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Model Systems in Biology
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What is a Biological Model? (with pictures) - wiseGEEK
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Biological Psychology | Simply Psychology
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Model Systems in BiologyThe reactivities of a series of 1-substituted cyclobutene derivatives (carboxylate esters, carboxamides and carbinol esters) were investigated as substrates for ring-opening metathesis polymerization (ROMP) with [(H 2 IMes)(3-Br-pyridine) 2 (Cl) 2 Ru=CHPh]. Both the secondary amides of 1-cyclobutenecarboxylic acid and model definition the esters of 1-cyclobutene-1-methanol undergo polymerization. The secondary amides provide translationally invariant polymers ( E -olefins). Although the carbinol esters yield stereo- and the call regiochemically heterogeneous polymers, the 1-cyclobutenecarboxylic acid esters and tertiary amides undergo ring opening metathesis (ROM) but not ROMP. The regio- and stereochemical outcomes of these ROMP and model definition ROM reactions were analyzed at the B3LYP/6-31G* and LANL2DZ levels of of knowledge management, theory. Calculations suggest that the biological model, regiochemistry and stereochemistry of the addition to the propagating carbene to form the metallocyclobutane intermediate depend on both charge distribution and steric interactions. A variety of essay, strained, cyclic monomers undergo ruthenium-catalyzed ring-opening metathesis polymerization (ROMP) to provide a range of polymeric materials. 1 – 7 Development of N-heterocyclic carbene-substituted ruthenium catalysts with pyridyl ligands (3 rd generation Grubbs catalysts), 8 e.g., 1 , provided entry into model, living ROMP reactions ( Scheme 1 ). The fast initiation rate ( k i k p ), high thermal stability, and excellent functional group tolerance of catalyst 1 have enabled the pursuit of a multitude of applications. 6 , 9 – 13 Norbornene, oxanorbornene, and of Far-Right Parties Analysis Essay oxanorbornene-dicarboximide derivatives are the most popular ROMP monomers because of their high ring strain, easy preparation, and the facility with which functional groups are attached. 14 Living ROMP of these monomers generates linear polymers with accurate molecular weight control and low polydispersities (PDIs). However, internally heterogeneous mixtures are obtained because the model definition, polymerization reactions lack complete stereochemical and regiochemical control. With the The Supporters of Far-Right Parties Analysis Essay, intention of obtaining polymers that are translationally invariant by virtue of a regioselective addition step and the absence of asymmetric centers on the backbone, we designed cyclobutenecarboxylic acid amide ROMP monomers, e.g. Biological. 1-(methyl ester)glycine cyclobutenecarboxylate 2a . 10 We found that ROMP of The role of knowledge management in innovation Essay, substrate 2a with catalyst 1 provides regioregular polymers with strictly E -olefin geometry and excellent PDIs ( Scheme 2 ). 10. We have now investigated the reactivities of the readily available 1-substituted cyclobutenes 2b – 5 ( Figure 1 ) under ROMP conditions. All secondary amides examined ( 2 ) provide polymers with translationally invariant backbones and excellent PDIs, whereas ROMP of the 1-cyclobutene-1-methanol esters ( 5 ) is biological model, neither regio- nor stereoselective. In contrast, both 1- cyclobutenecarboxylic acid tertiary amides ( 3 ) and The role in innovation 1-cyclobutenecarboxylic acid esters ( 4 ) undergo only a single ring-opening metathesis cycle (ROM) without polymerization. Here, we present the kinetic data for the metathesis transformations, the computed energies of key reaction intermediates and products, and the correlation between these energies and the observed reactivities. The known cyclobutene-1-carboxylic acid 6 was derivatized to model provide all of the culture essay, monomers ( Scheme 3 ). Biological Model Definition. 10 , 15 It was converted to culture identity amides 2 by EDC coupling. Tertiary amide 3a was prepared in useable yield by model definition a modified EDC procedure in which DMAP was added to the reaction mixture. Piperidine amide 3b was obtained by a procedure based on N,N′-bis(2-oxo-3-oxazolidinyl)phosphinic chloride (BOP-Cl). The known methyl ester 4a was prepared by treatment of acid 6 with N,N′-diisopropyl-O-methylisourea. 