Gas Electron Diffraction Analysis Research Articles

Interplay of Experiment and Theory: Determination of an Accurate Equilibrium Structure of 1-Methyluracil by the Gas Electron Diffraction Method and Coupled-Cluster Computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.

Preparation and Properties of Trifluorothioacetic Acid- S-(trifluoromethyl)ester, CF 3C(O)SCF 3

Trifluorothioacetic acid-S-(trifluoromethyl)ester, CF3C(O)SCF3, was prepared by reacting CF3C(O)Cl and AgSCF3 at 50 degrees C. The compound was characterized by (13)C-, (19)F-NMR, UV, and vibrational spectroscopy as well as by gas electron diffraction (GED) and quantum chemical calculations (HF, MP2, and B3LYP methods 6-31G(d) and 6-311+G(2df) basis sets). GED and vibrational spectroscopy result in the presence of a single conformer with C1 symmetry and synperiplanar orientation of the S-CF3 bond relative to the CO bond. This result is in agreement with quantum chemical calculations which predict the anti conformer to be higher in energy by about 4 kcal/mol. An assignment of the IR (gas) and Raman (liquid) spectra is proposed, and the GED analysis results in the following skeletal geometric parameters (r(a) and angle(a) values with 3sigma uncertainties; these parameters are thermal averages and are not inconsistent with calculated equilibrium values): C=O = 1.202(6) A, C-C = 1.525(10) A, S-C(sp(2)) = 1.774(3) A, S-C(sp(3)) = 1.824 (3) A. O=C-C = 118.7(21) degrees, O=C-S = 127.1(15) degrees, C-S-C = 99.8 (13) degrees.

Molecular Structure and Conformations of para-Methylbenzene Sulfonamide and ortho-Methylbenzene Sulfonamide: Gas Electron Diffraction and Quantum Chemical Calculations Study

The molecular structure and conformational properties of para-methylbenzene sulfonamide (4-MBSA) and ortho-methylbenzene sulfonamide (2-MBSA) have been studied by gas electron diffraction (GED) and quantum chemical methods (B3LYP/6-311+G** and MP2/6-31G**). Quantum chemical calculations predict the existence of two conformers for 4-MBSA with the S-N bond perpendicular to the benzene plane and the NH2 group either eclipsing or staggering the S-O bonds of the SO2 group. Both conformers possess CS symmetry. The eclipsed form is predicted to be favored by DeltaE = 0.63 kcal/mol (B3LYP) or 1.00 kcal/mol (MP2). According to the calculations, the S-N bond in 2-MBSA can possess planar direction opposite the methyl group (phi(C2C1SN) = 180 degrees ) or nonplanar direction (phi(C2C1SN) approximately 60 degrees ). In both cases, the NH2 group can adopt eclipsed or staggered orientation, resulting in a total of four stable conformers. The nonplanar eclipsed conformer (C1 symmetry) and the planar eclipsed form (CS symmetry) are predicted to be favored. According to the GED analysis, the saturated vapor over solid 4-MBSA at T = 151(3) degrees C consists as mixture of the eclipsed (78(19) %) and staggered (22(19) %) forms. The saturated vapor over solid 2-MBSA at T = 157(3) degrees C consists as a mixture of the nonplanar eclipsed (69(11) %) and planar eclipsed (31(11) %) forms.

Fluoroformyl Trifluoroacetyl Disulfide, FC(O)SSC(O)CF3: Synthesis, Structure in Solid and Gaseous States, and Conformational Properties

