Vibrational stark effect probes for nucleic acids

The vibrational Stark effect (VSE) has proven to be an effective method for the study of electric fields in proteins via the use of infrared probes. To explore the use of VSE in nucleic acids, we investigated the Stark spectroscopy of nine structurally diverse nucleosides. These nucleosides contained nitrile or azide probes in positions that correspond to both the major and minor grooves of DNA. The nitrile probes showed better characteristics and exhibited absorption frequencies over a broad range; that is, from 2253 cm-1 for 2'-O-cyanoethyl ribonucleosides 8 and 9 to 2102 cm(-1) for a 13C-labeled 5-thiocyanatomethyl-2'-deoxyuridine 3c. The largest Stark tuning rate observed was |Deltamu| = 1.1 cm(-1)/(MV/cm) for both 5-cyano-2'-deoxyuridine 1 and N2-nitrile-2'-deoxyguanosine 7. The latter is a particularly attractive probe because of its high extinction coefficient (epsilon = 412 M-1cm-1) and ease of incorporation into oligomers.     

Si~2Cl~6分子的内旋转能垒和振动基频的理论研究

用从头算方法HF/6-31G^*^*和密度函方法B3LYP/6-31G^*^*,对Si~2Cl~6分子的平衡几何构型进行优化,优化的结果与实验结果吻合得较好.并用上述两种不同的方法计算Si~2Cl~6分子的内旋转能垒,结果分别为8.786和6.694kJ/mol,其中DFT方法的计算结果与实验结果4.18kJ/mol吻合得较好.对Si~2Cl~6分子的振动基频进行计算.用HF/6-31G^*^*SQM力场所计算的频率理论值与实验值的平均误差为7.3cm^-^1,用B3LYP/6-31G^*^*未标度的力场所计算的频率理论值与实验值的平均误差为6.0cm^-^1.该密度泛函方法(B3LYP/~6-31G^*^*)的理论计算值比用HF/6-31G^*^*标度后的SQM力场计算的频率与实验值(除Si--Si键扭转振动基频之外的11条振动基频)吻合得更好.并给出了Si--Si键扭转振动基频的预测值。     

Si2Br6的分子振动光谱的理论研究

用量化从头算方法(HF/6-31G^*)和密度泛函方法(B3LYP/6-31G^*)以6-31G标准基组加一个极化函数,对Si₂Br₆分子的平衡几何构型和振动频率分别进行优化和计算,优化的结果与实验结果吻合得较好.按照Pulay的建议对HF/6-31G^*水平上所计算的谐性力场进行标度(标度因子取0.9).用HF/6-31G^*SQM力场所计算的基频预测值和实验值的平均误差为9.4cm^-1,最大误差为23.6cm^-1;用B₃LYP/6-31G^*未标度力场所计算的基频预测值和实验值的平均误差为8.6cm^-1,最大误差为16.6cm^-1;用该密度泛函方法所计算的基频预测值比用HF/6-31G^*的标度后的SQM力场所计算的基频预测值和实验值(除Si-Si键扭转振动基频之外的11条振动基频)吻合得更好.HF/6-31G^*和B3LYP/6-31G^*计算给出Si-Si键扭转振动基频的预测值分别为14cm^-1和9cm^-1.     

FT-IR, FT-Raman and UV spectral investigation; computed frequency estimation analysis and electronic structure calculations on 1-nitronaphthalene

In this work, the vibrational spectral analysis was carried out by using FT-Raman and FT-IR spectroscopy in the range 100-4000cm(-1) and 400-4000cm(-1) respectively, for 1-nitronaphthalene (C(10)H(7)NO(2)) molecule. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based density functional theory (DFT) and ab initio HF methods and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of total energy distribution (TED). The results of the calculations were applied to simulated spectra of the title compound, which show excellent agreement with observed spectra. The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The energy and oscillator strength calculated by time-dependent density functional theory (TD-DFT) complements with the experimental findings. Thermodynamic properties of the title compound at different temperatures have been calculated. Besides, frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) were performed.     

