Ab Initio Molecular Dynamics Study of Thiolate-Protected Gold Clusters and Their
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Trimethylsilyl Trifluoromethanesulfonate-Mediated Additions to Acetals, Nitrones, and Aminals Chelsea Safran
University of Richmond UR Scholarship Repository Honors Theses Student Research 4-1-2013 Trimethylsilyl trifluoromethanesulfonate-mediated additions to acetals, nitrones, and aminals Chelsea Safran Follow this and additional works at: http://scholarship.richmond.edu/honors-theses Recommended Citation Safran, Chelsea, "Trimethylsilyl trifluoromethanesulfonate-mediated additions to acetals, nitrones, and aminals" (2013). Honors Theses. Paper 71. This Thesis is brought to you for free and open access by the Student Research at UR Scholarship Repository. It has been accepted for inclusion in Honors Theses by an authorized administrator of UR Scholarship Repository. For more information, please contact [email protected]. Trimethylsilyl trifluoromethanesulfonate-mediated additions to acetals, nitrones, and aminals By Chelsea Safran Honors Thesis In Program In Biochemistry and Molecular Biology University of Richmond Richmond, VA Spring 2012 Advisor: Dr. C. Wade Downey This thesis has been accepted as part of the honors requirements in the Program in Biochemistry and Molecular Biology ______________________________ _________________ (advisor signature) (date) ______________________________ _________________ (reader signature) (date) Table of Contents i. Acknowledgements ii ii. Abstract iii iii. Chapter I: Introduction 1-4 iv. Chapter II: Amides 4-15 v. Chapter III: I. Bisthione Synthesis 16-18 II. Reactions with other N,O-acetals 18-22 vi. Chapter IV: I. Additions to Nitrones 22-25 II. Future Work 25 vii. Chapter V: Experimental I. N,O-acetal Formation 25-28 II. Addition to Nitrones 28-29 viii. Chapter VI: References 30 i Acknowledgments I would like to acknowledge my research Dr. Wade Downey for all of his time and dedication to my research for the past two years. -
1. INTRODUCTION Geometric Structure
1. INTRODUCTION Clusters, in general, are aggregates of atoms that are too large compared to atoms and molecules and too small compared to small pieces of crystals (bulk materials). Generally, clusters does not have the same structure or atomic arrangements as a bulk solid and can change its structure with the addition of just one or few atoms. As the number of atoms in the cluster increase, the bulk structure is established and the addition of atoms has no more effect on the structure. Of course there will be some rearrangement of the atoms on the surface of this bulk structure, but since the surface to volume ratio is very low in bulk material it can be neglected with a good approximation. However, in case of clusters, most of the atoms lie on the surface (extremely high surface to volume ratio) and such rearrangement produce a drastic effect. Owning to their high surface to volume ratio, the surface science from both chemical and physical point of view has become crucial in order to collect data and information about such systems. The ways to study such small cluster is nearly the same as the way they have been fabricated. With Bottom-up approach (chemical point of view) these clusters are formed from atoms and/or molecules by assembling it together to form the cluster, and there were many calculation based on this view point. Also these clusters can be fabricated, starting from the bulk material by reducing its dimension somehow, which is the Top-down approach. Geometric structure Usually the crystal structure of a large nanocluster is the same as the bulk structure of the material, with somewhat different lattice parameters (in general clusters are slightly contracted as compared to bulk). -
Labeling with Nanogold and Undecagold: Techniques and Results
Scanning Microscopy Volume 1996 Number 10 The Science of Biological Specimen Article 25 Preparation for Microscopy 8-15-1996 Labeling with Nanogold and Undecagold: Techniques and Results James F. Hainfeld Brookhaven National Laboratory, New York, [email protected] Follow this and additional works at: https://digitalcommons.usu.edu/microscopy Part of the Biology Commons Recommended Citation Hainfeld, James F. (1996) "Labeling with Nanogold and Undecagold: Techniques and Results," Scanning Microscopy: Vol. 1996 : No. 10 , Article 25. Available at: https://digitalcommons.usu.edu/microscopy/vol1996/iss10/25 This Article is brought to you for free and open access by the Western Dairy