Structure enhancement methodology using theory and experiment: gas-phase molecular structures using a dynamic interaction between electron diffraction, molecular mechanics, and ab initio data

A new method of incorporating ab initio theoretical data dynamically into the gas-phase electron diffraction (GED) refinement process has been developed to aid the structure determination of large, sterically crowded molecules. This process involves calculating a set of differences between parameters that define the positions of peripheral atoms (usually hydrogen), as determined using molecular mechanics (MM), and those which use ab initio methods. The peripheral-atom positions are then updated continually during the GED refinement process, using MM, and the returned positions are modified using this set of differences to account for the differences between ab initio and MM methods, before being scaled back to the average parameters used to define them, as refined from experimental data. This allows the molecule to adopt a completely asymmetric structure if required, without being constrained by the MM parametrization, whereas the calculations can be performed on a practical time scale. The molecular structures of tri-tert-butylphosphine oxide and tri-tert-butylphosphine imide have been re-examined using this new technique, which we call SEMTEX (Structure Enhancement Methodology using Theory and EXperiment).     

The molecular structure of tetra-tert-butyldiphosphine: an extremely distorted, sterically crowded molecule

The molecular structure of tetra-tert-butyldiphosphine has been determined in the gas phase by electron diffraction using the new DYNAMITE method and in the crystalline phase by X-ray diffraction. Ab initio methods were employed to gain a greater understanding of the structural preferences of this molecule in the gas phase, and to determine the intrinsic P-P bond energy, using recently described methods. Although the P-P bond is relatively long [GED 226.4(8) pm; X-ray 223.4(1) pm] and the dissociation energy is computed to be correspondingly small (150.6 kJ mol(-1)), the intrinsic energy of this bond (258.2 kJ mol(-1)) is normal for a diphosphine. The gaseous data were refined using the new Edinburgh structure refinement program ed@ed, which is described in detail. The molecular structure of gaseous P(2)Bu(t)(4) is compared to that of the isoelectronic 1,1,2,2-tetra-tert-butyldisilane. The molecules adopt a conformation with C(2) symmetry. The P-P-C angles returned from the gas electron diffraction refinement are 118.8(6) and 98.9(6) degrees, a difference of 20 degrees, whilst the C-P-C angle is 110.3(8) degrees. The corresponding parameters in the crystal are 120.9(1), 99.5(1) and 109.5(1) degrees. There are also large deformations within the tert-butyl groups, making the DYNAMITE analysis for this molecule extremely important.     

The gas-phase equilibrium structures of Si8O12(OSiMe3)8 and Si8O12(CHCH2)8

The equilibrium molecular structure of Si(8)O(12)(OSiMe(3))(8) has been determined in the gas phase by electron diffraction (GED). With OSi-containing substituents on the cage silicon atoms, this molecule contains a moiety, which would, if reproduced in a periodic manner, yield a zeolite-type structure. Extensive ab initio calculations were used to identify two conformers of this molecule, with D(4) and D(2) point-group symmetries; the D(4)-symmetric conformer was approximately 1.2 kJ mol(-1) lower in energy. With 132 atoms in each conformer, this is one of the largest studies to be undertaken using gas electron diffraction. Semiempirical molecular-dynamics (SE-MD) calculations were used to give amplitudes of vibration, vibrational distance corrections (differences between interatomic distances in the equilibrium structure and the vibrationally averaged distances that are given directly by the diffraction data), and anharmonic constants. The structure of Si(8)O(12)(CHCH(2))(8) has also been determined by GED. Calculations showed that the vinyl groups are fairly unhindered and rotate between three minimum-energy positions. Ultimately, all possible combinations of the vinyl groups in these low-energy positions were accounted for in the GED model.     

Tautomeric and conformational properties of malonamide, NH2C(O)-CH2-C(O)NH2: electron diffraction and quantum chemical study

The geometric structure of malonamide, NH2C(O)-CH2-C(O)NH2, has been investigated by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 approximations with 6-311++G(3df,pd) basis sets). Both GED and quantum chemistry result in the existence of a single diketo conformer in the gas phase. According to GED refinement this conformer possesses (sc,ac) conformation with one C=O bond in synclinal orientation (dihedral angle tau(O=C-C-C)=49.0(3.0) degrees) and the other C=O bond in anticlinal orientation (dihedral angle tau(O=C-C-C)=139.5(3.3) degrees). The experimental geometric parameters are reproduced very closely by the B3LYP method.     

