Review Of Experimental Gapt And Infrared Atomic Charges In Molecules

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)This review contains experimental values of polar tensors and generalized atomic polar tensor (GAPT) charges determined since the publication of the polar tensor formulism for infrared intensity interpretation in 1961. GAPT charges, also called mean dipole moment derivatives, for 167 atoms of 67 molecules are discussed and compared with infrared charges also determined completely from experimental intensities. The importance of the charge transfer and polarization dynamic contributions to the GAPT charge are emphasized as they differentiate this charge from most theoretically calculated charges. The inclusion of these dynamic contributions is shown to be necessary to provide adequate numerical descriptions of core electron ionization energy processes. These contributions are expected to be important in studies of chemical reactivity.276979991Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq)Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior (CAPES)CNPq [140711/2013-9]FAPESP [2014/21241-9, 09/09678-4]Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP

Review of experimental GAPT and infrared atomic charges in molecules

This review contains experimental values of polar tensors and generalized atomic polar tensor (GAPT) charges determined since the publication of the polar tensor formulism for infrared intensity interpretation in 1961. GAPT charges, also called mean dipole moment derivatives, for 167 atoms of 67 molecules are discussed and compared with infrared charges also determined completely from experimental intensities. The importance of the charge transfer and polarization dynamic contributions to the GAPT charge are emphasized as they differentiate this charge from most theoretically calculated charges. The inclusion of these dynamic contributions is shown to be necessary to provide adequate numerical descriptions of core electron ionization energy processes. These contributions are expected to be important in studies of chemical reactivity276979991CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQCOORDENAÇÃO DE APERFEIÇOAMENTO DE PESSOAL DE NÍVEL SUPERIOR - CAPESFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP140711/2013-9Sem informação2014/21241-9; 09/09678-

Atomic Charge Transfer-counter Polarization Effects Determine Infrared Ch Intensities Of Hydrocarbons: A Quantum Theory Of Atoms In Molecules Model.

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.1623224-3

Quantum Theory Of Atoms In Molecules/charge-charge Flux-dipole Flux Models For Fundamental Vibrational Intensity Changes On H-bond Formation Of Water And Hydrogen Fluoride.

The Quantum Theory of Atoms In Molecules/Charge-Charge Flux-Dipole Flux (QTAIM/CCFDF) model has been used to investigate the electronic structure variations associated with intensity changes on dimerization for the vibrations of the water and hydrogen fluoride dimers as well as in the water-hydrogen fluoride complex. QCISD/cc-pVTZ wave functions applied in the QTAIM/CCFDF model accurately provide the fundamental band intensities of water and its dimer predicting symmetric and antisymmetric stretching intensity increases for the donor unit of 159 and 47 km mol(-1) on H-bond formation compared with the experimental values of 141 and 53 km mol(-1). The symmetric stretching of the proton donor water in the dimer has intensity contributions parallel and perpendicular to its C2v axis. The largest calculated increase of 107 km mol(-1) is perpendicular to this axis and owes to equilibrium atomic charge displacements on vibration. Charge flux decreases occurring parallel and perpendicular to this axis result in 42 and 40 km mol(-1) total intensity increases for the symmetric and antisymmetric stretches, respectively. These decreases in charge flux result in intensity enhancements because of the interaction contributions to the intensities between charge flux and the other quantities. Even though dipole flux contributions are much smaller than the charge and charge flux ones in both monomer and dimer water they are important for calculating the total intensity values for their stretching vibrations since the charge-charge flux interaction term cancels the charge and charge flux contributions. The QTAIM/CCFDF hydrogen-bonded stretching intensity strengthening of 321 km mol(-1) on HF dimerization and 592 km mol(-1) on HF:H2O complexation can essentially be explained by charge, charge flux and their interaction cross term. Atomic contributions to the intensities are also calculated. The bridge hydrogen atomic contributions alone explain 145, 237, and 574 km mol(-1) of the H-bond stretching intensity enhancements for the water and HF dimers and their heterodimer compared with total increments of 149, 321, and 592 km mol(-1), respectively.14008430

