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     

Molecular mechanics (MM4) calculations on carbonyl compounds part I: aldehydes

Aliphatic aldehydes have been studied with the aid of the MM4 force field. The structures, moments of inertia, vibrational spectra, conformational energies, barriers to internal rotation, and dipole moments have been examined for six compounds (nine conformations). MM4 parameters have been developed to fit the indicated quantities to the wide variety of experimental data. Ab initio (MP2) and density functional theory (B3LYP) calculations have been used to augment and/or replace experimental data, as appropriate. Because more, and to some extent, better, data have become available since MM3 was developed, it was anticipated that the overall accuracy of the information calculated with MM4 would be better than with MM3. The best single measure of the overall accuracy of a force field is the accuracy to which the moments of inertia of a set of compounds (from microwave spectroscopy) can be reproduced. For all of the 20 moments (seven conformations) experimentally known for the aldehyde compounds, the MM4 rms error is 0.30%, while with MM3, the most accurate force field presently available, the rms error over the same set is 1.01%. The calculation of the vibrational spectra was also improved overall. For the four aldehydes that were fully analyzed (over a total of 78 frequencies), the rms errors with MM4 and MM3 are 18 and 38 cm^?1, respectively. These improvements came from several sources, but the major ones were separate parameters involving the carbonyl carbon for formaldehyde, the alkyl aldehydes and the ketones, and new crossterms featured in the MM4 force field that are not present in the MM3 version. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1396–1425, 2001     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

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.     

Force field calculations (MM3) on glyoxal,quinones, and related compounds

A general force field type of calculation has been devised in connection with MM3 to treat 1,2- and 1,4-diketones, both when they are not conjugated (as in derivatives of glyoxal) and when they are conjugated (as in derivatives of ortho- and para-benzoquinone). The molecular structures, moments of inertia, dipole moments, and vibrational spectra have been examined for about 15 compounds, some in several conformations. Ab initio calculations (6-31G*) have been used to determine quantities that have not been previously defined by experiment. In general, the force field permits the calculation of the structures with high accuracy, and the spectroscopic and conformational energy data with fair accuracy. © 1994 by John Wiley & Sons, Inc.     

Modified MM2 scheme for computation of O?C?N-containing systems

A modification of Allinger's MM2 force field for the anomeric effect in O? C? N systems is presented. For optimal consistency, it was parameterized by alternate use of ab initio (3-21G level) and X-ray results to account for the energetic and structural manifestations of the effect in the gas or condensed phase, respectively. The results obtained with the modified force field are in good agreement with those from both theoretical and experimental methods. The parameterization scheme explicitly treats all structural parameters of the C? O? C? N? C moiety as well as C? N bond lengths in tertiary amines contained within an anomeric unit. In addition, it includes directional H-bond type interactions. A limited number of parameters is put forward, in accord with the general MM2 force-field approach. © 1993 John Wiley & Sons, Inc.     

A comparative study of the structure and bonding of HOO,HOS, HSO,and HSS radicals by CNDO/2 and INDO methods

Equilibrium geometries, force constants, barriers to linearity, charge distributions, dipole moments, and electron spin density of HOO, HOS, HSO, and HSS radicals are calculated by CNDO/2 and INDO methods using respectively the original and some recently introduced scheme of parametrization. Three sets of calculations, namely, CNDO/2(sp), CNDO/2(spd), and INDO, are performed, and the results are compared with the ab initio and experimental values, wherever available. A good agreement is obtained for geometry in the case of CNDO/2 (sp) and INDO calculations. The performance of CNDO/2 (spd) calculations in this regard is quite unreliable. The stretching force constants are considerably overestimated by all the methods, while the bending force constants are in reasonable agreement with the ab initio values. With respect to dipole moments, the CNDO/2 values are in better agreement with the ab initio results than the INDO values. In all the cases, the dipole moment vector directions are in complete disagreement with the ab initio predictions.     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.     

On the use of conformationally dependent geometry trends from ab initio dipeptide studies to refine potentials for the empirical force field CHARMM

Previous 4-21G ab initio geometry optimizations of various conformations of the model dipeptides (N-acetyl N'methyl amides) of glycine (GLY) and the alanine (ALA) have been used to help refine the empirical force constants and equilibrium geometry in the CHARMM force field for peptides. Conformationally dependent geometry trends from ab initio calculations and positions of energy minima on the ab initio energy surfaces have been used as guides in the parameter refinement, leading to modifications in the bond stretch, angle bending, and some torsional parameters. Preliminary results obtained with these refined empirical parameters are presented for the protein Crambin. Results for the cyclic (Ala-Pro-DPhe)₂ are compared with those from other calculations. It seems that the dihedral angle fit achieved by the new parameters is significantly improved compared with results from force fields whose derivation does not include ab initio geometry trends.     

A molecular mechanics study of the Si?O bond and alkyl-silanes

The standard MM2 force field and program have been modified to include Si? O groups, the force constants being derived from ab initio wavefunctions, and using partial atomic charges calculated from the empirical algorithm CHARGE2. Molecular mechanics calculations have been carried out on disiloxane, dimethoxy-dimethylsilane, methyl silyl ether, and cyclotrisiloxane, and reasonable agreement has been obtained between the observed and calculated geometries. In addition, the energies obtained using the modified force field have been tested against experimental data on alkyl silanes where energetic and structural information is available. Again good agreement is obtained. The application of the force field to extended Si? O systems will also be discussed.     