Relativistic two-component calculations of electronic g-tensors that include spin polarization

The first two-component relativistic density-functional approach for the calculation of electronic g-tensors is reported that includes spin polarization using noncollinear spin-density functionals. The method is based on the relativistic Douglas-Kroll-Hess Hamiltonian and has been implemented into the ReSpect program package. Using three self-consistent-field calculations with orthogonal orientations of total magnetization J, the full g-matrix may be obtained. In contrast to previous spin-restricted two-component treatments, results with the new approach agree excellently with spin-polarized one-component calculations for light-atom radicals. Additionally, unlike one-component approaches, the method also reproduces successfully the negative deltag(parallel)-values of heavy-atom 2sigma radicals and the negative deltag(perpendicular) components in cysteinyl. The new method removes effectively the dilemma existing up to now regarding the simultaneous inclusion of spin polarization and higher-order spin-orbit effects in g-tensor calculations. It is straightforwardly applicable to higher than doublet spin multiplicities and has been implemented with hybrid functionals.     

Molecular structure of phthalocyaninatotin(II) studied by gas-phase electron diffraction and high-level quantum chemical calculations

The molecular structure of phthalocyaninatotin(II), Sn(II)Pc, is determined by density functional theory (DFT/B3LYP) calculations using various basis sets and gas-phase electron diffraction (GED). The quantum chemical calculations show that Sn(II)Pc has C4V symmetry, and this symmetry is consistent with the structure obtained by GED at 427 degrees C. GED locates the Sn atom at h(Sn) ) 112.8(48) pm above the plane defined by the four isoindole N atoms, and a N-Sn bond length of 226.0(10) pm is obtained. Calculation at the B3LYP/ccpVTZ/cc-pVTZ-PP(Sn) level of theory gives h(Sn) ) 114.2 pm and a N-Sn bond length of 229.4 pm. The phthalocyanine (Pc) macrocycle has a slightly nonplanar structure. Generally, the GED results are in good agreement with the X-ray structures and with the computed structure; however, the comparability between these three methods has been questioned. The N-Sn bond lengths determined by GED and X-ray are significantly shorter than those from the B3LYP predictions. Similar trends have been found for C-Sn bonds for conjugated organometallic tin compounds. Computed vibrational frequencies give five low frequencies in the range of 18-54 cm-1, which indicates a flexible molecule.     

Molecular structure of chloro-dodecafluorosubphthalocyanato boron(III) by gas-phase electron diffraction and quantum chemical calculations

The molecular structure of the chloro-dodecafluorosubphthalocyaninato boron(III) (F-SubPc) was determined with use of Gas Electron Diffraction (GED) and high-level quantum chemical calculations. The present results show that the F-SubPc molecule has a cone-shaped configuration, isoindole units are not planar, and the pyrrole ring has an envelope conformation. The structure parameters in the gas phase are determined. Some structural details can be observed such as the dihedral angle about the bond connecting the pyrrole ring and the benzene ring being ca. 174 degrees . High-level theoretical calculations with several extended basis sets for this molecule have been carried out. The calculations are in very good agreement with experimental methods: X-ray and GED. Nevertheless, some disagreements particularly related to the B-Cl bond distance found in GED are discussed. Vibrational frequencies were computed obtaining eight values below 100 cm-1 and three bending potentials were examined. They suggest that this molecule is very flexible.     

Tautomeric and conformational properties of malonamic acid methyl ester, NH2C(O)-CH2-C(O)OCH3: electron diffraction and quantum chemical study

The tautomeric and conformational properties of malonamic acid methyl ester, NH2C(O)-CH2-C(O)OCH3, have been investigated by means of gas-phase electron diffraction (GED) and quantum chemical calculations (HF, B3LYP, and MP2 approximations with different basis sets up to 6-311++G(3df,pd)). Both quantum chemistry and GED at 360(8) K result in the existence of a single diketo conformer in the gas phase. According to GED refinement, this conformer possesses an (ac, sc) conformation with dihedral angles C-C-C(NH2)=O of 140.3(3.0) degrees and C-C-C(OCH3)=O of 31.1(7.2) degrees. The experimental geometric parameters are reproduced very closely by MP2 and B3LYP methods with large basis sets.     

