Phosphoryl group differentiating α‐amino acids from β‐ and γ‐amino acids in prebiotic peptide formation

In recent years β‐amino acids have increased their importance enormously in defining secondary structures of β‐peptides. Interest in β‐amino acids raises the question: Why and how did nature choose α‐amino acids for the central role in life? In this article we present experimental results of MS and ³¹P NMR methods on the chemical behavior of N‐phosphorylated α‐alanine, β‐alanine, and γ‐amino butyric acid in different solvents. N‐Phosphoryl α‐alanine can self‐assemble to N‐phosphopeptides either in water or in organic solvents, while no assembly was observed for β‐ or γ‐amino acids. An intramolecular carboxylic–phosphoric mixed anhydride (IMCPA) is the key structure responsible for their chemical behaviors. Relative energies and solvent effects of three isomers of IMCPA derived from α‐alanine (2a–c), with five‐membered ring, and five isomers of IMCPA derived from β‐alanine (4a–e), with six‐membered ring, were calculated with density functional theory at the B3LYP/6‐31G** level. The lower relative energy (3.2 kcal/mol in water) of 2b and lower energy barrier for its formation (16.7 kcal/mol in water) are responsible for the peptide formation from N‐phosphoryl α‐alanine. Both experimental and theoretical studies indicate that the structural difference among α‐, β‐, and γ‐amino acids can be recognized by formation of IMCPA after N‐phosphorylation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 232–241, 2003     

Radical Stability Directs Electron Capture and Transfer Dissociation of β‐Amino Acids in Peptides

We report on the characteristics of the radical‐ion‐driven dissociation of a diverse array of β‐amino acids incorporated into α‐peptides, as probed by tandem electron‐capture and electron‐transfer dissociation (ECD/ETD) mass spectrometry. The reported results demonstrate a stronger ECD/ETD dependence on the nature of the amino acid side chain for β‐amino acids than for their α‐form counterparts. In particular, only aromatic (e.g., β‐Phe), and to a substantially lower extent, carbonyl‐containing (e.g., β‐Glu and β‐Gln) amino acid side chains, lead to N? C_β bond cleavage in the corresponding β‐amino acids. We conclude that radical stabilization must be provided by the side chain to enable the radical‐driven fragmentation from the nearby backbone carbonyl carbon to proceed. In contrast with the cleavage of backbones derived from α‐amino acids, ECD of peptides composed mainly of β‐amino acids reveals a shift in cleavage priority from the N? C_β to the C_α? C bond. The incorporation of CH₂ groups into the peptide backbone may thus drastically influence the backbone charge solvation preference. The characteristics of radical‐driven β‐amino acid dissociation described herein are of particular importance to methods development, applications in peptide sequencing, and peptide and protein modification (e.g., deamidation and isomerization) analysis in life science research.     

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.     

An Unexplored O2‐Involved Pathway for the Decarboxylation of Saturated Carboxylic Acids by TiO2 Photocatalysis: An Isotopic Probe Study

