Electron distribution on an intramolecular hydrogen bond: A semiempirical AM1 study

Dipole moments of seven molecules were studied by AM1, each containing an intramolecular hydrogen bond between a hydroxyl group and a carbonyl or nitro group as hydrogen acceptors. The hydrogen bond causes two electron shifts: from H to O within the hydroxyl group and from C to O within the carbonyl group. The latter is accompanied by withdrawal of electrons from even more distant atoms. If the total electron density change is expressed as a vector, its direction is close to the direction of the O-H bond. This electron redistribution is in agreement with the previous, somewhat, puzzling experimental results. However, it differs from the commonly accepted picture according to which electron density changes on the hydrogen acceptor moiety are less important than those on the O-H bond.Dedicated to Professor Viktor Gutmann on the occasion of his 70th birthday.     

Determination of solvation and specific interaction enthalpies of adamantane derivatives in aprotic solvents

Solution and solvation enthalpies at infinite dilution of 1-bromoadamantane, 1-adamantanol, and 2-adamantanone are reported at 298.15 K in a set of 14 aprotic solvents. The specific interaction enthalpies of the solid solutes are calculated using a methodology recently published by other authors. 1-Adamantanol’s specific interaction enthalpies show a good correlation with the Kamlet–Taft β scale.     

A semiempirical SCF MO study of the interaction of odorant molecules with a biological substrate

The AM 1 semiempirical SCF MO method developed by Dewar and co-workers has been employed to compute possible interaction processes of the odorant molecules cocaine, methyl benzoate, and benzaldehyde with the biological substrate lysine. The only process predicted as possible in each case was nucleophilic attack on the carbonyl carbons of each odorant by the nitrogen lone pairs on lysine. The remote amino group of lysine in each case was predicted to react with lower activation enthalpy than did the α-amino group, a prediction consistent with preliminary experimental data from these laboratories. Although the computed activation enthalpies were high (ca. 40 kcal mol^?1) for the gas-phase processes, it is conceivable that such processes could occur by alternate pathways with considerably lower ctivation energies in solvated media such as exists in the presence of mucus-containing olfactory binding protein in vertebrate olfactory reception. © 1992 John Wiley & Sons, Inc.     

Interactions of polar hydrogen bond donor solvents with ions: a theoretical study

Structural Chemistry - Intermolecular interactions between molecules of protic solvents (water, methanol, formic acid, formamide, methylamine and ammonia) and monatomic ions (Li+, Na+, K+,...     

Hydration of small anions: Calculations by the AM1 semiempirical method

The AM1 semiempirical molecular orbital method has been used to calculate successive heats of hydration of small anions, including hydride, hydroxide, and the halogen ions, for cluster sizes up to 11 water molecules surrounding the central anion. Heats of hydration agree with available experimental data to within a few kcal/mol. Structures, however, do not always agree well with available ab initio calculations on clusters with one or two water molecules. The results indicate that the AM1 semiempirical technique applied to finite-sized clusters must be used with caution in understanding how hydration affects the chemical reactions of anions.     

Smooth solvation method for d-orbital semiempirical calculations of biological reactions. 1. Implementation

The present paper describes the extension of a recently developed smooth conductor-like screening model for solvation to a d-orbital semiempirical framework (MNDO/d-SCOSMO) with analytic gradients that can be used for geometry optimizations, transition state searches, and molecular dynamics simulations. The methodology is tested on the potential energy surfaces for separating ions and the dissociative phosphoryl transfer mechanism of methyl phosphate. The convergence behavior of the smooth COSMO method with respect to discretization level is examined and the numerical stability of the energy and gradient are compared to that from conventional COSMO calculations. The present method is further tested in applications to energy minimum and transition state geometry optimizations of neutral and charged metaphosphates, phosphates, and phosphoranes that are models for stationary points in transphosphorylation reaction pathways of enzymes and ribozymes. The results indicate that the smooth COSMO method greatly enhances the stability of quantum mechanical geometry optimization and transition state search calculations that would routinely fail with conventional solvation methods. The present MNDO/d-SCOSMO method has considerable computational advantages over hybrid quantum mechanical/molecular mechanical methods with explicit solvation, and represents a potentially useful tool in the arsenal of multi-scale quantum models used to study biochemical reactions.     

