Correlations between MO Eigenvectors and the Thermochemistry of Simple Organic Molecules, Related to Empirical Bond Additivity Schemes

A bondingness term is further developed to aid in heat of formation (ΔfHº) calculations for C, N, O and S containing molecules. Bondingness originated from qualitative investigations into the antibonding effect in the occupied MOs of ethane. Previous work used a single parameter for bondingness to calculate ΔfHº in an alkane homologous series using an additivity scheme. This work modifies the bondingness algorithm and uses the term to parameterise a test group of 345 molecules consisting of 17 subgroups that include alkanes, alkenes, alkynes, alcohols, ethers, aldehydes, ketones, carboxylic acids, esters, amines, amides, diazenes, nitriles, nitroalkanes, nitrates, thiols and benzenoids. Comparing experimental with calculated ΔfHº values, a standard deviation for the residuals of 6.3 kJ mol 1 can be achieved using bondingness with a simple steric repulsion term (SSR) in a bond additivity scheme, and a standard deviation of 5.2 kJ mol 1 can be achieved using a Lennard-Jones potential. The method is compared with the group method of Pedley, which for a slightly smaller set of 338 molecules, a subset of the test set of 345 molecules, gives a standard deviation of 7.0 kJ mol 1. Bondingness, along with SSR or a Lennard-Jones potential, is parameterised in the lowest level of ab initio (HF-SCF) or semiempirical quantum chemical calculations. It therefore may be useful in determining the ΔfHº values for the largest molecules that are amenable to quantum chemical calculation. As part of our analysis we calculated the difference between the lowest energy conformer and the average energy of a mixture populated with higher energy conformers. This is the difference between the experimental ΔfHº value and the ΔfHº calculated for a single conformer. Example calculations which we have followed are given by Dale and Eliel et al.. Dale calculates the energy difference for molecules as large as hexane using relative energies based on the number of 1,4 gauche interactions. We have updated these values with constant increments ascertained by Klauda et al. as well as ab initio MP2 cc-pVDZ relative energies and have included calculations for heptane and octane

On the inner workings of Monte Carlo codes

We review state-of-the-art Monte Carlo (MC) techniques for computing fluid coexistence properties (Gibbs simulations) and adsorption simulations in nanoporous materials such as zeolites and metal-organic frameworks. Conventional MC is discussed and compared to advanced techniques such as reactive MC, configurational-bias Monte Carlo and continuous fractional MC. The latter technique overcomes the problem of low insertion probabilities in open systems. Other modern methods are (hyper-)parallel tempering, Wang-Landau sampling and nested sampling. Details on the techniques and acceptance rules as well as to what systems these techniques can be applied are provided. We highlight consistency tests to help validate and debug MC codes

Developing and validating Fuzzy-Border continuum solvation model with POlarizable Simulations Second order Interaction Model (POSSIM) force field for proteins

The accurate, fast and low cost computational tools are indispensable for studying the structure and dynamics of biological macromolecules in aqueous solution. The goal of this thesis is development and validation of continuum Fuzzy-Border (FB) solvation model to work with the Polarizable Simulations Second-order Interaction Model (POSSIM) force field for proteins developed by Professor G A Kaminski. The implicit FB model has advantages over the popularly used Poisson Boltzmann (PB) solvation model. The FB continuum model attenuates the noise and convergence issues commonly present in numerical treatments of the PB model by employing fixed position cubic grid to compute interactions. It also uses either second or first-order approximation for the solvent polarization which is similar to the second-order explicit polarization applied in POSSIM force field. The FB model was first developed and parameterized with nonpolarizable OPLS-AA force field for small molecules which are not only important in themselves but also building blocks of proteins and peptide side chains. The hydration parameters are fitted to reproduce the experimental or quantum mechanical hydration energies of the molecules with the overall average unsigned error of ca. 0.076kcal/mol. It was further validated by computing the absolute pKa values of 11 substituted phenols with the average unsigned error of 0.41pH units in comparison with the quantum mechanical error of 0.38pH units for this set of molecules. There was a good transferability of hydration parameters and the results were produced only with fitting of the specific atoms to the hydration energy and pKa targets. This clearly demonstrates the numerical and physical basis of the model is good enough and with proper fitting can reproduce the acidity constants for other systems as well. After the successful development of FB model with the fixed charges OPLS-AA force field, it was expanded to permit simulations with Polarizable Simulations Second-order Interaction Model (POSSIM) force field. The hydration parameters of the small molecules representing analogues of protein side chains were fitted to their solvation energies at 298.15K with an average error of ca.0.136kcal/mol. Second, the resulting parameters were used to reproduce the pKa values of the reference systems and the carboxylic (Asp7, Glu10, Glu19, Asp27 and Glu43) and basic residues (Lys13, Lys29, Lys34, His52 and Lys55) of the turkey ovomucoid third domain (OMTKY3) protein. The overall average unsigned error in the pKa values of the acid residues was found to be 0.37pH units and the basic residues was 0.38 pH units compared to 0.58pH units and 0.72 pH units calculated previously using polarizable force field (PFF) and Poisson Boltzmann formalism (PBF) continuum solvation model. These results are produced with fitting of specific atoms of the reference systems and carboxylic and basic residues of the OMTKY3 protein. Since FB model has produced improved pKa shifts of carboxylic residues and basic protein residues in OMTKY3 protein compared to PBF/PFF, it suggests the methodology of first-order FB continuum solvation model works well in such calculations. In this study the importance of explicit treatment of the electrostatic polarization in calculating pKa of both acid and basic protein residues is also emphasized. Moreover, the presented results demonstrate not only the consistently good degree of accuracy of protein pKa calculations with the second-degree POSSIM approximation of the polarizable calculations and the first-order approximation used in the Fuzzy-Border model for the continuum solvation energy, but also a high degree of transferability of both the POSSIM and continuum solvent Fuzzy Border parameters. Therefore, the FB model of solvation combined with the POSSIM force field can be successfully applied to study the protein and protein-ligand systems in water

