The aim of the study was to analyse where different organic molecules situated themselves in relation to the water surface of a water microdroplet and use the resulting data to compare three different forcefields in the simulation package GROMACS. The forcefields used were: General AMBER forcefield (GAFF), Optimized potentials for liquid simulations - all atoms (OPLS-AA), and CHARMM general force field (CGenFF). A library of 146 molecules were simulated using molecular dynamics. Out of the 146 molecules only 65 resulted in useful data for the comparison of the forcefields. The molecules were placed in the centre of a water microdroplet and their movements were simulated for a duration of 1 ns. The trajectories and positions of the molecules were stored and from each simulation a density profile was generated, showing where the molecules situated themselves. The distance from the peak of the density profile to the water surface was calculated and compared between the different forcefields. To analyse the data further some of the molecules were divided into subsets based on their functional groups to see if any trends were visible. Although inconclusive, the data suggested that different forcefields were more or less agreeable depending on the functional group of the molecules, for example OPLS-AA differed from CGenFF and GAFF in the case of alcohols.

A majority of research within the field of energetic materials have been centered around the stable crystalline phase, whilst there has been less about the amorphous phase and the implications of these types of material. In this study, Molecular Dynamics simulations with the General Amber Force Field (GAFF) is used to predict fundamental properties of the nitramine explosives HMX and CL-20 in the amorphous phase. Amorphous structures are obtained by compressing a molecular gas to 4 GPa followed by relaxation and equilibration. The simulations indicate that the amorphous phases of HMX and CL-20 have lower densities than the corresponding crystal phases, 12.7% and 7.3% respectively. Both HMX and CL-20 was found to compress more easily when subject to external pressure, the difference was most significant for HMX.As a second part of this study an amorphous composition of CL-20/HMX/Polyvinylacetate(PVAc) (50/45/5 -wt%) was studied. This was obtained by compressing a molecular gas to varying pressures followed by relaxation and equilibration. Results indicate that the simulated density around 1.64 [g/cm3 ] fall close to experimental observations of 1.7 [g/cm3 ]. The density was observed to not vary significantly for pressures higher than 0.4 [GP a] in accordance to experimental data.

L’avancée des infrastructures informatiques a permis l’émergence de la modélisation moléculaire. À cet effet, une multitude de modèles mathématiques sont aujourd’hui disponibles pour simuler différents systèmes chimiques. À l’aide de la modélisation moléculaire, différents types d’interactions chimiques ont été observés. À partir des systèmes les plus simples permettant l’utilisation de modèles quantiques rigoureux, une série d’approximations a été considérée pour rendre envisageable la simulation de systèmes moléculaires de plus en plus complexes. En premier lieu, la théorie de la fonctionnelle de densité dépendante du temps a été utilisée pour simuler les énergies d’excitation de molécules photoactives. De manière similaire, la DFT indépendante du temps a permis la simulation du pont hydrogène intramoléculaire de structures analogues au 1,3,5-triazapentadiène et la rationalisation de la stabilité des états de transition. Par la suite, la dynamique moléculaire et la mécanique moléculaire ont permis de simuler les interactions d’un trimère d’acide cholique et d’un pyrène dans différents solvants. Cette même méthodologie a été utilisée pour simuler les interactions d’un rotaxane-parapluie à l’interface d’un système biphasique. Finalement, l’arrimage moléculaire et les fonctions de score ont été utilisés pour simuler les interactions intermoléculaires entre une protéine et des milliers de candidats moléculaires. Les résultats ont permis de mettre en place une stratégie de développement d’un nouvel inhibiteur enzymatique. / The evolution of computer systems has led to the emergence of molecular modeling. To this end, a variety of mathematical models are now available to simulate various chemical systems. Using molecular modeling, different types of chemical interactions were observed. From the simplest systems allowing the use of rigorous quantum models, a series of approximations were considered in order to make possible the simulation of increasingly complex molecular systems. First, time-dependent density fonctional theory has been used to simulate the excitation energies of photoactive molecules. Similarly, time-independent DFT has enabled the simulation of intramolecular hydrogen bonding in the 1,3,5-triazapentadiene system and the rationalization of the stability of the transition states. Subsequently, molecular dynamics and molecular mechanics were used to simulate the interactions of a trimer of cholic acid with a pyrene in different solvents. This methodology was then used to simulate the interactions of an umbrella-rotaxane at the interface of a biphasic system. Finally, molecular docking and the concept of scoring functions were used to simulate the intermolecular interactions between a protein molecule and thousands of potential ligands. The results were then used to create a strategy for the development of a new enzyme inhibitor.

L’avancée des infrastructures informatiques a permis l’émergence de la modélisation moléculaire. À cet effet, une multitude de modèles mathématiques sont aujourd’hui disponibles pour simuler différents systèmes chimiques. À l’aide de la modélisation moléculaire, différents types d’interactions chimiques ont été observés. À partir des systèmes les plus simples permettant l’utilisation de modèles quantiques rigoureux, une série d’approximations a été considérée pour rendre envisageable la simulation de systèmes moléculaires de plus en plus complexes. En premier lieu, la théorie de la fonctionnelle de densité dépendante du temps a été utilisée pour simuler les énergies d’excitation de molécules photoactives. De manière similaire, la DFT indépendante du temps a permis la simulation du pont hydrogène intramoléculaire de structures analogues au 1,3,5-triazapentadiène et la rationalisation de la stabilité des états de transition. Par la suite, la dynamique moléculaire et la mécanique moléculaire ont permis de simuler les interactions d’un trimère d’acide cholique et d’un pyrène dans différents solvants. Cette même méthodologie a été utilisée pour simuler les interactions d’un rotaxane-parapluie à l’interface d’un système biphasique. Finalement, l’arrimage moléculaire et les fonctions de score ont été utilisés pour simuler les interactions intermoléculaires entre une protéine et des milliers de candidats moléculaires. Les résultats ont permis de mettre en place une stratégie de développement d’un nouvel inhibiteur enzymatique. / The evolution of computer systems has led to the emergence of molecular modeling. To this end, a variety of mathematical models are now available to simulate various chemical systems. Using molecular modeling, different types of chemical interactions were observed. From the simplest systems allowing the use of rigorous quantum models, a series of approximations were considered in order to make possible the simulation of increasingly complex molecular systems. First, time-dependent density fonctional theory has been used to simulate the excitation energies of photoactive molecules. Similarly, time-independent DFT has enabled the simulation of intramolecular hydrogen bonding in the 1,3,5-triazapentadiene system and the rationalization of the stability of the transition states. Subsequently, molecular dynamics and molecular mechanics were used to simulate the interactions of a trimer of cholic acid with a pyrene in different solvents. This methodology was then used to simulate the interactions of an umbrella-rotaxane at the interface of a biphasic system. Finally, molecular docking and the concept of scoring functions were used to simulate the intermolecular interactions between a protein molecule and thousands of potential ligands. The results were then used to create a strategy for the development of a new enzyme inhibitor.