Physical Organic Chemistry After 50 Years: It Has Changed, but Is It Still There?
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Chemistry Grade Level 10 Units 1-15
COPPELL ISD SUBJECT YEAR AT A GLANCE GRADE HEMISTRY UNITS C LEVEL 1-15 10 Program Transfer Goals ● Ask questions, recognize and define problems, and propose solutions. ● Safely and ethically collect, analyze, and evaluate appropriate data. ● Utilize, create, and analyze models to understand the world. ● Make valid claims and informed decisions based on scientific evidence. ● Effectively communicate scientific reasoning to a target audience. PACING 1st 9 Weeks 2nd 9 Weeks 3rd 9 Weeks 4th 9 Weeks Unit 1 Unit 2 Unit 3 Unit 4 Unit 5 Unit 6 Unit Unit Unit Unit Unit Unit Unit Unit Unit 7 8 9 10 11 12 13 14 15 1.5 wks 2 wks 1.5 wks 2 wks 3 wks 5.5 wks 1.5 2 2.5 2 wks 2 2 2 wks 1.5 1.5 wks wks wks wks wks wks wks Assurances for a Guaranteed and Viable Curriculum Adherence to this scope and sequence affords every member of the learning community clarity on the knowledge and skills on which each learner should demonstrate proficiency. In order to deliver a guaranteed and viable curriculum, our team commits to and ensures the following understandings: Shared Accountability: Responding -
Elimination Reactions E1, E2, E1cb and Ei
Elimination Reactions Dr. H. Ghosh Surendranath College, Kol-9 ________________________________________________ E1, E2, E1cB and Ei (pyrolytic syn eliminations); formation of alkenes and alkynes; mechanisms (with evidence), reactivity, regioselectivity (Saytzeff/Hofmann) and stereoselectivity; comparison between substitution and elimination. Substitution Reactions Elimination Reactions Elimination happens when the nucleophile attacks hydrogen instead of carbon Strong Base favor Elimination Bulky Nucleophile/Base favor Elimination High Temperature favors Elimination We know- This equation says that a reaction in which ΔS is positive is more thermodynamically favorable at higher temperature. Eliminations should therefore be favoured at high temperature Keep in Mind---- Mechanism Classification E1 Mechanism- Elimination Unimolecular E1 describes an elimination reaction (E) in which the rate-determining step is unimolecular (1) and does not involve the base. The leaving group leaves in this step, and the proton is removed in a separate second step E2 Mechanism- Elimination Bimolecular E2 describes an elimination (E) that has a bimolecular (2) rate-determining step that must involve the base. Loss of the leaving group is simultaneous with removal of the proton by the base Bulky t-butoxide—ideal for promoting E2 as it’s both bulky and a strong base (pKaH = 18). Other Organic Base used in Elimination Reaction These two bases are amidines—delocalization of one nitrogen’s lone pair on to the other, and the resulting stabilization of the protonated amidinium ion, E1 can occur only with substrates that can ionize to give relatively stable carbocations—tertiary, allylic or benzylic alkyl halides, for example. E1-Elimination Reaction not possible here The role of the leaving group Since the leaving group is involved in the rate-determining step of both E1 and E2, in general, any good leaving group will lead to a fast elimination. -
Prebiological Evolution and the Metabolic Origins of Life
Prebiological Evolution and the Andrew J. Pratt* Metabolic Origins of Life University of Canterbury Keywords Abiogenesis, origin of life, metabolism, hydrothermal, iron Abstract The chemoton model of cells posits three subsystems: metabolism, compartmentalization, and information. A specific model for the prebiological evolution of a reproducing system with rudimentary versions of these three interdependent subsystems is presented. This is based on the initial emergence and reproduction of autocatalytic networks in hydrothermal microcompartments containing iron sulfide. The driving force for life was catalysis of the dissipation of the intrinsic redox gradient of the planet. The codependence of life on iron and phosphate provides chemical constraints on the ordering of prebiological evolution. The initial protometabolism was based on positive feedback loops associated with in situ carbon fixation in which the initial protometabolites modified the catalytic capacity and mobility of metal-based catalysts, especially