Perfluoro effect on the electronic excited states of para-benzoquinone revealed by experiment and theory.

We report a comprehensive study on the electronic excited states of tetrafluoro-1,4-benzoquinone, through high-resolution vacuum ultraviolet photoabsorption spectroscopy and time-dependent density functional theory calculations performed within the nuclear ensemble approach. Absolute cross section values were experimentally determined in the 3.8-10.8 eV energy range. The present experimental results represent the highest resolution data yet reported for this molecule and reveal previously unresolved spectral structures. The interpretation of the results was made in close comparison with the available data for para-benzoquinone [Jones et al., J. Chem. Phys., 2017, 146, 184303]. While the dominant absorption features for both molecules arise from analogous π* ← π transitions, some remarkable differences have been identified. The perfluoro effect manifests in different ways: shifts in band positions and cross sections, appearance of features associated with excitations to σCF* orbitals, and spectrum broadening by quenching of either vibrational or Rydberg progressions. The level of agreement between experiment and theory is very satisfactory, yet that required the inclusion of nuclear quantum effects in the calculations. We have also discussed the role of temperature on the absorption spectrum, as well as the involvement of core-excited resonances in promoting dissociative electron attachment reactions in the 3-5 eV range.

Electronic structure and VUV photoabsorption measurements of thiophene.

The absolute photoabsorption cross sections for thiophene in the 5.0-10.7 eV range were measured using synchrotron radiation. New theoretical calculations performed at the time-dependent density functional theory level were used to qualitatively interpret the recorded photoabsorption spectrum. The calculations facilitated a re-analysis of the observed vibronic and Rydberg structures in the photoabsorption spectrum. Here a number of features have been re-assigned, while a number of other features have been assigned for the first time. This represents the most comprehensive and self-consistent assignment of the thiophene high-resolution photoabsorption spectrum to date.

Revisiting the photoabsorption spectrum of NH3 in the 5.4-10.8 eV energy region.

We present a comprehensive revisited experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectrum of ammonia, NH3, covering for the first time the full 5.4-10.8 eV energy-range, with absolute cross sections determined. The calculations on the vertical excitation energies and oscillator strengths were performed using the equation-of-motion coupled cluster method restricted to single and double excitation levels and used to help reanalyze the observed Rydberg structures in the photoabsorption spectrum. The VUV spectrum reveals several new features that are not previously reported in the literature, with particular reference to the vibrational progressions of the (D̃1E'←X̃1A1 '), the (F̃1E'←X̃1A1 '), and the (G̃1A2 ″←X̃1A1 ') absorption bands. In addition, new Rydberg members have been identified in nda1 '←1a2 ″D̃''1A2 ″←X̃1A1 ', where n > 3 has not been reported before as well as in nde″←1a2 ″F̃1E'←X̃1A1 ' and in nsa1 '←1a2 ″G̃1A2 ″←X̃1A1 '. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of ammonia in the Earth's atmosphere (0-50 km).

Probing the Lowest-Lying Electronic States of Acrylic Acid by Experimental and Theoretical Methods.

We report a combined experimental and theoretical study of the electronic state spectroscopy of acrylic acid (C3H4O2) in the gas phase, by high-resolution vacuum ultraviolet (VUV) photoabsorption measurements in the 4.0-10.8 eV energy range, together with ab initio calculations (vertical energies and oscillator strengths), which were used in the assignment of the valence transitions. We also discuss the Rydberg transitions for this molecular target, obtained using the experimental ionization energies available in the literature. The experimental spectrum presented in this paper represents the highest resolution data yet reported for acrylic acid and reveals new features not previously reported in the literature. The dominant transitions have been assigned to (π*(4a″) ← π(3a″)) and (π*(4a″) ← π(2a″)), the latter exhibiting excitation of the ν5'( a') C = O stretching mode with mean energy of 0.155 eV. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of acrylic acid in the upper stratosphere (20-50 km).

The influence of the localised charge of C- and N-termini on peptide self-assembly.

The charge of a peptide influences final assembled structures. It is important to consider not only global charge, but also local, such as that found on the terminal residues. This work investigates the change of peptide self-assembly through the selection of different amino acid sequences and by varying the local charge of the residues on the C- and N-termini.

Valence and lowest Rydberg electronic states of phenol investigated by synchrotron radiation and theoretical methods.

