The electrostatic properties of a molecule are often essential in determining its behavior; as such, the ability to approximate these electrostatic potentials computationally is often essential to obtaining a full understanding of how these molecules function. An approximate, analytical solution to the (linearized) Poisson-Boltzmann equation is proposed that is suitable for realistic biomolecules of virtually any size. A comparison with accepted numerical approaches on a large test set of biomolecular structures shows that the proposed method is considerably less expensive computationally, yet accurate enough to be considered as a possible alternative. The utility of the approach is demonstrated by computing and analyzing the electrostatic potential generated by full capsid of the tobacco ringspot virus (half a million atoms) at atomic resolution. The details of the potential distribution on the molecular surface sheds light on the mechanism behind the high selectivity of the capsid to the viral RNA. These results are generated with the modest computational power of a desktop PC. The applicability of the analytical approximation as an initial guess for traditional numerical methods as a means of improving the convergence of iterative solutions is investigated and found to be quite promising. / Master of Science

Computational methods are a convenient resource to solve drawbacks of drug research such as high cost, time-consumption, and high risk of failure. In order to get an optimum search of new drugs we need to design a rational approach to analyze the molecular forces that govern the interactions between the drugs and their target molecules. The objective of this project is to get an understanding of the interactions between drugs and proteins at the molecular level. The interaction energy, when protein and drugs react, has two components: non-covalent and covalent. The former accounts for the ionic interactions, the later accounts for electron transfer between the reactants. We study each energy component using the most popular analysis tools in computational chemistry such as docking scoring, molecular dynamics fluctuations, electron density change, molecular electrostatic potential (MEP), density of states projections, and the transmission function. We propose the probability of transfer of electrons (transmission function) between reactants in protein-drug complexes as an alternative tool for molecular recognition and as a direct correlator to the binding affinity. The quadratic correlation that exists between the electron transfer rate and the electronic coupling strength of the reactants allow a clear distinguishability between ligands. Thus, in order to analyze the binding affinity between the reactants, a calculation of the electronic coupling between them is more suitable than an overall energetic analysis such as free reaction energy.

abstract: The research of this dissertation involved quantitative characterization of electrostatic potential and charge distribution of semiconductor nanostructures using off-axis electron holography, as well as other electron microscopy techniques. The investigated nanostructures included Ge quantum dots, Ge/Si core/shell nanowires, and polytype heterostructures in ZnSe nanobelts. Hole densities were calculated for the first two systems, and the spontaneous polarization for wurtzite ZnSe was determined. Epitaxial Ge quantum dots (QDs) embedded in boron-doped silicon were studied. Reconstructed phase images showed extra phase shifts near the base of the QDs, which was attributed to hole accumulation in these regions. The resulting charge density was (0.03±0.003) holes/nm3, which corresponded to about 30 holes localized to a pyramidal, 25-nm-wide Ge QD. This value was in reasonable agreement with the average number of holes confined to each Ge dot determined using a capacitance-voltage measurement. Hole accumulation in Ge/Si core/shell nanowires was observed and quantified using off-axis electron holography and other electron microscopy techniques. High-angle annular-dark-field scanning transmission electron microscopy images and electron holograms were obtained from specific nanowires. The intensities of the former were utilized to calculate the projected thicknesses for both the Ge core and the Si shell. The excess phase shifts measured by electron holography across the nanowires indicated the presence of holes inside the Ge cores. The hole density in the core regions was calculated to be (0.4±0.2) /nm3 based on a simplified coaxial cylindrical model. Homogeneous zincblende/wurtzite heterostructure junctions in ZnSe nanobelts were studied. The observed electrostatic fields and charge accumulation were attributed to spontaneous polarization present in the wurtzite regions since the contributions from piezoelectric polarization were shown to be insignificant based on geometric phase analysis. The spontaneous polarization for the wurtzite ZnSe was calculated to be psp = -(0.0029±0.00013) C/m2, whereas a first principles' calculation gave psp = -0.0063 C/m2. The atomic arrangements and polarity continuity at the zincblende/wurtzite interface were determined through aberration-corrected high-angle annular-dark-field imaging, which revealed no polarity reversal across the interface. Overall, the successful outcomes of these studies confirmed the capability of off-axis electron holography to provide quantitative electrostatic information for nanostructured materials. / Dissertation/Thesis / Ph.D. Physics 2011

Abstract Charge density studies have been conducted on ten CB1 cannabinoid receptor antagonists via high resolution x-ray crystallography. Bond critical point values and various other properties derived from these studies including the electrostatic potential were analyzed in correlation to the affinity of each compound with the CB1 receptor. Correlation/anti-correlation was found between several properties and Ki. The data was also interpreted by principal component analysis with three principal components accounting for 85% of the data variation. Data mining was limit due to the low sample count and the requirements set for the inclusion of correlated/anti-correlated variables left fewer variables to analyze. The model presented is left for future interpretation.

