The effect of different terminations of cluster models was shown on the quantum-chemically calcul... more The effect of different terminations of cluster models was shown on the quantum-chemically calculated atomic charges, bonding population analysis and harmonic vibrational frequency of the inner OH group. As the basic model was proposed 32 atomic cluster of the brucite sheet in lizardite layer. The calculations were performed using Hartree-Fock method and 3-21G atomic basis set (HF/3-21G).
We report an inelastic neutron scattering (INS) study of a monosaccharide, 1,6-anhydro-b-D-glucop... more We report an inelastic neutron scattering (INS) study of a monosaccharide, 1,6-anhydro-b-D-glucopyranose, C 6 O 5 H 10 (levoglucosan). The assignment of the experimental vibrational spectrum measured in the range 30-4000 cm À1 on TOSCA spectrometer has been made by means of DFT calculations. To simulate crystal environment both molecular cluster and periodic models were used. The INS spectrum calculated with the periodic model is a better fit of the experiment than the cluster model. On the other hand the peaks between 630 and 730 cm À1 in the experimental INS assigned to OH torsional modes were reproduced better by the cluster calculations. The study has been completed by an alternative approach, molecular dynamics (MD) calculations, done at the same level of the DFT theory. The simulation trajectories were analyzed in both time and frequency space to determine the dynamical contributions to the observed spectra. Comparing the positions of the peaks in the power spectra and in the INS spectra, the former gave a better fit of the experimental ones in all the frequency ranges when compared to the spectra based on dynamical matrix. Our calculations, in general, underestimated the frequencies of the modes in the region between 500 and 1500 cm À1 by maximum of 30 cm À1. The power spectra of the velocity autocorrelation function for centre of mass of a molecule of levoglucosan show peaks below 160 cm À1 .
The electronic structure of the 001 and 110 ␣-alumina surfaces was Ž. determined by periodic Hart... more The electronic structure of the 001 and 110 ␣-alumina surfaces was Ž. determined by periodic Hartree᎐Fock method in statically relaxed geometries. Both 001 Ž. and 110 surfaces generate specific surface states into the energy gap. Significant influence of charge-transfer effect on the surface᎐adsorbate potential is possible in both cases studied. The inclusion of the exponential part to the standard potential forms was suggested for the description of the interaction potential in such cases.
Acta Crystallographica Section B Structural Science, 2005
The structure of deca-dodecasil 3R (DD-3R), Si120O240, a very well suited material for the synthe... more The structure of deca-dodecasil 3R (DD-3R), Si120O240, a very well suited material for the synthesis of inorganic/organic composites structured on a nanometer level, has been investigated in detail. So far, a highly complicated twinning has hampered its structure description at a desirable level of accuracy. This twinning has now been resolved and a new structure determination is presented. Structure refinement in the R\bar 3 space group revealed a large, unusually shaped atomic displacement ellipsoid for oxygen-bridging units (tetrahedra), bridging Si—O bonds shorter than expected and the linear Si—O—Si′ bond angle dictated by special positions at a threefold axis. A structure model based on a statistically disordered bridging O atom improved the accuracy of the Si—O bonds of interest, but provided unacceptable O—O contacts. To solve this dilemma, ab initio NVT molecular dynamics calculations were performed to study the possible configurations. Wavelet analysis of the time variatio...
The DFT method was used for modeling a partial decomposition of the structure of the thaumasite m... more The DFT method was used for modeling a partial decomposition of the structure of the thaumasite mineral. The four models with a consecutive decreasing of water content were prepared (T12 – 100 %, T9 – 75 %, T6 – 50 %, T3 – 25 %) and corresponding decomposition enthalpies were calculated. The results showed a good agreement with available experimental data for the decomposition reaction of the thaumasite structure.
Hexachlorobenzene (HCB), a representative of hydrophobic organic chemicals (HOC), belongs to the ... more Hexachlorobenzene (HCB), a representative of hydrophobic organic chemicals (HOC), belongs to the group of persistent organic pollutants (POPs) that can have harmful effects on humans and other biota. Sorption processes in soils and sediments largely determine the fate of HCB and the risks arising from the compound in the environment. In this context, especially HOC–organic matter interactions are intensively studied, whereas knowledge of HOC adsorption to mineral phases (e.g., clay minerals) is comparatively limited. In this work, we performed batch adsorption experiments of HCB on a set of twelve phyllosilicate mineral sorbents that comprised several smectites, kaolinite, hectorite, chlorite, vermiculite, and illite. The effect of charge and size of exchangeable cations on HCB adsorption was studied using the source clay montmorillonite STx-1b after treatment with nine types of alkali (M+: Li, K, Na, Rb, Cs) and alkaline earth metal cations (M2+: Mg, Ca, Sr, Ba). Molecular modeling...