Center at DigitalCommons@USU. It has been accepted for inclusion in Scanning Microscopy by an authorized administrator of DigitalCommons@USU. For more information, please contact [email protected]. Scanning Microscopy Supplement 10, 1996 (pages 309-325) 0892-953X/96$5.00+ .25 Scanning Microscopy International, Chicago (AMF O'Hare), IL 60666 USA LABELING WITH NANOGOLD AND UNDECAGOLD: TECHNIQUES AND RESULTS James F. Hainfeld Brookhaven National Laboratory, Biology Department, Upton, NY (Received for publication October 3, 1995 and in revised form August 15, 1996) Abstract Introduction A significant new development in gold labeling for The purpose of this review is to provide an intro microscopy has been achieved through the use of gold duction to the gold clusters (Nanogold, Undecagold, and cluster compounds that are covalently attached to FluoroNanogold), covering their properties and coupling antibodies or other probe molecules. These unique gold chemistry. Next, examples of their use in labeling of probes are smaller than most colloidal gold conjugates specific sites on biomolecules for high resolution struc and exhibit improved penetration into tissues, higher tural studies will be given; results using gold clusters in labeling densities, and allow many new probes to be immunolabeling will also be given. -
Furanosyl Oxocarbenium Ion Conformational Energy Landscape
DOI: 10.1002/chem.201900651 Full Paper & Stereoselectivity |Hot Paper| Furanosyl Oxocarbenium Ion Conformational Energy Landscape Maps as a Tool to Study the Glycosylation Stereoselectivity of 2-Azidofuranoses, 2-Fluorofuranoses and Methyl Furanosyl Uronates Stefan van der Vorm, Thomas Hansen, Erwin R. van Rijssel, Rolf Dekkers, Jerre M. Madern, Herman S. Overkleeft, Dmitri V. Filippov, Gijsbert A. van der Marel, and Jeroen D. C. Code*[a] Abstract: The 3D shape of glycosyl oxocarbenium ions de- ic furanoses by using a combined computational and experi- termines their stability and reactivity and the stereochemical mental approach. Surprisingly, all furanosyl donors studied course of SN1 reactions taking place on these reactive inter- react in a highly stereoselective manner to provide the 1,2- mediates is dictated by the conformation of these species. cis products, except for the reactions in the xylose series. The nature and configuration of functional groups on the The 1,2-cis selectivity for the ribo-, arabino- and lyxo-config- carbohydrate ring affect the stability of glycosyl oxocarbeni- ured furanosides can be traced back to the lowest-energy 3E um ions and control the overall shape of the cations. We or E3 conformers of the intermediate oxocarbenium ions. herein map the stereoelectronic substituent effects of the The lack of selectivity for the xylosyl donors is related to the C2-azide, C2-fluoride and C4-carboxylic acid ester on the sta- occurrence of oxocarbenium ions adopting other conforma- bility and reactivity of the complete suite of diastereoisomer- tions. Introduction and they may in fact outweigh steric effects. For example, pro- tonated iminosugars, that is, carbohydrates having the endocy- Stereoelectonic effects dictate the shape and behaviour of clic oxygen replaced by a nitrogen, may change their confor- molecules. -
Evolution of Size and Shape in the Colloidal Crystallization of Gold Nanoparticles Owen C
Published on Web 06/06/2007 Evolution of Size and Shape in the Colloidal Crystallization of Gold Nanoparticles Owen C. Compton and Frank E. Osterloh* Contribution from the Department of Chemistry, UniVersity of California, DaVis, One Shields AVenue, DaVis, California 95161 Received December 17, 2006; E-mail: [email protected] Abstract: The addition of dodecanethiol to a solution of oleylamine-stabilized gold nanoparticles in chloroform leads to aggregation of nanoparticles and formation of colloidal crystals. Based on results from dynamic light scattering and scanning electron microscopy we identify three different growth mechanisms: direct nanoparticle aggregation, cluster aggregation, and heterogeneous aggregation. These mechanisms produce amorphous, single-crystalline, polycrystalline, and core-shell type clusters. In the latter, gold nanoparticles encapsulate an impurity nucleus. All crystalline structures exhibit fcc or icosahedral packing and are terminated by (100) and (111) planes, which leads to truncated tetrahedral, octahedral, and icosahedral shapes. Importantly, most clusters in this system grow by aggregation of 60-80 nm structurally nonrigid clusters that form in the first 60 s of the experiment. The aggregation mechanism is discussed in terms of classical and other nucleation theories. Introduction and of its interfacial energy. Growth can only continue when Periodic arrangement of inorganic particles, or colloidal crystals have reached a critical nucleation size, beyond which crystals, continues to be of great academic -