Fluoroformyl trifluoroacetyl disulfide, FC(O)SSC(O)CF3, is prepared by quantitative reaction between FC(O)SCl and CF(3)C(O)SH. The conformational properties and geometric structure of the gaseous molecule have been studied by vibrational spectroscopy (IR(gas), Raman(liquid), IR(matrix)), gas electron diffraction (GED), and quantum chemical calculations (B3LYP and MP2 methods). The disulfide bond length derived from the GED analysis amounts 2.023(3) Angstroms, and the dihedral angle around this bond, phi(CS-SC), is 77.7(21) degrees, being the smallest dihedral angle measured for noncyclic disulfides in the gas phase. The compound exhibits a conformational equilibrium at room temperature having the most stable form C(1) symmetry with a synperiplanar (sp-sp) orientation of both carbonyl groups with respect to the disulfide bond. A second form was observed in IR spectra of the Ar matrix isolated compound at cryogenic temperatures, corresponding to a conformer that possess the carbonyl bond of the FC(O) moiety in antiperiplanar position with respect to the S-S single bond (ap-sp). A DeltaH degrees = - = 1.34(11) kcal/mol has been determined by IR(matrix) spectroscopy. The structure of single crystal of FC(O)SSC(O)CF3 was determinate by X-ray diffraction analysis at low temperature using a miniature zone melting procedure. The crystalline solid (monoclinic, P2(1)/n, a = 5.240(4)Angstroms, b = 23.319(17)Angstroms, c = 6.196(4)Angstroms, beta = 113.14(3) degrees) consists exclusively of the (sp-sp) conformation. The geometrical parameters agree with those obtained for the molecule in the gas phase.

Gas Electron Diffraction and Quantum-Mechanical Study of Dimethyloxalate

The geometrical structure and conformation of dimethyloxalate, CH3OC(O)–C(O)OCH3, have been studied by gas electron diffraction (GED) and quantum-chemical calculations (MP2 and B3LYP methods with 6-31G* and cc-pVTZ basis sets). The GED analysis with a dynamic model (T = 323 K) results in a mixture of two planar conformers, anti (C2h symmetry) and syn (C2v symmetry) orientation of the two C=O bonds. The energy difference between these conformers is 0.02(0.18) kcal/mol and barrier to internal rotation around the C–C bond is 0.44(0.41) kcal/mol. The CH3 groups occupy synperiplanar positions with respect to the C=O bonds. The following main geometrical parameters for the anti conformer (A and degrees) have been derived: rg(C–C) = 1.532(3), rg(C=O) = 1.203(2), rg(Csp3–O) = 1.436(3), rg(Csp2–O) = 1.333(3), ∠α(Csp2–Csp2–O) = 111.9(1.9), ∠α(Csp2–O–Csp3) = 116.3(1.6), ∠α(O–C= O) = 127.0(1.8).

Gas electron diffraction analysis on S-methyl thioacetate, CH3C(O)SCH3.

The molecular structure of S-methyl thioacetate, CH3C(O)SCH3, was determined by gas electron diffraction (GED) with the assistance of quantum chemical calculations (B3LYP/6-31G and MP2/6-31G). Experimental and theoretical methods result in a structure with syn conformation (C=O double bond syn with respect to the S-C(H3) single bond). The following skeletal geometric parameters were derived from the GED analysis (ra values with 3sigma uncertainties): C=O = 1.214(3), C-C = 1.499(5), S-C(sp2) = 1.781(6), S-C(sp3) = 1.805(6) angstroms, O=C-C = 123.4(8) degrees, O=C-S = 122.8(5) degrees and C-S-C = 99.2(9) degrees.

Tautomeric and Conformational Properties of Methyl Acetoacetate, CH3OC(O)−CH2−C(O)CH3: Electron Diffraction and Quantum Chemical Study

The tautomeric properties of methyl acetoacetate, CH3OC(O)−CH2−C(O)CH3, have been investigated in the gas phase by gas electron diffraction (GED), IR(matrix) spectroscopy, and quantum chemical calculations (the MP2 approximation with 6-31G** and 6-311G(2df) basis sets and the B3LYP method with 6-31G** and 6-31++G** basis sets). GED results in a mixture of 80(7)% enol tautomer and 20(7)% diketo form at 309(6) K. Only one enol form with the O−H bond adjacent to the methyl group, CH3OC(O)−CHC(OH)CH3, is present. The GED analysis cannot distinguish between the three diketo conformers which are predicted by quantum chemical calculations. IR(matrix) spectra confirm the presence of a mixture of enol and keto forms with the enol tautomer strongly prevailing. Quantum chemical calculations with the MP2 approximation predict a very small contribution of the enol tautomer, in contrast to the experiments. B3LYP calculations, however, reproduce the experimental tautomeric mixture very closely.

