70 research outputs found

    Understanding Gas and Energy Storage in Geological Formations with Molecular Simulations

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    Methane (CH4), the cleanest burning fossil fuel, has the potential to solve the energy crisis owing to the growing population and geopolitical tensions. Whilst highly calorific, realising its potential requires efficient storage solutions, which are safe and less energy-intensive during production and transportation. On the other hand, carbon dioxide (CO2), the by-product of human activities, exacerbates global heating driving climate change. CH4 is abundant in natural systems, in the form of gas hydrate and trapped gas within geological formations. The primary aim of this project was to learn how Nature could store such a large quantity of CH4 and how we can potentially extract and replace the in-place CH4 with atmospheric CO2, thereby reducing greenhouse gas emissions. We studied this question by applying molecular dynamics (MD) and Monte Carlo (MC) simulation techniques. Such techniques allow us to understand the behaviour of confined fluids, i.e., within the micropores of silica and kerogen matrices. Our simulations showed that CH4 hydrate in confinement could form under milder conditions than required, deviating from the typical methane-water phase diagram, complementing experimental observations. This research can contribute to artificial gas hydrate production via porous materials for gas storage. Besides that, the creation of 3D kerogen models via simulated annealing has enabled us to understand how maturity level affects the structural heterogeneity of the matrices and, ultimately CH4 diffusion. Immature and overmature kerogen types were identified to having fast CH4 diffusion. Subsequently, our proof-of-concept study demonstrated the feasibility of recovering CH4 via supercritical CO2 injection into kerogens. Insights from our study also explained why full recovery of CH4 is impossible. A pseudo-second-order rate law can predict the kinetics of such a process and the replacement quantity. A higher CO2 input required than the CH4 recovered highlights the possibility of achieving a net-zero future via geological CO2 sequestration

    Polarization effects at the surface of aqueous alkali halide solutions

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    The polarizability of ions, with its strong influence on their surface affinity, is one of the crucial pieces of the complex puzzle that determines the surface properties of electrolyte solutions. Here, we investigate the electrical and structural properties of alkali halide solutions at a concentration of about 1.3 M using molecular dynamics simulations of polarizable water and ions models. We show that capillary fluctuations have a dramatic impact on the sampled quantities and that without removing their smearing effect, it would be impossible to resolve the local structure of the interfacial region. This procedure allows us to investigate in detail the dependence of the permanent and induced dipoles on the distance from the interface. The enhanced resolution gives us access to the surface charges, estimated using the Gouy-Chapman theory, despite the Debye length being shorter than the amplitude of capillary fluctuations

    Applications of Molecular Dynamics simulations for biomolecular systems and improvements to density-based clustering in the analysis

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    Molecular Dynamics simulations provide a powerful tool to study biomolecular systems with atomistic detail. The key to better understand the function and behaviour of these molecules can often be found in their structural variability. Simulations can help to expose this information that is otherwise experimentally hard or impossible to attain. This work covers two application examples for which a sampling and a characterisation of the conformational ensemble could reveal the structural basis to answer a topical research question. For the fungal toxin phalloidin—a small bicyclic peptide—observed product ratios in different cyclisation reactions could be rationalised by assessing the conformational pre-organisation of precursor fragments. For the C-type lectin receptor langerin, conformational changes induced by different side-chain protonations could deliver an explanation of the pH-dependency in the protein’s calcium-binding. The investigations were accompanied by the continued development of a density-based clustering protocol into a respective software package, which is generally well applicable for the use case of extracting conformational states from Molecular Dynamics data

    Speeding-up Hybrid Functional based Ab Initio Molecular Dynamics using Multiple Time-stepping and Resonance Free Thermostat

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    Ab initio molecular dynamics (AIMD) based on density functional theory (DFT) has become a workhorse for studying the structure, dynamics, and reactions in condensed matter systems. Currently, AIMD simulations are primarily carried out at the level of generalized gradient approximation (GGA), which is at the 2nd rung of DFT-functionals in terms of accuracy. Hybrid DFT functionals which form the 4th rung in the accuracy ladder, are not commonly used in AIMD simulations as the computational cost involved is 100100 times or higher. To facilitate AIMD simulations with hybrid functionals, we propose here an approach that could speed up the calculations by ~30 times or more for systems with a few hundred of atoms. We demonstrate that, by achieving this significant speed up and making the compute time of hybrid functional based AIMD simulations at par with that of GGA functionals, we are able to study several complex condensed matter systems and model chemical reactions in solution with hybrid functionals that were earlier unthinkable to be performed.Comment: 45 pages, 9 figures, 5 table

    How molybdenum species cleave the phosphoester bond.

