Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide
Graphical abstract
Introduction
In peptides, the basic structural repeating unit is the carbonyl carbon to nitrogen bond, commonly known as the amide linkage. Amides are carboxylic acid derivatives, where an amine replaces the hydroxyl group, and the resulting peptide bonds formed via covalent linkages in the polypeptides confer structural rigidity and serve as structural materials in aqueous biochemical processes preventing hydrolysis [[1], [2], [3], [4], [5]]. The structure, dynamics, and overall bonding of aqueous solutions of these polyamides depend on the strength of the amide-water hydrogen bonding interactions. To study amide facilitated changes in structural and stretching dynamics of water molecules and the solvent effect on the amide moieties, we investigate water interactions with an exceptional tertiary amide DMF, consisting of two hydrophilic amino (NH2) and aldehyde (CHO) sites along with hydrophobic methyl groups. Moreover, it has been reported recently that the hydrophobic solubility may facilitate the stability of the protein in an aqueous environment [6]. DMF can act as both a proton donor and an acceptor. DMF can only be a proton acceptor (or H-bond acceptor) on substitution of the two hydrogen atoms of the amino group by methyl functionality in the simplest amide molecule formamide and it forms very weak CH…OW hydrogen bond [1]. Dialkyl substitution hinders NH…OC hydrogen bonding and makes DMF unique 3° amide to be studied. DMF is a common solvent in chemical reactions due to its low evaporation rate, and high dielectric constant [[7], [8], [9], [10]]. The dielectric constants are varied to make the aqueous mixtures useful solvents. On hydrating the DMF molecule, it undergoes structural changes, the behavior of water molecules in DMF-water mixtures vary with the surrounding solvent medium. In DMF solvation, water molecules form hydrogen bonds, and the hydrophobic interactions of the methyl functional groups affect the vicinal water molecules. The presence of a diverse environment in DMF attracts our attention to explore and comment on the structure, dynamics, and hydrogen bonding patterns prevailing in amide-water mixtures. Previously several experimental [[11], [12], [13], [14]] and theoretical studies [[15], [16], [17], [18], [19], [20], [21], [22], [23], [24]] on pure and aqueous DMF solutions were reported. The time-domain reflectometry (TDR) method was used to study the dielectric properties of DMF-water mixtures to understand hydrogen bonding and intramolecular rotations [25]. Molecular dynamics (MD) simulations using the OPLS all-atom force field showed the composition dependence and the clustering of water molecules in an aqueous solution of DMF [1]. It was seen that dipolar interactions existed between DMF and the solvent in pure solution, but hydrogen-bonded associations were not detected in the measurement of NMR chemical shift [26]. The calculation of the enthalpy of solution did not report the hydrophobic effect in mixtures of tetraalkylammonium ions [27]. In the DMF-water system, the physical properties like densities, viscosities, and the dynamical properties depicting molecular mobility like the diffusion coefficient vary as a function of solute composition and temperature variation [8,9]. These physicochemical properties [8,9,[28], [29], [30]] arise from the interactions of a single DMF molecule with its well-defined solvent environment, and the hydrogen bonds between water molecules and DMF result in the formation of water clusters. Two-dimensional correlation spectroscopy [31] found out the composition-dependent spectral shifts in the specific stretching bands. With the increase of the water content, two different regions were identified due to the appearance of CH and OH bands. [31] Numerous investigations [21,[32], [33], [34], [35], [36], [37], [38]] on the microscopic environment in mixtures of water and organic liquids revealed the interesting properties in the liquid structure arise from the water hydrogen-bonded structures [39]. Reorientation time correlation is a sensitive reporter of the intermolecular interactions of water molecules in amide-water mixtures [20,29,[40], [41], [42], [43], [44], [45]]. The measurement of the NMR spin-lattice relaxation times at 5, 25, and 45 °C depicted the hydrophilic and hydrophobic interactions between amide and water molecules and its impact on molecular reorientational dynamics [29]. Molecular dynamics study of aqueous amide mixtures addressed the relationship between concentration fluctuations and microheterogeneity [39]. Monte Carlo simulations [10] of dilute amide-water solutions performed at ambient conditions reported hydrogen bonds between the carbonyl oxygen of amide and the water molecules, but the solvent molecules around hydrophobic methyl showed little interaction with the solutes [10]. The other study [16] on the water-DMF interaction used the same simulation protocol and characterized CO…HW hydrogen bonds between the carboxyl oxygen site of DMF and water hydrogen by the calculations of the radial distribution functions. Statistical perturbation theory [16] was employed to monitor the stabilization of the DMF molecule, and it was observed that the energy changes involved in the hydration process stabilized DMF in its planar configuration. In this paper, we present the structural details that help in understanding the solvent structure around DMF, the phenomena of vibrational spectral diffusion of water molecules, and the strength and lifetime of hydrogen bonds affecting the dynamics in the amide-water systems.
Section snippets
Computational methods
First principles molecular dynamics (FPMD) [46] simulations of 50 water molecules and single DMF molecule were carried out in a cubic box with box vector 11.71 Å, using the Quickstep module [47] implemented in the CP2K [48] software package. The box length was calculated after performing the simulations within NpT ensemble. The dual centered Gaussian-type orbitals [47,49] and plane waves available within the Gaussian plane wave approach solve the self-consistent Kohn-Sham equations of density
Solvation shell structure in aqueous DMF
Structural detailing in liquid amides has drawn considerable interest in physical chemists. X-ray diffraction measurements determined the liquid structure of DMF [58], and later the structure was compared with the molecular structure of formamide (FA), declaring the absence of associated species in liquid DMF [59]. Understanding the atom-atom intermolecular interactions required support from reliable experimental and simulated radial distribution functions. To elucidate the intermolecular
Discussion
In this section, we compare the structural aspects of the amide solvation shell, spectral properties, and the dynamical response of the surrounding water molecules in N,N-dimethylformamide (DMF) with the earlier reported other aqueous amides studied using similar methods. Car-Parrinello molecular dynamics (CPMD) simulations with a single formamide (FA) dissolved in 31 solvent molecules, followed by the time-series wavelet analysis, calculated the time-dependent vibrational stretch frequencies. [
Conclusions
An aqueous solution of DMF was studied using first principles molecular dynamics simulation using the Perdew-Burke-Ernzerhof (PBE) [51,52] exchange-correlational functional and Grimme's D3 [55,56] dispersion correction using TZV2P basis set at a temperature of 330 K. The hydrophilic aldehyde carbonyl participates in hydrogen bond formation with the nearest neighboring water molecules. The DMF-water hydrogen bond between the CHO group and the corresponding hydrogen or oxygen atom of the adjacent
CRediT authorship contribution statement
Aritri Biswas: Formal analysis, Visualization, Validation, Writing - original draft. Bhabani S. Mallik: Investigation, Conceptualization, Methodology, Writing - review & editing, Supervision, Project administration, Funding acquisition.
Acknowledgments
The authors acknowledge financial support (EMR/2016/004965) for this work from the Department of Science and Technology, India. Aritri Biswas likes to thank the Ministry of Human and Resources Development, India, for the Ph.D. fellowship.
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