The journal of physical chemistry. B, Jan 13, 2015
We consider the impact of phosphatidic acid (namely 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on... more We consider the impact of phosphatidic acid (namely 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on the properties of a zwitterionic (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) bilayer used as a model system for protein-free cell membranes. For this purpose, experimental measurements were performed using differential scanning calorimetry and the Langmuir monolayer technique at physiological pH. Moreover, atomistic-scale molecular dynamics (MD) simulations were performed to gain information on the mixed bilayer's molecular organization. The results of the monolayer studies clearly showed that the DPPC/DOPA mixtures are non-ideal and the interactions between lipid species change from attractive, at low contents of DOPA, to repulsive, at higher contents of that component. In accordance with these results, the MD simulations demonstrated that both monoanionic and dianionic forms of DOPA have an ordering and condensing effect on the mixed bilayer at low concentrations. For the ...
Clathrate hydrates with polar guest molecules (dimethyl ether, ethylene oxide, trimethylene oxide... more Clathrate hydrates with polar guest molecules (dimethyl ether, ethylene oxide, trimethylene oxide, tetrahydrofuran, and tetrahydropyran) were studied by means of the density functional theory. A model of a large cage of structure-I clathrate was employed. Optimal configurations of encaged guests were investigated with a focus on the host-guest hydrogen bond formation. Weak hydrogen bonds were found to be formed by each guest, while for THP a strong hydrogen bond and formation of L-defect was also observed. This is in accord with previous computational and experimental studies. Steric factors were shown to play a key role for the strength of the hydrogen bond formed. Interestingly, the host-guest binding is influenced not only by the size of a guest molecule but also by its shape. This work demonstrates that both electronic and steric properties of a polar guest should be considered for a full description of clathrate systems.
... to reach ultimately the minimum, in our model located at the border of the Brillouin zone, an... more ... to reach ultimately the minimum, in our model located at the border of the Brillouin zone, and in the actual crystal corresponding to the lower Davydov component. ... petelenz@chemia.uj.edu. pl Handbook of Conducting Polymers, edited by TA Scotheim [?]Marcel Dekker, New ...
Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is... more Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.
A comprehensive theory of linear vibronic coupling in a coupled manifold of Frenkel and charge-tr... more A comprehensive theory of linear vibronic coupling in a coupled manifold of Frenkel and charge-transfer states in an infinite molecular crystal is presented and applied for sexithiophene. The approach, valid in the intermediate-coupling regime, includes up to three-particle terms of the Philpott expansion, with the vibronic wavefunctions represented in the Lang-Firsov basis. As a stringent test, the scheme is used to reproduce the complete set of available sexithiophene absorption and electroabsorption spectra within a unified theoretical framework. The input is based primarily on independent calculations and to some extent on independent experiments, with explicit fitting contained within the limits set by the estimated inherent errors of a priori parameter estimates. Reasonably good quantitative agreement with experimental spectra is achieved. The results resolve some existing interpretational ambiguities and expose some peculiarities of electric field effect on vibronic eigenstates of Frenkel parentage, highlighting the role of charge-transfer interactions.
ABSTRACT A model of vibronic coupling in a manifold of coupled Frenkel and charge transfer states... more ABSTRACT A model of vibronic coupling in a manifold of coupled Frenkel and charge transfer states is applied to evaluate the electric-field-induced shifts of lowest vibronic levels deriving from the lower Davydov component of the Frenkel exciton in sexithiophene. With respect to the isolated-molecule value, vibronic terms combined with the mixing between Frenkel and CT configurations amplify the field-induced shift by the factor of seven for the 0–0 line and by further 60% for the vibronic replica in the main progression-forming mode. Confirmation is found in the existing experimental literature.
The journal of physical chemistry. B, Jan 13, 2015
We consider the impact of phosphatidic acid (namely 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on... more We consider the impact of phosphatidic acid (namely 1,2-dioleoyl-sn-glycero-3-phosphate, DOPA) on the properties of a zwitterionic (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) bilayer used as a model system for protein-free cell membranes. For this purpose, experimental measurements were performed using differential scanning calorimetry and the Langmuir monolayer technique at physiological pH. Moreover, atomistic-scale molecular dynamics (MD) simulations were performed to gain information on the mixed bilayer's molecular organization. The results of the monolayer studies clearly showed that the DPPC/DOPA mixtures are non-ideal and the interactions between lipid species change from attractive, at low contents of DOPA, to repulsive, at higher contents of that component. In accordance with these results, the MD simulations demonstrated that both monoanionic and dianionic forms of DOPA have an ordering and condensing effect on the mixed bilayer at low concentrations. For the ...
