Tarek A. Mohamed

Spectra and Structure of Silicon-Containing Compounds. XXV. Raman and Infrared Spectra, r0 Structural Parameters, Vibrational Assignment, and Ab Initio Calculations of Ethyl Chlorosilane-Si-d2

The infrared (3200 to 400 cm−1) spectra of gaseous and solid and Raman (3200 to 20 cm−1) spectra of liquid and solid ethyl chlorosilane-Si-d2, CH3CH2SiD2Cl, have been recorded. Both the gauche and trans conformers have been identified in the fluid phases, but only the gauche conformer remains in the solid phase. Variable temperature (−105 to −150°C) studies of the infrared spectra of CH3CH2SiH2Cl dissolved in liquid krypton have been carried out. From these data, the enthalpy difference has been determined to be 78±11 cm−1 (0.93±0.13 kJ/mol), with the gauche conformer the more stable form. Utilizing the frequencies of the silicon-hydrogen stretches, from the chlorosilane-Si-d isotopomer, Si—H bond distances of 1.481 and 1.480 Å have been obtained for the gauche conformer and 1.481 Å for the trans conformer. Complete vibrational assignments are proposed for both isotopomers which are consistent with the predicted frequencies utilizing the force constants from ab initio MP2/6-31G(d) calculations. Both the infrared intensities and the Raman activities and depolarization values have been obtained from the ab initio calculations. Complete equilibrium geometries have been determined by ab initio calculations employing the 6-31(d), 6-311++G(d,p), and 6-311+G(2d,2p) basis sets with full electron correlation by the Moller–Plesset (MP) perturbation method to second order. Continuing the previously reported rotational constants from five different isotopomers and the ab initio predicted structural parameters, adjusted r0 parameters have been calculated, which are compared to the corresponding rs parameters. The results are discussed and the theoretical values are compared to the experimental values when appropriate.

Spectra and Structures of Silicon-Containing Compounds. XXIV.* Raman and Infrared Spectra, r0 Structural Parameters, Vibrational Assignment, Barriers to Internal Rotation, and Ab Initio Calculations of Ethylsilane

The infrared (3200 to 400 cm−1) and Raman (3200 to 20 cm−1) spectra of gaseous and solid ethylsilane, CH3CH2SiH3, have been recorded. Additionally, the Raman spectrum of the liquid has been obtained with quantitative depolarization values. The SiH3 torsional mode has been observed as sum and difference bands with the silicon-hydrogen stretching vibration. Utilizing the torsional fundamental frequency of 132 cm−1 the threefold periodic barrier of 590 cm−1 (7.06 kJ/mol) has been obtained. Utilizing the frequencies of the silicon-hydrogen stretches, Si-H bond distances of 1.485 and 1.484 Å have been obtained for the bonds gauche and trans to the methyl group, respectively. Using previously reported rotational constants from seven different isotopomers, the r0 parameters have been calculated and are compared to the corresponding rs parameters. A complete vibrational assignment is proposed that is consistent with the predicted frequencies utilizing the force constants from ab initio MP2/6-31G(d) calculations. Both the infrared intensities as well as the Raman activities and depolarization values have been obtained from the ab initio calculations. Complete equilibrium geometries have been determined by ab initio calculations employing the 6-31G(d), 6-311 + G(d,p), and 6-311+G(2d,2p) basis sets at levels of restricted Hartree–Fock (RHF) and/or Moller–Plesset (MP) to second order. The results are discussed and the theoretical values are compared to the experimental values when appropriate.

