Molekulární simulace ve strukturní analýze interkalátů

The samples of hydrotalcite intercalated with pyrenetetrasulphonate acid were obtained. Their structure cannot be precisely determined by the analysis of X-ray data. The amount of water in the interlayer space and the structure of the samples differed considerably in dependence on humidity. Convenient procedures and minimization strategy were established on the base of X-ray data in the molecular mechanic and the molecular dynamic simulations. A procedure for using of the supramol software was made. This software enables deterministic searching of conformational space. Initial models from supramol were minimized in the Cerius2 software using the Universal force field and then they were eventually optimized by the molecular dynamics. The arrangement of molecules of pyrenetetrasulphonate acid and water was determined in the interlayer space of hydrotalcite for three different samples with different interlayer distances: The sample 1 prepared by RH = 0%: 9.83A; the sample 2 prepared by RH = 84%: 13.63A; the sample 3 prepared RH = 40%-50%: 11.74A a 12.81A. The results of these structures proved a large variability of the arrangement of the molecules in the interlayer space. The sample No. 3 seems to be unstable.Interkalací pyrentetrasulfonové kyseliny do hydrotalcitových vrstev byly získány vzorky, jejichž struktura se analýzou difraktogramu nedá jednoznačně určit. V závislosti na relativní vlhkosti se značně lišilo množství mezivrstevné vody a struktura vzorku. Pro vyřešení struktur byly vytvořeny vhodné postupy a minimalizační strategie v molekulárně mechanických a molekulárně dynamických simulacích, které byly založeny na experimentálních výsledcích z rtg. difrakce. Pro nalezení vhodných iniciálních modelů byl vytvořen postup k použití programu supramol, určeného k deterministickému procházení prostoru možných konformací struktury. Iniciální modely z programu supramol byly následně minimalizovány v programu Cerius2 v silovém poli Universal a případně optimalizovány molekulární dynamikou. Bylo spočítáno uspořádání pyrentetrasulfonových kyselin a vody v mezivrství hydrotalcitu pro tři různé vzorky s následujícími mezirovinnými vzdálenostmi: Vzorek 1 připravený při RH = 0%: 9,83A; vzorek 2 při RH = 84%: 13,63A; vzorek 3 při RH = 40%-50%: 11,74A a 12,81A. Výsledky u těchto struktur prokázaly značnou variabilitu uspořádání molekul v mezivrství. Vzorek 3 se jeví jako neustálený.Katedra chemické fyziky a optikyDepartment of Chemical Physics and OpticsMatematicko-fyzikální fakultaFaculty of Mathematics and Physic

Molecular simulations in structure analysis of intercalates

The samples of hydrotalcite intercalated with pyrenetetrasulphonate acid were obtained. Their structure cannot be precisely determined by the analysis of X-ray data. The amount of water in the interlayer space and the structure of the samples differed considerably in dependence on humidity. Convenient procedures and minimization strategy were established on the base of X-ray data in the molecular mechanic and the molecular dynamic simulations. A procedure for using of the supramol software was made. This software enables deterministic searching of conformational space. Initial models from supramol were minimized in the Cerius2 software using the Universal force field and then they were eventually optimized by the molecular dynamics. The arrangement of molecules of pyrenetetrasulphonate acid and water was determined in the interlayer space of hydrotalcite for three different samples with different interlayer distances: The sample 1 prepared by RH = 0%: 9.83A; the sample 2 prepared by RH = 84%: 13.63A; the sample 3 prepared RH = 40%-50%: 11.74A a 12.81A. The results of these structures proved a large variability of the arrangement of the molecules in the interlayer space. The sample No. 3 seems to be unstable.Interkalací pyrentetrasulfonové kyseliny do hydrotalcitových vrstev byly získány vzorky, jejichž struktura se analýzou difraktogramu nedá jednoznačně určit. V závislosti na relativní vlhkosti se značně lišilo množství mezivrstevné vody a struktura vzorku. Pro vyřešení struktur byly vytvořeny vhodné postupy a minimalizační strategie v molekulárně mechanických a molekulárně dynamických simulacích, které byly založeny na experimentálních výsledcích z rtg. difrakce. Pro nalezení vhodných iniciálních modelů byl vytvořen postup k použití programu supramol, určeného k deterministickému procházení prostoru možných konformací struktury. Iniciální modely z programu supramol byly následně minimalizovány v programu Cerius2 v silovém poli Universal a případně optimalizovány molekulární dynamikou. Bylo spočítáno uspořádání pyrentetrasulfonových kyselin a vody v mezivrství hydrotalcitu pro tři různé vzorky s následujícími mezirovinnými vzdálenostmi: Vzorek 1 připravený při RH = 0%: 9,83A; vzorek 2 při RH = 84%: 13,63A; vzorek 3 při RH = 40%-50%: 11,74A a 12,81A. Výsledky u těchto struktur prokázaly značnou variabilitu uspořádání molekul v mezivrství. Vzorek 3 se jeví jako neustálený.Department of Chemical Physics and OpticsKatedra chemické fyziky a optikyFaculty of Mathematics and PhysicsMatematicko-fyzikální fakult

Application of Molecular Simulations in Complex Structural Analysis of Layered Materials

