3-chloro-1-butene: gas-phase molecular structure and conformations as determined by electron diffraction and by molecular mechanics and ab initio calculations

Gaseous 3-chloro-1-butene has been studied experimentally by electron diffraction (ED) at 20 and 180°C, and at these temperatures, 76(10)% and 62(10)%, respectively, of the most stable conformer i.e. the one having a hydrogen atom eclipsing the double bond, were found. The conformer with the chlorine atom eclipsing the C=C bond was also present. However, from the experimental data it was not possible to establish conclusive evidence for the conformer with an eclipsed CH₃ group. Molecular mechanics (MM) calculations and ab initio calculations using a 4-21 basis set were carried out with complete geometry optimization, and calculated parameters from each of the methods were used in combination with the ED data. Such calculations indicated the existence of all three conformers mentioned above. Least-squares analysis including constraints from the ab initio calculation gave as a result the following molecular structure (r_a distances and ??? angles) for the predominant conformer: r(C=C) = 1.337(6) Å, r(=C---C) = 1.503(4) Å, r(C---CH₃) = 1.522 Å, R(C---Cl) = 1.813(4) Å, <r(C---H)> = 1.089(18) Å, ???C=C---C = 122.9(2.1)°, ???C---C---C = 112.6(2.2)°, ???=C---C---Cl = 109.9(0.2)°, ???Cl---C---CH₃ = 109.3°. = 121.9° and = 110.0(1.3)°. The torsional angles were then τ(C=C---C---Cl> = −119.4° and τ(C=C---C---CH₃) = 120.3(2.1)°. Error limits are 2σ (σ includes estimates of systematic errors and correlations), parameters without quoted uncertainties are dependent or were constrained relative to another parameter. Combining the ED data with MM results yielded parameters consistent with those given above.     

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

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

The molecular structure of fluoromalononitrile as determined by gas-phase electron diffraction and ab initio calculations

The molecular structure of fluoromalononitrile was studied by means of gas-phase electron diffraction and quantum mechanical methods using HF/6-31G(d), MP2/6-311++G(2df,2pd) and DFT/B3LYP/6-31G(d), B3PW91/6-31G(d), B3LYP/6-311++G(2df,2pd) and B3PW91/6-311++G(2df,2pd). The r(g) and angle(alpha) structural parameters we obtained from the present analysis are: CC=1.487(5) A, CN=1.157(3) A, CF=1.386(5) A, CH=1.096 A (ass.), angleCCC=106.7(1.0) degrees , angleCCF=108.0(0.7) degrees , angleCCN=177.6(2.0) degrees . Uncertainties in parenthesis are 3sigma.     

Combined ab initio,electron diffraction,molecular mechanics and vibrational investigations of 1,1 -dimethyl-trans-2-decalone

The conformational behavior of 1,1'dimethyl-trans-2-decalone was studied by combined ab initio, electron diffraction, molecular mechanics and vibrational procedures, and the molecule was found to exist in a distorted all-chair ground state with average C-C, C-H and CO bond distances of r_g = 1.543 Å ± 0.002, r_g = 1.122 Å ± 0.007, and r_g = 1.236 Å ± 0.012, respectively. The ab initio calculations were performed on an STO-3G minimal basis and are indicative of the growing usefulness of quantum-mechanical techniques in the study of medium-sized molecular systems.     

The structure of trimethoxymethane in the gas phase,an electron diffraction,ab initio and molecular mechanics study

The structure of trimethoxymethane in the gas phase was studied by electron diffraction, ab initio molecular orbital calculations and molecular mechanics. The molecule was found to exist almost exclusively as an asymmetric all-staggered TGG conformer. The electron diffraction structural parameters (r_g distances, r_α angles) as obtained from geometrically consistent r_α-refinements are: r(C-O) central 1.382(6) Å, r(C-O) terminal 1.418(6) Å, r(C-H) 1.112(1) Å, ∠(O-C-O) in the gauche—gauche chain 115.0(1.0)°, in the gauche-anti chains 109.2(0.6)° ∠(C-O-C) 114.3(0.6)°, ∠(O-C-H)_Me 109.9(0.3)°, methyl torsion 68(6)°. The structure is adequately reproduced by molecular mechanics calculations applying Allinger's force field. The structures of methoxymethanes can be explained in terms of the anomeric effect. This is confirmed by ab initio calculations.     

