β‐Sheet to Helical‐Sheet Evolution Induced by Topochemical Polymerization: Cross‐α‐Amyloid‐like Packing in a Pseudoprotein with Gly‐Phe‐Gly Repeats

Protein‐mimics are of great interest for their structure, stability, and properties. We are interested in the synthesis of protein‐mimics containing triazole linkages as peptide‐bond surrogate by topochemical azide‐alkyne cycloaddition (TAAC) polymerization of azide‐ and alkyne‐modified peptides. The rationally designed dipeptide N₃‐CH₂CO‐Phe‐NHCH₂CCH ( 1 ) crystallized in a parallel β‐sheet arrangement and are head‐to‐tail aligned in a direction perpendicular to the β‐sheet‐direction. Upon heating, crystals of 1 underwent single‐crystal‐to‐single‐crystal polymerization forming a triazole‐linked pseudoprotein with Gly‐Phe‐Gly repeats. During TAAC polymerization, the pseudoprotein evolved as helical chains. These helical chains are laterally assembled by backbone hydrogen bonding in a direction perpendicular to the helical axis to form helical sheets. This interesting helical‐sheet orientation in the crystal resembles the cross‐α‐amyloids, where α‐helices are arranged laterally as sheets.     

Internal Rotation of Ester Linkage in Phenyl Benzoate and Hydroxybenzoic Acid Dimer as Models of Aromatic Polyesters Using Density Functional Theory

The internal rotation of the ester linkage was reinvestigated more quantitatively by using the density functional theory (DFT) in order to understand the characteristic stiffness and extendedness of polymer chain found in aromatic polyesters. Phenyl benzoate ( PB ) and p‐hydroxybenzoic acid (HBA) dimer ( HB ) were selected as models of aromatic polyesters. The relaxed potential energy surface (PES) scan was carried out along the internal rotation of three bonds (denoted as R, S and T, respectively) of the aromatic esters by using the hybrid DFT (B3LYP) with 6‐31G* basis set. The rotation of S bond, which mainly determines the linearity of the molecule, leads to the trans‐ and cis‐conformers of PB . Since the cis‐conformer of PB is 7.69 kcal·mol^–1 higher than the trans‐conformer, the cis‐conformer has little population at standard condition. HB does not have the cis‐conformer. In addition, the chain persistence length of 364 Å is obtained by the rotation matrix formalism using the structural parameters of HB . These agree with the experimental understanding that poly(p‐hydroxybenzoic acid) is the class of stiff and extended polymer.     

A new insight into the mechanism of 1,3‐dienes cationic polymerization. II. Structure of poly(1,3‐pentadiene) synthesized with tBuCl/TiCl4 initiating system

The microstructure of poly(1,3‐pentadiene) synthesized by cationic polymerization of 1,3‐pentadiene with ^tBuCl/TiCl₄ initiating system is analyzed using one‐dimensional‐ and two‐dimensional‐NMR spectroscopy. It is shown that unsaturated part of chain contains only homo and mixed dyads with trans?1,4‐, trans?1,2‐, and cis?1,2‐structures with regular and inverse (head‐to‐head or tail‐to‐tail) enchainment, whereas cis?1,4‐ and 3,4‐units are totally absent. The new quantitative method for the calculation of content of different structural units in poly(1,3‐pentadiene)s based on the comparison of methyl region of ¹³C NMR spectra of original and hydrogenated polymer is proposed. The signals of tert‐butyl head and chloromethyl end groups are identified in a structure of poly(1,3‐pentadiene) chain and the new approaches for the quantitative calculation of number‐average functionality at the α‐ and ω‐end are proposed. © 2013 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2013, 51, 3297–3307     

Designed Synthesis of a 1D Polymer in Twist‐Stacked Topology via Single‐Crystal‐to‐Single‐Crystal Polymerization