Title: Application of Molecular Simulations in Complex Structural Analysis of Layered Materials Author: RNDr. Marek Veteška Department: Department of Chemical Physics and Optics Supervisor: RNDr. Miroslav Pospíšil, Ph.D., Dept. of Chemical Physics and Optics Abstract: Techniques of molecular simulations were used together with experimental measurements (X-ray diffraction, thermogravimetry, infrared spectroscopy, elemental analysis and others) to clarify the structure properties of various types of layered materials. The structure of Zn-Al-layered double hydroxide intercalated by pyrenetetra- sulfonate acid was solved. Depending on the relative humidity, the samples showed different arrangements with three planes of water molecules and with either one or two planes of pyrenetetrasulfonate anions. At the same time considerable variability of anions arrangement was demonstrated. The adsorption behavior of natural montmorillonite and montmorillonite modified by tetramethylammonium cations in relation to aniline and phe- nol was explored. Adsorption features differed according to both the type of adsorbed molecules and the type of adsorbents. An important role was played by the plane of water molecules right above the surface which medi- ated adsorption of anilines. The water plane area was reduced by..

Molecular simulations in structure analysis of intercalates

The samples of hydrotalcite intercalated with pyrenetetrasulphonate acid were obtained. Their structure cannot be precisely determined by the analysis of X-ray data. The amount of water in the interlayer space and the structure of the samples differed considerably in dependence on humidity. Convenient procedures and minimization strategy were established on the base of X-ray data in the molecular mechanic and the molecular dynamic simulations. A procedure for using of the supramol software was made. This software enables deterministic searching of conformational space. Initial models from supramol were minimized in the Cerius2 software using the Universal force field and then they were eventually optimized by the molecular dynamics. The arrangement of molecules of pyrenetetrasulphonate acid and water was determined in the interlayer space of hydrotalcite for three different samples with different interlayer distances: The sample 1 prepared by RH = 0%: 9.83A; the sample 2 prepared by RH = 84%: 13.63A; the sample 3 prepared RH = 40%-50%: 11.74A a 12.81A. The results of these structures proved a large variability of the arrangement of the molecules in the interlayer space. The sample No. 3 seems to be unstable

Molecular simulations in structure analysis of intercalates

The samples of hydrotalcite intercalated with pyrenetetrasulphonate acid were obtained. Their structure cannot be precisely determined by the analysis of X-ray data. The amount of water in the interlayer space and the structure of the samples differed considerably in dependence on humidity. Convenient procedures and minimization strategy were established on the base of X-ray data in the molecular mechanic and the molecular dynamic simulations. A procedure for using of the supramol software was made. This software enables deterministic searching of conformational space. Initial models from supramol were minimized in the Cerius2 software using the Universal force field and then they were eventually optimized by the molecular dynamics. The arrangement of molecules of pyrenetetrasulphonate acid and water was determined in the interlayer space of hydrotalcite for three different samples with different interlayer distances: The sample 1 prepared by RH = 0%: 9.83A; the sample 2 prepared by RH = 84%: 13.63A; the sample 3 prepared RH = 40%-50%: 11.74A a 12.81A. The results of these structures proved a large variability of the arrangement of the molecules in the interlayer space. The sample No. 3 seems to be unstable

Molecular simulations in structure analysis of intercalates

The samples of hydrotalcite intercalated with pyrenetetrasulphonate acid were obtained. Their structure cannot be precisely determined by the analysis of X-ray data. The amount of water in the interlayer space and the structure of the samples differed considerably in dependence on humidity. Convenient procedures and minimization strategy were established on the base of X-ray data in the molecular mechanic and the molecular dynamic simulations. A procedure for using of the supramol software was made. This software enables deterministic searching of conformational space. Initial models from supramol were minimized in the Cerius2 software using the Universal force field and then they were eventually optimized by the molecular dynamics. The arrangement of molecules of pyrenetetrasulphonate acid and water was determined in the interlayer space of hydrotalcite for three different samples with different interlayer distances: The sample 1 prepared by RH = 0%: 9.83A; the sample 2 prepared by RH = 84%: 13.63A; the sample 3 prepared RH = 40%-50%: 11.74A a 12.81A. The results of these structures proved a large variability of the arrangement of the molecules in the interlayer space. The sample No. 3 seems to be unstable

Adsorption of phenol and aniline on natural and organically modified montmorillonite: experiment and molecular modelling

Natural and intercalated Wyoming montmorillonite (MMT) with the tetramethylammonium (TMA) cations were used for the adsorption of phenol and aniline. Laboratory experiments characterised by adsorption isotherms were compared with the results of molecular modelling simulations. Aniline adsorbed itself strongly on MMT; while using the TMA intercalates (TMA-MMT), its adsorption decreased. On the contrary, the adsorption of phenol on TMA-MMT was moderately higher than on the MMT surface. The MMT surface models were described by empirical force field used in molecular mechanics and dynamics. The Burchart–Universal force field was used in the Cerius2 modelling environment. The modelling results revealed the important role of water forming a moderately concentrated layer on the pure MMT surface. Water molecules enable the adsorption of aniline on MMT and, on the contrary, repel phenol molecules from MMT. In the case of TMA-MMT, lower amount of water near a silicate layer caused decrease in the aniline adsorption and, on the contrary, increase in the phenol adsorption.371197496