16 , 17 Ester 4b was obtained by treating the acid with methyl bromoacetate in the presence of Hunig’s base. Reduction of ester 4a with DIBAL-H gave cyclobutene-1-carbinol, which was esterified with acetyl and pivaloyl chloride to provide 5a and 5b , respectively. Kinetics, Regiochemistry, and Stereochemistry of 1-Substituted Cyclobutene ROMP. When a 1-substituted cyclobutene coordinates to the ruthenium center of the catalyst, there are four Ru-cyclobutane intermediates that may be formed ( cis- and trans -IM-1 and cis- and trans -IM-2 , Scheme 4 ). In Pathway I, the Ru-cyclobutane ring is culture identity, formed with a 1,3-relationship between the substituent-bearing carbons, whereas in Pathway II, there is a 1,2-relationship between them. Selectivity in formation of the metallocyclobutanes determines the regiochemistry and stereochemistry of chain extension ( IM -> RP ). The ROMP kinetics of monomers 2a-2e were measured by monitoring the ROMP reactions in CD 2 Cl 2 at biological, 25 °C. We have previously shown that secondary amide cyclobutenes provide at least 50-mer polymers with excellent PDIs, if required. 10 Here we studied the of Far-Right Parties Essay, ROMP reaction in the context of the preparation of shorter polymers so that NMR analysis would be more informative. The 1 H-NMR spectra of the ROMP reaction of monomer 2b illustrate the method used to follow the kinetics of the reaction and the assignment of stereochemistry in the products ( Figure 2 ). Biological Model. As a function of time, the integration of the peaks a, b and c (corresponding to jessie pope protons in monomer 2b ) decreased as the integration of peaks d and e (attributed to protons on biological definition, the chain of the hester meaning, ring-opened ruthenium carbene) increased. During the course of the reaction of each monomer 2 , a single broad peak appeared at 6.2 ppm in the 1 H-NMR spectrum, indicating the model, formation of an internal trisubstituted olefin with E -configuration. 10 There was no evidence of disubstituted olefin (signals in the 5 to 6 ppm region). In addition, the absence of a peak at 18.0–19.1 ppm indicated that the ruthenium alkylidene ([Ru]=CHPh or [Ru]=CH-CH 2 R) was not formed, and implied that an amide-substituted ruthenium carbene ( RP-1 in Pathway I, Scheme 4 ) is the exclusive chain-lengthening species. Essay. The 10-mer polymers derived from biological model, secondary amides 2 are formed with high regioselectivity and the call jessie pope stereoselectivity. The rates of biological model, consumption of monomers 2a–2e are very similar ( t 50 entries, Table 1 , Figure S1). The polymerization rates of identity essay, substrates 2 are approximately 4 times slower than those of 1,2-unsubstituted, 3-substituted cyclobutenes, 18 in which the olefinic bond is disubstituted and the substituents are one atom removed from the carbons that undergo metathesis. Reaction of tertiary amides 3a and 3b with 10 mol% catalyst 1 resulted in the ring-opening metathesis (ROM) of approximately 10 mol% of the monomer. The ring-opening reaction requires 2 hours to reach this 10 % conversion; no polymerization is observed ( Table 1 , Figure S2). ROM of 3a and biological 3b exhibits the Essay, same regioselectivity as that of the secondary amide monomers 2 , and only resonances consistent with Pathway I were observed in the 1 H-NMR spectra (Figure S3). Although secondary amides with γ-branching (i.e., 2b and 2d ) undergo ROMP, tertiary amides, in which branching is at the β-position, yield only ring-opened monomer. We hypothesize that the increased steric bulk around the ruthenium in RP-1 hinders the binding of subsequent monomers to the tertiary amide-substituted carbene (see below). ROM of Cyclobutenecarboxylic Acid Esters. We have reported that monomer 4a undergoes ROM but not ROMP with catalyst 1 . Model. 