p-π共轭分子的氨基面外弯曲振动模的拉曼光谱

拉曼光谱是一种用途广泛的无损分子检测技术,其能够提供化学物质的分子结构指纹信息.一种面外弯曲振动模被称作wagging振动,它的信号尤为特殊,其频率和强度都非常依赖于检测环境.以乙烯胺和苯胺为例,采用密度泛函理论计算研究了p-π共轭分子分别与水簇和银簇作用的平衡结构、成键作用和拉曼光谱.结果表明,弱相互作用,如分子与金属表面的弱吸附作用以及分子与水之间的氢键作用,均使氨基面外弯曲振动模(ωNH2)的拉曼信号发生显著的变化.考虑溶剂化效应后,氢键作用减弱,计算拉曼光谱趋于一致.通过进一步对电子结构的分析,解释了面外弯曲振动信号显著增强的原因,揭示了面外弯曲振动模与分子p-π共轭作用之间的关系.     

Density functional theory calculations of pressure effects on the vibrational structure of alpha-RDX

Pressure effects on the vibrational structure of alpha-RDX were examined using density functional theory (DFT) up to 4 GPa. The calculated vibrational frequencies at ambient conditions are in better agreement with experimental data than are previous single molecule calculations. The calculations showed the following pressure-induced changes: (i) larger shifts for lattice modes and for internal modes associated with the CH(2) and NO(2) groups as compared to the pressure shifts for modes associated with the triazine ring, (ii) enhancement of mixing between different vibrations, for example, between NN stretching and CH(2) scissor, wagging, twisting vibrations, and (iii) increase in mixing between translational lattice vibrations and the NO(2) wagging vibrations, reducing the distinction between internal and lattice modes. The calculated volume and lattice constants at ambient pressure are larger than the experimental values, due to the inability of the present density functional approach to correctly account for van der Waals forces. Consequently, the pressure-induced frequency shifts of many modes deviate substantially from experimental data for pressures below 1 GPa. With increasing pressure, both the lattice constants and the frequency shifts agree more closely with experimental values.     

Structural and vibrational theoretical analysis of protonated formaldehyde in its $$\tilde{X}^{1} A^{\prime}$$ ground electronic state

A structural and vibrational study of protonated formaldehyde (H₂COH⁺) in its ground electronic state, at the CCSD/cc-pVTZ theory level, is presented. The variation of the molecular structure with the torsion angle shows clear dependence of the H₂C wagging and COH angles. Anharmonic one- and two-dimensional vibrational models for two out-of-plane vibrational modes (H₂C torsion, and H₂C wagging) are constructed. Since H₂COH⁺ is classified under a G₄ non-rigid group, the vibrational Hamiltonians are factorized using the symmetry of the G₄ group and solved variationally. The one-dimensional results for torsion and wagging yield fundamental frequencies are 844.12 and 1,252.89 cm⁻¹, respectively. A two-dimensional COH angle + torsion model gives a torsion frequency of 762.32 cm⁻¹. Finally, a wagging + torsion model predicts frequencies of 931.93 and 1,255.82 cm⁻¹ for torsion and wagging, respectively. The variation of frequency values for torsion suggests an important coupling between this mode and the bending and wagging vibration modes.     

Study of disorder in different phases of tetratriacontane and a binary alkane mixture, using vibrational spectroscopy

Raman spectroscopy has been used to investigate the monoclinic crystal --> rotator --> melt phase transitions in n-C(34)H(70), for both real-time heating and cooling runs. Changes in band intensity and frequency in the CH2 bending, CH2 twisting, skeletal C-C stretching, and CH3 rocking regions revealed both transitions, particularly when using band components related to gauche bonds. In the room temperature infrared spectrum, the CH2 rocking-twisting and CH2 wagging progressions were observed and indexed for n-C(34)H(70) and a 2:1 (w/w) mixture of C(34)H(70) and C(36)D(74). This led to best estimates for the all-trans crystal core in both cases of 33 to 34 carbon atoms, indicating that the core corresponds to almost the whole of the C(34)H(70) molecule.     

