Supplementary Material
Optimization of empirical force field parameters for aldehydes.
Empirical force field calculations were performed with the program CHARMM
[1] using infinite cutoffs for the nonbond interactions. QM calculations were performed
with the Gaussian98 package [2], with all optimizations performed to default tolerances.
Aldehydes included in the parameter optimization are shown in Figure S1. Parameters
for acetaldehyde were transferred from propionaldehyde following optimization of
parameters for the later molecule.
Nonbonded Interaction Terms
The optimization of the interaction terms included only the refinement of the
partial atomic charges; Lennard-Jones parameters were transferred directly from the
CHARMM protein and nucleic acid force fields or, for chlorine, were obtained from
Jorgensen and coworkers [3]. Lennard-Jones parameters for the hydrogen on the
aldehyde correspond to those used for the H1 atom in the imidazole sidechain of
histidine. All atom types along with charges and internal parameters are included at the
end of the supplemental material.
Charge optimization involves the reproduction of HF/6-31G* minimum
interaction energies and geometries between water at the TIP3P internal geometry and the
various aldehyde compounds. The interaction orientations used are shown in Figure S2.
The interaction energies were calculated as the difference between the aldehyde-water
complex and the monomer species (i.e. aldehyde and water, separately).
Internal Parameters
Optimization of the internal parameters involved the reproduction of the
geometric, vibrational and energetic target data for the aldehydes. The bond, angle, and
dihedral force constants were obtained from the existing CHARMM protein sidechain
parameters for the aliphatic and aromatic portions of the aldehyde compounds (e.g. the
parameters for the phenyl moiety was obtained from the parameters for phenylalanine).
The only remaining internal terms that were not present in the parameter set were those
1
involving the atoms of the aldehyde moiety. The geometries of the aldehydes were
obtained from QM calculations at the MP2/6-31G* level of theory, and optimized by
performing energy minimizations in vacuo with infinite cutoffs. The vibrational
frequencies were calculated using the VIBRAN module, and the potential energy
distributions were calculated using the MOLVIB module [4] in CHARMM. A scaling
factor of 0.9 was used for QM HF/6-31G* frequencies [5] for empirical value
comparison. The dihedral parameters were optimized to reproduce the QM energy
barriers.
Results and Discussion
The CHARMM potential energy function has been optimized for a set of
aldehydes: acetaldehyde, propionaldehyde, benzaldehyde, and chloroacetaldehyde
(Figure S1). The optimization procedure was similar to previously described
developments of the parameters for other biomolecules. The parameter set for the
aldehydes was either optimized for agreement with QM calculations, or utilizing
previously existing parameters when appropriate. An iterative procedure was employed,
first optimizing the nonbonded parameters, then the internal or intramolecular parameters
followed by reevaluation of the nonbond terms.
Nonbonded Parameter Optimization
The partial charges were optimized using the interaction energy surface at the
HF/6-31G* level of theory. The minimum interaction energies and distances were
derived using the interaction orientations shown in Figure S2. The polar-neutral
compound charges were optimized to reproduce the QM aldehyde-water interaction
energies and distances, scaled by 1.16 and offset by –0.2 Å, respectively, to yield
acceptable condensed phase properties. The reasoning behind these values has been
described elsewhere [6]. As shown in Table SI, the agreement between the empirical and
QM data is generally quite good, validating the quality of the developed force field for
the treatment of nonbond interactions with the protein environment. It should be
emphasized that the selection of the HF/6-31G* level of theory for the QM calculations is
performed to maintain consistency with the remainder of the CHARMM22 force field
[7].
2
Table SI) Minimum interaction energies and distances for the optimized empirical
force field and the QM data for the aldehyde model compounds.
Interaction Energies
Empirical
QM
Propionaldehyde (0o)
O---HOH
O---HOH
H---OH2
Propionaldehyde (120o)
O---HOH
O---HOH
H---OH2
Chloroacetaldehyde
O---HOH
O---HOH
H---OH2
Cl---HOH
Benzaldehyde
O---HOH
O---HOH
H---OH2
Interaction Distances
Empirical
QM
-4.485
-2.654
-1.472
-4.490
-2.097
-1.469
1.85
2.69
2.36
1.86
2.52
2.42
-4.392
-5.149
-1.369
-4.540
-4.771
-1.420
1.85
1.84
2.37
1.86
1.85
2.43
-4.187
-4.823
-2.358
-0.097
-4.213
-4.711
-2.375
-0.192
1.85
1.84
2.28
2.43
1.90
1.88
2.20
3.25
-4.306
-1.658
-1.816
-4.523
-1.040
-1.568
1.85
3.08
2.35
1.86
2.75
2.42
Energies in kcal/mol and distances in Å. The HF/6-31G(d) QM calculated interaction energies
and distances were scaled by 1.16 and offset by –0.2 Å, respectively.
