S’han sintetitzat quatre alquil i aril (9 anthry1) carbinol (metil, fenil isopropil, terc-butil, i) que van revelar la rotació restringida al voltant de l'enllaç C9-C11. La seva energia lliure d'activació per a la rotació s'ha determinat, sent 11.0, 14.0, 21.7, i 9.8 kcal / mol, respectivament. Es descriuen l’aplicació mètodes de mesura del NOE i del temps de relaxació per a la determinació de l'energia d'activació per a la rotació de bons. El bon acord amb els valors obtinguts amb el mètode de la temperatura de coalescència confirma que l'enfocament basat NOE és una bona alternativa per a la determinació de les elevades barreres de rotació. Els càlculs de Mecànica Molecular (MM2) donen valors propers als experimentals. S’han preparat els carbamats homoquirals del 9-anthryl-terc-butylcarbinol i s’ha estudiat el seu equilibri conformacional. La configuració absoluta es va determinar mitjançant la comparació de les dades de RMN amb càlculs de MM. Els enantiòmers de l'alcohol es van obtenir després de la separació cromatogràfica dels derivats de carbamat i la seva hidròlisi. Els alcohols homoquirals van ser preparats per columna de cromatografia quiral directa. S’han detectat i o separat a temperatura ambient els confòrmers cisoid i transoid del 9,10 dipivaloylantracè i del 9,10-bis(1-imino-2,2-dimetilpropil)antracè. La transformació entre dues atropisómers va ser estudiada per RMN i modelat pels mètodes de MM. La difracció de raigs X es va realitzar per als derivats imino. El 9-antril-terc-butilcarbinol es va provar com a agent de solvatació quiral (CSA) en presència de formes racèmica de p-toluenesulfinate de mentil, 9-(1-amino-2,2- dimetilpropil)-9,19-dihydroantracè, àcid R-methoxyfenylacetic i 1-phenyl-1,2- ethanediol. Es formaren els complexes diastereòmers entre el reactiu quiral i cada enantiòmer d'aquests últims compostos. Un dels enantiòmers de 9-antril-tertbutylcarbinol va ser estudiat mitjançant NOE intermolecular i càlculs de dinàmica molecular. Es trobaren les principals diferencies termodinàmiques i estructurals. / Se han preparado Cuatro alquil- y aril- (9-antril)carbinols (metil, isopropil, tert-butil, y fenil) y mostraron la rotación restringida del enlace de C9-Cll. Su energía libre de activación para la rotación ha sido determinada, siendo 11.0, 14.0, 21.7, y 9.8 kcal/mol, respectivamente. Hemos determinado la energía de activación para la rotación de enlace C9-C11 por la aplicación de medidas de NOE y de tiempo de relajación. El buen acuerdo con los valores obtenidos con el método de temperatura coalescencia confirma que el método basado en el NOE es una buena alternativa para la determinación de barreras de rotatorión altas. La Mecánica Molecular (MM2) da valores cercanos a los experimentales. Se ha preparado el carbamato homochiral de 9-antril-tert-butilcarbinol y se ha estudiado su equilibrio conformacional. La configuración absoluta fue determinada por la comparación de los datos NMR con cálculos de MM. Los enantiomers del alcohol fueron obtenidos después de la separación cromatográfica de los carbamatos y tres su hidrólisis. Los mismos alcoholes se obtuvieron a través de una columna HPLC quiral Se han detectado o separado, a temperatura ambiente, los confórmeros cisoide y transoide del 9,10 dipivaloylantraceno y del 9,10-bis(1-imino-2,2- dimetilpropil)antraceno. La transformación entre los dos atropoisómeros se estudió por RMN i se modeló por métodes de MM. La difracción de rayos X se realitzó con los derivados imino. Se ha probado el 9-anthryl-tert-butylcarbinol como agente solvatación chiral (CSA) en presencia de las formas de racemicas de p-toluenesulfinato de mentilo, 9-(1-amino-2,2- dimetilpropil) - 9,19-dihydroanthracene, ácido de R-methoxyphenylacetic y 1-phenyl- 1,2-ethanediol. Se formaron los complejos diastereoisómericos el reactivo quiral y cada enantiomer de estos últimos compuestos. Uno de los enantiomers de 9-anthryltertbutylcarbinol fue estudiado por medio de NOE intermolecular y cálculos de dinámica moleculares. Las diferencias termodinámicas y estructurales principales fueron encontradas. / Four alkyl- and aryl-(9-anthry1)carbinols (methyl, isopropyl, tert-butyl, and phenyl) were synthesized and revealed restricted rotation about the C9-Cll bond. Their free energy of activation for rotation has been determined, being 11.0, 14.0, 21.7, and 9.8 kcal/mol, respectively. The application of NOE enhancement and relaxation time measurements for the determination of the activation energy for bond rotation is described. The good agreement with the values obtained with the coalescence temperature method bears out that the NOE based approach is a good alternative for the determination of high rotational barriers. Molecular Mechanics (MM2) calculations give values close to the experimental ones. The homochiral carbamates of 9-anthryl-tert-butylcarbinol were prepared and their conformational equilibrium was studied. The absolute configuration was determined by comparison of the NMR data with MM calculations. The enantiomers of the alcohol were obtained after chromatographic separation of carbamate derivatives and their hydrolysis. The same homochiral alcohols were prepared by direct chiral column chromatography Cisoid and transoid conformations of 9,10-dipivaloylanthracene and 9,10-bis(1-imino- 2,2-dimethylpropyl) anthracene were separated and detected for the former and isolated for the latter at room temperature. The transformation between two atropisomers was studied by NMR and modeled by MM methods. X-ray diffraction was performed for the imino derivatives. The 9-anthryl-tert-butylcarbinol was tested as a chiral solvating agent (CSA) in the presence of racemic forms of mentil-p-toluenesulfinate, 9-(1-amino-2,2- dimethylpropyl)-9,19-dihydroanthracene, R-methoxyphenylacetic acid and 1-phenyl- 1,2-ethanediol. Diastereomeric complexes were found to form between each enantiomer of these last two compounds. One of the enantiomers of 9-anthryltert-butylcarbinol was studied by means of intermolecular NOE and molecular dynamics calculations. Major thermodynamic and structural differences were found.

