Journal articles: 'Computational theoretical calculations'

1

Yao, Yitao, Marshall P. Tulin, and Ali R. Kolaini. "Theoretical and experimental studies of three-dimensional wavemaking in narrow tanks, including nonlinear phenomena near resonance." Journal of Fluid Mechanics 276 (October 10, 1994): 211–32. http://dx.doi.org/10.1017/s0022112094002533.

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In view of several practical ramifications of this problem, computational-analytical techniques for calculating waves induced by heaving arbitrary bodies in narrow tanks have been developed, including nonlinear wave groups produced near tank resonance. These feature computational near-field solutions matched with appropriate far-field solutions. In the linear case, the far field is provided by linear mode superposition. In the nonlinear case, the far field is described by a suitable nonlinear evolution equation of the cubic Schrödinger type. Matching techniques were developed. Calculations were successfully carried out and the results confirm the important effect of tank walls on added mass and damping.Results of computations have been compared with some data obtained with a conical wavemaker in a narrow tank. Pronounced nonlinear wave groups were obtained near resonance, and these are well reproduced in some detail by the nonlinear theory and computations, without considering any effects of dissipation.The related problem of resonant wave groups produced by a segmented paddle wavemaker has also been treated by analysis and subject to computation, with good general agreement with past experiments. The technique features matching near- and far-field computations using energy considerations.

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Juffer, André H. "Theoretical calculations of acid-dissociation constants of proteins." Biochemistry and Cell Biology 76, no. 2-3 (May 1, 1998): 198–209. http://dx.doi.org/10.1139/o98-034.

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The purpose of this review is to introduce several computational procedures for the determination of acid-dissociation constants (pKa) of titratable groups in proteins. Several concepts, such as continuum electrostatics and the exact meaning of intrinsic and apparent pKas, will be explained in some detail. Each of the methods will be judged on its merits, and some comparisons between the methods will be presented. While the emphasis of this review will be on theoretical formulations, the experimental determination by means of nuclear magnetic resonance will be briefly explained. The determination of individual pKa values by nuclear magnetic resonance in combination with computationally determined pKas can provide unique information about the pH-dependent properties of proteins and their complexes with peptides, DNA, and ligands.Key words: acid-dissociation constants, NMR, continuum electrostatics, dielectric constant of proteins, Monte Carlo, molecular dynamics.

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Zhou, Hua Xiang, Zheng Zhou, and Jing Ping Liu. "Theoretical and Computational Research of Heat Radiant Transfer in Cylinder." Applied Mechanics and Materials 628 (September 2014): 311–16. http://dx.doi.org/10.4028/www.scientific.net/amm.628.311.

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In order to obtain the radiation heat transfer theory and calculation methods, the movement of the gas particles, location, intensity, temperature, are researched in cylinder under different conditions with combustion system and the mode of heat transfer. Under high temperature conditions in the cylinder, the gas radiation heat transfer is researched in the complex heat transfer theory. A statistical correlation K narrow band model, a mean absorption coefficient, a gas line databases, by-line calculation method are found, through research and analysis emissivity, transmittance, absorption coefficient, typical models, mathematical equations, database, calculation methods. Examine the distribution performance of each database for different media concentration and temperature, a statistical narrow-band band parametric model accuracy is tested, using statistical narrow band model, the results of the use of by-line method. Research shows: selected spectral database, calculation method has a greater impact on the results. The research also shows the result coincides calculations based by-line HITEWP2010 database method, whether radiant heat or wall flux, statistical narrow band model. These are supplied to the internal combustion engine cylinder design.

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CAMARGO, Mairo Fabio. "COMPUTATIONAL THEORETICAL STUDY OF ENERGIES INVOLVED IN OZONE DECOMPOSITION BY CHLORINATED RADICALS IN THE HIGH ATMOSPHERE LAYERS." Periódico Tchê Química 08, no. 4 (August 20, 2007): 38–44. http://dx.doi.org/10.52571/ptq.v4.n08.2007.agosto/5_pgs_38_44.pdf.

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They had been analyzed by computational simulation, the mechanisms of the decomposition of ozone, catalyzed for atomic chlorine. The objective of the work was centered in the calculation of the surfaces of potential energy (PES) when the chlorine atom is forced if to approach to one of atoms of oxygen of ozone. The calculations had been effected using method DFT (B3LYP) associated to the bases of Dunning (cc-pVDZ, cc-pVTZ and cc-pVQZ). The calculations had been effected using the program of quantum calculations Gaussian03. The energy of joined activation is compatible with the experimental data of that the decomposition of ozone catalyzed for atomic chlorine is spontaneous, same to the low temperatures found in the stratosphere.

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MA, HAIBO, CHUNGEN LIU, and YUANSHENG JIANG. "BLOCK DENSITY MATRIX RENORMALIZATION GROUP WITH EFFECTIVE INTERACTIONS." Journal of Theoretical and Computational Chemistry 08, no. 05 (October 2009): 837–48. http://dx.doi.org/10.1142/s0219633609005064.

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Based on the contractor renormalization group (CORE) method and the density matrix renormalization group (DMRG) method, a new computational scheme, which is called the block density matrix renormalization group with effective interactions (BDMRG-EI), is proposed to deal with the numerical computation of quantum correlated systems. Different from the conventional CORE method in calculating the blocks and the fragments, where the DMRG method instead of the exact diagonalization is employed in BDMRG-EI, BDMRG-EI makes the calculations of larger blocks and fragments applicable. Integrating DMRG's advantage of high accuracy and CORE's advantage of low computational costs, BDMRG-EI can be widely used for the theoretical calculations of the ground state and low-lying excited states of large systems with simple or complicated connectivity. Test calculations on a 240 site one-dimensional chain and a double-layer polyacene oligomer containing 48 hexagons with the spin-1/2 Heisenberg Hamiltonian demonstrate the efficiency and potentiality of the method.