To synthesize a fully organic 1D polymer in a novel twist‐stacked topology, we designed a peptide monomer HC≡CCH₂‐NH‐Ile‐Leu‐N₃, which crystallizes with its molecules H‐bonded along a six‐fold screw axis. These H‐bonded columns pack parallelly such that molecules arrange head‐to‐tail, forming linear non‐covalent chains in planes perpendicular to the screw axis. The chains arrange parallelly to form molecular layers which twist‐stack along the screw axis. Crystals of this monomer, on heating, undergo single‐crystal‐to‐single‐crystal (SCSC) topochemical azide–alkyne cycloaddition (TAAC) polymerization to yield an exclusively 1,4‐triazole‐linked polymer in a twist‐stacked layered topology. This topologically defined polymer shows better mechanical strength and thermal stability than its unordered form, as evidenced by nanoindentation studies and thermogravimetric analysis, respectively. This work illustrates the scope of topochemical polymerizations for synthesizing polymers in pre‐decided topologies.     

Topochemical Syntheses of Polyarylopeptides Involving Large Molecular Motions: Frustrated Monomer Packing Leads to the Formation of Polymer Blends

We report the topochemical syntheses of three polyarylopeptides, wherein triazolylphenyl group is integrated into the backbone of peptide chains. We synthesized three different monomers having azide and arylacetylene as end-groups from glycine, L-alanine and L-valine. We crystallized these monomers and the crystal structures of two of them were determined by single-crystal X-ray diffractometry. Due to the steric constraints, both of these monomers crystallized with two molecules, viz. conformers A and B , in the asymmetric unit. Consistently, in both cases, the A -conformers are antiparallelly π -stacked and B -conformers are parallelly slip-stacked, exploiting weak interactions. Though the arrangements of molecules in the pristine crystals were unsuitable for topochemical reaction, upon heating, they undergo large motion inside the crystal lattice to reach a transient reactive orientation and thereby the self-sorted conformer stacks react to give a blend of triazole-linked polyarylopeptides having two different linkages. Due to the large molecular motion inside crystals, the product phase loses its crystallinity.     

Computational study of sulfoxides of thiacyclohexane, 4‐silathiacyclohexane, 4‐fluoro‐4‐silathiacyclohexane,and 4,4‐difluoro‐4‐silathiacyclohexane: Relative energies of conformations and sulfinyl oxygen stabilized pentacoordinate silicon in boat and twist structures

Second‐order Møller‐Plesset theory (MP2) has been used to calculate the equilibrium geometries and relative energies of the chair, 1,4‐twist, 2,5‐twist, 1,4‐boat, and 2,5‐boat conformations of thiacyclohexane 1‐oxide (tetrahydro‐2H‐thiopyran 1‐oxide), 4‐silathiacyclohexane 1‐oxide, cis‐ and trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide, and 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide. At the MP2/6‐311+G(d,p) level of theory, the chair conformer of axial thiacyclohexane 1‐oxide is 0.99, 5.61, 5.91, 8.57, and 7.43 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of equatorial thiacyclohexane 1‐oxide is 4.62, 6.31, 7.56, and 7.26 kcal/mol more stable (ΔE) than its respective 1,4‐twist and 2,5‐twist conformers and 1,4‐boat and 2,5‐boat transition states. The chair conformer of axial 4‐silathiacyclohexane 1‐oxide is 1.79, 4.26, 3.85, and 5.71 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The 2,5‐twist conformer of axial 4‐silathiacyclohexane 1‐oxide is stabilized by a transannular interaction between the sulfinyl oxygen and silicon, to give trigonal bipyramidal geometry at silicon. The chair conformer of equatorial 4‐silathiacyclohexane 1‐oxide is 2.47, 7.90, and 8.09 kcal/mol more stable (ΔE) than its respective 1,4‐twist, and 2,5‐twist conformers and 2,5‐boat transition state. The chair conformer of axial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 4.18 and 5.70 kcal/mol more stable than its 1,4‐twist conformer and 2,5‐boat transition state and 1.51 kcal/mol more stable than the chair conformer of equatorial cis‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide. The chair conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide is 5.02 and 6.11 kcal/mol more stable than its respective 1,4‐twist conformer and 2,5‐boat transition state, but is less stable than its 2,5‐twist conformer (ΔE = ?1.77 kcal/mol) and 1,4‐boat transition state (ΔE = ?1.65 kcal/mol). The 2,5‐twist conformer and 1,4‐boat conformer of axial trans‐4‐fluoro‐4‐silathiacyclohexane 1‐oxide are stabilized by intramolecular coordination of the sulfinyl oxygen with silicon that results in trigonal bipyramidal geometry at silicon. The chair conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is 3.02, 5.16, 0.90, and 6.21 kcal/mol more stable (ΔE) than its respective equatorial chair, 1,4‐twist, and 1,4‐boat conformers and 2,5‐boat transition state. The 1,4‐boat conformer of axial 4,4‐difluoro‐4‐silathiacyclohexane 1‐oxide is stabilized by a transannular coordination of the sulfinyl oxygen with silicon that results in a trigonal bipyramidal geometry at silicon. The relative energies of the conformers and transition states are discussed in terms of hyperconjugation, orbital interactions, nonbonded interactions, and intramolecular sulfinyl oxygen–silicon coordination. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Cationic polymerization of 1,3-pentadiene I. infrared, 1H-NMR and 13C-NMR investigations on the microstructure of poly(1,3-pentadiene) synthesized with cationic catalysts

