magistrsko delo
Dimitra Škrekovski (Author), Barbara Hribar (Mentor), Matija Strlič (Thesis defence commission member), Tomaž Urbič (Thesis defence commission member)

Abstract

Polielektroliti so skupina linearnih polimerov, katerih monomerne enote vsebujejo naboj. Običajno gre za ionizirajoče skupine, ki v vodnih raztopinah disociirajo na več-valentni poliion in nasprotno nabite protiione. Ioneni so vrsta polielektrolitov, katerih glavno verigo sestavljajo različno dolgi nizi metilenskih skupin, ločeni s pozitivno nabitimi kvarternimi dušikovimi atomi. Označujemo jih kot x,y-ionene, kjer x in y predstavljata število metilenskih skupin v monomerni enoti (poznamo npr. 3,3-, 4,5-, 6,6-, 9,12-ionene). S povečevanjem števila metilenskih skupin med zaporednimi duši-kovimi atom se gostota naboja na ionenu manjša, hidrofobnost pa povečuje. Cilj magi-strskega dela je bil določitev povprečne strukture raztopin 3,3- oz. 6,6-ionena s halo-genidnimi protiioni (F$^-$ oz. Br$^-$) s pomočjo molekulske dinamike. Lastnosti takšnih raz-topin so odvisne od gostote naboja na ionenu in vrste protiionov. Slednje imenujemo iono-specifični vplivi. Vrsta protiiona določa ali se bo le-ta zaradi ugodnih interakcij vezal na nabito skupino polielektrolita ali pa bo ostal prosto gibljiv v raztopini. Iono-specifični vplivi so izrednega pomena, saj sodelujejo pri veliki večini življensko po-membnih bioloških procesov, kot je membranski transport, osmotska regulacija, en-cimska aktivnost, adsorpcija, vplivajo pa tudi na strukturo in funkcijo proteinov, fosfo-lipidov, nukleinskih kislin in polisaharidov. S spreminjanjem gostote naboja na ionenu in vrste protiionov, sem preučila preplet zgoraj naštetih vplivov na prostorsko razpo-reditev protiionov in vodnih molekul v neposredni bližini ionena. Molekulska dinamika je ena izmed najpogosteje uporabljenih vrst računalniških simu-lacij. Simulacije v kemiji predstavljajo uporabno orodje za raziskovanje strukturnih, termodinamskih, dinamičnih in transportnih lastnosti sistema, reakcijskih mehani-zmov in karakteristik materialov. Prednost računalniških simulacij je, da z visoko stopnjo zanesljivosti podajo vpogled v dogajanje na atomistični skali, ki je zaradi veli-kega števila delcev v realnem sistemu nedosegljivo eksperimentu. V prvem delu magistrske naloge sem z lastnim programom izvedla Monte Carlo simulacijo Lennard-Jonesovega fluida, plina argona. Ta isti sistem sem simulirala tudi z molekulsko dinamiko v programu GROMACS. Z ujemanjem rezultatov obeh vrst si-mulacij (termodinamske spremenljivke, parska porazdelitvena funkcija), sem potrdila, da so rezultati neodvisni od izbire simulacijske metode. Osrednji del magistrskega dela so predstavljale simulacije raztopin polielektrolitov. Z molekulsko dinamiko sem v GROMACS-u simulirala štiri različne sisteme; raztopino 3,3- oz. 6,6-ionena s F$^-$ oz. Br$^-$ protiioni v vodi. Za atomistično obravnavo vseh delcev sistema, sem uporabila OPLS/AA polje sil, vodo pa sem predstavila s SPC/E mode-lom. 10-merni molekuli 3,3- in 6,6-ionena sem zgradila in geometrijsko optimizirala s programom Spartan, vhodno topologijo pa sem pripravila s serverjem TTPMKTOP, ki deluje v sklopu izbranega polja sil. Naboj (+1) sem asignirala izključno na dušikove atome, ostalim atomom v molekuli ionena pa sem pripisala naboj 0. S tem sem prido-bila dober vpogled v strukturo raztopine ob ionenu v odvisnosti od gostote naboja. Iz simulacijskih trajektorij sem izračunala parsko porazdelitveno funkcijo med različni-mi domenami sistema. Z ločeno obravnavo vsakega izmed strukturnih fragmenotov ionena sem določila orientacijo in razporeditev vodnih molekul ter protiionov ob po-sameznem delu verige. Iz porazdelitvenih funkcij med protiioni in kisikom oz. vodi-kom iz vode sem določila velikost radija hidratacije in orientacijo vodnih molekul v prvi hidratacijski lupini protiiona. S sočasnim upoštevanjem vseh porazdelitvenih funkcij sem določila podrobno strukturo povprečnih stanj, ki jih v takšnih raztopinah lahko opazimo v ravnotežju. Ugotovila sem, da imajo bromidni ioni razrahljano hidra-tacijsko lupino, s katere lahko sprostijo nekaj vode in se s prostim mestom kondenzira-jo na ionen. Fluoridni ioni imajo močno vezano in kompaktno hidratacijsko lupino, ki ob približevanju k ionenu ostane cela. Pokazala sem, da obe vrsti protiionov konden-zirata na 3,3-ionen, medtem ko na 6,6-ionenu kondenzirajo zgolj bromidni ioni. Za vsako izmed štirih raztopin (3,3-/6,6-ionen z F$^-$/Br$^-$ protiioni) sem izrisala podrobno skico najverjetnejših stanj raztopine ob verigi ionena v ravnotežju. Na skici sem upoš-tevala razmerja atomskih in ionskih radijev, molekulske geometrije udeleženih zvrsti in dimenzije SPC/E modela vode. Na koncu sem z Manningovo teorijo izračunala stopnjo kondenzacije za ionena obeh gostot naboja. Ugotovila sem, da Manningova kondenzacija protiionov na ionen poteče zgolj v primeru 3,3-ionena.

