PHYSICAL ORGANIC Chemistryl
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Brief Guide to the Nomenclature of Organic Chemistry
1 Brief Guide to the Nomenclature of Table 1: Components of the substitutive name Organic Chemistry (4S,5E)-4,6-dichlorohept-5-en-2-one for K.-H. Hellwich (Germany), R. M. Hartshorn (New Zealand), CH3 Cl O A. Yerin (Russia), T. Damhus (Denmark), A. T. Hutton (South 4 2 Africa). E-mail: [email protected] Sponsoring body: Cl 6 CH 5 3 IUPAC Division of Chemical Nomenclature and Structure suffix for principal hept(a) parent (heptane) one Representation. characteristic group en(e) unsaturation ending chloro substituent prefix 1 INTRODUCTION di multiplicative prefix S E stereodescriptors CHEMISTRY The universal adoption of an agreed nomenclature is a key tool for 2 4 5 6 locants ( ) enclosing marks efficient communication in the chemical sciences, in industry and Multiplicative prefixes (Table 2) are used when more than one for regulations associated with import/export or health and safety. fragment of a particular kind is present in a structure. Which kind of REPRESENTATION The International Union of Pure and Applied Chemistry (IUPAC) multiplicative prefix is used depends on the complexity of the provides recommendations on many aspects of nomenclature.1 The APPLIED corresponding fragment – e.g. trichloro, but tris(chloromethyl). basics of organic nomenclature are summarized here, and there are companion documents on the nomenclature of inorganic2 and Table 2: Multiplicative prefixes for simple/complicated entities polymer3 chemistry, with hyperlinks to original documents. An No. Simple Complicated No. Simple Complicated AND overall -
Singlet/Triplet State Anti/Aromaticity of Cyclopentadienylcation: Sensitivity to Substituent Effect
Article Singlet/Triplet State Anti/Aromaticity of CyclopentadienylCation: Sensitivity to Substituent Effect Milovan Stojanovi´c 1, Jovana Aleksi´c 1 and Marija Baranac-Stojanovi´c 2,* 1 Institute of Chemistry, Technology and Metallurgy, Center for Chemistry, University of Belgrade, Njegoševa 12, P.O. Box 173, 11000 Belgrade, Serbia; [email protected] (M.S.); [email protected] (J.A.) 2 Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, P.O. Box 158, 11000 Belgrade, Serbia * Correspondence: [email protected]; Tel.: +381-11-3336741 Abstract: It is well known that singlet state aromaticity is quite insensitive to substituent effects, in the case of monosubstitution. In this work, we use density functional theory (DFT) calculations to examine the sensitivity of triplet state aromaticity to substituent effects. For this purpose, we chose the singlet state antiaromatic cyclopentadienyl cation, antiaromaticity of which reverses to triplet state aromaticity, conforming to Baird’s rule. The extent of (anti)aromaticity was evaluated by using structural (HOMA), magnetic (NICS), energetic (ISE), and electronic (EDDBp) criteria. We find that the extent of triplet state aromaticity of monosubstituted cyclopentadienyl cations is weaker than the singlet state aromaticity of benzene and is, thus, slightly more sensitive to substituent effects. As an addition to the existing literature data, we also discuss substituent effects on singlet state antiaromaticity of cyclopentadienyl cation. Citation: Stojanovi´c,M.; Aleksi´c,J.; Baranac-Stojanovi´c,M. Keywords: antiaromaticity; aromaticity; singlet state; triplet state; cyclopentadienyl cation; substituent Singlet/Triplet State effect Anti/Aromaticity of CyclopentadienylCation: Sensitivity to Substituent Effect. -
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. -
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 -
Nomenclature of Alkanes
Nomenclature of alkanes methane CH4 ethane CH3CH3 propane CH3CH2CH3 butane CH3CH2CH2CH3 pentane CH3CH2CH2CH2CH3 hexane CH3CH2CH2CH2CH2CH3 heptane CH3CH2CH2CH2CH2CH2CH3 octane CH3CH2CH2CH2CH2CH2CH2CH3 nonane CH3CH2CH2CH2CH2CH2CH2CH2CH3 decane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH3 undecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3 dodecane CH3CH2CH2CH2CH2CH2CH2CH2CH2CH2CH2CH3 Funky groups/alkanes iso- CH3 R isopropyl HC R CH3 isobutane/isobutyl R = CH3/CH2R (4 C’s) R isopentane/isopentyl R = CH2CH3/CH2CH2R (5 C’s) R isohexane/isohexyl R = CH2CH2CH3/CH2CH2R (6 C’s) R neo- CH3 neopentyl H3C C CH2 R R CH3 neopentane R = H (5 C’s) neohaxane/neohexyl R = CH3/CH2R (6 C’s) R 1° primary (n-) 