The aerobic decarboxylation of saturated carboxylic acids (from C₂ to C₅) in water by TiO₂ photocatalysis was systematically investigated in this work. It was found that the split of C¹? C² bond of the acids to release CO₂ proceeds sequentially (that is, a C₅ acid sequentially forms C₄ products, then C₃ and so forth). As a model reaction, the decarboxylation of propionic acid to produce acetic acid was tracked by using isotopic‐labeled H₂¹⁸O. As much as ≈42 % of oxygen atoms of the produced acetic acids were from dioxygen (¹⁶O₂). Through diffuse reflectance FTIR measurements (DRIFTS), we confirmed that an intermediate pyruvic acid was generated prior to the cut‐off of the initial carboxyl group; this intermediate was evidenced by the appearance of an absorption peak at 1772 cm^?1 (attributed to C?O stretch of α‐keto group of pyruvic acid) and the shift of this peak to 1726 cm^?1 when H₂¹⁶O was replaced by H₂¹⁸O. Consequently, pyruvic acid was chosen as another model molecule to observe how its decarboxylation occurs in H₂¹⁶O under an atmosphere of ¹⁸O₂. With the α‐keto oxygen of pyruvic acid preserved in the carboxyl group of acetic acid, ≈24 % new oxygen atoms of the produced acetic acid were from molecular oxygen at near 100 % conversion of pyruvic acid. The other ≈76 % oxygen atoms were provided by H₂O through hole/OH radical oxidation. In the presence of conduction band electrons, O₂ can independently accomplish such C¹? C² bond cleavage of pyruvic acid to generate acetic acid with ≈100 % selectivity, as confirmed by an electrochemical experiment carried out in the dark. More importantly, the ratio of O₂ participation in decarboxylation increased along with the increase of pyruvic acid conversion, indicating the differences between non‐substituted acids and α‐keto acids. This also suggests that the O₂‐dependent decarboxylation competes with hole/OH‐radical‐promoted decarboxylation and depends on TiO₂ surface defects at which Ti_4c sites are available for the simultaneous coordination of substrates and O₂.     

Synthesis and conformational analysis of efrapeptins

The efrapeptin family of peptide antibiotics produced by the fungus Tolypocladium niveum, and the neo‐efrapeptins from the fungus Geotrichum candidumare inhibitors of F₁‐ATPase with promising antitumor, antimalaria, and insecticidal activity. They are rich in C^α‐dialkyl amino acids (Aib, Iva, Acc) and contain one β‐alanine and several pipecolic acid residues. The C‐terminus bears an unusual heterocyclic cationic cap. The efrapeptins C–G and three analogues of efrapeptin C were synthesized using α‐azido carboxylic acids as masked amino acid derivatives. All compounds display inhibitory activity toward F₁‐ATPase. The conformation in solution of the peptides was investigated with electronic CD spectroscopy, FT‐IR spectroscopy, and VCD spectroscopy. All efrapeptins and most efrapeptin analogues were shown to adopt helical conformations in solution. In the case of efrapeptin C, VCD spectra proved that a 3₁₀‐helix prevails. In addition, efrapeptin C was conformationally studied in detail with NMR and molecular modeling. Besides NOE distance restraints, residual dipolar couplings (RDC) observed upon partial alignment with stretched PDMS gels were used for the conformational analysis and confirmed the 3₁₀‐helical conformation.     

Convenient Procedure for Synthesis of N‐Protected β‐Aminomalonates and β‐Amino Acids From α‐Amidosulfones

A synthesis of N‐protected β‐aminomalonates starting from α‐amidosulfones under very mild and simple reaction conditions is described. Treatment of the sulfones with malonate esters in the presence of 2.5 equivalents of potassium carbonate affords the desired products in good yield. A variety of N‐Z and N‐Boc protected aliphatic and aromatic α‐aminosulfones and malonate esters have been successfully used as starting materials. Hydrolysis with concomitant decarboxylation of the N‐protected β‐aminomalonates provides a convenient access to racemic β‐amino acids.     

Sulfonamide‐Promoted Palladium(II)‐Catalyzed Alkylation of Unactivated Methylene C(sp3)H Bonds with Alkyl Iodides

The alkylation of unactivated β‐methylene C(sp³)? H bonds of α‐amino acid substrates with a broad range of alkyl iodides using Pd(OAc)₂ as the catalyst is described. The addition of NaOCN and 4‐Cl‐C₆H₄SO₂NH₂ was found to be crucial for the success of this transformation. The reaction is compatible with a diverse array of functional groups and proceeds with high diastereoselectivity. Furthermore, various β,β‐hetero‐dialkyl‐ and β‐alkyl‐β‐aryl‐α‐amino acids were prepared by sequential C(sp³)? H functionalization of an alanine‐derived substrate, thus providing a versatile strategy for the stereoselective synthesis of unnatural β‐disubstituted α‐amino acids.     