Theory supplemented by experiment. Electronic effects on the rotational stability of the amide group in p-substituted acetanilides

The electronic effect of polar substituents on the barrier of internal rotation around the amide carbon-nitrogen bond in a series of 10 p-substituted acetanilides is studied by applying density functional theory at the B3LYP/6-31G(d,p) level. The theoretical results are supplemented by experimental data on the amide C=O and N-H stretching mode frequency shifts. It is shown that computations at the theoretical level employed provide a valuable approach in studying the factors determining the conformational stability of the studied series of compounds. It is found that an excellent linear dependence between the barriers of rotation and frequency shifts exists. It is concluded that the variations of the amide C=O stretching mode frequency can be used for quantitative characterization of the amide group conformational flexibility in the studied series of acetanilides.     

Infrared and Raman matrix isolation studies of methylamine

Infrared (4000-50 cm^?1) and Raman spectra are reported of methylamine, methylamine-d₁ and methylamine-d₂ trapped in argon and nitrogen matrices at 4–20 K. An anomalous intensity variation was found for the NH₂ wagging mode of methylamine isolated in nitrogen matrices, while in argon matrices the NH₂ wagging absorption exhibited a complex structure due to matrix site effects. A normal coordinate analysis was carried out using a new assignment of the NHD twisting frequency. Barriers to internal rotation in argon and nitrogen matrices, calculated from the observed torsional frequencies, are compared with the gas phase value.     

Carbon-13 and proton magnetic resonance studies of some carbonyl-bis-(amino acid esters)

A number of carbonyl-bis-(amino acid esters) have been examined by proton and carbon-13 nuclear magnetic resonance techniques. All but one of the compounds were synthesized with two chiral centers of like-configuration. In one series, the diastereotopic nonequivalence of isopropyl methyl groups attached to the asymmetric centers is apparent in both the proton and the carbon spectra, and the relative magnitude of the observed nonequivalence increases slightly with increasing ‘bulk’ of the neighboring ester groups. Carbon-13 chemical shifts are reported, and a linear correlation of Taft σ* inductive constants with ester carbonyl carbon chemical shifts and with amide proton chemical shifts (for a series in which only variation of the ester substituent occurs) is presented. In addition, the effect in terms of chemical shift differences of keeping the same ester group at the asymmetric centers while varying the other substituent group, is examined.     

Photon-driven charge transfer and Herzberg-Teller vibronic coupling mechanism in surface-enhanced Raman scattering of p-aminothiophenol adsorbed on coinage metal surfaces: a density functional theory study

The chemical enhancement effects in surface-enhanced Raman scattering of p-aminothiophenol (PATP, it is also called p-mercaptoaniline or p-aminobenzenthiol) adsorbed on coinage metal surfaces with single thiol end or trapped into metal-molecule-metal junctions with both thiol and amino groups have been studied by density functional theory (DFT). We focus on the influence of photon-driven charge transfer (PDCT) and chemical bonding interaction (ground-state charge transfer) on the intensity enhancement and frequency shift in the surface Raman spectra of PATP. For comparison, the electronic structures and transitions of free PATP are studied first. The simulated pre-resonance UV Raman spectra illustrate that b(2) modes can be selectively enhanced via vibronic coupling. The fundamentals of all the b(2) modes in the frequency range of 1000 to 1650 cm(-1) are assigned in detail. For PATP adsorbed on coinage metals, the time-dependent-DFT calculations indicate that the low-lying CT excited state arises from the π bonding orbital of molecule to the antibonding s orbital of metallic clusters. Our results further show that the PDCT resonance-like Raman scattering mechanism enhances the totally symmetric vibrational modes and the NH(2) wagging vibration. Finally, the effect of chemical bonding interaction is also investigated. The amino group binding to metals gives a characteristic band of the NH(2) wagging mode with the large blueshift frequency and an intense Raman signal.     

