A Test of Improved Force Field Parameters for Urea: Molecular-Dynamics Simulations
of Urea Crystals
Gül Altınbaş Özpınar,a,b,c,# Frank R. Beierlein,b,c,# Wolfgang Peukert,c,d Dirk Zahn,b,c and
Timothy Clark*,b,c
a
Department of Chemistry, Natural Sciences, Architecture and Engineering Faculty, Bursa
Technical University, Osmangazi, 16000 Bursa, Turkey.
b
Computer-Chemie-Centrum and Interdisciplinary Center for Molecular Materials,
Friedrich-Alexander Universität Erlangen-Nürnberg, Nägelsbachstr. 25, 91052 Erlangen,
Germany.
c
Excellence Cluster Engineering of Advanced Materials, Friedrich-Alexander-Universität
Erlangen-Nürnberg, Nägelsbachstr. 49b 91052 Erlangen, Germany.
d
Lehrstuhl für Feststoff- und Grenzflächenverfahrenstechnik, Friedrich-AlexanderUniversität Erlangen-Nürnberg, Cauerstraße 4, 91058 Erlangen, Germany.
#
These authors contributed equally to this work
Table of Contents
1.
Force field parameters for urea used in this study...........................................
2.
RMSD, RMSF, energies and temperature during the initial MD simulations
of cubic, rectangular prismatic, and sheet urea crystals at 300 K in vacuo.....
3.
S3
S4
Average total energies of urea monomer and crystals in cubic, rectangular
prismatic, and sheet shapes obtained from the initial MD simulations in
vacuo at 300 K.................................................................................................
4.
Total and potential energies obtained from the “instantaneous heating” MD
simulation at 382 K..........................................................................................
5.
S9
RMSD and orientational order parameter obtained from the “instantaneous
heating” MD simulations at 300 and 350 K.....................................................
6.
S8
S10
RMSF and orientational order parameter mapped on the initial coordinates
of all C atoms in the system, as obtained from the “instantaneous heating”
MD simulation at 382 K..................................................................................
S12
S1
7.
Temperature and energy plots obtained from the “gradual heating”
simulations.......................................................................................................
8.
Snapshots from the MD simulation using the “gradual heating” protocol
and a heating rate of 20 K ns1........................................................................
9.
S14
S21
RMSD and orientational order parameter from the MD simulation using the
“gradual heating” protocol and a heating rate of 5 K ns-1...............................
S22
S2
1. Force field parameters for urea used in this study
Table S1. Improved general AMBER force field parameters from the previous study. [14]
Bond Parameters
Kra
rb
656 1.250
424 1.383
434 1.010
Angle Parametres
angle
K θc
θd
n –c –o
80 120.9
c –n –hn
30 120.0
hn –n –hn
35 120.0
n –c –n
70 118.6
Dihedral Parameters
torsion
no. of pathse Vn/2f
γg
nh
hn –n –c –o
1
2.5 180 -2
hn –n –c –o
1
2.0
0
1
Improper Dihedral Parameters
torsion
Vn/2f
γg
nh
n –n –c –o
10.5 180
2
c –hn –n –hn
1.1 180
2
Nonbonding Parameters
atom type
R*i
εj
hn
0.6000
0.0157
o
1.6612
0.2100
c
1.9080
0.0860
n
1.8240
0.1700
a
1 2 b

Force constant (kcal mol Å ). Bond distance (Å).
c
Force constant (kcal mol1 radian2). d Angle (deg.).
e
Number of bond paths that the total Vn/2 is divided into.
f
Magnitude of torsion (kcal mol1).
g
Phase offset (°).
h
The periodicity of the torsion. A negative value is not used in the computation but signifies
more than one component around a given bond.
i
(Å).
j
(kcal mol1).
bond
c –o
c -n
hn-n
Table S2. RESP charges used. [14]
Atoms RESP
0.884
C
-0.660
O
-0.888
N
0.388
H
S3
2. RMSD, RMSF, energies and temperature during the initial MD simulations of cubic,
rectangular, and flat urea crystals at 300 K in vacuo
2.5
330
Cubic
Cubic
Rectengular
Rectengular
Flat
Flat
320
2
Temperature (K)
310
RMSD
1.5
1
300
290
280
270
0.5
260
250
0
0
1000
2000
3000
4000
5000
6000
7000
8000
-150000
9000
0
10000
1000
2000
3000
4000
5000
6000
7000
8000
-150000
Cubic
Flat
-170000
Potential Energy (kcal/mol)
Total Energy (kcal/mol)
Rectengular
-160000
Flat
-170000
10000
Cubic
Rectengular
-160000
9000
-180000
-190000
-200000
-210000
-220000
-180000
-190000
-200000
-210000
-220000
-230000
-230000
-240000
-240000
-250000
-250000
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
0
1000
2000
3000
4000
5000
6000
7000
8000
9000
10000
Figure S1. RMSD (top left), total energy (bottom left), potential energy (bottom right) and
temperature (top right) during the initial simulations of cubic, rectangular prismatic, and sheet
urea crystals in vacuo at 300 K.
S4
Figure S2. Plots of the root-mean-square fluctuation [Å] (RMSF, top left, calculated for the
heavy atoms of each urea molecule), mean van der Waals (bottom left), electrostatic (top
right) and total interaction energies (bottom right) [kcal mol-1] of each urea molecule with the
rest of the system, as obtained from the initial simulations of the cubic urea crystal at 300 K in
vacuo. Values were mapped on the geometric centers of the average coordinates of the heavy
atoms in each urea molecule. The [001] surface corresponds to the “upper” and “lower”
crystal boundaries (plane with constant c-values).