iron-sulfur centers. A number of selection mechanisms, including catalytic efficiency and specificity, hydrolytic stability, and selective solubilization, are proposed as key determinants for autocatalytic reproduction exploited in protometabolic evolution. This evolutionary process led from autocatalytic networks within preexisting compartments to discrete, reproducing, mobile vesicular protocells with the capacity to use soluble sugar phosphates and hence the opportunity to develop nucleic acids. Fidelity of information transfer in the reproduction of these increasingly complex autocatalytic networks is a key selection pressure in prebiological evolution that eventually leads to the selection of nucleic acids as a digital information subsystem and hence the emergence of fully functional chemotons capable of Darwinian evolution. 1 Introduction: Chemoton Subsystems and Evolutionary Pathways Living cells are autocatalytic entities that harness redox energy via the selective catalysis of biochemical transformations. -
Chapter 3 • Ratio: Cnh2n+2
Organic Chemistry, 5th Edition Alkane Formulas L. G. Wade, Jr. • All C-C single bonds • Saturated with hydrogens Chapter 3 • Ratio: CnH2n+2 Structure and Stereochemistry • Alkane homologs: CH3(CH2)nCH3 of Alkanes • Same ratio for branched alkanes H H H H H H CH H C C C C H H H H C CCH Jo Blackburn H H H H H H Richland College, Dallas, TX H => Butane, C4H10 Dallas County Community College District Chapter 3Isobutane, C H 2 © 2003, Prentice Hall 4 10 Common Names Pentanes H H H H H H H CH • Isobutane, “isomer of butane” H C C C C C H H H • Isopentane, isohexane, etc., methyl H H H H H H H C CCC H branch on next-to-last carbon in chain. H H H H • Neopentane, most highly branched n-pentane, C5H12 isopentane, C5H12 • Five possible isomers of hexane, CH3 18 isomers of octane and 75 for H3C C CH3 decane! CH3 => => neopentane, C5H12 Chapter 3 3 Chapter 3 4 Longest Chain IUPAC Names • The number of carbons in the longest • Find the longest continuous carbon chain determines the base name: chain. ethane, hexane. (Listed in Table 3.2, • Number the carbons, starting closest to page 81.) the first branch. • If there are two possible chains with the • Name the groups attached to the chain, same number of carbons, use the chain using the carbon number as the locator. with the most substituents. • Alphabetize substituents. H3C CH CH CH • Use di-, tri-, etc., for multiples of same 2 3 CH3 substituent. -
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. -
4.2 Ionic Bonds Vocabulary: Ion – Polyatomic Ion – Ionic Bond – Ionic Compound – Chemical Formula – Subscript –
4.2 Ionic Bonds Vocabulary: Ion – Polyatomic ion – Ionic bond – Ionic compound – Chemical formula – Subscript – Crystal - An ion is an atom or group of atoms that has an electric charge. When a neutral atom loses a valence electron, it loses a negative charge. It becomes a positive ion. When a neutral atom gains an electron, it gains a negative charge and becomes a negative ion. Common Ions: Name Charge Symbol/Formula Lithium 1+ Li+ Sodium 1+ Na+ Potassium 1+ K+ Ammonium 1+ NH₄+ Calcium 2+ Ca²+ Magnesium 2+ Mg²+ Aluminum 3+ Al³+ Fluoride 1- F- Chloride 1- Cl- Iodide 1- I- Bicarbonate 1- HCO₃- Nitrate 1- NO₃- Oxide 2- O²- Sulfide 2- S²- Carbonate 2- CO₃²- Sulfate 2- SO₄²- Notice that some ions are made of several atoms. Ammonium is made of 1 nitrogen atom and 4 hydrogen atoms. Ions that are made of more than 1 atom are called polyatomic ions. Ionic bonds: When atoms that easily lose electrons react with atoms that easily gain electrons, valence electrons are transferred from one type to another. The transfer gives each type of atom a more stable arrangement of electrons. 1. Sodium has 1 valence electron. Chlorine has 7 valence electrons. 2. The valence electron of sodium is transferred to the chlorine atom. Both atoms become ions. Sodium atom becomes a positive ion (Na+) and chlorine becomes a negative ion (Cl-). 3. Oppositely charged particles attract, so the ions attract. An ionic bond is the attraction between 2 oppositely charged ions. The resulting compound is called an ionic compound. In an ionic compound, the total overall charge is zero because the total positive charges are equal to the total negative charges. -
Stereochemistry of Alkanes and Cycloalkanes
