<p> Block copolymers are composed of chemically distinct polymer chains that can be covalently linked in a variety of sequences and architectures. They are ubiquitous as ingredients of consumer products and also have applications in advanced plastics, drug delivery, advanced membranes, and next generation nano-lithographic patterning. The wide spectrum of possible block copolymer applications is a consequence of block copolymer self-assembly into periodic, meso-scale morphologies as a function of varying block composition and architecture in both melt and solution states, and the broad spectrum of physical properties that such mesophases afford. </p><p> Materials exploration and discovery has traditionally been pursued through an iterative process between experimental and theoretical/computational collaborations. This process is often implemented in a trial-and-error fashion, and from the computational perspective of generating phase diagrams, usually requires some existing knowledge about the competitive phases for a given system. Self-Consistent Field Theory (SCFT) simulations have proven to be both qualitatively and quantitatively accurate in the determination, or forward mapping, of block copolymer phases of a given system. However, it is possible to miss candidates. This is because SCFT simulations are highly dependent on their initial configurations, and the ability to map phase diagrams requires a priori knowledge of what the competing candidate morphologies are. The unguided search for the stable phase of a block copolymer of a given composition and architecture is a problem of global optimization. SCFT by itself is a local optimization method, so we can combine it with population-based heuristic algorithms geared at global optimization to facilitate forward mapping. In this dissertation, we discuss the development of two such methods: Genetic Algorithm + SCFT (GA-SCFT) and Particle Swarm Optimization + SCFT (PSO-SCFT). Both methods allow a population of configurations to explore the space associated with the numerous states accessible to a block copolymer of a given composition and architecture. </p><p> GA-SCFT is a real-space method in which a population of SCFT field configurations &ldquo;evolves&rdquo; over time. This is achieved by initializing the population randomly, allowing the configurations to relax to local basins of attraction using SCFT simulations, then selecting fit members (lower free energy structures) to recombine their fields and undergo mutations to generate a new &ldquo;generation&rdquo; of structures that iterate through this process. We present results from benchmark testing of this GA-SCFT technique on the canonical AB diblock copolymer melt, for which the theoretical phase diagram has long been established. The GA-SCFT algorithm successfully predicts many of the conventional mesophases from random initial conditions in large, 3-dimensional simulation cells, including hexagonally-packed cylinders, BCC-packed spheres, and lamellae, over a broad composition range and weak to moderate segregation strength. However, the GA-SCFT method is currently not effective at discovery of network phases, such as the Double-Gyroid (GYR) structure. </p><p> PSO-SCFT is a reciprocal space approach in which Fourier components of SCFT fields near the principal shell are manipulated. Effectively, PSO-SCFT facilitates the search through a space of reciprocal-space SCFT seeds which yield a variety of morphologies. Using intensive free energy as a fitness metric by which to compare these morphologies, the PSO-SCFT methodology allows us to agnostically identify low-lying competitive and stable morphologies. We present results for applying PSO-SCFT to conformationally symmetric diblock copolymers and a miktoarm star polymer, AB₄, which offers a rich variety of competing sphere structures. Unlike the GA-SCFT method we previously presented, PSO-SCFT successfully predicts the double gyroid morphology in the AB-diblock. Furthermore, PSO-SCFT successfully recovers the A₁₅ morphology at a composition where it is expected to be stable in the miktoarm system, as well as several competitive metastable candidates, and a new sphere morphology belonging to the hexagonal space group 191, which has not been seen before in polymer systems. Thus, we believe the PSO-SCFT method provides a promising platform for screening for competitive structures in a given block copolymer system.</p><p>

