Derivatives of Coenzyme F430 with a Covalently Attached α‐Axial Ligand. Part II

Coenzyme F430 pentamethyl ester 2 was partially hydrolyzed to a mixture of the five F430 tetramethyl esters 7 – 11 , which were separated by HPLC and identified by means of a full NMR characterization. The tetramethyl ester with a free COOH group at the side chain at C(3) of F430 was coupled to the N‐terminus of the peptidic spacer? ligand construct 12 selected and studied as described before. The UV/VIS and NMR spectra in CH₂Cl₂/3,3,3‐trifluoroethanol 6 : 1 show that the new derivative, the Ni^II(3³‐dehydroxy‐8³,12²,13³,18²‐tetra‐O‐methyl‐F430‐3³‐yl)‐L ‐prolyl‐L ‐prolyl‐N^π‐methyl‐L ‐histidine methyl ester ( 13 ), is an intramolecular, pentacoordinate, paramagnetic complex. In the same solvent system, the parent 3³,8³,12²,13³,18²‐penta‐O‐methyl‐F430 ( 2 ) is four coordinate and diamagnetic even in the presence of equimolar 1H‐imidazole. Protonation of the axially coordinating histidine residue of 13 gave the diamagnetic tetracoordinate base‐off form, which allowed us to establish the constitution of 13 by NMR.     

Synthesis,and Helix or Hairpin‐Turn Secondary Structures of ‘Mixed’ α/β‐Peptides Consisting of Residues with Proteinogenic Side Chains and of 2‐Amino‐2‐methylpropanoic Acid (Aib)

Twelve peptides, 1 – 12 , have been synthesized, which consist of alternating sequences of α‐ and β‐amino acid residues carrying either proteinogenic side chains or geminal dimethyl groups (Aib). Two peptides, 13 and 14 , containing 2‐methyl‐3‐aminobutanoic acid residues or a ‘random mix’ of α‐, β²‐, and β³‐amino acid moieties were also prepared. The new compounds were fully characterized by CD (Figs. 1 and 2), and ¹H‐ and ¹³C‐NMR spectroscopy, and high‐resolution mass spectrometry (HR‐MS). In two cases, 3 and 14 , we discovered novel types of turn structures with nine‐ and ten‐membered H‐bonded rings forming the actual turns. In two other cases, 8 and 11 , we found 14/15‐helices, which had been previously disclosed in mixed α/β‐peptides containing unusual β‐amino acids with non‐proteinogenic side chains. The helices are formed by peptides containing the amino acid moiety Aib in every other position, and their backbones are primarily not held together by H‐bonds, but by the intrinsic conformations of the containing amino acid building blocks. The structures offer new possibilities of mimicking peptide–protein and protein–protein interactions (PPI).     

Stereochemistry of the Methyl Group in (R)‐3‐Methylitaconate Derived by Rearrangement of 2‐Methylideneglutarate Catalysed by a Coenzyme B12‐Dependent Mutase

2‐Methylideneglutarate mutase is an adenosylcobalamin (coenzyme B₁₂)‐dependent enzyme that catalyses the equilibration of 2‐methylideneglutarate with (R)‐3‐methylitaconate. This reaction is believed to occur via protein‐bound free radicals derived from substrate and product. The stereochemistry of the formation of the methyl group of 3‐methylitaconate has been probed using a `chiral methyl group'. The methyl group in 3‐([²H₁,³H]methyl)itaconate derived from either (R)‐ or (S)‐2‐methylidene[3‐²H₁,3‐³H₁]glutarate was a 50 : 50 mixture of (R)‐ and (S)‐forms. It is concluded that the barrier to rotation about the C−C bond between the methylene radical centre and adjacent C‐atom in the product‐related radical [^.CH₂CH(⁻O₂CC=CH₂)CO₂⁻] is relatively low, and that the interaction of the radical with cob(II)alamin is minimal. Hence, cob(II)alamin is a spectator of the molecular rearrangement of the substrate radical to product radical.     