STEREOCHEMISTRY OF ALKANES AND CYCLOALKANES CONFORMATIONAL ISOMERS 1 CONFORMATIONAL ISOMERS • Stereochemistry concerned with the 3-D aspects of molecules • Rotation is possible around C-C bonds in open- chain molecules • A conformation is one of the many possible arrangements of atoms caused by rotation about a single bond, and a specific conformation is called a conformer (conformational isomer). 2 SOME VOCABULARY • A staggered conformation is the conformation in which all groups on two adjacent carbons are as far from each other as possible. • An eclipsed conformation is the conformation in which all groups on two adjacent carbons are as close to each other as possible. • Dihedral angle is angle between the substituents on two adjacent carbons; changes with rotation around the C-C bond 3 MORE VOCABULARY • Angle strain is the strain caused by the deformation of a bond angle from its normal value. • Steric strain is the repulsive interaction caused by atoms attempting to occupy the same space. • Torsional strain is the repulsive interaction between two bonds as they rotate past each other. Torsional strain is responsible for the barrier to rotation around the C-C bond. The eclipsed from higher in energy than the staggered form. 4 CONFORMATION OF ETHANE • Conformation- Different arrangement of atoms resulting from bond rotation • Conformations can be represented in 2 ways: 5 TORSIONAL STRAIN • We do not observe perfectly free rotation • There is a barrier to rotation, and some conformers are more stable than others • Staggered- most stable: -
Transition State Theory. I
MIT OpenCourseWare http://ocw.mit.edu 5.62 Physical Chemistry II Spring 2008 For information about citing these materials or our Terms of Use, visit: http://ocw.mit.edu/terms. 5.62 Spring 2007 Lecture #33 Page 1 Transition State Theory. I. Transition State Theory = Activated Complex Theory = Absolute Rate Theory ‡ k H2 + F "! [H2F] !!" HF + H Assume equilibrium between reactants H2 + F and the transition state. [H F]‡ K‡ = 2 [H2 ][F] Treat the transition state as a molecule with structure that decays unimolecularly with rate constant k. d[HF] ‡ ‡ = k[H2F] = kK [H2 ][F] dt k has units of sec–1 (unimolecular decay). The motion along the reaction coordinate looks ‡ like an antisymmetric vibration of H2F , one-half cycle of this vibration. Therefore k can be approximated by the frequency of the antisymmetric vibration ν[sec–1] k ≈ ν ≡ frequency of antisymmetric vibration (bond formation and cleavage looks like antisymmetric vibration) d[HF] = νK‡ [H2] [F] dt ! ‡* $ d[HF] (q / N) 'E‡ /kT [ ] = ν # *H F &e [H2 ] F dt "#(q 2 N)(q / N)%& ! ‡ $ ‡ ‡* ‡ (q / N) ' q *' q *' g * ‡ K‡ = # trans &) rot ,) vib ,) 0 ,e-E kT H2 qH2 ) q*H2 , gH2 gF "# (qtrans N) %&( rot +( vib +( 0 0 + ‡ Reaction coordinate is antisymmetric vibrational mode of H2F . This vibration is fully excited (high T limit) because it leads to the cleavage of the H–H bond and the formation of the H–F bond. For a fully excited vibration hν kT The vibrational partition function for the antisymmetric mode is revised 4/24/08 3:50 PM 5.62 Spring 2007 Lecture #33 Page 2 1 kT q*asym = ' since e–hν/kT ≈ 1 – hν/kT vib 1! e!h" kT h! Note that this is an incredibly important simplification. -
Analysis of Multipolar Linear Paul Traps for Ion–Atom Ultracold Collision Experiments
atoms Article Analysis of Multipolar Linear Paul Traps for Ion–Atom Ultracold Collision Experiments M. Niranjan *, Anand Prakash and S. A. Rangwala * Raman Research Institute, C. V. Raman Avenue, Sadashivanagar, Bangalore 560080, India; [email protected] * Correspondence: [email protected] (M.N.); [email protected] (S.A.R.) Abstract: We evaluate the performance of multipole, linear Paul traps for the purpose of studying cold ion–atom collisions. A combination of numerical simulations and analysis based on the virial theorem is used to draw conclusions on the differences that result, by considering the trapping details of several multipole trap types. Starting with an analysis of how a low energy collision takes place between a fully compensated, ultracold trapped ion and an stationary atom, we show that a higher order multipole trap is, in principle, advantageous in terms of collisional heating. The virial analysis of multipole traps then follows, along with the computation of trapped ion trajectories in the