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Qin, Xinming, Honghui Shang, Lei Xu, Wei Hu, Jinlong Yang, Shigang Li, and Yunquan Zhang. "The static parallel distribution algorithms for hybrid density-functional calculations in HONPAS package." International Journal of High Performance Computing Applications 34, no. 2 (May 9, 2019): 159–68. http://dx.doi.org/10.1177/1094342019845046.

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Hybrid density-functional calculation is one of the most commonly adopted electronic structure theories in computational chemistry and materials science because of its balance between accuracy and computational cost. Recently, we have developed a novel scheme called NAO2GTO to achieve linear scaling (Order-N) calculations for hybrid density-functionals. In our scheme, the most time-consuming step is the calculation of the electron repulsion integrals (ERIs) part, so creating an even distribution of these ERIs in parallel implementation is an issue of particular importance. Here, we present two static scalable distributed algorithms for the ERIs computation. Firstly, the ERIs are distributed over ERIs shell pairs. Secondly, the ERIs are distributed over ERIs shell quartets. In both algorithms, the calculation of ERIs is independent of each other, so the communication time is minimized. We show our speedup results to demonstrate the performance of these static parallel distributed algorithms in the Hefei Order-N packages for ab initio simulations.

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Schwenke, David W., Steven L. Mielke, and Donald G. Truhlar. "Variational reactive scattering calculations: computational optimization strategies." Theoretica Chimica Acta 79, no. 3-4 (1991): 241–69. http://dx.doi.org/10.1007/bf01113695.

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Sastre, S., R. Casasnovas, F. Muñoz, and J. Frau. "Isodesmic reaction for accurate theoretical pKa calculations of amino acids and peptides." Physical Chemistry Chemical Physics 18, no. 16 (2016): 11202–12. http://dx.doi.org/10.1039/c5cp07053h.

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Wang, Lin-Wang. "Novel Computational Methods for Nanostructure Electronic Structure Calculations." Annual Review of Physical Chemistry 61, no. 1 (March 2010): 19–39. http://dx.doi.org/10.1146/annurev.physchem.012809.103344.

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Brown, David A., Laurence P. Cuffe, Geraldine M. Fitzpatrick, Noel J. Fitzpatrick, William K. Glass, and Kara M. Herlihy. "Experimental and Theoretical Studies of Rotational Barriers in Aceto-, N-Methylaceto- and N-Phenylacetohydroxamic Acid." Collection of Czechoslovak Chemical Communications 66, no. 1 (2001): 99–108. http://dx.doi.org/10.1135/cccc20010099.

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Experimental and theoretical calculations for the E and Z forms of aceto-, N-methylaceto- and N-phenylacetohydroxamic acid are reported. The experimental method was NMR spectroscopy, while the computational methods included Hartree-Fock, Møller-Plesset and density functional theory calculations, with and without solvation, using either the Onsager or Tomasi's PCM method. In all calculations zero point energy corrections were included. The computed results when compared with the experimental ones show that, irrespective of the method used, the differences in the rotational barriers, ∆(E-TS) and ∆(Z-TS), are slight and below the 3 kcal mol-1 limit of the theoretical methods. In general the results using the PCM method were worse than the ones obtained from gas phase calculations or using the Onsager method, even though the PCM method is computationally most expensive. The calculations show, using either the Hartree-Fock or the B3LYP approach, that considering solvation using the Onsager method improves agreement with the experiment results. The calculated barrier heights, excluding the PCM method, agree broadly with the experimental results. Thus using the Onsager approach or gas phase calculations adequate results for barrier heights, but not for relative differences, were obtained.

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Xia, Jingjing, and Ping Wu. "A computational study on the thermal decomposition of di(tri)thiocarbonates." Journal of Theoretical and Computational Chemistry 15, no. 07 (November 2016): 1650061. http://dx.doi.org/10.1142/s0219633616500619.

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Alkyl methyl di(tri)thiocarbonates can be thermally decomposed into alkenes. In this paper, theoretical calculations were used to calculate the thermal decomposition procedures. Six compounds, including ethyl, isopropyl and [Formula: see text] dithiocarbonate and trithiocarbonate, were examined. For each decomposition, nine possible paths were considered, including the paths leading to the desired alkene products, as well as rearrangement and elimination reactions. This calculation was performed with the MP2/6-31G(d) method. Wiberg bond indices were also calculated to further reveal the reaction progress.

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Netz, Roland R., and William A. Eaton. "Estimating computational limits on theoretical descriptions of biological cells." Proceedings of the National Academy of Sciences 118, no. 6 (January 25, 2021): e2022753118. http://dx.doi.org/10.1073/pnas.2022753118.

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There has been much success recently in theoretically simulating parts of complex biological systems on the molecular level, with the goal of first-principles modeling of whole cells. However, there is the question of whether such simulations can be performed because of the enormous complexity of cells. We establish approximate equations to estimate computation times required to simulate highly simplified models of cells by either molecular dynamics calculations or by solving molecular kinetic equations. Our equations place limits on the complexity of cells that can be theoretically understood with these two methods and provide a first step in developing what can be considered biological uncertainty relations for molecular models of cells. While a molecular kinetics description of the genetically simplest bacterial cell may indeed soon be possible, neither theoretical description for a multicellular system, such as the human brain, will be possible for many decades and may never be possible even with quantum computing.

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Liu, Yanli, Hongtao Wu, Yuxuan Yang, Shangyuan Zou, Xuexiang Zhang, and Yaoyao Wang. "Symmetrical Workspace of 6-UPS Parallel Robot Using Tilt and Torsion Angles." Mathematical Problems in Engineering 2018 (June 21, 2018): 1–10. http://dx.doi.org/10.1155/2018/6412030.

