Quantum mechanical study of the conformational behavior of proline and 4R-hydroxyproline dipeptide analogues in vacuum and in aqueous solution

The conformational behavior of the title compounds has been investigated by Hartree-Fock, MP2, and DFT computations on the most significant structures related to variations of the backbone dihedral angles, cis/trans isomerism around the peptide bond, and diastereoisomeric puckering of the pyrrolidine ring. In vacuum the reversed gamma turn (gammal), characterized by an intramolecular hydrogen bridge, corresponds to the absolute energy minimum for both puckerings (up and down) of the pyrrolidine ring. An additional energy minimum is found in the helix region, but only for an up puckering of the pyrrolidine ring. When solvent effects are included by means of the polarizable continuum model the conformer observed experimentally in condensed phases becomes the absolute minimum. The down puckering is always favored over its up counterpart, albeit by different amounts (0.4-0.5 kcal/mol for helical structures and about 2 kcal/mol for gammal structures). In helical structures cis arrangements of the peptide bond are only slightly less stable than their trans counterparts. This is no longer true for gammal structures, because the formation of an intramolecular hydrogen bond is possible only for trans peptide bonds. In most cases, proline and hydroxyproline show the same general trends; however, the electronegative 4(R) substituent of hydroxyproline leads to a strong preference for up puckerings irrespective of the backbone conformation.     

SiCNN--a new stable isomer with Si(triple bond)C triple bonding

To predict potentially stable molecules with Si(triple bond)C triple bonding, theoretical calculations at the B3LYP/ 6-311G(d) and CCSD(T)/6-311G(2df) (single-point) levels were employed to study the structures, energetics, and isomerization of various SiCN2 isomers. A schematic potential energy surface (PES) of SiCN2 was established to discuss the kinetic stability of the isomers. A new isomer SiCNN was found to possess a typical Si(triple bond)C triple bond, as confirmed by comparative calculations at the B3LYP, QCISD, QCISD(T), CCSD, and CCSD(T) levels on the bond lengths of SiCNN and other experimentally or theoretically known species of RSiCH (R = H, F, Cl, OH). Moreover, SiCNN resides in a very deep potential, the stabilization barrier is at least 53.2 kcal mol(-1). Thus, SiCNN may be considered as the most kinetically stable isomer with Si(triple bond)C triple bonding known to date, and it may represent a very promising molecule for future experimental characterization. In addition, the stability of the other isomers, such as the four linear species SiNCN, SiNNC, NSiCN and NSiNC, a three-membered NNC ring isomer with exocyclic C-Si bonding, and a four-membered SiCNN ring isomer is discussed and compared with SiCNN.     

Understanding the role of stereoelectronic effects in determining collagen stability. 2. A quantum mechanical/molecular mechanical study of (Proline-Proline-Glycine)(n) polypeptides

The importance of vicinal and long-range interresidue effects in determining the stability of the collagen triple helix has been investigated by quantum mechanical (QM) and molecular mechanical (MM) computations on suitable model polypeptides, taking into account solvent effects by the polarizable continuum model (PCM). At the QM level, the PII conformation corresponds to an energy minimum for pentapeptide analogues incorporating the sequence Gly-Pro-Pro-Gly, irrespective of the down or up puckering of the pyrrolidine ring. However, our computations indicate that the alternation of down and up prolines characterizing collagen and collagen-like peptides is not due to an intrinsic preference of the Pro-Pro-Gly sequence. This result is confirmed by MM computations of longer polypeptides. Next, MM computations on model triple helices show that a better packing is obtained for specific values of backbone dihedrals, which, in turn, favor the alternation of down and up prolines along each chain.     

