Jarosław J Panek

Wyższa Szkoła Handlowa we Wrocławiu, Vrotslav, Lower Silesian Voivodeship, Poland

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Publications (40)113.42 Total impact

  • Kacper Błaziak · Jarosław J Panek · Aneta Jezierska ·
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    ABSTRACT: Quinoline derivatives are interesting objects to study internal reorganizations due to the observed excited-state-induced intramolecular proton transfer (ESIPT). Here, we report on computations for selected 12 quinoline derivatives possessing three kinds of intramolecular hydrogen bonds. Density functional theory was employed for the current investigations. The metric and electronic structure simulations were performed for the ground state and first excited singlet and triplet states. The computed potential energy profiles do not show a spontaneous proton transfer in the ground state, whereas excited states exhibit this phenomenon. Atoms in Molecules (AIM) theory was applied to study the nature of hydrogen bonding, whereas Harmonic Oscillator Model of aromaticity index (HOMA) provided data of aromaticity evolution as a derivative of the bridge proton position. The AIM-based topological analysis confirmed the presence of the intramolecular hydrogen bonding. In addition, using the theory, we were able to provide a quantitative illustration of bonding transformation: from covalent to the hydrogen. On the basis of HOMA analysis, we showed that the aromaticity of both rings is dependent on the location of the bridge proton. Further, the computed results were compared with experimental data available. Finally, ESIPT occurrence was compared for the three investigated kinds of hydrogen bridges, and competition between two bridges in one molecule was studied.
    The Journal of Chemical Physics 07/2015; 143(3):034301. DOI:10.1063/1.4926649 · 2.95 Impact Factor
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    Jarosław J Panek · Aneta Jezierska ·
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    ABSTRACT: The current study belongs to a series of investigations of polycyclic aromatic compounds containing intramolecular hydrogen bonds. Close proximity of the coupled aromatic system and hydrogen bridges gives rise to resonance-assisted hydrogen bonding phenomena. Substituted naphthols are ideally suited for this kind of investigation. The parent compound, 1-hydroxy-8-methoxy-3-methylnaphthalene, and its derivative, 1-bromo-5-hydroxy-4-isopropoxy-7-methylnaphthalene, both with known crystal structure, are investigated. Car-Parrinello molecular dynamics (CPMD) is chosen as a theoretical background for this study. Gas phase and solid state simulations are carried out. The effect of Grimme's dispersion corrections is also included. The report presents time evolution of structural parameters, spectroscopic signatures based on the CPMD simulations, and comparison with available experimental data. We show that the proton transfer phenomena do not occur within the simulations, which is consistent with evaluation based on the acidity of the donor and acceptor sites. The effects of the substitution in the aromatic system and change of the environment (gas vs. condensed phase) are of similar magnitude.
    Journal of Molecular Modeling 01/2015; 21(1):2550. DOI:10.1007/s00894-014-2550-8 · 1.74 Impact Factor
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    ABSTRACT: 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.
    The Journal of Chemical Physics 10/2013; 139(15):154312. DOI:10.1063/1.4825098 · 2.95 Impact Factor
  • Xueping Liu · Tomasz Bereźniak · Jarosław Jan Panek · Aneta Jezierska-Mazzarello ·
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    ABSTRACT: Zeatin, a cytokinin of the adenine family, originally isolated from Zea mays L., exhibits also bioeffects towards human cells: it is a potent acetylcholinesterase inhibitor and can potentially inhibit amyloid β-protein formation. The role of zeatin in neural disease treatment is yet to be established. This computational study describes a hierarchy of interactions between zeatin and a receptor, a protein from the nodulin family. DFT in hybrid and dispersion-corrected form as well as MP2 approaches were used to derive interaction energies. Docking procedure was employed to investigate the role of selected interaction for anchoring the ligand.
    Chemical Physics Letters 02/2013; 557:140–144. DOI:10.1016/j.cplett.2012.12.034 · 1.90 Impact Factor
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    ABSTRACT: 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. Electronic supplementary material The online version of this article (doi:10.1007/s10822-012-9597-3) contains supplementary material, which is available to authorized users.
