Molecular structure of phenylsilane: a study by gas-phase electron diffraction and ab initio molecular orbital calculations

The molecular structure of phenylsilane has been determined accurately by gas-phase electron diffraction and ab initio MO calculations at the MP2(f.c.)/6-31G* level. The calculations indicate that the perpendicular conformation of the molecule, with a Si–H bond in a plane orthogonal to the plane of the benzene ring, is the potential energy minimum. The coplanar conformation, with a Si–H bond in the plane of the ring, corresponds to a rotational transition state. However, the difference in energy is very small, 0.13 kJ mol⁻¹, implying free rotation of the substituent at the temperature of the electron diffraction experiment (301 K). Important bond lengths from electron diffraction are: <r_g(C–C)>=1.403±0.003 Å, r_g(Si–C)=1.870±0.004 Å, and r_g(Si–H)=1.497±0.007 Å. The calculations indicate that the C_ipso–C_ortho bonds are 0.010 Å longer than the other C–C bonds. The internal ring angle at the ipso position is 118.1±0.2° from electron diffraction and 118.0° from calculations. This confirms the more than 40-year old suggestion of a possible angular deformation of the ring in phenylsilane, in an early electron diffraction study by F.A. Keidel, S.H. Bauer, J. Chem. Phys. 25 (1956) 1218.     

An Ab Initio Molecular Orbital Theory and Density Functional Theory (DFT) Study of Conformers and Rotamers of 4-Substituted (Methyl, Hydroxymethyl, Methanoyl, Ethanoyl, Cyano, Fluoro, Chloro, Bromo, Acetoxy) Tetrahydro-2H-thiopyran-1,1-dioxides

The structures and energies of axial and equatorial conformers and rotamers of 4-substituted tetrahydro-2H-thiopyran-1,1-dioxides (tetrahydrothiopyran-1,1-dioxides, thiacyclohexane-1,1-dioxides, thiane-1,1-dioxides, and 1,1-dioxothianes; CH₃, CH₂OH, CHO, COCH₃, CN, F, Cl, Br, and OCOCH₃) were calculated using the hybrid density functionals B3LYP, B3P86, and B3PW91, as well as MP2 and the 6-31G(d), 6-31G(2d), 6-31G(3d), 6-31G(d,p), and 6-31+G(d) basis sets. MP2/6-31+G(d)/ /HF/6-31+G(d) [–G° = 1.73 kcal/mol], B3P86/6-31G(d) [–G° = 1.75 kcal/mol], and B3PW91/6-31G(d) [–G° = 1.85 kcal/mol] gave conformational free energy (G°) values at 180 K for 4-methyltetrahydro-2H-thiopyran-1,1-dioxide which were similar to the reported experimental values for methylcyclohexane (–G° = 1.80 kcal/mol), 4-methyltetrahydro-2H-thiopyran (–G° = 1.80 kcal/mol), and other 4-methyl-substituted heterocycles. All levels of theory showed that the conformational preferences of the 4-methanoyl (4-formyl), 4-ethanoyl (4-acetyl), and 4-cyano substituents were small. The HF calculations gave conformational free energy (G°) values for 4-chlorotetrahydro-2H-thiopyran-1,1dioxide which were closer to the experimental value than the MP2 and density functional methods. The best agreement with available experimental data for 4-bromotetrahydro-2H-thiopyran-1,1-dioxide was obtained from the HF/6-31G(2d), HF/6-31G(3d), and B3LYP/6-31G(2d) calculations, and, for 4-acetoxytetrahydro-2H-thiopyran-1,1-dioxide, from the HF/6–31G(3d) calculations. The conformational free energies (G°) and relative energies (E) of the conformers and rotamers have been compared with the correspondingly substituted cyclohexanes and tetrahydro-2H-thiopyrans and are discussed in terms of dipole–dipole (electrostatic) interactions and repulsive nonbonded interactions (steric) in the most stable axial and equatorial conformers. The axial S=O bond lengths are shorter than the equatorial S=O bond lengths and the C2–C3 bond lengths in the substituents with carbon-bonded to the ring are shorter than the C3–C4 and C4–C-5 bond lengths. In contrast, the C2–C3 bond lengths in the 4-halogen and 4-acetoxy substituents are longer than the C3–C4 and C4–C-5 bond lengths.     