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For the fast and efficient closed-loop real-time feedback control of 6-UPS parallel robot (6-UPS), a novel high efficiency calculation of the workspace is proposed and investigated. As a typical Nearly General Platform (NGP), 6-UPS has good symmetries. The symmetries effectively reduce computational cost and improve computational efficiency in the kinematics, singularity, dynamics, and optimization. To scrupulously demonstrate the symmetries of workspace, a novel algorithm is proposed. The modified Euler angles (T&T angles) are employed to represent the orientation matrix of 6-UPS, the inverse kinematics is analyzed, and the workspace of 6-UPS is obtained using the discretization algorithm. Meanwhile, the symmetries of the total orientation workspace are also proved. Compared with the traditional methods, the total orientation workspace reduces 5/6 computation cost, which means that the corresponding computation efficiency is increased by 6 times. Through theoretical and numerical calculations, the symmetries of the total orientation workspace of 6-UPS are verified. The proof of the symmetries lays a solid foundation for improving the computational efficiency of kinematics, dynamics, and control of 6-UPS.

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Gražulis, Saulius, Andrius Merkys, Antanas Vaitkus, Armel Le Bail, Daniel Chateigner, Linas Vilčiauskas, Stefaan Cottenier, Torbjörn Björkman, and Peter Murray-Rust. "Launching the Theoretical Crystallography Open Database." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1736. http://dx.doi.org/10.1107/s2053273314082631.

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As computational chemistry methods enjoy unprecedented growth, computer power increases and price/performance ratio drops, a large number of crystal structures can today be refined and their properties computed using modern theoretical approaches, such as DFT, post-HF, QM/MM, MCMM methods. Availability of several open source codes for computational and quantum chemistry and open-access crystallographic databases enables large scale computations of material structures and properties. We thus increasingly feel that an open collection of theoretically computed chemical structures would be a valuable resource for the scientific community. To address this need, we have launched a Theoretical Crystallography Open Database (TCOD, http://www.crystallography.net/tcod/). The TCOD sets a goal to collect a comprehensive set of computed crystal structures that would be made available under an Open Data license and invites all scientists to deposit their published results or pre-publication data. Accompanied with a large set of experimental structures in the COD database [1], the TCOD opens immediate possibilities for experimental and theoretical data cross-validation. To ensure high quality of deposited data, TCOD offers ontologies in a form of CIF [2] dictionaries that describe parameters of computed chemical and crystal structures, and an automated pipeline that checks each submitted structure against a set of community-specified criteria for convergence, computation quality and reproducibility. The scope of TCOD and validation tools make TCOD a high-quality, comprehensive theoretical structure database, useful in a broad range of disciplines. First-principle calculations are also of huge interest to simulate physical properties, either prospectively or for materials that do not grow as sufficiently large crystals. The property results can now be tested against the Material Properties Open Database [3] (http://www.materialproperties.org/) to ameliorate the used models.

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Ferraro, Diego, and Eduardo Villarino. "Calculations for a BWR Lattice with Adjacent Gadolinium Pins Using the Monte Carlo Cell Code Serpent v.1.1.7." Science and Technology of Nuclear Installations 2011 (2011): 1–4. http://dx.doi.org/10.1155/2011/659406.

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Monte Carlo neutron transport codes are usually used to perform criticality calculations and to solve shielding problems due to their capability to model complex systems without major approximations. However, these codes demand high computational resources. The improvement in computer capabilities leads to several new applications of Monte Carlo neutron transport codes. An interesting one is to use this method to perform cell-level fuel assembly calculations in order to obtain few group constants to be used on core calculations. In the present work theVTTrecently developedSerpent v.1.1.7cell-oriented neutronic calculation code is used to perform cell calculations of a theoretical BWR lattice benchmark with burnable poisons, and the main results are compared to reported ones and with calculations performed withCondor v.2.61, the INVAP's neutronic collision probability cell code.

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Zhang, Xinxing, Gerd Ganteför, Anastassia N. Alexandrova, and Kit Bowen. "Photoelectron spectroscopic and computational study of the PtMgH3,5− cluster anions." Physical Chemistry Chemical Physics 18, no. 28 (2016): 19345–49. http://dx.doi.org/10.1039/c6cp03243e.

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Nagayoshi, Kanade, Tohru Ikeda, Kazuo Kitaura, and Shigeru Nagase. "Computational Procedure of Lattice Energy Using the Ab Initio MO Method." Journal of Theoretical and Computational Chemistry 02, no. 02 (June 2003): 233–44. http://dx.doi.org/10.1142/s0219633603000537.

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Recently, we have proposed a computational procedure for calculations of lattice energies of molecular crystals using the ab initio MO method. This procedure does not use potential functions and is applicable to a variety of molecular crystals. The procedure has been successfully applied to calculation of packing structure of electron donor-acceptor complex, H3N–BF3, and hydrogen bonding crystal, CH3OH. In this work, we present a full account of the computational procedure. This method is applied to the packing structure calculations of hydrocarbon crystals, C2H2, C2H4 and C6H6. The lattice parameters optimized at the MP2/6-311++G** level are in good agreement with the experimental values. The basis set dependence of the lattice constants is also discussed for several crystals.

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Remsing, Richard C., and John D. Weeks. "Alchemical free energy calculations and umbrella sampling with local molecular field theory." Journal of Theoretical and Computational Chemistry 17, no. 03 (May 2018): 1840003. http://dx.doi.org/10.1142/s0219633618400035.

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Understanding the thermodynamic driving forces underlying any chemical process requires a description of the underlying free energy surface. However, computation of free energies is difficult, often requiring advanced sampling techniques. Moreover, these computations can be further complicated by the evaluation of any long-ranged interactions in the system of interest, such as Coulomb interactions in charged and polar media. Local molecular field theory is a promising approach to avoid many of the conceptual and computational difficulties associated with long-ranged interactions. We present frameworks for performing alchemical free energy calculations and non-Boltzmann sampling with local molecular field theory. We demonstrate that local molecular field theory can be used to perform these free energy calculations with accuracy comparable to traditional methodologies while eliminating the need for explicit treatment of long-ranged interactions in simulations.

