Quantum chemical DFT study of 4-azatricyclo [5.2.2.02,6] undecane-3,5,8-trione

Fourier-transform-Raman and infrared spectrum of 4-azatricyclo [5.2.2.0^2,6] undecane-3,5,8-trione were recorded and analyzed. The vibrational wavenumbers were examined theoretically using the Gaussian03 set of quantum chemistry codes, and the normal modes were assigned by potential energy distribution (PED) calculations. The first hyperpolarizability, predicted infrared intensities and Raman activities are reported. The calculated first hyperpolarizability is comparable with reported values of similar structures which makes this compound an attractive object for future studies of nonlinear optics. Optimized geometrical parameters of the compound are in agreement with similar reported structures. The red shift of the NH stretching wavenumber in the infrared spectrum from the computational wavenumber indicates the weakening of NH bond.     

Vibrational spectroscopy of synthetic stercorite H(NH4)Na(PO4)·4H2O--a comparison with the natural cave mineral

In order to mimic the chemical reactions in cave systems, the analogue of the mineral stercorite H(NH(4))Na(PO(4))·4H(2)O has been synthesised. X-ray diffraction of the stercorite analogue matches the stercorite reference pattern. A comparison is made with the vibrational spectra of synthetic stercorite analogue and the natural Cave mineral. The mineral in nature is formed by the reaction of bat guano chemicals on calcite substrates. A single Raman band at 920 cm(-1) (Cave) and 922 cm(-1) (synthesised) defines the presence of hydrogen phosphate in the mineral. In the synthetic stercorite analogue, additional bands are observed and are attributed to the dihydrogen and phosphate anions. The vibrational spectra of synthetic stercorite only partly match that of the natural stercorite. It is suggested that natural stercorite is more pure than that of synthesised stercorite. Antisymmetric stretching bands are observed in the infrared spectrum at 1052, 1097, 1135 and 1173 cm(-1). Raman spectroscopy shows the stercorite mineral is based upon the hydrogen phosphate anion and not the phosphate anion. Raman and infrared bands are found and assigned to PO(4)(3-), H(2)O, OH and NH stretching vibrations. Raman spectroscopy shows the synthetic analogue is similar to the natural mineral. A mechanism for the formation of stercorite is provided.     

Molecular dynamics simulation of liquid methanol. II. Unified assignment of infrared, Raman, and sum frequency generation vibrational spectra in methyl C-H stretching region

Vibrational spectra of methyl C-H stretching region are notoriously complicated, and thus a theoretical method of systematic assignment is strongly called for in condensed phase. Here we develop a unified analysis method of the vibrational spectra, such as infrared (IR), polarized and depolarized Raman, and ssp polarized sum frequency generation (SFG), by flexible and polarizable molecular dynamics simulation. The molecular model for methanol has been developed by charge response kernel model to allow for analyzing the methyl C-H stretching vibrations. The complicated spectral structure by the Fermi resonance has been unraveled by empirically shifting potential parameters, which provides clear information on the coupling mechanism. The analysis confirmed that for the IR, polarized Raman, and SFG spectra, two-band structure at about 2830 and 2950 cm(-1) results from the Fermi resonance splitting of the methyl C-H symmetric stretching and bending overtones. In the IR spectrum, the latter, higher-frequency band is overlapped with prominent asymmetric C-H stretching bands. In the depolarized Raman spectrum, the high frequency band at about 2980 cm(-1) is assigned to the asymmetric C-H stretching mode. In the SFG spectrum, the two bands of the splitted symmetric C-H stretching mode have negative amplitudes of imaginary nonlinear susceptibility χ(2), while the higher-frequency band is partly cancelled by positive imaginary components of asymmetric C-H stretching modes.     

