Puckering Coordinates of Monocyclic Rings by Triangular Decomposition

We describe a new method of describing the pucker of an N-member monocyclic ring using N−3 parameters. To accomplish this, three ring atoms define a reference plane, and the remainder of the ring is decomposed into triangular flaps. The angle of incidence for each flap upon the reference plane is then measured. The combination of these angles is characteristic of the ring\u27s pucker. This puckering coordinate system is compared to existing reduced parameter systems to describe rings using a cyclohexane molecule. We show that this method has the same descriptive power of previous systems while offering advantages in molecular simulations

Developing a triangular tessellation method for the analysis of medium ring pucker conformations

The main focus of this thesis is to investigate the relative conformational flexibilities of α-, β- and γ-cyclodextrins in water by analysing their macrocyclic ring puckering motion from Molecular Dynamics (MD) simulations. In particular, the puckering of the CDs is investigated through a coarse grained analysis of full atomistic simulations, where the CD conformational motions are studied on the macrocyclic scale rather than the atomistic scale. The flexibilities of the cyclodextrins (CDs) are then compared to their experimentally-observed aqueous solubility trend in order to try explain the anomalously flow solubility of β-cyclodextrin. β-CD has important applications in industry, such as the pharmaceutical industry, thus exploring the conformational reasons for its low solubility can help to design more effective cyclodextrin-based products in future. The ring puckering of the CDs is measured quantitatively using a reduced system of puckering coordinates based on the method of triangular tessellation. The triangular tessellation definition for monocylic 6-membered rings is first extended to 7- and 8-membered rings, and the corresponding puckering coordinates are derived mathematically. The macrocyclic CD rings are then simplified to monocyclic representations through an appropriate coarse graining of the molecules (specifically, α-, β- and γ-cyclodextrins are simplified to 6-, 7- and 8-sided rings, respectively), and the corresponding triangular tessellation definition is then used to measure their macrocyclic puckering. The rates of decay of the puckering motion are then calculated using time correlation functions, from which the relative flexibilities of the CDs is determined. Probability distributions are also used to investigate the ranges of the CD puckering. In addition, the horizontal contraction and expansion of the macrocyclic rings (termed """"breathing"""" herein) is analysed to supplement the puckering analysis. Puckering coordinates based on the triangular tessellation of 6-membered rings have been used previously to characterise all 38 canonical states of cyclohexane. In this thesis, a systematic procedure is developed to generate the triangular tessellation puckering coordinates of all the canonical states of 6-, 7- and 8-membered rings, and the coordinates for all canonical states of cycloheptane and cyclooctane are subsequently generated. These puckering coordinates can be useful not only in the conformational analysis of cyclohexane, cycloheptane and cyclooctane, but also to quantitatively characterise the conformations of 6-, 7- and 8-membered rings in general, both from experimental and computational studies

Developing methods to construct ring pucker free energy hypersurfaces applied to the analysis of glycosidase enzyme catalytic mechanisms