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Forouzesh, Negin, and Nikita Mishra. "An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor." Molecules 26, no. 8 (April 20, 2021): 2383. http://dx.doi.org/10.3390/molecules26082383.

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The binding free energy calculation of protein–ligand complexes is necessary for research into virus–host interactions and the relevant applications in drug discovery. However, many current computational methods of such calculations are either inefficient or inaccurate in practice. Utilizing implicit solvent models in the molecular mechanics generalized Born surface area (MM/GBSA) framework allows for efficient calculations without significant loss of accuracy. Here, GBNSR6, a new flavor of the generalized Born model, is employed in the MM/GBSA framework for measuring the binding affinity between SARS-CoV-2 spike protein and the human ACE2 receptor. A computational protocol is developed based on the widely studied Ras–Raf complex, which has similar binding free energy to SARS-CoV-2/ACE2. Two options for representing the dielectric boundary of the complexes are evaluated: one based on the standard Bondi radii and the other based on a newly developed set of atomic radii (OPT1), optimized specifically for protein–ligand binding. Predictions based on the two radii sets provide upper and lower bounds on the experimental references: −14.7(ΔGbindBondi)<−10.6(ΔGbindExp.)<−4.1(ΔGbindOPT1) kcal/mol. The consensus estimates of the two bounds show quantitative agreement with the experiment values. This work also presents a novel truncation method and computational strategies for efficient entropy calculations with normal mode analysis. Interestingly, it is observed that a significant decrease in the number of snapshots does not affect the accuracy of entropy calculation, while it does lower computation time appreciably. The proposed MM/GBSA protocol can be used to study the binding mechanism of new variants of SARS-CoV-2, as well as other relevant structures.

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Phan, Anh D., Cuong V. Nguyen, Pham T. Linh, Tran V. Huynh, Vu D. Lam, Anh-Tuan Le, and Katsunori Wakabayashi. "Deep Learning for the Inverse Design of Mid-Infrared Graphene Plasmons." Crystals 10, no. 2 (February 19, 2020): 125. http://dx.doi.org/10.3390/cryst10020125.

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We theoretically investigate the plasmonic properties of mid-infrared graphene-based metamaterials and apply deep learning of a neural network for the inverse design. These artificial structures have square periodic arrays of graphene plasmonic resonators deposited on dielectric thin films. Optical spectra vary significantly with changes in structural parameters. To validate our theoretical approach, we carry out finite difference time domain simulations and compare computational results with theoretical calculations. Quantitatively good agreements among theoretical predictions, simulations, and previous experiments allow us to employ this proposed theoretical model to generate reliable data for training and testing deep neural networks. By merging the pre-trained neural network with the inverse network, we implement calculations for inverse design of the graphene-based metameterials. We also discuss the limitation of the data-driven approach.

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Maung, Aung Phone, and Chung Hao Hsu. "A Study on Phonon-Mediated Thermal Transport and Lattice Thermal Conductivity Prediction Using First-Principles Calculations." Key Engineering Materials 847 (June 2020): 120–26. http://dx.doi.org/10.4028/www.scientific.net/kem.847.120.

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The systematic theoretical approaches and atomistic simulation programs to predict thermal properties of crystalline nanostructured materials within first-principles framework are studied here. Recent progress in computational power has enabled an accurate and reliable way to investigate nanoscale thermal transport in crystalline materials using first-principles based calculations. Extracting a large set of anharmonic force constants with low computational effort remains a big challenge in lattice dynamics and condensed-matter physics. This paper focuses on recent progress in first-principles phonon calculations for semiconductor materials and summarizes advantages and limitations of each approach and simulation programs by comparing accuracy of numerical solutions, computational load and calculating feasibility to a wide range of crystalline materials. This work also reviews and presents the coupling model of first-principles molecular dynamic (FPMD) approach that can extract anharmonic force constants directly and solution of linearized Boltzmann transport equation to predict phonon-mediated lattice thermal conductivity of crystalline materials.

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Mart�nez-N��ez, Emilio, Saulo A. V�zquez, and Ricardo A. Mosquera. "Conformational analysis of model compounds of vitamin D by theoretical calculations." Journal of Computational Chemistry 18, no. 13 (October 1997): 1647–55. http://dx.doi.org/10.1002/(sici)1096-987x(199710)18:13<1647::aid-jcc6>3.0.co;2-r.

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Piacente, Giovanni, Andrea Amadei, Marco D'Abramo, Isabella Daidone, and Massimiliano Aschi. "Theoretical-computational modeling of photo-induced charge separation spectra and charge recombination kinetics in solution." Phys. Chem. Chem. Phys. 16, no. 38 (2014): 20624–38. http://dx.doi.org/10.1039/c4cp02422b.

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A computational approach, based on molecular dynamics simulations and quantum-chemical calculations, is proposed for modelling the photo-induced charge separation and the kinetics of the subsequent charge recombination (CR) processes in solution.

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A, J. B. "Computational Chemistry: an Emphasis on Practical Calculations (Studies in Physical and Theoretical Chemistry 56)." Journal of Molecular Structure 212 (September 1989): 333. http://dx.doi.org/10.1016/0022-2860(89)85099-9.

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25

Heard, GL, and BF Yates. "Theoretical Evaluation of Alternative Pathways in the Stevens Rearrangement." Australian Journal of Chemistry 48, no. 8 (1995): 1413. http://dx.doi.org/10.1071/ch9951413.

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Ab initio and semi-empirical molecular orbital theory has been used to explore the ion-pair and lithium-catalysed pathways in the Stevens rearrangement of an alkylammonium ylide to an amine. These pathways represent alternatives to the concerted and free radical mechanisms which we have previously studied. Solvation effects have been included via a polarizable continuum model. Finally, the calculations have been extended to a set of experimentally observable compounds. For the nine systems studied here, the stepwise free radical pathway is predicted in every case to be the favourable mechanism for the Stevens rearrangement. Single-point MP2/6-31G(d) calculations on fully optimized PM3 geometries are shown to provide a useful method of including electron correlation at low computational cost.