Sulfonamide‐Promoted Palladium(II)‐Catalyzed Alkylation of Unactivated Methylene C(sp3)?H Bonds with Alkyl Iodides

The alkylation of unactivated β‐methylene C(sp³) H bonds of α‐amino acid substrates with a broad range of alkyl iodides using Pd(OAc)₂ as the catalyst is described. The addition of NaOCN and 4‐Cl‐C₆H₄SO₂NH₂ was found to be crucial for the success of this transformation. The reaction is compatible with a diverse array of functional groups and proceeds with high diastereoselectivity. Furthermore, various β,β‐hetero‐dialkyl‐ and β‐alkyl‐β‐aryl‐α‐amino acids were prepared by sequential C(sp³) H functionalization of an alanine‐derived substrate, thus providing a versatile strategy for the stereoselective synthesis of unnatural β‐disubstituted α‐amino acids.     

Facile Synthesis of Isoquinolines, β‐Carbolines,and 3‐Deazapurines

Isoquinoline, β‐carbolines, and 3‐deazapurines were prepared in 52–81% yields via oxidative decarboxylation of cyclic α‐amino acids using ammonium persulfate as an oxidant in the presence of catalytic silver.     

The mechanism of neutral amino acid decomposition in the gas phase. The elimination kinetics of N,N‐dimethylglycine ethyl ester,ethyl 1‐piperidineacetate,and N,N‐dimethylglycine

The gas‐phase elimination kinetics of the ethyl ester of two α‐amino acid type of molecules have been determined over the temperature range of 360–430°C and pressure range of 26–86 Torr. The reactions, in a static reaction system, are homogeneous and unimolecular and obey a first‐order rate law. The rate coefficients are given by the following equations. For N,N‐dimethylglycine ethyl ester: log k₁(s^?1) = (13.01 ± 3.70) ? (202.3 ± 0.3)kJ mol^?1 (2.303 RT)^?1 For ethyl 1‐piperidineacetate: log k₁(s^?1) = (12.91 ± 0.31) ? (204.4 ± 0.1)kJ mol^?1 (2.303 RT)^?1 The decompositon of these esters leads to the formation of the corresponding α‐amino acid type of compound and ethylene. However, the amino acid intermediate, under the condition of the experiments, undergoes an extremely rapid decarboxylation process. Attempts to pyrolyze pure N,N‐dimethylglycine, which is the intermediate of dimethylglycine ethyl ester pyrolysis, was possible at only two temperatures, 300 and 310°C. The products are trimethylamine and CO₂. Assuming log A = 13.0 for a five‐centered cyclic transition‐state type of mechanism in gas‐phase reactions, it gives the following expression: log k₁(s^?1) = (13.0) ? (176.6)kJ mol^?1 (2.303 RT)^?1. The mechanism of these α‐amino acids differs from the decarbonylation elimination of 2‐substituted halo, hydroxy, alkoxy, phenoxy, and acetoxy carboxylic acids in the gas phase. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33:465–471, 2001     

meso‐N,N′‐Oxalyl­divaline

The title compound, 2,2′‐(oxalyldiimino)bis(3‐methylbutanoic acid), C₁₂H₂₀N₂O₆, possesses a centre of symmetry. In the crystal, mol­ecules are connected by hydrogen bonds between ox­amide and carboxyl groups, similar to the pattern of the monoclinic forms of HO–Gly–CO–CO–Gly–OH and HO–Aib–CO–CO–Aib–OH (Gly is glycine and Aib is 2‐amino­isobutyric acid). The characteristic torsion angles in the title compound are close to those in peptide α‐helices.     

Synthesis of β‐Substituted γ‐Aminobutyric Acid Derivatives through Enantioselective Photoredox Catalysis

β‐Substituted chiral γ‐aminobutyric acids feature important biological activities and are valuable intermediates for the synthesis of pharmaceuticals. Herein, an efficient catalytic enantioselective approach for the synthesis of β‐substituted γ‐aminobutyric acid derivatives through visible‐light‐induced photocatalyst‐free asymmetric radical conjugate additions is reported. Various β‐substituted γ‐aminobutyric acid analogues, including previously inaccessible derivatives containing fluorinated quaternary stereocenters, were obtained in good yields (42–89 %) and with excellent enantioselectivity (90–97 % ee). Synthetically valuable applications were demonstrated by providing straightforward synthetic access to the pharmaceuticals or related bioactive compounds (S)‐pregabalin, (R)‐baclofen, (R)‐rolipram, and (S)‐nebracetam.     