Nitriding has been used for decades to improve the corrosion resistance of iron and steel materia... more Nitriding has been used for decades to improve the corrosion resistance of iron and steel materials. Moreover, iron nitrides (Fe x N) have been shown to give an outstanding catalytic performance in a wide range of applications. We demonstrate that nitriding also substantially enhances the reactivity of zerovalent iron nanoparticles (nZVI) used for groundwater remediation, alongside reducing particle corrosion. Two different types of Fe x N nanoparticles were synthesized by passing gaseous NH 3 /N 2 mixtures over pristine nZVI at elevated temperatures. The resulting particles were composed mostly of face-centered cubic (γ′-Fe 4 N) and hexagonal close-packed (εFe 2−3 N) arrangements. Nitriding was found to increase the particles' water contact angle and surface availability of iron in reduced forms. The two types of Fe x N nanoparticles showed a 20-and 5-fold increase in the trichloroethylene (TCE) dechlorination rate, compared to pristine nZVI, and about a 3-fold reduction in the hydrogen evolution rate. This was related to a low energy barrier of 27.0 kJ mol −1 for the first dechlorination step of TCE on the γ′Fe 4 N(001) surface, as revealed by density functional theory calculations with an implicit solvation model. TCE dechlorination experiments with aged particles showed that the γ′Fe 4 N nanoparticles retained high reactivity even after three months of aging. This combined theoretical-experimental study shows that Fe x N nanoparticles represent a new and potentially important tool for TCE dechlorination.
The density functional theory-based calculations were performed on stripe models of the single ka... more The density functional theory-based calculations were performed on stripe models of the single kaolinite layer. The calculations helped to explain why halloysite mineral, a member of the kaolinite group existing in a tubular form, has rolled tubes only in one way. In that form, aluminol octahedral sheet, terminated by surface hydroxyl groups, represents the inner surface of the nanotubes. The bending models with the inner surface formed by the SiO tetrahedral sheet showed significant structural instability with monotonically increasing strain energy as a function of the curvature. In contrast, for the bending models with the octahedral sheet as the inner surface, stabilization energetic minima were found at curvatures of about 10 nm. The calculations were also performed on the individual sheets (tetrahedral and octahedral) of the kaolinite layer to show their contribution to the bending strain. We found that the decrease of the bending energy and the layer stabilization with respect to the planar configuration for curvatures with radii R C > ∼5 nm can be attributed mainly to three factors(i) better match between octahedral and tetrahedral sheets, (ii) local structural changes of the SiO and AlOH polyhedral units, and (iii) increasing effectivity of hydrogen bonding of the outer surface OH groups.
Explicitly correlated MBPT-R12 and coupled cluster [up to CCSD(T)-R12] methods have been used in ... more Explicitly correlated MBPT-R12 and coupled cluster [up to CCSD(T)-R12] methods have been used in calculations of various (vibrationless) electrical properties for the LiH molecule, including the dipole and quadrupole moments, dipole and quadrupole polarizability tensors, dipole hyperpolarizability tensors, and the second dipole hyperpolarizability tensors. Generally, with extension of the basis set the R12 method did not lead to faster convergence for the calculated properties towards the basis limit. Nevertheless, R12 calculations serve as useful indicators to judge the reliability of the results, and substantially help in determining the accuracy. Results obtained with the 11s8p6d5fa9s8p6d5f basis and CCSD(T)-R12 calculated within this work should be close to the basis set limit.
