Infrared Spectral Assignment of Pyrimidine and Pyrazine in the CH Stretching Region by an Effective Spectroscopic Hamiltonian

Mid-Infrared spectra of pyrimidine (PM) and pyrazine (PZ) were recorded in the gas phase using a multi-pass long path gas cell. The IR band structure of these compounds above and below 3000 cm⁻¹ is very broad and contains many humps and shoulders. These humps and shoulders are due to various higher quantum excitation of low-frequency vibrational modes, which participate in Fermi resonance with the nearby CH stretch fundamentals and appears in this region. We constructed an Effective Spectroscopic Hamiltonian (ESH) in a mixed local mode (LM) normal mode (NM) basis to assign the various overtone and combination bands in the CH stretching region of these compounds. The CH stretching vibrations of both PZ and PM were treated as symmetrized anharmonic Morse oscillators in local coordinates and the in-plane deformations down to 1000 cm⁻¹ were treated as normal coordinates. The ESHs were diagonalized and the resulting eigenvalues were subsequently fitted in a given parameter space with the experimentally observed bands. The eigenvalues of the converged Hamiltonian are the anharmonic frequencies and the transition intensities were obtained by summing the squared eigenvector components. The overtone and combination transitions near 3000 cm⁻¹ of both PM and PZ were identified and assigned from the eigenvector coefficients of the ESH matrix. The wavefunctions of a pure CH stretch, overtone of the HCC in-plane bend and due to Type 1 Fermi coupling (resonance between a fundamental with an overtones of a low frequency mode, in this case resonance between the CH strech and the overtone of HCC in-plane bending modes) has been demonstrated pictorially.     

Frequencies and absorption intensities of the fundamental and the first overtone of NH stretching vibrations of pyrroleacetylene and pyrroleethylene complexes studied by density-functional-theory calculation

The structures of pyrroleacetylene and pyrroleethylene complexes which form an NH–π hydrogen bonding were calculated by density-functional-theory calculation. The wavenumbers and absorption intensities of the fundamental and the first overtone of NH stretching of the complexes were investigated to compare effects of the hydrogen bonding on the fundamental and the first overtone of the NH stretching mode. One-dimensional Schrödinger equation in consideration of molecular vibrational anharmonicity was used for the estimation of the wavenumbers and absorption intensities of NH stretching modes of the complexes; it was found that the NH–π hydrogen-bond formation induced lower wavenumber shift for both the fundamentals and first-overtones of NH stretching mode and it increases absorption intensities of the fundamentals and decreases those of first overtones of NH stretching mode.     

Structural properties of montmorillonite intercalated with tetraalkylammonium cations—Computational and experimental study

Several tetraalkylammonium (TAA) cations intercalated in layered clay mineral montmorillonite were studied by a combination of theoretical approach based on density functional theory (DFT) and infrared spectroscopy. DFT calculations revealed positions of TAA cations in the interlayer space and a dependence of d₀₀₁ parameter on the cation size. A finite difference method and molecular dynamic simulations were used to analyze and interpret vibrational modes observed in the experimental spectra with a specific focus on the CH₃ and CH₂ stretching modes. MD simulations on the tetraethylammonium-montmorillonite (TEA-M) model showed a high sensitivity of the position of the stretching vibrations of the CH₃ and CH₂ groups on the d₀₀₁ value. MD calculations also helped to distinguish vibrations of the parallel and perpendicular CH₃ groups of the tetramethylammonium-montmorillonite (TMA-M) which was not possible from the experimental infrared spectra because of many overlapping broad bands.     

The Raman spectra of serine and 3,3-dideutero-serine in aqueous solution

The Raman spectra of serine [α-amino-β-hydroxypropionic acid; HOCH₂CH(NH₃)⁺COO⁻] and 3,3-dideutero-serine [HOCD₂CH(NH₃)⁺COO⁻] in aqueous solution were studied in the range 4000–300 cm⁻¹. The data obtained for the deuterated compound are novel and provide compelling evidence that previously reported assignments for the undeuterated amino acid should be revised.     