    Journal of Computer-Aided Molecular Design 09/2012; 26(9):1045-53. DOI:10.1007/s10822-012-9597-3 · 2.99 Impact Factor
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    ABSTRACT: Properties of hydrogen bonds can induce changes in geometric or electronic structure parameters in the vicinity of the bridge. Here, we focused primarily on the influence of intramolecular H-bonding on the molecular properties in selected ortho-hydroxybenzaldehydes, with additional restricted insight into substituent effects. Static models were obtained in the framework of density functional theory at B3LYP/6-311+G(d,p) level. The electronic structure parameters evolution was analyzed on the basis of Atoms In Molecules (AIM) and Natural Bond Orbitals methods. The aromaticity changes related to the variable proton position and presence of substituents were studied using Harmonic Oscillator Model of Aromaticity (HOMA), Nucleus-Independent Chemical Shift (NICS) and AIM-based parameter of Matta and Hernández-Trujillo. Finally, Car-Parrinello molecular dynamics was applied to study variability of the hydrogen bridge dynamics. The interplay between effects of the substitution and variable position of the bridged proton was discussed. It was found that the hydrogen bond energies are ca. 9-10 kcal/mol, and the bridged proton exhibits some degree of penetration into the acceptor region. The covalent character of the studied hydrogen bond was most observable when the bridged proton reached the middle position between the donor and acceptor regions. The aromaticity indexes showed that the aromaticity of the central phenyl ring is strongly dependent on the bridged proton position. Correlations between these parameters were found and discussed. In the applied time-scale, the analysis of time evolution of geometric parameters showed that the resonance strengthening does not play a crucial role in the studied compounds.
    The Journal of Physical Chemistry A 11/2011; 116(1):460-75. DOI:10.1021/jp205730t · 2.69 Impact Factor
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    ABSTRACT: Adsorption of guest molecules on host surfaces can lead to dramatic changes in the spectral properties of the guest. One such effect is surface-enhanced infrared absorption (SEIRA), observed when the guest is adsorbed on, for example, thin films, metal surfaces, or nanotubes. p-Nitrobenzoic acid (p-NBA) exhibits a SEIRA effect when adsorbed on Ag and Au. Herein, the IR spectra of p-NBA adsorbed on a homemade rough Au surface, recorded in reflection mode with an angle of incidence of 16.5°, are reported. This SEIRA experiment reveals more bands than found by previous SEIRA studies. The intensities of both symmetric and asymmetric COO(-) and NO(2) stretching, in-plane CH, and C=C ring stretching modes are enhanced. Theoretical models constructed on the basis of density functional theory reveal the binding mode of p-NBA to gold "particles". The p-NBA anion binds to gold much more strongly than the neutral form, and interaction via the carboxylic oxygen atoms is preferred over the nitro group-gold contact. A significant charge transfer during chemisorption is found, which is considered to be crucial in leading to a high SEIRA enhancement factor.
    ChemPhysChem 09/2011; 12(13):2485-95. DOI:10.1002/cphc.201100067 · 3.42 Impact Factor
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    ABSTRACT: Mercury(II) has a strong affinity for the thiol groups in proteins often resulting in the disruption of their biological functions. In this study we present classical and first-principles, DFT-based molecular dynamics (MD) simulations of a complex of Hg(II) and proteinase K, a well-known serine protease with a very broad and diverse enzymatic activity. It contains a catalytic triad formed by Asp39, His69, and Ser224, which is responsible for its biological activity. It was found previously by X-ray diffraction experiments that the presence of Hg(II) inhibits the enzymatic action of proteinase K by affecting the stereochemistry of the triad. Our simulations predict that (i) the overall structure as well as the protein backbone dynamics are only slightly affected by the mercury cation, (ii) depending on the occupied mercury site, the hydrogen bonds of the catalytic triad are either severely disrupted (both bonds for mercury at site 1, and the His69-Ser224 contact for mercury at site 2) or slightly strengthened (the Asp39-His69 bond when mercury is at site 2), (iii) the network of hydrogen bonds of the catalytic triad is not static but undergoes constant fluctuations, which are significantly modified by the presence of the Hg(II) cation, influencing in turn the triad's ability to carry out the enzymatic function--these facts explain the experimental findings on the inhibition of proteinase K by Hg(II).
