Ability of the PM3 quantum‐mechanical method to model intermolecular hydrogen bonding between neutral molecules

The PM3 semiempirical quantum‐mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02–0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol−1 suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol−1 imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high‐resolution spectroscopic observations, gas electron diffraction data, and high‐level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1–0.2 Å for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1–2 kcal mol−1. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and O predict that donor strength follows the order F > O > N and acceptor strength follows the order N > O > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F‐H‐‐‐N bond to be the strongest and the N‐H‐‐‐F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two‐center repulsive forces brought about by the parameterization of the Gaussian core–core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum‐mechanical calculations can be applied to small biologic systems. © 1993 John Wiley & Sons, Inc.

[1]  M. B. Coolidge,et al.  Calculations of molecular vibrational frequencies using semiempirical methods , 1991 .

[2]  C. Korzeniewski,et al.  Evaluation of vibrational force fields derived by using semiempirical and ab initio methods , 1991 .

[3]  R. C. Cohen,et al.  Measurement of the intermolecular vibration--rotation tunneling spectrum of the ammonia dimer by tunable far infrared laser spectroscopy , 1991 .

[4]  David M. Hirst,et al.  A Computational Approach to Chemistry , 1990 .

[5]  J. T. Hougen,et al.  New measurements of microwave transitions in the water dimer , 1987 .

[6]  W. C. Herndon,et al.  An evaluation of water cluster geometries derived from semi-empirical AM1 calculations , 1988 .

[7]  K. Schröder.  A method for the separate computation of intermolecular vibrational frequencies with application on the H2O…HF and (H2O)n (n = 2–6) complexes , 1988 .

[8]  M. Frisch,et al.  Molecular orbital study of the dimers (AHn)2 formed from ammonia, water, hydrogen fluoride, phosphine, hydrogen sulfide, and hydrogen chloride , 1985 .

[9]  Michael J. S. Dewar,et al.  Ground states of molecules. XXV. MINDO/3. Improved version of the MINDO semiempirical SCF-MO method , 1975 .

[10]  W. Fabian.  AM1 calculations on the tautomerism of free and hydrated hydroxypyridines: Barriers to proton transfer in 2‐hydroxypyridine–pyrid‐2(1H)‐one and effect of solvation and self‐association , 1990 .

[11]  J. Watson.  Vibrational Spectra and Structure , 1977 .

[12]  H. J. Bernstein,et al.  The heat of dimerization of some carboxylic acids in the vapour phase determined by a spectroscopic method , 1969 .

[13]  R. Karaman,et al.  Correlation of singlet‐triplet gaps for aryl carbenes calculated by MINDO/3, MNDO, AM1, and PM3 with Hammett‐type substituent constants , 1991 .

[14]  An investigation of the relationship between sweetness and intramolecular hydrogen-bonding networks in hexuloses using the semiempirical molecular orbital method, AM1 , 1990 .

[15]  D. Weaver,et al.  An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies , 1991 .

[16]  C. Kozmutza,et al.  Counterpoise corrected calculations at the correlated level: A simplified method using LMOs , 1991 .

[17]  T. Dyke,et al.  Rotational spectra and structure of the ammonia–water complex , 1985 .

[18]  Larry A. Curtiss,et al.  Studies of molecular association in H2O and D2O vapors by measurement of thermal conductivity , 1979 .

[19]  H. Scheraga,et al.  A revised empirical potential for conformational, intermolecular, and solvation studies. 1. Evaluation of problem and description of model , 1978 .

[20]  W. M. Latimer,et al.  POLARITY AND IONIZATION FROM THE STANDPOINT OF THE LEWIS THEORY OF VALENCE. , 1920 .

[21]  Roger Hayward,et al.  The Hydrogen Bond , 1960 .

[22]  G. Buemi,et al.  Malondialdehyde and acetylacetone. An AM1 study of their molecular structures and keto–enol tautomerism , 1989 .

[23]  R. Voets,et al.  Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase by means of MINDO/3, MNDO, and AM1 , 1989 .

[24]  C. Reynolds.  Methyl chloride-formic acid van der Waals complex: a model for carbon as a hydrogen bond donor , 1990 .

[25]  Peter A. Kollman,et al.  A comparison of the AM1 and PM3 semiempirical models for evaluating model compounds relevant to catalysis by serine proteases , 1991 .