2° secondary (sec-, s-) 3° tertiary (tert-, t-) H C H C H3C 3 3 CH CH2 CH CH2 CH CH2 H C CH H C CH H3C CH3 3 3 3 3 n- often used with strait chain compounds though it is not actually necessary. sec- sec-butyl H the substituent is attached s-butyl to a 2° C of butane (4 C’s) H3C CH2 C R CH3 no other "sec-" group tert- tert-butyl CH3 a substituent is attached to t-butyl the 3° C of a 4 C H3C C R molecule/unit CH3 tert-pentyl CH3 a substituent is attached to t-pentyl the 3° of a 5 C molecule/unit H3C CH2 C R CH3 no other "tert-" group Form of name #-followed by substituent name followed by parent hydrocarbon name • Determine longest continuous chain. o This is the parent hydrocarbon o If compound has two or more chains of the same length, parent hydrocarbon is chain with greatest number of substituents • Cite the name of substituent before the name of the parent hydrocarbon along with the number of the carbon to which it is attached--Substituents are listed in alphabetical order – neglecting prefixes such as di- tri- tert- etc. -
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. -
Marvin Charton - Correlation Analyst Par Excellence
Int. J. Mol. Sci. 2005, 6, 3-10 International Journal of Molecular Sciences ISSN 1422-0067 © 2005 by MDPI www.mdpi.org/ijms/ Marvin Charton - Correlation Analyst Par Excellence John Shorter 29A, Meadowfields, Whitby, North Yorkshire, YO21 1QF, UK. (Emeritus Reader in Chemistry, University of Hull), email: [email protected] Received: 10 September 2004 / Accepted: 19 October 2004 / Published: 31 January 2005 Abstract: Since the late 1950s Marvin Charton, physical organic chemist, of Pratt Institute, Brooklyn, New York has studied structure-property relationships through correlation analysis, and has become one of the leading authorities in this field. Keywords: Hammett equation, correlation analysis, linear free energy relationships, substituent effects and constants, biological activity. Introduction Marvin Charton, of Pratt Institute, Brooklyn, New York, describes his research interests in his CV as follows: "The study of structure-property quantitative relationships in chemistry and biology by means of correlation analysis. Applications of this work include chemical reaction mechanisms, the estimation of chemical and physical properties and chemical reactivities of chemical compounds, the design of bioactive molecules including medicinal drugs and pesticides, and the prediction of environmental toxicities and other properties." His first paper in this field appeared in 1958 and he has now published over 150 research papers and review articles. Marvin's forebears came to the USA from eastern Europe in the late 19th century. His surname may sound French, but his ancestry was Polish, and the relatives who came from Poland to America had the name of Charton. He sometimes suggests, half in fun, that one of his ancestors may have accompanied Napoleon from France to Moscow in 1812, but during the great retreat, by the time they reached Poland he was a little tired of marching, so he absented himself, and found a good place to live and a nice Polish girl to marry... -
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. -
And Nitro- Oxy-Polycyclic Aromatic Hydrocarbons
This report contains the collective views of an international group of experts and does not necessarily represent the decisions or the stated policy of the United Nations Environment Programme, the International Labour Organization or the World Health Organization. Environmental Health Criteria 229 SELECTED NITRO- AND NITRO- OXY-POLYCYCLIC AROMATIC HYDROCARBONS First draft prepared by Drs J. Kielhorn, U. Wahnschaffe and I. Mangelsdorf, Fraunhofer Institute of Toxicology and Aerosol Research, Hanover, Germany Please note that the pagination and layout of this web version are not identical to the printed EHC Published under the joint sponsorship of the United Nations Environment Programme, the International Labour Organization and the World Health Organization, and produced within the framework of the Inter-Organization Programme for the Sound Management of Chemicals. The International Programme on Chemical Safety (IPCS), established in 1980, is a joint venture of the United Nations Environment Programme (UNEP), the International Labour Organization (ILO) and the World Health Organization (WHO). The overall objectives of the IPCS are to establish the scientific