Urea in Water: Structure, Dynamics, and Vibrational Echo Spectroscopy from First-Principles Simulations

Abstract

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.

Choline Chloride as a Nano‐Crowder Protects HP‐36 from Urea‐Induced Denaturation: Insights from Solvent Dynamics and Protein‐Solvent Interactions

“…The role of urea in slowing down the water dynamics has been recently described by Ojha et al. also . The addition of bulky choline ion affects the HB dynamics of water around protein backbone (both in PWC and PWUC) by manifold and hence it is reflected clearly in the timescale.…”

“…[85] The role of urea in slowing down the water dynamics has been recently described by Ojha et al also. [86] The addition of bulky choline ion affects the HB dynamics of water around protein backbone (both in PWC and PWUC) by manifold and hence it is reflected clearly in the timescale. In PWC (Figure 9a, blue curve), choline affects the dynamics of water in such a way that it facilitates the accumulation of the water molecules on the protein surface, which is evident from the g(r) plots (Figure 4a).…”

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations

“…This is justifiable because the numerical value of the transition dipole used for the calculation of the spectral dynamics alters the spectral intensity parametrically but it would not modify any of the spectral relaxation features. The value of κ ( μ 21 / μ 10 ) was found out using the known Eigen functions of Morse oscillators, and its value was found to be 1.34 . We have performed simulations of sodium and bromide ions dissolved in pure D 2 O, which allow us to have 214 OD modes for the dilute solution and 176 OD modes for the concentrated solution, thus enhancing the statistical averaging.…”

“…The value of κ (μ 21 / μ 10 ) was found out using the known Eigen functions of Morse oscillators, and its value was found to be 1.34. [26][27][28][29] We have performed simulations of sodium and bromide ions dissolved in pure D 2 O, which allow us to have 214 OD modes for the dilute solution and 176 OD modes for the concentrated solution, thus enhancing the statistical averaging. Each OD mode is considered as a decoupled stretching mode, hence the present study may be considered as an investigation of isolated OD modes in dilute and concentrated aqueous solutions of NaBr at different temperatures.…”

“…Nonlinear vibrational spectroscopic techniques like transient hole burning, two‐dimensional infrared (2D‐IR), three‐pulse photon echo peak shift (3PEPS), and pump‐probe experiments have enabled us to observe the dynamical evolution of the rapidly evolving hydrogen bond network and determine the timescales of associated vibrational spectral diffusion . There have been many experimental and simulation studies on the application of nonlinear vibrational spectroscopy to study hydrogen bond dynamics in liquid water and dilute ionic solutions, solute‐solvent complex formation in aqueous medium and also in hydrogen‐bonded nonaqueous solutions …”