Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models.

Circular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.

The ultraviolet and vacuum ultraviolet absorption spectrum of gamma-pyrone; the singlet states studied by configuration interaction and density functional calculations.

A synchrotron based vacuum ultraviolet absorption spectrum for γ-pyrone has been interpreted in terms of singlet excited electronic states using a variety of coupled cluster, configuration interaction, and density functional calculations. The extremely weak spectral onset at 3.557 eV shows eight vibrational peaks, which following previous analyses, are attributed to a forbidden 1A2 state. A contrasting broad peak with a maximum at 5.381 eV has a relatively high cross-section of 30 Mb; this arises from three overlapping states, where a 1A1 state dominates over progressively weaker 1B2 and 1B1 states. After fitting the second band to a polynomial Gaussian function and plotting the regular residuals over 20 vibrational peaks, we have had limited success in analyzing this fine structure. However, the small separation between these three states clearly shows that their vibrational satellites must overlap. Singlet valence and Rydberg state vibrational profiles were determined by configuration interaction using the CAM-B3LYP density functional. Vibrational analysis using both the Franck-Condon and Herzberg-Teller procedures showed that both procedures contributed to the profiles. Theoretical Rydberg states were evaluated by a highly focused CI procedure. The superposition of the lowest photoelectron spectral band on the vacuum ultraviolet spectrum near 6.4 eV shows that the 3s and 3p Rydberg states based on the 2B2 ionic state are present; those based on the other low-lying ionic state (X2B1) are destroyed by broadening; this is a dramatic extension of the broadening previously witnessed in our studies of halogenobenzenes.

Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane.

The mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-Tooth disease (CMT). GDAP1 is a distant member of the glutathione-S-transferase (GST) superfamily, with unknown enzymatic properties or functions at the molecular level. The structure of the cytosol-facing GST-like domain has been described, but there is no consensus on how the protein interacts with the mitochondrial outer membrane. Here, we describe a model for GDAP1 assembly on the membrane using peptides vicinal to the GDAP1 transmembrane domain. We used oriented circular dichroism spectroscopy (OCD) with synchrotron radiation to study the secondary structure and orientation of GDAP1 segments at the outer and inner surfaces of the outer mitochondrial membrane. These experiments were complemented by small-angle X-ray scattering, providing the first experimental structural models for full-length human GDAP1. The results indicate that GDAP1 is bound into the membrane via a single transmembrane helix, flanked by two peripheral helices interacting with the outer and inner leaflets of the mitochondrial outer membrane in different orientations. Impairment of these interactions could be a mechanism for CMT in the case of missense mutations affecting these segments instead of the GST-like domain.

High-level studies of the singlet states of quadricyclane, including analysis of a new experimental vacuum ultraviolet absorption spectrum by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet absorption spectrum (VUV) of quadricyclane (QC) is reported with energies up to 10.8 eV. Extensive vibrational structure has been extracted from the broad maxima by fitting short energy ranges of the VUV spectrum to high level polynomial functions and processing the regular residuals. Comparison of these data with our recent high-resolution photoelectron spectral of QC showed that this structure must be attributed to Rydberg states (RS). Several of these appear before the valence states at higher energies. Both types of states have been calculated by configuration interaction, including symmetry-adapted cluster studies (SAC-CI) and time dependent density functional theoretical methods (TDDFT). There is a close correlation between the SAC-CI vertical excitation energies (VEE) and both Becke 3-parameter hybrid functional (B3LYP), especially Coulomb-attenuating method-B3LYP determined ones. The VEE for several low-lying s-, p, d-, and f-RS have been determined by SAC-CI and adiabatic excitation energies by TDDFT methods. Searches for equilibrium structures for 11,3A2 and 11B1 states for QC led to rearrangement to a norbornadiene structure. Determination of the experimental 00 band positions, which show extremely low cross-sections, has been assisted by matching features in the spectra with Franck-Condon (FC) fits. Herzberg-Teller (HT) vibrational profiles for the RS are more intense than the FC ones, but only at high energy, and are attributed to up to ten quanta. The vibrational fine structure of the RS calculated by both FC and HT procedures gives an easy route to generating HT profiles for ionic states, which usually require non-standard procedures.

Excitation and fragmentation of the dielectric gas C4F7N: Electrons vs photons.

