Excited-state hydrogen bonding and deprotonation of esculetin in solution: a DFT/TDDFT study

The combined density functional theory (DFT) and time-dependent density functional theory (TDDFT) method was used to study the electronic spectral properties of different deprotonated forms of esculetin. By comparing the experimental absorption and fluorescence bands with the calculated electronic spectra, it is evidently demonstrated that the minor absorption and fluorescence bands observed at slightly longer wavelengths than the principal bands in experiments are predominantly from the de-H3 form of the esculetin monomer. Furthermore, we clarified the relationship between electronic spectral shifts and electronic excited-state intramolecular hydrogen bonding changes: the strengthening of intramolecular hydrogen bond can induce an electronic spectral blueshift while the intramolecular hydrogen bond weakening can result in an electronic spectral redshift.     

Spectral densities of infinite systems with strong electron correlations

Until now, solids with strongly correlated electrons can be treated only by model Hamiltonians. Even then a calculation of spectral densities is not simple, because the strong Coulomb interactions prevent us from treating correlations perturbatively. We show that projection and partitioning techniques are a very valuable tool here. The method is applied to computations of the density of states of transition metals, in particular, Ni. Here, the band narrowing and the sattlite peak at 6 eV due to correlations are reproduced. A second application concerns the spectral density of doped and undoped Cu(SINGLE BOND)O planes which are part of the high-T_c superconducting materials. © 1997 John Wiley & Sons, Inc. J Quant Chem 63: 645–653, 1997     

Spectral density analysis of nuclear spin—spin coupling: II. Hartree-Fock LCAO studies for homonuclear coupling constants

A spectral density function has been calculated for the indirect nuclear spin—spin coupling constant for homonuclear coupling. The ground state wavefunction is obtained with a normal ab-initio calculation. The sum over states approach for calculating the reduced coupling constant K is replaced by an integration over a spectral density function where the integration variable is the orbital exponent of a “scanning molecular orbital”. This results in a stable method for calculating K with reasonable accuracy. The spectral density function also gives information about which excited states give important contributions to K.Furthermore a residual spectral density function is defined that can be used as a test for the completeness of a set of virtual orbitals in a sum over states calculation.     

2-4’-甲酰基苯乙烯基苯并噻唑衍生物的合成和光谱特性

氮杂芪(azastilbene)衍生物及其盐类,是一类重要的功能化合物,和普通的芪类化合物相比,它的光谱响应范围可以大幅度地移向长波区。同时它具有很强的分子可极化率,对外场作用响应灵敏。     

Raman Optical Activity of Glucose and Sorbose in Extended Wavenumber Range

Raman optical activity (ROA) is pursued as a promising method for structural analyses of sugars in aqueous solutions. In the present study, experimental Raman and ROA spectra of glucose and sorbose obtained in an extended range (50–4000 cm⁻¹) are interpreted using molecular dynamics and density functional theory, with the emphasis on CH stretching modes. A reasonable theoretical basis for spectral interpretation was obtained already at the harmonic level. Anharmonic corrections led to minor shifts of band positions (up to 25 cm⁻¹) below 2000 cm⁻¹, while the CH stretching bands shifted more, by ∼180 cm⁻¹, and better reproduced the experiment. However, the anharmonicities could be included on a relatively low approximation level only, and they did not always improve the harmonic band shapes. The dependence on the structure and conformation shows that the CH stretching ROA spectral pattern is a sensitive marker useful in saccharide structure studies.     

Separating Vibrational Coherences in Ground/Excited Electronic States of Solvent/Solute Following Non-Resonant/Resonant Impulsive Excitation

In a quest to track down the origin of coherent vibrational motions observed in femtosecond pump-probe transients, whether they arise from ground/excited electronic state of solute or are contributed by the solvent, we demonstrate a method for extricating vibrations under resonant and non-resonant impulsive excitations using a diatomic solute in condensed phase (iodine in carbon tetrachloride) with aid of spectral dispersion of the chirped broadband probe. Most importantly, we show how a sum over intensities for a select region of detection wavelengths and Fourier transform of data over select temporal window untwine contributions from vibrational modes of different origins. Thus, in a single pump-probe experiment, vibrational features specific to solute as well as solvent are disentangled that are otherwise spectrally overlapping and are non-separable in conventional (spontaneous/stimulated) Raman spectroscopy employing narrowband excitation. We envision wide-ranging applications of this method to unveil vibrational features in complex molecular systems.     

A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: strengthening and weakening

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally.     