Includes bibliographical references.Carbohydrates consist of one or more sub-units usually various 5- and 6-membered cycles (furanoses and pyranoses) which can twist, bend or flip into a variety of conformers that differ in strain - this is ring puckering. These puckers notably the strained puckering conformers are observed during enzymatically assisted bond formation or cleavage of the glycosidic bonds of carbohydrate substrates. In this thesis, the free energy of ring puckering is calculated by implementing the Hill-Reilly reduced coordinate pucker description into the sampling enhancing Free Energies from Adaptive Reaction Coordinate Forces (FEARCF) method. FEARCF non-Boltzmann simulations of prototypical sugars β-Dribose and β-D-glucose converged to yield free energy pucker surfaces and volumes when using several semi-empirical QM methods - AM1, PM3, PM3CARB-1 and SCC-DFTB. From this, the accessible puckering conformations and minimum free energy paths of puckering were reasoned An analysis of the furanose and pyranose free energy pucker surfaces and volumes compared with both Density Functional Theory RB3LYP/6-311++G** optimised structures and a Hartree-Fock free energy surface revealed that SCC-DFTB provides the best semi-empirical description of 5- and 6- membered carbohydrate ring deformation. This illustrates that necessary high energy ring conformations observed in enzymatic binding sites requires the enzyme to induce and preserve high energy conformations required for successful hydrolyses and synthesis of the glycosidic bond. To further test this hypothesis, a 5- and 6-membered cycle were studied within enzymatic environments. The polysaccharide cellulose contains β 1-4 linked glucose subunit and is degraded by cellulase, a glycosidase. Specifically, the retaining cellobiohydrolase I (CBHI) of Trichoderma Reesei which cleaves cellobiose units from crystalline cellulose.The free energy volumes of puckering for the glucose sub-unit (in the catalytic position of an 8 unit cellulosic fragment - cellooctaose) were calculated and explored in vacuum, water and in the active site of CBHI. It was observed that the binding pocket of enzymes limits the ring pucker and that the active site amino acids preferentially stabilise certain puckering conformations. For CBHI, the first part of the glycosidase reaction is the glycosylation step. This was driven to completion during SCC-DFTB QM/MD FEARCF calculations where GLU212, ASP214 and GLU217 and part of the substrate were treated quantum mechanically. The general hybrid orbital method was used to connect the QM and MM regions. The free energy barriers of glycosylation were computed and the puckering statistics during the conversion of cellooctaose to products were correlated with this. Guanosine, a 5-membered ribose derivative is phosphorylated by Purine Nucleoside Phosphorylase (PNP) in order to salvage the guanine base. The effect of the PNP protein environment on ring pucker was studied by using FEARCF SCC-DFTB QM/MD non Boltzmann free energy calculations to quantify the pucker change induced in guanosine when changing environment from vacuum, to water and to the protein. In vacuo, the E4 and E1 pucker conformers were observed as minima. Upon solvation, the puckering phase space became less restricted with the 3T4 and 2T3 pucker conformers as minima. In the PNP active site pucker became restricted with only the 4E conformer observed

Visualisation of Cyclic and Multi-Branched Molecules with VMD

We report the addition of two visualisation algorithms, termed PaperChain and Twister, to the freely available Visual Molecular Dynamics (VMD) package. These algorithms produce visualisations of complex cyclic molecules and multi-branched polysaccharides and are a generalization and optimization of those we previously developed in a standalone package for carbohydrates. PaperChain highlights each ring in a molecular structure with a polygon, which is coloured according to the ring pucker. Twister traces glycosidic bonds with a ribbon that twists according to the relative orientation of successive sugar residues. Combination of these novel algorithms and new ring selection statements with the large set of visualisations already available in VMD allows for unprecedented flexibility in the level of detail displayed for glycoconjugate, glycoprotein and carbohydrate-binding protein structures, as well as other cyclic structures. We highlight the efficacy of these algorithms with selected illustrative examples, clearly demonstrating the value of the new visualisations, not only for structure validation, but also for facilitating insights into molecular structure and mechanism

Sodium ion interactions with aqueous glucose: Insights from quantum mechanics, molecular dynamics, and experiment

In the last several decades, significant efforts have been conducted to understand the fundamental reactivity of glucose derived from plant biomass in various chemical environments for conversion to renewable fuels and chemicals. For reactions of glucose in water, it is known that inorganic salts naturally present in biomass alter the product distribution in various deconstruction processes. However, the molecular-level interactions of alkali metal ions and glucose are unknown. These interactions are of physiological interest as well, for example, as they relate to cation-glucose cotransport. Here, we employ quantum mechanics (QM) to understand the interaction of a prevalent alkali metal, sodium, with glucose from a structural and thermodynamic perspective. The effect on B-glucose is subtle: a sodium ion perturbs bond lengths and atomic partial charges less than rotating a hydroxymethyl group. In contrast, the presence of a sodium ion significantly perturbs the partial charges of α-glucose anomeric and ring oxygens. Molecular dynamics (MD) simulations provide dynamic sampling in explicit water, and both the QM and the MD results show that sodium ions associate at many positions with respect to glucose with reasonably equivalent propensity. This promiscuous binding nature of Na + suggests that computational studies of glucose reactions in the presence of inorganic salts need to ensure thorough sampling of the cation positions, in addition to sampling glucose rotamers. The effect of NaCl on the relative populations of the anomers is experimentally quantified with light polarimetry. These results support the computational findings that Na + interacts similarly with a- and B-glucose