Spectra and structure of silicon-containing compounds. Part XXXVIII: Infrared and Raman spectra, vibrational assignment, conformational stability, and ab initio calculations of vinyldifluorosilane

Infrared spectra (3500-50 cm(-1)) of gaseous and solid, and Raman spectrum (3500-30 cm(-1)) of liquid vinyldifluorosilane, CH(2)z.dbnd6;CHSiF(2)H, are reported. Both the cis and gauche rotamers have been identified in the fluid phases. From temperature-dependent FT-infrared spectra of krypton solutions, it is shown that the cis conformer is more stable than the gauche form by 119+/-12 cm(-1) (1.42+/-0.14 kJ mol(-1)). At ambient temperature there is 53+/-2% of the gauche conformer present. Complete vibrational assignments are provided for the cis conformer and several modes are identified for the gauche form. Harmonic force constants, fundamental frequencies, infrared intensities, and Raman activities have been obtained from MP2/6-31G(d) calculations with full electron correlation. The optimized geometries and conformational stabilities have also been obtained from ab initio MP2/6-31G(d), MP2/6-311+G(d,p), and MP2/6-311+G(2d,2p) calculations with full electron correlation as well as from density functional theory calculations (DFT) by the B3LYP method. The SiH bond distances (r(0)) of 1.472 and 1.471 A have been obtained for the cis and gauche conformers, respectively, from the silicon-hydrogen stretching frequencies. These results are compared to the corresponding quantities of the corresponding carbon analogue as well as with some similar molecules.

Synthesis, antimicrobial activity, structural and spectral characterization and DFT calculations of Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile

Co(II), Ni(II), Cu(II) and Pd(II) complexes of 4-amino-5-pyrimidinecarbonitrile (APC) have been synthesized and characterized using elemental analysis, magnetic susceptibility, mass spectrometry, infrared (4000-200 cm(-1)), UV-Visible (200-1100 nm), (1)H NMR and ESR spectroscopy as well as TGA analysis. The molar conductance measurements in DMSO imply non-electrolytic complexes, formulated as [M(APC)2Cl2] where M=Co(II), Ni(II), Cu(II) and Pd(II). The infrared spectra of Co(II), Ni(II) and Cu(II) complexes indicate a bidentate type of bonding for APC through the exocyclic amino and adjacent pyrimidine nitrogen as donors whereas APC coordinated to Pd(II) ion as a monodentated ligand via a pyrimidine nitrogen donor. The magnetic measurements and the electronic absorption spectra support distorted octahedral geometries for Co(II), Ni(II) and Cu(II) complexes however a square planar complex was favored for the Pd(II) complex (C2h skeleton symmetry). In addition, we carried out B3LYP and ω-B97XD geometry optimization at 6-31G(d) basis set except for Pd(II) where we implemented LanL2DZ/6-31G(d) combined basis set. The computational results favor all trans geometrical isomers where amino N, pyrimidine N and Cl are trans to each other (structure 1). Finally, APC and its divalent metal ion complexes were screened for their antibacterial activity, and the synthesized complexes were found to be more potent antimicrobial agents than APC against one or more microbial species.

Raman, infrared and NMR spectral analysis, normal coordinate analysis and theoretical calculations of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione and its thiol tautomer.

Raman (3400-100 cm(-1)) and infrared (4000-200 cm(-1)) spectra of 5-(methylthio)-1,3,4-thiadiazole-2(3H)-thione (C3H4N2S3; MTT) were measured in the solid state, and the (1)H/(13)C NMR spectra were obtained in DMSO-d6. Initially, twelve structures were proposed as a result of thiol-thione tautomerism and the internal rotation about the C-S bonds. The energies and vibrational frequencies of the optimized structures were calculated using the 6-31G(d) basis set with the methods of MP2 and DFT/B3LYP with Gaussian 98 quantum calculations. Additionally, (1)H/(13)C NMR chemical shifts were predicted for the thiol (structure 5) and thione (structure 9) tautomers by means of B3LYP/6-311+G(d,p) calculations utilizing the GIAO approximation and the PCM solvation model. After complete relaxation of twelve candidate isomers, the thione tautomer (structure 9) was favored owing to its low energy and its predicted real spectral frequencies. These results agree with the recorded infrared and Raman results, in addition to the observed/calculated (1)H and (13)C NMR spectra. Aided by normal coordinate analysis and potential energy distributions (PEDs), complete vibrational assignments have been proposed for all observed fundamentals for the thione tautomer. With the aid of MP2/6-31G(d) potential surface scans, CH3, CH3S, and SH barriers to internal rotations were estimated with the optimized structural parameters from the MP2 method with the 6-31G(d) basis set. The results are discussed herein and compared with similar model compounds whenever appropriate.