Continous gradient temperature Raman Spectroscopy identifies flexible sites in proline and alanine peptides

Continuous gradient temperature Raman spectroscopy (GTRS) applies the temperature gradients utilized in differential scanning calorimetry (DSC) to Raman spectroscopy, providing a straightforward technique to identify molecular rearrangements that occur near phase transitions. Herein we apply GTRS and DSC to the solid dipeptides Ala-Pro, Pro-Ala, and the mixture Ala-Pro/Pro-Ala 2:1. A simple change in residue order resulted in dramatic changes in thermal stability and properties. Characteristic Pro vibrations were observed at ∼75 °C higher temperature in Pro-Ala than Ala-Pro. The appearance/disappearance of characteristic vibrational modes with increasing temperature showed that a double peak in the Ala-Pro major phase transition (174–184 °C) was due to a gauche to anti 165° rotation of H₃CC*NH₃ about C*. CH₂ rocking and wagging frequencies present in Pro-Ala were not observed in Ala-Pro. For Ala-Pro, the Ala ⁺NH_3, and Pro COO⁻ sites were flexible whereas the Pro ring moiety was not; since the OCN (C)₂ amide bond is planar the CNC moiety keeps the Pro ring rigid. For Pro-Ala, CH₂ sites in the Pro ring were flexible and the OCNH amide bond is perpendicular to the Pro ring. Since the mass of the Pro ring is significantly larger than the mass of the flexible Ala ⁺NH₃ moiety, Pro-Ala absorbs more thermal energy, corresponding to a higher phase transition temperature (240–260 °C). Ala-Pro, Pro-Ala, and Ala-Pro/Pro-Ala 2:1 exhibited α-helix, β-sheet, α-helix secondary structure conformations, respectively.     

Fourier transformed infrared spectral investigations of molecular interactions in propionic acid–2-propanol binary system

FTIR spectra of propionic acid (PA), 2-propanol (PROH) and its binary mixtures with varying molefraction of the PA were recorded in the region 500–3500 cm^?1, to investigate the formation of hydrogen bonded complexes in a mixed system. The observed features in ν(CO), ν(CO) and δ(COH) of PA, ν(CO) of PROH and δ(COH) of PA + PROH have been explained in terms of the hydrogen bonding interactions between PROH and PA and dipole–dipole interaction. The dipole moment derivative for the above mentioned vibrational modes have also been predicted from the integrated absorbance. The intrinsic linewidth for the vibrational modes ν(CO) and δ(COH) of PA has been elucidated using Bondarev and Mardaeva model.     

Theoretical calculations of the substituent effect on molecular properties of the RCN⋯HF hydrogen-bonded complexes with R = NH2, CH3O,CH3, OH,SH, H,Cl, F,CF3, CN and NO2

DFT calculations with B3LYP and PBE1PBE functionals and 6–311++G(d,p) basis set have been performed in order to obtain molecular geometries, binding energies and vibrational properties of the RCN?HF H-bonded complexes with R = NH₂, CH₃O, CH₃, OH, SH, H, Cl, F, CF₃, CN and NO₂. As expected, it has been verified as a red-shift of the HF stretching frequency (ν_HF), in conformity with the elongation of the bond after complexation. On the other hand, the CN stretching frequency (ν_CN) is blue-shifted and corresponds to a shortening of the bond. The binding energies (ΔE_c), including BSSE and ZPVE corrections, show a linear correlation with several structural, electronic and vibrational properties. In particular, an important linear dependence between the binding energy and the calculated dipole moment of the free RCN molecule (μ_RCN) has been found. This result suggests that μ_RCN can be a useful quantity in order to predict the ability of this fragment to form a hydrogen-bond. The IR intensities of stretching and bending modes of complexed HF acid fragment are adequately interpreted through the atomic polar tensor of the hydrogen atom in HF using the modified CCFO model for infrared intensities. The new vibrational modes arising from complexation show several interesting features.     

Vibrational spectroscopy and DFT calculations of 1,3-dibromo-2,4,6-trimethylbenzene: Anharmonicity,coupling and methyl group tunneling

The Raman, IR and INS spectra of 1,3-dibromo-2,4,6-trimethylbenzene (DBMH) were recorded in the 80–3200 cm⁻¹ range. The molecular conformation and vibrational spectra of DBMH were computed at the MPW1PW91/LANL2DZ level. Except for the methyl 2 environment, the agreement between the DFT calculations and the neutron diffraction structure is almost perfect (deviations < 0.01 Å for bond lengths, <0.2° for angles). The frequencies of the internal modes of vibration were calculated with the harmonic and anharmonic approximations; the later method yields results that are in remarkable agreement with the spectroscopic data, resulting in a confident assignment of the vibrational bands. Thus, no scaling is necessary. The coupling, in phase or anti-phase, of the motions of symmetrical CBr and CMe bonds is highlighted. Our DFT calculations suggest that the torsion of methyl groups 4 and 6 is hindered in deep wells, whereas methyl group 2 is a quasi-free rotor. The failure of the calculations to determine the frequencies of the methyl torsional modes is explained as follows: DFT does not consider the methyl spins and assumes localization of the protons, whereas the methyl groups must be treated as quantum rotors.     