    Molecular Diversity 02/2011; 15(1):215-26. DOI:10.1007/s11030-010-9256-3 · 1.90 Impact Factor
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    ABSTRACT: We have studied substituent effects on the properties of the intramolecular hydrogen bond of some ortho-hydroxy Schiff bases using density functional theory (DFT) based first-principle molecular dynamics (FPMD) and path integral molecular dynamics. The studied compounds possess a strong intramolecular hydrogen bond (r((O⋅⋅⋅N)) ≤ 2.6 Å), which can be tuned by substitution to either (i) enhance the basicity of the acceptor moiety by induction effects or (ii) decrease the hydrogen bond length through steric repulsion. DFT calculations and FPMD were employed to investigate structural and dynamical properties of the selected molecules, while quantum effects on the structural properties were assessed using path integral FPMD. The simulations were performed in vacuo and in the solid state to study the influence of the environment on the hydrogen bond and spectroscopic properties. We give computational support to the suggestion that induction effects are less effective to tune the intramolecular hydrogen bond properties of the discussed ortho-hydroxy Schiff bases than the steric or the environmental effects.
    The Journal of Chemical Physics 01/2011; 134(3):034308. DOI:10.1063/1.3528721 · 2.95 Impact Factor
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    ABSTRACT: In the field of enzymatic catalysis, creating activity from a non catalytic scaffold is a daunting task. Introduction of a catalytically active moiety within a protein scaffold offers an attractive means for the creation of artificial metalloenzymes. With this goal in mind, introduction of a biotinylated d6-piano-stool complex within streptavidin (SAV) affords enantioselective artificial transfer-hydrogenases for the reduction of prochiral ketones. Based on an X-ray crystal structure of a highly selective hybrid catalyst, displaying significant disorder around the biotinylated catalyst [η6-(p-cymene)Ru(Biot-p-L)Cl], we report on molecular dynamics simulations to shed light on the protein–cofactor interactions and contacts. The results of these simulations with classical force field indicate that the SAV-biotin and SAV-catalyst complexes are more stable than ligand-free SAV. The point mutations introduced did not affect significantly the overall behavior of SAV and, unexpectedly, the P64G substitution did not provide additional flexibility to the protein scaffold. The metal-cofactor proved to be conformationally flexible, and the S112K or P64G mutants proved to enhance this effect in the most pronounced way. The network of intermolecular hydrogen bonds is efficient at stabilizing the position of biotin, but much less at fixing the conformation of an extended biotinylated ligand. This leads to a relative conformational freedom of the metal-cofactor, and a poorly localized catalytic metal moiety. MD calculations with ab initio potential function suggest that the hydrogen bonds alone are not sufficient factors for full stabilization of the biotin. The hydrophobic biotin-binding pocket (and generally protein scaffold) maintains the hydrogen bonds between biotin and protein. Electronic supplementary material The online version of this article (doi:10.1007/s10822-010-9369-x) contains supplementary material, which is available to authorized users.
