Comparative performance of MM3(92) and two TINKER MM3 versions for the modeling of carbohydrates

The 1992 version of MM3 was largely used for modeling mono-, di-, and trisaccharides. In later versions of MM3 improvements were made in some parameters that may be important for carbohydrates. This corrected MM3 force field is part of the Tinker package, freely available (as its 4.1 version), and included in the Chem 3D Ultra 8.0 package (as the 3.7 version). The latter version lacks the corrections to the standard bond lengths produced by electronegativity and anomeric effects, whereas the Tinker 4.1 version only lacks the latter correction. The present work compares the performance of the three MM3 versions (and in some cases, DFT and/or HF/ab initio procedures) on several carbohydrate model problems as the chair and rotamer equilibria in 2-hydroxy- and 2-methoxytetrahydropyran, hydrogen bonding in cis-2,3-dihydroxytetrahydropyran, and the potential energy surfaces around the glycosidic bonds of two sulfated disaccharides and two trisaccharides. Tinker MM3 can be used accurately to estimate carbohydrate energies and geometries, and-with the help of some programming-to pursue studies on the potential energy surfaces of di- and trisaccharides. In most cases results obtained using the three MM3 versions are similar, although large energy differences are obtained when comparing a rotameric distribution around a O-C-O-H dihedral, which is almost forced to the exo-anomeric position by the Tinker versions. In other systems smaller energy differences are found, but they can nevertheless lead to a different global minimum when comparing conformers of similar energy. MM3(92) establishes better the differences between the bond lengths in both anomers, as an expected expression of the anomeric correction.     

Molecular mechanics calculations (MM3) on sulfones

The structures of several sulfones, including dimethyl sulfone, methyl ethyl sulfone, methyl vinyl sulfone, and diphenyl sulfone, have been fit with the MM3 force field to existing experimental data from electron diffraction and microwave spectroscopy. The vibrational spectra have also been fit for six of these compounds. The torsional parameters for the aliphatic sulfones were fit to ab initio 6-31G data. Heats of formation were also fit. © 1993 John Wiley & Sons, Inc.     

Mass spectrometric study of ring-chain tautomers of 3-amino(hydroxy)pyrazolidines

The mass spectrometric fragmentation of substituted 3-amino-, 3-hydrazino-, and 3-hydroxypyrazolidines has been studied. In the gas phase these compounds exist partly as the acyclic tautomers.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 10, pp. 1334–1338, 1986.     

Molecular mechanics calculations (MM2 and MM3) on enamines and aniline derivatives

The MM2 and MM3 force fields have been extended to cover this class of compounds. Structures, vibrational spectra, and other data for 13 compounds were examined and can be reproduced satisfactorily by MM3. Except for the spectra, the other data can be reproduced somewhat less well by MM2. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on conjugated hydrocarbons

The MM3 molecular mechanics program has been extended to conjugated systems. A VESCF method is applied to the pi-system to calculate bond orders, from which various stretching and torsional parameters are obtained. The procedure gives somewhat better results than the analogous MM2 calculations. It has been applied to a study of 81 compounds of aromatic and other conjugated hydrocarbons, as well as 45 alkenes and unconjugated polyenes. The structures calculated are generally in good agreement with experiment, and the heats of formation of these compounds can be calculated with a rms value of 0.62 kcal/mol, which may be compared with the average experimental error of 0.61 kcal/mol. In addition, vibrational frequencies for five representative conjugated model structures are calculated, with an rms value of 46 cm^?1, and from these, other properties such as entropy can be calculated.     

Molecular mechanics calculations (MM3) on bicycloalkyl hydrocarbons

A series of bicycloalkyl hydrocarbons were studied using molecular mechanics methods (MM3), and the results were compared with the experimental data available. Five compounds were studied: bicyclopropyl, bicyclobutyl, bicyclopentyl, bicyclohexyl and 2,3-dimethylbutane. In general, the MM3 results are in good agreement with experimental values. Predicted structures and conformations are given for the bicyclopentyl previously uninvestigated experimentally.     