Keywords

ionen;iono-specifični vplivi;gostota naboja;simulacija Monte Carlo;parska porazdelitvena funkcija;magistrska dela;

Data

Language: Slovenian
Year of publishing:
Typology: 2.09 - Master's Thesis
Organization: UL FKKT - Faculty of Chemistry and Chemical Technology
Publisher: [D. Škrekovski]
UDC: 544.6.018.47-036.5:544.272(043.2)
COBISS: 193903619 Link will open in a new window
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Downloads: 7
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Other data

Secondary language: English
Secondary title: The effect of charge-density on the distribution of counter-ions in aqueous solutions of ionenes - computer simulation
Secondary abstract: Polyelectrolytes are linear polymers in which monomer units carry a charge. These charges usually originate from ionizing groups which in aqueous solutions dissociate into multivalent polyion and oppositely charged counter-ions. Ionenes are polyelectro-lytes consisting of hydrophobic methylene strings separated by positively charged qua-ternary nitrogen atoms. They are referred to as x,y-ionenes, where x and y represent the number of methylene groups between adjacent nitrogens (we know e.g. 3,3-, 4,5-, 6,6-, 9,12-ionenes). As the number of methylene groups between positively charged nitro-gens increases, charge-density of ionene decreases and hydrophobicity increases. The aim of this master's thesis was to determine the average structure of 3,3-/6,6-ionene solutions with added halogenide counter-ions (F$^-$ and Br$^-$) with molecular dynamics. The properties of such solutions depend on the charge-density of the ionene and on the type of counter-ions. The latter is known as ion-specific effects. The type of counter-ions determines whether they bind to the charged groups on the ionene due to favoura-ble interactions or remain mobile in the solution. Ion-specific effects are extremely important, as they occur in majority of vital biological processes, e.g., in membrane transport, osmotic regulation, enzymatic activity regulation, adsorption. They also affect the structure and function of proteins, phospholipids, nucleic acids, and polysac-charides. By varying the charge-density of the ionene and the type of added counter-ions we studied the interplay of both effects on the spatial distribution of counter-ions and water molecules around the ionene. Molecular dynamics is one of the most frequently used types of computer simulations. Simulations in chemistry represent a useful tool for determining the structural, ther-modynamic, dynamic and transport properties of a system, reaction mechanisms and material characteristics. The advantage of simulations is the insight they give us into the events happening at atomic scale while still possessing a high degree of reliability. Such small scales are not accessible to experiments due to high number of particles that make up real matter. In the first part of my master's thesis, we performed Monte Carlo simulations of Len-nard-Jones fluid, gaseous argon, using our own programme. The same system was simulated by molecular dynamic with GROMACS software. Matching results (ther-modynamic variables, pair distribution functions) of both types of simulation con-firmed that the simulation outcome doesn’t depend on the method used to obtain it. The main part of our work were simulations of polyelectrolyte solutions. Molecular dynamics simulations of four different systems; aqueous solutions of 3,3- or 6,6-ionene with added F$^-$ or Br$^-$ counter-ions, were performed in GROMACS. OPLS/AA force-field was applied for atomistic treatment of our system. SPC/E water model was used. 10-meres of 3,3- and 6,6-ionene were built and geometrically optimized using Spartan software. Topology was generated by TTPMKTOP server. The charge (+1) was as-signed to the nitrogen atoms exclusively while all the other ionene atoms remained electrically neutral. Pair distribution functions (RDF) between various sites were ob-tained from simulation trajectories. For this purpose, ionene was divided into its con-sisting fragments and each type was treated as an individual group for RDF calcula-tions. This way a detailed insight into orientation and arrangement of water and coun-ter-ions around different parts of ionene molecule was obtained. Radius of hydration and orientation of water molecules in the first hydration shell of counter-ions was de-termined by counter-ion-water oxygen/hydrogen distribution functions. By simultane-ously taking in account all the results the average states of these solutions at equilibri-um were found. We proved that bromides tend to have weakly bound hydration shells from which they lose some of the water molecules upon condensation on ionene chain. Fluorides on the other hand possess tight and compact hydration shell which they al-ways keep intact. We showed that both types of counter-ions condense on 3,3-ionene while the condensation on 6,6-ionene happens only with bromide ions. For each of the four solutions (3,3-/6,6-ionene with F$^-$/Br$^-$ counter-ions) a detailed sketch of the aver-age states at equilibrium was made taking in account the appropriate atomic and ionic radii, molecular geometry of the species involved and SPC/E water model dimensions. In the end Manning’s degree of condensation for both types of ionenes was calculated. We determined that Manning’s counter-ion condensation happens only in the case of 3,3-ionene.
Secondary keywords: ionene;ion-specific effects;charge-density;Monte Carlo simulation;molecular dynamics;pair distribution function;Polielektroliti;Molekularna dinamika;Univerzitetna in visokošolska dela;
Type (COBISS): Master's thesis/paper
Study programme: 1000375
Embargo end date (OpenAIRE): 1970-01-01
Thesis comment: Univ. v Ljubljani, Fak. za kemijo in kemijsko tehnologijo, smer Kemija
Pages: 1 spletni vir (1 datoteka PDF ( 86 str.))
ID: 23502172