    Journal of Computer-Aided Molecular Design 09/2010; 24(9):719-732. DOI:10.1007/s10822-010-9369-x · 2.99 Impact Factor
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    ABSTRACT: The structure, proton transfer, and vibrational dynamics under ambient conditions of a selected ortho-hydroxy Schiff base type compound, 2-(N-methyl-alpha-iminoethyl)-4-chlorophenol, containing a very short intramolecular hydrogen bond, were investigated computationally in the gas phase and in the crystal by density functional theory (DFT) based first-principle molecular dynamics (FPMD). It is found that the proton is well localized on the nitrogen side of the O...H...N bridge in the crystal phase, in agreement with X-ray diffraction experiments, while a more labile proton is located most of the time on the oxygen side in a vacuum. Environmental effects on this very strong hydrogen bond thus appear crucial and lead to drastic changes of the infrared (IR) spectrum: The computed gas-phase IR spectrum shows a very broad absorption band that covers frequencies from about 1000 to 3000 cm(-1) assigned to the labile proton. In mere contrast, a much more localized absorption band around 2600-2700 cm(-1) is predicted in the crystal phase. Finally, effects of the quantization of the proton motion on the hydrogen bond structure were estimated in two ways. First, we constructed the one-dimensional (1D) potential energy surface (PES) for the proton along the O...H...N bridge in a vacuum. The 1D Schrodinger equation was then solved. Next, path integral molecular dynamics (PIMD) was performed in the solid state. Inclusion of quantum effects does not affect the observed change of the most probable tautomer, upon going from the gas phase to the crystal.
    The Journal of Physical Chemistry B 12/2009; 114(1):242-53. DOI:10.1021/jp903501m · 3.30 Impact Factor
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    ABSTRACT: Physicochemical properties of 1,3-dihydro-1-hydroxy-3-morpholin-4-yl-2,1-benzoxaborole (IIa) and 1,3-dihydro-1- hydroxy-2,1-benzoxaborole (IIb) were investigated using a combination of spectroscopic and computational approaches. The compound IIa belongs to the group represented by the prototypical benzoxaborole IIb, which exhibits receptor activity toward sugars in aqueous solution. Additionally, the IIb can serve as a pattern structure for physicochemical description of benzoxaborole derivatives. The infrared and Raman spectroscopy measurements were performed in solvents and in the solid state. Furthermore, experimental findings served as a reference data source for further computational investigations. DFT calculations in vacuo were used to estimate the binding energy of the dimeric forms, indicating the strength of the intermolecular hydrogen bonds. AIM and ELF theories were applied to give an insight into the electronic structure of the studied compounds. The last part of this study contains Car–Parrinello molecular dynamics investigations in the solid state. Computational results indicated that the key intermolecular feature, the pair of hydrogen bonds, is rather harmonic and the extent of the anharmonicity is temperature dependent as shown by the OH stretching envelope calculations performed for IIa. Inclusion of the quantum effects in the proton motion does not significantly change the qualitative description of the intermolecular H-bond dynamics of the investigated compound. Copyright © 2010 John Wiley & Sons, Ltd.
    Journal of Physical Organic Chemistry 11/2009; 23(5):451 - 460. DOI:10.1002/poc.1625 · 1.38 Impact Factor
  • Aneta Jezierska · Jarosław J. Panek · Riccardo Mazzarello ·
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    ABSTRACT: Density functional theory-based methods were employed to obtain static and dynamical descriptions of the molecular properties of 2-hydroxy-N-methylbenzamide and 2-hydroxy-N-methylthiobenzamide; compounds containing O–H···O and O–H···S strong, intramolecular hydrogen bonds. These compounds are important as analogues of commercial analgesic and antipyretic medicines. In the current study the classical Kohn–Sham method was applied to develop static models describing the geometric parameters and proton potentials. The topological analysis of the electron density was performed via atoms in molecules theory. Subsequently, Car–Parrinello molecular dynamics investigations were performed in vacuo and in the solid state. The geometric and spectroscopic properties were investigated and compared with available experimental data. The influence of quantum effects on the intramolecular hydrogen bond properties were studied via path integral molecular dynamics in the solid state for 2-hydroxy-N-methylbenzamide. We found that the proton behavior depends strongly on the type of acceptor: the sulfur-containing bridge has significantly smaller proton flexibility than the oxygen-bearing analogue, which is reflected in the electronic structure and bridge dynamics.
