All-trans- and t,T,t,C,t,T,t-deca-1,3,5,7,9-Pentaenes: Ab Initio Structures,Vibrational Analyses,and Some Regularities in the Series of Related Molecules

Total geometry optimization and calculation of the force constants for all-transand t,T,t,C,t,T,tdeca-1,3,5,7,9-pentaene were carried out at the ab initio, HF/6-31G level. The HF/6-31G//HF/ 6-31G force fields were modified using empirical scale factors transferred from trans-buta-1,3-diene augmented by an additional scale factor for the central formal carbon-carbon double bond coordinates (determined previously for all-trans-hexa-1,3,5-triene). The total number of scale factors was seven. The vibrational problems for both decapentaenes were solved using the respective scaled HF/6-31G//HF/6-31G force field. Infrared intensities and Raman activities were calculated from the unscaled HF/6-31G//HF/6-31G force fields. Complete assignment of all the fundamental vibrational frequencies is given. Geometrical parameters, vibrational frequencies and force constants are compared with the corresponding values of buta-1,3-diene, hexa-1,3,5-triene and octa-1,3,5,7-tetraene. Regularities in the properties of this molecular series are discussed. Special attention is given to the possibility of using the vibrational spectra for detection of distortions from the regular trans structure of these oligoenes.     

Molecular modeling of ring-chain equilibria for the ring-opening cross-metathesis of cis,cis-1,5-dimethyl-cycloocta-1,5-diene with ethylene at T=298.15 K

The molecular modeling of ring-opening cross-metathesis of cis,cis-1,5-dimethyl-cycloocta-1,5-diene (1,5-DM-COD), cis,cis-1,6-dimethyl-cycloocta-1,5-diene (1,6-DM-COD) and cis,cis-cycloocta-1,5-diene (COD) with ethylene (ethenolysis) at T=298.15 K using the B3LYP/6-31G(d,p) level of theory reveals that ring-chain equilibrium constants are dependent on the nature of cyclic diene. The ring-chain equilibria for the ethenolysis of 1,5-DM-COD is completely shifted to the formation of monomeric 2-methyl-hexa-1,5-diene.     

Vibrational analysis of trans,Trans,trans-2,3,4,5-tetrachlorohexa-1,3,5-trienes

Infrared and Raman spectra of t,T,t-2,3,4,5-tetrachlorohexa-1,3,5-triene were measured in liquid and crystalline phases. It is suggested that the non-planar structure of this compound may be due to the 1–3 effect. In the liquid state a mixture of rotational isomers, of C₂ and C_i symmetry, was confirmed by the freezing-out of some characteristic bands in the 1600 cm⁻¹ region in the IR and Raman spectra of the t,T,t-compound. Normal coordinate analysis was carried out using force constant values from the force field previously determined for chloroderivatives of buta-1,3-diene. A complete assignment of observed frequencies is proposed.     

An Ab Initio Study and NBO Analysis of the Stability and Conformational Properties of Hexakis(trimethylelementhyl)benzene (Element = C,Si, Ge,and Sn)

