The Huisgen Reaction: Milestones of the 1,3‐Dipolar Cycloaddition
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Stabilizing a Different Cyclooctatetraene Stereoisomer
Stabilizing a different cyclooctatetraene stereoisomer Longfei Lia,b, Ming Leia,1, Yaoming Xieb, Henry F. Schaefer IIIb,1, Bo Chenc, and Roald Hoffmannc,1 aState Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China; bCenter for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602; and cDepartment of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 Contributed by Roald Hoffmann, July 27, 2017 (sent for review June 6, 2017; reviewed by Henry Rzepa and Jay S. Siegel) An unconventional cis-cis-cis-trans or (Z,Z,Z,E) structure B of cyclo- (Z,Z,Z,E)-COT octatetraene (COT) is calculated to lie only 23 kcal/mol above the A Second COT Isomer. As did the above-cited authors, we located the well-known tub-shaped (Z,Z,Z,Z) isomer A; one example of this type (Z,Z,Z,E) isomer of COT (B) as a local minimum on its potential of structure is known. The barrier for B returning to A is small, energy surface. Throughout this paper, we use the ωB97X-D/cc- 3 kcal/mol. However, by suitable choice of substituents, the (Z,Z,Z,E) pVTZ (density functional theory method using the ωb97X-D func- isomer can be made to lie in energy below the tub-shaped structure. tional with correlation-consistent polarized valence triple-zeta basis Steric, clamping, and electronic strategies are proposed for achieving set) method of calculation (details are provided in SI Appendix) t B this. -
On Conducting Polymer Coated Electrodes: a Versatile Platform for the Modification of Electrode Surfacesa
Full Paper http://www.paper.edu.cn ‘‘Click’’ on Conducting Polymer Coated Electrodes: A Versatile Platform for the Modification of Electrode Surfacesa Yan Li, Weixia Zhang, Jing Chang, Jinchun Chen, Guangtao Li,* Yong Ju* Two types of N-substituted pyrroles with azide and terminal alkyne groups have been synthesized and electropolymerized. ‘‘Click’’ chemistry, specifically Huisgen 1,3-dipolar cycloaddition, was used as a general method for functionalization of the polypyrrole films. Several model compounds, including redox active (quinone), bioactive (cholic acid) and recognition elements (carbohydrate and thymi- dine) could easily be attached onto the electrode surfaces without loss of functionality or the elec- troactivity of the underlying conducting polymers. The results suggest that the polypyrrole films are clickable and provide a novel biocompatible and versatile platform for efficient modifications on electrode surfaces. Introduction catalysis.[1,2] A key factor in such investigations and applications is the achievement of an efficient interface The immobilization of functional units, such as electro- between the functional groups and the conductive active, bioactive and biological recognition elements, onto surface.[3,4] conductive surfaces is of enormous interest, both in Compared to various protocols developed for confining studies of functional groups themselves and in numerous functional units onto solid surfaces, electrodeposition of applications ranging from disease diagnosis to electro- conducting polymers offers a simple and -
The Case of Sterimol Steric Parameters A
Conformational Effects on Physical-Organic Descriptors – the Case of Sterimol Steric Parameters A. V. Brethomé,† S. P. Fletcher†* and R. S. Paton†§* †Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK §Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA Abstract Mathematical relationships which relate chemical structure with selectivity have provided quantitative insights underlying catalyst design and informing mechanistic studies. Flexible compounds, however, can adopt several distinct geometries and so can be challenging to describe using a single structure-based descriptor. How best to quantify the structural characteristics of an ensemble of structure poses both practical and technical difficulties. In this work we introduce an automated computational workflow which can be used to obtain multidimensional Sterimol parameters for a conformational ensemble of a given substituent from a single command. The Boltzmann-weighted Sterimol parameters obtained from this approach are shown to be useful in multivariate models of enantioselectivity, while the range of values from conformers within 3 kcal/mol of the most stable structure provides a visual way to capture a possible source of uncertainty arising in the resulting models. Implementing our approach requires no programming expertise and can be executed from within a graphical user interface using open-source programs. Introduction Steric effects are key nonbonding interactions influencing molecular conformation and -