Produktion av nya energetiska material är dyrt. Målet med detta arbete är att utveckla en metod som uppskattar Chapman-Jouget detonationstrycket och detonationshastigheten hos nya CHNO-sprängämnen. En sådan metod möjliggör valet att bara syntetisera och testa de mest lovande kandidaterna som nya energetiska material, därmed undviks resursslösande arbete. Den här metoden använder sig av density functional theory (DFT) och den elektrostatiska potentialen till att uppskatta bildningsentalpier och kristalldensiteter. Beräkningarna gjordes på traditionella sprängämnen och de beräknade detonationstrycken och detonatioshastigheterna visade bra överensstämmelse med experimentell data. Detonationstrycken hamnade inom ±10% och detonatioshastigheterna inom ±5% av experimentell data. / Producing new energetic materials is expensive. This work aims to develop a method of estimating the Chapman-Jouget detonation pressure and the detonation velocity of potential new CHNO explosives. This would allow choosing the most promising candidates for synthesis and testing thus avoiding wasting resources. This method utilizes density functional theory (DFT) and the electrostatic potential to estimate heats of formation and crystal densities. The calculations were performed on traditionally used explosives and the calculated detonation pressures and detonation velocities showed good accordance with experimental data. The calculated detonation pressures fell within ±10% and the detonation velocities within ±5% of experimental data.

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Kvantkemiska studier av reaktiviteten hos guldnanopartiklar Au3-Au11 och Au13 mot O- centrerade molekylradikaler OH , OOH , OCH3   och H2O undersöks. Olika molekylära ytegenskaper tas med i beräkningen, elektrostatiska ytpotentialen, den genomsnittliga lokala joniseringsenergin, electron attachment energy och spinndensiteten (VS(r), IS(r), TS(r), ES(r) och S(r)). De erhållna resultaten gäller slutna och öppna skalsystem. Där system med slutna skal bildas från växelverkan mellan en guldklusterradikal och en fri radikal, och system med öppna skal bildas från växelverkan mellan ett jämnt antal guldatomer med en fri radikal. För system med slutna skal Aux-R (där x = 3, 5, 7, 9 eller 11 och R är en O-centrerad radikal) finns det en övergripande trend av bindningsenergin gentemot ES(r), vilket återspeglar elektrofilictiten hos guldnanopartiklar. Multivariata modeller visar vidare hur de olika parametrarna korrelerar gentemot varandra för system med slutna skal.För strukturerna Aux-R (där x=3-11) medl ägst bindningsenergi, dvs. inklusive både slutna och öppna skalsystem, är den tydligaste trenden bindningsenergi vs minimum i ES(r) och parametern TS(r). Vid jämförelse av resultaten av interaktionerna med de fria radikalerna med H2O är trenden alltid tydligast för H2O. I linje med tidigare studier finns det även en korrelation av bindningsenergierna med VS,max och ES,min för H2O. Slutligen sträcker sig trenden med bindningsenergi vs ES,min vidare till systemet som innehåller den icke-plana Au13-strukturen. Denna studie visar kopplingen mellan reaktiviteten hos guldnanopartiklar mot fria radikaler till den lokala ES(r), samtidigt som bidraget från andra ytegenskaper visas. Detta kan vara av betydelse för fortsatta studier kring naturen av interaktioner av guldnanopartiklar. / The nature of gold nanoparticle interactions towards molecular radicals are investigated. Quantum chemical studies of the reactivity of gold nanoparticles Au3-Au11 and Au13 towards O-centered molecular radicals OH , OOH , OCH3   and H2O are performed. Different molecular surface properties are taken into account; the surface electrostatic potential, average local ionization energy, electron attachment energy and spin density (VS(r), IS(r), TS(r), ES(r) and S(r)). The obtained results concern closed and open shell systems. Where closed shell systems are formed from the interaction of a radical gold cluster and a free radical, and open shell systems are formed from the interaction of an even number of gold atoms with a free radical. For closed shell systems Aux-R (where x = 3, 5, 7, 9 or 11 and R is an O-centered radical) there is an overall trend of the binding energy vs the local electron attachment energy, reflecting the electrophilicity of the gold nanoparticles. Multivariate plots further show how the different parameters correlate together for closed shell systems. Looking at the lowest energy structures Aux-R (where x = 3-11), i.e. including closed and open shell systems, the clearest trend is of binding energy vs minima in the local electron attachment energy ES,min and the TS(r) parameter. When comparing the results of the interactions with the free radicals with H2O, the trend is always clearest for H2O. Concurring with previous trends, there is a correlation of the binding energies with VS,max and ES,min for H2O. Lastly, the trend of Binding energy vs ES,min further extends to systems containing the non-planar Au13 structure. This study extends the reactivity of gold nanoparticles towards free radicals to the local electron attachment energy, while showing the contribution of other surface properties. This might be of importance for further studies concerning the nature of gold nanoparticle interactions.

Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

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