C4F7N is a promising candidate for the replacement of sulfur hexafluoride as an insulating medium, and it is important to understand the chemical changes initiated in the molecule by collision with free electrons, specifically the formation of neutral fragments. The first step of neutral fragmentation is electronic excitation, yet neither the absorption spectrum in the vacuum ultraviolet (VUV) region nor the electron energy loss spectrum have previously been reported. Here, we experimentally probed the excited states by VUV photoabsorption spectroscopy and electron energy loss spectroscopy (EELS). We found that the distribution of states populated upon electron impact with low-energy electrons is significantly different from that following photoabsorption. This difference was confirmed and interpreted with ab initio modeling of both VUV and EELS spectra. We propose here a new computational protocol for the simulation of EELS spectra combining the Born approximation with approximate forms of correlated wave functions, which allows us to calculate the (usually very expensive) scattering cross sections at a cost similar to the calculation of oscillator strengths. Finally, we perform semi-classical non-adiabatic dynamics simulations to investigate the possible neutral fragments of the molecule formed through electron-induced neutral dissociation. We show that the product distribution is highly non-statistical.

The ionic and ground states of gamma-pyrone. The photoionization spectrum studied by synchrotron radiation and interpreted by configuration interaction and density functional calculations.

A synchrotron-based photoionization spectrum up to 27 eV represents a considerable improvement in resolution over early He(I) and He(II) spectra. Symmetry-adapted coupled cluster calculations of the ionic state sequence give the sequence of state vertical ionization energies (VIE) as 12B2 < 12B1 < 12A2 < 22B1 < 12A1. Generally, these symmetry-adapted cluster configuration interactions VIE match reasonably well with the experimental spectrum over this wide energy range. Density functional calculations of the corresponding adiabatic terms (AIE) were also performed. Higher energy ionic states were determined by complete active space self-consistent field methods; these include all π-ionizations and some σ-ionic states. These were analyzed by Franck-Condon (FC) procedures and compared with an experiment. The spectral onset is complex, where two states, later shown to be the 12B2 and 12B1 states, are strongly overlapping. The superposition of the FC vibrational structure in the 12B2 and 12B1 states accounts for most of the peaks arising at the onset of the photoelectron spectra. However, the small separation between these two ionic states makes vibronic interaction fairly inevitable. In the absence of Herzberg-Teller analyses for ionic states, we have sought and determined a transition state between the 12B2 and 12B1 states, showing that vibronic coupling does occur. The lack of degradation in the vibrational envelope of the higher of the two states contrasts with our previous work on the halogenobenzenes, where overlapping state envelopes led to considerable widening of the line width at half-height of the higher energy states.

Controlled modulation of the dynamics of the Deinococcus grandis Dps N-terminal tails by divalent metals.

DNA-binding proteins from starved cells (Dps) are small multifunctional nanocages expressed by prokaryotes in acute oxidative stress conditions or during the starvation-induced stationary phase, as a bacterial defense mechanism. Dps proteins protect bacterial DNA from damage by either direct binding or by removing precursors of reactive oxygen species from solution. The DNA-binding properties of most Dps proteins studied so far are related to their unordered, flexible, N- and C-terminal extensions. In a previous work, we revealed that the N-terminal tails of Deinoccocus grandis Dps shift from an extended to a compact conformation depending on the ionic strength of the buffer and detected a novel high-spin ferrous iron center in the proximal ends of those tails. In this work, we further explore the conformational dynamics of the protein by probing the effect of divalent metals binding to the tail by comparing the metal-binding properties of the wild-type protein with a binding site-impaired D34A variant using size exclusion chromatography, dynamic light scattering, synchrotron radiation circular dichroism, and small-angle X-ray scattering. The N-terminal ferrous species was also characterized by Mössbauer spectroscopy. The results herein presented reveal that the conformation of the N-terminal tails is altered upon metal binding in a gradual, reversible, and specific manner. These observations may point towards the existence of a regulatory process for the DNA-binding properties of Dps proteins through metal binding to their N- and/or C-terminal extensions.

The excited states of azulene: A study of the vibrational energy levels for the lower ππ*-valence states by configuration interaction and density functional calculations, and theoretical studies of the Rydberg states.

