 Campo Grande strain and Bm86 is 0.2% higher than that between Bm86 Campo Grande strain and Bm95 antigens. The identities were 96.5% and 96.3% respectively. Major suggestive differences in hydrophobicity were predicted among the sequences in two specific regions.

A novel representation for apoptosis protein subcellular localization prediction using support vector machine.

PubMed

Zhang, Li; Liao, Bo; Li, Dachao; Zhu, Wen

2009-07-21

Apoptosis, or programmed cell death, plays an important role in development of an organism. Obtaining information on subcellular location of apoptosis proteins is very helpful to understand the apoptosis mechanism. In this paper, based on the concept that the position distribution information of amino acids is closely related with the structure and function of proteins, we introduce the concept of distance frequency [Matsuda, S., Vert, J.P., Ueda, N., Toh, H., Akutsu, T., 2005. A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci. 14, 2804-2813] and propose a novel way to calculate distance frequencies. In order to calculate the local features, each protein sequence is separated into p parts with the same length in our paper. Then we use the novel representation of protein sequences and adopt support vector machine to predict subcellular location. The overall prediction accuracy is significantly improved by jackknife test.

Correlation of MFOLD-predicted DNA secondary structures with separation patterns obtained by capillary electrophoresis single-strand conformation polymorphism (CE-SSCP) analysis.

PubMed

Glavac, Damjan; Potocnik, Uros; Podpecnik, Darja; Zizek, Teofil; Smerkolj, Sava; Ravnik-Glavac, Metka

2002-04-01

We have studied 57 different mutations within three beta-globin gene promoter fragments with sizes 52 bp, 77 bp, and 193 bp by fluorescent capillary electrophoresis CE-SSCP analysis. For each mutation and wild type, energetically most-favorable predicted secondary structures were calculated for sense and antisense strands using the MFOLD DNA-folding algorithm in order to investigate if any correlation exists between predicted DNA structures and actual CE migration time shifts. The overall CE-SSCP detection rate was 100% for all mutations in three studied DNA fragments. For shorter 52 bp and 77 bp DNA fragments we obtained a positive correlation between the migration time shifts and difference in free energy values of predicted secondary structures at all temperatures. For longer 193 bp beta-globin gene fragments with 46 mutations MFOLD predicted different secondary structures for 89% of mutated strands at 25 degrees C and 40 degrees C. However, the magnitude of the mobility shifts did not necessarily correlate with their secondary structures and free energy values except for the sense strand at 40 degrees C where this correlation was statistically significant (r = 0.312, p = 0.033). Results of this study provided more direct insight into the mechanism of CE-SSCP and showed that MFOLD prediction could be helpful in making decisions about the running temperatures and in prediction of CE-SSCP data patterns, especially for shorter (50-100 bp) DNA fragments. Copyright 2002 Wiley-Liss, Inc.

Spectral structure of electron antineutrinos from nuclear reactors.

PubMed

Dwyer, D A; Langford, T J

2015-01-09

Recent measurements of the positron energy spectrum obtained from inverse beta decay interactions of reactor electron antineutrinos show an excess in the 4 to 6 MeV region relative to current predictions. First-principles calculations of fission and beta decay processes within a typical pressurized water reactor core identify prominent fission daughter isotopes as a possible origin for this excess. These calculations also predict percent-level substructures in the antineutrino spectrum due to Coulomb effects in beta decay. Precise measurement of these substructures can elucidate the nuclear processes occurring within reactors. These substructures can be a systematic issue for measurements utilizing the detailed spectral shape.

Study of the structure of yrast bands of neutron-rich 114-124Pd isotopes

NASA Astrophysics Data System (ADS)

Chaudhary, Ritu; Devi, Rani; Khosa, S. K.

2018-02-01

The projected shell model calculations have been carried out in the neutron-rich 114-124Pd isotopic mass chain. The results have been obtained for the deformation systematics of E(2+1) and E(4+1)/E({2}+1) values, BCS subshell occupation numbers, yrast spectra, backbending phenomena, B( E2) transition probabilities and g-factors in these nuclei. The observed systematics of E(2+1) values and R_{42} ratios in the 114-124Pd isotopic mass chain indicate that there is a decrease of collectivity as the neutron number increases from 68 to 78. The occurrence of backbending in these nuclei as well as the changes in the calculated B( E2) transition probabilities and g -factors predict that there are changes in the structure of yrast bands in these nuclei. These changes occur at the spin where there is crossing of g-band by 2-qp bands. The predicted backbendings and predicted values of B( E2)s and g-factors in some of the isotopes need to be confirmed experimentally.

Predicting the melting temperature of ice-Ih with only electronic structure information as input.

PubMed

Pinnick, Eric R; Erramilli, Shyamsunder; Wang, Feng

2012-07-07

The melting temperature of ice-Ih was calculated with only electronic structure information as input by creating a problem-specific force field. The force field, Water model by AFM for Ice and Liquid (WAIL), was developed with the adaptive force matching (AFM) method by fitting to post-Hartree-Fock quality forces obtained in quantum mechanics∕molecular mechanics calculations. WAIL predicts the ice-Ih melting temperature to be 270 K. The model also predicts the densities of ice and water, the temperature of maximum density of water, the heat of vaporizations, and the radial distribution functions for both ice and water in good agreement with experimental measurements. The non-dissociative WAIL model is very similar to a flexible version of the popular TIP4P potential and has comparable computational cost. By customizing to problem-specific configurations with the AFM approach, the resulting model is remarkably more accurate than any variants of TIP4P for simulating ice-Ih and water in the temperature range from 253 K and 293 K under ambient pressure.

Ion Engine Plume Interaction Calculations for Prototypical Prometheus 1

NASA Technical Reports Server (NTRS)

Mandell, Myron J.; Kuharski, Robert A.; Gardner, Barbara M.; Katz, Ira; Randolph, Tom; Dougherty, Ryan; Ferguson, Dale C.

2005-01-01

Prometheus 1 is a conceptual mission to demonstrate the use of atomic energy for distant space missions. The hypothetical spacecraft design considered in this paper calls for multiple ion thrusters, each with considerably higher beam energy and beam current than have previously flown in space. The engineering challenges posed by such powerful thrusters relate not only to the thrusters themselves, but also to designing the spacecraft to avoid potentially deleterious effects of the thruster plumes. Accommodation of these thrusters requires good prediction of the highest angle portions of the main beam, as well as knowledge of clastically scattered and charge exchange ions, predictions for grid erosion and contamination of surfaces by eroded grid material, and effects of the plasma plume on radio transmissions. Nonlinear interactions of multiple thrusters are also of concern. In this paper we describe two- and three-dimensional calculations for plume structure and effects of conceptual Prometheus 1 ion engines. Many of the techniques used have been validated by application to ground test data for the NSTAR and NEXT ion engines. Predictions for plume structure and possible sputtering and contamination effects will be presented.

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

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

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Phase stabilities of pyrite-related MTCh compounds (M=Ni, Pd, Pt; T=Si, Ge, Sn, Pb; Ch=S, Se, Te): A systematic DFT study

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

Bachhuber, Frederik; School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland; Krach, Alexander

2015-03-15

Pyrite-type and related systems appear for a wide range of binary and ternary combinations of transition metals and main group elements that form Zintl type dumbbell anion units. Those representatives with 20 valence electrons exhibit an extraordinary structural flexibility and interesting properties as low-gap semiconductors or thermoelectric and electrode materials. This work is devoted to the systematic exploration of novel compounds within the class of MTCh compounds (M=Ni, Pd, Pt; T=Si, Ge, Sn, Pb; Ch=S, Se, Te) by means of density functional calculations. Their preferred structures are predicted from an extended scheme of colored pyrites and marcasites. To determine theirmore » stabilities, competing binary MT{sub 2} and MCh{sub 2} boundary phases are taken into account as well as ternary M{sub 3}T{sub 2}Ch{sub 2} and M{sub 2}T{sub 3}Ch{sub 3} systems. Recently established stability diagrams are presented to account for MTCh ordering phenomena with a focus on a not-yet-reported ordering variant of the NiAs{sub 2} type. Due to the good agreement with experimental data available for several PtTCh systems, the predictions for the residual systems are considered sufficiently accurate. - Graphical abstract: Compositional and structural stability of MTCh compounds is investigated from first principle calculations. A conceptional approach is presented to study and predict novel stable and metastable compounds and structures of low gap semiconductors with TCh dumbbell units that are isoelectronic and structurally related to pyrite (FeS{sub 2}). - Highlights: • Study of compositional stability of MTCh vs. M{sub 3}T{sub 2}Ch{sub 2} and M{sub 2}T{sub 3}Ch{sub 3} compounds. • Study of structural stability of known and novel MTCh compounds. • Prediction of novel stable and metastable structures and compounds isoelectronic to pyrite, FeS{sub 2}.« less

Stabilization of flat aromatic Si6 rings analogous to benzene: ab initio theoretical prediction.

PubMed

Zdetsis, Aristides D

2007-12-07

It is shown by ab initio calculations, based on density functional (DFT/B3LYP), and high level coupled-cluster [CCSD(T)] and quadratic CI [QCISD(T)] methods, that flat aromatic silicon structures analogous to benzene (C6H6) can be stabilized in the presence of lithium. The resulting planar Si6Li6 structure is both stable and aromatic, sharing many key characteristics with benzene. To facilitate possible synthesis and characterization of these species, routes of formation with high exothermicity are suggested and several spectral properties (including optical absorption, infrared, and Raman) are calculated.

First-Principles Study of Antimony Doping Effects on the Iron-Based Superconductor CaFe(SbxAs1-x)2

NASA Astrophysics Data System (ADS)

Nagai, Yuki; Nakamura, Hiroki; Machida, Masahiko; Kuroki, Kazuhiko

2015-09-01

We study antimony doping effects on the iron-based superconductor CaFe(SbxAs1-x)2 by using the first-principles calculation. The calculations reveal that the substitution of a doped antimony atom into As of the chainlike As layers is more stable than that into FeAs layers. This prediction can be checked by experiments. Our results suggest that doping homologous elements into the chainlike As layers, which only exist in the novel 112 system, is responsible for rising up the critical temperature. We discuss antimony doping effects on the electronic structure. It is found that the calculated band structures with and without the antimony doping are similar to each other within our framework.

The prediction of a new high-pressure phase of hafnia using first-principles computations

NASA Astrophysics Data System (ADS)

Al-Khatatbeh, Y.; Tarawneh, K.; Hamad, B.

2018-02-01

Using density functional theory (DFT) calculations, we predicted a new high- pressure phase of hafnia (HfO2). We found the hexagonal phase (Ni2In-type structure; space group: P63 /mmc) to be the stable phase at ultrahigh pressures greater than ~386 GPa. Our findings are consistent with recent calculations performed on the similar dioxide ZrO2 [M. Durandurdu, J. Solid State Chem. 230, 233 (2015)] where this phase has been claimed to be the most stable at pressures greater than 380 GPa. The Birch-Murnaghan equation of state (BM- EOS) of the new phase shows that this phase is more compressible and less dense than Fe2P-type phase. Additionally, the hardness calculations using a scaling model confirmed that our newly predicted phase has a similar hardness compared to the other HfO2 phases, indicating that none of the HfO2 phases can be considered to be superhard.

Ag@ZnO core-shell nanoparticles study by first principle: The structural, magnetic and optical properties

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

Cheng, Hai-Xia; Wang, Xiao-Xu; Beijing Computing Center, Beijing 100094

Ag@ZnO core-shell nanoparticles of around 72 atoms have been investigated by the density functional theory, revealing proving for the first time that the core-shell structure exhibits a shrinkage phenomenon from outer shell in agreement with the other studies in literatures. Our calculations predict that the Ag@ZnO core-shell structure is a ferromagnetic spin polarized state, and the magnetism mainly stems from the spin splitting of 2p electrons of O atoms. In addition, the total and partial DOS of Ag@ZnO indicate that the nanostructure is a half-metallic nanoparticle and has the characters of the p-type semiconductor. Furthermore, the optical properties calculations showmore » that the absorption edge of Ag@ZnO have a red shift and good photocatalysis compare to that of the bulk ZnO. These results of the Ag@ZnO core-shell structure obtain a well agreement with the experimental measurement. - Graphical abstract: Geometric structure of (a) Ag@ZnO core-shell nanostructure; (b) the core of Ag; (c) the shell of ZnO The core-shell nanoparticle Ag@ZnO contains Ag inner core of radius of 4 Å and ZnO outer shell with thickness of 2 Å. Ag@ZnO core-shell nanoparticles of around 72 atoms have been proved for the first time that the core-shell structure exhibit a shrinkage phenomenon from outer shell. Our calculations predict that the Ag@ZnO core-shell structure is a half-metallic nanoparticle and has the characters of the p-type semiconductor. The absorption edge of Ag@ZnO have a red shift and get good photo-catalysis compare to that of the bulk ZnO.« less

Contact Prediction for Beta and Alpha-Beta Proteins Using Integer Linear Optimization and its Impact on the First Principles 3D Structure Prediction Method ASTRO-FOLD

PubMed Central

Rajgaria, R.; Wei, Y.; Floudas, C. A.

2010-01-01

An integer linear optimization model is presented to predict residue contacts in β, α + β, and α/β proteins. The total energy of a protein is expressed as sum of a Cα – Cα distance dependent contact energy contribution and a hydrophobic contribution. The model selects contacts that assign lowest energy to the protein structure while satisfying a set of constraints that are included to enforce certain physically observed topological information. A new method based on hydrophobicity is proposed to find the β-sheet alignments. These β-sheet alignments are used as constraints for contacts between residues of β-sheets. This model was tested on three independent protein test sets and CASP8 test proteins consisting of β, α + β, α/β proteins and was found to perform very well. The average accuracy of the predictions (separated by at least six residues) was approximately 61%. The average true positive and false positive distances were also calculated for each of the test sets and they are 7.58 Å and 15.88 Å, respectively. Residue contact prediction can be directly used to facilitate the protein tertiary structure prediction. This proposed residue contact prediction model is incorporated into the first principles protein tertiary structure prediction approach, ASTRO-FOLD. The effectiveness of the contact prediction model was further demonstrated by the improvement in the quality of the protein structure ensemble generated using the predicted residue contacts for a test set of 10 proteins. PMID:20225257

Electronic and optical properties of titanium nitride bulk and surfaces from first principles calculations

NASA Astrophysics Data System (ADS)

Mehmood, Faisal; Pachter, Ruth; Murphy, Neil R.; Johnson, Walter E.

2015-11-01

Prediction of the frequency-dependent dielectric function of thin films poses computational challenges, and at the same time experimental characterization by spectroscopic ellipsometry remains difficult to interpret because of changes in stoichiometry and surface morphology, temperature, thickness of the film, or substrate. In this work, we report calculations for titanium nitride (TiN), a promising material for plasmonic applications because of less loss and other practical advantages compared to noble metals. We investigated structural, electronic, and optical properties of stoichiometric bulk TiN, as well as of the TiN(100), TiN(110), and TiN(111) outermost surfaces. Density functional theory (DFT) and many-body GW methods (Green's (G) function-based approximation with screened Coulomb interaction (W)) were used, ranging from G0W0, GW0 to partially self-consistent sc-GW0, as well as the GW-BSE (Bethe-Salpeter equation) and time-dependent DFT (TDDFT) methods for prediction of the optical properties. Structural parameters and the band structure for bulk TiN were shown to be consistent with previous work. Calculated dielectric functions, plasma frequencies, reflectivity, and the electron energy loss spectrum demonstrated consistency with experiment at the GW0-BSE level. Deviations from experimental data are expected due to varying experimental conditions. Comparison of our results to spectroscopic ellipsometry data for realistic nanostructures has shown that although TDDFT may provide a computationally feasible level of theory in evaluation of the dielectric function, application is subject to validation with GW-BSE calculations.

Local and average structure of Mn- and La-substituted BiFeO{sub 3}

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

Jiang, Bo; Selbach, Sverre M., E-mail: selbach@ntnu.no

2017-06-15

The local and average structure of solid solutions of the multiferroic perovskite BiFeO{sub 3} is investigated by synchrotron X-ray diffraction (XRD) and electron density functional theory (DFT) calculations. The average experimental structure is determined by Rietveld refinement and the local structure by total scattering data analyzed in real space with the pair distribution function (PDF) method. With equal concentrations of La on the Bi site or Mn on the Fe site, La causes larger structural distortions than Mn. Structural models based on DFT relaxed geometry give an improved fit to experimental PDFs compared to models constrained by the space groupmore » symmetry. Berry phase calculations predict a higher ferroelectric polarization than the experimental literature values, reflecting that structural disorder is not captured in either average structure space group models or DFT calculations with artificial long range order imposed by periodic boundary conditions. Only by including point defects in a supercell, here Bi vacancies, can DFT calculations reproduce the literature results on the structure and ferroelectric polarization of Mn-substituted BiFeO{sub 3}. The combination of local and average structure sensitive experimental methods with DFT calculations is useful for illuminating the structure-property-composition relationships in complex functional oxides with local structural distortions. - Graphical abstract: The experimental and simulated partial pair distribution functions (PDF) for BiFeO{sub 3}, BiFe{sub 0.875}Mn{sub 0.125}O{sub 3}, BiFe{sub 0.75}Mn{sub 0.25}O{sub 3} and Bi{sub 0.9}La{sub 0.1}FeO{sub 3}.« less

Synthetic cannabinoids: In silico prediction of the cannabinoid receptor 1 affinity by a quantitative structure-activity relationship model.

PubMed

Paulke, Alexander; Proschak, Ewgenij; Sommer, Kai; Achenbach, Janosch; Wunder, Cora; Toennes, Stefan W

2016-03-14

The number of new synthetic psychoactive compounds increase steadily. Among the group of these psychoactive compounds, the synthetic cannabinoids (SCBs) are most popular and serve as a substitute of herbal cannabis. More than 600 of these substances already exist. For some SCBs the in vitro cannabinoid receptor 1 (CB1) affinity is known, but for the majority it is unknown. A quantitative structure-activity relationship (QSAR) model was developed, which allows the determination of the SCBs affinity to CB1 (expressed as binding constant (Ki)) without reference substances. The chemically advance template search descriptor was used for vector representation of the compound structures. The similarity between two molecules was calculated using the Feature-Pair Distribution Similarity. The Ki values were calculated using the Inverse Distance Weighting method. The prediction model was validated using a cross validation procedure. The predicted Ki values of some new SCBs were in a range between 20 (considerably higher affinity to CB1 than THC) to 468 (considerably lower affinity to CB1 than THC). The present QSAR model can serve as a simple, fast and cheap tool to get a first hint of the biological activity of new synthetic cannabinoids or of other new psychoactive compounds. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Optically induced lattice deformations, electronic structure changes, and enhanced superconductivity in YBa 2Cu 3O 6.48

DOE PAGES

Mankowsky, R.; Fechner, M.; Forst, M.; ...

2017-02-28

Resonant optical excitation of apical oxygen vibrational modes in the normal state of underdoped YBa 2Cu 3O 6+x induces a transient state with optical properties similar to those of the equilibrium superconducting state. Amongst these, a divergent imaginary conductivity and a plasma edge are transiently observed in the photo-stimulated state. Femtosecond hard x-ray diffraction experiments have been used in the past to identify the transient crystal structure in this non-equilibrium state. Here, we start from these crystallographic features and theoretically predict the corresponding electronic rearrangements that accompany these structural deformations. Using density functional theory, we predict enhanced hole-doping of themore » CuO 2 planes. The empty chain Cu dy2-z2 orbital is calculated to strongly reduce in energy, which would increase c-axis transport and potentially enhance the interlayer Josephson coupling as observed in the THz-frequency response. From these results, we calculate changes in the soft x-ray absorption spectra at the Cu L-edge. As a result, femtosecond x-ray pulses from a free electron laser are used to probe changes in absorption at two photon energies along this spectrum and provide data consistent with these predictions.« less

Quantum chemical ab initio prediction of proton exchange barriers between CH{sub 4} and different H-zeolites

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

Tuma, Christian; Sauer, Joachim, E-mail: js@chemie.hu-berlin.de

2015-09-14

A hybrid MP2:DFT (second-order Møller–Plesset perturbation theory–density functional theory) method that combines MP2 calculations for cluster models with DFT calculations for the full periodic structure is used to localize minima and transition structures for proton jumps at different Brønsted sites in different frameworks (chabazite, faujasite, ferrierite, and ZSM-5) and at different crystallographic positions of a given framework. The MP2 limit for the periodic structures is obtained by extrapolating the results of a series of cluster models of increasing size. A coupled-cluster (CCSD(T)) correction to MP2 energies is calculated for cluster models consisting of three tetrahedra. For the adsorption energies, thismore » difference is small, between 0.1 and 0.9 kJ/mol, but for the intrinsic proton exchange barriers, this difference makes a significant (10.85 ± 0.25 kJ/mol) and almost constant contribution across different systems. The total values of the adsorption energies vary between 22 and 34 kJ/mol, whereas the total proton exchange energy barriers fall in the narrow range of 152–156 kJ/mol. After adding nuclear motion contributions (harmonic approximation, 298 K), intrinsic enthalpy barriers between 134 and 141 kJ/mol and apparent energy barriers between 105 and 118 kJ/mol are predicted for the different sites examined for the different frameworks. These predictions are consistent with experimental results available for faujasite, ferrierite, and ZSM-5.« less

An orientation sensitive approach in biomolecule interaction quantitative structure-activity relationship modeling and its application in ion-exchange chromatography.