CH⋯Ni interactions and cyano-bridged heteronuclear polymeric complexes studied by vibrational spectroscopy and quantum chemistry calculations

Three 1D bimetallic M(II)/Ni(II) (M = Cu, Zn and Cd) complexes, [Cu(OHepy)₂Ni(CN)₄]_n (1), [Zn(OHepy)₂Ni(CN)₄]_n (2) and [Cd(OHepy)₂Ni(CN)₄]_n (3) (2-(2-hydroxyethyl)pyridine abbreviated to OHepy), have been synthesized and characterized by FT-IR and Raman spectroscopy, elemental, thermal analyses and single crystal X-ray diffraction techniques. FT-IR and Raman spectra of OHepy have been experimentally and theoretically investigated in the region of 4000–250 cm⁻¹. The corresponding vibrational assignments of OHepy are examined by means of B3LYP hybrid density functional theory (DFT) method together with 6-311++G(d, p) basis set. Moreover, reliable vibrational assignments have been made on the basis of potential energy distribution (PED). The structures of the complexes consist of one-dimensional polymeric chain M(OHepy)₂NCNi(CN)₂CNM(OHepy)²⁻, in which the M(II) and Ni(II) atoms are linked by CN groups. The nickel atom is fourfold coordinated with four cyanide-carbon atoms in a square planar arrangement and the metal(II) atoms are sixfold coordinated with two cyanide nitrogen, two OHepy nitrogen and two OHepy oxygen atoms, in a distorted octahedral arrangement. In all the complexes adjacent chains are connected by π⋯π, CH⋯Ni and OH⋯N hydrogen bonding interactions to form two and three dimensional networks.     

A theoretical study on the alkene insertion step in Rh-Yanphos catalyzed hydroformylation

This paper studied the mechanism of the alkene insertion elementary step in the asymmetric hydroformylation （AHF） catalyzed by RhH（CO）2[（R,S）-Yanphos] using four alkene substrates （CH2=CH- Ph, CH2=CH-Ph-（p）-Me, CH2=CH-C（==O）OCH3 and CH2=CH-OC（=O）-Ph, abbreviated as A1-A4）. Interestingly, the equatorial vertical coordination mode （A mode） with respect to the Rh center was found for AI and A2 but not for A3 and A4, although the equatorial in-plane coordination mode （E mode） was found for A1 -A4. The relative energy of the E mode of the -q2-intermediates is lower than that of the A mode. In the alkene insertion step, Path 1 is more favorable than Path 2 for this system. As for AI and A2, there could be a transformation between 2eq and 2ax.     

DFT study of the IR and Raman spectra of a fluorescent dendron built from cyclotriphosphazene core

Combined experimental and theoretical studies on molecular structure of the zero generation dendron, built from the hexafunctional cyclotriphosphazene core, with five OC₆H₄(CH₂)₂NHSO₂C₁₀H₆N(CH₃)₂ terminal groups and one oxybenzaldehyde group G₀ are reported. The Fourier transform Raman and IR spectra of G₀ have been recorded. Conformations of low energy isomers of G₀ have been studied at quantum-chemical level. The optimized geometry has been calculated by density functional (DFT) method at the PBE/TZ2P level of theory. The theoretical geometrical parameters, harmonic vibrational frequencies, IR intensities and Raman scattering activities are predicted in a good agreement with the experimental data. It was found that dendron molecule G₀ has a concave lens structure with planar OC₆H₄CHO fragments and slightly non-planar cyclotriphosphazene core. Relying on DFT calculations the bands of the core and terminal groups were assigned. The frequencies of ν(NH) bands in the IR spectrum reveal the presence of the H-bonds in the dendron.     