[26]  T. Katagi.  AM1 study of acid‐catalyzed hydrolysis of maleamic (4‐amino‐4‐oxo‐2‐butenoic) acids , 1990 .

[27]  A. Raudino,et al.  Hydrogen bonding and rotation barriers: A comparison between MNDO and AM1 results , 1988 .

[28]  J. A. Odutola,et al.  Water dimer tunneling states with K=0 , 1988 .

[29]  Brian J. Smith,et al.  Transition structures for the interchange of hydrogen atoms within the water dimer , 1990 .

[30]  L. Burggraf,et al.  Hydration of small anions: Calculations by the AM1 semiempirical method , 1991 .

[31]  Amiram Goldblum,et al.  Improvement of the hydrogen bonding correction to MNDO for calculations of biochemical interest , 1987 .

[32]  Eamonn F. Healy,et al.  Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model , 1985 .

[33]  F. L. Pilar,et al.  Elementary Quantum Chemistry , 1968 .

[34]  S. Scheiner,et al.  Basis sets for molecular interactions. 1. Construction and tests on (HF)2 and (H2O)2 , 1987 .

[35]  A. Lledós,et al.  Comparison of semiempirical and bsse corrected møller-plesset ab initio calculations on the direct addition of water to formaldehyde , 1990 .

[36]  G. Buemi.  Intramolecular hydrogen bonding of malondialdehyde and its monothio and dithio analogues studied by the PM3 method , 1990 .

[37]  G. T. Fraser,et al.  Does Ammonia Hydrogen Bond? , 1987, Science.

[38]  H. Ågren.  Comparison of Ab Initio quantum chemistry with experiment for small molecules. The state of the art. Edited by Rodney J. Bartlett, D. Reidel Publishing Company, 1985 , 1987 .

[39]  T. R. Dyke,et al.  Partially deuterated water dimers: Microwave spectra and structure , 1980 .

[40]  M. Dewar,et al.  Ground States of Molecules. 38. The MNDO Method. Approximations and Parameters , 1977 .

[41]  Brian J. Smith,et al.  Characterization of the bifurcated structure of the water dimer , 1991 .

[42]  D. Millen,et al.  The nature of the hydrogen bond to water in the gas phase , 1992 .

[43]  H. Schaefer,et al.  An analysis of the infrared and Raman spectra of the formic acid dimer (HCOOH)2 , 1987 .

[44]  F. B. van Duijneveldt,et al.  SCF, MP2, and CEPA‐1 calculations on the OH ‥ O hydrogen bonded complexes (H2O)2 and (H2O‐H2CO) , 1990 .

[45]  J. Bertrán,et al.  An AM1 study of the preferential solvation of ammonium ion in ammonia—water mixtures , 1988 .

[46]  A. Hüttermann,et al.  The Hydrogen Bond , 1940, Nature.

[47]  Giles Henderson.  Heat of dimerization of formic acid by FTIR , 1987 .

[48]  G. Buemi.  AM1 study of tautomerism and intramolecular hydrogen bonding in thiomalondialdehyde and thioacetylacetone , 1990 .

[49]  S. Scheiner,et al.  Basis sets for molecular interactions. 2. Application to H3NHF, H3NHOH, H2OHF, (NH3)2, and H3CHOH2 , 1987 .

[50]  A. Engdahl,et al.  On the structure of the water trimer. A matrix isolation study , 1987 .

[51]  L. L. Connell,et al.  Rotational coherence spectroscopy of 1‐naphthol‐(water)2 clusters: Structural evidence for a cyclic hydrogen‐bonded trimer , 1991 .

[52]  J. Novoa,et al.  The nature of intramolecular hydrogen-bonded and non-hydrogen-bonded conformations of simple di- and triamides , 1991 .

[53]  John S. Muenter,et al.  THE STRUCTURE OF WATER DIMER FROM MOLECULAR BEAM ELECTRIC RESONANCE SPECTROSCOPY: PARTIALLY DEUTERATED DIMERS , 1977 .

[54]  J. L. Derissen,et al.  A reinvestigation of the molecular structure of acetic acid monomer and dimer by gas electron diffraction , 1971 .

[55]  G. Buemi.  AM1 study of intramolecular hydrogen bonding in the dithio analogues of malondialdehyde and acetylacetone , 1989 .