We present the experimental high-resolution vacuum ultraviolet (VUV) photoabsorption spectra of phenol covering for the first time the full 4.3-10.8 eV energy-range, with absolute cross sections determined. Theoretical calculations on the vertical excitation energies and oscillator strengths were performed using time-dependent density functional theory and the equation-of-motion coupled cluster method restricted to single and double excitations level. These have been used in the assignment of valence and Rydberg transitions of the phenol molecule. The VUV spectrum reveals several new features not previously reported in the literature, with particular reference to the 6.401 eV transition, which is here assigned to the 3sσ/σ(∗)(OH)←3π(3a″) transition. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of phenol in the earth's atmosphere (0-50 km).

Toluene Valence and Rydberg Excitations as Studied by ab initio Calculations and Vacuum Ultraviolet (VUV) Synchrotron Radiation.

The electronic spectroscopy of isolated toluene in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 4.0-10.8 eV energy range, with absolute cross-section measurements derived. We present the first set of ab initio calculations (vertical energies and oscillator strengths), which we use in the assignment of valence and Rydberg transitions of the toluene molecule. The spectrum reveals several new features not previously reported in the literature, with particular relevance to 7.989 and 8.958 eV, which are here tentatively assigned to the π*(17a') ← σ(15a') and 1π*(10a″) ← 1π(14a') transitions, respectively. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of toluene in the upper stratosphere (20-50 km).

Valence and Ionic Lowest-Lying Electronic States of Isobutyl Formate Studied by High-Resolution Vacuum Ultraviolet Photoabsorption, Photoelectron Spectroscopy, and Ab Initio Calculations.

The highest resolution vacuum ultraviolet photoabsorption spectrum of isobutyl formate, C5H10O2, yet reported is presented over the energy range 4.5-10.7 eV (275.5-118.0 nm) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series observed in the photoabsorption spectrum have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. Calculations have also been carried out to determine the ionization energies and fine structure of the lowest ionic state of isobutyl formate and are compared with a newly recorded photoelectron spectrum (from 9.0 to 27.0 eV). The value of the first ionization energy was determined to be 10.508 eV (adiabatic) and 10.837 eV (vertical). New vibrational structure is observed in the first photoelectron band, predominantly resulting from C-O and C═O stretches of the molecule. The photoabsorption cross sections have been used to calculate the photolysis lifetime of isobutyl formate in the upper stratosphere (20-50 km), indicating that the hydroxyl radical processes will be the main loss process for isobutyl formate.

Electronic State Spectroscopy of Halothane As Studied by ab Initio Calculations, Vacuum Ultraviolet Synchrotron Radiation, and Electron Scattering Methods.

We present the first set of ab initio calculations (vertical energies and oscillator strengths) of the valence and Rydberg transitions of the anaesthetic compound halothane (CF3CHBrCl). These results are complemented by high-resolution vacuum ultraviolet photoabsorption measurements over the wavelength range 115-310 nm (10.8-4.0 eV). The spectrum reveals several new features that were not previously reported in the literature. Spin-orbit effects have been considered in the calculations for the lowest-lying states, allowing us to explain the broad nature of the 6.1 and 7.5 eV absorption bands assigned to σ*(C-Br) ← nBr and σ*(C-Cl) ← n(Cl) transitions. Novel absolute photoabsorption cross sections from electron scattering data were derived in the 4.0-40.0 eV range. The measured absolute photoabsorption cross sections have been used to calculate the photolysis lifetime of halothane in the upper stratosphere (20-50 km).

Electronic excitation of furfural as probed by high-resolution vacuum ultraviolet spectroscopy, electron energy loss spectroscopy, and ab initio calculations.

The electronic spectroscopy of isolated furfural (2-furaldehyde) in the gas phase has been investigated using high-resolution photoabsorption spectroscopy in the 3.5-10.8 eV energy-range, with absolute cross section measurements derived. Electron energy loss spectra are also measured over a range of kinematical conditions. Those energy loss spectra are used to derive differential cross sections and in turn generalised oscillator strengths. These experiments are supported by ab initio calculations in order to assign the excited states of the neutral molecule. The good agreement between the theoretical results and the measurements allows us to provide the first quantitative assignment of the electronic state spectroscopy of furfural over an extended energy range.