This study deals with cationic polymerization of the cis- and trans-isomers of 1,3-pentadiene. The microstructure of the polymer chains is studied by ¹H-NMR, ¹³C-NMR and IR spectroscopies. It is shown that the trans-diene gives strictly trans-1,4 and trans-1,2 residual linear insaturations, whereas the cis-isomer yields also cis-1,4, cis-1,2 and 3,4-units whose overall content can reach 10 mol-%. According to the cyclization degree of the macromolecules, ranging from 30 to 70 mol-%, the number of trans-(1,2+1,4) units varies between 33 to 65 mol-% and that of trans-1,2 units between 4 and 20 mol-%. An analytical method is proposed to evaluate the average number of rings present in the polycyclic sequences. It is found that the cyclic fragments of the polymer chains consist of bi- or tri-cyclohexane fused rings containing α tetrasubstituted double bond.     

Functional Monomers and Polymers. 165. Dehydrochlorination of Head‐to‐Tail 1,4‐rans‐Poly‐(‐1‐Chlorobutadiene) Prepared by Inclusion Polymerization in Deoxycholic Acid Canals

Thermal and chemical dehydrochlorination of head‐to‐tail 1,4‐trans‐poly(‐1‐chlorobutadiene) prepared by inclusion polymerization in deoxycholic acid canals resulted in formation of a trans‐polyacetylene‐type polymer. The dehydrochiorinated polymer was characterized by UV/VIS, IR, Raman, and ESR spectroscopy. The number of conjugated double bonds in the polymer was about 10–20. Doping with iodine was also studied.     

Photoisomerization of cis‐1,2‐di(1‐Methyl‐2‐naphthyl)ethene at 77 K in Glassy Media

cis‐1,2‐Di(1‐methyl‐2‐naphthyl)ethene, c‐ 1,1 , undergoes photoisomerization in methylcyclohexane, isopentane and diethyl ether/isopentane/ethanol glasses at 77 K. On 313 nm excitation the fluorescence of c‐ 1,1 is replaced by fluorescence from t‐ 1,1 . Singular value decomposition reveals that the spectral matrices behave as two component systems suggesting conversion of a stable c‐ 1,1 conformer to a stable t‐ 1,1 conformer. However, the fluorescence spectra are λ_exc dependent. Analysis of global spectral matrices shows that c‐ 1,1 is a mixture of two conformers, each of which gives one of four known t‐ 1,1 conformers. The λ_exc dependence of the c‐ 1,1 fluorescence spectrum is barely discernible. Structure assignments to the resolved fluorescence spectra are based on the principle of least motion and on calculated geometries, energy differences and spectra of the conformers. The relative shift of the c‐ 1,1 conformer spectra is consistent with the shift of the calculated absorption spectra. The calculated structure of the most stable conformer of c‐ 1,1 agrees well with the X‐ray crystal structure. Due to large deviations of the naphthyl groups from the ethenic plane in the conformers of both c‐ and t‐ 1,1 isomers, minimal motion of these bulky substituents accomplishes cis → trans interconversion by rotation about the central bond.     