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Carlsson, Håkan, and Ebbe Nordlander. "Computational Modeling of the Mechanism of Urease." Bioinorganic Chemistry and Applications 2010 (2010): 1–8. http://dx.doi.org/10.1155/2010/364891.

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In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).

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Sanz, Javier Fern�ndez, and Alain Dargelos. "Theoretical analysis of the electronic spectrum of GeH4 fromab initio CI calculations." Journal of Computational Chemistry 11, no. 9 (October 1990): 1017–20. http://dx.doi.org/10.1002/jcc.540110903.

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Zhao, Cheng Yan, Ai Ping Fu, Hong Liang Li, Ping Wang, Yong Xu, and Yun Bo Duan. "Theoretical Study of Stereoselectivity for Syn-Selective Cross-Aldol Reactions of Aldehydes Catalyzed by Chiral Diamine Organocatalysts." Advanced Materials Research 798-799 (September 2013): 59–62. http://dx.doi.org/10.4028/www.scientific.net/amr.798-799.59.

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Quantum mechanical calculations have been performed to study the stereoselectivities in the direct cross-aldol reactions of aldehydes catalyzed by simple chiral diamines. The detailed computational studies on the stereochemistry-controlling step of the subject reactions have been presented by DFT calculations at the B3LYP/6-31G* level. The poor agreement between the calculated and the observed diastereomeric ratio and enantiomeric excess values is obtained for all diamines catalysts. Further M06-2X calculations can provide a reasonable explanation for the observed syn-selectivities of the asymmetric cross-aldol reaction between propionaldehyde and 4-nitrobenzaldehyde.

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CHEMOURI, HAFIDA, WAFAA BENCHOUK, and SIDI MOHAMED MEKELLECHE. "REGIOSELECTIVITY OF HETERO DIELS–ALDER REACTIONS BETWEEN 1-AZA-1,3-BUTADIENE DERIVATIVES AND DIMETHYLVINYLAMINE: A THEORETICAL INVESTIGATION." Journal of Theoretical and Computational Chemistry 05, no. 04 (December 2006): 707–18. http://dx.doi.org/10.1142/s0219633606002581.

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The regioselectivity of hetero Diels–Alder reactions between 1-aza-1,3-butadiene derivatives and dimethylvinylamine is elucidated by means of several theoretical approaches, namely, the Gazquez–Mendez rule based on the calculation of local softnesses, barrier activation calculations, maximum hardness principle, and the Houk rule based on the FMO theory. The calculations were performed at the B3LYP/6-31G(d) level of theory, and the obtained results are in agreement with available experimental results. Moreover, the present analysis shows that these inverse electron demand polar cycloadditions present a linear relationship between the activation barriers of the favored ortho regio-isomers and the inverse of electrophilicity differences of the reagents.

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Amara, Sarah, Noureddine Tchouar, and Salah Belaidi. "Computational Study of some Double Headed Acyclo-C-Nucleosides." International Letters of Chemistry, Physics and Astronomy 61 (November 2015): 1–11. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.61.1.

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In the present paper we have a focus in a study of theoretical characterization of three double headed acyclo-C-nucleosides, which are a recent target of experimental studies. The structural and electronic properties of double headed acyclo-C-nucleosides, 1,4-bis (3-mercapto-1H-1,2,4-triazol-5-yl) butane-1,2,3,4-tetrol, 1,4-bis (4-amino-5-mercapto-4H-1,2,4-triazol-3-yl) butane-1,2,3,4-tetrol and 5,5'-(1,2,3,4-tetrahydroxybutane-1,4-diyl) bis (1,3,4-oxadiazole-2(3H)-thione), have been investigated theoretically by performing semi-empirical molecular orbital, ab initio Hartree-Fock (HF) and Density Functional Theory (DFT) calculations. Geometries of the three molecules are optimized at the level of Austin Model 1 (AM1). The electronic properties and relative energies of the molecules have been calculated by HF and DFT in the ground state.

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YAO, YUAN, WEI-WEI HAN, YI-HAN ZHOU, QUAN LUO, and ZE-SHENG LI. "CATALYTIC REACTION MECHANISM OF HUMAN PHOTORECEPTOR RETINOL DEHYDROGENASE: A THEORETICAL STUDY." Journal of Theoretical and Computational Chemistry 07, no. 04 (August 2008): 565–78. http://dx.doi.org/10.1142/s0219633608003964.

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Human photoreceptor retinol dehydrogenase (hRDH8) catalyzes the reduction of all-trans-retinal to all-trans-retinol with NADPH as a rate-limiting step in the visual cycle. Based on the docking results of the substrate to the 3D structure of hRDH8 which is generated by homology modeling method, three quantum chemical calculation models with different sizes were used to investigate the catalytic reaction mechanism of hRDH8 with the aid of density functional theory. The calculations indicate that hRDH8 employs a general acid/base mechanism that a proton is transferred to the keto oxygen of the substrate after the pro-S hydride of NADPH transfer to keto carbon of the substrate. The H-transfer order is converse to that in the proposed mechanism of 17ß-hydroxysteroid dehydrogenase 1, which is highly related to the hRDH8 sequence. Tyr155 always provides the proton to the keto oxygen of the substrate whether unprotonated Lys159 is considered or not in the calculation models. However, protonated Lys159 changes the initial mechanism and replaces Tyr155 to provide the proton to the keto oxygen of the substrate. Moreover, protonated Lys159 can also decrease very effectively the Gibbs free energy barrier to make the reaction indeed energetically feasible. The role of Lys159 in hRDH8 is different from that in 17ß-hydroxysteroid dehydrogenase 1. The solvent effect calculations indicate that the reaction is more feasible energetically in the protein electrostatic environment than in the gas phase.

