Yes / A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca2+, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca2+ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22*, substantially over-estimates the binding strength between Ca2+ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium–acetate and calcium–malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard–Jones interaction between Ca2+ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate–Ca2+ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22* parameter set.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / The force fields used in computer simulations play an important role in describing a particular system. In order to estimate the accuracy of a force field, physical or thermodynamic properties are usually compared with simulation results. Recently, we have been developing a force field which is called the Kirkwood-Buff Force Field (KBFF). This force field is established by transforming experimental data into Kirkwood-Buff (KB) integrals and then attempting to reproduce those KBIs with molecular dynamic (MD) simulations. Here we investigate a variety of intermolecular interactions in aqueous solutions through KB theory and molecular simulations. First, we describe a force field for the simulation of alkali halide aqueous solutions. These models are developed specifically to reproduce the experimentally determined Kirkwood-Buff integrals and solution activities as a function of molality. Additionally, other experimentally known properties including ion diffusion constants, relative permittivities, the densities and heats of mixing are reproduced by these models. Second, In an effort to understand the interactions which occur between amino acids in solution we have developed new force fields for simple amino acids and their analogs including glycine, betaine, β-alanine, dl-alanine, NH4Cl, NH4Br, N(CH3)4Cl, N(CH3)4Br, CH3NH3Cl, and CH3COONa. The new force fields reproduce the experimental Kirkwood-Buff integrals which describe the relative distribution of all the species in a solution mixture. Furthermore, it is shown that these simple amino acids can be understood in terms of the interactions of their functional groups and that, to a very good approximation, the transferability and additivity usually assumed in the development of biomolecular force fields appear to hold true. Third, an analysis of the effect of a cosolvent on the association of a solute in solution is presented by using the Kirkwood-Buff theory of solutions. The derived expressions provide a foundation for the investigation of cosolvent effects on molecular and biomolecular equilibria, including protein association, aggregation, and cellular crowding. Finally, in an effort to understand peptide aggregation at the atomic level we have performed simulations of polyglycine ((gly)n) using our recently developed force fields. Experimentally, the association of glycine polypeptides increases with n. Our force fields reproduce this behavior, and we investigated the reasons behind this trend. In addition to studying closed ensembles, we also simulate these systems in a semi-open ensemble that was designed to mimic cellular environments typically open to water, using a simple direct approach. The differences between the two ensembles are investigated and compared with our recent theoretical descriptions of aggregating systems using Kirkwood-Buff theory.

Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated. A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems. A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs.  In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted. The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.

The detrimental effects of rising CO₂ levels on the global climate have made carbon abatement technologies one of the most widely researched areas of recent times. In this thesis, we first present a techno-economic analysis of a novel approach to directly capture CO₂ from air (Air Capture) using highly selective adsorbents. Our process modeling calculations suggest that the monetary cost of Air Capture can be reduced significantly by identifying adsorbents that have high capacities and optimum heats of adsorption. The search for the best performing material is not limited to Air Capture, but is generally applicable for any adsorption-based separation. Recently, a new class of nanoporous materials, Metal-Organic Frameworks (MOFs), have been widely studied using both experimental and computational techniques. In this thesis, we use a combined quantum chemistry and classical simulations approach to predict macroscopic properties of MOFs. Specifically, we describe a systematic procedure for developing classical force fields that accurately represent hydrocarbon interactions with the MIL-series of MOFs using Density Functional Theory (DFT) calculations. We show that this force field development technique is easily extended for screening a large number of complex open metal site MOFs for various olefin/paraffin separations. Finally, we demonstrate the capability of DFT for predicting MOF topologies by studying the effect of ligand functionalization during CuBTC synthesis. This thesis highlights the versatility and opportunities of using multiscale modeling approach that combines process modeling, classical simulations and quantum chemistry calculations to study nanoporous materials for adsorptive separations.