Conformational study of fosinopril sodium in solution using NMR and molecular modeling

Two conformers of fosinopril sodium in methanol were unambiguously established using 2D NMR methods and variable‐temperature NMR experiments. Differences in their conformational structure were shown to be related to the rotational energy barrier about the amide bond and hydrophobic interaction. The relationship between the 3D structure and activity is discussed. It is suggested that the trans‐conformer may be more biologically active owing to its stacking structure and strong hydrophobic interaction and the cis‐conformer could be more easily hydrolyzed because of its extended structure. Copyright © 2003 John Wiley & Sons, Ltd.     

Dependence of the luminescent properties and chain length of poly[2‐methoxy‐5‐(2′‐ethyl‐hexyloxy)‐1,4‐phenylene vinylene] on the formation of cis‐vinylene bonds during Gilch polymerization

The presence of cis‐vinylene bonds in Gilch‐polymerized poly[2‐methoxy‐5‐(2′‐ethyl‐hexyloxy)‐1,4‐phenylene vinylene] is reported. Through fractionation, species with a weight‐average molecular weight of less than 37,000 exhibited an abnormal blueshift of photoluminescence spectra in toluene solutions, and this was attributed to the presence of cis‐vinylene bonds, as verified by NMR spectroscopy. Surprisingly, the fractionated species (～1 wt %) with a weight‐average molecular weight of 5000 were mostly linked by the cis‐vinylene bonds. The concentration decreased with the molecular weight until a molecular weight of 37,000 was reached; at that point, the polymer chains contained mainly trans‐vinylene bonds. Obviously, the formation of cis‐vinylene bonds strongly inhibited the growth of polymer chains during Gilch polymerization. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 2520–2526, 2005     

Low-temperature 15N NMR spectra of reduced 1,3-heterocyclic systems

The ¹⁵N NMR spectra of the O-inside cis-fused conformer of perhydropyrido[1,2-c][1,3]thiazine shows a shielding of the nitrogen of 23.0 ppm relative to the trans-fused conformer. In contrast, ¹⁵N shifts for the cis-and trans-fused conformers of perhydro-oxazolo[3,4-a]pyridine and perhydrothiazolo[3,4-a]pyridine show corresponding shieldings of only 0.6 and 2.5 ppm, respectively.     

Carbon-13 NMR of polybutadiene

By using the carbon-13 NMR technique, it is shown that there are no cis-1,4–trans-1,4 linkages in a n-BuLi-catalyzed polybutadiene. The polymer consists of “blocks” of cis-1,4 units and trans-1,4 units separated by isolated vinyl units. Preliminary evidence suggests this might also be true for other types of 1,3-diene polymerization. Some of the implications of this finding on the mechanism of polymerization are discussed. Tacticity triad distributions are readily determined in polybutadienes with high 1,2 addition contents.     

Conformational Panorama and Chirality Controlled Structure–Energy Relationship in a Chiral Carboxylic Acid Dimer

Chirality recognition in dimers of tetrahydro‐2‐furoic acid (THFA) was studied in a conformer‐specific manner using rotational spectroscopy and theoretical approaches. THFA shows a strong preference for the trans‐ over the cis‐COOH configuration. Two drastically different scenarios are possible for the detectable (THFA)₂: a kinetically preferred dimer bound by feeble interactions between two trans THFAs or a thermodynamically favored dimer with a double hydrogen‐bonded ring structure between two cis subunits. To identify the conformers responsible for the extremely dense rotational spectra observed, it was essential not only to locate several hundred homo/heterochiral (THFA)₂ minima in ab initio calculations but also to evaluate the energetic connectivities among the minima. The study further reveals an interesting chirality dependent structure–energy ordering relationship. A method for enantiomeric excess (ee) determination of THFA is presented using a recently proposed chiral self‐tag approach.     