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Zhang, Yaowen, Shutong Yang, and Canglong Wang. "First-principles calculations for point defects in MAX phases Ti2AlN." Modern Physics Letters B 30, no. 09 (April 10, 2016): 1650101. http://dx.doi.org/10.1142/s0217984916501013.

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This paper outlines general physical issues associated with performing computational numerical simulations of primary point defects in MAX phases Ti2AlN. First-principles solutions are possible due to the development of computational resources of software and hardware. The calculation accuracy is a good agreement with the experimental results. As an important application of our simulations, the results could provide a theoretical guidance for future experiments and application of Ti2AlN. For example, the N mono-vacancy is the most difficult to form. On the contrary, the mono-vacancy formation in Ti2AlN is energetically most favorable for the Al atom. The essence of the phenomena is explained by the calculated density of state (DOS).

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Rocha, Rênica Alves de Morais, Thaís Forest Giacomello, Antonio Maia de Jesus Chaves Neto, Gunar Vingre Da Silva Mota, and Fabio Luiz Paranhos Costa. "Carbon-13 Nuclear Magnetic Resonance Chemical Shift Calculation Protocol Applied to Rigid Triterpenes Molecules." Advanced Science, Engineering and Medicine 12, no. 8 (August 1, 2020): 995–1001. http://dx.doi.org/10.1166/asem.2020.2636.

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Nuclear magnetic resonance spectroscopy is one of the most powerful experimental techniques for obtaining three-dimensional structures of complex molecules, mainly for the analysis of the relative and absolute configurations of organic compounds. For this reason, this has become one of the most promising tools in the field of chemistry. From the theoretical point of view, advanced computational protocols have been developed for calculating nuclear magnetic resonance, mainly hydrogen-1 and carbon-13, parameters of isolated molecules, in which the environmental effects are neglected. These effects are predominantly related to the inherently large size of such systems, making conventional ab initio theories either very computationally demanding or even prohibitive. Despite the current advances in spectroscopic techniques, instances of revision of structures erroneously established for natural products are still common in the literature. Therefore, it is still necessary the development of quantum-chemical protocols that may assist in the correct structural determination of these compounds. This work aimed to test a universal scaling factor, based on a linear regression, for the calculation of carbon-13 nuclear magnetic resonance chemical shifts for rigid molecules, which has low computational cost and great accuracy to aid in the structural determination of natural products. The carbon-13 chemical shifts were calculated using the mPW1PW91/3-21G level of theory. Scaled chemical shifts were obtained according to the relation: 1.14x(calculated chemical shifts)–4.71. To test the application of the created scaling factor to problems related to stereochemistry, we investigated its ability to differentiate pentacyclic triterpenes regioisomers. Our results show that the mPW1PW91/3-21G//PM7 level of theory applied to the calculations, together with the use of the scaling factor, is an efficient and low-cost tool as an alternative to computational requirement approaches, usually applied to the calculation of carbon-13 nuclear magnetic resonance chemical shifts.

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Frau, J., J. Donoso, F. Muñoz, and F. García Blanco. "Theoretical calculations of β-lactam antibiotics. V. AM1 calculations of hydrolysis of cephalothin in gaseous phase and influence of the solvent." Journal of Computational Chemistry 14, no. 12 (December 1993): 1545–52. http://dx.doi.org/10.1002/jcc.540141217.

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Li, G. S., B. Maigret, D. Rinaldi, and M. F. Ruiz-L�pez. "Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations." Journal of Computational Chemistry 19, no. 15 (November 30, 1998): 1675–88. http://dx.doi.org/10.1002/(sici)1096-987x(19981130)19:15<1675::aid-jcc1>3.0.co;2-k.

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Ferrer, Santiago Melchor, and Jose Molina Molina. "Theoretical calculations on C30H12 bowl-shaped hydrocarbons: NMR shielding constants, stability, and aromaticity." Journal of Computational Chemistry 20, no. 13 (October 1999): 1412–21. http://dx.doi.org/10.1002/(sici)1096-987x(199910)20:13<1412::aid-jcc8>3.0.co;2-f.

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Rulíšek, Lubomír, Kasper P. Jensen, Kristoffer Lundgren, and Ulf Ryde. "The reaction mechanism of iron and manganese superoxide dismutases studied by theoretical calculations." Journal of Computational Chemistry 27, no. 12 (September 2006): 1398–414. http://dx.doi.org/10.1002/jcc.20450.

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Ghasemi, Ashraf Sadat, Mahsan Deilam, and Fereydoun Ashrafi. "INVESTIGATION OF MOLECULAR STRUCTURE AND EXPERIMENTAL AND THEORETICAL SPECTROSCOPIC STUDIES OF ANTICANCER DRUGS - A REVIEW." Ciência e Natura 38, no. 2 (May 31, 2016): 1124. http://dx.doi.org/10.5902/2179460x21525.

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In many literatures, both experimental and computational study on molecular structure and spectroscopic assignments of anticancer drugs has been reported. The molecular geometry was obtained from the X-ray structure determination exprimentally and optimized using computational chemistry methods like Density Functional Theory (DFT) method. In this review, we have investigated calculations based on density functional theory at the B3LYP/6-31G(d,p) and B3LYP/6-311++G(d,p) levels of theory. From the optimized geometry of the molecules, Molecular structure (bond lengths, bond angles and torsion angles) and vibrational assignments have been obtained.

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POOLMEE, P., and S. HANNONGBUA. "THEORETICAL INVESTIGATION ON ENERGY GAP OF FLUORENE-THIOPHENE COPOLYMER." Journal of Theoretical and Computational Chemistry 03, no. 04 (December 2004): 481–89. http://dx.doi.org/10.1142/s0219633604001227.

