Literature DB >> 23187683

Optimization of parameters for semiempirical methods VI: more modifications to the NDDO approximations and re-optimization of parameters.

James J P Stewart1.   

Abstract

Modern semiempirical methods are of sufficiepan class="Chemical">nt accuracy when used inclass="Chemical">pan> the modeling of molecules of the same type as used as reference data in the papan> class="Disease">rameterization. Outside that subset, however, there is an abundance of evidence that these methods are of very limited utility. In an attempt to expand the range of applicability, a new method called PM7 has been developed. PM7 was parameterized using experimental and high-level ab initio reference data, augmented by a new type of reference data intended to better define the structure of parameter space. The resulting method was tested by modeling crystal structures and heats of formation of solids. Two changes were made to the set of approximations: a modification was made to improve the description of noncovalent interactions, and two minor errors in the NDDO formalism were rectified. Average unsigned errors (AUEs) in geometry and ΔHf for PM7 were reduced relative to PM6; for simple gas-phase organic systems, the AUE in bond lengths decreased by about 5% and the AUE in ΔHf decreased by about 10%; for organic solids, the AUE in ΔHf dropped by 60% and the reduction was 33.3% for geometries. A two-step process (PM7-TS) for calculating the heights of activation barriers has been developed. Using PM7-TS, the AUE in the barrier heights for simple organic reactions was decreased from values of 12.6 kcal/mol(-1) in PM6 and 10.8 kcal/mol(-1) in PM7 to 3.8 kcal/mol(-1). The origins of the errors in NDDO methods have been examined, and were found to be attributable to inadequate and inaccurate reference data. This conclusion provides insight into how these methods can be improved.

Entities:  

Year:  2012        PMID: 23187683      PMCID: PMC3536963          DOI: 10.1007/s00894-012-1667-x

Source DB:  PubMed          Journal:  J Mol Model        ISSN: 0948-5023            Impact factor:   1.810


  23 in total

1.  The Cambridge Structural Database: a quarter of a million crystal structures and rising.

Authors:  Frank H Allen
Journal:  Acta Crystallogr B       Date:  2002-05-29

2.  Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation.

Authors:  James J P Stewart
Journal:  J Mol Model       Date:  2003-12-04       Impact factor: 1.810

3.  Nucleophilic attack on phosphate diesters: a density functional study of in-line reactivity in dianionic, monoanionic, and neutral systems.

Authors:  Xabier Lopez; Annick Dejaegere; Fabrice Leclerc; Darrin M York; Martin Karplus
Journal:  J Phys Chem B       Date:  2006-06-15       Impact factor: 2.991

4.  Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs.

Authors:  Petr Jurecka; Jirí Sponer; Jirí Cerný; Pavel Hobza
Journal:  Phys Chem Chem Phys       Date:  2006-03-07       Impact factor: 3.676

5.  Activation energies of pericyclic reactions: performance of DFT, MP2, and CBS-QB3 methods for the prediction of activation barriers and reaction energetics of 1,3-dipolar cycloadditions, and revised activation enthalpies for a standard set of hydrocarbon pericyclic reactions.

Authors:  Daniel H Ess; K N Houk
Journal:  J Phys Chem A       Date:  2005-10-27       Impact factor: 2.781

6.  Density functional theory augmented with an empirical dispersion term. Interaction energies and geometries of 80 noncovalent complexes compared with ab initio quantum mechanics calculations.

Authors:  Petr Jurecka; Jirí Cerný; Pavel Hobza; Dennis R Salahub
Journal:  J Comput Chem       Date:  2007-01-30       Impact factor: 3.376

7.  Seemingly simple stereoelectronic effects in alkane isomers and the implications for Kohn-Sham density functional theory.

Authors:  Stefan Grimme
Journal:  Angew Chem Int Ed Engl       Date:  2006-07-03       Impact factor: 15.336

8.  RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I.

Authors:  Gerd B Rocha; Ricardo O Freire; Alfredo M Simas; James J P Stewart
Journal:  J Comput Chem       Date:  2006-07-30       Impact factor: 3.376

9.  Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

Authors:  Stefan Grimme
Journal:  J Comput Chem       Date:  2006-11-30       Impact factor: 3.376

10.  Accurate interaction energies of hydrogen-bonded nucleic acid base pairs.

Authors:  Jirí Sponer; Petr Jurecka; Pavel Hobza
Journal:  J Am Chem Soc       Date:  2004-08-18       Impact factor: 15.419

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  232 in total

1.  Empirical correction for PM7 band gaps of transition-metal oxides.

Authors:  Xiang Liu; Karl Sohlberg
Journal:  J Mol Model       Date:  2016-01-06       Impact factor: 1.810

2.  Revealing the nature of intermolecular interaction and configurational preference of the nonpolar molecular dimers (H₂)₂, (N₂)₂, and (H₂)(N₂).

Authors:  Tian Lu; Feiwu Chen
Journal:  J Mol Model       Date:  2013-11-01       Impact factor: 1.810

Review 3.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

4.  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

5.  Benchmarking semiempirical and DFT methods for the interaction of thiophene and diethyl sulfide molecules with a Ti(OH)4(H2O) cluster.

Authors:  Alexander V Vorontsov; Panagiotis G Smirniotis
Journal:  J Mol Model       Date:  2017-07-13       Impact factor: 1.810

6.  Modeling and Prediction of Solvent Effect on Human Skin Permeability using Support Vector Regression and Random Forest.

Authors:  Hiromi Baba; Jun-ichi Takahara; Fumiyoshi Yamashita; Mitsuru Hashida
Journal:  Pharm Res       Date:  2015-06-02       Impact factor: 4.200

7.  Nucleic acid reactivity: challenges for next-generation semiempirical quantum models.

Authors:  Ming Huang; Timothy J Giese; Darrin M York
Journal:  J Comput Chem       Date:  2015-05-06       Impact factor: 3.376

8.  Far-infrared spectroscopy of salt penetration into a collagen fiber scaffold.

Authors:  Maya Mizuno; Akira Yamada; Kaori Fukunaga; Hiroaki Kojima
Journal:  J Biol Phys       Date:  2015-03-13       Impact factor: 1.365

9.  Application of semiempirical electronic structure theory to compute the force generated by a single surface-mounted switchable rotaxane.

Authors:  Karl Sohlberg; Gloria Bazargan; Joseph P Angelo; Choongkeun Lee
Journal:  J Mol Model       Date:  2017-01-13       Impact factor: 1.810

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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