Infrared spectrum of 4-methoxypicolinic acid N-oxide: computation of asymmetric O-H stretching band

In this article we studied the strong intramolecularly hydrogen-bonded system 4-methoxypicolinic acid N-oxide. The potential energy surface V = V(rOH,rOO) and the corresponding dipole moment function were calculated using the DFT B3LYP/6-31+G(d,p) level of approximation. The time-independent vibrational Schr?dinger equation was solved using a rectangular grid basis set and shifted Gaussian basis set. The vibrational spectrum and metric parameters were also calculated. Effects of deuteration were considered. The calculated vibrational spectra were compared with the experimental spectra. The vibrational transition corresponding to asymmetric O-H stretching that occurs at about 1400 cm-1 compares well with the experimentally assigned O-H asymmetric stretching band centered at 1380 cm-1. The corresponding asymmetric O-D stretching band was predicted to be at 1154 cm-1, while the experimental O-D band was not assigned due to its very low intensity. Several overtones and hot transitions of significant intensities were located in the vicinity of the fundamental O-H stretching frequency, effectively broadening the infrared absorption attributed to the O-H stretching mode. This is in a good agreement with the observed broad protonic absorptions found in the infrared spectra of the title compound and its analogs. We have shown that the Gaussian basis set is the method of choice for a two-dimensional vibrational problem that requires several hundreds of vibrational basis functions and when high accuracy of the eigenvalues is required or when extending the calculations to more vibrational degrees of freedom. We have also demonstrated that for a large number of basis functions the Gramm-Schmidt orthogonalization procedure outperforms symmetric and canonical orthogonalization schemes.     

Raman under nitrogen. The high-resolution Raman spectroscopy of crystalline uranocene, thorocene, and ferrocene

The utility of recording Raman spectroscopy under liquid nitrogen, a technique we call Raman under nitrogen (RUN), is demonstrated for ferrocene, uranocene, and thorocene. Using RUN, low-temperature (liquid nitrogen cooled) Raman spectra for these compounds exhibit higher resolution than previous studies, and new vibrational features are reported. The first Raman spectra of crystalline uranocene at 77 K are reported using excitation from argon (5145 A) and krypton (6764 A) ion lasers. The spectra obtained showed bands corresponding to vibrational transitions at 212, 236, 259, 379, 753, 897, 1500, and 3042 cm(-1), assigned to ring-metal-ring stretching, ring-metal tilting, out-of-plane CCC bending, in-plane CCC bending, ring-breathing, C-H bending, CC stretching and CH stretching, respectively. The assigned vibrational bands are compared to those of uranocene in THF, (COT)2-, and thorocene. All vibrational frequencies of the ligands, except the 259 cm(-1) out-of-plane CCC bending mode, were found to increase upon coordination. A broad, polarizable band centered about approximately 460 cm(-1) was also observed. The 460 cm(-1) band is greatly enhanced relative to the vibrational Raman transitions with excitations from the krypton ion laser, which is indicative of an electronic resonance Raman process as has been shown previously. The electronic resonance Raman band is observed to split into three distinct bands at 450, 461, and 474 cm(-1) with 6764 A excitation. Relativistic density functional theory is used to provide theoretical interpretations of the measured spectra.     

An infrared and Raman spectroscopic study of natural zinc phosphates

Zinc phosphates are important in the study of the phosphatisation of metals. Raman spectroscopy in combination with infrared spectroscopy has been used to characterise the zinc phosphate minerals. The minerals may be characterised by the patterns of the hydroxyl stretching vibrations in both the Raman and infrared spectra. Spencerite is characterised by a sharp Raman band at 3516 cm(-1) and tarbuttite by a single band at 3446 cm(-1). The patterns of the Raman spectra of the hydroxyl stretching region of hopeite and parahopeite are different in line with their differing crystal structures. The Raman spectrum of the PO4 stretching region shows better band separated peaks than the infrared spectra which consist of a complex set of overlapping bands. The position of the PO4 symmetric stretching mode can be used to identify the zinc phosphate mineral. It is apparent that Raman spectroscopy lends itself to the fundamental study of the evolution of zinc phosphate films.     