Gas phase structure and conformational properties of trifluoroacetic anhydride, CF 3C(O)OC(O)CF 3

The geometric structure of trifluoroacetic anhydride, CF 3C(O)OC(O)CF 3, has been studied by gas electron diffraction (GED) and quantum chemical calculations (MP2 and B3LYP with 6-31G * basis sets). The GED analysis results in a single conformer with synperiplanar orientation of the two CO bonds. This analysis, however, cannot discriminate between a planar equilibrium structure ( C 2v symmetry) with large amplitude torsional motions around the OC bonds and a nonplanar equilibrium structure (C 2 symmetry) with a low barrier at the planar arrangement. An effective dihedral angle φ(COCO=18(4)° is obtained. Both quantum chemical methods predict a nonplanar equilibrium structure of C 2 symmetry and φ(COCO)=16.5° and 13.9°, respectively.

Structure and Conformation of Perfluoromethyloxalate, CF3OC(O)C(O)OCF3, in the Crystal and in the Gas Phase

The geometric structure and conformational properties of perfluoromethyloxalate, CF3OC(O)C(O)OCF3, have been studied in the gas phase by gas electron diffraction (GED) and in the solid state by X-ray crystallography. The experimental investigations were supplemented by quantum chemical calculations using the MP2 and B3LYP methods with 6-31G* and 6-31++G(2df) basis sets, respectively. The GED analysis results for the gaseous state in a mixture of two planar conformers with both CO bonds antiperiplanar (ap) to each other (C2h symmetry) or both CO bonds synperiplanar (sp) to each other (C2v symmetry). The ratio ap:sp of 58(12)%:42(12)% corresponds to ΔG0 = 0.19(37) kcal/mol. This value is reproduced satisfactorily by the quantum chemical calculations: 0.42 kcal/mol (MP2) and 0.67 kcal/mol (B3LYP). The presence of a mixture of two conformers with nearly equal contributions is confirmed by the IR(gas) spectrum. In the solid state, four independent molecules with ap conformation (Ci symmetry) occur in the unit cell.

Structures and Conformations of ((Trifluoroacetyl)imido)(trifluoromethyl)sulfur Fluoride, CF3C(O)NS(F)CF3

The molecular structure and conformational properties of ((trifluoroacetyl)imido)(trifluoromethyl)sulfur fluoride, CF 3 C(O)N=S(F)CF 3 , were determined by gas electron diffraction (GED) and vibrational spectroscopy (IR (gas) and Raman (liquid)). Furthermore, quantum chemical calculations (HF, MP2, and B3LYP with 6-31G* basis sets) were performed. The vibrational spectra were assigned by comparison with related molecules and calculated (HF and B3LYP) frequencies and intensities. According to the GED analysis the main conformer (90(6)%) possesses an anti-syn structure with anti orientation of the N-C bond relative to the F-S-CF 3 bisector and syn orientation of the C=O bond relative to the N=S bond. The second conformer (10(6)%) possesses a syn-syn structure. The experimental Gibbs free energy difference (ΔG° = 1.3(4) kcal/mol) is reproduced correctly by the two quantum chemical methods (1.35 kcal/mol from MP2 and 1.04 kcal/mol from B3LYP). The conformational properties of this compound are in contrast to those of imidosulfurous difluorides, RNSF 2 , and dichlorides, RN=SCl 2 , for which only syn structures around the N=S double bond were observed.

Gas Phase Structure of Methyl Trifluoromethanesulfonate, CH3OSO2CF3, and Conformational Properties of Covalent Sulfonates

The molecular structure of methyl trifluoromethanesulfonate (CH3OSO2CF3, methyl triflate) was investigated by gas electron diffraction (GED) and quantumchemical calculations (HF/3-21G* and B3LYP/6-31G*). The GED analysis revealed a gauche conformation (methyl group gauche with respect to CF3 group) with a dihedral angle φ(C−O−S−C) = 89(7)°. This value is reproduced correctly by the calculations. Some calculated bond lengths and bond angles, however, differ from experimental values by up to ±0.07 Å and ±6°. Additional B3LYP/6-31G* calculations have been performed for some covalent sulfonates. The potential functions for internal rotation around the S−O single bond in FOSO2F and ClOSO2F possess minima for gauche and trans orientation of the O−X (X = F or Cl) bond. The trans minima are 1.6 and 1.3 kcal mol-1 higher in energy. The potential functions for triflic acid, HOSO2CF3, for CH3OSO2Cl and CH3OSO2F possess minima only for gauche structures and maxima for trans orientation. These results are in partial contrast to previous experimental studies.

