Charge-transfer transitions in the vacuum-ultraviolet of protein circular dichroism spectra

Circular dichroism (CD) is widely used in the structural characterization and secondary structure determination of proteins. The vacuum UV region (below 190 nm), where charge-transfer transitions have an influence on the CD spectra, can be accessed using synchrotron radiation circular dichroism (SRCD) spectroscopy. Recently, charge-transfer transitions in a conformationally diverse set of dipeptides have been characterized ab initio using complete active space self-consistent field calculations, and the relevant charge distributions have been parametrized for use in the matrix method for calculations of protein CD. Here, we present calculations of the vacuum UV CD spectra of 71 proteins, for which experimental SRCD spectra and X-ray crystal structures are available. The theoretical spectra are calculated considering charge-transfer and side chain transitions. This significantly improves the agreement with experiment, raising the Spearman correlation coefficient between the calculated and the experimental intensity at 175 nm from 0.12 to 0.79. The influence of the conformation on charge-transfer transitions is analyzed in detail, showing that the n --> pi* charge-transfer transitions are most important in alpha-helical proteins, whereas in beta strand proteins the pi --> pi* charge-transfer transition along the chain in the amino- to carboxy-end direction is most dominant.     

The electronic absorption spectra of nine substituted phenols

A new technique—photoacoustic spectroscopy (PAS)—is used for the first time to record the u.v.-vis spectra of nine substituted phenols. The π-π* electronic transitions analogous to benzene first primary and secondary transitions could be detected from the PAS spectra in comparison with the u.v. solution and vapour phase spectra recorded by conventional methods. Detection of singlet → triplet absorptions from the PAS spectra, with significant intensity, is considered to be an important feature which transitions are in general either not observed or observed with weak intensity, by conventional methods. The analyses show that a few excited state combinations observed in the u.v.-vis PAS spectra compare well with such combinations in the ground state observed in the near i.r. PAS spectra of the molecules.     

High-resolution absorption spectra of diphenylnmethylenes

High-resolution absorption spectra of the following diphenylmethylenes (DPM_s) dispersed in benzophenone crystals at liquid-helium temperatures are presented: DPM-h₁₀, DPM-d₁₀, 4-chloro-DPM, and 4-bromo-DPM. The substituent effects concerning the electronic structure, transition energy and intensity are discussed. From polarization measurements, the electronic configurations of the ground and the first excited triplet states of these DPM_s are assigned as (pπ)¹(pσ)¹ and (pσ)¹(π*)¹, respectively. Further studies reveal a second excited triplet state, designated as (pπ)¹(π*)¹, which lies less than 1000 cm^-1 above the first excited triplet state of DPM. Diffuse broad bands appear as common features in all the spectra. Such diffuseness is discussed in terms of electron-phonon coupling of the low-lying excited states.     

The absorption and circular dichroism spectra of chiral olefins

Absorption and CD spectra over the quartz and vacuum UV region down to 165 nm are reported for a range of chiral alkenes in the vapour phase and in solution from +70° to ?185°C. A major couplet of oppositely-signed CD bands with comparable band areas, near 48 and 55 kK, is observed in a number of dissymmetric olefins and in some cases a weaker Rydberg CD absorption is found at lower frequency. The Rydberg CD band is characterised by its sharp vibronic structure in the vapour phase and by large blue-shifts produced on passing to the condensed phase and by a reduction in temperature. The olefin couplet of major CD bands with opposite sign is assigned to a near-complete mixing of the electric-dipole π_x→π_x^* and the magnetic-dipole π_x→π_y^* excitations, producing a pair of isotiopic absorption bands with the same polarisation and comparable dipole strengths associated with the CD couplet. Three mixing mechanisms are discussed; sterically-induced π-bond torsion, a first-order static field model, and a second-order dynamic-coupling model dependent, respectively, upon the effective charge and upon the mean polarisability of dissymmetrically-located substituent. The latter two models give the octant rule previously proposed empirically connecting the sign of the rotational strength of the lower- and higher-frequency member of the olefin CD couplet with the position of the substituent in the chromophore coordinate frame.     

Modeling of phytochrome absorption spectra

Phytochromes constitute one of the six well‐characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high‐resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV‐vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes. © 2013 Wiley Periodicals, Inc.     

The absorption spectra of the phenoxyl radical in solid argon

Vacuum ultraviolet photolysis of phenol, phenol-d₆ and anisole during condensation with excess argon at 20 K has produced and trapped the phenoxyl radical as evidenced by structured absorptions at 397.2 and 628.1 nm. A broad photosensitive 416 ± 2 nm band is tentatively assigned to the phenol cation.     