用局部拟合主成分回归计算光度分析法测定黄连生物碱

针对具有样本数据非无匀分布和非线性特点的光度分析问题，提聘种局部拟合 主成分回归法，用于中药多组分计算测定。该方法根据待测样本与各已知样本光度 分析数据的欧式距离确定相应的权值，将部分权值较大的样本组成校正集，并用分 段线性拟合算法建立待测样本的校正预测模型，将其用于分析黄连的药根碱、巴巴 亭和小檗碱等三种生物碱，所得预测均方根误差分别为0.023,0.0400和0.052，优 于主成分回归法、偏最小二乘法以及人工神经元网络法所得结果。这表明，本方法 用于中药光度分析能获得较为准确的计算分析结果。     

Excited state reactivity index theory application for small moieties

This study aims to use the concept of ground‐state reactivity index formalism within density functional theory (DFT) to predict the behavior of the excited state through the response function produced by weak electric field on chlorinated methanes and chlorinated benzenes. A comparison was made between the geometry of ground state and the excited state for those moieties through configuration interaction (CI) method with Austin Model 1 Hamiltonian over the optimized geometry of DFT at the ground state. Results obtained through these two methodologies suggested that in terms of polarizability and heat of formation, DFT can reproduce the excited state qualitatively. Again, those results can be further validated through UV spectral data, generated using CI method. The reactivity index proposition at ground state shows the potential of DFT to simulate excitation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A hierarchical transition state search algorithm

A hierarchical transition state search algorithm is developed and its implementation in the density functional theory program deMon2k is described. This search algorithm combines the double ended saddle interpolation method with local uphill trust region optimization. A new formalism for the incorporation of the distance constrain in the saddle interpolation method is derived. The similarities between the constrained optimizations in the local trust region method and the saddle interpolation are highlighted. The saddle interpolation and local uphill trust region optimizations are validated on a test set of 28 representative reactions. The hierarchical transition state search algorithm is applied to an intramolecular Diels-Alder reaction with several internal rotors, which makes automatic transition state search rather challenging. The obtained reaction mechanism is discussed in the context of the experimentally observed product distribution.     

用EM算法改进鸟枪法蛋白质鉴定中的无标记定量方法

蛋白质定量是探索疾病发生发展状况和寻找新药靶标的重要手段。在shotgun蛋白组学中,目前常用定量方法包括综合同位素标记后的质谱峰强度方法和无标记定量方法。根据数据类型无标记定量方法可以分为两类:基于鉴定蛋白的质谱数的方法和基于质谱峰强度的方法。本研究主要用EM算法改进基于鉴定蛋白质谱数的定量方法,并用免疫印迹实验获得的酵母全蛋白的丰度来验证EM算法改进后定量的有效性结果表明,改进后的质谱数和蛋白丰度的相关性比改进前有一定的提高。同时,利用这些数据对主要的几种基于鉴定蛋白的质谱数的模型进行了比较,发现PAI模型最好,SpS模型次之,emPAI模型最不适合于蛋白质定量。     

Resolving Electronic Transitions in Synthetic Fluorescent Protein Chromophores by Magnetic Circular Dichroism

The detailed electronic structures of fluorescent chromophores are important for their use in imaging of living cells. A series of green fluorescent protein chromophore derivatives is examined by magnetic circular dichroism (MCD) spectroscopy, which allows the resolution of more bands than plain absorption and fluorescence. Observed spectral patterns are rationalized with the aid of time‐dependent density functional theory (TDDFT) computations and the sum‐over‐state (SOS) formalism, which also reveals a significant dependence of MCD intensities on chromophore conformation. The combination of organic and theoretical chemistry with spectroscopic techniques also appears useful in the rational design of fluorescence labels and understanding of the chromophore's properties. For example, the absorption threshold can be heavily affected by substitution on the phenyl ring but not much on the five‐member ring, and methoxy groups can be used to further tune the electronic levels.     

Vibronic Dynamics of Photodissociating ICN from Simulations of Ultrafast X-Ray Absorption Spectroscopy

Ultrafast UV-pump/soft-X-ray-probe spectroscopy is a subject of great interest since it can provide detailed information about dynamical photochemical processes with ultrafast resolution and atomic specificity. Here, we focus on the photodissociation of ICN in the ¹Π₁ excited state, with emphasis on the transient response in the soft-X-ray spectral region as described by the ab initio spectral lineshape averaged over the nuclear wavepacket probability density. We find that the carbon K-edge spectral region reveals a rich transient response that provides direct insights into the dynamics of frontier orbitals during the I−CN bond cleavage process. The simulated UV-pump/soft-X-ray-probe spectra exhibit detailed dynamical information, including a time-domain signature for coherent vibration associated with the photogenerated CN fragment.     

Origin of the anomalous two-photon absorption in fluorescent protein DsRed

The red fluorescent protein DsRed displays a two-photon excitation band around 760 nm which is not accompanied by any feature in the corresponding one-photon spectral region (380 nm). By means of time-dependent density functional theory, we are able to explain such an effect, as arising from an electronic excitation of the DsRed chromophore with ability to couple with a charge-transfer state, through an effective two-photon absorption channel.     