    Theoretical Chemistry Accounts 11/2009; 124(5):319-330. DOI:10.1007/s00214-009-0612-2 · 2.23 Impact Factor
  • Aneta Jezierska · Jarosław J Panek ·
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    ABSTRACT: The presence of intramolecular hydrogen bonds influences the binding energy, tautomeric equilibrium, and spectroscopic properties of various classes of organic molecules. This article discusses the O-H...S bridge, one of the less commonly investigated types of intramolecular interactions. 3-mercapto-1,3-diphenylprop-2-en-1-one was considered as the model structure. This compound exhibits photochromic properties. Car-Parrinello molecular dynamics (CPMD) was applied to investigate the spectroscopic and molecular properties of this compound in the gas phase and in the solid state. The second part of the study is devoted to the effects of the quantization of nuclear motions, with special attention to the O-H...S moiety. Path integral molecular dynamics (PIMD) of the molecular crystal of 3-mercapto-1,3-diphenylprop-2-en-1-one was carried out for this purpose. The employment of this fully quantum mechanical technique enables one to study, in a time-averaged sense, the zero-point motion important for flat potential energy surfaces. Finally, the potentials of mean force (Pmfs) were calculated from the CPMD and PIMD data obtained for the solid-state calculations. The effect of including quantum nuclear motion was investigated. In the studied compound, quantum effects shortened the H-bridge and provided a better description of the free energy minimum. The computational results place this uncommon intramolecular H-bonding among the class of strong hydrogen bonds with large red shifts of O-H stretching modes, which correspond well with previously presented experimental data in the literature concerning this structure.
    Journal of Computational Chemistry 06/2009; 30(8):1241-50. DOI:10.1002/jcc.21158 · 3.59 Impact Factor
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    ABSTRACT: We were able to test the Bent-Walsh rule by examining geometric parameters in the vicinity of the ipso-carbon atom of H-bonded complexes of para-substituted phenol/phenolate and aniline/anilide derivatives for the three cases (i) a versus alpha, (ii) alpha versus d(CO) or d(CN), and (iii) a versus d(CO) or d(CN), where alpha is the ring valence angle at the ipso-carbon atom (C1 substituted by OH or O(-) or NH(2) or NH(-)) and a is the arithmetic mean of the two C(ipso)-C(ortho) bond lengths. The data for nonequilibrium H-bonded complexes of unsubstituted phenol/phenolate and aniline/anilide with the respective bases F(-) and CN(-) and acids HF and HCN showed the same dependence of a on d(CX) (X = O, N) as the data for equilibrium complexes of para-Y-substituted phenol/phenolate and aniline/anilide derivatives (Y = NO, NO(2), CHO, COMe, CONH(2), Cl, F, H, Me, OMe, OH) with the same bases and acids. The slope of these dependencies was negative, as expected. In the remaining cases (a versus alpha and alpha versus d(CO) or d(CN)), the slopes for simulated complexes followed the Bent-Walsh rule. Finally, for the equilibrium complexes in which the substituent effect was included, the slopes of the trend lines for the substituted systems were opposite. This is because in the a versus alpha relationships, electonegativity and the resonance effect act in the same direction, whereas for the other two cases, these effects are opposite, and the resonance effect dominates.
    The Journal of Physical Chemistry A 05/2009; 113(19):5800-5. DOI:10.1021/jp8109258 · 2.69 Impact Factor
  • Jarosław J Panek · Thomas R Ward · Aneta Jezierska · Marjana Novic ·
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    ABSTRACT: Due to its highly specific and very strong binding, the (strept)avidin-biotin system forms the basis for numerous applications in the life sciences: immunoassays, DNA detection systems, affinity chromatography, etc. Fine-tuning of the ligand binding abilities of this system might provide new technologies with relevance to nanoscale research. Here, we report our computational investigations on wild type (WT) and modified streptavidin (SAV), assessing the impact of fluorination of tryptophan residues on biotin binding ability. Complexes of biotin with four SAV protein variants (WT-SAV, 4fW-SAV, 5fW-SAV and 6fW-SAV) were studied. We found that protein stability and folding are predicted to be weakly affected by fluorination. The host protein binding pocket decreases its ability to form numerous hydrogen bonds to biotin in the case of the 4fW-SAV variant. Conversely, the 5fW-SAV mutant is predicted to have an even more stable ligand-host hydrogen bonding network than WT-SAV. Thermodynamic perturbation investigations predict a decrease in biotin binding free energy from 3.0 to 6.5 kcal/mol per tetrameric host, with the 5fW-SAV mutant being least affected. Overall, the computational findings indicate that 6fW-SAV and, especially, 5fW-SAV to be promising variants of streptavidin for potential modifiable picomolar binding of the biotin ligand family.