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In this work, HOMO-LUMO energy gap and the lowest excitation energy of poly [2,7-(9,9-dihexylfluorene)-co-alt-2,5-(decylthiophene) were performed by different methods. The obtained results indicate that TDDFT(B3LYP/6-31G*)//B3LYP/6-31G* calculations can be useful to provide reliable energetic and structural results of this polymer. The HOMO-LUMO predictions were not accurately obtained as compared to the experimental results. The inverse chain length approximation by using TDDFT(B3LYP/6-31G*)//B3LYP/6-31G* calculations provides energy gap of 2.50 eV, which is in an excellent agreement with the experimental data. However, it was found that the HOMO-LUMO energy gaps obtained from B3LYP calculations were still far from the experimental data.

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Mao, James X., Phillip Walsh, Peter Kroll, and Kevin A. Schug. "Simulation of Vacuum Ultraviolet Absorption Spectra: Paraffin, Isoparaffin, Olefin, Naphthene, and Aromatic Hydrocarbon Class Compounds." Applied Spectroscopy 74, no. 1 (September 13, 2019): 72–80. http://dx.doi.org/10.1177/0003702819875132.

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The advent of a new vacuum ultraviolet (VUV) spectroscopic absorption detector for gas chromatography has enabled applications in many areas. Theoretical simulations of VUV spectra using computational chemistry can aid the new technique in situations where experimental spectra are unavailable. In this study, VUV spectral simulations of paraffin, isoparaffin, olefin, naphthene, and aromatic (PIONA) compounds using time-dependent density functional theory (TDDFT) methods were investigated. Important factors for the simulations, such as functionals/basis sets and formalism of oscillator strength calculations, were examined and parameters for future PIONA compound simulations were obtained by fitting computational results to experimental spectra. The simulations produced satisfactory correlations between experimental observations and theoretical calculations, and enabled potential analysis applications for complex higher distillate fuels, such as diesel fuel. Further improvement of the methods was proposed.

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Pokluda, J., M. Černý, P. Šandera, and M. Šob. "Calculations of theoretical strength: State of the art and history." Journal of Computer-Aided Materials Design 11, no. 1 (January 2004): 1–28. http://dx.doi.org/10.1007/s10820-004-4567-2.

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Hong, Gong-Yi, Xiangqian Hu, Fan Wang, and Le-Min Li. "An approach to reduce the computational effort in accurate DFT calculations." Chemical Physics 290, no. 2-3 (May 2003): 163–70. http://dx.doi.org/10.1016/s0301-0104(03)00118-6.

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Ćosić, Rajko, Aleš Vítek, and René Kalus. "Photoabsorption spectra of small mercury clusters: a computational study." Physical Chemistry Chemical Physics 20, no. 45 (2018): 28871–80. http://dx.doi.org/10.1039/c8cp04858d.

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Photoabsorption spectra of small Hg_N clusters (N = 2–5) have been calculated using a diatomics-in-molecules interaction model and an atoms-in-molecules approach for transition probability calculations.

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Zhang, Xuesheng, Xiaona Lin, Zihao Zhang, Licong Dong, Xinlong Sun, Desheng Sun, and Kehong Yuan. "Artificial Intelligence Medical Ultrasound Equipment: Application of Breast Lesions Detection." Ultrasonic Imaging 42, no. 4-5 (June 16, 2020): 191–202. http://dx.doi.org/10.1177/0161734620928453.

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Breast cancer ranks first among cancers affecting women’s health. Our work aims to realize the intelligence of the medical ultrasound equipment with limited computational capability, which is used for the assistant detection of breast lesions. We embed the high-computational deep learning algorithm into the medical ultrasound equipment with limited computational capability by two techniques: (1) lightweight neural network: considering the limited computational capability of ultrasound equipment, a lightweight neural network is designed, which greatly reduces the amount of calculation. And we use the technique of knowledge distillation to train the low-precision network helped with the high-precision network; (2) asynchronous calculations: consider four frames of ultrasound images as a group; the image of the first frame of each group is used as the input of the network, and the result is respectively fused with the images of the fourth to seventh frames. An amount of computation of 30 GFLO/frame is required for the proposed lightweight neural network, about 1/6 of that of the large high-precision network. After trained from scratch using the knowledge distillation technique, the detection performance of the lightweight neural network (sensitivity = 89.25%, specificity = 96.33%, the average precision [AP] = 0.85) is close to that of the high-precision network (sensitivity = 98.3%, specificity = 88.33%, AP = 0.91). By asynchronous calculation, we achieve real-time automatic detection of 24 fps (frames per second) on the ultrasound equipment. Our work proposes a method to realize the intelligence of the low-computation-power ultrasonic equipment, and successfully achieves the real-time assistant detection of breast lesions. The significance of the study is as follows: (1) The proposed method is of practical significance in assisting doctors to detect breast lesions; (2) our method provides some practical and theoretical support for the development and engineering of intelligent equipment based on artificial intelligence algorithms.

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Apelian, Diran, M. M. Makhlouf, and D. Saha. "CDS Method for Casting Aluminium-Based Wrought Alloy Compositions: Theoretical Framework." Materials Science Forum 519-521 (July 2006): 1771–76. http://dx.doi.org/10.4028/www.scientific.net/msf.519-521.1771.

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A novel process named Controlled Diffusion Solidification (CDS) has been developed to circumvent problems that are typically associated with casting wrought aluminum alloy compositions into near net shaped components. The process involves bringing two precursor alloys of precisely controlled composition, temperature, and quantity into intimate contact, and then casting the resultant alloy using a conventional casting process to yield a component of predetermined composition with a microstructure that is similar to that of semi-solid processed alloys. Describing the many interactions that occur during solidification of aluminum alloys in a consistent manner is virtually impossible without the use of computational tools that are based on thermodynamic models. In this paper, we describe how the CALPHAD method, which allows calculating all the necessary data from thermodynamic model parameters, was used along with theoretical calculations and empirical rules to allow describing the Gibbs free energy of each phase in the alloy system and yield quantitative data that guided the development and optimization of the CDS method.