PubMed

Kittelmann, Jörg; Lang, Katharina M H; Ottens, Marcel; Hubbuch, Jürgen

2017-01-27

Quantitative structure-activity relationship (QSAR) modeling for prediction of biomolecule parameters has become an established technique in chromatographic purification process design. Unfortunately available descriptor sets fail to describe the orientation of biomolecules and the effects of ionic strength in the mobile phase on the interaction with the stationary phase. The literature describes several special descriptors used for chromatographic retention modeling, all of these do not describe the screening of electrostatic potential by the mobile phase in use. In this work we introduce two new approaches of descriptor calculations, namely surface patches and plane projection, which capture an oriented binding to charged surfaces and steric hindrance of the interaction with chromatographic ligands with regard to electrostatic potential screening by mobile phase ions. We present the use of the developed descriptor sets for predictive modeling of Langmuir isotherms for proteins at different pH values between pH 5 and 10 and varying ionic strength in the range of 10-100mM. The resulting model has a high correlation of calculated descriptors and experimental results, with a coefficient of determination of 0.82 and a predictive coefficient of determination of 0.92 for unknown molecular structures and conditions. The agreement of calculated molecular interaction orientations with both, experimental results as well as molecular dynamic simulations from literature is shown. The developed descriptors provide the means for improved QSAR models of chromatographic processes, as they reflect the complex interactions of biomolecules with chromatographic phases. Copyright © 2016 Elsevier B.V. All rights reserved.

Theoretical prediction of a novel inorganic fullerene-like family of silicon-carbon materials

NASA Astrophysics Data System (ADS)

Wang, Ruoxi; Zhang, Dongju; Liu, Chengbu

2005-08-01

In an effort to search for new inorganic fullerene-like structures, we designed a series of novel silicon-carbon cages, (SiC) n ( n = 6-36), based on the uniformly hybrid Si-C four- and six-membered-rings, and researched their geometrical and electronic structures, as well as their relative stabilities using the density function theory. Among these cages, the structures for n = 12, 16, and 36 were found to been energetically more favorable. The calculated disproportionation energy and binding energy per SiC unit show that the (SiC) 12 cage is the most stable one among these designed structures. The present calculations not only indicate that silicon-carbon fullerenes are promised to be synthesized in future, but also provide a new way for stabilizing silicon cages by uniformly doping carbon atoms into silicon structures.

Stability and superconducting properties of GaH5 at high pressure

NASA Astrophysics Data System (ADS)

Ning, Yan-Li; Yang, Wen-Hua; Zang, Qing-Jun; Lu, Wen-Cai

2017-11-01

Using genetic algorithm (GA) method combined with first-principles calculations, the structures, dynamical and thermodynamic stabilities of GaH5 were studied. The calculated results suggested that at the pressure range 150-400 GPa, the P21/m phase of GaH5 is the most favorable phase and dynamically stable, but thermodynamically it is unstable and can decompose into GaH3 and H2. The superconducting property of GaH5 was further calculated, and the predicted superconducting transformation temperature Tc of GaH5 P21/m phase is about 35.63 K at 250 GPa. Besides, we compared the GaH5 and GaH3 superconducting properties, and found that GaH3-Pm-3n structure has a larger DOS near Fermi level than GaH5-P21/m structure, which may be the main reason causing higher Tc of GaH3 than GaH5.

Structure, spectra and antioxidant action of ascorbic acid studied by density functional theory, Raman spectroscopic and nuclear magnetic resonance techniques.

PubMed

Singh, Gurpreet; Mohanty, B P; Saini, G S S

2016-02-15

Structure, vibrational and nuclear magnetic resonance spectra, and antioxidant action of ascorbic acid towards hydroxyl radicals have been studied computationally and in vitro by ultraviolet-visible, nuclear magnetic resonance and vibrational spectroscopic techniques. Time dependant density functional theory calculations have been employed to specify various electronic transitions in ultraviolet-visible spectra. Observed chemical shifts and vibrational bands in nuclear magnetic resonance and vibrational spectra, respectively have been assigned with the help of calculations. Changes in the structure of ascorbic acid in aqueous phase have been examined computationally and experimentally by recording Raman spectra in aqueous medium. Theoretical calculations of the interaction between ascorbic acid molecule and hydroxyl radical predicted the formation of dehydroascorbic acid as first product, which has been confirmed by comparing its simulated spectra with the corresponding spectra of ascorbic acid in presence of hydrogen peroxide. Copyright © 2015 Elsevier B.V. All rights reserved.

Identifying Few-Molecule Water Clusters with High Precision on Au(111) Surface.

PubMed

Dong, Anning; Yan, Lei; Sun, Lihuan; Yan, Shichao; Shan, Xinyan; Guo, Yang; Meng, Sheng; Lu, Xinghua

2018-06-01

Revealing the nature of a hydrogen-bond network in water structures is one of the imperative objectives of science. With the use of a low-temperature scanning tunneling microscope, water clusters on a Au(111) surface were directly imaged with molecular resolution by a functionalized tip. The internal structures of the water clusters as well as the geometry variations with the increase of size were identified. In contrast to a buckled water hexamer predicted by previous theoretical calculations, our results present deterministic evidence for a flat configuration of water hexamers on Au(111), corroborated by density functional theory calculations with properly implemented van der Waals corrections. The consistency between the experimental observations and improved theoretical calculations not only renders the internal structures of absorbed water clusters unambiguously, but also directly manifests the crucial role of van der Waals interactions in constructing water-solid interfaces.

Temperature effects on prevalent structures of hydrated Fe{sup +} complexes: Infrared spectroscopy and DFT calculations of Fe{sup +}(H{sub 2}O){sub n} (n = 3–8)

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

Ohashi, Kazuhiko, E-mail: kazu@chem.kyushu-univ.jp; Sekiya, Hiroshi; Sasaki, Jun

2014-12-07

Hydrated Fe{sup +} ions are produced in a laser-vaporization cluster source of a triple quadrupole mass spectrometer. The Fe{sup +}(H{sub 2}O){sub n} (n = 3–8) complexes are mass-selected and probed with infrared (IR) photodissociation spectroscopy in the OH-stretch region. Density functional theory (DFT) calculations are also carried out for analyzing the experimental IR spectra and for evaluating thermodynamic quantities of low-lying isomers. Solvation through H-bonding instead of direct coordination to Fe{sup +} is observed already at n = 3, indicating the completion of the first hydration shell with two H{sub 2}O molecules. Size dependent variations in the spectra for nmore » = 5–7 provide evidence for the second-shell completion at n = 6, where a linearly coordinated Fe{sup +}(H{sub 2}O){sub 2} subunit is solvated with four H{sub 2}O molecules. Overall spectral features for n = 3–8 agree well with those predicted for 2-coordinated structures. DFT calculations predict that such 2-coordinated structures are lowest in energy for smaller n. However, 4-coordinated isomers are predicted to be more stable for n = 7 and 8; the energy ordering is in conflict with the IR spectroscopic observation. Examination of free energy as a function of temperature suggests that the ordering of the isomers at warmer temperatures can be different from the ordering near 0 K. For n = 7 and 8, the 4-coordinated isomers should be observed at low temperatures because they are lowest in enthalpy. Meanwhile, outer-shell waters in the 2-coordinated structures are bound less rigidly; their contribution to entropy is rather large. The 2-coordinated structures become abundant at warmer temperatures, owing to the entropy effect.« less

Exploring the high-pressure behavior of the three known polymorphs of BiPO{sub 4}: Discovery of a new polymorph

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

Errandonea, D., E-mail: daniel.errandonea@uv.es; García-Domene, B.; Gomis, O.

We have studied the structural behavior of bismuth phosphate under compression. We performed x-ray powder diffraction measurements up to 31.5 GPa and ab initio calculations. Experiments were carried out on different polymorphs: trigonal (phase I) and monoclinic (phases II and III). Phases I and III, at low pressure (P < 0.2–0.8 GPa), transform into phase II, which has a monazite-type structure. At room temperature, this polymorph is stable up to 31.5 GPa. Calculations support these findings and predict the occurrence of an additional transition from the monoclinic monazite-type to a tetragonal scheelite-type structure (phase IV). This transition was experimentally found after the simultaneous applicationmore » of pressure (28 GPa) and temperature (1500 K), suggesting that at room temperature the transition might by hindered by kinetic barriers. Calculations also predict an additional phase transition at 52 GPa, which exceeds the maximum pressure achieved in the experiments. This transition is from phase IV to an orthorhombic barite-type structure (phase V). We also studied the axial and bulk compressibility of BiPO{sub 4}. Room-temperature pressure-volume equations of state are reported. BiPO{sub 4} was found to be more compressible than isomorphic rare-earth phosphates. The discovered phase IV was determined to be the less compressible polymorph of BiPO{sub 4}. On the other hand, the theoretically predicted phase V has a bulk modulus comparable with that of monazite-type BiPO{sub 4}. Finally, the isothermal compressibility tensor for the monazite-type structure is reported at 2.4 GPa showing that the direction of maximum compressibility is in the (0 1 0) plane at approximately 15° (21°) to the a axis for the case of our experimental (theoretical) study.« less

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.

PubMed

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-14

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiC x O 6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations

NASA Astrophysics Data System (ADS)

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-01

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Crystal structure and phase stability of tungsten borides

NASA Astrophysics Data System (ADS)

Li, Quan; Zhou, Dan; Ma, Yanming; Chen, Changfeng

2013-03-01

We address the longstanding and controversial issue of ground-state structures of technically important tungsten borides using a first-principles structural search method via a particle-swarm optimization (PSO) algorithm. We have explored a large set of stable chemical compositions (convex hull) and clarified the ground-state structures for a wide range of boron concentrations, including W2B, W3B2,WB,W2B3, WB2,W2B5, WB3, and WB4. We further assessed relative stability of various tungsten borides and compared the calculated results with previously reported experimental data. The phase diagram predicted by the presented calculations may serve as a useful guide for synthesis of a variety of tungsten borides. This work was supported by DOE Grant No. DE-FC52-06NA26274.

T-Epitope Designer: A HLA-peptide binding prediction server.

PubMed

Kangueane, Pandjassarame; Sakharkar, Meena Kishore

2005-05-15

The current challenge in synthetic vaccine design is the development of a methodology to identify and test short antigen peptides as potential T-cell epitopes. Recently, we described a HLA-peptide binding model (using structural properties) capable of predicting peptides binding to any HLA allele. Consequently, we have developed a web server named T-EPITOPE DESIGNER to facilitate HLA-peptide binding prediction. The prediction server is based on a model that defines peptide binding pockets using information gleaned from X-ray crystal structures of HLA-peptide complexes, followed by the estimation of peptide binding to binding pockets. Thus, the prediction server enables the calculation of peptide binding to HLA alleles. This model is superior to many existing methods because of its potential application to any given HLA allele whose sequence is clearly defined. The web server finds potential application in T cell epitope vaccine design. http://www.bioinformation.net/ted/

Effect of substituents on prediction of TLC retention of tetra-dentate Schiff bases and their Copper(II) and Nickel(II) complexes.

PubMed

Stevanović, Nikola R; Perušković, Danica S; Gašić, Uroš M; Antunović, Vesna R; Lolić, Aleksandar Đ; Baošić, Rada M

2017-03-01

The objectives of this study were to gain insights into structure-retention relationships and to propose the model to estimating their retention. Chromatographic investigation of series of 36 Schiff bases and their copper(II) and nickel(II) complexes was performed under both normal- and reverse-phase conditions. Chemical structures of the compounds were characterized by molecular descriptors which are calculated from the structure and related to the chromatographic retention parameters by multiple linear regression analysis. Effects of chelation on retention parameters of investigated compounds, under normal- and reverse-phase chromatographic conditions, were analyzed by principal component analysis, quantitative structure-retention relationship and quantitative structure-activity relationship models were developed on the basis of theoretical molecular descriptors, calculated exclusively from molecular structure, and parameters of retention and lipophilicity. Copyright © 2016 John Wiley & Sons, Ltd.

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions,

The Opacity of TiO from a Coupled Electronic State Calculation Parameterized by ab initio and Experimental Data

NASA Technical Reports Server (NTRS)

Schwenke, David W.; Huo, Winifred (Technical Monitor)

1998-01-01

We have carried out ab initio electronic structure calculations of the spin-orbit and rotation-orbit couplings among the 14 lowest electronic states of TiO and used them to predict ro-vibrational energy levels. We report on the qualitative results as well as our progress in optimizing our Hamiltonian parameters in order to improve agreement with experimental line positions.

Dimer formation of perylene: An ultracold spectroscopic and computational study

NASA Astrophysics Data System (ADS)

Birer, Ö.; Yurtsever, E.

2015-10-01

The electronic spectra of perylene inside helium nanodroplets recorded by the depletion method are presented. The results show two broad peaks in addition to sharp monomer vibronic transitions due to dimer formation. In order to understand the details of the spectra, first the dimer formation is studied by DFT and SCS-MP2 calculations and then the electronic spectra are calculated at the minima of the potential energy surface (PES). Theoretical calculations show that there are two low-lying energetically degenerate dimer structures; namely a parallel displaced one and a rotated stacked one. PES around these minima is very flat with a number of local minima at higher energies which at the experimental temperatures cannot be populated. Even though thermodynamically these two structures are equally populated, dynamical considerations point out that in helium droplet the parallel displaced geometry is encouraged by the natural alignment of the molecules due to the acquired angular momentum following the pick-up process. The calculated spectrum of the parallel displaced geometry predicts the positions of the dimer transitions within 30 nm of the experimental spectrum. Furthermore, the difference between the two dimer transitions is accurately predicted to be about 25 nm while the experimental difference was about 20 nm. Such a small difference could only be detected due to the ultracold conditions helium nanodroplets provided.

Structural dynamics payload loads estimates

NASA Technical Reports Server (NTRS)

Engels, R. C.

1982-01-01

Methods for the prediction of loads on large space structures are discussed. Existing approaches to the problem of loads calculation are surveyed. A full scale version of an alternate numerical integration technique to solve the response part of a load cycle is presented, and a set of short cut versions of the algorithm developed. The implementation of these techniques using the software package developed is discussed.

Structure, Kinetics, and Thermodynamics of the Aqueous Uranyl(VI) Cation

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

Kerisit, Sebastien N.; Liu, Chongxuan

2013-08-20

Molecular simulation techniques are employed to gain insights into the structural, kinetic, and thermodynamic properties of the uranyl(VI) cation (UO22+) in aqueous solution. The simulations make use of an atomistic potential model (force field) derived in this work and based on the model of Guilbaud and Wipff (Guilbaud, P.; Wipff, G. J. Mol. Struct. (THEOCHEM) 1996, 366, 55-63). Reactive flux and thermodynamic integration calculations show that the derived potential model yields predictions for the water exchange rate and free energy of hydration, respectively, that are in agreement with experimental data. The water binding energies, hydration shell structure, and self-diffusion coefficientmore » are also calculated and discussed. Finally, a combination of metadynamics and transition path sampling simulations is employed to probe the mechanisms of water exchange reactions in the first hydration shell of the uranyl ion. These atomistic simulations indicate, based on two-dimensional free energy surfaces, that water exchanges follow an associative interchange mechanism. The nature and structure of the water exchange transition states are also determined. The improved potential model is expected to lead to more accurate predictions of uranyl adsorption energies at mineral surfaces using potential-based molecular dynamics simulations.« less

Crystal Structure and Superconductivity of PH 3 at High Pressures

DOE PAGES

Liu, Hanyu; Li, Yinwei; Gao, Guoying; ...

2016-01-20

Here, we performed systematic structure search on solid PH 3 at high pressures using particle swarm optimization method. Furthermore, at 100-200 GPa, the search led to two structures consisting of P-P bonds that different from these predicted for H 2S. Phonon and electron-phonon calculations indicate both structures are dynamically stable and superconductive. Particularly, the estimated critical temperature for the monoclinic (C2/m) phase of 83 K at 200 GPa is in excellent agreement with a recent experimental report.

Synthesis, NMR, FT-IR, X-ray structural characterization, DFT analysis and isomerism aspects of 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione.

PubMed

Barakat, Assem; Al-Najjar, Hany J; Al-Majid, Abdullah Mohammed; Soliman, Saied M; Mabkhot, Yahia Nasser; Shaik, Mohammed Rafi; Ghabbour, Hazem A; Fun, Hoong-Kun

2015-08-05

The synthesis and spectral characterization of the 5-(2,6-dichlorobenzylidene)pyrimidine-2,4,6(1H,3H,5H)-trione;3 was reported. The solid state molecular structure of 3 was studied using X-ray crystallography. The relative stabilities of the seven possible isomers of 3 were calculated by DFT/B3LYP method using 6-311 G(d,p) basis set. The calculated total energies and thermodynamic parameters were used to predict the relative stabilities of these isomers. The effect of solvent polarity on the relative stability of these isomers was studied at the same level of theory using PCM. It was found that the keto form, (T0), is the most stable isomer both in the gaseous state and solution. In solution, the calculated total energies of all isomers are decreased indicating that all isomers are stabilized by the solvent effect. The vibrational spectra of the most stable isomer, 3(T0) are calculated using the same level of theory and the results are compared with the experimentally measured FTIR spectra. Good correlation was obtained between the experimental and calculated vibrational frequencies (R(2)=0.9992). The electronic spectra of 3(T0) in gas phase as well as in solutions were calculated using the TD-DFT method. All the predicted electronic transitions showed very little spectral shifts and increase in the intensity of absorption due to solvent effect. Also the (1)H- and (13)C-NMR chemical shifts of the stable isomer were calculated and the results were correlated with the experimental data. Good correlations between the experimental and calculated chemical shifts were obtained. Copyright © 2015 Elsevier B.V. All rights reserved.

A novel Multi-Agent Ada-Boost algorithm for predicting protein structural class with the information of protein secondary structure.

PubMed

Fan, Ming; Zheng, Bin; Li, Lihua

2015-10-01

Knowledge of the structural class of a given protein is important for understanding its folding patterns. Although a lot of efforts have been made, it still remains a challenging problem for prediction of protein structural class solely from protein sequences. The feature extraction and classification of proteins are the main problems in prediction. In this research, we extended our earlier work regarding these two aspects. In protein feature extraction, we proposed a scheme by calculating the word frequency and word position from sequences of amino acid, reduced amino acid, and secondary structure. For an accurate classification of the structural class of protein, we developed a novel Multi-Agent Ada-Boost (MA-Ada) method by integrating the features of Multi-Agent system into Ada-Boost algorithm. Extensive experiments were taken to test and compare the proposed method using four benchmark datasets in low homology. The results showed classification accuracies of 88.5%, 96.0%, 88.4%, and 85.5%, respectively, which are much better compared with the existing methods. The source code and dataset are available on request.

Three-dimensional effects for radio frequency antenna modeling

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

Carter, M.D.; Batchelor, D.B.; Stallings, D.C.

1994-10-15

Electromagnetic field calculations for radio frequency (rf) antennas in two dimensions (2-D) neglect finite antenna length effects as well as the feeders leading to the main current strap. The 2-D calculations predict that the return currents in the sidewalls of the antenna structure depend strongly on the plasma parameters, but this prediction is suspect because of experimental evidence. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform three-dimensional (3-D) modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused bymore » feeders to the main current strap and conducting sidewalls are considered. The modeling shows that the feeders affect the launched power spectrum in an indirect way by forcing the driven rf current to return in the antenna structure rather than the plasma, as in the 2-D model. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading predicted from that predicted in the 2-D model. For some plasma parameters, the combined 3-D effects can lead to a reduction in the predicted loading by as much as a factor of 2 from that given by the 2-D model, even with end-effect corrections for the 2-D model.« less

Three-dimensional effects for radio frequency antenna modeling

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

Carter, M.D.; Batchelor, D.B.; Stallings, D.C.

1993-12-31

Electromagnetic field calculations for radio frequency (rf) antennas in two dimensions (2-D) neglect finite antenna length effects as well as the feeders leading to the main current strap. The 2-D calculations predict that the return currents in the sidewalls of the antenna structure depend strongly on the plasma parameters, but this prediction is suspect because of experimental evidence. To study the validity of the 2-D approximation, the Multiple Antenna Implementation System (MAntIS) has been used to perform three-dimensional (3-D) modeling of the power spectrum, plasma loading, and inductance for a relevant loop antenna design. Effects on antenna performance caused bymore » feeders to the main current strap and conducting sidewalls are considered. The modeling shows that the feeders affect the launched power spectrum in an indirect way by forcing the driven rf current to return in the antenna structure rather than the plasma, as in the 2-D model. It has also been found that poloidal dependencies in the plasma impedance matrix can reduce the loading predicted from that predicted in the 2-D model. For some plasma parameters, the combined 3-D effects can lead to a reduction in the predicted loading by as much as a factor of 2 from that given by the 2-D model, even with end-effect corrections for the 2-D model.« less

Determination of Irreducible Water Saturation from nuclear magnetic resonance based on fractal theory — a case study of sandstone with complex pore structure

NASA Astrophysics Data System (ADS)

Peng, L.; Pan, H.; Ma, H.; Zhao, P.; Qin, R.; Deng, C.