    Journal of Molecular Modeling 03/2009; 15(3):257-66. DOI:10.1007/s00894-008-0382-0 · 1.74 Impact Factor
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    ABSTRACT: A phenethyl containing piperidinium compound was synthesized and the results of an X-ray crystallographic and computational analysis of this compound are reported. The compound, 1-[2-(2-methoxyphenyl)ethyl]piperidinium chloride, contains a C–H···O contact, which stabilizes the experimentally found conformation. Additionally, an ionic bond between N–H···Cl atoms is present as shown by the crystallographic measurements. The presence of these two contacts prompted us to perform further theoretical studies. The first part of the computational investigations was carried out on the basis of the Car-Parrinello molecular dynamics (CPMD) in the solid-state using experimental parameters and conditions as a starting point of the simulation. The time evolution of the interatomic distances of the atoms involved in the N–H···Cl interaction was investigated. Vibrational features of the compound were studied by predicted and power spectra. In addition, static models, based on density functional theory (DFT) and second-order Møller-Plesset perturbation calculus, were built to describe the geometric and electronic structure parameters. Finally, the details of the ionic bridge were analyzed using the natural bond orbitals (NBO) approach. The electron density topology was investigated by the atoms in molecules (AIM) theory. In summary, the ionic bridge modifies the spectroscopic properties of the bridge proton. The negative charge of the chloride anion is partially delocalized via the ammonium moiety to the organic subunit.
    Journal of Molecular Structure 11/2008; 891(1-3):184-191. DOI:10.1016/j.molstruc.2008.03.022 · 1.60 Impact Factor
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    ABSTRACT: The hydrogen-bonded isoelectronic complexes of aniline with HF/F- and an ionic form of aniline with HF were investigated by use of computational methods: Symmetry-Adapted Perturbation Theory (SAPT), Atoms in Molecules (AIM), and Natural Bond Orbitals (NBO) approaches. All computations were based on structural models previously generated at the B3LYP/6-311+(d,p) level. The differences between neutral (Ph-NH2...HF)and anionic (Ph-NH2...F- and Ph-NH-...HF) complexes were clearly outlined. The discussed charged complexes serve as Lewis acids and base, HF and F-, respectively. It was found that electrostatic and induction energy terms, obtained as a result of the SAPT method, are most dependent on the type of H-bonding (i.e.,charged or neutral). The electrostatic term is the most distinctive between the neutral and charge-assisted hydrogen bonds in the investigated two-body systems, whereas the latter is more significant in the case of weaker interactions (larger H...B distances). Application of Principal Component Analysis (PCA) to energy components obtained from the SAPT procedure indicated that all of them are relatively well intercorrelated.The above-mentioned terms together with the exchange energy terms are the most important contributions ofthe main principal component, which describes 95% of the total variance. Comparison of AIM parameters in bond critical points for modeled H-bond systems shows a good agreement with those from equilibrium complexes, both experimental and calculated ones. It was found that charged H-bonded complexes exhibit larger fluctuation of electron density and its Laplacian in bond critical points, in line with SAPT analysis. NBO results confirmed the effect of the strength of interaction on property changes both in the region of H-bonding and outside of it. The latter, more distant consequences follow the Bent-Walsh rule for all studied complexes.
