Mateusz Z. Brela

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.

Born–Oppenheimer Molecular Dynamics Study on Proton Dynamics of Strong Hydrogen Bonds in Aspirin Crystals, with Emphasis on Differences between Two Crystal Forms

In this study, the proton dynamics of hydrogen bonds for two forms of crystalline aspirin was investigated by the Born-Oppenheimer molecular dynamics (BOMD) method. Analysis of the geometrical parameters of hydrogen bonds using BOMD reveals significant differences in hydrogen bonding between the two crystalline forms of aspirin, Form I and Form II. Analysis of the trajectory for Form I shows spontaneous proton transfer in cyclic dimers, which is absent in Form II. Quantization of the O-H stretching modes allows a detailed discussion on the strength of hydrogen-bonding interactions. The focal point of our study is examination of the hydrogen bond characteristics in the crystal structure and clarification of the influence of hydrogen bonding on the presence of the two crystalline forms of aspirin. In the BOMD method, thermal motions were taken into account. Solving the Schrödinger equation for the snapshots of 2D proton potentials, extracted from MD, gives the best agreement with IR spectra. The character of medium-strong hydrogen bonds in Form I of aspirin was compared with that of weaker hydrogen bonds in aspirin Form II. Two proton minima are present in the potential function for the hydrogen bonds in Form I. The band contours, calculated by using one- and two-dimensional O-H quantization, reflect the differences in the hydrogen bond strengths between the two crystalline forms of aspirin, as well as the strong hydrogen bonding in the cyclic dimers of Form I and the medium-strong hydrogen bonding in Form II.

Car–Parrinello Molecular Dynamics Simulations of Infrared Spectra of Crystalline Vitamin C with Analysis of Double Minimum Proton Potentials for Medium-Strong Hydrogen Bonds

We studied proton dynamics of a hydrogen bonds of the crystalline l-ascorbic acid. Our approach was based on the Car-Parrinello molecular dynamics. The focal point of our study was simulation of the infrared spectra of l-ascorbic acid associated with the O-H stretching modes that are very sensitive to the strength of hydrogen bonding. In the l-ascorbic acid there are four kinds of hydrogen bonds. We calculated their spectra by using anharmonic approximation and the time course of the dipole moment function as obtained from the Car-Parrinello simulation. The quantization of the nuclear motion of the protons was made to perform detailed analysis of strength and properties of hydrogen bonds. We presented double minimum proton potentials with small value of barriers for medium-strong hydrogen bonds. We have also shown the difference character of medium-strong hydrogen bonds compared to weaker hydrogen bonds in the l-ascorbic acid.

Tetrazole substituted polymers for high temperature polymer electrolyte fuel cells

While tetrazole (TZ) has much lower basicity than imidazole and may not be fully protonated in the presence of phosphoric acid (PA), DFT calculations suggest that the basicity of TZ groups can be increased by the introduction of a 2,6-dioxy-phenyl-group in position 5 of TZ. This structure allows hydrogen bonds between TZ protons and ether oxygen atoms, and thereby establishes a resonance stabilised, co-planar structure for tetrazolium ions. Molecular electrostatic potential (MEP) calculations also indicate that tetrazolium ions possess two sites for proton hopping. This makes such materials interesting for use in a high temperature fuel cell (HT PEMFC). Based on these findings, two polymers incorporating the proposed TZ groups were synthesised, formed into membranes, doped with PA and tested for fuel cell relevant properties. At room temperature, TZ-PEEN and commercial meta-PBI showed an equilibrium uptake of 0.5 and 4.7 mol PA per mol heterocycle, respectively, indicating that PBI has higher affinity for PA than TZ-PEEN. The highest achieved PA uptake was ca. 110 wt%, resulting in a proton conductivity of 25 mS cm−1 at 160 °C with a low activation energy of about 35 kJ mol−1. In a first HT PEMFC test at 160 °C, a peak power density of 287 mW cm−2 was achieved.

Experimental and theoretical investigations of the NiII complex with N-phosphorylated thiourea iPrNHC(S)NHP(O)(OPh)2

The N-phosphorylated thiourea iPrNHC(S)NHP(O)(OPh)2 (HL) has been synthesized by the reaction of iPrNH2 and (PhO) 2P(O)NCS. Recrystallization of HL from aqueous acetone leads to [iPrNH3]+[P(O)2(OPh)2]- in a quantitative yield. Reaction of the deprotonated HL with NiCl2 leads to violet [NiL2] crystals with a 1,3-N,S-coordination mode of the ligands. Static DFT and ab initio molecular dynamics studies indicated that [NiL2] is stabilized predominantly by intramolecular N-H⋯OP hydrogen bonding and dynamically by secondary CPh-H⋯S interactions. All compounds have been characterized by IR, diffuse reflectance, UV-vis and NMR spectroscopy, single crystal X-ray diffraction analysis and elemental analysis. Thermal properties investigated in an air atmosphere by means of TGA revealed a residue corresponding to NiPS3.