NBO analysis and vibrational spectra of 2,6-bis(p-methyl benzylidene cyclohexanone) using density functional theory

Vibrational analysis of the 2,6-bis(p-methyl benzylidene cyclohexanone) [PMBC] compound was carried out by using NIR FT-Raman and FT-IR spectroscopic techniques. The equilibrium geometry, various bonding features and harmonic vibrational frequencies of PMBC have been investigated with the help of B3LYP/6-31G(d) density functional theory method. The optimized geometry clearly demonstrates cyclohexanone ring chair conformation is changed into half-chair conformation. The shortening of C–H bond length and blue shifting of the CH stretching wavenumber suggest the existence of improper weak C–HO hydrogen bonding, which is confirmed by the natural bond orbital analysis. The Mulliken population analysis on atomic charges and the HOMO–LUMO energy are also calculated.     

Reaction of 1-alkynylsilanes with triallylborane—competition between 1,1- and 1,2-allylboration

The reaction of triallylborane (All₃B, 1) with various 1-alkynylsilanes of the type Me₃Si–CCR¹ [R¹=H (2a), Me (2b), Ph (2c), CC–SiMe₃ (2d), SiMe₃ (2e)], Ph₃Si–CCPh (3) MeCC–SiMe₂SiMe₂–CCMe (4) and Me₂Si(Cl)–CCPh (5) was studied. Triallylborane 1 turned out to be much more reactive than other triorganoboranes R₃B (e.g. R=Et, Ph). In the cases of 2 and 5, the products are organometallic-substituted alkenes 6 and 11, respectively, with the boryl and silyl group in cis-positions as the result of selective 1,1-allylboration (via cleavage of the Si–C bond) or mixtures of such and other alkenes 7 or 8 because of competition between 1,1- and 1,2-allylboration (the composition of these mixtures depends on the polarity of the solvent). In the case of 4, the 1,2-dihydro-1,2-disilaborepine derivative 12 is formed selectively (twofold 1,1-allylboration). The alkyne 3 did not react with 1. The products were characterised by ¹H-, ¹¹B-, ¹³C- and ²⁹Si-NMR spectroscopy.     

A computational study of the effect of an external electric field on the geometry of selected donor–acceptor complexes

To understand the effect of Au and thiol atoms in octane molecule, a structural and charge density analysis has been carried out by high level ab initio quantum chemical calculations using MP2 and B3PW91 methods with the basis sets 6-311G(d,p) and LANL2DZ. The optimized geometries, specifically, the geometry obtained from both levels reveal the effect of S- and Au-atoms in octane molecule. An introduction of sulfur atom in octane molecule lengthen its backbone C–C bond distances, and further adding of Au-atom at the terminals of octane dithiolate stabilizes these distances. The bond densities of the C–C bonds of octane are 1.6 eÅ⁻³, these values are decreased significantly and the charges are largely depleted, when thiol and Au-atoms added in the octane molecule. The presence of negative Laplacian ²ρ(r) at bond critical points of C–C and C–H bonds, indicate, the charges are concentrated in these bonds, confirm that these bonds exhibit an open shell type interaction. The moderate values of density and the negative Laplacian of S–C bonds confirm the covalent character. The positive ²ρ(r) value of Au–S bonds, characterize, the bonding interaction is a closed shell interaction. The combined observed low value of electron density and the positive Laplacian of Au–S bond comprises, the gold and S interaction is not a covalent interaction, but it is a very weak coordination bond interaction. The small positive value of total energy density in Au–S bond indicates, the charges in these bonds are highly depleted and this is further confirmed by the Laplacian of bond characterization.     