The gas-phase molecular structure of 1,1-diethynylsilacyclobutane as determined by means of electron diffraction and ab initio calculations

As a continuation of our systematic investigation of the effect of substituents on the ring geometry and dynamics in silacyclobutanes and in order to explore the role of the silicon atom as a mediator for electronic interactions between the attached fragments, we studied the molecular structure of 1,1-diethynylsilacyclobutane (DESCB) by means of gas-phase electron diffraction and ab initio calculations. The structural refinement of the electron diffraction data yielded the following bond lengths (r_a) and bond angles (uncertainties are 3σ): r(Si–C)=1.874(2) Å, r(Si–C)=1.817(1) Å, (C–Si–C)=79.2(6)°, (C–Si–C)=106.5(6)°. The geminal Si–CC moieties were found to be bent outwards by 3.1(15)° and the puckering angle was determined to be 30.0(15)°. The evidently short Si–C bond length, which was also reproduced by the ab initio calculations, could be rationalized as being the consequence of the electronic interaction between the outer π charges of the triple bond and the 3pπ orbitals at the silicon atom. It is also likely that the conjugation of the geminal ethynyl groups leads to an enhancement of this bond contraction. Electrostatic interactions and the subsequent reduction of the covalent radius of the silicon atom may also contribute to this bond shortening. It has been found that the endocyclic Si–C bond length fits nicely within a scheme describing a monotonous decrease of the Si–C bond length with the increase of the electronegativity of the substituent in various geminally substituted silacyclobutanes.A series of related silacyclobutanes and acyclic diethynylsilanes have been studied by applying various ab initio methods and their optimized structures were compared to the structure of DESCB. Among these compounds are 1,1-dicyanosilacyclobutane (DCYSCB), which is isoelectronic to DESCB, 1,1-diethynylcyclobutane (DECB) which is isovalent to DESCB, monoethynylsilacyclobutane (MESCB) and monocyanosilacyclobutane (MCYSCB). Searching for reasonable support for the explanation of the structural results of DESCB we performed detailed natural population analysis as well as Mulliken population analysis (MPA) on DESCB and other related molecules. In contrast to the Mulliken charges, the natural atomic charges provided helpful information concerning the bonding properties in DESCB and the corresponding compounds. By varying the size of some basis sets, we could demonstrate the validity of the repeatedly discussed dependency of the Mulliken MPA on the basis set.For the performance of the quantum mechanical calculations we employed the following methods and basis sets: HF/6-31G(d,p), DFT/B3PW91/6-31G(d), DFT/B3PW91/6-311++G(d,p), MP2/6-31G(d,p) and MP2/6-311++G(d,p).     

The equilibrium molecular structure of 2-cyanopyridine from combined analysis of gas-phase electron diffraction and microwave data and results of ab initio calculations

Structural Chemistry - The gas-phase electron diffraction study of 2-cyanopyridine was carried out for the first time. Results of ab initio structure calculations performed at the CCSD(T) level of...     

Structure and conformation of cyclobutylsilane: an electron diffraction and ab initio study

A gas electron diffraction study of cyclobutylsilane results in a mixture of equatorial and axial conformers, with the equatorial confomer slightly more stable (Δ G = 0.8 ± 0.4 kJ mol⁻¹). The cyclobutyl ring is distorted with the adjacent bonds longer (C₁---C₂ = 1.573 (4) Å) than the opposite bonds (C₂---C₃ = 1.557 (4) Å). The experimental values for the energy difference between the two conformers and for the geometric parameters are reproduced very well by ab initio calculations. The importance of silicon 3d orbitals in the interpretation of ring distortion is ambiguous, but on the basis of the ab initio calculations the participation of silicon 3d functions is negligible.     

Accurate equilibrium structures obtained from gas-phase electron diffraction data: sodium chloride

A novel method has been developed to allow the accurate determination of equilibrium gas-phase structures from experimental data, thus allowing direct comparison with theory. This new method is illustrated through the example of sodium chloride vapor at 943 K. Using this approach the equilibrium structures of the monomer (NaCl) and the dimer (Na(2)Cl(2)), together with the fraction of vapor existing as dimer, have been determined by gas-phase electron diffraction supplemented with data from microwave spectroscopy and ab initio calculations. Root-mean-square amplitudes of vibration (u) and distance corrections (r(a) - r(e)) have been calculated explicitly from the ab initio potential-energy surfaces corresponding to the vibrational modes of the monomer and dimer. These u and (r(a) - r(e)) values essentially include all of the effects associated with large-amplitude modes of vibration and anharmonicity; using them we have been able to relate the ra distances from a gas-phase electron diffraction experiment directly to the re distances from ab initio calculations. Vibrational amplitudes and distance corrections are compared with those obtained by previous methods using both purely harmonic force fields and those including cubic anharmonic contributions, and the differences are discussed. The gas-phase equilibrium structural parameters are r(e)(Na-Cl)(monomer) = 236.0794(4) pm; r(e)(Na-Cl)(dimer) = 253.4(9) pm; and <(e)ClNaCl = 102.7(11) degrees. These results are found to be in good agreement with high-level ab initio calculations and are substantially more precise than those obtained in previous structural studies.     