Molecular mechanics (MM3) calculations on alkyl radicals

The MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on azoxy compounds

The MM3 force field has been extended to include azoxy compounds and also the related amine oxides, both aliphatic and aromatic. The structures of nine molecules were all well fit. The heats of formation for the aliphatic compounds were also well fit, and the vibrational spectra of eight compounds were also fit to the accuracy expected for such calculations. Because many of the experimental data needed to derive the force field were either lacking or were inadequate, ab initio calculations on structures, optimized at the MP2/6-31G* level, were used as needed. © 1994 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) parameterization for oxocarbenium ions

The physical properties of a diverse group of 12 oxocarbenium ions have been studied with ab initio calculations at the MP2/6‐31+G* level of theory. Based on theoretically derived properties such as molecular equilibrium geometry, dipole moment, and vibrational frequencies, a molecular mechanics (MM3) force field has been developed with the assistance of the programs TORSMART and MPMSR, components of our artificial parameter development and refinement method. The MM3 force field is now able to reproduce bond lengths, bond angles, moments of inertia, dipole moments, torsional energy profiles, and vibrational frequencies of oxocarbenium ions, which will allow further studies of glycoside hydrolysis and their rates of reaction. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 329–339, 2000     

A molecular mechanics (MM3) study of fluorinated hydrocarbons

A molecular mechanics study of small saturated hydrocarbons (up to C-6), substituted by up to six fluorines was carried out with the MM3 force field. Perfluorobutane and Teflon were also studied. A parameter set was developed for use in the calculation of bond lengths, bond angles, torsion angles, conformational energies, barriers to rotation, dipole moments, moments of inertia and vibrational frequencies for these compounds. The results are in good agreement with experiment when only one or two fluorines are present, but some rather large discrepancies were noted when the F/H ratio becomes high. These can be taken into account only by using a force field more complicated than MM3. Some of the requirements of such a force field are delineated. Some pertinent ab initio results are also reported in this article.     

Intensities of infrared bands in molecular mechanics (MM3)

The MM3 molecular mechanics program calculates a fair representation of vibrational frequencies for molecules. To make this information more useful, a qualitative intensity calculation has been added, as is described herein. Because each bond in the molecule is assigned a dipole moment, and the vibrational amplitudes are known from the frequency calculation, the change in dipole moment corresponding to each normal mode is readily calculated. In some cases a charge flux has to be added empirically for bond stretchings. This relatively simple calculation has been applied to a number of different functional groups, and gives band intensities adequate for dividing the bands into very strong, strong, medium, weak, or very weak (forbidden) categories. © 1992 by John Wiley & Sons, Inc.     

Molecular mechanics (MM3) calculations on lithium amide compounds

The MM3 force field has been extended to deal with the lithium amide molecules that are widely used as efficient catalysts for stereoselective asymmetric synthesis. The MM3 force field parameters have been determined on the basis of the ab initio MP2/6-31G* and/or DFT (B3LYP/6-31G*, B3-PW91/6-31G*) geometry optimization calculations. To evaluate the electronic interactions specific to the lithium amides derived from the diamine molecules properly, the Lewis bonding potential term for the interaction between the lithium atom and the nonbonded adjacent electronegative atom such as nitrogen was introduced into the MM3 force field. The bond dipoles were evaluated correctly from the electronic charges on the atoms calculated by fitting to the electrostatic potential at points selected. The MM3 results on the molecular structures, conformational energies, and vibrational spectra show good agreement with those from the quantum mechanical calculations.     

Stabilization of the tautomers HP(OH)2 and P(OH)3 of hypophosphorous and phosphorous acids as ligands

Treatment of [CpRu(PPh(3))(2)Cl] 1 with the stoichiometric amount of H(3)PO(2) or H(3)PO(3) in the presence of chloride scavengers (AgCF(3)SO(3) or TlPF(6)) yields compounds of formula [CpRu(PPh(3))(2)(HP(OH)(2))]Y (Y = CF(3)SO(3) 2a or PF(6) 2b) and [CpRu(PPh(3))(2)(P(OH)(3))]Y (Y = CF(3)SO(3) 3aor PF(6) 3b) which contain, respectively, the HP(OH)(2) and P(OH)(3) tautomers of hypophosphorous and phosphorous acids bound to ruthenium through the phosphorus atom. The triflate derivatives 2a and 3a react further with hypophosphorous or phosphorous acids to yield, respectively, the complexes [CpRu(PPh(3))(HP(OH)(2))(2)]CF(3)SO(3) 4 and [CpRu(PPh(3))(P(OH)(3))(2)]CF(3)SO(3) 5 which are formed by substitution of one molecule of the acid for a coordinated triphenylphosphine molecule. The compounds 2 and 3 are quite stable in the solid state and in solutions of common organic solvents, but the hexafluorophosphate derivatives undergo easy transformations in CH(2)Cl(2): the hypophosphorous acid complex 2b yields the compound [CpRu(PPh(3))(2)(HP(OH)(2))]PF(2)O(2) 6, whose difluorophosphate anion originates from hydrolysis of PF(6)(-); the phosphorous acid complex 3b yields the compound [CpRu(PPh(3))(2)(PF(OH)(2))]PF(2)O(2) 7, which is produced by hydrolysis of hexafluorophosphate and substitution of a fluorine for an OH group of the coordinated acid molecule. All the compounds have been characterized by elemental analyses and NMR measurements. The crystal structures of 2a, 3a and 7 have been determined by X-ray diffraction methods.     

