Ring polymer dynamics for rigid tops with an improved integrator

Operator Formulation of Feynman Path Centroid Dynamics for Rotations

An operator formulation of centroid molecular dynamics (CMD) for rotational degrees of freedom is presented. The quasi-density operator concept was introduced by Jang and Voth [J. Chem. Phys 111, 2357 (1999)] and is used to obtain a phase-space mapping without the need for discretized path integrals. The approach allows the calculation of approximate Kubo-transformed time correlation functions. The particle on a ring is chosen as an illustrative example. Numerical results demonstrate that the proposed approach leads to accurate results when compared with exact diagonalization calculations for linear operators. At very low temperatures, it is found that rotational CMD yields results that are in exact agreement with the quantum dynamics of a spin-1 system.

Electrolyte clusters as hydrogen sponges: diffusion Monte Carlo simulations

We carry out Diffusion Monte Carlo simulations of up to five hydrogen molecules aggregated with two Stockmayer clusters that solvate a single lithium ion. The first one contains six point dipole solvent particles with parameters tuned to emulate nitromethane. The second cluster is a relative large system investigated recently [G. DiEmma, S. Kalette, and E. Curotto, Chem. Phys. Lett. 2019, 725, 80-86]. In both cases we find that the aggregated hydrogen molecules perturb significantly the ground state of the host cluster and form a distorted tetrahedral cage around the Li⁺ ion. The fifth hydrogen molecule is absorbed by the larger Stockmayer cluster while remaining in the proximity of the solvated charge.

Hydroxide Ion Mechanism for Long-Range Proton Pumping in the Third Proton Transfer of Bacteriorhodopsin

In bacteriorhodopsin, representative light-driven proton pump, five proton transfers yield vectorial active proton translocation, resulting in a proton gradient in microbes. Third proton transfer occurs from Asp96 to the Schiff base on the photocycle, which is expected to be a long-range proton transfer via the Grotthuss mechanism through internal water molecules. Here, large-scale quantum molecular dynamics simulations are performed for the third proton transfer, where all the atoms (~50000 atoms) are treated quantum-mechanically. The simulations demonstrate that two reaction paths exist along the water wire, namely, via hydronium and via hydroxide ions. The free energy analysis confirms that the path via hydroxide ions is considerably favorable and consistent with the observed lifetime of the transient water wire. Therefore, the proposed hydroxide ion mechanism, as in the first proton transfer, is responsible for the third long-range proton transfer.

In situ examination of a charged amino acid-induced structural change in lipid bilayers by sum frequency generation vibrational spectroscopy

The interactions between amino acids (AAs) and membranes represent various short-range and long-range interactions for biological phenomena; however, they are still poorly understood. In this study, we used cationic lysine and arginine as AA models, and systematically investigated the interactions between charged AAs and lipid bilayers using sum frequency generation vibrational spectroscopy (SFG-VS) in situ and in real time. The AA-induced dynamic structural changes of the lipid bilayer were experimentally monitored using the spectral features of CD₂, CD₃, the lipid head phosphate, and carbonyl groups in real time. Time-dependent SFG changes in the structure of the lipid bilayer provide direct evidence for the different interactions of lysine and arginine with the membrane. It was found that the discrepancy between lysine and arginine in binding with the lipid bilayer is due to the nature of the terminal functional groups. Arginine exhibits a more drastic impact on the membrane than lysine. SFG responses of the acyl chains, phosphate groups, and carbonyl groups provide evidence that the interaction between AAs and the membrane most likely follows an electrostatics and hydrogen bond-induced defect model. This work presents an exemplary method for comprehensive investigations of interactions between membranes and other functionally significant substances.

Quest for Inexpensive Hydrogen Isotopic Fractionation: Do We Need 2D Quantum Confining in Porous Materials or Are Rough Surfaces Enough? The Case of Ammonia Nanoclusters

We study the adsorption energetics and quantum properties of the molecular hydrogen isotopes H₂, D₂, and T₂ onto the surface of rigid ammonia nanoclusters with quantum simulations and accurate model potential energy surfaces (PES). A highly efficient diffusion Monte Carlo (DMC) algorithm for rigid rotors allowed us to accurately define zero-point adsorption energies for the three isotopes, as well as the degree of translational and rotational delocalization that each affords on the surface. From the data emerges that the quantum adsorption energy (E_ads) of T₂ can be up to twice the one of H₂ at 0 K, suggesting the possibility of exploiting some form of solid ammonia to selectivity separate hydrogen isotopes at low temperatures (≃20 K). This is discussed by focusing on the structural motif that may be more effective for the task. The analysis of the contributions to E_ads, however, surprisingly indicates that the average kinetic energy (E^kin) and rotation energy (E_rot^kin) of T₂ can also be, respectively, 2 times and 20 times higher than those of H₂; this finding markedly deviates from what is predicted for hydrogen molecules inside carbon nanotubes (CNT) or metallic-organic frameworks (MOF), where E^kin and E_rot^kin is higher for H₂ due to the unavoidable effects of confinement and hindrance to its rotational motion. The rationale for these differences is provided by the geometrical distributions for the rigid rotors, which reveal an increasingly stronger coupling between rotational and translational degrees of freedom upon increasing the isotopic mass. This effect has never been observed before on adsorbing surfaces (e.g., graphite) and is induced by a strongly anisotropic and anharmonic bowl-like potential experienced by the rotors.