The structures, vibrational frequencies, and potential energy functions of several molecules in their ground and excited electronic states were determined using various spectroscopic and theoretical methods. High-level ab initio and density functional theory (DFT) calculations were utilized to investigate the previously reported structures and vibrational spectra of 1,3- disilacyclobutane (13DSCB) and its 1,1,3,3-d4 (13DSCB-d4) isotopomer. These calculations confirmed the finding from earlier microwave work that the CSiC angles of the 13DSCB ring are unexpectedly larger than the SiCSi angles. The calculated vibrational spectra using density functional theory agreed well with the experimental data and showed CH2 modes to have unusually low values. The calculations also confirmed that the individual molecules in the vapor phase are puckered whereas in the solid they become planar. The one-dimensional potential energy surfaces (PESs) for the ring inversion vibration of 2-cyclohexen-1-one and its 2,6,6-d3 isotopomer in its ground and singlet S1(n,π*) electronic states were determined using ultraviolet cavity ringdown spectroscopy (CRDS). The CRDS data allowed several of the quantum states of the ring inversion vibration to be determined for both the ground and excited electronic states, and the data were fit very well with PESs with high barriers to inversion. The infrared and Raman spectra and DFT calculations were utilized to complete a vibrational assignment of 2CHO and 2CHO-d3. A remarkable agreement was seen between the experimental and calculated spectra. The fluorescence excitation spectra (FES) and the single-vibronic level fluorescence (SVLF) spectra of jet-cooled 1,4-dihydronaphthalene (14DHN) were acquired to determine its ring-puckering potential energy function for the ground and singlet S1(π,π*) electronic states. Ultraviolet, infrared, and Raman spectra were also recorded to complement the analysis. The potential energy functions showed that the molecule is planar in both the ground and S1(π,π*) states. A complete vibrational assignment was carried out for 14DHN using the infrared and Raman data and aided by DFT calculations. The ab intio calculations carried out on 2-methyl-2-cyclopenten-1-one (2MCP) showed that the molecule can have 3 different conformers. Infrared and Raman spectra of the liquid-phase molecule were recorded and analyzed to complement the theoretical calculations.

Dialkylstannylene acetals are tin-containing species employed extensively as intermediates to facilitate high-yielding and regioselective monosubstitution reactions of diols or polyols with various electrophiles, which is an important application of organotin compounds in organic synthesis. Although an abundance of experimental studies of these reactions have been reported, the mechanism of the reaction has not been well defined. High-level theoretical methods are used in this thesis to investigate the chemistry of organotin systems at a molecular level. This involves the exploration of the geometry characteristics of the gas-phase structures along the reaction paths in order to understand the mechanism of the organotin-mediated alkylations of diols. Alkylation reactions which require strict conditions can be dramatically enhanced by the presence of nucleophiles. The effects of added nucleophiles were examined computationally by comparing reaction profiles obtained for alkylations of dimethylstannylene acetals in the presence of different nucleophiles.

<p> This dissertation contains investigations based on Molecular Dynamics (MD) of a variety of systems, from small atomic clusters to polymers in solution and in their condensed phases. The overall research is divided in three parts. First, I tested a new thermostat in the literature on the thermal equilibration of a small cluster of Lennard-Jones (LJ) atoms. The proposed thermostat is a Hamiltonian thermostat based on a logarithmic oscillator with the outstanding property that the mean value of its kinetic energy is constant independent of the mass and energy. I inspected several weak-coupling interaction models between the LJ cluster and the logarithmic oscillator in 3D. In all cases I show that this coupling gives rise to a kinetic motion of the cluster center of mass without transferring kinetic energy to the interatomic vibrations. This is a failure of the published thermostat because the temperature of the cluster is mainly due to vibrations in small atomic clusters This logarithmic oscillator cannot be used to thermostat any atomic or molecular system, small or large. </p><p> The second part of the dissertation is the investigation of the inherent structure of the polymer polyethylene glycol (PEG) solvated in three different solvents: water, water with 4% ethanol, and ethyl acetate. PEG with molecular weight of 2000 Da (PEG₂₀₀₀) is a polymer with many applications from industrial manufacturing to medicine that in bulk is a paste. However, its structure in very dilute solutions deserved a thorough study, important for the onset of aggregation with other polymer chains. I introduced a modification to the GROMOS 54A7 force field parameters for modeling PEG₂₀₀₀ and ethyl acetate. Both force fields are new and have now been incorporated into the database of known residues in the molecular dynamics package Gromacs. This research required numerous high performance computing MD simulations in the ARGO cluster of GMU for systems with about 100,000 solvent molecules. My findings show that PEG₂₀₀₀ in water acquires a ball-like structure without encapsulating solvent molecules. In addition, no hydrogen bonds were formed. In water with 4% ethanol, PEG₂₀₀₀ acquires also a ball-like structure but the polymer ends fluctuate folding outward and onward, although the general shape is still a compact ball-like structure. </p><p> In contrast, PEG₂₀₀₀ in ethyl acetate is quite elongated, as a very flexible spaghetti that forms kinks that unfold to give rise to folds and kinks in other positions along the polymer length. The behavior resembles an ideal polymer in a &thetas; solvent. A Principal Component Analysis (PCA) of the minima composing the inherent structure evidences the presence of two distinct groups of ball-like structures of PEG₂₀₀₀ in water and water with 4% ethanol. These groups give a definite signature to the solvated structure of PEG₂₀₀₀ in these two solvents. In contrast, PCA reveals several groups of avoided states for PEG₂₀₀₀ in ethyl acetate that disqualify the possibility of being an ideal polymer in a &thetas; solvent. </p><p> The third part of the dissertation is a work in progress, where I investigate the condensed phase of PEG₂₀₀₀ and study the interface between the condensed phase and the three different solvents under study. With a strategy of combining NPT MD simulations at different temperatures and pressures, PEG₂₀₀₀ condensed phase displays the experimental density within a 1% discrepancy at 300 K and 1 atm. This is a very encouraging result on this ongoing project. </p><p>

