Notes

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As estimated by comparing the model study and DFT band structure, the dominant electron coupling strengths are found to be nearly independent of XC functionals, which further establishes the utility of the SK-TB model.The protein folding process often proceeds through partially folded transient states. Therefore, a structural understanding of these disordered states is crucial for developing mechanistic models of the folding process. Characterization of unfolded states remains challenging due to their disordered nature, and incorporating multiple methods is necessary. Combining the time-resolved x-ray solution scattering (TRXSS) signal with molecular dynamics (MD), we are able to characterize transient partially folded states of bovine α-lactalbumin, a model system widely used for investigation of molten globule states, during its unfolding triggered by a temperature jump. We track the unfolding process between 20 µs and 70 ms and demonstrate that it passes through three distinct kinetic states. The scattering signals associated with these transient species are then analyzed with TRXSS constrained MD simulations to produce protein structures that are compatible with the input signals. Without utilizing any experimentally extracted kinetic information, the constrained MD simulation successfully drove the protein to an intermediate molten globule state; signals for two later disordered states are refined to terminal unfolded states. From our examination of the structural characteristics of these disordered states, we discuss the implications disordered states have on the folding process, especially on the folding pathway. Finally, we discuss the potential applications and limitations of this method.In this article, a systematic examination of the electronic and optical properties of partially fluorinated graphene is presented. In order to capture a large variety of fluorination degrees and configurations, different sizes of the supercell combining with various degrees of fluorination are considered. On top of periodic density functional theory, the G0W0 method and the G0W0Γ method within many-body Green's function framework are employed. Including the description of electron-hole interactions, the optical spectra based on the Bethe-Salpeter equation are calculated. Two-sided fluorination with compact fluorination arrangements is energetically most favorable. The fluorination degree has a determined impact on the bandgap value in the system, while the fluorination pattern strongly influences the characteristics of the bands in the electronic structures. Depending on the polarization of the applied electromagnetic field, the optical absorption spectra of the same structure could vary significantly. These interesting results suggest the potential applications of partially fluorinated graphene as optoelectronic materials.Using ab initio electronic structure methods with flexible atomic orbital basis sets, we investigated the electronic structure and stability of reduction products of selected representative cations (C+) constituting ionic liquids. We found that an electron attachment to such cations leads to the neutral radicals, whereas a subsequent attachment of another (i.e., excess) electron leads to adiabatically stable anions only in two cases [P(CH3)4]- and [MeMePyr]-. The possibility of the formation of various dimers (such as CC+, CC, and CC-) was also considered, and the resulting systems were characterized by predicting their lowest energy structures, ionization potentials, electron affinities, and susceptibilities to the fragmentation process. Among the cations studied, only the [MeMePyr]+ was found to form a typical Rydberg radical (MeMePyr) and double-Rydberg anion ([MeMePyr]-), whereas the remaining cations were predicted to form neutral radicals of a primarily valence (MeMeIm and MePy) or mixed Rydberg-valence [P(CH3)4] character. Our calculations confirmed the stability of all CC+ and CC dimers against fragmentation yielding the corresponding monomers (the binding energies of 12.2-20.5 kcal/mol and 11.3-72.3 kcal/mol were estimated for CC+ and CC dimers, respectively). [(MeMePyr)2]- was identified as the only adiabatically stable CC- dimeric anion having its vertical electron detachment energy of 0.417 eV. We also found that in the [(MeMePyr)2]- anionic state, three outermost electrons are described by Rydberg orbitals, which results in the (σ)2(σ*)1 configuration.A hydrogen-bonded CHF⋯HF complex was characterized by FTIR matrix isolation spectroscopy and ab initio calculations. Three possible structures of this complex were found at the coupled-cluster with single, double, and perturbative triple excitations [CCSD(T)/L3a_3] level of theory. The comparison between the experiment and theory reveals that the most stable structure with the binding energy of 6.48 kcal/mol is formed upon x-ray irradiation of isolated CH2F2 molecules in noble gas matrices (Ne, Ar, Xe). This species appears to be the first known intermolecular complex of monofluorocarbene, and its identification was unambiguously proved by IR absorptions corresponding to HF deformation (libration), CF stretching, H-C-F bending, and CH and HF stretching modes. It is worth noting that the corresponding spectral features in an argon matrix were previously tentatively ascribed to CH2F2 +· and HF⋯CHF-· [L. Andrews and F. T. Prochaska, J. Chem. Phys. GW3965 cell line 70, 4714 (1979)], but the calculations performed in the present study definitely support the re-assignment. The observed CHF⋯HF complex can be converted to the parent CH2F2 under the action of light with λ less then 525 nm. The plausible mechanism of this conversion using the conical intersection concept is discussed.Oxygen in its elemental form shows a variety of magnetic properties in its condensed phases; in particular, the epsilon solid phase loses its magnetism. These phenomena reflect the nature of the intermolecular forces present in the solid and the changes that arise with variations in pressure and temperature. In this study, we use intermolecular potentials obtained with unrestricted ab initio methods to model the singlet state of the oxygen tetramer [(O2)4], which is the unit cell, consistent with the non-magnetic character of this phase. To do this, we perform an analysis of the coupled-uncoupled representations of the spin operator together with a pairwise approximation and the Heisenberg Hamiltonian. We start from unrestricted potentials for the dimer calculated at a high level as well as different density functional theory (DFT) functionals and then apply a finite model to predict the properties of the epsilon phase. The results obtained in this way reproduce well the experimental data in the entire pressure range below 60 GPa.
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