几个荧光蛋白发色团双光子吸收性质的理论研究

实验测得的荧光蛋白的单、双光子吸收光谱在低频和高频区域都表现出明显不同的特征。为了揭示这些不同点的起源和研究荧光蛋白的构–效关系,我们详细研究了三种荧光蛋白发色团(一种增强型蓝绿色荧光蛋白的中性发色团和两种红色荧光蛋白的阴离子发色团)的单、双光子吸收特性,分别计算了纯的和振动分辨的电子谱。计算结果表明：光谱线形与计算采用的交换相关密度泛函及谱截面计算所采用的近似关系密切;如果在计算光谱截面时,我们利用长程修正的交换相关泛函CAM-B3LYP来计算几何和电子结构参数,然后把Franck-Condon (FC)效应和包含Herzberg-Teller (HT)效果的电-声耦合效应都考虑进去,理论计算的光谱与实验测定的光谱可以很好地符合;对于两种离子态的发色团,HT电-声耦合效应使得对应于基态到第一激发态跃迁的双光子吸收最强峰相对于单光子吸收的最强峰发生了蓝移,但HT电-声耦合效应对高频的双光子吸收谱没有太大的影响;分子内电荷转移是导致高频区的双光子吸收明显强于单光子吸收的主要原因。     

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.     

Absorption spectra of first-row transition metal complexes of bacteriochlorins: a theoretical analysis

A theoretical study on a family of divalent transition metal bacteriochlorin complexes (M-BC, where M = Mn, Fe, Co, Ni Cu, and Zn) has been carried out to elucidate their potentialities as active molecules in photodynamic therapy (PDT). To draw a complete picture of their electronic properties, both for the ground and excited states, these complexes have been studied by the means of density functional theory (DFT). The time-dependent DFT (TDDFT) approach was used to interpret the electronic spectra, while solvent effects were taken into account by explicitly considering both two water molecules coordinated to the central metal atom and the contribution from the solvent bulk. Particular attention has been devoted to the analysis of the so-called Q bands, since these can be particularly important for medical applications. Metal substitution and environment (solvent) effects have been analyzed, and good agreement is found between computed and available UV-vis spectra. These theoretical data, especially those relative to the metallobacteriochlorins not yet completely characterized at the experimental level, could give some hints for future medical applications.     

An explicitly correlated local coupled cluster method for calculations of large molecules close to the basis set limit

A new explicitly correlated local coupled-cluster method with single and double excitations and a perturbative treatment of triple excitations [DF-LCCSD(T0)-F12x (x = a,b)] is presented. By means of truncating the virtual orbital space to pair-specific local domains (domain approximation) and a simplified treatment of close, weak and distant pairs using LMP2-F12 (pair approximation) the scaling of the computational cost with molecular size is strongly reduced. The basis set incompleteness errors as well as the errors due to the domain approximation are largely eliminated by the explicitly correlated terms. All integrals are computed using efficient density fitting (DF) approximations. The accuracy of the method is investigated for 52 reactions involving medium size molecules. A comparison of DF-LCCSD(T0)-F12x reaction energies with canonical CCSD(T)-F12x calculations shows that the errors introduced by the domain approximation are indeed very small. Care must be taken to keep the errors due to the additional pair approximation equally small, and appropriate distance criteria are recommended. Using these parameters, the root mean square (RMS) deviations of DF-LCCSD(T0)-F12a calculations with triple-ζ basis sets from estimated CCSD(T) complete basis set (CBS) limits and experimental data amount to only 1.5 kJ mol(-1) and 2.9 kJ mol(-1), respectively. For comparison, the RMS deviation of the CCSD(T)/CBS values from the experimental values amounts to 3.0 kJ mol(-1). The potential of the method is demonstrated for five reactions of biochemical or pharmacological interest which include molecules with up to 61 atoms. These calculations show that molecules of this size can now be treated routinely and yield results that are close to the CCSD(T) complete basis set limits.     

