PhotochemCAD‡: A Computer-Aided Design and Research Tool in Photochemistry

A database of absorption and fluorescence spectra, including molar absorption coefficients and fluorescence quantum yields, has been compiled for 125 photochemically relevant compounds. An accompanying program enables calculation of oscillator strengths, natural radiative lifetimes, transition dipole moments, Forster energy-transfer rates, multicomponent analysis, simulations of fluorescence spectra upon energy transfer among linear arrays of pigments, calculations of blackbody radiator curves at different temperatures and Lorentzian and Gaussian peak distributions. The program runs under Windows 95 and is equipped with extensive literature references and help features.     

Generation of substructure identification rules using feature-combinations from tandem mass spectra

Software to interpret tandem mass spectra, entitled Method for Analyzing Patterns in Spectra (MAPS), has been developed to provide substructure information for an automated compound identification system, This software consists of several program modules which manipulate databases of tandem mass spectra and substructure information, generate substructure identification rules, and apply these rules to the tandem mass spectra of unknown compounds to identify components of their structure. The MAPS rule generation program has been modified to generate rules based on specific combinations of spectral features that occur concertedly. False positives are drastically reduced by searching for “feature-combinations” that have 100% uniqueness with respect to a reference database of compounds. Recall is increased by the determination of multiple feature-combinations indicative of the presence of a given substructure. Strategies were developed in the algorithm for the discovery of feature-combinations that avoid the computation “explosion” that occurs when working with a large number of spectral features. The rules developed have the form: “IF feature-eombination a (FC a) or FC b,..., or FC x, THEN substructure SSn is present.”     

An activation analysis system for short-lived radioisotopes including automatic dead-time corrections with a microcomputer

A system based on an IBM-PC microcomputer coupled to a Canberra Series 80 multichannel analyser has been developed for activation analysis with short-lived radioisotopes. The data transfer program can store up to 77 gamma-ray spectra on a floppy disk. A spectrum analysis program, DVC, has been written to determine peak areas interactively, to correct the counting losses, and to calculate elemental concentrations.     

GammaLab: a suite of programs for k0-NAA and gamma-ray spectrum analysis

The GammaLab is a collection of computer codes, written in MATLAB, for performing calculations involved in k ₀ neutron activation analysis. The main features of the program include calibrations including energy-channel, energy-FWHM and energy-efficiency for different geometries, background subtraction, nuclide identification, spectral interference correction, elemental concentration and limit of detection determination. The data input is taken from two files one is the spectrum file stored in IAEA ASCII format and other is report file containing peak energy and peak area data. The information about sample, irradiation and counting conditions, background spectra are retrieved from QAQCData database. GammaLab takes nuclear data such as gamma lines, emission probabilities, half-lives, and k ₀ factors from NucData database. The sample results which contain elemental concentrations with uncertainties are stored in the QAQCData database. The program has been evaluated by analyzing several hundred spectra and results were found satisfactory.     

Nonplanar property study of antifungal agent tolnaftate-spectroscopic approach

Vibrational analysis of the thionocarbamate fungicide tolnaftate which is antidermatophytic, antitrichophytic and antimycotic agent, primarily inhibits the ergosterol biosynthesis in the fungus, was carried out using NIR FT-Raman and FTIR spectroscopic techniques. The equilibrium geometry, various bonding features, harmonic vibrational wavenumbers and torsional potential energy surface (PES) scan studies have been computed using density functional theory method. The detailed interpretation of the vibrational spectra has been carried out with the aid of VEDA.4 program. Vibrational spectra, natural bonding orbital (NBO) analysis and optimized molecular structure show the clear evidence for electronic interaction of thionocarbamate group with aromatic ring. Predicted electronic absorption spectrum from TD-DFT calculation has been compared with the UV-vis spectrum. The Mulliken population analysis on atomic charges and the HOMO-LUMO energy were also calculated. Vibrational analysis reveals that the simultaneous IR and Raman activation of the C-C stretching mode in the phenyl and naphthalene ring provide evidence for the charge transfer interaction between the donor and acceptor groups and is responsible for its bioactivity as a fungicide.     

Simulation of atomic spectra—II. Mutual spectral interferences of rare earth elements in the inductively coupled plasma

This article is an electronic publication in Spectrochimica Acta Electronica (SAE), the electronic section of Spectrochimica Acta B (SAB). The hardcopy text, comprising the main article and an appendix, is accompanied by a diskette with a program, data files, and a manual. The text details the purpose of the work, with emphasis on the spectroscopic aspects, and the appendix provides the essential information for accessing the diskette and using program and data. Additional tutorial guidance is provided by the manual.