Fingerprints of carbon defects in vibrational spectra of gallium nitride (GaN) consider-ing the isotope effect

This work examines the carbon defects associated with recently reported and novel peaks of infrared (IR) absorption and Raman scattering appearing in GaN crystals at carbon ($^{12}C$) doping in the range of concentrations from $3.2*10^{17}$ to $3.5*10^{19} cm^{-3}$. 14 unique vibrational modes of defects are observed in GaN samples grown by hydride vapor phase epitaxy (HVPE) and then compared with defect properties predicted from first-principles calculations. The vibrational frequency shift in two $^{13}C$ enriched samples related to the effect of the isotope mass indicates six distinct configurations of the carbon-containing point defects. The effect of the isotope replacement is well reproduced by the density functional theory (DFT) calculations. Specific attention is paid to the most pronounced defects, namely tri-carbon complexes($C_N=C=C_N$) and carbon substituting for nitrogen $C_N$. The position of the transition level (+/0) in the bandgap found for $C_N=C=C_N$ defects by DFT at 1.1 eV above the valence band maximum, suggest that $(C_N=C=C_N)^+$ provides compensation of ${C_N}^-$. $C_N=C=C_N$ defects are observed to be prominent, yet have high formation energies in DFT calculations. Regarding ${C_N}$ defects, it is shown that the host Ga and N atoms are involved in the defect's delocalized vibrations and significantly affect the isotopic frequency shift. Much more faint vibrational modes are found from di-atomic carbon-carbon and carbon-hydrogen (C-H) complexes. Also, we note changes of vibrational mode intensities of $C_N$, $C_N=C=C_N$, C-H, and $C_N-C_i$ defects in the IR absorption spectra upon irradiation in the defect-related UV/visible absorption range. Finally, it is demonstrated that the resonant enhancement of the Raman process in the range of defect absorption above 2.5 eV enables the detection of defects at carbon doping concentrations as low as $3.2*10^{17} cm^{-3}$

Association between Antibodies to the MR 67,000 Isoform of Glutamate Decarboxylase (GAD) and Type 1 (Insulin-Dependent) Diabetes Mellitus with Coexisting Autoimmune Polyendocrine Syndrome Type II

By using an immunoprecipitation assay, we analysed reactivity of autoantibodies to human recombinant GAD65 and GAD67 in sera from patients with autoimmune polyendocrine syndrome Type II (APS II) with and without Type 1 (insulin-dependent) diabetes mellitus (IDDM) compared to patients with organ-specific autoimmunity. Overall antibodies to GAD65 were correlated with IDDM in all study groups, whereas GAD67 antibodies were associated with IDDM when APS II coexists. Antibodies to GAD65 and GAD67 were detected in 13 (44.8%) and 7 (24.1%) out of 29 APS II patients with IDDM, but in only 4 (13.8%) and 2 (6.9%) out of 29 APS II patients without IDDM, respectively (p < 0.05). In short-standing IDDM (< 1 year), antibodies to GAD67 were significantly more frequent in patients with APS II (5 of 9 [55.6%] subjects) compared to matched diabetic patients without coexisting polyendocrinopathy (1 of 18 [5.6%] subjects) (p < 0.02). The levels of GAD65 (142 ± 90 AU) and GAD67 antibodies (178 ± 95 AU) were significantly higher in patients with polyglandular disease than in patients with isolated IDDM (91 ± 85 AU and 93 ± 57 AU) (p < 0.02). Interestingly, all 11 GAD67 antibody positive subjects also had GAD65 antibodies (p < 0.0001), and in 10 of 11 anti-GAD67 positive sera the GAD67 antibodies could be blocked by either GAD67 or GAD65, suggesting the presence of cross-reactive autoantibodies. No correlation was observed between GAD antibodies and age, sex or any particular associated autoimmune disease, besides IDDM. GAD antibodies were present in only 1 of 6 (16.7%) patients with APS Type I, in 1 of 26 (3.9%) patients with autoimmune thyroid disease but in none of the patients with Addison's disease (n = 16), pernicious anaemia (n = 7) or normal controls (n = 50). Our data suggest distinct antibody specificities reactive to GAD isoforms in APS II and IDDM, which might reflect different mechanisms of autoimmune response in IDDM with coexisting autoimmune polyendocrine autoimmunity