A new vacuum ultraviolet absorption (VUV) spectrum of azulene vapor has been obtained by using a synchrotron radiation source. The onset of the ultraviolet spectrum, previously reported by Sidman et al., has been analyzed in detail by Franck-Condon (FC) and Herzberg-Teller (HT) methods. The photoelectron spectral profile identifies the 3px-Rydberg state 00 band to be 131 cm-1 from the VUV maximum. Excited state energy levels were calculated by three independent methods: the wide scan VUV spectrum was correlated with symmetry adapted cluster configuration interaction calculations. The low energy portion of the spectrum was studied by both time dependent density functional theoretical methods (TDDFT) and multi-reference multi-root CI (MRD-CI). Equilibrium structures were determined for valence states at the TDDFT level. Rydberg states were determined by both TDDFT and MRD-CI. The FC + HT analyses were performed on the TDDFT wave-functions. The HT intensity profiles are generally low in intensity, relative to the FC ones; however, HT is dominant in the second singlet state (S2, 11A1). As a result, numerous non-symmetric modes, their overtones, and combination bands show considerable intensity in that band. Energies obtained from use of extremely diffuse s-, p-, d-, or f-character functions enabled realistic extrapolation to the IE1 for many Rydberg states (RS). The lowest RS (3b13s) based on IE2 lies at 4.804 eV with a quantum defect of 0.714. Differentiation between valence and RS is readily made using the second moments of the charge distribution.

Superanionic Solvent-Free Liquid Enzymes Exhibit Enhanced Structures and Activities.

The surface of a carboxylate-enriched octuple mutant of Bacillus subtilis lipase A (8M) is chemically anionized to produce core (8M)-shell (cationic polymer surfactants) bionanoconjugates in protein liquid form, which are termed anion-type biofluids. The resultant lipase biofluids exhibit a 2.5-fold increase in hydrolytic activity when compared with analogous lipase biofluids based on anionic polymer surfactants. In addition, the applicability of the anion-type biofluid using Myoglobin (Mb) that is well studied in anion-type solvent-free liquid proteins is evaluated. Although anionization resulted in the complete unfolding of Mb, the active α-helix level is partially recovered in the anion-type biofluids, and the effect is accentuated in the cation-type Mb biofluids. These highly active anion-type solvent-free liquid enzymes exhibit increased thermal stability and provide a new direction in solvent-free liquid protein research.

The ground and ionized states of azulene: A combined study of the vibrational energy levels by photoionization, configuration interaction, and density functional calculations.

A synchrotron-based photoionization spectrum of azulene shows a significant additional vibrational fine structure when compared to previous studies. This spectrum was successfully analyzed by using Franck-Condon (FC) methods. Previously reported zero-kinetic-energy electron spectra for azulene have been reinterpreted in FC terms, leading to some alternative assignments to the earlier work. The sequence of ionic states has been determined by using ab initio configuration interaction (CI) methods, leading to reliable theoretical values for both the calculated adiabatic ionization energy (AIE) and vertical ionization energy (VIE). VIEs were calculated by both symmetry-adapted cluster (SAC-CI), together with Green's function (GF) and Tamm-Dancoff approximation (TDA), and single excitation CI methods; AIEs for highest states of each symmetry were determined by open-shell self-consistent field (SCF) methods at the restricted Hartree-Fock level. Complete active space SCF was used for the pairs of 12A2 + 22A2 and 12B1 + 22B1 states, each of which occurs as antisymmetric and symmetric (higher energy) combinations. The combined ionic state sequences (AIE and VIE) from these methods are 12A2 < 12B1 < 22A2 < 22B1. The photoelectron spectrum (PES) shows a series of broadbands above 11 eV, each of which is attributed to more than one ionization. The calculated PES sequence of states of up to 19 eV shows that the SAC-CI and GF results are in almost exact agreement. The internal spacing of the bands is best reproduced by the simpler GF and TDA methods. States involving simultaneous ionization and electronic excitation are considered by both SAC-CI and TDA methods.

The vacuum ultraviolet absorption spectrum of norbornadiene: Vibrational analysis of the singlet and triplet valence states of norbornadiene by configuration interaction and density functional calculations.

A synchrotron-based vacuum ultraviolet (VUV) absorption spectrum of norbornadiene (NBD) is reported, and the extensive vibrational structure obtained has been analyzed. The previously known 5b13s-Rydberg state has been reinterpreted by comparison with our recent high-resolution photoelectron spectral analysis of the X2B1 ionic state. Additional vibrational details in the region of this Rydberg state are observed in its VUV spectrum when compared with the photoelectron 2B1 ionic state; this is attributed to the underlying valence state structure in the VUV. Valence and Rydberg state energies have been obtained by configuration interaction and time-dependent density functional theoretical methods. Several low-lying singlet valence states, especially those that arise from ππ* excitations, conventionally termed NV1 to NV4, have been examined in detail. Their Franck-Condon (FC) and Herzberg-Teller (HT) profiles have been investigated and fitted to the VUV spectrum. Estimates of the experimental 00 band positions have been made from these fits. The anomaly of the observed UV absorption by the 1A2 state of NBD is attributed to HT effects. Generally, the HT components are less than 10% of the FC terms. The calculated 5b13s lowest Rydberg state also shows a low level of HT components. The observed electron impact spectra of NBD have been analyzed in detail in terms of triplet states.