The program primarily concerns the simulation of the spectra of rare earth elements (REE) as interferents in 80-pm wide spectral windows centred about the wavelengths of 26 prominent lines of Ce, La, Nd, Pr, and Sm. The program essentially covers the model described in Spectrochim. Acta 43B, 1365 (1988) and the database is identical to the experimental database published in Spectrochim. Acta 44B, 31 (1989). Accordingly, the data are for an inductively coupled plasma (ICP). The program enables the user to simulate spectra with the spectral bandwidth as an optional variable. The user may then generate spectra of both single REEs, without or with analyte, and mixtures of REEs of any composition, also without or with analyte, whereby for spectra with analyte the display includes the blank spectrum. Displays are accompanied by legends providing a set of essential numerical data. In addition, particular program options allow the generation of numerical data only, one of them being the calculation of true detection limits. This option permits it to perform, within the limited scope of the database, line selection for complex REE samples in a rational way.

The program operates, in principle, with the default values of the ICP Doppler temperature (6800 K) and “average” ICP a-parameter of the Voigt profile (0.5), but these values may be optionally modified. Similarly, the user may add new data files to the base and thus also apply the program for other purposes and outside the REE environment, such as model studies in general, and for learning or teaching, as explained in the manual on the diskette. The tutorial part of this manual provides the user not only with elementary instructions for using the program as a practical tool, but also incorporates a variety of instructive examples, including a brief “course” on spectral line profiles and spectral interferences.     

Modern strategies for PC-supported spectral analysis of 1D NMR data

 Analysis of high-resolution NMR spectra elucidation has been known for many years. Hard-and software development now permits the implementation of such programs on personal computers. The structural information hidden in complex proton NMR spectra becomes easily accessible by using graphical user interfaces and direct data exchange between programs. A new mode has been implemented in 1D WIN-NMR to support the analysis of multiplet patterns with first order rules. Structure display, direct export mechanisms to the simulation program WIN-DAISY, and an archiving possibility complete the state-of-the-art data analysis. Some practical examples are given. Received: 25 October 1996/Revised: 6 March 1997/Accepted: 10 March 1997     

NAA with the improved relative method and the interactive computer program EPAA

The program EPAA has been written to perform neutron activation analysis calculations on a personal computer. It reads gamma-ray spectra from disk, calculates peak areas using interactive computer graphics, corrects interferences, and calculates the concentrations of the elements chosen by the user with the improved relative standardization method. This method is suitable for use with reactors with reproducible neutron fluxes. Calibrations are performed for all elements in standard counting geometries and are used for subsequent analyses over a long period of time.     

Energy transfer dynamics in light-harvesting assemblies templated by the tobacco mosaic virus coat protein

Picosecond time-resolved fluorescence spectroscopy was used to characterize energy transfer between chromophores displayed on a rod assembly of tobacco mosaic virus coat protein. The incorporation of donor chromophores with broad and overlapping absorption and emission spectra creates an "antenna" with a large absorption cross section, which can convey excitation energy over large distances before transfer to an acceptor chromophore. The possibility for both donor-to-donor and donor-to-acceptor transfer results in complex kinetic behavior at any single wavelength. Thus, to describe the various pathways of energy transfer within this system accurately, a global lifetime analysis was performed to obtain decay associated spectra. We found the energy transfer from donor to acceptor chromophores occurs in 187 ps with an efficiency of 36%. A faster decay component of 70 ps was also observed from global lifetime analysis and is attributed to donor-to-donor transfer. Although more efficient three-chromophore systems have been demonstrated, a two-chromophore system was studied here to facilitate analysis.     

ForceFit: A code to fit classical force fields to quantum mechanical potential energy surfaces

The ForceFit program package has been developed for fitting classical force field parameters based upon a force matching algorithm to quantum mechanical gradients of configurations that span the potential energy surface of the system. The program, which runs under UNIX and is written in C++, is an easy‐to‐use, nonproprietary platform that enables gradient fitting of a wide variety of functional force field forms to quantum mechanical information obtained from an array of common electronic structure codes. All aspects of the fitting process are run from a graphical user interface, from the parsing of quantum mechanical data, assembling of a potential energy surface database, setting the force field, and variables to be optimized, choosing a molecular mechanics code for comparison to the reference data, and finally, the initiation of a least squares minimization algorithm. Furthermore, the code is based on a modular templated code design that enables the facile addition of new functionality to the program. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures

The structural characterization of proteins and peptides isolated in minute quantities requires the most efficient use of available sample. A mass spectrometer data system was programmed to continuously evaluate incoming liquid chromatography/mass spectrometry data against a user-defined array of information. The resulting conclusions were used to automatically set and modify acquisition parameters in real time to collect collision-induced dissociation spectra for selected ions (tandem mass spectrometry). This approach has provided a mechanism to target specific subsets of masses in a complex mixture and/or to discriminate selectively against masses that are known or not of interest. Masses of contaminants or peptide masses derived from known proteins can be automatically recorded and removed from further consideration for collision-induced dissociation analysis. Once recorded, these “libraries” of masses can be used across multiple analyses. This technique directs the mass spectrometer data system to focus on the analysis of masses significant to the user, even if their signal intensities are well below the intensities of contaminating masses. When combined with a database search program to correlate tandem mass spectra to known protein sequences, the identity of the protein can be established unequivocally by using less than 100 fmol of sample.     

