Piotr Durlak

Car-Parrinello and path integral molecular dynamics study of the hydrogen bond in the chloroacetic acid dimer system.

We have studied the double proton transfer (DPT) reaction in the cyclic dimer of chloroacetic acid using both classical and path integral Car-Parrinello molecular dynamics. We also attempt to quantify the errors in the potential energy surface that arise from the use of a pure density functional. In the classical dynamics a clear reaction mechanism can be identified, where asynchronized DPT arises due to coupling between the O-H stretching oscillator and several low energy intermolecular vibrational modes. This mechanism is considerably altered when quantum tunneling is permitted in the simulation. The introduction of path integrals leads to considerable changes in the thermally averaged molecular geometry, leading to shorter and more centered hydrogen bond linkages.

Investigations of the Very Short Hydrogen Bond in the Crystal of Nitromalonamide via Car–Parrinello and Path Integral Molecular Dynamics

In this paper are presented the results of theoretical studies of the structure in proton motion in a very short O···O and two weak N-H···O intramolecular hydrogen bonds in the nitromalonamide crystal. The dynamics of proton motion in hydrogen bonds were investigated in the NVT ensemble at 298 K using the Car-Parrinello and the path integral molecular dynamics. A very large delocalization of proton in the slightly asymmetrical single well of free energy potential of O-H···O intramolecular hydrogen bond was noted especially in the path integral simulation where quantum effects are taken into account. This hydrogen bond is very strong with the estimated energy of hydrogen bond ca. -27 kcal/mol. The nature of intra- and intermolecular interactions was studied by means of quantum theory of atoms in molecules. The infrared spectra were calculated and compared with available experimental data. CPMD vibrational results appear to be in good agreement with the experimental ones.

A Car-Parrinello and path integral molecular dynamics study of the intramolecular lithium bond in the lithium 2-pyridyl-N-oxide acetate

Lithium bonding in lithium 2-pyridyl-N-oxide acetate has been investigated using classic Car-Parrinello molecular dynamics (CPMD) and the path integral approach [path integrals molecular dynamics (PIMD)]. The simulations have been performed in 300 K. Structures, energies, and lithium trajectories have been determined. The CPMD results show that the lithium atom is generally equidistant between heavy atoms in the (O...Li...O) bridge. Applying quantum effects through the PIMD leads to similar conclusion. The theoretical lithium 2-pyridyl-N-oxide acetate infrared spectrum has also been determined using the CPMD calculations. This shows very good agreement with available experimental results and reproduces well the broad low-frequency band observed experimentally. In order to gain deeper understanding of the nature of the lithium bonding topological analysis of the electron localization function has been applied.

The mechanism of Claisen rearrangement of allyl phenyl ether from the perspective of topological analysis of the ELF

The Claisen rearrangement of allyl phenyl ether to 6-(prop-2-en-1-yl) cyclohexa-2,4-dien-1-one has been studied by means of Bonding Evolution Theory (BET), which combines the topological analysis of the electron localization function (ELF) and catastrophe theory. The reaction can be presented as consisting of 10 main steps separated by fold and cusp catastrophes. The description of the mechanism of C–O bond breaking is complicated and depends on the DFT method used. It proceeds through a heterolytic cleavage (B3LYP, M052x) with the formation of the V3(O) non-bonding basin in step II (M052x) or with electron density resonating between oxygen and carbon atoms in step II (B3LYP). The C–C bond between the allyl group and the phenol ring is formed after the TS in step VIII. The reaction is terminated by the formation of two localized CC bonds in the phenyl ring in steps IX and X. The localization of Vi=1,2(C,C) basins – typical of localized double bonds – in the phenyl ring proves the process of dearomatisation. The electronic structure of the transition structure distinguishes the non-bonding electron density concentrated in the vicinity of the C2 atom, represented by the V(C2) basin, with a population of 0.28e. This basin is a “bridgehead” for the “construction” of the C–C bond between the phenyl ring and the allyl group.

Enormous lattice distortion through an isomorphous phase transition in an organic–inorganic hybrid based on haloantimonate(III)

Bis(diisobutylammonium) octabromodiantimonate(III), [(i-C4H9)2NH2]2Sb2Br8, has been synthesized. The differential scanning calorimetric measurements indicate a reversible, first-order phase transition at 222/229 K (cooling/heating). The single crystal X-ray diffraction studies reveal that the phase transition is isomorphous and is accompanied by a huge distortion of the crystal lattice. By comparison of the crystal structures of [(i-C4H9)2NH2]2Sb2Br8 and [(i-C4H9)2NH2]2Sb2Cl8, an analogous mechanism of the phase transition of the former is proposed. The change of the electronic structure of the complex during the phase transition was analyzed by UV-vis spectroscopy. A low-frequency dielectric relaxation process appears over phase I (below the room temperature) and corresponds to the dynamics of dipolar diisobutylammonium cations. The detailed analysis of the molecular motions of the organic cations studied by means of proton magnetic resonance (1H NMR) in a wide temperature range indicates a leading role of the methyl groups in the relaxation mechanism. A variable-temperature investigation of the infrared spectra of [(i-C4H9)2NH2]2Sb2Br8 confirms, in turn, the influence of the diisobutylammonium cation dynamics on the molecular mechanism of the structural transformation at 229 K.