cis‐trans Peptide‐Bond Isomerization in α‐Methylproline Derivatives

α‐Methyl‐L ‐proline is an α‐substituted analog of proline that has been previously employed to constrain prolyl peptide bonds in a trans conformation. Here, we revisit the cis‐trans prolyl peptide bond equilibrium in derivatives of α‐methyl‐L ‐proline, such as N‐Boc‐protected α‐methyl‐L ‐proline and the hexapeptide H‐Ala‐Tyr‐αMePro‐Tyr‐Asp‐Val‐OH. In Boc‐α‐methyl‐L ‐proline, we found that both cis and trans conformers were populated, whereas, in the short peptide, only the trans conformer was detected. The energy barrier for the cis‐trans isomerization in Boc‐α‐methyl‐L ‐proline was determined by line‐shape analysis of NMR spectra obtained at different temperatures and found to be 1.24 kcal/mol (at 298 K) higher than the corresponding value for Boc‐L ‐proline. These findings further illuminate the conformationally constraining properties of α‐methyl‐L ‐proline.     

Conformational analysis,part 43. A theoretical and LIS/NMR investigation of the conformations of substituted benzamides

A refined Lanthanide‐Induced‐Shift Analysis (LISA) is used with molecular mechanics and ab initio calculations to investigate the conformations of benzamide ( 1 ), N‐methylbenzamide ( 2 ), N,N‐dimethylbenzamide ( 3 ) and the conformational equilibria of 2‐fluoro ( 4 ), 2‐chloro ( 5 ) and N‐methyl‐2‐methoxy benzamide ( 6 ). The amino group in 1 is planar in the crystal but is calculated to be pyramidal with the CO/phenyl torsional angle (ω) of 20–25°. The LISA analysis gave acceptable agreement factors (Rcryst ≤ 1%) for the ab initio geometries when ω was decreased to 0°, the other geometries were not as good. In 2 , the N‐methyl is coplanar with the carbonyl group in all the geometries. Good agreement was obtained for the RHF geometries, with ω 25°, the other geometries were only acceptable with increased values of ω. In 3 , good agreement for the RHF and PCModel geometries was found when ω was changed from the calculated values of 40° (RHF) and 90° (PCModel) to ca. 60°, the X‐ray and B3LYP geometries were not as good. The two substituted compounds 4 , 5 and 6 are interconverting between the cis (O,X) and trans (O,X) conformers. The more stable trans conformer is planar in 4 and 6 but the cis form non‐planar. Both the cis and trans conformers of 5 are non‐planar. There is an additional degree of freedom in 6 due to the 2‐methoxy group, which can be either planar or orthogonal to the phenyl ring in both conformers. The conformer ratios were obtained from the LISA analysis to give Ecis‐Etrans in 4 > 2.3 kcal/mol (CDCl₃) and 1.7 kcal/mol (CD₃CN), in 5 0.0 kcal/mol (CD₃CN) and in 6 > 2.5 kcal/mol (CDCl₃) and 2.0 kcal/mol (CD₃CN). These values were used with the observed versus calculated ¹H shifts to determine the conformer ratios and energies in DMSO solvent to give Ecis‐Etrans 1.1, ?0.1 and 1.8 kcal/mol for ( 4 ), ( 5 ) and ( 6 ). Comparison of the observed versus calculated conformer energies show that both the MM and ab initio calculations overestimate the NH..F hydrogen bond in ( 4 ) by ca. 2 kcal/mol. Copyright © 2015 John Wiley & Sons, Ltd.     

Conformational analysis. Part 40: a theoretical and NMR investigation of the conformations of cis‐ and trans‐cyclopentane‐1,3‐diol