Time-domain calculations of the polarized Raman spectra, the transient infrared absorption anisotropy, and the extent of delocalization of the OH stretching mode of liquid water

The polarized Raman spectrum and the time dependence of the transient infrared (TRIR) absorption anisotropy are calculated for the OH stretching mode of liquid water (neat liquid H2O) by using time-domain formulations, which include the effects of both the diagonal frequency modulations (of individual oscillators) induced by the interactions between the dipole derivatives and the intermolecular electric field, and the off-diagonal (intermolecular) vibrational coupling described by the transition dipole coupling (TDC) mechanism. The IR spectrum of neat liquid H2O and the TRIR anisotropy of a liquid mixture of H2O/HDO/D2O are also calculated. It is shown that the calculated features of these optical signals, including the temperature dependence of the polarized Raman and IR spectra, are in reasonable agreement with the experimental results, indicating that the frequency separation between the isotropic and anisotropic components of the polarized Raman spectrum and the rapid decay (approximately 0.1 ps) of the TRIR anisotropy of the OH stretching mode of neat liquid H2O are mainly controlled by the resonant intermolecular vibrational coupling described by the TDC mechanism. Comparing with the time evolution of vibrational excitations, it is suggested that the TRIR anisotropy decays in the time needed for the initially localized vibrational excitations to delocalize over a few oscillators. It is also shown that the enhancement of the dipole derivatives by the interactions with surrounding molecules is an important factor in generating the spectral profiles of the OH stretching Raman band. The time-domain behavior of the molecular motions that affect the spectroscopic features is discussed.     

Vibrational analysis of I2*- x nCO2 clusters (n = 1-10): a first principle study on microsolvation

Structure, stability, and vibrational IR and Raman spectra of I(2)(*-) x nCO(2) clusters (n = 1-10) are reported based on first-principle electronic structure calculations. Several close-lying minimum energy structures are predicted for these solvated clusters following the quasi Newton-Raphson procedure of geometry optimization. Search strategy based on Monte-Carlo simulated annealing is also applied to find out the global minimum energy structures of these clusters. Successive addition of solvent CO(2) molecules to the negatively charged diatomic solute, I(2)(*-), is fairly symmetrical. Energy parameters of these solvated clusters are calculated following second-order Moller-Plesset perturbation (MP2) as well as coupled cluster theory with 6-311+G(d) set of basis function (I atom is treated with 6-311G(d) set of basis function). The excess electron in these solvated clusters is observed to be localized mainly over the two I atoms. Average interaction energy between the anionic solute, I(2)(*-), and a solvent CO(2) molecule is approximately 129 meV in I(2)(*-) x nCO(2) clusters, and the average interaction energy between two solvent CO(2) molecules is approximately 85 meV in the case of neutral (CO(2))(n) clusters at MP2 level of theory. IR spectra show similar features in all these solvated clusters, depicting a strong band at approximately 2330 cm(-1) for C-O stretching and a weak band at approximately 650 cm(-1) for CO(2) bending modes. Degeneracy of the bending mode of a free solvent CO(2) unit gets lifted when it interacts with the charged solute I(2)(*-) to form a molecular cluster because of the change in structure of solvent CO(2) units. The vibrational band at the bending region of CO(2) in the Raman spectra of these anionic clusters shows a characteristic feature for the formation of I(2)(*-) x nCO(2) clusters showing a Raman band at approximately 650 cm(-1).     

DFT and Raman spectroscopy of porphyrin derivatives: Tetraphenylporphine (TPP)