Molecular structures of free quinuclidine and its adducts with metal trihydrides, MH3 (M=B, Al or Ga), studied by gas-phase electron diffraction, X-ray diffraction and quantum chemical calculations

The structure of quinuclidine, HC(CH(2)CH(2))(3)N, has been re-investigated by quantum chemical calculations and by gas-phase electron diffraction (GED). The GED data, together with published rotational constants, have been analysed using the SARACEN method to determine the most reliable structure (r(h1)) for the gaseous molecule. The structures of two adducts of quinuclidine with group 13 trihydride molecules, MH(3) (M=B, Al), have also been determined by GED and quantum chemical calculations. The effect of the coordination of these hydrides to the quinuclidine nitrogen atom has been investigated, and the structural changes and energetics of adduct formation are discussed. We also present the crystal structure of quinuclidine borane.     

The structure of glycerol in the liquid state: a neutron diffraction study

Neutron diffraction coupled with hydrogen/deuterium isotopic substitution has been used to investigate the structure of the pure cryoprotectant glycerol in the liquid state at 298 K and 1 atm. The neutron diffraction data were used to constrain a 3 dimensional computational model that is experimentally relevant using the empirical potential structure refinement (EPSR) technique. These simulations lead to a model structure of the glycerol molecule that is consistent with the experimental data. Interestingly, from interrogation of this structure, it is found that the number of hydrogen bonds per molecule is larger than had previously been suggested. Furthermore, converse to previous work, no evidence for intra-molecular hydrogen bonds is found. These results highlight the importance and relevance of using experimental data to inform computational modelling of even simple liquid systems.     

Conformational structure of gaseous 3-chloropropanoyl chloride by electron diffraction, normal coordinate analysis, and ab initio molecular orbital, and density functional theory calculations

The molecular and conformational structures of 3-chloropropanoyl chloride (CH(2)Cl-CH(2)-C(=O)Cl) have been studied by using gas-phase electron diffraction (GED) data obtained at 22 degrees C (295 K) and ab initio molecular orbital (MO) and density functional theory (DFT) calculations up to the levels of MP4(SDQ) and B3LYP using larger basis sets. Normal coordinate calculations (NCA) taking into account nonlinear vibrational effects were also used in the analyses. The title compound may have up to four low-energy conformers in the gas phase, labeled according to the position of each of the two chlorine atoms in relation to the CCC propanoyl backbone, labeling the carbonyl chlorine torsion angle first: AA, AG, GG, and GA; where A is anti (ideal C-C-C-Cl torsion angle of approximately 180 degrees) and G is gauche (ideal C-C-C-Cl torsion angle of approximately 60 degrees). It has been judged from the experimental GED data and the theoretical calculations, as well as from previously published infrared (IR) studies on the molecule in both the liquid phase and in argon-trapped matrices at 10 K, that the gas phase consists of a mixture of at least three conformers: AA (most stable), AG, and GG, with the possibility of a smaller contribution (<10%) from the higher-energy GA form. The GA conformer cannot be ruled out by the GED experimental data. Relevant structural parameter values obtained from the GED least-squares refinements, with calculated ab initio MO MP2/6-31+G(2d,p) values used as constraints, were as follows (AA values with estimated 2sigma uncertainties): Bond lengths (r(h1)): r(C-C(=O)) = 1.505(4) A, r(C-CH(2)Cl) = 1.520(4) A, r(C=O) = 1.197(4) A, r(C(=O)-Cl) = 1.789(3) A, and r(C-Cl) = 1.782(3) A. Bond angles (angle(h1)): angle CCC = 111.5(11) degrees , angle CCO = 127.0(5) degrees, angle CC(O)Cl = 112.5(3) degrees, and angle CCCl = 110.3(3) degrees. Torsion angles (phi(C-C) = phi(ClCCC)): for AA, phi(1)(C-C(O)) = phi(2)(C-CH(2)Cl) = 180 degrees (assumed for true C(s) symmetry); for AG, phi(1)(C-C(O)) = -140(5) degrees, phi(2)(C-CH(2)Cl) = 76(13) degrees; for GG, phi(1)(C-C(O)) = 46(8) degrees, phi(2)(C-CH(2)Cl) = 77(14) degrees; for GA, phi(1)(C-C(O)) = 67.9 degrees (assumed), phi(2)(C-CH(2)Cl) = 177.8 degrees (assumed). The non-AA conformers all have chiral C(1) symmetry with twice the statistical weight (multiplicity) of C(s). The MP2/6-31+G(2d,p) calculated composition (%) based on the zero-point energy (ZPE) corrected energy differences, and the statistical weights for conformers: AA/AG/GG/GA = 28/35/28/9 was assumed in the final GED refinement. The more recent literature concerning the title molecule, as well as for several related molecules, has been examined and a survey has been attempted in the present article. The new experimental results for 3-chloropropanoyl chloride are discussed and compared with the previously published findings.     