Comparison of AM1 and ab initio calculation of the carbon-carbon bond rotation in ethylene glycol diacetate

The C-C glycol bond rotational energy in ethylene diacetate as a polyester model was compared using the semiempirical method AM1 and an ab initio method with an STO-3G basis set. The results were qualitatively much different depending on the method used. Ab initio calculations showed the expected minima at 180 and near 60 (69.6) degrees dihedral angle with maxima at 0 and 120 degrees. The AM1 rotational curve indicated an apparent minimum at a 90 degree dihedral angle, a shallow, apparent maximum at 180 degrees and an apparent maximum at 0 degrees which could not be confirmed as minima or maxima via frequency calculations. Ethylene diacetate analog compounds with one or two ester oxygens replacing methylene group(s) gave curves with AM1 having the general shape for ethylene diacetate by the ab initio method, indicating a parameterization problem for the otherwise very useful AM1 to correctly handle a compound with only two carbons between the two electronegative oxygen atoms thus rendering this method currently unsuitable for examination of rotational energy barriers of such polyester model compounds.     

An examination of intermolecular and intramolecular hydrogen bonding in biomolecules by AM1 and MNDO/M semiempirical molecular orbital studies

The recent NMDO/M modification and parameterization of the MNDO molecular orbital method has been used to analyze intermolecular hydrogen bonding between amino acids and water, and intramolecular hydrogen bonding in monosaccharides. The results have been compared to AM1 calculations on the same systems. The MNDO/M calculations gave values which were similar to ab initio calculations with respect to the intermolecular interactions, but yielded significantly poorer results for the intramolecular interactions. The AM1 procedure performed better on the intramolecular interactions than the MNDO/M procedure, but frequently provided unfavorable three-centered hydrogen bonding geometries for the intermolecular interactions.     

Parameterization of semiempirical methods to treat nucleophilic attacks to biological phosphates: AM1/d parameters for phosphorus

 This paper reports a new AM1/d model for phosphorus that can be used to model nucleophilic attack of phosphates relevant for biological phosphate hydrolysis reactions. The parameters were derived from a quantum dataset calculated with hybrid density-functional theory [B3LYP/6-311++G(3df,2p)//B3LYP/6-31++G(d,p)] of phosphates and phosphoranes in various charge states, and on transitions states for nucleophilic attacks. A suite of non-linear optimization methods is outlined for semiempirical parameter development based on integrated evolutionary (genetic), Monte Carlo simulated annealing and direction set minimization algorithms. The performance of the new AM1/d model and the standard AM1 and MNDO/d models are compared with the density-functional results. The results demonstrate that the strategy of developing semiempirical parameters specific for biological reactions offers considerable promise for application to large-scale biological problems. Received: 15 January 2002 / Accepted: 6 September 2002 / Published online: 28 March 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: D.M. York e-mail: york@chem.umn.edu Acknowledgements. D.M.Y. is grateful for financial support provided by the National Institutes of Health (grant 1R01-GM62248-01A1) and the Donors of The Petroleum Research Fund, administered by the American Chemical Society, and the Minnesota Supercomputing Institute through a 6-month research scholar award (X.L.). Computational resources were provided by the Minnesota Supercomputing Institute.     

Diatomics-in-molecules calculation of interaction of molecular hydrogen with a lithium metal cluster

Interaction of H₂ with a lithium metal surface simulated by eight Li atoms is studied using the DIM method. Two variables are examined, the distance of H₂ from the surface and the HH separation. The adsorption proceeds adiabatically. Associative chemisorption is predicted to be energetically more favourable than dissociative.     

Electronic and structural properties of the metalloporphyrin structural isomers: semiempirical AM1 and PM3 calculations

Semiempirical calculations using AM1 and PM3 have been performed on the zinc(II) and magnesium(II) complexes of nine structural isomers of tetrapyrrole macrocycles such as porphyrin, porphycene, corrphycene and hemiporphycene, N-confused porphyrin and other isomers that have not been synthesized. The optimized geometry and the bond parameters obtained compare favorably with results obtained from X-ray and spectral studies. Heats of formation, ionization potentials, HOMO-LUMO energy differences, dipole moments, and the splitting of HOMOs and LUMOs of the metal complexes of each of these isomers are also reported and compared with experimental results. The “four-orbital model” of Gouterman remains valid for the investigated structural isomers. The present study represents an unusually appropriate opportunity to study, via molecular orbital methods, the interaction between various metal ions, and the electronic and geometrical environment of the central cavity of the closely related isomeric macrocycles. The major outcome of this study is the verification of the expected differential behavior of metal ions employed in the present study as a sophisticated probe of cavity properties which also suggests that this procedure can be extended to other metal complexes. This study also serves as an interesting prototype for more elaborate ab initio calculations. However, such calculations on the presently investigated macrocyclic systems may have to be performed at a higher level than MP2 or DFT to account for the unusual delocalization, as suggested by a recent study by Schaefer and co-workers on delocalized [10]annulene (H.M. Sulzbach, H.F. Schaefer, W. Klopper and H.P. Luthi, J. Am. Chem. Soc., 118 (1996) 3519).     

