Conformational stability from variable temperature infrared spectra of xenon solutions, r0 structural parameters, and ab initio calculations of cyclopropylisocyanate

Infrared spectra (4000 to 400 cm(-1)) of the gas and variable temperature xenon solutions, and the Raman spectrum of the liquid have been recorded for cyclopropylisocyanate. The enthalpy difference has been determined to be 77 ± 8 cm(-1) (0.92 ± 0.10 kJ/mol) with the trans form more stable than the cis conformer with 59 ± 2% present at ambient temperature. By utilizing three rotational constants for each conformer, combined with structural parameters predicted from MP2(full)/6-311+G(d,p) calculations, the adjusted r(0) parameters have been obtained. Heavy atom structural parameters for the trans [cis] conformers are the following: distances (?) (C-C(2,3)) = 1.509(3) [1.509(3)], (C(2)-C(3)) = 1.523(3) [1.521(3)], (C-N) = 1.412(3) [1.411(3)], (N═C) =1.214(3) [1.212(3)], (C═O) = 1.163(3) [1.164(3)]; angles (°) ∠CCN = 116.7(5) [120.1(5)], ∠CNC = 136.3(5) [137.6(5)]. The centrifugal distortion constants have been predicted from ab initio and DFT calculations and are compared to the experimentally determined values.     

Conformational stability, r0 structural parameters, and vibrational assignments of mono-substituted cyclobutanes: fluorocyclobutane

Variable temperature (-55 to -100°C) studies of the infrared spectra (3500-400 cm(-1)) of fluorocyclobutane, c-C(4)H(7)F, dissolved in liquid xenon have been carried out as well as the infrared spectra of the gas. By utilizing eight pairs of conformers at 10 different temperatures, the enthalpy difference between the more stable equatorial conformer and the axial form has been determined to be 496±40 cm(-1) (5.93±0.48 kJ/mol). The percentage of the axial conformer present at ambient temperature is estimated to be 8±1%. The ab initio MP2(full) average predicted energy difference from a variety of basis sets is 732±47 cm(-1) (9.04±0.44 kJ/mol) and the average value of 602±20 cm(-1) from density functional theory predictions by the B3LYP method are significantly larger than the experimentally determined enthalpy value. By utilizing previously reported microwave rotational constants for the equatorial and axial conformers combined with ab initio MP2(full)/6-311+G(d,p) predicted structural values, adjusted r(0) parameters have been obtained. The determined heavy atom structural parameters for the equatorial [axial] conformer are: distances (?) C-F=1.383(3) [1.407(3)], C(α)-C(β)=1.543(3) [1.546(3)], C(β)-C(γ)=1.554(3) [1.554(3)] and angles (°) ∠C(α)C(β)C(γ)=85.0(5) [89.2(5)], ∠C(β)C(α)C(β)=89.3(5) [89.2(5)], ∠F-(C(β)C(α)C(β))=117.4(5) [109.2(5)] and a puckering angle of 37.4(5) [20.7(5)]. The conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios and vibrational frequencies have been obtained for both conformers from MP2(full)/6-31G(d) ab initio calculations and compared to experimental values where available. The results are discussed and compared to the corresponding properties of some other monosubstituted cyclobutanes with halogen and pseudo-halogen substituents.     

Molecular structure of 1,5-diazabicyclo[3.1.0]hexane as determined by gas electron diffraction and quantum-chemical calculations

The equilibrium molecular structure and conformation of 1,5-diazabicyclo[3.1.0]hexane (DABH) has been studied by the gas-phase electron-diffraction method at 20 degrees C and quantum-chemical calculations. Three possible conformations of DABH were considered: boat, chair, and twist. According to the experimental and theoretical results, DABH exists exclusively as a boat conformation of C s symmetry at the temperature of the experiment. The MP2 calculations predict the stable chair and twist conformations to be 3.8 and 49.5 kcal mol(-1) above the boat form, respectively. The most important semi-experimental geometrical parameters of DABH (r(e), A and angle)e), deg) are (N1-N5) = 1.506(13), (N1-C6) = 1.442(2), (N1-C2) = 1.469(4), (C2-C3) = 1.524(7), (C6-N1-C2) = 114.8(8), (N5-N1-C2) = 107.7(4), (N1-C2-C3) = 106.5(9), and (C2-C3-C4) = 104.0(10). The natural bond orbital (NBO) analysis has shown that the most important stabilization factor in the boat conformation is the n(N) --> sigma*(C-C) anomeric effect. The geometry calculations and NBO analysis have been performed also for the bicyclohexane molecule.     

