Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations.
Deepak OjhaAmalendu ChandraPublished in: The journal of physical chemistry. B (2019)
Aqueous solution of urea at a concentration of 4.0 M is studied by using ab initio molecular dynamics simulation. The radial and spatial distribution functions reveal no significant disruption of the local solvent structure by urea even at such a rather high concentration. Although the static structural features are not altered in any significant manner, the translational, rotational, and vibrational dynamics are found to show noticeable slowing down. The diffusion coefficient of urea is found to be three times lower than that of bulk water molecules. Similarly, orientational relaxation of water molecules in the solvation shell of urea is found to be about 5.0 ps which is significantly higher than the average value of 3.8 ps found for all water molecules. The vibrational dynamics is investigated through calculations of frequency-time correlation function (FTCF), joint frequency probability, and frequency-structure correlation functions. The timescale of vibrational spectral diffusion as determined from FTCF is found to be 2.7 ps which is higher than the known calculated timescale of ∼2 ps for spectral diffusion of pure water for similar levels of calculations. The third-order polarization and the corresponding vibrational echo intensity of OD modes are calculated within the Condon and second-order cumulant approximations. The timescales of loss of correlation in the vibrational echo spectrum are calculated from the time dependence of the slope of the 3-pulse photon echo (S3PE) function. The timescales obtained from S3PE are found to be in agreement with the FTCF. The slowing down of vibrational, translational, and rotational dynamics means that urea affects the properties of water from a dynamical perspective.
Keyphrases
- molecular dynamics simulations
- density functional theory
- molecular dynamics
- molecular docking
- magnetic resonance
- diffusion weighted imaging
- energy transfer
- optical coherence tomography
- blood pressure
- diffusion weighted
- ionic liquid
- high resolution
- dna methylation
- single cell
- ultrasound guided
- computed tomography
- fluorescent probe