quadrupole, hexapole, octopole and do-decapole radio frequency traps. A detailed analysis of the motion of trapped ions as a function of the amplitude, phase and stability of the ion’s motion is used to evaluate the experimental prospects for such traps. The present analysis has the virtue of providing definitive answers for the merits of the various configurations, using first principles. Keywords: ion trapping; ion–atom collisions; linear multipole traps; virial theorem Citation: Niranjan, M.; Prakash, A.; Rangwala, S.A. Analysis of Multipolar Linear Paul Traps for 1. Introduction Ion–Atom Ultracold Collision Linear multipole Paul trap configurations are emerging as a natural choice for a wide Experiments. -
Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium Sp
Article Cite This: Biochemistry 2019, 58, 1246−1259 pubs.acs.org/biochemistry Transition State Analysis of the Reaction Catalyzed by the Phosphotriesterase from Sphingobium sp. TCM1 † † † ‡ ‡ Andrew N. Bigley, Dao Feng Xiang, Tamari Narindoshvili, Charlie W. Burgert, Alvan C. Hengge,*, † and Frank M. Raushel*, † Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States ‡ Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States *S Supporting Information ABSTRACT: Organophosphorus flame retardants are stable toxic compounds used in nearly all durable plastic products and are considered major emerging pollutants. The phospho- triesterase from Sphingobium sp. TCM1 (Sb-PTE) is one of the few enzymes known to be able to hydrolyze organo- phosphorus flame retardants such as triphenyl phosphate and tris(2-chloroethyl) phosphate. The effectiveness of Sb-PTE for the hydrolysis of these organophosphates appears to arise from its ability to hydrolyze unactivated alkyl and phenolic esters from the central phosphorus core. How Sb-PTE is able to catalyze the hydrolysis of the unactivated substituents is not known. To interrogate the catalytic hydrolysis mechanism of Sb-PTE, the pH dependence of the reaction and the effects of changing the solvent viscosity were determined. These experiments were complemented by measurement of the primary and ff ff secondary 18-oxygen isotope e ects on substrate hydrolysis and a determination of the e ects of changing the pKa of the leaving group on the magnitude of the rate constants for hydrolysis. Collectively, the results indicated that a single group must be ionized for nucleophilic attack and that a separate general acid is not involved in protonation of the leaving group. -
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 -
There Are Three Major Biological Molecules Classified As Ketone Bodies
There are three major biological molecules classified as ketone bodies: These ketone bodies are water soluble and do not need specific transporters to cross membranes. Synthesis of acetoacetate 1. React two acetyl-CoA molecules with each other using thiolase. This is called acetoacetyl-CoA. What is the second product? 2. React a third acetyl-CoA molecule with acetoacetyl-CoA. This step is catalyzed by hydroxymethylglutaryl-CoA synthase (HMG-CoA synthase). a. Deprotonate C2 of acetyl-CoA. You have created a great nucleophile. b. React your newly formed carbanion nucleophile with the electrophilic carbonyl C3 of acetoacetyl-CoA. c. Protonate the oxyanion. d. Use water as a nucleophile to react with the electrophilic carbonyl of the thioester of the newly added acetyl-CoA unit. This results in a carboxylate functional group. e. Your product should contain a 5-carbon chain, which starts with a thioester to CoA, ends with a carboxylate, and has a hydroxyl and a methyl group attached to C3. This is β-hydroxy-β- methylglutaryl-CoA (HMG-CoA). 3. An acetyl-CoA group is eliminated. This step is catalyzed by hydroxymethylglutaryl-CoA lyase (HMG- CoA lyase). a. A base deprotonates the hydroxyl group of β-hydroxy-β-methylglutaryl-CoA. b. A pair of electrons from the oxyanion moves to form a carbonyl. C2 leaves as a carbanion [which delocalizes into the adjacent thioester carbonyl]. c. The first product is acetoacetate. d. The carbanion picks up the proton and leaves as acetyl-CoA. Formation of acetone from acetoacetate This occurs in a non-enzymatic fashion because of the arrangement of the ketone in the β position from the carboxylate in acetoacetate and causes problems since acetone builds up.