Structural analysis of adsorption processes of 5FU and imiquimodon hydrogels using AMBER/PM3 hybrid model

AMBER/PM3 hybrid model allowed determining the structural properties of 5FU and imiquimod individually and after the adsorption of chitosan hydrogels crosslinked with genipin, respectively. It was observed that the Gibbs free energy (ΔG) decreases with the adsorption, but indicates thermodynamic stability and spontaneity in both processes; ΔG was verified by the increase in the dipole moments. On the one hand, the partition coefficient established the hydrophilic character with respect to the water present in the hydrogel, which increases with the adsorption. The FTIR showed that there were displacements in the signals, however, the hydrogen bond bands attributed to the formation of new bonds to perform the adsorption of the drugs were observed. The adsorption was verified by the MESP and the surface analysis, where the distribution of nucleophilic and electrophilic zone was observed.O modelo hibrido AMBER/PM3 permitiu determinar as propriedades estruturadas do 5FU e imiquimod individualmente e depois da adsorção em hidrogeles de quitosano entrecruzados com genipina, respectivamente. Observou-se que o poder livre de Gibbs (ΔG) diminui com a adsorção, sem embargo, em ambos os processos se encontró estabilidade termodinâmica e espontaneidad; ΔG foi verificado através do aumento nos momentos de dipolares. Por outro lado, o coeficiente de divisão estabeleceu o carácter hidrofílico em relação à água presente no hidrogel, o qual aumenta com a adsorção. El FTIR evidenció que existem deslocamentos em las señales. Se observe as bandas de puente de hidrógeno, atribuições à formação de enlaces, para realizar a adsorção dos fármacos. A adsorção foi verificada através do MESP e os análises de superfície, em donde se apreciou a distribuição de zonas nucleofílicas e eletrofílicas.El modelo hibrido AMBER/PM3permitió determinar las propiedades estructurales del 5FU e imiquimod individualmente y después de la adsorción en hidrogeles de quitosano entrecruzados con genipina, respectivamente. Se observó que la energía libre de Gibbs (ΔG) disminuye con la adsorción, sin embargo, en ambos procesos se encontró estabilidad termodinámica y espontaneidad; ΔG fue verificado mediante el incremento en los momentos dipolares. Por otro lado, el coeficiente de partición estableció el carácter hidrofìlico con respecto al agua presente en el hidrogel, el cual aumenta con la adsorción. El FTIR evidenció que existen desplazamientos en las señales. Se observaron las bandas de puente de hidrógeno, atribuidas a la formación de enlaces, para realizar la adsorción de los fármacos. La adsorción fue verificada mediante los MESP y los análisis de superficie, en donde se apreció la distribución de zonas nucleofílicas y electrofílicas

