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We further use the degree of deshielding on the proton as a measure of the hydrogen bonding interactions and evaluate the strength of the bifurcated short hydrogen bond as compared to its linear counterpart.A comprehensive description of the spin dynamics underlying the formation of Ortho-Deuterium Induced Polarization (ODIP) is presented. ODIP can serve as a tool for enhancing Nuclear Magnetic Resonance (NMR) signals of 2H nuclei, being important probes of molecular structure and dynamics. To produce ODIP, in the first step, the D2 gas is brought to thermal equilibrium at low temperature, here 30 K, so that the ortho-component, corresponding to the total spin of the 2H nuclei equal to 0 and 2, is enriched, here to 92%. In the second step, the orthodeuterium molecule is attached to a substrate molecule using a suitable hydrogenation catalyst such that the symmetry of the two 2H nuclei is broken. As a result, the non-thermal spin order of orthodeuterium is converted into enhancement of observable NMR signals. In this work, we perform a theoretical study of ODIP and calculate the shape of ODIP spectra and their dependence on the magnetization flip angle. These results are compared with experiments performed for a number of substrates; good agreement between experimental and calculated ODIP spectra is found. We also discuss the performance of NMR techniques for converting anti-phase ODIP spectral patterns into in-phase patterns, which are more suitable for signal detection and for transferring ODIP to heteronuclei, here to 13C spins. Experimental procedures reported here allowed us to reach signal enhancement factors of more than 1000 for 2H nuclei in the liquid phase. These results are useful for extending the scope of spin hyperpolarization to the widely used 2H nuclei.Plasmon-tunable tip pyramids (PTTPs) are reproducible and efficient nanoantennas for tip-enhanced Raman spectroscopy (TERS). Their fabrication method is based on template stripping of a segmented gold pyramid with a size-adjustable nanopyramid end, which is capable of supporting monopole localized surface plasmon resonance (LSPR) modes leading to high spectral enhancement when its resonance energy is matched with the excitation laser energy. Here, we describe in detail the PTTP fabrication method and report a statistical analysis based on 530 PTTPs' and 185 ordinary gold micropyramids' templates. Our results indicate that the PTTP method generates probes with an apex diameter smaller than 30 nm on 92.4% of the batch, which is a parameter directly related to the achievable TERS spatial resolution. Moreover, the PTTPs' nanopyramid edge size L, a critical parameter for LSPR spectral tuning, shows variability typically smaller than 12.5%. The PTTP's performance was tested in TERS experiments performed on graphene, and the results show a spectral enhancement of up to 72-fold, which is at least one order of magnitude higher than that typically achieved with gold micropyramids. Imaging resolution is in the order of 20 nm.The problem of determining the rate of rare events in dynamical systems is quite well-known but still difficult to solve. Recent attempts to overcome this problem exploit the fact that dynamic systems can be represented by a linear operator, such as the Koopman operator. Mathematically, the rare event problem comes down to the difficulty in finding invariant subspaces of these Koopman operators K. In this article, we describe a method to learn basis functions of invariant subspaces using an artificial neural network.The non-equilibrium stationary coherences that form in donor-acceptor systems are investigated to determine their relationship to the efficiency of energy transfer to a neighboring reaction center. It is found that the effects of asymmetry in the dimer are generally detrimental to the transfer of energy. Four types of systems are examined, arising from combinations of localized trapping, delocalized (Forster) trapping, eigenstate dephasing, and site basis dephasing. In the cases of site basis dephasing, the interplay between the energy gap of the excited dimer states and the environment is shown to give rise to a turnover effect in the efficiency under weak dimer coupling conditions. Furthermore, the nature of the coherences and associated flux is interpreted in terms of pathway interference effects. Dihydroqinghaosu In addition, regardless of the cases considered, the ratio of the real part and the imaginary part of the coherences in the energy-eigenbasis tends to a constant value in the steady state limit.A general procedure for the optimization of atomic density-fitting basis functions is designed with the balance between accuracy and numerical stability in mind. Given one-electron wavefunctions and energies, weights are assigned to the product densities, modeling their contribution to the exchange and second-order correlation energy, and a simple weighted error measure is minimized. Generally contracted Gaussian auxiliary basis sets are optimized to match the wavefunction basis sets [D. N. Laikov, Theor. Chem. Acc. 138, 40 (2019)] for all 102 elements in a scalar-relativistic approximation [D. N. Laikov, J. Chem. Phys. 150, 061103 (2019)].In triplet-triplet annihilation based photon upconversion, controlling triplet energy transfer (TET) through the system is key to unlocking higher efficiencies. In this work, we vary the size of colloidally synthesized CdSe nanocrystals (NCs) to examine the effects on TET during photon upconversion, using steady-state measurements and transient absorption spectroscopy. As the CdSe NC size increases, the photon upconversion quantum yield (QY) decreases due to the decrease in the rate of TET from CdSe to the surface bound anthracene transmitter ligand, as expected for the Marcus description of energy transfer from the transmitter to the NC. Long microsecond transmitter lifetimes are critical to high photon upconversion QYs.Single-atom alloys can be effective catalysts and have been compared to supported single-atom catalysts. To rationally design