Internal parameter optimization
Internal parameters were optimized to reproduce the MP2/6-31G* geometries,
vibrations and conformational energies of the aldehyde moieties; the remainder of the
internal parameters were directly transferred from the CHARMM22 force field for
proteins. Shown in Tables SII and SIII are the empirical and QM bonds and angles,
respectively, for the aldehyde moieties. Overall, the agreement between the empirical and
QM data is satisfactory, indicating the internal aspect of the force field to yield
reasonable geometries. The largest discrepancies are due to the use of common atom
types for the aldehyde group in all four model compounds. For example, in acetaldehyde
and propionaldehyde, the O-C bond is to long in the empirical model as compared to the
QM target data, while the opposite is true to the O-C bond in chloroacetaldehyde and
benzaldehyde. A similar trend occurs with the O-C-CB(CG) angle. Such differences
3
may be eliminated via the use of additional atom types. However, the small magnitude of
the changes did not warrant such an addition in the present case
Table SII) Comparison of the empirical and QM bond lengths for the aldehyde moieties
on the model compounds.
Bond
Empirical
QM
Acetaldehyde
HA-C
1.111
O-C
1.203
C-CB
1.516
Propionaldehyde
HA-C
1.110
O-C
1.204
C-CB
1.530
Chloracetaldehyde
HA-C
1.111
O-C
1.204
C-CB
1.519
CB-CL
1.777
Benzaldehyde
HA-C
1.110
O-C
1.206
C-CG
1.489
Average Difference
RMS Difference
Bond lengths in Å
4
Difference
1.096
1.188
1.508
0.015
0.015
0.008
1.096
1.188
1.508
0.014
0.016
0.022
1.106
1.220
1.519
1.777
0.004
-0.016
0.001
0.000
1.110
1.227
1.480
-0.001
-0.021
0.009
0.005
0.013
Table SIII) Comparison of the empirical and QM valence for the aldehyde moieties on
the model compounds.
Angles
Acetaldehyde
HA-C-O
HA-C-CB
O-C-CB
Propionaldehdye
HA-C-O
HA-C-CB
O-C-CB
C-CB-CG
Chloroacetaldehyde
HA-C-O
HA-C-CB
O-C-CB
C-CB-CL
Benzaldehyde
HA-C-O
HA-C-CG
O-C-CG
C-CG-CD1
C-CG-CD2
Average Difference
RMS Difference
Empirical
QM
Difference
121.0
116.5
122.5
120.2
115.0
124.8
0.8
1.5
-2.3
120.9
116.1
123.0
114.5
120.2
115.0
124.8
113.8
0.7
0.9
-1.8
0.8
121.0
116.4
122.6
111.9
122.5
116.5
121.0
111.8
-1.4
-0.2
1.6
0.1
120.8
114.4
124.8
120.8
119.8
120.5
115.2
124.3
119.9
119.7
0.3
-0.8
0.6
0.8
0.0
0.1
1.1
Angles in degrees.
Force constants were optimized initially to reproduce vibrational spectra, with
emphasis on the reproduction of both frequencies and assignments. Tables SIV to SVI
show good agreement between the empirical and QM models. Notable is the quality of
the low frequency regions, as those modes will typically have the largest displacements in
MD simulations, thereby having the largest impact on the results from MD simulations.
5
Table SIV: Comparison of Empirical and Quantum Mechanical Vibrational Frequencies
(cm-1) for Propionaldehyde.
Mode
Empirical
Empirical assignments
QM
QM assignments
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
139.0
256.7
259.7
682.9
769.9
813.8
1007.0
1027.8
1079.8
1150.6
1256.3
1349.2
1408.7
1415.1
1428.8
1429.0
1438.2
1740.5
2900.3
2909.3
2917.4
2941.8
2959.1
2960.7
CC tor.
CCC sciss.
CC tor.
OCC def.
CH2 rock.
CC str.
CH3 rock.
CH3 rock.'
CC str.
CH wag.
CH2 twist
CH2 wag.
CH2 sciss.
CH3 sym. def.