The effect of substitutions of central cations in the octahedral sheet of trioctahedral phyllosil... more The effect of substitutions of central cations in the octahedral sheet of trioctahedral phyllosilicates on the inner hydroxyl group was studied applying quantum-mechanical B3LYP/DZP method on cluster models of the solid. Changes of the geometry and of the stretching vibration of the inner hydroxyl group were observed. Calculated vibrational frequencies correlate with experimental spectra of 2:1 trioctahedral minerals of the talc type. The simulation of infrared spectra in the region of the stretching vibration of the inner OH groups was performed for several concentrations of the Ni 2þ cation in the trioctahedral sheet. Simulated spectra are in good agreement with experimental ones of synthetic talc minerals containing different concentrations of the Ni 2þ cation.
The study of electrical conductivity, Raman and IR spectra, and microhardness of both polycrystal... more The study of electrical conductivity, Raman and IR spectra, and microhardness of both polycrystalhne and single crystalline forms of samples has proved that the kind of inco~rat~on of ~ngsten into the YSZ lattice is a unction of its concentration. However, the influence of tungsten impurity on the investigated physical properties of YSZ is rather weak. The electrical conductivity does not change markedly its character with an exception of an anomaly at 0.142 wt% W03. The observed decrease of the intensities of the defect-induced Raman bands can be caused by the strong electronic influence of W"+ ions on their environment and by the decrease of the number of oxygen vacancies in the structure. The dependence of the microhardness on the temperature is stepwise. The inhomogeneities observed are connected with different impurity phases. Tbe microhardness is inde~ndent of the presence of tungsten above 375°C which indicates the absence of tungsten containing impurity phases at these temperatures.
ABSTRACTIn this work, we study CdTe thin films used in CdTe/CdS solar cells with a substrate conf... more ABSTRACTIn this work, we study CdTe thin films used in CdTe/CdS solar cells with a substrate configuration, which allows for better control in forming the junction, and the possibility for using flexible non-transparent substrates. We studied the properties of CdTe films grown at 450° and 550°C, with and without a CuxTe layer, and before and after CdCl2 treatment. We analyzed the structural and electro-optical properties using electron backscatter diffraction (EBSD), cathodoluminescence (CL) and X-ray diffraction (XRD), and investigated how the film structure, stress, and defect structure changes with the different growth conditions.
Solvation Effects on Molecules and Biomolecules, 2008
The importance of hydrogen bonds and solvent effects in soil and environmental chemistry is demon... more The importance of hydrogen bonds and solvent effects in soil and environmental chemistry is demonstrated in this chapter. Humic substances as one of the major soil constituents are modeled by means of representative functional groups. Their capability to form hydrogen bonds is demonstrated on interactions with selected sets of polar molecules, anions and acidic pesticides, particularly 2,4-dichlorophenoxyacetic. It was shown that anionic species form complexes of similar strength as corresponding neutral molecules if solvent effects are taken into account. Of all functional groups carboxyl showed the highest chemical activity in the formation of complexes. The calculations demonstrate that the solvent effect substantially lowers the complex formation energies, especially in case of charged systems. The soil minerals kaolinite and goethite studied in this work possess very active surfaces, which are formed from hydroxyl groups. These OH groups are very flexible and able to act as a proton donor or acceptor for hydrogen bond formation. Polar molecules (e.g., H2O, acetic acid) form strongly bound complexes via multiple hydrogen bonds. It was shown that strong sorbent sites exist on irregular clay mineral surfaces formed on the corner and edges of clay mineral particles
Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide... more Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide was studied using density functional theory (DFT) calculations combined with molecular dynamics (MD). The important step made here lies in the use of a periodic DFT method enabling the study of a mineral surface of different protonation states, in strong contrast with previous molecular modeling studies limited to single protonation state corresponding to the point of zero charge. Different surface OH groups and MCPA proton states were used to mimic the strong effects of pH on the outer- and inner-sphere surface complexes that are theoretically possible, together with their binding energies, and their bond lengths. Modeling both a solvated and a protonated (110) goethite surface provided a major breakthrough in the acidic adsorption regime. An outer-sphere complex and a monodentate inner-sphere complex with the neutral MCPA molecule were found to be the most energetically stable adsorba...