Raman and infrared spectra, conformational stability, normal coordinate analysis, ab initio calculations and vibrational assignment of 1‐chloro‐1‐methylsilacyclobutane

The Raman spectrum (3500–30 cm−1) of liquid 1-chloro-1-methylsilacyclobutane, c-C3H6SiCl(CH3), was recorded and quantitative depolarization values were obtained. Additionally, the infrared (3500–40 cm−1) spectra of the gas and solid were recorded. Both the axial and equatorial (with respect to the methyl group) conformers were identified in the fluid phases. Variable temperature (−55 to −100 °C) studies of the infrared spectra of the sample dissolved in liquid xenon were carried out. From these data, the enthalpy difference was determined as 178 ± 15 cm−1 (2.13 ± 0.18 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 of the equatorial conformer were also identified. The vibrational assignments are supported by normal coordinate calculations utilizing ab initio force constants. Complete equilibrium geometries, conformational stabilities, harmonic force fields, infrared intensities, Raman activities and depolarization ratios were 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 with those obtained for some similar molecules. Copyright

Vibrational assignments, normal coordinate analysis, B3LYP calculations and conformational analysis of methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1- carbodithioate

The Raman and infrared spectra of solid methyl-5-amino-4-cyano-3-(methylthio)-1H-pyrazole-1-carbodithioate (MAMPC, C7H8N4S3) were measured in the spectral range of 3700-100 cm(-1) and 4000-200 cm(-1) with a resolution of 4 and 0.5 cm(-1), respectively. Room temperature 13C NMR and (1)H NMR spectra from room temperature down to -60 °C were also recorded. As a result of internal rotation around C-N and/or C-S bonds, eighteen rotational isomers are suggested for the MAMPC molecule (Cs symmetry). DFT/B3LYP and MP2 calculations were carried out up to 6-311++G(d,p) basis sets to include polarization and diffusion functions. The results favor conformer 1 in the solid (experimentally) and gaseous (theoretically) phases. For conformer 1, the two -CH3 groups are directed towards the nitrogen atoms (pyrazole ring) and CS, while the -NH2 group retains sp2 hybridization and C-CN bond is quasi linear. To support NMR spectral assignments, chemical shifts (δ) were predicted at the B3LYP/6-311+G(2d,p) level using the method of Gauge-Invariant Atomic Orbital (GIAO) method. Moreover, the solvent effect was included via the Polarizable Continuum Model (PCM). Additionally, both infrared and Raman spectra were predicted using B3LYP/6-31G(d) calculations. The recorded vibrational, 1H and 13C NMR spectral data favors conformer 1 in both the solid phase and in solution. Aided by normal coordinate analysis and potential energy distributions, confident vibrational assignments for observed bands have been proposed. Moreover, the CH3 barriers to internal rotations were investigated. The results are discussed herein are compared with similar molecules whenever appropriate.

Infrared and NMR spectra, tautomerism, vibrational assignment, normal coordinate analysis, and quantum mechanical calculations of 4-amino-5-pyrimidinecarbonitrile.