Myoglobin Reconstituted with Ni Tetradehydrocorrin as a Methane‐Generating Model of Methyl‐coenzyme M Reductase

Myoglobin reconstituted with Ni tetradehydrocorrin was investigated as a model of F430‐containing methyl‐coenzyme M reductase, which catalyzes anaerobic methane generation. The Ni^II tetradehydrocorrin complex has a Ni^II/Ni^I redox potential of ?0.34 V vs. SHE and EPR spectroscopy indicates the formation of a Ni^I species upon reduction by dithionite. This redox potential is approximately 0.31 V more positive than that of F430. The Ni^I tetradehydrocorrin moiety is bound to the apo‐form of myoglobin to yield the reconstituted protein. Methane gas is generated in the reaction of the model with methyl iodide in the presence of the reconstituted protein under reductive conditions, whereas the Ni^I complex itself does not produce methane gas. This is the first example of a protein‐based functional model of F430‐containing methyl‐coenzyme M reductase.     

Didehydroaspartate Modification in Methyl‐Coenzyme M Reductase Catalyzing Methane Formation

All methanogenic and methanotrophic archaea known to date contain methyl‐coenzyme M reductase (MCR) that catalyzes the reversible reduction of methyl‐coenzyme M to methane. This enzyme contains the nickel porphinoid F₄₃₀ as a prosthetic group and, highly conserved, a thioglycine and four methylated amino acid residues near the active site. We describe herein the presence of a novel post‐translationally modified amino acid, didehydroaspartate, adjacent to the thioglycine as revealed by mass spectrometry and high‐resolution X‐ray crystallography. Upon chemical reduction, the didehydroaspartate residue was converted into aspartate. Didehydroaspartate was found in MCR I and II from Methanothermobacter marburgensis and in MCR of phylogenetically distantly related Methanosarcina barkeri but not in MCR I and II of Methanothermobacter wolfeii, which indicates that didehydroaspartate is dispensable but might have a role in fine‐tuning the active site to increase the catalytic efficiency.     

Conformational analysis of the disaccharide methyl α‐d‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d‐mannopyranoside monohydrate

The crystal structure of methyl α‐d ‐mannopyranosyl‐(1→3)‐2‐O‐acetyl‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₆O₁₂·H₂O, ( II ), has been determined and the structural parameters for its constituent α‐d ‐mannopyranosyl residue compared with those for methyl α‐d ‐mannopyranoside. Mono‐O‐acetylation appears to promote the crystallization of ( II ), inferred from the difficulty in crystallizing methyl α‐d ‐mannopyranosyl‐(1→3)‐β‐d ‐mannopyranoside despite repeated attempts. The conformational properties of the O‐acetyl side chain in ( II ) are similar to those observed in recent studies of peracetylated mannose‐containing oligosaccharides, having a preferred geometry in which the C2—H2 bond eclipses the C=O bond of the acetyl group. The C2—O2 bond in ( II ) elongates by ～0.02 Å upon O‐acetylation. The phi (?) and psi (ψ) torsion angles that dictate the conformation of the internal O‐glycosidic linkage in ( II ) are similar to those determined recently in aqueous solution by NMR spectroscopy for unacetylated ( II ) using the statistical program MA′AT, with a greater disparity found for ψ (Δ = ～16°) than for ? (Δ = ～6°).     