Raman spectrum of the meso tetraphenylporphine (TPP) deposited onto smooth copper surface as thin film were recorded in the region 200–1700 cm⁻¹. To investigate the effect of meso-phenyl substitution rings on the vibrational spectrum of free base porphyrin, we calculated Raman and infrared (IR) spectra of the meso-tetraphenylporphine (TPP), meso tetramethylporphine (TMP), copper (II)porphine (CuPr) and free base porphine (FBP) at the B3LYP/6-311+G(d,p) level of the density functional theory (DFT). The observed Raman spectrum of the TPP is assigned based on the calculated its Raman spectrum in connection with the calculated spectra of the TMP, CuPr and FBP by taking into account of their corresponding vibrational motions of the Raman modes of frequencies. Results of the calculations clearly indicated that the meso tetraphenyl substitution rings are totally responsible for the observed Raman bands at ∼1593, 1234 and 1002 cm⁻¹. The calculated and observed Raman spectra also suggested that the observed Raman band with a medium intense at 962 cm⁻¹ might result from the surface plasmon effect. Furthermore, the observed Raman bands with medium intense at ∼334 and ∼201 cm⁻¹ are as results of the dimerization or aggregation of the TPP or would be that related to intramolecular interaction. We also calculated IR spectra of these molecules at same level of the theory. To investigate the solvent effect on the vibrational spectrum of porphine, the Raman and IR spectra of the TPP and FBP are calculated in solution phase where water used as solvent. The results of these calculation indicated that there is no any significant effect on the vibrational spectrum of the TPP.     

Vibrational spectra and reinvestigation of the crystal structure of a polymeric copper(II)-orotate complex, [Cu(μ-HOr)(H2O)2]n: The performance of new DFT methods, M06 and M05-2X, in theoretical studies

The crystal and molecular structure of a polymeric Cu(II)-orotate complex, [Cu(μ-HOr)(H₂O)₂]_n, has been reinvestigated by single crystal X-ray diffraction. It is shown that several synergistic interactions: two axial Cu-O interactions; intramolecular and intermolecular hydrogen bonds; and π-π stacking between the uracil rings contribute to the stability of the crystal structure. The Raman and FT-IR spectra of the title complex are reported for the first time. Comprehensive theoretical studies have been performed by using three unrestricted DFT methods: B3LYP; and the recently developed M06, and M05-2X density functionals. Clear-cut assignments of all the bands in the vibrational spectra have been made on the basis of the calculated potential energy distribution, PED. The very strong Raman band at 1219 cm⁻¹ is diagnostic for the N1-deprotonation of the uracil ring and formation of the copper-nitrogen bond, in this complex. The Cu-O (carboxylate) stretching vibration is observed at 287 cm⁻¹ in the IR spectrum, while the Cu-N (U ring) stretching vibration is assigned to the strong Raman band at 263 cm⁻¹. The molecular structure and vibrational spectra (frequencies and intensities) calculated by the M06 functional method are very similar to the results obtained by the B3LYP method, but M06 performs better than B3LYP in calculations of the geometrical parameters and vibrational frequencies of the interligand O-H?O hydrogen bonding. Unfortunately, the M05-2X method seriously overestimates the strength of interligand hydrogen bond.     

Effect of water on the formamide-intercalation of kaolinite

The molecular structures of low defect kaolinite completely intercalated with formamide and formamide-water mixtures have been determined using a combination of X-ray diffraction, thermoanalytical techniques, DRIFT and Raman spectroscopy. Expansion of the kaolinite to 10.09 A was observed with subtle differences whether the kaolinite was expanded with formamide or formamide-water mixtures. Thermal analysis showed that greater amounts of formamide could be intercalated into the kaolinite in the presence of water. New infrared bands were observed for the formamide intercalated kaolinites at 3648, 3630 and 3606 cm(-1). These bands are attributed to the hydroxyl stretching frequencies of the inner surface hydroxyls hydrogen bonded to formamide with water, formamide and interlamellar water. Bands were observed at similar positions in the Raman spectrum. At liquid nitrogen temperature, the 3630 cm(-1) Raman band separated into two bands at 3633 and 3625 cm(-1). DRIFT spectra showed the hydroxyl deformation mode at 905 cm(-1). Changes in the molecular structure of the formamide are observed through both the NH stretching vibrations and the amide 1 and 2 bands. Upon intercalation of kaolinite with formamide, bands are observed at 3460, 3344, 3248 and 3167 cm(-1) attributed to the NH stretching vibration of the NH involved with hydrogen bonded to the oxygens of the kaolinite siloxane surface. In the DRIFT spectra of the formamide intercalated kaolinites bands are observed at 1700 and 1671 cm(-1) and are attributed to the amide 1 and amide 2 vibrations.     