As a reliable, convenient, and advantageous tool in the theoretical investigations of bioorganic, inorganic, and organometallic chemistry, density functional theory (DFT) computations have provided chemists with numerous significant insights. The understanding of mechanisms of chemical reactions, and the design and development of catalysts have been greatly promoted by the employment of DFT. In this dissertation, the applications of DFT computations in the catalytic bioorganic, inorganic, and organometallic systems were studied. Phosphoramidate hydrolysis catalyzed by human histidine triad nucleotide binding protein 1 (hHint1) was investigated using a cluster-model DFT approach, and the key involvement of the histidine triad as a proton shuttle was discussed in the proposed mechanism. The IEFPCM-Bondi-B3LYP/BS1 methodology was demonstrated as a reliable, and time-saving model in computing the reduction potentials of transition metal complexes. Moderate accuracy (MAD = 0.233 V, mean absolute deviation) and good linear correlation (R2 = 0.93) between computed and experimental reduction potentials of the 49 studied species are osberved. The fluxionality of cyclohexenyl manganese tricarbonyl [(C6H9)Mn(CO)3] was investigated using DFT computations, which uncovered a previously uncharacterized “closed” Cs agostomer. The intramolecular oxidative amination of an alkene catalyzed by the extreme π-loading N-heterocyclic carbene pincer Tantalum(V) bis(imido) complex was also computationally analyzed, and the mechanisms of the formation of oxidative amination product, reduction product, and hydroamination product were investigated. The computational results are consistent with the experimentally observed product ratios and selectivity.

Yes / Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future. / veski

<p>The notion of autonomous laboratories is of much interest to the chemical science community.  Promises of increased efficiency and throughput of discovery, beyond that of automated platforms, has already begun to be fulfilled by autonomous continuous flow reactors and desktop robots.  For fully autonomous laboratories to be further realized, various components in these systems require automation.  Herein this work, are presented multiple data-driven statistical methods for automating and optimizing various chemical systems and processes.  Presented are: the development and deployment of a general stochastic optimization algorithm, a machine learning-based solvent selection pipeline for organic transformations, a generalized data-dependent scoring methodology for antibody assay development, the prototyping of an automated platform for ion-molecule reactions inside a linear ion trap, and a review on recent developments for machine learning and mass spectrometry.  In summary, these works present various components for furthering the automation of chemistry.</p>

The dramatic expansion of the electronics industry over the past 40 years has been based on the progressive reduction in size of the silicon-based semiconductor components of integrated circuits. The miniaturisation of semi-conductor circuits cannot, however, continue indefinitely, and we are rapidly approaching the stage where quantum effects will prevent further dramatic improvements in computer performance using existing technology. As a result, the field of molecular electronics, which seeks to identify and develop much smaller molecular analogues of the transistors that make up integrated circuits, has expanded rapidly over the past few years. Recent studies suggested that extended metal atom chains (EMAC) may have many potential applications in molecular electronics, but it is clear that this potential can only be realised if we establish a link between the fundamental electronic properties of these systems and the transport of electrons. For this reason the ultimate goal of this thesis is to relate the electronic structure of extended metal chains to their electron transport properties. We address the problem using non-equilibrium Green’s function, in conjugation with density functional theory. In the results sections of this thesis we present calculations on tricobalt, trichromium and trinickel chains. Our data suggested that in the trimetal chains, the dominant electron transport channel is the σ manifold, while the π systems establish the contact with the electrodes. The implication of this is that even when the highly polarized π channels are strongly rehybridised by the applied electric field, current flow is not affected. In the trichromium systems we find that the distortion of the chain away from the symmetric equilibrium structure does not perturb the current flow but rather enhances it. Our rather counter intuitive conclusion is therefore that ‘broken wires’ (highly unsymmetric) are more efficient conductors than their symmetric counterparts. We have performed calculation on longer penta- and heptacobalt structures chains to establish the extent to which longer structures attenuate the conductance. Our calculations show significant oscillations of the conductance due to development of a one-dimensional band structure about the Fermi level. The evolution of the electron transport properties in cobalt chains with different length is a complex one, but it is clear that narrowing the band gap in longer chains makes it increasingly likely that the Fermi level will be in resonance with one or more of the orbitals of the extended metal atom chain.