ABSTRACT a b s t r a c t Structural and vibrational features of Na-montmorillonite and montmorill... more ABSTRACT a b s t r a c t Structural and vibrational features of Na-montmorillonite and montmorillonite intercalated with tetram-ethylammonium cation (TMA +) were characterized theoretically and experimentally. Theoretical study was performed using density functional theory with inclusion of dispersion corrections. The analysis of the hydrogen bonds in the calculated models has shown that the Na + cations coordinated by six water molecules (Na-M model) are bound to montmorillonite layers by moderate hydrogen bonds between water molecules and basal oxygen atoms of the tetrahedral sheets. Hydrated Na + cations are stabi-lized by relatively strong hydrogen bonds among water molecules. In the intercalate model, the TMA + cation is fixed in the interlayer space by weak hydrogen bonds between the methyl groups and basal oxygen atoms of montmorillonite layers. The calculated vibrational spectra are in a good agreement with the measured infrared spectra. The detailed analysis of the simulated vibrational spectra allowed unambiguous identification of corresponding bands in the measured spectra and their assignment to the particular vibrational modes. For example, calculations clearly distinguished between AlMgOH and AlAlOH stretching vibrations and also between the coupled vibrations of the methyl groups of the TMA + cations.
An extensive theoretical study has been carried out to determine barriers for the proton exchange... more An extensive theoretical study has been carried out to determine barriers for the proton exchange reactions of C2-C4 alkanes in ZSM-5. It was found that cluster size and cavity structure are very important for predicting this barrier. A decrement of up to 20 kcal/mol was observed when employing the periodic model instead of using the small cluster model. Effects of basis set quality and electron correlation to the activation energy are positive and in combination could contribute up to 8 kcal/mol. An extrapolation scheme for estimating the reaction barrier that takes into account effects of cluster size, basis set quality, and electron correlation has been proposed. The regioselectivity and the chain length were discussed. Keywords ZSM-5 zeolite Á Proton exchange Á Density functional theory Á Activation barrier Dedicated to Professor Marco Antonio Chaer Nascimento and published as part of the special collection of articles celebrating his 65th birthday.
Molecular simulations using density functional theory (DFT/PBE and DFT/tight-binding (DFTB)) have... more Molecular simulations using density functional theory (DFT/PBE and DFT/tight-binding (DFTB)) have been performed to study wetting processes of model nanopore segments in humic substances (HS). A complex of two poly (acrylic acid) trimers (trimer complex, TC) ...
The effect of different terminations of cluster models was shown on the quantum-chemically calcul... more The effect of different terminations of cluster models was shown on the quantum-chemically calculated atomic charges, bonding population analysis and harmonic vibrational frequency of the inner OH group. As the basic model was proposed 32 atomic cluster of the brucite sheet in lizardite layer. The calculations were performed using Hartree-Fock method and 3-21G atomic basis set (HF/3-21G).
We report an inelastic neutron scattering (INS) study of a monosaccharide, 1,6-anhydro-b-D-glucop... more We report an inelastic neutron scattering (INS) study of a monosaccharide, 1,6-anhydro-b-D-glucopyranose, C 6 O 5 H 10 (levoglucosan). The assignment of the experimental vibrational spectrum measured in the range 30-4000 cm À1 on TOSCA spectrometer has been made by means of DFT calculations. To simulate crystal environment both molecular cluster and periodic models were used. The INS spectrum calculated with the periodic model is a better fit of the experiment than the cluster model. On the other hand the peaks between 630 and 730 cm À1 in the experimental INS assigned to OH torsional modes were reproduced better by the cluster calculations. The study has been completed by an alternative approach, molecular dynamics (MD) calculations, done at the same level of the DFT theory. The simulation trajectories were analyzed in both time and frequency space to determine the dynamical contributions to the observed spectra. Comparing the positions of the peaks in the power spectra and in the INS spectra, the former gave a better fit of the experimental ones in all the frequency ranges when compared to the spectra based on dynamical matrix. Our calculations, in general, underestimated the frequencies of the modes in the region between 500 and 1500 cm À1 by maximum of 30 cm À1. The power spectra of the velocity autocorrelation function for centre of mass of a molecule of levoglucosan show peaks below 160 cm À1 .
The electronic structure of the 001 and 110 ␣-alumina surfaces was Ž. determined by periodic Hart... more The electronic structure of the 001 and 110 ␣-alumina surfaces was Ž. determined by periodic Hartree᎐Fock method in statically relaxed geometries. Both 001 Ž. and 110 surfaces generate specific surface states into the energy gap. Significant influence of charge-transfer effect on the surface᎐adsorbate potential is possible in both cases studied. The inclusion of the exponential part to the standard potential forms was suggested for the description of the interaction potential in such cases.
