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Thematische Bibliographien / Semiempirical quantum-mechanical methods / Zeitschriftenartikel

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Zeitschriftenartikel zum Thema „Semiempirical quantum-mechanical methods“

Autor: Grafiati

Veröffentlicht am 28. Juni 2021

Zuletzt aktualisiert am 17. Februar 2022

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1

Diller, David J., Christine Humblet, Xiaohua Zhang und Lance M. Westerhoff. „Computational alanine scanning with linear scaling semiempirical quantum mechanical methods“. Proteins: Structure, Function, and Bioinformatics 78, Nr. 10 (13.05.2010): 2329–37. http://dx.doi.org/10.1002/prot.22745.

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2

Řezáč, Jan, und Pavel Hobza. „Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods“. Journal of Chemical Theory and Computation 8, Nr. 1 (22.12.2011): 141–51. http://dx.doi.org/10.1021/ct200751e.

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3

Christensen, Anders S., Tomáš Kubař, Qiang Cui und Marcus Elstner. „Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications“. Chemical Reviews 116, Nr. 9 (13.04.2016): 5301–37. http://dx.doi.org/10.1021/acs.chemrev.5b00584.

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4

Wollacott, Andrew M., und Kenneth M. Merz. „Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures“. Journal of Chemical Theory and Computation 3, Nr. 4 (30.05.2007): 1609–19. http://dx.doi.org/10.1021/ct600325q.

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5

Titmuss, Stephen J., Peter L. Cummins, Andrey A. Bliznyuk, Alistair P. Rendell und Jill E. Gready. „Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods applied to enzyme reactions“. Chemical Physics Letters 320, Nr. 1-2 (März 2000): 169–76. http://dx.doi.org/10.1016/s0009-2614(00)00215-3.

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6

Ibrahim, Mahmoud A. A. „Performance Assessment of Semiempirical Molecular Orbital Methods in Describing Halogen Bonding: Quantum Mechanical and Quantum Mechanical/Molecular Mechanical-Molecular Dynamics Study“. Journal of Chemical Information and Modeling 51, Nr. 10 (26.09.2011): 2549–59. http://dx.doi.org/10.1021/ci2002582.

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7

Kříž, Kristian, und Jan Řezáč. „Benchmarking of Semiempirical Quantum-Mechanical Methods on Systems Relevant to Computer-Aided Drug Design“. Journal of Chemical Information and Modeling 60, Nr. 3 (15.02.2020): 1453–60. http://dx.doi.org/10.1021/acs.jcim.9b01171.

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8

Yilmazer, Nusret Duygu, Pascal Heitel, Tobias Schwabe und Martin Korth. „Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data“. Journal of Theoretical and Computational Chemistry 14, Nr. 01 (Februar 2015): 1540001. http://dx.doi.org/10.1142/s0219633615400015.

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The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.

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9

Hostaš, Jiří, Jan Řezáč und Pavel Hobza. „On the performance of the semiempirical quantum mechanical PM6 and PM7 methods for noncovalent interactions“. Chemical Physics Letters 568-569 (Mai 2013): 161–66. http://dx.doi.org/10.1016/j.cplett.2013.02.069.

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10

Titmuss, Stephen J., Peter L. Cummins, Alistair P. Rendell, Andrey A. Bliznyuk und Jill E. Gready. „Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions. II. An energy decomposition analysis“. Journal of Computational Chemistry 23, Nr. 14 (04.09.2002): 1314–22. http://dx.doi.org/10.1002/jcc.10122.

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11

Pichierri, Fabio. „Computation of the permanent dipole moment of α-chymotrypsin from linear-scaling semiempirical quantum mechanical methods“. Journal of Molecular Structure: THEOCHEM 664-665 (Dezember 2003): 197–205. http://dx.doi.org/10.1016/j.theochem.2003.09.003.