Clathrate hydrates with polar guest molecules (dimethyl ether, ethylene oxide, trimethylene oxide... more Clathrate hydrates with polar guest molecules (dimethyl ether, ethylene oxide, trimethylene oxide, tetrahydrofuran, and tetrahydropyran) were studied by means of the density functional theory. A model of a large cage of structure-I clathrate was employed. Optimal configurations of encaged guests were investigated with a focus on the host-guest hydrogen bond formation. Weak hydrogen bonds were found to be formed by each guest, while for THP a strong hydrogen bond and formation of L-defect was also observed. This is in accord with previous computational and experimental studies. Steric factors were shown to play a key role for the strength of the hydrogen bond formed. Interestingly, the host-guest binding is influenced not only by the size of a guest molecule but also by its shape. This work demonstrates that both electronic and steric properties of a polar guest should be considered for a full description of clathrate systems.
... to reach ultimately the minimum, in our model located at the border of the Brillouin zone, an... more ... to reach ultimately the minimum, in our model located at the border of the Brillouin zone, and in the actual crystal corresponding to the lower Davydov component. ... petelenz@chemia.uj.edu. pl Handbook of Conducting Polymers, edited by TA Scotheim [?]Marcel Dekker, New ...
Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is... more Traditionally, infrared band assignment for the protonated water clusters, such as H(+)(H2O)5, is based on their lowest energy isomer. Recent experiments extend the observation spectral window to lower frequencies, for which such assignment appears to be inadequate. Because this hydrogen-bonded system is highly anharmonic, harmonic spectral calculations are insufficient for reliable interpretation. Consequently, we have calculated the IR spectrum of several isomers of the protonated water pentamer using an inherently anharmonic methodology, utilizing dipole and velocity autocorrelation functions computed from ab initio molecular dynamic trajectories. While the spectrum of H(+)(H2O)5 is universally assumed to represent the branched Eigen isomer, we find a better agreement for a mixture of a ring and linear isomers. The first has an Eigen core and contributes at high frequencies, whereas the latter accounts for all prominent low-frequency bands. Interestingly, its core is neither a classical Eigen nor a Zundel cation, but rather has hybrid geometry. Such an isomer may play a role in proton conductance along short proton wires.
A comprehensive theory of linear vibronic coupling in a coupled manifold of Frenkel and charge-tr... more A comprehensive theory of linear vibronic coupling in a coupled manifold of Frenkel and charge-transfer states in an infinite molecular crystal is presented and applied for sexithiophene. The approach, valid in the intermediate-coupling regime, includes up to three-particle terms of the Philpott expansion, with the vibronic wavefunctions represented in the Lang-Firsov basis. As a stringent test, the scheme is used to reproduce the complete set of available sexithiophene absorption and electroabsorption spectra within a unified theoretical framework. The input is based primarily on independent calculations and to some extent on independent experiments, with explicit fitting contained within the limits set by the estimated inherent errors of a priori parameter estimates. Reasonably good quantitative agreement with experimental spectra is achieved. The results resolve some existing interpretational ambiguities and expose some peculiarities of electric field effect on vibronic eigenstates of Frenkel parentage, highlighting the role of charge-transfer interactions.
ABSTRACT A model of vibronic coupling in a manifold of coupled Frenkel and charge transfer states... more ABSTRACT A model of vibronic coupling in a manifold of coupled Frenkel and charge transfer states is applied to evaluate the electric-field-induced shifts of lowest vibronic levels deriving from the lower Davydov component of the Frenkel exciton in sexithiophene. With respect to the isolated-molecule value, vibronic terms combined with the mixing between Frenkel and CT configurations amplify the field-induced shift by the factor of seven for the 0–0 line and by further 60% for the vibronic replica in the main progression-forming mode. Confirmation is found in the existing experimental literature.
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Papers by Waldemar Kulig