G2 ab initio calculations on three-membered rings: Role of hydrogen atoms

G2 ab initio calculations on all ABX three-membered rings (TMRs) that can be derived from cyclopropane by systematic substitution of the (SINGLE BOND)CH₂ groups by (SINGLE BOND)NH or (SINGLE BOND)O groups have been performed. Our results show that the decrease in the A(SINGLE BOND)B bond length as the electronegativity of X increases is significantly larger than that found for the corresponding acyclic analogs. In general, a systematic substitution of the (SINGLE BOND)CH₂ groups of cyclopropane by (SINGLE BOND)NH or (SINGLE BOND)O groups implies significant geometric changes that are not reflected in a parallel change of the corresponding conventional ring strain energy (CRSE). When the electronegativity of the groups forming the TMR increases the effect on the CRSE of the system is small, although the charge delocalization inside the ring decreases. The near constancy of the CRSE along the series can be explained in terms of the charge redistribution of the system where the (SINGLE BOND)CH₂ groups play a crucial role. There are, however, significant changes in the hydrogenation energies of the TMR investigated; our results show that, when in an ABX three-membered ring, the electronegativity of X increases the hydrogenation energy of A(SINGLE BOND)B bond decreases and vice versa. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1072–1086, 1998     

Calculation of bond dissociation energies for oxygen containing molecules by ab initio and density functional theory methods

Two ab initio (ROHF and MP2), one local (SVWN), four hybrid (BHandH, BHandHLYP, Becke3LYP, and Becke3P86), and two nonlocal (BLYP and BP86) density functional theory (DFT) methods are used for calculating the dissociation energies of molecules that contain H(SINGLE BOND)O, O(SINGLE BOND)O and O(SINGLE BOND)C bonds. The sensitivity to the basis set of the prediction of bond dissociation energies with DFT methods was tested with Becke3LYP on the H(SINGLE BOND)O dissociation energy of water. The 6–31 + G(d) methods are chosen as the smallest basis set which produces reasonable results. The calculated values for all other ab initio and DFT methods were performed with these basis sets and then compared with the experimental data. The suitability of DFT methods for computing reliable bond dissociation energies of oxygen containing molecules is discussed. © 1996 John Wiley & Sons, Inc.     

Molecular structure and binding energies of monosubstituted hexacarbonyls of chromium,molybdenum, and tungsten: Relativistic density functional study

Relativistic density functional calculations have been carried out for the group VI transition metal carbonyls M(CO)₅L (M=Cr, Mo, W; L=OH₂, NH₃, PH₃, PMe₃, N₂, CO, OC (isocarbonyl), CS, CH₂, CF₂, CCl₂, NO⁺). The optimized molecular structures and M(SINGLE BOND)L bond dissociation energies, as well as the metal–carbonyl bond energy of the trans CO group, have been calculated. Besides the marked dependence of the trans M(SINGLE BOND)CO bond length on the type of ligand L, such an effect on the that bond energy is also observed. For the chromium compounds, the trans Cr(SINGLE BOND)CO bond length varies from 184 to 199 pm and its bond energy from 242 to 150 kJ/mol. For the molybdenum compounds, the range is 197 to 216 pm and 253 to 128 kJ/mol and, for tungsten, 198 to 214 pm and 293 to 159 kJ/mol. The observed trends can be explained with the π acceptor strength of the L ligand. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1985–1992, 1997     

The structure of 1-chlorosilatrane: An ab initio molecular orbital and a density functional theory study