Acta Crystallographica Section B Structural Science, 2005
The structure of deca-dodecasil 3R (DD-3R), Si120O240, a very well suited material for the synthe... more The structure of deca-dodecasil 3R (DD-3R), Si120O240, a very well suited material for the synthesis of inorganic/organic composites structured on a nanometer level, has been investigated in detail. So far, a highly complicated twinning has hampered its structure description at a desirable level of accuracy. This twinning has now been resolved and a new structure determination is presented. Structure refinement in the R\bar 3 space group revealed a large, unusually shaped atomic displacement ellipsoid for oxygen-bridging units (tetrahedra), bridging Si—O bonds shorter than expected and the linear Si—O—Si′ bond angle dictated by special positions at a threefold axis. A structure model based on a statistically disordered bridging O atom improved the accuracy of the Si—O bonds of interest, but provided unacceptable O—O contacts. To solve this dilemma, ab initio NVT molecular dynamics calculations were performed to study the possible configurations. Wavelet analysis of the time variatio...
The DFT method was used for modeling a partial decomposition of the structure of the thaumasite m... more The DFT method was used for modeling a partial decomposition of the structure of the thaumasite mineral. The four models with a consecutive decreasing of water content were prepared (T12 – 100 %, T9 – 75 %, T6 – 50 %, T3 – 25 %) and corresponding decomposition enthalpies were calculated. The results showed a good agreement with available experimental data for the decomposition reaction of the thaumasite structure.
Hexachlorobenzene (HCB), a representative of hydrophobic organic chemicals (HOC), belongs to the ... more Hexachlorobenzene (HCB), a representative of hydrophobic organic chemicals (HOC), belongs to the group of persistent organic pollutants (POPs) that can have harmful effects on humans and other biota. Sorption processes in soils and sediments largely determine the fate of HCB and the risks arising from the compound in the environment. In this context, especially HOC–organic matter interactions are intensively studied, whereas knowledge of HOC adsorption to mineral phases (e.g., clay minerals) is comparatively limited. In this work, we performed batch adsorption experiments of HCB on a set of twelve phyllosilicate mineral sorbents that comprised several smectites, kaolinite, hectorite, chlorite, vermiculite, and illite. The effect of charge and size of exchangeable cations on HCB adsorption was studied using the source clay montmorillonite STx-1b after treatment with nine types of alkali (M+: Li, K, Na, Rb, Cs) and alkaline earth metal cations (M2+: Mg, Ca, Sr, Ba). Molecular modeling...
Nitriding has been used for decades to improve the corrosion resistance of iron and steel materia... more Nitriding has been used for decades to improve the corrosion resistance of iron and steel materials. Moreover, iron nitrides (Fe x N) have been shown to give an outstanding catalytic performance in a wide range of applications. We demonstrate that nitriding also substantially enhances the reactivity of zerovalent iron nanoparticles (nZVI) used for groundwater remediation, alongside reducing particle corrosion. Two different types of Fe x N nanoparticles were synthesized by passing gaseous NH 3 /N 2 mixtures over pristine nZVI at elevated temperatures. The resulting particles were composed mostly of face-centered cubic (γ′-Fe 4 N) and hexagonal close-packed (εFe 2−3 N) arrangements. Nitriding was found to increase the particles' water contact angle and surface availability of iron in reduced forms. The two types of Fe x N nanoparticles showed a 20-and 5-fold increase in the trichloroethylene (TCE) dechlorination rate, compared to pristine nZVI, and about a 3-fold reduction in the hydrogen evolution rate. This was related to a low energy barrier of 27.0 kJ mol −1 for the first dechlorination step of TCE on the γ′Fe 4 N(001) surface, as revealed by density functional theory calculations with an implicit solvation model. TCE dechlorination experiments with aged particles showed that the γ′Fe 4 N nanoparticles retained high reactivity even after three months of aging. This combined theoretical-experimental study shows that Fe x N nanoparticles represent a new and potentially important tool for TCE dechlorination.