Valence and ionic lowest-lying electronic states of ethyl formate as studied by high-resolution vacuum ultraviolet photoabsorption, He(I) photoelectron spectroscopy, and ab initio calculations.

The highest resolution vacuum ultraviolet photoabsorption spectrum of ethyl formate, C2H5OCHO, yet reported is presented over the wavelength range 115.0-275.5 nm (10.75-4.5 eV) revealing several new spectral features. Valence and Rydberg transitions and their associated vibronic series, observed in the photoabsorption spectrum, have been assigned in accordance with new ab initio calculations of the vertical excitation energies and oscillator strengths. Calculations have also been carried out to determine the ionization energies and fine structure of the lowest ionic state of ethyl formate and are compared with a newly recorded He(I) photoelectron spectrum (from 10.1 to 16.1 eV). New vibrational structure is observed in the first photoelectron band. The photoabsorption cross sections have been used to calculate the photolysis lifetime of ethyl formate in the upper stratosphere (20-50 km).

Anisotropy spectra for enantiomeric differentiation of biomolecular building blocks.

All biopolymers are composed of homochiral building blocks, and both D-sugars and L-amino acids uniquely constitute life on Earth. These monomers were originally enantiomerically differentiated under prebiotic conditions. Particular progress has recently been made in support of the photochemical model for this differentiation: the interaction of circularly polarized light with racemic molecules is currently thought to have been the original source for life's biological homochirality. The differential asymmetric photoreactivity of particular small molecules can be characterized by both circular dichroism and anisotropy spectroscopy. Anisotropy spectroscopy, a novel derivative of circular dichroism spectroscopy, records the anisotropy factor g = Δε/ε as a function of the wavelength. Anisotropy spectroscopy promisingly affords the wavelength-dependent determination of the enantiomeric excess (ee) inducible into chiral organic molecules by photochemical irradiation with circularly polarized light. Anisotropy spectra of small molecules therefore provide unique means for characterizing the different photochemical behaviors between enantiomers upon exposure to various wavelengths of circularly polarized light. This chapter will: (1) present the theory and configuration of anisotropy spectroscopy; (2) explain experimentally recorded anisotropy spectra of selected chiral biomolecules such as amino acids; and (3) discuss the relevance of these spectra for the investigation of the origin of the molecular homochirality observed in living organisms. This review describes a new chiroptical technique that is of significance for advances in asymmetric photochemistry and that is also highly relevant for the European Space Agency Rosetta Mission, which will determine enantiomeric excesses (ees) in chiral organic molecules in cometary ices when it lands on Comet 67P/Churyumov-Gerasimenko in November 2014.

Determination of degree of ionization of poly(allylamine hydrochloride) (PAH) and poly[1-[4-(3-carboxy-4 hydroxyphenylazo)benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO) in layer-by-layer films using vacuum photoabsorption spectroscopy.

Electrostatic and hydrophobic interactions govern most of the properties of supramolecular systems, which is the reason determining the degree of ionization of macromolecules has become crucial for many applications. In this paper, we show that high-resolution ultraviolet spectroscopy (VUV) can be used to determine the degree of ionization and its effect on the electronic excitation energies of layer-by-layer (LbL) films of poly(allylamine hydrochloride) (PAH) and poly[1-[4-(3-carboxy-4 hydroxyphenylazo)benzene sulfonamido]-1,2-ethanediyl, sodium salt] (PAZO). A full assignment of the VUV peaks of these polyelectrolytes in solution and in cast or LbL films could be made, with their pH dependence allowing us to determine the pK(a) using the Henderson-Hasselbach equation. The pK(a) for PAZO increased from ca. 6 in solution to ca. 7.3 in LbL films owing to the charge transfer from PAH. Significantly, even using solutions at a fixed pH for PAH, the amount adsorbed on the LbL films still varied with the pH of the PAZO solutions due to these molecular-level interactions. Therefore, the procedure based on a comparison of VUV spectra from solutions and films obtained under distinct conditions is useful to determine the degree of dissociation of macromolecules, in addition to permitting interrogation of interface effects in multilayer films.

Electronically excited states of formic acid investigated by theoretical and experimental methods.