New Chiral Auxiliaries for the [3+2]-Cycloaddition of Nonstabilised Azomethine Ylides
New Chiral Auxiliaries For The [3+2]-Cycloaddition Of Nonstabilised Azomethine Ylides Allan Rostrup Forup Jensen A thesis submitted in partial fulfilment of the degree of Doctor of Philosophy Christopher Ingold Laboratories University College London London 20 Gordon Street WC1H OAJ ProQuest Number: 10610918 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 10610918 Published by ProQuest LLC(2017). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106- 1346 /\cjmowieugemenis First and foremost I wish to thank my supervisor, Professor K. J. Hale, for the constant support, encouragement and guidance he has provided throughout the duration of this project. I also wish to take this opportunity to thank my sponsor, Rhone- Poulenc-Rorer, without whom this project would not have been possible. I also wish to thank past and present members of the Hale group for their friendship and encouragement. In particular, Dr. J. Cai was an invaluable help and inspiration. For their friendship and enormous support through good and bad times, Rukpong Tupprasoot, Neha Jogiya, Andrew Calabrese, Dr. Gurpreet Bhatia, Marc Hummersone, Rafaqat Hussain, also deserve to be mentioned. -
Heterocycles 2 Daniel Palleros
Heterocycles 2 Daniel Palleros Heterocycles 1. Structures 2. Aromaticity and Basicity 2.1 Pyrrole 2.2 Imidazole 2.3 Pyridine 2.4 Pyrimidine 2.5 Purine 3. Π-excessive and Π-deficient Heterocycles 4. Electrophilic Aromatic Substitution 5. Oxidation-Reduction 6. DNA and RNA Bases 7. Tautomers 8. H-bond Formation 9. Absorption of UV Radiation 10. Reactions and Mutations Heterocycles 3 Daniel Palleros Heterocycles Heterocycles are cyclic compounds in which one or more atoms of the ring are heteroatoms: O, N, S, P, etc. They are present in many biologically important molecules such as amino acids, nucleic acids and hormones. They are also indispensable components of pharmaceuticals and therapeutic drugs. Caffeine, sildenafil (the active ingredient in Viagra), acyclovir (an antiviral agent), clopidogrel (an antiplatelet agent) and nicotine, they all have heterocyclic systems. O CH3 N HN O O N O CH 3 N H3C N N HN N OH O S O H N N N 2 N O N N O CH3 N CH3 caffeine sildenafil acyclovir Cl S N CH3 N N H COOCH3 nicotine (S)-clopidogrel Here we will discuss the chemistry of this important group of compounds beginning with the simplest rings and continuing to more complex systems such as those present in nucleic acids. Heterocycles 4 Daniel Palleros 1. Structures Some of the most important heterocycles are shown below. Note that they have five or six-membered rings such as pyrrole and pyridine or polycyclic ring systems such as quinoline and purine. Imidazole, pyrimidine and purine play a very important role in the chemistry of nucleic acids and are highlighted. -
Steric Effects Vs. Electron Delocalization
RSC Advances PAPER View Article Online View Journal | View Issue Steric effects vs. electron delocalization: a new look into the stability of diastereomers, conformers Cite this: RSC Adv.,2021,11, 20691 and constitutional isomers† Sopanant Datta and Taweetham Limpanuparb * A quantum chemical investigation of the stability of compounds with identical formulas was carried out on 23 classes of compounds made of C, N, P, O and S atoms as core structures and halogens H, F, Cl, Br and I as Received 13th April 2021 substituents. All possible structures were generated and investigated by quantum mechanical methods. The Accepted 24th May 2021 prevalence of a formula in which its Z configuration, gauche conformation or meta isomer is the most stable DOI: 10.1039/d1ra02877d form is calculated and discussed. Quantitative and qualitative models to explain the stability of the 23 classes rsc.li/rsc-advances of halogenated compounds were also proposed. hyperconjugation in a similar vein to the ethane case,17,18 but Creative Commons Attribution-NonCommercial 3.0 Unported Licence. 