Deuteron 1D and 2D NMR spectroscopy was used to study the dynamics of water molecules within the mesoporous material MCM-41. The deuteron spectra show three magnetization components for a sample hydrated to a 0.2 monolayer level. One component was assigned to the pore surface silanol group deuterons that exhibit a broad Gaussian line of 32.6 kHz FWHM and the other components were assigned to the water deuterons. At room temperature one water deuteron component has a powder pattern line shape (splitting of about 4.2 kHz and population of about 61%) and the other has a Lorentzian line shape (about 388 Hz FWHM and population of 39%). Magnetization exchange occurs between these components. An exchange model, based on multi-site exchange, was constructed and used to analyse the results for exchange. For the 0.2 monolayer sample the rate of magnetization exchange out of the hydration site where the water deuterons exhibit a Lorentzian line in the deuteron spectra is 1.3 ms. 2D measurements at 233 K and room temperature confirmed the magnetization exchange scenario for the two water deuteron sites. Combining the deuteron results with proton-silicon cross polarization magic angle spinning experiments together with heat treatment of the sample, definitive hydration site identification for MCM-41 was achieved. This study has shown that the water molecules bound to the hydrogen-bonded silanol groups produce the powder pattern while water molecules bound to the single silanol groups produce the Lorentzian line. This represents a necessary first step toward a meaningful modeling of NMR observables in terms of site-specific water molecule coordination and dynamics in MCM-41.