2017-12-01

The irreducible water saturation (Swir) is a vital parameter for permeability prediction and original oil and gas estimation. However, the complex pore structure of the rocks makes the parameter difficult to be calculated from both laboratory and conventional well logging methods. In this study, an effective statistical method to predict Swir is derived directly from nuclear magnetic resonance (NMR) data based on fractal theory. The spectrum of transversal relaxation time (T2) is normally considered as an indicator of pore size distribution, and the micro- and meso-pore's fractal dimension in two specific range of T2 spectrum distribution are calculated. Based on the analysis of the fractal characteristics of 22 core samples, which were drilled from four boreholes of tight lithologic oil reservoirs of Ordos Basin in China, the positive correlation between Swir and porosity is derived. Afterwards a predicting model for Swir based on linear regressions of fractal dimensions is proposed. It reveals that the Swir is controlled by the pore size and the roughness of the pore. The reliability of this model is tested and an ideal consistency between predicted results and experimental data is found. This model is a reliable supplementary to predict the irreducible water saturation in the case that T2 cutoff value cannot be accurately determined.

Structure, ferroelectric ordering, and semiempirical quantum calculations of lanthanide based metal-organic framework: [Nd(C4H5O6)(C4H4O6)][3H2O

NASA Astrophysics Data System (ADS)

Ahmad, Bhat Zahoor; Want, Basharat

2016-04-01

We investigate the structure and ferroelectric behavior of a lanthanide based metal-organic framework (MOF), [Nd(C4H5O6)(C4H4O6)][3H2O]. X-ray crystal structure analyses reveal that it crystallizes in the P41212 space group with Nd centres, coordinated by nine oxygen atoms, forming a distorted capped square antiprismatic geometry. The molecules, bridged by tartrate ligands, form a 2D chiral structure. The 2D sheets are further linked into a 3D porous framework via strong hydrogen-bonding scheme (O-H…O ≈ 2.113 Å). Dielectric studies reveal two anomalies at 295 K and 185 K. The former is a paraelectric-ferroelectric transition, and the later is attributed to the freezing down of the motion of the hydroxyl groups. The phase transition is of second order, and the spontaneous polarization in low temperature phase is attributed to the ordering of protons of hydroxyl groups. The dielectric nonlinearity parameters have been calculated using Landau- Devonshire phenomenological theory. In addition, the most recent semiempirical models, Sparkle/PM7, Sparkle/RM1, and Sparkle/AM1, are tested on the present system to assay the accuracy of semiempirical quantum approaches to predict the geometries of solid MOFs. Our results show that Sparkle/PM7 model is the most accurate to predict the unit cell structure and coordination polyhedron geometry. The semiempirical methods are also used to calculate different ground state molecular properties.

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

Noise produced by turbulent flow into a rotor: Users manual for noise calculation

NASA Technical Reports Server (NTRS)

Amiet, R. K.; Egolf, C. G.; Simonich, J. C.

1989-01-01

A users manual for a computer program for the calculation of noise produced by turbulent flow into a helicopter rotor is presented. These inputs to the program are obtained from the atmospheric turbulence model and mean flow distortion calculation, described in another volume of this set of reports. Descriptions of the various program modules and subroutines, their function, programming structure, and the required input and output variables are included. This routine is incorporated as one module of NASA's ROTONET helicopter noise prediction program.

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

Azadi, Sam, E-mail: s.azadi@ucl.ac.uk; Cohen, R. E.; Department of Earth- and Environmental Sciences, Ludwig Maximilians Universität, Munich 80333

We studied the low-pressure (0–10 GPa) phase diagram of crystalline benzene using quantum Monte Carlo and density functional theory (DFT) methods. We performed diffusion quantum Monte Carlo (DMC) calculations to obtain accurate static phase diagrams as benchmarks for modern van der Waals density functionals. Using density functional perturbation theory, we computed the phonon contributions to the free energies. Our DFT enthalpy-pressure phase diagrams indicate that the Pbca and P2{sub 1}/c structures are the most stable phases within the studied pressure range. The DMC Gibbs free-energy calculations predict that the room temperature Pbca to P2{sub 1}/c phase transition occurs at 2.1(1)more » GPa. This prediction is consistent with available experimental results at room temperature. Our DMC calculations give 50.6 ± 0.5 kJ/mol for crystalline benzene lattice energy.« less

DFT approach to (benzylthio)acetic acid: Conformational search, molecular (monomer and dimer) structure, vibrational spectroscopy and some electronic properties

NASA Astrophysics Data System (ADS)

Sienkiewicz-Gromiuk, Justyna

2018-01-01

The DFT studies were carried out with the B3LYP method utilizing the 6-31G and 6-311++G(d,p) basis sets depending on whether the aim of calculations was to gain the geometry at equilibrium, or to calculate the optimized molecular structure of (benzylthio)acetic acid (Hbta) in the forms of monomer and dimer. The minimum conformational energy search was followed by the potential energy surface (PES) scan of all rotary bonds existing in the acid molecule. The optimized geometrical monomeric and dimeric structures of the title compound were compared with the experimental structural data in the solid state. The detailed vibrational interpretation of experimental infrared and Raman bands was performed on the basis of theoretically simulated ESFF-scaled wavenumbers calculated for the monomer and dimer structures of Hbta. The electronic characteristics of Hbta is also presented in terms of Mulliken atomic charges, frontier molecular orbitals and global reactivity descriptors. Additionally, the MEP and ESP surfaces were computed to predict coordination sites for potential metal complex formation.

Electronic structure modeling of InAs/GaSb superlattices with hybrid density functional theory

NASA Astrophysics Data System (ADS)

Garwood, T.; Modine, N. A.; Krishna, S.

2017-03-01

The application of first-principles calculations holds promise for greatly improving our understanding of semiconductor superlattices. Developing a procedure to accurately predict band gaps using hybrid density functional theory lays the groundwork for future studies investigating more nuanced properties of these structures. Our approach allows a priori prediction of the properties of SLS structures using only the band gaps of the constituent materials. Furthermore, it should enable direct investigation of the effects of interface structure, e.g., intermixing or ordering at the interface, on SLS properties. In this paper, we present band gap data for various InAs/GaSb type-II superlattice structures calculated using the generalized Kohn-Sham formulation of density functional theory. A PBE0-type hybrid functional was used, and the portion of the exact exchange was tuned to fit the band gaps of the binary compounds InAs and GaSb with the best agreement to bulk experimental values obtained with 18% of the exact exchange. The heterostructures considered in this study are 6 monolayer (ML) InAs/6 ML GaSb, 8 ML InAs/8 ML GaSb and 10 ML InAs/10 ML GaSb with deviations from the experimental band gaps ranging from 3% to 11%.

Structural, optoelectronic, and thermoelectric properties of AZn13 (A=Na, K, Ca, Sr, Ba) compounds

NASA Astrophysics Data System (ADS)

Basit, Abdul; Murtaza, G.; Mahmood, Asif; Yar, Abdullah; Muhammad, S.

2016-08-01

We report the structural, electronic, optical, and thermoelectric properties of the five cubic alkali-earth transition-metals AZn13 (A-Na, K, Ca, Sr, Ba) using density functional theory. Structural properties, electronic structures and optical behaviors are calculated explicitly via highly accurate contemporary full potential-linearized augmented plane wave (FP-LAPW) method. The investigated ground state data of these materials is quite close to the experimental information. The modified Becke-Johnson (mBJ) predicts the intermetallic nature of AZn13 (A-Na, K, Ca, Sr, Ba) materials. The complex dielectric function of these intermetallic compounds has been calculated and the observed noticeable peaks are examined through mBJ. With the help of complex dielectric function, the other important optical parameters like reflectivities, conductivities and refractive indices of AZn13 (A-Na, K, Ca, Sr, Ba) have been calculated as a function of energy. The optical response suggests that AZn13 (A-Na, K, Ca, Sr, Ba) compounds can be used for the optoelectronic devices. Further, the thermoelectric properties have been calculated through BoltzTraP program, the calculated values for different thermoelectric parameters recommend that these AZn13 (A-Na, K, Ca, Sr, Ba) materials are the suitable candidates for thermoelectric applications.

Propargyl + O 2 Reaction in Helium Droplets: Entrance Channel Barrier or Not?

DOE PAGES

Moradi, Christopher P.; Morrison, Alexander M.; Klippenstein, Stephen J.; ...

2013-09-09

A combination of liquid He droplet experiments and multireference electronic structure calculations is used to probe the potential energy surface for the reaction between the propargyl radical and O 2. Infrared laser spectroscopy is used to probe the outcome of the low temperature, liquid He-mediated reaction. Bands in the spectrum are assigned to the acetylenic CH stretch (ν 1), the symmetric CH 2 stretch (ν 2), and the antisymmetric CH 2 stretch (ν 13) of the trans-acetylenic propargyl peroxy radical (•OO—CH 2—C≡CH). The observed band origins are in excellent agreement with previously reported anharmonic frequency computations for this species. Themore » Stark spectrum of the ν 1 band provides further evidence that the reaction leads only to the trans-acetylenic species. There are no other bands in the CH 2 stretching region that can be attributed to any of the other three propargyl peroxy isomers/conformers that are predicted to be minimum energy structures ( gauche-acetylenic, cis-allenic, and trans-allenic). There is also no evidence for the kinetic stabilization of a van der Waals complex between propargyl and O 2. A combination of multireference and coupled-cluster electronic structure calculations is used to probe the potential energy surface in the neighborhood of the transition state connecting reactants with the acetylenic adduct. The multireference based evaluation of the doublet-quartet splitting added to the coupled-cluster calculated quartet state energies yields what are likely the most accurate predictions for the doublet potential curve. As a result, this calculation suggests that there is no saddle point for the addition process, in agreement with the experimental observations. Other calculations suggest the possible presence of a small submerged barrier.« less

Scalability improvements to NRLMOL for DFT calculations of large molecules

NASA Astrophysics Data System (ADS)

Diaz, Carlos Manuel

Advances in high performance computing (HPC) have provided a way to treat large, computationally demanding tasks using thousands of processors. With the development of more powerful HPC architectures, the need to create efficient and scalable code has grown more important. Electronic structure calculations are valuable in understanding experimental observations and are routinely used for new materials predictions. For the electronic structure calculations, the memory and computation time are proportional to the number of atoms. Memory requirements for these calculations scale as N2, where N is the number of atoms. While the recent advances in HPC offer platforms with large numbers of cores, the limited amount of memory available on a given node and poor scalability of the electronic structure code hinder their efficient usage of these platforms. This thesis will present some developments to overcome these bottlenecks in order to study large systems. These developments, which are implemented in the NRLMOL electronic structure code, involve the use of sparse matrix storage formats and the use of linear algebra using sparse and distributed matrices. These developments along with other related development now allow ground state density functional calculations using up to 25,000 basis functions and the excited state calculations using up to 17,000 basis functions while utilizing all cores on a node. An example on a light-harvesting triad molecule is described. Finally, future plans to further improve the scalability will be presented.

Spectroscopic and molecular structure investigation of 2-furanacrylic acid monomer and dimer using HF and DFT methods

NASA Astrophysics Data System (ADS)

Ghalla, H.; Issaoui, N.; Govindarajan, M.; Flakus, H. T.; Jamroz, M. H.; Oujia, B.

2014-02-01

In the present work, we reported a combined experimental and theoretical study on molecular structure and vibrational spectra of 2-furanacrylic acid (abbreviated as 2FAA). The FT-IR and FT-Raman spectra of 2FAA have been recorded in the regions 4000-400 and 4000-100 cm-1. The spectra were interpreted in terms of fundamentals modes, combination and overtone bands. The monomer and dimer structures of the title molecule have been obtained from Hartree-Fock (HF) and density functional theory (DFT) B3LYP methods with 6-311++G(d,p) as basis set calculations. The vibrational frequencies were calculated by DFT method and compared with the experimental frequencies, which yield good agreement between observed and calculated frequencies. Intermolecular OH⋯O hydrogen bonds are discussed in dimer structure of the molecule. The infrared and Raman spectra were also predicted from the calculated intensities. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. A study on the electronic properties, such as excitation energies, oscillator strength, wavelengths, HOMO and LUMO energies, are performed by time-dependent DFT (TD-DFT) approach. In addition, Milliken atomic charges, possible charge transfer, natural bond orbital (NBO) and AIM topological analysis were performed. Moreover, molecular electrostatic potential (MEP) and the thermodynamic properties (heat capacity, entropy, and enthalpy) of the title compound at different temperatures were calculated in gas phase.

Experimental and computational prediction of glass transition temperature of drugs.

PubMed

Alzghoul, Ahmad; Alhalaweh, Amjad; Mahlin, Denny; Bergström, Christel A S

2014-12-22

Glass transition temperature (Tg) is an important inherent property of an amorphous solid material which is usually determined experimentally. In this study, the relation between Tg and melting temperature (Tm) was evaluated using a data set of 71 structurally diverse druglike compounds. Further, in silico models for prediction of Tg were developed based on calculated molecular descriptors and linear (multilinear regression, partial least-squares, principal component regression) and nonlinear (neural network, support vector regression) modeling techniques. The models based on Tm predicted Tg with an RMSE of 19.5 K for the test set. Among the five computational models developed herein the support vector regression gave the best result with RMSE of 18.7 K for the test set using only four chemical descriptors. Hence, two different models that predict Tg of drug-like molecules with high accuracy were developed. If Tm is available, a simple linear regression can be used to predict Tg. However, the results also suggest that support vector regression and calculated molecular descriptors can predict Tg with equal accuracy, already before compound synthesis.

Prediction of the Effective Thermal Conductivity of Powder Insulation

NASA Astrophysics Data System (ADS)

Jin, Lingxue; Park, Jiho; Lee, Cheonkyu; Jeong, Sangkwon

The powder insulation method is widely used in structural and cryogenic systems such as transportation and storage tanks of cryogenic fluids. The powder insulation layer is constructed by small particle powder with light weight and some residual gas with high porosity. So far, many experiments have been carried out to test the thermal performance of various kinds of powder, including expanded perlite, glass microspheres, expanded polystyrene (EPS). However, it is still difficult to predict the thermal performance of powder insulation by calculation due to the complicated geometries, including various particle shapes, wide powder diameter distribution, and various pore sizes. In this paper, the effective thermal conductivity of powder insulation has been predicted based on an effective thermal conductivity calculationmodel of porous packed beds. The calculation methodology was applied to the insulation system with expanded perlite, glass microspheres and EPS beads at cryogenic temperature and various vacuum pressures. The calculation results were compared with previous experimental data. Moreover, additional tests were carried out at cryogenic temperature in this research. The fitting equations of the deformation factor of the area-contact model are presented for various powders. The calculation results show agood agreement with the experimental results.

Fe-Cluster Compounds of Chalcogenides: Candidates for Rare-Earth-Free Permanent Magnet and Magnetic Nodal-Line Topological Material.

PubMed

Zhao, Xin; Wang, Cai-Zhuang; Kim, Minsung; Ho, Kai-Ming

2017-12-04

Fe-cluster-based crystal structures are predicted for chalcogenides Fe 3 X 4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe 3 X 4 compounds and exhibit interesting magnetic and electronic properties. In particular, we show that Fe 3 Te 4 can be a good candidate as a rare-earth-free permanent magnet and Fe 3 S 4 can be a magnetic nodal-line topological material.

An efficient method for the prediction of deleterious multiple-point mutations in the secondary structure of RNAs using suboptimal folding solutions

PubMed Central

Churkin, Alexander; Barash, Danny

2008-01-01

Background RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the predicted structure of the wild type. The secondary structure predictions are performed using the Vienna RNA package. A more efficient implementation of RNAmute is needed, however, to extend from the case of single point mutations to the general case of multiple point mutations, which may often be desired for computational predictions alongside mutagenesis experiments. But analyzing multiple point mutations, a process that requires traversing all possible mutations, becomes highly expensive since the running time is O(nm) for a sequence of length n with m-point mutations. Using Vienna's RNAsubopt, we present a method that selects only those mutations, based on stability considerations, which are likely to be conformational rearranging. The approach is best examined using the dot plot representation for RNA secondary structure. Results Using RNAsubopt, the suboptimal solutions for a given wild-type sequence are calculated once. Then, specific mutations are selected that are most likely to cause a conformational rearrangement. For an RNA sequence of about 100 nts and 3-point mutations (n = 100, m = 3), for example, the proposed method reduces the running time from several hours or even days to several minutes, thus enabling the practical application of RNAmute to the analysis of multiple-point mutations. Conclusion A highly efficient addition to RNAmute that is as user friendly as the original application but that facilitates the practical analysis of multiple-point mutations is presented. Such an extension can now be exploited prior to site-directed mutagenesis experiments by virologists, for example, who investigate the change of function in an RNA virus via mutations that disrupt important motifs in its secondary structure. A complete explanation of the application, called MultiRNAmute, is available at [1]. PMID:18445289

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.

Machine Learning Estimates of Natural Product Conformational Energies

PubMed Central

Rupp, Matthias; Bauer, Matthias R.; Wilcken, Rainer; Lange, Andreas; Reutlinger, Michael; Boeckler, Frank M.; Schneider, Gisbert

2014-01-01

Machine learning has been used for estimation of potential energy surfaces to speed up molecular dynamics simulations of small systems. We demonstrate that this approach is feasible for significantly larger, structurally complex molecules, taking the natural product Archazolid A, a potent inhibitor of vacuolar-type ATPase, from the myxobacterium Archangium gephyra as an example. Our model estimates energies of new conformations by exploiting information from previous calculations via Gaussian process regression. Predictive variance is used to assess whether a conformation is in the interpolation region, allowing a controlled trade-off between prediction accuracy and computational speed-up. For energies of relaxed conformations at the density functional level of theory (implicit solvent, DFT/BLYP-disp3/def2-TZVP), mean absolute errors of less than 1 kcal/mol were achieved. The study demonstrates that predictive machine learning models can be developed for structurally complex, pharmaceutically relevant compounds, potentially enabling considerable speed-ups in simulations of larger molecular structures. PMID:24453952

Accurate Binding Free Energy Predictions in Fragment Optimization.

PubMed

Steinbrecher, Thomas B; Dahlgren, Markus; Cappel, Daniel; Lin, Teng; Wang, Lingle; Krilov, Goran; Abel, Robert; Friesner, Richard; Sherman, Woody

2015-11-23

Predicting protein-ligand binding free energies is a central aim of computational structure-based drug design (SBDD)--improved accuracy in binding free energy predictions could significantly reduce costs and accelerate project timelines in lead discovery and optimization. The recent development and validation of advanced free energy calculation methods represents a major step toward this goal. Accurately predicting the relative binding free energy changes of modifications to ligands is especially valuable in the field of fragment-based drug design, since fragment screens tend to deliver initial hits of low binding affinity that require multiple rounds of synthesis to gain the requisite potency for a project. In this study, we show that a free energy perturbation protocol, FEP+, which was previously validated on drug-like lead compounds, is suitable for the calculation of relative binding strengths of fragment-sized compounds as well. We study several pharmaceutically relevant targets with a total of more than 90 fragments and find that the FEP+ methodology, which uses explicit solvent molecular dynamics and physics-based scoring with no parameters adjusted, can accurately predict relative fragment binding affinities. The calculations afford R(2)-values on average greater than 0.5 compared to experimental data and RMS errors of ca. 1.1 kcal/mol overall, demonstrating significant improvements over the docking and MM-GBSA methods tested in this work and indicating that FEP+ has the requisite predictive power to impact fragment-based affinity optimization projects.

Structural stability, elastic and thermodynamic properties of Au-Cu alloys from first-principles calculations

NASA Astrophysics Data System (ADS)

Kong, Ge-Xing; Ma, Xiao-Juan; Liu, Qi-Jun; Li, Yong; Liu, Zheng-Tang

2018-03-01

Using first-principles calculations method based on density functional theory (DFT) with the Perdew-Burke-Ernzerhof (PBE) implementation of the generalized gradient approximation (GGA), we investigate the structural, elastic and thermodynamic properties of gold-copper intermetallic compounds (Au-Cu ICs). The calculated lattice parameters are in excellent agreement with experimental data. The elastic constants show that all the investigated Au-Cu alloys are mechanically stable. Elastic properties, including the shear modulus, Young's modulus, Poisson's ratio and Pugh's indicator, of the intermetallic compounds are evaluated and discussed, with special attention to the remarkable anisotropy displayed by Au-Cu ICs. Thermodynamic and transport properties including the Debye temperature, thermal conductivity and melting point are predicted from the averaged sound velocity and elastic moduli, using semi-empirical formulas.

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.

