The interplay of thio(seleno)amide/vinylogous thio(seleno)amide "resonance" and the anisotropic effect of thiocarbonyl and selenocarbonyl functional groups

Amino-substituted thio(seleno)acrylamides 1-4 were synthesized and their 1H and 13C NMR spectra assigned. Both the NMR data and the results of theoretical calculations at the ab initio level of theory were employed to elucidate the adopted structures of the compounds in terms of E/Z isomerism and s-cis/s-trans configuration. In the case of the asymmetrically N(Me)Ph-substituted compounds, ab initio GIAO-calculated ring current effects of the N-phenyl group were applied to successfully determine the preferred conformer bias. The restricted rotations about the two C-N partial double bonds were studied by DNMR and the barriers to rotation (DeltaG(c)++) determined at the coalescence temperatures, and these were discussed with respect to the structural differences between the compounds. The barriers to rotation were also calculated at the ab initio level of theory where the best results (R(2) = 0.8746) were obtained only with inclusion of the solvent at the SCIPCM-HF/6-31G* level of theory. The calculations also provided means of assessing structural influences which were not available due to inaccessible rotation barriers. By means of natural bond orbital (NBO) analysis of 1-4, the occupation numbers of nitrogen lone pairs and bonding/antibonding pi/pi orbitals were shown to quantitatively describe thio(seleno)amide/vinylogous thio(seleno)amide "resonance". Finally, the thio(seleno)carbonyl anisotropic effect was quantitatively calculated by the GIAO method and visualized by isochemical shielding surfaces (ICSS). Only marginal differences between the two anisotropic effects were calculated and are therefore of questionable utility for previous and future applications with respect to stereochemical assignments.     

Structural characterization of poly(diethylsiloxane) in the crystalline, liquid crystalline and isotropic phases by solid-state 17O NMR spectroscopy and ab initio MO calculations

The structure of poly(diethylsiloxane) (PDES) has been characterized using solid-state NMR of (17)O. The sample studied had a weight-average molecular weight of 2.45 x 10(5). The sample was prepared by utilizing the cationic ring-opening polymerization of (17)O-enriched hexacyclotrisiloxane. Solid-state NMR of (17)O-enriched PDES was measured on the low-temperature beta(1) phase, the high-temperature beta(2) phase, the two-phase system consisting of the liquid crystal and isotropic liquid phase and the isotropic phase. From these data, the molecular structure and dynamics of PDES in the various phases were characterized via the chemical shifts of (17)O, and electric field gradient parameters were determined from NMR and ab initio molecular orbital (MO) calculations. In addition to the solid-state NMR of (1)H, (13)C and (29)Si previously reported on these samples, knowledge of the dynamic behavior of PDES as inferred from the NMR of (17)O in the present study was enhanced significantly. Further, the potential of combining the experimental NMR of (17)O with ab initio MO calculations to characterize the dynamics of polymers containing oxygen is demonstrated.     

Exocyclic push–pull conjugated compounds. Part 3. An experimental NMR and theoretical MO ab initio study of the structure, the electronic properties and barriers to rotation about the exocyclic partial double bond in 2-exo-methylene- and 2-cyanoimino-quinazolines and -benzodiazepines

The structure of a number of 2-exo-methylene substituted quinazolines and benzodiazepines, respectively, 1, 3a,b, 4 (X=–CN,–COOEt) and their 2-cyanoimino substituted analogues 2, 3c,d (X=–CN,–SO₂C₆H₄–Me(p) was completely assigned by the whole arsenal of 1D and 2D NMR spectroscopic methods. The E/Z isomerism at the exo-cyclic double bond was determined by both NMR spectroscopy and confirmed by ab initio quantum chemical calculations; the Z isomer is the preferred one, its amount proved dependent on steric hindrance. Due to the push–pull effect in this part of the molecules the restricted rotation about the partial C²,C¹¹ and C²,N¹¹ double bonds, could also be studied and the barrier to rotation measured by dynamic NMR spectroscopy. The free energies of activation of this dynamic process proved very similar along the compounds studied but being dependent on the polarity of the solvent. Quantum chemical calculations at the ab initio level were employed to prove the stereochemistry at the exo-cyclic partial double bonds of 1–4, to calculate the barriers to rotation but also to discuss in detail both the ground and the transition state of the latter dynamic process in order to better understand electronic, inter- and intramolecular effects on the barrier to rotation which could be determined experimentally. In the cyanoimino substituted compounds 2, 3c,d, the MO ab initio calculations evidence the isomer interconversion to be better described by the internal rotation process than by the lateral shift mechanism.     

