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.     

CNDO/2 (complete neglect of differential overlap)-method for third-row molecules

An extension of the CNDO/2 method to compounds containing third-row elements (Germanium, Arsenic, Selenium and Bromine) is presented. Bond lengths, bond angles, dipole moments, and ionization potentials are considered.     

Towards an Understanding of the Carbon-Carbon Bond

In this essay, the classical question of “the influence of the number and kind of substituents on the strength of the C? C bond”, is pursued with the modern tools of contemporary physical organic chemistry. Based on the work of Karl Ziegler, the products and kinetics of thermolysis of a large number of highly branched aliphatic hydrocarbons and phenyl- or cyano-substituted derivatives were investigated. For each class of compounds, a linear relationship was found between the free enthalpy of activation of the homolytic cleavage of the weakest C? C bond and the strain energy in the ground state. These relationships permitted a quantitative separation of steric and electronic effects on the cleavage of C? C bonds. The influence of the size of the substituent groups on bond angles, bond lengths, and the conformational behavior of model compounds was studied by means of experimental structure determinations and force field calculations. C? C bond lengths up to 164 pm, bond angles at tetracoordinate carbon as large as 126°, and unusual eclipsed and gauche preferred conformations were found.     

Theoretical study of ketenimine: Geometry,electronic properties,force constants and barriers to inversion and rotation

Non-empirical calculations of the structure and properties of ketenimine have been performed using nine Gaussian basis sets. Values for the bond lengths and angles, HOMO and LUMO energies, atomic charges, overlap populations, dipole moments, bond energies, force constants and barriers to nitrogen inversion and internal rotation are predicted.     

Structural model of dioxouranium(VI) with hydrazono ligands

Synthesis and characterization of several new coordination compounds of dioxouranium(VI) heterochelates with bidentate hydrazono compounds derived from 1-phenyl-3-methyl-5-pyrazolone are described. The ligands and uranayl complexes have been characterized by various physico-chemical techniques. The bond lengths and the force constant have been calculated from asymmetric stretching frequency of OUO groups. The infrared spectral studies showed a monobasic bidentate behaviour with the oxygen and hydrazo nitrogen donor system. The effect of Hammett's constant on the bond distances and the force constants were also discussed and drawn. Wilson's matrix method, Badger's formula, Jones and El-Sonbati equations were used to determine the stretching and interaction force constant from which the UO bond distances were calculated. The bond distances of these complexes were also investigated.     

Molecular mechanics (MM4) study of amines

The MM4 force field has been extended to include aliphatic amines. About 20 amines have been examined to obtain a set of useful molecular mechanics parameters for this class. The vibrational spectra of seven amines (172 frequencies) calculated by MM4 have an overall rms error of 27 cm(-1), compared with corresponding MM4 value of 24 cm(-1) for alkanes. The rms and signed average errors of the moments of inertia of nine simple amines compared with the experimental data were 0.18% and -0.004%, respectively. The heats of formation of 30 amines were also studied. The MM4 weighted standard deviation is 0.41 kcal/mol, compared with experiment. Electronegativity effects occur in the hydrocarbon portion of an amine from the nitrogen, and are accounted for by including electronegativity induced changes in bond lengths and angles, and induced dipole-dipole interactions in the molecule. Negative hyperconjugation results from the presence of the lone pair of electrons on nitrogen, and leads to the Bohlmann bands in the infrared, and also to strong and unusual geometric changes in the molecules (Bohlmann effect), all of which are fairly well accounted for. The conformational energies in amines appear to be less straightforward than those for most other classes of molecules, apparently because of the Bohlmann effect, and these are probably not yet completely understood. In general, the agreement between the MM4 calculated results and the available data is reasonably good.     

Transferability of the electronic structure characteristics of saturated molecules

The common quantum mechanical problem for the total class of saturated hydrocarbons has been stated and solved within the framework of the effective Hamiltonian method. A quantum mechanical substantiation of the transferability of the electronic structure characteristics (bond dipole moments, bond energies, and bond force constants) as well as the investigation of the origin of transferability have been considered for the stated class of chemical compounds.     