Study of NH stretching vibrations in small ammonia clusters by infrared spectroscopy in He droplets and ab initio calculations

Infrared spectra of the NH stretching vibrations of (NH3)n clusters (n = 2-4) have been obtained using the helium droplet isolation technique and first principles electronic structure anharmonic calculations. The measured spectra exhibit well-resolved bands, which have been assigned to the nu1, nu3, and 2nu4 modes of the ammonia fragments in the clusters. The formation of a hydrogen bond in ammonia dimers leads to an increase of the infrared intensity by about a factor of 4. In the larger clusters the infrared intensity per hydrogen bond is close to that found in dimers and approaches the value in the NH3 crystal. The intensity of the 2nu4 overtone band in the trimer and tetramer increases by a factor of 10 relative to that in the monomer and dimer, and is comparable to the intensity of the nu1 and nu3 fundamental bands in larger clusters. This indicates the onset of the strong anharmonic coupling of the 2nu4 and nu1 modes in larger clusters. The experimental assignments are compared to the ones obtained from first principles electronic structure anharmonic calculations for the dimer and trimer clusters. The anharmonic calculations were performed at the M?ller-Plesset (MP2) level of electronic structure theory and were based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structures. In general, there is excellent (<20 cm(-1)) agreement between the experimentally measured band origins for the N-H stretching frequencies and the calculated anharmonic vibrational frequencies. However, the calculations were found to overestimate the infrared intensities in clusters by about a factor of 4.     

Vibrational analysis of hydroxyacetone

In order to be able to fully understand the vibrational dynamics of monosaccharide sugars, we started with hydroxyacetone CH2OHCOCH3, and glycolaldehyde CH2OHCOH, which are among the smallest molecules that contain hydroxyl and carbonyl group on neighboring carbon atoms. This sterical configuration is characteristic for saccharides and determines their biochemical activity. In this work vibrational analysis of hydroxyacetone was undertaken by performing the normal coordinate analysis for glycolaldehyde first, and transferring these force constants to hydroxyacetone. The observed Raman and infrared bands for 90 wt.% solution of hydroxyacetone in water (acetol) were used as a first approximation for the bands of free hydroxyacetone. The number of observed Raman and infrared bands for acetol exceeds the number of calculated values for the most stable hydroxyacetone conformer with Cs symmetry, which suggests more than one conformer of hydroxyacetone in water solution. In particular, there are two bands both in infrared (1083 and 1057 cm(-1)) and in Raman spectrum (1086.5 and 1053 cm(-1)) that are assigned to the CO stretching mode and this is one of the indicators of several hydroxyacetone conformers in the solution. Additional information was obtained from low temperature Raman spectra: at 240 K a broad asymmetric band centered around 280 cm(-1) appears, suggesting a disorder in the orientation of hydroxyl groups. Glassy state forms at approximately 150K. The broad band at 80 cm(-1) is assigned to frozen torsions of hydroxymethyl groups.     

Vapor Phase Vibrational Spectra for Re(2)O(7) and the Infrared Spectrum of Gaseous HReO(4). Molecular Shapes of Mn(2)O(7), Tc(2)O(7), and Re(2)O(7)

The Raman and infrared spectra of gas phase Re(2)O(7) are reported. The experimental vibrational spectra of molecular Tc(2)O(7) and Re(2)O(7) are compared with calculated spectra. The results of these studies agree with a nonlinear M-O-M bridge for Tc(2)O(7) and Re(2)O(7). For infrared intensity calculations, the point charge approximation is used, while for the Raman calculations a combination of bond and atom polarizabilities is adopted. Pure Re(2)O(7) was prepared from rhenium wire, but attempts to prepare it from rhenium powder and oxygen always led to infrared spectra showing serious contamination from a species containing an -OH linkage. Detailed experiments identified this molecule as HReO(4), a unique transition metal analogue of the perhalic acids, and a partial infrared spectrum of this molecule is reported.     