single-atom alloys and other surfaces with localized ensembles, it is crucial to understand variations in reactivity when varying the dopant and the ensemble size. link2 Here, we examined hydrogen adsorption on surfaces embedded with localized clusters and discovered general trends. Counterintuitively, increasing the amount of a more reactive metal sometimes makes a surface site less reactive. link3 This behavior is due to the hybridization and splitting of narrow peaks in the electronic density of states of many of these surfaces, making them analogous to free-standing nanoclusters. When a single-atom alloy has a peak just below the Fermi energy, the corresponding two-dopant cluster often has weaker adsorption than the single-atom alloy due to splitting of this peak across the Fermi energy. Furthermore, single-atom alloys have qualitatively different behaviors than larger ensembles. Specifically, the adsorption energy is a U-shaped function of the dopant's group for single-atom alloys. Additionally, adsorption energies on single-atom alloys correlate more strongly with the dopant's p-band center than with the d-band center.Polarizable force fields based on classical Drude oscillators offer a practical and computationally efficient avenue to carry out molecular dynamics (MD) simulations of large biomolecular systems. To treat the polarizable electronic degrees of freedom, the Drude model introduces a virtual charged particle that is attached to its parent nucleus via a harmonic spring. Traditionally, the need to relax the electronic degrees of freedom for each fixed set of nuclear coordinates is achieved by performing an iterative self-consistent field (SCF) calculation to satisfy a selected tolerance. This is a computationally demanding procedure that can increase the computational cost of MD simulations by nearly one order of magnitude. To avoid the costly SCF procedure, a small mass is assigned to the Drude particles, which are then propagated as dynamic variables during the simulations via a dual-thermostat extended Lagrangian algorithm. To help clarify the significance of the dual-thermostat extended Lagrangian propagation in the context of the polarizable force field based on classical Drude oscillators, the statistical mechanics of a dual-temperature canonical ensemble is formulated. The conditions for dynamically maintaining the dual-temperature properties in the case of the classical Drude oscillator are analyzed using the generalized Langevin equation.The single-reference coupled-cluster method has proven very effective in the ab initio description of atomic and molecular systems, but its successful application is limited to states dominated by a single Slater determinant, which is used as the reference. In cases where several determinants are important in the wave function expansion, i.e., we have to deal with nondynamic correlation effects, a multi-reference version of the coupled-cluster method is required. The multi-reference coupled-cluster approaches are based on the effective Hamiltonian formulation providing a two-step procedure, in which dynamic correlation effects can be efficiently evaluated by the wave operator, while nondynamic correlation contributions are given by diagonalization of the effective Hamiltonian in the final step. There are two classical multi-reference coupled-cluster formulations. In this paper, the focus is on the so-called Fock-space coupled-cluster method in its basic version with one- and two-particle operators in the exponent. Computational schemes using this truncation of the cluster operator have been successfully applied in calculations in one- and two-valence sectors of the Fock space. In this paper, we show that the approach can be easily extended and effectively employed in the three-valence sector calculations.Water is at the heart of almost all biological phenomena, without which no life that we know of would have been possible. It is a misleadingly complex liquid that exists in near coexistence with the vapor phase under ambient conditions. Confinement within a hydrophobic cavity can tip this balance enough to drive a cooperative dewetting transition. For a nanometer-scale pore, the dewetting transition leads to a stable dry state that is physically open but impermeable to ions. This phenomenon is often referred to as hydrophobic gating. Numerous transmembrane protein ion channels have now been observed to utilize hydrophobic gating in their activation and regulation. Here, we review recent theoretical, simulation, and experimental studies that together have started to establish the principles of hydrophobic gating and discuss how channels of various sizes, topologies, and biological functions can utilize these principles to control the thermodynamic properties of water within their interior pores for gating and regulation. Exciting opportunities remain in multiple areas, particularly on direct experimental detection of hydrophobic dewetting in biological channels and on understanding how the cell may control the hydrophobic gating in regulation of ion channels.Broad-spectrum antiviral drugs are urgently needed to stop the Coronavirus Disease 2019 pandemic and prevent future ones. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is related to the SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), which have caused the previous outbreaks. The papain-like protease (PLpro) is an attractive drug target due to its essential roles in the viral life cycle. As a cysteine protease, PLpro is rich in cysteines and histidines, and their protonation/deprotonation modulates catalysis and conformational plasticity. Here, we report the pKa calculations and assessment of the proton-coupled conformational dynamics of SARS-CoV-2 in comparison to SARS-CoV and MERS-CoV PLpros using the recently developed graphical processing unit (GPU)-accelerated implicit-solvent continuous constant pH molecular dynamics method with a new asynchronous replica-exchange scheme, which allows computation on a single GPU card. The calculated pKa's support the catalytic roles of the Cys-His-Asp triad.