The effect of cryogenic sample cooling on X-ray absorption spectra

It is common for samples to be cooled to near liquid He temperature (4 K) during measurement of their X-ray absorption spectra (XAS). This procedure is believed to improve spectrum quality either by minimizing radiation damage, or by decreasing thermal motions of atoms. The actual benefits realized by cooling are rarely assessed, since that would require duplicate measurements at multiple temperatures, followed by duplicate data analyses. With a cryostat installed, it is difficult to measure room temperature or hotter spectra, which often requires removing the cryostat from the beam path.Here we investigate the effect of cooling and show that it is not globally useful in X-ray absorption spectroscopy. Photolysis does not occur, or its consequences are not controlled by cooling. Secondary photochemical damage is delayed and is remote from the absorption site. Thermal motions do not usually contribute significantly to disorder and consequent damping of EXAFS, either because vibrational amplitudes are small, or because static disorder and structural complexity affect EXAFS in the same way but more profoundly.The low probability of photochemical effects on XAS is in contrast to the situation with crystallography of biological specimens, where photochemical damage anywhere in the sample degrades the data set regardless of proximity to atoms of one specific element. Thermal disorder becomes important in certain types of samples and when the Debye-Waller factor is itself used as a tool. In most cases, it is more efficient to first measure room temperature spectra, and then repeat measurement using a cryostat of only those spectra where the objectives of the analysis justify an attempt to gain more information.     

Infrared absorption spectra of As-Se glasses

IR absorption spectra of As-Se glasses have been studied over a wide range of compositions. Various two-phonon, multiphonon (combination tones) and impurity absorptions have been identified. Compositional variation of relative band intensities has been explained in terms of the chemically ordered network model.     

Electronic absorption spectra and EPR spectra of irradiated silicate glasses

The election absorption spectra of sodium silicate glasses in the visible region and the EPR spectra of -irradiated two-component alkali silicate glasses have been studied. It has been established that the electron absorption spectra of these glasses have two bands in the visible region of the spectrum, while the EPR line with g=2.01 consists of two components. A comparison of the absorption spectral data with the EPR spectra showed that the band having a maximum around 4400 å and the -component of the doublet with g=2.01 are associated with the same hole center, of the type Si-O^–... Me⁺ while the band having a maximum around 6200 å and the -component of the doublet arise from a hole center of the type Si-O^–. The change in the ratio of the intensities of the - and -components with changes in the concentration and type of alkali metal is explained.     

The electronic absorption spectra of pyridine azides, solvent-solute interaction

The electronic absorption spectra of: 2-, 3-, and 4-azidopyridines have been investigated in a wide variety of polar and non-polar solvents. According to Onsager model, the studied spectra indicate that the orientation polarization of solvent dipoles affects the electronic spectrum much stronger than the induction polarization of solvent dipoles. The effect of solvent dipole moment predominates that of solvent refractive index in determining the values of band maxima of an electronic spectrum. The spectra of azidopyridines differ basically from these of pyridine or mono-substituted pyridine. Results at hand indicate that the azide group perturbs the pyridine ring in the case of 3-azidopyridine much more than it does in the case of 2-azidopyridine. This result agrees with the predictions of the resonance theory. Although the equilibrium <==> azide tetrazole is well known, yet the observed spectra prove that such an equilibrium does not exist at the studied conditions. The spectra of the studied azidopyridines are characterized by the existence of overlapping transitions. Gaussian analysis is used to obtain nice, resolved spectra. All the observed bands correspond to pi-->pi* transitions, n-->pi* may be overlapped with the stronger pi-->pi* ones.     

Infrared absorption spectra of 2,2-dibromobutane

The possible existence of geometrically isomeric forms of the title compound, CH₃CBr₂CH₂CH₃, has been investigated by i.r. spectroscopy. It was found that the general features of the spectra can be interpreted reasonably in terms of only one conformation of the molecules in the liquid state. Further confirmation of this view, based on a brief comparison of the liquid phase spectra of CH₃CBr₂CH₂CH₃ and CH₃CHBrCHBrCH₃ is given. Vibrational assignments have been made for most of the fundamental bands assuming C_s molecular symmetry.     

Infrared absorption spectra of trialkyl orthovanadates

Conclusions The IR spectra of seven trialkyl orthovanadates were studied. The absorption bands of the V=O and V-O bonds in the spectra of these compounds are found respectively in the 960–1012 and 600–662 cm^–1 regions.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 12, pp. 2812–2814, December, 1972.     

Predicting absorption spectra of silver-ligand complexes

The detailed structures of most of ligand-stabilized metal nanoclusters (NCs) remain unknown due to the absence of crystal structure data for them. In such a situation, quantum-chemical modeling is of particular interest. We compared the performance of different theoretical methods of geometry optimization and absorption spectra calculation for silver-thiolate complexes. We showed that the absorption spectra calculated with the ADC(2) method were consistent with the spectra obtained with CC2 method. Three DFT functionals (B3LYP, CAM-B3LYP, and M06-2X) failed to reproduce the CC2 absorption spectra of the silver-thiolate complexes.