Ab initio molecular orbital and density functional theory were used to investigate energetic and structural properties of the various conformations of hexa-tertbutylbenzene (1), hexakis(trimethylsilyl)benzene (2), hexakis (trimethylgermyl)benzene (3), and hexakis(trimethylstannyl)benzene (4). HF/3-21G//HF/3-21G and B3LYP/3-21G//HF/3-21G results revealed that the Twist-Boat (TB) conformer of compound 1 is more stable than the 1-Chair (C), 1-Boat (B), and 1-Planar (P) conformers. B3LYP/3-21G//HF/3-21G results show that the 1- TB conformer is more stable than 1- C, 1- B, and 1- P conformers of about 1.13, 4.34, and 99.94 kcal mol^?1 , respectively. Contrary to the stability order of compound 1 conformers, the C conformer of compounds 2–4 is more stable than TB, B, and P conformations, as calculated by B3LYP/3-21G//HF/3-21G and HF/3-21G//HF/3-21G levels of theory. The energy gap between the C and P conformers in compounds 1–4 is decreased in the following order: ΔE(4: C, P) < ΔE (3: C, P) < ΔE(2: C, P) < ΔE (1: C, P). This fact can be explained in terms of the increase of C _aromatic -M (M═C, Si, Ge, and Sn) bond lengths and the decrease of steric (van der Waals) repulsions in the previously discussed compounds. For compounds 1–3, the calculations were also performed at the B3LYP/ 6-31G*//HF/3-21G level of theory. However, the comparison showed that the results at B3LYP/3-21G//HF/3-21G methods correlated well with those obtained at the B3LYP/6-31G*// HF/6-31G method. Further, NBO analysis revealed that in compounds 1–4, the resonance energy associated with the σ_M-C1 to σ*_C2-C3 delocalization is 5.20, 9.68, 11.15, and 12.27 kcal mol^?1, respectively. These resonance energy values could explain the easiness of the ring flipping processes of C, B, and TB conformers of compounds 4 to 1. Also, the NBO results showed that by an increase of the σ_M-C1 → σ *_C2-C3 resonance energies in compounds 1–4, the σ_M-C1 bonding orbital occupancies decrease. This fact could fairly explain the increase of the C_aryl-M bond length from compound 1 to 4. The NBO results are also in good agreement with the calculated energy barriers for the ring flipping of the chair conformations in compounds 1–4, as calculated by B3LYP and HF methods.     

ISOMER COMPOSITION and SPECTRA OF THE DARK and LIGHT ADAPTED FORMS OF ARTIFICIAL BACTERIORHODOPSINS*

Abstract– The isomer composition and spectral properties of 15 artificial bacteriorhodopsin (bR) pigments, based on a series of retinal analogs with polyene residue modified below C₉ are determined for both dark-adapted (DA) and light-adapted (LA) forms. Similarly to native bR, in all cases only two isomers, C₁₃=C₁₄cis (13-cis) and M-trans, are observed. However, the artificial DA pigments have a lower 13-d.s content than native DA bR (? 66%) while the corresponding LA pigments have a much higher 13-cis content (11-69%) than native LA bR (<2%). Thus, in variance with the native pigment, in all of the artificial systems light also induced the reversed all-trans13-cis process. The data are accounted for in terms of specific steric interactions between the polyene and the protein binding site which allow a (C₁₅-anti)(C_ls-syn) isomerization during the photocycle of the artificial pigments, but not in the case of native bR. This accounts for the high proton pumping efficiency of the natural pigment. The nature of a highly red shifted light-adapted form of two of the artificial pigments is investigated and discussed. It is also shown that, in variance with native bR, several artificial pigments exhibit identical absorption spectra for their 13-cis and all-trans isomers. It is concluded that the spectral data for the above species of artificial pigments do not lead to a clear molecular model for the origin of the spectral shift between 13-cis and all-trans bR.     

Synthesis, X-ray characterization, NMR and ab initio molecular-orbital studies of some cadmium(II) macrocyclic Schiff-base complexes with two 2-aminoethyl pendant arms

Three new pendant arm Schiff-base macrocyclic complexes, [CdLⁿ]²⁺ (n = 5, 6, 7), have been prepared via cyclocondensation of 2,6-diacetylpyridine with three different branched hexaamines in the presence of Cd(II). The ligands are 15-, 16- and 17-membered pentaaza macrocycles having two 2-aminoethyl pendant arms [L⁵ = 2,13-dimethyl-6,9-bis(aminoethyl)-3,6,9,12,18-pentaazabicyclo[12.3.1]octadeca-1(18),2,12,14,16-pentaene, L⁶ = 2,14-dimethyl-6,10-bis(aminoethyl)-3,6,10,13,19-pentaazabicyclo[13.3.1]nonadeca-1(19),2,13,15,17-pentaene and L⁷ = 2,15-dimethyl-6,11-bis(aminoethyl)-3,6,11,14,20-pentaazabicyclo[14.3.1]eicosa-1(20),2,14,16,18-pentaene]. All complexes were investigated by IR, ¹H and ¹³C NMR, COSY(H,H) and HETCOR(H,C) spectroscopy and X-ray diffraction. In the solid state structure of each complex the Cd(II) ion is situated centrally within an approximately planar pentaaza macrocyclic ring, binding to the five nitrogen atoms, and also to the two pendant amines which are located on opposite sides of the macrocyclic plane. ab initio HF-MO calculations using a standard 3-21G* basis set have been used to verify that these similar basic structures correspond to energy minima in the gas phase.     