Stability, Elastic Properties, and Deformation of LiBN2: A Potential High-Energy Material.

PubMed

Zhu, Chunye; Zhu, Wenjun; Yang, Yanqiang

2018-05-15

Searching for high-energy-density materials is of great interest in scientific research and for industrial applications. Using an unbiased structure prediction method and first-principles calculations, we investigated the phase stability of LiBN 2 from 0 to100 GPa. Two new structures with space groups P4̅2 1 m and Pnma were discovered. The theoretical calculations revealed that Pnma LiBN 2 is stable with respect to a mixture of 1 / 3 Li 3 N, BN, and 1 / 3 N 2 above 22 GPa. The electronic band structure revealed that Pnma LiBN 2 has an indirect band gap of 2.3 eV, which shows a nonmetallic feature. The Pnma phase has a high calculated bulk modulus and shear modulus, indicating its incompressible nature. The microscopic mechanism of the structural deformation was demonstrated by ideal tensile shear strength calculations. It is worth mentioning that Pnma LiBN 2 is dynamically stable under ambient conditions. The decomposition of this phase is exothermic, releasing an energy of approximately 1.23 kJ/g at the PBE level. The results provide new thoughts for designing and synthesizing novel high-energy compounds in ternary systems.

Chemical Shifts of the Carbohydrate Binding Domain of Galectin-3 from Magic Angle Spinning NMR and Hybrid Quantum Mechanics/Molecular Mechanics Calculations.

PubMed

Kraus, Jodi; Gupta, Rupal; Yehl, Jenna; Lu, Manman; Case, David A; Gronenborn, Angela M; Akke, Mikael; Polenova, Tatyana

2018-03-22

Magic angle spinning NMR spectroscopy is uniquely suited to probe the structure and dynamics of insoluble proteins and protein assemblies at atomic resolution, with NMR chemical shifts containing rich information about biomolecular structure. Access to this information, however, is problematic, since accurate quantum mechanical calculation of chemical shifts in proteins remains challenging, particularly for 15 N H . Here we report on isotropic chemical shift predictions for the carbohydrate recognition domain of microcrystalline galectin-3, obtained from using hybrid quantum mechanics/molecular mechanics (QM/MM) calculations, implemented using an automated fragmentation approach, and using very high resolution (0.86 Å lactose-bound and 1.25 Å apo form) X-ray crystal structures. The resolution of the X-ray crystal structure used as an input into the AF-NMR program did not affect the accuracy of the chemical shift calculations to any significant extent. Excellent agreement between experimental and computed shifts is obtained for 13 C α , while larger scatter is observed for 15 N H chemical shifts, which are influenced to a greater extent by electrostatic interactions, hydrogen bonding, and solvation.

Thermal structure of oceanic transform faults

USGS Publications Warehouse

Behn, M.D.; Boettcher, M.S.; Hirth, G.

2007-01-01

We use three-dimensional finite element simulations to investigate the temperature structure beneath oceanic transform faults. We show that using a rheology that incorporates brittle weakening of the lithosphere generates a region of enhanced mantle upwelling and elevated temperatures along the transform; the warmest temperatures and thinnest lithosphere are predicted to be near the center of the transform. Previous studies predicted that the mantle beneath oceanic transform faults is anomalously cold relative to adjacent intraplate regions, with the thickest lithosphere located at the center of the transform. These earlier studies used simplified rheologic laws to simulate the behavior of the lithosphere and underlying asthenosphere. We show that the warmer thermal structure predicted by our calculations is directly attributed to the inclusion of a more realistic brittle rheology. This temperature structure is consistent with a wide range of observations from ridge-transform environments, including the depth of seismicity, geochemical anomalies along adjacent ridge segments, and the tendency for long transforms to break into small intratransform spreading centers during changes in plate motion. ?? 2007 Geological Society of America.

Prediction of possible CaMnO3 modifications using an ab initio minimization data-mining approach.

PubMed

Zagorac, Jelena; Zagorac, Dejan; Zarubica, Aleksandra; Schön, J Christian; Djuris, Katarina; Matovic, Branko

2014-10-01

We have performed a crystal structure prediction study of CaMnO3 focusing on structures generated by octahedral tilting according to group-subgroup relations from the ideal perovskite type (Pm\\overline 3 m), which is the aristotype of the experimentally known CaMnO3 compound in the Pnma space group. Furthermore, additional structure candidates have been obtained using data mining. For each of the structure candidates, a local optimization on the ab initio level using density-functional theory (LDA, hybrid B3LYP) and the Hartree--Fock (HF) method was performed, and we find that several of the modifications may be experimentally accessible. In the high-pressure regime, we identify a post-perovskite phase in the CaIrO3 type, not previously observed in CaMnO3. Similarly, calculations at effective negative pressure predict a phase transition from the orthorhombic perovskite to an ilmenite-type (FeTiO3) modification of CaMnO3.

The solid-state terahertz spectrum of MDMA (Ecstasy) - A unique test for molecular modeling assignments

NASA Astrophysics Data System (ADS)

Allis, Damian G.; Hakey, Patrick M.; Korter, Timothy M.

2008-10-01

The terahertz (THz, far-infrared) spectrum of 3,4-methylene-dioxymethamphetamine hydrochloride (Ecstasy) is simulated using solid-state density functional theory. While a previously reported isolated-molecule calculation is noteworthy for the precision of its solid-state THz reproduction, the solid-state calculation predicts that the isolated-molecule modes account for only half of the spectral features in the THz region, with the remaining structure arising from lattice vibrations that cannot be predicted without solid-state molecular modeling. The molecular origins of the internal mode contributions to the solid-state THz spectrum, as well as the proper consideration of the protonation state of the molecule, are also considered.

Intramolecular hydrogen bonding in myricetin and myricitrin. Quantum chemical calculations and vibrational spectroscopy

NASA Astrophysics Data System (ADS)

Vojta, Danijela; Dominković, Katarina; Miljanić, Snežana; Spanget-Larsen, Jens

2017-03-01

The molecular structures of myricetin (3,3‧,4‧,5,5‧,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the Cdbnd O stretching bands is suggested.

Fast bi-directional prediction selection in H.264/MPEG-4 AVC temporal scalable video coding.

PubMed

Lin, Hung-Chih; Hang, Hsueh-Ming; Peng, Wen-Hsiao

2011-12-01

In this paper, we propose a fast algorithm that efficiently selects the temporal prediction type for the dyadic hierarchical-B prediction structure in the H.264/MPEG-4 temporal scalable video coding (SVC). We make use of the strong correlations in prediction type inheritance to eliminate the superfluous computations for the bi-directional (BI) prediction in the finer partitions, 16×8/8×16/8×8 , by referring to the best temporal prediction type of 16 × 16. In addition, we carefully examine the relationship in motion bit-rate costs and distortions between the BI and the uni-directional temporal prediction types. As a result, we construct a set of adaptive thresholds to remove the unnecessary BI calculations. Moreover, for the block partitions smaller than 8 × 8, either the forward prediction (FW) or the backward prediction (BW) is skipped based upon the information of their 8 × 8 partitions. Hence, the proposed schemes can efficiently reduce the extensive computational burden in calculating the BI prediction. As compared to the JSVM 9.11 software, our method saves the encoding time from 48% to 67% for a large variety of test videos over a wide range of coding bit-rates and has only a minor coding performance loss. © 2011 IEEE

First-principles calculations for elastic properties of OsB 2 under pressure

NASA Astrophysics Data System (ADS)

Yang, Jun-Wei; Chen, Xiang-Rong; Luo, Fen; Ji, Guang-Fu

2009-11-01

The structure, elastic properties and elastic anisotropy of orthorhombic OsB 2 are investigated by density functional theory method with the ultrasoft pseudopotential scheme in the frame of the generalized gradient approximation (GGA) as well as local density approximation (LDA). The obtained structural parameters, elastic constants, elastic anisotropy and Debye temperature for OsB 2 under pressure are consistent with the available experimental data and other theoretical results. It is found that the elastic constants, bulk modulus and Debye temperature of OsB 2 tend to increase with increasing pressure. It is predicted that OsB 2 is not a superhard material from our calculations.

Exploration on anion ordering, optical properties and electronic structure in K3WO3F3 elpasolite

NASA Astrophysics Data System (ADS)

Atuchin, V. V.; Isaenko, L. I.; Kesler, V. G.; Lin, Z. S.; Molokeev, M. S.; Yelisseyev, A. P.; Zhurkov, S. A.

2012-03-01

Room-temperature modification of potassium oxyfluorotungstate, G2-K3WO3F3, has been prepared by low-temperature chemical route and single crystal growth. Wide optical transparency range of 0.3-9.4 μm and forbidden band gap Eg=4.32 eV have been obtained for G2-K3WO3F3 crystal. Meanwhile, its electronic structure has been calculated with the first-principles calculations. The good agreement between the theorectical and experimental results have been achieved. Furthermore, G2-K3WO3F3 is predicted to possess the relatively large nonlinear optical coefficients.

Density functional theory studies on molecular structure and vibrational spectra of NLO crystal L-phenylalanine phenylalanium nitrate for THz application

NASA Astrophysics Data System (ADS)

Amalanathan, M.; Hubert Joe, I.; Rastogi, V. K.

2011-12-01

Molecular structure, FT-IR and Raman spectra of L-phenylalanine phenylalanium nitrate have been investigated using density functional theory calculation. The polarizability and hyperpolarizability value of the crystal is also calculated. Natural bond orbital analysis confirms the presence of intramolecular charge transfer and the hydrogen bonding interaction. Simultaneous activation of ring C sbnd C stretching modes shows the non-centrosymmetric symmetry. Terahertz time-domain spectroscopy has been used to detect the absorption spectra in the frequency range from 0.05 to 1.3 THz. Theoretically predicted β value exhibits the high nonlinear optical activity.

Application of binding free energy calculations to prediction of binding modes and affinities of MDM2 and MDMX inhibitors.

PubMed

Lee, Hui Sun; Jo, Sunhwan; Lim, Hyun-Suk; Im, Wonpil

2012-07-23

Molecular docking is widely used to obtain binding modes and binding affinities of a molecule to a given target protein. Despite considerable efforts, however, prediction of both properties by docking remains challenging mainly due to protein's structural flexibility and inaccuracy of scoring functions. Here, an integrated approach has been developed to improve the accuracy of binding mode and affinity prediction and tested for small molecule MDM2 and MDMX antagonists. In this approach, initial candidate models selected from docking are subjected to equilibration MD simulations to further filter the models. Free energy perturbation molecular dynamics (FEP/MD) simulations are then applied to the filtered ligand models to enhance the ability in predicting the near-native ligand conformation. The calculated binding free energies for MDM2 complexes are overestimated compared to experimental measurements mainly due to the difficulties in sampling highly flexible apo-MDM2. Nonetheless, the FEP/MD binding free energy calculations are more promising for discriminating binders from nonbinders than docking scores. In particular, the comparison between the MDM2 and MDMX results suggests that apo-MDMX has lower flexibility than apo-MDM2. In addition, the FEP/MD calculations provide detailed information on the different energetic contributions to ligand binding, leading to a better understanding of the sensitivity and specificity of protein-ligand interactions.

Synthesis, characterization of (3E)-1-(6-chloro-2-methyl-4-phenyl quinolin-3-Yl)-3-aryl prop-2-en-1-ones through IR, NMR, single crystal X-ray diffraction and insights into their electronic structure using DFT calculations

NASA Astrophysics Data System (ADS)

Sarveswari, S.; Srikanth, A.; Arul Murugan, N.; Vijayakumar, V.; Jasinski, Jerry P.; Beauchesne, Hanna C.; Jarvis, Ethan E.

2015-02-01

3E-1-(6-Chloro-2-methyl-4-phenylquinolin-3-yl)-3-arylprop-2-en-1-ones were synthesized and characterized by FTIR, 1H NMR, 13C NMR, HSQC, DEPT-135. In addition the compound 3E-1-(6-chloro-2-methyl-4-phenylquinolin-3-yl)-3-(2,5-dimethoxyphenyl)prop-2-en-1-one was subjected to the single crystal X-ray diffraction studies. Density functional theory calculations were carried out for this chalcone and its derivatives to investigate into their electronic structure, chemical reactivity, linear and non-linear optical properties. The structure predicted from DFT for chalcone is in good agreement with the structure from XRD measurement.

Data-directed RNA secondary structure prediction using probabilistic modeling

PubMed Central

Deng, Fei; Ledda, Mirko; Vaziri, Sana; Aviran, Sharon

2016-01-01

Structure dictates the function of many RNAs, but secondary RNA structure analysis is either labor intensive and costly or relies on computational predictions that are often inaccurate. These limitations are alleviated by integration of structure probing data into prediction algorithms. However, existing algorithms are optimized for a specific type of probing data. Recently, new chemistries combined with advances in sequencing have facilitated structure probing at unprecedented scale and sensitivity. These novel technologies and anticipated wealth of data highlight a need for algorithms that readily accommodate more complex and diverse input sources. We implemented and investigated a recently outlined probabilistic framework for RNA secondary structure prediction and extended it to accommodate further refinement of structural information. This framework utilizes direct likelihood-based calculations of pseudo-energy terms per considered structural context and can readily accommodate diverse data types and complex data dependencies. We use real data in conjunction with simulations to evaluate performances of several implementations and to show that proper integration of structural contexts can lead to improvements. Our tests also reveal discrepancies between real data and simulations, which we show can be alleviated by refined modeling. We then propose statistical preprocessing approaches to standardize data interpretation and integration into such a generic framework. We further systematically quantify the information content of data subsets, demonstrating that high reactivities are major drivers of SHAPE-directed predictions and that better understanding of less informative reactivities is key to further improvements. Finally, we provide evidence for the adaptive capability of our framework using mock probe simulations. PMID:27251549

Metallic behavior in the graphene analogue Ni 3(HITP) 2 and a strategy to render the material a semiconductor.

DOE PAGES

Foster, Michael E.; Sohlberg, Karl; Spataru, Dan Catalin; ...

2016-06-19

The metal organic framework material Ni 3(2,3,6,7,10,11 - hexaiminotriphenylene) 2, (Ni 3(HITP) 2) is composed of layers of extended conjugated planes analogous to graphene. We carried out Density functional theory (DFT) calculations to model the electronic structure of bulk and monolayer Ni 3(HITP) 2. The layered 3D material is metallic, similar to graphene. Our calculations predict that there is appreciable band dispersion not only in-plane, but perpendicular to the stacking planes as well, suggesting that, unlike graphene, the conductivity may be nearly isotropic. In contrast, a 2D monolayer of the material exhibits a band gap, consistent with previously published results.more » Insight obtained from studies of the evolution of the material from semiconducting to metallic as the material is transitioned from 2D to 3D suggests the possibility of modifying the material to render it semiconducting by changing the metal center and inserting spacer moieties between the layers. Furthermore, the DFT calculations predict that the modified material will be structurally stable and exhibit a band gap.« less

Structure, stability, thermodynamic properties, and infrared spectra of the protonated water octamer H(+)(H2O)8.

PubMed

Karthikeyan, S; Park, Mina; Shin, Ilgyou; Kim, Kwang S

2008-10-16

We investigated various two-dimensional (2D) and three-dimensional (3D) structures of H (+)(H 2O) 8, using density functional theory (DFT), Moller-Plesset second-order perturbation theory (MP2), and coupled cluster theory with single, double, and perturbative triple excitations (CCSD(T)). The 3D structure is more stable than the 2D structure at all levels of theory on the Born-Oppenheimer surface. With the zero-point energy (ZPE) correction, the predicted structure varies depending on the level of theory. The DFT employing Becke's three parameters with Lee-Yang-Parr functionals (B3LYP) favors the 2D structure. At the complete basis set (CBS) limit, the MP2 calculation favors the 3D structure by 0.29 kcal/mol, and the CCSD(T) calculation favors the 3D structure by 0.27 kcal/mol. It is thus expected that both 2D and 3D structures are nearly isoenergetic near 0 K. At 100 K, all the calculations show that the 2D structure is much more stable in free binding energy than the 3D structure. The DFT and MP2 vibrational spectra of the 2D structure are consistent with the experimental spectra. First-principles Car-Parrinello molecular dynamics (CPMD) simulations show that the 2D Zundel-type vibrational spectra are in good agreement with the experiment.

Derivation of force field parameters for SnO2-H2O surface systems from plane-wave density functional theory calculations.

PubMed

Bandura, A V; Sofo, J O; Kubicki, J D

2006-04-27

Plane-wave density functional theory (DFT-PW) calculations were performed on bulk SnO2 (cassiterite) and the (100), (110), (001), and (101) surfaces with and without H2O present. A classical interatomic force field has been developed to describe bulk SnO2 and SnO2-H2O surface interactions. Periodic density functional theory calculations using the program VASP (Kresse et al., 1996) and molecular cluster calculations using Gaussian 03 (Frisch et al., 2003) were used to derive the parametrization of the force field. The program GULP (Gale, 1997) was used to optimize parameters to reproduce experimental and ab initio results. The experimental crystal structure and elastic constants of SnO2 are reproduced reasonably well with the force field. Furthermore, surface atom relaxations and structures of adsorbed H2O molecules agree well between the ab initio and force field predictions. H2O addition above that required to form a monolayer results in consistent structures between the DFT-PW and classical force field results as well.

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.

Lattice and Valence Electronic Structures of Crystalline Octahedral Molybdenum Halide Clusters-Based Compounds, Cs2[Mo6X14] (X = Cl, Br, I), Studied by Density Functional Theory Calculations.

PubMed

Saito, Norio; Cordier, Stéphane; Lemoine, Pierric; Ohsawa, Takeo; Wada, Yoshiki; Grasset, Fabien; Cross, Jeffrey S; Ohashi, Naoki

2017-06-05

The electronic and crystal structures of Cs 2 [Mo 6 X 14 ] (X = Cl, Br, I) cluster-based compounds were investigated by density functional theory (DFT) simulations and experimental methods such as powder X-ray diffraction, ultraviolet-visible spectroscopy, and X-ray photoemission spectroscopy (XPS). The experimentally determined lattice parameters were in good agreement with theoretically optimized ones, indicating the usefulness of DFT calculations for the structural investigation of these clusters. The calculated band gaps of these compounds reproduced those experimentally determined by UV-vis reflectance within an error of a few tenths of an eV. Core-level XPS and effective charge analyses indicated bonding states of the halogens changed according to their sites. The XPS valence spectra were fairly well reproduced by simulations based on the projected electron density of states weighted with cross sections of Al K α , suggesting that DFT calculations can predict the electronic properties of metal-cluster-based crystals with good accuracy.

Investigation of different physical aspects such as structural, mechanical, optical properties and Debye temperature of Fe2ScM (M=P and As) semiconductors: A DFT-based first principles study

NASA Astrophysics Data System (ADS)

Ali, Md. Lokman; Rahaman, Md. Zahidur

2018-04-01

By using first principles calculation dependent on the density functional theory (DFT), we have investigated the mechanical, structural properties and the Debye temperature of Fe2ScM (M=P and As) compounds under various pressures up to 60 GPa. The optical properties have been investigated under zero pressure. Our calculated optimized structural parameters of both the materials are in good agreement with other theoretical predictions. The calculated elastic constants show that Fe2ScM (M=P and As) compounds are mechanically stable under external pressure below 60 GPa. From the elastic constants, the shear modulus G, the bulk modulus B, Young’s modulus E, anisotropy factor A and Poisson’s ratio ν are calculated by using the Voigt-Reuss-Hill approximation. The Debye temperature and average sound velocities are also investigated from the obtained elastic constants. The detailed analysis of all optical functions reveals that both compounds are good dielectric material.

Theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis-, and trans-1,2-difluoroethylenes

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

Nozirov, Farhod, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com; Stachów, Michał, E-mail: michal.stachow@gmail.com; Kupka, Teobald, E-mail: teobaldk@gmail.com, E-mail: farhod.nozirov@gmail.com

2014-04-14

A theoretical prediction of nuclear magnetic shieldings and indirect spin-spin coupling constants in 1,1-, cis- and trans-1,2-difluoroethylenes is reported. The results obtained using density functional theory (DFT) combined with large basis sets and gauge-independent atomic orbital calculations were critically compared with experiment and conventional, higher level correlated electronic structure methods. Accurate structural, vibrational, and NMR parameters of difluoroethylenes were obtained using several density functionals combined with dedicated basis sets. B3LYP/6-311++G(3df,2pd) optimized structures of difluoroethylenes closely reproduced experimental geometries and earlier reported benchmark coupled cluster results, while BLYP/6-311++G(3df,2pd) produced accurate harmonic vibrational frequencies. The most accurate vibrations were obtained using B3LYP/6-311++G(3df,2pd)more » with correction for anharmonicity. Becke half and half (BHandH) density functional predicted more accurate {sup 19}F isotropic shieldings and van Voorhis and Scuseria's τ-dependent gradient-corrected correlation functional yielded better carbon shieldings than B3LYP. A surprisingly good performance of Hartree-Fock (HF) method in predicting nuclear shieldings in these molecules was observed. Inclusion of zero-point vibrational correction markedly improved agreement with experiment for nuclear shieldings calculated by HF, MP2, CCSD, and CCSD(T) methods but worsened the DFT results. The threefold improvement in accuracy when predicting {sup 2}J(FF) in 1,1-difluoroethylene for BHandH density functional compared to B3LYP was observed (the deviations from experiment were −46 vs. −115 Hz)« less

Electronic and optical properties of titanium nitride bulk and surfaces from first principles calculations

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

Mehmood, Faisal; General Dynamics Information Technology, Inc., Dayton, Ohio 45433; Pachter, Ruth, E-mail: ruth.pachter@us.af.mil

Prediction of the frequency-dependent dielectric function of thin films poses computational challenges, and at the same time experimental characterization by spectroscopic ellipsometry remains difficult to interpret because of changes in stoichiometry and surface morphology, temperature, thickness of the film, or substrate. In this work, we report calculations for titanium nitride (TiN), a promising material for plasmonic applications because of less loss and other practical advantages compared to noble metals. We investigated structural, electronic, and optical properties of stoichiometric bulk TiN, as well as of the TiN(100), TiN(110), and TiN(111) outermost surfaces. Density functional theory (DFT) and many-body GW methods (Green'smore » (G) function-based approximation with screened Coulomb interaction (W)) were used, ranging from G{sub 0}W{sub 0}, GW{sub 0} to partially self-consistent sc-GW{sub 0}, as well as the GW-BSE (Bethe-Salpeter equation) and time-dependent DFT (TDDFT) methods for prediction of the optical properties. Structural parameters and the band structure for bulk TiN were shown to be consistent with previous work. Calculated dielectric functions, plasma frequencies, reflectivity, and the electron energy loss spectrum demonstrated consistency with experiment at the GW{sub 0}-BSE level. Deviations from experimental data are expected due to varying experimental conditions. Comparison of our results to spectroscopic ellipsometry data for realistic nanostructures has shown that although TDDFT may provide a computationally feasible level of theory in evaluation of the dielectric function, application is subject to validation with GW-BSE calculations.« less

Experimental validation of finite element and boundary element methods for predicting structural vibration and radiated noise

NASA Technical Reports Server (NTRS)

Seybert, A. F.; Wu, T. W.; Wu, X. F.

1994-01-01

This research report is presented in three parts. In the first part, acoustical analyses were performed on modes of vibration of the housing of a transmission of a gear test rig developed by NASA. The modes of vibration of the transmission housing were measured using experimental modal analysis. The boundary element method (BEM) was used to calculate the sound pressure and sound intensity on the surface of the housing and the radiation efficiency of each mode. The radiation efficiency of each of the transmission housing modes was then compared to theoretical results for a finite baffled plate. In the second part, analytical and experimental validation of methods to predict structural vibration and radiated noise are presented. A rectangular box excited by a mechanical shaker was used as a vibrating structure. Combined finite element method (FEM) and boundary element method (BEM) models of the apparatus were used to predict the noise level radiated from the box. The FEM was used to predict the vibration, while the BEM was used to predict the sound intensity and total radiated sound power using surface vibration as the input data. Vibration predicted by the FEM model was validated by experimental modal analysis; noise predicted by the BEM was validated by measurements of sound intensity. Three types of results are presented for the total radiated sound power: sound power predicted by the BEM model using vibration data measured on the surface of the box; sound power predicted by the FEM/BEM model; and sound power measured by an acoustic intensity scan. In the third part, the structure used in part two was modified. A rib was attached to the top plate of the structure. The FEM and BEM were then used to predict structural vibration and radiated noise respectively. The predicted vibration and radiated noise were then validated through experimentation.

Predicting the potentials, solubilities and stabilities of metal-acetylacetonates for non-aqueous redox flow batteries using density functional theory calculations

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

Kucharyson, J. F.; Cheng, L.; Tung, S. O.

New active materials are needed to improve the performance and reduce the cost of non-aqueous redox flow batteries (RFBs) for grid-scale energy storage applications. Efforts to develop better performing materials, which have largely been empirical, would benefit from a better understanding of relationships between structural, electronic and RFB-relevant functional properties. This paper focuses on metal-acetylacetonates, a class of metal coordination complexes that has shown promise for use in RFBs, and describes correlations between their experimentally measured standard potentials, solubilities, and stabilities (cycle lifes), and selected chemical, structural and electronic properties determined from Density Functional Theory (DFT) calculations. The training setmore » consisted of 16 complexes including 5 different metals and 11 different substituents on the acetylacetonate ligand. Standard potentials for those compounds were calculated and are in good agreement with experimentally measured results. A predictive equation based on the solvation energies and dipole moments, two easily computed properties, reasonably modeled the experimentally determined solubilities. Importantly, we were able to identify a descriptor for the stability of acetylacetonates. The experimentally determined stability, quantified as the cycle life to a given degree of degradation, correlated with the percentage of the highest occupied (HOMO) or lowest unoccupied molecular orbital (LUMO) on the metal of the complex. This percentage is influenced by the degree of ligand innocence (irreducibility), and complexes with the most innocent ligands yielded the most stable redox reactions. To this end, VO(acetylacetonate)(2) and Fe(acetylacetonate)(3), with nearly 80% of the HOMO and LUMO on the metal, possessed the most stable oxidation and reduction half-reactions, respectively. The structure-function relationships and correlations presented in this paper could be used to predict new, highly soluble and stable complexes for RFB applications.« less

MODBASE, a database of annotated comparative protein structure models

PubMed Central

Pieper, Ursula; Eswar, Narayanan; Stuart, Ashley C.; Ilyin, Valentin A.; Sali, Andrej

2002-01-01

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server. PMID:11752309

First-principles calculations of two cubic fluoropervskite compounds: RbFeF3 and RbNiF3

NASA Astrophysics Data System (ADS)

Mubarak, A. A.; Al-Omari, Saleh

2015-05-01

We present first-principles calculations of the structural, elastic, electronic, magnetic and optical properties for RbFeF3 and RbNiF3. The full-potential linear augmented plan wave (FP-LAPW) method within the density functional theory was utilized to perform the present calculations. We employed the generalized gradient approximation as exchange-correlation potential. It was found that the calculated analytical lattice parameters agree with previous studies. The analysis of elastic constants showed that the present compounds are elastically stable and anisotropic. Moreover, both compounds are classified as a ductile compound. The calculations of the band structure and density functional theory revealed that the RbFeF3 compound has a half-metallic behavior while the RbNiF3 compound has a semiconductor behavior with indirect (M-Γ) band gap. The ferromagnetic behavior was studied for both compounds. The optical properties were calculated for the radiation of up to 40 eV. A beneficial optics technology is predicted as revealed from the optical spectra.

Assessment of quantitative structure-activity relationship of toxicity prediction models for Korean chemical substance control legislation

PubMed Central

Kim, Kwang-Yon; Shin, Seong Eun; No, Kyoung Tai

2015-01-01

Objectives For successful adoption of legislation controlling registration and assessment of chemical substances, it is important to obtain sufficient toxicological experimental evidence and other related information. It is also essential to obtain a sufficient number of predicted risk and toxicity results. Particularly, methods used in predicting toxicities of chemical substances during acquisition of required data, ultimately become an economic method for future dealings with new substances. Although the need for such methods is gradually increasing, the-required information about reliability and applicability range has not been systematically provided. Methods There are various representative environmental and human toxicity models based on quantitative structure-activity relationships (QSAR). Here, we secured the 10 representative QSAR-based prediction models and its information that can make predictions about substances that are expected to be regulated. We used models that predict and confirm usability of the information expected to be collected and submitted according to the legislation. After collecting and evaluating each predictive model and relevant data, we prepared methods quantifying the scientific validity and reliability, which are essential conditions for using predictive models. Results We calculated predicted values for the models. Furthermore, we deduced and compared adequacies of the models using the Alternative non-testing method assessed for Registration, Evaluation, Authorization, and Restriction of Chemicals Substances scoring system, and deduced the applicability domains for each model. Additionally, we calculated and compared inclusion rates of substances expected to be regulated, to confirm the applicability. Conclusions We evaluated and compared the data, adequacy, and applicability of our selected QSAR-based toxicity prediction models, and included them in a database. Based on this data, we aimed to construct a system that can be used with predicted toxicity results. Furthermore, by presenting the suitability of individual predicted results, we aimed to provide a foundation that could be used in actual assessments and regulations. PMID:26206368

Theoretical study on Curcumin: A comparison of calculated spectroscopic properties with NMR, UV vis and IR experimental data

NASA Astrophysics Data System (ADS)

Benassi, Rois; Ferrari, Erika; Lazzari, Sandra; Spagnolo, Ferdinando; Saladini, Monica

2008-12-01

The main target of this study is a high-level computational analysis of Curcumin, employing DFT approach with two different sets of basis functions (B3LYP/6-31G ∗ and B3LYP/6-311G ∗∗). Accurate quantum mechanical studies, both in vacuum and in methanol medium, are carried out with the aim to analyze the conformational equilibria, to find the most stable equilibrium structure and to define the nature of the molecular orbitals, fundamental to explain Curcumin binding characteristic. Our theoretical calculations, performed at B3LYP/6-31G ∗ and B3LYP/6-311G ∗∗ levels both in vacuum and in methanol medium, confirm that the keto-enolic forms are more stable than the di-keto one, whose extremely low population suggests that this structure should not influence Curcumin properties. Keto-enolic form C results the most stable, independently on calculation level and solvent (methanol) effect. HOMO and LUMO molecular orbitals are calculated for all the structures with the two sets of basis with very similar results. MEPs show that the negative charge is localized on the oxygen atoms, which, in the keto-enolic forms, point in the same direction enabling metal coordination. NMR, UV-vis and FT-IR experimental data are employed in the comparison with electronic and conformational properties of Curcumin resulting from theoretical calculations. The two different calculation levels (B3LYP/6-31G ∗ and B3LYP/6-311G ∗∗) give very similar results. Good linear correlations between the experimental 1H and 13C NMR chemical shifts ( δexp), in methanol- d4 (MeOD) and DMSO- d6 (DMSO), and calculated magnetic isotropic shielding tensors ( σcalc) are found ( δexp = a · σcalc + b). A good prediction of UV-vis experimental maximum absorption ( λmax) on the basis of conformer populations is obtained. A linear relation with a good correlation coefficient is observed plotting the FT-IR experimental wavenumbers vs . the calculated ones, allowing to predict FT-IR spectra.

Predicting Keto-Enol Equilibrium from Combining UV/Visible Absorption Spectroscopy with Quantum Chemical Calculations of Vibronic Structures for Many Excited States. A Case Study on Salicylideneanilines.

PubMed

Zutterman, Freddy; Louant, Orian; Mercier, Gabriel; Leyssens, Tom; Champagne, Benoît

2018-06-21

Salicylideneanilines are characterized by a tautomer equilibrium, between an enol and a keto form of different colors, at the origin of their remarkable thermochromic, solvatochromic, and photochromic properties. The enol form is usually the most stable but appropriate choice of substituents and conditions (solvent, crystal, host compound) can displace the equilibrium toward the keto form so that there is a need for fast prediction of the keto:enol abundance ratio. Here we demonstrate the reliability of a combined theoretical-experimental method, based on comparing simulated and measured UV/visible absorption spectra, to determine this keto/enol ratio. The calculations of the excitation energies, oscillator strengths, and vibronic structures of both enol and keto forms are performed for all excited states absorbing in the relevant (visible and near-UV) wavelength range at the time-dependent density functional theory level by accounting for solvent effects using the polarizable continuum model. This approach is illustrated for two salicylideneaniline derivatives, which are present, in solution, under the form of keto-enol mixtures. The results are compared to those of chemometric analysis as well as ab initio predictions of the reaction free enthalpies.

Analyzing Aeroelasticity in Turbomachines

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Srivastava, R.

2003-01-01

ASTROP2-LE is a computer program that predicts flutter and forced responses of blades, vanes, and other components of such turbomachines as fans, compressors, and turbines. ASTROP2-LE is based on the ASTROP2 program, developed previously for analysis of stability of turbomachinery components. In developing ASTROP2- LE, ASTROP2 was modified to include a capability for modeling forced responses. The program was also modified to add a capability for analysis of aeroelasticity with mistuning and unsteady aerodynamic solutions from another program, LINFLX2D, that solves the linearized Euler equations of unsteady two-dimensional flow. Using LINFLX2D to calculate unsteady aerodynamic loads, it is possible to analyze effects of transonic flow on flutter and forced response. ASTROP2-LE can be used to analyze subsonic, transonic, and supersonic aerodynamics and structural mistuning for rotors with blades of differing structural properties. It calculates the aerodynamic damping of a blade system operating in airflow so that stability can be assessed. The code also predicts the magnitudes and frequencies of the unsteady aerodynamic forces on the airfoils of a blade row from incoming wakes. This information can be used in high-cycle fatigue analysis to predict the fatigue lives of the blades.

Mixed cerium-platinum oxides: Electronic structure of [CeO]Pt{sub n} (n = 1, 2) and [CeO{sub 2}]Pt complex anions and neutrals

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

Ray, Manisha; Kafader, Jared O.; Topolski, Josey E.

The electronic structures of several small Ce–Pt oxide complexes were explored using a combination of anion photoelectron (PE) spectroscopy and density functional theory calculations. Pt and Pt{sub 2} both accept electron density from CeO diatomic molecules, in which the cerium atom is in a lower-than-bulk oxidation state (+2 versus bulk +4). Neutral [CeO]Pt and [CeO]Pt{sub 2} complexes are therefore ionic, with electronic structures described qualitatively as [CeO{sup +2}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −}, respectively. The associated anions are described qualitatively as [CeO{sup +}]Pt{sup −2} and [CeO{sup +}]Pt{sub 2}{sup −2}, respectively. In both neutrals and anions, the most stable molecularmore » structures determined by calculations feature a distinct CeO moiety, with the positively charged Ce center pointing toward the electron rich Pt or Pt{sub 2} moiety. Spectral simulations based on calculated spectroscopic parameters are in fair agreement with the spectra, validating the computationally determined structures. In contrast, when Pt is coupled with CeO{sub 2}, which has no Ce-localized electrons that can readily be donated to Pt, the anion is described as [CeO{sub 2}]Pt{sup −}. The molecular structure predicted computationally suggests that it is governed by charge-dipole interactions. The neutral [CeO{sub 2}]Pt complex lacks charge-dipole stabilizing interactions, and is predicted to be structurally very different from the anion, featuring a single Pt–O–Ce bridge bond. The PE spectra of several of the complexes exhibit evidence of photodissociation with Pt{sup −} daughter ion formation. The electronic structures of these complexes are related to local interactions in Pt-ceria catalyst-support systems.« less

Vibrational analysis, NBO analysis, NMR, UV-VIS, hyperpolarizability analysis of Trimethadione by density functional theory

NASA Astrophysics Data System (ADS)

Vijayachamundeeswari, S. P.; Yagna Narayana, B.; Jone Pradeepa, S.; Sundaraganesan, N.

2015-11-01

Trimethadione (TMD) is an anticonvulsant drug widely used against absences seizures. We have characterised the TMD by various spectra including UV-VIS, IR, Raman, GC-MS and NMR. In this work, we made use of Density Functional Theory (DFT) B3LYP method with 6-31G (d, p) basis set, to calculate the molecular structure of TMD, and predicted its infrared, Raman and ultraviolet spectra for the first time. FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm-1 and 3500-50 cm-1, respectively. The vibrational frequencies were calculated and scaled values were compared with the experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes. The optimized geometry parameters were calculated. NMR chemical shifts of the molecule were calculated using the gauge independent atomic orbital (GIAO) method. The predicted first hyperpolarizibility also shows that the molecule might have convincingly good nonlinear optical (NLO) activities. The calculated HOMO-LUMO energy gap discloses that charge transfer occurs within the molecule.

Development of a New Model for Accurate Prediction of Cloud Water Deposition on Vegetation

NASA Astrophysics Data System (ADS)

Katata, G.; Nagai, H.; Wrzesinsky, T.; Klemm, O.; Eugster, W.; Burkard, R.

2006-12-01

Scarcity of water resources in arid and semi-arid areas is of great concern in the light of population growth and food shortages. Several experiments focusing on cloud (fog) water deposition on the land surface suggest that cloud water plays an important role in water resource in such regions. A one-dimensional vegetation model including the process of cloud water deposition on vegetation has been developed to better predict cloud water deposition on the vegetation. New schemes to calculate capture efficiency of leaf, cloud droplet size distribution, and gravitational flux of cloud water were incorporated in the model. Model calculations were compared with the data acquired at the Norway spruce forest at the Waldstein site, Germany. High performance of the model was confirmed by comparisons of calculated net radiation, sensible and latent heat, and cloud water fluxes over the forest with measurements. The present model provided a better prediction of measured turbulent and gravitational fluxes of cloud water over the canopy than the Lovett model, which is a commonly used cloud water deposition model. Detailed calculations of evapotranspiration and of turbulent exchange of heat and water vapor within the canopy and the modifications are necessary for accurate prediction of cloud water deposition. Numerical experiments to examine the dependence of cloud water deposition on the vegetation species (coniferous and broad-leaved trees, flat and cylindrical grasses) and structures (Leaf Area Index (LAI) and canopy height) are performed using the presented model. The results indicate that the differences of leaf shape and size have a large impact on cloud water deposition. Cloud water deposition also varies with the growth of vegetation and seasonal change of LAI. We found that the coniferous trees whose height and LAI are 24 m and 2.0 m2m-2, respectively, produce the largest amount of cloud water deposition in all combinations of vegetation species and structures in the experiments.

Discriminating a deep gallium antisite defect from shallow acceptors in GaAs using supercell calculations

DOE PAGES

Schultz, Peter A.

2016-03-01

For the purposes of making reliable first-principles predictions of defect energies in semiconductors, it is crucial to distinguish between effective-mass-like defects, which cannot be treated accurately with existing supercell methods, and deep defects, for which density functional theory calculations can yield reliable predictions of defect energy levels. The gallium antisite defect GaAs is often associated with the 78/203 meV shallow double acceptor in Ga-rich gallium arsenide. Within a conceptual framework of level patterns, analyses of structure and spin stabilization can be used within a supercell approach to distinguish localized deep defect states from shallow acceptors such as B As. Thismore » systematic approach determines that the gallium antisite supercell results has signatures inconsistent with an effective mass state and cannot be the 78/203 shallow double acceptor. Lastly, the properties of the Ga antisite in GaAs are described, total energy calculations that explicitly map onto asymptotic discrete localized bulk states predict that the Ga antisite is a deep double acceptor and has at least one deep donor state.« less

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.

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

WANG,YIFENG; XU,HUIFANG

Correctly identifying the possible alteration products and accurately predicting their occurrence in a repository-relevant environment are the key for the source-term calculation in a repository performance assessment. Uraninite in uranium deposits has long been used as a natural analog to spent fuel in a repository because of their chemical and structural similarity. In this paper, a SEM/AEM investigation has been conducted on a partially alternated uraninite sample from a uranium ore deposit of Shinkolobwe of Congo. The mineral formation sequences were identified: uraninite {yields} uranyl hydrates {yields} uranyl silicates {yields} Ca-uranyl silicates or uraninite {yields} uranyl silicates {yields} Ca-uranyl silicates.more » Reaction-path calculations were conducted for the oxidative dissolution of spent fuel in a representative Yucca Mountain groundwater. The predicted sequence is in general consistent with the SEM observations. The calculations also show that uranium carbonate minerals are unlikely to become major solubility-controlling mineral phases in a Yucca Mountain environment. Some discrepancies between model predictions and field observations are observed. Those discrepancies may result from poorly constrained thermodynamic data for uranyl silicate minerals.« less

Penta-SiC5 monolayer: A novel quasi-planar indirect semiconductor with a tunable wide band gap

NASA Astrophysics Data System (ADS)

Naseri, Mosayeb

2018-03-01

In this paper, by using of the first principles calculations in the framework of the density functional theory, we systematically investigated the structure, stability, electronic and optical properties of a novel two-dimensional pentagonal monolayer semiconductors namely penta-SiC5 monolayer. Comparing elemental silicon, diamond, and previously reported 2D carbon allotropes, our calculation shows that the predicted penta-SiC5 monolayer has a metastable nature. The calculated results indicate that the predicted monolayer is an indirect semiconductor with a wide band gap of about 2.82 eV by using Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional level of theory which can be effectively tuned by external biaxial strains. The obtained exceptional electronic properties suggest penta-SiC5 monolayer as promising candidates for application in new electronic devices in nano scale.

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.

A Micromechanics-Based Method for Multiscale Fatigue Prediction

NASA Astrophysics Data System (ADS)

Moore, John Allan

An estimated 80% of all structural failures are due to mechanical fatigue, often resulting in catastrophic, dangerous and costly failure events. However, an accurate model to predict fatigue remains an elusive goal. One of the major challenges is that fatigue is intrinsically a multiscale process, which is dependent on a structure's geometric design as well as its material's microscale morphology. The following work begins with a microscale study of fatigue nucleation around non- metallic inclusions. Based on this analysis, a novel multiscale method for fatigue predictions is developed. This method simulates macroscale geometries explicitly while concurrently calculating the simplified response of microscale inclusions. Thus, providing adequate detail on multiple scales for accurate fatigue life predictions. The methods herein provide insight into the multiscale nature of fatigue, while also developing a tool to aid in geometric design and material optimization for fatigue critical devices such as biomedical stents and artificial heart valves.

