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.     

利用太赫兹时域光谱鉴别爆炸物2,4-DNT和 2,6-DNT

利用太赫兹时域光谱测得了2,4-DNT和 2,6-DNT在0.3-2.0THz频谱范围的吸收谱和折射谱。借助高斯03程序对2,6-DNT进行结构优化和频率计算。2,6-DNT在1.09, 1.36 and 1.55 THz有三个明显吸收并被归因于分子间的相互作用。本文使用太赫兹光谱法对2,4-DNT和 2,6-DNT混合物做了定量分析。分析的结果与实际值基本一致,相对误差约为8%。     

Theoretical and experimental study of the inelastic neutron scattering spectra of β-5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one

The inelastic neutron scattering (INS) spectra of β-5-Nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (β-NTO) are presented to 1400 cm⁻¹. The β-NTO vibrational frequencies observed differ considerably from the -NTO vibrational frequencies and normal mode frequency calculations for the isolated molecule. The INS spectrum contains detail unobserved in the previous IR studies, including combinations and overtones of the phonon and internal modes of β-NTO. The INS spectra are compared with periodic DFT calculations to show that the periodic DFT results correctly predict the solid-state molecular vibrational frequencies.     

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.     

Noncovalent interactions between modified cytosine and guanine DNA base pair mimics investigated by terahertz spectroscopy and solid-state density functional theory

Modified cytosine and guanine nucleobases cocrystallize in a hydrogen bonding configuration similar to that observed in native DNA. The noncovalent interactions binding these base pairs in the crystalline solid were investigated using terahertz (THz) spectroscopy and solid-state density functional theory (DFT). While stronger hydrogen bonding interactions are responsible for the general molecular orientations in the crystalline state, it is the weaker dipole-dipole and dispersion forces that determine the overall packing arrangement. The inclusion of dispersion interactions in the DFT calculations was found to be necessary to accurately simulate the unit cell structure and THz vibrational spectrum. Using properly modeled intermolecular potentials, the lattice vibrational motions of the cytosine and guanine derivatives were calculated. The vibrational characters of the modes exhibited by the DNA base pair mimic in the THz region were primarily rotational motions and are indicative of the energies and the nature of vibrations that would likely be observed between similar base pairs in DNA molecules.     

Terahertz Time-Domain Spectroscopy of Naphthalene and Naphthols

Low-energy vibrational modes have been investigated in polycrystalline naphthalene and its derivatives naphthols using terahertz time-domain spectroscopy (THz-TDS) over the frequency range from 17 to 73 cm^–1 (0.5–2.2 THz) at room temperature. We propose that naphthalene and naphthols show spectral features originating from intermolecular vibrational modes. Because of the collective origin of the observed modes, the absorption spectra are highly sensitive to the overall structure and configuration of the molecules, as well as their environments. For light-sensitive materials, the THz-TDS procedure can avoid effects like photobleaching.     

Studies of Solvent Effects on Structure and Low Frequency Vibrational Spectra of 2,4-Dinitrotoluene

Solvent effects on 2,4-dinitrotoluene(2,4-DNT) molecule in different solvents(toluene,ethanol,and water) were studied via DFT PCM method at B3LYP/6-311+G(d,p) level. The influences of these solvents on the molecular structure,vibrational spectra,charge distribution,and dipole moment were studied as well. The results show that PCM computations are successful in describing the vibrational spectra of 2,4-DNT molecules in these solutions and the solvent effects on the low frequency vibrational spectra are weak.     

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.     

20种α-氨基酸的太赫兹光谱及其分子结构的相关性

应用太赫兹时域光谱(THz-TDS)技术, 在室温下对构成蛋白质的20种基本氨基酸的多晶粉末压片样品进行了光谱测试分析. 结果表明, 所有氨基酸对THz波反应非常灵敏, 在0.2-3.0 THz的有效频谱范围内, 表现出各自特征吸收峰, 故而利用THz光谱可以有效地区别不同种类的氨基酸. 我们以新数据验证和补充了前人的研究结果, 建立了以氨基酸分子结构及其THz光谱特征为基础的分类方案, 讨论并揭示了氨基酸分子的结构差异与其THz吸收光谱之间的相关性. 认知这些相关性将有助于鉴定氨基酸分子, 促进THz光谱学的理论研究以及在生物医学领域的推广应用.     

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.     

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.     

Application of THz Vibrational Spectroscopy to Molecular Characterization and the Theoretical Fundamentals: An Illustration Using Saccharide Molecules

This work illustrates several theoretical fundamentals for the application of THz vibrational spectroscopy to molecular characterization in the solid state using two different types of saccharide systems as examples. Four subjects have been specifically addressed: (1) the qualitative differences in the molecular vibrational signatures monitored by THz and mid‐IR vibrational spectroscopy; (2) the selection rules for THz vibrational spectroscopy as applied to crystalline and amorphous systems; (3) a normal mode simulation, using α‐l ‐xylose as an example; and (4) a rigorous mode analysis to quantify the percentage contributions of the intermolecular and intramolecular vibrations to the normal mode of interest.     

