Molecular structure of carphedon as studied by gas electron diffraction and quantum chemical calculations

The gas-phase structure and conformational properties of carphedon (C₁₂H₁₄N₂O₂, phenylpiracetam, 2-oxo-4-phenyl-1-pyrrolidineacetamide) have been determined by gas electron diffraction (GED) and quantum chemical calculations (B3LYP and MP2 with 6-31G and cc-pVDZ basis sets). Since quantum chemical calculations demonstrate that the orientation of the acetamide group is fixed by a strong intramolecular N–H(amide)···O(pyrrolidone) hydrogen bond, the number of possible conformers is reduced considerably. Depending on the conformation of the pyrrolidine ring, envelope with out-of-plane C4 atom and acetamide group on the same side of the plane (“+”) or envelope with C4 and acetamide group on opposite sides (“?”), and on the orientation of the phenyl ring, axial (Ax), or equatorial (Eq), four relevant conformations, Ax?, Ax+, Eq?, and Eq+, exist. According to both quantum chemical methods (B3LYP and MP2 with cc-pVDZ basis sets) these four conformers differ by less than 2 kcal/mol in free energies. However, the two methods predict different relative free energies. The GED data were analyzed with different models. With a single-conformer model the best fit of the experimental GED intensities (agreement factor R _f = 4 %) is obtained with the Ax+ conformer. Using a two-conformer model the fit improves considerable for a 50(11):50(11) mixture of Ax? and Eq+ conformers (R _f = 2.7 %). No further improvement is obtained with a three-conformer model and large uncertainties for relative contributions occur. The geometric parameters of gaseous carphedon are compared with those in the crystal phase, where two molecules are connected by two intermolecular N–H···O hydrogen bonds, and with gas-phase values of piracetam.     

Molecular structures of phthalocyaninatozinc and hexadecafluorophthalocyaninatozinc studied by gas-phase electron diffraction and quantum chemical calculations

The molecular structures of phthalocyaninatozinc (HPc-Zn) and hexadecafluorophthalocyaninatozinc (FPc- Zn) are determined using the gas electron diffraction (GED) method and high-level density functional theory (DFT) quantum chemical calculations. Calculations at the B3LYP/6-311++G** level indicate that the equilibrium structures of HPc-Zn and FPc-Zn have D4h symmetry and yield structural parameters in good agreement with those obtained by GED at 480 and 523 degrees C respectively. The calculated force fields indicate that both molecules are flexible. Normal coordinate calculations on HPc-Zn yield five vibrational frequencies (one degenerate) in the range 22-100 cm(-1), and ten vibrational frequencies ranging from 13 to 100 cm(-1) (three degenerate) for FPc-Zn. The high-level force field calculations confirm most of the previous vibrational assignments, and some new ones are suggested. The out-of-plane vibration of the Zn atom in HPc-Zn was studied in detail optimizing models in which the distance from the Zn atom to the two symmetry equivalent diagonally opposed N atoms (h) was fixed. The calculations indicate that the vibrationally activated vertically displacement of the Zn atom is accompanied by distortion of the ligand from D4h to C2v symmetry. The average height, h, at the temperature of the GED experiment was calculated to be 14.5 pm. Small structural changes indicate that a full F substitution on the benzo-subunits do not significantly alter the geometry, however there are indications that the benzo-subunits may shrink slightly with perfluorination.     

Molecular structure and conformations of benzenesulfonamide: gas electron diffraction and quantum chemical calculations

The molecular structure and conformational properties of benzenesulfonamide, C6H5SO2NH2, were studied by gas electron diffraction (GED) and quantum chemical methods (MP2 and B3LYP with different basis sets). The calculations predict the presence of two stable conformers with the NH2 group eclipsing or staggering the SO2 group. The eclipsed form is predicted to be favored by about 0.5 kcal/mol. According to GED, the saturated vapor over solid benzenesulfonamide at a temperature of 150(5) degrees C consists of the eclipsed conformer. The GED intensities, however, possess a very low sensitivity toward the vapor composition, and contributions of the anti conformer of up to 75% (at the 0.05 level of significance) or up to 55% (at the 0.25 level of significance) cannot be excluded. The molecule possesses C(sS) symmetry with the S-N bond perpendicular to the ring plane.     

