Vibrational spectra and structures of urazole and 4-methylurazole: DFT calculations of the normal modes in aqueous solution and in the solid state,and the influence of hydrogen bonding

Solid-state IR and Raman as well as aqueous solution state Raman spectra are reported for urazole, 4-methylurazole and their deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of the molecules can be interpreted using models with hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments. Solid-state pseudopotential-plane-wave DFT calculations, using the PW91 functional were also carried out, reflecting the importance of intermolecular hydrogen bonding in the solid state.     

Vibrational spectra and structures of the anions of urazole and 4-methylurazole: DFT calculations of the normal modes and the influence of hydrogen bonding

Solid state IR and Raman as well as aqueous solution state Raman spectra are reported for the anions of urazole and 4-methylurazole, and their N-deuterated derivatives. DFT calculations, at the B3-LYP/cc-pVTZ level, established that the structures and vibrational spectra of both anions can be interpreted using a model that incorporates hydrogen-bonded water molecules, in conjunction with the polarizable continuum solvation method. In the case of the urazole anion it is shown that deprotonation occurs primarily at N1 rather than N4, but there is also evidence for the second tautomer both in the solid state and in aqueous solution. The vibrational spectra were computed at the optimised molecular geometry in each case, enabling normal coordinate analysis, which yielded satisfactory agreement with the experimental IR and Raman data. Computed potential energy distributions of the normal modes provided detailed vibrational assignments.     

Vibrational spectroscopic studies and DFT calculations on tribromoacetate and tribromoacetic acid in aqueous solution

Aqueous solutions of sodium tribromoacetate (NaCBr3CO2) and its corresponding acid (CBr3COOH) have been studied using Raman and infrared spectroscopy. The spectra of the species in solution were assigned according to symmetry Cs. Characteristic bands of CBr3CO2-(aq) and the tribromoacetic acid, CBr3COOH(aq), are discussed. For the hydrated anion, the CO2 group, the symmetric CO2 stretching mode at 1332 cm(-1) and the asymmetric stretching mode at 1651 cm(-1) are characteristic while the CO mode at 1730 cm(-1) is characteristic for the spectra of the acid. The stretching mode, νC-C at 912cm(-1) for CBr3CO2-(aq) is 10 cm(-1) lower in the anion compared with that of the acid. These characteristic modes are compared to those in acetate, CH3CO2-(aq). Coupling of the modes are fairly extensive and therefore DFT calculations have been carried out in order to compare the measured spectra with the calculated ones. The geometrical parameters such as bond length and bond angles of the tribromoacetate, and tribromoacetic acid have been obtained and may be compared with the ones published for other acetates and their conjugated acids. CBr3COOH(aq) is a moderately strong acid and the pKa value derived from quantitative Raman measurements is equal to -0.23 at 23°C. The deuterated acid CBr3COOD in heavy water has been measured as well and the assignments were given.     

The influence of short strong hydrogen bonding on the structure and the physicochemical properties of alkyl-N-iminodiacetic acids in solid state and aqueous systems

Alkyl-N-iminodiacetic acids with varying alkyl chain lengths have been prepared and characterized with respect to structure, acidic properties, and ability to form aggregates in water. The alkyl-N-iminodiacetic acids are the group of ligands with the lowest molecule weight which can be characterized as chelating surfactants, compounds with surface chemical properties which at the same time have a high ability to bind metal ions. The solid alkyl-N-iminodiacetic acids have a unique structure with neutral zwitterionic units linked together to polymer chains through a short strong hydrogen bond, d(O(-H)...O) approximately 2.46 A, and where the nu(O-H) stretching vibration at ca. 720 cm(-1) supports the presence of such a hydrogen bond. The polymer chains are cross-linked together to bilayers through relatively strong hydrogen bonds between ammonium and carboxylate groups, and where the parallel alkyl groups are interdigitating each other; the bilayer surface consists of hydrophilic iminodiacetic acid groups. The acidic properties of monomeric alkyl-N-iminodiacetic acids in water are in the expected ranges with pK(a) values of about 1.7, 2.3, and 10.3. n-Octadecyl-N-iminodiacetic acid, present as aggregates in water, displays very acidic properties of the first proton, and a substantially weakened acidity of the second proton, pK(a2) = 5.5-7.5, depending on ionic strength, and pK(a3) = 9.5-10.5. This pattern of the acidic constants strongly indicates that the polymer structure with short strong hydrogen bonds is maintained in the aggregates and that such bonds can exist in aqueous systems if they are supported by a strong and rigid backbone structure, as the bilayers of well-organized long interdigitating alkyl chains in the studied systems. Hydrogenbis(methyl-N-iminodiacetic acid) perchlorate precipitates from perchloric acidic solutions of methyl-N-iminodiacetic acid. The structure is built up of dimers of zwitterionic methyl-N-iminodiacetic acid units linked together by an extra proton in a short strong hydrogen bond, d(O(-H)...O) approximately 2.456(6) A, and nu(O-H) = 789 cm(-1).     