FT-IR, FT-Raman vibrational spectra and molecular structure investigation of 2-chloro-4-methylaniline: A combined experimental and theoretical study

In this work, the experimental and theoretical vibrational spectra of 2-chloro-4-methylaniline (2Cl4MA, C₇H₈NCl) were studied. FT-IR and FT-Raman spectra of 2Cl4MA in the liquid phase have been recorded in the region 4000–400 cm⁻¹ and 3500–50 cm⁻¹, respectively. The structural and spectroscopic data of the molecule in the ground state have been calculated by using Hartree-Fock (HF) and density functional method (B3LYP) with the 6-31G(d), 6-31G(d,p), 6-31+G(d,p), 6-31++G(d,p) and 6-311G(d), 6-311G(d,p), 6-311+G(d,p), 6-311++G(d,p) basis sets. The vibrational frequencies have been calculated and scaled values have been compared with experimental FT-IR and FT-Raman spectra. The observed and calculated frequencies are found to be in good agreement. The complete assignments were performed on the basis of the total energy distribution (TED) of the vibrational modes, calculated with scaled quantum mechanics (SQM) method. The DFT-B3LYP/6-311++G(d,p) calculations have been found more reliable than the ab initio HF/6-311++G(d,p) calculations for the vibrational study of 2Cl4MA. The optimized geometric parameters (bond lengths and bond angles) were compared with experimental values of aniline and p-methylaniline molecules.     

A density functional theory study on boundary of “superreduced” transition metal carbonyl anions [M(CO)n](M=Cr, n=5, 4, 3, z=2, 4, 6; M=Mn, n=5, 4, 3, z=1, 3, 5; M=Fe, n=4, 3, 2, z=2, 4, 6; M=Co, n=4, 3, 2, z=1, 3, 5)

A nonlocal density functional theory (DFT) method has been applied to the calculations on optimized geometry, Mulliken atomic net charges and interatomic Mulliken bond orders as well as total bonding energies (E) in the binary transition metal carbonyl anions with different reduced states [M(CO)_n]^z− (M=Cr, n=5, 4, 3, z=2, 4, 6; M=Mn, n=5, 4, 3, z=1, 3, 5; M=Fe, n=4, 3, 2, z=2, 4, 6; M=Co, n=4, 3, 2, z=1, 3, 5). For comparison of relative stability, a relative stabilization energy D is defined as D=E([M(CO)_n]^z−)−nE(CO). The calculated C–O distances are lengthened monotonously with the increase of the anionic charge, but the M–C distances are significantly lengthened only in the higher reduced states. The relative stabilization energy calculated is a considerable negative value in the lower reduced states, but a larger positive value in the higher reduced states. The DFT calculations show that with the increase of the anionic charge, the Mulliken net charges on the M, C, and O atoms all increase, however, an excess of the anionic charge is mainly located at the central metal atom. The calculated C–O Mulliken bond orders decrease consistently with the increase of the anionic charge, but the M–C bond orders exhibit an irregular behavior. However, the total bond orders calculated clearly explain the higher reduced states to be considerably unstable. From analysis of the calculated results, it is deduced that the stability of the binary transition metal carbonyl anions [M(CO)_n]^z− studied are associated with the coordination number n and the anionic charge z, further, it is possible for the anions studied to be stable if n≥z, conversely, it is impossible when n<z.     

Theoretical study of 3d‐metal mononitrides using DFT method

3d‐Metal mononitrides are studied using the density functional theory method. The lowest spin state for these dimers is obtained using the B3LYP hybrid functional with the 6‐311+G* basis set. The equilibrium geometries, vibrational frequencies, binding energies, Mulliken, and natural orbital population analysis charges, natural orbital electronic configuration, electron affinity, and ionization potential are obtained. Mulliken as well as natural orbital population analysis charges indicate that for all dimers, in cations most of the positive charge localized on the transition metal atom where in anions most of the negative charge localized on nitrogen atom. The binding energies for 3d‐metal mononitrides are higher than those for monocarbides and monoxides. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Theoretical evaluation of atomic charges to be integrated into conformational analyses of neutral lipids

