MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries

Journal of Computational Chemistry

Volumn 20, Issue 7, 1999, Pages 730-748

  Halgren, Thomas A ^a  

^a MERCK RESEARCH LABORATORIES   (United States)

Author keywords

Conformational energy; Force field; Hydrogen bonding; Intermolecular interactions; Scaled quantum mechanics

Indexed keywords

EID: 0001242234     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(199905)20:7<730::AID-JCC8>3.0.CO;2-T     Document Type: Article

References (64)

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37. This modified basis set (denoted 6-31G′ in ref. 2) differs from standard 6-31G* by using exponents for polanzation functions that are more representative of those found in basis sets optimized for the correlation energy. The Gaussian exponents used are 0.80 for H; 0.60, 0.85, 1.20, and 1.65 for C, N, O, and F, respectively; and 0.50, 0.65, and 0.80 for P, S, and Cl.
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42. cc-pVTZ(-f) refers to the triple-zeta correlation-consistent basis set of Dunning, excluding f functions on second-row elements and d functions on hydrogen; see: Dunning, T. H. J Chem Phys 1989, 90, 1007.
43. The LMP2/cc-pVTZ(-f) and GVB-LMP2/cc-pVTZC-O calculations were performed using Jaguar v3.5 (Schrodinger, Inc., Portland OR). The conformational energies differ slightly from those reported in refs. 28(a) and 28(b) because these workers used MP2(FrozenCore)/6-31G* geometries whereas MP2(FULL)/6-31G* geometries are used in this work.
44. Using the same set of conformational comparisons with the exception of the cyclooctane and cyclononane comparisons added here, the Friesner group showed that errors versus experiment are significantly reduced when zero point corrections [ref. 28(a)] are added. For the expanded set, however, we found that the fits for cyclooctane and cyclononane, which are already degraded by sizable post-MP2 correlation corrections (compare entries in the final three columns of Table III), are significantly worsened by MP2/6-31G*-based zero point corrections of -0.54 and -0.33 kcal/mol, respectively. As a result, while zero point corrections do reduce the RMSD for the LMP2 model to 0.31 kcal/mol, for the overall data set they actually raise the RMSDs for the "LMP4" and GVB-LMP2 models to 0.37 kcal/mol in each case.
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46. The trend in the modified MMFF94 results given in Table VI of ref. 4 indicates that this point would be reached at an aliphatic hydrogen charge of approximately +0.15.
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49. The CHARMM 22 calculations for cyclohexanol and cyclopentanol required that residue topology entries for these structures be added to the distributed July 1997 version of the top_all22_model.inp file and that H-OH1-CT1-CT2 torsional and OH1-CT1-CT2 and CT1-CT2-CT1 angle-bending parameters be added to the distributed par_all22_ prot.inp file. The parameter entries were set equal to the existing H-OH1-CT1-CT3, OH1-CT1-CT3, and CT2-CT1-CT1 entries. The residue topology entries could be generated unambiguously from atom types and charges defined for other model compounds.
50. To carry out these calculations for the broadest set of complexes that lay reasonably within the defined parameterization for CHARMM 22, residue topology entries for dimethyl ether, ammonia, ammonium cation, hydrogen sulfide, and dimethyl sulfide were added to the distributed July 1997 version of the top_all22_model.inp file by modifying related topology entries that contained the requisite chemical moieties. The associated charges could be unambiguously assigned from charges defined for existing residue types except in the case of dimethyl sulfide, where assigned sulfur (S) and carbon (CT3) charges of -0.10 and -0.22 represent a compromise. In addition, the extension required the addition of parameters for CT3-S-CT3, CT3-OH1-CT3 (used in dimethyl ether), and HS-S-HS angle bending and for HA-CT3-S-CT3 torsion. The first and last of these were cloned from existing CT3-S-CT2 and HA-CT2-S-CT3 (identical to HA-CT3-S-CT2) parameters; the second and third, which we did not feel would seriously affect the computed interaction energies, were assigned values based on MMFF94 (i.e., for CT3-OH1-CT3 a force constant of 86.0 and an ideal angle of 107°, and for HS-S-H a force constant of 53.0 and an ideal angle of 93.4°).
51. s structure for the ammonia dimer, and the stacked, "pancake" structure for the N-methylacetamide dimer.
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58. a values of 4.76 for ammonium ion and 5.17 for pyridinium ion as listed in A. Streitweiser, Jr.; C. H. Heath-cock, Introduction to Organic Chemistry, 2nd ed.; Macmillan: New York, 1981. That neither this source nor any other that we could find lists acidity/basicity information for thiophene is consistent with the general knowledge that thiophene is nonbasic.
59. Kaminski, G.; Jorgensen, W. L. J Phys Chem 1996, 100, 18010-18013. For example, they found in liquid-phase studies for butane, methanol, and N-methylacetamide that MMFF94 yields densities and heats of vaporization that are too low by 20-30%.
60. In addition, B. L. Bush (Merck Research Laboratories) applied perturbation theory to small organic solutes such as methane, ethane, propane, and methanol, and found that MMFF94 free energies for gas to water transfer are typically too positive (too hydrophobic), indicating insufficient van der Waals attraction between hydrocarbon moieties and water. Our own studies (unpublished) of the methane dimer using very large basis sets and very high levels of electron correlation confirm that MMFF94 vdW well depths for aliphatic hydrogen and carbon are too small in magnitude and that effective MMFF94 radii are slightly too large.
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64. The evaluation suite can be accessed at http://ccl.osc.edu/ cca/data/ff_evaluation_suite via the Web or at ftp://ccl.osc.edu/pub/chemistry/data/ff_evaluation_ suite. Alternatively, the test suite can be accessed via ftp at ccl.osc.edu; cd to pub/ chemistry/ data/ ff_evaluation_ suite. This location is part of the Computational Chemistry List archive site maintained by the Ohio Supercomputer Center.