17O solid-state NMR and first-principles calculations of sodium trimetaphosphate (Na3P3O9), tripolyphosphate (Na5P3O10), and pyrophosphate (Na4P2O7)

The assignment of high-field (18.8 T) (17)O MAS and 3QMAS spectra has been completed by use of first-principles calculations for three crystalline sodium phosphates, Na 3P 3O 9, Na 5P 3O 10, and Na 4P 2O 7. In Na 3P 3O 9, the calculated parameters, quadrupolar constant ( C Q), quadrupolar asymmetry (eta Q), and the isotropic chemical shift (delta cs) correspond to those deduced experimentally, and the calculation is mandatory to achieve a complete assignment. For the sodium tripolyphosphate Na 5P 3O 10, the situation is more complex because of the free rotation of the end-chain phosphate groups. The assignment obtained with ab initio calculations can however be confirmed by the (17)O{ (31)P} MAS-J-HMQC spectrum. Na 4P 2O 7 (17)O MAS and 3QMAS spectra show a complex pattern in agreement with the computed NMR parameters, which indicate that all of the oxygens exhibit very similar values. These results are related to structural data to better understand the influence of the oxygen environment on the NMR parameters. The findings are used to interpret those results observed on a binary sodium phosphate glass.     

Determination of the electron affinity of the acetyloxyl radical (CH3COO) by low-temperature anion photoelectron spectroscopy and ab initio calculations

The electronic structure and electron affinity of the acetyloxyl radical (CH3COO) were investigated by low-temperature anion photoelectron spectroscopy and ab initio calculations. Photoelectron spectra of the acetate anion (CH3COO-) were obtained at two photon energies (355 and 266 nm) and under three different temperatures (300, 70, and 20 K) with use of a new low-temperature ion-trap photoelectron spectroscopy apparatus. In contrast to a featureless spectrum at 300 K, a well-resolved vibrational progression corresponding to the OCO bending mode was observed at low temperatures in the 355 nm spectrum, yielding an accurate electron affinity for the acetyloxyl radical as 3.250 +/- 0.010 eV. This experimental result is supported by ab initio calculations, which also indicate three low-lying electronic states observed in the 266 nm spectrum. The calculations suggest a 19 degrees decrease of the OCO angle upon detaching an electron from acetate, consistent with the vibrational progression observed experimentally.     

Complete 13C NMR chemical shifts assignment for cholesterol crystals by combined CP-MAS spectral editing and ab initio GIPAW calculations with dispersion forces

We report here the first fully ab initio determination of (13)C NMR spectra for several crystal structures of cholesterol, observed in various biomaterials. We combine Gauge-Including Projector Augmented Waves (GIPAW) calculations at relaxed structures, fully including dispersion forces, with Magic Angle Spinning Solid State NMR experiments and spectral editing to achieve a detailed interpretation of the complex NMR spectra of cholesterol crystals. By introducing an environment-dependent secondary referencing scheme in our calculations, not only do we reproduce the characteristic spectral features of the different crystalline polymorphs, thus clearly discriminating among them, but also closely represent the spectrum in the region of several highly overlapping peaks. This, in combination with spectral editing, allows us to provide a complete peak assignment for monohydrate (ChM) and low-temperature anhydrous (ChAl) crystal polymorphs. Our results show that the synergy between ab initio calculations and refined experimental techniques can be exploited for an accurate and efficient NMR crystallography of complex systems of great interest for biomaterial studies. The method is general in nature and can be applied for studies of various complex biomaterials.     

