X-ray scattering and density-functional theory calculations to study the presence of hydrogen-bonded clusters in liquid N-methylacetamide

A structural investigation of liquid N-methylacetamide (NMA) is performed by x-ray scattering and density functional theory (DFT). Experimental data are analyzed to yield the total structure function SM(Q) and the pair correlation function g(r). The DFT calculations, using the standard triple zeta valence basis set augmented by a diffuse function for carbon, nitrogen and oxygen atoms, are performed on the one hand to study the structure and stability of the two possible conformers cis and trans. On the other hand, they are meant to examine some possible clusters which may describe the intermolecular arrangement in liquid NMA. Among two series of dimers and trimers associations, the spectra are particularly interpreted in terms of: Trans NMA dimers and trimers which resemble the short-range crystal structure, mixed cis and trans trimers and cis cyclic trimers. The H-bonding parameters and the intermolecular energy for each model are described.     

Intermolecular association in liquid N-methylacetamide as studied by x-ray scattering

A structural investigation of liquid N methylacetamide was performed at 308 K using x-ray scattering. To extract the molecular form factor F1(q), the geometry of the conformer which has been found in the crystal is considered. The intermolecular structure function DM(q) is interpreted in terms of H-bonding interactions. The crystal N...O distance is taken into accounted and the number of H bond(s) is assumed to be, respectively, equal to one and two. The liquid structure can be described by a linear dimer or chainlike trimer similar to the ones existing in the crystal. The structure factors SM(q) extracted from these clusters fairly agree with the experimental one beyond q=2.5 A(-1).     

Molecular structure of (cyanomethoxy)(dimethylamino)methane as studied by gas-phase electron diffraction and quantum-chemical calculations

The molecular structure of (cyanomethoxy)(dimethylamino)methane in the gas phase is investigated by means of gas-phase electron diffraction and quantum-chemical studies for the first time. It is shown that in the gaseous state, (cyanomethoxy)(dimethylamino)methane is a mixture of gauche-anti (65%) and anti-gauche (35%) conformers. The slight influence of the anomeric effect on the compound’s structural parameters was noted.     

Hydrogen-bonding interactions in acetic acid monohydrates and dihydrates by density-functional theory calculations

Equilibrium structures and the respective binding energies of acetic acid monohydrates and dihydrates have been determined by density-functional theory calculations with different basis sets, including 6-31+G(3d,p), 6-311++G(d,p), and 6-311++G(3df,3pd). Given that the C=O and OH groups in acetic acid provide the predominant hydrogen-bonding interactions with water, six stable conformer structures have been found each for the monohydrate and syn-dihydrate. Of the three syn- and three anti-conformers of acetic acid with water, the most stable monohydrate structure is found to be that of the syn-conformer bonding with water in a cyclic double H-bonded geometry. Similarly, the syn-conformer bonding with two water molecules in a cyclic double H-bonded geometry has also been determined to be the most stable among the six plausible structures for the syn-dihydrate. Frequency analysis of the stable conformers has been performed and the vibrational spectra of the most stable monohydrate and dihydrate structures are compared with the experimental gas-phase and matrix data. Furthermore, the calculated binding energies between an acetic acid and a water molecule for both monohydrate and dihydrate are larger than that between two water molecules, which supports our recent experimental observation of coevaporation of acetic acid with water upon annealing acetic acid on ice.     

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.     

Structure of H(D)TaO3 determined by powder X-ray and neutron diffraction

Pure crystalline samples of HTaO₃ and DTaO₃ have been prepared. The crystal structure has been solved using powder X-ray and neutron diffraction (at 2 K and room temperature) and has been shown to consist of Ta(O,OH)₆ octahedra sharing vertices with the oxygen atoms displaced toward the vacant perovskite A sites. The compound is isomorphous with HNbO₃, D_xWO₃, and D_xReO₃ and contains hydrogen atoms as hydroxide groups.     

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.     

Hydrogen bonding of N-methylacetamide in CDCl3 solution studied by NMR and IR spectra

The amide proton NMR chemical shifts have been widely used for the determination of the population fraction of the non-hydrogen-bonded states in studies of hydrogen bonding in peptides and proteins. However, in such works the determination of the limiting chemical shifts for the fully hydrogen-bonded state and for the non-hydrogen-bonded state is quite problematic, because they cannot be measured directly. In the present study, we carried out variable-temperature ¹H NMR and IR measurements for N-methylacetamide in CDCl₃ solution. We derived the expression for the limiting chemical shift for the fully hydrogen-bonded state as a function of IR band intensity and chemical shift. According to the equation, we determined the values of the limiting shifts at various temperatures. The present method may be applicable to other hydrogen-bonding systems.     