Competitive formation of cis and trans derivatives in the nucleophilic substitution reactions of cyclophosphazenes having a mono-spiro P-NHR group

Nucleophilic substitution reactions of N(3)P(3)Cl(4)[NH(CH(2))(3)NMe] (1) and N(3)P(3)Cl(4)[NH(CH(2))(3)O] (2) with mono-functional alcohols (methanol, 2,2,2-trifluoroethanol, phenol) and a secondary amine (pyrrolidine) were used to investigate the relationship between the incoming nucleophile and the proportions of products with substituents that are cis or trans to the spiro NH moiety. The reaction products were characterized by elemental analysis, mass spectrometry, (1)H and (31)P NMR spectroscopy and the configurational isomers by X-ray crystallography. Six products have been characterised with the substituent cis to the spiro NH group for the alcohol (methanol, phenol) and pyrrolidine derivatives of both compounds 1 and 2, compared to just one derivative with the substituent trans to the spiro NH group, that for the pyrrolidine derivative of compound 2. For each reaction the relative proportions of cis and trans isomers were determined by (31)P NMR measurements of the reaction mixtures. It was found that the reactions of compound 1 with all three alcohols and of compound 2 with methanol lead to exclusive formation of isomers with the substituent cis to the NH moiety, whereas all other reactions lead to mixtures of cis and trans isomers in different ratios under standard reaction conditions. However, when crown ether is included in the reaction medium for the reactions of compound 2 with both 2,2,2-trifluoroethanol and phenol, it is found that only cis isomers are formed. All these results are rationalised in terms of the competition between at least two effects; the cis-directing effect by hydrogen bonding of the incoming nucleophile to the spiro N-H group already present on the cyclophophazene ring and the cis-directing effect of the sodium cation coordinating to the oxygen lone pairs of the P-O moiety of the spiro ring.     

Substituted 2-azabicyclo[2.1.1]hexanes as constrained proline analogues: implications for collagen stability

Among the proteinogenic amino acids, only proline is a secondary amine and only proline has a saturated ring. Electronegative substituents on C-4 (that is, C(gamma)) have a substantial effect on the trans/cis ratio of the prolyl peptide bond and the pucker of the pyrrolidine ring. 2-Azabicyclo[2.1.1]hexane is, in essence, a proline analogue with two C(gamma) atoms, one in each of the two prevalent ring puckers of proline. Here, 2-azabicyclo[2.1.1]hexane analogues of 2S-proline, (2S,4S)-4-hydroxyproline, and (2S,4S)-4-fluoroproline residues were synthesized, and their trans/cis ratios were shown to be invariant in a particular solvent. Thus, the substitution of a proline residue on C-4 affects the trans/cis ratio by altering the pucker of its pyrrolidine ring. This finding has implications for the conformation of collagen, which has an abundance of 2S-proline and (2S,4R)-4-hydroxyproline residues, and can be stabilized by (2S,4R)-4-fluoroproline and (2S,4S)-4-fluoroproline residues.     

Stereoelectronic effects on collagen stability: the dichotomy of 4-fluoroproline diastereomers

Collagen is the most abundant protein in animals. Natural collagen consists of a triple helix of (Xaa-Yaa-Gly)n chains, in which the Xaa and Yaa residues are often l-proline. Here, a (2S,4S)-4-fluoroproline (flp) residue is shown to be greatly stabilizing in the Xaa position (but destabilizing in the Yaa position). In contrast, a (2S,4R)-4-fluoroproline (Flp) residue is shown to be greatly destabilizing in the Xaa position (but stabilizing in the Yaa position). The dichotomous effect of the diastereomers appears to arise from a gauche effect, which alters pyrrolidine ring pucker and hence properly (or improperly) preorganizes main-chain dihedral angles. Thus, the rational use of stereoelectronic effects can enhance the conformational stability of a protein.     

Effect of 3-hydroxyproline residues on collagen stability

Collagen is an integral part of many types of connective tissue in animals, especially skin, bones, cartilage, and basement membranes. A fibrous protein, collagen has a triple-helical structure, which is comprised of strands with a repeating Xaa-Yaa-Gly sequence. l-Proline (Pro) and 4(R)-hydroxy-l-proline (4-Hyp) residues occur most often in the Xaa and Yaa positions. The 4-Hyp residue is known to increase markedly the conformational stability of a collagen triple helix. In natural collagen, a 3(S)-hydroxy-l-proline (3-Hyp) residue occurs in the sequence: 3-Hyp-4-Hyp-Gly. Its effect on collagen stability is unknown. Here, two host-guest peptides containing 3-Hyp are synthesized: (Pro-4-Hyp-Gly)(3)-3-Hyp-4-Hyp-Gly-(Pro-4-Hyp-Gly)(3) (peptide 1) and (Pro-4-Hyp-Gly)(3)-Pro-3-Hyp-Gly-(Pro-4-Hyp-Gly)(3) (peptide 2). The 3-Hyp residues in these two peptides diminish triple-helical stability in comparison to Pro. This destabilization is small when 3-Hyp is in the natural Xaa position (peptide 1). There, the inductive effect of its 3-hydroxyl group diminishes slightly the strength of the interstrand 3-HypC=O.H-NGly hydrogen bond. The destabilization is large when 3-Hyp is in the nonnatural Yaa position (peptide 2). There, its pyrrolidine ring pucker leads to inappropriate mainchain dihedral angles and interstrand steric clashes. Thus, the natural regioisomeric residues 3-Hyp and 4-Hyp have distinct effects on the conformational stability of the collagen triple helix.     