[56]  J. J. Esperilla,et al.  Overestimation of the coupling component in the CP technique. Application of the indirect counterpoise correction to the H2OHF hydrogen‐bonded system , 1990 .

[57]  G. T. Fraser,et al.  Microwave spectrum of the CH3OH-NH3 complex , 1988 .

[58]  James J. P. Stewart,et al.  Reply to “Comments on a comparison of AM1 with the recently developed PM3 method” , 1990 .

[59]  Z. Latajka,et al.  On the reliability of SCF ab initio calculations of vibrational frequencies and intensities of hydrogen-bonded systems , 1989 .

[60]  R. Karaman,et al.  Correlation of the acidity of substituted phenols, anilines, and benzoic acids calculated by MNDO, AM1, and PM3 with Hammett‐type substituent constants , 1990 .

[61]  K. Swamy,et al.  Pentacoordinated molecules. 85. Influence of hydrogen bonding on the formation of boat and chair conformations of six-membered rings in spirocyclic tetraoxyphosphoranes , 1991 .

[62]  Andrey A. Bliznyuk,et al.  MNDO/M Calculations on hydrogen bonded systems , 1988 .

[63]  E. Davidson,et al.  AM1 studies on the potential energy surface for the proton transfer in protonated water clusters, H+(H2O)n , 1989 .

[64]  T. Steitz,et al.  Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[65]  R. Bohn,et al.  Matrix infrared and Raman spectra of the inequivalent submolecules in the ammonia dimer , 1991 .

[66]  Janet E. Del Bene,et al.  An ab initio molecular orbital study of the structures and energies of neutral and charged bimolecular complexes of NH3 with the hydrides AHn (A = N, O, F, P, S, and Cl) , 1989 .

[67]  C. E. Dykstra,et al.  Polarization counterpoise corrections to correlated hydrogen bond interaction energies , 1987 .

[68]  J. Mullens,et al.  Theoretical study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted phenolate ions in the gas phase by means of MINDO/3, MNDO, and AM1 , 1990 .

[69]  M. Huggins.  The Structure of Benzene , 1922, Nature.

[70]  J. Dannenberg,et al.  An AM1 molecular orbital study of hydrogen bonding in crystalline nitroanilines , 1989 .

[71]  D. A. Sullivan,et al.  Gas-Phase Ion and Neutral Thermochemistry , 1988 .

[72]  E. Coitiño,et al.  AM1 study of hydrogen bonded complexes of water , 1989 .

[73]  H. Schaefer,et al.  Extensive theoretical studies of the hydrogen‐bonded complexes (H2O)2, (H2O)2H+, (HF)2, (HF)2H+, F2H−, and (NH3)2 , 1986 .

[74]  George P. Ford,et al.  The optimized ellisoidal cavity and its application to the self‐consistent reaction field calculation of hydration energies of cations and neutral molecules , 1992 .

[75]  Michael Wolfe,et al.  J+ = J , 1994, ACM SIGPLAN Notices.

[76]  Ian H. Williams,et al.  Theoretical modelling of specific solvation effects upon carbonyl addition , 1987 .

[77]  Applications of the simulated annealing method to intermolecular interactions , 1991 .

[78]  Peter A. Kollman,et al.  Catalytic pathway of serine proteases: classical and quantum mechanical calculations , 1991 .

[79]  T. R. Dyke,et al.  Group theoretical classification of the tunneling–rotational energy levels of water dimer , 1977 .

[80]  C. E. Dykstra,et al.  Structures, stabilities, and intermolecular vibrational frequencies of small ammonia complexes by molecular mechanics for clusters analysis , 1990 .

[81]  J. Gready,et al.  Mechanistic aspects of biological redox reactions involving NADH 2: A combined semiempirical and ab initio study of hydride‐ion transfer between the NADH analogue, 1‐methyl‐dihydronicotinamide, and folate and dihydrofolate analogue substrates of dihydrofolate reductase , 1990 .

[82]  J. Dannenberg.  An AM1 and ab initio molecular orbital study of water dimer , 1988 .

[83]  J. Stewart.  Optimization of parameters for semiempirical methods I. Method , 1989 .

[84]  Jacek Koput,et al.  PM3 study of the proton affinities of 2‐, 3‐, and 4‐monosubstituted pyridines in the gas phase , 1991 .

[85]  C. E. Dykstra,et al.  Improved counterpoise corrections for the abinitio calculation of hydrogen bonding interactions , 1986 .