Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra.

Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and ß-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.

Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI.

Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.

Clinically Manifesting, Naturally Occurring Fowl Glioma in a Leghorn Chicken in Germany.

Fowl glioma-inducing virus (FGV), a strain of avian leukosis virus (ALV) subgroup A, is the causal agent of fowl glioma characterized by multiple nodular astrocytic growths, gliosis, and lymphocytic encephalitis. Also associated with FGV infection are cases of cerebellar hypoplasia, perineuromas, and nonsuppurative myocarditis. Though fowl glioma has been recognized in several countries, most reports of FGV infection come from Japan. A 9-mo-old brown leghorn from a German farm with nine leghorns was presented to a veterinarian with an impaired general health with torticollis, tremor, and incoordination. Histopathology revealed multifocal nodular astrocytic growths, gliosis, and a lymphoplasmacytic encephalitis. Immunohistochemically, neoplastic astrocytes showed positivity for anti-ALV antibody. FGV was detected in the brain with nested reverse transcription-polymerase chain reaction (RT-PCR) and subsequent sequencing of PCR product. The remaining eight birds were screened for the presence of ALV with real-time RT-PCR. Four leghorns tested positive for exogenous ALV in nested RT-PCR with an identical nucleotide sequence as the leghorn with neurological symptoms. To the authors' knowledge this is the first report of a natural FGV infection in a brown leghorn in Germany with clinical manifestation.

Glioma aviar de manifestación clínica y natural en un pollo Leghorn en Alemania. El virus inductor del glioma del pollo (FGV), una cepa del subgrupo A del virus de la leucosis aviar (ALV), es el agente causal del glioma del pollo caracterizado por crecimientos astrocíticos nodulares múltiples, gliosis y encefalitis linfocítica. También se asocian con la infección por este virus, casos de hipoplasia cerebelar, perineuromas y miocarditis no supurativa. Aunque el glioma aviar se ha reconocido en varios países, la mayoría de los informes de infección por el virus inductor del glioma del pollo provienen de Japón. Un pollo Leghorn marrón de nueve meses de edad proveniente de una granja alemana con nueve aves Leghorns fue remitido a una clínica veterinaria con problemas de salud en general, tortícolis, temblores y falta de coordinación. La histopatología reveló crecimientos astrocíticos nodulares multifocales, gliosis y encefalitis linfoplasmocítica. Inmunohistoquímicamente, los astrocitos neoplásicos mostraron reacción positiva para anticuerpos contra el virus de la leucosis aviar. El virus inductor del glioma del pollo se detectó en el cerebro mediante transcripción reversa y reacción en cadena de la polimerasa anidada (RT-PCR) y con secuenciación posterior del producto de PCR. Las ocho aves restantes se examinaron para detectar la presencia del virus de la leucosis aviar mediante RT-PCR en tiempo real. Cuatro aves Leghorn dieron positivo para virus exógenos de leucosis mediante RT-PCR anidada y con una secuencia de nucleótidos idéntica a la del ave Leghorn con síntomas neurológicos. De acuerdo con el conocimiento de los autores, este es el primer informe de una infección natural por el virus inductor del glioma del pollo en un ave Leghorn marrón en Alemania que presentaba manifestaciones clínicas.

Spin-state dependence of exchange-correlation holes.

Applications of density-functional theory (DFT) in computational chemistry rely on an approximate exchange-correlation (xc) functional. However, existing approximations can fail dramatically for open-shell molecules, in particular for transition-metal complexes or radicals. Most importantly, predicting energy differences between different spin-states with approximate exchange-correlation functionals remains extremely challenging. Formally, it is known that the exact xc functional should be spin-state dependent, but none of the available approximations feature such an explicit spin-state dependence [C. R. Jacob and M. Reiher, Int. J. Quantum Chem., 2012, 112, 3661-3684]. Thus, to find novel approximations for the xc functional for open-shell systems, the development of spin-state dependent xc functionals appears to be a promising avenue. Here, we set out to shed light on the spin-state dependence of the xc functional by investigating the underlying xc holes, which we extract from configuration interaction calculations for model systems. We analyze the similarities and differences between the xc holes of the lowest-energy singlet and triplet states of the dihydrogen molecule, the helium atom, and the lithium dimer. To shed further light on the spin-state dependence of these xc holes we also discuss exact conditions that can be derived from the spin structure of the reduced two-electron density matrix. Altogether, our results suggest several possible routes towards the construction of explicitly spin-state dependent approximations for the xc functional.