Vibrational anharmonic calculations in solution: performance of various DFT approaches

We report anharmonic spectra calculated for formaldehyde in acetonitrile solution using the quartic force field obtained for various DFT/solvent coupled models. A statistical study has been carried out for each mode by using several classes of DFT functionals and comparing them to the reference ab-initio CCSD(T)/cc-pVQZ calculations. Results lead to the recommended use of hybrid functionals associated with the 6-31+G** basis set and the Polarized Continuum model (PCM) to predict the expected shifts relative to the gas phase.     

Vibrational spectra of isomeric pyridinic carboxylic acids in solid state and in solution and their SERS studies in silver sol

Raman spectroscopic studies of three isomeric pyridinic carboxylic acids, viz. picolinic, nicotinic and iso-nicotinic acid in solid state, in aqueous solution and in silver hydrosol, in the frequency range 900–1750 cm⁻¹, have been made. Assignments of the observed bands have been proposed in relation to the molecular forms present in solid state and in solution. Different degrees of intensity enhancements of the Raman bands in surface-enhanced Raman scattering (SERS) have been observed in all the three isomeric molecules. In iso-nicotinic acid, the intensity enhancement has been found to be minimum. Comparisons of Raman spectra in aqueous solution with those due to SERS in silver sol indicate that picolinic and nicotinic acid adsorb perpendicularly to the sol surface whereas in iso-nicotinic acid it occurs via donation of a π-electron of the aromatic ring, i.e. the plane of the ring lies parallel to the surface of the sol.     

1H NMR spectra of alcohols in hydrogen bonding solvents: DFT/GIAO calculations of chemical shifts

Proton nuclear magnetic resonance (NMR) shifts of aliphatic alcohols in hydrogen bonding solvents have been computed on the basis of density functional theory by applying the gauge‐including atomic orbital method to geometry‐optimized alcohol/solvent complexes. The OH proton shifts and hydrogen bond distances for methanol or ethanol complexed with pyridine depend very much on the functional employed and very little on the basis set, provided it is sufficiently large to give the correct quasi‐linear hydrogen bond geometry. The CH proton shifts are insensitive to both the functional and the basis set. NMR shifts for all protons in several alcohol/pyridine complexes are calculated at the Perdew, Burke and Ernzerhof PBE0/cc‐pVTZ//PBE0/6‐311 + G(d,p) level in the gas phase. The results correlate with the shifts for the pyridine‐complexed alcohols, determined by analysing data from the NMR titration of alcohols against pyridine. More pragmatically, computed shifts for a wider range of alcohols correlate with experimental shifts in neat pyridine. Shifts for alcohols in dimethylsulfoxide, based on the corresponding complexes in the gas phase, correlate well with the experimental values, but the overall root mean square difference is high (0.23 ppm), shifts for the OH, CH OH and other CH protons being systematically overestimated, by averages of 0.42, 0.21 and 0.06 ppm, respectively. If the computed shifts are corrected accordingly, a very good correlation is obtained with a gradient of 1.00 ± 0.01, an intercept of 0.00 ± 0.02 ppm and a root mean square difference of 0.09 ppm. This is a modest improvement on the result of applying the CHARGE programme to a slightly different set of alcohols. Some alcohol complexes with acetone and acetonitrile were investigated both in the gas phase and in a continuum of the relevant solvent. Copyright © 2015 John Wiley & Sons, Ltd.     