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    217 p.Metal species have a great impact on the biochemistry of living systems. It has been reported that polyoxomolybdates exhibit anti-tumor activity similar to that of commercial drugs. However, the mechanism by which these species are effective against cancer has been an elusive topic. It is believed that their activity is related to their interaction with phosphoester' containing biomolecules.Experimental studies have demonstrated that molybdenum species can cause cleavage in different model phosphoester molecules.However, the complex chemistry of molybdates has made these experimental studies difficult to interpret. We used computational methodologies to shed light on the phosphoesterase activity of molybdenum species in different reaction models. The study employed density functional theory to explore the mechanistic details of hydrolysis reactions of phosphate monoesters and diestersin the presence of different molybdenum species.The study results on the speciation of MoO2Cl2(DMF)2 supported the experimental findings that reported DMF release and Mo¿Clbond breakage. Two different NPP hydrolysis pathways were proposed depending on the complex concentration. Lower concentrations disfavoured the formation of polynuclear species, and the hydrolysis proceeded through less favourable mononuclear intermediates. With enough complex concentration, a nucleation process was favoured over the phosphate interaction. After theformation of dinuclear species, the incorporation of NPP and its consequent hydrolysis showed lower energetic barriers than theuncatalysed reaction. We also examined heptamolybdate as it was reported to hydrolyse NPP while its nuclearity decreased.Pentanuclear active species proposed by experimentals showed a higher activation barrier for its hydrolysis and cannot beconsidered as a catalyst. The study proposed a dinuclear compound resulting from heptamolybdate fragmentation as the catalytic species, which decreased the energetic barrier compared to the non¿catalysed reaction. With DNA and RNA models BNPP andHPNP, the calculations supported the experimental findings that heptamolybdate can hydrolyse phosphodiester molecules without fragmentation. With phosphate diesters, the hydrolysis proceeded through more compact mechanisms than with phosphatemonoesters, in which phosphorane structures are formed.The study revealed that the dinuclear species and the heptamolybdate cluster provide a structural motif that catalyses the hydrolysisof these phosphates. The molybdate structure generally augments the electrophilia of the phosphorous atom and can deprotonateand activate the nucleophile, favouring associative mechanisms. This information can aid in designing effective and non¿toxicphosphoesterases.DIP

    Studying the properties of molecular photoactive materials via the methods of computational chemistry

