*2.1. Car–Parrinello Molecular Dynamics (CPMD)*

The CPMD [36] computations were performed in the crystalline phase for three crystals taken from the Cambridge Crystallographic Data Centre (CCDC) [75]. Their CCDC codes are as follows: (A)—919101, (B)—908102 and (C)—908103 [51]. The molecular structures of the studied complexes are presented in Figures 1 and 2. Two different sets of structures were chosen to thoroughly describe the intermolecular hydrogen bonds present in these systems. The simulations of the monomers of the (A), (B) and (C) were conducted in the gas phase with the box edges set to: a = b = c = 15 Å. The Perdew–Burke–Ernzerhof

functional (PBE) [76] and the norm-conserving Troullier-Martins pseudopotentials [77] were applied. The plane-wave kinetic energy cutoff was set to 100 Ry. The models for crystalline-phase simulations were constructed based on experimental data—the details of which are presented in Table 1. The periodic boundary conditions (PBCs) with real-space electrostatic summations for the eight nearest neighbors in each direction were employed during the crystalline phase computations. Additionally, simulations were performed for dimers in the gas phase as well. The sizes of the corresponding simulation boxes were benchmarked and adjusted to calculate the Hartree potential using the Hockney solver of the Poisson equation. The edges of the corresponding boxes for the dimers were equal to: a = 18 Å b = 21 Å c = 18 Å for the (D) dimer and a = 22 Å b = 18 Å c = 18 Å for the (E) dimer.

**Figure 1.** Crystalline (first row) and gaseous phases (second row) of (**A**) 2,6-difluorobenzamide, (**B**) 5-hydroxyquinoline, and (**C**) co-crystal of 4-hydroxybenzoic acid and quinoxaline. For clarity, the oxygen donor atoms for (**C**) are denoted as OD1, OD2 and OD3—this adopted nomenclature is used throughout the study. Dotted line indicates the intermolecular hydrogen bond. Color coding: white—hydrogen, grey—carbon, red—oxygen, blue—nitrogen, green—fluorine.

**Figure 2.** Dimers taken from the crystalline phase of (**D**) 2,6-difluorobenzamide and (**E**) 4 hydroxybenzoic acid to study intermolecular hydrogen bonds. Dotted line indicates the intermolecular hydrogen bond.


**Table 1.** CCDC code and unit cell data for the investigated compounds.

Subsequently, Car–Parrinello molecular dynamics (CPMD) [36] simulations were performed with the CPMD 4.3 suite of programs [78]. During the computations, the time step was set to 3 a.u., while the fictitious electron mass (EMASS) parameter was equal to 400 a.u. in both phases. The temperature was controlled by the Nosé–Hoover thermostat [79,80] and it was set to 297 K. The obtained CPMD trajectories were divided into equilibration (first 10,000 steps were excluded from the data analysis) and the production run. The CPMD production runs of the crystalline models were collected for ca. 72 ps and 42 ps for crystalline and gas-phase systems, respectively (monomers dynamics in the gas phase was simulated only to obtain the spectroscopic signatures of the O-H, C-H and N-H functional groups). Molecular dynamics corresponding to the models chosen to study dimer interactions were propagated for ca. 45 ps. The post-processing included the analysis of metric and spectroscopic properties. The vibrational features were studied using the Fourier transform of the atomic velocity autocorrelation function. This type of analysis enabled the decomposition of the computed IR spectra. The O-H and N-H stretching was obtained to give a deeper insight into spectroscopic signatures in the investigated hydrogen bridges. The metric parameters analysis was performed with the assistance of the VMD 1.9.3 program [81], while the Fourier transform power spectra of the atomic velocity were computed using home-made scripts. The graphs were obtained with the Gnuplot [82] program. The experimental unit cells were visualized and analyzed using the Mercury [83] program. The visualizations presented in Figures 1 and 2 were prepared in the SAMSON suite of programs [84].