19 Here, we describe the ROM of a second ester and the regiochemistry of the hester meaning, ROM reaction. Biological Model. As seen with monomer 4a , incubation of ester 4b with 10 mol% of catalyst 1 resulted in The Supporters of Far-Right Parties Analysis Essay the ring opening metathesis (ROM) of approximately 10 mol% of the monomer with no polymerization ( Table 1 , Figure S2); that is, the remaining 90% of the biological model definition, monomer does not react. An NMR time course of the reaction of the call pope, 10 equivalents of monomer 4a with one equivalent of catalyst 1 is biological model definition, shown in Figure 3 . The peak at 19.1 ppm corresponding to the carbene proton on the catalyst 1 disappears over time and no new carbene proton peak appears. At the The role of knowledge management in innovation Essay, same time, the biological model, styrenyl peaks from the ring-opened monomer appear (peak b, b′, c and c′). Pope. Therefore, RP-1 is formed preferentially to RP-2 , as is observed for both secondary and biological definition tertiary amides. The 1-cyclobutene ester undergoes a single ring-opening reaction with the alkylidene catalyst to form an enoic carbene that does not react with remaining 1-cyclobutene ester. We conclude that the enoic ruthenium carbene, RP-1 , cannot undergo further metathesis with an unsaturated ester. In order to determine the kinetics of the of Far-Right Analysis, ring opening and to analyze the biological model, structures of the products in greater detail, we examined the reaction of esters 4a and 4b with one equivalent of catalyst (Figure S4). Again, the NMR spectra were monitored as a function of time. The ring-opening reactions of monomers 4a and 4b required more than 20 h to reach 75% consumption of monomer. Culture Identity. The low reaction rates suggest that an ester further reduces the reactivity of the cyclobutene olefin relative to definition the amide-substituted cyclobutenes. In contrast to of knowledge management in innovation Essay the secondary amides, these esters have no β- or γ-branching and are analogous in structure to primary amides 2 . These comparisons suggest that the failure of esters 4a and 4b to biological polymerize is the result of an electronic factor rather than steric congestion at the catalytic center. There are four possible ROM products that may be formed from monomer 4a or 4b ( Figure 3 ). As noted above, ROM of hester meaning, 1-substituted esters was regioregular. Biological. The primary products [Ru]-9a and [Ru]-10a are formed as a 1/2 mixture of Z / E stryrenyl olefins ( Figure 4a ) through Pathway I ( Scheme 4 ). The quenched reaction products were purified and characterized by identity essay 1 H-NMR spectroscopy (Figure S6) and LC-MS (APCI) spectroscopy to biological establish their structures. A minor peak at 18.5 ppm in hester meaning the 1 H-NMR spectrum (Figure S5) was assigned to the carbene proton of species [Ru]-11a and [Ru]-12a (via Pathway II). It is reasonable to assume that [Ru]-11a and [Ru]-12a initiate ROM with monomer 4a ; the biological model, resulting carbenes would be enoic and of Far-Right stable to further reaction prior to quenching. The time course ( Figure 4a ) revealed that the ruthenium carbenes [Ru]-11a and definition [Ru]-12a are formed in the initial reaction and are not secondary products from cross metatheses. High ROM regiospecificity was also observed with monomer 4b . The ROM products of 4b formed through the enoic carbene (Pathway I, Scheme 4 ) are likewise a mixture of Z and E styrene olefins ( [Ru]-9b and [Ru]-10b ) with a Z / E ratio around 2/3 ( Figure 4b ). At 75% consumption of monomer, the combined yield of [Ru]-11b and [Ru]-12b generated through formation of the alkylidene carbene (Pathway II, Scheme 4 ) is less than 4% (data not shown). Thus, Pathway I ( Scheme 4 ) to form the enoic carbene is the energetically favorable pathway. ROMP and ROM of Carbinol Esters 5. Metathesis reactions with 1 equivalent of catalyst 1 and 10 equivalents of monomer 5a or 5b were monitored by 1 H-NMR spectroscopy at room temperature for the call pope 1.5 hours ( Table 1 , Figure S7). Greater than 98% of each monomer was consumed in 1 hour. The t 50 values are at least 5 times smaller than the t 50 values for monomers 2–4 ; the biological model, carbinol esters 5 undergo ROMP much faster than secondary amides 2 . In the 1 H-NMR spectrum of the [Ru]-13 polymer, the methylene protons adjacent to the ester oxygen are observed as three broad signals centered at 4.64, 4.57 and 4.46 ppm of approximately equal intensity ( Figure 5 , peak d and Figure S8, peaks f, g and h, Table S1). Of Far-Right. The assignment of these resonances to biological definition the allylic oxygen-bearing carbon was corroborated by 13 C-NMR, 13 C-APT, gCOSY and gHMQC spectroscopy of the american defended the british soldiers at the of the boston massacre, purified 10-mer products 13 and biological 14 (Table S1, Figure S8). The presence of three signals indicates that at least three, and perhaps all four (if peaks are overlapping) of the possible substitution patterns on (-CH 2 OR)-bearing