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New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
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10.1063/1.2801988
/content/aip/journal/jcp/127/20/10.1063/1.2801988
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/20/10.1063/1.2801988

Figures

Image of FIG. 1.
FIG. 1.

(Color online) Schematic representation of the active and auxiliary orbitals in the GHO method.

Image of FIG. 2.
FIG. 2.

(Color online) Alanine dipeptide with atomic labels in the definition of the CHARMM27 parameter set.

Image of FIG. 3.
FIG. 3.

(Color online) Potential energy curves with the STO-3G basis set and the a1 partitioning.

Image of FIG. 4.
FIG. 4.

(Color online) Potential energy curves with the cc-pVDZ basis set and the a1 partitioning.

Image of FIG. 5.
FIG. 5.

(Color online) Interaction energy between the alanine dipeptide and the water molecule as a function of the distance between the water oxygen and 18-CT3 with the A1 conformation and a1 partitioning.

Image of FIG. 6.
FIG. 6.

(Color online) Interaction energy between the alanine dipeptide and the water molecule as a function of the distance between the water oxygen and 13-CT3 with the A2 conformation and a3 partitioning.

Image of FIG. 7.
FIG. 7.

(Color online) Interaction energy between the alanine dipeptide and the water molecule as a function of the distance between the water oxygen and 1-CT3 with the A3 conformation and a2 partitioning.

Image of FIG. 8.
FIG. 8.

(Color online) Interaction energy between the alanine dipeptide and the water molecule as a function of the distance between the water oxygen and 1-CT3 with the A3 conformation and a4 partitioning.

Image of FIG. 9.
FIG. 9.

(Color online) The OPLS-AA parameter set is used. Other parameters are same as those in Fig. 8.

Image of FIG. 10.
FIG. 10.

(Color online) The structure of the cysteine dipeptide.

Image of FIG. 11.
FIG. 11.

(Color online) The structure of the proline dipeptide.

Image of FIG. 12.
FIG. 12.

(Color online) Interaction energy between the cysteine dipeptide and the water molecule as a function of the distance from 13-CT2 to the water oxygen with the C1 conformation and c1 partitioning.

Image of FIG. 13.
FIG. 13.

(Color online) Interaction energy between the cysteine dipeptide and the water molecule as a function of the distance between 17-HS to the water oxygen with the C1 conformation and c2 partitioning.

Image of FIG. 14.
FIG. 14.

(Color online) Interaction energy between the proline dipeptide and the water molecule as a function of the distance from 12-CP2 to the water oxygen with the P1 conformation and p1 partitioning.

Tables

Generic image for table
Table I.

QM/MM partitionings of dipeptides.

Generic image for table
Table II.

Optimized bond length (Å) and angles (degree) for the a1 partitioning with the STO-3G basis set.

Generic image for table
Table III.

Mass-weighted RMSD for the a1 partitioning with the STO-3G basis set.

Generic image for table
Table IV.

Optimized bond length (Å) and angles (degree) for the a1 partitioning with the cc-pVDZ basis set.

Generic image for table
Table V.

Mass-weighted RMSD for the a1 partitioning with the cc-pVDZ basis set.

Generic image for table
Table VI.

Optimized bond length (Å) and angles (degree) for the a2 partitioning with the cc-pVDZ basis set.

Generic image for table
Table VII.

Mass-weighted RMSD for the a2 partitioning with the cc-pVDZ basis set.

Generic image for table
Table VIII.

(Recalculated using the a1 partitioning) The energy values (in hartrees) according to the dihedral angle for a1 partitioning.

Generic image for table
Table IX.

Internal coordinates of the complexes of water and dipeptides.

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/content/aip/journal/jcp/127/20/10.1063/1.2801988
2007-11-26
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/20/10.1063/1.2801988
10.1063/1.2801988
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