Proton Dynamics in Strong (Short) Intramolecular H-Bond. DFT Study of the KH Maleate Crystal

Molecular Dynamics Simulation of Association Processes in Aqueous Solutions of Maleate Salts of Drug-like Compounds: The Role of Counterion

The study of the formation of microstructures during the interaction of a protonated drug-like compound (API) with a maleic acid monoanion sheds light on the assembly processes in an aqueous solution at the molecular level. Molecular dynamics (MD) simulations coupled with density functional theory (DFT) calculations made it possible to find initial hydrogen bonding motifs during the assembly process, leading to the formation of heterodimers and trimers. The process of trimer formation [protonated API—maleic acid monoanion—protonated API] proceeds through the formation of three intermolecular H-bonds by the CO₂⁻ group of the maleic acid monoanion in both systems. The total enthalpy/energy of these H-bonds is more than 70 kJ/mol. Thus, the maleic acid monoanion plays a key role in the processes of association in aqueous solution, and the interaction of the maleic acid monoanion with API is more preferable than the interaction of API molecules with each other. DFT computations in the discrete continuum approximation reveal the spectral features of heterodimers and trimers, and the ATR-IR spectra confirmed these findings. MD simulations followed by DFT calculations made it possible to describe the initial stages of the formation of pharmaceutical cocrystals in an aqueous solution.

Choline Hydrogen Dicarboxylate Ionic Liquids by X-ray Scattering, Vibrational Spectroscopy and Molecular Dynamics: H-Fumarate and H-Maleate and Their Conformations

We explore the structure of two ionic liquids based on the choline cation and the monoanion of the maleic acid. We consider two isomers of the anion (H-maleate, the cis-isomer and H-fumarate, the trans-isomer) having different physical chemical properties. H-maleate assumes a closed structure and forms a strong intramolecular hydrogen bond whereas H-fumarate has an open structure. X-ray diffraction, infrared and Raman spectroscopy and molecular dynamics have been used to provide a reliable picture of the interactions which characterize the structure of the fluids. All calculations indicate that the choline cation prefers to connect mainly to the carboxylate group through OH⋯O interactions in both the compounds and orient the charged head N(CH3)3+ toward the negative portion of the anion. However, the different structure of the two anions affects the distribution of the ionic components in the fluid. The trans conformation of H-fumarate allows further interactions between anions through COOH and CO2- groups whereas intramolecular hydrogen bonding in H-maleate prevents this association. Our theoretical findings have been validated by comparing them with experimental X-ray data and infrared and Raman spectra.

Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density

Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.

N-Tosyl-L-proline benzene hemisolvate: a rare example of a hydrogen-bonded carboxylic acid dimer with symmetrically disordered H atoms

The carboxylic acid group is an example of a functional group which possess a good hydrogen-bond donor (-OH) and acceptor (C=O). For this reason, carboxylic acids have a tendency to self-assembly by the formation of hydrogen bonds between the donor and acceptor sites. We present here the crystal structure of N-tosyl-L-proline (TPOH) benzene hemisolvate {systematic name: (2S)-1-[(4-methylbenzene)sulfonyl]pyrrolidine-2-carboxylic acid benzene hemisolvate}, C₁₂H₁₅NO₄S·0.5C₆H₆, (I), in which a cyclic R₂²(8) hydrogen-bonded carboxylic acid dimer with a strong O-(1/2H)...(1/2H)-O hydrogen bond is observed. The compound was characterized by single-crystal X-ray diffraction and NMR spectroscopy, and crystallizes in the space group I2 with half a benzene molecule and one TPOH molecule in the asymmetric unit. The H atom of the carboxyl OH group is disordered over a twofold axis. An analysis of the intermolecular interactions using the noncovalent interaction (NCI) index showed that the TPOH molecules form dimers due to the strong O-(1/2H)...(1/2H)-O hydrogen bond, while the packing of the benzene solvent molecules is governed by weak dispersive interactions. A search of the Cambridge Structural Database revealed that the disordered dimeric motif observed in (I) was found previously only in six crystal structures.

Cl···Cl interactions in molecular crystals: insights from the theoretical charge density analysis

The structure, IR harmonic frequencies and intensities of normal vibrations of 20 molecular crystals with the X-Cl···Cl-X contacts of different types, where X = C, Cl, and F and the Cl···Cl distance varying from ~3.0 to ~4.0 Å, are computed using the solid-state DFT method. The obtained crystalline wave functions have been further used to define and describe quantitatively the Cl···Cl interactions via the electron-density features at the Cl···Cl bond critical points. We found that the electron-density at the bond critical point is almost independent of the particular type of the contact or hybridization of the ipso carbon atom. The energy of Cl···Cl interactions, E(int), is evaluated from the linking E(int) and local electronic kinetic energy density at the Cl···Cl bond critical points. E(int) varies from 2 to 12 kJ/mol. The applicability of the geometrical criterion for the detection of the Cl···Cl interactions in crystals with two or more intermolecular Cl···Cl contacts for the unique chlorine atom is not straightforward. The detection of these interactions in such crystals may be done by the quantum-topological analysis of the periodic electron density.