The molecular geometries of the 1-chloro-, 1-fluoro-, 1-methyl-, and 1-hydrogenosilatranes were fully optimized by the restricted Hartree-Fock (HF) method supplemented with 3-21G, 3-21G(d), 6-31G(d), and CEP-31G(d) basis sets; by MP2 calculations using 6-31G(d) and CEP-31G(d) basis sets; and by GGA-DFT calculations using 6-31G(d5) basis set with the aim of locating the positions of the local minima on the energy hypersurface. The HF/6-31G(d) calculations predict long (>254 pm) and the MP2/CEP calculations predicted short (∼225 pm) equilibrium Si(SINGLE BOND)N distances. The present GGA-DFT calculations reproduce the available gas phase experimental Si(SINGLE BOND)N distances correctly. The solid phase experimental results predict that the Si(SINGLE BOND)N distance is shorter in 1-chlorosilatrane than in 1-fluorosilatrane. In this respect the HF results show a strong basis set dependence, the MP2/CEP results contradict the experiment, and the GGA-DFT results in electrolytic medium agree with the experiment. The latter calculations predict that 1-chlorosilatrane is more polarizable than 1-fluorosilatrane and also support a general Si(SINGLE BOND)N distance shortening trend for silatranes during the transition from gas phase to polar liquid or solid phase. The calculations predict that the ethoxy links of the silatrane skeleton are flexible. Consequently, it is difficult to measure experimentally the related bond lengths and bond and torsion angles. This is the probable origin of the surprisingly large differences for the experimental structural parameters. On the basis of experimental analogies, ab initio calculations, and density functional theory (DFT) calculations, a gas phase equilibrium (r_e) geometry is predicted for 1-chlorosilatrane. The semiempirical methods predict a so-called exo minimum (at above 310 pm Si(SINGLE BOND)N distance); however, the ab initio and GGA-DFT calculations suggest that this form is nonexistent. The GGA-DFT geometry optima were characterized by frequency analysis. © 1996 by John Wiley & Sons, Inc.     

Molybdenum (VI) dioxodihalides: Agreement with experiment and prediction of unknown properties through density functional theory

Density functional calculations are reported for the molecular structures, harmonic vibrational frequencies, UV/visible spectra, and oxo-transferability of MoO₂X₂ (X = F, Cl, Br, I). Available experimental data have been used to check the validity of the theoretical calculations. Given the good agreement between theory and gas-phase experiment, predictions have been issued for the less studied members of this family of compounds. Furthermore, electronic spectra of the full series have been computed for the first time. For all transitions studied, excitation energies decrease in the order F > Cl > Br > I. Finally, the labilization of Mo(SINGLE BOND)O bonds generated by the HOMO(SINGLE BOND)LUMO transition, which is related to the oxygen-atom transfer reaction in the active site of molybdenum oxidoreductases, was also investigated. For MoO₂Cl₂ and MoO₂Br₂ compounds, the HOMO-LUMO transition yields a considerable lengthening of the Mo(SINGLE BOND)O bond, yet not requiring a large excitation energy. © 1997 John Wiley & Sons, Inc.     

A comparative study of O2, CO,and NO binding to iron–porphyrin

Minimum-energy structures of O₂, CO, and NO iron–porphyrin (FeP) complexes, computed with the Car–Parrinello molecular dynamics, agree well with the available experimental data for synthetic heme models. The diatomic molecule induces a 0.3–0.4 Å displacement of the Fe atom out of the porphyrin nitrogen (N_p) plane and a doming of the overall porphyrin ring. The energy of the iron–diatomic bond increases in the order Fe(SINGLE BOND)O₂ (9 kcal/mol) < Fe(SINGLE BOND)CO (26 kcal/mol) < Fe(SINGLE BOND)NO (35 kcal/mol). The presence of an imidazole axial ligand increases the strength of the Fe(SINGLE BOND)O₂ and Fe(SINGLE BOND)CO bonds (15 and 35 kcal/mol, respectively), with few structural changes with respect to the FeP(CO) and FeP(O₂) complexes. In contrast, the imidazole ligand does not affect the energy of the Fe(SINGLE BOND)NO bond, but induces significant structural changes with respect to the FeP(NO) complex. Similar variations in the iron–imidazole bond with respect to the addition of CO, O₂, and NO are also discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 69: 31–35, 1998     

Density functional study of chlorine–oxygen compounds related to the ClO self-reaction