He I photoelectron spectra and valence synchrotron photoionization for XC(O)SCl (X = F, Cl) compounds

Small penta-atomic molecules like FC(O)SCl and ClC(O)SCl have been analyzed by using both photoelectron spectroscopy (PES) and results derived from the use of synchrotron radiation in the same energy range. For this second experiment total ion yield (TIY), photoelectron photoion coincidence (PEPICO), and partial ion yield (PIY) spectra have been recorded. This set of data together with results obtained by computational chemistry allow us to study electronic properties and the ionization channels of both species. Thus, whereas the photodissociation behavior of FC(O)SCl can be divided into three well-defined energy regions, the fragmentation dynamics of ClC(O)SCl seems to be more complex. Nevertheless, simultaneous evaluation of the PES and valence synchrotron photoionization studies helps to clarify the molecular ionization processes.     

Two-photon spectroscopy of dipole-forbidden transitions

We have investigated the applicability of CNDO/S-type methods for the calculation of optical spectra of molecules with the special implication that the calculations should not only describe the intense, dipole-allowed transitions which dominate the one-photon absorption spectrum but also those transitions which are one-photon forbidden in first-order approximation. We show that such a method is well suited to predict dipole allowed and dipole forbidden transitions at a similar level of accuracy if double excited configurations are taken into account. In spite of the lack of perfect pairing in NDO methods there are still two types of states which exhibit a different sensitivity towards correlation effects. Therefore, the approximation by which we describe the R-dependence of the Coulomb repulsion gains much more importance than in cases where mainly dipole allowed transitions are of interest. These findings confirm results obtained earlier from theories for which the pairing theorem is valid. The calculated data show an excellent stability with respect to further increase of the number of configurations if at least about 200 energy selected configurations are taken into account.     

A dynamic mean field theory for dissipative interacting many-electron systems: Markovian formalism and its implementation

To demonstrate its applicability for realistic open systems, we apply the dynamic mean field quantum dissipative theory to simulate the photo-induced excitation and nonradiative decay of an embedded butadiene molecule. The Markovian approximation is adopted to further reduce the computational time, and the resulting Markovian formulation assumes a variation of Lindblad's semigroup form, which is shown to be numerically stable. In the calculation, all 22 valence electrons in the butadiene molecule are taken as the system and treated explicitly while the nuclei of the molecules are taken as the immediate bath of the system. It is observed that (1) various excitations decay differently, which leads to different peak widths in the absorption spectra; and (2) the temperature dependences of nonradiative decay rates are distinct for various excitations, which can be explained by the different electron-phonon couplings.     

Density functional theory study of vibronic structure of the first absorption Qx band in free-base porphin

Harmonic vibrational frequencies and vibronic intensities in the first S(0)-->S(1) (pipi( *)) absorption band of free-base porphin (H(2) P) are investigated by hybrid density functional theory (DFT) with the standard B3LYP functional. The S(0)-S(1) transition probability is calculated using time-dependent DFT with account of Franck-Condon (FC) and Herzberg-Teller (HT) contributions to the electric-dipole transition moments including displacements along all 108 vibrational modes. Two weak wide bands observed in the gas phase absorption spectra of the H(2) P molecule at 626 and 576 nm are interpreted as the 0-0 band of the X(1) A(g)-->1B(3u) transition and the 0-1 band with largest contributions from the nu(10)(a(g))=1610 cm(-1) and nu(19)(b(1g))=1600 cm(-1) modes, respectively, in agreement with previous tentative assignments. Both bands are induced by the HT mechanism, while the FC contributions are negligible. A number of fine structure bands, including combination of two vibrational quanta, are obtained and compared with available spectra from supersonic jet and Shpolskij matrices. Both absorption and fluorescence spectra are interpreted on ground of the linear coupling model and a good fulfillment of the mirror-symmetry rule.     

Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

The electronic absorption spectra of pyridine and nicotine in aqueous solution have been computed using a multistep approach. The computational protocol consists in studying the solute solvation with accurate molecular dynamics simulations, characterizing the hydrogen bond interactions, and calculating electronic transitions for a series of configurations extracted from the molecular dynamics trajectories with a polarizable QM/MM scheme based on the fluctuating charge model. Molecular dynamics simulations and electronic transition calculations have been performed on both pyridine and nicotine. Furthermore, the contributions of solute vibrational effect on electronic absorption spectra have been taken into account in the so called vertical gradient approximation. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Effective method to compute vibrationally resolved optical spectra of large molecules at finite temperature in the gas phase and in solution