Explicit Solvent Modeling of IR and UV–Vis Spectra of 1-Ethyl-3-methylimidazolium Bis(trifluoromethylsulfonyl)imide Ionic Liquid

Explicit solvent modeling of absorption spectra of 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide has been performed. Fourier transform of the autocorrelation function of the dipole moment calculated from ab initio molecular dynamics (AIMD) simulations has been used to obtain the IR spectrum of the bulk liquid. A sequential molecular dynamics (MD)/time-dependent density functional theory procedure has been applied to calculate the UV-vis spectrum. Description of both spectra is improved by an explicit solvent model with respect to gas-phase calculations or an implicit solvent model, with good agreement between computed spectra and experimental data. The major factor contributing to the improvement has been found to be the better description of structures of cation-anion pairs sampled from MD simulations. AIMD with Fourier transform has been demonstrated to be a powerful methodology for calculating bulk IR spectra of ionic liquids.

Analysis of the bonding between two M(μ-NAr(#)) monomers in the dimeric metal(II) imido complexes {M(μ-NAr(#))}2 [M = Si, Ge, Sn, Pb; Ar(#) = C6H3-2,6-(C6H2-2,4,6-R3)2]. The stabilizing role played by R = Me and iPr.

The nature of the bonding between the two M(μ-NAr(#)) imido monomers [M = Si, Ge, Sn, Pb; Ar(#) = C6H3-2,6-(C6H2-2,4,6-R3)2; R = Me, iPr] in the {M(μ-NAr(#))}2 dimer is investigated with the help of a newly developed energy and density decomposition scheme as well as molecular dynamics. The approach combines the extended transition state energy decomposition method with the natural orbitals for chemical valence density decomposition scheme within the same theoretical framework. The dimers are kept together by two σ bonds and two π bonds. The σ bonding has two major contributions. The first is a dative transfer of charge from nitrogen to M. It amounts to -188 kcal/mol for {Si(μ-NAr(#))}2, -152 kcal/mol for {Ge(μ-NAr(#))}2 with -105 kcal/mol for {Sn(μ-NAr(#))}2, and -79 kcal/mol for {Pb(μ-NAr(#))}2. The second is a charge buildup within the ring made up of the two dimers. It amounts to -82 kcal/mol for M = Si with -61 kcal/mol for M = Ge and ∼-50 kcal/mol for M = Sn and Pb. We finally have π bonding with a donation of charge from M to nitrogen. It has a modest contribution of ∼-30 kcal/mol. The presence of isopropyl (iPr) groups is further shown to stabilize{M(μ-NAr(#))}2 [M = Si, Ge, Sn, Pb; Ar(#) = C6H3-2,6-(C6H2-2,4,6-iPr3)2] compared to the methylated derivatives (R = Me) through attractive van der Waals dispersion interactions.

ETS-NOCV Decomposition of the Reaction Force: The HCN/CNH Isomerization Reaction Assisted by Water

The partitioning of the reaction force based on the extended‐transition‐state natural orbital for chemical valence (ETS‐NOCV) scheme has been proposed. This approach, together with the analysis of reaction electronic flux (REF), has been applied in a description of the changes in the electronic structure along the IRC pathway for the HCN/CNH isomerization reaction assisted by water. Two complementary ways of partitioning the system into molecular fragments have been considered (“reactant perspective” and “product perspective”). The results show that the ETS‐NOCV picture is fully consistent with REF and bond‐order changes. In addition, proposed ETS‐NOCV decomposition of the reaction force allows for the quantitative assessment of the influence of the observed bond‐breaking and bond‐formation processes, providing detailed information about the reaction‐driving and reaction‐retarding force components within the assumed partitioning scheme.

Polymorphism driven optical properties of an anil dye

Red crystals of N,N′-bis(3-methoxysalicylidene)-1,5-diiminonaphthalene were obtained after Schiff base condensation in ethanol. Recrystallization from acetone afforded yellow crystals, a process which is reversible and reproducible. Single crystal X-ray diffraction evidences two polymorphs differing in their space group and dihedral angle between aromatic moieties. DFT periodic calculations further confirmed the existence of two minima on the potential energy surface corresponding to red and yellow crystals. The red polymorph irreversibly (monotropically) transforms at 165–190 °C into the yellow one with a 3% increase of the unit cell volume, as shown by X-ray powder diffraction and periodic DFT calculations. Both polymorphs are thermochromic but only the red one displays photochromism upon irradiation at λ = 365 nm, which is reversible and exhibits a relatively slow thermal relaxation. A temperature induced cis/trans-keto equilibrium is for the first time identified for an N-salicylidene aniline derivative. Static DFT molecular and periodic calculations as well as ab initio Born–Oppenheimer dynamics simulations were performed to characterize the stability of both polymorphs and to determine the relative populations of the enol/cis-keto/trans-keto isomers at various temperatures.

ETS-NOCV decomposition of the reaction force for double-proton transfer in formamide-derived systems

The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide–thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of the reaction force, considering the intra-fragments strain and the inter-fragments interaction terms, and further—the electrostatic, Pauli-repulsion and orbital interaction components, with the latter being decomposed into the NOCV components. Two methods of the system partitioning into the fragments were considered (‘reactant perspective’/bond-formation, ‘product perspective’ / bond-breaking). In agreement with previous studies, the results indicate that the major changes in the electronic structure occur in the transition state region; the bond-breaking processes are, however, initiated already in the reactant region, prior to entering the TS region. The electrostatic contributions were identified as the main factor responsible for the increase in the activation barrier in the order R1 < R2 < R3.