Physical, Mechanical and Chemical Aging of Polyurea Nanocomposites

Two component polyurea systems, on one hand, are gaining popularity as corrosion and abrasion resistant coatings and linings while on the other hand there are a few polyurea compositions being used as barrier against blast and ballistic threats to protect nation\u27s critical infrastructure. Physical properties of polymer composites can be tailored with appropriate choice of type, size and amount of reinforcement. In general, nano-sized reinforcements provide better reinforcing over conventional reinforcements due to higher surface to volume ratio. In this dissertation, the first aim is to study effect of nanoreinforcement addition on the overall character (mechanical, chemical and microstructural) of different polyurea systems. Control tensile strength, dynamic mechanical and nanoindentation properties of these composites are used as parameters to rank the mechanical performance of these composites. Evaluation of synergistic effects of various environmental factors such as temperature, humidity, light, etc. on the performance of composite materials is the second challenge addressed in this research work. Selective composites are subject to hygrothermal cycling and ultraviolet (UV) radiation and stabilities studies for long durations. The severity of the effect of these exposures are measured in terms of the tensile strength of composites at predetermined time intervals. Change in the chemical makeup of these composites due to hygrothermal and UV exposures is studied using Fourier transformed infrared (FTIR) spectroscopy. Atomic force microscopy (AFM) is used to study the changes in polyurea microstructure due to addition of nanoreinforcements and subsequent aging. Long term mechanical performance of polyurea nanocomposites is evaluated using time temperature superposition (TTS) principle. Effects of different amounts of nano reinforcement on the elastic properties in polyurea nanocomposites are studied using molecular dynamics (MD) simulations

A Proposed Framework for Strengthening Mitigations of Offshore Jacket Structures and its Application

Master's thesis in Offshore technology : Structural EngineeringThe majority of offshore platforms and jacket structures are currently passing their assigned lifetime both on the Norwegian Continental Shelf (NCS), the Gulf of Mexico (GoM), the United Kingdom Continental Shelf (UKCS) and other parts of the world. The concern about ageing related issues and how to solve them is a major concern and presents a significant challenge in all sectors of the offshore oil and gas industry. The reason for mitigation and extending the lifetime of platforms are because there are still plenty of oil reserves left in existing fields. These fields are too small for stand-alone development and the construction of new platforms. Therefore, the use of existing infrastructure is a necessary and efficient solution. In addition, there are several monetary and environmental factors for extending the lifetime of platforms instead of decommissioning them. Mitigation of existing jacket platforms is especially a major concern, because the majority of offshore platforms around the world are jacket-type structures. However, the standards and codes that are available does not provide a detailed guideline for strengthening mitigation of offshore jacket structures. There is not sufficient information about the process and the necessary solutions for extending the lifetime of a jacket structure. In addition, the information is scattered among several codes, guidelines, standards and numerous published articles. To address this issue, a detailed framework is proposed that show a more precise and general guideline for the mitigation of an offshore jacket structure. A literature review is done to assess and collect the available information and present it in a clear overview. The proposed framework is more detailed and provides a list of mitigation techniques on an offshore jacket structure. It provides a better solution by addressing the issues related to the weld, the legs and braces, corrosion damage and structural integrity. At last, the significance of the proposed framework is highlighted through a case study where the proposed mitigation techniques are applied on an existing offshore jacket structure. The results from the case study are discussed and finally conclusions are drawn about the applicability and significance of the proposed framework

Computations on non-covalent assemblies: Supramolecular organization and transport properties

The aim of this Thesis is to rationalize, from a theoretical perspective, the structural, electronic, optical and transport properties of different electroactive non-covalent assemblies of special relevance in the field of organic electronics. The ultimate goal is to establish valuable supramolecular structure-property relationships. In particular, this Thesis is focused on three types of systems: hole transporting materials (HTM), donor–acceptor supramolecular complexes and supramolecular polymers. For each system, the spotlight has been put on different relevant electronic processes. In the first part, the structural organization of several supramolecular polymers is studied. In particular, the relation between the supramolecular organization and the properties of interest (e.g. chiral behavior, or optical properties) of the selected systems. In the second part the charge transport properties of hole transporting materials, donor–acceptor supramolecular complexes are studied. On one hand the effect of H-bonding and the size of the HTM in the electronic mobilities is investigated. On the other hand, the kinectics of the photoinduced electron transfer on donor–acceptor supramolecular complexes in solution is simulated. Finally, the effects that become relevant for energy transport at the typical distances found in non-covalent assemblies are analyzed. These findings are used to simulate the exciton dynamics along one supramolecular polymer and, in particular the role of the charge transfer states in the exciton transport is analyzed

Purpose Tailoring of Bioactive-Biocompatible Polymers as Soluble Drug Carriers and Hydrogels for Drug Delivery Systems

During the PhD course I have studied poly(amido amine)s based nanostructured systems, that can be considered as part of the huge field of the polymer therapeutics. After a brief intrpduction about polymer therapeutics and a general review concerning poly(amidoamines), the work done during the PhD course is reported, divided in the following main chapters: Kinetic study of PAAs synthesis in organic solvents; Synthesis of new polymeric precursors of PAA-drug or PAA-protein conjugate by disulfide bond; Synthesis of nano-structured PAA-Cholesterol conjugates; Syntesys of cross linked polyplexes for applications in gene delivery; Glass surface functionalization for AFM imaging of lipid systems