"Catalysts are involved at some stage in the manufacture process of virtually all commercially produced chemical product. Among the materials used as catalysts, metal oxides are one of the most used due to their versatility and wide range of physical properties. Identifying the principles of surface to adsorbate charge transfer is key to a better understanding of metal oxide materials as both catalysts and gas sensors. Using density functional theory (DFT), we modeled the adsorption of small molecules over stoichiometric and reduced metal oxide surfaces of group IV metals and quantify the effect of electron transfer upon adsorption. We found that charge transfer only occurs during the adsorption process of an adsorbate more electronegative than the surface. We also found a correlation between the work function of the metal oxide, and the ionic adsorption of the oxygen molecule. Mixed phase rutile/anatase catalysts show increased reactivity compared with the pure phases alone. However, the mechanism causing this effect is not fully understood. Using DFT and the +U correction we calculated the bands offsets between the phases taking into account the effect of the interface. We found rutile to have both higher conduction and valence band offsets than anatase, leading to an accumulation of electrons in the anatase phase accompanied by hole accumulation in the rutile phase. We also probed the electronic structure of our heterostructure and found a gap state caused by electrons localized in undercoordinated Ti atoms which were present within the interfacial region. Interfaces between bulk materials and between exposed surfaces both showed electron trapping at undercoordinated sites. Finally, we studied the effect of the size of gold nanoparticles in the catalytic properties of gold decorated titania surfaces. We found that the adsorption energy of several intermediates reactives in the CO oxidation and water gas shift reaction does not change with the size of the nanoparticles. In conclusion, the factor that affects the reactivity of the system is the density of undercoodinated gold atoms on the interface perimeter."

Electron scattering cross sections have been computed for pyridine and pyrimidine using the static-exchange approximation with model potential to account for dynamic electron correlation. To obtain well-converged orbitals, we have expanded all partial waves to a maximum angular momentum of l = 60 for both targets. We have obtained total cross sections for electron scattering energies to 20 eV. Both targets display similar features, namely a dipole-induced increase in the integrated cross section at scattering energies below 5 eV, and peaks corresponding to resonances in b1, a2, and b1 symmetries. These resonances were investigated through a Siegert eigenstate analysis and Breit-Wigner fit of the SECP eigenphase sums. They were also compared to the virtual orbitals obtained from a minimum basis set Hartree-Fock calculation on both targets. We consider electron scattering resonances from cis-diamminedichloroplatinum, [Pt(NH3)2Cl2], the ligand molecular species Cl2 (1Sigma+g ), and the isolated transition metal center Pt in a nondegenerate atomic state (1S) at the SECP level of theory. As a rigorous comparison to the single-state, single-configuration SECP level results of these smaller, yet electron dense targets, we have also considered scattering from ground state Cl2 and Pt in the 1S and 3D states in the multichannel configuration-interaction (MCCI) approximation originally developed for photoionization for scattering up to 10 eV. Photoionization cross sections and angular distributions in the recoil frame (RFPAD) and molecular frame (MFPAD) have been computed for inner-shell C 1s and Cl 2p ionization from the chloroalkanes chloromethane and chloroethane, with ionization leading to a variety of ionic fragment states. We have also computed valence level ionization from the nitro molecule nitromethane CH3NO2 leading to the dissociation of the CN bond. All of these calculations were performed in the frozen-core Hartree-Fock approximation. Even at this level of theory, we obtain computed results that compare well to the photoelectronphotoion coincidence measurements. The fullerene C20 is the smallest fullerene predicted to exist, with most relevant structural calculations suggesting the reduction of the icosahedral symmetry into one in which the target species possesses at maximum only a dihedral axis. We have computed positron scattering cross sections for the molecule in two low-symmetry structural isomers Ci and C2, within the HF approximation. Density functional expressions were used to incorporate important positron-electron interactions within the calculation. We have found similar cross sections and resonance features for both isomers, including a positron scattering resonance whose density is found within the framework of the fullerene cluster.