The infrared (4000-200 cm(-1)) spectrum for 4-amino-5-pyrimidinecarbonitrile (APC, C5H4N4) was acquired in the solid phase. In addition, the (1)H and (13)C NMR spectra of APC were obtained in DMSO-d6 along with its mass spectrum. Initially, six isomers were hypothesized and then investigated by means of DFT/B3LYP and MP2(full) quantum mechanical calculations using a 6-31G(d) basis set. Moreover, the (1)H and (13)C NMR chemical shifts were predicted using a GIAO approximation at the 6-311+G(d,p) basis set and the B3LYP method with (and without) solvent effects using PCM method. The correlation coefficients showed good agreement between the experimental/theoretical chemical shift values of amino tautomers (1 and 2) rather than the eliminated imino tautomers (3-6), in agreement with the current quantum mechanical calculations. Structures 3-6 are less stable than the amino tautomers (1 and 2) by about 5206-8673 cm(-1) (62.3-103.7 kJ/mol). The MP2(full)/6-31G(d) computational results favor the amino structure 1 with a pyramidal NH2 moiety and calculated real vibrational frequencies, however; structure 2 is considered a transition state owing to the calculated imaginary frequency. It is worth mentioning that, the calculated structural parameters suggest a strong conjugation between the amino nitrogen and pyrimidine ring. Aided by frequency calculations, normal coordinate analysis, force constants and potential energy distributions (PEDs), a complete vibrational assignment for the observed bands is proposed herein. Finally, NH2 internal rotation barriers for the stable non-planar isomer (1) were carried out using MP2(full)/6-31G(d) optimized structural parameters. Our results are discussed herein and compared to structural parameters for similar molecules whenever appropriate.

Analysis of UV and vibrational spectra (FT-IR and FT-Raman) of hexachlorocyclotriphosphazene based on normal coordinate analysis, MP2 and DFT calculations

The Raman (1400-100 cm(-1)) and infrared (4000-400 cm(-1)) of solid hexachlorocyclotriphosphazene, P(3)N(3)Cl(6) (HCCTP) were recorded. The conformational energies were calculated using MP2 and DFT (B3LYP and B3PW91) methods utilizing a variety of basis sets up to 6-311+G(d). On the basis of D(3h) symmetry, the simulated vibrational spectra of P(3)N(3)Cl(6) from MP2 and DFT methods were in excellent agreement with those obtained experimentally. Additionally, Frontier Molecular Orbitals and electronic transitions were predicted using steady state and time dependent DFT(B3LYP)/PCM calculations respectively, each employing the 6-311+G(d,p) optimized structural parameters. The predicted wavelengths were in excellent agreement with experimental values when CH(2)Cl(2) was used as solvent. The (14)N and (31)P chemical shifts were predicted with B3LYP/6-311+G(2d,p) calculations using the GIAO technique with solvent effect modeled using the PCM method. The computed structural parameters of the planar P(3)N(3)Cl(6) (D(3h)) agree well with experimental values from both X-ray and electron diffraction data with slight distortions observed due to lattice defects in the solid phase. The experimental/computational results favor a slightly distorted D(3h) symmetry for the title compound in the gas and solid phases and in solution (τPNPN and τNPNP ranged from 0.018° to 0.90°). Aided by normal coordinate analysis, and the simulated vibrational spectra utilizing MP2, B3LYP and B3PW91 methods at 6-31G(d) basis set, revised and complete vibrational assignments for all fundamentals are provided herein.

Infrared, 1H and 13C NMR spectra, structural charcterization and DFT calculations of novel adenine-cyclodiphosp(V)azane derivatives

Adenine tetrachlorocyclodiphospha(V)zane derivatives (III(a-c)) were prepared by the reaction of hexachlorocyclodiphospha(V)zane derivatives (I(a-c)) and adenine (II) as precursors. The synthesized compounds and their structures (III(a-c)) were firmly characterized (based on the presence of an inversion center) using FT-IR (4000-200 cm(-1)), UV-vis. (190-800 nm), (1)H, (13)C NMR and Mass spectral measurements in addition to C, H, N, P elemental analysis. The compounds (III(a-c)) were found to be a 1:2 molar ratio of (I(a-c)) and adenine (II) adducts, respectively. Confident and complete vibrational assignments are proposed for nearly all fundamental vibrations, along with detailed interpretation for all observed signals in both (1)H and (13)C NMR spectra of the investigated phospha(V)zanes (III(a-c)). In addition, unconstrained geometry optimization of III(a-c) were carried out by means of DFT-B3LYP/3-21G(d) calculations to provide new insight into the structural parameters and molecular geometries of compounds III(a-c). The results are reported herein and compared with similar molecules whenever appropriate.