Locked conformations for proline pyrrolidine ring: synthesis and conformational analysis of cis- and trans-4-tert-butylprolines

The motional restrictions of the proline pyrrolidine ring allow this secondary amine amino acid to act as a turn inducer in many peptides and proteins. The pyrrolidine ring is known to exhibit two predominant pucker modes (i.e., C-4 (Cgamma) exo and endo envelope conformers whose ratio can be controlled by proper substituents in the ring). In nature, the exo puckered 4(R)-hydroxy-l-proline plays a crucial role as a building block in collagen and collagen-like structures. It has been previously concluded that the electronegativity of the 4-cis-substituent increases the endo puckering while the electronegativity of the 4-trans-substituent favors the exo puckering. Here, we have introduced a sterically demanding tert-butyl group at C-4 in trans- and cis-configurations. In the case of trans-substitution, the induced puckering effect on the pyrrolidine ring was studied with X-ray crystallography and 1H NMR spectral simulations. Both cis- and trans-4-tert-butyl groups strongly favor pseudoequatorial orientation, thereby causing opposite puckering effects for the pyrrolidine ring, cis-exo and trans-endo for l-prolines, in contrast to the effects observed in the case of electronegative C-4 substituents. The syntheses and structural analysis are presented for the conformationally constrained 4-tert-butylprolines. The prolines were synthesized from 4-hydroxy-l-proline, substitution with t-BuCuSPhLi being the key transformation. This reaction gave N-Boc-trans-4-tert-butyl-l-proline tert-butyl ester in 94% ee and 57% de. Enantioselectivity was increased to 99.2% ee by crystallization of N-Boc-trans-4-tert-butyl-l-proline in the final step of the synthesis.     

Studies on the constituents of Broussonetia species VIII. Four new pyrrolidine alkaloids, broussonetines R, S, T, and V and a new pyrroline alkaloid, broussonetine U, from Broussonetia kazinoki Sieb

Four new pyrrolidine alkaloids, broussonetines R, S, T, and V and a new pyrroline alkaloid, broussonetine U were isolated from the branches of Broussonetia kazinoki SIEB. (Moraceae) in low yield. Broussonetines R, S and T were formulated as (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(1R)-1-hydroxy-3-[6-(4-hydroxybutyl)-cyclohexy-2-on-1(6)-enyllpropyl] pyrrolidine (1), (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(1R,10S)-1,10,13-trihydroxytridecyl] pyrrolidine (2), (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(1R,5S)-1,5, 13-trihydroxy-10-oxo-tridecyl] pyrrolidine (3). And broussonetines U and V were proposed to be (2S,3S,4S)-2-hydroxymethyl-3, 4-dihydroxy-5-(9-oxo-13-hydroxytridecyl)-5-pyrroline (4), (2R,3S,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(E)-9-oxo-13-hydroxy-3-tridecenyl] pyrrolidine (5), respectively, by spectroscopic and chemical methods.     