Discovery, Characterization, and Development of Small
DISCOVERY, CHARACTERIZATION, AND DEVELOPMENT OF SMALL MOLECULE INHIBITORS OF GLYCOGEN SYNTHASE Buyun Tang Submitted to the faculty of the University Graduate School in partial fulfillment of the requirements for the degree Doctor of Philosophy in the Department of Biochemistry and Molecular Biology, Indiana University June 2020 Accepted by the Graduate Faculty of Indiana University, in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Doctoral Committee ______________________________________ Thomas D. Hurley, Ph.D., Chair ______________________________________ Peter J. Roach, Ph.D. April 30, 2020 ______________________________________ Millie M. Georgiadis, Ph.D. ______________________________________ Steven M. Johnson, Ph.D. ______________________________________ Jeffrey S. Elmendorf, Ph.D. ii © 2020 Buyun Tang iii Dedication I dedicate this work to my beloved family, my grandparents, my parents, and my brother. iv Acknowledgement First and foremost, I would like to express my deepest gratitude to my thesis advisor, Dr. Thomas D. Hurley. I am grateful to have him as my research mentor over the past four years. He has continuously guided, supported, and inspired me during my study at IUSM. His passion for science and devotion of mentorship offered me the best training experience I could ever receive in graduate school. His easygoing personality reminded me of all the wonderful times inside and outside of the lab. I remember him instructing me handling crystal instrument hand by hand, flying with me to San Diego for a conference, and driving me to a farm restaurant at Illinois. Dr. Hurley is not only an outstanding research mentor, but also a trustful friend. I deeply thank him for all his time, patience, and encouragement along my graduate training. -
Transformation of Doped Graphite Into Cluster- Encapsulated Fullerene Cages
ARTICLE DOI: 10.1038/s41467-017-01295-9 OPEN Transformation of doped graphite into cluster- encapsulated fullerene cages Marc Mulet-Gas1, Laura Abella2, Maira R. Cerón 3, Edison Castro 3, Alan G. Marshall1,4, Antonio Rodríguez-Fortea 2, Luis Echegoyen3, Josep M. Poblet 2 & Paul W. Dunk 1 An ultimate goal in carbon nanoscience is to decipher formation mechanisms of highly ordered systems. Here, we disclose chemical processes that result in formation of high- 1234567890 symmetry clusterfullerenes, which attract interest for use in applications that span biome- dicine to molecular electronics. The conversion of doped graphite into a C80 cage is shown to occur through bottom-up self-assembly reactions. Unlike conventional forms of fullerene, the iconic Buckminsterfullerene cage, Ih-C60, is entirely avoided in the bottom-up formation mechanism to afford synthesis of group 3-based metallic nitride clusterfullerenes. The effects of structural motifs and cluster–cage interactions on formation of compounds in the solvent- extractable C70–C100 region are determined by in situ studies of defined clusterfullerenes under typical synthetic conditions. This work establishes the molecular origin and mechanism that underlie formation of unique carbon cage materials, which may be used as a benchmark to guide future nanocarbon explorations. 1 National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310, USA. 2 Departament de Química Física i Inorgànica, Universitat Rovira i Virgili, Tarragona 43007, Spain. 3 Department of Chemistry, University of Texas at El Paso, El Paso, TX 79968, USA. 4 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306, USA. Marc Mulet-Gas and Laura Abella contributed equally to this work. -
Increased Glycosidic Bond Stabilities in 4-C-Hydroxymethyl Linked Disaccharides ⇑ Gour Chand Daskhan, Narayanaswamy Jayaraman