CH3 asym. def.
CH3 asym. def.'
CH rock.
CO str.
CH3 str.
CH str.
CH2 str.
CH2 str.
CH3 str.
CH3 str.
138.9
256.6
259.4
683.0
769.3
813.5
1006.9
1027.8
1079.8
1150.5
1256.6
1349.4
1408.5
1415.1
1428.8
1428.9
1438.3
1740.5
2900.2
2909.2
2917.4
2941.7
2959.1
2960.7
CC tor.
CCC sciss.
CC tor.
OCC def.
CH2 rock
CC str.
CH3 rock
CH3 rock'
CC str.
CH wag
CH2 twist
CH2 wag
CH2 sciss.
CH3 sym. def.
CH3 asym. def.
CH3 asym. def.'
CH rock
CO str.
CH3 str.
CH str.
CH2 str.
CH2 str.
CH3 str.
CH3 str.
6
Table SV: Comparison of Empirical and Quantum Mechanical Vibrational Frequencies
(cm-1) for Chloroacetaldehyde.
Mode
Empirical
Empirical assignments
QM
QM assignments
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
7.6
321.9
498.3
807.0
831.5
1032.6
1128.8
1257.4
1349.2
1419.7
1486.5
1733.6
2868.8
2902.4
2913.0
CC def.
CCCl sciss.
OCC def.
CH2 rock.
CCl str.
CC str.
CH wag.
CH2 twist.
CH2 wag.
CH rock.
CH2 sciss.
CO str.
CH2 str.
CH2 str.
CH str.
3.8
261.3
441.5
687.5
798.2
1005.3
1015.5
1160.0
1257.1
1360.9
1423.3
1685.4
2862.7
2975.2
3038.1
CC tor.
CCCl sciss.
OCC def.
CH2 rock.
CCl str.
CH wag.
CC str.
CH2 twist.
CH2 wag.
CH rock.
CH2 sciss.
CO str.
CH str.
CH2 str.
CH2 str.
7
Table SVI: Comparison of Empirical and Quantum Mechanical Vibrational Frequencies
(cm-1) for Benzaldehyde.
Mode
Empirical
Empirical assignments
QM
QM assignments
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
88.7
229.4
239.8
404.2
414.4
472.4
621.4
651.3
691.6
768.9
786.0
882.3
951.2
953.2
975.6
1000.9
1024.0
1024.8
1036.5
1144.2
1211.5
1219.0
1352.5
1387.2
1425.9
1440.4
1468.0
1486.8
1515.0
1756.3
2908.1
3054.5
3055.1
3056.4
3056.7
3060.1
CC tor.
CC wag.
CC def.
CC str.
asym. tor.
asym. tor.'
OOC def.
puckering
asym. def.'
CH wag
asym. def.
CH wag
CH wag
trigonal def.
CC str.
CC wag.
CC str.
CC wag.
CH wag.
CC str.
CH def.
CH def.
CH rock.
CH rock.
CH def.
CC str.
CH def.
CH def.
CH def.
CO str.
CH str.
CH str.
CH str.
CH str.
CH str.
CH str.
106.7
211.8
215.3
374.8
413.7
419.2
477.7
593.1
624.9
690.6
793.1
801.8
828.6
848.7
856.2
952.0
963.3
1003.2
1061.5
1147.8
1153.1
1188.7
1282.3
1361.4
1396.9
1426.7
1463.9
1566.3
1582.9
1664.6
2809.0
3029.0
3042.7
3053.3
3061.7
3067.2
CC tor.
CC def.
CC wag.
asym. tor.
CC wag.
asym. def.
puckering
asym. def.'
asym. def.
CC wag.
CH wag.
CC str.
CH wag.
CH wag.
CH wag.
CH wag.
trigonal def.
CC str.
CC str.
CH def.
CH def.
CC str.
CH def.
CH rock.
CC str.
CH def.
CH def.
CC str.
CC str.
CO str.
CH str.
CH str.
CH str.
CH str.
CH str.
CH str.
