Co-reporter:Irena Majerz
Helvetica Chimica Acta 2016 Volume 99( Issue 4) pp:286-295
Publication Date(Web):
DOI:10.1002/hlca.201500183
The influence of the proton transfer on the geometry of donor and acceptor molecule in benzoic acid–pyridine complexes is investigated by theoretical calculations at the B3LYP/6-311++G** level of theory. Systematic shifts of the H-atom in the H-bond are reflected in the geometry of the COOH group and the lengths of aromatic ring bond lengths of the proton acceptor. Changes in electron densities have been studied by atoms in molecules analysis. A systematic natural bond orbital analysis has been performed to study the proton transfer mechanism. Two donor orbitals are engaged in the proton transfer process which is accompanied by a change in orbital delocalization of H-atom that can switch between two donor orbitals so the path of proton transfer in intermolecular H-bond is not determined by the orbital shape. Theoretical results have been confirmed by experimental results published previously.
Co-reporter:Irena Majerz and Teresa Dziembowska
The Journal of Physical Chemistry A 2016 Volume 120(Issue 41) pp:8138-8147
Publication Date(Web):September 30, 2016
DOI:10.1021/acs.jpca.6b05928
The HOMA index calculated for [2.2]paracyclophanes in the solid state reveals a slight decrease of aromaticity. Interactions between aromatic rings of [2.2]paracyclophane have been investigated using AIM and NCI analysis in both crystal and optimized [2.2]paracyclophane structures. AIM analysis showed that the C···C bond path between the two aromatic rings is present only in few [2.2]paracyclophanes. The NCI approach visualized the dispersion and repulsive interactions between the aromatic rings of every [2.2]paracyclophane. Combination of AIM and the NCI approach is necessary for determining and identifying nonbonded interactions in [2.2]paracyclophanes.
Co-reporter:Irena Majerz and Matthias J. Gutmann
RSC Advances 2015 vol. 5(Issue 116) pp:95576-95584
Publication Date(Web):02 Nov 2015
DOI:10.1039/C5RA06733B
The neutron structure of 3-methylpyridinium 2,6-dichloro-4-nitrophenolate measured at different temperatures is used to discuss the structural parameters of the OHN intermolecular hydrogen bridges with the proton moving. The experimental and optimized structures, with the precise location of the proton, are used to explain the mechanism of proton transfer in the OHN hydrogen bridge.
Co-reporter:Irena Majerz, Ireneusz Natkaniec
Chemical Physics Letters 2014 Volume 608() pp:289-294
Publication Date(Web):21 July 2014
DOI:10.1016/j.cplett.2014.05.088
Highlights
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The low-temperature INS spectrum of 2,4,6-trimethylpyridinium pentachlorophenolate is presented.
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Comparison of experimental spectrum with theoretical spectrum calculated for this complex and the complex components.
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The low frequency range of the spectrum has been investigated to find the proton bridge vibrations.
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Influence of the hydrogen bond on the librations of the methyl group in the proton acceptor has been shown.
Co-reporter:Irena Majerz and Teresa Dziembowska
The Journal of Physical Chemistry A 2014 Volume 118(Issue 34) pp:7118-7129
Publication Date(Web):August 5, 2014
DOI:10.1021/jp5047672
The influence of substituents and environment on the aromaticity of the naphthalene ring is shown for a series of peri- and para-substituted naphthalenes. Crystal structure geometries are compared with the single molecule structures in vacuum (optimized at the B3LYP/6-311++G** level) and with structures determined in media of different polarity. The harmonic oscillator model of aromaticity (HOMA) index of the naphthalene rings has been used to characterize the aromaticity of the investigated molecules. It has been shown that the ellipticity of the C2–C3 (C6–C7) bonds can be applied as a measure of participation of the quinoid resonance structure and through-resonance effect between the para-substituents.