1. Introduction the reasoning underlying the preference for meta isomer is still Steric effects, non-bonded interactions leading to avoidance of lacking. spatial congestion of atoms or groups, are oen the central In addition to carbon-backbone compounds in Table 1, there theme in the discussion of stability of diastereomers, are many experimental and theoretical studies for other back- 21 ] 22,23 ] 24 conformers and constitutional isomers. Reasoning based on bones discussed in this paper, namely, C3, C N, C P, 25–31 32 33,34 35 36,37 38–40 41 steric effects is relatively intuitive and gives rise to a generally N]N, N]P, P]P, C–N, C–P, C–O, C–S, N– 38,42–44 38,43 38,43,45,46 38,42,47 47 48,49 50 accepted rule of thumb that an E conguration, anti conformer N, N–P, P–P, N–O, N–S, P–O, P–S, O– 38,42,51,52 53,54 38,55 and para isomer in diastereomers, conformational and consti- O, O–S, and S–S. -
Combined Experimental and Theoretical Study of Poly(Aniline-Co-Pyrrole) Oligomer
ORE Open Research Exeter TITLE Combined experimental and theoretical study of poly(aniline-co-pyrrole) oligomer AUTHORS Kamran, Muhammad; Ullah, Habib; Shah, Anwar-ul-Haq A.; et al. JOURNAL Polymer DEPOSITED IN ORE 15 March 2016 This version available at http://hdl.handle.net/10871/20729 COPYRIGHT AND REUSE Open Research Exeter makes this work available in accordance with publisher policies. A NOTE ON VERSIONS The version presented here may differ from the published version. If citing, you are advised to consult the published version for pagination, volume/issue and date of publication Combined Experimental and Theoretical Study of Poly(Aniline-co-Pyrrole) Oligomer Habib Ullah*,a,b, Muhammad Kamranb, Salma Bibic, Anwar-ul-Haq A. Shah*,b, Asif A. Tahira, Khurshid Ayub*,d aEnvironment and Sustainability Institute (ESI), University of Exeter, Penryn Campus, Penryn, Cornwall TR10 9FE, UK bInstitute of Chemical Sciences, University of Peshawar, 25120 Peshawar, Pakistan cNational Centre of Excellence in Physical Chemistry, University of Peshawar, 25120 Peshawar, Pakistan. dDepartment of Chemistry, COMSATS Institute of Information Technology, University Road, Tobe Camp, 22060 Abbottabad, Pakistan * To whom corresponding should be addressed Email: [email protected] Abstract Quantum mechanical calculations are performed to establish the structure of an oligomer of aniline and pyrrole [Poly(Ani-co-Py)], through comparison of experimental and theoretically calculated properties, including conductivity. The copolymer was synthesized through chemical oxidative polymerization and then confirmed from the experimental IR, UV-vis, mass spectra, elemental, XRD, TGA, and SEM analysis. Quantum mechanical calculations are performed at Density Functional Theory (DFT) and Time dependent DFT (TD-DFT) methods for the electronic and spectroscopic properties of the oligomer. -
Reactions of Pyrrole, Imidazole, and Pyrazole with Ozone
Environmental Science Water Research & Technology View Article Online PAPER View Journal | View Issue Reactions of pyrrole, imidazole, and pyrazole with † Cite this: Environ. Sci.: Water Res. ozone: kinetics and mechanisms Technol., 2020, 6,976 Agnes Tekle-Röttering,‡a Sungeun Lim, ‡bc Erika Reisz,d Holger V. Lutze,efgj Mohammad Sajjad Abdighahroudi, e Sarah Willach,e Winfried Schmidt,af Peter R. Tentscher,h Daniel Rentsch, i Christa S. McArdell, b Torsten C. Schmidt *efg and Urs von Gunten*bc Five-membered nitrogen-containing heterocyclic compounds (azoles) belong to potential moieties in com- plex structures where transformations during ozonation can occur. This study focused on the azole–ozone chemistry of pyrrole, imidazole, and pyrazole as model compounds. Reaction kinetics and ozonation