Soft mode and related behaviour in the SmA and SmC* phases of a ferroelectric liquid crystalline polymer by dielectric spectroscopy

Anomalous dielectric relaxation behaviour is observed in the ferroelectric liquid crystalline polymer (viz. ferroelectric copolysiloxane (R)-COPS 11-10) around the ferroelectric SmC* to paraelectric SmA phase transition. Measurements have been performed on sample of thickness ~10 mum in indium-tin-oxide coated cell in the frequency range 10 Hz to 13 MHz. With increase of temperature, a gradual shift of the soft mode frequency towards the higher frequency side was observed, while a decrease in the relaxation strength was seen with the corresponding increase in temperature. The shifts of the soft modes in the SmC* and SmA phase are considered to be due to change in the viscosity of the polymer, as an increase in viscosity increases fluctuations of the coupling between the dipoles in the network even far from the paraelectric-ferroelectric phase transition. Application of a bias field causes a shift of the critical frequency towards the higher frequency side, while the dielectric strength ( Δε) decreases under the bias field. The Cole-Cole fitting parameters obtained from the best fit of the dielectric constant data are found to be consistent with other similar materials. Another relaxation mode (molecular mode) was also observed which comes into play in both the smectic phases (SmC* and SmA) and contributes to the dielectric permittivity.     

Soft mode and related behaviour in the SmA and SmC* phases of a ferroelectric liquid crystalline polymer by dielectric spectroscopy

Anomalous dielectric relaxation behaviour is observed in the ferroelectric liquid crystalline polymer (viz. ferroelectric copolysiloxane (R)-COPS 11-10) around the ferroelectric SmC* to paraelectric SmA phase transition. Measurements have been performed on sample of thickness ～10 μm in indium-tin-oxide coated cell in the frequency range 10 Hz to 13 MHz. With increase of temperature, a gradual shift of the soft mode frequency towards the higher frequency side was observed, while a decrease in the relaxation strength was seen with the corresponding increase in temperature. The shifts of the soft modes in the SmC* and SmA phase are considered to be due to change in the viscosity of the polymer, as an increase in viscosity increases fluctuations of the coupling between the dipoles in the network even far from the paraelectric-ferroelectric phase transition. Application of a bias field causes a shift of the critical frequency towards the higher frequency side, while the dielectric strength (δε) decreases under the bias field. The Cole-Cole fitting parameters obtained from the best fit of the dielectric constant data are found to be consistent with other similar materials. Another relaxation mode (molecular mode) was also observed which comes into play in both the smectic phases (SmC% and SmA) and contributes to the dielectric permittivity.     

Molecular structure, vibrational spectra and photochemistry of 2-methyl-2H-tetrazol-5-amine in solid argon

In this work, the molecular structure, infrared spectrum and UV photochemistry of 2-methyl-2H-tetrazol-5-amine (2MTA) isolated in solid argon (10 K) were investigated. The experimental studies were supported by extensive DFT(B3LYP)/6-311++G(d,p) calculations. The infrared spectrum of matrix-isolated 2MTA was fully assigned and correlated with structural properties. Taking into consideration the observed frequency of the NH2 wagging mode, it is suggested that, in the matrixes, the amine group becomes slightly more planar than in the gas phase, due to matrix-packing effects. In situ UV irradiation (lambda > 235 nm) of the matrix-isolated 2MTA monomer is shown to induce three main primary photochemical processes: (1) tautomerization to mesoionic 3-methyl-1H-tetrazol-3-ium-5-aminide; (2) nitrogen elimination, with production of 1-methyl-1H-diazirene-3-amine; (3) ring cleavage leading to production of methyl azide and cyanamide. Following the primary photoproducts, secondary reactions were observed, leading to spectroscopic observation of methylenimine and isocyanidric acid.     