Reactions of Methyl Diazoacetate with (E)‐ and (Z)‐1,2‐Bis(trifluoromethyl)ethene‐1,2‐dicarbonitrile: Novel and Unanticipated Pathways

The cycloadditions of methyl diazoacetate to 2,3‐bis(trifluoromethyl)fumaronitrile ((E)‐ BTE ) and 2,3‐bis(trifluoromethyl)maleonitrile ((Z)‐ BTE ) furnish the 4,5‐dihydro‐1H‐pyrazoles 13 . The retention of dipolarophile configuration proceeds for (E)‐ BTE with > 99.93% and for (Z)‐ BTE with > 99.8% (CDCl₃, 25°), suggesting concertedness. Base catalysis (1,4‐diazabicyclo[2.2.2]octane (DABCO), proton sponge) converts the cycloadducts, trans‐ 13 and cis‐ 13 , to a 94 : 6 equilibrium mixture (CDCl₃, r.t.); the first step is N‐deprotonation, since reaction with methyl fluorosulfonate affords the 4,5‐dihydro‐1‐methyl‐1H‐pyrazoles. Competing with the cis/trans isomerization of 13 is the formation of a bis(dehydrofluoro) dimer (two diastereoisomers), the structure of which was elucidated by IR, ¹⁹F‐NMR, and ¹³C‐NMR spectroscopy. The reaction slows when DABCO is bound by HF, but F^? as base keeps the conversion to 22 going and binds HF. The diazo group in 22 suggests a common intermediate for cis/trans isomerization of 13 and conversion to 22 : reversible ring opening of N‐deprotonated 13 provides 18 , a derivative of methyl diazoacetate with a carbanionic substituent. Mechanistic comparison with the reaction of diazomethane and dimethyl 2,3‐dicyanofumarate, a related tetra‐acceptor‐ethylene, brings to light unanticipated divergencies.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

N‐(tert‐Butoxycarbonyl)‐O‐allyl‐l‐seryl‐α‐aminoisobutyryl‐l‐valine methyl ester: a protected tripeptide with an allylated serine residue

The title compound [systematic name (6S,12S)‐methyl 6‐(allyloxymethyl)‐12‐isopropyl‐2,2,9,9‐tetramethyl‐4,7,10‐trioxo‐3‐oxa‐5,8,11‐triazatridecan‐13‐oate], C₂₁H₃₇N₃O₇, containing the little studied O‐allyl‐l ‐serine residue [Ser(All)], crystallizes in the monoclinic space group C2 with one molecule in the asymmetric unit. The compound is an analogue of the Ser140‐Val142 segment of the water channel aquaporin‐4 (AQP4). It forms a distorted type‐II β‐turn with a P_II–3_10L–P_II backbone conformation (P_II is polyproline II). The overall backbone conformation is markedly different from that of the CO(Pro139)–Val142 stretch of rat AQP4, but is quite similar to the corresponding segment of human AQP4, despite significant differences at the level of the individual residues. The side chain of the Ser(All) residue adopts a gauche conformation relative to the backbone CO—C^α and C^α—N bonds. The H atoms of the two CH₂ groups in the Ser(All) side chain are almost eclipsed. The crystal packing of the title compound is divided into one‐molecule‐thick layers, each layer having a hydrophilic core and distinct hydrophobic interfaces on either side.     

Structural insights into methyl‐ or methoxy‐substituted 1‐(α‐aminobenzyl)‐2‐naphthol structures: the role of C—H…π interactions

Aminobenzylnaphthols are a class of compounds containing a large aromatic molecular surface which makes them suitable candidates to study the role of C—H…π interactions. We have investigated the effect of methyl or methoxy substituents on the assembling of aromatic units by preparing and determining the crystal structures of (S,S)‐1‐{(4‐methylphenyl)[(1‐phenylethyl)amino]methyl}naphthalen‐2‐ol, C₂₆H₂₅NO, and (S,S)‐1‐{(4‐methoxyphenyl)[(1‐phenylethyl)amino]methyl}naphthalen‐2‐ol, C₂₆H₂₅NO₂. The methyl group influenced the overall crystal packing even if the H atoms of the methyl group did not participate directly either in hydrogen bonding or C—H…π interactions. The introduction of the methoxy moiety caused the formation of new hydrogen bonds, in which the O atom of the methoxy group was directly involved. Moreover, the methoxy group promoted the formation of an interesting C—H…π interaction which altered the orientation of an aromatic unit.     