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    V této práci jsou nejprve rychle nastíněny principy teorie funkcionálu elektronové hustoty (DFT), spolu s praktickými metodami hledání nejníže energeticky postavených struktur organických molekul a predikování jejich spektroskopických a elektronických vlastností. Poté jsou prezentovány výsledky teoretické analýzy geometrie a elektronové struktury dvou druhů molekul v kombinaci s experimentálními výsledky. Nejprve jsou diskutovány alloxazin, lumazin a jejich deriváty, souhrnně nazývané flaviny, které reprezentují molekulární materiály. Naproti tomu, struktury na bázi polythiofenu reprezentují polymerní materiály. V případě flavinů byla nejprve nalezena nejlepší možná korelace teoretických absorpčních spekter s experimentálními na základě výpočtů se třemi různými bázovými soustavami v kombinaci s funkcionálem B3LYP. Dobrá shoda byla nalezena pomocí metod B3LYP/6-31+G** a B3LYP/aug-cc-PVDZ, které dosáhly korelačních koeficientů 0.95 a 0.96. Naproti tomu soustava def2SVP dosáhla pouze 0.94. V tomto kontextu se tak metoda B3LYP/6-31+G** jeví jako nejefektivnější vzhledem k náročnosti na výpočetní kapacitu. Měřením absorpčních spekter vybraných flavinů ve směsi dimethylsulfoxidu (DMSO) a vody byla získána spektra jednotlivých izomerů – alloxazinové a isoalloxazinové formy. Reakce těchto molekul na změny koncentrace DMSO a vody bude předmětem dalšího studia. U polythiofenů byly studovány optické a elektrické vlastnosti na modelových oktamerech, zatímco geometrie a konformace adamantylovaných substitutentů byly z důvodu vysoké výpočetní náročnosti modelovány na trimerových molekulách. Bylo zjištěno, že thiofenový řetězec s postranními methyladamantylovými skupinami vykazuje vyšši rigiditu než řetězec substituovaný ethyladamantylem, což bylo později potvrzeno krystalografickou analýzou a skenováním povrchu pomocí mikroskopie atomárních sil. Byly nalezeny krystalické struktury s parametry srovnatelnými s poly(3-hexylthiofenem) (P3HT). Na základě tohoto výzkumu byly navržený nové páteřní řetězce pro možnou syntézu, jako hlavní doporučení se zde jeví snížení počtu substituentů, aby adamantylový postranní řetězec byl přítomen pouze na každém druhém či třetím thiofenu. Zde prezentované molekuly jsou zajímavými kandidáty pro využití v optoelektronice, a teoretické predikce dosahují dobrou shodu s experimentem, přestože jejich srovnání není vždy triviální, jako je tomu například u postranních řetězců polythiofenu.In this work, the principles of theoretical density functional theory are briefly discussed first, together with the method of searching for lowest-energy structures of molecules and predicting the spectroscopic and electronic properties. Afterwards, the results of the theoretical analysis of the geometry and electronic structure of two types of molecules is presented, combined with experimental results. First, the alloxazine and lumazine, considered together as flavins, and their derivatives represent molecular materials, while adamantyl substituted polythiophenes represent polymer materials. With respect to the flavins, different basis sets, together with the B3LYP functional, were used to find the best possible fit to experimental absorption spectra. Here, the B3LYP/6-31+G** and B3LYP/aug-cc-PVDZ methods proved to have the best correlation, with correlation coefficients 0.95 and 0.96, respectively, while the def2SVP set reached 0.94. In this context, the B3LYP/6-31+G** method seems to be the most cost-efficient. By measuring the absorption spectra of selected flavins in a mixture of dimethylsulfoxide (DMSO) and water, the spectra of flavin isomers – the alloxazine and isoalloxazine form were gained. The response of these molecules to changes in the concentration of DMSO and water will be the object of further study. For the polythiophenes, the electronic and optical properties were theoretically investigated using model octamers, while the conformations of the adamantylated side chains were considered using trimer molecules, due to a high computational complexity. Here, the methyladamantyl thiophene was found to have a more rigid structure compared to the ethyladamantyl substituted chain, which was later confirmed via crystallographic analysis and atomic force microscopy scans. Crystal structures were confirmed to be present, with lattice parameters comparable to poly(3-hexylthiophene) (P3HT). Inspired by this research, different polymer backbones based on polythiophene were considered for future synthesis. The main recommendation here is to lower the amount of side substituents, so that only one in two or one in three thiophenes bear an adamantylated side chain. Overall, the molecules presented here are interesting candidates for future use in optoelectronics, and the theoretical predictions generally agree with experimental results, although the comparison with experiment is not always trivial, e.g., in the case of the polythiophene side chains.

    Molecular dynamics study of structure and reactions at the hydroxylated Mg(0001)/bulk water interface

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    A molecular level understanding of the aqueous Mg corrosion mechanism will be essential in developing improved alloys for battery electrodes, automobile parts, and biomedical implants. The structure and reactivity of the hydroxylated surface is expected to be key to the overall mechanism because (i) it is predicted to be the metastable surface state (rather than the bare surface) under a range of conditions and (ii) it provides a reasonable model for the outer corrosion film/water interface. We investigate the structure, interactions, and reactivity at the hydroxylated Mg(0001)/water interface using a combination of static Density Functional Theory calculations and second-generation Car–Parrinello ab initio molecular dynamics. We carry out detailed structural analyses into, among other properties, near-surface water orientations, favored adsorption sites, and near-surface hydrogen bonding behavior. Despite the short timescale (tens of ps) of our molecular dynamics run, we observe a cathodic water splitting event; the rapid timescale for this reaction is explained in terms of near-surface water structuring lowering the reaction barrier. Furthermore, we observe oxidation of an Mg surface atom to effectively generate a univalent Mg species (Mg+). Results are discussed in the context of understanding the Mg corrosion mechanism: For example, our results provide an explanation for the catalytic nature of the Mg corrosion film toward water splitting and a feasible mechanism for the generation of the univalent Mg species often proposed as a key intermediate