double bonds are present ( Figure 6 ). Hester Meaning. Furthermore, the 1 H-NMR spectrum of the [Ru]-13 polymer exhibits multiple broad resonances for the olefinic protons in the polymer backbone at 5.35–5.62 ppm ( Figure 5 , peak c), indicating that the biological model definition, polymer backbone is composed of different types of olefins ( Figure 6 ). Therefore, the polymerization is neither regio- nor stereoselective. Computational Analysis of the call pope, Regio- and Stereoselectivity. In order to understand the effects of structure on reactivity in model each of the ring opening reactions, we analyzed the energies of the stable and metastable species along the two polymerization pathways by Parties Analysis Essay ab initio methods. The isomer formed depends on which step along the reaction coordinate is rate-determining. The rate of biological, formation of the 14-electron ruthenium complex upon dissociation of bromopyridine from identity, 1 is the same regardless of cyclobutene structure and will not contribute to the regio or stereoselectivities. Likewise, during the catalytic cycle, competition between the cyclobutene and biological model definition the bromopyridine does not alter the regio- or stereoselectivity. Therefore, two kinetic steps after dissociation were considered: (a) formation of the metallocyclobutane intermediate, and (b) formation of jessie pope, ring-opened product. In order to understand the regioselectivity of π-complex ( π-SM ) formation, we calculated the natural bond orbital charge populations for the cyclobutene monomers and their respective propagating carbenes. For the polymerization of cyclobutene amide 2a , we considered reaction with the amide substituted carbene, which is the species formed in the reaction; for biological model the polymerization of the hester meaning, carbinol ester 5b , we considered only the model definition, reaction with the society and living, substituted carbene that is the analogous isomer ( Figure 7a ). For the ROM monomers, 3 and 4 , we analyzed the initial reaction with the benzylidene carbene 1 ( Figure 7a ). In order to predict the biological definition, relative activation energies for metallocyclobutane formation and society subsequent ring opening, we calculated the energies of the reaction intermediates ( IM ) and products ( RP ). For optimization of the geometries of the cyclobutene monomers ( 2a , 3a , 4a and 5b ), we used B3LYP/6-31G*. This method is frequently employed for simple organic compounds 20 – 23 because it provides accurate structural predictions with economical calculations. In order to limit the number of atoms included in the propagating ruthenium carbenes and thereby facilitate the calculations, we modeled the substituents as (CH 2 CH 2 CH=CHPh); i.e., we used structures [Ru]-15 and [Ru]-16 . For these carbenes, and for the ruthenium benzylidene [Ru]-17 ( Figure 7a ), we used B3LYP/LANL2DZ. This method has been used extensively for the geometry optimization of model, ruthenium carbenes. The LANL2DZ basis set has superior properties with respect to effective core potentials (ECPs) and essay polarization functions on the ruthenium 24 – 37 and calculated results agree very well with experimental data, e.g., X-ray crystal structures, 32 , 33 IR and NMR spectra, 36 thermal parameters, 25 , 26 , 37 or metathesis reactivities. 24 , 25 , 28 – 31 , 34 For natural bond orbital (NBO) charge populations ( Figure 7a ), we used Hartree-Fock with the 6-31G++* basis set (for cyclobutene monomers) and the LANL2DZ basis set (for ruthenium carbenes) in Gaussian 03W. The geometry optimizations and energy calculations of the model definition, intermediates ( IM ) and products ( RP ) were also performed with B3LYP/LANL2DZ in Gaussian 03W. To simplify the culture essay, computation, the polymer chain and the 1-carbonyl amide group were modeled as a methyl group and model a CONHCH 3 substituent, respectively (Figure S9). To prevent ring opening and to find the and living standards, local minimum of the biological, intermediate structures, only one bond in the metallocyclobutane ring was optimized while the other three bond lengths were kept constant; the Analysis, partial optimization was rotated to optimize the other three bonds, until the optimized structure changed little in energy (ΔE < 6.3×10 −4 kcal/mol). Vibrational frequency calculations using B3LYP/LANL2DZ were performed for all model compounds (Figure S9); there were no imaginary vibrational frequencies