Co-reporter:Irena Majerz and Teresa Dziembowska
The Journal of Physical Chemistry A 2012 Volume 116(Issue 23) pp:5629-5636
Publication Date(Web):May 23, 2012
DOI:10.1021/jp212449m
For a series of 2,4,6-trinitroanilines substituted with bulky groups, the influence of intramolecular hydrogen bonds, electronic substituents effect, and steric hindrance on aromaticity of the molecules in crystals and their analogues optimized at the B3LYP/6-311++G** level were studied. The HOMA index was used as a measure of the aromaticity, while the parameter ΔP was a description of the distortion of the benzene ring from planarity. Conformation of the nonplanar ring in crystal and optimized structures was also described using the puckering parameters. A comparison of the data for crystal and optimized structures showed an important effect of the intermolecular interactions on aromaticity of the overcrowded nitroanilines. The packing effects were analyzed using the simplified PCM model of solvents. NBO analysis illustrated the changes of orbitals upon dearomatisation.
Co-reporter:Irena Majerz
The Journal of Physical Chemistry A 2012 Volume 116(Issue 30) pp:7992-8000
Publication Date(Web):July 9, 2012
DOI:10.1021/jp300942n
The directionality of inter- and intramolecular OHO hydrogen bonds has been compared. For intramolecular bridges it is determined by an orbital formed in the proton transfer process. For intermolecular bonds, the hydrogen-bonded proton is attached to two lone pairs of the acceptor and the OHO angle is not fixed but can change in a broad range. Depending on the OHO angle, the interaction changes continuously from electrostatic interaction to strong OHO hydrogen bond.
Co-reporter:Irena Majerz and Matthias J. Gutmann
RSC Advances 2011 vol. 1(Issue 2) pp:219-228
Publication Date(Web):29 Jul 2011
DOI:10.1039/C1RA00219H
The structure of the complex of 3,5-dinitrobenzoaic acid with 3,5-dimethylpyridine was studied by neutron diffraction at 330, 300, 270, 240, 210, 180, 150, 120, 90, 60, and 30 K. The O⋯H bond length gradually changes from 1.403(10) Å at 300 K to 1.424(4) Å at 30 K. The proton shifts in the hydrogen bridge towards the acceptor nitrogen atom. Temperature-dependent changes in the strong OHN hydrogen bond are used to discuss the proton transfer mechanism.
Co-reporter:Irena Majerz;Teresa Dziembowska
European Journal of Organic Chemistry 2011 Volume 2011( Issue 2) pp:280-286
Publication Date(Web):
DOI:10.1002/ejoc.201000978
Abstract
The influence of intramolecular hydrogen bonds and steric hindrance on distortion from planarity of the benzene ring and its aromaticity is shown for a series of substituted 2,4,6-trinitroanilines. The crystal structure geometry and thegeometry optimized at the B3LYP/6-311++G** level are compared with analogues without intramolecular hydrogen bonds. The HOMA index and the parameter ΔP describing the distortion from planarity of the benzene ring were used to characterize the aromacity of the investigated molecules. NBO and AIM analysis were also applied.
Co-reporter:Irena Majerz and Ivar Olovsson
Physical Chemistry Chemical Physics 2010 vol. 12(Issue 20) pp:5462-5467
Publication Date(Web):08 Apr 2010
DOI:10.1039/B925489G
The quantum-mechanically derived reaction coordinates (QMRC) for the proton transfer in O–H–O hydrogen bonds have been derived from ab initio calculations of potential-energy surfaces. A comparison is made between the QMRC and the corresponding bond-order reaction coordinates (BORC) derived by applying the Pauling bond order concept together with the principle of conservation of bond order. In agreement with earlier results for N–H–N+ hydrogen bonds there is virtually perfect agreement between the QMRC and BORC curves for intermolecular O–H–O hydrogen bonds. For intramolecular O–H–O hydrogen bonds, the donor and acceptor parts of the molecule impose strong constraints on the O⋯O distance and the QMRC does not follow the BORC relation in the whole range. The neutron-determined proton positions are located close to the theoretically calculated potential-energy minima, and where the QMRC and the BORC curves coincide with each other. The results confirm the universal character of intermolecular hydrogen bonds: BORC is identical with QMRC and the proton can be moved from donor to acceptor keeping its valency equal to 1. The shape of PES for intramolecular hydrogen bonds is more complex as it is sensitive to the geometry of the molecule as well as of the hydrogen bridge.