Geometrical parameters, vibrational frequencies, relative stabilities, and dissociation energies of the three stable Cl₂O₂ isomers and the OClO and ClOO radicals were investigated by density functional theory (DFT). The present analysis shows that DFT using hybrid functionals is capable of describing these systems to at least the same degree of accuracy as ab initio methods. The average absolute bond-length deviation of ClClO₂, ClOOCl, and ClO₂ from experimental results is 0.024/0.027 Å, with a maximum deviation for the dichlorine peroxide O(SINGLE BOND)O bond equal to 0.072/0.063 Å, for the B3PW91 and B3LYP functionals, respectively. The average absolute bond-angle deviation for the hybrid functionals is 0.8°. Harmonic vibrational frequencies calculated with DFT give for all Cl(SINGLE BOND)O compounds good agreement with experiments. The dissociation energies of ClOOCl, OClO, and ClOO were found to be in good agreement with experiments, the average error being less than 1.2 kcal/mol. The two isomers chloryl chloride (ClClO₂) and dichlorine peroxide (ClOOCl) were found to be approximately 9 kcal/mol more stable than the chlorine chlorite (ClOClO) isomer. The ClOO isomer is predicted to be 3.0 kcal/mol more stable than OClO, in accordance with the experimental value of 4 kcal/mol. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 203–217, 1998     

Silaacetylene: A possible target for experimental studies

The equilibrium geometries and transition states for interconversion of the CSiH₂ isomers in the singlet electronic ground state are optimized at the MP2 and CCSD(T) levels of theory using a TZ2P basis set. The heats of formation, vibrational frequencies, infrared intensities, and rotational constants are also predicted. There are three energy minima on the CSiH₂ potential energy surface. Energy calculations at CCSD(T)/TZ2P(fd) + ZPE predict that the global energy minimum is silavinylidene (1), which is 34.1 kcal mol⁻¹ lower in energy than trans-bent silaacetylene (2) and 84.1 kcal mol⁻¹ more stable than the vinylidene isomer (3). The barrier for rearrangement 2→1 is calculated at the same level of theory to be 5.1 kcal mol⁻¹, while for the rearrangement 3→2 a barrier of 2.7 kcal mol⁻¹ is predicted. The natural bond orbital (NBO) population scheme indicates a clear polarization of the C(SINGLE BOND)Si bonds toward the carbon end. A significant ionic contribution to the C(SINGLE BOND)Si bonds of 1 and 2 is suggested by the NBO analysis. The C(SINGLE BOND)Si bond length of trans-bent silaacetylene (2) is longer than previously calculated [1.665 Å at CCSD(T)/TZ2P)]. The calculated carbon-silicon bond length of 2 is in the middle between the C(SINGLE BOND)Si double bond length of 1 (1.721 Å) and the C(SINGLE BOND)Si triple bond of the linear form HCSiH (4), which is 1.604 Å. Structure 4 is a higher-order saddle point on the potential energy surface. © 1996 by John Wiley & Sons, Inc.     

Ab initio studies of three-membered ring formation through intramolecular nucleophilic substitution

Three-membered ring (3MR) forming processes of ⁻X(SINGLE BOND)CH₂(SINGLE BOND)CH₂(SINGLE BOND)F and ⁻CH₂(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH₂(SINGLE BOND)F (X(DOUBLE BOND)CH₂, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (S_Ni) are studied theoretically using the ab initio molecular orbital method with the 6–31+G* basis set. When electron correlation effects are considered, the activation (ΔG^≠) and reaction energies (ΔG⁰) are lowered by ca. 10 kcal mol⁻¹, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (−TΔS^≠) at 298 K to ΔG^≠ is very small, and the reactions are enthalpy controlled. The ΔG^≠ and ΔG⁰ values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell–Evans–Polanyi principle applies well to all these reaction series. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 1773–1784, 1997     

Estimates of the structure and dimerization energy of polyacetylene from ab initio calculations on finite polyenes