Conformational analyses of large molecules as fatty acids and triglycerides are usually amenable by molecular mechanics. A correct evaluation of the electrostatic energy term is thus crucial in determining reliable results. In this contribution, we have considered the most abundant fatty acids in biomembranes, i.e., lauric, stearic, oleic, and elaidic acid, and the corresponding triglycerides, i.e., trilaurin, tristearin, triolein, and trielaidin, and estimated the Mulliken and potential-derived charges both at the semiempirical AM 1 and ab initio HF MO STO -3G level. Atomic charges obtained by the Mulliken population analysis do not take into account the full geometry of the molecule. On the contrary, the change of conformation, due to different chains length or the presence of a trans or cis double bond, greatly influences the repartition of the potential-derived charges. A systematic comparative analysis shows that charges calculated by AM 1 are not suitable because as they do not reproduce potential-derived charges obtained by ab initio. © 1993 John Wiley & Sons, Inc.     

Crystal and molecular structure, hydrogen bond and electrostatic interactions of bis(1-methylisonicotinate)hydrogen perchlorate studied by X-ray diffraction, DFT calculations, FT-IR, Raman and NMR spectroscopes

The crystal structure of bis(1-methylisonicotinate)hydrogen perchlorate, (MIN)₂H·ClO₄, has been studied by X-ray diffraction, DFT calculations, FT-IR, Raman, ¹H and ¹³C NMR spectra. The crystals are monoclinic, space group P2₁/n, with a pair of MIN molecules bridged by a short asymmetrical O·H·O hydrogen bond of 2.461(5) Å. The COO groups are twisted by 80.55° with respect to the plane of the pyridine ring. The anion interacts electrostatically with the positively charged nitrogen atoms of the neighbouring MIN molecules. The most stable conformer of isolated (MIN)₂H·ClO₄ and two homoconjugated cations, (MIN)₂H, have been analyzed by the B3LYP/6-31G(d,p) calculations in order to determine the influence of the anion on the hydrogen bonds in MIN·H·MIN unit. The FT-IR spectrum of the (MIN)₂H·ClO₄ shows a broad and intense absorption in the 1500–400 cm⁻¹ region, typical of short hydrogen bonds. The isotopic ratio, νOHO/νODO, is close to unity, indicating that the hydrogen bond is acentric (pseudo-type A).     

Infrared and Raman spectra, conformational stability, normal coordinate analysis, ab initio calculations, and vibrational assignment of 1-fluoro-1-methylsilacyclobutane

The infrared (3500–40 cm⁻¹) spectra of gaseous and solid 1-fluoro-1-methylsilacyclobutane, c-C₃H₆SiF(CH₃), have been recorded. Additionally, the Raman spectrum (3500–30 cm⁻¹) of the liquid has been recorded and quantitative depolarization values have been obtained. Both the axial and equatorial (with respect to the methyl group) conformers have been identified in the fluid phases. Variable temperature (−55–−100°C) studies of the infrared spectra of the sample dissolved in liquid xenon have been carried out. From these data, the enthalpy difference has been determined to be 267±10 cm⁻¹ (3.19±0.12 kJ mol⁻¹), with the axial conformer being the more stable form and the only conformer remaining in the polycrystalline solid. A complete vibrational assignment is proposed for the axial conformer and many of the fundamentals for the equatorial conformer have also been identified. The vibrational assignments are supported by normal coordinate calculations utilizing ab initio force constants. Complete equilibrium geometries have been determined for both rotamers by ab initio calculations employing the 6-31G* and 6-311++G** basis sets at the levels of restricted Hartree–Fock (RHF) and/or Moller–Plesset (MP) to second order. The results are discussed and compared to those obtained for some similar molecules.     

Implications of hyperconjugative effects on bond lengths of allylic systems. An NBO investigation

The influence of hyperconjugative interactions on bond lengths of some allylic compounds (H₂CCH–CH₂–M(CH₃)₃; M=C, Si, Ge) has been investigated through NBO calculations using ab initio and density functional methods. The optimized structural parameters, at the B3LYP/6-31+G(d,p) and HF/6-31+G(d,p) levels, showed a good agreement with the resonance theory. Partial geometry optimization with orbital interactions removed confirmed the observations and revealed that σ→σ* interactions, together with the more common σ→π* ones, play an important role in determining the variations in bond lengths on going from C to Ge.     