Carbohydrate Research 346 (2011) 2394–2400 Contents lists available at SciVerse ScienceDirect Carbohydrate Research journal homepage: www.elsevier.com/locate/carres Increased glycosidic bond stabilities in 4-C-hydroxymethyl linked disaccharides ⇑ Gour Chand Daskhan, Narayanaswamy Jayaraman Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India article info abstract Article history: Three new hydroxymethyl-linked non-natural disaccharide analogues, containing an additional methy- Received 25 May 2011 lene group in between the glycosidic linkage, were synthesized by utilizing 4-C-hydroxymethyl-a-D- Received in revised form 24 August 2011 glucopyranoside as the glycosyl donor. A kinetic study was undertaken to assess the hydrolytic stabilities Accepted 25 August 2011 of these new disaccharide analogues toward acid-catalyzed hydrolysis, at 60 °C and 70 °C. The studies Available online 2 September 2011 showed that the disaccharide analogues were stable, by an order of magnitude, than naturally-occurring disaccharides, such as, cellobiose, lactose, and maltose. The first order rate constants were lower than Keywords: that of methyl glycosides and the trend of hydrolysis rate constants followed that of naturally-occurring Acid hydrolysis disaccharides. -Anomer showed faster hydrolysis than the b-anomer and the presence of axial hydroxyl Carbohydrates a Disaccharide analogues group also led to faster hydrolysis among the disaccharide analogues. Energy minimized structures, Glycosidic bond derived through molecular modeling, showed that dihedral angles around the glycosidic bond in disac- Kinetics charide analogues were nearly similar to that of naturally-occurring disaccharides. Oxocarbenium ion Ó 2011 Elsevier Ltd. All rights reserved. 1. Introduction determined to be important, prior to heterolysis of C1–O1 bond. -
Two Distinct Fluorescent Quantum Clusters of Gold Starting from Metallic Nanoparticles by Ph-Dependent Ligand Etching
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Springer - Publisher Connector Nano Res (2008) 1: 333 340 DOI 10.1007/s12274-008-8035-2 00333 Research Article Two Distinct Fluorescent Quantum Clusters of Gold Starting from Metallic Nanoparticles by pH-Dependent Ligand Etching Madathumpady Abubaker Habeeb Muhammed1, Subramani Ramesh1, Sudarson Sekhar Sinha2, Samir Kumar Pal2, and Thalappil Pradeep1( ) 1 DST Unit on Nanoscience (DST UNS), Department of Chemistry and Sophisticated Analytical Instrument Facility, Indian Institute of Technology Madras, Chennai 600 036, India 2 Unit for Nanoscience and Technology, Department of Chemical, Biological and Macromolecular Sciences, Satyendra Nath Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India Received: 30 July 2008 / Revised: 26 August 2008 / Accepted: 27 August 2008 ©Tsinghua Press and Springer-Verlag 2008. This article is published with open access at Springerlink.com ABSTRACT Two fl uorescent quantum clusters of gold, namely Au25 and Au8, have been synthesized from mercaptosuccinic acid-protected gold nanoparticles of 4 5 nm core diameter by etching with excess glutathione. While etching at pH ~3 yielded Au25, that at pH 7 8 yielded Au8. This is the fi rst report of the synthesis of two quantum clusters starting from a single precursor. This simple method makes it possible to synthesize well-defined clusters in gram quantities. Since these clusters are highly fl uorescent and are highly biocompatible due to their low metallic content, they can be used for diagnostic applications. KEYWORDS Gold cluster, glutathione, pH, ligand etching, fl uorescence Nanoparticles with a variety of shapes and sizes have but different, fluorescence emissions ranging from been synthesized as they offer numerous possibilities ultraviolet to near infrared with increasing number of to study size and shape-dependent variations of core atoms [6]. -
Functionalization of Gold Nanoparticles by Inorganic Entities
nanomaterials Review Functionalization of Gold Nanoparticles by Inorganic Entities Frédéric Dumur 1,* , Eddy Dumas 2 and Cédric R. Mayer 3,4,* 1 Aix Marseille Univ, CNRS, ICR, UMR 7273, F-13397 Marseille, France 2 Institut Lavoisier de Versailles, UMR CNRS 8180, Université de Versailles Saint-Quentin-en-Yvelines, F-78035 Versailles, France; [email protected] 3 Laboratoire LuMin, FRE CNRS 2036, CNRS, Université Paris-Sud, ENS Paris-Saclay, Université Paris-Saclay, F-91405 Orsay CEDEX, France 4 Département de Chimie, UFR des Sciences, Université de Versailles Saint-Quentin-en-Yvelines, F-78035 Versailles, France * Correspondence: [email protected] (F.D.); [email protected] (C.R.M.); Tel.: +33-0491289059 (F.D.) Received: 25 February 2020; Accepted: 13 March 2020; Published: 18 March 2020 Abstract: The great affinity of gold surface for numerous electron-donating groups has largely contributed to the rapid development of functionalized gold nanoparticles (Au-NPs). In the last years, a new subclass of