Molecular structure of caffeine as determined by gas electron diffraction aided by theoretical calculations

The molecular structure of caffeine (3,7-dihydro-1,3,7-trimethyl-1H-purine-2,6-dione) was determined by means of gas electron diffraction. The nozzle temperature was 185 °C. The results of MP2 and B3LYP calculations with the 6-31G⁷ basis set were used as supporting information. These calculations predicted that caffeine has only one conformer and some of the methyl groups perform low frequency internal rotation. The electron diffraction data were analyzed on this basis. The determined structural parameters (r_g and ∠_α) of caffeine are as follows: <r(NC)_ring> = 1.382(3) Å; r(CC) = 1.382(←) Å; r(CC) = 1.446(18) Å; r(CN) = 1.297(11) Å; <r(NC_methyl)> = 1.459(13) Å; <r(CO)> = 1.206(5) Å; <r(CH)> = 1.085(11) Å; ∠N₁C₂N₃ = 116.5(11)°; ∠N₃C₄C₅ = 121. 5(13)°; ∠C₄C₅C₆ = 122.9(10)°; ∠C₄C₅N₇ = 104.7(14)°; ∠N₉–C₄=C₅ = 111.6(10)°; <∠NCH_methyl> = 108.5(28)°. Angle brackets denote average values; parenthesized values are the estimated limits of error (3σ) referring to the last significant digit; left arrow in parentheses means that this parameter is bound to the preceding one.     

Molecular structure and conformations of 2,2-di-tert-butyl-1,3-diaza-2-silacyclopentane: gas electron diffraction and quantum chemical calculations

The geometric structure and conformational properties of the saturated five-membered-ring compound 2,2-di-tert-butyl-1,3-diaza-2-silacyclopentane, (t-Bu)(2)Si(NH)(2)(CH(2))(2), was investigated by gas electron diffraction and quantum chemical methods (B3LYP and MP2 with 6-31G basis sets). The compound exists as a mixture of two conformers, both possessing a twist conformation and C(2) symmetry. In the prevailing form (76(6) % at 305 K) the N-H bonds stagger the adjacent CH(2) groups, and in the minor form the N-H bonds eclipse the CH(2) groups. This conformational mixture corresponds to a free energy difference of DeltaG degrees = 0.69(19) kcal/mol. The B3LYP method predicts a preference for the eclipsed conformer. The largest torsion occurs around the C-C bond with tau(NCCN) = 29.2(24) degrees. The degree of puckering in the title compound is considerably smaller than that in silacyclopentane with tau(CCCC) = 49.7(14) degrees. This has been rationalized by larger angle strain in the title compound.     

Molecular structure of propargylgermane (2-propynylgermane) determined by gas-phase electron diffraction and quantum chemical calculations

The molecular structure of propargylgermane, HCCCH₂GeH₃, has been determined by gas-phase electron diffraction. The electron-diffraction investigation has been supported by density functional theory and ab initio calculations. The r_a value of the bond lengths (pm) are: r(C–Ge)=197.2(1); r(C–C)=143.9(2); r(CC)=123.1(1); r(H–C_acetylene)=108.5(3); r(C–H)=111.6(3) and r(Ge–H_average)=153.7(2). The Ge–C–C angle is 111.7(1)° and the C–CC angle is 178.3(4)°. The uncertainties are one standard deviation from the least-squares refinement.     

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.     

Molecular structure of noradrenaline according to gas-phase electron diffraction data and quantum chemical calculations

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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.     

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.     

Structure and conformational properties of diacetyl sulfide in the gaseous and condensed phases explored by gas electron diffraction, single-crystal X-ray diffraction, vibrational spectroscopy, and quantum chemical calculations.

