QTAIMC study of the X–H/H⋯O bond order indices (X=O, N, C) in molecular systems

Proton transfer between sulfonic acids and various propylamines by density functional theory calculations

CONTEXT

Proton transfer in acid-base systems is not well understood. Some acid-base reactions do not proceed to the extent that is expected from the difference in the pK_a values between the base and acid in aqueous solutions, yet some do. In that regard, we have computationally studied the process of proton transfer from the acids of varying strength (benzenesulfonic acid (BSu), methansulfonic acid (MsO), and sulfuric acid (SA)) to the amines with different numbers of propyl substituents on the nitrogen atom (propylamine (PrA), dipropylamine (DPrA), and tripropylamine (TPrA)) upon complexation. Density functional theory calculations were used to thoroughly examine the energetic and structural aspects of the molecular complexes and/or ionic pairs resulting from the acid-base interaction. The potential energy curves along the proton transfer coordinate in these acid-amine systems were analyzed. The change in free energies accompanying the molecular complexes and ionic pair formations was calculated, and the relationship between the energy values and the ΔРА parameter (difference in proton affinity of the acid anion and amine) was established. The larger ΔРА values were found to be unfavorable for the formation of ionic pairs. Using structural, energy, QTAIM, and NBO analyses, we determined that the hydrogen bonds in the molecular complexes PrA-MsO and PrA-BSu are stronger than those in their corresponding ionic pairs. The ionic pairs with the TPrA cation possess the strongest hydrogen bonds of all the ionic pairs being studied, regardless of the anion. The results showed that hydrogen bonding interactions in the molecular complexes contribute significantly to the energies of the acid-base interaction, while in the ionic pairs, the most important energy contribution comes from Coulomb interactions, followed by hydrogen bonding and dispersion forces. The ionic pairs with propylammonium, dipropylammonium, and tripropylammonium cations have stronger ion-ion interactions than tetrapropylammonium (TetPrA)-containing ionic pairs with the same anions. This effect rises with the order of the cation: TetPrA → TPrA → DPrA → PrA, and the sequence of anions is SA → BSu → MsO. The results obtained here expand the concept of acid-base interaction and provide an alternative to experimental searches for suitable acids and bases to obtain new types of protic ionic liquids.

METHODS

All quantum-chemical calculations were carried out by using the DFT/B3LYP-GD3/6-31++G(d,p) level as implemented in the Gaussian 09 software package. For the resulting structures, the electron density distribution was analyzed by the "atoms in molecules" (QTAIM) and the natural bond orbital (NBO) methods on the wave functions obtained at the same level of theory by AIMAll Version 10.05.04 and Gaussian NBO Version 3.1 programs, respectively.

Experimental and theoretical charge density, intermolecular interactions and electrostatic properties of metronidazole

Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P2₁/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)_max = 1.12 Å^-1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen-Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N-O and C-NO₂ exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O-H...N, C-H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.

Direct air capture of CO-2 - topological analysis of the experimental electron density (QTAIM) of the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4

Chemical bonding and all intermolecular interactions in the highly insoluble carbonate salt of a 2,6-pyridine-bis(iminoguanidine), (PyBIGH2)(CO3)(H2O)4, recently employed in the direct air capture of CO2 via crystallization, have been analyzed within the framework of the quantum theory of atoms in molecules (QTAIM) based on the experimental electron density derived from X-ray diffraction data obtained at 20 K. Accurate hydrogen positions were included based on an analogous neutron diffraction study at 100 K. Topological features of the covalent bonds demonstrate the presence of multiple bonds of various orders within the PyBIGH2 2+ cation. Strong hydrogen bonds define ribbons comprising carbonate anions and water molecules. These ribbons are linked to stacks of essentially planar dications via hydrogen bonds from the guanidinium moieties and an additional one to the pyridine nitro-gen. The linking hydrogen bonds are approximately perpendicular to the anion-water ribbons. The observation of these putative interactions provided motivation to characterize them by topological analysis of the total electron density. Thus, all hydrogen bonds have been characterized by the properties of their (3,-1) bond critical points. Weaker interactions between the PyBIGH2 2+ cations have similarly been characterized. Integrated atomic charges are also reported. A small amount of cocrystallized hydroxide ion (∼2%) was also detected in both the X-ray and neutron data, and included in the multipole model for the electron-density refinement. The small amount of additional H+ required for charge balance was not detected in either the X-ray or the neutron data. The results are discussed in the context of the unusually low aqueous solubility of (PyBIGH2)(CO3)(H2O)4 and its ability to sequester atmospheric CO2.