Structure of the 2-isopropylaminoethanol isolated molecule: Conformational analysis and intramolecular interactions

In this paper, a systematic exploration of all the possible conformers of 2-isopropylaminoethanol (2-IPAE) was carried out using the Density Functional Theory (B3LYP) and the 6-311++G(d,p) basis set. At this level, 66 unique conformers within a Gibbs energy range of ca. 31 kJ mol⁻¹ were found in the potential energy surface and their geometrical and thermodynamic properties were determined and discussed. A significant molecular strain was evidenced by the dihedrals and distances between non-bonded hydrogen atoms. According to the geometrical parameters, a O–H···N hydrogen bond was found to be present in the three most stable conformers, representing 68% of the conformational composition at 298.15 K. The energetic and geometrical data derived from the DFT calculations were further complemented by a NBO analysis of the most stable conformers.     

Why N-methyleneformamide, CH2N–CHO, prefers gauche-conformation? A DFT/NBO study

Three possible stable conformations of N-methyleneformamide were studied using Weinhold's Natural bond orbital method. Wavefunctions for the NBO analysis were obtained using B3LYP hybrid functional with 6-311+G(d,p) extended basis set. gauche conformation was predicted to be more stable than trans conformation by ≈2.3 kcal/mol in agreement with earlier studies. At the same time it was found that this preference is due to the strong π_C1–N2↔π_C3–O4 and σ_C3–H5↔n_σN2 repulsive interactions in the planar conformations, and additional conjugative stabilization of the gauche conformation.     

Determination of the bond-angle distribution in vitreous B2O3 by B double rotation (DOR) NMR spectroscopy

The B–O–B bond angle distributions for both ring and non-ring boron sites in vitreous B₂O₃ have been determined by ¹¹B double rotation (DOR) NMR and multiple-quantum (MQ) DOR NMR. The [B₃O₆] boroxol rings are observed to have a mean internal B–O–B angle of 120.0±0.7° with a small standard deviation, σ_R=3.2±0.4°, indicating that the rings are near-perfect planar, hexagonal structures. The rings are linked predominantly by non-ring [BO₃] units, which share oxygens with the boroxol ring, with a mean B_ring–O–B_non-ring angle of 135.1±0.6° and σ_NR=6.7±0.4°. In addition, the fraction of boron atoms, f, which reside in the boroxol rings has been measured for this sample as f=0.73±0.01.     

Studies of the surface wettability and hydrothermal stability of methyl-modified silica films by FT-IR and Raman spectra

Fourier transform infrared (FT-IR) and Raman spectroscopy were employed to study the hydrothermal stability and the influence of surface functional groups on the surface wettability of methyl-modified silica films. The surface free energy parameters of the silica films were determined using the Lifshitz-van der Waals/acid–base approach. The thermal decomposition mechanisms of the CH₃ groups in the methyl-modified silica material are proposed. The results show that with the increase of methyltriethoxysilane (MTES)/tetraethylorthosilicate (TEOS) ratio, the surface free energy and surface wettability of the silica films decrease greatly. This is mainly because of the contribution of the acid–base term; the intensity of Si–CH₃ groups increases at the expense of the intensity of O–H groups in the samples. The surfaces of the methyl-modified silica films exhibited predominantly monopolar electron-donicity. The contact angle on the silica film surface reaches its maximum value when calcination is performed at 350 °C. Thermogravimetric analysis implies that some low molecular weight species, such as H₂, CH₄, and C, are eliminated upon thermal decomposition of the –CH₃ groups. The Si–CH₃ and –CH₃ vibrational bands diminish in intensity as the calcination temperature is increased, disappearing completely when the calcination temperature is increased to 600 °C. When the calcination temperature is increased to 750 °C, the free carbon and CSi₄ species will be formed.     

