Electronic g-factors for ESR spectra of a number of diatomic molecules with a ground X3Î£- state and their electronic spin-rotational coupling constants have been calculated by a linear response method. General expressions are used for the second order correction to the electronic g-factor which account for spin-orbit coupling induced admixtures from all excited triplet states to the ground state orbital magnetism. First order corrections - the spin-Zeeman kinetic energy contribution and the one-electron spin-Zeeman gauge contribution - to the g-factor are also accounted for. Calculated g-factors and spin-rotational coupling constants are in a good agreement with available experimental data. In particular, the positive, anomalous, sign of the spin-rotational coupling constant of the PF radical is reproduced.
Linear response theory has been applied for calculations of g-tensors of organic radicals in order to test the range of validity of restricted Hartree-Fock reference states. The g-values were calculated for the benzene cation (C6H6+), the benzene anion (C6H6-), hydropyrazine (C4H5N2), the dihydropyrazine cation (C4H6N2+), the aniline radical (C6H5NH), the p-benzoquinone anion (C6H4O2-), phenoxyl (C6H5O), the nitrobenzene anion (C6H5NO2-), and the nitropyridine anion (C5H4N2O2-). Influence of variations of structural parameters on the g-tensor components were investigated. Calculated g-values were in excellent agreement with experiment for six out of nine radicals. Two radicals - the p-benzoquinone anion and aniline radical - showed minor discrepancies, while the g-tensor of the phenoxyl radical was incorrect. The problem with the phenoxyl radical was traced to a complex electronic structure and optical spectrum. Results consistent with experiment could in that case only be obtained with electron correlated calculations.
Currently, much experimental effort is being invested in the engineering of phytochromes, a large superfamily of photoreceptor proteins, into fluorescent proteins suitable for bioimaging in the near-infrared regime. In this work, we gain insight into the potential of computational methods to contribute to this development by investigating how well representative quantum chemical methods reproduce recently recorded red-light absorption and emission maxima of synthetic derivatives of the bilin chromophores of phytochromes. Focusing on the performance of time-dependent density functional theory but using also the ab initio CIS(D), CC2 and CASPT2 methods, we explore how various methodological considerations influence computed spectra and find, somewhat surprisingly, that density functionals lacking exact exchange reproduce the experimental measurements with smaller errors than functionals that include exact exchange. Thus, for the important class of chromophores that bilins constitute, the widely established trend that hybrid functionals give more accurate excitation energies than pure functionals does not apply.
Amyloid diseases such as Alzheimer's and spongiform encephalopathies evolve from aggregation of proteins due to misfolding of the protein structure. Early disease handling require sophisticated but yet simple techniques to follow the complex properties of the aggregation process. Conjugated polyelectrolytes (CPEs) have shown promising capabilities acting as optical biological sensors, since they can specifically bind to polypeptides both in solution and in solid phase. The structural changes in biomolecules can be monitored by changes of the optical spectra of the CPEs, both in absorption and emission modes. Notably, the studied CPEs possess multi-photon excitation capability, making them potential for in vivo imaging using laser scanning microscopy. Aggregation of proteins depends on concentration, temperature and pH. The optical effect on the molecular probe in various environments must also be investigated if applied in these environments. Here we present the results of quantum efficiency and two-photon absorption cross-section of three CPEs: POMT, POWT and PTAA in three different pH buffer systems. The extinction coefficient and quantum efficiency were measured. POMT was found to have the highest quantum efficiency being approximately 0.10 at pH 2.0. The two-photon absorption cross-section was measured for POMT and POWT and was found to be more than 18-25 times and 7-11 times that of Fluorescein, respectively. We also show how POMT fluorescence can be used to distinguish conformational differences between amyloid fibrils formed from reduced and non-reduced insulin in spectrally resolved images recorded with a laser scanning microscope using both one- and two-photon excitation. © 2007 Elsevier B.V. All rights reserved.
The geometric and electronic structure of condensed phase organic conducting polymer PEDOT:PSS blends has been investigated by periodic density functional theory (DFT) calculations with a generalized-gradient approximation (GGA) functional, and a plane wave basis set. The influence of the degree of doping of the PEDOT polymer on structural and optical parameters such as the reflectivity, absorbance, conductivity, dielectric function, refractive index and the energy-loss function is studied. A flip from the benzoid to the quinoid structure is observed in the calculations when the neutral PEDOT is doped by negatively charged PSS. Also the optical properties are affected by the doping. In particular, the reflectivity was found to be very sensitive to the degree of doping, where higher doping implies higher reflectivity. The reflectivity is highly anisotropic, with the dominant contribution stemming from the direction parallel to the PEDOT polymer chain.
