We study, with molecular dynamics simulations, a lysozyme protein immersed in a water-trehalose solution upon cooling. The aim is to understand the cryoprotectant role played by this disaccharide through the modifications that it induces on the slow dynamics of protein hydration water with its presence. The α-relaxation shows a fragile to strong crossover about 20° higher than that in the bulk water phase and 15° higher than that in lysozyme hydration water without trehalose. The protein hydration water without trehalose was found to show a second slower relaxation exhibiting a strong to strong crossover coupled with the protein dynamical transition. This slower relaxation time importantly appears enormously slowed down in our cryoprotectant solution. On the other hand, this long-relaxation in the presence of trehalose is also connected with a stronger damping of the protein structural fluctuations than that found when the protein is in contact with the pure hydration water. Therefore, this appears to be the mechanism through which trehalose manifests its cryoprotecting function.In this work, a Raman bond model that partitions the Raman intensity to interatomic charge flow modulations or Raman bonds is extended from the static limit to frequency dependent cases. This model is based on damped response theory and, thus, enables a consistent treatment of off-resonance and resonance cases. Model systems consisting of pyridines and silver clusters are studied using time dependent density functional theory to understand the enhancement mechanisms of surface-enhanced Raman scattering (SERS). The Raman bonds in the molecule, the inter-fragment bond, and the cluster are mapped to the enhancement contributions of the molecular resonance mechanism, the charge transfer mechanism, and the electromagnetic mechanism. The mapping quantifies the interference among the coupled mechanisms and interprets the electromagnetic mechanism as charge flow modulations in the metal. The dependence of the enhancement on the incident frequency, the molecule-metal bonding, and the applied electric field is interpreted and quantified. The Raman bond framework offers an intuitive and quantitative interpretation of SERS mechanisms.The recently developed real-time nuclear-electronic orbital (RT-NEO) approach provides an elegant framework for treating electrons and selected nuclei, typically protons, quantum mechanically in nonequilibrium dynamical processes. However, the RT-NEO approach neglects the motion of the other nuclei, preventing a complete description of the coupled nuclear-electronic dynamics and spectroscopy. In this work, the dynamical interactions between the other nuclei and the electron-proton subsystem are described with the mixed quantum-classical Ehrenfest dynamics method.  https://www.selleckchem.com/products/Puromycin-2HCl.html  The NEO-Ehrenfest approach propagates the electrons and quantum protons in a time-dependent variational framework, while the remaining nuclei move classically on the corresponding average electron-proton vibronic surface. This approach includes the non-Born-Oppenheimer effects between the electrons and the quantum protons with RT-NEO and between the classical nuclei and the electron-proton subsystem with Ehrenfest dynamics. Spectral features for vibrational modes involving both quantum and classical nuclei are resolved from the time-dependent dipole moments. This work shows that the NEO-Ehrenfest method is a powerful tool to study dynamical processes with coupled electronic and nuclear degrees of freedom.We describe a coupled cluster framework for coupled systems of electrons and harmonic phonons. Neutral and charged excitations are accessed via the equation-of-motion version of the theory. Benchmarks on the Hubbard-Holstein model allow us to assess the strengths and weaknesses of different coupled cluster approximations, which generally perform well for weak to moderate coupling. Finally, we report progress toward an implementation for ab initio calculations on solids and present some preliminary results on finite-size models of diamond with a linear electron-phonon coupling. We also report the implementation of electron-phonon coupling matrix elements from crystalline Gaussian type orbitals within the PySCF program package.Conical intersections are ubiquitous in chemical systems but, nevertheless, extraordinary points on the molecular potential energy landscape. They provide ultra-fast radiationless relaxation channels, their topography influences the product branching, and they equalize the timescales of the electron and nuclear dynamics. These properties reveal optical control possibilities in the few femtosecond regime. In this theoretical study, we aim to explore control options that rely on the carrier envelope phase of a few-cycle IR pulse. The laser interaction creates an electronic superposition just before the wave packet reaches the conical intersection. The imprinted phase information is varied by the carrier envelope phase to influence the branching ratio after the conical intersection. We test and analyze this scenario in detail for a model system and show to what extent it is possible to transfer this type of control to a realistic system like uracil.How a substrate modulates properties of water upon it and how far the perturbation is present remain to be fundamental questions in surface science. To answer these questions, we develop a layer-by-layer exfoliation method to identify physically meaningful water layers upon a substrate through molecular dynamics simulations under ambient conditions. The results show a qualitatively consistent long-ranged layer-by-layer propagation of the atomic structure, irrespective of whether the substrate is soft, solid, hydrophobic, or hydrophilic. The capillary-wave fluctuation of a water layer upon air or oil diverges with long wavelength but is truncated upon solid substrates by an effective field, which exhibits a long-ranged decay but its strength is almost irrelevant with substrate chemistry. The distinction in the water structure and atomic dynamics due to substrate specificity is mostly limited to the outmost layer. We conclude a long-ranged layering organization and a short-ranged substrate-dependent specificity for interfacial water.