How strong is hydrogen bonding in ionic liquids? Combined X-ray crystallographic, infrared/Raman spectroscopic, and density functional theory study

Hydrogen bonding in ionic liquids based on the 1-(2'-hydroxylethyl)-3-methylimidazolium cation ([C₂OHmim](+)) and various anions ([A](-)) of differing H-bond acceptor strength, viz. hexafluorophosphate [PF6](-), tetrafluoroborate [BF₄](-), bis(trifluoromethanesulfonimide) [Tf₂N](-), trifluoromethylsulfonate [OTf](-), and trifluoroacetate [TFA](-), was studied by a range of spectroscopic and computational techniques and, in the case of [C₂OHmim][PF6], by single crystal X-ray diffraction. The first quantitative estimates of the energy (E(HB)) and the enthalpy (-ΔH(HB)) of H-bonds in bulk ILs were obtained from a theoretical analysis of the solid-state electron-density map of crystalline [C₂OHmim][PF6] and an analysis of the IR spectra in crystal and liquid samples. E(HB) for OH···[PF6](-) H-bonds amounts to ~3.4-3.8 kcal·mol(-1), whereas weaker H-bonds (2.8-3.1 kcal·mol(-1)) are formed between aromatic C2H group of imidazolium ring and the [PF6](-) anion. The enthalpy of the OH···[A](-) H-bonds follows the order: [PF6] (2.4 kcal·mol(-1)) < [BF₄] (3.3 kcal·mol(-1)) < [Tf₂N] (3.4 kcal·mol(-1)) < [OTf] (4.7 kcal·mol(-1)l) < [TFA] (6.2 kcal·mol(-1)). The formation of aggregates of self-associated [C₂OHmim](+) cations is present in liquid [C₂OHmim][PF6], [C₂OHmim][BF₄], and [C₂OHmim][Tf₂N], with the energy of the OH···OH H-bonds amounting to ~6 kcal·mol(-1). Multiple secondary interactions in the bulk ILs influence their structure, vibrational spectra, and H-bond strength. In particular, these interactions can blue-shift the stretching frequencies of the CH groups of the imidazolium ring in spite of red-shifting CH···[A](-) H-bonds. They also weaken the H-bonding in the IL relative to the isolated ion pairs, with these anticooperative effects amounting to ca. 50% of the E(HB) value.

Is there a simple way to reliable simulations of infrared spectra of organic compounds?

To assess the ability of the quantum-chemical computations to reproduce the experimental relative intensities in the infrared (IR) spectra of both the gas- and condensed-phase systems, the hybrid DFT functional B3LYP has been applied to simulation of IR spectra for species containing from three to twelve first- or second-row atoms, both in the gas phase and in CCl4 solutions. The results demonstrate that B3LYP, combined with the highly compact double-ζ basis set 6-31+G* and "scaled quantum mechanics" techniques, offers excellent quantitative performance in the calculations of relative IR intensities and frequencies (ν ≤ 2200 cm(-1)) for the bands of vibrations of medium-size isolated molecules, whereas it produces unsatisfactory results for the solutions of the same species. Neither larger basis sets nor implicit treatment of the media effects improve the agreement of the simulated spectra with the condensed-phase experiment. At the same time, some preliminary results suggest that explicit modeling of media effects could offer better quality of the IR spectral simulations for the condensed-phase systems.

Intermolecular hydrogen bond energies in crystals evaluated using electron density properties: DFT computations with periodic boundary conditions

The hydrogen bond (H-bond) energies are evaluated for 18 molecular crystals with 28 moderate and strong O-H···O bonds using the approaches based on the electron density properties, which are derived from the B3LYP/6-311G** calculations with periodic boundary conditions. The approaches considered explore linear relationships between the local electronic kinetic G(b) and potential V(b) densities at the H···O bond critical point and the H-bond energy E(HB). Comparison of the computed E(HB) values with the experimental data and enthalpies evaluated using the empirical correlation of spectral and thermodynamic parameters (Iogansen, Spectrochim. Acta Part A 1999, 55, 1585) enables to estimate the accuracy and applicability limits of the approaches used. The V(b)-E(HB) approach overestimates the energy of moderate H-bonds (E(HB) < 60 kJ/mol) by ~20% and gives unreliably high energies for crystals with strong H-bonds. On the other hand, the G(b)-E(HB) approach affords reliable results for the crystals under consideration. The linear relationship between G(b) and E(HB) is basis set superposition error (BSSE) free and allows to estimate the H-bond energy without computing it by means of the supramolecular approach. Therefore, for the evaluation of H-bond energies in molecular crystals, the G(b) value can be recommended to be obtained from both density functional theory (DFT) computations with periodic boundary conditions and precise X-ray diffraction experiments.