Convenient QSAR model for predicting the complexation of structurally diverse compounds with beta-cyclodextrins.

PubMed

Pérez-Garrido, Alfonso; Morales Helguera, Aliuska; Abellán Guillén, Adela; Cordeiro, M Natália D S; Garrido Escudero, Amalio

2009-01-15

This paper reports a QSAR study for predicting the complexation of a large and heterogeneous variety of substances (233 organic compounds) with beta-cyclodextrins (beta-CDs). Several different theoretical molecular descriptors, calculated solely from the molecular structure of the compounds under investigation, and an efficient variable selection procedure, like the Genetic Algorithm, led to models with satisfactory global accuracy and predictivity. But the best-final QSAR model is based on Topological descriptors meanwhile offering a reasonable interpretation. This QSAR model was able to explain ca. 84% of the variance in the experimental activity, and displayed very good internal cross-validation statistics and predictivity on external data. It shows that the driving forces for CD complexation are mainly hydrophobic and steric (van der Waals) interactions. Thus, the results of our study provide a valuable tool for future screening and priority testing of beta-CDs guest molecules.

Density functional theory studies on the electronic, structural, phonon dynamical and thermo-stability properties of bicarbonates MHCO3, M = Li, Na, K

NASA Astrophysics Data System (ADS)

Duan, Yuhua; Zhang, Bo; Sorescu, Dan C.; Johnson, J. Karl; Majzoub, Eric H.; Luebke, David R.

2012-08-01

The structural, electronic, phonon dispersion and thermodynamic properties of MHCO3 (M = Li, Na, K) solids were investigated using density functional theory. The calculated bulk properties for both their ambient and the high-pressure phases are in good agreement with available experimental measurements. Solid phase LiHCO3 has not yet been observed experimentally. We have predicted several possible crystal structures for LiHCO3 using crystallographic database searching and prototype electrostatic ground state modeling. Our total energy and phonon free energy (FPH) calculations predict that LiHCO3 will be stable under suitable conditions of temperature and partial pressures of CO2 and H2O. Our calculations indicate that the {{HCO}}_{3}^{-} groups in LiHCO3 and NaHCO3 form an infinite chain structure through O⋯H⋯O hydrogen bonds. In contrast, the {{HCO}}_{3}^{-} anions form dimers, ({{HCO}}_{3}^{-})_{2}, connected through double hydrogen bonds in all phases of KHCO3. Based on density functional perturbation theory, the Born effective charge tensor of each atom type was obtained for all phases of the bicarbonates. Their phonon dispersions with the longitudinal optical-transverse optical splitting were also investigated. Based on lattice phonon dynamics study, the infrared spectra and the thermodynamic properties of these bicarbonates were obtained. Over the temperature range 0-900 K, the FPH and the entropies (S) of MHCO3 (M =Li, Na, K) systems vary as FPH(LiHCO3) > FPH(NaHCO3) > FPH(KHCO3) and S(KHCO3) > S(NaHCO3) > S(LiHCO3), respectively, in agreement with the available experimental data. Analysis of the predicted thermodynamics of the CO2 capture reactions indicates that the carbonate/bicarbonate transition reactions for Na and K could be used for CO2 capture technology, in agreement with experiments.

Electronic structure of PPP@ZnO from all-electron quasiarticle calculations

NASA Astrophysics Data System (ADS)

Höffling, Benjamin; Nabok, Dimitri; Draxl, Claudia; Condensed Matter Theory Group, Humboldt University Berlin Team

We investigate the electronic properties of poly(para-phenylene) (PPP) adsorbed on the non-polar (001) surface of rocksalt (rs) ZnO using all-electron density functional theory (DFT) as well as quasiparticle (QP) calculations within the GW approach. A particular focus is put on the electronic band discontinuities at the interface, where we investigate the impact of quantum confinement, molecular polarization, and charge rearrangement. For our prototypical system, PPP@ZnO, we find a type-I heterostructure. Comparison of the band offsets derived from a QP-treatment of the hybrid system with predictions based on mesoscopic methods, like the Shockley-Anderson model or alignment via the electrostatic potential, reveals the inadequacy of these simple approaches for the prediction of the electronic structure of such inorganic/organic heterosystems. Finally, we explore the optical excitations of the interface compared to the features of the pristine components and discuss the methodological implications for the ab-initio treatment of interface electronics.

Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

PubMed Central

Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

2015-01-01

Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

Automated use of mutagenesis data in structure prediction.

PubMed

Nanda, Vikas; DeGrado, William F

2005-05-15

In the absence of experimental structural determination, numerous methods are available to indirectly predict or probe the structure of a target molecule. Genetic modification of a protein sequence is a powerful tool for identifying key residues involved in binding reactions or protein stability. Mutagenesis data is usually incorporated into the modeling process either through manual inspection of model compatibility with empirical data, or through the generation of geometric constraints linking sensitive residues to a binding interface. We present an approach derived from statistical studies of lattice models for introducing mutation information directly into the fitness score. The approach takes into account the phenotype of mutation (neutral or disruptive) and calculates the energy for a given structure over an ensemble of sequences. The structure prediction procedure searches for the optimal conformation where neutral sequences either have no impact or improve stability and disruptive sequences reduce stability relative to wild type. We examine three types of sequence ensembles: information from saturation mutagenesis, scanning mutagenesis, and homologous proteins. Incorporating multiple sequences into a statistical ensemble serves to energetically separate the native state and misfolded structures. As a result, the prediction of structure with a poor force field is sufficiently enhanced by mutational information to improve accuracy. Furthermore, by separating misfolded conformations from the target score, the ensemble energy serves to speed up conformational search algorithms such as Monte Carlo-based methods. Copyright 2005 Wiley-Liss, Inc.

Universal fragment descriptors for predicting properties of inorganic crystals

NASA Astrophysics Data System (ADS)

Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

2017-06-01

Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

Universal fragment descriptors for predicting properties of inorganic crystals.

PubMed

Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

2017-06-05

Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

Insufficient Hartree–Fock Exchange in Hybrid DFT Functionals Produces Bent Alkynyl Radical Structures

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

Oyeyemi, Victor B.; Keith, John A.; Pavone, Michele

2012-01-11

Density functional theory (DFT) is often used to determine the electronic and geometric structures of molecules. While studying alkynyl radicals, we discovered that DFT exchange-correlation (XC) functionals containing less than ~22% Hartree–Fock (HF) exchange led to qualitatively different structures than those predicted from ab initio HF and post-HF calculations or DFT XCs containing 25% or more HF exchange. We attribute this discrepancy to rehybridization at the radical center due to electron delocalization across the triple bonds of the alkynyl groups, which itself is an artifact of self-interaction and delocalization errors. Inclusion of sufficient exact exchange reduces these errors and suppressesmore » this erroneous delocalization; we find that a threshold amount is needed for accurate structure determinations. Finally, below this threshold, significant errors in predicted alkyne thermochemistry emerge as a consequence.« less

Fe-Cluster Compounds of Chalcogenides: Candidates for Rare-Earth-Free Permanent Magnet and Magnetic Nodal-Line Topological Material

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

Zhao, Xin; Wang, Cai-Zhuang; Kim, Minsung

Here, Fe-cluster-based crystal structures are predicted for chalcogenides Fe 3X 4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Additionally, using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe 3X 4 compounds and exhibit interesting magnetic and electronic properties. In particular, we show that Fe 3X 4 can be a good candidatemore » as a rare-earth-free permanent magnet and Fe 3X 4 can be a magnetic nodal-line topological material.« less

Fe-Cluster Compounds of Chalcogenides: Candidates for Rare-Earth-Free Permanent Magnet and Magnetic Nodal-Line Topological Material

DOE PAGES

Zhao, Xin; Wang, Cai-Zhuang; Kim, Minsung; ...

2017-11-13

Here, Fe-cluster-based crystal structures are predicted for chalcogenides Fe 3X 4 (X = S, Se, Te) using an adaptive genetic algorithm. Topologically different from the well-studied layered structures of iron chalcogenides, the newly predicted structures consist of Fe clusters that are either separated by the chalcogen atoms or connected via sharing of the vertex Fe atoms. Additionally, using first-principles calculations, we demonstrate that these structures have competitive or even lower formation energies than the experimentally synthesized Fe 3X 4 compounds and exhibit interesting magnetic and electronic properties. In particular, we show that Fe 3X 4 can be a good candidatemore » as a rare-earth-free permanent magnet and Fe 3X 4 can be a magnetic nodal-line topological material.« less

Pressure-induced structural phase transition in transition metal carbides TMC (TM = Ru, Rh, Pd, Os, Ir, Pt): a DFT study

NASA Astrophysics Data System (ADS)

Manikandan, M.; Rajeswarapalanichamy, R.; Iyakutti, K.

2018-03-01

First-principles calculations based on density functional theory was performed to analyse the structural stability of transition metal carbides TMC (TM = Ru, Rh, Pd, Os, Ir, Pt). It is observed that zinc-blende phase is the most stable one for these carbides. Pressure-induced structural phase transition from zinc blende to NiAs phase is predicted at the pressures of 248.5 GPa, 127 GPa and 142 GPa for OsC, IrC and PtC, respectively. The electronic structure reveals that RuC exhibits a semiconducting behaviour with an energy gap of 0.7056 eV. The high bulk modulus values of these carbides indicate that these metal carbides are super hard materials. The high B/G value predicts that the carbides are ductile in their most stable phase.

Approximate method for calculating free vibrations of a large-wind-turbine tower structure

NASA Technical Reports Server (NTRS)

Das, S. C.; Linscott, B. S.

1977-01-01

A set of ordinary differential equations were derived for a simplified structural dynamic lumped-mass model of a typical large-wind-turbine tower structure. Dunkerley's equation was used to arrive at a solution for the fundamental natural frequencies of the tower in bending and torsion. The ERDA-NASA 100-kW wind turbine tower structure was modeled, and the fundamental frequencies were determined by the simplified method described. The approximate fundamental natural frequencies for the tower agree within 18 percent with test data and predictions analyzed.

Structure and Randomness of Continuous-Time, Discrete-Event Processes

NASA Astrophysics Data System (ADS)

Marzen, Sarah E.; Crutchfield, James P.

2017-10-01

Loosely speaking, the Shannon entropy rate is used to gauge a stochastic process' intrinsic randomness; the statistical complexity gives the cost of predicting the process. We calculate, for the first time, the entropy rate and statistical complexity of stochastic processes generated by finite unifilar hidden semi-Markov models—memoryful, state-dependent versions of renewal processes. Calculating these quantities requires introducing novel mathematical objects (ɛ -machines of hidden semi-Markov processes) and new information-theoretic methods to stochastic processes.

Ternary chalcogenides C s 2 Z n 3 S e 4 and C s 2 Z n 3 T e 4 : Potential p -type transparent conducting materials

DOE PAGES

Shi, Hongliang; Saparov, Bayrammurad; Singh, David J.; ...

2014-11-11

Here we report prediction of two new ternary chalcogenides that can potentially be used as p-type transparent conductors along with experimental synthesis and initial characterization of these previously unknown compounds, Cs 2Zn 3Ch 4 (Ch = Se, Te). In particular, the structures are predicted based on density functional calculations and confirmed by experiments. Phase diagrams, electronic structure, optical properties, and defect properties of Cs 2Zn 3Se 4 and Cs 2Zn 3Te 4 are calculated to assess the viability of these materials as p-type TCMs. Cs 2Zn 3Se 4 and Cs 2Zn 3Te 4, which are stable under ambient air, displaymore » large optical band gaps (calculated to be 3.61 and 2.83 eV, respectively) and have small hole effective masses (0.5-0.77 m e) that compare favorably with other proposed p-type TCMs. Defect calculations show that undoped Cs2Zn3Se4 and Cs2Zn3Te4 are p-type materials. However, the free hole concentration may be limited by low-energy native donor defects, e.g., Zn interstitials. Lastly, non-equilibrium growth techniques should be useful for suppressing the formation of native donor defects, thereby increasing the hole concentration.« less

Predicting full-field dynamic strain on a three-bladed wind turbine using three dimensional point tracking and expansion techniques

NASA Astrophysics Data System (ADS)

Baqersad, Javad; Niezrecki, Christopher; Avitabile, Peter

2014-03-01

As part of a project to predict the full-field dynamic strain in rotating structures (e.g. wind turbines and helicopter blades), an experimental measurement was performed on a wind turbine attached to a 500-lb steel block and excited using a mechanical shaker. In this paper, the dynamic displacement of several optical targets mounted to a turbine placed in a semi-built-in configuration was measured by using three-dimensional point tracking. Using an expansion algorithm in conjunction with a finite element model of the blades, the measured displacements were expanded to all finite element degrees of freedom. The calculated displacements were applied to the finite element model to extract dynamic strain on the surface as well as within the interior points of the structure. To validate the technique for dynamic strain prediction, the physical strain at eight locations on the blades was measured during excitation using strain-gages. The expansion was performed by using both structural modes of an individual cantilevered blade and using modes of the entire structure (three-bladed wind turbine and the fixture) and the predicted strain was compared to the physical strain-gage measurements. The results demonstrate the ability of the technique to predict full-field dynamic strain from limited sets of measurements and can be used as a condition based monitoring tool to help provide damage prognosis of structures during operation.

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

Verma, U. P.; Nayak, V.

Quantum mechanical first principle calculations have been performed to study the electronic and structural properties of TiN and TiAs in zinc blende (ZB) and rock salt (RS) structures. The full-potential linearized augmented plane wave (FP-LAPW) method has been used within the framework of density functional theory (DFT). The exchange correlation functional has been solved employing generalized gradient approximation (GGA). Our predicted results for lattice constants are in good agreement with the earlier findings. The electronic band structures of TiX are metallic in both the phases.

Measurements and Modeling of Soot Formation and Radiation in Microgravity Jet Diffusion Flames. Volume 4

NASA Technical Reports Server (NTRS)

Ku, Jerry C.; Tong, Li; Greenberg, Paul S.

1996-01-01

This is a computational and experimental study for soot formation and radiative heat transfer in jet diffusion flames under normal gravity (1-g) and microgravity (0-g) conditions. Instantaneous soot volume fraction maps are measured using a full-field imaging absorption technique developed by the authors. A compact, self-contained drop rig is used for microgravity experiments in the 2.2-second drop tower facility at NASA Lewis Research Center. On modeling, we have coupled flame structure and soot formation models with detailed radiation transfer calculations. Favre-averaged boundary layer equations with a k-e-g turbulence model are used to predict the flow field, and a conserved scalar approach with an assumed Beta-pdf are used to predict gaseous species mole fraction. Scalar transport equations are used to describe soot volume fraction and number density distributions, with formation and oxidation terms modeled by one-step rate equations and thermophoretic effects included. An energy equation is included to couple flame structure and radiation analyses through iterations, neglecting turbulence-radiation interactions. The YIX solution for a finite cylindrical enclosure is used for radiative heat transfer calculations. The spectral absorption coefficient for soot aggregates is calculated from the Rayleigh solution using complex refractive index data from a Drude- Lorentz model. The exponential-wide-band model is used to calculate the spectral absorption coefficient for H20 and C02. It is shown that when compared to results from true spectral integration, the Rosseland mean absorption coefficient can provide reasonably accurate predictions for the type of flames studied. The soot formation model proposed by Moss, Syed, and Stewart seems to produce better fits to experimental data and more physically sound than the simpler model by Khan et al. Predicted soot volume fraction and temperature results agree well with published data for a normal gravity co-flow laminar flames and turbulent jet flames. Predicted soot volume fraction results also agree with our data for 1-g and 0-g laminar jet names as well as 1-g turbulent jet flames.

Activity of N-coordinated multi-metal-atom active site structures for Pt-free oxygen reduction reaction catalysis: Role of *OH ligands

DOE PAGES

Holby, Edward F.; Taylor, Christopher D.

2015-03-19

We report calculated oxygen reduction reaction energy pathways on multi-metal-atom structures that have previously been shown to be thermodynamically favorable. We predict that such sites have the ability to spontaneously cleave the O₂ bond and then will proceed to over-bind reaction intermediates. In particular, the *OH bound state has lower energy than the final 2 H₂O state at positive potentials. Contrary to traditional surface catalysts, this *OH binding does not poison the multi-metal-atom site but acts as a modifying ligand that will spontaneously form in aqueous environments leading to new active sites that have higher catalytic activities. These *OH boundmore » structures have the highest calculated activity to date.« less

Electron and positron states in HgBa2CuO4

NASA Astrophysics Data System (ADS)

Barbiellini, B.; Jarlborg, T.

1994-08-01

Local-density-calculations of the electronic structure of HgBa2CuO4 have been performed with the self-consistent linear muffin-tin orbital method. The positron-density distribution and its sensitivity due to different potentials are calculated. The annihilation rates are computed in order to study the chemical bonding and to predict the Fermi-surface signal. Comparisons are made with previous calculations on other high-Tc copper oxides concerning the Fermi-surface properties and electron-positron overlap. We discuss the possibility of observing the Fermi surface associated with the Cu-O planes in positron-annihilation experiments.

Electronic structure of boron based single and multi-layer two dimensional materials

NASA Astrophysics Data System (ADS)

Miyazato, Itsuki; Takahashi, Keisuke

2017-09-01

Two dimensional nanosheets based on boron and Group VA elements are designed and characterized using first principles calculations. B-N, B-P, B-As, B-Sb, and B-Bi are found to possess honeycomb structures where formation energies indicate exothermic reactions. Contrary to B-N, the cases of B-P, B-As, B-Sb, and B-Bi nanosheets are calculated to possess narrow band gaps. In addition, calculations reveal that the electronegativity difference between B and Group VA elements in the designed materials is a good indicator to predict the charge transfer and band gap of the two dimensional materials. Hydrogen adsorption over defect-free B-Sb and B-Bi results in exothermic reactions, while defect-free B-N, B-P, and B-As result in endothermic reactions. The layerability of the designed two dimensional materials is also investigated where the electronic structure of two-layered two dimensional materials is strongly coupled with how the two dimensional materials are layered. Thus, one can consider that the properties of two dimensional materials can be controlled by the composition of two dimensional materials and the structure of layers.

Crystal growth, electronic structure and optical properties of Sr2Mg(BO3)2

NASA Astrophysics Data System (ADS)

Lv, Xianshun; Wei, Lei; Wang, Xuping; Xu, Jianhua; Yu, Huajian; Hu, Yanyan; Zhang, Huadi; Zhang, Cong; Wang, Jiyang; Li, Qinggang

2018-02-01

Single crystals of Sr2Mg(BO3)2 (SMBO) were grown by Kyropoulos method. X-ray powder diffraction (XRD) analysis, transmission spectrum, thermal properties, band structure, density of states and charge distribution as well as Raman spectra of SMBO were described. The as-grown SMBO crystals show wide transparency range with UV cut-off below 180 nm. A direct band gap of 4.66 eV was obtained from the calculated electronic structure results. The calculated band structure and density of states results indicated the top valence band is determined by O 2p states whereas the low conduction band mainly consists of Sr 5s states. Twelve Raman peaks were observed in the experimental spectrum, fewer than the number predicted by the site group analysis. Raman peaks of SMBO were assigned combining first-principle calculation and site group analysis results. The strongest peak at 917 cm-1 in the experimental spectrum is assigned to symmetric stretching mode A1‧(ν1) of free BO3 units. SMBO is a potential Raman crystal which can be used in deep UV laser frequency conversion.

A comparative experimental and quantum chemical study on monomeric and dimeric structures of 3,5-dibromoanthranilic acid.

PubMed

Karabacak, Mehmet; Cinar, Mehmet

2012-10-01

This study presents the structural and spectroscopic characterization of 3,5-dibromoanthranilic acid with help of experimental techniques (FT-IR, FT-Raman, UV, NMR) and quantum chemical calculations. The vibrational spectra of title compound were recorded in solid state with FT-IR and FT-Raman in the range of 4000-400 and 4000-50 cm(-1), respectively. The vibrational frequencies were also computed using B3LYP method of DFT with 6-311++G(d,p) basis set. The fundamental assignments were done on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanical (SQM) method. The (1)H, (13)C and DEPT NMR spectra were recorded in DMSO solution and calculated by gauge-invariant atomic orbitals (GIAO) method. The UV absorption spectra of the compound were recorded in the range of 200-400 nm in ethanol, water and DMSO solutions. Solvent effects were calculated using time-dependent density functional theory and CIS method. The ground state geometrical structure of compound was predicted by B3LYP method and compared with the crystallographic structure of similar compounds. All calculations were made for monomeric and dimeric structure of compound. Moreover, molecular electrostatic potential (MEP) and thermodynamic properties were performed. Mulliken atomic charges of neutral and anionic form of the molecule were computed and compared with anthranilic acid. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantum Monte Carlo study of the phase diagram of solid molecular hydrogen at extreme pressures

PubMed Central

Drummond, N. D.; Monserrat, Bartomeu; Lloyd-Williams, Jonathan H.; Ríos, P. López; Pickard, Chris J.; Needs, R. J.

