Literature DB >> 17902157

QUILD: QUantum-regions interconnected by local descriptions.

Marcel Swart1, F Matthias Bickelhaupt.   

Abstract

A new program for multilevel (QM/QM and/or QM/MM) approaches is presented that is able to combine different computational descriptions for different regions in a transparent and flexible manner. This program, designated QUILD (for QUantum-regions Interconnected by Local Descriptions), uses adapted delocalized coordinates (Int J Quantum Chem 2006, 106, 2536) for efficient geometry optimizations of equilibrium and transition-state structures, where both weak and strong coordinates may be present. The Amsterdam Density Functional (ADF) program is used for providing density functional theory and MM energies and gradients, while an interface to the ORCA program is available for including RHF, MP2, or semiempirical descriptions. The QUILD optimization setup reduces the number of geometry steps needed for the Baker test-set of 30 organic molecules by approximately 30% and for a weakly-bound test-set of 18 molecules by approximately 75% compared with the old-style optimizer in ADF, i.e., a speedup of roughly a factor four. We report two examples of using geometry optimizations with numerical gradients, for spin-orbit relativistic ZORA and for excited-state geometries. Finally, we show examples of its multilevel capabilities for a number of systems, including the multilevel boundary region of amino acid residues, an S(N)2 reaction in the gas-phase and in solvent, and a DNA duplex. (c) 2007 Wiley Periodicals, Inc.

Entities:  

Mesh:

Substances:

Year:  2008        PMID: 17902157     DOI: 10.1002/jcc.20834

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  12 in total

1.  Unraveling differences in aluminyl and carbene coordination chemistry: bonding in gold complexes and reactivity with carbon dioxide.

Authors:  Diego Sorbelli; Leonardo Belpassi; Paola Belanzoni
Journal:  Chem Sci       Date:  2022-03-31       Impact factor: 9.969

2.  Molecule-like and lattice vibrations in metal clusters.

Authors:  Krishnadas Kumaranchira Ramankutty; Huayan Yang; Ani Baghdasaryan; Jeremie Teyssier; Valentin Paul Nicu; Thomas Buergi
Journal:  Phys Chem Chem Phys       Date:  2022-06-08       Impact factor: 3.945

3.  Differential stabilization of adenine quartets by anions and cations.

Authors:  Tushar van der Wijst; Bernhard Lippert; Marcel Swart; Célia Fonseca Guerra; F Matthias Bickelhaupt
Journal:  J Biol Inorg Chem       Date:  2009-11-27       Impact factor: 3.358

4.  Supramolecular ring structures of 7-methylguanine: a computational study of its self-assembly and anion binding.

Authors:  Gábor Paragi; Zoltán Kupihár; Célia Fonseca Guerra; F Matthias Bickelhaupt; Lajos Kovács
Journal:  Molecules       Date:  2012-12-27       Impact factor: 4.411

5.  H2O2 Oxidation by FeIII-OOH Intermediates and Its Effect on Catalytic Efficiency.

Authors:  Juan Chen; Apparao Draksharapu; Davide Angelone; Duenpen Unjaroen; Sandeep K Padamati; Ronald Hage; Marcel Swart; Carole Duboc; Wesley R Browne
Journal:  ACS Catal       Date:  2018-09-06       Impact factor: 13.084

6.  Analysis of Vibrational Circular Dichroism Spectra of Peptides: A Generalized Coupled Oscillator Approach of a Small Peptide Model Using VCDtools.

Authors:  Mark A J Koenis; Lucas Visscher; Wybren J Buma; Valentin P Nicu
Journal:  J Phys Chem B       Date:  2020-02-21       Impact factor: 2.991

7.  What Singles out Aluminyl Anions? A Comparative Computational Study of the Carbon Dioxide Insertion Reaction in Gold-Aluminyl, -Gallyl, and -Indyl Complexes.

Authors:  Diego Sorbelli; Leonardo Belpassi; Paola Belanzoni
Journal:  Inorg Chem       Date:  2022-01-05       Impact factor: 5.165

8.  B-DNA Structure and Stability: The Role of Nucleotide Composition and Order.

Authors:  Celine Nieuwland; Trevor A Hamlin; Célia Fonseca Guerra; Giampaolo Barone; F Matthias Bickelhaupt
Journal:  ChemistryOpen       Date:  2022-01-27       Impact factor: 2.630

9.  B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands.

Authors:  Giampaolo Barone; Célia Fonseca Guerra; F Matthias Bickelhaupt
Journal:  ChemistryOpen       Date:  2013-08-16       Impact factor: 2.911

Review 10.  Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent.

Authors:  Trevor A Hamlin; Marcel Swart; F Matthias Bickelhaupt
Journal:  Chemphyschem       Date:  2018-04-19       Impact factor: 3.102

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.