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      The Effective Fragment Molecular Orbital Method for Fragments Connected by Covalent Bonds

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      PLoS ONE
      Public Library of Science

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          Abstract

          We extend the effective fragment molecular orbital method (EFMO) into treating fragments connected by covalent bonds. The accuracy of EFMO is compared to FMO and conventional ab initio electronic structure methods for polypeptides including proteins. Errors in energy for RHF and MP2 are within 2 kcal/mol for neutral polypeptides and 6 kcal/mol for charged polypeptides similar to FMO but obtained two to five times faster. For proteins, the errors are also within a few kcal/mol of the FMO results. We developed both the RHF and MP2 gradient for EFMO. Compared to ab initio, the EFMO optimized structures had an RMSD of 0.40 and 0.44 Å for RHF and MP2, respectively.

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          Most cited references46

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          Self-consistent molecular orbital methods. XXIII. A polarization-type basis set for second-row elements

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            Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements

            Several modifications that have been made to the NDDO core-core interaction term and to the method of parameter optimization are described. These changes have resulted in a more complete parameter optimization, called PM6, which has, in turn, allowed 70 elements to be parameterized. The average unsigned error (AUE) between calculated and reference heats of formation for 4,492 species was 8.0 kcal mol−1. For the subset of 1,373 compounds involving only the elements H, C, N, O, F, P, S, Cl, and Br, the PM6 AUE was 4.4 kcal mol−1. The equivalent AUE for other methods were: RM1: 5.0, B3LYP 6–31G*: 5.2, PM5: 5.7, PM3: 6.3, HF 6–31G*: 7.4, and AM1: 10.0 kcal mol−1. Several long-standing faults in AM1 and PM3 have been corrected and significant improvements have been made in the prediction of geometries. Figure Calculated structure of the complex ion [Ta6Cl12]2+ (footnote): Reference value in parenthesis Electronic supplementary material The online version of this article (doi:10.1007/s00894-007-0233-4) contains supplementary material, which is available to authorized users.
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              Distributed multipole analysis, or how to describe a molecular charge distribution

              A.J. Stone (1981)
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                23 July 2012
                : 7
                : 7
                : e41117
                Affiliations
                [1 ]Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
                [2 ]NRI, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
                German Cancer Research Center, Germany
                Author notes

                Conceived and designed the experiments: CS. Performed the experiments: CS. Analyzed the data: CS DF JJ. Contributed reagents/materials/analysis tools: CS. Wrote the paper: CS DF JJ.

                Article
                PONE-D-12-06195
                10.1371/journal.pone.0041117
                3402534
                22844433
                2a0ff050-855c-4407-8017-6ac99235dba9
                Steinmann et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 22 February 2012
                : 19 June 2012
                Page count
                Pages: 11
                Categories
                Research Article
                Biology
                Computational Biology
                Macromolecular Structure Analysis
                Protein Structure
                Chemistry
                Applied Chemistry
                Chemical Properties
                Intermolecular Forces
                Chemical Biology
                Computational Chemistry
                Ab Initio Methods
                Molecular Mechanics
                Quantum Chemistry
                Theoretical Chemistry
                Computer Science
                Computer Modeling

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                Uncategorized

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