2015-01-01

Establishing the phase diagram of hydrogen is a major challenge for experimental and theoretical physics. Experiment alone cannot establish the atomic structure of solid hydrogen at high pressure, because hydrogen scatters X-rays only weakly. Instead, our understanding of the atomic structure is largely based on density functional theory (DFT). By comparing Raman spectra for low-energy structures found in DFT searches with experimental spectra, candidate atomic structures have been identified for each experimentally observed phase. Unfortunately, DFT predicts a metallic structure to be energetically favoured at a broad range of pressures up to 400 GPa, where it is known experimentally that hydrogen is non-metallic. Here we show that more advanced theoretical methods (diffusion quantum Monte Carlo calculations) find the metallic structure to be uncompetitive, and predict a phase diagram in reasonable agreement with experiment. This greatly strengthens the claim that the candidate atomic structures accurately model the experimentally observed phases. PMID:26215251

Periodic density functional theory study of spin crossover in the cesium iron hexacyanochromate prussian blue analog

NASA Astrophysics Data System (ADS)

Wojdeł, Jacek C.; Moreira, Ibério de P. R.; Illas, Francesc

2009-01-01

This paper presents a detailed theoretical analysis of the electronic structure of the CsFe[Cr(CN)6] prussian blue analog with emphasis on the structural origin of the experimentally observed spin crossover transition in this material. Periodic density functional calculations using generalized gradient approximation (GGA)+U and nonlocal hybrid exchange-correlation potentials show that, for the experimental low temperature crystal structure, the t2g6eg0 low spin configuration of FeII is the most stable and CrIII (S =3/2, t2g3eg0) remains the same in all cases. This is also found to be the case for the low spin GGA+U fully relaxed structure with the optimized unit cell. A completely different situation emerges when calculations are carried out using the experimental high temperature structure. Here, GGA+U and hybrid density functional theory calculations consistently predict that the t2g4eg2 FeII high spin configuration is the ground state. However, the two spin configurations appear to be nearly degenerate when calculations are carried out for the geometries arising from a GGA+U full relaxation of the atomic structure carried out at experimental high temperature lattice constant. A detailed analysis of the energy difference between the two spin configurations as a function of the lattice constant strongly suggests that the observed spin crossover transition has a structural origin with non-negligible entropic contributions of the high spin state.

Quantitative structure-retention relationship models for the prediction of the reversed-phase HPLC gradient retention based on the heuristic method and support vector machine.

PubMed

Du, Hongying; Wang, Jie; Yao, Xiaojun; Hu, Zhide

2009-01-01

The heuristic method (HM) and support vector machine (SVM) were used to construct quantitative structure-retention relationship models by a series of compounds to predict the gradient retention times of reversed-phase high-performance liquid chromatography (HPLC) in three different columns. The aims of this investigation were to predict the retention times of multifarious compounds, to find the main properties of the three columns, and to indicate the theory of separation procedures. In our method, we correlated the retention times of many diverse structural analytes in three columns (Symmetry C18, Chromolith, and SG-MIX) with their representative molecular descriptors, calculated from the molecular structures alone. HM was used to select the most important molecular descriptors and build linear regression models. Furthermore, non-linear regression models were built using the SVM method; the performance of the SVM models were better than that of the HM models, and the prediction results were in good agreement with the experimental values. This paper could give some insights into the factors that were likely to govern the gradient retention process of the three investigated HPLC columns, which could theoretically supervise the practical experiment.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship.

PubMed

Wang, Xueding; Xu, Yilian; Yang, Lu; Lu, Xiang; Zou, Hao; Yang, Weiqing; Zhang, Yuanyuan; Li, Zicheng; Ma, Menglin

2018-03-01

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Electronic structure modeling of InAs/GaSb superlattices with hybrid density functional theory

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

Garwood, Tristan; Modine, Normand A.; Krishna, S.

2016-12-18

The application of first-principles calculations holds promise for greatly improving our understanding of semiconductor superlattices. By developing a procedure to accurately predict band gaps using hybrid density functional theory, it lays the groundwork for future studies investigating more nuanced properties of these structures. Our approach allows a priori prediction of the properties of SLS structures using only the band gaps of the constituent materials. Furthermore, it should enable direct investigation of the effects of interface structure, e.g., intermixing or ordering at the interface, on SLS properties. In this paper, we present band gap data for various InAs/GaSb type-II superlattice structuresmore » calculated using the generalized Kohn-Sham formulation of density functional theory. A PBE0-type hybrid functional was used, and the portion of the exact exchange was tuned to fit the band gaps of the binary compounds InAs and GaSb with the best agreement to bulk experimental values obtained with 18% of the exact exchange. The heterostructures considered in this study are 6 monolayer (ML) InAs/6 ML GaSb, 8 ML InAs/8 ML GaSb and 10 ML InAs/10 ML GaSb with deviations from the experimental band gaps ranging from 3% to 11%.« less

RDC-enhanced structure calculation of a β-heptapeptide in methanol.

PubMed

Rigling, Carla; Ebert, Marc-Olivier

2017-07-01

Residual dipolar couplings (RDCs) are a rich source of structural information that goes beyond the range covered by the nuclear Overhauser effect or scalar coupling constants. They can only be measured in partially oriented samples. RDC studies of peptides in organic solvents have so far been focused on samples in chloroform or DMSO. Here, we show that stretched poly(vinyl acetate) can be used for the partial alignment of a linear β-peptide with proteinogenic side chains in methanol. 1 D CH , 1 D NH , and 2 D HH RDCs were collected with this sample and included as restraints in a simulated annealing calculation. Incorporation of RDCs in the structure calculation process improves the long-range definition in the backbone of the resulting 3 14 -helix and uncovers side-chain mobility. Experimental side-chain RDCs of the central leucine and valine residues are in good agreement with predicted values from a local three-state model. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.

2017-09-01

In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

Ab initio and DFT studies of the structure and vibrational spectra of anhydrous caffeine

NASA Astrophysics Data System (ADS)

Srivastava, Santosh K.; Singh, Vipin B.

2013-11-01

Vibrational spectra and molecular structure of anhydrous caffeine have been systematically investigated by second order Moller-Plesset (MP2) perturbation theory and density functional theory (DFT) calculations. Vibrational assignments have been made and many previous ambiguous assignments in IR and Raman spectra are amended. The calculated DFT frequencies and intensities at B3LYP/6-311++G(2d,2p) level, were found to be in better agreement with the experimental values. It was found that DFT with B3LYP functional predicts harmonic vibrational wave numbers more close to experimentally observed value when it was performed on MP2 optimized geometry rather than DFT geometry. The calculated TD-DFT vertical excitation electronic energies of the valence excited states of anhydrous caffeine are found to be in consonance to the experimental absorption peaks.

An Applied Method for Predicting the Load-Carrying Capacity in Compression of Thin-Wall Composite Structures with Impact Damage

NASA Astrophysics Data System (ADS)

Mitrofanov, O.; Pavelko, I.; Varickis, S.; Vagele, A.

2018-03-01

The necessity for considering both strength criteria and postbuckling effects in calculating the load-carrying capacity in compression of thin-wall composite structures with impact damage is substantiated. An original applied method ensuring solution of these problems with an accuracy sufficient for practical design tasks is developed. The main advantage of the method is its applicability in terms of computing resources and the set of initial data required. The results of application of the method to solution of the problem of compression of fragments of thin-wall honeycomb panel damaged by impacts of various energies are presented. After a comparison of calculation results with experimental data, a working algorithm for calculating the reduction in the load-carrying capacity of a composite object with impact damage is adopted.

Determination of NMR chemical shifts for cholesterol crystals from first-principles

NASA Astrophysics Data System (ADS)

Kucukbenli, Emine; de Gironcoli, Stefano

2011-03-01

Solid State Nuclear Magnetic Resonance (NMR) is a powerful tool in crystallography when combined with theoretical predictions. So far, empirical calculations of spectra have been employed for an unambiguous identification. However, many complex systems are outside the scope of these methods. Our implementation of ultrasoft and projector augmented wave pseudopotentials within ab initio gauge including projector augmented plane wave (GIPAW) method in Quantum Espresso simulation package allows affordable calculations of NMR spectra for systems of thousands of electrons. We report here the first ab initio determination of NMR spectra for several crystal structures of cholesterol. Cholesterol crystals, the main component of human gallstones, are of interest to medical research as their structural properties can shed light on the pathologies of gallbladder. With our application we show that ab initio calculations can be employed to aid NMR crystallography.

TensorCalculator: exploring the evolution of mechanical stress in the CCMV capsid

NASA Astrophysics Data System (ADS)

Kononova, Olga; Maksudov, Farkhad; Marx, Kenneth A.; Barsegov, Valeri

2018-01-01

A new computational methodology for the accurate numerical calculation of the Cauchy stress tensor, stress invariants, principal stress components, von Mises and Tresca tensors is developed. The methodology is based on the atomic stress approach which permits the calculation of stress tensors, widely used in continuum mechanics modeling of materials properties, using the output from the MD simulations of discrete atomic and C_α -based coarse-grained structural models of biological particles. The methodology mapped into the software package TensorCalculator was successfully applied to the empty cowpea chlorotic mottle virus (CCMV) shell to explore the evolution of mechanical stress in this mechanically-tested specific example of a soft virus capsid. We found an inhomogeneous stress distribution in various portions of the CCMV structure and stress transfer from one portion of the virus structure to another, which also points to the importance of entropic effects, often ignored in finite element analysis and elastic network modeling. We formulate a criterion for elastic deformation using the first principal stress components. Furthermore, we show that von Mises and Tresca stress tensors can be used to predict the onset of a viral capsid’s mechanical failure, which leads to total structural collapse. TensorCalculator can be used to study stress evolution and dynamics of defects in viral capsids and other large-size protein assemblies.

Experimental Verification of a Progressive Damage Model for IM7/5260 Laminates Subjected to Tension-Tension Fatigue

NASA Technical Reports Server (NTRS)

Coats, Timothy W.; Harris, Charles E.

1995-01-01

The durability and damage tolerance of laminated composites are critical design considerations for airframe composite structures. Therefore, the ability to model damage initiation and growth and predict the life of laminated composites is necessary to achieve structurally efficient and economical designs. The purpose of this research is to experimentally verify the application of a continuum damage model to predict progressive damage development in a toughened material system. Damage due to monotonic and tension-tension fatigue was documented for IM7/5260 graphite/bismaleimide laminates. Crack density and delamination surface area were used to calculate matrix cracking and delamination internal state variables to predict stiffness loss in unnotched laminates. A damage dependent finite element code predicted the stiffness loss for notched laminates with good agreement to experimental data. It was concluded that the continuum damage model can adequately predict matrix damage progression in notched and unnotched laminates as a function of loading history and laminate stacking sequence.

Combined DFT and BS study on the exchange coupling of dinuclear sandwich-type POM: comparison of different functionals and reliability of structure modeling.

PubMed

Yin, Bing; Xue, GangLin; Li, JianLi; Bai, Lu; Huang, YuanHe; Wen, ZhenYi; Jiang, ZhenYi

2012-05-01

The exchange coupling of a group of three dinuclear sandwich-type polyoxomolybdates [MM'(AsMo7O27)2](12-) with MM' = CrCr, FeFe, FeCr are theoretically predicted from combined DFT and broken-symmetry (BS) approach. Eight different XC functionals are utilized to calculate the exchange-coupling constant J from both the full crystalline structures and model structures of smaller size. The comparison between theoretical values and accurate experimental results supports the applicability of DFT-BS method in this new type of sandwich-type dinuclear polyoxomolybdates. However, a careful choice of functionals is necessary to achieve the desired accuracy. The encouraging results obtained from calculations on model structures highlight the great potential of application of structure modeling in theoretical study of POM. Structural modeling may not only reduce the computational cost of large POM species but also be able to take into account the external field effect arising from solvent molecules in solution or counterions in crystal.

Effects of nitrogenous substituent groups on the benzene dication

NASA Astrophysics Data System (ADS)

Forgy, C. C.; Schlimgen, A. W.; Mazziotti, D. A.

2018-05-01

The benzene dication possesses a pentagonal-pyramidal structure with a hexacoordinated carbon. In contrast, halogenated benzene dications retain a similar structure to their parent molecules. In this work, we report on theoretical studies of the structures of the dications of benzene with nitrogenous substituents. We find that the nitrobenzene dication favours a near ideal pentagonal-pyramidal structure, while the aniline dication favours a flat, hexagonal structure. Reduced-density-matrices methods give predictions in agreement with available ab initio calculations and experiment. These results are also compared with those from the Hartree-Fock method and density functional theory.

Errors in the Calculation of 27Al Nuclear Magnetic Resonance Chemical Shifts

PubMed Central

Wang, Xianlong; Wang, Chengfei; Zhao, Hui

2012-01-01

Computational chemistry is an important tool for signal assignment of 27Al nuclear magnetic resonance spectra in order to elucidate the species of aluminum(III) in aqueous solutions. The accuracy of the popular theoretical models for computing the 27Al chemical shifts was evaluated by comparing the calculated and experimental chemical shifts in more than one hundred aluminum(III) complexes. In order to differentiate the error due to the chemical shielding tensor calculation from that due to the inadequacy of the molecular geometry prediction, single-crystal X-ray diffraction determined structures were used to build the isolated molecule models for calculating the chemical shifts. The results were compared with those obtained using the calculated geometries at the B3LYP/6-31G(d) level. The isotropic chemical shielding constants computed at different levels have strong linear correlations even though the absolute values differ in tens of ppm. The root-mean-square difference between the experimental chemical shifts and the calculated values is approximately 5 ppm for the calculations based on the X-ray structures, but more than 10 ppm for the calculations based on the computed geometries. The result indicates that the popular theoretical models are adequate in calculating the chemical shifts while an accurate molecular geometry is more critical. PMID:23203134

Role of conformational sampling in computing mutation-induced changes in protein structure and stability.

PubMed

Kellogg, Elizabeth H; Leaver-Fay, Andrew; Baker, David

2011-03-01

The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling. Copyright © 2010 Wiley-Liss, Inc.

Failure analysis of thick composite cylinders under external pressure

NASA Technical Reports Server (NTRS)

Caiazzo, A.; Rosen, B. W.

1992-01-01

Failure of thick section composites due to local compression strength and overall structural instability is treated. Effects of material nonlinearity, imperfect fiber architecture, and structural imperfections upon anticipated failure stresses are determined. Comparisons with experimental data for a series of test cylinders are described. Predicting the failure strength of composite structures requires consideration of stability and material strength modes of failure using linear and nonlinear analysis techniques. Material strength prediction requires the accurate definition of the local multiaxial stress state in the material. An elasticity solution for the linear static analysis of thick anisotropic cylinders and rings is used herein to predict the axisymmetric stress state in the cylinders. Asymmetric nonlinear behavior due to initial cylinder out of roundness and the effects of end closure structure are treated using finite element methods. It is assumed that local fiber or ply waviness is an important factor in the initiation of material failure. An analytical model for the prediction of compression failure of fiber composites, which includes the effects of fiber misalignments, matrix inelasticity, and multiaxial applied stresses is used for material strength calculations. Analytical results are compared to experimental data for a series of glass and carbon fiber reinforced epoxy cylinders subjected to external pressure. Recommendations for pretest characterization and other experimental issues are presented. Implications for material and structural design are discussed.

Curved Displacement Transfer Functions for Geometric Nonlinear Large Deformation Structure Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran; Lung, Shun-Fat

2017-01-01

For shape predictions of structures under large geometrically nonlinear deformations, Curved Displacement Transfer Functions were formulated based on a curved displacement, traced by a material point from the undeformed position to deformed position. The embedded beam (depth-wise cross section of a structure along a surface strain-sensing line) was discretized into multiple small domains, with domain junctures matching the strain-sensing stations. Thus, the surface strain distribution could be described with a piecewise linear or a piecewise nonlinear function. The discretization approach enabled piecewise integrations of the embedded-beam curvature equations to yield the Curved Displacement Transfer Functions, expressed in terms of embedded beam geometrical parameters and surface strains. By entering the surface strain data into the Displacement Transfer Functions, deflections along each embedded beam can be calculated at multiple points for mapping the overall structural deformed shapes. Finite-element linear and nonlinear analyses of a tapered cantilever tubular beam were performed to generate linear and nonlinear surface strains and the associated deflections to be used for validation. The shape prediction accuracies were then determined by comparing the theoretical deflections with the finiteelement- generated deflections. The results show that the newly developed Curved Displacement Transfer Functions are very accurate for shape predictions of structures under large geometrically nonlinear deformations.

Transverse charge and magnetization densities: Improved chiral predictions down to b=1 fms

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

Alarcon, Jose Manuel; Hiller Blin, Astrid N.; Vicente Vacas, Manuel J.

The transverse charge and magnetization densities provide insight into the nucleon’s inner structure. In the periphery, the isovector components are clearly dominant, and can be computed in a model-independent way by means of a combination of chiral effective field theory (cEFT) and dispersion analysis. With a novel N=D method, we incorporate the pion electromagnetic formfactor data into the cEFT calculation, thus taking into account the pion-rescattering effects and r-meson pole. As a consequence, we are able to reliably compute the densities down to distances b1 fm, therefore achieving a dramatic improvement of the results compared to traditional cEFT calculations, whilemore » remaining predictive and having controlled uncertainties.« less

pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring.

PubMed

Jiménez-García, Brian; Pons, Carles; Fernández-Recio, Juan

2013-07-01

pyDockWEB is a web server for the rigid-body docking prediction of protein-protein complex structures using a new version of the pyDock scoring algorithm. We use here a new custom parallel FTDock implementation, with adjusted grid size for optimal FFT calculations, and a new version of pyDock, which dramatically speeds up calculations while keeping the same predictive accuracy. Given the 3D coordinates of two interacting proteins, pyDockWEB returns the best docking orientations as scored mainly by electrostatics and desolvation energy. The server does not require registration by the user and is freely accessible for academics at http://life.bsc.es/servlet/pydock. Supplementary data are available at Bioinformatics online.

Predicting the stability of ternary intermetallics with density functional theory and machine learning

NASA Astrophysics Data System (ADS)

Schmidt, Jonathan; Chen, Liming; Botti, Silvana; Marques, Miguel A. L.

2018-06-01

We use a combination of machine learning techniques and high-throughput density-functional theory calculations to explore ternary compounds with the AB2C2 composition. We chose the two most common intermetallic prototypes for this composition, namely, the tI10-CeAl2Ga2 and the tP10-FeMo2B2 structures. Our results suggest that there may be ˜10 times more stable compounds in these phases than previously known. These are mostly metallic and non-magnetic. While the use of machine learning reduces the overall calculation cost by around 75%, some limitations of its predictive power still exist, in particular, for compounds involving the second-row of the periodic table or magnetic elements.

Mesh Convergence Requirements for Composite Damage Models

NASA Technical Reports Server (NTRS)

Davila, Carlos G.

2016-01-01

The ability of the finite element method to accurately represent the response of objects with intricate geometry and loading renders the finite element method as an extremely versatile analysis technique for structural analysis. Finite element analysis is routinely used in industry to calculate deflections, stress concentrations, natural frequencies, buckling loads, and much more. The method works by discretizing complex problems into smaller, simpler approximations that are valid over small uniform domains. For common analyses, the maximum size of the elements that can be used is often be determined by experience. However, to verify the quality of a solution, analyses with several levels of mesh refinement should be performed to ensure that the solution has converged. In recent years, the finite element method has been used to calculate the resistance of structures, and in particular that of composite structures. A number of techniques such as cohesive zone modeling, the virtual crack closure technique, and continuum damage modeling have emerged that can be used to predict cracking, delaminations, fiber failure, and other composite damage modes that lead to structural collapse. However, damage models present mesh refinement requirements that are not well understood. In this presentation, we examine different mesh refinement issues related to the representation of damage in composite materials. Damage process zone sizes and their corresponding mesh requirements will be discussed. The difficulties of modeling discontinuities and the associated need for regularization techniques will be illustrated, and some unexpected element size constraints will be presented. Finally, some of the difficulties in constructing models of composite structures capable of predicting transverse matrix cracking will be discussed. It will be shown that to predict the initiation and propagation of transverse matrix cracks, their density, and their saturation may require models that are significantly more refined than those that have been contemplated in the past.

Isochoric structural recovery in molecular glasses and its analog in colloidal glasses

NASA Astrophysics Data System (ADS)

Banik, Sourya; McKenna, Gregory B.