Activation of the sulfhydryl group by Mo centers: kinetics of reaction of benzyl radical with a binuclear Mo(micro-SH)Mo complex and with arene and alkane thiols

This paper provides evidence from kinetic experiments and electronic structure calculations of a significantly reduced S-H bond strength in the Mo(micro-SH)Mo function in the homogeneous catalyst model, CpMo(micro-S)(2)(micro-SH)(2)MoCp (1, Cp = eta(5)-cyclopentadienyl). The reactivity of 1 was explored by determination of a rate expression for hydrogen atom abstraction by benzyl radical from 1 (log(k(abs)/M(-)(1) s(-)(1)) = (9.07 +/- 0.38) - (3.62 +/- 0.58)/theta) for comparison with expressions for CH(3)(CH(2))(7)SH, log(k(abs)/M(-)(1) s(-)(1)) = (7.88 +/- 0.35) - (4.64 +/- 0.54)/theta, and for 2-mercaptonaphthalene, log(k(abs)/M(-)(1) s(-)(1)) = (8.21 +/- 0.17) - (4.24 +/- 0.26)/theta (theta = 2.303RT kcal/mol, 2sigma error). The rate constant for hydrogen atom abstraction at 298 K by benzyl radical from 1 is 2 orders of magnitude greater than that from 1-octanethiol, resulting from the predicted (DFT) S-H bond strength of 1 of 73 kcal/mol. The radical CpMo(micro-S)(3)(micro-SH)MoCp, 2, is revealed, from the properties of slow self-reaction, and exclusive cross-combination with reactive benzyl radical, to be a persistent free radical.     

Relation of chemical structure to reactivity in complete oxidation on oxide contact catalysts for open-chain hydrocarbons

It is shown that the relative reactivities of alkanes, alkenes, alkynes, and cyclopropane in complete oxidation decreases with increase in the energy of the bond broken in the rate-limiting step: for alkanes from ethane upwards this is a C-C bond, for unsaturated hydrocarbons it is the -type C-C bond, and for methane it is a C-H bond.     

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     

Quantum treatment of hydrogen nuclei in primary kinetic isotope effects in a thermal [1,5]-sigmatropic hydrogen (or deuterium) shift from (Z)-1,3-pentadiene

The geometric and kinetic isotope effects (GIE and KIE) for thermal [1,5]-sigmatropic H and D shifts of (Z)-1,3-pentadiene were studied by including the direct quantum effect of the migrating H or D nucleus in the multi-component molecular orbital-Hartree-Fock (MC_MO-HF) method. Based on the results, the C(1)-D bond lengths are 0.007 Angstrom shorter than the C1-H bond lengths in both the reactant (A) and the transition states (TS), whereas other bond lengths resemble those between H and D. The ratio of the rate constant (k(H)/k(D)) of the reaction for the thermal [1,5]-H and D shifts determined using the MC_MO-HF method (8.28) is closer to the experimental value (12.2) than that determined using either the conventional restricted Hartree-Fock (4.10) or restricted M?ller-Plesset second-order perturbation (3.79) methods.     

Molecular mechanics of organic halides: Part IV. Monobromides and non-geminal dibromides

A molecular-mechanical hydrocarbon force field is extended to apply to saturated organic bromides, including non-geminal dibromides. Simultaneous calculation of molecular geometries, dipole moments, conformer energies and barriers to internal rotation is provided for. Results are reported for 34 molecules, acyclic and cyclic, representing altogether 78 structural variants. Variability in bond lengths and dihedral angles, and the “repulsive gauche effect”, are touched on in the discussion.     

Molecular geometries and heats of formation of C60 and C70 as computed by MM2-87

MM2-87 calculations have been performed on C₆₀ (buckminsterfullerence; footballene) and C₇₀ with full energy minimization. The steric energies for C₆₀ and C₇₀ were computed to be 179.9 and 177.9 kcal/mol, respectively. The heats of formation for C₆₀ is found to be more stable than C₆₀. The two bond lengths for C₆₀ were computed to be 1.393 and 1.444 Å. Eight different bond lengths were found for C₇₀ ranging from 1.386 to 1.452 Å. Bond angles, dihedral angles, and moments of inertia are also reported for the compounds.     

Remarks on the molecular mechanical calculations of functionalized hydrocarbons

Molecular mechanical calculations for hetero-substituted hydrocarbons present certain difficulties that are not encountered in dealing with hydrocarbons. Ways are proposed to overcome such difficulties, sometimes by two-step or iterative computation. The following topics are considered: fitting the force field by using data from studies in solution; ways to estimate atomic charges or, alternatively, bond moments; ways to account for field effects upon atomic charges and bond moments.     