nanocomposite has emerged, based on the association of inorganic molecular entities (IME) with Au-NPs. This highly extended and diversified subclass was promoted by the synergy between the intrinsic properties of the shell and the gold core. This review—divided into four main parts—focuses on an introductory section of the basic notions related to the stabilization of gold nanoparticles and defines in a second part the key role played by the functionalizing agent. Then, we present a wide range of inorganic molecular entities used to prepare these nanocomposites (NCs). In particular, we focus on four different types of inorganic systems, their topologies, and their current applications. -
Characterization of Glycosyl Dioxolenium Ions and Their Role in Glycosylation Reactions
ARTICLE https://doi.org/10.1038/s41467-020-16362-x OPEN Characterization of glycosyl dioxolenium ions and their role in glycosylation reactions Thomas Hansen 1,4, Hidde Elferink2,4, Jacob M. A. van Hengst1, Kas J. Houthuijs 2, Wouter A. Remmerswaal 1, Alexandra Kromm2, Giel Berden 3, Stefan van der Vorm 1, Anouk M. Rijs 3, Hermen S. Overkleeft1, Dmitri V. Filippov1, Floris P. J. T. Rutjes2, Gijsbert A. van der Marel1, Jonathan Martens3, ✉ ✉ ✉ Jos Oomens 3 , Jeroen D. C. Codée 1 & Thomas J. Boltje 2 1234567890():,; Controlling the chemical glycosylation reaction remains the major challenge in the synthesis of oligosaccharides. Though 1,2-trans glycosidic linkages can be installed using neighboring group participation, the construction of 1,2-cis linkages is difficult and has no general solution. Long-range participation (LRP) by distal acyl groups may steer the stereoselectivity, but contradictory results have been reported on the role and strength of this stereoelectronic effect. It has been exceedingly difficult to study the bridging dioxolenium ion intermediates because of their high reactivity and fleeting nature. Here we report an integrated approach, using infrared ion spectroscopy, DFT computations, and a systematic series of glycosylation reactions to probe these ions in detail. Our study reveals how distal acyl groups can play a decisive role in shaping the stereochemical outcome of a glycosylation reaction, and opens new avenues to exploit these species in the assembly of oligosaccharides and glycoconju- gates to fuel biological research. 1 Leiden University, Leiden Institute of Chemistry, Einsteinweg 55, 2333 CC Leiden, The Netherlands. 2 Radboud University Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands. -
Controlling the Stereoselectivity of Glycosylation Via Solvent Effects
Canadian Journal of Chemistry Controlling the Stereoselectivity of Glycosylation via Solvent Effects Journal: Canadian Journal of Chemistry Manuscript ID cjc-2016-0417.R1 Manuscript Type: Invited Review Date Submitted by the Author: 16-Sep-2016 Complete List of Authors: Kafle, Arjun; University of New Mexico Liu, Jun; University of New Mexico Cui, Lina; University of New Mexico, Chemistry and Chemical Biology; University Draftof New Mexico, UNM Comprehensive Cancer Center Glycosylation, Stereoselectivity, Synthesis, Solvent effect, Carbohydrate Keyword: chemistry https://mc06.manuscriptcentral.com/cjc-pubs Page 1 of 29 Canadian Journal of Chemistry Controlling the Stereoselectivity of Glycosylation via Solvent Effects Arjun Kafle, Jun Liu, and Lina Cui* Address: Department of Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, U.S.A. Corresponding author: e-mail: [email protected]; Tel: 505-277-6519; Fax: 505-277-2609 Invited Review Dedicated to Prof. David R. Bundle onDraft the occasion of his retirement (Special Issue for Prof. Bundle) 1 https://mc06.manuscriptcentral.com/cjc-pubs Canadian Journal of Chemistry Page 2 of 29 Abstract: This review covers a special topic in carbohydrate chemistry – solvent effects on the stereoselectivity of glycosylation reactions. Obtaining highly stereoselective glycosidic linkages is one of the most challenging tasks in organic synthesis, as it is affected by various controlling factors. One of the least understood factors is the effect of solvents. We have described the known solvent effects while providing both general rules and specific examples. We hope this review will not only help fellow researchers understand the known aspects of solvent effects and use that in their experiments, moreover we expect more studies on this topic will be started and continued to expand our understanding of the mechanistic aspects of solvent effects in glycosylation reactions.