2018-06-01

Concentrated colloidal dispersions have been regarded as models for molecular glasses. One of the many ways to compare the behavior in these two different systems is by comparing the structural recovery or the physical aging behavior. However, recent investigations from our group to examine structural recovery in thermosensitive colloidal dispersions have shown contrasting results between the colloidal and the molecular glasses. The differences in the behaviors of the two systems have led us to pose this question: Is structural recovery behavior in colloidal glasses truly distinct from that of molecular glasses or is the conventional experimental condition (isobaric temperature-jumps) in determining the structural recovery in molecular glasses different from the experimental condition in the colloidal experiments (concentration- or volume fraction-jumps); i.e., are colloidal glasses inherently different from molecular glasses or not? To address the question, we resort to model calculations of structural recovery in a molecular glass under constant volume (isochoric) conditions following temperature only- and simultaneous volume- and temperature-jumps, which are closer to the volume fraction-jump conditions used in the thermosensitive-colloidal experiments. The current model predictions are then compared with the signatures of structural recovery under the conventional isobaric state in a molecular glass and with structural recovery behavior in colloidal glasses following volume fraction-jumps. We show that the results obtained from the experiments conducted by our group were contrasting to classical molecular glass behavior because the basis of our comparisons were incorrect (the histories were not analogous). The present calculations (with analogous histories) are qualitatively closer to the colloidal behavior. The signatures of "intrinsic isotherms" and "asymmetry of approach" in the current isochoric model predictions are quite different from those in the classical isobaric conditions while the "memory" signatures remain essentially the same. While there are qualitative similarities between the current isochoric model predictions and results from colloidal glasses, it appears from the calculations that the origins of these are different. The isochoric histories in the molecular glasses have compensating effects of pressure and departure from equilibrium which determines the structure dependence on mobility of the molecules. On the other hand, in the colloids it simply appears that the volume fraction-jump conditions simply do not exhibit such structure mobility dependence. The determining interplay of thermodynamic phase variables in colloidal and molecular systems might be very different or at least their correlations are yet to be ascertained. This topic requires further investigation to bring the similarities and differences between molecular and colloidal glass formers into fuller clarity.

Thermal expansion and specific heat of Cr2TeO6 and Fe2TeO6 by first principles calculations

NASA Astrophysics Data System (ADS)

Mishra, Vinayak

2018-05-01

Cr2TeO6 and Fe2TeO6 crystallize in tetragonal structure. These compounds are formed in nuclear reactors. Therefore, study of thermal expansion of these compounds is important. In this paper, using WIEN2k code we have calculated the volume dependent total energies E(V) of these materials at zero kelvin. Subsequently, we have applied the quasi harmonic approximation, in order to include the thermal effects. Using our calculations, we have predicted the thermal expansion and specific heat at high temperatures. The calculated properties for Fe2TeO6 are in very good agreement with the reported experimental results.

Static characteristics design of hydrostatic guide-ways based on fluid-structure interactions

NASA Astrophysics Data System (ADS)

Lin, Shuo; Yin, YueHong

2016-10-01

With the raising requirements in micro optical systems, the available machines become hard to achieve the process dynamic and accuracy in all aspects. This makes compact design based on fluid/structure interactions (FSI) important. However, there is a difficulty in studying FSI with oil film as fluid domain. This paper aims at static characteristic design of a hydrostatic guide-way with capillary restrictors based on FSI. The pressure distribution of the oil film land is calculated by solving the Reynolds-equation with Galerkin technique. The deformation of structure is calculated by commercial FEM software, MSC. Nastran. A matlab program is designed to realize the coupling progress by modifying the load boundary in the submitting file and reading the deformation result. It's obvious that the stiffness of the hydrostatic bearing decreases with the weakening of the bearing structure. This program is proposed to make more precise prediction of bearing stiffness.

Compositional bowing of band energies and their deformation potentials in strained InGaAs ternary alloys: A first-principles study

NASA Astrophysics Data System (ADS)

Khomyakov, Petr A.; Luisier, Mathieu; Schenk, Andreas

2015-08-01

Using first-principles calculations, we show that the conduction and valence band energies and their deformation potentials exhibit a non-negligible compositional bowing in strained ternary semiconductor alloys such as InGaAs. The electronic structure of these compounds has been calculated within the framework of local density approximation and hybrid functional approach for large cubic supercells and special quasi-random structures, which represent two kinds of model structures for random alloys. We find that the predicted bowing effect for the band energy deformation potentials is rather insensitive to the choice of the functional and alloy structural model. The direction of bowing is determined by In cations that give a stronger contribution to the formation of the InxGa1-xAs valence band states with x ≳ 0.5, compared to Ga cations.

Preliminary design methods for fiber reinforced composite structures employing a personal computer

NASA Technical Reports Server (NTRS)

Eastlake, C. N.

1986-01-01

The objective of this project was to develop a user-friendly interactive computer program to be used as an analytical tool by structural designers. Its intent was to do preliminary, approximate stress analysis to help select or verify sizing choices for composite structural members. The approach to the project was to provide a subroutine which uses classical lamination theory to predict an effective elastic modulus for a laminate of arbitrary material and ply orientation. This effective elastic modulus can then be used in a family of other subroutines which employ the familiar basic structural analysis methods for isotropic materials. This method is simple and convenient to use but only approximate, as is appropriate for a preliminary design tool which will be subsequently verified by more sophisticated analysis. Additional subroutines have been provided to calculate laminate coefficient of thermal expansion and to calculate ply-by-ply strains within a laminate.

First-principles predictions of structural, mechanical and electronic properties of βTiNb under high pressure

NASA Astrophysics Data System (ADS)

Wang, Z. P.; Fang, Q. H.; Li, J.; Liu, B.

2018-04-01

Structural, mechanical and electronic properties of βTiNb alloy under high pressure have been investigated based on the density functional theory (DFT). The dependences of dimensionless volume ratio, elastic constants, bulk modulus, Young's modulus, shear modulus, ductile/brittle, anisotropy and Poisson's ratio on applied pressure are all calculated successfully. The results reveal that βTiNb alloy is mechanically stable under pressure below 23.45 GPa, and the pressure-induced phase transformation could occur beyond this critical value. Meanwhile, the applied pressure can effectively promote the mechanical properties of βTiNb alloy, including the resistances to volume change, elastic deformation and shear deformation, as well as the material ductility and metallicity. Furthermore, the calculated electronic structures testify that βTiNb alloy performs the metallicity and the higher pressure reduces the structural stability of unit cell.

DFT investigations on mechanical stability, electronic structure and magnetism in Co2TaZ (Z = Al, Ga, In) heusler alloys

NASA Astrophysics Data System (ADS)

Khandy, Shakeel Ahmad; Gupta, Dinesh C.

2017-12-01

Ferromagnetic Heusler compounds have vast and imminent applications for novel devices, smart materials thanks to density functional theory (DFT) based simulations, which have scored out a new approach to study these materials. We forecast the structural stability of Co2TaZ alloys on the basis of total energy calculations and mechanical stability criteria. The elastic constants, robust spin-polarized ferromagnetism and electron densities in these half-metallic alloys are also discussed. The observed structural aspects calculated to predict the stability and equilibrium lattice parameters agree well with the experimental results. The elastic parameters like elastic constants, bulk, Young’s and shear moduli, poison’s and Pugh ratios, melting temperatures, etc have been put together to establish their mechanical properties. The elaborated electronic band structures along with indirect band gaps and spin polarization favour the application of these materials in spintronics and memory device technology.

Development of bovine serum albumin-water partition coefficients predictive models for ionogenic organic chemicals based on chemical form adjusted descriptors.

PubMed

Ding, Feng; Yang, Xianhai; Chen, Guosong; Liu, Jining; Shi, Lili; Chen, Jingwen

2017-10-01

The partition coefficients between bovine serum albumin (BSA) and water (K BSA/w ) for ionogenic organic chemicals (IOCs) were different greatly from those of neutral organic chemicals (NOCs). For NOCs, several excellent models were developed to predict their logK BSA/w . However, it was found that the conventional descriptors are inappropriate for modeling logK BSA/w of IOCs. Thus, alternative approaches are urgently needed to develop predictive models for K BSA/w of IOCs. In this study, molecular descriptors that can be used to characterize the ionization effects (e.g. chemical form adjusted descriptors) were calculated and used to develop predictive models for logK BSA/w of IOCs. The models developed had high goodness-of-fit, robustness, and predictive ability. The predictor variables selected to construct the models included the chemical form adjusted averages of the negative potentials on the molecular surface (V s-adj - ), the chemical form adjusted molecular dipole moment (dipolemoment adj ), the logarithm of the n-octanol/water distribution coefficient (logD). As these molecular descriptors can be calculated from their molecular structures directly, the developed model can be easily used to fill the logK BSA/w data gap for other IOCs within the applicability domain. Furthermore, the chemical form adjusted descriptors calculated in this study also could be used to construct predictive models on other endpoints of IOCs. Copyright © 2017 Elsevier Inc. All rights reserved.

A Computational Approach From Gene to Structure Analysis of the Human ABCA4 Transporter Involved in Genetic Retinal Diseases.

PubMed

Trezza, Alfonso; Bernini, Andrea; Langella, Andrea; Ascher, David B; Pires, Douglas E V; Sodi, Andrea; Passerini, Ilaria; Pelo, Elisabetta; Rizzo, Stanislao; Niccolai, Neri; Spiga, Ottavia

2017-10-01

The aim of this article is to report the investigation of the structural features of ABCA4, a protein associated with a genetic retinal disease. A new database collecting knowledge of ABCA4 structure may facilitate predictions about the possible functional consequences of gene mutations observed in clinical practice. In order to correlate structural and functional effects of the observed mutations, the structure of mouse P-glycoprotein was used as a template for homology modeling. The obtained structural information and genetic data are the basis of our relational database (ABCA4Database). Sequence variability among all ABCA4-deposited entries was calculated and reported as Shannon entropy score at the residue level. The three-dimensional model of ABCA4 structure was used to locate the spatial distribution of the observed variable regions. Our predictions from structural in silico tools were able to accurately link the functional effects of mutations to phenotype. The development of the ABCA4Database gathers all the available genetic and structural information, yielding a global view of the molecular basis of some retinal diseases. ABCA4 modeled structure provides a molecular basis on which to analyze protein sequence mutations related to genetic retinal disease in order to predict the risk of retinal disease across all possible ABCA4 mutations. Additionally, our ABCA4 predicted structure is a good starting point for the creation of a new data analysis model, appropriate for precision medicine, in order to develop a deeper knowledge network of the disease and to improve the management of patients.

A nonlinear fracture mechanics approach to the growth of small cracks

NASA Technical Reports Server (NTRS)

Newman, J. C., Jr.

1983-01-01

An analytical model of crack closure is used to study the crack growth and closure behavior of small cracks in plates and at notches. The calculated crack opening stresses for small and large cracks, together with elastic and elastic plastic fracture mechanics analyses, are used to correlate crack growth rate data. At equivalent elastic stress intensity factor levels, calculations predict that small cracks in plates and at notches should grow faster than large cracks because the applied stress needed to open a small crack is less than that needed to open a large crack. These predictions agree with observed trends in test data. The calculations from the model also imply that many of the stress intensity factor thresholds that are developed in tests with large cracks and with load reduction schemes do not apply to the growth of small cracks. The current calculations are based upon continuum mechanics principles and, thus, some crack size and grain structure exist where the underlying fracture mechanics assumptions become invalid because of material inhomogeneity (grains, inclusions, etc.). Admittedly, much more effort is needed to develop the mechanics of a noncontinuum. Nevertheless, these results indicate the importance of crack closure in predicting the growth of small cracks from large crack data.

Performance of combined fragmentation and retention prediction for the identification of organic micropollutants by LC-HRMS.

PubMed

Hu, Meng; Müller, Erik; Schymanski, Emma L; Ruttkies, Christoph; Schulze, Tobias; Brack, Werner; Krauss, Martin

2018-03-01

In nontarget screening, structure elucidation of small molecules from high resolution mass spectrometry (HRMS) data is challenging, particularly the selection of the most likely candidate structure among the many retrieved from compound databases. Several fragmentation and retention prediction methods have been developed to improve this candidate selection. In order to evaluate their performance, we compared two in silico fragmenters (MetFrag and CFM-ID) and two retention time prediction models (based on the chromatographic hydrophobicity index (CHI) and on log D). A set of 78 known organic micropollutants was analyzed by liquid chromatography coupled to a LTQ Orbitrap HRMS with electrospray ionization (ESI) in positive and negative mode using two fragmentation techniques with different collision energies. Both fragmenters (MetFrag and CFM-ID) performed well for most compounds, with average ranking the correct candidate structure within the top 25% and 22 to 37% for ESI+ and ESI- mode, respectively. The rank of the correct candidate structure slightly improved when MetFrag and CFM-ID were combined. For unknown compounds detected in both ESI+ and ESI-, generally positive mode mass spectra were better for further structure elucidation. Both retention prediction models performed reasonably well for more hydrophobic compounds but not for early eluting hydrophilic substances. The log D prediction showed a better accuracy than the CHI model. Although the two fragmentation prediction methods are more diagnostic and sensitive for candidate selection, the inclusion of retention prediction by calculating a consensus score with optimized weighting can improve the ranking of correct candidates as compared to the individual methods. Graphical abstract Consensus workflow for combining fragmentation and retention prediction in LC-HRMS-based micropollutant identification.

Displacement Theories for In-Flight Deformed Shape Predictions of Aerospace Structures

NASA Technical Reports Server (NTRS)

Ko, William L.; Richards, W. L.; Tran, Van t.

2007-01-01

Displacement theories are developed for a variety of structures with the goal of providing real-time shape predictions for aerospace vehicles during flight. These theories are initially developed for a cantilever beam to predict the deformed shapes of the Helios flying wing. The main structural configuration of the Helios wing is a cantilever wing tubular spar subjected to bending, torsion, and combined bending and torsion loading. The displacement equations that are formulated are expressed in terms of strains measured at multiple sensing stations equally spaced on the surface of the wing spar. Displacement theories for other structures, such as tapered cantilever beams, two-point supported beams, wing boxes, and plates also are developed. The accuracy of the displacement theories is successfully validated by finite-element analysis and classical beam theory using input-strains generated by finite-element analysis. The displacement equations and associated strain-sensing system (such as fiber optic sensors) create a powerful means for in-flight deformation monitoring of aerospace structures. This method serves multiple purposes for structural shape sensing, loads monitoring, and structural health monitoring. Ultimately, the calculated displacement data can be visually displayed to the ground-based pilot or used as input to the control system to actively control the shape of structures during flight.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

PubMed

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Interaction between polymer constituents and the structure of biopolymers

NASA Technical Reports Server (NTRS)

Rein, R.

1974-01-01

The paper reviews the current status of methods for calculating intermolecular interactions between biopolymer units. The nature of forces contributing to the various domains of intermolecular separations is investigated, and various approximations applicable in the respective regions are examined. The predictive value of current theory is tested by establishing a connection with macroscopic properties and comparing the theoretical predicted values with those derived from experimental data. This has led to the introduction of a statistical model describing DNA.

Computational Discovery of New Materials Under Pressure

NASA Astrophysics Data System (ADS)

Zurek, Eva

The pressure variable opens the door towards the synthesis of materials with unique properties, ie. superconductivity, hydrogen storage media, high-energy density and superhard materials, to name a few. Indeed, recently superconductivity has been observed below 203 K and 103 K in samples of compressed sulfur dihydride and phosphine, respectively. Under pressure elements that would not normally combine may form stable compounds, or may mix in novel proportions. As a result using our chemical intuition developed at 1 atm to theoretically predict stable phases is bound to fail. In order to enable our search for superconducting hydrogen-rich systems under pressure, we have developed XtalOpt, an open-source evolutionary algorithm for crystal structure prediction. New advances in XtalOpt that enable the prediction of unit cells with greater complexity will be described. XtalOpt has been employed to find the most stable structures of hydrides with unique stoichiometries under pressure. The electronic structure and bonding of the predicted phases has been analyzed by detailed first-principles calculations based on density functional theory. The results of our computational experiments are helping us to build chemical and physical intuition for compressed solids.

First-principle study of pressure-induced phase transitions and electronic properties of electride Y2C

NASA Astrophysics Data System (ADS)

Feng, Caihui; Shan, Jingfeng; Xu, Aoshu; Xu, Yang; Zhang, Meiguang; Lin, Tingting

2017-10-01

Trigonal yttrium hypocarbide (Y2C), crystallizing in a layered hR3 structure, is an intriguing quasi-two-dimensional electride metal with potential application for the next generation of electronics. By using an efficient structure search method in combination with first-principles calculations, we have extensively explored the phase transitions and electronic properties of Y2C in a wide pressure range of 0-200 GPa. Three structural transformations were predicted, as hR3 → oP12 → tI12 → mC12. Calculated pressures of phase transition are 20, 118, and 126 GPa, respectively. The high-pressure oP12 phase exhibits a three-dimensional extended C-Y network built up from face- and edge-sharing CY8 hendecahedrons, whereas both the tI12 and mC12 phases are featured by the presence of C2 units. No anionic electrons confined to interstitial spaces have been found in the three predicted high-pressure phases, indicating that they are not electrides. Moreover, Y2C is dynamically stable and also energetically stable relative to the decomposition into its elemental solids.

An Experimental and Computational Investigation into the Gas-Phase Acidities of Tyrosine and Phenylalanine: Three Structures for Deprotonated Tyrosine

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

Bokatzian, Samantha S.; Stover, Michele L.; Plummer, Chelsea E.

Using mass spectrometry and correlated molecular orbital theory, three deprotonated structures were revealed for the amino acid tyrosine. The structures were distinguished experimentally by ion/molecule reactions involving proton transfer and trimethylsilyl azide. Gas-phase acidities from proton transfer reactions and from G3(MP2) calculations generally agree well. The lowest energy structure, which was only observed experimentally using electrospray ionization from aprotic solvents, is deprotonated at the carboxylic acid group and is predicted to be highly folded. A second unfolded carboxylate structure is several kcal/mol higher in energy and primarily forms from protic solvents. Protic solvents also yield a structure deprotonated at themore » phenolic side chain, which experiments find to be intermediate in energy to the two carboxylate forms. G3(MP2) calculations indicate that the three structures differ in energy by only 2.5 kcal/mol, yet they are readily distinguished experimentally. Structural abundance ratios are dependent upon experimental conditions, including the solvent and accumulation time of ions in a hexapole. Under some conditions, carboxylate ions may convert to phenolate ions. For phenylalanine, which lacks a phenolic group, only one deprotonated structure was observed experimentally when electrosprayed from protic solvent. This agrees with G3(MP2) calculations that find the folded and unfolded carboxylate forms to differ by 0.3 kcal/mol.« less

A quantum chemical calculation of the potential energy surface in the formation of HOSO 2 from OH + SO 2

NASA Astrophysics Data System (ADS)

Sitha, Sanyasi; Jewell, Linda L.; Piketh, Stuart J.; Fourie, Gerhard

2011-01-01

The formation of HOSO 2 from OH and SO 2 has been thoroughly investigated using several different methods (MP2=Full, MP2=FC, B3LYP, HF and composite G∗ methods) and basis sets (6-31G(d,p), 6-31++G(d,p), 6-31++G(2d,2p), 6-31++G(2df,2p) and aug-cc-pVnZ). We have found two different possible transition state structures, one of which is a true transition state since it has a higher energy than the reactants and products (MP2=Full, MP2=FC and HF), while the other is not a true transition state since it has an energy which lies between that of the reactants and products (B3LYP and B3LYP based methods). The transition state structure (from MP2) has a twist angle of the OH fragment relative to the SO bond of the SO 2 fragment of -50.0°, whereas this angle is 26.7° in the product molecule. Examination of the displacement vectors confirms that this is a true transition state structure. The MP2=Full method with a larger basis set (MP2=Full/6-31++G(2df,2p)) predicts the enthalpy of reaction to be -112.8 kJ mol -1 which is close to the experimental value of -113.3 ± 6 kJ mol -1, and predicts a rather high barrier of 20.0 kJ mol -1. When the TS structure obtained by the MP2 method is used as the input for calculating the energetics using the QCISD/6-31++G(2df,2p) method, a barrier of 4.1 kJ mol -1 is obtained (ZPE corrected). The rate constant calculated from this barrier is 1.3 × 10 -13 cm 3 molecule -1 s -1. We conclude that while the MP2 methods correctly predict the TS from a structural point of view, higher level energy corrections are needed for estimation of exact barrier height.

Closed coronal structures. V - Gasdynamic models of flaring loops and comparison with SMM observations

NASA Technical Reports Server (NTRS)

Peres, G.; Serio, S.; Vaiana, G.; Acton, L.; Leibacher, J.; Rosner, R.; Pallavicini, R.

1983-01-01

A time-dependent one-dimensional code incorporating energy, momentum and mass conservation equations, and taking the entire solar atmospheric structure into account, is used to investigate the hydrodynamic response of confined magnetic structures to strong heating perturbations. Model calculation results are compared with flare observations which include the light curves of spectral lines formed over a wide range of coronal flare temperatures, as well as determinations of Doppler shifts for the high temperature plasma. It is shown that the numerical simulation predictions are in good overall agreement with the observed flare coronal plasma evolution, correctly reproducing the temporal profile of X-ray spectral lines and their relative intensities. The predicted upflow velocities support the interpretation of the blueshifts as due to evaporation of chromospheric material.