H-bond network in amino acid cocrystals with H2O or H2O2. The DFT study of serine-H2O and serine-H2O2

The structure, IR spectrum, and H-bond network in the serine-H(2)O and serine-H(2)O(2) crystals were studied using DFT computations with periodic boundary conditions. Two different basis sets were used: the all-electron Gaussian-type orbital basis set and the plane wave basis set. Computed frequencies of the IR-active vibrations of the titled crystals are quite different in the range of 10-100 cm(-1). Harmonic approximation fails to reproduce IR active bands in the 2500-2800 frequency region of serine-H(2)O and serine-H(2)O(2). The bands around 2500 and 2700 cm(-1) do exist in the anharmonic IR spectra and are caused by the first overtone of the OH bending vibrations of H(2)O and a combination vibration of the symmetric and asymmetric bendings of H(2)O(2). The quantum-topological analysis of the crystalline electron density enables us to describe quantitatively the H-bond network. It is much more complex in the title crystals than in a serine crystal. Appearance of water leads to an increase of the energy of the amino acid-amino acid interactions, up to ~50 kJ/mol. The energy of the amino acid-water H-bonds is ~30 kJ/mol. The H(2)O/H(2)O(2) substitution does not change the H-bond network; however, the energy of the amino acid-H(2)O(2) contacts increases up to 60 kJ/mol. This is caused by the fact that H(2)O(2) is a much better proton donor than H(2)O in the title crystals.

A model proton-transfer system in the condensed phase: NH4(+)OOH(-), a crystal with short intermolecular H-bonds

The crystal structure of NH(4)(+)OOH(-) is determined from single-crystal x-ray data obtained at 150 K. The crystal belongs to the space group P2(1)/c and has four molecules in a unit cell. The structure consists of discrete NH(4)(+) and OOH(-) ions. The OOH(-) ions are linked by short hydrogen bonds (2.533 Å) to form parallel infinite chains. The ammonium ions form links between these chains (the N⋯O distances vary from 2.714 to 2.855 Å) giving a three-dimensional network. The harmonic IR spectrum and H-bond energies are computed at the Perdew-Burke-Ernzerhof (PBE)/6-31G(∗∗) level with periodic boundary conditions. A detailed analysis of the shared (bridging) protons' dynamics is obtained from the CPMD simulations at different temperatures. PBE functional with plane-wave basis set (110 Ry) is used. At 10 K the shared proton sits near the oxygen atom, only a few proton jumps along the chain are detected at 70 K while at 270 K numerous proton jumps exist in the trajectory. The local-minimum structure of the space group Cc is localized. It appears as a result of proton transfer along a chain. This process is endothermic (∼2 kJ/mol) and is described as P2(1)/c↔2Cc. The computed IR spectrum at 10 K is close to the harmonic one, the numerous bands appear at 70 K while at 270 K it shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1). The advantages of the NH(4)(+)OOH(-) crystal as a promising model for the experimental and DFT based molecular dynamics simulation studies of proton transfer along the chain are discussed.

Density functional study of the proton transfer effect on vibrations of strong (short) intermolecular O-H...N/O-...H-N+ hydrogen bonds in aprotic solvents

The structure and spectroscopic properties of the 1:1 complexes of substituted pyridines with benzoic acid and phenol derivatives in aprotic solvents are studied using B3LYP functional combined with the polarizable continuum model approximation. Two extreme structures are investigated: the state without (HB) and with proton transfer (PT). In the presence of an external electric field the O...N distance is contracted and the PT state does appear. The PT state of both the pyridine-benzoic and the pyridine-phenol complexes displays the only IR-active band in the 2800-1800 frequency region, which is located around 2000 cm(-1). However, the nature of the band is different for these two complexes. In the pyridine-benzoic acid complex it is practically a pure stretching vibration of the HN(+) group, while in the pyridine-phenol complex it is the mixed vibration of the bridging proton. A specific feature of the PT state in the pyridine-phenol complex is an IR-intensive band near 600 cm(-1), associated with the asymmetric stretching vibrations of the O(-)...HN(+) fragment. Its intensity is reciprocally proportional to the O...N distance. The appearance of this band provides an efficient criterion to differentiate between the HB and PT states of the 1:1 complexes of phenols with pyridines in aprotic solvents.