Final optimization of the dihedral parameters for the C-C bond, where one C is
the carbonyl carbon, was based on reproduction of the QM energy surface for rotation
about that bond. Figure S3 shows the respective surfaces for propionaldehyde,
chloroacetaldehyde and benzaldehyde. As is evident, the agreement in all three cases is
8
quite good. The largest discrepancy occurs in the regions about the minima for
benzaldehyde, where the empirical model has a more gradual increase in energy as the
dihedral deviates from the minimum energy orientation. Such deviation is required to
avoid significantly overestimating the energy barriers, related to limitations in the form of
the potential energy function. Having the empirical model more flexible than the QM
model insures that the force field won’t force the sampling a limited region of the
dihedral conformational space; this approach is consistent with the remainder of the
CHARMM force field. In all cases the internal parameters for propionaldehyde were
directly transferred to acetaldehyde, such that the later molecule was not explicitly
parameterized. Overall, the developed force field accurately describes both the
geometries and distortions of the aldehyde moieties, validating its utility in MD
simulations of the selected aldehydes.
9
Figure S1: Structures of the aldehydes molecules used for CHARMM parameterization.
Figure S2: Interaction orientations of the optimized aldehyde moieties with water. For
orientations A and B, the C-O-H(water) angle was fixed at 120˚.
10
Figure S3: Comparison of Emprical (CHARMM) and Quantum Mechanical (ab initio)
dihedral energy surfaces for propionaldehyde, chloroacetaldehyde and benzaldehyde.
11
Additional simulation result referred to in section: “Thiolate forms of
Cys243”.
Figure S4: Radial distribution function, g(r), between oxygen atoms of TIP3P water
molecules and the center of the benzyl moiety of benzaldehyde from simulations where
Cys243 was modeled as a thiol (black) and as a thiolate (red).
Additional MM simulation results described in section: “Glu209 versus
Glu333 in substrate bound MM simulation”
Figure S5: Distance plot between carboxylate oxygen of Glu209 to Sulfur of Cys-243
(left) and with backbone amide proton of Ala411 (right).
12
Figure S6: Distance plot between carboxylate oxygen of Glu333 to Sulfur of Cys-243
(left) and with hydroxyl proton on NAD ribose (right).
References
1. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M.
CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics
Calculations. J. Comput. Chem. 1983; 4:187-217.
2. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR,
Zakrzewski VG, Montgomery JA, Jr., Stratmann RE, Burant JC, Dapprich S, Millam JM,
Daniels AD, Kudin KN, Strain MC, Farkas O, Tomasi J, Barone V, Cossi M, Cammi R,
Mennucci B, Pomelli C, Adamo C, Clifford S, Ochterski J, Petersson GA, Ayala PY, Cui
Q, Morokuma K, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Cioslowski J,
Ortiz JV, Baboul AG, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I,
Gomperts R, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A,
Gonzalez C, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Andres JL,
Gonzalez C, Head-Gordon M, Replogle ES, Pople JA (1998). Gaussian 98. Gaussian,
Inc., Pittsburgh, PA.
3. Jorgensen WL, Binning RC, Bigot B. Structures and Properties of Organic Liquids: nButane and 1,2-Dichloroethane and Their Conformational Equilibria. J Am Chem Soc
1981; 103:4393-4399.
13
4. Kuczera, K., Wiorkiewicz, JK, Karplus M. MOLVIB: Program for the Analysis of
Molecular Vibrations. CHARMM, 1983; Harvard University.
5. Scott AP, Radom L. Harmonic Vibrational Frequencies: An Evaluation of HartreeFock, Moller-Plesset, Quadratic Configuration Interaction, Density Functional Theory,
and Semiempirical Scale Factors. J Phys Chem 1996; 100:16502-16513.
6. MacKerell Jr. AD, Bashford D, Bellott M, Dunbrack Jr. RL, Evanseck JD, Field MJ,
Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK,
Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher III WE, Roux B,
Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin
D, Karplus M. All-atom empirical potential for molecular modeling and dynamics studies
of proteins. J Phys Chem B 1998; 102:3586-3616.
7. MacKerell AD., Jr. Atomistic Models and Force Fields. In Computational
Biochemistry and Biophysics (Becker OM, MacKerell AD, Jr., Roux B, Watanabe M,
eds.), New York: Marcel Dekker, Inc., 2001. p 7-38.
14
* Topology and Parameter Stream File for aldehydes
* This file should be streamed in CHARMM following input of
* top_all22_prot.inp: mass list must be altered (see below)
* and
* par_all22_prot.inp
*
! the following line has to be added to the mass list
! in top_all22_prot.inp
!MASS 196 CL 35.453000 CL ! Chlorine Atom
read rtf card append
* Topology for aldehydes
*
!acetaldehyde additions, ssc & adm, jr., 2/01
RESI AALD
0.00
! Acetaldehyde
GROUP
!