Structure of tri-tert-butylsilane by electron diffraction and molecular mechanics

A model force field for silanes is constructed by extending the model field MUB-2 to include silicon, for the following purposes: the calculation, via normal coordinate analyses, of amplitudes of vibration and shrinkage corrections for use in gas-phase electron-diffraction analyses, and the calculation of molecular structure by means of molecular mechanics. All of these applications are carried out in conjunction with an electron-diffraction study of [(CH₃)₃C]₃SiH. Evidence of significant steric strain is obtained in both the diffraction and the molecular-mechanics investigations. Diffraction results include the structural parameters (±3σ) r_g(Si-C) = 1.934(6) Å, r_g(C-C) = 1.548(3) Å, r_g(C-H) = 1.121(9) Å, ∠HSiC = 105.3(1.3)°, (∠SiCC)_av = 111.5(0.5)°, ∠CCH = 110.0(1.5)°, t-butyl torsion = 10(3)°, t-butyl tilt = 2.7(2.4)°. Experimental and calculated structures and amplitudes are in satisfactory agreement. The present compound is found to be appreciably less strained than its hydrocarbon analog [(CH₃)₃C]₃CH, somewhat more strained than [(CH₃)₃Si]₃CH, and much more strained than [(CH₃)₃Si]₃SiH. Molecular-mechanics results are presented for the present compound and its carbon and silicon analogs.     

Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.     

Planar 1,3lambda4delta2,2,4-benzodithiadiazine and its nonplanar 5,6,7,8-tetrafluoro derivative: gas-phase structures studied by electron diffraction and ab initio calculations

The gas-phase molecular structures of 1,3lambda4delta2,2,4-benzodithiadiazine and 5,6,7,8-tetrafluoro-1,3lambda4delta2,2,4-benzodithiadiazine have been investigated by ab initio calculations and electron diffraction using the SARACEN method of structural analysis. Important structural parameters (r(h1) structure) for the parent compound were found to be: 1.546(3), r(S-N) 1.697(5), r(C-S) 1.784(5), and r(C-N) 1.393(6) A. For the tetrafluoro derivative, these are (r(h1) structure): 1.552(3), r(S-N) 1.723(8), r(C-S) 1.812(9), and r(C-N) 1.396(7) A. Furthermore, the GED experiment (Gas Electron Diffraction) quite convincingly demonstrates the nonplanarity of the former and the planarity of the latter in agreement with DFT calculations; but the results contradict calculations at the MP2 level. The effect of the fluorine atoms on the conformations of the molecules is discussed.     

Molecular structures of Se(SCH3)2 and Te(SCH3)2 using gas-phase electron diffraction and ab initio and DFT geometry optimisations

The molecular structures of Se(SCH(3))(2) and Te(SCH(3))(2) were investigated using gas-phase electron diffraction (GED) and ab initio and DFT geometry optimisations. While parameters involving H atoms were refined using flexible restraints according to the SARACEN method, parameters that depended only on heavy atoms could be refined without restraints. The GED-determined geometric parameters (r(h1)) are: rSe-S 219.1(1), rS-C 183.2(1), rC-H 109.6(4) pm; angleS-Se-S 102.9(3), angleSe-S-C 100.6(2), angleS-C-H (mean) 107.4(5), phiS-Se-S-C 87.9(20), phiSe-S-C-H 178.8(19) degrees for Se(SCH(3))(2), and rTe-S 238.1(2), rS-C 184.1(3), rC-H 110.0(6) pm; angleS-Te-S 98.9(6), angleTe-S-C 99.7(4), angleS-C-H (mean) 109.2(9), phiS-Te-S-C 73.0(48), phiTe-S-C-H 180.1(19) degrees for Te(SCH(3))(2). Ab initio and DFT calculations were performed at the HF, MP2 and B3LYP levels, employing either full-electron basis sets [3-21G(d) or 6-31G(d)] or an effective core potential with a valence basis set [LanL2DZ(d)]. The best fit to the GED structures was achieved at the MP2 level. Differences between GED and MP2 results for rS-C and angleS-Te-S were explained by the thermal population of excited vibrational states under the experimental conditions. All theoretical models agreed that each compound exists as two stable conformers, one in which the methyl groups are on the same side (g(+)g(-) conformer) and one in which they are on different sides (g(+)g(+) conformer) of the S-Y-S plane (Y = Se, Te). The conformational composition under the experimental conditions could not be resolved from the GED data. Despite GED R-factors and ab initio and DFT energies favouring the g(+)g(+) conformer, it is likely that both conformers are present, for Se(SCH(3))(2) as well as for Te(SCH(3))(2).     