Three‐Residue Turns in α/β‐Peptides and Their Application in the Design of Tertiary Structures

A new three‐residue turn was serendipitously discovered in α/β hybrid peptides derived from alternating C‐linked carbo‐β‐amino acids (β‐Caa) and L ‐Ala residues. The three‐residue β‐α‐β turn at the C termini, nucleated by a helix at the N termini, resulted in helix‐turn (HT) supersecondary structures in these peptides. The turn in the HT motif is stabilized by two H bonds—CO(i?2)–NH(i), with a seven‐membered pseudoring (γ turn) in the backward direction, and NH(i?2)–CO(i), with a 13‐membered pseudoring in the forward direction (i being the last residue)—at the C termini. The study was extended to generalize the new three‐residue turn (β‐α‐β) by using different α‐ and β‐amino acids. Furthermore, the HT motifs were efficiently converted, by an extension with helical oligomers at the C termini, into peptides with novel helix‐turn‐helix (HTH) tertiary structures. However, this resulted in the destabilization of the β‐α‐β turn with the concomitant nucleation of another three‐residue turn, α‐β‐β, which is stabilized by 11‐ and 15‐membered bifurcated H bonds. Extensive NMR spectroscopic studies were carried out to delineate the secondary and tertiary structures in these peptides, which are further supported by molecular dynamics (MD) investigations.     

4‐Amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one (metamitron) and 4‐amino‐6‐methyl‐3‐phenyl‐1,2,4‐triazin‐5(4H)‐one (isometamitron)

The title structures, both C₁₀H₁₀N₄O, are substitutional isomers. The N—N bond lengths are longer and the C=N bond lengths are shorter by ca 0.025 Å than the respective average values in the C=N—N=C group of asymmetric triazines; the assessed respective bond orders are 1.3 and 1.7. There are N—H⋯O and N—H⋯N hydrogen bonds in both structures, with 4‐­amino‐3‐methyl‐6‐phenyl‐1,2,4‐triazin‐5(4H)‐one containing a rare bifurcated N—H⋯N,N hydrogen bond. The structures differ in their mol­ecular stacking and the hydrogen‐bonding patterns.     

N‐(tert‐Butoxycarbonyl)‐α‐aminoisobutyryl‐α‐aminoisobutyric acid methyl ester: two polymorphic forms in the space group P21/n

The title compound (systematic name: methyl 2‐{2‐[(tert‐butoxycarbonyl)amino]‐2‐methylpropanamido}‐2‐methylpropanoate), C₁₄H₂₆N₂O₅, (I), crystallizes in the monoclinic space group P2₁/n in two polymorphic forms, each with one molecule in the asymmetric unit. The molecular conformation is essentially the same in both polymorphs, with the α‐aminoisobutyric acid (Aib) residues adopting ϕ and ψ values characteristic of α‐helical and mixed 3₁₀‐ and α‐helical conformations. The helical handedness of the C‐terminal residue (Aib2) is opposite to that of the N‐terminal residue (Aib1). In contrast to (I), the closely related peptide Boc‐Aib‐Aib‐OBn (Boc is tert‐butoxycarbonyl and Bn is benzyl) adopts an α_L‐P_II backbone conformation (or the mirror image conformation). Compound (I) forms hydrogen‐bonded parallel β‐sheet‐like tapes, with the carbonyl groups of Aib1 and Aib2 acting as hydrogen‐bond acceptors. This seems to represent an unusual packing for a protected dipeptide containing at least one α,α‐disubstituted residue.     

