Zwitter Ionization of Glycine at Outer Space Conditions due to Microhydration by Six Water Molecules

Intramolecular and Water Mediated Tautomerism of Solvated Glycine

Understanding tautomerism and characterizing solvent effects on the dynamic processes pose significant challenges. Using enhanced-sampling molecular dynamics based on state-of-the-art deep learning potentials, we investigated the tautomeric equilibria of glycine in water. We observed that the tautomerism between neutral and zwitterionic glycine can occur through both intramolecular and intermolecular proton transfers. The latter proceeds involving a contact anionic-glycine-hydronium ion pair or separate cationic-glycine-hydroxide ion pair. These pathways with comparable barriers contribute almost equally to the reaction flux.

Unraveling Water Solvation Effects with Quantum Mechanics/Molecular Mechanics Semiclassical Vibrational Spectroscopy: The Case of Thymidine

We introduce a quantum mechanics/molecular mechanics semiclassical method for studying the solvation process of molecules in water at the nuclear quantum mechanical level with atomistic detail. We employ it in vibrational spectroscopy calculations because this is a tool that is very sensitive to the molecular environment. Specifically, we look at the vibrational spectroscopy of thymidine in liquid water. We find that the C═O frequency red shift and the C═C frequency blue shift, experienced by thymidyne upon solvation, are mainly due to reciprocal polarization effects, that the molecule and the water solvent exert on each other, and nuclear zero-point energy effects. In general, this work provides an accurate and practical tool to study quantum vibrational spectroscopy in solution and condensed phase, incorporating high-level and computationally affordable descriptions of both electronic and nuclear problems.

Anharmonic Assignment of the Water Octamer Spectrum in the OH Stretch Region

We interface the quasi-classical trajectory approach with an ab initio potential energy surface for water to assign the vibrational spectroscopical features of the OH stretch region of the water octamer cluster, which is considered to be a precursor of ice. An attempt by Li et al. to assign their recent reference experiment involved lower-level calculations based on an ad hoc scaled harmonic approach. Differently from the conclusions of this previous assignment, which invoked the contribution of 5 conformers and a solvated form of the water heptamer in the spectrum, we find out that the spectroscopic features can be related to the 4 conformers of the octamer lying lower in energy.

Ultrafast Roaming Mechanisms in Ethanol Probed by Intense Extreme Ultraviolet Free-Electron Laser Radiation: Electron Transfer versus Proton Transfer

Ultrafast H₂⁺ and H₃⁺ formation from ethanol is studied using pump-probe spectroscopy with an extreme ultraviolet (XUV) free-electron laser. The first pulse creates a dication, triggering H₂ roaming that leads to H₂⁺ and H₃⁺ formation, which is disruptively probed by a second pulse. At photon energies of 28 and 32 eV, the ratio of H₂⁺ to H₃⁺ increases with time delay, while it is flat at a photon energy of 70 eV. The delay-dependent effect is ascribed to a competition between electron and proton transfer. High-level quantum chemistry calculations show a flat potential energy surface for H₂ formation, indicating that the intermediate state may have a long lifetime. The ab initio molecular dynamics simulation confirms that, in addition to the direct emission, a small portion of H₂ undergoes a roaming mechanism that leads to two competing pathways: electron transfer from H₂ to C₂H₄O²⁺ and proton transfer from C₂H₄O²⁺ to H₂.

Understanding the Role of Intramolecular Ion-Pair Interactions in Conformational Stability Using an Ab Initio Thermodynamic Cycle

Intramolecular ion-pair interactions yield shape and functionality to many molecules. With proper orientation, these interactions overcome steric factors and are responsible for the compact structures of several peptides. In this study, we present a thermodynamic cycle based on isoelectronic and alchemical mutation to estimate the intramolecular ion-pair interaction energy. We determine these energies for 26 benchmark molecules with common ion-pair combinations and compare them with results obtained using intramolecular symmetry-adapted perturbation theory. For systems with long linkers, the ion-pair energies evaluated using both approaches deviate by less than 2.5% in the vacuum phase. The thermodynamic cycle based on density functional theory facilitates calculations of salt-bridge interactions in model tripeptides with continuum/microsolvation modeling and four large peptides: 1EJG (crambin), 1BDK (bradykinin), 1L2Y (a mini-protein with a tryptophan cage), and 1SCO (a toxin from the scorpion venom).

Effect of (H2O)n (n = 0–3, 13) on the NH3 + OH reaction in the gas and liquid phases

We studied the effect of water clusters on the NH₃ + OH reaction at both the DFT and CCSD(T) levels. The calculated rate constants for the pure reaction are 2.07 × 10⁻¹³ and 1.35 × 10⁻¹³ cm³ molecule⁻¹ s⁻¹ in the gas and liquid phases, respectively, and the gas-phase rate constants are consistent with the corresponding experimental result (1.70 × 10⁻¹³ cm³ molecule⁻¹ s⁻¹), while the liquid-phase rate constants are slightly smaller than the experimental value (5.84 × 10⁻¹² cm³ molecule⁻¹ s⁻¹). In the gas phase, the presence of (H₂O)_n (n = 1–3) decreases the rate constant compared to the pure NH₃ + OH reaction, and these results are in agreement with many reported H₂O-catalyzed reactions. For the liquid phase reaction, compared with the case of n = 0–3, when the size of the water molecule cluster surrounding the OH radical is n = 13, the rate constant of the title reaction increases. Our study also shows that proton transfer is also a factor which accelerates the liquid phase NH₃ + OH reaction.

We used DFT and CCSD(T) methods with PCM solvation model to study the water cluster effect and solvation effect on the NH₃ + OH reaction.