含硫氨基酸的太赫兹光谱

利用太赫兹时域光谱(THz-TDS)技术研究室温条件下多晶含硫氨基酸L-蛋氨酸(Met)和L-半胱氨酸(Cys)的光谱特性, 得到相应的吸收谱和折射率谱, 表明含硫氨基酸在THz波段具有区别于其它氨基酸的显著特征. 在实验测量的有效光谱范围0.2～2.8 THz内, L-蛋氨酸的THz吸收峰分别位于1.06, 1.88和2.70 THz; L-半胱氨酸的吸收峰分别位于1.40, 1.70, 2.33和2.61 THz, 两种氨基酸的平均折射率均为1.44. 利用GAUSSIAN 03软件包中的Hartree-Fock理论计算了蛋氨酸双分子的低频振动谱, 表明了与蛋氨酸各吸收峰对应的分子微观振动模式, 并对实验光谱进行了解析讨论.     

Modified corrections for London forces in solid-state density functional theory calculations of structure and lattice dynamics of molecular crystals

Dispersion forces are critical for defining the crystal structures and vibrational potentials of molecular crystals. It is, therefore, important to include corrections for these forces in periodic density functional theory (DFT) calculations of lattice vibrational frequencies. In this study, DFT was augmented with a correction term for London-type dispersion forces in the simulations of the structures and terahertz (THz) vibrational spectra of the dispersion-bound solids naphthalene and durene. The parameters of the correction term were modified to best reproduce the experimental crystal structures and THz spectra. It was found that the accurate reproduction of the lattice dimensions by adjusting the magnitude of the applied dispersion forces resulted in the highest-quality fit of the calculated vibrational modes with the observed THz absorptions. The method presented for the modification of the dispersion corrections provides a practical approach to accurately simulating the THz spectra of molecular crystals, accounting for inherent systematic errors imposed by computational and experimental factors.     

丙氨酸晶体太赫兹振动光谱的实验和理论研究

利用太赫兹时域光谱和低频拉曼光谱仪研究了丙氨酸晶体在0.2-2.6 THz 范围内的太赫兹吸收和拉曼散射光谱. 研究表明: 在该低频范围有四个振动模式, 其中两个只具有拉曼活性, 其余两个同时具有红外和拉曼活性. 基于B3LYP杂化密度泛函的自洽场晶体轨道法对丙氨酸周期性结构进行了理论研究和光谱计算. 通过比较实验和理论结果, 指认了实验光谱特征峰所属的不可约表示. 通过理论计算得到的图形, 得出在此低频范围的振动模式主要包含分子间氢键的扭转和摇摆运动.     

Importance of accurate spectral simulations for the analysis of terahertz spectra: citric acid anhydrate and monohydrate

The terahertz (THz) spectra of crystalline solids are typically uniquely sensitive to the molecular packing configurations, allowing for the detection of polymorphs and hydrates by THz spectroscopic techniques. It is possible, however, that coincident absorptions may be observed between related crystal forms, in which case careful assessment of the lattice vibrations of each system must be performed. Presented here is a THz spectroscopic investigation of citric acid in its anhydrous and monohydrate phases. Remarkably similar features were observed in the THz spectra of both systems, requiring the accurate calculation of the low-frequency vibrational modes by solid-state density functional theory to determine the origins of these spectral features. The results of the simulations demonstrate the necessity of reliable and rigorous methods for THz vibrational modes to ensure the proper evaluation of the THz spectra of molecular solids.     

Semi-Empirical Model to Retrieve Finite Temperature Terahertz Absorption Spectra using Morse Potential

Terahertz (THz) absorption is a fingerprint property of materials, due to the underlying low-frequency vibration/phonon modes being strongly dependent on the chemical constitutions and microscopic structures. The low excitation energies (0.414-41.4 meV) are related to two intrinsic properties of THz vibrations: the potential energy surfaces (PESs) are shallow, and the vibrationally excited states are usually populated via thermal fluctuations. The shallow PESs make the vibrations usually anharmonic, leading to redshifted vibrational excited state absorption; combined with considerable vibrational excited states population, characteristic THz signals are usually redshifted and congested with varying degrees at different temperatures. Combining existing experimental THz spectra at low temperatures, first principles vibration analysis, and the Morse potential, we developed a semi-empirical model to evaluate the anharmonicity of the low-frequency modes. The model was benchmarked with purine molecular crystal to generate THz spectra at different temperatures, the results were consistent with experiments. The good agreement suggests this model would facilitate the application of THz spectroscopy in molecular crystal characterization.     