ATOM HA HR1 0.06
!
HB3
ATOM C CD
0.12
!
|
ATOM O O
-0.32
! HB1-CB-HB2
ATOM CB CT3 -0.13
!
|
ATOM HB1 HA 0.09
!
O=C
ATOM HB2 HA 0.09
!
|
ATOM HB3 HA 0.09
!
HA
BOND HA C C CB CB HB1
CB HB2
BOND CB HB3
DOUBLE C O
IMPH CB C O HA
ACCE O
IC o c cb hb1
0.0 0.0 0.0
0.0 0.0
IC hb2 cb c o
0.0 0.0 120.0
0.0 0.0
IC hb3 cb c o
0.0 0.0 -120.0
0.0 0.0
IC ha o *c cb 0.0 0.0 180.0
0.0 0.0
PATCHING FIRST NONE LAST NONE
15
RESI PALD
0.00
! Propionaldehyde
GROUP
!
ATOM O O
-0.32
!
HG3
ATOM C CD
0.12
!
|
ATOM CB CT2 -0.04
! HG1-CG-HG2
ATOM HB1 HA 0.09
!
|
ATOM HB2 HA 0.09
! HB1-CB-HB2
ATOM HA HR1 0.06
!
|
GROUP
! O=C
ATOM CG CT3 -0.27
!
|
ATOM HG1 HA
0.09
!
HA
ATOM HG2 HA
0.09
!
ATOM HG3 HA
0.09
BOND HA C C CB CB HB1 CB HB2
BOND CB CG CG HG1 CG HG3 CG HG2
DOUBLE C O
IMPH CB C O HA
ACCE O
IC o c cb cg
0.0 0.0
0.0
0.0 0.0
IC cg cb c ha
0.0 0.0 180.0
0.0 0.0
IC hb1 cb c o
0.0 0.0 120.0
0.0 0.0
IC hb2 cb c o
0.0 0.0 -120.0
0.0 0.0
IC c cb cg hg1 0.0 0.0 180.0 0.0 0.0
IC c cb cg hg2 0.0 0.0 60.0
0.0 0.0
IC c cb cg hg3 0.0 0.0 -60.0
0.0 0.0
PATCHING FIRST NONE LAST NONE
RESI CALD
0.00
! Chloroacetaldehyde
GROUP
!
CL
ATOM O O
-0.34 !
|
ATOM C CD
0.19 !HB1-CB-HB2
ATOM CB CT2
-0.08 !
|
ATOM HB1 HA
0.09 ! O=C
ATOM HB2 HA
0.09 !
|
ATOM CL CL
-0.04 !
HA
ATOM HA HR1
0.09
BOND HA C C CB CB HB1 CB HB2
BOND CB CL
DOUBLE C O
IMPH CB C O HA
ACCE O
IC o c cb cl
0.0 0.0
180.0
IC cl cb c ha
0.0 0.0
0.0
IC ha o *c cb
0.0 0.0
0.0
IC cl c *cb hb1
0.0 0.0
120.0
16
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
IC hb1 c *cb hb2
0.0 0.0
120.0
PATCHING FIRST NONE LAST NONE
0.0 0.0
!benzaldehyde additions, ssc & adm, jr., 2/01
RESI BALD
0.00
! Benzaldehyde
GROUP
!
ATOM HA HR1 0.05
!
HZ
ATOM C CD
0.16
!
|
ATOM O O
-0.33
!
CZ
ATOM CG CA
0.12
!
// \
GROUP
!HE1-CE1
CE2-HE2
ATOM CD1 CA -0.115 !
|
||
ATOM HD1 HP 0.115
!HD1-CD1
CD2-HD2
GROUP
!
\\
/
ATOM CE1 CA -0.115
!
CG
ATOM HE1 HP 0.115
!
|
GROUP
!
O=C
ATOM CZ CA -0.115
!
|
ATOM HZ HP 0.115
!
