Literature DB >> 20711513

An implicit solvent model for SCC-DFTB with Charge-Dependent Radii.

Guanhua Hou1, Xiao Zhu, Qiang Cui.   

Abstract

Motivated by the need of rapidly exploring the potential energy surface of chemical reactions that involve highly charged species, we have developed an implicit solvent model for the approximate density functional theory, SCC-DFTB. The solvation free energy is calculated using the popular model that employs Poisson-Boltzmann for electrostatics and a surface-area term for non-polar contributions. To balance the treatment of species with different charge distributions, we make the atomic radii that define the dielectric boundary and solute cavity depend on the solute charge distribution. Specifically, the atomic radii are assumed to be linearly dependent on the Mulliken charges and solved self-consistently together with the solute electronic structure. Benchmark calculations indicate that the model leads to solvation free energies of comparable accuracy to the SM6 model (especially for ions), which requires much more expensive DFT calculations. With analytical first derivatives and favorable computational speed, the SCC-DFTB based solvation model can be effectively used, in conjunction with high-level QM calculations, to explore the mechanism of solution reactions. This is illustrated with a brief analysis of the hydrolysis of mono-methyl mono-phosphate ester (MMP) and tri-methyl mono-phosphate ester (TMP). Possible future improvements are also briefly discussed.

Entities:  

Year:  2010        PMID: 20711513      PMCID: PMC2918909          DOI: 10.1021/ct1001818

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  37 in total

1.  Reactivity of phosphate monoester monoanions in aqueous solution. 1. Quantum mechanical calculations support the existence of "anionic zwitterion" MeO(+)(H)PO(3)(2-) as a key intermediate in the dissociative hydrolysis of the methyl phosphate anion.

Authors:  Marc Bianciotto; Jean-Claude Barthelat; Alain Vigroux
Journal:  J Am Chem Soc       Date:  2002-06-26       Impact factor: 15.419

2.  Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges.

Authors:  Aleksandr V Marenich; Ryan M Olson; Casey P Kelly; Christopher J Cramer; Donald G Truhlar
Journal:  J Chem Theory Comput       Date:  2007-11       Impact factor: 6.006

Review 3.  Mechanisms and free energies of enzymatic reactions.

Authors:  Jiali Gao; Shuhua Ma; Dan T Major; Kwangho Nam; Jingzhi Pu; Donald G Truhlar
Journal:  Chem Rev       Date:  2006-08       Impact factor: 60.622

4.  Charge-dependent model for many-body polarization, exchange, and dispersion interactions in hybrid quantum mechanical/molecular mechanical calculations.

Authors:  Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2007-11-21       Impact factor: 3.488

5.  Application of the computationally efficient self-consistent-charge density-functional tight-binding method to magnesium-containing molecules.

Authors:  Zheng-Li Cai; Philip Lopez; Jeffrey R Reimers; Qiang Cui; Marcus Elstner
Journal:  J Phys Chem A       Date:  2007-06-08       Impact factor: 2.781

6.  The H2O2+OH-->HO2+H2O reaction in aqueous solution from a charge-dependent continuum model of solvation.

Authors:  Bojana Ginovska; Donald M Camaioni; Michel Dupuis
Journal:  J Chem Phys       Date:  2008-07-07       Impact factor: 3.488

7.  Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes.

Authors:  Demian Riccardi; Patricia Schaefer; Yang Yang; Haibo Yu; Nilanjan Ghosh; Xavier Prat-Resina; Peter König; Guohui Li; Dingguo Xu; Hua Guo; Marcus Elstner; Qiang Cui
Journal:  J Phys Chem B       Date:  2006-04-06       Impact factor: 2.991

8.  Description of phosphate hydrolysis reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) theory. 1. Parameterization.

Authors:  Yang Yang; Haibo Yu; Darrin York; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2008       Impact factor: 6.006

9.  Generalized born model with a simple smoothing function.

Authors:  Wonpil Im; Michael S Lee; Charles L Brooks
Journal:  J Comput Chem       Date:  2003-11-15       Impact factor: 3.376

10.  Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.

Authors:  Shina C L Kamerlin; Maciej Haranczyk; Arieh Warshel
Journal:  Chemphyschem       Date:  2009-05-11       Impact factor: 3.102

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  10 in total

1.  VR-SCOSMO: A smooth conductor-like screening model with charge-dependent radii for modeling chemical reactions.

Authors:  Erich R Kuechler; Timothy J Giese; Darrin M York
Journal:  J Chem Phys       Date:  2016-04-28       Impact factor: 3.488

2.  Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase.

Authors:  Quin H Hu; Murphi T Williams; Irina Shulgina; Carl J Fossum; Katelyn M Weeks; Lauren M Adams; Clorice R Reinhardt; Karin Musier-Forsyth; Sanchita Hati; Sudeep Bhattacharyya
Journal:  ACS Catal       Date:  2020-08-14       Impact factor: 13.084

3.  Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.

Authors:  Xiu Yang; Huan Lei; Peiyuan Gao; Dennis G Thomas; David L Mobley; Nathan A Baker
Journal:  J Chem Theory Comput       Date:  2018-01-29       Impact factor: 6.006

4.  A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions.

Authors:  Guanhua Hou; Xiao Zhu; Marcus Elstner; Qiang Cui
Journal:  J Chem Theory Comput       Date:  2012-11-13       Impact factor: 6.006

5.  QM/MM analysis suggests that Alkaline Phosphatase (AP) and nucleotide pyrophosphatase/phosphodiesterase slightly tighten the transition state for phosphate diester hydrolysis relative to solution: implication for catalytic promiscuity in the AP superfamily.

Authors:  Guanhua Hou; Qiang Cui
Journal:  J Am Chem Soc       Date:  2011-12-08       Impact factor: 15.419

6.  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

7.  Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.

Authors:  Daniel Roston; Qiang Cui
Journal:  J Am Chem Soc       Date:  2016-08-31       Impact factor: 15.419

8.  Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

Authors:  Guanhua Hou; Qiang Cui
Journal:  J Am Chem Soc       Date:  2013-07-09       Impact factor: 15.419

9.  Eliminating Transition State Calculations for Faster and More Accurate Reactivity Prediction in Sulfa-Michael Additions Relevant to Human Health and the Environment.

Authors:  Piers A Townsend; Elliot H E Farrar; Matthew N Grayson
Journal:  ACS Omega       Date:  2022-07-21

10.  Field-SEA: a model for computing the solvation free energies of nonpolar, polar, and charged solutes in water.

Authors:  Libo Li; Christopher J Fennell; Ken A Dill
Journal:  J Phys Chem B       Date:  2013-12-13       Impact factor: 2.991

  10 in total

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