    Adsorption Kinetics and Phase Behavior of Particles Adsorbed at an Interface

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    The ability to predict the adsorption dynamic, phase behavior, and surface pressure of a monolayer of adsorbed particles in two-dimensional systems are key aspects of many current research areas. Examples include phase transitions in amphiphilic monolayers, emulsion stability due to particle adsorption at interfaces, and melting at an interface. In this thesis, a new approach for deriving the equation of state for a two-dimensional lattice gas is proposed, based on arguments similar to those used in the derivation of the Langmuir-Szyszkowski equation of state for localized adsorption. This work aims to predict the adsorption kinetics and phase behavior of a system composed of many hard-core particles based on kinetic arguments and the Gibbs adsorption isotherm. To that purpose, the random sequential adsorption with a surface diffusion model is used to samples the configuration of the system at different coverage. This configuration is used to calculate the thermodynamic properties of the system where many interesting collective phenomena are observed. The determination of phase behavior and, in particular, the nature of phase transitions in two-dimensional systems is often clouded by finite-size effects and by access to the appropriate thermodynamic regime. We address these issues using our new model. Insight into coexistence regions and phase transitions is obtained through direct visualization of the system at any fractional surface coverage via local bond orientation order. The analysis of the bond orientation correlation function for each individual configuration confirms that first-order phase transition occurs in a two-step liquid-hexatic-solid transition at high surface coverage. The next part of this work concentrates on reversible adsorption by introducing a desorption process into our model and varying the equilibrium rate constant as a control parameter. We find that an exact prediction of the temporal evolution of fractional surface coverage and the surface pressure dynamics of reversible adsorption can be achieved by the use of the blocking function of a system with irreversible adsorption of highly mobile particles. For systems out of equilibrium, we observe several features of glassy dynamics, such as slow relaxation dynamics, the memory effect, and aging. In particular, the analysis of our system in the limit of small desorption probability shows simple aging behavior with a power-law decay. A detailed discussion of Gibbs adsorption isotherm for non-equilibrium adsorption is given, which exhibits a hysteresis between this system and its equilibrium counterpart. The next chapter focus on the adsorption kinetics and the thermodynamic properties of a binary mixture on a square lattice are studied using the random sequential adsorption with surface diffusion (RSAD). We compare the adsorption of binary species with different equilibrium rate constants and effective rates of adsorption to a surface and find that the temporal evolution of surface coverages of both species can be obtained through the use of the blocking function of a system with irreversible adsorption of highly diffusive particles. Binary mixtures, when one of the components follows the random sequential adsorption (RSA) without surface diffusion and the other follows the RSAD model, display competitive adsorption in addition to cooperative phenomena. Specifically, (i) species replacement occurs over a long period of time, while the total coverage remains unchanged after a short time, (ii) the presence of the RSAD component shifts the jamming coverage to the higher values, and (iii) the maximum jamming coverage is obtained when the effective adsorption of the RSA type components is lower than the other adsorbing particles. Then our new approach is used to analyze the interfacial behavior of asphaltenes at the water/oil interface. RSAD method reveals the phase transition of asphaltenes at the interface from disordered to ordered phase at high coverage due to the steric hindrance effect. This ordered phase is consistent with the observation of birefringence within asphaltenes laden interfaces upon contracting the aged droplet. Corresponding surface pressure obtained from this model is equal to the surface pressure that a droplet containing asphaltenes solution loses its Laplacian shape over the contraction experiment. Another outcome of this model is the observation of dynamic frustration within the dense interfacial layers due to the fast increase of surface coverage in comparison with interfacial diffusion either during spontaneous adsorption or during interfacial area reduction. As a result, the interfacial layer could enter into a metastable glass state that would slowly relax towards a crystalline state with time. Finally, we investigated the phase behavior of particles adsorbed at the liquid/vapor interface using molecular dynamic simulations (MD). The results obtained from these simulations provide complementary insight about the orientation of particles at the interface and the formation of micelles in a real experiment such as pendant drop and Langmuir trough
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