Structure, stability and vibrational spectrum of the hydrogen-bonded complex between HNO3 and H2O. Ab initio and DFT studies

The structure, stability and vibrational spectrum of the binary complex between HONO2 and H2O have been investigated using ab initio calculations at SCF and MP2 levels with different basis sets and B3LYP/6-31G(d,p) calculations. Full geometry optimization was made for the complex studied. It was established that the hydrogen-bonded H2O...HONO2 complex has a planar structure. The corrected values of the dissociation energy at the SCF and MP2 levels and B3LYP calculations are indicative of relatively strong OH...O hydrogen-bonded interaction. The changes in the vibrational characteristics (vibrational frequencies and infrared intensities) arising from the hydrogen bonding between HONO2 and H2O have been estimated by using the ab initio calculations at SCF and MP2 levels and B3LYP/6-31G(d,p) calculations. It was established that the most sensitive to the complexation is the stretching O-H vibration from HONO2. In agreement with the experiment, its vibrational frequency in the complex is shifted to lower wavenumbers. The predicted frequency shift with the B3LYP/6-31G(d,p) calculations (-439 cm(-1)) is in the best agreement with the experimentally measured (-498 cm(-1)). The intensity of this vibration increases dramatically upon hydrogen bonding. The ab initio calculations at the SCF level predict an increase up to five times; at the MP2 level up to 10 times and the B3LYP/6-31G(d,p) predicted increase is up to 17 times. The good agreement between the predicted values of the frequency shifts and those experimentally observed show that the structure of the hydrogen-bonded complex H2O...HONO2 is reliable.     

Vibrational assignments and electronic structure calculations for 3-acetylcoumarin

Laser Raman (3500-50 cm(-1)) and IR (4000-400 cm(-1)) spectral measurements have been made on the laboratory prepared solid 3-acetylcoumarin. Molecular electronic energy, equilibrium geometrical structure and harmonic vibrational spectra have been computed at the RHF/6-31G(d,p) and B3LYP/6-31G(d,p) levels of theory. A complete vibrational assignment aided by the theoretical harmonic frequency analysis has been proposed. The B3LYP/6-31G(d,p) geometrical parameters, and frequencies of the C=O in the pyrone and acetyl group are in good agreement with experiment. The difference in the frequencies due to the two carbonyl groups, 50 cm(-1), which is attributed to the conjugation effect, is accounted for by the B3LYP to be 56cm(-1).     

Vibrational spectroscopic analysis of 2-bromobenzoic and anthranilic acids: a combined experimental and theoretical study

In this work, the vibrational spectral analysis was carried out by using Raman and infrared spectroscopy in the range 100-4000 cm(-1) and 50-4000 cm(-1) respectively, for the title molecules. The molecular structure, fundamental vibrational frequencies and intensity of the vibrational bands are interpreted with the aid of structure optimizations and normal coordinate force field calculations based on Hartee-Fock (HF) and density functional theory (DFT) method and different basis sets combination. The complete vibrational assignments of wavenumbers were made on the basis of potential energy distribution (PED). The scaled B3LYP/6-311++G(d,p) results show the best agreement with the experimental values over the other methods. The effects due to the substitutions of amino group and halogen bond were investigated. The results of the calculations were applied to simulate spectra of the title compounds, which show excellent agreement with observed spectra.     

How Sensitive is the Amide I Vibration of the Polypeptide Backbone to Electric Fields?

Site‐selective isotopic labeling of amide carbonyls offers a nonperturbative means to introduce a localized infrared probe into proteins. Although this strategy has been widely used to investigate various biological questions, the dependence of the underlying amide I vibrational frequency on electric fields (or Stark tuning rate) has not been fully determined, which prevents it from being used in a quantitative manner in certain applications. Herein, through the use of experiments and molecular dynamics simulations, the Stark tuning rate of the amide I vibration of an isotopically labeled backbone carbonyl in a transmembrane α‐helix is determined to be approximately 1.4 cm^?1/(MV/cm). This result provides a quantitative basis for using this vibrational model to assess local electric fields in proteins, among other applications. For instance, by using this value, we are able to show that the backbone region of a dipeptide has a surprisingly low dielectric constant.     

异丙醇的O-H伸缩振动泛频光谱和分子构像

使用高灵敏的光腔衰荡光谱(CavityRingDownSpectroscopy)技术测出了异丙醇的O-H伸缩v=4、5振动泛频光谱,每个振动能级都有三个吸收峰,被归属为分子构像的O-H伸缩泛频吸收.给出了光腔衰荡光谱的振动泛频吸收的谱带强度公式,并求得分子不同构像在不同振动能级的O-H伸缩泛频吸收的谱带强度;同时利用局域模理论,求得分子各O-H伸缩局域模振子的机械频率(X1)、非谐性(X2)以及解离能(D).用密度泛函(DFT)B3LYP/6-31+G*理论方法优化了分子的各种可能构像,验证了分子存在反式(trans)和偏转(gauche)两种稳定构像,计算的分子的O-H伸缩频率及构像稳定性同实验结果是一致的.     