Ab Initio Molecular Dynamics Study of the Very Short O−H···O Hydrogen Bonds in the Condensed Phases

In this paper are presented the results of theoretical studies of the structure and proton motion in very short O···O intramolecular hydrogen bonds in two molecular crystals. A comparison was conducted between 3-cyano-2,4-pentanedione (I) and 4-cyano-2,2,6,6-tetramethyl-3,5-heptanedione (II) in the solid state. The dynamics of proton motion in the O-H···O hydrogen bond were investigated in he NVT ensemble at 298 and 50 K, respectively, for crystals I and II using Car-Parrinello and path integral molecular dynamics. Very large delocalization of the bridging proton was noted especially in the path integral simulation where quantum effects are taken into account. The infrared spectrum was calculated, and a comparative vibrational analysis was performed. CPMD vibrational results appear to be in qualitative agreement with the experimental ones.

Proton transfer dynamics in the propionic acid dimer from path integral molecular dynamics calculations

The double proton transfer process in the cyclic dimer of propionic acid in the gas phase was studied using a path integral molecular dynamics method. Structures, energies and proton trajectories were determined. Very large amplitude motions of the skeleton of a propionic acid molecule were observed during the simulations, and almost free rotation of the C2H5 group around the Cα-C bond. A double-well symmetric potential with a very small energy barrier was determined from the free energy profile for the proton motions. Infrared spectra for different isotopomers were calculated, and comparative vibrational analysis was performed. The vibrational results from CPMD appear to be in qualitative agreement with the experimental ones.

Crystal structural analysis of methyl-substituted pyrazines with anilic acids: a combined diffraction, inelastic neutron scattering, 1H-NMR study and theoretical approach

The crystal and molecular structures of (1) 2-methylpyrazine (2MP) with 2,5-dichloro-3,6-dihydroxy-p-quinone (chloranilic acid, CLA), (2) 2-methylpyrazine (2MP) with 2,5-dibromo-3,6-dihydroxy-p-quinone (bromanilic acid, BRA), (3) 2,3,5-trimethylpyrazine (TrMP) with 2,5-dichloro-3,6-dihydroxy-p-quinone (chloranilic acid, CLA), and (4) 2,3,5-trimethylpyrazine (TrMP) with 2,5-dibromo-3,6-dihydroxy-p-quinone (bromanilic acid, BRA) were analyzed in terms of the number of independent methyl groups in their crystal structure. The inelastic neutron back-scattering spectra at low temperature (4–40 K) were discussed in terms of methyl group tunnelling. The INS spectra were compared with the temperature dependence of the 1H-NMR spin–lattice relaxation time, particularly at low temperatures, where CH3 tunnelling is postulated. The infrared and Raman spectra at room temperature were recorded for all complexes under investigation. Furthermore, the vibrational spectra were discussed in terms of the structure of molecules and their interactions. The structural phase transition of the TrMP·CLA complex at 171/175 K (cooling/heating) was characterized by DSC and single-crystal X-ray diffraction. Full-geometry optimization was carried out in the solid state in order to obtain the minimum structures and bonding properties. The results are in very good agreement with the experimental data. The infrared spectrum in the harmonic approximation was calculated and a comparative vibrational analysis was performed. CRYSTAL09 vibrational results appear to be in good agreement with the experimental results.

Widely used hardly known. An insight into electric and dynamic properties of formamidinium iodide

The simple organic crystal formamidinium iodide (FAI) appeared to be a novel semiconducting material in a wide temperature range. The electric properties of FAI and the role of formamidinium cation (FA+) in the molecular mechanism of the solid-to-solid phase transitions (at 345 K (III → II) and 388 K (II → I)) were analysed. The creation of the ferroelastic domain structure in phases III and II was proved on the basis of observation under a polarizing microscope. Moreover, the molecular arrangement of dipolar organic FA+ was studied by 1H NMR (spin-lattice relaxation time) and vibrational spectroscopy supported by density functional theory. The theoretical results show a good agreement with the experimental data. The infrared spectrum in a harmonic approximation was calculated and a comparative vibrational analysis was performed. All used techniques showed that the prototypic phase I exhibits the feature of plastic phase.

Car-Parrinello and Path Integral Molecular Dynamics Study of the Proton Transfer in the Intramolecular Hydrogen Bonds in the Ketohydrazone-Azoenol System

Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD) simulations were carried out for 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) (Sudan I) in vacuo and in the solid state at 298 K. The fast proton transfer (FPT) and tautomerism in the ketohydrazone-azoenol systems have been analyzed on the basis of CPMD and PIMD methods level. The two-dimensional free-energy landscape of reaction coordinate δ-parameter and RN···O distances shows the NH tautomer to be more favorable in the gas phase as well as in the solid state according to the CP and PI results, respectively. The hydrogen between the nitrogen and the oxygen atoms adopts a starkly asymmetrical position in the double potential well. The molecular geometry and energy barrier for the intramolecular proton transference were calculated, and the value found suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the two-dimensional average index of π-delocalization ⟨λ⟩ landscape of time evolutions of RN1···O1 and RC1═O1 distances for both the crystals indicate that the hydrogen bonds in the crystals of 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) have characteristic properties for the type of bonding model: resonance-assisted hydrogen bonds and low-barrier hydrogen bonds, without the existence of equilibrium in the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.