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12

Tahir, Iqmal, Karna Wijaya und Titik Subarni. „MODELING OF ALKYL SALICYLATE COMPOUNDS AS UV ABSORBER BASED ON ELECTRONIC TRANSITION BY USING SEMIEMPIRICAL QUANTUM MECHANICS ZINDO/s CALCULATION“. Indonesian Journal of Chemistry 2, Nr. 1 (05.06.2010): 64–72. http://dx.doi.org/10.22146/ijc.21934.

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Modeling of several alkyl salicylates based on electronic transition by using semiempriical mechanical quantum ZINDO/s calculation has been done. Object of these research were assumed only alkyl salicylates of C4 (butyl) until C8 (octyl) homologue with 4-7 example structures of each homologue. All of the computation have been performed using quantum chemistry - package software Hyperchem 6.0. The research covered about drawing each of the structure, geometry optimization using semiempirical AM1 algorithm and followed with single point calculation using semiempirical ZINDO/s technique. ZINDO/s calculations used a defined criteria that is singly excited - Configuration Interaction (CI), gap of HOMO-LUMO energy transition was 2 and degeneracy level was 3. Analysis of the theoretical spectra was focused in the UV-B (290-320 nm) and UV-C (200-290 nm) area. The result showed that modeling of the compound can be used for predicting the type of UV protection activity depending with the electronic transition in the UV area. Modification of the alkyl homologue relatively did not change the value of wavelength absorbtion to indicate the UV protection activity. Alkyl salicylate compounds were predicted as UV-C sunscreen or relatively the compounds have protection effect for UV-C. Keywords: alkyl salicylate, sunscreen, semiempirical methods

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13

Raha, Kaushik, Arjan J. van der Vaart, Kevin E. Riley, Martin B. Peters, Lance M. Westerhoff, Hwanho Kim und Kenneth M. Merz. „Pairwise Decomposition of Residue Interaction Energies Using Semiempirical Quantum Mechanical Methods in Studies of Protein−Ligand Interaction“. Journal of the American Chemical Society 127, Nr. 18 (Mai 2005): 6583–94. http://dx.doi.org/10.1021/ja042666p.

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14

Řezáč, Jan. „Description of halogen bonding in semiempirical quantum‐mechanical and self‐consistent charge density‐functional tight‐binding methods“. Journal of Computational Chemistry 40, Nr. 17 (03.04.2019): 1633–42. http://dx.doi.org/10.1002/jcc.25816.

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15

Pérez-Tabero, Sergio, Berta Fernández, Enrique M. Cabaleiro-Lago, Emilio Martínez-Núñez und Saulo A. Vázquez. „New Approach for Correcting Noncovalent Interactions in Semiempirical Quantum Mechanical Methods: The Importance of Multiple-Orientation Sampling“. Journal of Chemical Theory and Computation 17, Nr. 9 (23.08.2021): 5556–67. http://dx.doi.org/10.1021/acs.jctc.1c00365.

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16

Miriyala, V. M., und J. Řezáč. „Testing Semiempirical Quantum Mechanical Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules“. Journal of Physical Chemistry A 122, Nr. 10 (23.02.2018): 2801–8. http://dx.doi.org/10.1021/acs.jpca.8b00260.

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17

Greatbanks, Stephen P., Jill E. Gready, Ajay C. Limaye und Alistair P. Rendell. „Comparison of enzyme polarization of ligands and charge-transfer effects for dihydrofolate reductase using point-charge embeddedab initio quantum mechanical and linear-scaling semiempirical quantum mechanical methods“. Journal of Computational Chemistry 21, Nr. 9 (15.07.2000): 788–811. http://dx.doi.org/10.1002/(sici)1096-987x(20000715)21:9<788::aid-jcc7>3.0.co;2-q.

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18

Gogonea, Valentin, Lance M. Westerhoff und Kenneth M. Merz. „Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian“. Journal of Chemical Physics 113, Nr. 14 (08.10.2000): 5604–13. http://dx.doi.org/10.1063/1.1290608.