On the evidence of the electron diffraction pattern of the vapor, of the IR spectrum of the matrix-isolated molecule, and of quantum chemical calculations, the diacetyl sulfide molecule, CH3C(O)SC(O)CH3, adopts a planar heavy-atom skeleton with the [sp,ap] conformation. Other conformations contribute little (<1%) to the population of the gaseous molecules at normal temperatures. Salient structural parameters (r(a) structure, distances (in A), angles (in deg), and 3sigma uncertainties in parentheses) were as follows: r(C=O) 1.198(2)/1.196(2), r(C-S) 1.787(3)/1.808(3), r(C-C) 1.483(4)/1.472(4), angleC-S-C 108.8(9), angleS-C=O 125.7(6)/115.1(6), and angleS-C-C 121.1(7)/111.2(7). The structure of a single crystal at 150 K [monoclinic, P2(1)/n, a = 4.2230(7) A, b = 11.2105(17) A, c = 12.332(2) A, beta = 94.544(16) degrees] also reveals planar molecules with the same conformation and dimensions close to those of the gaseous molecule. Changes in the vibrational spectra of the compound accompanying the transition from the vapor to the condensed phases are attributed not to the presence of more than one conformer but to differences in the local environment of the two carbonyl groups. The properties deduced are compared with those of other compounds of the type CH3C(O)XC(O)CH3 (X = CH2, NH, or O).     

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.     

Structural and thermochemical studies of pyrrolidine borane and piperidine borane by gas electron diffraction and quantum chemical calculations

Structural Chemistry - The gaseous structures, thermochemical properties and dehydrogenation reaction energy profiles of the borane complexes of pyrrolidine and piperidine have been investigated...     

The molecular structure of different species of cuprous chloride from gas-phase electron diffraction and quantum chemical calculations

The molecular geometry of gaseous cuprous chloride oligomers was determined by gas-phase electron diffraction at two different temperatures. Quantum chemical calculations were also performed for Cu(n)Cl(n) (n=1-4) molecules. A complex vapor composition was found in both experiments. Molecules of Cu(3)Cl(3) and Cu(4)Cl(4) were present at the lower temperature (689 K), while dimeric molecules (Cu(2)Cl(2)) were found in addition to the trimers and tetramers at the higher temperature (1333 K). All Cu(n)Cl(n) species were found to have planar rings by both experiment and computation. The bond lengths from electron diffraction (r(g)) at 689 K are 2.166+/-0.008 A and 2.141+/-0.008 A and the Cu-Cl-Cu bond angles are 73.9+/-0.6 degrees and 88.0+/-0.6 degrees for the trimer and the tetramer, respectively. At 1333 K the bond lengths are 2.254+/-0.011 A, 2.180+/-0.011 A, and 2.155+/-0.011 A, and the Cu-Cl-Cu bond angles 67.3+/-1.1 degrees, 74.4+/-1.1 degrees, and 83.6+/-1.1 degrees for the dimer, trimer, and tetramer, respectively.     

Molecular structure and internal rotation in 2,3,5,6-tetrafluoroanisole as studied by gas-phase electron diffraction and quantum chemical calculations

The geometric structure of 2,3,5,6-tetrafluoroanisole and the potential function for internal rotation around the C(sp2)-O bond were determined by gas electron diffraction (GED) and quantum chemical calculations. Analysis of the GED intensities with a static model resulted in near-perpendicular orientation of the O-CH3 bond relative to the benzene plane with a torsional angle around the C(sp2)-O bond of tau(C-O) = 67(15) degrees. With a dynamic model, a wide single-minimum potential for internal rotation around the C(sp2)-O bond with perpendicular orientation of the methoxy group [tau(C-O) = 90 degrees] and a barrier of 2.7 +/- 1.6 kcal/mol at planar orientation [tau(C-O) = 0 degrees] was derived. Calculated potential functions depend strongly on the computational method (HF, MP2, or B3LYP) and converge adequately only if large basis sets are used. The electronic energy curves show internal structure, with local minima appearing because of the interplay between electron delocalization, changes in the hybridization around the oxygen atom, and the attraction between the positively polarized hydrogen atoms in the methyl group and the fluorine atom at the ortho position. The internal structure of the electronic energy curves mostly disappears if zero-point energies and thermal corrections are added. The calculated free energy barrier at 298 K is 2.0 +/- 1.0 kcal/mol, in good agreement with the experimental determination.     