Conformational stability of cyclobutanol from temperature dependent infrared spectra of xenon solutions, r0 structural parameters, ab initio calculations and vibrational assignment

Variable temperature (-55 to -100 degrees C) studies of the infrared spectra (4000-400 cm(-1)) of cyclobutanol, c-C4H7OH dissolved in liquid xenon have been carried out. The infrared spectrum (4000-100 cm(-1)) of the gas has also been recorded. From these data two of the four possible stable conformers have been confidently identified and their order of stabilities has been experimentally determined where the first indicator is for the position of attachment of the hydroxyl group on the bent cyclobutyl ring (Eq=equatorial or Ax=axial) and the second one (t=trans, g=gauche) is the relative position of the hydroxyl rotor, i.e. rotation around the ring C-O bond. The enthalpy difference between the most stable Eq-t conformer and the second most stable rotamer, Eq-g, has been determined to be 200+/-50 cm(-1) (2.39+/-0.60 kJ/mol). This experimentally determined order is consistent with the order of stability predicted by ab initio calculations Eq-t>Eq-g>Ax-g>Ax-t. Evidence was obtained for the third conformer Ax-g which is predicted by ab initio calculations to be less stable by more than 650cm(-1) than the Eq-t form. The percentage of each conformer at ambient temperature is estimated to be Eq-t (50%), Eq-g (47%) and Ax-g (3%). The conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios and vibrational frequencies have been obtained for all of the conformers from MP2(full)/6-31G(d) ab initio calculations. The optimized geometries and conformational stabilities have been obtained from ab initio calculations utilizing several different basis sets up to MP2(full)/aug-cc-pVTZ and from density functional theory calculations by the B3LYP method. By utilizing previously reported microwave rotational constants for the Eq-t conformer combined with ab initio MP2(full)/6-311+G(d,p) predicted structural values, adjusted r0 parameters have been obtained. The determined heavy atom structural parameters for the Eq-t conformer are: the distances C1-C4=1.547(5) angstroms, C4-C6=1.552(5)angstroms, C-O=1.416(5) angstroms and angles angleC6C4C1=86.6(5) degrees , angleC4C1C5=88.9(5) degrees and angleC6C5C1C4=22.8(5) degrees . The results are discussed and compared to the corresponding properties of some similar molecules.     

Microwave, infrared and Raman spectra, r0 structural parameters, ab initio calculations and vibrational assignment of 1-fluoro-1-silacyclopentane

The microwave spectrum (6500-18 ,500 MHz) of 1-fluoro-1-silacyclopentane, c-C(4)H(8)SiHF has been recorded and 87 transitions for the (28)Si, (29)Si, (30)Si, and (13)C isotopomers have been assigned for a single conformer. Infrared spectra (3050-350 cm(-1)) of the gas and solid and Raman spectrum (3100-40 cm(-1)) of the liquid have also been recorded. The vibrational data indicate the presence of a single conformer with no symmetry which is consistent with the twist form. Ab initio calculations with a variety of basis sets up to MP2(full)/aug-cc-pVTZ predict the envelope-axial and envelope-equatorial conformers to be saddle points with nearly the same energies but much lower energy than the planar conformer. By utilizing the microwave rotational constants for seven isotopomers ((28)Si, (29)Si, (30)Si, and four (13)C) combined with the structural parameters predicted from the MP2(full)/6-311+G(d,p) calculations, adjusted r(0) structural parameters have been obtained for the twist conformer. The heavy atom distances in A? are: r(0)(SiC(2)) = 1.875(3); r(0)(SiC(3)) = 1.872(3); r(0)(C(2)C(4)) = 1.549(3); r(0)(C(3)C(5)) = 1.547(3); r(0)(C(4)C(5)) = 1.542(3); r(0)(SiF) = 1.598(3) and the angles in degrees are: [angle]CSiC = 96.7(5); [angle]SiC(2)C(4) = 103.6(5); [angle]SiC(3)C(5) = 102.9(5); [angle]C(2)C(4)C(5) = 108.4(5); [angle]C(3)C(5)C(4) = 108.1(5); [angle]F(6)Si(1)C(2) = 110.7(5); [angle]F(6)Si(1)C(3) = 111.6(5). The heavy atom ring parameters are compared to the corresponding r(s) parameters. Normal coordinate calculations with scaled force constants from MP2(full)/6-31G(d) calculations were carried out to predict the fundamental vibrational frequencies, infrared intensities, Raman activities, depolarization values, and infrared band contours. These experimental and theoretical results are compared to the corresponding quantities of some other five-membered rings.     