S5
Figure S3. Plots of the root-mean-square fluctuation [Å] (RMSF, top, calculated for the
heavy atoms of each urea molecule), mean van der Waals, electrostatic and total interaction
energies (bottom) [kcal mol-1] of each urea molecule with the rest of the system, as obtained
from the initial simulations of the rectangular prismatic urea crystal at 300 K in vacuo. Values
were mapped on the geometric centers of the average coordinates of the heavy atoms in each
urea molecule.
S6
FigureS4 Plots of the root-mean-square fluctuation [Å] (RMSF, top left, calculated for the
heavy atoms of each urea molecule), mean electrostatic (top right), van der Waals (bottom
left) and total interaction energies (bottom right) [kcal mol-1] of each urea molecule with the
rest of the system, as obtained from the initial simulations of the sheet urea crystal at 300 K in
vacuo. The b coordinate axis was scaled by a factor of 10 to improve clarity. Values were
mapped on the geometric centers of the average coordinates of the heavy atoms in each urea
molecule.
S7
3. Average total energies of urea monomer and crystals in cubic, rectangular prismatic,
and sheet shapes obtained from the initial MD simulations in vacuo at 300 K
Table S3. Average total energies [kcal mol-1] of urea monomer and crystals in cubic,
rectangular prismatic, and sheet shapes obtained from the MD simulations in vacuo at 300K
Number of urea molecules
Sheet
Rectangular
prismatic
Cubic
Monomer
Average Etotal
1220
1125
-201353.9636
-196506.9957
1152
1
-203462.7163
-153.7973
S8
4. Total and potential energies obtained from the “instantaneous heating” MD
simulation at 382 K
Figure S5. Plot of total (green) and potential (black) energies obtained from the
“instantaneous heating” MD simulation at 382 K.
S9
5. RMSD and orientational order parameter obtained from the “instantaneous heating”
MD simulations at 300 and 350 K.
Figure S6. RMSD (left) and orientational order parameter (right) calculated for all C atoms
obtained from the “instantaneous heating” protocol MD simulation at 300 K. The first 500 ps
(restrained MD, heat-up) were omitted for the analyses.
S10
Figure S7. RMSD (left) and orientational order parameter (right) calculated for all C atoms
obtained from the “instantaneous heating” protocol MD simulation at 350 K. The first 500 ps
(restrained MD, heat-up) were omitted for the analyses.
S11
6. RMSF and orientational order parameter mapped on the initial coordinates of all C
atoms in the system, as obtained from the “instantaneous heating” MD simulation at 382
K.
Figure S8. RMSF (left) and orientational order parameter (right) calculated for all C atoms
mapped on the initial coordinates of all C atoms in the system, as obtained from the
“instantaneous heating” protocol MD simulation at 382 K. The viewing angle corresponds to
“side view” in Figure 4 in the main text. The first 500 ps (restrained MD, heat-up) were
omitted for the analyses.
S12
Figure S9. RMSF (left) and orientational order parameter (right) calculated for all C atoms
mapped on the initial coordinates of all C atoms in the system, as obtained from the
“instantaneous heating” protocol MD simulation at 382 K. The viewing angle corresponds to
“side view rotated by 45°” in Figure 4 in the main text. The first 500 ps (restrained MD, heatup) were omitted for the analyses.
S13
7. Temperature and energy plots from the “gradual heating” simulations
gradual heating (30K/ns)
Figure S10. Temperature vs. time in the “gradual heating” simulation with a heating rate of
30 K/ns.
S14
gradual heating (20K/ns)
Figure S11. Temperature vs. time in the “gradual heating” simulation with a heating rate of
20 K/ns.
S15
gradual heating (10K/ns)
Figure S12. Temperature vs. time in the “gradual heating” simulation with a heating rate of
10 K/ns.
S16
gradual heating (5K/ns)
Figure S13. Temperature vs. time in the “gradual heating” simulation with a heating rate of 5
K/ns.
S17
melting interval
7.4 ns
405.5 K
7.85 ns
419 K
gradual heating (30 K/ns)
Figure S14. Total (green) and potential energies (black) in the “gradual heating” simulation
with a heating rate of 30 K/ns.
S18
melting interval
9.5 ns
403 K
10.0 ns
413 K
gradual heating (20 K/ns)
Figure S15. Total (green) and potential energies (black) in the “gradual heating” simulation
with a heating rate of 20 K/ns.
S19
melting interval
15.9 ns
403 K
16.45 ns
408.5 K
gradual heating (10 K/ns)
Figure S16. Total and potential energies (black) in the “gradual heating” simulation with a
heating rate of 10 K/ns.
S20
8. Snapshots from the MD simulation using the “gradual heating” protocol and a
heating rate of 20 K ns1
Figure S17. Snapshots from the MD simulation using the “gradual heating” protocol and a
heating rate of 20 K ns1.
S21
9. RMSD and orientational order parameter from the MD simulation using the “gradual
heating” protocol and a heating rate of 5 K ns-1
Figure S18. RMSD (left) and orientational order parameter (right) calculated for all C atoms
obtained from the “gradual heating” protocol MD simulation and a heating rate of 5 K ns-1.
The first 500 ps (restrained MD, heat-up) were omitted for the analyses.
S22