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought

Nitrification is a fundamental process in terrestrial nitrogen cycling. However, detailed information on how climate change affects the structure of nitrifier communities is lacking, specifically from experiments in which multiple climate change factors are manipulated simultaneously. Consequently, our ability to predict how soil nitrogen (N) cycling will change in a future climate is limited. We conducted a field experiment in a managed grassland and simultaneously tested the effects of elevated atmospheric CO2, temperature, and drought on the abundance of active ammonia-oxidizing bacteria (AOB) and archaea (AOA), comammox (CMX) Nitrospira, and nitrite-oxidizing bacteria (NOB), and on gross mineralization and nitrification rates. We found that N transformation processes, as well as gene and transcript abundances, and nitrifier community composition were remarkably resistant to individual and interactive effects of elevated CO2 and temperature. During drought however, process rates were increased or at least maintained. At the same time, the abundance of active AOB increased probably due to higher NH4+ availability. Both, AOA and comammox Nitrospira decreased in response to drought and the active community composition of AOA and NOB was also significantly affected. In summary, our findings suggest that warming and elevated CO2 have only minor effects on nitrifier communities and soil biogeochemical variables in managed grasslands, whereas drought favors AOB and increases nitrification rates. This highlights the overriding importance of drought as a global change driver impacting on soil microbial community structure and its consequences for N cycling

Benzyne in V4334 Sqr: A Quest for the Ring with SOFIA/EXES

Large aromatic molecules are ubiquitous in both circumstellar and interstellar environments. Detection of small aromatic molecules, such as benzene (C6H6) and benzyne (C6H4), are rare in astrophysical environments. Detection of such species will have major implications for our understanding of the astrochemistry involved in the formation of the molecules necessary for life, including modeling the chemical pathways to the formation of larger hydrocarbon molecules. We conducted a search for the infrared 18 μm spectral signature of benzyne in V4334 Sgr with the Stratospheric Observatory for Infrared Astronomy (SOFIA)/Echelon-Cross-Echelle Spectrograph (EXES) finding no evidence for a feature at the sensitivity of our observations

Amplitude measurements of Faraday waves

A light reflection technique is used to measure quantitatively the surface elevation of Faraday waves. The performed measurements cover a wide parameter range of driving frequencies and sample viscosities. In the capillary wave regime the bifurcation diagrams exhibit a frequency independent scaling proportional to the wavelength. We also provide numerical simulations of the full Navier-Stokes equations, which are in quantitative agreement up to supercritical drive amplitudes of 20%. The validity of an existing perturbation analysis is found to be limited to 2.5% overcriticaly.Comment: 7 figure

Measurement of the Eta Production in Proton Proton Collisions with the COSY Time of Flight Spectrometer

The reaction pp -> pp eta was measured at excess energies of 15 and 41 MeV at an external target of the Juelich Cooler Synchrotron COSY with the Time of Flight Spectrometer. About 25000 events were measured for the excess energy of 15 MeV and about 8000 for 41 MeV. Both protons of the process pp eta were detected with an acceptance of nearly 100% and the eta was reconstructed by the missing mass technique. For both excess energies the angular distributions are found to be nearly isotropic. In the invariant mass distributions strong deviations from the pure phase space distributions are seen.Comment: 15 pages, 14 figures, 4 table