Ab initio calculations at the Hartree-Fock (HF) and the second-order Møller-Plesset (MP2) levels are performed for finite polyenes C_2nH_2n+2 to estimate the structure and dimerization energy (E_dim) of polyacetylene. The effect of electron correlation on the structure of finite polyenes is analyzed in detail. The MP3/6–31G* C(DOUBLE BOND)C and C(SINGLE BOND)C bond lengths in polyacetylene are estimated by a simple extrapolation method using empirical corrections for the MP2 deficiencies, yielding values [C(DOUBLE BOND)C(MP3) ∼ 1.36 Å and C(SINGLE BOND)C(MP3) ∼ 1.44 Å] that are in a good agreement with experiment (C(DOUBLE BOND)C (DOUBLE BOND) 1.36 Å and C(SINGLE BOND)C (DOUBLE BOND) 1.44–1.45 Å). Comparison is also made with other theoretical estimates of polyacetylene structure. E_dim is approximated by the energy difference between the equilibrium and hypothetical polyenic structures. It is estimated that E_dim is ∼ 1.4–1.5 kcal/mol (0.06–0.07 eV) per carbon-carbon bond at the HF level with 4–21G and 6–31G* basis sets and ∼ 0.3–0.5 kcal/mol (0.013–0.022 eV) at the MP2 level with the 6–31G* basis set. It is concluded that E_dim is very sensitive to the level of approximation employed so that a proper treatment of electron correlation is essential to obtain a reliable estimate of the dimerization energy. © 1997 John Wiley & Sons, Inc.     

Theoretical study of ester enolate–imine condensation route to β-lactams

The condensation reaction of the enolate of methyl acetate with formaldimine to afford a β-lactam was studied using the MP2-FC/6-31+G* level of theory taking into account the electrostatic effect of the solvent by means of a self-consistent reaction field continuum model. The reaction is a stepwise process with three main steps: the formation of the C3(SINGLE BOND)C4 bond, the closure of the β-lactam ring, and the elimination of the methoxide ion. The formation of the C3(SINGLE BOND)C4 bond is rate determining and according to our calculations is not a reversible step. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1826–1833, 1998     

Hydrogen-bonding interactions of the trifluoromethyl group: 2-Trifluoromethylvinyl alcohol

As part of our investigation of intramolecular hydrogen bonding and its geometrical consequences, ab initio molecular orbital calculations on 2-trifluoromethylphenol and 2-trifluoromethylvinyl alcohol and their parent structures were performed at the MP2/6–31+G^** level of theory. The intramolecular hydrogen bonding in 2-trifluoromethylvinyl alcohol appears stronger than that in 2-trifluoromethylphenol as witnessed by the shorter F...H interaction (1.96 Å) and the greater bond length changes in the rest of the molecule, as compared with the respective parent molecules. Beyond the geometrical characteristics, the energetics of hypothetical isodesmic reactions and the small shift of the O(SINGLE BOND)H stretching frequency indicate that these C(SINGLE BOND)F...H(SINGLE BOND)O interactions are rather weak. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 62: 645–652, 1997     

Structural and energetic relations between β turns

A systematic quantum chemical study on the structure and stability of the major types of β-turn structures in peptides and proteins was performed at different levels of ab initio MO theory (MP2/6-31G*, HF/6-31G*, HF/3-21G) considering model turns of the general type Ac(SINGLE BOND)X_aa(SINGLE BOND)Y_aa(SINGLE BOND)NHCH₃ with the amino acids glycine, l - and d -alanine, aminoisobutyric acid, and l -proline. The influence of correlation effects, zero-point vibration energies, thermal energies, and entropies on the turn formation was examined. Solvent effects on the turn stabilities were estimated employing quantum chemical continuum approaches (Onsager's self-consistent reaction field and Tomasi's polarizable continuum models). The results provide insight into the geometry and stability relations between the various β-turn subtypes. They show some characteristic deviations from the widely accepted standard rotation angles of β turns. The stability order of the β-turn subtypes depends strongly on the amino acid type. Thus, the replacement of l -amino acids in the two conformation-determining turn positions by d - or α,α-disubstituted amino acid residues generally increases the turn formation tendency and can be used to favor distinct β-turn subtypes in peptide and protein design. The β-turn subtype preferences, depending on amino acid structure modifications, can be well illustrated by molecular dynamics simulations in the gas phase and in aqueous solution. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18 : 1415–1430, 1997     

Hydrogen bonding properties of oxygen and nitrogen acceptors in aromatic heterocycles