Synthesis with structural and electronic characterization of homoleptic Fe(II)- and Fe(III)-fluorinated phenolate complexes

Four Fe(III) compounds and one Fe(II) compound containing mononuclear, homoleptic, fluorinated phenolate anions of the form [Fe(OAr)(m)](n-) have been prepared in which Ar(F) = C(6)F(5) and Ar' = 3,5-C(6)(CF(3))(2)H(3): (Ph(4)P)(2)[Fe(OAr(F))(5)], 1, (Me(4)N)(2)[Fe(OAr(F))(5)], 2, {K(18-crown-6)}(2)[Fe(OAr(F))(5)], 3a, {K(18-crown-6)}(2)[Fe(OAr')(5)], 3b, and {K(18-crown-6)}(2)[Fe(OAr(F))(4)], 6. Two dinuclear Fe(III) compounds have also been prepared: {K(18-crown-6)}(2)[(OAr(F))(3)Fe(μ(2)-O)Fe(OAr(F))(3)], 4, and {K(18-crown-6)}(2)[(OAr(F))(3)Fe(μ(2)-OAr(F))(2)Fe(OAr(F))(3)], 5. These compounds have been characterized with UV-vis spectroscopy, elemental analysis, Evans method susceptibility, and X-ray crystallography. All-electron, geometry-optimized DFT calculations on four [Ti(IV)(OAr)(4)] and four [Fe(III)(OAr)(4)](-) species (Ar = 2,3,5,6-C(6)Me(4)H, C(6)H(5), 2,4,6-C(6)Cl(3)H(2), C(6)F(5)) with GGA-BP and hybrid B3LYP basis sets demonstrated that, under D(2d) symmetry, π donation from the O 2p orbitals is primarily into the d(xy) and d(z(2)) orbitals. The degree of donation is qualitatively consistent with expectations based on ligand Br?nsted basicity and supports the contention that fluorinated phenolate ligands facilitate isolation of nonbridged homoleptic complexes due to their reduced π basicity at oxygen.     

The <Emphasis Type="Italic">r</Emphasis><Subscript>0</Subscript> structural parameters of equatorial and axial chlorocyclobutane,conformational stability from temperature dependent infrared spectra of xenon solutions,and vibrational assignments

Variable temperature (?55 to ?100 °C) studies of the infrared spectra (4,000–400 cm^?1) of chlorocyclobutane, c-C₄H₇Cl, dissolved in liquid xenon have been carried out. The infrared spectrum (4,000–100 cm^–1) of the gas has also been recorded. For this puckered ring molecule the enthalpy difference between the more stable equatorial conformer and the axial form, has been determined to be 361 ± 17 cm^?1 (4.32 ± 0.20 kJ/mol). This stability order is consistent with that predicted by ab initio calculations but the ?H is much lower than the average energy value of 646 ± 73 cm^?1 obtained from the MP2 ab initio calculations or 611 ± 28 cm^?1 from the B3LYP density functional theory calculations. The percentage of the axial conformer present at ambient temperature is estimated to be 15 ± 1%. By utilizing previously reported microwave rotational constants for both conformers combined with ab initio MP2(full)/6–311+G(d,p) predicted structural values, adjusted r ₀ parameters have been obtained. The determined heavy atom structural parameters for the equatorial conformer are: the distances C–Cl = 1.783(5), C₁–C₄ = 1.539(3), C₄–C₆ = 1.558(3) Å, and angles ∠C₆C₄C₁ = 86.9(5), ∠C₄C₁C₅ = 89.7(5)°, and for the axial conformer are: the distances C–Cl = 1.803(5), C₁–C₄ = 1.547(3), C₄–C₆ = 1.557(3) Å, and angles ∠C₆C₄C₁ = 86.3(5), ∠C₄C₁C₅ = 88.9(5) and the puckering angles for the equatorial and axial conformers are 30.7(5)° and 22.3(5)°, respectively. The conformational stabilities, harmonic force fields, infrared intensities, Raman activities, depolarization ratios and vibrational frequencies have been obtained for both conformers from MP2(full)/6-31G(d) ab initio calculations and compared to experimental values where available. The results are discussed and compared to the corresponding properties of some similar molecules.     

