First-Principle Molecular Dynamics Study of Selected Schiff and Mannich Bases: Application of Two-Dimensional Potential of Mean Force to Systems with Strong Intramolecular Hydrogen Bonds

The electron attachment effect on the structure and properties of ortho-hydroxyaryl Schiff and Mannich bases - the hydrogen/proton transfer processes

The attachment of electrons is known to significantly influence some chemical and biological processes. The chemical differences between Schiff and Mannich bases are characterized by strong intramolecular hydrogen bonds, resulting from the presence of, respectively, single or double carbon-nitrogen bonds in the chelate rings. Differences are especially visible in the hydrogen transfer processes from molecular (O-H⋯N) to the proton transfer (O⋯H-N) forms. The reaction in a Schiff base occurs as an ordinary hydrogen transfer from a donor to an acceptor, while in a Mannich base the transfer of hydrogen occurs simultaneously with a C-N bond scission leading to an intermolecular complex. The attachment of electrons preserves the overall structural topology of the reactants; however, due to differences in electron affinities, reactions switch from endothermic to exothermic and reaction rates in the anionic systems are significantly higher. The difference in electron affinities for particular reactants comes from the fundamental differences in electron binding mechanisms, leading to the valence-bound or dipole-bound states. The observed mechanisms are closely related to the nature and size of the LUMOs of the parent molecules. The transition state of the Mannich base corresponds to the σ and π orbital conversion and possesses the characteristics of the valence-bound state and the dipole-bound electronic state.

Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.

Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car-Parrinello Molecular Dynamics and Electronic Structure Inspection

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

Inter- vs. Intramolecular Hydrogen Bond Patterns and Proton Dynamics in Nitrophthalic Acid Associates

Noncovalent interactions are among the main tools of molecular engineering. Rational molecular design requires knowledge about a result of interplay between given structural moieties within a given phase state. We herein report a study of intra- and intermolecular interactions of 3-nitrophthalic and 4-nitrophthalic acids in the gas, liquid, and solid phases. A combination of the Infrared, Raman, Nuclear Magnetic Resonance, and Incoherent Inelastic Neutron Scattering spectroscopies and the Car-Parrinello Molecular Dynamics and Density Functional Theory calculations was used. This integrated approach made it possible to assess the balance of repulsive and attractive intramolecular interactions between adjacent carboxyl groups as well as to study the dependence of this balance on steric confinement and the effect of this balance on intermolecular interactions of the carboxyl groups.

Theoretical study of intramolecular hydrogen bond in selected symmetric "proton sponges" on the basis of DFT and CPMD methods

"Proton sponges," derivatives of prototypic 1,8-bis(dimethylamino)naphthalene (DMAN), exhibit remarkable basicity, which made them interesting for various experimental and theoretical studies. The details of bridged proton dynamics in protonated DMAN and its derivative denoted as TMGN (1,8-bis(tetramethylguanidino)naphthalene) were investigated on the basis of density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) methods. Special attention was paid to the effects of symmetry of the molecular skeleton and the type of substituent on the bridged proton neighborhood statistics and dynamics. The metric parameter analyses of hydrogen bridge provided us with a conclusion that proton migration events in TMGNH⁺ are less numerous than in DMANH⁺, which can be rationalized by noticing the slower dynamics of large substituents of TMGN with respect to the smaller -N(Me)₂ groups of DMAN. The atomic velocity power spectra served as computational models of the vibrational signatures associated with the presence of the intramolecular hydrogen bond. A broad feature was registered for hydrogen bonds present in both compounds. The computations were verified by experimental data available.

N-H⋯O versus O-H⋯O: density functional calculation and first principle molecular dynamics study on a quinoline-2-carboxamide N-oxide

N-oxide-type compounds are the object of current research interest due to the presence of resonance-assisted N–H⋯O hydrogen bonds. Here, the metric and spectroscopic parameters of N-methyl-quinoline-2-carboxamide 1-oxide were computed on the basis of density functional theory and Car-Parrinello molecular dynamics. Computations were performed in vacuo and in solid state; for both phases additional simulations with Grimme’s dispersion correction were carried out. The approaches used were able to reproduce correctly the structural aspects of the studied compound and shed more light on the hydrogen bonding with special focus on bridge proton mobility. Proton transfer phenomena were found not to occur in the investigated compound, and the bridge proton was localized to the donor site. This observation is in agreement with the classical theory of the acidity of donor–acceptor sites. The presence of hydrogen bonding was confirmed using atoms-in-molecules theory. The computational results were compared with available experimental data.