Short-range order effects in amorphous polycondensates as studied by spin polarized diffuse neutron scattering and simulation

Short-range order effects in amorphous polycondensates, including the technologically important bisphenol-A-polycarbonate, have been investigated by elastic diffuse neutron scattering with spin polarization analysis. Selectively deuterated samples of each polycondensate have been used in order to vary the scattering contrast and thereby emphasize different pair correlations. The technique of spin polarization analysis allowed a reliable separation of the coherent scattering and an intensity calibration on the basis of the incoherent scattering as an internal standard. Thus, (d/d)_coh has been measured directly by this method. The experimental results are compared to calculated cross-sections from computer-generated structures. Simulations have been performed with the amorphous cell method which models the static structure of the amorphous polymer in full chemical detail on the basis of a random coil conformation. The results of the simulations yield a fertily ground for the discussion of the measured cross-sections, though a direct comparison with the experiment is not always satisfactory. The observed discrepancies indicate a still insufficient structural relaxation of the simulated structures.Dedicated to Professor Dr. E. W. Fischer of the occasion of his 65th birthday.     

Molecular structure of tris(dipivaloylmethanato)lutetium(iii) studied by gas electron diffraction and ab initio and DFT calculations

Combined gas electron diffraction/mass spectrometry (GED/MS) was used to determine the molecular structure of tris(dipivaloylmethanato)lutetium(III), Lu(dpm)(3)(dpm = 2,2,6,6-tetramethyl-heptane-3,5-dionato). Up to about 520-570 K the vapour consisted only of molecules Lu(dpm)(3). The experimental data recorded at 408(5) K indicate that the molecules have D(3) symmetry. The bond distances (r(h1)) in the chelate ring are Lu-O 2.197(6) Angstrom, C-O 1.270(4) Angstrom and C-C 1.390(6) Angstrom . Theoretical computations at the HF and DFT levels with basis sets up to 6-311G* afford structures similar to those found experimentally, with a distorted LuO(6) antiprism.     

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.     

Geometric structure and electronic properties of neutral and anionic Fe2C3 and Fe2C4 clusters, as obtained by density-functional calculations

We calculated the geometrical structures and electronic properties of neutral and anionic Fe2Cn clusters (n = 3,4) using a density-functional method that employs linear combinations of atomic orbitals as basis sets, standard nonlocal norm-conserving pseudopotentials, and the generalized gradient approximation to exchange and correlation. We show that the ground-state structures of Fe2C3 and Fe2C4 are essentially the same in the neutral and anionic states, namely, planar rings that feature nonadjacent Fe atoms. For the anionic clusters, these findings contrast with previously published results.     

Lanthanide(III) complexes with a tetrapyridine pendant-armed macrocyclic ligand: 1H NMR structural determination in solution, X-ray diffraction, and density-functional theory calculations

Complexes between the tetrapyridyl pendant-armed macrocyclic ligand (L) and the trivalent lanthanide ions have been synthesized, and structural studies have been made both in the solid state and in aqueous solution. The crystal structures of the La, Ce, Pr, Gd, Tb, Er, and Tm complexes have been determined by single-crystal X-ray crystallography. In the solid state, all the cation complexes show a 10-coordinated geometry close to a distorted bicapped antiprism, with the pyridine pendants situated alternatively above and below the main plane of the macrocycle. The conformations of the two five-membered chelate rings present in the complexes change along the lanthanide series. The La(III) and Ce(III) complexes show a lambdadelta (or deltalambda) conformation, while the complexes of the heavier lanthanide ions present lambdalambda (or deltadelta) conformation. The cationic [Ln(L)]3+ complexes (Ln = La, Pr, Eu, Tb, and Tm) were also characterized by theoretical calculations at the density-functional theory (DFT) B3LYP level. The theoretical calculations predict a stabilization of the lambdalambda (or deltadelta) conformation on decreasing the ionic radius of the Ln(III) ion, in agreement with the experimental evidence. The solution structures show a good agreement with the calculated ones, as demonstrated by paramagnetic NMR measurements (lanthanide induced shifts and relaxation rate enhancements). The 1H NMR spectra indicate an effective D2 symmetry of the complexes in D2O solution. The 1H lanthanide induced shifts (LIS) observed for the Ce(III), Tm(III), and Yb(III) complexes can be fit to a theoretical model assuming that dipolar contributions are dominant for all protons. The resulting calculated values are consistent with highly rhombic magnetic susceptibility tensors with the magnetic axes being coincident with the symmetry axes of the molecule. In contrast with the solid-state structure, the analysis of the LIS data indicates that the Ce(III) complexes present a lambdalambda (or deltadelta) conformation in solution.     

The molecular structure of N-fluorobis(trifluoromethanesulfonyl)imide, NF(SO(2)CF(3))(2), as studied in the gas phase by electron diffraction restrained by ab initio calculations

The structure of N-fluorobis(trifluoromethylsulfonyl)imide, prepared by a relatively safe and easy method, has been determined by gas-phase electron diffraction (GED), employing the SARACEN method, with flexible restraints based on the MP2/6-311G* structure, and by X-ray crystallography at 150 K. The strongly electron-withdrawing CF(3) and SO(2)CF(3) groups make the C-S and N-S distances long, averaging 187.7(3) and 171.7(3) pm, respectively, in the gas phase. The gas consists of two conformers, one (75%) with a CF(3) group on each side of the SNS plane, one anti-periplanar and one syn-periplanar to the further N-S bond (ap, sp), and the other with both CF(3) groups on the same side, i.e. denoted ap, ap. These conformers have very different SNS angles, 126.9(9) degrees and 117.1(17) degrees respectively. In the crystal all molecules have the ap, sp conformation, with parameters similar to those found for this conformer in the gas phase.