The electronic structure of the poly-pyridine conjugated polymer has been investigated by resonant and non-resonant inelastic X-ray scattering and X-ray absorption spectroscopies using synchrotron radiation. The measurements were made for both the carbon and nitrogen contents of the polymer. The analysis of the spectra has been carried out in comparison with molecular orbital calculations taking the repeat-unit cell as a model molecule of the polymer chain. The simulations indicate no significant differences in the absorption and in the non-resonant X-ray scattering spectra for the different isomeric geometries, while some isomeric dependence of the resonant spectra is predicted. The resonant emission spectra show depletion of the electron bands in line with symmetry selection and momentum conservation rules. The effect is most visual for the carbon spectra; the nitrogen spectra are dominated by lone pair n orbital emission of symmetry and are less frequency dependent.
First principle quantum chemical methods have been employed in the calculations of the linear and nonlinear ground state absorption in platinum-organic compounds, some of which include charge-transfer groups. The theoretical results show several ways to tailor the linear absorption to a desired wave length region. Spin-orbit induced transitions are discussed and characterized. The nonlinear absorption cross-sections are strongly enhanced by the introduction of charge-transfer units, whereas the linear oscillator strengths remain essentially unaffected by the same ligand substitutions. The charge-transfer substitutions are also accompanied by red-shifts in the linear absorption spectra. © 2002 Elsevier Science B.V. All rights reserved.
The "in-crystal" frequency of the anharmonic and uncoupled OH stretching vibration of HDO molecules in LiClO4.3H2O(s) has been calculated by quantum-mechanical ab initio and model potential methods and compared with the experimental infrared frequency from isotope-isolated HDO molecules. The effects of the nearest neighbours as well as of the crystalline environment have been investigated by the two computational techniques. In both cases, the one-dimensional potential for an anharmonic OH oscillator was constructed from point-wise energy calculations and the Schrodinger equation for the protonic motion in this potential well was solved by a variational procedure. In the ab initio calculations, vibrational potentials were constructed from RHF and MP2 type calculations of point-charge embedded ClO4-.HDO and (Li+)2.(ClO4-)2.HDO clusters using DZP and TZP basis sets. For the LiClO4.3H2O(s) crystal, the ab initio OH frequency is in close quantitative agreement with experiment when electron correlation by MP2 and the crystal field are included: 3537 cm-1 (MP2(TZP)) versus the experimental value of 3556 cm-1. Inclusion of the crystal field is essential and can in this crystal be satisfactorily represented by Ewald field-consistent point charges outside the hydrogen-bonded ClO4-...HDO cluster. In the model potential calculations, analytical intermolecular pair potential functions from the literature were used in conjunction with an experimental intramolecular potential function for the OH stretching motion. The particular intermolecular model chosen here yields an absolute OH frequency 160 cm-1 below experiment. These calculations exemplify some of the difficulties encountered when employing analytical model potentials in vibrational studies.
A theoretical investigation of phenylene ethynylene macrocycles and oligomers aggregation was carried out. Two types of stacked supramolecular organization were investigated at the MP2 level: the intermolecular aggregation of macrocycles and the intramolecular conformational ordering of long oligomers. For the neutral monomer and ortho- and meta-macrocycles bound states of p-p stacked pairs were found, having binding energies of ~-0.061, -0.378 and -0.81 eV, respectively. The relative stability between ortho- and meta-phenylene ethynylene chains and helices as function of the oligomer length n, in gas phase was also studied. The results show that p-p interactions stabilize the helical structures for long oligomers. © 2001 Elsevier Science B.V. All rights reserved.
Uncoupled OH and OD stretching bands of HDO molecules have been calculated for an ionic aqueous solution, based on the trajectories from a classical statistical-mechanical computer simulation and subsequent quantum-mechanical calculations of the vibrational energy levels. Each V(r(OH)) potential function has been constructed as a sum of intra- and intermolecular energies, where different intermolecular water-water potential functions from the literature (MCY, TIPS2, RWK2 and CF2) have been tested in conjunction with the experimentally derived HMS intramolecular potential. In this way, vibrational densities-of-states as well as infrared absorption bands have been calculated for HDO molecules in the bulk and in the ionic hydration shells (Li+, HCOO-). Calculated frequencies and band widths for the TIPS2 and MCY potentials are fairly close to experimental values. The calculated OH shift between the gas and liquid water phases is - 303 cm-1 with the TIPS2 potential, as compared to the experimental value of - 307 cm-1. The MCY potential gives - 260 cm-1, while RWK2 as well as the CF2 potentials give rise to a non-negligible number of spurious frequencies. Water molecules in the first hydration shell of Li+ exhibit only slightly lower stretching frequencies than bulk water. The frequencies of the OH and OD groups of HDO molecules bonded to the formate oxygen atoms are lower than in bulk water, while the frequency of the OH/OD group pointing away from the formate ion is higher compared to bulk water.