The vertical excitation energies of 17 boron-dipyrromethene (BODIPY) core structures with a variety of substituents and ring sizes are benchmarked using time-dependent density functional theory (TD-DFT) with nine different functionals combined with the cc-pVTZ basis set. When compared to experimental measurements, all functionals provide mean absolute errors (mean AEs) greater than 0.3 eV, larger than the 0.1-0.3 eV differences typically expected from TD-DFT. Due to the high linear correlation of TD-DFT results with experiment, most functionals can be used to predict excitation energies if corrected empirically. Using the CAM-B3LYP functional, 0-0 transition energies are determined, and while the absolute difference is improved (mean AE = 0.478 eV compared to 0.579 eV), the correlation diminishes substantially (R(2) = 0.961 to 0.862). Two very recently introduced charge transfer (CT) indices, q(CT) and d(CT), and electron density difference (EDD) plots demonstrate that CT does not play a significant role for most of the BODIPYs examined and, thus, cannot be the source of error in TD-DFT. To assess TD-DFT methods, vertical excitation energies are determined utilizing TD-HF, configuration interaction CIS and CIS(D), equation of motion EOM-CCSD, SAC-CI, and Laplace-transform based local coupled-cluster singles and approximate doubles LCC2* methods. Moreover, multireference CASSCF and CASPT2 vertical excitation energies were also obtained for all species (except CASPT2 was not feasible for the four largest systems). The SAC-CI/cc-pVDZ, LCC2*/cc-pVDZ, and CASPT2/cc-pVDZ approaches are shown to have the smallest mean AEs of 0.154, 0.109, and 0.100 eV, respectively; the utility of the LCC2* approach is demonstrated for eight extended BODIPYs and aza-BODIPYs. We found that the problems with TD-DFT arise from difficulties in dealing with the differential electron correlation (as assessed by comparing CCS, CC2, LR-CCSD, CCSDR(T), and CCSDR(3) vertical excitation energies for five compounds) and from contributions of multireference character and double excitations (from analysis of the CASSCF wave functions).

Orientation and alignment parameters have been computed from first principles for the photodissociation of the HF and DF diatomic molecules. The calculations are entirely ab initio and the break-up dynamics of the molecule is treated rigorously taking account of the electronically nonadiabatic dynamics on three coupled adiabatic electronic potential energy curves. The potential energy curves and spin–orbit interactions, which have been previously reported [J. Chem. Phys. 113, 1870 (2000)], are computed using ab initio molecular electronic structure computer codes. These are then used to compute photofragmentation T matrix elements using a time-dependent quantum mechanical wave packet treatment and from these a complete set of anisotropy parameters with rank up to K=3 is computed. The predicted vector correlations and alignment parameters are presented as a function of energy for HF and DF initially in both their ground and first excited vibrational states. The parameters predicted for the molecules which are initially in their excited vibrational states display a pronounced sharp energy dependence arising from the nodal structure of the initial vibrational wavefunction. The theoretical results are analyzed using a simple model of the dynamics and it is demonstrated how the magnitude and relative phases of the photofragmentation T matrix elements can be deduced from the experimentally measured alignment parameters. No experimental measurements have yet been made of alignment parameters for hydrogen halide diatomics and the present results provide the first predictions of these quantities which may be compared with future experimental observations.

Hepatitis C virus (HCV) infection is a major cause of liver disease and hepatocellular carcinoma. Glycan shielding has been proposed to be a mechanism by which HCV masks broadly neutralizing epitopes on its viral glycoproteins. However, the role of altered glycosylation in HCV resistance to broadly neutralizing antibodies is not fully understood. Here, we have generated potent HCV neutralizing antibodies hu5B3.v3 and MRCT10.v362 that, similar to the previously described AP33 and HCV1, bind to a highly conserved linear epitope on E2. We utilize a combination of in vitro resistance selections using the cell culture infectious HCV and structural analyses to identify mechanisms of HCV resistance to hu5B3.v3 and MRCT10.v362. Ultra deep sequencing from in vitro HCV resistance selection studies identified resistance mutations at asparagine N417 (N417S, N417T and N417G) as early as 5days post treatment. Comparison of the glycosylation status of soluble versions of the E2 glycoprotein containing the respective resistance mutations revealed a glycosylation shift from N417 to N415 in the N417S and N417T E2 proteins. The N417G E2 variant was glycosylated neither at residue 415 nor at residue 417 and remained sensitive to MRCT10.v362. Structural analyses of the E2 epitope bound to hu5B3.v3 Fab and MRCT10.v362 Fab using X-ray crystallography confirmed that residue N415 is buried within the antibody-peptide interface. Thus, in addition to previously described mutations at N415 that abrogate the β-hairpin structure of this E2 linear epitope, we identify a second escape mechanism, termed glycan shifting, that decreases the efficacy of broadly neutralizing HCV antibodies.