Computational study of sulfoxides of thiacyclohexane, 4‐silathiacyclohexane, 4‐fluoro‐4‐silathiacyclohexane,and 4,4‐difluoro‐4‐silathiacyclohexane: Relative energies of conformations and sulfinyl oxygen stabilized pentacoordinate silicon in boat and twist structures

Second‐order Møller‐Plesset theory (MP2) has been used to calculate the equilibrium geometries and relative energies of the chair, 1,4‐twist, 2,5‐twist, 1,4‐boat, and 2,5‐boat conformations of thiacyclohexane 1‐oxide (tetrahydro‐2H‐thiopyran 1‐oxide), 4‐silathiacyclohexane 1‐oxide, cis‐ and trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide, and 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide. At the MP2/6‐311+G(d,p) level of theory, the chair conformer of axial thiacyclohexane 1‐oxide is 0.99, 5.61, 5.91, 8.57, and 7.43 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of equatorial thiacyclohexane 1‐oxide is 4.62, 6.31, 7.56, and 7.26 kcal/mol more stable (ΔE) than its respective 1,4‐twist and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of axial 4‐silathiacyclohexane 1‐oxide is 1.79, 4.26, 3.85, and 5.71 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The 2,5‐twist conformer of axial 4‐silathiacyclohexane 1‐oxide is stabilized by a transannular interaction between the sulfinyl oxygen and silicon, to give trigonal bipyramidal geometry at silicon. The chair conformer of equatorial 4‐silathiacyclohexane 1‐oxide is 2.47, 7.90, and 8.09 kcal/mol more stable (ΔE) than its respective 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The chair conformer of axial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 4.18 and 5.70 kcal/mol more stable than its 1,4‐twist conformer and 2,5‐boat transition state and 1.51 kcal/mol more stable than the chair conformer of equatorial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide. The chair conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 5.02 and 6.11 kcal/mol more stable than its respective 1,4‐twist conformer and 2,5‐boat transition state, but is less stable than its 2,5‐twist conformer (ΔE = ?1.77 kcal/mol) and 1,4‐boat transition state (ΔE = ?1.65 kcal/mol). The 2,5‐twist conformer and 1,4‐boat conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The chair conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is 3.02, 5.16, 0.90, and 6.21 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 1,4‐boat conformers and 2,5‐boat transition state. The 1,4‐boat conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in a trigonal bipyramidal geometry at silicon. The relative energies of the conformers and transition states are discussed in terms of hyperconjugation, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen–silicon coordination. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Microwave spectrum of 3-butyne-1-thiol: evidence for intramolecular S-H...pi hydrogen bonding

The microwave spectrum of 3-butyne-1-thiol has been studied by means of Stark-modulation microwave spectroscopy and quantum-chemical calculations employing the B3LYP/6-311++G(3df,2pd), MP2/aug-cc-pVTZ, MP2/6-311++G(3df,2pd), and G3 methods. Rotational transitions attributable to two conformers of this molecule were assigned. One of these conformers possesses an antiperiplanar arrangement of the atoms S-C1-C2-C3, while the other is synclinal and stabilized by the formation of an intramolecular hydrogen bond between the H-atom of the thiol group and the pi-electrons of the C[triple bond]C triple bond. The energy difference between these conformers was estimated to be 1.7(4) kJ mol(-1) by relative intensity measurements, with the hydrogen-bonded conformer being lower in energy. The spectra of five vibrationally excited states of the synclinal conformer were observed, and an assignment of these states to particular vibrational modes was made with the aid of a density functional theory (DFT) calculation of the vibrational frequencies at the B3LYP/6-311++G(3df,2pd) level of theory.     

Electron diffraction and quantum-chemical studies of the conformational properties of the 1,3-benzenedisulfochloride molecule

A combined electron diffraction (T = 394(5) K) and quantum-chemical (MP2/6-31G**) study has been performed to investigate the molecular structure of 1,3-benzenedisulfochloride (1,3-BDSC). The 1,3-BDSC molecule was found to exist as the trans (I) and cis (II) stable conformers where the planes containing S-Cl bonds are perpendicular to the plane of the benzene ring. The energy of conformer I is 0.13 kJ/mol lower than that of conformer II. The mutual effect of the sulfochloride groups was found to be absent, which is evident from the coincident bond lengths and angles in the two conformers. The main structural parameters of the conformers are r _h1(C-H)_av = 1.103(4) Å, r _h1(C-C)_av = 1.401(3) Å, r _h1(C-S) = 1.767(4) Å, r _h1(S=O) = 1.422(3) Å, r _h1(S-Cl) = 2.048(4) Å, ∠Cl-S-O = 106.6(2)°, ∠C-S-Cl = 100.4(5)°, ∠ O-S-O = 123.2(5)°.     