This thesis provides an introduction to and analysis of the problem of determining nuclear magnetic resonance (NMR) relaxation times of porous media by using the so-called Carr-Purcell-Meiboom-Gill (CPMG) technique. We introduce the principles of NMR, the CPMG technique and the signals produced, porous effects on the NMR relaxation times and discuss various numerical methods for the inverse problem of extracting the relaxation times from CPMG signals. The numerical methods for solving Fredholm integral equations of the first kind are sketched from a series expansion perspective. A method of using arbitrary constituent functions for improving the performance of non-negative least squares (NNLS) is developed and applied to several synthesized data sets and real experimental data sets of saturated porous glass gels. The data sets were obtained by the author of this thesis and the experimental procedure will be presented. We discuss the imperfections in the assumptions on the physical and numerical models, the numerical schemes, and the experimental results, which may lead to new research possibilities.

Nuclear magnetic resonance (NMR) spectroscopy technique is becoming exceedingly significant due to its capability of studying protein structures in solution. However, NMR protein structure determination has remained a laborious and costly process until now, even with the help of currently available computer programs. After the NMR spectra are collected, the main road blocks to the fully automated NMR protein structure determination are peak picking from noisy spectra, resonance assignment from imperfect peak lists, and structure calculation from incomplete assignment and ambiguous nuclear Overhauser enhancements (NOE) constraints. The goal of this dissertation is to propose error-tolerant and highly-efficient methods that work well on real and noisy data sets of NMR protein structure determination and the closely related protein structure prediction problems. One major contribution of this dissertation is to propose a fully automated NMR protein structure determination system, AMR, with emphasis on the parts that I contributed. AMR only requires an input set with six NMR spectra. We develop a novel peak picking method, PICKY, to solve the crucial but tricky peak picking problem. PICKY consists of a noise level estimation step, a component forming step, a singular value decomposition-based initial peak picking step, and a peak refinement step. The first systematic study on peak picking problem is conducted to test the performance of PICKY. An integer linear programming (ILP)-based resonance assignment method, IPASS, is then developed to handle the imperfect peak lists generated by PICKY. IPASS contains an error-tolerant spin system forming method and an ILP-based assignment method. The assignment generated by IPASS is fed into the structure calculation step, FALCON-NMR. FALCON-NMR has a threading module, an ab initio module, an all-atom refinement module, and an NOE constraints-based decoy selection module. The entire system, AMR, is successfully tested on four out of five real proteins with practical NMR spectra, and generates 1.25A, 1.49A, 0.67A, and 0.88A to the native reference structures, respectively. Another contribution of this dissertation is to propose novel ideas and methods to solve three protein structure prediction problems which are closely related to NMR protein structure determination. We develop a novel consensus contact prediction method, which is able to eliminate server correlations, to solve the protein inter-residue contact prediction problem. We also propose an ultra-fast side chain packing method, which only uses local backbone information, to solve the protein side chain packing problem. Finally, two complementary local quality assessment methods are proposed to solve the local quality prediction problem for comparative modeling-based protein structure prediction methods.