A comparative effect of ring annelation on cation-benzene and anion-benzene

DFT/B3LYP calculations were carried out on several π-complexes formed by cations and anions with annelated benzene, respectively. The binding energies obtained with standard method were corrected by basis set superposition error (BSSE) and zero-point energy (ZPE) during the geometry optimization for all complexes at the same levels of theory, respectively. Some different aspects of the π–cation have been compared to those of π–anion, involving in binding energy changes in effect of ring annelation, the aromaticity of the ring upon complexation, Mulliken and NBO charge-transfer. The effect of BSSE correction during the optimization is very important in some π–anion complexes whether or not using diffuse functions in basis set, and results with at least one set of diffuse functions 6-31+G(d) basis set is a little better than results obtained by 6-31G(d, p) basis set for some π–anion especially for F⁻ complexes.     

The vibrational and NMR spectra,conformations and ab initio calculations of aminomethylene,propanedinitrile and itsN-methyl derivatives

The IR and Raman spectra of aminomethylene propanedinitrile (AM) [H₂N-CH=C(CN)₂], (methylamino)methylene propanedinitrile (MAM) [CH₃NH-CH=C(CN)₂] and (dimethylamino)methylene propanedinitrile (DMAM) [(CH₃)₂N-CH=C(CN)₂] as solids and solutes in various solvents have been recorded in the region 4000-50 cm^–1. AM and DMAM can exist only as one conformer. From the vibrational and NMR spectra of MAM in solutions, the existence of two conformers with the methyl group orientedanti andsyn toward the double C=C bond were confirmed. The enthalpy difference H ⁰ between the conformers was measured to be 3.7±1.4 kJ mol^–1 from the IR spectra in acetonitrile solution and 3.4±1.1 kJ mol^–1 from the NMR spectra in DMSO solution. Semiempirical (AM1, PM3, MNDO, MINDO3) and ab initio SCF calculations using a DZP basis set were carried out for all three compounds. The calculations support the existence of two conformersanti andsyn for MAM, withanti being 7.8 kJ mol^–1 more stable thansyn from ab initio and 8.6, 13.4, 11.6, and 10.8 kJ mor^–1 from AM1, PM3, MNDO, and MINDO3 calculations, respectively. Finally, complete assignments of the vibrational spectra for all three compounds were made with the aid of normal coordinate calculations employing scaled ab initio force constants. The same scale factors were optimized on the experimental frequencies of all three compounds, and a very good agreement between calculated and experimental frequencies was achieved.     

Synthesis of 1,1′-binaphthyl-2,2′-diamine from 2-naphthol under atmospheric pressure

A practical protocol to obtain 1,1'-binaphthyl-2,2'-diamine was developed from 2-naphthol and 2-naphthylhydrazine under mild conditions:solvent-free,125-130℃,atmospheric pressure.The convenient procedure makes the process amenable for large-scale synthesis of the versatile compound.     

A quantum chemical study of red-shift and blue-shift hydrogen bonds in bimolecular and trimolecular methylhydrazine-hydrate complexes

This study presents a theoretical discussion of the geometry and molecular parameters of the methylhydrazine-hydrate complex. Using B3LYP/6-311++G(d,p) calculations, two geometries for the methylhydrazine-hydrate complex were analyzed by considering the interaction between water in: (i) a lone nitrogen pair assisted by a methyl (I); and (ii) the nitrogen of the NH₂ group (II). These geometries were examined by examining the formation of (N···H) hydrogen bonds, which were characterized using ChelpG charge transfer amounts, as well as by means of topological parameters derived from Quantum Theory of Atoms in Molecules (QTAIM) calculations. In a qualitative evaluation, both complexes (a) and (b) were compared with the corresponding trimolecular system (c) formed by methylhydrazine and two water molecules. A conclusion was then obtained by means of vibrational analysis, in which, in addition to δυ(H–O) red-shifts in water molecules, the stretch frequency of the H–C bond of methyl group shifted upwards, indicating the formation of a blue-shifting hydrogen bond in the methylhydrazine-bihydrate complex.