Raman bandshape analysis and DFT study of CO and CH stretching modes of NN-Dibutyl formamide in DMSO solvent`

The study reports the inter-molecular interactions and dynamics of CO and CH stretching modes of NN- Dibutyl Formamide (DBF) in DMSO solvent using Raman spectroscopic technique. The Raman band of CO and CH stretching modes have been deconvoluted into two distinct bands for neat as well as in DMSO solvent. Peak wavenumbers of CO stretching modes show red shift while CH stretching modes shows blue shift with the increase in solvent concentrations. The optimized geometric parameters, vibrational wavenumbers, Mulliken atomic charges and natural bond orbitals of the molecule has been computed using Density Functional Theory (DFT) method with basis set 6-31 +G (d, p). In addition, the same basis set has been carried out with counterpoise keyword accounting BSSE calculation on monomer and dimer states with DMSO solvent to present an appropriate interacting environment. IEF-PCM solvation model has also been computed using the same basis set and compares the geometrical parameters and vibrational wavenumbers of the molecules and in their complexes. In order to get a complete study of the DBF + DMSO complexes, explicit solvation model has also been calculated for Monomer DBF in two solvent molecules. Theoretical calculations of frequencies have been compared with the experimental findings and the results are found in good agreement.     

Thermal effect on microstructure vibration of SiO2 thin films

The microstructure of amorphous SiO₂ thin film is a random network structure in which a large amount of [SiO₄] is interconnected with a specific SiOSi bond angle. The SiO₂ thin films used in this paper were prepared by ion beam sputtering and electron beam evaporation deposition techniques. Two-dimensional correlation spectroscopy analysis techniques were used in this study. By measuring the infrared temperature spectrum, we obtained the two-dimensional correlation synchronous spectrum and asynchronous spectrum, and decomposed the in-phase and out-phase asymmetric stretching vibration characteristics of SiOSi. As the temperature increases, the spectral transmittance of the vibrating peak decreases, and the relative change of in-phase asymmetric stretching vibration absorption peak is higher than that of the out-phase asymmetric stretching vibration absorption peak.     

Comparative DFT study of Raman spectra of phosphorus-containing dendrimers built from thiophosphoryl,cyclotriphosphazene and phthalocyanine cores

The FT Raman spectra of the zero and first generations of phosphorus-containing dendrimers built from thiophosphoryl, cyclotriphosphazene and phthalocyanine core with terminal oxybenzaldehyde groups have been recorded and analyzed. The structural optimization and normal mode analysis were performed for dendrimers on the basis of the density functional theory (DFT). The calculated geometrical parameters, harmonic vibrational frequencies and Raman scattering activities are predicted in a good agreement with the experimental data. The experimental Raman spectra of dendrimers were interpreted by means of potential energy distribution. Relying on DFT calculations the lines of the cores, repeating units and terminal groups of dendrimers were assigned.The influence of the encirclement on the line frequencies and intensities was studied and due to the predictable, controlled and reproducible structure of dendrimers the information, usually inaccessible is obtained. The strong line at 1600 cm⁻¹ show marked changes of intensity in dependence of aldehyde (CHO) or azomethyne (CHN) substituents in the aromatic ring. The polarizabilities and lipophilicity of dendrimers were estimated.     

Polymer brushes on hydrogen-terminated silicon substrates via stable Si—C bond

A universal and straightforward method for the preparation of polymer brushes via the formation of Si-C bond on silicon substrates through the UV-induced photopolymerization is demonstrated.     

Vibrational spectra of fluorene, 1-methylfluorene and 1,8-dimethylfluorene

In this paper, we report the gas phase infrared spectra of fluorene and its methylated derivatives using a heated multipass cell and argon as a carrier gas. The observed spectra in the 4000–400 cm⁻¹ range have been fitted using the modified scaled quantum mechanical force field (SQMFF) calculation with the 6-311G** basis. The advantage of using the modified SQMFF method is that it scales the force constants to find the best fit to the observed spectral lines by minimizing the fitting error. In this way we are able to assign all the observed fundamental bands in the spectra. With consecutive methyl substitutions two sets of bands are found to shift in a systematic way. The set of four aromatic CH stretching vibrations around 3000 cm⁻¹ shifts toward lower frequencies while the single most intense aromatic CH out-of-plane bending mode around 750 cm⁻¹ shifts toward higher frequencies. The reason for shifting of aromatic CH stretching frequency toward lower wave numbers with gradual methyl substitution has been attributed to the lengthening of the CH bonds due to the +I effect of the methyl groups to the ring current as revealed from the calculations. While the unexpected shifting of the aromatic CH out-of-plane bend toward higher wave numbers with increasing methyl substitution is ascribed to the lowering of the number of adjacent aromatic CH bonds on the plane of the benzene ring with gradual methyl substitutions.     