Vibrational and NMR spectra of mono- and di-chlorothiolacetic acids in relation to rotational isomerism and hydrogen bonding

The vibrational spectra of mono- and di-chlorothiolacetic acids have been measured in liquid and gaseous states and solutions, and vibrational assignments have been proposed. The experimental material shows that these molecules are present as a mixture of two rotational isomers. The energy of the two isomers in the liquid state is almost the same.     

Vibrational overtone spectra of chloroanilines--evidence for intramolecular hydrogen bonding in o-chloroaniline

The near infrared vibrational overtone absorption spectra of liquid phase aniline and chloroanilines are reported. The analysis of the observed CH and NH local mode mechanical frequency values shows that intramolecular hydrogen bonding occurs between NH2 group and chlorine atom in o-chloroaniline. This observation supports the conclusion drawn from microwave spectroscopic studies reported earlier.     

IR and NMR spectra,intramolecular hydrogen bonding and conformations of para-tert-butyl-aminothiacalix[4]arene in solid state and chloroform solution

It is demonstrated that dissolution of aminothiacalix[4]arene in chloroform results in transformation of 1,3-alternate conformation, adopted in single-crystal and bulk polycrystalline solids, to the pinched-cone form. This conformer is stabilised by the intramolecular hydrogen bonds of two distal amino-groups acting as H-donors with another two amino moieties that appear as H-acceptors. The H-bonds cause quite small (ca. 10–20 cm^?1) red shift of the IR bands of the NH₂ stretching vibrations, which suggests rather weak NH?N hydrogen bonding. This latter is sufficient to stabilize the pinched-cone conformation in the chloroform solution, but the energy gap between the pinched-cone and other conformations is small, and solid-state intermolecular forces easily overcome it, leading to realisation of the 1,3-alternate conformer. The comparison of the DFT computed and experimental vibrational and NMR spectra demonstrates good quality of present quantum-chemical computations, allows complete interpretation of the spectra and reveals simple IR and NMR spectroscopic markers of the conformers of aminothiacalix[4]arenes.     

Vibrational spectra of triiodomesitylene: combination of DFT calculations and experimental studies. Effects of the environment

A study of the internal vibrations of triiodomesitylene (TIM) is presented. It is known from X-rays diffraction at 293 K that the molecule has nearly D(3h) symmetry because of the large delocalization of the methyl protons. By using Raman and infrared spectra recorded at room temperature, a first assignment is done by comparing TIM vibrations with those of 1,3,5-triiodo- and 1,3,5-trimethyl-benzene. This assignment is supported by DFT calculations by using the MPW1PW91 functional with the LanL2DZ(d,p) basis set and assuming C(3h) symmetry. The agreement between the calculated and experimental frequencies is very good: always better than 97% for the observed skeletal vibrations. The calculations overestimate the methyl frequencies by 7%, and experiment shows only broad features for these excitations. Because a neutron diffraction study had established that the TIM conformation at 14 K is not exactly trigonal, new theoretical calculations were done with C(s) symmetry. This shows that all previous E' and E' modes of vibration are split by 2-12 cm(-1). This is confirmed by infrared, Raman, and inelastic neutron scattering spectra recorded below 10 K. Apart from two frequencies, all the TIM skeleton vibrations have been detected and assigned by using C(s) symmetry. For the methyl vibrations, experiment has confirmed the splitting of the previously degenerate modes; only some small discrepancies remain in the assignment. This is partly due to the difference of the model conformation used in the calculations and the crystallographic one. All these results confirm that each of the three methyl groups has not only its own tunnel splitting but also a different specific spectroscopic behavior for all the molecular modes.     

Vibrational spectra and fundamental structural assignments from HF and DFT calculations of methyl benzoate

The Fourier transform Raman and Fourier transform infrared spectra of methyl benzoate (MB) were recorded in the liquid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities, depolarization ratios, reduced masses were calculated by Hartree-Fock (HF) and density functional B3LYP method with the 6-311+G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental values. The thermodynamic functions of the title compound were also performed at HF/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. A detailed interpretations of the infrared and Raman spectra of methyl benzoate is reported. The theoretical spectrograms for FT-IR spectra of the title molecule have been constructed.     