Interaction of the phospholipid head group with representative quartz and aluminosilicate structures: an ab initio study

Silica dust particles in the form of quartz (but not kaolin) have been hypothesized to promote pulmonary diseases such as silicosis. The hypothesis is that quartz and kaolin have a comparable membranolytic potential on a specific surface area basis, and they have a comparable cytotoxic potential for lavaged pulmonary macrophages. Suppression of the cytotoxic activity occurs when these dust particles are treated with dipalmitoylphosphatidylcholine (DPPC), a common phospholipid component of the lung pulmonary surfactant. However, the enzyme phospholipase A2 is known to digest the phospholipid component more readily in the presence of quartz than kaolin. Since surface silanol (Si-OH) and aluminol (Al-OH) groups may interact differently with the phospholipid, an understanding of the selective removal of phospholipid by PLA2 may explain in vivo differences in cytotoxicity between quartz and kaolin. To develop some insight into this phenomenon, the interaction between a phospholipid and silica particles was examined by performing ab initio DFT calculations on clusters constructed with small (one or two silica tetrahedral units) representative parts of the silicate surface and the phospholipid head group. The clusters consisted of a phospholipid head group or functional groups from the head group complexed with Si(OSiH 3) 3OH, Al(OSiH 3) 3OH (-) or Al(OSiH 3) 3OH 2. Fully optimized geometries of the complexes were used to determine binding energies, -OH vibrational frequency shifts, and NMR chemical shieldings. Results indicate that interaction of the protonated aluminol group (Al-OH 2 (+)) with the phosphate portion of the head group is strongest, while interaction of the -OH 2 (+) group with the trimethyl-choline moiety of the head group is weakest. The presence of the choline moiety increased the magnitude of the -OH vibrational frequency shifts, and the shifts were significantly larger in complexes with protonated aluminol groups relative to silanol complexes. Analysis of ChelpG atomic charges shows that a net transfer of charge occurs from the silica unit to the head group within the complexes.     

1H chemical shifts in NMR. Part 21--prediction of the 1H chemical shifts of molecules containing the ester group: a modelling and ab initio investigation

The 1H NMR spectra of 24 compounds containing the ester group are given and assigned. These data were used to investigate the effect of the ester group on the 1H chemical shifts in these molecules. These effects were analysed using the CHARGE model, which incorporates the electric field, magnetic anisotropy and steric effects of the functional group for long-range protons together with functions for the calculation of the two- and three-bond effects. The effect of the ester electric field was given by considering the partial atomic charges on the three atoms of the ester group. The anisotropy of the carbonyl group was reproduced with an asymmetric magnetic anisotropy acting at the midpoint of the carbonyl bond with values of Deltachi(parl) and Deltachi(perp) of 10.1 x 10(-30) and -17.1 x 10(-30) cm3 molecule(-1). An aromatic ring current (=0.3 times the benzene ring current) was found to be necessary for pyrone but none for maleic anhydride. This result was confirmed by GIAO calculations. The observed 1H chemical shifts in the above compounds were compared with those calculated by CHARGE and the ab initio GIAO method (B3LYP/6-31G**). For the 24 compounds investigated with 150 1H chemical shifts spanning a range of ca 10 ppm, the CHARGE model gave an excellent r.m.s. error (obs - calc) of <0.1 ppm. The GIAO calculations gave a very reasonable r.m.s. error of ca 0.2 ppm although larger deviations of ca 0.5 ppm were observed for protons near to the electronegative atoms. The accurate predictions of the 1H chemical shifts given by the CHARGE model were used in the conformational analysis of the vinyl esters methyl acrylate and methyl crotonate. An illustration of the use of the CHARGE model in the prediction of the 1H spectrum of a complex organic molecule (benzochromen-6-one) is also given.     

A resonance Raman study of octopus bathorhodopsin with deuterium labeled retinal chromophores.