The density functional theory-based calculations were performed on stripe models of the single ka... more The density functional theory-based calculations were performed on stripe models of the single kaolinite layer. The calculations helped to explain why halloysite mineral, a member of the kaolinite group existing in a tubular form, has rolled tubes only in one way. In that form, aluminol octahedral sheet, terminated by surface hydroxyl groups, represents the inner surface of the nanotubes. The bending models with the inner surface formed by the SiO tetrahedral sheet showed significant structural instability with monotonically increasing strain energy as a function of the curvature. In contrast, for the bending models with the octahedral sheet as the inner surface, stabilization energetic minima were found at curvatures of about 10 nm. The calculations were also performed on the individual sheets (tetrahedral and octahedral) of the kaolinite layer to show their contribution to the bending strain. We found that the decrease of the bending energy and the layer stabilization with respect to the planar configuration for curvatures with radii R C > ∼5 nm can be attributed mainly to three factors(i) better match between octahedral and tetrahedral sheets, (ii) local structural changes of the SiO and AlOH polyhedral units, and (iii) increasing effectivity of hydrogen bonding of the outer surface OH groups.
Explicitly correlated MBPT-R12 and coupled cluster [up to CCSD(T)-R12] methods have been used in ... more Explicitly correlated MBPT-R12 and coupled cluster [up to CCSD(T)-R12] methods have been used in calculations of various (vibrationless) electrical properties for the LiH molecule, including the dipole and quadrupole moments, dipole and quadrupole polarizability tensors, dipole hyperpolarizability tensors, and the second dipole hyperpolarizability tensors. Generally, with extension of the basis set the R12 method did not lead to faster convergence for the calculated properties towards the basis limit. Nevertheless, R12 calculations serve as useful indicators to judge the reliability of the results, and substantially help in determining the accuracy. Results obtained with the 11s8p6d5fa9s8p6d5f basis and CCSD(T)-R12 calculated within this work should be close to the basis set limit.
The effect of substitutions of central cations in the octahedral sheet of trioctahedral phyllosil... more The effect of substitutions of central cations in the octahedral sheet of trioctahedral phyllosilicates on the inner hydroxyl group was studied applying quantum-mechanical B3LYP/DZP method on cluster models of the solid. Changes of the geometry and of the stretching vibration of the inner hydroxyl group were observed. Calculated vibrational frequencies correlate with experimental spectra of 2:1 trioctahedral minerals of the talc type. The simulation of infrared spectra in the region of the stretching vibration of the inner OH groups was performed for several concentrations of the Ni 2þ cation in the trioctahedral sheet. Simulated spectra are in good agreement with experimental ones of synthetic talc minerals containing different concentrations of the Ni 2þ cation.
The study of electrical conductivity, Raman and IR spectra, and microhardness of both polycrystal... more The study of electrical conductivity, Raman and IR spectra, and microhardness of both polycrystalhne and single crystalline forms of samples has proved that the kind of inco~rat~on of ~ngsten into the YSZ lattice is a unction of its concentration. However, the influence of tungsten impurity on the investigated physical properties of YSZ is rather weak. The electrical conductivity does not change markedly its character with an exception of an anomaly at 0.142 wt% W03. The observed decrease of the intensities of the defect-induced Raman bands can be caused by the strong electronic influence of W"+ ions on their environment and by the decrease of the number of oxygen vacancies in the structure. The dependence of the microhardness on the temperature is stepwise. The inhomogeneities observed are connected with different impurity phases. Tbe microhardness is inde~ndent of the presence of tungsten above 375°C which indicates the absence of tungsten containing impurity phases at these temperatures.
ABSTRACTIn this work, we study CdTe thin films used in CdTe/CdS solar cells with a substrate conf... more ABSTRACTIn this work, we study CdTe thin films used in CdTe/CdS solar cells with a substrate configuration, which allows for better control in forming the junction, and the possibility for using flexible non-transparent substrates. We studied the properties of CdTe films grown at 450° and 550°C, with and without a CuxTe layer, and before and after CdCl2 treatment. We analyzed the structural and electro-optical properties using electron backscatter diffraction (EBSD), cathodoluminescence (CL) and X-ray diffraction (XRD), and investigated how the film structure, stress, and defect structure changes with the different growth conditions.