Vibrational analysis of 2-[4-(<Emphasis Type="Italic"> N</Emphasis> -dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole

The infrared absorption spectra of 2-[4-( N -dodecanoylamino)phenyl]-5-(4-nitrophenyl)-1,3,4-oxadiazole (also denoted AF51) in solution and in the solid state as well as the solid-state Raman spectrum of the powdered compound are compared with the infrared linear dichroic (LD) spectra recorded at two orthogonal polarizations. The IR-LD spectra were measured in an anisotropic solvent-the nematic liquid crystal ZLI-1695 (Merck). The solvent spectrum taken under precisely the same experimental conditions and polarized radiation azimuths was subtracted from the polarized sample spectra in order to achieve pure oriented spectra of the compound studied. These spectra were further processed using a stepwise reduction procedure that allows for assignment of vibrational modes having mutually orthogonal dipole moments.     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

Enhanced raman spectra of molecules adsorbed on small metal particles

The Raman spectra of benzene adsorbed on small nickel and platinum particles have been measured. The spectra are strongly enhanced, compared with those wavelengths, where no enhancement has been observed. The spectra of benzene adsorbed on platinum and nickel particles are rather similar. The most intensive vibrational band is the totally symmetric breathing mode, which dominates the spectrum. Besides the Raman active vibrations, some other weak vibrational modes are observed, which may be assigned to normally infrared and inactive vibrational transitions. The enhanced Raman effect seems to be dependent on the particle size and shape. Therefore it is important to investigate the behaviour of small metallic particles. First results of pyridine bonded to Ag₂ and Ag₃ are reported.     

FT-IR, FT-Raman spectra and ab initio DFT vibrational analysis of p-bromophenoxyacetic acid

The Fourier transform Raman and Fourier transform infrared spectra of p-bromophenoxyacetic acid were recorded in the solid phase. The equilibrium geometry, harmonic vibrational frequencies, infrared intensities and Raman scattering activities were calculated by HF and DFT (B3LYP) method with the 6-31G(d,p) basis set. The scaled theoretical wavenumbers showed very good agreement with the experimental ones. A detailed interpretation of the infrared and Raman spectra of p-bromophenoxyacetic acid is reported on the basis of the calculated potential energy distribution. The theoretical spectrograms for the IR spectrum of the title molecule have been constructed.     

Assignment of rovibrational transitions of propyne in the region of 2934-2952 cm(-1) measured by two-color IR-vacuum ultraviolet laser photoion-photoelectron methods

The infrared (IR) spectrum of propyne in the region of 2934-2952 cm(-1) has been recorded by the IR-vacuum ultraviolet (VUV)-photoion method. The spectrum is shown to consist of two near-resonant, but noncoupled vibrational bands: the nu2 symmetric methyl C-H stretching vibrational band and a combination vibrational band nucs. The previously unobserved Q line of the nucs band is observed. The rotational transition lines of the nu2=1 band produces IR-VUV-pulsed field ionization-photoelectron (IR-VUV-PFI-PE) signal at the C3H4+ (nu2+=1) photoionization threshold. The rotational transition lines associated with the nucs band do not produce IR-VUV-PFI-PE signal. Rotational transition lines of both vibrational bands are assigned and simulated; and ab initio calculations further confirm the assignment.     

An investigation on a broad infrared band with the maximum at approximately 1300 cm(-1) in magnesia cement,phase 3

In magnesia cement, phase 3, a broad and strong infrared band was observed with the maximum at approximately 1300 and 1050 cm(-1) in the H and D systems, respectively. To clarify the origin of the 1300 cm(-1) band the temperature dependency of the infrared spectra of the H system was observed and the spectra analyzed on the basis of a strong vibrational coupling of the OH stretching with lattice modes. The fitting was quite well, giving rise to the origin of the 1300 cm(-1) band of the OH stretching.