Quantum-Chemical Study of Electronic and Steric Structure of Vinyltetrazoles: I. 2-Substituted 5-Vinyltetrazoles

The total Mulliken charges on the carbon atoms of the vinyl group, populations of S-trans-(N¹)conformers, and internal rotation energies were calculated ab initio (HF/6-31G**, MP2/6-31G**, and MP2/6-31G**//AM1) for a series of 2R-5-vinyltetrazoles (R = CH₃, C₂H₅, i-C₃H₇, t-C₄H₉, C₆H₅). The calculation results were compared to the available experimental data.     

Excess molar volumes of (cyclohexanone+trichloromethane,or 1,2-dichloroethane,or trichloroethene,or 1,1,1-trichloroethane,or cyclohexane) at T=308.15 K,and of (cyclohexanone+dichloromethane) at T=303.15 K

Excess molar volumes V_m^E have been measured using a dilatometric technique for mixtures of cyclohexanone (C₆H₁₀O) with trichloromethane (CHCl₃), 1,2-dichloroethane (CH₂ClCH₂Cl), trichloroethene (CHClCCl₂), 1,1,1-trichloroethane (CCl₃CH₃), and cyclohexane (c-C₆H₁₂) at T=308.15 K, and for cyclohexanone+dichloromethane (CH₂Cl₂) at T=303.15 K. Throughout the entire range of the mole fraction χ of C₆H₁₀O, V_m^E has been found to be positive for χ C₆H₁₀O+(1−χ)c-C₆H₁₂, and negative for χ C₆H₁₀O+(1−χ)CH₂Cl₂, χ C₆H₁₀O+(1−χ)CHClCCl₂, χ C₆H₁₀O+(1−χ)CHCl₃, and χ C₆H₁₀O+(1−χ) CCl₃CH₃. For χ C₆H₁₀O+(1−χ)CH₂ClCH₂Cl, V_m^E has been found to be positive at lower values of χ and negative at high values of χ, with inversion of sign from positive to negative values of V_m^E for this system occurring at χ∼0.78. Values of V_m^E for the various systems have been fitted by the method of least squares with smoothing equation, and have been discussed from the viewpoint of the existence specific interactions between the components.     

A facile synthesis of 2-ethynylpyrroles by ButOK-assisted room temperature deprotection of 2-(acylethynyl)pyrroles

Available N-substituted 2-(acylethynyl)pyrroles undergo room temperature deprotection in the Bu^tOK/THF system to give 2-ethynylpyrroles in 82–92% yields. Quantum-chemical calculations (B2PLYP/6-311G**//B3LYP/6-311G**+C-PCM/THF) show that the cleavage of ethynyl–acyl bond via the proton transfer from Bu^tOK with formation of potassium acylate and 2-methylpropene is thermo-dynamically much more preferred compared to alternative nucleophilic attack of tert-butoxide anion at the acyl carbon (ΔG = –35.1 vs. –2.7 kcal mol^-1).     