双色双共振-多光子电离光谱研究小分子的碰撞诱导转动能量转移

用双色双共振多光子电离光谱方法测量了NO分子A~(2∑+)(v=0)态的转动能量转移, 得到了由R-F能量转移导致的转动可分辨的弛豫光谱, 计算了转动态-态转移速率常数。用以转移能量为基础的指数和幂指数能隙模型, 对碰撞弛豫态分布进行计算机模拟, 并从计算值与实验值的比较讨论了能隙模型存在的不足。用同法对I_2分子B∏(O_u~+)态的测量, 得到由转动能量转移导致的谱线展宽及交叠并作了分析。     

The synthesis, photoluminescence and energy transfer mechanism of a reactive Eu(III)-complex intermediate of white light phosphor

A reactive Eu(III)-complex intermediate of white light phosphor was synthesized using benzoylactone, 1,10-phenanthroline and undecylenic acid as ligands. The structure of the complex was characterized by elemental analysis and FT-IR spectra. The luminescent properties were investigated by fluorescence spectra and UV?Cvis absorption spectra. The results indicate that the complex emitted the characteristic peaks of the Eu(III) ion when being excited at 367?nm, revealing that the complex can be excited by 365?nm of ultraviolet. The energy of the highest occupied molecular orbital and the lowest unoccupied molecular orbital as well as the singlet state and triplet state energy level of the ligands were calculated with the Gaussian03 program package. Intramolecular energy transfer mechanism was studied and an energy transfer diagram was sketched to illuminate the energy transfer process. The Eu(III)-copolymer was synthesized by the free radical copolymerization of the Eu(III)-complex and methyl methacrylate. XRD analysis indicates that the Eu(III)-complex in the copolymer was dispersed much more uniformly into the polymer matrix than that in the doped polymer. The photoluminescent properties of the Eu(III)-polymer suggest that the Eu(III)-complex is a good candidate of red light moiety in white light phosphor.     

A new computer program for QSAR-analysis: ARTE-QSAR

A new computer program has been designed to build and analyze quantitative-structure activity relationship (QSAR) models through regression analysis. The user is provided with a range of regression and validation techniques. The emphasis of the program lies mainly in the validation of QSAR models in chemical applications. ARTE-QSAR produces an easy interpretable output from which the user can conclude if the obtained model is suitable for prediction and analysis.     

Ultrafast energy transfer and structural dynamics in DNA

Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.     

YTaO4：Gd,Eu体系光致发光中的能量传递

Yttrium orthotantalate co doped by Eu 3+ and Gd 3+ has been synthesized by solid state method. The emission and excitation spectra of YTaO4: Gd, Eu are studied in detail. In the excitation spectra of Eu 3+5D 0→ 7F2 transition emission in YTaO4:Gd, Eu, there appear excitations of Gd3+ and TaO43- group, which indicate energy transfer from Gd 3+ and TaO4 3- group to Eu 3+ in the process of luminescence. The excitation spectra of Gd 3+ emission(λ=312 5 nm) including strong excitation of charge transfer of group show energy transfer from host lattice to Gd 3+ . So there are two ways of energy transfer in YTaO4:Gd,Eu system. The strong evidences from excitation spectra, emission spectra and diffusive reflection spectra of this system show that Gd 3+ can play an intermediate role in the process of luminescence. There is energy transfer from TaO 3- 4 to Gd 3+ and finally to Eu 3+ via the charge transfer state and spectral overlap. The energy transfer from TaO 3- 4 to Gd 3+ is a dominating process in this system.     

Computerized data acquisition and processing for Shpol'skii high-resolution spectrofluorimetry

The program described provides simultaneously digital control of a high-resolution spectrofluorimeter, acquisition of analog signals and data storage, and contains graphics processing to visualize spectra. Automatic evaluation software, which evaluates peak heights and calculates concentrations is included. The program runs on an IBM PC-AT2 (or compatible) equipped with interface cards; it is composed of distinct modules which are obtained through a menu. The system has been applied to the determination of 13 polynuclear aromatic hydrocarbons (PAHs); it offers high selectivity, excellent detection limits, and rapidity of data acquisition. Results obtained for 9 PAHs in a standard urban dust (SRM-1649) were satisfactory.     

Tuning the Surface Structure and Optical Properties of CdSe Clusters Using Coordination Chemistry

A series of nonstoichiometric CdSe clusters with lowest energy electronic absorptions between 409 - 420 nm has been prepared from cadmium 1-naphthoate, 2-naphthoate, 4-thiomethyl-1-naphthaote, and 1-naphthalene thiolate complexes and diphenylphosphine selenide (DPPSe). Pair distribution function analysis of X-ray diffraction data, ligand exchange experiments, and NMR molecular weight analyses suggest the nanocrystal core changes minimally among these clusters despite significant changes to their absorption and luminescence spectra. Photoluminescence excitation spectra obtained at 77 K reveal an energy transfer process between the surface-trapped excited state and the naphthalene-containing ligands that leads to ligand phosphorescence. A Dexter energy transfer mechanism is proposed to explain the observation of ligand phosphorescence on excitation of the cluster. These compounds demonstrate that cluster absorption and trap luminescence can be controlled with surface coordination chemistry.