products were determined by kinetic and analytical methods including NMR, LC-HRMS/MS, HPLC-UV, and IC-MS. 1 Analyses of reactive oxygen species ( O2, ˙OH, H2O2), quantum chemical computations (Gibbs energies), and kinetic simulations were used to further support the proposed reaction mechanisms. The species-specific 6 −1 Creative Commons Attribution-NonCommercial 3.0 Unported Licence. second-order rate constants for the reactions of ozone with pyrrole and imidazole were (1.4 ± 1.1) × 10 M −1 5 −1 −1 s and (2.3 ± 0.1) × 10 M s , respectively. Pyrazole reacted more slowly with ozone at pH 7 (kapp =(5.6± 0.9) × 101 M−1 s−1). Maleimide was an identified product of pyrrole with a 34% yield. Together with other prod- ucts,formate,formamide,andglyoxal,CandNmassbalancesof∼50% were achieved. Imidazole reacted with ozone to cyanate, formamide, and formate (∼100% yields per transformed imidazole, respectively) with a closed mass balance. -
Computational Measurement of Steric Effects: the Size of Organic Substituents Computed by Ligand Repulsive Energies
J. Org. Chem. 1999, 64, 7707-7716 7707 Computational Measurement of Steric Effects: the Size of Organic Substituents Computed by Ligand Repulsive Energies David P. White,*,1 Jan C. Anthony,2 and Ademola O. Oyefeso2 Department of Chemistry, University of North CarolinasWilmington, 601 South College Rd., Wilmington, North Carolina 28403-3297 Received December 8, 1998 Ligand repulsive energies, ER, have been demonstrated to provide reliable steric parameters for ligands in organometallic systems. ER values have now been computed for 167 different organic substituents. Three different fragments were employed for the calculation of the ligand repulsive energies: CH3,CH2COOH, and Cr(CO)5 . All compounds were modeled using molecular mechanics. Two different force fields were employed: Allinger’s MMP2 and Rappe´’s Universal Force Field (UFF). Both molecular dynamics and stochastic mechanics were used to determine the lowest energy conformer for each species. Steric sizes were compared against standard steric measures in organic chemistry: Taft-Dubois steric parameter, E′S, A-values, cone angles, θ, and solid angles, ΩS. Good correlations between ER and the model-based steric measures (θ and ΩS) were found. Experimental- based measures, E′S and A-values, showed a mix of steric and electronic effects. On the basis of these correlations, the use of CH3,CH2COOH, and Cr(CO)5 fragments for steric size quantification was critically examined. Introduction outlined above would respond identically to steric effects. Therefore, Dubois chose a single standard: the acid- Over 100 years ago the importance of the size of a catalyzed esterification of carboxylic acids in methanol substituent in determining the rate of a given transfor- at 40 °C. -
CONCISE STUDY NOTES for BG 4Th Semester (UNIT: Amines and Heterocyclic Compounds)
CONCISE STUDY NOTES FOR BG 4th Semester (UNIT: Amines and Heterocyclic Compounds) Syllabus Amines: Classification and factors affecting basicity of amines. Mechanistic details (wherever applicable) of methods of formation of alkyl and arylamines through reduction of nitro compounds and nitriles. Gabriel-Phthalamide reaction and Hofmann rearrangement. Mechanisms involved in the formation and reactions of arenediazonium salts including Azo coupling. Heterocyclic compounds bearing one nitrogen atom: Stuctural features of pyrrole, pyrrolidine, pyridine and piperidine and comparative account of their basic strength. Aromaticity and electrophilic substitution reactions of pyrrole and their comparison with those of furan and thiophene.Mechanisms involved in the preparations of Indole and quinoline using Fischer-Indole and Bishlier-Napierlaski syntheses. Amines: Their classification Alkyl, aryl and ar-alkyl derivatives of ammonia are known as amines General formula is RNH2, R2NH, R3NH, where R can be any alkyl, aryl or aralkyl group. Amines are classified in to primary, secondary and tertiary amines depending upon the number of Hydrogen atoms in ammonia replaced by alkyl or aryl group. If one of hydrogen atom in NH3 is replaced by alkyl or aryl group, the derivative of ammonia so obtained is known as primary amine, if two hydrogen atoms in ammonia are replaced by alkyl, aryl or ar-alkyl groups, the derivative obtained is known as secondary amine, while as if all H atoms in ammonia are replaced by alkyl aryl or aralkyl groups, a tertiaty amine is obtained as shown below: The R groups can be alkyl, aryl or aralkyl groups. Further a secondary or tertiary amine may contain same or different R groups. -
