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Nanomechanical Stability of Aβ Tetramers and Fibril-like Houses: Molecular Dynamics Models.
The extrapolations are done both without and with a basis-set correction based on density-functional theory. The mean absolute deviations from experiment for these extrapolations are 0.46 kcal/mol and 0.51 kcal/mol, respectively. Orbital optimization methods used to obtain improved convergence of the SHCI energies are also discussed.We report a synchrotron radiation vacuum ultraviolet photoionization study of the hydroperoxyl radical (HO2), a key reaction intermediate in combustion and atmospheric chemistry as well as astrochemistry, using double imaging photoelectron photoion coincidence spectroscopy. The HO2 radical is formed in a microwave discharge flow tube reactor through a set of reactions initiated by F atoms in a CH4/O2/He gas mixture. The high-resolution threshold photoelectron spectrum of HO2 in the 11 eV-12 eV energy range is acquired without interferences from other species and assigned with the aid of theoretically calculated adiabatic ionization energies (AIEs) and Franck-Condon factors. The three vibrational modes of the radical cation HO2+, the H-O stretch, the H-O-O bend, and the O-O stretch, have been identified, and their individual frequencies are measured. In addition, the AIEs of the X3A″ ground state and the a1A' first excited electronic state of HO2+ are experimentally determined at 11.359 ± 0.003 eV and 11.639 ± 0.005 eV, respectively, in agreement with high-level theoretically computed results. Furthermore, the former AIE value provides validation of thermochemical networks used to extract the enthalpy of formation of the HO2 radical.Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. Rapamycin solubility dmso When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.Electron-phonon coupling plays a central role in the transport properties and photophysics of organic crystals. Successful models describing charge- and energy-transport in these systems routinely include these effects. Most models for describing photophysics, on the other hand, only incorporate local electron-phonon coupling to intramolecular vibrational modes, while nonlocal electron-phonon coupling is neglected. One might expect nonlocal coupling to have an important effect on the photophysics of organic crystals because it gives rise to large fluctuation in the charge-transfer couplings, and charge-transfer couplings play an important role in the spectroscopy of many organic crystals. Here, we study the effects of nonlocal coupling on the absorption spectrum of crystalline pentacene and 7,8,15,16-tetraazaterrylene. To this end, we develop a new mixed quantum-classical approach for including nonlocal coupling into spectroscopic and transport models for organic crystals. Importantly, our approach does not assume that the nonlocal coupling is linear, in contrast to most modern charge-transport models. We find that the nonlocal coupling broadens the absorption spectrum non-uniformly across the absorption line shape. In pentacene, for example, our model predicts that the lower Davydov component broadens considerably more than the upper Davydov component, explaining the origin of this experimental observation for the first time. By studying a simple dimer model, we are able to attribute this selective broadening to correlations between the fluctuations of the charge-transfer couplings. Overall, our method incorporates nonlocal electron-phonon coupling into spectroscopic and transport models with computational efficiency, generalizability to a wide range of organic crystals, and without any assumption of linearity.We present an extension of the locally enhanced sampling method. A restraint potential is introduced to drive the many-replica system to the canonical ensemble corresponding to the physical, single-replica system. Convergence properties are demonstrated using a model rugged two-dimensional potential, for which sampling by conventional equilibrium molecular dynamics is inefficient. Restrained locally enhanced sampling (RLES) is found to explore the space of configurations with an efficiency comparable to that of temperature replica exchange. To demonstrate the potential of RLES for realistic applications, the method is used to fold the 12-residue tryptophan zipper miniprotein in explicit solvent. The RLES algorithm can be incorporated into existing LES implementations with minor code modifications.Programmable self-assembly is one of the most promising strategies for making ensembles of nanostructures from synthetic components. Yet, predicting the phase behavior that emerges from a complex mixture of many interacting species is difficult, and designing such a system to exhibit a prescribed behavior is even more challenging. In this article, I develop a mean-field model for predicting linker-mediated interactions between DNA-coated colloids, in which the interactions are encoded in DNA molecules dispersed in solution instead of in molecules grafted to particles' surfaces. As I show, encoding interactions in the sequences of free DNA oligomers leads to new behavior, such as a re-entrant melting transition and a temperature-independent binding free energy per kBT. This unique phase behavior results from a per-bridge binding free energy that is a nonlinear function of the temperature and a nonmonotonic function of the linker concentration, owing to subtle entropic contributions. To facilitate the design of experiments, I also develop two scaling limits of the full model that can be used to select the DNA sequences and linker concentrations needed to program a specific behavior or favor the formation of a prescribed target structure.
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