S-trifluoromethyldisulfanyl sulfinylimine, CF 3SSNSO: structure and conformation in the electronic ground and excited states

The molecular structure of S-trifluoromethyldisulfanyl sulfinylimine, CF 3SNSO, was determined by gas electron diffraction (GED) and quantum chemical calculations ( HF 3-21 G∗ , HF 6-31 G∗ , BPW91 6-31 G∗ and B3 PW91 6-31 G∗ ). Experimental and theoretical methods result in a structure with a planar SSNSO skeleton and the CF 3 group out of this plane. The SS single bond possesses anti-orientation relative to the NS double bond and the SN single bond synorientation with respect to the SO double bond. The following skeletal parameters ( r a values with 3σ uncertainties) were derived from the GED analysis: SO, 1.458 (4) Å; SN, 1.523(6) Å; SN, 1.681(6) Å; SC, 1.824(7) Å; SS, 2.016(4) Å; NSO, 116.3(17)°; SNS, 125.9(13)°; SSN, 97.9(14)°; SSC, 103.9(12)°; and CSSN, 81.3(94)°. The Raman (liquid) and UV (gas) spectra were recorded. Using the time-dependent theory of Raman scattering, the evaluation of the Raman excitation profiles together with UV data results in the dimensionless displacements (Δ) in normal coordinates for the excited state. These were transformed to internal coordinate values (δ).

(Trifluoromethyl)sulfanyl sulfinylimine, CF 3SNSO. Structure and conformation in the electronic ground and excited states

The molecular structure of (trifluoromethyl)sulfanyl sulfinylimine, CF 3SNSO, was determined by gas electron diffraction (GED) and ab initio calculations ( HF 3–21 G∗ , HF 6–31+ G∗ and MP2 6–31+ G∗ ). Experimental and theoretical methods result in a structure with planar CSNSO skeleton (C s symmetry), anti orientation of the SC bond relative to the NS bond and syn orientation of the SN bond relative to the SO double bond (anti-syn structure). The following skeletal parameters ( r a values with 3σ uncertainties) were derived in the GED analysis: SC, 1.831(4) Å; SN, 1.684(5) Å; NS, 1.538(6) Å; SO, 1.453(6) Å; CSN, 94.6(8)°; SNS, 120.6(6)°; NSO: 116.5(8)°. A normal coordinate analysis based on FTIR (gas), FTIR (matrix) and Raman (liquid) spectra was performed. The UV (gas) spectrum was recorded and interpretation of the resonance Raman effect leads to the conclusion that the molecular symmetry (C s) is retained upon electronic excitation.

The Anomeric Effect in (Fluoromethyl)dimethylamine, CH2FN(CH3)2

The molecular structure of (fluoromethyl)dimethylamine, CH2FN(CH3)2, has been determined by gas electron diffraction (GED), ab initio (HF/3-21G(*) (polarization functions only at nitrogen), and MP2/6-311G(2d,p)), and local density functional (VWN/TZVP) calculations. According to the GED analysis only the anti conformer (C−F bond antiperiplanar to the nitrogen lone pair) is present. The following skeletal geometric parameters (ra distances and ∠α angles with 3σ error limits) were obtained: N−CH2F = 1.408(13) Å, N−CH3 = 1.466(9) Å, C−F = 1.410(5) Å, (C−N−C)mean = 111.6(10)°, and N−C−F = 115.9(24)°. The results are discussed on the basis of the generalized anomeric effect. The theoretical calculations predict a second stable conformer with synclinal orientation of the C−F bond and 4.5−5.3 kcal mol-1 higher in energy.