Polymethylated DOTA ligands. 2. Synthesis of rigidified lanthanide chelates and studies on the effect of alkyl substitution on conformational mobility and relaxivity

M4DOTA, [(2S,5S,8S,11S)-4,7,10-tris-carboxymethyl-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]acetic acid (2e), and M4DOTMA, (R)-2-[(2S,5S,8S,11S)-4,7,10-tris-((R)-1-carboxyethyl)-2,5,8,11-tetramethyl-1,4,7,10-tetraazacyclododecan-1-yl]propionic acid (3e), are derivatives of ligand DOTA (1e) that form sterically crowded lanthanide chelates. M4DOTMA forms highly symmetric and totally rigid single Y(3+) and Yb(3+) species in which the ring substituents occupy corner positions in a square antiprismatic arrangement as shown by molecular mechanics calculations and by a quantitative interpretation of the relative magnitudes of the paramagnetic (1)H NMR shifts of dipolar origin. The NMR spectrum of YbM4DOTMA(-) displays two intense methyl peaks outside the 0-10 ppm range whose shift difference is strongly temperature dependent. YbM4DOTMA(-) (3d) could be a useful probe in magnetic resonance thermometric imaging. With only four methyl substituents on the tetraaza ring, M4DOTA forms three Yb(3+) species in solution. The methyl substituents prevent the inversion of configuration of the ethylenic groups but not of the acetate arms. Although the methyl groups are likely to preferably occupy ring corner positions, the dipolar equations do not allow one to distinguish with certainty between the two available corner (equatorial) orientations. Reliably applying the dipolar equations is less obvious than usually assumed. A single methyl substituent as in ligand MDOTA (5e) suffices to rigidify the tetraaza cycle but not the acetate arms. Racemic YbMDOTA(-) (5d) is present in solution as four totally asymmetric topomers with the methyl groups occupying either one of the two equatorial positions. A complete assignment of the solution structures on the basis of the dipolar equations is again uncertain. The nuclear magnetic relaxation dispersion curves of the Gd(3+) chelates of all the methylated DOTA ligands including DOTMA, (R)-2-[4,7,10-tris-((R)-carboxyethyl)- 1,4,7,10- tetraazacyclododecan-1-yl]propionic acid, are very similar, and intermolecular conformational processes appear to have no influence on the relaxivity of these small complexes for which the relaxation T(1) is mainly determined by the rotational correlation time (tau(r)). The hydration number of the Tb(3+) chelates measured by fluorescence decreases from DOTMA to M4DOTMA presumably because steric crowding leads to an increase of the metal-water distance.     

Studies on the constituents of Broussonetia species. VII. Four new pyrrolidine alkaloids, broussonetines M, O, P, and Q, as inhibitors of glycosidase, from Broussonetia kazinoki SIEB

Four new pyrrolidine alkaloids, broussonetines M, O, P, and Q, were isolated from the branches of Broussonetia kazinoki SIEB, (Moraceae). Broussonetines M, O, P, and Q were formulated as (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(10S)-10,13-dihydroxy-tri decyl]pyrrolidine (1), (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(E)9-oxo-13-hydroxy-3- tridecenyl]pyrrolidine (2), (2R,3R,4R,5R)-2-hydroxymethyl-3,4-dihydroxy-5-[(E)10-oxo-13-hydroxy-3-++ +tridecenyl]pyrrolidine (3), and (2R,3S,4R,5R)-2-hydroxymethyl-3-hydroxy-4-(beta-D-glucopyranosyloxy++ +)-5-[10-oxo-13-(beta-D-glucopyranosyloxy)tridecyl]pyrrolidine (4) respectively, by spectroscopic and chemical methods. 1-4 inhibited beta-glucosidase, beta-galactosidase and beta-mannosidase.     

Chiral pyridylamino-ruthenium(II) complexes: synthesis, structure and catalytic properties in Diels-Alder reactions

Half-sandwich complexes [(eta(6)-arene)RuCl(pyam)][SbF(6)] (pyam = L(n) = N-(2-pyridylmethyl)-(R)-1-phenylethylamine (L(1)), N-(2-pyridylmethyl)-(R)-1-naphthylethylamine (L(2)), N-(2-quinolylmethyl)-(R)-1-naphthylethylamine (L(3)), N-(2-pyridylmethyl)-(R)-1-cyclohexylethylamine (L(4)), N-(2-pyridylmethyl)-(1R,2S,4R)-1-bornylamine (L(5))) have been synthetised and characterised. Treatment of these compounds with AgSbF(6) generates dicationic complexes [(eta(6)-arene)Ru(pyam)(H(2)O)](2+) which act as enantioselective catalysts for the Diels-Alder reactions of methacrolein and cyclopentadiene. The catalytic reactions occur quickly at room temperature with good exo : endo selectivity (from 84 : 16 to 98 : 2) and moderate enantioselectivity (up to 74% ee). The molecular structures of the chloride complexes (R(Ru),S(N),R(C))-[(eta(6)-p-MeC(6)H(4)iPr)RuClL(1)][SbF(6)], (R(Ru),S(N),S(C2))-[(eta(6)-p-MeC(6)H(4)iPr)RuClL(5)][SbF(6)], and that of the aqua complex (R(Ru),S(N),S(C2))-[(eta(6)-p-MeC(6)H(4)iPr)RuL(5)(H(2)O)][SbF(6)](2), were determined by X-ray diffractometric methods. The distinctive variations observed in the molecular structures of these complexes only concern the puckering parameters of the metallacycle and the relative disposition of substituents within this ring. A clear trend to localise the most steric demanding substituents at equatorial positions is evident from the structural study.     