Electron propagator theory study of N-/O-methylglycine conformers

The low-lying conformers of N-/O-methylglycine are studied by ab initio calculations at the B3LYP, MP3, and MP4(SDQ) levels of theory with the aug-cc-pVDZ basis set. The conformers having the intramolecular hydrogen bonds N-H...O=C or O-H...N are more stable than the others. Vertical ionization energies for the valence molecular orbitals of each conformer predicted with the electron propagator theory in the partial third-order quasiparticle approximation are in good agreement with the experimental data available in the literatures. The relative energies of the conformers and comparison between the simulated and the experimental photoelectron spectra demonstrate that there are at least three and two conformers of N- and O-methylglycine, respectively, in the gas-phase experiments. The intramolecular hydrogen bonding O-H...N effects on the molecular electronic structures are discussed for the glycine methyl derivatives, on the basis of the ab initio electronic structure calculations, natural orbital bond, and atoms-in-molecules analyses. The intramolecular hydrogen bonding O-H...N interactions hardly affect the electronic structures of the O-NH2-CH2-C(=O)-O-CH3 and alpha-methylated NH2-CH2-C(CH3)OOH conformers, while the similar intramolecular interactions lead to the significantly lower-energy levels of the highest occupied molecular orbitals for the N-(CH3-NH-CH2-COOH) and beta-methylated (NH2-CH2-CH2-COOH) conformers.     

Conformations of alpha-aminobutyric acid in the gas phase.

A laser-ablation molecular-beam Fourier transform microwave (LA-MB-FTMW) spectrometer has been successfully applied to the structural study of alpha-aminobutyric acid. Three neutral conformers have been identified in the gas phase by comparing their experimental rotational and 14N nuclear quadrupole coupling parameters with those predicted by ab initio calculations at the MP2/6-311++G(d,p) level. The most stable conformer is stabilized by a bifurcated amine-to-carbonyl hydrogen bond (N--HO=C) and a cis-COOH group, and the side-chain adopts a configuration with a torsion angle tau(C(gamma)-C(beta)-C(alpha)-C') of about 180 degrees. The second most stable conformer exhibits the same configuration for the amino acid skeleton but adopts a different orientation for the side chain with tau(C(gamma)-C(beta)-C(alpha)-C') approximately -60 degrees. In the third conformer an intramolecular hydrogen bond is established between the hydroxyl group and the nitrogen atom (NH--O), with a side-chain orientation similar to that of the most stable conformer.     

Gas-phase structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane

The geometric structure and conformational properties of 3,3,6,6-tetramethyl-1,2,4,5-tetroxane (diacetone diperoxide) have been studied by gas electron diffraction and quantum chemical calculations (MP2 and B3LYP methods with 6-31G(d,p) and 6-311+G(2df,p) basis sets). The molecule possesses a chair conformation with C2h symmetry and the following geometric parameters for the six-membered ring (rh1 values) have been determined: O-O = 1.463(5) A, C-O = 1.432 (4) A, O-C-O = 108.2(7) degrees, C-O-O = 107.7(4) degrees, phi(C-O-O-C) = 63.7(4) degrees, and phi(O-O-C-O) = -63.9(4) degrees. A small contribution of less than 3.5% of a twist conformer with C2 symmetry cannot be excluded. Quantum chemical calculations predict a contribution between 1 and 2%. Additional calculations for the parent compound 1,2,4,5-tetroxane (diformaldehyde diperoxide) demonstrate that methyl substitution at the carbon atoms has a minor effect on the ring geometry but a strong effect on the conformational properties. Methyl substitution reduces the energy difference between twist and chair conformers by more than 5 kcal/mol.     

Molecular structure and conformational stability of allylisocyanate—post-Hartree–Fock and density functional theory studies

The molecular structure and conformational stability of allylisocyanate (CH₂CHCH₂NCO) molecule was studied using the ab initio and DFT methods. The geometries of possible conformers, C-gauche (δ=120°, θ=0°) (δ=C=C–C–N and θ=C–C–N=C) and C-cis N-trans (δ=0° and θ=180°) were optimized employing HF/6-31G^*, MP2/6-31G^* levels of theory of ab initio and BLYP, B3LYP, BPW91 and B3PW91 methods of DFT implementing the atomic basis set 6-311+G(d,p). The structural and physical parameters of the above conformers were discussed with the experimental and theoretical values of the related molecules, methylisocyanate and 3-fluoropropene. It has been found that the N=C=O bond angle is not linear as the experimental result for both the conformers and the theoretical bond angle is 173°. The rotational potential energy surfaces have been performed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The Fourier decomposition potentials were analysed at the HF/6-31G^*, and MP2/6-31G^* levels of theory. The HF/6-31G^* level of theory predicted that the C-gauche conformer is more stable than the C-cis N-trans conformer by 0.41 kJ/mol, but the MP2 and DFT methods predicted the C-cis N-trans conformer is found to be more stable than the C-gauche conformer. The calculated chemical hardness value at the HF/6-31G^* level of theory predicted the C-cis N-trans form is more stable than C-gauche form, whereas the chemical hardness value at the MP2/6-31G^* level of theory favours the slight preference towards the C-gauge conformer.     