Solvation Effects on Molecules and Biomolecules, 2008
The importance of hydrogen bonds and solvent effects in soil and environmental chemistry is demon... more The importance of hydrogen bonds and solvent effects in soil and environmental chemistry is demonstrated in this chapter. Humic substances as one of the major soil constituents are modeled by means of representative functional groups. Their capability to form hydrogen bonds is demonstrated on interactions with selected sets of polar molecules, anions and acidic pesticides, particularly 2,4-dichlorophenoxyacetic. It was shown that anionic species form complexes of similar strength as corresponding neutral molecules if solvent effects are taken into account. Of all functional groups carboxyl showed the highest chemical activity in the formation of complexes. The calculations demonstrate that the solvent effect substantially lowers the complex formation energies, especially in case of charged systems. The soil minerals kaolinite and goethite studied in this work possess very active surfaces, which are formed from hydroxyl groups. These OH groups are very flexible and able to act as a proton donor or acceptor for hydrogen bond formation. Polar molecules (e.g., H2O, acetic acid) form strongly bound complexes via multiple hydrogen bonds. It was shown that strong sorbent sites exist on irregular clay mineral surfaces formed on the corner and edges of clay mineral particles
Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide... more Interaction between the goethite surface and 4-chloro-2-methylphenoxyacetic acid (MCPA) herbicide was studied using density functional theory (DFT) calculations combined with molecular dynamics (MD). The important step made here lies in the use of a periodic DFT method enabling the study of a mineral surface of different protonation states, in strong contrast with previous molecular modeling studies limited to single protonation state corresponding to the point of zero charge. Different surface OH groups and MCPA proton states were used to mimic the strong effects of pH on the outer- and inner-sphere surface complexes that are theoretically possible, together with their binding energies, and their bond lengths. Modeling both a solvated and a protonated (110) goethite surface provided a major breakthrough in the acidic adsorption regime. An outer-sphere complex and a monodentate inner-sphere complex with the neutral MCPA molecule were found to be the most energetically stable adsorba...
ABSTRACT a b s t r a c t Structural and vibrational features of Na-montmorillonite and montmorill... more ABSTRACT a b s t r a c t Structural and vibrational features of Na-montmorillonite and montmorillonite intercalated with tetram-ethylammonium cation (TMA +) were characterized theoretically and experimentally. Theoretical study was performed using density functional theory with inclusion of dispersion corrections. The analysis of the hydrogen bonds in the calculated models has shown that the Na + cations coordinated by six water molecules (Na-M model) are bound to montmorillonite layers by moderate hydrogen bonds between water molecules and basal oxygen atoms of the tetrahedral sheets. Hydrated Na + cations are stabi-lized by relatively strong hydrogen bonds among water molecules. In the intercalate model, the TMA + cation is fixed in the interlayer space by weak hydrogen bonds between the methyl groups and basal oxygen atoms of montmorillonite layers. The calculated vibrational spectra are in a good agreement with the measured infrared spectra. The detailed analysis of the simulated vibrational spectra allowed unambiguous identification of corresponding bands in the measured spectra and their assignment to the particular vibrational modes. For example, calculations clearly distinguished between AlMgOH and AlAlOH stretching vibrations and also between the coupled vibrations of the methyl groups of the TMA + cations.
An extensive theoretical study has been carried out to determine barriers for the proton exchange... more An extensive theoretical study has been carried out to determine barriers for the proton exchange reactions of C2-C4 alkanes in ZSM-5. It was found that cluster size and cavity structure are very important for predicting this barrier. A decrement of up to 20 kcal/mol was observed when employing the periodic model instead of using the small cluster model. Effects of basis set quality and electron correlation to the activation energy are positive and in combination could contribute up to 8 kcal/mol. An extrapolation scheme for estimating the reaction barrier that takes into account effects of cluster size, basis set quality, and electron correlation has been proposed. The regioselectivity and the chain length were discussed. Keywords ZSM-5 zeolite Á Proton exchange Á Density functional theory Á Activation barrier Dedicated to Professor Marco Antonio Chaer Nascimento and published as part of the special collection of articles celebrating his 65th birthday.
Molecular simulations using density functional theory (DFT/PBE and DFT/tight-binding (DFTB)) have... more Molecular simulations using density functional theory (DFT/PBE and DFT/tight-binding (DFTB)) have been performed to study wetting processes of model nanopore segments in humic substances (HS). A complex of two poly (acrylic acid) trimers (trimer complex, TC) ...
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