The resonance Raman spectrum of octopus bathorhodopsin in the fingerprint region and in the ethylenic-Schiff base region have been obtained at 80 K using the "pump-probe" technique as have its deuterated chromophore analogues at the C7D; C8D; C8,C7D2; C10D; C11D; C11, C12D2; C14D; C15D; C14, C15D2; and N16D positions. While these data are not sufficient to make definitive band assignments, many tentative assignments can be made. Because of the close spectral similarity between the octopus bathorhodopsin spectrum and that of bovine bathorhodopsin, we conclude that the essential configuration of octopus bathorhodopsin's chromophore is all-trans like. The data suggest that the Schiff base, C = N, configuration is trans (anti). The observed conformationally sensitive fingerprint bands show pronounced isotope shifts upon chromophore deuteration. The size of the shifts differ, in certain cases, from those found for bovine bathorhodopsin. Thus, the internal mode composition of the fingerprint bands differs somewhat from bovine bathorhodopsin, suggesting a somewhat different in situ chromophore conformation. An analysis of the NH bend frequency, the Schiff base C = N stretch frequency, and its shift upon Schiff base deuteration suggests that the hydrogen bonding between the protonated Schiff base with its protein binding pocket is weaker in octopus bathorhodopsin than in bovine bathorhodopsin but stronger than that found in bacteriorhodopsin's bR568 pigment.     

Frequency shifts due to the interference of resolved peaks in magnitude-mode Fourier-transform ion cyclotron resonance mass spectra

We have obtained relationships for frequency shifts resulting from the interference of spectral components for the magnitude mode Fourier transform. The approximation of a weak perturbation of well resolved peaks has been used. Both the low- and high-pressure limits for Fourier-transform ion cyclotron resonance (FTICR) operation have been considered. We have found that the shifts can be either negative or positive, depending on the initial phase and/or the choice of the time-domain interval. The magnitude of shifts generally does not exceed the peak width. In the approximation of small perturbations the shifts produced by multiple peaks are additive. We have compared theoretical results with experimental shifts for isotopic clusters of multiply charged insulin. Up to 1 ppm frequency variations were experimentally observed for the insulin 5+ charge state, consistent with theoretical estimates. The peak interference is of particular significance in the case of bio-molecular mass spectra having a large number of peaks and covering a considerable dynamic range (i.e., relative abundance). We conclude that the common mass measurement procedure based on the location of the magnitude mode maxima of well resolved peaks can result in systematic mass measurement errors. The relationships obtained provide corrections for the frequency shifts and thus improve the mass measurement accuracy.     

Quantum chemistry predicted correlations between geometric isomerism (conformation) of -OH and =NH substituents and typical group frequencies of nucleic acid bases: cytosine

Results of a search for correlations between typical group mode frequencies and conformation of -OH and =NH substituents is reported. The study is based on quantum chemical data (HF/6-31G (d, p) and MP2 (full)/6-31G (d, p) approximations) of 13 isomers of cytosine. It is closely related to investigations of stability and energetics of all isomers of the more common nucleic acid bases, which revealed correlations between conformation (geometric isomerism) of OH and =NH substituents on the one hand and conversion energies, relaxation of internal structural parameters, electric field gradients, etc. on the other hand. In the majority of cases alteration of conformation of these substituents is accompanied by systematic frequency shifts of stretching, in-plane and out-of-plane bending (torsional) modes conventionally assigned to such groups and by alteration of quantum chemically predicted estimates of harmonic valence force constants and structural parameters dominating the mode frequencies. For identification of group modes 'fractional' mass (other than 'natural' mass) isotope shifts of frequency and normal vectors proved useful. Likewise, estimation of effects of force constant and structural parameter alterations on frequency shifts by first order perturbation theory of the FG problem of partial structures contributed valuable insight into the origin of the shifts.     

An infrared study on Langmuir–Blodgett films of 14,15-bis(hydroxyimino)-13-thiaoctacosane

The Langmuir–Blodgett (LB) films of 14,15-bis(hydroxyimino)-13-thiaoctacosane (TOC) on aluminium plated substrates were investigated using Fourier transform infrared (FTIR), grazing angle (GAIR) and horizontal attenuated total reflectance (HATR) techniques. The LB films of TOC can be transferred onto the solid substrate successfully. The molecular structure of LB films was analysis by comparing the GAIR and HTAR spectra. The intense bands at 2848 and 2918 cm⁻¹ are assigned to symmetric ν_s(CH₂) and asymmetric ν_a(CH₂) stretching vibrations of methylene groups. These peaks suggest that the alkyl chains in TOC are nearly in all-trans conformational state. The presence in the infrared spectra of several bands due to the methylene wagging and twisting modes and of the splitting of the bands due to the methylene scissoring mode at 1467 and 1459 cm⁻¹ and the CH₂ rocking mode at 720 and 731 cm⁻¹ also indicates that in films of TOC alkyl chains are in the all-trans conformation and packed in either an orthorhombic or a monoclinic structure with an orthorhombic subcell containing two mutually orthogonal molecules. Another conclusion presented in this paper that the alkyl chain tilt, which is the angle between the axis, which bisects the C–C bonds and the surface normal, was quite large by comparing the GAIR and HATR spectra.     