Synthesis of a Derivative of the Peptaibol‐Antibiotic Trichovirin I 1B by Means of the ‘Azirine/Oxazolone Method’

According to the earlier published synthesis of the C‐terminal nonapeptide of Trichovirin I 1B, Z‐Ser(^tBu)‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 5 ), the complete tetradecapeptide Z‐Aib‐Asn(Trt)‐Leu‐Aib‐Pro‐Ser(^tBu)‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 11b ), a protected Trichovirin I 1B, has now been prepared by means of the ‘azirine/oxazolone method’. With the exception of the N‐terminal Aib(1), all Aib residues were introduced by the coupling of the corresponding amino or peptide acids with 2,2‐dimethyl‐2H‐azirine‐3‐(N‐methyl‐N‐phenylamine) ( 1a ) and methyl N‐(2,2‐dimethyl‐2H‐azirin‐3‐yl)‐L ‐prolinate ( 3a ) as the Aib and Aib‐Pro synthons, respectively. Single crystals of two segments, i.e., the N‐terminal hexapeptide Z‐Aib‐Asn(Trt)‐Leu‐Aib‐Pro‐Ser(^tBu)‐OMe ( 23 ) and the C‐terminal octapeptide Z‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 17 ), were obtained and their structures have been established by X‐ray crystallography. Following the same strategy, the C‐terminal nonapeptide of Trichovirin I 4A, Z‐Ala‐Val‐Aib‐Pro‐Aib‐Leu‐Aib‐Pro‐Leuol ( 26 ), was also synthesized and characterized by X‐ray crystallography.     

The peptide NCbz‐Val‐Tyr‐OMe and aromatic π–π interactions

The peptide N‐benzyloxycarbonyl‐L‐valyl‐L‐tyrosine methyl ester or NCbz‐Val‐Tyr‐OMe (where NCbz is N‐benzyloxycarbonyl and OMe indicates the methyl ester), C₂₃H₂₈N₂O₆, has an extended backbone conformation. The aromatic rings of the Tyr residue and the NCbz group are involved in various attractive intra‐ and intermolecular aromatic π–π interactions which stabilize the conformation and packing in the crystal structure, in addition to N—H...O and O—H...O hydrogen bonds. The aromatic π–π interactions include parallel‐displaced, perpendicular T‐shaped, perpendicular L‐shaped and inclined orientations.     

Synthesis of an Enantiomerically Pure 1,3‐Thiazole‐5(4H)‐thione and Its Stereoselective 1,3‐Dipolar Cycloaddition with an Azomethine Ylide

Starting from the enantiomerically pure 2H‐azirin‐3‐amines (R,S)‐ 4 and (S,S)‐ 4 , the enantiomeric, optically active 4‐benzyl‐4‐methyl‐2‐phenyl‐1,3‐thiazole‐5(4H)‐thiones (R)‐ 1 and (S)‐ 1 , respectively, have been prepared (Schemes 2 and 3). In each case, the reaction of 1 with N‐(benzylidene)[(trimethylsilyl)methyl]amine ( 2 ) in HMPA in the presence of CsF and trimethylsilyl triflate gave a mixture of four optically active spirocyclic cycloadducts (Scheme 4). Separation by preparative HPLC yielded two pure diastereoisomers, e.g., (4R,5R,9S)‐ 10 and (4R,5R,9R)‐ 10 . The regioisomeric compounds 11 were obtained as a mixture of diastereoisomers. The products were formed by a 1,3‐dipolar cycloaddition of 1 with in situ generated azomethine ylide 3 , which attacks 1 stereoselectively from the sterically less‐hindered side, i.e., with (R)‐ 1 the attack occurs from the re‐side and in the case of (S)‐ 1 from the si‐side.     