Experimental and theoretical studies of 45Sc NMR interactions in solids

Solid-state 45Sc NMR spectroscopy, ab initio calculations, and X-ray crystallography are applied to examine the relationships between 45Sc NMR interactions and molecular structure and symmetry. Solid-state 45Sc (I = 7/2) magic-angle spinning (MAS) and static NMR spectra of powdered samples of Sc(acac)3, Sc(TMHD)3, Sc(NO3)3.5H2O, Sc(OAc)3, ScCl3.6H2O, ScCl3.3THF, and ScCp3 have been acquired. These systems provide a variety of scandium coordination environments yielding an array of distinct 45Sc chemical shielding (CS) and electric field gradient (EFG) tensor parameters. Acquisition of spectra at two distinct magnetic fields allows for the first observations of scandium chemical shielding anisotropy (CSA). 45Sc quadrupolar coupling constants (CQ) range from 3.9 to 13.1 MHz and correlate directly with the symmetry of the scandium coordination environment. Single-crystal X-ray structures were determined for Sc(TMHD)3, ScCl3.6H2O, and Sc(NO3)3.5H2O to establish the hitherto unknown scandium coordination environments. A comprehensive series of ab initio calculations of EFG and CS tensor parameters are in excellent agreement with the observed parameters. Theoretically determined orientations of the NMR interaction tensors allow for correlations between NMR tensor characteristics and scandium environments. Solid-state 45Sc, 13C, and 19F NMR experiments are also applied to characterize the structures of the microcrystalline Lewis acid catalyst Sc(OTf)3 (for which the crystal structure is unknown) and a noncrystalline, microencapsulated, polystyrene-supported form of the compound.     

Vibrational spectra, NMR and theoretical studies of the enantiomers and rotamers of alpha-cypermethrin

NMR, infrared and Raman vibrational spectra of alpha-cypermethrin have been measured at room temperature. Infrared spectra were also recorded to low temperature. The spectra were analyzed by means of ab initio calculations. The conformational space of both enantiomers and some rotamers A, B and C of alpha-cypermethrin has been scanned using molecular dynamics and complemented with functional density calculations that optimize the geometry of the lowest-energy conformers of each species as obtained in the simulations. The vibrational frequencies and the 1H and 13C NMR chemical shifts were assigned using functional density calculations. The molecular electrostatic potential maps were obtained and analyzed.     

Theoretical and experimental study of the structure and vibration spectra of 4,4′-carbonyl-di-morpholine

4,4′-Carbonyl-di-morpholine was synthesized and characterized by X-ray diffraction, the FTIR and NMR spectra. The extended MO calculations using density functional theory (DFT) and self-consistent field molecular orbital Hartree-Fock theory were carried out. The results of the calculations were compared with experimental data. The experimental and calculated results were supported each other. The performance of a hybrid B3LYP density functional was compared with the ab initio restricted Hartree-Fock method. With the basis sets of the 6-311G** quality, the DFT calculated bond lengths, dipole moments and harmonic vibrations were predicted in a very good agreement with available experimental data.     

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.     

Investigation of the configuration of alkyl phenyl ketone phenylhydrazones from ab initio 1H NMR chemical shifts

Using ab initio GIAO calculations the experimental 1H NMR spectra of the E and Z isomers of alkyl phenyl ketone phenylhydrazones R1-C(Ph) = N-NH-Ph (R1 = Me, Et, iPr, and tBu) have been re-interpreted and deviations from Karabatsos' rule or from the assignment of Bellamy and Hunter have been discussed in the light of the optimized geometrical structures.     