Analysis of vibrational spectra of 4-amino-2,6-dichloropyridine and 2-chloro-3,5-dinitropyridine based on density functional theory calculations

This work deals with the vibrational spectroscopy of 4-amino-2,6-dichloropyridine (ADCP) and 2-chloro-3,5-dinitropyridine (CDNP) by means of quantum chemical calculations. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G(*) and B3LYP/6-311+G(**) methods and basis set combinations, and was scaled using various scale factors which yields a good agreement between observed and calculated frequencies. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on scaled density functional force field. The results of the calculations were applied to simulated infrared and Raman spectra of the title compounds, which showed excellent agreement with the observed spectra.     

Simulation of IR and Raman spectral based on scaled DFT force fields: a case study of 2-amino 4-hydroxy 6-trifluoromethylpyrimidine, with emphasis on band assignment

This work deals with the vibrational spectroscopy of 2-amino 4-hydroxy 6-triflouromethylpyrimidine (AHFMP) by means of quantum chemical calculations. The mid and far FTIR and FT-Raman spectra were measured in the condensed state. The fundamental vibrational frequencies and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6-31G* and B3LYP/6-311+G** method and basic set combinations. Normal co-ordinate calculations were performed with the DFT force field corrected by a recommended set of scaling factors yielding fairly good agreement between observed and calculated frequencies. Simulation of infrared and Raman spectra utilizing the results of these calculations led to excellent overall agreement with the observed spectral patterns. The SQM approach applying selective scaling of the DFT force field was shown to be superior to the uniform scaling method in its ability to allow for making modifications in the band assignment, resulting in more accurate simulation of IR and Raman Spectra.     

Vibrational spectra and structure of benzil and its 18O- and d10-labelled derivatives: a quantum chemical and experimental study

Geometry and vibrational spectroscopic data of benzil-d0 benzil-d10 and benzil-18O calculated at various levels of theory (RHF/6-31G*, B3LYP/6-31G*, BLYP/6-31G*) are reported. The theoretical results are discussed mainly in terms of the comparisons with infrared (4000-100 cm(-1)) and Raman (4000-50 cm(-1)) spectral data. The calculated isotopic frequency shifts, induced by the 18O- and d10-labeling, are in a good agreement with the measured values. A complete vibrational assignment was made with the help of ab initio force field calculations. The data thus obtained were used for reassigning some vibrational frequencies. The results of the optimized molecular structure obtained on the basis of RHF and the DFT calculations are presented and compared with the experimental X-ray diffraction for the benzil-d0 single crystal. It turns out that the best structural parameters are predicted by the B3LYP/6-31G* method.     

Molecular geometry and vibrational studies of 3,5-diamino-1,2,4-triazole using quantum chemical calculations and FT-IR and FT-Raman spectroscopies

The 3,5-diamino-1,2,4-triazole (guanazole) was investigated by vibrational spectroscopy and quantum methods. The solid phase FT-IR and FT-Raman spectra were recorded in the region 4000-400 cm(-1) and 3600-50 cm(-1) respectively, and the band assignments were supported by deuteration effects. The results of energy calculations have shown that the most stable form is 1H-3,5-diamino-1,2,4-triazole under C1 symmetry. For this form, the molecular structure, harmonic vibrational wave numbers, infrared intensities and Raman activities were calculated by the ab initio/HF and DFT/B3LYP methods using 6-31G* basis set. The calculated geometrical parameters of the guanazole molecule using B3LYP methodology are in good agreement with the previously reported X-ray data, and the scaled vibrational wave number values are in good agreement with the experimental data. The normal vibrations were characterized in terms of potential energy distribution (PEDs) using VEDA 4 program.     

Observation of the predissociated, quasilinear B(1A') state of CHF by optical-optical double resonance

We report the first observation of the predissociative B state of a halocarbene molecule. Rovibronic energy levels were measured in the B(1A') state of CHF by fluorescence dip detected optical-optical double resonance spectroscopy via the A state. The origin was found to lie 30 817.4 cm-1 above the zero point level of the X state. Rotational transitions within six purely bending states, and states involving one or two quanta of CF-stretch were observed, including the vibrational angular momentum components. Interpretation of the spectrum, with support of ab initio calculations, shows that CHF is quasilinear in the B state with a small (-200 cm-1) barrier to linearity which lies below the zero-point level. The rotational constant, B=1.04 to 1.09 cm-1, depending on vibrational state, again in good agreement with theory. All observed B state levels were predissociative, as evidenced by Lorentzian line broadening. Linewidths varied with initial state from 0.7-10.8 cm-1, corresponding to excited state lifetimes of 0.5-8 ps.     