DFT study of Raman spectra of phosphorus-containing dendrimers built from thiophosphoryl core

The FT-Raman spectra of the first and second generations of phosphorus-containing dendrimers with terminal benzaldehyde and P–Cl groups have been recorded and analyzed. The structural optimization and normal mode analysis were performed for dendrimers on the basis of the density functional theory (DFT). The calculated geometrical parameters, harmonic vibrational frequencies and Raman scattering activities are predicted in a good agreement with the experimental data. The experimental Raman spectra of dendrimers were interpreted by means of potential energy distribution. Relying on DFT calculations the lines of the core, repeating units and terminal groups of dendrimers were assigned.The influence of the encirclement on the line frequencies and intensities was studied and due to the predictable, controlled and reproducible structure of dendrimers the information, usually inaccessible is obtained. The strong line at 1600 cm⁻¹ show marked changes of intensity in dependence of aldehyde (CHO) or azomethyne (CHN) substituents in the aromatic ring. The polarizabilities and lipophilicity of the eleven generations of dendrimers were estimated based on the calculated values of the first generations.     

Vibrational spectroscopy of a crystallographically unsettled uranyl carbonate: Structural impact and model

Room-temperature vibrational and photoluminescence (PL) spectra of a natural, rare hydrated calcium copper uranyl carbonate mineral, voglite (Ca₂Cu(UO₂)(CO₃)₄·6H₂O) are recorded and discussed in details. Vibrational spectroscopy gives information about the structure of voglite, which is still missing due to its unknown crystallographic features. By comparison with other uranyl carbonates and sulfates, a strong Raman line occurring at 834 cm⁻¹ is assigned to the ν₁(UO₂)²⁺ symmetric stretching vibration rather than to the ν₂(CO₃)²⁻ out-of-plane bending vibration. The ν₃(UO₂)²⁺ antisymmetric stretching vibration is tentatively identified at 897 cm⁻¹ from infrared (IR) spectroscopy. Several well resolved bands found at 1074,1092, 1381, 1566 cm⁻¹ in the Raman and 1046, 1114, 1145, 1376, 1426, 1510, 1561 cm⁻¹ in the IR are ascribed to symmetric and antisymmetric stretching motions of the carbonate units. The presence of all these intense vibrational bands points to different CO bond lengths. The infrared water band is well structured, suggesting a few different OH moieties in the crystal. Original micro-PL spectra show a manifold of vibronic features whose energy spacing is close to the frequency of the symmetric OUO stretching vibration and confirms the uranium origin of the most intense Raman band. The study suggests that voglite structure has no inversion centers, a low symmetry, and contains molecular units similar to those of the parent phases, andersonite or liebigite, like uranyl tricarbonate clusters (UTC). The existence of these UTCs in voglite is confirmed by density functional theory calculations. A new assignment of all vibrational modes is proposed.     

Oxidation and reduction of nanodiamond particles in colloidal solutions by laser irradiation or radio-frequency plasma treatment

Functionalized nanodiamond particles (NDs) represent carbon nanomaterial with unique properties for various applications. Here we report on a new approach to surface modification of NDs by their exposure to radio frequency (RF) plasma or laser irradiation (LI) plasma directly in aqueous solution. By using grazing angle reflectance Fourier transform infrared spectroscopy and supporting analysis by X-ray photoelectron spectroscopy, zeta-potential, and Kelvin force microscopy we show that surface chemistry of NDs produced by detonation process (DNDs) or high-pressure high-temperature process (HPHT NDs) works in different way. Moieties on as-received NDs are dominated by COOH and COC groups due to wet chemical cleaning procedures. On DNDs, both RF and LA treatment lead to removal of sp² shell and additional oxidation of the surface to C OC groups. On HPHT NDs the RF treatment leads to reduction of COC groups that are transformed into COH and CH moieties. Thus at least partial hydrogenation of colloidal HPHT NDs seems feasible.     

Structural studies of methyl brevifolincarboxylate in solid state by means of NMR spectroscopy and DFT calculations

Methyl brevifolincarboxylate isolated from the herb of Potentilla argentea L. (Rosaceae) is a representative of the naturally occurring polyphenols. The compound is of pharmaceutical interest mainly because of its antiviral and antioxidant properties. ¹³C NMR spectra were recorded for solution and solid phase. ¹³C CPMAS spectra were assigned by comparison with solution data, dipolar dephasing and short contact time experiments. The correctness of assignments was verified by GIAO DFT calculations of shielding constants. The differences between the solution and solid state chemical shift values were explained in terms of orientation of OH groups and intramolecular hydrogen bonds. The splitting of the C1O resonance shows that there exists a polymorphism in the solid phase, which might be due to the formation of intramolecular hydrogen bond involving carbonyl or methoxy oxygen (i.e. C10OH⋯OC or C10OH⋯OCH₃).