The conformations of cis‐ ( 1 ) and trans‐cyclopentane‐1,3‐diol ( 2 ) have been studied by ab initio (Gaussian 98) and molecular mechanics (PCMODEL) calculations and by NMR spectroscopy. The calculations gave two low‐energy conformations for ( 1 ), 1A and 1B , both with axial hydroxyl groups. Two conformations with equatorial hydroxyl groups ( 1C and 1D ) were found but with much higher energy (ca 4.0 kcal mol^?1). Five low‐energy conformers were found for 2 . Four were envelope conformations and one a half‐chair. The complete analysis of the 400 MHz ¹H NMR spectra of 1 in a variety of solvents and 2 in chloroform was performed by extensive decoupling experiments, iterative computer analysis and spectral simulation. This gave all the H,H couplings in the molecule, including in 1 a long‐range ⁴J(H,H) coupling between H‐2cis and H‐4,5cis. The ³J(H,H) couplings were used to determine the conformer populations in these molecules. This was initially achieved using the Haasnoot, de Leeuw and Altona equation. to obtain the conformer couplings. It was found that this equation was not accurate for the C·CH₂·CH₂·C fragment in these molecules and the following equation was derived for this fragment from five‐ and six‐ membered cyclic compounds in fixed conformations: (1) The conformer populations were obtained by calculating the conformer couplings which were then compared with the observed couplings. Compound 1 in benzene solution is an approximately equal mixture of conformers 1A and 1B with small (<4%) amounts of 1C and 1D . In the polar solvents acetone and acetonitrile the populations of 1A and 1B are again equal, with 20% of 1C and <2% of 1D . In 2 the major conformers are 2B and 2D with small amounts of 2C , 2E and 2A . These novel findings are considered with previous data on cyclopentanol and cis‐ and trans‐cyclopentane‐1,2‐diol and it is shown that the axial hydroxyl substituent at the fold of the envelope appears to be a major factor in determining the conformational energies of these compounds. Copyright © 2003 John Wiley & Sons, Ltd.     

Polymerization of 2‐pentene with Ni(II) α‐diimine complex/M‐MAO catalyst and structure of the polymer

Polymerization of 2‐pentene with [ArN?C(An)C(An)·NAr)NiBr₂ (Ar?2,6‐iPr₂C₆H₃)] ( 1‐Ni) /M‐MAO catalyst was investigated. A reactivity between trans‐2‐pentene and cis‐2‐pentene on the polymerization was quite different, and trans‐2‐pentene polymerized with 1‐Ni /M‐MAO catalyst to give a high molecular weight polymer. On the other hand, the polymerization of cis‐2‐butene with 1‐Ni /M‐MAO catalyst did not give any polymeric products. In the polymerization of mixture of trans‐ and cis‐2‐pentene with 1‐Ni /M‐MAO catalyst, the M_n of the polymer increased with an increase of the polymer yields. However, the relationship between polymer yield and the M_n of the polymer did not give a strict straight line, and the M_w/M_n also increased with increasing polymer yield. This suggests that side reactions were induced during the polymerization. The structures of the polymer obtained from the polymerization of 2‐ pentene with 1‐Ni /M‐MAO catalyst consists of ? CH₂? CH₂? CH(CH₂CH₃)? , ? CH₂? CH₂? CH₂? CH(CH₃)? , ? CH₂? CH(CH₂CH₂CH₃)? , and methylene sequence ? (CH₂)_n? (n ≥ 5) units, which is related to the chain walking mechanism. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 2858–2863, 2008     

Pressure Effect on Conformational Equilibria of Analog Peptides in Aqueous Solution by Raman Spectroscopy

We investigated the pressure effect on the conformational equilibria of glycinamide (GA) and 2-chloroacetamide (MCA) in aqueous solution by Raman spectroscopy. Scattering intensities in the CH₂ scissoring mode of GA and the NH₂ rocking mode of MCA in aqueous solution were decomposed into two component bands by ab initio MO calculations at the HF/6-31G(d,p) level. From the pressure dependence of the Raman band intensities, we determined the difference in the partial molar volume (PMV) between the cis and trans conformers of each for GA and MCA. The volume changes for the isomerization of the cis to trans conformer are ?(1.9 ± 0.3) and ?(1.5 ± 0.3) cm³-mol^?1 for GA and MCA, respectively. The volume difference between the cis and trans conformers is due to the hydration effect, which seems to be mainly the result of local effects of solute–solvent interactions in both cases. This contribution is due to the influence of the solute–solvent interaction with water molecules on the PMV of the cis conformer being less than that of the trans conformer.