The QM/MM-QTAIM approach reveals the nature of the different reactivity of cephalosporins in the active site of L1 metallo-β-lactamase

We combine the QM/MM and the QTAIM approaches to predict the reactivity of cephalosporins in the active site of L1 metallo-β-lactamase.

QTAIM Assessment of the Intra- and Intermolecular Bonding in a Bis(nitramido-oxadiazolate) Energetic Ionic Salt at 20 K

Accurate experimental determination of the electron density distribution for the energetic ionic salt bis(ammonium) 2,2'-dinitramido-5,5'-bis(1-oxa-3,4-diazolate) dihydrate (1) is obtained from multipole modeling of single-crystal X-ray diffraction data collected at 20 K. The intra- and intermolecular bonding is assessed in terms of the quantum theory of atoms in molecules (QTAIM) with a view to better understanding the physicochemical properties in relation to chemical bonding. Topological analysis reveals stronger bonding for the N-NO₂ bond relative to energetic nitramines RDX and HMX and the indication of a trend between this and impact sensitivity of nitro-containing energetic materials is noted. The intermolecular bonding of 1 is dominated by classical H-bonds but includes multiple π-bonding interactions and interactions between H-bond donor and acceptor atoms where bond paths are deflected by H atoms. There also exists a weak O···O interaction between end-on nitro groups, as well as an intramolecular ring-forming 1,5-type interaction. An anharmonic description of thermal motion was required to obtain the best fitting model, despite the low temperature of the study. The experimental study was complemented by periodic boundary DFT calculations at the experimental geometry as well as gas phase calculations on the isolated dianion.

Pancake Bonding in π-Stacked Trimers in a Salt of Tetrachloroquinone Anion

The crystal structure of [4-damp])₂ [Cl₄ Q]₃ (4-damp=4-dimethylamino-N-methylpyridinium, Cl₄ Q=tetrachloroquinone) salt is built up from slipped columnar stacks of quinoid rings composed of closely bound trimers with the intra-trimer separation distance of 2.84 Å and total charge of -2 whereas the inter-trimer distance is 3.59 Å. The individual rings exhibit partial negative charges that are distributed unevenly among the three Cl₄ Qs in the trimer. The strong interactions within a trimer (Cl₄ Q)₃^2- have a partially covalent character with two-electron/multicentered bonding, that is extended over three rings, plausibly termed as "pancake bonding". The electron pairing within this multicentre bond leads to the fact that the crystals are diamagnetic and act as insulators. The studies of the structure and nature of bonding are based on X-ray charge density analysis and density functional theory.

Experimental Charge-Density Study of the Intra- and Intermolecular Bonding in TKX-50

The intra- and intermolecular bonding in the known phase of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate, TKX-50, has been analyzed on the basis of the experimentally determined charge density distribution from high-resolution X-ray diffraction data obtained at 20 K. This was compared to the charge density obtained from DFT calculations with periodic boundary conditions using both direct calculations and derived structure factors. Results of topological analysis of the electron density corroborate that TKX-50 is best described as a layered structure linked primarily by a number of hydrogen bonds as well as by a variety of other interactions. Additional bonding interactions were identified, including a pair of equivalent 1,5-type intramolecular closed-shell interactions in the dianion. Refinement of anharmonic motion was shown to be essential for obtaining an adequate model, despite the low temperature of the study. Although generally unusual, the implementation of anharmonic refinement provided a significant improvement compared to harmonic refinement of both traditional and split-core multipole models.

Experimental evidence of a 3-centre, 2-electron covalent bond character of the central O–H–O fragment on the Zundel cation in crystals of Zundel nitranilate tetrahydrate

Charge density of the Zundel cation in the solid state reveals a covalent nature of its central O–H–O fragment.

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.