Proton transfer from water to aromatic N-heterocyclic anions from DFT-MD simulations

The phenomenon of proton transfer from water to six N-heterocyclic anions and free energy landscapes of this process are studied using both electronic structure calculations and first principles molecular metadynamics simulations. Our investigation involves microhydrated and aqueous phase interaction of water with six aromatic heterocyclic anions relevant to chemistry and biology: imidazolide, pyrrolide, benzimidazolide, 2-cyanopyrrolide, indolide, and indazolide. The basic structures of all these heterocyclic anions differ by substituted functional groups as well as fused rings. We study the proton transfer reaction and the minimum number of required water molecules for the reaction in hydrated microclusters. We find out that at least four water molecules are necessary for hydrated clusters to facilitate the intracluster proton transfer reaction from water to anions except for pyrrolide, for which this magic number is 3. To obtain the reaction free energy and activation barrier of the proton transfer process in an aqueous solution, the metadynamics method based first principles molecular dynamics simulations were performed. The complete proton transfer was observed in aqueous solutions for all the anions. The water molecule directly involved in proton transfer becomes acidic due to the cooperative effect of neighboring water molecules. From the metadynamics simulation, we obtain the values of activation barrier for the proton transfer processes from neutral water to anions, and the highest activation barrier is obtained for benzimidazolide, whereas the lowest activation barrier is obtained for pyrrolide. The structures and free energy profiles of the process for all the anions are discussed, and a comparative outlook of the study is presented here.

Ab initio metadynamics calculations of dimethylamine for probing pKb variations in bulk vs. surface environments

Free energy landscape obtained from ab initio metadynamics calculations for dimethylamine protonation at the air–water interface.

Heterogeneous Occupancy and Vibrational Dynamics of Spatially Patterned Water Molecules

We performed first-principles molecular dynamics simulations of relatively dilute aqueous solutions of sulfate and thiosulfate dianions to analyze the structure, dynamics, and vibrational spectral properties of water molecules around the solute, especially the spatially patterned solvent molecules in the first solvation layer and the extended layers. This study also involves the investigation of dynamics of dangling OH groups in these layers and their role in patterning the water molecules around the dianions. Structural evaluation of the systems is carried out by radial distribution functions, number integrals, and spatial distribution functions. The lifetime of dangling OH groups inside the solvation shell is compared more to that of the bulk. By constructing the O-H groups in three ensembles (S1, S2, and S3) around the anion, we show that the frequency distribution of OH modes in the S1 ensemble show red-shifting for both sulfate and thiosulfate. The O-H groups in the S2 ensemble of the sulfate-water system show red-shifting by 10 cm^-1, while in the case of thiosulfate-water, these O-H groups show blue-shifting by 8 cm^-1. The water molecules in S1 and S2 subensembles have slower dynamics compared to those in the bulk (S3). The dynamics of various kinds of hydrogen bonds were characterized by hydrogen bond population correlation functions. The spectral diffusion of solvation shell O-H modes was performed through a frequency-time correlation function. We find a significant amount of orientational retardation of water molecules in the S1 layer and moderate retardation in the S2 layer as compared to that in the bulk, S3 layer. All these findings, the red shift of the OH stretching frequency in S1 and S2 layers, slowing down of the orientational dynamics of OH vectors in S1 and S2 layers, and less diffusivity of water in S1 and S2 layers, show the long-range kosmotropic effect of multivalent sulfate and thiosulfate oxyanions. Due to the long-range effect, heterogeneous occupancy of water molecules is observed, and the water molecules are found to arrange in a patterned manner in the vicinity of anions with varied local density.

Time-dependent vibrational spectral analysis of first principles trajectory of methylamine with wavelet transform

The fluctuation dynamics of amine stretching frequencies, hydrogen bonds, dangling N-D bonds, and the orientation profile of the amine group of methylamine (MA) were investigated under ambient conditions by means of dispersion-corrected density functional theory-based first principles molecular dynamics (FPMD) simulations. Along with the dynamical properties, various equilibrium properties such as radial distribution function, spatial distribution function, combined radial and angular distribution functions and hydrogen bonding were also calculated. The instantaneous stretching frequencies of amine groups were obtained by wavelet transform of the trajectory obtained from FPMD simulations. The frequency-structure correlation reveals that the amine stretching frequency is weakly correlated with the nearest nitrogen-deuterium distance. The frequency-frequency correlation function has a short time scale of around 110 fs and a longer time scale of about 1.15 ps. It was found that the short time scale originates from the underdamped motion of intact hydrogen bonds of MA pairs. However, the long time scale of the vibrational spectral diffusion of N-D modes is determined by the overall dynamics of hydrogen bonds as well as the dangling ND groups and the inertial rotation of the amine group of the molecule.