Literature DB >> 27074247

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.

Anders S Christensen1, Tomáš Kubař, Qiang Cui1, Marcus Elstner.   

Abstract

Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.

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Year:  2016        PMID: 27074247      PMCID: PMC4867870          DOI: 10.1021/acs.chemrev.5b00584

Source DB:  PubMed          Journal:  Chem Rev        ISSN: 0009-2665            Impact factor:   60.622


  217 in total

1.  Generalized Gradient Approximation Made Simple.

Authors: 
Journal:  Phys Rev Lett       Date:  1996-10-28       Impact factor: 9.161

2.  Quantum mechanics simulation of protein dynamics on long timescale.

Authors:  H Liu; M Elstner; E Kaxiras; T Frauenheim; J Hermans; W Yang
Journal:  Proteins       Date:  2001-09-01

3.  PDDG/PM3 and PDDG/MNDO: improved semiempirical methods.

Authors:  Matthew P Repasky; Jayaraman Chandrasekhar; William L Jorgensen
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

4.  A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

Authors:  Kaushik Raha; Kenneth M Merz
Journal:  J Am Chem Soc       Date:  2004-02-04       Impact factor: 15.419

5.  Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution.

Authors:  Hao Hu; Marcus Elstner; Jan Hermans
Journal:  Proteins       Date:  2003-02-15

6.  Deriving effective mesoscale potentials from atomistic simulations.

Authors:  Dirk Reith; Mathias Pütz; Florian Müller-Plathe
Journal:  J Comput Chem       Date:  2003-10       Impact factor: 3.376

7.  Optimization of parameters for semiempirical methods IV: extension of MNDO, AM1, and PM3 to more main group elements.

Authors:  James J P Stewart
Journal:  J Mol Model       Date:  2004-03-02       Impact factor: 1.810

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

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

9.  Intercalators. 1. Nature of stacking interactions between intercalators (ethidium, daunomycin, ellipticine, and 4',6-diaminide-2-phenylindole) and DNA base pairs. Ab initio quantum chemical, density functional theory, and empirical potential study.

Authors:  David Reha; Martin Kabelác; Filip Ryjácek; Jirí Sponer; Judit E Sponer; Marcus Elstner; Sándor Suhai; Pavel Hobza
Journal:  J Am Chem Soc       Date:  2002-04-03       Impact factor: 15.419

10.  Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: applications to structural and energetic analysis.

Authors:  Marcus Elstner; Qiang Cui; Petra Munih; Efthimios Kaxiras; Thomas Frauenheim; Martin Karplus
Journal:  J Comput Chem       Date:  2003-04-15       Impact factor: 3.376

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  46 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.  Unravelling the molecular effect of ocellatin-1, F1, K1 and S1, the frog-skin antimicrobial peptides to enhance its therapeutics-quantum and molecular mechanical approaches.

Authors:  P Chandra Sekar; D Meshach Paul; E Srinivasan; R Rajasekaran
Journal:  J Mol Model       Date:  2021-01-03       Impact factor: 1.810

4.  Perspective: Quantum mechanical methods in biochemistry and biophysics.

Authors:  Qiang Cui
Journal:  J Chem Phys       Date:  2016-10-14       Impact factor: 3.488

5.  Chirality-induced spin polarization places symmetry constraints on biomolecular interactions.

Authors:  Anup Kumar; Eyal Capua; Manoj K Kesharwani; Jan M L Martin; Einat Sitbon; David H Waldeck; Ron Naaman
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-22       Impact factor: 11.205

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.  Improvement of d-d interactions in density functional tight binding for transition metal ions with a ligand field model: assessment of a DFTB3+U model on nickel coordination compounds.

Authors:  Stepan Stepanovic; Rui Lai; Marcus Elstner; Maja Gruden; Pablo Garcia-Fernandez; Qiang Cui
Journal:  Phys Chem Chem Phys       Date:  2020-12-07       Impact factor: 3.676

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.  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

10.  Thermodynamics study of biokerosene from coconut and palm kernel oils and JP-8 aircraft fuels in the gas phase by the DFT method.

Authors:  Edimilson S Moraes; Gustavo F Reis; Jorddy Cruz; Klaus Cozzolino; Abel F G Neto; Tarciso Andrade-Filho; Antonio M J C Neto
Journal:  J Mol Model       Date:  2020-03-16       Impact factor: 1.810

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