A normal coordinate analysis of monomethylhydrazine and its bidentate nickel (II) chloride complex

A full normal coordinate analysis (NCA) has been carried out on monomethylhydrazine and N-deuterated monomethylhydrazine. The C_3ν symmetry of the methyl group is lost; nevertheless the concept of specific methyl group modes is still valuable. The NN stretching mode is relatively pure enabling it to be used as a criteria of coordination. An NCA has also been carried out for the bidentate nickel complex NiCl₂(NH₂NHCH₃)₂. Interesting effects are observed for the wagging and twisting modes of the NH₂ group on coordination.     

Structural, odd-even chain alternation and thermal investigation of a homologous series of anhydrous silver(I) n-alkanoates

Molecular and lattice structures of a homologous series (n(c) = 8-20, inclusive) of silver (I) n-alkanoates are determined from X-ray Powder Diffraction, Solid State spin decoupled (13)C-NMR and variable temperature Fourier Transform Infrared Spectroscopies. The compounds crystallize in a monoclinic crystal system with hydrocarbon chains in the fully extended all-trans conformation. Moreover, the chains are tilted ca. 75° with respect to the metal basal plane and are arranged as methyl(tail)-to-methyl(tail) bilayers within a lamellar. The methyl chain ends, from different layers in the bilayer, do not overlap but are in such close proximity to cause methyl-methyl interactions. In a molecule, two carboxylate groups bind in a syn-syn type bridging bidentate mode to two silver atoms to form an eight-membered structure. Intramolecular silver-silver and intermolecular Ag-O-Ag interactions stabilize the head group and promote the formation of layer type polymeric sheets. Though the compounds are nearly isostructural, odd-even chain alternation is observed in density, anti-symmetric stretching vibrations of methyl and unusually, carboxylate (head) groups, as a result of packing differences of hydrocarbon chains within the crystal lattice. These arise from the relative vertical distances between polymeric sheets, which are not in the same plane. Thus, for odd chain length compounds, where those distances are less than for even chains, more ordered packing and hence higher densities are observed for these adducts. Also, the numbers and natures of the thermotropic phase transitions are chain length dependent and irreversible.     

Effect of surface coverage on the conformation and mobility of C18-modified silica gels

C18-modified silica gels with surface coverages of 2 to 8.2 micromol m(-2), were prepared by different synthetic pathways and characterized by Fourier Transform infrared spectroscopy (FTIR), solid-state nuclear magnetic resonance (NMR) spectroscopy, and chromatographic measurements. The effects of temperature and bonding density on the conformational order of C18-modified silica gels were studied in detail by FTIR spectroscopy. The silane functionality and degree of cross-linking of silane ligands on the silica surface were evaluated by 29Si cross-polarization magic-angle spinning (CP/MAS) NMR and the structural order and mobility of the alkyl chains were investigated by 13C CP/MAS NMR spectroscopy. CH2 symmetric and anti-symmetric stretching bands and CH2 wagging bands were used as IR probes to monitor the conformational order and flexibility of the alkyl chains in the C18 phases. Qualitative information about the conformational order was obtained from frequency shifts of the CH2 symmetric and anti-symmetric stretching bands. The relative amounts of kink/gauche-trans-gauche, double-gauche, and end-gauche conformers in the alkyl chains were determined by analysis of CH2 wagging bands. These results indicate that surface coverage plays a dominant role in the conformational order of C18-modified silica gels. The FTIR and NMR data are discussed in the context of the chromatographic shape-selectivity differences.