Car–Parrinello Molecular Dynamics Trajectory and Energy Data for Aqueous Solvation of Neutral Indole-3-Acetic Acid

Dataset Description This dataset contains computational data supporting the study entitled "Aqueous Solvation and Hydrogen Bonding of Neutral Indole-3-Acetic Acid Investigated by Car–Parrinello Molecular Dynamics and Electron-Density Analyses", submitted to Scientific Reports. The study investigates the structural, dynamical, and electronic characteristics of hydrogen-bond interactions between neutral indole-3-acetic acid (IAA) and water molecules using Car–Parrinello molecular dynamics (CPMD) simulations combined with electron-density-based analyses. Computational Methodology The CPMD simulations were performed using CPMD version 4.3 within the density functional theory (DFT) framework, employing the PBE exchange–correlation functional, Vanderbilt ultrasoft pseudopotentials, and a plane-wave kinetic-energy cutoff of 25 Ry. The aqueous system consists of one neutral IAA molecule and 90 water molecules in a cubic periodic simulation cell with a side length of 15.0 Å, corresponding to an approximate density of 0.90 g cm⁻³. The simulation was performed at a target ionic temperature of 300 K using Nosé–Hoover chain thermostats, a time step of 0.1209 fs, and a fictitious electronic mass of 400 a.u. The total simulation time was approximately 42 ps. Representative IAA–water configurations extracted from the CPMD trajectory were subsequently subjected to electronic-structure calculations at the M06-2X/6-311++G(d,p) level using Gaussian 16. Electron-density analyses were performed using Multiwfn 3.7, employing the Quantum Theory of Atoms in Molecules (QTAIM), Reduced Density Gradient (RDG), and Interaction Region Indicator (IRI) approaches. Dataset Contents 1. TRAJEC.xyz – Molecular Dynamics Trajectory Atomic coordinates recorded during the CPMD simulation of neutral IAA surrounded by 90 water molecules. The trajectory provides the structural information used to investigate hydration-shell organization, radial distribution functions (RDFs), intermolecular distances, hydrogen-bond geometries, and coordination dynamics. 2. ENERGY – Energy and Temperature Data Simulation output containing energy-related and temperature data recorded during the CPMD simulation. These data were used to monitor the stability of the simulation, electronic adiabaticity, and ionic temperature, supporting the analysis presented in Figure 2 of the associated manuscript. 3. Geometry.rar and QTAIM_RDG_IRI.rar – Electronic-Structure and Electron-Density Analysis Files The Geometry.rar archive additionally contains Cartesian coordinate files in XYZ format (.xyz), including the initial molecular configuration used in the CPMD simulation. Compressed archive containing Gaussian input files (.gjf) and formatted checkpoint files (.fchk) associated with representative IAA–water configurations selected from the CPMD trajectory. The selected configurations represent different intermolecular separations involving the three principal hydration sites: N–H···OW interaction involving H19. O–H···OW interaction involving H22. C=O···HW interaction involving O13. The .gjf files provide molecular geometries and computational input information, whereas the .fchk files contain electronic-structure information used for electron-density analyses. These files support the QTAIM topological characterization presented in Table 2 and the RDG and IRI analyses illustrated in Figures 6–8 of the associated manuscript. To reproduce the QTAIM, RDG, and IRI analyses, the .fchk files should be loaded into Multiwfn 3.7. The program can be used to calculate bond critical points and associated topological descriptors, generate volumetric grid data (cube files), and produce the numerical data required for RDG and IRI scatter plots. The resulting cube files can be visualized using VMD or other compatible molecular visualization software to reconstruct the interaction isosurfaces presented in Figures 6–8 of the associated manuscript. The deposited .fchk files provide the electronic-structure information needed to regenerate these analyses without repeating the original Gaussian electronic-structure calculations. The RDG and IRI isosurfaces were generated using isovalues of 0.5 and 1.0, respectively, in Multiwfn 3.7. These parameters can be used to reproduce the interaction surfaces presented in Figures 6–8 of the associated manuscript. Data Reuse and Reproducibility The deposited files enable independent examination of the CPMD trajectory, simulation energy and temperature behavior, and electronic-density properties of selected IAA–water configurations. The electronic-structure files can be used with compatible analysis software, including Multiwfn, to examine bond critical points, electron-density distributions, and interaction regions. Associated Publication Manuscript: Aqueous Solvation and Hydrogen Bonding of Neutral Indole-3-Acetic Acid Investigated by Car–Parrinello Molecular Dynamics and Electron-Density Analyses. Journal: Scientific Reports (submitted). Corresponding Author Luciano RibeiroUniversidade Estadual de Goiás, Anápolis, Goiás, BrazilEmail: [e-mail]