Molecular mechanics (MM3) parameterization of hydroxylamine and methyl derivatives

Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6-31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp³)—O(sp³) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.     

Photorearrangement of ylidene tautomers of azinyl(o-nitrophenyl)-carbomethoxymethanes

The photochemical properties of ylidene tautomers of azinyl (o-nitrophenyl) carbomethoxy-methanes have been examined. Photolysis at the absorption wavelength of the ylidene tautomer results in selective rearrangement of a type hitherto unknown in o-nitro-styrenes, involving transfer of an oxygen atom to exocyclic carbon, and reduction of the nitro group to nitroso.Deceased.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2323–2327, October, 1989.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of positively charged conjugated nitrogen-containing compounds

Ab initio calculations have been carried out on s-trans-N-vinylmethyleneammonium, pyridinium, and related compounds to obtain rotational barriers, structures, and vibrational frequencies. The restricted Hartree-Fock (RHF) level of theory with 6-31G** basis set was used for these calculations. In addition, the MM2(91) and MM3(94) force fields have been parameterized to calculate these positively charged nitrogen-containing compounds. A bond order term was incorporated in the force field to reproduce accurately the rotational barriers of s-trans-N-vinylmethyleneammonium and related compounds. Molecular mechanics geometries and vibrational frequencies compare well with those calculated by ab initio methods. © 1996 by John Wiley & Sons, Inc.     

Ab initio and molecular mechanics (MM2 and MM3) calculations of nonconjugated positively charged nitrogen-containing compounds

High-level ab initio calculations have been performed on N-methyl-N-methyleneammonium and related compounds to obtain accurate rotational barriers, structures, and vibrational frequencies. The 6-31G** basis set has been utilized at the Hartree-Fock level of theory for these calculations because little experimental data are available. The MM2(91) and MM3(94) force fields have been parameterized to include these nonconjugated charged nitrogen-containing compounds. Molecular mechanics geometries and vibrational frequencies compare well with the ab initio results. © 1995 John Wiley & Sons, Inc.     

(3R,4S)-isostreptenol III from Penicillium purpurogenum MM

Abstract

In continuation of the search for new compounds from the terrestrial fungus Penicillium purpurogenum MM, (3R,4S)-isostreptenol III (1), a further new natural compound is reported. The chemical structure of 1 was confirmed by extensive 1D and 2D NMR and ESI HR mass measurements, and by comparison with literature data. The absolute configuration was determined by ab initio calculations of ECD, ORD, and NMR data. The antimicrobial and cytotoxic activities of the crude extract and 1 were reported using a set of microorganisms and by the brine shrimp assay, respectively.     

Conformational analysis of jet-cooled tryptophan analogs and Histamine using the MM3(94) force field: Comparison with experiment

MM3(94) has been used to predict the conformers of nitrogen-containing aromatic heterocycles with polar aliphatic sidechains. Computations were done for cases in which experimental gas-phase rotational constants have been determined and include histamine and analogs of tryptophan. The agreement with experiment for the tryptophan analogs is better than earlier MM2(87) computations but still not complete. A fairly good match can be made to experimental rotational constants of four histamine conformers, but other conformers are also predicted that may not be important experimentally. A comparison can be made with ab initio calculations undertaken for histamine. Similar structures were generally predicted, but there were significant discrepancies with MM3 in relative conformer energies. © 1995 by John Wiley & Sons, Inc.