Conformational study of the structure of free 12-thiacrown-4 and some of its cation metal complexes

Conformational search of 12-thiacrown-4, 12t4, was performed using the CONFLEX method and the MMFF94S force field whereby 156 conformations were predicted. Optimized geometries of the 156 predicted conformations were calculated at the HF, B3LYP, CAM-B3LYP, M06, M06L, M062x and M06HF levels using the 6-311G** basis set. The correlation energy was recovered at the MP2 level using the same 6-311G** basis set. Optimized geometries at the MP2/6-311G** level and G3MP2 energies were calculated for some of the low energy conformations. The D ₄ conformation was predicted to be the ground state conformation at all levels of theory considered in this work. Comparison between the dihedral angles of the predicted conformations indicated that for the stability of 12t4, a SCCS dihedral angle of 180° requirement is more important than a gauche CSCC dihedral angle requirement. Conformational search was performed also for the 12t4?CAg⁺, Bi³⁺, Cd²⁺, Cu⁺ and Sb³⁺ cation metal complexes using the CONFLEX method and the CAChe-augmented MM3 and MMFF94S force fields. Conformations with relative energies less than 10?kcal/mol at the MP2/6-31+G*//HF/6-31+G* level, with double zeta quality basis set on the metal cations, were considered for computations at the same levels as those used for free 12t4, using also the 6-311G** basis set. The cc-pVTZ-pp basis set was used for the metal cations. The predicted ground state conformations of the 12t4?CAg⁺, Bi³⁺, Cd²⁺, Cu⁺ and Sb³⁺ cation metal complexes are the C ₄, C ₄, C ₄, C _2v and C ₄ conformations, respectively. This is in agreement with the experimental X-ray data for the 12t4?CAg⁺ and Cd²⁺ cation metal complexes, but experimentally by X-ray, the 12t4?CBi³⁺ and Cu⁺ cation metal complexes have C _s and C ₄ structures, respectively.     

Synthesis of thietanyl-substituted pyrimidine-2,4(1H,3H)-dions

Reactions of 6-methylpyrimidine-2,4(1H,3H)-dione or 5-hydroxy-6-methyl-pyrimidine-2,4(1H,3H)-dione with 2-chloromethylthiirane afforded the corresponding substituted 1-(thietan-3-yl)pyrimidine-2,4(1H,3H)-diones. The calculations in the framework of approximations PBE/3z, B3LYP/6-31G++(d,p) and MP2/6-31G++(d,p) showed that the alkylation occurred at the atom N¹ of the pyrimidine ring.     

Quantification of benzene,toluene, ethylbenzene and o-xylene in internal combustion engine exhaust with time-weighted average solid phase microextraction and gas chromatography mass spectrometry

A new and simple method for benzene, toluene, ethylbenzene and o-xylene (BTEX) quantification in vehicle exhaust was developed based on diffusion-controlled extraction onto a retracted solid-phase microextraction (SPME) fiber coating. The rationale was to develop a method based on existing and proven SPME technology that is feasible for field adaptation in developing countries. Passive sampling with SPME fiber retracted into the needle extracted nearly two orders of magnitude less mass (n) compared with exposed fiber (outside of needle) and sampling was in a time weighted-averaging (TWA) mode. Both the sampling time (t) and fiber retraction depth (Z) were adjusted to quantify a wider range of C_gas. Extraction and quantification is conducted in a non-equilibrium mode. Effects of C_gas, t, Z and T were tested. In addition, contribution of n extracted by metallic surfaces of needle assembly without SPME coating was studied. Effects of sample storage time on n loss was studied. Retracted TWA–SPME extractions followed the theoretical model. Extracted n of BTEX was proportional to C_gas, t, D_g, T and inversely proportional to Z. Method detection limits were 1.8, 2.7, 2.1 and 5.2 mg m⁻³ (0.51, 0.83, 0.66 and 1.62 ppm) for BTEX, respectively. The contribution of extraction onto metallic surfaces was reproducible and influenced by C_gas and t and less so by T and by the Z. The new method was applied to measure BTEX in the exhaust gas of a Ford Crown Victoria 1995 and compared with a whole gas and direct injection method.     