A study on the secondary structure of the metalloregulatory protein CueR: effect of pH, metal ions and DNA.

The response of CueR towards environmental changes in solution was investigated. CueR is a bacterial metal ion selective transcriptional metalloregulator protein, which controls the concentration of copper ions in the cell. Although several articles have been devoted to the discussion of the structural and functional features of this protein, CueR has not previously been extensively characterized in solution. Here, we studied the effect of change in pH, temperature, and the presence of specific or non-specific binding partners on the secondary structure of CueR with circular dichroism (CD) spectroscopy. A rather peculiar reversible pH-dependent secondary structure transformation was observed, elucidated and supplemented with pKa estimation by PROPKA and CpHMD simulations suggesting an important role of His(76) and His(94) in this process. CD experiments revealed that the presence of DNA prevents this structural switch, suggesting that DNA locks CueR in the α-helical-rich form. In contrast to the non-cognate metal ions HgII, CdII and ZnII, the presence of the cognate AgI ion affects the secondary structure of CueR, most probably by stabilizing the metal ion and DNA-binding domains of the protein.

Reduction of enzymatic degradation of insulin via encapsulation in a lipidic bicontinuous cubic phase.

Oral delivery of the protein drug insulin is not currently possible due to rapid degradation of the secondary structure in low pH conditions in the stomach and under the influence of digestive enzymes in the gastrointestinal tract. Effective oral delivery of insulin and other protein- or peptide-based drugs will, therefore, require encapsulation in a material or nanoparticle. Herein we investigate the ability of the lipid bicontinuous cubic phase formed by two lipids, monoolein (MO) and phytantriol (PT), to protect encapsulated insulin from degradation by the enzyme chymotrypsin, typically found in the small intestine. High encapsulation efficiency (>80%) was achieved in both lipid cubic phases with retention of the underlying cubic nanostructure. Release of insulin from the cubic matrix was shown to be diffusion-controlled; the release rate was dependent on the cubic nanostructure and consistent with measured diffusion coefficients for encapsulated insulin. Encapsulation was shown to significantly retard enzymatic degradation relative to that in water, with the protective effect lasting up to 2 h, exemplifying the potential of these materials to protect the encapsulated protein payload during oral delivery.

High-level studies of the ionic states of norbornadiene and quadricyclane, including analysis of new experimental photoelectron spectra by configuration interaction and coupled cluster calculations.

Synchrotron-based photoelectron spectra (PES) of norbornadiene (NBD) and quadricyclane (QC) differ significantly from those in previous studies. The adiabatic ionization energy (AIE1) for NBD, assigned to the 2B1 state at 8.279 eV, shows a progression of 18 members with decreasing vibration frequency from 390 cm-1 to 340 cm-1; our calculated frequency is 381 cm-1. Similarly, the AIE1 for QC at 7.671 eV, assigned to the 2B2 state, discloses a vibrational progression of nine or more members with vibration frequency decreasing from 703 cm-1 to 660 cm-1; our calculated vibration frequency is 663 cm-1. These AIEs, determined by coupled cluster and fourth order Møller-Plesset perturbation theory, were very similar to the corresponding second order perturbation theory results. The calculated AIE symmetry sequences are 2B1 < 2A1 < 2A2 < 2B2 for NBD and 2B2 < 2A2 < 2B1 < 2A1 for QC. The overall PES vertical ionization energy profiles for both compounds were closely reproduced by Tamm-Dancoff approximation energies and intensities. The vibrational structure of the ionic states, determined using Franck-Condon methods, gave a good account of the observed spectra, but the observed envelopes for both IE1 are complex sets of vibrations, rather than single progressions. The NMR spectra for QC showed residual second order properties at 300 MHz; both QC and NBD have been theoretically analyzed in greater detail using AA/BB/CC/XX/ spectra, where all H are coupled; the magnetic shielding and spin-spin coupling constants obtained are similar to experimental values.

Circular dichroism, anisotropy and absorption spectroscopy of chlorophyll b in methanol and mixed methanol-water solutions.