The directionality and relative strengths of hydrogen bonds to monocyclic aromatic heterocycles were investigated using crystal structure data and theoretical calculations. Surveys of the Cambridge Structural Database for hydrogen bonds between C^(sp3)(SINGLE BOND)O(SINGLE BOND)H and aromatic fragments containing one or more nitrogen and/or oxygen heteroatoms showed that hydrogen bonds to nitrogen atoms are much more abundant than to oxygen. Distinct preferred orientations were also revealed in these surveys. Theoretical calculations were performed on the interaction of methanol with pyridine, pyrimidine, pyrazine, pyridazine, oxazole, isoxazole, 1,2,4-oxadiazole, and furan as models for the heterocyclic fragments. The intermolecular potential surface was thoroughly scanned using a model potential that accurately described the electrostatic forces (derived from distributed multipole analysis) with empirical parameters for the repulsion and dispersion terms. Minima on this surface agreed well with the observed orientations in the data base and they were typically deeper for nitrogen than for oxygen acceptors, although the hydrogen bond strength and geometry was influenced by other heteroatoms in the ring. These results were confirmed by highly accurate intermolecular perturbation theory calculations, which also estimated the deviations from hydrogen bonding in the traditional nitrogen lone pair direction that could occur with negligible reduction in the interaction energy. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2060–2074, 1997     

π-Bonding contribution to restricted internal rotations in saccharides

Extensive semiempirical SCF-MO calculations confirm that the exo-anomeric effect in methyl O-, N- and S-glycosides deals with an interaction of π-character along the C₁(SINGLE BOND)Y₁ bond in a X₅(SINGLE BOND)C₁(SINGLE BOND)Y₁(SINGLE BOND)Me moiety (where X = O, S; Y = O, NH, S). The bond-order between orbitals of pπ symmetry on C₁ and Y₁ serves as a measure of all significant molecular orbital interactions responsible for the exo-anomeric stabilization. The set of simpler compounds X(SINGLE BOND)CH₂(SINGLE BOND)Y (X = OH, SH, SeH, TeH; Y = OH, SH, SeH, TeH, NH₂) on which the anomeric effect has been well studied was also calculated and it is noticeable that the π-bond-orders accord with the results of other analyses of the ab initio wave function accounting for the anomeric effect. Although the AM1 and the PM3 parameterizations of MNDO do not accurately reproduce the anomeric effect energetic, they do reproduce accordingly the expected variations in the molecular conformations of complex carbohydrates, and thus it follows that there are maximal π-bond-orders for the synclinal arrangement around the C₁(SINGLE BOND)Y₁ bond. In addition, the π-bond-orders show the same behavior for conformational preferences around the C₁(SINGLE BOND)C′₁ and the C₅(SINGLE BOND)C₆ bonds in methyl C-glycosides and in the hydroxymethyl group of α-D -glucose, respectively. © 1996 by John Wiley & Sons, Inc.     

Synthesis and properties of polycarbosilanes with the meta-linkage bending unit by hydrosilylation polymerization

The polycarbosilanes (PCS) with meta-linkage bending unit ((SINGLE BOND)Me₂Si(SINGLE BOND)m(SINGLE BOND)C₆H₄(SINGLE BOND)Me₂Si(SINGLE BOND)CH₂CH₂(SINGLE BOND)) were successfully synthesized in mild conditions by hydrosilylation in the presence of [Pt{(CH₂(DOUBLE BOND)CHSiMe₂)₂O}₂]. The PCS obtained were soluble in various solvents owing to the lowering of the crystallinity. These properties are well compared with those of the PCS [(SINGLE BOND)Me₂Si(SINGLE BOND)p(SINGLE BOND)C₆H₄(SINGLE BOND)Me₂Si(SINGLE BOND)CH₂CH₂(SINGLE BOND)]_n. © 1996 John Wiley & Sons, Inc.     

