SUPPMAT1018.DOC 463KB Jun 05 2011 09:30:50 PM

Supplementary Material for “Calculation of
Relative Solvation Free Energy Differences by
Thermodynamic Perturbation Method:
Dependence of the Free Energy Results on the
Simulation Length” by M. Rami Reddy and
Mark D. Erion

Figure Captions:

Figure 6:

Plot of accumulated relative solvation free energy change as a

function of  for the transformation of 1,1,1-trifluoroacetone ( =1) to
acetone ( =0). These calculated results were obtained using different MD
simulation lengths (153, 306, 510, 714 and 1530 ps) and the same starting
configurations.

Figure 7:

Plot of accumulated relative solvation free energy change as a

function of  for the transformation of 1,1,1-trichloroacetone ( =1) to
acetone ( =0). These calculated results were obtained using different MD
simulation lengths (153, 306, 510, 714 and 1530 ps) and the same starting
configurations.

Figure 8:

Plot of accumulated relative solvation free energy change as a

function of  for the transformation of 2,3-butanedione ( =1) to acetone (
=0). These calculated results were obtained using different MD simulation
lengths (153, 306, 510, 714 and 1530 ps) and the same starting
configurations.

Figure 9:

Plot of accumulated relative solvation free energy change as a

function of  for the transformation of formaldehyde hydrate ( =1) to

formaldehyde ( =0). These calculated results were obtained using different
MD simulation lengths (153, 306, 510, 714 and 1530 ps) and the same
starting configurations.

Table IV: List of final atomic coordinates and CHELPG charges for the
structures of compounds 1 –9 following energy optimization at the 6-31G**
basis set level.
Acetaldehyde
ATOM
1 H ACT