HA
GROUP
ATOM CD2 CA -0.115
ATOM HD2 HP 0.115
GROUP
ATOM CE2 CA -0.115
ATOM HE2 HP 0.115
BOND HA C C CG CG CD1 CG CD2
BOND CD1 HD1 CD2 HD2 CD1 CE1 CD2 CE2
BOND CE1 HE1 CE2 HE2 CE1 CZ CE2 CZ
BOND CZ HZ
DOUBLE C O
IMPH CG C O HA
ACCE O
IC O C CG CD1
0.0
0.0
0.0
IC HA O *C CG
0.0
0.0 180.0
IC CD1 C *CG CD2
0.0
0.0 -177.9600
IC C CG CD1 CE1
0.0
0.0 -177.3700
IC CE1 CG *CD1 HD1
0.0
0.0 179.7000
IC C CG CD2 CE2
0.0
0.0 177.2000
IC CE2 CG *CD2 HD2
0.0
0.0 -178.6900
IC CG CD1 CE1 CZ
0.0
0.0
-0.1200
IC CZ CD1 *CE1 HE1
0.0
0.0 -179.6900
IC CZ CD2 *CE2 HE2
0.0
0.0 -179.9300
IC CE1 CE2 *CZ HZ
0.0
0.0 179.5100
PATCHING FIRST NONE LAST NONE
end
17
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
read para card append
* Parameters of Benzaldehyde
*
BONDS
!
!V(bond) = Kb(b - b0)**2
!
!Kb: kcal/mole/A**2
!b0: A
!
!atom type Kb
b0
!
!benzaldehyde and model compounds, the RESI names on each line indicate the
!model compound that should be used to parametrize the particular term
!NOTE: only change terms in the benzaldehyde section. DO NOT change any other
!terms.
!
O
CD
720.000 1.2050 ! acetaldehyde
HR1 CD
330.000 1.1100 ! acetaldehyde
CD
CA
300.000 1.4798 ! benzaldehyde
CT2 CL
220.000 1.7768 ! chloroacetaldehyde
!********************************
ANGLES
!
!V(angle) = Ktheta(Theta - Theta0)**2
!
!V(Urey-Bradley) = Kub(S - S0)**2
!
!Ktheta: kcal/mole/rad**2
!Theta0: degrees
!Kub: kcal/mole/A**2 (Urey-Bradley)
!S0: A
!
!atom types Ktheta Theta0 Kub S0
!
O
CD
HR1 75.000
121.0000 ! acetaldehyde
HR1 CD
CT3 20.000
116.0000 ! acetaldehyde
O
CD
CT3 140.000
123.0000 ! acetaldehyde
CT3 CT2 CD
60.000
113.8000 ! propionaldehyde
O
CD
CT2 140.000
125.0000 ! propionaldehyde
HR1 CD
CT2 35.000
115.0000 ! propionaldehyde
CD
CT2 CL
65.000
111.8215 ! chloroacetaldehyde
HA
CT2 CL
35.000
108.9905 ! chloroacetaldehyde
18
HR1 CD
CA
15.000
115.0000 ! benzaldehyde
O
CD CA
75.000
124.0000 ! benzaldehyde
CD CA CA
45.000
119.8000 ! benzaldehyde
!********************************************
DIHEDRALS
!
!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
!
!Kchi: kcal/mole
!n: multiplicity
!delta: degrees
!
!atom types
Kchi n delta
!
O
CD CT2 CT3
1.050 1
180.00 ! propionaldehyde
O
CD CT2 CT3
0.400 2
180.00 !
O
CD CT2 CT3
0.600 3
180.00 !
O
CD CT2 CT3
0.100 4
180.00 !
O
CD CT2 CL
0.100 1
0.00 ! chloracetaldehyde
O
CD CT2 CL
1.000 2
180.00 !
O
CD CT2 CL
0.550 3
180.00 !
O
CD CA CA
1.000 2
0.00 ! benzaldehyde
HR1 CD CA CA
3.200 2
180.00 ! benzaldehyde
CD CA CA HP
4.200 2
180.00 ! benzaldehyde
CD CA CA CA
3.100 2
180.00 ! benzaldehyde
!********************************************
IMPROPER
!
!V(improper) = Kpsi(psi - psi0)**2
!
!Kpsi: kcal/mole/rad**2
!psi0: degrees
!note that the second column of numbers (0) is ignored
!
!atom types
Kpsi
psi0
!
CT3 CD O HR1 28.0000
0 180.0000 ! acetaldehyde
CT2 CD O HR1 28.0000
0 180.0000 ! propionaldehyde
CA CD O HR1 14.0000
0 180.0000 ! benzaldehyde
!*****************************
NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 5/08/91, suggested cutoff scheme
19
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon
Rmin/2 ignored eps,1-4
Rmin/2,1-4
!
!********************************
CL 0.000000 -0.030000 1.908200 ! from Jorgensen/BOSS
! for choroacetaldehyde
!********************************
end
20