Molecular structures of benzoic acid and 2-hydroxybenzoic acid, obtained by gas-phase electron diffraction and theoretical calculations

The structures of benzoic acid (C6H5COOH) and 2-hydroxybenzoic acid (C6H4OHCOOH) have been determined in the gas phase by electron diffraction using results from quantum chemical calculations to inform restraints used on the structural parameters. Theoretical methods (HF and MP2/6-311+G(d,p)) predict two conformers for benzoic acid, one which is 25.0 kJ mol(-1) (MP2) lower in energy than the other. In the low-energy form, the carboxyl group is coplanar with the phenyl ring and the O-H group eclipses the C=O bond. Theoretical calculations (HF and MP2/6-311+G(d,p)) carried out for 2-hydroxybenzoic acid gave evidence for seven stable conformers but one low-energy form (11.7 kJ mol(-1) lower in energy (MP2)) which again has the carboxyl group coplanar with the phenyl ring, the O-H of the carboxyl group eclipsing the C=O bond and the C=O of the carboxyl group oriented toward the O-H group of the phenyl ring. The effects of internal hydrogen bonding in 2-hydroxybenzoic acid can be clearly observed by comparison of pertinent structural parameters between the two compounds. These differences for 2-hydroxybenzoic acid include a shorter exocyclic C-C bond, a lengthening of the ring C-C bond between the substituents, and a shortening of the carboxylic single C-O bond.     

Molecular structure,conformation, and large amplitude motion of barbituric acid as studied by gas-phase electron diffraction and quantum chemical calculations

Structural Chemistry - B3LYP and MP2(Full) calculations with large basis sets predict the planar equilibrium structure of barbituric acid and reveal large amplitude ring puckering motion which is...     

Structure and conformational properties of N-pentafluorosulfur(sulfuroxide difluoride imide) SF5N=S(O)F2: vibrational analysis, gas electron diffraction, and quantum chemical calculations

The molecular structure and conformational properties of N-pentafluorosulfur(sulfuroxide difluoride imide), SF5N=S(O)F2, have been studied by vibrational spectroscopy (IR (gas) and Raman (liquid)), by gas electron diffraction (GED), and by quantum chemical calculations (MP2 and B3LYP with (6-31G(d) and 6-311+G(2df) basis sets). According to GED, the prevailing conformer possesses a syn structure (N-SF5 bond synperiplanar with respect to the bisector of the SF2 group). Splitting of the symmetric N=S=O stretching vibration in gas and liquid spectra demonstrates the presence of a second conformer (11(5)%) with anticlinal orientation of the N-SF5 bond according to quantum chemical calculations. The geometric structure, conformational properties, and vibrational frequencies are well reproduced by quantum chemical calculations.     

Molecular structure and benzene ring deformation of three ethynylbenzenes from gas-phase electron diffraction and quantum chemical calculations

The molecular structures of ethynylbenzene and s-triethynylbenzene have been accurately determined by gas-phase electron diffraction and ab initio/DFT MO calculations and are compared to that of p-diethynylbenzene from a previous study [Domenicano, A.; Arcadi, A.; Ramondo, F.; Campanelli, A. R.; Portalone, G.; Schultz, G.; Hargittai, I. J. Phys. Chem. 1996, 100, 14625]. Although the equilibrium structures of the three molecules have C2v, D3h, and D2h symmetry, respectively, the corresponding average structures in the gaseous phase are best described by nonplanar models of Cs, C3v, and C2v symmetry, respectively. The lowering of symmetry is due to the large-amplitude motions of the substituents out of the plane of the benzene ring. The use of nonplanar models in the electron diffraction analysis yields ring angles consistent with those from MO calculations. The molecular structure of ethynylbenzene reported from microwave spectroscopy studies is shown to be inaccurate in the ipso region of the benzene ring. The variations of the ring C-C bonds and C-C-C angles in p-diethynylbenzene and s-triethynylbenzene are well interpreted as arising from the superposition of independent effects from each substituent. In particular, experiments and calculations consistently show that the mean length of the ring C-C bonds increases by about 0.002 A per ethynyl group. MO calculations at different levels of theory indicate that though the length of the C[triple bond]C bond of the ethynyl group is unaffected by the pattern of substitution, the C(ipso)-C(ethynyl) bonds in p-diethynylbenzene are 0.001-0.002 A shorter than the corresponding bonds in ethynylbenzene and s-triethynylbenzene. This small effect is attributed to conjugation of the two substituents through the benzene ring. Comparison of experimental and MO results shows that the differences between the lengths of the C(ipso)-C(ethynyl) and C(ipso)-C(ortho) bonds in the three molecules, 0.023-0.027 A, are correctly computed at the MP2 and B3LYP levels of theory but are overestimated by a factor of 2 when calculated at the HF level.