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A combined effective fragment potential–fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin
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10.1063/1.3517110
/content/aip/journal/jcp/134/3/10.1063/1.3517110
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/3/10.1063/1.3517110

Figures

Image of FIG. 1.
FIG. 1.

FMO/EFP optimized geometry of hydrated chignolin [colored by chemical elements as light gray (H), dark gray (C), blue (N), and red (O)] optimized at the RHF/6–31G(d) level of theory. Root mean square deviation (RMSD) is calculated from the Cartesian coordinates of all atoms.

Image of FIG. 2.
FIG. 2.

Fragmentation of (a) neutral tetraglycine and (b) zwitterionic tetraglycine. The covalent bonds detached in FMO are shown with two dots.

Image of FIG. 3.
FIG. 3.

(a) The solute structure of hydrated chignolin in Fig. 1, shown with sticks colored by chemical elements (cyan, red, and blue) for solution (FMO/EFP), overlaid with the gas phase optimized structure of chignolin (black) and the RMSD between them. (b) FMO/EFP structure overlaid with that from NMR (black).

Image of FIG. 4.
FIG. 4.

Superposition of the FMO/EFP geometry of hydrated neutral tetraglycine [colored by chemical elements as light gray (H), dark gray (C), blue (N), and red (O)] and the corresponding ab initio QM/EFP geometry, optimized at the RHF/cc-pVDZ level of theory, with water layers, (a) 2.5 Å, (b) 3.0 Å, (c) 3.5 Å, (d) 4.0 Å, and (e) 4.5 Å. RMSD between FMO/EFP and QM/EFP optimized geometries is calculated for all atoms.

Image of FIG. 5.
FIG. 5.

Superposition of the FMO/EFP geometry of the hydrated zwitterionic tetraglycine [colored by chemical elements as light gray (H), dark gray (C), blue (N), and red (O)] and the corresponding ab initio QM/EFP geometry, optimized at the RHF/cc-pVDZ level of theory, with water layers, (a) 2.5 Å, (b) 3.0 Å, (c) 3.5 Å, (d) 4.0 Å, and (e) 4.5 Å. RMSD between FMO/EFP and QM/EFP optimized geometries is calculated for all atoms.

Image of FIG. 6.
FIG. 6.

Superposition of the solute coordinates of the zwitterionic (atoms in black) and neutral (colored by the element) tetraglycine optimized at the RHF/cc-pVDZ level of theory, with water layers, (a) 2.5 Å, (b) 3.0 Å, (c) 3.5 Å, (d) 4.0 Å, and (e) 4.5 Å. RMSD between FMO/EFP for the neutral and zwitterionic geometries is calculated for all solute atoms. Hydrogen atoms are not shown.

Tables

Generic image for table
Table I.

Errors (kJ/mol) in the FMO2/EFP energies of hydrated tetraglycine relative to the corresponding conventional RHF/EFP energies at the RHF/cc-pVDZ level using the respective optimized geometries.

Generic image for table
Table II.

Relative energy contributions (kJ/mol) for FMO-RHF/EFP (solvent by EFP) and the full FMO-RHF (FMO solvent) for hydrated zwitterionic tetraglycine relative to the neutral form: the internal solute ΔE solu and solvent ΔE solv energies, as well as the solute–solvent interaction ΔE solu–solv. The cc-pVDZ basis set is used. The number of water molecules is shown in parentheses.

Generic image for table
Table III.

Interaction energies (kJ/mol) between the zwitterionic tetraglycine and water molecules forming hydrogen bonds with the COO group with the cc-pVDZ basis set (extracted from the large fully optimized structures with the thickness of water layers given in angstrom). The number of water molecules directly interacting with the carboxyl group is shown in parentheses. Below, “full” means that solvent was treated as FMO fragments.

Generic image for table
Table IV.

Hydrogen bond lengths (angstrom) between the COO group of the hydrated zwitterionic tetraglycine and EFP water molecules (optimized with cc-pVDZ). There are 5–6 hydrogen bonds formed between COO and solvent. The numbers in parentheses are the intramolecular hydrogen bond lengths of the solute. The superscripts denote one of the two oxygen atoms of the COO group, shown here to distinguish hydrogen bonds.

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/content/aip/journal/jcp/134/3/10.1063/1.3517110
2011-01-20
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: A combined effective fragment potential–fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/3/10.1063/1.3517110
10.1063/1.3517110
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