Absolute cross-section values are reported from high-resolution vacuum ultraviolet (VUV) photoabsorption measurements of gas-phase formic acid (HCOOH) in the photon energy range 4.7-10.8 eV (265-115 nm), together with quantum chemical calculations to provide vertical energies and oscillator strengths. The combination of experimental and theoretical methods has allowed a comprehensive assignment of the electronic transitions. The VUV spectrum reveals various vibronic features not previously reported in the literature, notably associated with (3pa'←10a'), (3p'a'←10a'), (3sa'←2a″) and (3pa'←2a″) Rydberg transitions. The assignment of vibrational features in the absorption bands reveal that the C=O stretching, v3'a', the H'-O-C' deformation, v5'a', the C-O stretching, v6'a', and the O=C-O' deformation, v7'a' modes are mainly active. The measured absolute photoabsorption cross sections have also been used to estimate the photolysis lifetime of HCOOH in the upper stratosphere (30-50 km), showing that solar photolysis is an important sink at altitudes above 30 km but not in the troposphere. Potential energy curves for the lowest-lying electronic excited states, as a function of the C=O coordinate, are obtained employing time dependent density functional theory (TD-DFT). These calculations have shown the relevance of internal conversion from Rydberg to valence character governing the nuclear dynamics, yielding clear evidence of the rather complex multidimensional nature of the potential energy surfaces involved.

Soluble factor requirements for the autostimulatory growth of B lymphoblasts immortalized by Epstein-Barr virus.

B lymphoblasts immortalized by the Epstein-Barr virus (EBV) exhibit autocrine growth stimulation--that is they release a soluble activity to which they respond by growth. A minimally supplemented serum-free medium conditioned by lymphoblastoid cells in their log phase of growth (LCL-CM) was found to contain autostimulatory activity allowing us to explore the mechanism of autocrine growth for these cell-types in defined conditions. Below cell densities capable of supporting autonomous growth, continued proliferation in serum-free medium was dependent on both added LCL-CM and transferrin. Neither activity alone was capable of sustaining growth. At higher cell densities, transferrin by itself was sufficient to maintain the autocrine loop. The action of the autostimulatory factor appeared to reside in its ability to prime cells continually for a proliferative response to transferrin by enhancing the expression of transferrin receptors at the lymphoblast surfaces. The implications of these findings for normal B cell physiology and their possible relation to oncogenesis are discussed.

The FGF receptor-1 tyrosine kinase domain regulates myogenesis but is not sufficient to stimulate proliferation.

Ligand-stimulated activation of FGF receptors (FGFRs) in skeletal muscle cells represses terminal myogenic differentiation. Skeletal muscle cell lines and subsets of primary cells are dependent on FGFs to repress myogenesis and maintain growth. To understand the intracellular events that transduce these signals, MM14 skeletal muscle cells were transfected with expression vectors encoding chimeric receptors. The chimeras are comprised of the PDGF beta receptor (PDGFbetaR) extracellular domain, the FGFR-1 intracellular domain, and either the PDGFbetaR or FGFR-1 transmembrane domain. The chimeric receptors were autophosphorylated upon PDGF-BB stimulation and are capable of stimulating mitogen-activated protein kinase activity. Activation of the tyrosine kinase domain of either chimera repressed myogenesis, suggesting intracellular responses regulating skeletal muscle differentiation are transduced by activation of the FGFR-1 tyrosine kinase. Unexpectedly, we found that activation of either chimeric receptor failed to stimulate cellular proliferation. Thus, it appears that regulation of skeletal muscle differentiation by FGFs requires only activation of the FGFR tyrosine kinase. In contrast, stimulation of proliferation may require additional, as yet unidentified, signals involving the receptor ectodomain, the FGF ligand, and heparan sulfate either alone, or in combination.

Viral-encoded cyclins.

D-type cyclin homologs have been found in the genomes of herpesviruses associated with neoplasias. They appear to exploit features of G(1) cyclins but extend their properties to allow for deregulation of the cell cycle. Advances in the study of the molecular basis for these novel features as well as the potential role of viral cyclins in tumorigenesis are addressed.

E2F-1 but not E2F-4 can overcome p16-induced G1 cell-cycle arrest.