Tautomeric and conformational properties of dimethyl malonate, CH3OC(O)-CH2-C(O)OCH3: electron diffraction and quantum chemical study

The geometric structure of dimethyl malonate, CH₃OC(O)-CH₂-C(O)OCH₃, was studied by gas electron diffraction (GED) and quantum chemical methods. We conclude that only diketo conformers exist in the gas phase. According to the GED refinement, a mixture of two diketo conformers is present: 69(10)% (ac,ac) conformer with C₂ symmetry (both CO bonds anticlinal relative to the opposite C-C bond) and 31(10)% (sp,ac) conformer with C₁ symmetry (one CO bond with synperiplanar, the other CO bond with anticlinal orientation). Ab initio calculations, however, predict a preference of the (sp,ac) conformer rather than the (ac,ac) form.     

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.     

The Crystal and Molecular Structure of 1-Methyl-1-Thionia-Cyclohexane Iodide

Crystals of 1-methyl-1-thionia-cyclohexane iodide are orthorhombic with space group Pna2₁, a = 18.036, b = 6.611, c = 7.420 Å, Z = 4. The crystal structure was solved by the heavy-atom method. Very strong parameter interactions prevented least-squares refinement of atoms other than S and I. The molecule adopts the chair conformation with the methyl group in equatorial position.     

Vibrational spectroscopy (FT-IR and FT-Raman) investigation, and hybrid computational (HF and DFT) analysis on the structure of 2,3-naphthalenediol

The FT-IR and FT-Raman vibrational spectra of 2,3-naphthalenediol (C(10)H(8)O(2)) have been recorded using Bruker IFS 66V spectrometer in the range of 4000-100 cm(-1) in solid phase. A detailed vibrational spectral analysis has been carried out and the assignments of the observed fundamental bands have been proposed on the basis of peak positions and relative intensities. The optimized molecular geometry and vibrational frequencies in the ground state are calculated by using the ab initio Hartree-Fock (HF) and DFT (LSDA and B3LYP) methods with 6-31+G(d,p) and 6-311+G(d,p) basis sets. There are three conformers, C1, C2 and C3 for this molecule. The computational results diagnose the most stable conformer of title molecule as the C1 form. The isotropic computational analysis showed good agreement with the experimental observations. Comparison of the fundamental vibrational frequencies with calculated results by HF and DFT methods. Comparison of the simulated spectra provides important information about the capability of computational method to describe the vibrational modes. A study on the electronic properties, such as absorption wavelengths, excitation energy, dipole moment and Frontier molecular orbital energies, are performed by time dependent DFT approach. The electronic structure and the assignment of the absorption bands in the electronic spectra of steady compounds are discussed. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. On the basis of the thermodynamic properties of the title compound at different temperatures have been calculated. The statistical thermodynamic properties (standard heat capacities, standard entropies, and standard enthalpy changes) and their correlations with temperature have been obtained from the theoretical vibrations.     