Molecular vibration mode assignment of nematic liquid crystal 5CB on Terahertz spectra

Using DFT/B3LYP/6-311++G** method, the molecular structure and absorption spectra in terahertz (THz) range of liquid crystal 5CB are investigated. In a frequency range 0–15 THz, an assignment of the vibrational modes corresponding to absorption frequencies is performed using potential energy distribution for the first time. It is found that the cyano group radical (–CN) do actively take part in the strongest THz absorption of 1.743, 3.942, 5.169 and 14.769 THz in different vibration modes. The results suggest that the strong polar group should be avoided in designing liquid crystal molecule and mixtures in order to reduce the absorption intensity in THz range.     

Vibrational coupling in carboxylic acid dimers

The vibrational level splitting in the ground electronic state of carboxylic acid dimers mediated by the doubly hydrogen-bonded networks are investigated using pure and mixed dimers of benzoic acid with formic acid as molecular prototypes. Within the 0-2000-cm(-1) range, the frequencies for the fundamental and combination vibrations of the two dimers are experimentally measured by using dispersed fluorescence spectroscopy in a supersonic jet expansion. Density-functional-theory calculations predict that most of the dimer vibrations are essentially in-phase and out-of-phase combinations of the monomer modes, and many of such combinations show significantly large splitting in vibrational frequencies. The infrared spectrum of the jet-cooled benzoic acid dimer, reported recently by Bakker et al. [J. Chem. Phys. 119, 11180 (2003)], has been used along with the dispersed fluorescence spectra to analyze the coupled g-u vibrational levels. Assignments of the dispersed fluorescence spectra of the mixed dimer are suggested by comparing the vibronic features with those in the homodimer spectrum and the predictions of density-functional-theory calculation. The fluorescence spectra measured by excitations of the low-lying single vibronic levels of the mixed dimer reveal that the hydrogen-bond vibrations are extensively mixed with the ring modes in the S1 surface.     

Vibrational spectra of copper sulfate hydrates investigated with low-temperature Raman spectroscopy and terahertz time domain spectroscopy

In this paper, the vibrational spectra of copper sulfate hydrates (CuSO(4)·xH(2)O, x = 5, 3, 1, 0) have been investigated with low-temperature Raman spectroscopy and terahertz time domain spectroscopy (THz-TDS). It is found that the four groups of Raman bands between 90 and 4000 cm(-1) can be assigned to lattice vibration as well as intramolecular vibrations of a copper complex, sulfate group, and water molecules. The variation of vibrational spectra during the dehydrated process are discussed in detail considering the transformation of the crystal structure, especially the bands between 3000 and 3500 cm(-1), which are attributed to the ν(1) and ν(3) modes of water molecules. In addition, as a complement of Raman spectra, the THz spectra at 0.1-3 THz indicate the absorption due to the low-frequency lattice vibration and hydrogen bond.     

萘醌及其衍生物的太赫兹时域光谱研究

用太赫兹(THz)时域光谱技术研究了室温条件下的萘醌及其衍生物1,2-萘醌、1,2-萘醌-4-磺酸钠、甲萘醌、白花丹素、胡桃醌的光谱特征,得到了各自的吸收谱和折射率。结果表明,萘醌及其衍生物在此波段有不同的吸收特征,利用太赫兹时域光谱能够鉴别分子结构存在微小差别的化合物。在对样品的吸收谱进行比较的基础上,讨论了分子结构和分子间晶格振动与THz光谱特征吸收的关系。     

蒽醌及其衍生物的THz时域光谱研究

利用太赫兹(terahertz,THz)时域光谱技术室温下进行了蒽醌及其衍生物2_甲基蒽醌、蒽醌_2_磺酸钠、蒽醌_2,6_二磺酸钠、蒽醌_2,7_二磺酸钠在10～55cm-1(0.3～1.65THz)频谱范围内的光谱测量。结果表明,蒽醌及其衍生物在此波段有不同的吸收特征,它们的吸收可能是由于晶格振动引起的。THz时域光谱不仅能够鉴别分子结构存在微小差别的化合物而且还能鉴别同分异构体。     

Molecular analysis of water clusters: Calculation of the cluster structures and vibrational spectrum using density functional theory

Density functional theory (DFT) is applied to obtain absorption spectra at THz frequencies for molecular clusters of H₂O. The vibrational modes of the clusters are calculated. Coupling among molecular vibrational modes explains their spectral features associated with THz excitation. THz excitation is associated with vibrational frequencies which are here calculated within the DFT approximation of electronic states. This is done for both isolated molecules and collections of molecules in a cluster. The principal result of the paper is that a crystal-like cluster of 38 water molecules together with a continuum solvent background is sufficient to replicate well the experimental vibrational frequencies.     