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Abgaryan, Karine, Ilya Mutigullin, and Dmitriy Bazhanov. "Multiscale Computational Model of Nitride Semiconductor Nanostructures." Advanced Materials Research 560-561 (August 2012): 1133–37. http://dx.doi.org/10.4028/www.scientific.net/amr.560-561.1133.

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Theoretical multiscale model of nitride semiconductor nanostructure is proposed. The model combines various computational methods such as density functional theory, molecular dynamics and kinetic Monte Carlo. As a first step of implementation of proposed approach ab initio calculations of structural and electronic properties of two different structures InN/Si and AlN/AlGaN/GaN heterostructures were carried out. In particular, the influence of oxygen on InN/Si adhesion energy was studied. AlN, GaN, AlxGa1-xN (x=0.33) spontaneous and piezoelectric polarizations as well as sheet carrier concentrations at GaN/AlGaN interface were calculated. Obtained value for sheet carrier concentration at GaN/AlGaN interface is close to experimental data.

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LAGUNOVA, Yuliya Andreevna, Stanislav Anatol’evich MAYOROV, and Gennadiy Alexeevich BOYARSKIH. "Statistical analysis of stress-strain state of bearing jaw crusher." NEWS of the Ural State Mining University 1, no. 2 (June 15, 2020): 159–71. http://dx.doi.org/10.21440/2307-2091-2020-2-159-171.

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The relevance of the work. When creating particularly large machines and systems, in the case of their 3D modeling and detailed study, the load on the central processor of the computer, as well as on the graphic and RAM modules, increases, which significantly slows down the design process and calculations. In the article, a statistical analysis of the stress-strain state of the jaw crusher bearing is carried out to establish the correspondence of the theoretical and actual structural models taking into account all workloads. The objectives of the study. Consider the task of selecting a simpler and “easier” for the calculation model programs, not difficult to parameterize, compared with the original bearing model, but providing accuracy in the calculation in an acceptable range of errors. To analyze the stress-strain state of the bearing assembly with various geometric parameters. Research methodology. In the calculations, the finite element method was used. Used specialized software package APM WinMachine. A computational experiment was conducted. A correlation analysis of the theoretical and actual structural model of the bearing is carried out. Results. Mathematical models of the metal structures of bearings of various sections are given and the locations of the highest stresses are identified. Calculation errors and correlation dependencies of stresses are established taking into account the Pearson, Fisher criteria and the construction of the Taylor series. Conclusions. The results of a computational experiment satisfy the requirements and can be used to solve further problems of designing bearing assemblies. In the future, a parameter-dependent model can be created that makes it easier to calculate using any type of bearing

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Min, Ahreum, Ahreum Ahn, Cheol Joo Moon, Ji Hoon Lee, Yeon Guk Seong, Seong Keun Kim, and Myong Yong Choi. "Conformational structures of jet-cooled acetaminophen–water clusters: a gas phase spectroscopic and computational study." Physical Chemistry Chemical Physics 19, no. 6 (2017): 4840–48. http://dx.doi.org/10.1039/c6cp06863d.

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Jet-cooled acetaminophen (AAP)–water clusters, AAP–(H₂O)₁, have been investigated by a combination of theoretical calculations and R2PI, UV–UV HB, IR-dip, IR–UV HB techniques in the gas phase.

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Milenković, Dejan, Jasmina M. Dimitrić Marković, Dušan Dimić, Svetlana Jeremić, Dragan Amić, Marijana Stanojević Pirković, and Zoran S. Marković. "Structural characterization of kaempferol: a spectroscopic and computational study." Macedonian Journal of Chemistry and Chemical Engineering 38, no. 1 (May 20, 2019): 49. http://dx.doi.org/10.20450/mjcce.2019.1333.

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Calculations based on the density functional theory, with the B3LYP functional and the 6-311++G(d,p) basis set, were performed with the aim of confirming the molecular structure and spectroscopic characteristics of kaempferol, a naturally occurring flavonoid molecule. The electronic structure of kaempferol was examined using NBO analysis. The assigning of the experimentally obtained IR and Raman spectra was performed after the best-fit-based comparison with theoretical spectra. The 13C and 1H NMR experimental spectra were related to the theoretically obtained values of the chemical shifts determined by the GIAO method. The correlation coefficient and the average absolute error values proved B3LYP-D3 to be an adequate method in describing the NMR parameters of kaempferol. Molecular docking analysis was carried out in order to identify the potency of inhibition of the title molecule against human procalcitonin. The inhibition activity was obtained for 10 conformations of ligand inside the protein.

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CHEN, LIPING, XINJUAN HOU, LINGYUN ZHU, SHIWEI YIN, and Z. SHUAI. "THEORETICAL DESIGN OF LIGHT-EMITTING POLYMERS — SUBSTITUTION EFFECTS OF EXCITED STATE ORDERING OF POLYDIACETYLENE AND POLYACETYLENE." Journal of Theoretical and Computational Chemistry 05, spec01 (January 2006): 391–400. http://dx.doi.org/10.1142/s0219633606002337.

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The excited states structure, essential in determining the light-emitting properties, in a correlated electron system behaves differently from the one-electron system. Previous investigations show that upon proper chemical substitution, the non-emissive polyacetylene (PA) can be designed to be strongly light-emitting materials. On the basis of the correlated quantum chemical calculations within the INDO/EOM-CCSD approach, we systematically studied both the pristine and substituted polydiacetylene (PDA) about the low-lying excited states orderings. PDA possesses high mobility, but it is non-emissive. We predict that it is impossible to cause PDA to be light-emitting. From these numerical results, we propose a simple and practical rule to design conjugated light-emitting polymers, which require only a molecular orbital calculation instead of sophisticated correlated calculations. This rule is derived from physical pictures of correlated electron model, and is found to be in agreement with the existing experiments for various substituted PA and poly(p-phenylenebutadiynylene) (PPPB).

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Journal articles on the topic 'Computational theoretical calculations'

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