Impact of proton transfer phenomena on the electronic structure of model Schiff bases: an AIM/NBO/ELF study

Understanding of the electronic structure evolution due to a proton dynamics is a key issue in biochemistry and material science. This paper reports on density functional theory calculations of Schiff bases containing short, strong intramolecular hydrogen bonds where the bridged proton is located: (i) at the donor site, (ii) strongly delocalized, and (iii) at the acceptor site. The mobility of the bridged proton and its influence on the molecular structure and properties of the chosen Schiff base derivatives have been investigated on the basis of Atoms in Molecules, Natural Bond Orbitals, and Electron Localization Function theories. It has been observed that the extent of the bridged proton delocalization is strongly modified by the steric and inductive effects present in the studied compounds introduced by various substituents. It has been shown that: (i) potential energy profiles for the proton motion are extremely dependent on the substitution of the aromatic ring, (ii) the topology of the free electron pairs present at the donor∕acceptor site, as well as their electron populations, are affected qualitatively by the bridged proton position, (iii) the distortion of the molecular structure due to the bridged proton dynamics includes the atomic charge fluctuations, which are in some cases non-monotonic, and (iv) topology of the ELF recognizes events of proton detachment from the donor and attachment to the acceptor. The quantitative and qualitative results shed light onto molecular consequences of the proton transfer phenomena.

Comparison of resonance assisted and charge assisted effects in strengthening of hydrogen bonds in dipyrrins

This paper deals with the study of two types of hydrogen bonding: a quasi-aromatic hydrogen bonding in dipyrromethene and the ionic one in dipyrromethane. The study focuses on two phenomena-the proton transfer process and tautomeric equilibrium. Metric parameters and spectroscopic assignments have been calculated; this allowed a further comparison of spectral features calculated with four methods (Car-Parrinello molecular dynamics (CPMD), ab initio, density functional theory (DFT), and numerical calculation of anharmonic vibrational levels via a solution of the corresponding 1D Schrödinger equation). A significant dynamics of the bridged proton and bent vibration of pyrrole fragments in dipyrromethane have been exposed by the CPMD calculations. The prevailing of the ionic effect over the π-electronic coupling in the strengthening of the hydrogen bonding has been shown on the basis of the calculated structural, electron-topological, and spectral data as well as potential energy surface (PES). The analysis of the aromaticity and electronic state of pyrrole and chelate moieties depending on the tautomeric equilibrium by the quantum theory of atoms in molecules (QTAIM) method was conducted. The principle divergence in the behavior of aromaticity of the chelate chains in the analyzed compounds was demonstrated.

Triple hydrogen bonding in a circular arrangement: ab initio, DFT and first-principles MD studies of tris-hydroxyaryl enamines

First-principles Car-Parrinello molecular dynamics, ab initio (MP2) and density functional schemes have been used to explore the tautomeric equilibrium in three tris(amino(R)methylidene)cyclohexane-1,3,5-triones (R = hydrogen, methyl or phenyl group). The dynamic nature of the cyclic hydrogen bonding has been studied by the first-principles MD method. The comparison of the results obtained by aforesaid methods has been accomplished on the basis of calculations of structural and spectroscopic characteristics of the compounds. The conformational analysis of the studied compounds has been carried out at the MP2/6-31+G(d,p) and B3LYP/6-31+G(d,p) levels of theory. The influence of steric and electronic effects on the cyclic hydrogen bonding has been analysed. The extent of the proton delocalization has been modified by the substituents according to the sequence: hydrogen < phenyl < methyl. This fact is verified by the spectroscopic and structural data as well as the energy potential curve. A prevalence of the keto-enamine tautomeric form has been observed in the static ab initio and DFT models, and confirmed by the first-principles MD.

Car-Parrinello simulation of the vibrational spectrum of a medium strong hydrogen bond by two-dimensional quantization of the nuclear motion: application to 2-hydroxy-5-nitrobenzamide

The nature of medium strong intra- and intermolecular hydrogen bonding in 2-hydroxy-5-nitrobenzamide in the crystal phase was examined by infrared spectroscopy and Car-Parrinello molecular dynamics simulation. The focal point of our study was the part of the infrared spectra associated with the O-H and N-H stretching modes that are very sensitive to the strength of hydrogen bonding. For spectra calculations we used an isolated dimer and the fully periodic crystal environment. We calculated the spectra by using harmonic approximation, the time course of the dipole moment function as obtained from the Car-Parrinello simulation, and the quantization of the nuclear motion of the proton for an instantaneous snapshot of the structures in one and two dimensions. Although quantitative assessment of the agreement between the computed and experimental band contour is difficult due to the fact that the experimental band is very broad, we feel that the most reasonable qualitative agreement with the experiment is obtained from snapshot structures and two-dimensional quantization of the proton motion. We have also critically examined the methods of constructing the one-dimensional proton potential. Perspectives are given for the treatment of nuclear quantum effects in biocatalysis.