Spectroscopic characterization,X-ray structure and DFT studies on 4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]-N-methylthiazol-2-amine

The titled molecule 4-[3-(2,5-dimethylphenyl)-3-methylcyclobutyl]-N-methylthiazol-2-amine (C₁₇H₂₂N₂S) is synthesized and characterized by ¹H NMR, ¹³C NMR, IR, and X-ray single crystal determination. The compound crystallizes in the monoclinic space group P2_1/c with a = 6.3972(4) Å, b = 9.4988(6) Å, c = 26.016(2) Å and β = 93.496(7)°. In addition to the molecular geometry from the X-ray determination, vibrational frequencies and gauge, including the atomic orbital (GIAO), ¹H and ¹³C NMR chemical shift values of the titled compound in the ground state are calculated using the density functional (B3LYP) method with 6-31G(d), 6-31++G(d,p) and 6-311+G(2d,p) basis sets. The calculated results show that the optimized geometries can well reproduce the crystal structure. Moreover, the theoretical vibrational frequencies and chemical shift values show good agreement with the experimental values. The predicted nonlinear optical properties of the titled compound are greater than those of urea. DFT calculations of the molecular electrostatic potentials and frontier molecular orbitals of the titled compound are carried out at the B3LYP/6-31G(d) level of theory.     

Theoretical study on the insertion reactions of the germylenoid H2GeClMgCl with RH (R = F, OH, NH2)

The insertion reactions of the germylenoid H₂GeClMgCl with RH (R = F, OH, NH₂) have been studied by using the DFT B3LYP and QCISD methods. The geometries of the stationary points on the potential energy surfaces of the reactions were optimized at the B3LYP/6-311+G(d, p) level of theory. The calculated results indicate that all the mechanisms of the three insertion reactions are identical to each other. The QCISD/6-311++G(d, p)//B3LYP/6-311+G(d, p) calculated potential energy barriers for the three insertion reactions of R = F, OH, and NH₂ are 164.62, 193.30, and 200.73 kJ mol^?1, and the reaction energies for the three reactions are ?57.46, ?35.65, and ?22.22 kJ mol^?1, respectively. Under the same situation, the insertion reactions should occur easily in the following order H-F > H-OH > H-NH₂. In THF solvent the insertion reactions get more difficult than in gas phase.     

Structural studies on bulky phosphines: X-ray crystal structures of [2,4,6-(t-Bu)3C6H2P(SiMe3)2] and

The crystal and molecular structures of two bulky phosphines containing the 2,4,6-(t-Bu)₃C₆H₂ group are reported. Compound1, [2,4,6-(t-Bu)₃C₆H₂P(SiMe₃)₂], crystallizes in the monoclinic space group P2₁/c; a = 9.450(8), b = 17.154(6), c = 17.790(5)Å, β = 101.19(5)°. Compound2,

, also crystallizes in the monoclinic space group P2₁/c: a = 18.224(5), b = 9.394(2), c = 12.321(2)Å, β = 107.28(2)°. Structural features resulting as a consequence of the bulky 2,4,6-(tBu)₃C₆H₂ group, in particular the geometry at phosphorus, are discussed.     

The standard thermodynamic functions of ethyl-, formyl-, and benzoylferrocene in the ideal gas state

The standard enthalpies of formation of gaseous ethylferrocene, formylferrocene, and benzoylferrocene were calculated at the B3LYP/6-311+G(3df,2p)//B3LYP/6-31G(d,p) level of density functional theory using the method of isodesmic reactions. The absolute entropy, heat capacity, and enthalpy were calculated for ethylferrocene and formylferrocene by statistical thermodynamics methods over the temperature range 100–1000 K. The molecular constants necessary for calculations (structural parameters, vibrational frequencies, and internal rotation potential) were estimated at the B3LYP/6-31G(d,p) level. Empirical estimates were used to check the reliability and mutual consistency of literature experimental data on the enthalpies of formation and entropies of several ferrocene derivatives. Unreliable data were revealed and more reliable estimates of their errors were obtained.     