Theoretical analysis of the terahertz spectrum of the high explosive PETN.

The experimental solid-state terahertz (THz) spectrum (3 to 120 cm(-1)) of the high explosive pentaerythritol tetranitrate (PETN, C(5)H(6)N(4)O(12)) has been modeled using solid-state density functional theory (DFT) calculations. Solid-state DFT, employing the BP density functional, is in best qualitative agreement with the features in the previously reported THz spectrum. The crystal environment of PETN includes numerous intermolecular hydrogen-bonding interactions that contribute to large (up to 80 cm(-1)) calculated shifts in molecular normal-mode positions in the solid state. Comparison of the isolated-molecule and solid-state normal-mode calculations for a series of density functionals reveals the extent to which the inclusion of crystal-packing interactions and the relative motions between molecules are required for correctly reproducing the vibrational structure of solid-state THz spectra. The THz structure below 120 cm(-1) is a combination of both intermolecular (relative rotations and translations) and intramolecular (torsions, large amplitude motions) vibrational motions. Vibrational-mode analyses indicate that the first major feature (67.2 cm(-1)) in the PETN THz spectrum contains all of the optical rotational and translational cell modes and no internal (molecular) vibrational modes.     

Simultaneous photon absorption as a probe of molecular interaction and hydrogen-bond cooperativity in liquids

We have investigated the simultaneous absorption of near-infrared photons by pairs of neighboring molecules in liquid methanol. Simultaneous absorption by two OH-stretching modes is found to occur at an energy higher than the sum of the two absorbing modes. This frequency shift arises from interaction between the modes, and its value has been used to determine the average coupling between neighboring methanol molecules. We find a rms coupling strength of 46+/-1 cm(-1), larger than can be explained from a transition-dipole coupling mechanism, suggesting that hydrogen-bond mediated interactions also contribute to the coupling. The most important aspect of simultaneous vibrational absorption is that it allows for a quantitative investigation of hydrogen-bond cooperativity. We derive the extent to which the hydrogen-bond strengths of neighboring molecules are correlated by comparing the line shape of the absorption band caused by simultaneous absorption with that of the fundamental transition. Surprisingly, neighboring hydrogen bonds in methanol are found to be strongly correlated, and from the data we obtain an estimate for the hydrogen-bond correlation coefficient of 0.69+/-0.12.     

β-丙氨酸的THz时域光谱研究

运用THz时域光谱测试技术(THz-TDS)与理论模拟相结合的方法, 研究了β-丙氨酸在THz波段的光谱特性. 在室温氮气环境中, 得到了样品在0.2～2.4 THz波段的吸收谱和折射率谱, 表明其特征吸收峰位于2.11 THz处, 平均折射率为1.96. 同时利用Gaussian 03软件的半经验理论计算了该分子在0.1～10.0 THz的振动吸收谱, 其在0.2～2.4 THz波段的吸收峰与实验相互对应, 且峰位符合较好. 研究了分子低频的振动模式, 并给出了分子的构象参数.     

Infrared and Raman spectroscopic characterization of the hydrogen-bonding network in l-serine crystal

The IR spectra (4000–400 cm⁻¹) of neat and isotopically substituted (ND/OD ≤ 10% D and ≅30% D) polycrystalline l-serine (α-amino-β-hydroxypropionic acid; HO–CH₂–CH(NH₃)⁺–COO⁻) were recorded in the temperature range 300–10 K and assigned. The isotopic-doping/low-temperature methodology, which allows for decoupling of individual proton vibrational modes from the crystal bulk vibrations, was used for estimating the lengths and energies of the different H-bonds present in l-serine crystal. To this end, the frequency shifts observed in both the NH/OH stretching and out-of-plane bending spectral regions (relatively to reference values for these vibrations in non-hydrogen-bonded l-serine molecules) were used, together with previously developed empirical correlations between these spectral parameters and the H-bond properties. In addition, the room-temperature Raman spectrum (4000–150 cm⁻¹) of a single crystal of neat l-serine was also recorded and interpreted. A systematic comparison was made between the spectroscopic data obtained currently for l-serine and previously for dl-serine, revealing that the vibrational spectra of the two crystals reflect well the different characteristics of their hydrogen-bond networks, and also correlate accurately with the different susceptibility of the two crystals to pressure-induced strain.     

Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Terahertz time-domain spectra of aromatic carboxylic acids incorporated in nano-sized pores of mesoporous silicate.

Terahertz time-domain spectroscopy (THz-TDS) is used to study the intra- and intermolecular vibrational modes of aromatic carboxylic acids, for example, o-phthalic acid, benzoic acid, and salicylic acid, which form either intra- or intermolecular hydrogen bond(s) in different ways. Incorporating the target molecules in nano-sized spaces in mesoporous silicate (SBA-16) is found to be effective for the separate detection of intramolecular hydrogen bonding modes and intermolecular modes. The results are supported by an analysis of the differences in the peak shifts, which depend on temperature, caused by the different nature of the THz absorption. Raman spectra revealed that incorporating the molecules in the nano-sized pores of SBA-16 slightly changes the molecular structures. In the future, THz-TDS using nanoporous materials will be used to analyze the intra- and intermolecular vibrational modes of molecules with larger hydrogen bonding networks such as proteins or DNA.     

Charge transfer interaction and terahertz studies of a nonlinear optical material L-glutamine picrate: A DFT study

Charge transfer interaction, vibrational spectra, and DFT computation of l-glutamine picrate has been analyzed. The equilibrium geometry, bonding features, and harmonic vibrational wavenumbers have been investigated with the help of B3LYP density functional theory method. The natural bond orbital analysis confirms the occurrence of strong intramolecular hydrogen bonding in the molecule. Terahertz time-domain spectroscopy was used to detect the absorption spectra in the frequency range from 0.025 to 2.8 THz. The vibrational modes found in molecular crystalline materials should be described as phonon modes with strong coupling to the intramolecular vibrations.     

Polarization and temperature dependent spectra of poly(3-hydroxyalkanoate)s measured at terahertz frequencies

Temperature-dependent terahertz (THz) absorption spectra of poly(3-hydroxyalkanoate)s (PHAs) were measured by using a Fourier transform far-infrared (FT-FIR) spectrometer and a THz time-domain spectrometer over a temperature range of 10 K to 465 K with a liquid helium cryostat and a heating cell. Clear differences were observed between the spectra of crystalline and amorphous polyhydroxybutyrate (PHB), indicating that the absorption peaks observed in the THz spectra originated in the higher-order conformation of PHB. The polarization spectra of a stretched PHB sample were measured, and the direction of the vibrational transition moment was determined. The temperature dependences of the spectra reveal frequency shifts and broadening of the absorption peaks with temperature, suggesting large anharmonicity of the vibrational potential. The temperature shift behaviour is quite different in each transition. Some of the transitions show a blue shift, which cannot be explained by a simple anharmonic potential model. Frequency shifts of the peaks were mainly observed below 10 THz, which suggests a large anharmonicity of the vibrational potential at lower frequencies.     

Investigation of (1R,2S)‐(−)‐Ephedrine by Cryogenic Terahertz Spectroscopy and Solid‐State Density Functional Theory

The terahertz (THz) spectrum of the pharmaceutical (1R,2S)‐(?)‐ephedrine from 8.0 to 100.0 cm^?1 is investigated at liquid‐nitrogen (78.4 K) temperature. The spectrum exhibits several distinct features in this range that are characteristic of the crystal form of the compound. A complete structural analysis and vibrational assignment of the experimental spectrum is performed using solid‐state density functional theory (DFT) and cryogenic single‐crystal X‐ray diffraction. Theoretical modeling of the compound includes an array of density functionals and basis sets with the final assignment of the THz spectrum performed at a PW91/6‐311G(d,p) level of theory, which provides excellent solid‐state simulation agreement with experiment. The solid‐state analysis indicates that the seven experimental spectral features observed at low temperature consist of 13 IR‐active vibrational modes. Of these modes, nine are external crystal vibrations and provide approximately 57 % of the predicted spectral intensity. This study demonstrates that the THz spectra of complex pharmaceuticals may be well reproduced by solid‐state DFT calculations and that inclusion of the crystalline environment is necessary for realistic and accurate simulations.