Calcium and calmodulin are implicated in mediating the Ca2+-dependent regulation of gap junctions that are essential for the intercellular transmission of molecules such as nutrients, metabolites, metal ions and signal messengers (< 1000 Da) through its specialized cell membrane channels and communication to extracellular environment. To understand the key determinants for calcium and calmodulin regulation of gap junction, in this study, we identified a calmodulin binding domain in the second half of the intracellular loop of Cxonnexin50 (the major gap junction protein found in an eye lens) using peptide fragments that encompass predicted CaM binding sites and various biophysical methods. Our study provides the first direct evidence that CaM binds to a specific region of the ubiquitous gap junction protein Cx50 in a Ca2+-dependent manner. Furthermore, two novel CaM binding regions in cytosolic loop and C-termini of Connexin43 (the most ubiquitous connexin) have been shown to interact with CaM with different binding modes in the presence of Ca2+ using high resolution NMR. Our results also elucidate the molecular determinants of regulation of gap junction by multiple CaM targeting regions and provide insight into the molecular basis of gap junction gating mechanism and the binding of CaM to the cytoslic region Cx43-3p as the major regulation site. Upon response to the cytosolic calcium increase, CaM binds to the cytosolic loop to result in the conformational change of gap junction and close the channel. It is possible for CaM to use an adjacent region as an anchor close to the regulation site to allow for fast response. Since a large number of residues in the Cxs mutated in human diseases reside at the highly identified CaM binding sites in Cxs, our studies provide insights into define the critical cellular changes and molecular mechanisms contributing to human disease pathogenesis as part of an integrated molecular model for the calcium regulation of GJs. In addition, we have applied the grafting approach to probe the metal binding capability of predicted EF-hand motifs within the streptococcal hemoprotein receptor (Shr) of Streptococcus pyrogenes as well as the nonstructural protein 1 (nsP1) of Sindbis virus and Poxvirus. This fast and robust method allows us to analyze putative EF-hand proteins at genome-wide scale and to further visualize the evolutionary scenario of the EF-hand protein family. Further, mass spectrometry has also been applied to probe modification of proteins such as CaM labeling by florescence dye and 7E15 by PEG.

Wood is our most important renewable resource. We need better quality and quantity both according to the wood itself and the processes that are using wood as a raw material. Hence, the understanding of the chemical composition of the wood is of high importance. Improved and new methods for analyzing wood are important to achieve better knowledge about both refining processes and raw material. The combination of NMR and multivariate analyses (MVA) is a powerful method for these analyses but so far it has been limited mainly to 1D NMR. In this project, we have developed methods for combining 2D NMR and MVA in both wood analysis and metabolomics. This combination was used to compare samples from normal wood and tension wood, and also trees with a down regulation of a pectin responsible gene. Dissolving pulp was also examined using the same combination of 2D-NMR and MVA, together with FT-IR and solid state 13C CP-MAS NMR. Here we focused on the difference between wood type (softwood and hardwood), process type (sulfite and sulfate) and viscosity. These methods confirmed and added knowledge about the dissolving pulp. Also reactivity was compared in relation to morphology of the cellulose and pulp composition. Based on the method and software used in the wood analysis projects, a new method called HSQC-STOCSY was developed. This method is especially suited for assignment of substances in complex mixtures. Peaks in 2D NMR spectra that correlate between different samples are plotted in correlation plots resembling regular NMR spectra. These correlation plots have great potential in identifying individual components in complex mixtures as shown here in a metabolic data set. This method could potentially also be used in other areas such as drug/target analyses, protein dynamics and assignment of wood spectra.

Deuteron 1D and 2D NMR spectroscopy was used to study the dynamics of water molecules within the mesoporous material MCM-41. The deuteron spectra show three magnetization components for a sample hydrated to a 0.2 monolayer level. One component was assigned to the pore surface silanol group deuterons that exhibit a broad Gaussian line of 32.6 kHz FWHM and the other components were assigned to the water deuterons. At room temperature one water deuteron component has a powder pattern line shape (splitting of about 4.2 kHz and population of about 61%) and the other has a Lorentzian line shape (about 388 Hz FWHM and population of 39%). Magnetization exchange occurs between these components. An exchange model, based on multi-site exchange, was constructed and used to analyse the results for exchange. For the 0.2 monolayer sample the rate of magnetization exchange out of the hydration site where the water deuterons exhibit a Lorentzian line in the deuteron spectra is 1.3 ms. 2D measurements at 233 K and room temperature confirmed the magnetization exchange scenario for the two water deuteron sites. Combining the deuteron results with proton-silicon cross polarization magic angle spinning experiments together with heat treatment of the sample, definitive hydration site identification for MCM-41 was achieved. This study has shown that the water molecules bound to the hydrogen-bonded silanol groups produce the powder pattern while water molecules bound to the single silanol groups produce the Lorentzian line. This represents a necessary first step toward a meaningful modeling of NMR observables in terms of site-specific water molecule coordination and dynamics in MCM-41.