Calculation of relative energies of permethylated oligosilane conformers in vapor and in alkane solution

The geometries of 35 conformers of Me(SiMe2)nMe (n = 4, 1; n = 5, 2; n = 6, 3; n = 7, 4) were optimized at the MP2/VTDZ level, and CCSD(T) single-point calculations were done at three MP2/VTDZ conformer geometries of 1. The relative ground-state energies of the conformers of 1-4 in the gas phase were obtained from the MP2/VTDZ electronic energy, zero-point vibrational energy, and thermal corrections at 0, 77, and 298 K. Relative energies in an alkane solvent at 77 and 298 K were obtained by the addition of solvation energies, obtained from the SM5.42R model. The calculated energies of 26 of the conformers (n = 4-6) have been least-squares fitted to a set of 15 additive increments associated with each Si-Si bond conformation and each pair of adjacent bond conformations, with mean deviations of 0.06-0.20 kcal/mol. An even better fit for the energies of 24 conformers (mean deviations, 0.01-0.09 kcal/mol) has been obtained with a larger set of 19 increments, which also contained contributions from selected combinations of conformations of three adjacent bonds. The utility of the additive increments for the prediction of relative conformer energies in the gas phase and in solution has been tested on the remaining nine conformers (n = 6, 7). With the improved increment set, the average deviation from the SM5.42R//MP2 results for solvated conformers at 298 K was 0.18 kcal/mol, and the maximum error was 0.98 kcal/mol.     

Comprehensive conformational analysis of the nucleoside analogue 2'-beta-deoxy-6-azacytidine by DFT and MP2 calculations

A comprehensive conformational analysis of isolated 2'-beta-deoxy-6-azacytidine (d6AC), an analogue of therapeutically active 6-azacytidine (6AC), has been performed by means of ab initio calculations at the MP2/6-311++G(2df,pd)//DFT B3LYP/6-31G(d,p) level of theory. Among the 81 conformers located within a 7.83 kcal/mol Gibbs energy range at T = 298.15 K, 38 contain syn-oriented bases with respect to 2'-deoxyribose; the other conformers include anti-oriented bases. Energetic analysis of these conformers shows that conformational equilibrium of isolated d6AC at T = 298.15 K is shifted to syn conformation with a syn/anti ratio estimated as 61.4%:38.6%. As far as the sugar conformation is concerned, 40 conformers contain north (N) (with 0.3 degrees < or = P < or = 40.1 degrees), and the rest possess south (S) (with 157.1 degrees < or = P < or = 207.0 degrees) puckers, where P is the pseudorotational angle of the furanose ring. The S/N occupancy ratio is estimated as 80.2%:19.8% (T = 298.15 K). The two most stable conformers are energetically quasidegenerate and correspond to both C2'-endo/syn conformers differing only by orientation of the O3'H hydroxyl group. They are both stabilized by means of similar intramolecular H-bonds, i.e., O5'H...O2, C2'H2...O2, and C2'H2...O5'. As examined by AIM criteria, from 1 to 3 H-bonds per conformer were identified among 13 possible interactions: O5'H...O2, O5'H...N6, O3'H...O5', O5'H...O3', C1'H...O2, C2'H2...O2, C2'H2...O5', C3'H...O2, C3'H...N6, C5'H1...O2, C5'H2...O2, C5'H1...N6, and C5'H2...N6. The biological effect of d6AC is conceived as an inhibition of replicative DNA polymerase caused by an unusual orientation of the sugar residue against the base in the only A form DNA-like conformer.     

Conformational stability from variable temperature infrared spectra of krypton solutions, ab initio calculations, vibrational assignment, and r0 structural parameters of 1,3-difluoropropane