Synthesis of poly(2‐oxazoline)s with side chain methyl ester functionalities: Detailed understanding of living copolymerization behavior of methyl ester containing monomers with 2‐alkyl‐2‐oxazolines

Poly(2‐oxazoline)s with methyl ester functionalized side chains are interesting as they can undergo a direct amidation reaction or can be hydrolyzed to the carboxylic acid, making them versatile functional polymers for conjugation. In this work, detailed studies on the homo‐ and copolymerization kinetics of two methyl ester functionalized 2‐oxazoline monomers with 2‐methyl‐2‐oxazoline, 2‐ethyl‐2‐oxazoline, and 2‐n‐propyl‐2‐oxazoline are reported. The homopolymerization of the methyl ester functionalized monomers is found to be faster compared to the alkyl monomers, while copolymerization unexpectedly reveals that the methyl ester containing monomers significantly accelerate the polymerization. A computational study confirms that methyl ester groups increase the electrophilicity of the living chain end, even if they are not directly attached to the terminal residue. Moreover, the electrophilicity of the living chain end is found to be more important than the nucleophilicity of the monomer in determining the rate of propagation. However, the monomer nucleophilicity can be correlated with the different rates of incorporation when two monomers compete for the same chain end, that is, in copolymerizations. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2649–2661     

Uncovering stereochemical relations in a compound with a stereogenic N—O axis: methyl 2‐(4‐methyl‐2‐thio­xo‐2,3‐di­hydro­thia­zol‐3‐yl­oxy)­propanoate

The geometry of racemic methyl 2‐(4‐methyl‐2‐thio­xo‐2,3‐di­hydro­thia­zol‐3‐yl­oxy)­propanoate, C₈H₁₁NO₃S₂, (I), is characterized by a distorted heterocyclic five‐membered ring and an enantiomorphic N‐alkoxy substituent, which is inclined at an angle of −68.8° to the thia­zole­thione plane in (M)‐(I). The unit cell consists of a 1:1 ratio of R,P‐ and S,M‐configured mol­ecules of (I). The combination of a P configuration at the N—O axis and an R configuration at the asymmetric propanoate C_β atom on one side, and an S,M configuration on the other side, is considered to originate from steric interactions. The largest substituent at the asymmetric propanoate C_β atom, i.e. the methoxycarbonyl group, resides above the methyl substituent; the medium‐sized propanoate γ‐methyl substituent points in the opposite direction with respect to the N—O bond, whereas the H atom is located above the C=S double bond of the thiazolethione subunit.     

First Synthesis of 3‐O‐Functionalized Cellulose Ethers via 2,6‐Di‐O‐Protected Silyl Cellulose

The present paper describes the synthesis of 2,6‐di‐O‐thexyldimethylsilyl cellulose as a novel 2,6‐di‐O‐protected cellulose derivative. This material was obtained by reacting cellulose in N,N‐dimethylacetamide/LiCl solution with thexyldimethylchlorosilane and imidazole for 24 h at 100°C. In a typical subsequent reaction the residual OH‐group in position 3 could be completely etherified without loss of any protecting groups. Treatment with tetrabutylammonium fluoride leads to the novel compounds 3‐O‐allyl and 3‐O‐methyl cellulose. The structures of all polymers are revealed by means of one‐ (¹H and ¹³C) and two‐dimensional (COSY and HMQC) NMR techniques.     

The absolute configuration of (2S,4S)‐ and (2R,4R)‐2‐tert‐butyl‐4‐methyl‐3‐(4‐tolyl­sulfon­yl)‐1,3‐oxazolidine‐4‐carbaldehyde

The title enanti­omorphic compounds, C₁₆H₂₃NO₄S, have been obtained in an enanti­omerically pure form by crystallization from a diastereomeric mixture either of (2S,4S)‐ and (2R,4S)‐ or of (2R,4R)‐ and (2S,4R)‐2‐tert‐butyl‐4‐methyl‐3‐(4‐tolyl­sulfon­yl)‐1,3‐oxazolidine‐4‐carbaldehyde. These mixtures were prepared by an aziridination rearrangement process starting with (S)‐ or (R)‐2‐tert‐butyl‐5‐methyl‐4H‐1,3‐dioxine. The crystal structures indicate an envelope conformation of the oxazolidine moiety for both compounds.