Literature DB >> 30215645

Extending the perturbed matrix method beyond the dipolar approximation: comparison of different levels of theory.

Laura Zanetti-Polzi1, Sara Del Galdo, Isabella Daidone, Marco D'Abramo, Vincenzo Barone, Massimiliano Aschi, Andrea Amadei.   

Abstract

Some years ago we developed a theoretical-computational hybrid quantum/classical methodology, the Perturbed Matrix Method (PMM), to be used in conjunction with molecular dynamics simulations for the investigation of chemical processes in complex systems, that proved to be a valuable tool for the simulation of relevant experimental observables, e.g., spectroscopic signals, reduction potentials, kinetic constants. In typical PMM calculations the quantum sub-part of the system, the quantum centre, is embedded into an external perturbing field providing a perturbation operator explicitly calculated up to the dipolar terms. In this paper we further develop the PMM approach, beyond the dipolar terms in the perturbation operator expansion, by including explicitly the quadrupolar terms and/or by expanding the perturbation operator on each atom of the quantum centre. These different levels of the perturbation operator expansion, providing different levels of theory, have been tested by calculating three different spectroscopic observables: the spectral signal of liquid water and aqueous benzene due to the lowest energy electronic excitation and the infrared amide I band of aqueous trans-N-methylacetamide. All the systems tested show that, even though the previous PMM level of theory is already capable of reproducing the main features of the spectral signal, the higher levels of theory improve the quantitative reproduction of the spectral details.

Entities:  

Year:  2018        PMID: 30215645     DOI: 10.1039/c8cp04190c

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  9 in total

1.  Rationalizing Sequence and Conformational Effects on the Guanine Oxidation in Different DNA Conformations.

Authors:  Alessandro Nicola Nardi; Alessio Olivieri; Marco D'Abramo
Journal:  J Phys Chem B       Date:  2022-06-07       Impact factor: 3.466

Review 2.  Theoretical Modeling of Redox Potentials of Biomolecules.

Authors:  Cheng Giuseppe Chen; Alessandro Nicola Nardi; Andrea Amadei; Marco D'Abramo
Journal:  Molecules       Date:  2022-02-05       Impact factor: 4.411

3.  Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches.

Authors:  Jesús Lucia-Tamudo; Gustavo Cárdenas; Nuria Anguita-Ortiz; Sergio Díaz-Tendero; Juan J Nogueira
Journal:  J Chem Inf Model       Date:  2022-06-30       Impact factor: 6.162

4.  Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents.

Authors:  Emanuele Falbo; Marco Fusè; Federico Lazzari; Giordano Mancini; Vincenzo Barone
Journal:  J Chem Theory Comput       Date:  2022-09-27       Impact factor: 6.578

5.  Effects of Environmental and Electric Perturbations on the pKa of Thioredoxin Cysteine 35: A Computational Study.

Authors:  Valeria D'Annibale; Donatella Fracassi; Paolo Marracino; Guglielmo D'Inzeo; Marco D'Abramo
Journal:  Molecules       Date:  2022-09-30       Impact factor: 4.927

6.  CPL Spectra of Camphor Derivatives in Solution by an Integrated QM/MD Approach.

Authors:  Sara Del Galdo; Marco Fusè; Vincenzo Barone
Journal:  Front Chem       Date:  2020-07-07       Impact factor: 5.221

7.  Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design.

Authors:  Laura Zanetti-Polzi; Micholas Dean Smith; Chris Chipot; James C Gumbart; Diane L Lynch; Anna Pavlova; Jeremy C Smith; Isabella Daidone
Journal:  ChemRxiv       Date:  2020-11-06

8.  Theoretical Characterization of the Reduction Potentials of Nucleic Acids in Solution.

Authors:  Valeria D'Annibale; Alessandro Nicola Nardi; Andrea Amadei; Marco D'Abramo
Journal:  J Chem Theory Comput       Date:  2021-02-23       Impact factor: 6.006

9.  Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics.

Authors:  Giordano Mancini; Sara Del Galdo; Balasubramanian Chandramouli; Marco Pagliai; Vincenzo Barone
Journal:  J Chem Theory Comput       Date:  2020-08-11       Impact factor: 6.006

  9 in total

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