Computational Prediction and Rational Design of Novel Clusters, Nanoparticles, and Solid State Materials

The creation of new materials is absolutely essential for developing new technologies. However, experimental efforts toward the material discovery are usually based on trial-and-error approach and thus require a huge amount of time and money. Alternatively, computational predictions can now provide a more systematic, rapid, inexpensive, and reliable method for the design of novel materials with properties suitable for new technologies. This dissertation describes the technique of theoretical predictions and presents the results on the successfully predicted and already produced (in some cases) unusual molecules, clusters, nanoparticles, and solids. The major part of scientific efforts in this dissertation was devoted to rationalizing of size- and composition-dependent properties of the materials based on understanding of their electronic structure and chemical bonding. It was shown that understanding relations between bonding and geometric structure, bonding and stability, and bonding and reactivity is an important step toward rational design of new, yet unknown materials with unusual properties. Our findings led to the discovery of the first simplest inorganic double helix structures, which can be used in the design of novel molecular devices. A significant part of this work also deals with the pseudo John-Teller effect, which potentially can be a powerful tool for rationalizing and predicting molecular and solid state structures, their deformations, transformations, and properties. Therefore, the works on the pseudo Jahn-Teller effect presented in this dissertation can be considered the steps toward further generalization and elevation of the pseudo Jahn-Teller effect to a higher level of understanding of the origin of molecular and solid state properties

Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2

The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes, such as cell adhesion and recognition. To understand the process of protein glycosylation, the reaction mechanisms of the participating enzymes need to be known. However, the reaction mechanism of retaining glycosyltransferases has not yet been sufficiently explained. Here we investigated the catalytic mechanism of human isoform 2 of the retaining glycosyltransferase polypeptide UDP-GalNAc transferase by coupling two different QM/MM-based approaches, namely a potential energy surface scan in two distance difference dimensions and a minimum energy reaction path optimisation using the Nudged Elastic Band method. Potential energy scan studies often suffer from inadequate sampling of reactive processes due to a predefined scan coordinate system. At the same time, path optimisation methods enable the sampling of a virtually unlimited number of dimensions, but their results cannot be unambiguously interpreted without knowledge of the potential energy surface. By combining these methods, we have been able to eliminate the most significant sources of potential errors inherent to each of these approaches. The structural model is based on the crystal structure of human isoform 2. In the QM/MM method, the QM region consists of 275 atoms, the remaining 5776 atoms were in the MM region. We found that ppGalNAcT2 catalyzes a same-face nucleophilic substitution with internal return (SNi). The optimized transition state for the reaction is 13.8 kcal/mol higher in energy than the reactant while the energy of the product complex is 6.7 kcal/mol lower. During the process of nucleophilic attack, a proton is synchronously transferred to the leaving phosphate. The presence of a short-lived metastable oxocarbenium intermediate is likely, as indicated by the reaction energy profiles obtained using high-level density functionals

A stereoelectronic and thermodynamic study of b-D-methyl glucose conformational changes related to anomeric centre reactivity