The infrared spectra (3200-400 cm(-1)) of krypton solutions of 1,3-difluoropropane, FCH2CH2CH2F, at variable temperatures (-105 to -150 degrees C) have been recorded. Additionally, the infrared spectra (3200-50 cm(-1)) of the gas and solid have been recorded as well as the Raman spectrum of the liquid. From a comparison of the spectra of the fluid phases with that in the solid, all of the fundamental vibrations of the C2 conformer (gauche-gauche) where the first gauche indicates the form for one of the CH2F groups and the second gauche the other CH2F, and many of those for the C1 form (trans-gauche) have been identified. Tentative assignments have been made for a few of the fundamentals of the other two conformers, i.e. C2v (trans-trans) and Cs (gauche-gauche'). By utilizing six pairs of fundamentals for these two conformers in the krypton solutions, an enthalpy difference of 277 +/- 28 cm(-1) (3.31 +/- 0.33 kJ mol(-1)) has been obtained for the C2 versus C1 conformer with the C2 conformer the more stable form. For the C2v conformer, the enthalpy difference has been determined to be 716 +/- 72 cm(-1) (8.57 +/- 0.86 kJ mol(-1)) and for the Cs form 971 +/- 115 cm(-1) (11.6 +/- 1.4 kJ mol(-1)). It is estimated that there is 64 +/- 3% of the C2 form, 34 +/-3% of the C1 form, 1% of the C2v form and 0.6% of the Cs conformer present at ambient temperature. Equilibrium geometries and total energies of the four stable conformers have been determined from ab initio calculations with full electron correlation by the perturbation method to second order as well as by hybrid density functional theory calculations with the B3LYP method using a number of basis sets. The MP2 calculations predict the C1 conformer stability to be slightly higher than the experimentally determined value whereas for the C2v and Cs conformers the predicted energy difference is much larger than the experimental value. The B3LYP calculations predict a better energy difference for both the C1 and C2v as well as for the Cs conformers than the MP2 values. A complete vibrational assignment is proposed for the C2 conformer and many of the fundamentals have been identified for the C1 form based on the force constants, relative intensities and rotational-vibrational band contours obtained from the predicted equilibrium geometry parameters. By combining previously reported rotational constants for the C2 and C1 conformers with ab initio MP2/6-311 + G(d, p) predicted parameters, adjusted r0 parameters have been obtained for both conformers. Comparisons are made with the parameters obtained for some other molecules containing the FCH2 group. The spectroscopic and theoretical results are compared to the corresponding properties for some similar molecules.     

Cubane-type heterometallic sulfido clusters: incorporation of two metal fragments into a dinuclear ReS(mu-S)2ReS core affording bimetallic M2Re2(mu 3-S)4 clusters (M = Ru,Pt, Cu) or trimetallic MM'Re2(mu 3-S)4 clusters via incomplete cubane-type MRe2(mu 3-S)(mu 2-S)3 intermediates (M = Ru,Rh, Ir; M' = Mo,W, Pd,Ru, Rh)

Reactions of a dirhenium tetra(sulfido) complex [PPh(4)](2)[ReS(L)(mu-S)(2)ReS(L)] (L = S(2)C(2)(SiMe(3))(2)) with a series of group 8-11 metal complexes in MeCN at room temperature afforded either the cubane-type clusters [M(2)(ReL)(2)(mu(3)-S)(4)] (M = CpRu (2), PtMe(3), Cu(PPh(3)) (4); Cp = eta(5)-C(5)Me(5)) or the incomplete cubane-type clusters [M(ReL)(2)(mu(3)-S)(mu(2)-S)(3)] (M = (eta(6)-C(6)HMe(5))Ru (5), CpRh (6), CpIr (7)), depending on the nature of the metal complexes added. It has also been disclosed that the latter incomplete cubane-type clusters can serve as the good precursors to the trimetallic cubane-type clusters still poorly precedented. Thus, treatment of 5-7 with a range of metal complexes in THF at room temperature resulted in the formation of novel trimetallic cubane-type clusters, including the neutral clusters [[(eta(6)-C(6)HMe(5))Ru][W(CO)(3)](ReL)(2)(mu(3)-S)(4)], [(CpM)[W(CO)(3)](ReL)(2)(mu(3)-S)(4)] (M = Rh, Ir), [(Cp*Ir)[Mo(CO)(3)](ReL)(2)(mu(3)-S)(4)], [[(eta(6)-C(6)HMe(5))Ru][Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)], and [(Cp*Ir)[Pd(PPh(3))](ReL)(2)(mu(3)-S)(4)] (13) along with the cationic clusters [(Cp*Ir)(CpRu)(ReL)(2)(mu(3)-S)(4)][PF(6)] (14) and [(Cp*Ir)[Rh(cod)](ReL)(2)(mu(3)-S)(4)][PF(6)] (cod = 1,5-cyclooctadiene). The X-ray analyses have been carried out for 2, 4, 7, 13, and the SbF(6) analogue of 14 (14') to confirm their bimetallic cubane-type, bimetallic incomplete cubane-type, or trimetallic cubane-type structures. Fluxional behavior of the incomplete cubane-type and trimetallic cubane-type clusters in solutions has been demonstrated by the variable-temperature (1)H NMR studies, which is ascribable to both the metal-metal bond migration in the cluster cores and the pseudorotation of the dithiolene ligand bonded to the square pyramidal Re centers, where the temperatures at which these processes proceed have been found to depend upon the nature of the metal centers included in the cluster cores.     