Effect of substituents (NH_2,OH,F) on structures and stability of lithofluorosilylenoids

Ｓｉｌｙｌｅｎｅｉｓｔｈｅｓｉｍｉｌａｒｉｔｙｏｆｓｉｌｉｃｏｎｔｏｃａｒｂｅｎｅ,ａｎｄ,ｌｉｋｅｃａｒｂｅｎｅｉｎｏｒｇａｎｉｃｒｅａｃｔｉｏｎｓ,ｉｔｐｌａｙｓａｖｅｒｙｉｍｐｏｒｔａｎｔｒｏｌｅｉｎｏｒｇａｎｏｓｉｌｉｃｏｎｒｅａｃｔｉｏｎｓ.Ｉｎｒｅｃｅｎｔｙｅａｒｓ,ｔｈｅｒｅｈａｖｅｂｅｅｎｍａｎｙｒｅｐｏｒｔｓｏｎｓｉｌｙｌｅｎｅｓｉｎｑｕａｎｔｕｍｃｈｅｍｉｃａｌｒｅｓｅａｒｃｈｅｓ[1—3].Ｉｎｖｅｓｔｉｇａｔｉｏｎｏｎｉｔｓｏｒｇａｎｉｃｒｅａｃｔｉｏｎｓｈｏｗｓｔｈａｔｒｅａｌｉ…     

Regioselective coupling of pentafluorophenyl substituted alkynes: mechanistic insight into the zirconocene coupling of alkynes and a facile route to conjugated polymers bearing electron-withdrawing pentafluorophenyl substituents

The reaction of Cp(2)ZrCl(2) with 2 equiv of BuLi at -78 degrees C, followed by the addition of an unsymmetrical tetra- or pentafluorophenyl substituted alkyne R(1)C[triple bond]CAr(f) (R(1), Ar(f) = (CH(2))(4)Me, p-C(6)F(4)H; Me, p-C(6)F(4)H; Ph, C(6)F(5)), resulted in regioselective couplings of these alkynes to zirconacyclopentadienes in which the Ar(f) substituents preferentially adopt the 3,4-positions (beta beta) of the zirconacyclopentadiene ring. With Cp(2)Zr(py)(Me(3)SiC[triple bond]CSiMe(3)) as the zirconocene reagent, the couplings could be carried out at room temperature; however, at higher temperatures significant quantities of the 2,4-fluoroaryl substituted (alpha beta) isomers were also formed. None of the conditions employed produced the 2,5-fluoroaryl substituted (alpha alpha) isomers. These fluoroaryl-substituted zirconacyclopentadienes were readily converted to butadienes via reactions with acids. The zirconacyclopentadiene Cp(2)ZrC(4)-2,5-Ph(2)-3,4-(C(6)F(5))(2), which resulted from the coupling of PhC[triple bond]C(C(6)F(5)), was converted to the corresponding thiophene by reaction with S(2)Cl(2), and to an arene by reaction with MeO(2)CC[triple bond]CCO(2)Me/CuCl. Mechanistic studies on zirconocene couplings of (p-CF(3)C(6)H(4))C[triple bond]C(p-MeC(6)H(4)) indicate that the observed regioselectivities are determined by an electronic factor that controls the orientation of at least one of the two alkynes as they are coupled. Additionally, these studies suggest an unsymmetrical transition state for the zirconocene coupling of alkynes, and this is supported by DFT calculations. The reaction of [(C(6)F(5))C[triple bond]CCH(2)](2)CH(2) with Cp(2)Zr(py)(Me(3)SiC[triple bond]CSiMe(3)) resulted in a zirconacyclopentadiene in which the pentafluorophenyl substituents have been forced into the 2,5-positions (alpha alpha). Zirconocene coupling of the diyne (C(6)F(5))C[triple bond]C-1,4-C(6)H(4)-C[triple bond]C(C(6)F(5)) provided a route to conjugated polymers bearing electron-withdrawing pentafluorophenyl groups.     