Unusual conformational-determining interactions in oxymethylpyridines: An ab initio study and an improved method for refining molecular mechanics parameters

The conformational preferences of oxymethylpyridines have been investigated by ab initio calculations and compared to similar calculations for oxymethylbenzene. The C? O bond in the pyridine compounds was found to prefer eclipsing with a C? C bond in the ring, in agreement with previous observations but in disaccord with tentative MM2 calculations. The effect was most pronounced in the 2-substituted pyridine. The benzene compound, on the other hand, showed good agreement between the energies from MM2, MM3, and ab initio calculations. The conformational preferences are discussed in terms of stereoelectronic interactions. New MM2 and MM3 parameters were determined from ab initio calculations on nonstationary points on the energy hypersurface. The parameterization method is discussed. © 1995 by John Wiley & Sons, Inc.     

Molecular mechanics calculations on carbonyl compounds. III. Cycloketones

Molecular mechanics (MM4) calculations were carried out on cycloketones for ring sizes ranging from 4 to 11 carbon atoms. The MM4 relative energies for the various conformations of the cycloketones were compared to density functional theory (DFT) calculations (B3LYP/6‐31G*), which were also carried out in this work. For small ring sizes (n=4–6), calculated molecular geometries, dipole moments, moments of inertia, and vibrational spectra were compared to experimental data. The axial–equatorial energy differences in methyl‐substituted cyclohexanones were also calculated by MM4 and compared to ab initio, DFT, and experimental results. The results of the MM4 studies on cycloketones showed significant improvement from those of MM3 calculations performed in parallel with the MM4 calculations. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1451–1475, 2001     

Alcohols,ethers, carbohydrates,and related compounds. I. The MM4 force field for simple compounds

Simple alcohols and ethers have been studied with the MM4 force field. The structures of 13 molecules have been well fit using the MM4 force field. Moments of inertia have been fit with rms percentage errors as indicated: 18 moments for ethers, 0.28%; 21 moments for alcohols, 0.22%. Rotational barriers and conformational equilibria have also been examined, and the experimental and ab initio results are reproduced substantially better with MM4 than they were with MM3. Much of the improvement comes from the use of additional interaction terms in the force constant matrix, of which the torsion-bend and torsion-torsion are particularly important. Induced dipoles are included in the calculation, and dipole moments are reasonably well fit. It has been possible for the first time to fit conformational energetic data for both open chain and cyclic alcohols (e.g., propanol and cyclohexanol) with the same parameter set. For vibrational spectra, over a total of 82 frequencies, the rms error is 27 cm(-1), as opposed to 38 cm(-1) with MM3. Both the alpha and beta bond shortening resulting from the presence of the electronegative oxygen atom in the molecule are well reproduced. The electronegativity of the oxygen is sufficient that one must also include not only the alpha and beta electronegativity effects on bond lengths, but also on angle distortions, if structures are to be well reproduced. The heats of formation of 32 alcohols and ethers were fit overall to within experimental error (weighted standard deviation error 0.26 kcal/mol).     

A CNDO/INDO molecular orbital formalism for the elements H to Br. applications

The CNDO/INDO molecular orbital formalism introduced in the preceding paper has been applied to a large number of atom combinations up to bromine under the inclusion of the first transition metal series. The results are compared with experimental data (geometries, ionization potentials, dipole moments) or with the results of sophisticatedab initio calculations (one electron energies, net charges, atomic populations). The semiempirical model reproduces for a wide range of molecules the experimental andab initio data with remarkable success.     

Conformational energies and rotational barriers in 3-methyl-1-butene and 1-butene: An ab initio and molecular mechanics study

The calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3-methyl-1-butene is not in agreement with experimental data. In order to reparametrize the C_sp2-C_sp3-C_sp-C_sp3 torsional angle, 3-methyl-1-butene and 1-butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6-31G* and MP3/6-31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3-methyl-1-butene and 1-butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.     

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.     

A molecular mechanics study of conformational trends in simple alcohols and ethers. Part I: Geometric trends

We have modified the MM2(80) molecular mechanics force field for alcohols and ethers to reproduce geometric trends predicted by ab initio calculations with the 4-21G basis set. The results obtained with the modified force field are consistent with experimental evidence.     

Ab initio molecular calculations with pseudopotentials: Higher quality calculations on Li2, LiH,and BeH2

New psudopotentials of higher quality have been used in ab initio molecular calculations. Simple molecular systems like Li₂, LiH, and BeH₂ have been investigated with varying basis sets. Energy, geometrical parameters, and dipole moments have been determined. The convergence properties of the various quantities have been investigated. They show characteristic behavior, e.g., stationary value for the energy where such behavior may be expected.     

Molecular mechanics study of conformational trends in simple alcohols and ethers. II. Intramolecular hydrogen bonding

In this article we present an extension of our modified MM2(80) force field MM2MOD in which a potential function for hydrogen bonding in alcohols and ethers is included. The results of applying MM2(85), MM2(87), and MM2MOD on ethylene glycol, 2-methoxyethanol and 1,3-propanediol are reported and compared with available experimental data and ab initio results. It is concluded that hydrogen bonding plays an important role in determining the molecular conformations of these systems. © 1992 by John Wiley & Sons, Inc.