Probing quantum and dynamic effects in concerted proton-electron transfer reactions of phenol-base compounds

The oxidation of three phenols, which contain an intramolecular hydrogen bond to a pendent pyridine or amine group, has been shown, in a previous experimental study, to undergo concerted proton-electron transfer (CPET). In this reaction, the electron is transferred to an outer-sphere oxidant, and the proton is transferred from the oxygen to nitrogen atom. In the present study, this reaction is studied computationally using a version of Hammes-Schiffer's multistate continuum theory where CPET is formulated as a transmission frequency between neutral and cation vibrational-electronic states. The neutral and cation proton vibrational wave functions are computed from one-dimensional potential energy surfaces (PESs) for the transferring proton in a fixed heavy atom framework. The overlap integrals for these neutral/cation wave functions, considering several initial (i.e., neutral) and final (i.e., cation) vibrational states, are used to evaluate the relative rates of oxidation. The analysis is extended to heavy atom configurations with various proton donor-acceptor (i.e., O-N) distances to assess the importance of heavy atom "gating". Such changes in d(ON) dramatically affect the nature of the proton PESs and wave functions. Surprisingly, the most reactive configurations have similar donor-acceptor distances despite the large (~0.2 Å) differences in the optimized structures. These theoretical results qualitatively reproduce the experimental faster reactivity of the reaction of the pyridyl derivative 1 versus the CH(2)-pyridyl 2, but the computed factor of 5 is smaller than the experimental 10(2). The amine derivative is calculated to react similarly to 1, which does not agree with the experiments, likely due to some of the simplifying assumptions made in applying the theory. The computed kinetic isotope effects (KIEs) and their temperature dependence are in agreement with experimental results.

The photoinduced isomerization and its implication in the photo-dynamical processes in two simple Schiff bases isolated in solid argon

Two Schiff bases: 2-(1-(methylimino)methyl)-phenol (SMA) and its chlorosubstituted derivative 2-(1-(methylimino)methyl)-6-chlorophenol (SMAC), and SMA complexes with water were studied by infrared matrix isolation spectroscopy and DFT/B3LYP/6-311G++(2d,2p) quantum chemical calculations. SMA and SMAC bases trapped in an argon matrix from the vapor above the liquid and solid samples have the most stable enol conformation with intramolecular O-H···N bonding. Irradiation (λ > 320 nm) leads in both bases to a rotational isomerization reaction in which the scission of the O-H···N bond occurs and the C(H)NCH(3) and OH groups are turned by 180° around the C-C and C-O bonds, respectively. In SMAC a competitive photoreaction channel yields the trans-keto tautomer. The identification of the two SMAC photoproducts evidences that in the excited enol form of this compound two processes compete with each other: the rotational isomerization and intramolecular proton transfer (ESIPT). In the argon matrices doped with SMA and H(2)O the SMA-water complexes were identified and characterized spectroscopically. Interaction of SMA with one or two water molecules does not affect the photochemistry of SMA.

Car-Parrinello simulation of hydrogen bond dynamics in sodium hydrogen bissulfate

We studied proton dynamics of a short hydrogen bond of the crystalline sodium hydrogen bissulfate, a hydrogen-bonded ferroelectric system. Our approach was based on the established Car-Parrinello molecular dynamics (CPMD) methodology, followed by an a posteriori quantization of the OH stretching motion. The latter approach is based on snapshot structures taken from CPMD trajectory, calculation of proton potentials, and solving of the vibrational Schrodinger equation for each of the snapshot potentials. The so obtained contour of the OH stretching band has the center of gravity at about 1540 cm(-1) and a half width of about 700 cm(-1), which is in qualitative agreement with the experimental infrared spectrum. The corresponding values for the deuterated form are 1092 and 600 cm(-1), respectively. The hydrogen probability densities obtained by solving the vibrational Schrodinger equation allow for the evaluation of potential of mean force along the proton transfer coordinate. We demonstrate that for the present system the free energy profile is of the single-well type and features a broad and shallow minimum near the center of the hydrogen bond, allowing for frequent and barrierless proton (or deuteron) jumps. All the calculated time-averaged geometric parameters were in reasonable agreement with the experimental neutron diffraction data. As the present methodology for quantization of proton motion is applicable to a variety of hydrogen-bonded systems, it is promising for potential use in computational enzymology.