Weak C-H...O and C-H...F-C hydrogen bonds in the oxirane-trifluoromethane dimer

The oxirane-trifluoromethane dimer generated in a supersonic expansion has been characterized by Fourier transform microwave spectroscopy. The rotational spectra of the parent species and of its two (13)C isotopomers in combination with ab initio calculations have been used to establish a C(s)() geometry for the dimer with the two monomers bound by one C-H.O and two C-H.F-C hydrogen bonds. An overall bonding energy of about 6.7 kJ/mol has been derived from the centrifugal distortion analysis. The lengths of the C-H.O and C-H.F hydrogen bonds, r(O.H) and r(F.H), are 2.37 and 2.68 A, respectively. The C-H.F-C interactions give rise to the HCF(3) internal rotation motion barrier of 0.55(1) kJ/mol, which causes the A-E splittings observed in the rotational spectra. The analysis of the structural and energetic features of the C-H.O and C-H.F-C interactions allows us to classify them as weak hydrogen bonds. Ab initio calculations predict these weak interactions to produce blue shifts in the C-H vibrational frequencies and shortenings of the C-H lengths.     

Conformational properties of methyl vinyl sulfone: Ab initio geometry optimization and vibrational analysis

An ab initio conformational analysis of methyl vinyl sulfone (CH₂CHSO₂CH₃) has been carried out. Molecular geometry optimizations have been performed at the HF and MP2 levels of the theory. Relative energies of the stationary points have been determined by using different approaches, including electron correlation corrections up to the third order. The IR and Raman spectra of the liquid have been measured and a vibrational assignment is proposed. The height of the barrier to the methyl group internal rotation has been estimated. Theoretical calculations and vibrational spectra have shown that the predominant conformation of methyl vinyl sulfone has the C=C bond eclipsed with one of the S=O bonds. Similar eclipsed forms have been found in vinyl fluoro sulfone, vinyl chloro sulfone and divinyl sulfone by ab initio HF calculations.     

Stereomutations of two-bladed propeller derivatives: ortho-substituted diaryl ethylene and diaryl ketone

Stereochemical analysis, supported by ab initio computations, predicts the existence of three possible stable helical conformers for o,o'-diisopropyl-1,1'-diphenylethylene (1) and o,o'-diisopropylbenzophenone (2). At low temperature the NMR spectra of 1 showed distinct sets of signals for these conformers, thus allowing the measurement of the three barriers involved in the related stereomutation processes to be obtained (DeltaG=6.45, 4.65, and < or =4.0 kcal mol(-1)). The NMR spectra also indicate that the asymmetric conformer (C1 point group) is the most stable one in solution, as anticipated by calculations. X-ray diffraction confirmed that this structure is that adopted in the crystalline state. On the other hand, o,o'-diisopropylbenzophenone (2) is predicted by calculations to exist essentially as a C2-type conformer, a result that was confirmed by the low-temperature NMR spectra. The interconversion barrier for the enantiomeric forms of this conformer was also measured (DeltaG=6.3(5) kcal mol(-1)).     

Static and dynamic stereochemistry of the conformational atropisomers of tetra(o-tolyl)benzene

[graph: see text] Whereas only one atropisomer of 1,2,4,5-tetra(o-tolyl)benzene was observed by X-ray diffraction in the solid, five conformational atropisomers were detected by low-temperature NMR in solution. Their structures were assigned by a combination of NOE experiments, solvent effect, and ab initio calculations. Variable temperature dynamic NMR and bidimensional EXSY experiments allowed the barrier for the interconversion of these atropisomers to be determined (deltaG(double dagger) = 15.3 kcal mol(-1)).     

