| Phys. Chem. Chem. Phys., 2004,
6 |
|
Additions and corrections
Computer simulation studies on the solvation of aliphatic hydrocarbons in 6.9 M aqueous urea solution |
Daniel Trzesniak, Nico F. A. van der Vegt and Wilfred F. van Gunsteren
Phys. Chem. Chem. Phys., 2004, 6, 697 (DOI: 10.1039/b314105e). Amendment published 3rd August 2004
To our dismay we have found out that in the calculations reported in this paper the Van der Waals parameters for the urea carbon and oxygen were interchanged from the values as given in ref. 20 of the paper (L. J. Smith, H. J. C. Berendsen and W. F. van Gunsteren, J. Phys. Chem. B, 2004, 108, 1065). The correct Van der Waals parameters are listed in Table 1. We have repeated the calculations with the correct urea model and found that the data previously reported are not greatly affected and the conclusions drawn remain unchanged. The main consequence of the swap is that with the correct urea model urea hydrogen bonding to other species is stronger and the solution density increases to approach the appropriate experimental value (ref. 20). Because the convergence of the thermodynamic integrations became slower we extended the simulation times by about 50%. With the correct urea model preferential urea interaction with the hydrocarbons increases slightly. The free energy, solutesolvent energy and solutesolvent entropy calculated with the correct urea model of ref. 20 are presented in Table 2. The values reported in our paper (within parentheses) were kept for comparison. The solvation free energies in 6.9 M urea (column 6) and transfer free energies (last column) are nearly unchanged. Note that both 
Uuv and TSuv (columns 3 and 4) slightly decrease due to the larger solution density. Solutesolvent energy and entropy changes of solute transfer between water and 6.9 M urea (columns 7 and 8) increase in absolute magnitude but also without affecting the previously given interpretation. The radial distribution functions (RDF) presented in Figs. 3 and 5 of the original paper remain practically identical and are not shown. The KirkwoodBuff (KB) analysis shows some numerical changes, because it is extremely sensitive to long range fluctuations in the RDFs. Even tiny bumps in the RDF lead to considerable changes in the KB integrals. Table 3 and Table 4 show the KB analysis for the solutes and the cavities respectively. Even with these numerical changes, the qualitative behaviour remains unchanged and thus the interpretation given before is still valid. The authors would like to apologise for the inconvenience to the reader.
Table 1 Van der Waals parameters for urea. The carbon and oxygen values had been interchanged in the previously published version
Urea atom
|
103C61/2/kJ1/2 mol1/2 nm3
|
103C121/2/kJ1/2 mol1/2 nm6
|
 /nm
|
 /kJ mol1
|
| C | 69.906 | 3.6864 | 0.375 | 0.43933 |
| O | 48.620 | 1.2609 | 0.296 | 0.87870 |
Table 2 Corrected values for the thermodynamic quantities in kJ mol1 (at 298 K and 1 atm) associated with the solvation of aliphatic hydrocarbons. σ denotes the hard-sphere diameter in nm. Uuv: solutesolvent potential energy (eqn. (3)). Suv: solutesolvent entropy (eqns. (2) and (5)). GS: free enthalpy of solvation (eqn. (2)). The values in parentheses are those previously published
Solute
|
|
6.9 M ureawater
|
Transfer
|
Uuv
|
TSuv
|
GS
|
Uuv
|
TSuv
|
GS
|
sim
| sim
| exp
| sim
|
sim
| sim
| exp
| sim
|
| Methane |
0.370 |
16.6 (15.8) |
25.8 (24.6) |
9.1 |
9.2 (8.8) |
3.1 (2.3) |
3.6 (2.4) |
0.8 |
0.5 (0.1) |
| Ethane |
0.438 |
27.7 (25.9) |
34.2 (32.6) |
8.0 |
6.5 (6.7) |
6.0 (4.2) |
5.1 (3.5) |
0.4 |
0.9 (0.7) |
| Propane |
0.506 |
36.6 (34.4) |
43.0 (40.8) |
8.1 |
6.4 (6.4) |
7.3 (5.1) |
5.1 (2.9) |
0.1 |
2.2 (2.2) |
| i-Butane |
0.555 |
45.2 (39.3) |
53.2 (47.4) |
9.2 |
8.0 (8.1) |
10.2 (4.3) |
7.9 (2.1) |
0.5 |
2.3 (2.2) |
| n-Butane |
0.565 |
47.0 (44.0) |
53.0 (50.1) |
8.2 |
6.0 (6.1) |
10.6 (8.6) |
7.9 (6.0) |
0.5 |
2.7 (2.6) |
| Neo-pentane |
0.589 |
50.8 (48.3) |
58.5 (55.8) |
9.8 |
7.7 (7.5) |
10.9 (8.4) |
8.7 (6.0) |
0.7 |
2.2 (2.4) |
Table 3 Corrected values for the hydrocarbon solute first shell coordination numbers nu for urea and nw for water,
KirkwoodBuff excess coordination numbers 
uGSu and
wGSw and preferential binding parameter
= u(GSu GSw). The values in parentheses are those previously published
Solute
|
nu
solute
|
nw
solute
|
uGSu solute
|
wGSw solute
|
solute
|
| Methane |
3.2 (3.3) |
15.3 (15.2) |
0.27 (0.17) |
0.00 (0.77) |
0.27 (0.03) |
| Ethane |
4.8 (4.8) |
15.6 (16.6) |
1.42 (0.13) |
5.96 (2.28) |
2.45 (0.28) |
| Propane |
4.5 (5.3) |
19.2 (18.3) |
0.40 (0.01) |
0.07 (2.77) |
0.41 (0.51) |
| i-Butane |
5.8 (5.8) |
20.8 (20.5) |
0.67 (0.87) |
6.04 (1.08) |
1.76 (0.67) |
| n-Butane |
5.9 (6.6) |
20.3 (20.7) |
0.96 (2.80) |
6.43 (10.99) |
2.12 (4.78) |
| Neo-pentane |
6.2 (6.3) |
21.8 (21.0) |
0.02 (0.33) |
5.13 (5.18) |
0.91 (1.27) |
Table 4 Corrected values for the hydrocarbon solute cavity first shell coordination numbers
nu for urea and nw for water, KirkwoodBuff excess coordination numbers uGSu and
wGSw and preferential binding parameter
= u(GSu GSw). See also caption of Table 3. The values in parentheses are those previously published
Cavity
|
nu cavity
|
nw cavity
|
uGSu cavity
|
wGSw cavity
|
cavity
|
| Methane |
1.8 (2.9) |
17.2 (18.7) |
0.88 (1.69) |
0.23 (1.50) |
0.92 (1.96) |
| Ethane |
2.4 (3.8) |
24.4 (21.4) |
1.46 (1.36) |
0.39 (1.36) |
1.53 (1.11) |
| Propane |
2.5 (3.9) |
30.8 (28.7) |
1.67 (4.10) |
0.40 (4.58) |
1.74 (4.92) |
| i-Butane |
2.6 (4.5) |
33.1 (30.4) |
1.95 (4.70) |
0.46 (4.74) |
2.03 (5.56) |
| n-Butane |
2.8 (4.2) |
34.3 (31.1) |
1.55 (3.88) |
0.29 (2.45) |
1.60 (4.32) |
| Neo-pentane |
3.7 (4.8) |
32.6 (29.7) |
1.11 (5.04) |
0.05 (4.52) |
1.12 (5.86) |
The Royal Society of Chemistry apologises for these errors and any
consequent inconvenience to authors and readers.
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