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Ce travail théorique vise à étudier, via les méthodes Premiers Principes, les propriétés des complexes de métaux de transitions, left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-} pour un usage en batterie. Pour cette étude ab-initio, les composés mono et bi-nucléaires ont été retenus. La pertinance de notre modélisation a été validée sur les composés mononucléaires. Nous nous sommes interessé au complexes de Fe, Ru et Cu pour lesquels une validation expérimentale était possible. Notre étude a principalement consisté à faire varier les degrés de liberté que nous possédons pour optimiser le voltage et la cinétique de chargement des batteries. Pour cela, nous avons fait varier le TM = Fe, Ru, et Cu, la nature des contre-ions Ci^{-}=PF_{6}^{-}, TFSI^{-} et ClO_{4}^{-} en interaction avec le polymère lors du processus de charge, ainsi que la longeur de la chaîne alkyl qui sépare les deux monomers dans le cas des composés binucléaires. Le composé à base de Fe avec une chaîne -left(CH_{2}right)_{n=6}- a été retenu comme le meilleur candidat pour une application batterie. Le composé à base Ru montre un comportement proche de celui du Fe, quant-au complexe de Cu, il présente des changements de géométrie locale sous chargement trop importants, le rendant peu apte à conduire à une cinétique efficace. Cette étude nous a permis de déterminer que l'approximation PBE était le meilleur choix possible pour modéliser nos complexes dans les conditions de fonctionnement en batterie (dans le champ créé par les contre-ions) et que l'approximation PBE0, généralement utilisée dans la littérature, ne pouvait rendre compte de la physico-chimie de nos composés dans de telles conditions.De surcroît, nous avons dévelopé pour le complexe de Fe, un potentiel atomistique de type “Champ de forces” de manière à pouvoir aborder les aspects dynamiques impliquant de plus grandes tailles de boîte de simulation. Ici, nous modélisons une structure 3D, totalement réticulée à partir de nos monomères à base de Fe. Nous nous sommes servi de la base de donnés DFT que nous avions généré (énergies, géométries, état de spin et fréquences vibrationnelles calculées) pour ajuster les paramètres entrant dans l'écriture du modèle. La construction de la géométrie initiale du polymère 3D a nécessité l'écriture d'un code de calcul visant à produire un arrangement complétement réticulé et à assigner les charges effectives issues des calculs DFT. Ce modèle nous a permis de déterminer les coefficients de diffusion des contre-ions pour les états totalement chargé et non-chargé. Un calcul plus ambitieux vise à déterminer les chemins de diffusion des contre-ions lors d'un processus de chargement en considérant un seul centre de degré d'oxydation 3+ au centre du polymère 3D, pour lequel les centres actifs possèdent un degré d'oxidation 2+. Les contre-ions assurent la neutralité globale.Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modeling / Abstract Standard redox potentials for mono and bi-nuclear transition metal (TM) complexes left[Mleft(dmbpyright)_{3}right]^{n+}nCi^{-}, have been investigated using First Principles Calculation. Three metal centers are investigated: Fe, Ru, and Cu. Our modeling is validated on mono-nuclear compounds. This approach consists in determining the best small polymer (bi-nuclear) made out of these monomers for a battery application. For that, we varied the three available degrees of freedom i.e., the nature of the central TM atom (Fe, Ru, and Cu), counter-ions Ci=PF_{6}^{-}, TFSI^{-} and ClO_{4}^{-} in interaction with the polymer, and the alkyl chain -left(CH_{2}right)_{n}- of length n that connects both mono-nuclear in the bi-nuclear compound. The Iron compound with -left(CH_{2}right)_{n=6}- is found to be the best candidate. The left[Culeft(dmbpyright)_{2}right]^{n+}nCi^{-} complex shows too much structure deformation upon loading, making it less reliable for cathode material. Moreover, we studied two XC functional, PBE and PBE0 and found, for three complexes PBE approximation retains the ligand field picture whereas PBE0 functional induces an exaggerated and unexpected band dispersion by dissolving the ligand field picture expected for the octahedral environment of the TM in the studied complexes. These findings validate that hybrid functional for which it was designed to localize and cancel self-interaction error does not work for all system. More particularly, the PBE0 approximation fails to model the three complexes (Fe, Ru, and Cu) in functional conditions (in the field made by the counter-ions).Abstract Further, we have developed an atomistic potential relying on the Force Field scheme for the Iron complex in order to study the dynamical properties of this compound at larger simulation scale (3D reticulated polymerization made of our Fe complex monomers). We made an intensive use of our DFT data (energies, geometries, spin-state configurations and calculated vibrational properties) to develop the required parameters entering the model. Moreover, computational techniques (written python language) were developed specifically to create a 3D structure of transition metal complexes satisfying the condition to be fully reticulated. Bounding conditions had to be designed and a procedure aiming at fixing reliable and physical effective charges on each atom of the simulation cell (compatible with DFT results) were developed. Our first simulations have been attached to calculate the diffusion coefficients of the counter-ions in both the fully loaded and unloaded states. A more ambitious and realistic calculation aims at investigating the paths of the counter-ions when one single center starts to be loaded in an unloaded environment.Abstract Keyword: Polymer, Electrochemistry, Li-ion Battery, DFT, Force Field development, 3D structure, Atomistic modeling