Molecular dynamics simulation of the dielectric constant of water: the effect of bond flexibility

The role of bond flexibility on the dielectric constant of water is investigated via molecular dynamics simulations using a flexible intermolecular potential SPC/Fw [Y. Wu, H. L. Tepper, and G. A. Voth, J. Chem. Phys. 128, 024503 (2006)]. Dielectric constants and densities are reported for the liquid phase at temperatures of 298.15 K and 473.15 K and the supercritical phase at 673.15 K for pressures between 0.1 MPa and 200 MPa. Comparison with both experimental data and other rigid bond intermolecular potentials indicates that introducing bond flexibility significantly improves the prediction of both dielectric constants and pressure-temperature-density behavior. In some cases, the predicted densities and dielectric constants almost exactly coincide with experimental data. The results are analyzed in terms of dipole moments, quadrupole moments, and equilibrium bond angles and lengths. It appears that bond flexibility allows the molecular dipole and quadrupole moment to change with the thermodynamic state point, and thereby mimic the change of the intermolecular interactions in response to the local environment.     

Molecular parameters for the prediction of polyurethane structures

Recent efforts to determine the structures of poly(MDI/diol) hard segments in polyurethane elastomers have relied on the structures determined by single-crystal x-ray methods for diphenylmethane urethane model compounds. We have surveyed the structure of six model compounds, and have derived average values for the bond lengths, bond angles, and bond torsion angles for use in future analyses. The applicability of these averages to polymer structures is discussed, and the data are used to derive models for the poly(MDI-butanediol) chain which are found to be consistent with the fiber repeat determine by x-ray methods.     

An improved empirical force field for saturated hydrocarbons

A new molecular mechanics force field for alkanes is presented. The force field aims to eliminate some identified failures of the well-known MM2 force field. The new energy function gives an improved prediction of the rotational barriers of highly congested molecules, a better calculation of short nonbonded contacts, and the correct reproduction of bond elongation in small torsion angles. The calculation of sublimation enthalpies is also improved. The standard deviation of the formation enthalpies for a set of 54 compounds is 0.63 kcal/mol; this compares with the reported value of 0.42 calculated with MM2 and MM3 for different sets. The force field parameters were obtained using a least squares method.     

Parametrization in the AM 1 method

Parameter definition is considered for the AM 1 method, which is a new modification of MNDO incorporating better correction for atomic-core repulsion, so the promising approach can be used to calculate energy and structural characteristics for molecules and adducts. Calculations have been performed on heats of formation, ionization potentials, and dipole moments for various compounds, as well as structure parameters (bond lengths and bond and torsion angles), which are close to the standard ones and reproduce experimental values satisfactorily.Translated from Teoreticheskaya i Éksperimental'naya Khimiya, Vol. 24, No. 6, pp. 713–717, November–December, 1988.     

Effects of chain length on the rates of C-C bond dissociation in linear alkanes and polyethylene

Molecular dynamics modeling of C-C bond dissociation is performed for a series of linear alkanes and polyethylene macromolecules with the chain lengths ranging from one to a thousand constituent ethylene monomers (PE-1-PE-1000). The rate constants obtained in molecular dynamics calculations are compared with those determined using variational transition state theory with the same potential energy surface. The results of simulations demonstrate a significant accelerating effect of chain length on the rates of C-C bond scission. Per-bond rate constant values increase with the increasing chain length, up to an order of magnitude, in the sequence of linear alkanes from PE-1 (ethane) to PE-5 (decane); this dependence becomes saturated for longer chain lengths. Stiffening the potentials of bending and especially the torsional degrees of freedom diminishes the accelerating effect of chain length, while constraining the bond distances for all C-C bonds except the one undergoing dissociation has no effect. The results of the calculations are compared with existing experimental data on the dependences of the rates of thermal decomposition of linear alkanes on the alkane chain length.     

Chemical ionization pathways of polyfluorinated chemicals—A connection to environmental atmospheric processes

A systematic mass spectrometry study of an industrially prolific class of polyfluorinated compounds known as telomers was conducted. The study specifically focused upon polyfluorinated alcohols along with corresponding saturated and alpha,beta-unsaturated fluoroacids. Within each class differing fluoroalkyl chain length homologues were investigated, using negative and positive chemical ionization mass spectrometry (NCI and PCI). In the case of the fluoroalcohols, NCI resulted in the production of more elaborate spectra than the other classes. Moreover, it showed the interesting production of HF(2)(-) and the complex of this species, along with F(-), with the parent molecule. These complexes resulted in the formation of the novel H(2)F(3)(-) ion. Results show that there is significant intra-molecular hydrogen bonding that occurs for these compounds, which influences the molecules fragmentation. This bonding will also influence the fate and disposition through environmental processes (e.g., V(P), k(OH), K(OW), K(OA)) which are affected by molecular geometry. Furthermore, there is an increased accumulation and persistence potential for the molecule as a function of the fluorocarbon chain length. We have shown that in conjunction with the use of mass spectroscopy the engertics of environmental processes for polyfluorinated materials can be established.