Computer simulations of model fluids

Alkoholi so zanimive organske spojine, ki se pogosto uporabljajo kot reaktanti ali topila pri reakcijah v kemijskih procesih, podobno pa jih lahko v različnih vlogah zasledimo tudi pri številnih bioloških procesih. Zato so pogosto predmet različnih znanstvenih raziskav. V tem diplomskem delu smo se osredotočili na izomerne spojine heksan-1-ol, heksan-2-ol, heksan-3-ol in 3,3-dimetilbutanol, naš cilj pa je bil s pomočjo računalniških simulacij molekulske dinamike in izbranega modela na osnovi polja sil TraPPE–UA raziskati njihove lastnosti na molekularnem nivoju. Računalniške simulacije smo pričeli z energijsko minimizacijo sistema, sledilo je uravnoteženje v ansamblu NVT, uravnoteženje v ansamblu NPT, na koncu pa še izvedba produkcijskega koraka simulacije, ki je priskrbel osnovne rezultate simulacije. S primerjavo rezultatov simulacij za nekatere termodinamske lastnosti modelnega sistema z eksperimentalnimi rezultati alkohola iz literature, smo preučili, kako dobro izbran model opiše raziskovani sistem. Ugotovili smo, da je uporabljeno polje sil TraPPE–UA nekoliko boljše opisalo primarne alkohole kot sekundarne alkohole. Zanimale so nas tudi strukturne lastnosti alkoholov, zato smo iz rezultatov simulacije izračunali radialne in prostorske porazdelitvene funkcije, na njihovi osnovi pa še povprečno število vodikovih vezi na hidroksilno skupino alkohola. Izkazalo se je, da lahko v povprečju največ vodikovih vezi tvorijo molekule primarnih alkoholov. Porazdelitev intramolekularnih razdalj od atoma C1 do C4 pri različnih modelnih alkoholih je zanimivo pokazala tudi to, da je rotacija terc-butilne skupine okoli vezi med atomoma C2 in C3 v modelu očitno zelo omejena.Alcohols are interesting organic compounds that are often used as reactants or solvents in chemical processes, but they also play various roles in many biological processes. As such, they are often the subject of various researches. In this work, we focused on hexan-1-ol, hexan-2-ol, hexan-3-ol, and 3,3-dimethylbutanol. Our goal was to investigate their properties at the molecular level using the computer simulations of molecular dynamics and a selected model based on the TraPPE–UA force field. We started the computer simulations with the energy minimization of the system, followed by the equilibration in the NVT ensemble, the equilibration in the NPT ensemble, and finished with the production step that provided the basic simulation results. By comparing the simulation results for some thermodynamic properties of the simulated system with the experimental results of alcohol from the literature, we investigated how well the chosen model describes the studied system. We found that the TraPPE–UA force field describes the studied primary alcohols slightly better than the secondary alcohols. Since we were also interested in the structural properties of the studied alcohols, we calculated the radial and spatial distribution functions from the simulation results and based on them the average number of hydrogen bonds per hydroxyl group of the alcohol. It turned out that the molecules of primary alcohols can form the most hydrogen bonds on average. Interestingly, the distribution of intramolecular distances from the C1 to the C4 atom in different model alcohols also showed that the rotation of the tert-butyl group around the bond between the C2 and C3 atoms in the model is apparently very limited