Molecular structure and conformation of cyclopropylbenzene as determined by ab initio molecular orbital calculations, pulsed-jet fourier transform microwave spectroscopic, and gas-phase electron diffraction investigations

Ab initio computational, microwave spectroscopic, and electron diffraction techniques have been used to study the gas-phase structure of cyclopropylbenzene. Theoretical calculations at the HF, B3LYP, and MP2 levels for basis sets 6-31G(d) and 6-311G(d) have been carried out. Both MP2 and B3LYP calculations showed the bisected form to be lower in energy (245/157 and 660/985 cal mol(-1), respectively, for basis sets 6-311G(d)/6-31G(d)). Rotational constants for the bisected form of the parent and eight singly substituted (13)C isotopic species were obtained. The selection rules of the observed rotational transitions and the facts that eight (rather than six) singly substituted (13)C isotopers are observed and assigned and that seven of the compound's nine carbon atoms lie in the molecule's symmetry plane required the molecule to exist in the bisected conformation. No transition from the perpendicular form was observed in the pulsed-jet microwave experiment. Gas-phase electron diffraction data were collected at a nozzle-tip temperature of 265 K. Least squares analyses were carried out using ED data alone and with the inclusion of microwave rotational constants. The principal structural results (r(g) and angle(alpha)) obtained from the combined ED/MW least-squares analysis are r(C-H)(av) = 1.093(6) A, r(C(7)-C(8))(v) = 1.514(20) A, r(C(8)-C(9))(d) = 1.507(26) A, r(C(7)-C(1)) = 1.520(25) A, r(C-C)(Ph) = 1.395(1) A, angleC(1)C(7)C(8) = 119.6(17) degrees, angleC(2)C(1)C(7) = 122.5(25) degrees, angleC(1)C(2)C(3) = 120.9(35) degrees, angleHC(8)C(9) = 116.7(20) degrees, angleHCC(Ph) = 120.0 degrees (assumed).     

1,2-Dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3): conformational structure and vibrational properties by gas-phase electron diffraction, infrared and Raman spectroscopy, and ab initio molecular orbital and density functional theory calculations

The molecular structure and conformational properties of 1,2-dibromoethyl-trichlorosilane (CH2BrCHBrSiCl3) have been investigated using gas-phase electron diffraction (GED) data recorded at a temperature of 100 degrees C, together with ab initio molecular orbital (MO) and density functional theory (DFT) calculations, infrared (IR) and Raman spectroscopy in the liquid and solid phases, and normal coordinate analysis (NCA). The molecule exists in the gas- and liquid phases as a mixture of three conformers, gauche(-) [G(-)], with a refined torsion angle phi(BrCCBr)=-71(6) degrees, anti [A], with a torsion angle phi(BrCCBr) approximately -170 degrees , and gauche(+) [G(+)], with a torsion angle phi(BrCCBr) approximately +70 degrees . The second torsion angle of importance, the rotation about the CSi bond, has been refined to a value of +175(13) degrees . Torsion angles were only refined for the more abundant G(-) conformer. In the solid phase, only the G(-) conformer was observed. The temperature-dependent Raman spectra have provided an estimate of the relative conformational entropies, DeltaS. The obtained composition from GED refinements was (%) G(-)/A/G(+)=64(27)/23(13)/13(18) (values with estimated 2sigma uncertainties), giving a conformational stability order in agreement with both the Raman enthalpy measurements and the ab initio MO and DFT calculations using the 6-311G(d) basis set and scaled zero-point energies. Relevant structural parameter values obtained from the GED refinements (with the ab initio HF values used as constraints) were as follows (G(-) values with estimated 2sigma uncertainties): bond lengths (r(g)):r(C-C)=1.501(18)A, r(SiC)=1.865(15)A, r(CBr)=1.965(8)A (average), r(SiCl)=2.028(3)A (average). Bond angles ( anglealpha):angleCCSi=114.1(33) degrees , angleC1C2Br=114.0(21) degrees , angleCSiCl=109.6(7) degrees (average). Experimental IR/Raman and obtained vibrational wavenumbers based on both the unscaled, fixed-scaled as well as the scale-refined quantum-mechanical force fields [HF/6-311G(d)] are presented. The results are discussed and compared with some similar molecules from the literature.     

The molecular structure of cyclohexanone determined by gas-phase electron diffraction,including microwave data

The electron diffraction data for gaseous cyclohexanone, collected at 371 K, combined with microwave rotational constants, can be explained by a single chair conformation. Least-squares analysis of the observed data led to an r_g, r_α-structure with the following geometrical parameters: r_CO = 1.229 Å, r_C1C2 = 1.503 Å, r_C1C2 = 1.542 Å, r_C3C4 = 1.545 Å, r_CH = 1.088 Å, ∠ C-CO-C = 115.3°, ∠ CO-C-C = 111.5°, ∠ C-C-C = 110.8°, ∠ H-C-H = 106°. The sp₂ -hybridized part of the ring is less puckered, whereas the sp³ part is more puckered than in cyclohexane.     

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.