BACKGROUND: The transition from G1 to S phase is the key regulatory step in the mammalian cell cycle. This transition is regulated positively by G1-specific cyclin-dependent kinases (cdks) and negatively by the product of the retinoblastoma tumour suppressor gene, pRb. Hypophosphorylated pRb binds to and inactivates the E2F transcription factor, which controls the expression of genes required for S-phase progression. Hyperphosphorylation of pRb in late G1 phase results in the accumulation of active E2F, a critical event in the progression to S phase. The E2F factor is not a single entity, but rather represents a family of highly related molecules, all of which bind to pRb or the pRb-related proteins p107 and p130. RESULTS: In this study, we have used specific inhibitors of cdks to explore the requirements for cell-cycle progression from G1 to S phase. Expression of p16Ink4, which specifically inhibits cyclin D-directed cdks, blocks cells in G1 phase; this block can be overcome by expression of the viral proteins that inactivate pRb or by E2F-1. Importantly however, the G1 arrest is not overcome by overexpression of E2F-4. By using chimeric E2F proteins, containing amino-acid sequences from E2F-1 and E2F-4, we have shown that their differential abilities to overcome a p16-imposed arrest is determined by their respective amino-terminal regions. We also demonstrate that E2F-1 can promote entry into S phase without concomitant phosphorylation of pRb. In contrast to the p16-mediated G1 block, G1 arrest mediated by the cdk inhibitors p21Cip1 or p27Kip1 cannot be bypassed either by inactivation of pRb or overexpression of E2F family members. CONCLUSIONS: These data demonstrate that the role of the cyclin D-directed cdks in promoting the progression of cells from G1 into S phase is wholly to activate an E2F-1-like activity through phosphorylation, thus preventing the formation of the E2F-pRb complex. The cyclin E-cdk2 complex is also required for the G1/S transition but has a different and as yet undefined role. We also provide evidence for a functional difference between E2F-1 and E2F-4, dependant upon the region that contains the DNA-binding and dimerization domains. These results indicate that these two E2F family members are likely to regulate the expression of different subsets of E2F-responsive promoters.

Germline variable region gene segment derivation of human monoclonal anti-Rh(D) antibodies. Evidence for affinity maturation by somatic hypermutation and repertoire shift.

To date, there has been no systematic study of the process of affinity maturation of human antibodies. We therefore sequenced the variable region genes (V genes) of 14 human monoclonal antibodies specific for the erythrocyte Rh(D) alloantigen and determined the germline gene segments of origin and extent of somatic hypermutation. These data were correlated with determinations of antibody affinity. The four IgM antibodies (low affinity) appear to be derived from two germline heavy chain variable region gene segments and one or two germline light chain variable region gene segments and were not extensively mutated. The 10 IgG antibodies (higher affinity) appear to be derived from somatic hypermutation of these V gene segments and by use of new V gene segments or V gene segment combinations (repertoire shift). Affinity generally increased with increasing somatic hypermutation; on average, there were 8.9 point mutations in the V gene segments of the four IgM antibodies (Ka = 1-4 x 10(7)/M-1) compared with 19 point mutations in the V gene segments of the 10 IgG antibodies. The four highest affinity antibodies (Ka = 0.9-3 x 10(9)/M-1) averaged 25.5 point mutations. The use of repertoire shift and somatic hypermutation in affinity maturation of human alloantibodies is similar to data obtained in inbred mice immunized with haptens.

E1A control of gene expression is mediated by sequences 5' to the transcriptional starts of the early viral genes.

A product of the adenovirus E1A gene is a positive regulator of early viral gene expression. In this report we show that E1A regulates at the transcriptional level and that sequences located 5' to the early viral regions contain sites which confer regulation by the E1A gene product. We constructed chimeric genes in which the sequences at the 5' end of the E2A, E3, and E4 regions were fused to the structural sequences of either the herpes simplex virus thymidine kinase gene, the bacterial gene encoding the enzyme neomycin phosphotransferase, or the chloramphenicol acetyltransferase gene. In all cases, expression of the chimeric genes was induced by a product of the E1A region. It was also found that the insertion of a fragment from the left-hand end of the adenovirus type 5 genome into a plasmid harboring the thymidine kinase gene resulted in elevated frequencies of transformation of TK- cells to TK+. The elevated transformation frequencies were only detected when the insert and tk gene were covalently joined. This effect occurred even when the insert was several kilobase upstream from, and regardless of its orientation to, the transcriptional initiation site of the tk gene. We propose that this region of the adenovirus type 5 genome harbors a cis-acting enhancer of transcription.