    The Journal of Physical Chemistry A 10/2008; 112(40):9895-905. DOI:10.1021/jp803592v · 2.69 Impact Factor
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    ABSTRACT: The molecular structure and properties of phenylboronic acid were investigated experimentally using X-ray structural analysis and spectroscopic methods. Infrared (IR) spectroscopy measurements were performed to assess the hydrogen bonding strength. The experimental part is enhanced by computational results concerning the geometrical and electronic structure. The molecular dimer (basic structural motif) was investigated on the basis of density functional theory (DFT) and Møller–Plesset second order (MP2) perturbation theory. The basis-set superposition error (BSSE) was calculated to correct the binding energy. Atoms in molecules (AIM) and topological analysis of electron localization function (ELF) were applied to study the intermolecular hydrogen bond properties and localization pattern for the neighborhood of the boron atom. The anharmonicity of the hydrogen bond potential function was studied by solving the time-independent Schrödinger equation. Potential energy distribution (PED) analysis of the normal modes was performed to identify the characteristic frequencies of the studied system. Subsequently, the interaction energy for the dimeric form was decomposed using the symmetry-adapted perturbation theory (SAPT) scheme. Car–Parrinello molecular dynamics (CPMD) gave an insight into dynamical processes occurring in the phenylboronic acid dimer in vacuo. The hydrogen bridge protons in the phenylboronic acid are not shifted significantly toward the acceptor. Lower dimerization energy with respect to the carboxylic acid dimers is explained on the basis of the interaction energy decomposition as the effect of diminished induction term. The employment of SAPT and CPMD approaches is a step forward in the understanding of the physico-chemical nature of the large family represented by the investigated compound. Copyright © 2008 John Wiley & Sons, Ltd.
    Journal of Physical Organic Chemistry 05/2008; 21(6):472 - 482. DOI:10.1002/poc.1389 · 1.38 Impact Factor
  • Aneta Jezierska · Jarosław J Panek · Aleksander Koll ·
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    ABSTRACT: Car-Parrinello molecular dynamics simulations in vacuum and in the solid state are performed on a strongly anharmonic system, namely, 2-(N-diethylamino-N-oxymethyl)-4,6-dichlorophenol, to investigate its molecular and spectroscopic properties. The investigated compound contains two slightly different molecules in the crystal cell with very short intramolecular hydrogen bonds (of 2.400 and 2.423 A), as determined previously by neutron diffraction. The vibrational properties of the compound are studied on the basis of standard approaches, that is, Fourier transformation of the autocorrelation functions of the atomic velocities and dipole moments. Then, the trajectory obtained from ab initio molecular dynamics is sampled and the obtained snapshots are used to solve the vibrational Schrödinger equations and to calculate the O--H stretching envelope as a superposition of the 0-->1 transition. Using an envelope method, the a posteriori quantum effects are included in the O--H stretching. In addition, NMR spectra are calculated also using the obtained snapshots. One- and two-dimensional potentials of mean force (1D and 2D pmf) are derived to explain the details of the proton dynamics. The computational results are supported by NMR experimental data. In addition, the calculated results are compared with previously published X-ray, neutron diffraction, and spectroscopic descriptions. A detailed analysis of the bridged proton's dynamics is thus obtained. The application of 1D and 2D pmf in a system with a strong bridged-proton delocalization is also demonstrated.
    ChemPhysChem 04/2008; 9(6):839-46. DOI:10.1002/cphc.200700769 · 3.42 Impact Factor

Publication Stats

509 Citations
113.42 Total Impact Points


  • 2000-2015
    • Wyższa Szkoła Handlowa we Wrocławiu
      Vrotslav, Lower Silesian Voivodeship, Poland
  • 1999-2013
    • University of Wroclaw
      • Faculty of Chemistry
      Vrotslav, Lower Silesian Voivodeship, Poland
  • 2009
    • Pierre and Marie Curie University - Paris 6
      • Laboratoire de Physique Théorique de la Matière Condensée (LPTMC)
      Lutetia Parisorum, Île-de-France, France
  • 2004-2009
    • National Institute of Chemistry
      Lubliano, Ljubljana, Slovenia