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19

Reddy, Krishna N., und Martin A. Locke. „Prediction of Soil Sorption (Koc) of Herbicides Using Semiempirical Molecular Properties“. Weed Science 42, Nr. 3 (September 1994): 453–61. http://dx.doi.org/10.1017/s0043174500076761.

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Relationships between soil sorption normalized to organic carbon (Koc) and molecular properties of 71 herbicides were examined. The Koc values were obtained from the literature. Various molecular properties were calculated by quantum mechanical methods using molecular modeling software. The quantitative structure activity relationship (QSAR) models based on four molecular properties, van der Waals volume (VDWv), molecular polarizability (α), dipole moment (μ), and energy of highest occupied molecular orbital (eHOMO), together accounted for 70% of the variation in Koc. Herbicides were broadly divided into six families based on structural similarities, and separate equations were established for each group. The three descriptors, VDWv, α, and μ, along with either energy of lowest unoccupied molecular orbital (eLUMO), or electrophilic superdelocalizability (SE), or eHOMO appeared to be determinants and accounted for 82 to 99% of the variation in Koc. Applicability of these models was tested for one herbicide analogue and 10 metabolites. The QSAR models appear to be specific to structurally similar chemicals. The QSAR models could be developed to predict Koc of structurally similar compounds even before they are synthesized or for some of the metabolites of existing herbicides. Models of this type can also be developed to create priority lists for testing, so that time, money, and efforts can be focused on the potentially most hazardous chemicals.

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20

Sastry, Kumara, D. D. Johnson, Alexis L. Thompson, David E. Goldberg, Todd J. Martinez, Jeff Leiding und Jane Owens. „Optimization of Semiempirical Quantum Chemistry Methods via Multiobjective Genetic Algorithms: Accurate Photodynamics for Larger Molecules and Longer Time Scales“. Materials and Manufacturing Processes 22, Nr. 5 (04.06.2007): 553–61. http://dx.doi.org/10.1080/10426910701319506.

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21

Heimel, G., D. Somitsch, P. Knoll und E. Zojer. „Ab Initio Study of Vibrational Anharmonic Coupling Effects in Oligo(para-phenylenes)“. MRS Proceedings 708 (2001). http://dx.doi.org/10.1557/proc-708-bb3.10.

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ABSTRACTIn this study we present a theoretical approach to simulate vibrational anharmonic coupling effects seen in the Raman spectra of oligo(para-phenylenes). Quantum chemical ab inito methods are applied to determine anharmonic force constants and energy corrections on the harmonic vibrational frequencies of the isolated molecules. Semiempirical methods are applied to compute Raman intensities of fundamentals and combination bands. This methodology is then used to characterize a previously unassigned Fermi resonance around 1600 cm-1. The evolution of this quantum mechanical resonance with oligomer length and planarity is compared to experimental data.

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22

Tarnowska, M., S. Oldziej, A. Liwo, Z. Grzonka und E. Borowski. „Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods“. European Biophysics Journal 21, Nr. 4 (September 1992). http://dx.doi.org/10.1007/bf00185122.

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23

Mezentseva, Natalya, Vladislav Aleksandrovich Sadykov, Vasilii Ivanovich Avdeev und Vladimir L'vovich Kuznetsov. „Analysis of the Structural Specificity of ZrO2 Nanoparticles in Pillared Clays by Modeling of the Condensation Process in ZrOCl2*8H2O Solutions“. MRS Proceedings 894 (2005). http://dx.doi.org/10.1557/proc-0894-ll06-05.

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AbstractA combination of quantum-chemical approaches including DFT, semiempirical PM3 and molecular mechanics (force field MM+) methods has been applied for analysis of the structure of polynuclear hydroxocomplexes of Zr in diluted solutions of its oxochloride as precursors of zirconia nanoparticles in zirconia-pillared clays. Relative stability of complexes differing by their size and shape has been estimated.

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