basis for assessment of the risk to human health and the environment from exposure to chemicals, through international peer review processes, as a prerequisite for the promotion of chemical safety, and to provide technical assistance in strengthening national capacities for the sound management of chemicals. The Inter-Organization Programme for the Sound Management of Chemicals (IOMC) was established in 1995 by UNEP, ILO, the Food and Agriculture Organization of the United Nations, WHO, the United Nations Industrial Development Organization, the United Nations Institute for Training and Research and the Organisation for Economic Co- operation and Development (Participating Organizations), following recommendations made by the 1992 UN Conference on Environment and Development to strengthen cooperation and increase coordination in the field of chemical safety. -
II. Nomenclature Rules for Alkenes 1. the Parent Name Will Be the Longest
1 Lecture 9 II. Nomenclature Rules For Alkenes 1. The parent name will be the longest carbon chain that contains both carbons of the double bond. Drop the -ane suffix of the alkane name and add the –ene suffix. Never name the double bond as a prefix. If a double bond is present, you have an alkene, not an alkane. alkane + -ene = alkene 2. Begin numbering the chain at the end nearest the double bond. Always number through the double bond and identify its position in the longest chain with the lower number. In the older IUPAC rules the number for the double bond was placed in front of the stem name with a hyphen. Under the newer rules, the number for the double bond is placed right in front of “ene”, with hyphens. We will use the newer rules for specifying the location of pi bonds. 1 2 3456 H3CCHCH CH 2 CH2 CH3 hex-2-ene (newer rules) 2-hexene (older rules) 3. Indicate the position of any substituent group by the number of the carbon atom in the parent (longest) chain to which it is attached. CH 1 2 345 3 H3CCHCHCHCH2 CH CH3 6 7 CH3 Numbering is determined by the double bond, not the branches, because the double bond has 5,6-dimethylhept-3-ene (newer rules) higher priority than any alkyl branch. 5,6-dimethyl-3-heptene (older rules) 4. Number cycloalkenes so that the double bond is 1,2 (number through the double bond). Number in the direction about the ring so that the lowest number is used at the first point of difference. -
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. -
One-Pot Synthesis of CF3-Substituted Pyrazolines/Pyrazoles from Electron
FULL PAPER DOI: 10.1002/ejoc.201301852 One-Pot Synthesis of CF3-Substituted Pyrazolines/Pyrazoles from Electron- Deficient Alkenes/Alkynes and CF3CHN2 Generated in situ: Optimized Synthesis of Tris(trifluoromethyl)pyrazole Evgeniy Y. Slobodyanyuk,[a] Olexiy S. Artamonov,[b] Oleg V. Shishkin,[c] and Pavel K. Mykhailiuk*[a,d] Keywords: Synthetic methods / Nitrogen heterocycles / Fluorine / Multicomponent reactions / Cycloaddition The [3+2] cycloaddition of CF3CHN2, generated in situ, with three-component reaction between CF3CH2NH2·HCl, electron-deficient alkenes/alkynes affords CF3-substituted NaNO2, and the substrate proceeds at room temperature in pyrazolines/pyrazoles in quantitative yields. The one-pot dichloromethane/water. Introduction In 1968, Atherton and Fields prepared CF3-substituted Pyrazolines play an important role in drug discovery and pyrazolines by [3+2] cycloaddition between CF3CHN2 and organic synthesis: they exhibit a broad spectrum of bio- alkenes.[8] The transformation, however, was technically logical activities (Figure 1),[1,2] and serve as precursors to challenging, because it required (i) generation of the [3] [4] [5] [9,10] cyclopropanes, pyrazoles, and diamines. Considering toxic, potentially explosive gas CF3CHN2 from [6,7] that more than 45 drugs contain the CF3 group, CF3- CF3CH2NH2·HCl and NaNO2 and (ii) purification of the substituted pyrazolines look to be promising molecules for reagent by two vacuum distillations at –80 and –196 °C.[11] medicinal chemists. Therefore, this method has had very little practical applica- Figure 1. Bioactive pyrazolines.[1,2] [12,13] [a] Organic Chemistry Department, Taras Shevchenko National tion so far. In this context, we have developed a safe, University of Kyiv, one-pot procedure to prepare CF3-substituted pyrazolines Volodymyrska 64, Kyiv 01601, Ukraine without isolation of the dangerous CF CHN .