Vibrational spectra and gas phase structures of fluorine fluorosulfate (FOSO 2F) and chlorine fluorosulfate (ClOSO 2F)

Infrared spectra in the gaseous state, and in the matrix and Raman spectra in the solid state, were recorded for the halogen fluorosulfates XOSO 2F, X = F, Cl. The absence of frequency splittings in the matrix spectra demonstrates the presence of one single conformer for both compounds. The assignments of the fundamental vibrations are supported by normal coordinate analyses based on frequencies and isotopic shifts. The molecular structures of both compounds were determined by gas electron diffraction (GED) and ab initio calculations ( HF 3-21 G∗ and HF 6-31 G∗ . According to the GED analysis and in agreement with the ab initio calculations gauche conformers with dihedral angles τ (FSOX) ≈ 70° are preferred in both fluorosulfates. The calculations predict the trans forms, τ(FSOX) ≈ 180°, to be higher in energy by about 10 kJ mol −1 for X = F and by about 8 kJ mol −1 for X = Cl.

Conformations and structures of thiophosphanes containing one, two and three PS bonds. A gas electron diffraction and ab initio study

Abstract The conformations and geometric structures of thiophosphanes which contain one PS bond, X 2 PSY, two PS bonds, XP(SY) 2 and three PS bonds, P(SY) 3 are studied by ab initio calculations and gas electron diffraction (GED). For compounds of the type X 2 PSY (X  H or F and YH, CH 3 or F) the calculations predict two possible conformations with the SY bond either synperiplanar to the phosphorus lone pair (Θ (1pPSY)  0°) or antiperiplanar (Θ = 180°). The synperiplanar structure is preferred in compounds with equivalent substituents (H 2 PSH and F 2 PSF), whereas the antiperiplanar form is preferred for mixed substituents (F 2 PSH, F 2 PSCH 3 and H 2 PSF). A GED study of (CF 3 ) 2 PSCF 3 results in a synperiplanar structure (Θ = 0°), confirming this observation. Calculations for HP(SH) 2 result in three stable structures, syn—syn ( C s symmetry), syn—anti ( C 1 symmetry) and anti—anti ( C s symmetry). The relative energies are predicted to be 0, 0.46 and 1.26 kcal mol −1 (HF/3-21G*). In the case of HP(SCF 3 ) 2 the calculated energy of the syn—anti form relative to the syn—syn form depends on the basis set; −1.32 kcal mol −1 for HF/3-21G* and 0.23 kcal mol −1 for HF/6-31G**. According to the GED analysis, the prevailing conformer of this thiophosphane is syn—syn with a possible small contribution of the syn—anti form. The parent thiophosphane with three PS bonds, P(SH) 3 , posseses five possible conformations, two of which have C 3 symmetry, two C s symmetry and one C 1 symmetry. For P(SCF 3 ) 3 two of these five forms possess unreasonably short F⋰F contacts between neighboring CF 3 groups and do not form stable structures. According to the GED analysis the main conformer of P(SCF) 3 ) 3 possesses C 3 symmetry with all CF 3 groups syn to the phosphorus lone pair (Θ 1 = Θ 2 = Θ 3 = 29(4)°). Small contributions ( C s and/or C 1 structures cannot be excluded.

Is the molecular structure of 1,4,7-trithiacyclononane([9]aneS3) as symmetrical in the gas phase as it is in the crystal? An electron diffraction study

The molecular structure of [9]aneS3 has been studied by gas electron diffraction (GED) and by molecular-mechanics calculations (MM2). Four molecular models have been fitted to the experimental data, one having D3 symmetry, one C3 symmetry, one C2 symmetry and one C1 symmetry. The D3 model was incompatible with the GED data and was discarded. The C1 model gave the lowest R-factor in the GED analysis, and the C2 model gave only a slightly poorer fit to the data. The C3 model, which corresponds to the conformation observed in the crystalline state, could not be completely excluded, but the model gave a significantly worse fit to the GED data than the C2 and C1 models. MM2 calculations also favoured the C1 model, but with the C3 model only 0.13 kJ mol–1 higher in strain energy. The C2 and D3 models were higher in energy by 8.3 and 9.9 kJ mol–1 respectively.

Determination of structures of molecules of lower halides of transition elements by gas electron-diffraction analysis. I. Titanium trichloride

Determination of structures of molecules of lower halides of transition elements by gas electron-diffraction analysis. I. Titanium trichloride