Reciprocity of steric and stereoelectronic effects in the collagen triple helix

In previous work, we demonstrated that 4-fluoroproline residues can contribute greatly to the conformational stability of the collagen triple helix, and that this stability arises from stereoelectronic effects that fix the pucker of the pyrrolidine ring and thereby preorganize the backbone properly for triple-helix formation. Here, we take a reciprocal approach, demonstrating that the steric effect of a 4-methyl group confers stability similar to that from a 4-fluoro group in the opposite configuration. Such fundamental interplay between steric and stereoelectronic effects is heretofore unknown in proteins-natural or synthetic-and provides a new means to modulate conformational stability.     

Theory of the cooperative transition between two ordered conformations of poly(L-proline). II. Molecular theory in the absence of solvent.

Phenomenological theories of the transition between helical form I (cis peptide bond) and helical form II (trans peptide bond) of poly(-L-proline), which is a typical order in equilibrium order transition, have been presented by Schwarz (using the parameters s, sigma, beta', and beta' in a 2 X 2 matrix formulation) and by the present authors (using the parameters s, sigma betaC, and betaN in a 4 X 4 matrix formulation). A molecular theory of the same transition has been formulated to account for the phenomenological parameters. The statistical weights of regular helical sequences with and without junctions between the two forms were computed from empirical potential energy functions. Two puckering conformations of the pyrrolidine ring, i.e., with the Cgamma atom down and up, were allowed, and the free energy was computed for chains with four types of puckering, viz., regular down, regular up, random A, and random B, in the latter two of which the up and down puckerings were randomly distributed. The random A and random B chains have higher energy than those with regular down or up puckering, in both forms I and II. From both an energetical and a free energetical point of view, form I is more stable than form II under vacuum at room temperature. The dependence of the relative stabilities of form I and form II under vacuum on chain length was examined from both an energy and free energy point of view. The four parameters, s, sigma, beta', and beta', which describe the transitions in Schwarz's theory, were calculated from the statistical weights of various types of sequences. It was found that the thermally induced transition between form I and II under vacuum occurs with the pyrrolidine rings remaining in the down conformation. The calculated values of s suggest that form I is more stable than form II in the regular down chain, while form II is more stable than form I in the regular up chain under vacuum at room temperature. The calculated values of sigma for regular down and regular up pyrrolidine ring puckering are in good agreement with experimental observations, whereas those for random A and random B puckering are much smaller than the experimental values. A theory for the effect of solvent on the parameters s, sigma, beta', and beta' (at constant temperature) is developed, and the computations involving solvent effects are described in the next paper.     

Self-selection in the self-assembly of isomeric supramolecular squares from unsymmetrical bis(4-pyridyl)acetylene ligands

A new approach wherein steric interactions between substituents of unsymmetrical bis(4-pyridyl)acetylene ligands dictate the self-selection of single isomers of [4 + 4] self-assembled squares is presented. Each [4 + 4] self-assembly is characterized by multinuclear (31)P and (1)H NMR spectroscopies and electrospray ionization mass spectrometry. NMR spectroscopic studies are used to provide a means of evaluating the efficiency of bulky substituents at proximal or remote positions relative to the Pt-N bonding motif to direct self-selection. Molecular modeling using the MMFF force field is utilized to determine the relative energy of different isomers of each assembly, and modeling results reasonably explain the trend in self-selectivity with varying pyridyl substitution.     