Inter- and intramolecular hydrogen bond in methyl 2-hydroxy-9H-1-carbazole carboxylate: effect of solvents and acid concentration

The photo-physics of methyl 2-hydroxy-9H-1-carbazazole carboxylate (MPCC) in different solvents and cyclohexane-trifluoroethanol (TFE) mixtures has been studied by means of absorption, fluorescence, fluorescence excitation spectra, time dependence spectrofluoremetery and AM1 semi-empirical quantum mechanical calculations. Only one small Stoke’s shifted fluorescence band is observed under all the environments, indicating that the geometry of the molecule is not changed much on excitation to the first singlet state (S₁) and excited state intramolecular proton transfer (ESIPT) is not viable both in the ground (S₀) and S₁ states at the room temperature. AM1 calculation shows that the ESIPT is still endothermic in S₁ state. Single exponential decay is observed in the fluorescence from MPCC in all the solvents except acetonitrile and methanol. This suggests that in these two solvents, at least two different conformers are present in the S₀ state, whose absorption spectra are not different from each other. Spectral characteristics of MPCC in cyclohexane as a function of TFE have shown a slight blue shift in the λ_max^ab, decrease in the ε_max, red shift in the λ_max^fl and decrease in the φ_fl. This suggests that intermolecular hydrogen bonding is playing a major role in the deactivation of the fluorescence intensity than the intramoleuclar hydrogen bonding (IHB). Spectral properties of MPCC were also studied as a function of acid–base concentrations. pK_a values for different prototropic equilibriums were determined in S₀ and S₁ states and discussed.     

A model study of the interaction of a hydrogen bond with a π-electron system

A semi-empirical CNDO/2 calculation of the structure of the diimide-hydrogen fluoride hydrogen bonded complex is reported. The results are compared to calculations on a similar saturated system in an attempt to elucidate the effect of a neighboring -system on a hydrogen bond, and to uncomplexed diimide to study the effect of the hydrogen bond on the -system.     

Communication: Frequency shifts of an intramolecular hydrogen bond as a measure of intermolecular hydrogen bond strengths

Infrared-ultraviolet double resonance spectroscopy has been applied to study the infrared spectra of the supersonically cooled gas phase complexes of formic acid, acetic acid, propionic acid, formamide, and water with 9-hydroxy-9-fluorenecarboxylic acid (9HFCA), an analog of glycolic acid. In these complexes each binding partner to 9HFCA can function as both proton donor and acceptor. Relative to its frequency in free 9HFCA, the 9-hydroxy (9OH) stretch is blue shifted in complexes with formic, acetic, and propionic acids, but is red shifted in the complexes with formamide and water. Density functional calculations on complexes of 9HFCA to a variety of H bonding partners with differing proton donor and acceptor abilities reveal that the quantitative frequency shift of the 9OH can be attributed to the balance struck between two competing intermolecular H bonds. More extensive calculations on complexes of glycolic acid show excellent consistency with the experimental frequency shifts.     

AM1 semiempirical searching for suitable thiophene derivatives that will enable thiophenes to act as a diene in the diels-alder reactions

The AM1 semiempirical method was used for theoretical searching of activation of thiophene as a diene for the Diels-Alder reaction. The reactivity of thiophene, electron-withdrawing and electron-donating substituted thiophenes, as well as the S-methylthiophenium ion were studied as the diene for Diels-Alder reactions by evaluating their frontier orbital energies and by calculating reaction barriers with activated and deactivated dienophiles. It was demonstrated that slight activation of the thiophene ring can be obtained with both electron-donating and electron-withdrawing groups attached to the thiophene ring. It was predicted that the actual transformation of thiophenes into the corresponding S-methylthiophenium anions is the best means of activating the thiophenes. The calculated activation energies for normal (non-activated) dienophiles are moderate so mild reaction conditions are predicted. If dienophiles are activated with electron-donating substituents, AM1 calculations predict a two step cycloaddition reaction with a very small activation barrier.