Crystal structure and density functional theory study on structural properties and energies of a isonicotinohydrazide compound

An X-ray and a theoretical study of the structure of the isoniazid derivative N'-(4-dimethylaminobenzylidene)-isonicotinohydrazide monohydrate (1) are reported. In this work, we will report a combined experimental and theoretical study on the molecular structure, vibrational spectra and energies of N'-(4-dimethylaminobenzylidene)-isonicotinohydrazide monohydrate. The calculated parameters are in good agreement with the corresponding X-ray diffraction values. The FTIR spectrum in the range of 400-4000 cm-1 of N'-(4-dimethylaminobenzylidene)-isonicotinohydrazide monohydrate has been recorded. The molecular geometry and vibrational frequencies and energies in the ground state are calculated by using the DFT (B3LYP, PBE1PBE) methods with 6-311G** basis sets. The calculated HOMO and LUMO energies also confirm that charge transfer occurs within the molecule. The geometries and normal modes of vibrations obtained from B3LYP/PBE1PBE/6-311G** calculations are in good agreement with the experimentally observed data.     

马钱子碱分子结构和振动光谱的密度泛函理论研究

用密度泛函理论B3LYP/6-31G*方法对天然药材马钱子中的生物碱马钱子碱的几何构型进行了优化,得到马钱子碱分子的平衡结构参数,并同实验结构进行了比较.计算了上述分子在平衡构型下的振动谐力场和振动基频.针对不同的振动模式,提出了相应的校正因子,并据此对计算频率进行了校正.理论计算和实验测定频率的平均误差为19.0cm-1.根据DFT计算的振动模式和IR光谱强度值对目标分子的实验振动基频进行了完善的和合理的指认和解释.     

The O-H stretching mode of a prototypical photoacid as a local dielectric probe

We investigate the OH stretch vibrational frequency shifts of a prototype photoacid, 2-naphthol (2N), when dissolved in solvents of low polarity. We combine femtosecond mid-infrared spectroscopy and a theoretical model based on the Pullin-van der Zwan-Hynes perturbative approach to explore vibrational solvatochromic effects in the ground S(0) and the first electronically excited (1)L(b) states. The model is parametrized using density functional theory (DFT), at the B3LYP/TZVP and TD-B3LYP/TZVP levels for the 2N chromophore in the S(0) and (1)L(b) states, respectively. From the agreement between experiment and theory we conclude that vibrational solvatochromic effects are dominated by the instantaneous dielectric response of the solvent, while time-dependent nuclear rearrangements are of secondary importance.     

Coupled-cluster calculations of vibrational Raman optical activity spectra

We present the first calculations of Raman optical activity spectra at the coupled-cluster level of theory. Calculations are presented for (S)-methyloxirane and compared to recent experimental gas-phase measurements as well as the results obtained at the Hartree-Fock and density functional level of theory using the popular B3LYP functional. For the experimentally relevant frequency region of 400-1600 cm(-1), the Hartree-Fock, B3LYP and coupled-cluster spectra are very similar when the same force field is used, and the results also agree well with experiment. For high-frequency vibrational modes, differences in the ROA difference parameters are observed and are analyzed. The new coupled-cluster ROA code will allow for critical benchmarking of the accuracy of modern exchange-correlation functionals in the calculation of ROA spectra.     

Vibrational spectroscopy for glycine adsorbed on silicon clusters: Harmonic and anharmonic calculations for models of the Si(1 0 0)-2 × 1 surface

The vibrational spectroscopy of a glycine molecule adsorbed on a silicon surface is studied computationally, using different clusters as models for the surface. Harmonic frequencies are computed using density functional theory (DFT) with the B3LYP functional. Anharmonic frequency calculations are carried out using vibrational self-consistent field (VSCF) algorithms on an improved PM3 potential energy surface. The results are compared with experiments on Glycine@Si(1 0 0)-2 × 1.

The main findings are: (1) Agreement of the computed frequencies with experiment improves with cluster size. (2) The anharmonic calculations are generally in better agreement with experiment than the harmonic ones. The improvements due to anharmonicity are most significant for hydrogenic stretching. (3) An important part of the anharmonic effects is due to anharmonic coupling between different normal modes of the system. (4) The anharmonic coupling between glycine vibrational modes is much larger than the anharmonic coupling between glycine and “phonon” (cluster) modes.

Implications of the results for surface vibrational spectroscopy are discussed.