Determination of absolute configuration using X-ray diffraction

Methods for determination of absolute structure using X-ray crystallography are described, with an emphasis on applications for absolute configuration assignment of enantiopure light-atom organic compounds. The ability to distinguish between alternative absolute structures by X-ray crystallography is the result of a physical phenomenon called resonant scattering, which introduces small deviations from the inherent inversion symmetry of single-crystal X-ray diffraction patterns. The magnitude of the effect depends on the elements present in the crystal and the wavelength of the X-rays used to collect the diffraction data, but it is always very weak for crystals of compounds containing no element heavier than oxygen. The precision of absolute structure determination by conventional least squares refinement appears to be unduly pessimistic for light-atom materials. Recent developments based on Bijvoet differences, quotients and Bayesian statistics enable better and more realistic precision to be obtained. The new methods are sensitive to statistical outliers, and techniques for identifying these are summarised.     

Chlorodifluoroacetyl cyanide, ClF2CC(O)CN: synthesis, structure, and spectroscopic characterization

The novel molecule difluorochloroacetyl cyanide, ClF(2)CC(O)CN, has been characterized by IR (gas phase, Ar matrix), Raman (liquid), (19)F and (13)C NMR, and photoelectron (PES) spectroscopies; photoionization mass spectrometry (PIMS); and gas electron diffraction (GED). The conformational properties of ClF(2)CC(O)CN have been studied by joint application of vibrational spectroscopy, GED, and quantum chemical calculations. The existence of two conformers is detected in the gas and liquid phases, in which the C-Cl bond adopts gauche and syn orientations with respect to the C═O group. The computed enthalpy difference is in harmony with the experimental results of the gauche being more stable than the syn conformer by ΔH° = 1.3 kcal mol(-1) (MP2/cc-pVTZ). The valence electronic properties and the possible ionization and dissociation processes of the title compound are studied using the PES and PIMS. The experimental first vertical ionization energy of 12.0 eV corresponds to the ejection of an electron of the oxygen lone pairs. Taking into account the properties and broad applications of acyl cyanides, ClF(2)CC(O)CN is a promising new precursor in preparative chemistry.     

Molecular structure and conformational composition of 1,3-dihydroxyacetone studied by combined analysis of gas-phase electron diffraction data, rotational constants, and results of theoretical calculations. Ideal gas thermodynamic properties of 1,3-dihydroxyacetone

The molecular structure of 1,3-dihydroxyacetone (DHA) has been studied by gas-phase electron diffraction (GED), combined analysis of GED and microwave (MW) data, ab initio, and density functional theory calculations. The equilibrium re structure of DHA was determined by a joint analysis of the GED data and rotational constants taken from the literature. The anharmonic vibrational corrections to the internuclear distances (re-ra) and to the rotational constants (B(i)e-B(i)0) needed for the estimation of the re structure were calculated from the B3LYP/cc-pVTZ cubic force field. It was found that the experimental data are well reproduced by assuming that DHA consists of a mixture of three conformers. The most stable conformer of C2v symmetry has two hydrogen bonds, whereas the next two lowest energy conformers (Cs and C1 symmetry) have one hydrogen bond and their abundance is about 30% in total. A combined analysis of GED and MW data led to the following equilibrium structural parameters (re) of the most abundant conformer of DHA (the uncertainties in parentheses are 3 times the standard deviations): r(C=O)=1.215(2) A, r(C-C)=1.516(2) A, r(C-O)=1.393(2) A, r(C-H)=1.096(4) A, r(O-H)=0.967(4) A, angleC-C=O=119.9(2) degrees, angleC-C-O=111.0(2) degrees, angleC-C-H=108.2(7) degrees, angleC-O-H=106.5(7) degrees. These structural parameters reproduce the experimental B(i)0 values within 0.05 MHz. The experimental structural parameters are in good agreement with those obtained from theoretical calculations. Ideal gas thermodynamic functions (S degrees (T), C degrees p(T), and H degrees (T)-H degrees (0)) of DHA were calculated on the basis of experimental and theoretical molecular parameters obtained in this work. The enthalpy of formation of DHA, -523+/-4 kJ/mol, was calculated by the atomization procedure using the G3X method.     

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.