Collagen stability: insights from NMR spectroscopic and hybrid density functional computational investigations of the effect of electronegative substituents on prolyl ring conformations

Collagen-like peptides of the type (Pro-Pro-Gly)(10) fold into stable triple helices. An electron-withdrawing substituent at the H(gamma)(3) ring position of the second proline residue stabilizes these triple helices. The aim of this study was to reveal the structural and energetic origins of this effect. The approach was to obtain experimental NMR data on model systems and to use these results to validate computational chemical analyses of these systems. The most striking effects of an electron-withdrawing substituent are on the ring pucker of the substituted proline (Pro(i)) and on the trans/cis ratio of the Xaa(i-1)-Pro(i) peptide bond. NMR experiments demonstrated that N-acetylproline methyl ester (AcProOMe) exists in both the C(gamma)-endo and C(gamma)-exo conformations (with the endo conformation slightly preferred), N-acetyl-4(R)-fluoroproline methyl ester (Ac-4R-FlpOMe) exists almost exclusively in the C(gamma)-exo conformation, and N-acetyl-4(S)-fluoroproline methyl ester (Ac-4S-FlpOMe) exists almost exclusively in the C(gamma)-endo conformation. In dioxane, the K(trans/cis) values for AcProOMe, Ac-4R-FlpOMe, and Ac-4S-FlpOMe are 3.0, 4.0, and 1.2, respectively. Density functional theory (DFT) calculations with the (hybrid) B3LYP method were in good agreement with the experimental data. Computational analysis with the natural bond orbital (NBO) paradigm shows that the pucker preference of the substituted prolyl ring is due to the gauche effect. The backbone torsional angles, phi and psi, were shown to correlate with ring pucker, which in turn correlates with the known phi and psi angles in collagen-like peptides. The difference in K(trans/cis) between AcProOMe and Ac-4R-FlpOMe is due to an n-->pi interaction associated with the Bürg-Dunitz trajectory. The decrease in K(trans/cis) for Ac-4S-FlpOMe can be explained by destabilization of the trans isomer because of unfavorable electronic and steric interactions. Analysis of the results herein along with the structures of collagen-like peptides has led to a theory that links collagen stability to the interplay between the pyrrolidine ring pucker, phi and psi torsional angles, and peptide bond trans/cis ratio of substituted proline residues.     

Design and stereoselective synthesis of four peptide nucleic acid monomers with cyclic structures in backbone

Four isomers of the monomer of peptide nucleic acid (PNA) were derived from (2S,4R)‐4‐hydroxyproline; they had different stereochemistries at the C² and C⁴ positions in the pyrrolidine ring. These different backbone conformations corresponding to four different stereochemistries were realized through a combination of inversions at the C² and the C⁴ positions in pyrrolidine ring. The obtained backbone frameworks were reacted with N‐benzoyl thymine to give the corresponding PNA monomers. Spectroscopic comparison of the resultant monomers confirmed their stereochemistries. J. Heterocyclic Chem., (2011).     

The impact of pyrrolidine hydroxylation on the conformation of proline-containing peptides

[structure: see text] A series of eight dipeptides of the general formula Ac-Phe-Pro-NHMe was synthesized and the thermodynamics of the cis --> trans isomerization about the central amide bond were studied by NMR. Pro* represents the following prolines: l-proline (Pro), l-trans-4-hydroxyproline (Hyp), l-cis-4-hydroxyproline (hyp), l-cis-4-methoxyproline (hyp[OMe]), l-trans-3-hydroxyproline (3-Hyp), l-cis-3-hydroxyproline (3-hyp), l-2,3-trans-3,4-cis-3,4-dihydroxyproline (DHP), and l-2,3-cis-3,4-trans-3,4-dihydroxyproline (dhp). The conformation of the pyrrolidine ring in each case is discussed in light of previous structural studies, analysis of potential stereoelectronic effects, and NMR data. Hydroxy substituents at C-4 have a greater impact on cis --> trans isomerization than analogous substituents at C-3 as a result of the intervening bond distances and bridging groups. The position of the equilibrium and its dependence on temperature are a reflection of both enthalpic and entropic factors, the latter being complicated in this study by an Ar-Pro interaction in the cis conformation. The substituents on the pyrrolidine ring determine the conformation of the five-membered ring, which in turn influences the strength of the Ar-Pro interaction, backbone dihedral angles, and the relative energy of the cis and trans species. The ultimate position of the equilibrium depends on a complex blend of steric, electronic, and conformational factors.