Vibrational spectra and structure of 1-phenyltetrazole and 5-chloro-1-phenyltetrazole: A combined study by low temperature matrix isolation and solid state FTIR spectroscopy and DFT calculations

Infrared spectra of 1-phenyltetrazole (C₇N₄H₆) and 5-chloro-1-phenyltetrazole (C₇N₄H₅Cl) isolated in argon matrixes (T=8 K) and in the solid state (at room temperature) were studied. DFT(B3LYP)/6-31G* calculations predict the minimum energy conformation of 1-phenyltetrazole as being non-planar, with the two rings (phenyl and tetrazole) twisted by 29°. For 5-chloro-1-phenyltetrazole, the optimized dihedral angle between the two rings is larger (48°). The theoretically calculated IR spectra of both compounds fit well the spectra observed experimentally. This allowed a reliable assignment of observed IR absorption bands.     

The structure of fosfomycin salts in solution and in the solid state by nuclear magnetic resonance spectroscopy and DFT calculations

Two samples of fosfomycin salts, the calcium and the disodium ones, were used to record their NMR spectra both in solution and in the solid state. The existence of fosfomycin in a neutral and two ionized structures (mono and dianion) was considered to interpret the spectra that were solved using the GIAO calculated chemical shifts of the minimum energy conformations. Although the starting materials were dianions, the spectra in solution show the presence of monoanions.     

Excited-state hydrogen bonding and deprotonation of esculetin in solution: a DFT/TDDFT study

The combined density functional theory (DFT) and time-dependent density functional theory (TDDFT) method was used to study the electronic spectral properties of different deprotonated forms of esculetin. By comparing the experimental absorption and fluorescence bands with the calculated electronic spectra, it is evidently demonstrated that the minor absorption and fluorescence bands observed at slightly longer wavelengths than the principal bands in experiments are predominantly from the de-H3 form of the esculetin monomer. Furthermore, we clarified the relationship between electronic spectral shifts and electronic excited-state intramolecular hydrogen bonding changes: the strengthening of intramolecular hydrogen bond can induce an electronic spectral blueshift while the intramolecular hydrogen bond weakening can result in an electronic spectral redshift.     

Vibrational spectra, structure and hydrogen bonding of 5-tert-butylpyrazole and its zinc complexes

New zinc complexes [L₂ZnX₂] with X=Cl (I), Br (II), I (III) and NO₃ (IV), [L₃Zn(OClO₃)]ClO₄ (V) and [L₄Zn](ClO₄)₂ (VI) with 5-tert-butylpyrazole as ligand L were synthesized and characterized by infrared-, Raman-, mass- and NMR-spectroscopy. The assignment of the vibrational frequencies for the complexes in the range of 4000–80 cm⁻¹ is proposed. Analysis of the IR spectra in the range of ν_NH frequencies shows that 5-tert-butylpyrazole forms cyclic associates in the solid using intermolecular NHN hydrogen bonds. This was proven by a crystal structure determination, which showed that L exists as tetramers in the solid state. In solution there is an equilibrium between tetramers and monomers and, probably, dimers or trimers. In the complexes, the NH-groups of L form intramolecular H-bonds with the X-group. The intramolecular H-bond in VI has interionic character and partially dissociates in solution at high dilution. Ligand vibrations that are sensitive to the coordination and the dependence of their frequencies on the anionic group X has been revealed.     

Sodium hydride clusters in solid hydrogen and neon: infrared spectra and theoretical calculations

Laser-ablated sodium atom reactions with H2 have been investigated in solid molecular hydrogens and neon. The NaH molecule and (NaH)2,3,4 clusters were identified by IR spectra with isotopic substitution (HD and D2) and comparison to frequencies calculated by density functional theory and the MP2 method. The use of para-hydrogen enriched samples provides evidence for a (H2)nNaH subcomplex surrounded by the solid hydrogen matrix cage. The ionic rhombic (NaH)2 dimer is characterized by strong absorptions at 761.7, 759.1, and 757.0 cm(-1), respectively, in solid neon, para-hydrogen, and normal hydrogen matrices. The cyclic sodium hydride trimer and tetramer clusters are also observed. Although the spontaneous reaction of two Li and H2 to form (LiH)2 occurs on annealing in solid H2, the formation of (NaH)2 requires near uv photoexcitation.     

