Hydration of N-Hydroxyurea from Ab Initio Molecular Dynamics Simulations

Abstract

N-Hydroxyurea (HU) is an important chemotherapeutic agent used as a first-line treatment in conditions such as sickle cell disease and β-thalassemia, among others. To date, its properties as a hydrated molecule in the blood plasma or cytoplasm are dramatically understudied, although they may be crucial to the binding of HU to the radical catalytic site of ribonucleotide reductase, its molecular target. The purpose of this work is the comprehensive exploration of HU hydration. The topic is studied using ab initio molecular dynamic (AIMD) simulations that apply a first principles representation of the electron density of the system. This allows for the calculation of infrared spectra, which may be decomposed spatially to better capture the spectral signatures of solute-solvent interactions. The studied molecule is found to be strongly hydrated and tightly bound to the first shell water molecules. The analysis of the distance-dependent spectra of HU shows that the E and Z conformers spectrally affect, on average, 3.4 and 2.5 of the closest H₂O molecules, respectively, in spheres of radii of 3.7 Å and 3.5 Å, respectively. The distance-dependent spectra corresponding to these cutoff radii show increased absorbance in the red-shifted part of the water OH stretching vibration band, indicating local enhancement of the solvent's hydrogen bond network. The radially resolved IR spectra also demonstrate that HU effortlessly incorporates into the hydrogen bond network of water and has an enhancing effect on this network. Metadynamics simulations based on AIMD methodology provide a picture of the conformational equilibria of HU in solution. Contrary to previous investigations of an isolated HU molecule in the gas phase, the Z conformer of HU is found here to be more stable by 17.4 kJ·mol^-1 than the E conformer, pointing at the crucial role that hydration plays in determining the conformational stability of solutes. The potential energy surface for the OH group rotation in HU indicates that there is no intramolecular hydrogen bond in Z-HU in water, in stark contrast to the isolated solute in the gas phase. Instead, the preferred orientation of the hydroxyl group is perpendicular to the molecular plane of the solute. In view of the known chaotropic effect of urea and its N-alkyl-substituted derivatives, N-hydroxyurea emerges as a unique urea derivative that exhibits a kosmotropic ordering of nearby water. This property may be of crucial importance for its binding to the catalytic site of ribonucleotide reductase with a concomitant displacement of a water molecule.

Keywords: N-hydroxyurea; ab initio molecular dynamics; density functional theory; hydration.

Figure 1

The studied conformers of hydroxyurea: (a) E-hydroxyurea; (b) Z-hydroxyurea. Italicized numbers indicate the atom numbering scheme used in this work.

Figure 2

(a) Oxygen–oxygen radial distribution function of liquid water from AIMD simulations (red) and from X-ray diffraction measurements [56] (black). (b) Infrared absorption spectrum of liquid water on the decadic molar absorptivity scale from AIMD simulations (red) and from spectroscopic measurements [57] (black).

Figure 3

Free energy profiles for the rotation around (a) OCNO dihedral angle ($\varphi$) in hydroxyurea (red) and (b) CNOH dihedral angle ($\omega$) in E-hydroxyurea (green) and Z-hydroxyurea (blue).

Figure 4

The time evolution of the CNOH dihedral angle ($\omega$) in E-hydroxyurea during a selected microcanonical equilibrium AIMD trajectory (cyan) and during the well-tempered metadynamics trajectory, with $\omega$ as the collective variable (magenta).

Figure 5

Normalized distribution functions of molecular dipole moments of E-hydroxyurea (green dots) and Z-hydroxyurea (blue dots) along with the respective fits to normal distribution (dashed lines).

Figure 6

Radial distribution functions for H₉···O_w pairs (solid lines) and O₈···H_w pairs (dashed lines) in E-hydroxyurea (green) and Z-hydroxyurea (blue).

Figure 7

Radial distribution functions for O₄···H_w pairs in E-hydroxyurea (green) and Z-hydroxyurea (blue).

Figure 8

Radial distribution functions for H₅···O_w (orange), H₆···O_w (cyan), and H₇···O_w (magenta) pairs in (a) E-hydroxyurea and (b) Z-hydroxyurea.

Figure 9

Intramolecular radial distribution function for O₄···H₉ pair in Z-hydroxyurea.

Figure 10

Instantaneous snapshot of the hydration shell of (a) E-hydroxyurea and (b) Z-hydroxyurea. Atoms are colored as follows: C (cyan), O (red), N (blue), and H (gray).

Figure 11

The radially resolved IR spectrum of aqueous (a) E-hydroxyurea and (b) Z-hydroxyurea. The center of mass of HU molecule is located at $r=0$. The local spectral intensity is indicated by color scale.

Figure 12

The distance-dependent IR spectrum of aqueous (a) E-hydroxyurea and (b) Z-hydroxyurea. The center of mass of HU molecule is located at $R_c=0$. The cutoff distance in Å is indicated by color scale. The inset shows the modulation of the distance-dependent spectra at a probing frequency 320 cm⁻¹ in E-hydroxyurea (green) and Z-hydroxyurea (blue).

Figure 13

The distance-dependent IR spectrum of aqueous E-hydroxyurea at $R_c=3.7$ Å (green) and Z-hydroxyurea at $R_c=3.5$ Å (blue), compared with the bulk water IR spectrum (red).