Impact of Rigidity on Molecular Self-Assembly
Impact of Rigidity on Molecular Self-Assembly Ella M. King1,2, Matthew A. Gebbie1,3, Nicholas A. Melosh1,4* *E-mail: [email protected] 1Geballe Laboratory for Advanced Materials, Stanford University, Stanford, CA 94305 2Department of Physics, Harvard University, Cambridge, MA 02138 3Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706 4Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305 Abstract Rigid, cage-like molecules, like diamondoids, show unique self-assembly behavior, such as templating 1-D nanomaterial assembly via pathways that are typically blocked for such bulky substituents. We investigate molecular forces between diamondoids to explore why molecules with high structural rigidity exhibit these novel assembly pathways. The rigid nature of diamondoids significantly lowers configurational entropy, and we hypothesize that this influences molecular interaction forces. To test this concept, we calculated the distance-dependent impact of entropy on assembly using molecular dynamics simulations. To isolate pairwise entropic and enthalpic contributions to assembly, we considered pairs of molecules in a thermal bath, fixed at set intermolecular separations but otherwise allowed to freely move. By comparing diamondoids to linear alkanes, we draw out the impact of rigidity on the entropy and enthalpy of pairwise interactions. We find that linear alkanes actually exhibit stronger van der Waals interactions than diamondoids at contact, because the bulky structure of diamondoids induces larger net atomic separations. Yet, we also find that diamondoids pay lower entropic penalties when assembling into contact pairs. Thus, the cage-like shape of diamondoids introduces an enthalpic penalty at contact, but the penalty is counterbalanced by entropic effects. -
1,3-Dipolar Cycloaddition of Azomethine Ylides Generated from Aziridines in Supercritical Carbon Dioxide Paulo J
Tetrahedron Letters 47 (2006) 5475–5479 1,3-Dipolar cycloaddition of azomethine ylides generated from aziridines in supercritical carbon dioxide Paulo J. S. Gomes, Cla´udio M. Nunes, Alberto A. C. C. Pais, Teresa M. V. D. Pinho e Melo* and Luis G. Arnaut Department of Chemistry, Coimbra University, 3004-535 Coimbra, Portugal Received 8 March 2006; revised 26 May 2006; accepted 30 May 2006 Abstract—The 1,3-dipolar cycloaddition of azomethine ylides with DMAD in supercritical carbon dioxide is reported. The photo- lysis reaction conditions were optimized with a suitable adjustment of pressure, temperature, irradiation time and co-solvent concen- tration leading to a more efficient reaction than in neat acetonitrile. Similar results were observed using thermal reaction conditions. Supercritical carbon dioxide with a minute co-solvent addition is shown to be a very efficient medium for promoting this type of cycloadditions. Ó 2006 Elsevier Ltd. All rights reserved. Over the last decade, supercritical fluids (SCF) received ology for the synthesis of nitrogen-heterocyclic significant attention as a new class of environmentally compounds. We chose the 1,3-dipolar cycloaddition friendly solvents for organic synthesis. Supercritical flu- of azomethine ylides generated from aziridines as the ids have properties intermediate between the gas and the model reaction. Aziridines (1) undergo electrocyclic ring liquid phases that can be tuned simply by changing the opening in a disrotatory manner upon irradiation and pressure and temperature. In particular, changes of pres- conrotatory ring opening upon thermolysis, giving sure close to the critical point enable drastic changes in azomethine ylides (2), which participate in 1,3-dipolar density and viscosity.