The spectroscopic properties of chlorophyll (Chl) strongly depend on interactions with other Chl molecules, a fact that nature exploits in light harvesting by photosynthetic proteins. In solution, complex Chl aggregates are formed that depend not only on the solvent, but also on the detailed preparation procedure. Here we report synchrotron radiation circular dichroism (SRCD) spectra of Chlb in methanol (MeOH) and MeOH/H2O mixtures; in the latter, water molecules assist in the formation of Chl aggregates as Chlb is too hydrophobic to dissolve in water. The magnitude of the most prominent CD signal increases up to 100-fold over time (2-15 hours) when the water content is increased from 0 to 50% in volume, the signal is non-conservative (almost exclusively negative), and sensitive to sample preparation. Three different types of signature CD spectra (Types A to C) are identified depending on preparation, and the change in CD signal over time and with temperature is further analyzed with anisotropy spectroscopy (ratio of simultaneously recorded CD to absorption) and principal component analysis (PCA). We show that CD is clearly superior to pure absorption spectroscopy in identifying structural changes, and anisotropy spectroscopy further increases the sensitivity towards smaller structural changes. PCA on temperature dependent CD data show that depending on preparation, and thus the type of aggregate as revealed by the CD signature, either one (Type A) or two chiral species (Type B) are identified in the spectra, further evidencing the complex nature of Chlb aggregates. Furthermore, the CD signal decreases linearly with volume when a sample of Chlb in MeOH/H2O (i.e., a sample of Chlb aggregates) is diluted, which implies that the aggregation process is irreversible: once aggregates are formed, they largely do not revert back to monomers. However, anisotropy spectroscopy reveals that there are small changes in the aggregates, not directly noticeable in CD and absorption. The work presented here demonstrates, compared to absorption spectroscopy, a clear advantage of CD and anisotropy spectroscopy in studying the complex evolution of Chl samples with time and temperature.

Absolute Photoabsorption Cross-Sections of Methanol for Terrestrial and Astrophysical Relevance.

We investigate the methanol absorption spectrum in the range 5.5-10.8 eV to provide accurate and absolute cross-sections values. The main goal of this study is to provide a comprehensive analysis of methanol electronic-state spectroscopy by employing high-resolution vacuum ultraviolet (VUV) photoabsorption measurements together with state-of-the-art quantum chemical calculation methods. The VUV spectrum reveals several new features that are not previously reported in literature, for n > 3 in the transitions (nsσ(a') ← (2a″)) (1A' ← X̃1A') and (nsσ, npσ, npσ', ndσ ← (7a')) (1A' ← X̃1A'), and with particular relevance to vibrational progressions of the CH3 rocking mode, v11'(a″), mode in the (3pπ(a″) ← (2a″)) (21A' ← X̃1A') absorption band at 8.318 eV. The measured absolute photoabsorption cross-sections have subsequently been used to calculate the photolysis lifetime of methanol in the Earth's atmosphere from the ground level up to the limit of the stratosphere (50 km altitude). This shows that solar photolysis plays a negligible role in the removal of methanol from the lower atmosphere compared with competing sink mechanisms. Torsional potential energy scans, as a function of the internal rotation angle for the ground and first Rydberg states, have also been calculated as part of this investigation.

The vacuum ultraviolet spectrum of cyclohepta-1, 3, 5-triene: Analysis of the singlet and triplet excited states by ab initio and density functional methods.

The vacuum ultraviolet (VUV) spectrum for cyclohepta-1,3,5-triene up to 10.8 eV shows several broad bands, which are compared with electron impact spectra. Local curve fitting exposed groups of sharp vibrational peaks, which are assigned to Rydberg states. The vertical excitation profile of the VUV spectrum, reproduced by time dependent density functional theory (TDDFT), gives a good interpretation of the principal regions of absorption. Fourth order Möller-Plessett perturbation theory, including single, double, and quadruple excitations, showed that the lowest singlet and triplet states retain CS symmetry. This contrasts with TDDFT where several low-lying excited states are planar. Detailed vibrational analysis of the first UV band was performed by Franck-Condon, Herzberg-Teller, and their combined methods. These show the dominance of mid-range frequencies, while the lowest frequency (75 cm-1) has negligible importance. In contrast, the second excited (Rydberg) state shows a major progression with separations of 115 (6) cm-1. This is interpreted by re-analysis of the X2A' ionic state at the anharmonic level. Extremely low exponent Gaussian functions enabled several low-lying Rydberg state energies to be determined theoretically; extrapolation of the 3s-, 4s-, and 5s-Rydberg state calculated energies gives the adiabatic ionization energy as 7.837 eV (4) with δ 0.964 (2). Similarly, extrapolation of the centroids of the observed Rydberg states gave the vertical ionization energy (VIE) as VIE1 = 8.675 ± 0.077, close to the photoelectron spectroscopy VIE value [8.55 (1) eV].