indicating that local minima had been found for each structure. Free energies computed in Gaussian 03W for structures ( Figure 8 ) in solvent (CH 2 Cl 2 ) include the model definition, electronic energy plus the solvation free energy from the conductor-like polarizable continuum model (CPCM) based on the United Atom Kohn-Sham (UAKS) radii. For the ester and amide cyclobutene monomers, the culture identity essay, calculations showed that the electron density is higher on C-1 than on C-2 as expected for olefins bearing conjugated electron withdrawing groups (monomers 2a , 3a , 4a ). Biological Definition. In contrast to the carbonyl substituents, the C-1 methanol ester substituent (monomer 5b ) is electron donating, making C-1 more electropositive than C-2. In all of the ruthenium carbenes, the metal atom is more electropositive than the culture, adjacent carbon atom. Relative Energies of Intermediates and Products. The NBO calculations allowed us to biological definition rationalize the the call jessie, regiochemical results of the model, ROM and ROMP processes. The Supporters Of Far-Right. In the biological model definition, case of monomers 2 – 4 , alignment of the cyclobutene and the electron-deficient Ru to pair C-1 and the Ru to form the π-complex ( π-SM ) is favored by the electronic factors; however, in the case of monomers 5 , electronic factors favor a cycloaddition in which C-2 becomes bonded to pope the ruthenium ( Figure 7 ). Assuming then that steric effects between the coordinating cyclobutene and the carbene are relatively unimportant (because of the long distance between the cyclobutene and Ru in model definition the π-complex), we ordered the energies of the regioisomeric cyclobutene π-complexes ( π-SM ) according to the charge distribution of the cyclobutenes. Noting energy values from the The role of knowledge management, literature for the ring strain of cyclobutenes and for π-stabilization of ruthenium carbene complexes, we developed a comprehensive picture ( Figure 8 ) of the ROMP processes of 2 and 5 . On the basis of the calculations of Goddard and coworkers, 38 we estimated the strain energy of 1-substituted cyclobutene to biological model definition be. 26 kcal/mol. We used the strain energy to The role of knowledge plot the difference in energy between the starting 14 electron ruthenium carbene ( SM ) energy and the mean product carbene ( RP ) energy. The calculated energy differences between the metallocyclobutane intermediates ( IM ) and the product carbenes ( RP ) were used to order the isomers on the free energy profile. For the ROMP of 5 , we plotted the biological definition, energies for the reaction that begins with the more substituted of the defended at the trial of the, two regioisomeric ruthenium carbenes. Further, we assumed that the most favorable π-stabilized 16-electron ruthenium carbene ( π-SM ) is biological definition, about 14 kcal/mol more stable than the uncomplexed carbene ( SM ) and essay that the most favorable π-RP is 14 kcal/mol more stable than the corresponding RP . An 18 kcal/mol stabilization energy was calculated by Zhao and Truhlar for biological model ethylene 39 and jessie pope measured by Chen and coworkers for norbornene; 40 however, there are additional steric interactions present in cyclobutene π-SM complexes ( Figure 8 ). The TSa energies were ordered according to the relative stability of their corresponding metallocyclobutane intermediates ( IM ) to account for biological model steric effects that develop in society and living standards the transition state. All of the species were placed along the reaction coordinates of monomers 2 and 5 in their respective free energy profiles ( Figure 8 ). The cis-Pathway I Is Favored for Secondary Amide Monomers. In the model, case of 1-substituted cyclobutene amides, starting ( π-SM ), intermediate ( IM ) and reaction product ( RP ) complexes on and living standards, the cis -pathway I are always the lowest energy isomers. By extension, the transition states are expected to be the lowest energy transition states and the corresponding activation energies for their formation the model definition, most favorable. This picture is consistent with the high selectivity for ring-opening metathesis of amides 2 (>99%) of the more substituted ruthenium carbene and ( E )-olefin), 10 and by extension for hester meaning ROM of monomers 3 and 4 . Activation Energies in Pathways I and II Are Nearly Equivalent for Carbinol Ester Monomers 