Numerical Solution of the Drop Population Balance Equation Using Weighted Residual and Finite Volume Methods

This article presents a comparison of numerical results obtained by two different approximations of population balances—the spectral orthogonal collocation and finite volume methods. In particular, the population balance equation for a homogeneous dispersed liquid–liquid system in a batch reactor was considered in the present numerical study. The focus was placed on the accuracy of the numerical approximation of the particle property density distribution. An advantage of the finite volume method is the easy of distributing the points in a nonuniform discretization. It is supposed that the spectral-element orthogonal collocation method may benefit by dividing the computational domain into elements of various polynomial orders. For the present problems studied, the orthogonal collocation in the spectral framework does not perform as well as the finite volume method.     

Chemical potential perturbation: a method to predict chemical potentials in periodic molecular simulations

A new method, called chemical potential perturbation (CPP), has been developed to predict the chemical potential as a function of density in periodic molecular simulations. The CPP method applies a spatially varying external force field to the simulation, causing the density to depend upon position in the simulation cell. Following equilibration the homogeneous (uniform or bulk) chemical potential as a function of density can be determined relative to some reference state after correcting for the effects of the inhomogeneity of the system. We compare three different methods of approximating this correction. The first method uses the van der Waals density gradient theory to approximate the inhomogeneous Helmholtz free energy density. The second method uses the local pressure tensor to approximate the homogeneous pressure. The third method uses the Triezenberg-Zwanzig definition of surface tension to approximate the inhomogeneous free energy density. If desired, the homogeneous pressure and Helmholtz free energy can also be predicted by the new method, as well as binodal and spinodal densities of a two-phase fluid region. The CPP method is tested using a Lennard-Jones (LJ) fluid at vapor, liquid, two-phase, and supercritical conditions. Satisfactory agreement is found between the CPP method and an LJ equation of state. The efficiency of the CPP method is compared to that for Widom's method under the tested conditions. In particular, the new method works well for dense fluids where Widom's method starts to fail.     

电感耦合等离子体发射光谱中的光谱干扰

光谱干扰是电感耦合等离子体发射光谱(ICP-AES)中的主要干拢。已有不少文献作了报道。CIP发射光谱的波长表,为研究光谱干扰提供了可靠的数据和资料。本文试对这方面的文献进行了归纳和分析。光谱干扰包括光谱线的重叠和背景。在ICP-AES中,有以下几种类型的光谱干扰不可忽视:     

Ultrafast infrared spectroscopy of riboflavin: dynamics, electronic structure, and vibrational mode analysis

Femtosecond time-resolved infrared spectroscopy was used to study the vibrational response of riboflavin in DMSO to photoexcitation at 387 nm. Vibrational cooling in the excited electronic state is observed and characterized by a time constant of 4.0 +/- 0.1 ps. Its characteristic pattern of negative and positive IR difference signals allows the identification and determination of excited-state vibrational frequencies of riboflavin in the spectral region between 1100 and 1740 cm (-1). Density functional theory (B3LYP), Hartree-Fock (HF) and configuration interaction singles (CIS) methods were employed to calculate the vibrational spectra of the electronic ground state and the first singlet excited pipi* state as well as respective electronic energies, structural parameters, electronic dipole moments and intrinsic force constants. The harmonic frequencies of the S 1 excited state calculated by the CIS method are in satisfactory agreement with the observed band positions. There is a clear correspondence between computed ground- and excited-state vibrations. Major changes upon photoexcitation include the loss of the double bond between the C4a and N5 atoms, reflected in a downshift of related vibrations in the spectral region from 1450 to 1720 cm (-1). Furthermore, the vibrational analysis reveals intra- and intermolecular hydrogen bonding of the riboflavin chromophore.     

Structure of aqueous solutions of group IIIA metals perchlorates by near infrared spectroscopy

The state of water in aqueous solutions of group IIIA metal perchlorates at 25°C was studied by the IR spectroscopy in the range of 5400–7500 cm^?1. The optical density values of the solution measured at different wavelengths were combined in a matrix of experimental data of the uniform dimension. The matrices were chemometrically analyzed. A number, spectra, and concentration profiles of the spectral forms existing in the solution were determined. By the principal component method, the IR spectra of the studied systems are grouped into the mathematical clusters according to the nature of the cation-water interaction in the solution. The combined use of the infrared spectroscopy and chemometric analysis showed that the structural changes in the solution predicted by the generalized phenomenological model are due to the existence and interconversion of the spectral forms.     

SPECTRAL PROPERTIES OF CHLOROPHYLL a MONOLAYERS: MONOLAYERS OF CHLOROPHYLL a AND PHEOPHYTIN AT A GAS-WATER INTERFACE*

Abstract— Surface and spectral properties of chlorophyll a monolayers were studied at a nitrogen-water interface. Direct spectral analysis of Chl monolayers indicated that compression results in a heterogenous mixture of Chl species. Fourth derivative and difference spectra showed the presence of minor bands at 692, 726 and 748 nm. The state of compression determines the quantity and type of spectral species formed. A Chl monolayer on an acid subphase results in the formation of a long wavelength absorbing species (705 nm) similar to that of pheophytin. The half-band width, optical density/monolayer, and extinction coefficients of Chl monolayers are given. It is concluded that in the monolayer the formation of various aggregated species of Chl can be induced.