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.     

Angle-dependent terahertz time-domain spectroscopy of amino acid single crystals

The measurement of absorption spectra using angle-dependent terahertz (THz) time-domain spectroscopy for amino acid single crystals of l-cysteine and l-histidine is reported for the first time. Linearly polarized THz radiation enables us to observe angle-dependent far-infrared absorption spectra of amino acid single crystals and determine the direction of the oscillating dipole of the molecules in the 20-100 cm(-1) range. By comparing the THz spectra of a single crystal and powder, we found that there was a clear hydrogen-bond peak in the crystal spectrum as a result of the larger hydrogen-bond network. The low-temperature THz spectra of amino acid microcrystals showed more intermolecular vibrational modes than those measured at room temperature. An ab initio frequency calculation of a single amino acid molecule was used to predict the intramolecular vibrational modes. The validity of the calculation models was confirmed by comparing the results with experimentally obtained data in the Raman spectral region.     

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.     

乐果分子的太赫兹时域光谱研究

研究了有机磷农药乐果在0.2~2.5 THz波段的光谱特性。应用密度泛函理论的Becke-3-Lee-Yang-Parr(B3LYP)方法计算了乐果分子在THz波段的振动吸收谱,同时利用THz时域光谱系统(THz-TDS)测得了乐果在此波段的吸收谱和折射率谱。根据理论计算结果,借助于Gaussian View软件对乐果的THz吸收谱进行了指认,并给出了与光谱特征吸收对应的分子振动构象。研究表明:乐果分子在THz波段存在吸收峰,理论计算与实验结果符合较好,且乐果分子在THz波段的吸收是由分子内和分子间振动共同引起。本研究证明了将THz-TDS技术用于乐果分子探测和识别的可行性,为THz时域光谱技术在其它农药分子识别和残留检测中的应用提供了有益的借鉴。     

Terahertz spectroscopy of enantiopure and racemic polycrystalline valine

Experimental and computational THz (or far-infrared) spectra of polycrystalline valine samples are reported. The experimental spectra have been measured using THz time-domain spectroscopy. Spectra of the pure enantiomers, both D and L, as well as the dl racemate have been taken at room temperature and low temperature (78 K). The spectra of the pure D and L enantiomers are essentially identical, and they are markedly different from the DL racemate. In addition, a temperature-dependent study of L-valine was undertaken in which the absorption maxima were found to red shift as a function of increasing temperature. The vibrational absorption spectra (frequencies and intensities) were calculated using the harmonic approximation with the Perdew-Burke-Ernzerhof (PBE) functional, localized atomic orbital basis sets, and periodic boundary conditions. The calculated and experimental spectra are in good qualitative agreement. A general method of quantifying the degree to which a calculated mode is intermolecular versus intramolecular is demonstrated, with the intermolecular motions further separated into translational versus rotational/librational motion. This allows straightforward comparison of spectra calculated using different basis sets or other constraints.     

DFT and ab initio study of structure of dyes derived from 2-hydroxy and 2,4-dihydroxy benzoic acids

We present a detailed analysis of the structural, infrared spectra and visible spectra of a series of azo dyes preparation of salicylic acid and 2,4-dihydroxy benzoic acid derivatives as the coupling component. The preparation of these azo dyes with salicylic acid and 2,4-dihydroxy benzoic acid derivatives (salicylic acid, methyl salicylate, ethyl salicylate, butyl salicylate, methyl 2,4-dihydroxy benzoate, ethyl 2,4-dihydroxy benzoate, salicylaldehyde, salicylamide, 2,4-dihydroxy benzamide, salicylaldoxime) have been investigated theoretically by performing HF and DFT levels of theory using the standard 6-31G* basis set. The optimized geometries and calculated vibrational frequencies are evaluated via comparison with experimental values. The vibrational spectral data obtained from solid phase FT-IR spectra are assigned modes based on the results of the theoretical calculations. The observed spectra are found to be in good agreement with the calculations.     

Ground-state spectral features of molecular clusters RDX excited at THz frequencies

Calculations are presented of ground state resonance structure at THz frequencies for molecular clusters of the high explosive RDX using density functional theory (DFT). The spectral features of this resonance structure are due to coupling of resonance modes for ground state excitation. In particular, the coupling among ground state resonance modes provides a reasonable molecular level interpretation of spectral features associated with THz excitation of molecular clusters. THz excitation is associated with frequencies that are characteristically perturbative to molecular electronic states, in contrast to frequencies that can induce appreciable electronic state transition. Owing to this characteristic of THz excitation, one is able to make a direct association between local oscillations about ground-state minima of molecules, either isolated or comprising a cluster, and THz excitation spectra. The DFT software GAUSSIAN was used for the calculations of ground state resonance structure presented here.     

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.