Comparison between post-Hartree-Fock and DFT methods for the study of strength and mechanism of cleavage of Hg(SINGLE BOND)C bond

A parallel MP2 and DFT study was performed for mercury dihalides and for representative organomercury compounds including a Hg(SINGLE BOND)C bond. From a methodological point of view, medium-size basis sets provide reliable general trends for a number of properties already at the HF level. However, quantitative results can only be obtained including correlation energy by post-Hartree-Fock (even at the MP2 level) or density functional models and adding f-polarization functions on Hg. At this level, geometrical parameters are sufficiently accurate for most purposes and reliable thermodynamic data can be obtained using isodesmic reactions. The advantage of the DF approach resides, besides the shorter computation times, in the lower dependence of the results on the basis set. From a more general point of view, all the computations indicate that Hg(SINGLE BOND)C bond breaking is favored, decreasing the electronegativity of further substituents. We have next investigated the reaction mechanism for cleavage of the Hg(SINGLE BOND)C bond by halogenic acids. Our results show that the reaction occurs through a one-step mechanism in which, however, bond forming and breaking are not completely synchronous. © 1997 John Wiley & Sons, Inc.     

An original route to poly[silylene-co-(2,4-disilapentane-2,4-diyl)] oligomers,efficient precursors of silicon carbide-based ceramics with variable C/Si ratios

Novel oligomers possessing a backbone formed of ((TRIPLE BOND)Si(SINGLE BOND)CH₂(SINGLE BOND)Si(TRIPLE BOND)) and (SINGLE BOND)Si(SINGLE BOND)_n units were prepared by the copolycondensation of bis(chlorosilyl)methanes and various dichlorosilanes in the presence of sodium, in refluxing toluene. The effect of the respective molar ratios of comonomers on the yields and the structure of the copolymers was investigated. The role of substituents on silicon atoms in the ability of these materials to provide convenient ceramic precursors upon pyrolysis was examined. When (TRIPLE BOND)Si(SINGLE BOND)H bonds were present, thermal cross-linking was readily performed and ceramics possessing variable C/Si ratios were prepared.     

Effect of inclusion of electron correlation in MM3 studies of cyclic conjugated compounds

Electron correlation at the Møller–Plesset second-order level was incorporated into the π-system portion of MM3 calculations for several conformers of [10]annulene, [18]annulene, bicyclo[5.3.1]undecapentaene, and bicyclo[4.4.1]undecapentaene. The conformers with “localized” C(SINGLE BOND)C π bonds (strongly alternating bond lengths) were found to be of lower energy than their counterparts with “delocalized” C(SINGLE BOND)C π bonds (similar bond lengths) before correlation energy was included. Correlation always lowered the energies of the delocalized conformation more than it did that of the localized conformation, such that often the latter was found to be more stable after correlation energy was included in the calculation. When a delocalized structure was not at a stationary point on the MM3 energy surface, such comparison could not be made. An example is the porphin molecule. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 475–487, 1998     

A density functional study of Fe(SINGLE BOND)N2, Fe(SINGLE BOND)N+2, and Fe(SINGLE BOND)N−2

The interaction of an iron atom with molecular nitrogen was studied using density functional theory. Calculations were of the all-electron type and both conventional local and gradient-dependent models were used. A ground state of linear structure was found for Fe(SINGLE BOND)N₂, with 2S + 1 = 3, whereas the triangular Fe(SINGLE BOND)N₂ geometry, of C_2v symmetry, was located 2.1 kcal/mol higher in energy, at least for the gradient-dependent model. The reversed order was found using the conventional local approximation. In Fe(SINGLE BOND)N₂, the N(SINGLE BOND)N bond is strongly perturbed by the iron atom: It has a bond order of 2.4, a vibrational frequency of 1886 cm⁻¹, and an equilibrium bond length of 1.16 Å: These values are 3.0, 2359 cm⁻¹, and 1.095 Å, respectively, for the free N₂ molecule. With the gradient-dependent model and corrections for nonsphericity of the Fe atom, a very small binding energy, 8.8 kcal/mol, was calculated for Fe(SINGLE BOND)N₂. Quartet ground states were found for both Fe(SINGLE BOND)N⁺₂ and Fe(SINGLE BOND)N⁻₂. The adiabatic ionization potential, electron affinity, and electronegativity were also computed; the predicted values are 7.2, 1.22, and 4.2 eV, respectively. © 1997 John Wiley & Sons, Inc.