Thermochemical properties of 4-N,N-dialkylamino-7-nitrobenzofurazan derivatives (alkyl = methyl,ethyl)

The standard (p° = 0.1 MPa) molar enthalpies of formation, at T = 298.15 K, in the gaseous phase, for two nitrobenzofurazan derivatives, 4-N,N-dimethylamino-7-nitrobenzofurazan (DMANBF) and 4-N,N-diethylamino-7-nitrobenzofurazan (DEANBF), were derived from their enthalpies of combustion and sublimation, obtained by static bomb calorimetry and by the Knudsen effusion technique, respectively. The results are compared with the corresponding data calculated by the G3(MP2)//B3LYP approach. Computationally, the molecular structures of both compounds were established and the geometrical parameters were determined at the B3LYP/6-31G(d) level of theory.     

High performance liquid chromatographic determination of diazinon, permethrin, DEET (N, N-diethyl-m-toluamide), and their metabolites in rat plasma and urine

A rapid method was developed for the analysis of the insecticide (A) diazinon (O,O-diethyl O-2-isopropyl-6-methylpyridimidinyl) phosphorothioate, its metabolites (B) diazoxon (O,O-diethyl O-2-isopropyl-6-methylpyridimidinyl) phosphate, and (C) 2-isopropyl-6-methyl-4-pyrimidinol, the insecticide (D) permethrin [3-(2,2-dichloro-ethenyl)-2,2-dimethylcyclopropanecarboxylic acid (3-phenoxyphenyl)methylester], its metabolites (E) m-phenoxybenzyl alcohol, and (F) m-phenoxybenzoic acid, the insect repellent (G) DEET (N,N-diethyl-m-toluamide), and its metabolites (H) m-toluamide and (I) m-toluic acid in rat plasma and urine. The method is based on using C₁₈ Sep-Pak cartridges (Waters Corporation, Milford, Mass., U.S.A.) for solid phase extraction and high performance liquid chromatography with a reversed phase C₁₈ column, and absorbance detection at 230 nm for compounds A, B, and C, and at 210 nm for compounds D–I. The compounds were separated using a gradient from 1% to 99% acetonitrile in water (pH 3.0) at a flow rate ranging between 1 and 1.7 mL/min in a period of 17 min. The limits of detection were ranged between 20 and 100 ng/mL, while limits of quantification were 80–200 ng/mL. The relationship between peak areas and concentration was linear over a range of 100–1000 ng/mL. This method was applied to determine the above insecticides and their metabolites following dermal administration in rats.     

Performance of theoretical methods and basis sets on the molecular structure, atomisation and ionisation energies, electron affinity, and vibrational spectrum of silylene

This work compares the performance of theoretical methods and basis sets on the molecular structure, atomisation and ionisation energies, electron affinity, and vibrational spectrum of silylene. Silylene, its cation and anion have been studied in ¹ A ₁, ² A ₁ and ² B ₁ states, respectively, in the gas phase and C_2v symmetry. The methods considered are second-order Møller-Plesset perturbation theory (MP2), the density functional theory (DFT), Gaussian-2 (G2) and complete basis set methods (CBS-4M and CBS-Q). The basis sets used are 6-31G(d,p), 6-311G(d,p), 6-31++G(d,p) and 6-311++G(d,p). The functional used for the DFT method is B3LYP. Silylene and its cation and anion have been optimised using the MP2 and DFT methods and the named basis sets. Single-point energy calculations (G2, CBS-4M and CBS-Q) were performed using MP2/6-311++G(d,p) structures and these energies have been used to calculate atomisation energy, ionisation energy and adiabatic electron affinity. Frequency calculations were also done and the raw vibrational frequencies were assigned. It is interesting to note the close similarity between the predicted parameters and some of the available literature values. The results obtained are consistent and converge with different basis sets with improved size and quality. However, the parameters obtained are very much method dependent.