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Recent theoretical studies have shown that charge transport in high-mobility organic semiconductors is limited by low-frequency vibrations because of strong non-local electron-phonon interaction. Here we investigate two high-electron-mobility organic semiconductors with similar molecular structures but considerably different crystal packings, TCNQ and F2-TCNQ, and reveal the relationship between the experimental low-frequency Raman spectra and the calculated contributions of various vibrational modes to the electron-phonon interaction. We suggest that the combination of Raman spectroscopy with solid-state DFT is a powerful tool for probing electron-phonon interaction and focused search for high-mobility organic semiconductors.

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Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)-glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded ß-sheet structure. The 1 µs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898-915 (2011)]. These structures are stabilized by the short (+)N-H⋯O(-) bonds. Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm(-1). It is caused by the asymmetric stretching vibrations of the (+)N-H⋯O(-) fragment. Result of the present paper suggests that infrared spectroscopy in the 2000-2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.

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The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.

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The relationship between the d(H...A) distance (A=O, N) and the topological properties at the H...A bond critical point of 37 strong (short) hydrogen bonds occurring in 26 molecular crystals are analyzed using the quantum theory of atoms in molecules (QTAIM). Ground-state wave functions of the three-dimensional periodical structures representing the accurate experimental geometries calculated at the B3LYP/6-31G** level of approximation were used to obtain the QTAIM electron density characteristics. The use of an electron-correlated method allowed us to reach the quantitatively correct values of electron density rhob at the H...A bond critical point. However, quite significant differences can appear for small absolute values of the Laplacian (<0.5 au). The difference between the H...O and H...N interactions is described using the rhob versus d(H...A) dependence. It is demonstrated that the values of parameters in this dependence are defined by the nature of the heavy atom forming the H...A bond. An intermediate (or transit) region separating the shared and closed-shell interactions is observed for the H-bonded crystals in which the bridging proton can move from one heavy atom to another. The crystalline environment changes the location of the bridging proton in strong H-bonded systems; however, the d(O-H)/d(H...O) ratio is approximately the same for both the gas-phase complexes and molecular crystals with a linear or near-linear O-H...O bond.

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Outersphere reorganization energies (lambda) for intramolecular electron and hole transfer are studied in anion- and cation-radical forms of complex organic substrates (p-phenylphenyl-spacer-naphthyl) in polar (water, 1,2-dichloroethane, tetrahydrofuran) and quadrupolar (supercritical CO2) solvents. Structure and charge distributions of solute molecules are obtained at the HF/6-31G(d,p) level. Standard Lennard-Jones parameters for solutes and the nonpolarizable simple site-based models of solvents are used in molecular dynamics (MD) simulations. Calculation of lambda is done by means of the original procedure, which treats electrostatic polarization of a solvent in terms of a usual nonpolarizable MD scheme supplemented by scaling of reorganization energies at the final stage. This approach provides a physically relevant background for separating inertial and inertialless polarization responses by means of a single parameter epsilon(infinity), optical dielectric permittivity of the solvent. Absolute lambda values for hole transfer in 1,2-dichloroethane agree with results of previous computations in terms of the different technique (MD/FRCM, Leontyev, I. V.; et al. Chem. Phys. 2005, 319, 4). Computed lambda values for electron transfer in tetrahydrofuran are larger than the experimental values by ca. 2.5 kcal/mol; for the case of hole transfer in 1,2-dichloroethane the discrepancy is of similar magnitude provided the experimental data are properly corrected. The MD approach gives nonzero lambda values for charge-transfer reaction in supercritical CO2, being able to provide a uniform treatment of nonequilibrium solvation phenomena in both quadrupolar and polar solvents.

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To examine the effects of transarticular loading on articular cartilage and subchondral bone, we used a canine model that we had developed previously, in which a standardized load of approximately 2000 newtons is delivered across the patellofemoral joint. The purpose of the study was to define and describe the initial changes, as seen on histopathological and magnetic resonance-imaging studies, that occur in the early stages after injury to the joint by transarticular loading. Scanning electron microscopy was used to define the extent and characteristics of the fractures produced in the subchondral bone of four patellae that were examined on the day of loading. We found multiple, extensive fractures through the zone of calcified cartilage and the subchondral bone, frequently with step-off displacement, and with little or no change in the gross appearance of the articular cartilage. Specimens from four patellae were examined histologically two weeks after loading, and the observed changes were correlated with those that had been demonstrated by scanning electron microscopy. Fractures through the zone of calcified cartilage and the subchondral bone, with step-off displacement, were prominent. Clefts were present in the surface of the articular cartilage and, in some areas, there was a focal loss of proteoglycan from the extracellular matrix, as indicated by the complete absence of staining with safranin O. Six dogs were examined one year after loading. There was healing of the subchondral fractures and restoration of proteoglycan in the extracellular matrix. However, superficial clefts and fissures were still present in the articular cartilage. Sequential magnetic resonance-imaging studies were also carried out on these six dogs, at two, eight, sixteen, thirty-six, and fifty-two weeks after loading. Two weeks after loading, all knees had soft-tissue swelling, effusion, and a decreased marrow signal in the medullary cavity of the patella. The decreased marrow signal and effusion were still present eight weeks after the impact, and then the findings gradually returned to normal. One year after loading, it was found that the histopathological changes had not been progressive; in fact, they had been ameliorated and, to some extent, reversed by repair processes. The early, severe magnetic resonance-imaging changes had also been reversed, so that this study demonstrated normal findings by one year after loading.

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Intact canine metacarpophalangeal and metatarsophalangeal joints were subjected to a variety of loads in vitro. Intraarticular fracture occurred in 19 joints loaded to an average force of 2.4 +/- 0.4 kN with a corresponding loading rate of 88 +/- 23 kN/s. The remaining 29 joints were without gross evidence of fracture with an average load and loading rate of 1.7 +/- 0.9 kN and 64 +/- 32 kN/s, respectively. In the fractured specimens, damage to the zone of calcified cartilage and subchondral bone was much more extensive than was initially evident by gross inspection when assessed by scanning electron microscopy. Cracks with associated step-off displacement at the zone of calcified cartilage were found distant to the gross fractures. These findings were confirmed histologically. In addition, cracks localized to the zone of calcified cartilage were commonly identified histologically in specimens loaded in the range of 1.9-2.8 kN, but were not grossly fractured. The contact area determined with pressure-sensitive film increased with increasing load up to the point of fracture. The average pressure generated at the articular cartilage surface at the time of fracture in this model is > or = 40 MPa, and the fracture occurred at the contact site. Our findings suggest that failure in acute transarticular loading begins in the zone of calcified cartilage and subsequently involves the subchondral bone and overlying cartilage. This type of injury may contribute to the development of osteoarthritis after intraarticular fracture, or at high loads that do not result in gross fracture.

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