The authors present a new method for the computation of vibrationally resolved optical spectra of large molecules, including the Duschinsky rotation of the normal modes and the effect of thermal excitation. The method automatically selects the relevant vibronic contributions to the spectrum, independently of their frequency, and it is able to provide fully converged spectra with moderate computational times, both in vacuo and in solution. By describing the electronic states in the frame of the density functional theory and its time-dependent extension, they computed the room temperature absorption spectra of coumarin C153 and trans-stilbene in cyclohexane and the phosphorescence spectrum of porphyrazine in gas phase, showing that the method is fast and efficient. The comparison with experiment for trans-stilbene and coumarin C153 is very satisfactory, confirming the progress made toward a reliable method for the computation and interpretation for the optical spectra of large molecules.     

Infrared reflectance spectra of some optically biaxial crystals: on the origin of isosbestic-like points in the polarized reflectance spectra

An investigation of the IR polarized reflectance spectra of the orthorhombic K2SO4, KHSO4 and monoclinic CaSO4 x 2H2O, K2Ni(SO4)2 x 6H2O, (NH4)2Ni(SO4)2 x 6H2O was performed in order to explain the appearance of particular intersection points in their spectra. The analogy in the origin of the appearance of intersection points and the well-known isosbestic points in UV-vis and IR spectra was discussed. The reason for such an appearance was identified in the way that the individual reflectances (for radiation polarized along principal dielectric axes) sum up to give the reflectance under arbitrary polarization. This summation may also produce supplementary bands in the reflectance spectra, not predicted by the group theory. It was shown that relatively large LO-TO splitting is needed for the supplementary band(s) to appear, but also the overlapping region must be taken into account.     

Character of the thermal motion of water molecules according to the data on quasielastic incoherent scattering of slow neutrons

The paper discusses the applicability of quasi-crystalline approximation to describing the thermal motion of water molecules in their normal and supercooled states. The problem is subjected to the critical analysis of experimental data on incoherent scattering of slow neutrons based on theories developed by Singwi-Sjolander [1] and Oskotsky [2] modified to duly take into account the limited applicability range of diffusion approximation. The applicability conditions of quasi-crystalline approximation are shown to be consistently satisfied only when water is in supercooled state and within a narrow temperature range above the melting temperature.     

Ground state and phase transitions in a system of arg-cysteamines self-assembled on a Au(111) crystal surface

The translational and orientation order of arg-cysteamine molecules chemiabsorbed on the Au(111) crystal surface is considered. Couplings between carbon, nitrogen, and hydrogen atoms of the n-alkanethiols are approximated by the Lennard-Jones potential. Moreover, hydrogen bonds between oxygen and nitrogen and dipole-dipole interactions of the dipole moments of different atomic groups are taken into account. It is found that molecules are arranged in a 2 x 2 lattice and have the total symmetry C6 x Z2. The critical temperature of the phase transition to the tilted state Tc1, which breaks the symmetry C6, is estimated to be extremely high. The spontaneous breakdown of the remaining symmetry Z2 leads to the twisted state of the molecules and has the critical temperature Tc2=340 K.     

Solvent effect on the singlet excited-state lifetimes of nucleic acid bases: A computational study of 5-fluorouracil and uracil in acetonitrile and water

The first comprehensive quantum mechanical study of solvent effects on the behavior of the two lowest energy excited states of uracil derivatives is presented. The absorption and emission spectra of uracil and 5-fluorouracil in acetonitrile and aqueous solution have been computed at the time-dependent density-functional theory level, using the polarizable continuum model (PCM) to take into account bulk solvent effects. The computed spectra and the solvent shifts provided by our method are close to their experimental counterpart. The S0/S1 conical intersection, located in the presence of hydrogen-bonded solvent molecules by CASSCF (8/8) calculations, indicates that the mechanism of ground-state recovery, involving out-of-plane motion of the 5 substituent, does not depend on the nature of the solvent. Extensive explorations of the excited-state surfaces in the Franck-Condon (FC) region show that solvent can modulate the accessibility of an additional decay channel, involving a dark n/pi* excited state. This finding provides the first unifying explanation for the experimental trend of 5-fluorouracil excited-state lifetime in different solvents. The microscopic mechanisms underlying solvent effects on the excited-state behavior of nucleobases are discussed.     

