Literature DB >> 27782516

Perspective: Quantum mechanical methods in biochemistry and biophysics.

Qiang Cui1.   

Abstract

In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.

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Year:  2016        PMID: 27782516      PMCID: PMC5065567          DOI: 10.1063/1.4964410

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  185 in total

1.  Theoretical perspectives on proton-coupled electron transfer reactions.

Authors:  S Hammes-Schiffer
Journal:  Acc Chem Res       Date:  2001-04       Impact factor: 22.384

2.  Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins.

Authors:  C Clementi; H Nymeyer; J N Onuchic
Journal:  J Mol Biol       Date:  2000-05-19       Impact factor: 5.469

3.  Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitations.

Authors:  S Mukamel
Journal:  Annu Rev Phys Chem       Date:  2000       Impact factor: 12.703

Review 4.  Quantum mechanical methods for enzyme kinetics.

Authors:  Jiali Gao; Donald G Truhlar
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

Review 5.  Great metalloclusters in enzymology.

Authors:  Douglas C Rees
Journal:  Annu Rev Biochem       Date:  2001-11-09       Impact factor: 23.643

6.  Quantum chemistry can locally improve protein crystal structures.

Authors:  Ulf Ryde; Kristina Nilsson
Journal:  J Am Chem Soc       Date:  2003-11-26       Impact factor: 15.419

7.  Many-body force field models based solely on pairwise Coulomb screening do not simultaneously reproduce correct gas-phase and condensed-phase polarizability limits.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2004-06-01       Impact factor: 3.488

8.  Direct calculation of electron density in density-functional theory.

Authors: 
Journal:  Phys Rev Lett       Date:  1991-03-18       Impact factor: 9.161

9.  Density-functional theory-symmetry-adapted intermolecular perturbation theory with density fitting: a new efficient method to study intermolecular interaction energies.

Authors:  A Hesselmann; G Jansen; M Schütz
Journal:  J Chem Phys       Date:  2005-01-01       Impact factor: 3.488

Review 10.  Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis.

Authors:  Richard A Friesner; Victor Guallar
Journal:  Annu Rev Phys Chem       Date:  2005       Impact factor: 12.703

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  19 in total

1.  Benchmarking density functional tight binding models for barrier heights and reaction energetics of organic molecules.

Authors:  Maja Gruden; Ljubica Andjeklović; Akkarapattiakal Kuriappan Jissy; Stepan Stepanović; Matija Zlatar; Qiang Cui; Marcus Elstner
Journal:  J Comput Chem       Date:  2017-07-24       Impact factor: 3.376

Review 2.  Molecular Dynamics Simulations of Membrane Permeability.

Authors:  Richard M Venable; Andreas Krämer; Richard W Pastor
Journal:  Chem Rev       Date:  2019-02-12       Impact factor: 60.622

3.  Exploring the applicability of density functional tight binding to transition metal ions. Parameterization for nickel with the spin-polarized DFTB3 model.

Authors:  Milena Vujović; Mioy Huynh; Sebastian Steiner; Pablo Garcia-Fernandez; Marcus Elstner; Qiang Cui; Maja Gruden
Journal:  J Comput Chem       Date:  2018-10-09       Impact factor: 3.376

4.  Accurate Backbone 13 C and 15 N Chemical Shift Tensors in Galectin-3 Determined by MAS NMR and QM/MM: Details of Structure and Environment Matter.

Authors:  Jodi Kraus; Rupal Gupta; Manman Lu; Angela M Gronenborn; Mikael Akke; Tatyana Polenova
Journal:  Chemphyschem       Date:  2020-06-04       Impact factor: 3.102

5.  Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Authors:  Rommie E Amaro; Adrian J Mulholland
Journal:  Nat Rev Chem       Date:  2018-04-11       Impact factor: 34.035

6.  Multi-level free energy simulation with a staged transformation approach.

Authors:  Shingo Ito; Qiang Cui
Journal:  J Chem Phys       Date:  2020-07-28       Impact factor: 3.488

7.  Differences in the Nature of the Phosphoryl Transfer Transition State in Protein Phosphatase 1 and Alkaline Phosphatase: Insights from QM Cluster Models.

Authors:  Rui Lai; Qiang Cui
Journal:  J Phys Chem B       Date:  2020-10-08       Impact factor: 2.991

8.  Intermolecular interactions in the condensed phase: Evaluation of semi-empirical quantum mechanical methods.

Authors:  Anders S Christensen; Jimmy C Kromann; Jan H Jensen; Qiang Cui
Journal:  J Chem Phys       Date:  2017-10-28       Impact factor: 3.488

9.  Emerging Diversity in Lipid-Protein Interactions.

Authors:  Valentina Corradi; Besian I Sejdiu; Haydee Mesa-Galloso; Haleh Abdizadeh; Sergei Yu Noskov; Siewert J Marrink; D Peter Tieleman
Journal:  Chem Rev       Date:  2019-02-13       Impact factor: 60.622

10.  Analysis of Density Functional Tight Binding with Natural Bonding Orbitals.

Authors:  Xiya Lu; Juan Duchimaza-Heredia; Qiang Cui
Journal:  J Phys Chem A       Date:  2019-08-15       Impact factor: 2.781

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