An ab initio MO study on the structures and electronic states of hydrogen-bonded O3- HF and SO2-HF complexes

Ab initio molecular orbital (MO) calculations have been carried out for base-hydrogen fluoride (HF) complexes (base = O3 and SO2) in order to elucidate the structures and energetics of the complexes. The ab initio calculations were performed up to the QCISD(T)/6-311++G(d,p) level of theory. In both complexes, hydrogen-bonded structures where the hydrogen of HF orients toward one of the oxygen atoms of bases were obtained as stable forms. The calculations showed that cis and trans isomers exist in both complexes. All calculations for the SO2-HF complex indicated that the cis form is more stable in energy than the trans form. On the other hand, in O3-HF complexes, the stable structures are changed by the ab initio levels of theory used, and the energies of the cis and trans forms are close to each other. From the most sophisticated calculations (QCISD(T)/6-311++G(d,p)//QCISD/6-311+G(d) level), it was predicted that the complex formation energies for cis SO2-HF, trans SO2-HF, cis O3-HF, and trans O3-HF are 6.1, 5.7, 3.4, and 3.6 kcal/mol, respectively, indicating that the binding energy of HF to SO2 is larger than that of O3. The harmonic vibrational frequencies calculated for cis O3-HF and cis SO2-HF complexes were in good agreement with the experimental values measured by Andrews et al. Also, the calculated rotation constants for cis SO2-HF agreed with the experiment.     

Molecular structure, spectroscopy and matrix photochemistry of fluorocarbonyl iodide, FC(O)I

The molecular structure of FC(O)I has been determined by gas electron diffraction. High-level ab initio methods, including coupled-cluster and the new correlation-consistent basis sets for fourth row elements, have been used to calculate the structure of FC(O)I. A comprehensive vibrational spectroscopic study (both IR and Raman) complemented by high-level calculations has also been performed. Furthermore, UV, mass, and NMR spectra have been recorded for FC(O)I. The matrix photochemistry of FC(O)I has been studied with a low-pressure mercury lamp and with a high-pressure xenon lamp in combination with interference and cut-off filters. UV photolysis revealed the formation of the OC. IF and OC.FI complexes and further photolysis of these complexes at lambda>320 nm resulted in a re-formation of FC(O)I. The structural conformation of the complexes has been characterized by comparing shifts in their CO and IF vibrational modes with respect to those of the free species. The structures, vibrational properties, and stability of the complexes were analyzed with the aid of coupled-cluster ab initio calculations.     

Vibrational frequencies and infrared intensities of the hydrogen-bonded complexes of nitrous acid with ethers: ab initio and DFT studies

The vibrational spectra of the binary complexes formed by HONO-trans and HONO-cis with dimethyl and diethyl ethers have been investigated using ab initio calculations at the SCF and MP2 levels with 6-311++G(d,p) basis set and B3LYP calculations with 6-31G(d,p) and 6-31+G(d,p) basis sets. Full geometry optimisation was made for the complexes studied. The accuracy of the ab initio calculations have been estimated by comparison between the predicted values of the vibrational characteristics (vibrational frequencies and infrared intensities) and the available experimental data. It was established, that the methods, used in this study are well adapted to the problem under examination. The predicted values with the B3LYP calculations are very near to the results, obtained with 6-311++G(d,p)/MP2. The ab initio and DFT calculations show that the changes in the vibrational characteristics (vibrational frequencies and infrared intensities) upon hydrogen bonding for the hydrogen-bonded complex (CH3)2O...HONO-trans are larger than for the complex (CH3)2O...HONO-cis.     

Rotational spectrum of a chiral alpha-hydroxyester: conformation stability and internal rotation barrier heights of methyl lactate

High resolution spectrum of methyl lactate, a chiral alpha-hydroxyester, has been investigated using a molecular jet Fourier transform microwave spectrometer. High level ab initio calculations were employed to study the conformational isomerism of methyl lactate. The observed rotational spectrum confirms that the most stable conformer has an intramolecular hydrogen bond of OH...O==C type, as predicted by the ab initio calculations. The internal rotation barrier heights of the ester methyl group and the alpha-carbon methyl group were calculated to be 5.4 and 14.5 kJ mol(-1) at the MP2/aug-cc-pVDZ level of theory for the most stable conformer. The internal rotation splittings due to the ester methyl group were observed and analyzed and the ester methyl group tunneling barrier height was determined experimentally to be 4.762 (3) kJ mol(-1).