Ab initio spectroscopy and photoinduced cooling of the trans-stilbene molecule

We present a theoretical study of the S(0)-->S(1) and S(0)<--S(1) vibronic spectra for trans-stilbene. Franck-Condon spectra in the harmonic approximation are generated for the complete system with 72 degrees of freedom by means of an analytic time-dependent approach accounting for Dushinsky rotations and thermal effects. The force fields are computed by means of density functional theory (DFT) and time-dependent DFT, on the one hand, and ab initio complete active space self-consistent field theory, on the other hand. The B3LYP functional shows that almost planar potential energy surface minima are found for the S(0) and S(1) state. Imposing C(2h) symmetry constraints, we obtain low-temperature high-resolution Franck-Condon spectra for both absorption and emission which are in reasonably good agreement with the experimental spectra measured by Syage et al. [J. Chem. Phys. 81, 4685 (1984)] in supersonic jets. Due to thermal population of low-energy modes, the room temperature absorption spectrum is very broad. An almost structureless band which extends over several thousand cm(-1) is obtained from the present theory and agrees with the experimental absorption band shape. Finally, within the harmonic model, we study the effect of photoexcitation on the energy distribution in the excited S(1) state. We find noticeable cooling of approximately 20 K within a frequency interval spanning from -400 to 200 cm(-1) around the 0-0 transition. This indicates that photoinduced cooling must be taken into account when considering the dynamics of the photoinduced isomerization of trans-stilbene. Moreover, this is not the final word, as anharmonicity of the low frequency modes must be taken into account to obtain a full picture which would explain both the energy dependence of the isomerization rates as well as the dependence on the pressure of an external buffer gas.     

Excited state ab initio and Franck-Condon simulation of S1 → S0 fluorescence excitation spectra of p-, m-, and o-difluorobenzenes

Although difluorobenzenes (DFBs) are well-known organic molecules to understand the electronic structure and spectroscopy of benzene and its derivatives, few theoretical investigations have been performed to simulate their fine spectra and assign their vibrational bands. In this work, the fluorescence excitation (FEX) spectra of the first excited singlet states for three DFBs molecules (para-, meta- and ortho-difluorobenzene) were simulated by the Franck-Condon calculations with the displaced harmonic oscillator approximation plus the distorted correction. The calculated results indicated that the spectral profiles of three DFBs are primarily described by the Franck-Condon progression of their totally symmetric vibrational modes. Specifically, it is found that modes v(3) and v(5) of para-DFB, v(8) and v(9) of meta-DFB, and ortho-DFB play the most important roles in the fluorescence spectra. By taking into account the contributions of the distorted effect, we could assign most of the dominant overtones from the nontotally symmetric vibrational modes, and the results agree well with the experimental assignments. Some inferred and unassigned vibrational transitions in experiment were confirmed according to the present calculated results. In addition, in the simulated fluorescence spectra, we tentatively assigned several combination bands with relative moderate intensity and weak vibrational lines which appeared in the experimental observations but the corresponding assignments were not given. The present work reproduced satisfactorily the experimental FEX spectra of p-, m-, and o-DFBs derivatives and provided a useful method to simulate the FEX spectra of dihalogenated benzene molecules.     

Structure,tautomerism, and features of 1-(5-acetyl-2,4-dihydroxyphenyl)-3-(furan-2-yl)prop-2-en-1-one (FC) and 1,1′-(4,6-dihydroxybenzene-1,3-diyl)bis[3-(furan-2-yl)prop-2-en-1-one] (FDC)

Quantum chemistry studies of various tautomeric/rotameric forms of the furanyl analogues of acetyl dihydroxychalcone (FC) and dihydroxydichalcone (FDC) have shown that the thermodynamically most stable molecules are planar. In the crystalline solid phase, both molecules are more (FDC) or less (FC) non-planar. Two relatively strong intramolecular H-bonds, whose existence is evidenced by X-ray, computational, and spectral investigations, stabilize the planar geometry and influence the features of the lowest energy tautomers/rotamers of both compounds. Extending to the visible region, the electronic absorption of FC and FDC is accompanied by an intramolecular electron density shift, a property that could have analytical implications.