Study of the thymine molecule: equilibrium structure from joint analysis of gas-phase electron diffraction and microwave data and assignment of vibrational spectra using results of ab initio calculations

Thymine is one of the nucleobases which forms the nucleic acid (NA) base pair with adenine in DNA. The study of molecular structure and dynamics of nucleobases can help to understand and explain some processes in biological systems and therefore it is of interest. Because the scattered intensities on the C, N, and O atoms as well as some bond lengths in thymine are close to each other the structural problem cannot been solved by the gas phase electron diffraction (GED) method alone. Therefore the rotational constants from microvawe (MW) studies and differences in the groups of N-C, C=O, N-H, and C-H bond lengths from MP2 (full)/cc-pVQZ calculations were used as supplementary data. The analysis of GED data was based on the C(s) molecular symmetry according to results of the structure optimizations at the MP2 (full) level using 6-311G (d,p), cc-pVTZ, and cc-pVQZ basis sets confirmed by vibrational frequency calculations with 6-311G (d,p) and cc-pVTZ basis sets. Mean-square amplitudes as well as harmonic and anharmonic vibrational corrections to the internuclear distances (r(e)-r(a)) and to the rotational constants (B(e)(k)-B(0)(k), where k = A, B, C) were calculated from the quadratic (MP2 (full)/cc-pVTZ) and cubic (MP2 (full)/6-311G (d,p)) force constants (the latter were used only for anharmonic corrections). The harmonic force field was scaled using published IR and Raman spectra of the parent and N1,N3-dideuterated species, which were for the first time completely assigned in the present work. The main equilibrium structural parameters of the thymine molecule determined from GED data supplemented by MW rotational constants and results of MP2 calculations are the following (bond lengths in Angstroms and bond angles in degrees with 3sigma in parentheses): r(e) (C5=C6) = 1.344 (16), r(e) (C5-C9) = 1.487 (8), r(e) (N1-C6) = 1.372 (3), r(e) (N1-C2) = 1.377 (3), r(e) (C2-N3) = 1.378 (3), r(e) (N3-C4) = 1.395 (3), r(e) (C2=O7) = 1.210 (1), r(e) (C4=O8) = 1.215 (1), angle e (N1-C6=C5) = 123.1 (5), angle e (C2-N1-C6) = 123.7 (5), angle e (N1-C2-N3) = 112.8 (5), angle e (C2-N3-C4) = 128.0 (5), angle e (N3-C4-C5) = 114.8 (5), angle e (C6=C5-C9) = 124.4 (9). The experimental structural parameters are in good agreement with those from MP2 (full) calculations with use of cc-pVTZ and cc-pVQZ basis sets.     

Effect of trimethylsilyl substitution on the chemical properties of triarylphosphines and their corresponding metal-complexes: solubilising effect in supercritical carbon dioxide

The donor strengths of the following triarylphosphine ligands P(Ar)(2)(Ar')(Ar = Ar'= 4-Me(3)SiC(6)H(4), 1b; 4-Me(3)CC(6)H(4), 1d; 4-F(3)CC(6)H(4), 1e; Ar = C(6)H(5), Ar'= 4-Me(3)SiC(6)H(4), 1c) have been evaluated experimentally and theoretically. The measurements of the J(P-Se) coupling constants of the corresponding synthesised selenides Se=P(Ar)(2)(Ar'), 2b,c and the DFT calculation of the energies of the phosphine lone-pair (HOMO) reveal insignificant influence on the electronic properties of the substituted phosphines when the trimethylsilyl group is attached to the aryl ring, in marked contrast to the strong electronic effect of the trifluoromethyl group. These triarylphosphine ligands P(Ar)(2)(Ar') reacted with (eta5-C(5)H(5))Co(CO)(2), (eta5-C(5)H(5))Co(CO)I(2) or PdCl(2) to yield the new compounds (eta5-C(5)H(5))Co(CO)[P(Ar)(2)(Ar')], 3b,d; (eta5-C(5)H(5))CoI(2)[P(Ar)(2)(Ar')], 4b-e; and PdCl(2)[P(Ar)(2)(Ar')](2), 5b,c respectively. These complexes have been characterized and their spectroscopic properties compared with those reported for the known triphenylphosphine complexes. Again, the contrast of the (31)P NMR and (13)C NMR chemical shifts or C-O or M-Cl stretching frequencies, when applied, does not show an important electronic effect on the metal complex of the trimethylsilyl substituted phosphines with respect to P(C(6)H(5))(3) derivatives. Solubility measurements of complexes 3a and 3b in scCO(2) were performed. We conclude that Me(3)Si groups on the triarylphosphine improve the solubility of the corresponding metal complex in scCO(2).