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Decomposition of energy and free energy changes by following the flow of work along reaction path
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10.1063/1.3243080
/content/aip/journal/jcp/131/14/10.1063/1.3243080
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/14/10.1063/1.3243080
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

MEP and MFEP of alanine dipeptide isomerization projected onto the Ramachandran plot. A total of 40 replicas are used in the chain for optimizing a cyclic path. Isomerization starts from the configuration (replica 1) by going first through (replica 11) and then (replica 29), and finally back to itself (replica 41). The contour plot is generated via minimized structures of alanine dipeptide in vacuum restrained at different values of and .

Image of FIG. 2.
FIG. 2.

Profiles of potential energy differences and accumulated works along the MEP (Fig. 1) of alanine dipeptide isomerization in vacuum. is the contour length in Ångström and replica 1 is used as the reference state. Indexes of several replicas are placed on the top for clarity.

Image of FIG. 3.
FIG. 3.

Decomposition of accumulated work (potential energy differences) between selected replicas on MEP of alanine dipeptide isomerization in vacuum (Fig. 1). The top figure defines atom names. Superscripts correspond to replica indexes. For example, is the accumulated work of going from replica 1 to replica 16 and is the accumulated work of going from replica 41 to replica 16 in a reversed direction. Replica 41 is equivalent to replica 1 on a cyclic path with 40 replicas.

Image of FIG. 4.
FIG. 4.

The profile of free energy differences along the MFEP (Fig. 1) of alanine dipeptide isomerization in explicit water. is the contour length in Ångström and replica 1 is used as the reference state. The profile of potential energy differences along MEP in vacuum is also shown for comparison. Indexes of several replicas are placed on the top for clarity.

Image of FIG. 5.
FIG. 5.

Decomposition of accumulated work (free energy differences) between selected replicas on the MFEP (Fig. 1) of alanine dipeptide isomerization in explicit water. Correspondent decompositions on MEP in vacuum are also shown for comparison.

Image of FIG. 6.
FIG. 6.

Decomposition of accumulated work (free energy differences) between selected replicas on the MFEP (Fig. 1) of alanine dipeptide isomerization in explicit water.

Image of FIG. 7.
FIG. 7.

Correlation between , [ (free energy difference in explicit water) (potential energy difference in vacuum)], and the averaged number of hydrogen bonds that an alanine dipeptide forms with water in an all-atom MD simulation. See text for the details of simulation.

Image of FIG. 8.
FIG. 8.

(a) Molecular structures of the reaction complex [methyl-carboxylic-acid-methyl ester (MCME)], ethanol, , and seven water molecules) in reactant and TI states; water molecules that are important for causing reaction barrier are also highlighted. (b) Profiles of potential energy differences and accumulated works on the MEP for forming TI during transesterification. Close agreement between potential energy differences and accumulated works can be seen. Profiles of potential energy differences in MEP using only the atoms of reacting cluster (MCME, ethanol, and ), , and atoms of WC, , are shown for comparison.

Image of FIG. 9.
FIG. 9.

Decomposition of the accumulated work between the reactant cluster and TI along MEP (Fig. 8).

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/content/aip/journal/jcp/131/14/10.1063/1.3243080
2009-10-12
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Decomposition of energy and free energy changes by following the flow of work along reaction path
http://aip.metastore.ingenta.com/content/aip/journal/jcp/131/14/10.1063/1.3243080
10.1063/1.3243080
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