Vibrational spectra of 1-methylthymine: matrix isolation, solid state and theoretical studies

The infrared spectra of 1-methylthymine (1-MeT) in argon and nitrogen cryogenic matrices are presented, for the first time. The molecular structure, conformations, vibrational frequencies, infrared intensities and Raman scattering activities of 1-MeT have been calculated by the DFT(B3LYP), MP2 and HF methods using the D95V** basis set. The theoretically predicted intensity pattern of the IR and Raman bands has proved to be of great help in assigning the experimental spectra. Rigorous normal coordinate analysis has been performed, at each level of theory. The unequivocal and complete vibrational assignment for 1-MeT has been made on the basis of the calculated potential energy distribution (PED). Comparison of the experimental matrix isolation spectra with the theoretical results has revealed that the B3LYP method is superior to both the MP2 and HF methods in predicting the frequencies of uracil derivatives. The MP2 method consistently underestimates the frequencies of the out-of-plane gamma(C=O) and gamma(C-H) bending modes, while the HF method yields the reverse order of the frequencies of two nu(C=O) stretching vibrations. Investigation of the frequency shift of several bands, on passing from matrix isolation to solid state spectra, has provided information on the strength of intermolecular hydrogen bonding in the crystal of 1-MeT. Several ambiguities in the earlier assignments of the vibrational spectra of polycrystalline 1-MeT have been clarified.     

Time-domain calculations of the infrared and polarized Raman spectra of tetraalanine in aqueous solution

The IR and polarized (isotropic and anisotropic) Raman spectra are calculated for the amide I band of tetraalanine ((Ala)4) in aqueous solution by using a time-domain computational method, which includes the effects of the diagonal frequency modulations (of individual peptide groups), the off-diagonal (interpeptide) vibrational couplings, and structural dynamics. It is shown that the calculated band profiles, especially the existence of a large negative noncoincidence effect (i.e., large frequency separations between the IR, isotropic Raman, and anisotropic Raman bands, with the isotropic Raman being higher in frequency), are in reasonable agreement with the experimental results. This negative noncoincidence effect derives from two conditions: the positive coupling between the amide I vibrations of peptide groups and the angle larger than 90 degrees between the transition dipoles of the coupled vibrations. This result means that the dynamically changing structures mainly in the polyproline II and beta-type conformations containing some repeated interconversions obtained from the molecular dynamics calculation are consistent with the existence of a large negative noncoincidence effect, as far as the structures satisfy the above two conditions. It is also shown that the electric fields from solvent water molecules induce larger frequency shifts than those of intrachain interactions, with rapid underdamped oscillatory modulations ( approximately 43 fs) due to the librational motions of water molecules that give rise to motional narrowing effect on the spectra. The reason for the difference from the behavior seen for the O-H stretching mode of liquid water is discussed. The time-domain analysis of the mode identity shows that the system proceeds halfway to complete mode mixing with a similar time scale ( approximately 60 fs), suggesting the importance of the nonadiabatic effect, which is included in a natural way in the present computational method.     

Vibrational overtone spectra of o-fluorophenol and the "anomalous" order of intramolecular hydrogen bonding strengths

The near infrared vibrational overtone absorption spectrum of liquid phase o-fluorophenol is examined in the region deltav=2, 3 and 4. The OH frequencies are compared with that of o-chlorophenol and phenol. Considering the relative electronegativities of all halogens, one might expect the order of intramolecular hydrogen bond strength for o-fluorophenol to be the greatest among all halogenophenols. It is evident that o-fluorophenol forms a weaker intramolecular hydrogen bond (an anomalous trend) contrary to that expected from relative electronegativities of halogens. The local mode mechanical frequency values and anharmonicity values obtained from fitting the overtones are analysed. Our observation is in agreement with the previous experimental as well as the recent theoretical vibrational analysis of halogenophenols using density functional theory (B3LYP). The overtone spectra of o-fluorophenol in carbon tetrachloride in different concentrations are also examined. It is noted that the OH-red shift which arises due to the intermolecular bond formation between the cis and trans conformers of o-fluorophenol (dimerization) increases with concentration.