1

X
Y
Z
-1.148 -1.225 -.001 .1230

ATOM

2 C ACT

1

-1.162

-.143

.000 -.3753

ATOM

3 C ACT

1

.241

.396

.000 .6128

ATOM

4 H ACT

1

.322 1.490

.000 -.0358

ATOM

5 H ACT

1

-1.695

.221 -.874 .1014

ATOM

6 H ACT

1

-1.695

.220

.875 .1015

ATOM

7 O ACT

1

1.218

-.278

.000 -.5277

Acetone
ATOM
1 H ACE

1

2.133

.068

Z
q
-.002 .1409

ATOM

2 C ACE

1

1.288 -.607

.000 -.5152

ATOM

3 C ACE

1

ATOM

4 C ACE

ATOM

X

Y

.000

.187

.000 .8032

1

-1.288 -.607

.000 -.5206

5 H ACE

1

1.334 -1.251

-.874 .1314

ATOM

6 H ACE

1

1.335 -1.249

.875 .1315

ATOM

7 O ACE

1

.000 1.379

.000 -.5787

ATOM

8 H ACE

1

-2.133

.067

.001 .1434

ATOM

9 H ACE

1

-1.333 -1.251

.874 .1321

ATOM

10 H ACE

1

-1.335 -1.249 -.875

Pyruvic Acid

X

Y

.1321
Z

ATOM

1 H PYR

1

-2.737

-.271

.000 .1409

ATOM

2 C PYR

1

-1.769

-.750

.000 -.4724

ATOM

3 C PYR

1

-.700

.307

.000 .5988

ATOM

4 C PYR

1

.745

-.219

.000 .6967

ATOM

5 O PYR

1

-.903 1.474

.000 -.4802

ATOM

6 H PYR

1

-1.664 -1.386

.872 .1376

ATOM

7 H PYR

1

-1.665-1.387

-.871 .1376

ATOM

8 O PYR

1

1.645

.739

q

.000 -.6636

q

ATOM

9 O PYR

1

ATOM

10 H PYR

1

1,1,1-Trifluoroacetone

.996 -1.379
2.508

.000 -.5818

.346

X

.000

.4863

Y

Z

q
.1393

ATOM

1 H CF3

1

-2.848

-.484

.000

ATOM

2 C CF3

1

-1.834

-.855

.000 -.3728

ATOM

3 C CF3

1

-.885

.312

.000 .5332

ATOM

4 C CF3

1

.608

-.043

.000 .6455

ATOM

5 F CF3

1

1.370 1.019

.000 -.2185

ATOM

6 F CF3

1

.898 -.769 -1.068 -.2324

ATOM

7 F CF3

1

.898 -.769 1.068 -.2324

ATOM

8 O CF3

1

-1.206 1.451

.000 -.4801

ATOM

9 H CF3

1

-1.665 -1.472

.875 .1091

ATOM

10 H CF3

1

-1.665 -1.472 -.876 .1091

1,1,1-Trichloroacetone

X

Y

Z

q

ATOM

1 H CCL

1

-.941

.024 -1.778

.1574

ATOM

2 C CCL

1

-1.134

.017 -.713

.3893

ATOM

3 C CCL

1

ATOM

4 Cl CCL

1

ATOM

5 Cl CCL

1

1.152 1.463

ATOM

6 Cl CCL

1

1.153 -1.418 -.565 .0491

ATOM

7 O CCL

1

-1.786 1.150 -.291 -.6057

ATOM

8 O CCL

1

-1.852 -1.121

ATOM

9 H CCL

1

-2.589 1.249 -.779 .4526

1

-2.100 -1.143

ATOM

10 H

CCL

.252
.050

2,3-Butanedione

.004 -.014 -.4260
-.073 1.747 .0792

X

-.451 .0620

-.454 -.6081
.460 .4503
Y

Z

ATOM

1 H BUT

1

-2.790 -.076

.000 .1485

ATOM

2 C BUT

1

-1.900

.538

.000 -.4767

ATOM

3 C BUT

1

-.686 -.349

.000 .5827

ATOM

4 C BUT

1

.686

.349

.000

.5875

q

ATOM

5 O BUT

1

-.728 -1.539

ATOM

6 H BUT

1

-1.890 1.183 -.871 .1336

ATOM

7 H BUT

1

-1.890 1.184

.871 .1336

ATOM

8 C

BUT

1

1.900

-.538

.000 -.5068

ATOM

9 O

BUT

1

.728 1.539

.000 -.5211

ATOM

10 H BUT

1

ATOM

11 H BUT

1

1.890 -1.184 -.871 .1412

ATOM

12 H BUT

1

1.891 -1.183

2.790

Cyclopropanone

X

.000 -.5212

.076

Y

.000 .1574
.871 .1412
Z

q

ATOM

1 H CPR

1

ATOM

2 C CPR

1

ATOM

3 C CPR

1

-.384

.000

.000 .6462

ATOM

4 C CPR

1

.852

.779

.000 -.4167

ATOM

5 H CPR

1

1.148 -1.277

.908 .1761

ATOM

6 H CPR

1

1.148 1.277

.908 .1761

ATOM

7 H CPR

1

1.148 1.278 -.908 .1762

ATOM

8 O CPR

1

Formaldehyde

1.148 -1.278 -.908 .1762
.852 -.779

-1.564
X

.000 -.4167

.000

Y

.000 -.5174

Z

ATOM

1 H FMD

1

ATOM

2 C FMD

1

.520

.000

.000 .4465

ATOM

3 O FMD

1

-.665

.000

.000 -.4609

ATOM

4 H FMD

1

1.101

.926

.000

Formaldehyde Hydrate

1.101 -.926

q

X

Y

-.564 1.281

.000 .0072

.0072
Z

q

ATOM

1 H FMH

1

.022 .0140

ATOM

2 C FMH

1

-1.298

.476

.018 .4789

ATOM

3 H FMH

1

-2.350

.769

.038 .0054

ATOM

4 O FMH

1

-.972 -.667 -.005 -.4771

ATOM

5 O FMH

1

1.867 .134 -.078 -.8061

ATOM

6 H FMH

1

1.134 -.463 -.126 .3888

ATOM

7 H FMH

1

2.412 -.178

.625 .3961

Equilibrium geometries for all 9 compounds were obtained from ab initio
optimized coordinates (Table IV). Partial atomic charges were obtained
using CHELPG to fit the charges to the quantum mechanical electrostatic
potential computed from ab initio 6-31G** wave functions calculated with
Gaussian 94 (Table IV). Force constants and Van der waal’s parameters for
all the atoms were obtained from similar chemical species within the
AMBER database, except the force field parameters related to the following
atoms.

Van der waal’s parameters
Compound name
1,1,1-Trifluoroacetone
1,1,1-Trichlroacetone

Atom Name
F

1.70
Cl

kcal/mol

R*(Å)
0.08

0.25 

2.07

Torsional parameters
Torsion

Vn /2



n

HO – OH – CT – OH

0.57

0.0

3

HC – CT – OH – OH

0.20

0.0

3

O=C–C=O

1.75

180.0

2