Co-reporter:Irena Majerz, Ivar Olovsson
Journal of Molecular Structure 2010 Volume 968(1–3) pp:48-51
Publication Date(Web):8 April 2010
DOI:10.1016/j.molstruc.2010.01.018
The influence of the OHO angle in the hydrogen bond on the potential-energy surface has been studied. The OHO angle has been artificially changed from 140° to 180° to study the influence of the angle on the location of the energy minimum relative to QMRC, the minimum energy reaction path, and BORC, the bond-order reaction path. In the intermolecular hydrogen bond QMRC and BORC are identical, independent on the OHO angle. The intramolecular hydrogen bond is very sensitive to a change in the OHO angle. The agreement between the theoretical results is confirmed by available experimental neutron data.
Co-reporter:Emilia Kwiatkowska, Irena Majerz
Chemical Physics Letters 2010 Volume 484(4–6) pp:134-138
Publication Date(Web):7 January 2010
DOI:10.1016/j.cplett.2009.11.018
Abstract
The potential energy curves for proton motion in the intermolecular hydrogen bonds in phenol–tertiary amine complexes have been analyzed to investigate the location of the energy minimum. The proton donor and proton acceptor properties of the complex components are the main parameters which determine the location of the minimum. Also substituent effect in phenols as well as the different proton acceptors can shift the potential energy curve for proton motion against the reaction coordinate.
Co-reporter:Irena Majerz, Ireneusz Natkaniec
Chemical Physics Letters 2008 Volume 465(1–3) pp:86-91
Publication Date(Web):3 November 2008
DOI:10.1016/j.cplett.2008.09.056
Abstract
Experimental INS (Inelastic Neutron Scattering) spectrum of t-butanol was compared with theoretical spectra of t-butanol monomer and OHO hydrogen bonded dimer calculated at B3LYP/6-31++G∗∗ level. Formation of the OHO hydrogen bond was reflected in shifting of the bands of the stretching and bending vibrations of OH group as well as arising of the bridge vibrations in the low frequency range. INS spectroscopy appeared to be an important tool to investigate the low frequency range of the vibrational spectrum where out-of-plane OH deformation bands and hydrogen bridge stretching and bending bands are located.
Co-reporter:Lucjan Jerzykiewicz, Adam Sroka, Irena Majerz
Journal of Pharmaceutical Sciences (December 2016) Volume 105(Issue 12) pp:3487-3495
Publication Date(Web):1 December 2016
DOI:10.1016/j.xphs.2016.08.029
The crystal structure of fenamic acid-acridine complex is determined by X-ray diffraction. The strong OHN hydrogen bond linking the complex components and other interactions responsible for packing of the molecules into a crystal are investigated within the Quantum Theory of Atom in Molecule theory. The crystal structure is compared with the structure optimized at B3LYP/6-311++G** level and with the theoretical structures optimized under systematically changed pressure. Analysis of the lattice constants, hydrogen bond lengths, and angles of the inter- and intramolecular hydrogen bond under compression is performed. The structural transformation observed at 5 GPa is connected with a change in the intermolecular OHN hydrogen bond. The proton shifts to acceptor and a new interaction in the crystal appears.
Co-reporter:Irena Majerz and Ivar Olovsson
Physical Chemistry Chemical Physics 2010 - vol. 12(Issue 20) pp:NaN5467-5467
Publication Date(Web):2010/04/08
DOI:10.1039/B925489G
The quantum-mechanically derived reaction coordinates (QMRC) for the proton transfer in O–H–O hydrogen bonds have been derived from ab initio calculations of potential-energy surfaces. A comparison is made between the QMRC and the corresponding bond-order reaction coordinates (BORC) derived by applying the Pauling bond order concept together with the principle of conservation of bond order. In agreement with earlier results for N–H–N+ hydrogen bonds there is virtually perfect agreement between the QMRC and BORC curves for intermolecular O–H–O hydrogen bonds. For intramolecular O–H–O hydrogen bonds, the donor and acceptor parts of the molecule impose strong constraints on the O⋯O distance and the QMRC does not follow the BORC relation in the whole range. The neutron-determined proton positions are located close to the theoretically calculated potential-energy minima, and where the QMRC and the BORC curves coincide with each other. The results confirm the universal character of intermolecular hydrogen bonds: BORC is identical with QMRC and the proton can be moved from donor to acceptor keeping its valency equal to 1. The shape of PES for intramolecular hydrogen bonds is more complex as it is sensitive to the geometry of the molecule as well as of the hydrogen bridge.