Includes bibliographical references.The major part of this thesis focuses on investigating the rationale for ring deformation of -D-methyl glucose in glycosidase reactions (for example, cellulose hydrolysis). The investigation is computational and is done in isolation from the enzyme binding pocket and incoming nucleophile. What is the effect of the C1-O1 bond breaking process on key glucose properties is the central question asked and answered in this thesis. A battery of ab initio methods is used to uncover details of the glucose ring pucker free energy volumes. The free energy volumes were computed using the Free Energy from Adaptive Reaction Coordinate Forces (FEARCF) method. The bond stretch of the C1-O1 bond in -D-methyl glucose serves as a sugar model for hydrolysis, following the DN*AN mechanism. The FEARCF method has been employed as it was previously shown to generate molecular sampling traversing all of pucker phase space resulting in a multidimensional free energy surfaces (or volumes). Density functional theory and post SCF analysis have been used to investigate the stereoelectronic changes that occur during ring deformation. In particular, changes involving the anomeric carbon, that is the C1-O1, C1-O5 bond distances, electron densities and charges of the C1, O5 and O1 atoms

Análise estrutural e conformacional de carboidratos depositados no Protein Data Bank

Os carboidratos são bem conhecidos por suas características físico-químicas, biológicas, funcionais e terapêuticas. Infelizmente, sua natureza química impõe sérios desafios para a elucidação estrutural desses fenômenos, prejudicando não apenas a profundidade de nossa compreensão dos carboidratos, mas também o desenvolvimento de novas aplicações biotecnológicas e terapêuticas baseadas nessas moléculas. No passado recente, a quantidade de informações estruturais, obtidas principalmente da cristalografia de raios-X, aumentou progressivamente, assim como sua qualidade. Nesse contexto, o presente trabalho apresenta uma análise global das informações sobre carboidratos disponíveis em todo o principal banco de dados de estruturas cristalográficas, Protein Data Bank (PDB). A partir de estruturas de alta qualidade, fica claro que a maioria dos dados está altamente concentrada em alguns tipos de resíduos, principalmente em suas formas monossacarídicas e com um nível limitado de ramificação. As geometrias adotadas pelas ligações glicosídicas podem estar principalmente associadas aos tipos de ligações em vez dos resíduos, enquanto o nível de distorção dos monossacarídeos, baseado em medições do puckering, foi caracterizado, quantificado e localizado em uma paisagem de equilíbrio pseudo-rotacional - não apenas para mínimos locais, mas também para estados de transição. Além disso, foi realizado um ajuste de parâmetros já existentes para simulações de dinâmica molecular de hexopiranose (GROMOS53a6GLYC), a fim de descrever corretamente o equilíbrio de conformações presentes nos monossacarídeos in silico. Essas análises qualitativas e quantitativas oferecem uma imagem global do conteúdo estrutural de carboidratos no PDB, potencialmente apoiando a construção de novos modelos para fenômenos biológicos relacionados a carboidratos no nível atomístico. Além disso, o cuidado com a representação correta dessas moléculas auxilia em estudos futuros sobre as propriedades terapêuticas e atomísticas dessas importantes biomoléculas.Carbohydrates are well known for their physico-chemical, biological, functional and therapeutic characteristics. Unfortunately, their chemical nature impose severe challenges for the structural elucidation of these phenomena, impairing not only the depth of our understanding of carbohydrates, but also the development of new biotechnological and therapeutic applications based on these molecules. In the recent past, the amount of structural information, obtained mainly from X-ray crystallography, has increased progressively, as well as its quality. In this context, the current work presents a global analysis of the carbohydrate information available on the entire Protein Data Bank. From high quality structures, it is clear that most of the data is highly concentrated on a few set of residue types, mainly on their monosaccharidic forms and with a limited level of branching. The geometries adopted by glycosidic linkages can be mostly associated to the types of linkages instead of the residues, while the level of puckering distortion was characterized, quantified and located in a pseudorotational equilibrium landscape - not only to local minima, but also to transitional states. Furthermore an adjustment of already existing parameters for hexopyranoses molecular dynamics simulations (GROMOS53a6GLYC) was performed, in order to correctly describe the equilibrium of conformations present in monosaccharides in silico. These qualitative and quantitative analyses offer a global picture of carbohydrate structural content on PDB, potentially supporting the building of new models for carbohydrate related biological phenomena at the atomistic level. In addition, the care for the correct representation of these molecules in silico aids in future studies regarding the therapeutical and atomistic properties of such important biomolecules