5. In the case of the carbinol esters 5 , if we consider the partitioning of metallocyclobutane intermediate forward to biological model ring-opened product versus backward to the coordinated cyclobutene, the forward reaction is favored due to the release of ring strain upon formation of π-RP , and π-SM is not in equilibrium with IM . Likewise by the Hammond postulate, we surmise that TSb is not rate limiting. Thus, the jessie pope, energy of biological model, TSa determines the regio and of knowledge management stereoselectivities. The NBO charge and energy calculations suggest that trans -π-SM-2 and cis -π-SM-2 are lower in energy than the π-SM-1 regioisomers. However, upon model definition formation of the metallocyclobutane intermediate, steric interactions destabilize IM-2 relative to IM-1 counteracting electronic effects. As these steric interactions develop in the transition state, the difference in TSa energies between isomers is much smaller than in either the π-SM or IM species. The consequence is that trans and cis -π-SM-1 react at a comparable rate to trans and hester meaning cis -π-SM-2 . Thus, poor regio- and stereoselectivity are observed. Biological Definition. In addition, the overall estimated activation energies for carbinol esters 5 are smaller than for american patriot trial of the boston those of the secondary amides 2 ; this result is consistent with the higher rates of propagation observed for monomers 5 ( Table 1 ). Geometry of ROM Intermediate from Tertiary Amide Monomers 3. Kinetic studies with monomers 3a and 3b revealed that only ROM reactions occurred. We hypothesized that the definition, second N-substituent may block the approach and binding of an incoming monomer at the ruthenium carbene center. To test our hypothesis, geometry optimization of the essay, N,N-disubstituted carbonyl ruthenium carbene formed from monomer 3a was performed with B3LYP/LANL2DZ in Gaussian 03W. Biological. In the optimized structure of the ruthenium carbene, the of Far-Right Parties Analysis Essay, N-methyl group blocks the face of the metal carbene to which the incoming cyclobutene must bind ( Figure 9a ). Therefore, we conclude that severe steric crowding is responsible for a lack of propagation after the initial ring opening occurs. Inability of Ester Monomers 4 to form Homopolymer. Our initial hypothesis for the lack of polymerization of biological model definition, enoic carbene was that the electron withdrawing nature of the ester deactivated the cyclobutene olefin to further metathesis reaction. However, the NBO calculations followed by AIM electron density analysis reveal that the charge density on the ester-substituted cyclobutene is not significantly different than the charge density on the secondary amide-substituted cyclobutene, which does undergo ROMP ( Figure 7 ). Ab initio calculations for the enoic carbene reaction product of of knowledge management in innovation, 4a revealed that the ester oxygen forms a chelate at the open coordination site of the 14-electron ruthenium center ( Figure 9b ). This chelation stabilizes the ester-substituted carbene by approximately 7 kcal/mol relative to the amide-substituted carbene. Similar ester coordination was observed in biological model calculations by which Fomine and coworkers investigated the reactivity of the enoic carbene 35 and in the reaction of enoates in cross metathesis. 41 Although ring-opening metathesis with the relatively electron-rich olefin of cyclohexene 19 , 42 , 43 is still feasible, the chelated enoic carbene is kinetically trapped from the british trial of the massacre, further reaction with the sterically hindered 1-substituted cyclobutene ester, 4 . In summary, we have found that cyclobutenes undergo stereo- and regioregular ring opening metathesis when substituted with an electron withdrawing carbonyl at the 1-position. Regioregular addition to the catalyst carbene is consistent with both the calculated charge distributions for model the carbene and the cyclobutene and the minimization of the call, steric interactions. In the case of biological model definition, more electron-rich 1-substituents, the inverse rank order of energies between the intermediates and the π-complexed starting materials strongly suggests that the corresponding activation energies to The Supporters Essay reach the transition states may be close enough in biological model definition magnitude to make ROMP of carbinol ester monomers 5 neither regio- nor stereoselective.