The ground and ionic states of cyclohepta-1,3,5-triene and their relationship to norcaradiene states: New 1H and 13C NMR spectra and analysis of a new experimental photoelectron spectrum by ab initio methods.

The strong inter-relationship between cyclohepta-1,3,5-triene (CHT) and norcaradiene (NCD) systems observed in some reactions has been extended to include the energy surfaces for some low-lying ionic states. Equilibrium structures for ionic states of CHT with 2A' symmetry were routinely found; the structures emerging with 2A'' symmetry were NCD ionic states. A detailed analysis of these surfaces as a function of the C1 to C6 distance showed that while minima occurred for both state symmetries, curve crossing occurs in CS symmetry, which is avoided by distortion to C1 symmetry. The CHT → NCD structural change is attributed to initial conrotatory closure of the singly occupied molecular orbital. A new synchrotron-based photoelectron spectrum (PES) for CHT up to 25 eV shows little vibrational structure. We have assigned the PES up to 17 eV using a variety of theoretical methods. The calculated lowest ionic state, X2A', is predicted to have a very low vibrational frequency of 87 cm-1, leading to a high density of vibrational states. The Franck-Condon envelopes calculated for the two lowest states are almost completely contained within the envelope of the lowest PES band. A comparison of the predicted PES of CHT and NCD showed much closer agreement of the PES with that of CHT. An analysis of the 1H and 13C nuclear magnetic resonance (NMR) spectra of CHT showed no evidence of NCD. The increased chemical shifts arising from the higher frequencies used here lead to significant changes in appearance when compared with earlier NMR spectra.

On the delocalization length in RNA single strands of cytosine: how many bases see the light?

The interplay between multiple chromophores in nucleic acids and photosynthetic proteins gives rise to complex electronic phenomena and largely governs the de-excitation dynamics. Electronic coupling between bases in the excited states of single strands of DNA and RNA may extend over several bases and likely protects nucleic acids from harmful UV damage. Here we report on the coupling between bases in single RNA strands of cytosine and find that the excited state is delocalized over up to five bases at neutral pH, where all bases are non-protonated (i.e. neutral). Delocalization is over four bases at 278 nm excitation, while it involves five bases at shorter wavelengths of 188 nm and 201 nm. This is in contrast to only nearest-neighbour interactions for corresponding DNA strands as previously reported. The current results seemingly corroborate earlier findings of larger spatial communication in RNA than in DNA strands of adenine, but there is no obvious link between the overall structure of strands and delocalization lengths. RNA cytosine strands form a tight helix, while comparatively, adenine strands show less tight packing, also compared to their DNA counterparts, and yet exhibit even higher delocalisation.

The electronically excited states of cyclooctatetraene-An analysis of the vacuum ultraviolet absorption spectrum by ab initio configuration interaction methods.

A new synchrotron-based study of the vacuum ultraviolet (VUV) absorption spectrum for cyclooctatetraene (COT) shows a series of broad peaks. A significant sharp structure was extracted from the strongest band between 5.9 and 6.3 eV by fitting this range of the spectrum to a polynomial; the regular residuals show a set of sharp peaks. Comparison of this region of the VUV with the photoelectron spectrum demonstrates the presence of several Rydberg states, all based on the lowest observed ionization energy ionic state. The UV onset contains a broad band in the range 4.0 eV-5.3 eV. Theoretical vertical excitation energies, determined by configuration interaction (CI) studies at the multireference multiroot singles and doubles CI level, enabled interpretation of the principal absorption bands of the VUV spectrum. Adiabatic excitation energies (AEEs) for several singlet and triplet valence states (V) were evaluated by multiconfiguration self-consistent field methods. Theoretical Rydberg series AEEs were obtained by use of extremely diffuse Gaussian orbitals in highly correlated wave-functions. The second moments of the charge distribution identify which roots are valence or Rydberg states. A contrast was found between some density functional methods and Hartree-Fock (HF) wave-functions during single-excitation CI, when degenerate orbitals were involved in the leading configurations. The 7a16e* state contained the expected 8-membered ring in the density functional theory calculations. The HF wave-functions led to a 1,5-cross-ring interaction which converged on a singlet excited state of a bicyclo[3,3,0]octatriene; this is reminiscent of the photochemical conversion of COT to semibullvalene.