Two-photon spectroscopy of fluorescent proteins is a powerful bioimaging tool. Considerable effort has been made to measure absolute two-photon absorption (TPA) for the available fluorescent proteins. Being a technically involved procedure, there is significant variation in the published experimental measurements even for the same protein. In this work, we present a time-dependent density functional theory (TDDFT) study on isolated chromophores comparing the ability of four functionals (PBE0, B3LYP, CAM-B3LYP, and LC-BLYP) combined with the 6-31+G(d,p) basis set to reproduce averaged experimental TPA energies and cross sections. The TDDFT energies and TPA cross sections are also compared to corresponding CC2/6-31+G(d,p) results for excitation to S1 for the five smallest chromophores. In general, the computed TPA energies are less functional dependent than the TPA cross sections. The variation between functionals is more pronounced when higher-energy transitions are studied. Changes to the conformation of a chromophore are shown to change the TPA cross-section considerably. This adds to the difficulty of comparing an isolated chromophore to the one embedded in the protein environment. All functionals considered give moderate agreement with the corresponding CC2 results; in general, the TPA cross sections determined by TDDFT are 1.5-10 times smaller than the corresponding CC2 values for excitation to S1. LC-BLYP and CAM-B3LYP give erroneously large TPA cross sections in the higher-energy regions. On the other hand, B3LYP and PBE0 yield values that are of the same order of magnitude and in some cases very close to the averaged experimental data. Thus, based on the results reported here, B3LYP and PBE0 are the preferred functionals for screening chromphores for TPA. However, at best, TDDFT can be used to semiquantitatively scan chromophores for potential TPA probes and highlight spectroscopic peaks that could be present in the mature protein.

High resolution ion imaging study of BrCl photolysis in the wavelength range 330-570 nm Quasiclassical and quantum mechanical modeling of the breakdown of the axial recoil approximation observed in the near threshold photolysis of IBr and Br 2The photodissociation of jet-cooled IBr molecules has been investigated at numerous excitation wavelengths in the range 440-685 nm using a state-of-art ion imaging spectrometer operating under optimal conditions for velocity mapping. Image analysis provides precise threshold energies for the ground, I( 2 P 3/2 )ϩBr( 2 P 3/2 ), and first excited ͓I( 2 P 3/2 )ϩBr( 2 P 1/2 )͔ dissociation asymptotes, the electronic branching into these two active product channels, and the recoil anisotropy of each set of products, as a function of excitation wavelength. Such experimental data have allowed mapping of the partial cross-sections for parallel ͑i.e., ⌬⍀ϭ0) and perpendicular ͑i.e., ⌬⍀ϭϮ1) absorptions and thus deconvolution of the separately measured ͑room temperature͒ parent absorption spectrum into contributions associated with excitation to the A 3 ⌸(1), B 3 ⌸(0 ϩ ) and 1 ⌸(1) excited states of IBr. Such analyses of the continuous absorption spectrum of IBr, taken together with previous spectroscopic data for the bound levels supported by the A and B state potentials, has allowed determination of the potential energy curves for, and ͑R independent͒ transition moments to, each of these excited states. Further wave packet calculations, which reproduce, quantitatively, the experimentally measured wavelength dependent product channel branching ratios and product recoil anisotropies, serve to confirm the accuracy of the excited state potential energy functions so derived and define the value ͑120 cm Ϫ1 ) of the strength of the coupling between the bound (B) and dissociative (Y ) diabatic states of 0 ϩ symmetry.

We report a full dimensional, ab initio based potential energy surface for CH(5) (+). The ab initio electronic energies and gradients are obtained in direct-dynamics calculations using second-order Møller-Plesset perturbation theory with the correlation consistent polarized valence triple zeta basis. The potential energy and the dipole moment surfaces are fit using novel procedures that ensure the full permutational symmetry of the system. The fitted potential energy surface is tested by comparing it against additional electronic energy calculations and by comparing normal mode frequencies at the three lowest-lying stationary points obtained from the fit against ab initio ones. Well-converged diffusion Monte Carlo zero-point energies, rotational constants, and projections along the CH and HH bond lengths and the tunneling coordinates are presented and compared with the corresponding harmonic oscillator and standard classical molecular dynamics ones. The delocalization of the wave function is analyzed through comparison of the CH(5) (+) distributions with those obtained when all of the hydrogen atoms are replaced by (2)H and (3)H. The classical dipole correlation function is examined as a function of the total energy. This provides a further probe of the delocalization of CH(5) (+).

We report a potential energy surface and calculations of power spectra for CH 5 ϩ. The potential surface is obtained by precise fitting of MP2/cc-pVTZ electronic energies and gradients, which are obtained in classical direct-dynamics calculations. The power spectra are obtained using standard microcanonical classical and novel quasiclassical calculations of the velocity autocorrelation function, from which the power spectrum is obtained in the usual way. Both calculations agree qualitatively that the overall spectrum is quite complex; however, the latter calculations indicate that some spectral features may be assignable.

The synthesis of the first examples of tellurophenes exhibiting phosphorescence in the solid state and under ambient conditions (room temperature and in air) is reported. Each of these main-group-element-based emitters feature pinacolboronates (BPin) as ring-appended side groups. The nature of the luminescence observed was also investigated using computational methods.