This thesis provides an introduction to and analysis of the problem of determining nuclear magnetic resonance (NMR) relaxation times of porous media by using the so-called Carr-Purcell-Meiboom-Gill (CPMG) technique. We introduce the principles of NMR, the CPMG technique and the signals produced, porous effects on the NMR relaxation times and discuss various numerical methods for the inverse problem of extracting the relaxation times from CPMG signals. The numerical methods for solving Fredholm integral equations of the first kind are sketched from a series expansion perspective. A method of using arbitrary constituent functions for improving the performance of non-negative least squares (NNLS) is developed and applied to several synthesized data sets and real experimental data sets of saturated porous glass gels. The data sets were obtained by the author of this thesis and the experimental procedure will be presented. We discuss the imperfections in the assumptions on the physical and numerical models, the numerical schemes, and the experimental results, which may lead to new research possibilities.

Nuclear magnetic resonance (NMR) spectroscopy technique is becoming exceedingly significant due to its capability of studying protein structures in solution. However, NMR protein structure determination has remained a laborious and costly process until now, even with the help of currently available computer programs. After the NMR spectra are collected, the main road blocks to the fully automated NMR protein structure determination are peak picking from noisy spectra, resonance assignment from imperfect peak lists, and structure calculation from incomplete assignment and ambiguous nuclear Overhauser enhancements (NOE) constraints. The goal of this dissertation is to propose error-tolerant and highly-efficient methods that work well on real and noisy data sets of NMR protein structure determination and the closely related protein structure prediction problems. One major contribution of this dissertation is to propose a fully automated NMR protein structure determination system, AMR, with emphasis on the parts that I contributed. AMR only requires an input set with six NMR spectra. We develop a novel peak picking method, PICKY, to solve the crucial but tricky peak picking problem. PICKY consists of a noise level estimation step, a component forming step, a singular value decomposition-based initial peak picking step, and a peak refinement step. The first systematic study on peak picking problem is conducted to test the performance of PICKY. An integer linear programming (ILP)-based resonance assignment method, IPASS, is then developed to handle the imperfect peak lists generated by PICKY. IPASS contains an error-tolerant spin system forming method and an ILP-based assignment method. The assignment generated by IPASS is fed into the structure calculation step, FALCON-NMR. FALCON-NMR has a threading module, an ab initio module, an all-atom refinement module, and an NOE constraints-based decoy selection module. The entire system, AMR, is successfully tested on four out of five real proteins with practical NMR spectra, and generates 1.25A, 1.49A, 0.67A, and 0.88A to the native reference structures, respectively. Another contribution of this dissertation is to propose novel ideas and methods to solve three protein structure prediction problems which are closely related to NMR protein structure determination. We develop a novel consensus contact prediction method, which is able to eliminate server correlations, to solve the protein inter-residue contact prediction problem. We also propose an ultra-fast side chain packing method, which only uses local backbone information, to solve the protein side chain packing problem. Finally, two complementary local quality assessment methods are proposed to solve the local quality prediction problem for comparative modeling-based protein structure prediction methods.

Quantum information processing devices promise to solve some problems more efficiently than their classical counterparts. The source of the speedup is the structure of quantum theory itself. In that sense, the physical units that are the building blocks of such devices are its power. The quest then is to find or manufacture a system that behaves according to quantum theory, and yet is controllable in such a way that the desired algorithms can be implemented. Candidate systems are benchmarked against general criteria to evaluate their success. In this thesis, I advance a particular system and present the progress made towards each of these criteria. The system is a three-qubit 13C solid-state nuclear magnetic resonance (NMR) based quantum processor. I report results concerning system characterization and control, pseudopure state preparation, and quantum error correction. I also report on using the system to test a central question in the foundation of quantum mechanics.