Efficient Access to Enantiopure γ4‐Amino Acids with Proteinogenic Side‐Chains and Structural Investigation of γ4‐Asn and γ4‐Ser in Hybrid Peptide Helices

Hybrid peptides composed of α‐ and β‐amino acids have recently emerged as new class of peptide foldamers. Comparatively, γ‐ and hybrid γ‐peptides composed of γ⁴‐amino acids are less studied than their β‐counterparts. However, recent investigations reveal that γ⁴‐amino acids have a higher propensity to fold into ordered helical structures. As amino acid side‐chain functional groups play a crucial role in the biological context, the objective of this study was to investigate efficient synthesis of γ⁴‐residues with functional proteinogenic side‐chains and their structural analysis in hybrid‐peptide sequences. Here, the efficient and enantiopure synthesis of various N‐ and C‐terminal free‐γ⁴‐residues, starting from the benzyl esters (COOBzl) of N‐Cbz‐protected (E)‐α,β‐unsaturated γ‐amino acids through multiple hydrogenolysis and double‐bond reduction in a single‐pot catalytic hydrogenation is reported. The crystal conformations of eight unprotected γ⁴‐amino acids (γ⁴‐Val, γ⁴‐Leu, γ⁴‐Ile, γ⁴‐Thr(OtBu), γ⁴‐Tyr, γ⁴‐Asp(OtBu), γ⁴‐Glu(OtBu), and γ‐Aib) reveals that these amino acids adopted a helix favoring gauche conformations along the central C^γ? C^β bond. To study the behavior of γ⁴‐residues with functional side chains in peptide sequences, two short hybrid γ‐peptides P1 (Ac‐Aib‐γ⁴‐Asn‐Aib‐γ⁴‐Leu‐Aib‐γ⁴‐Leu‐CONH₂) and P2 (Ac‐Aib‐γ⁴‐Ser‐Aib‐γ⁴‐Val‐Aib‐γ⁴‐Val‐CONH₂) were designed, synthesized on solid phase, and their 12‐helical conformation in single crystals were studied. Remarkably, the γ⁴‐Asn residue in P1 facilitates the tetrameric helical aggregations through interhelical H bonding between the side‐chain amide groups. Furthermore, the hydroxyl side‐chain of γ⁴‐Ser in P2 is involved in the interhelical H bonding with the backbone amide group. In addition, the analysis of 87 γ⁴‐residues in peptide single‐crystals reveal that the γ⁴‐residues in 12‐helices are more ordered as compared with the 10/12‐ and 12/14‐helices.     

The effect of amino acid backbone length on molecular packing: crystalline tartrates of glycine, β‐alanine, γ‐aminobutyric acid (GABA) and dl‐α‐aminobutyric acid (AABA)

We report a novel 1:1 cocrystal of β‐alanine with dl ‐tartaric acid, C₃H₇NO₂·C₄H₆O₆, (II), and three new molecular salts of dl ‐tartaric acid with β‐alanine {3‐azaniumylpropanoic acid–3‐azaniumylpropanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₃H₇NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (III)}, γ‐aminobutyric acid [3‐carboxypropanaminium dl ‐tartrate, C₄H₁₀NO₂⁺·C₄H₅O₆⁻, (IV)] and dl ‐α‐aminobutyric acid {dl ‐2‐azaniumylbutanoic acid–dl ‐2‐azaniumylbutanoate dl ‐tartaric acid–dl ‐tartrate, [H(C₄H₉NO₂)₂]⁺·[H(C₄H₅O₆)₂]⁻, (V)}. The crystal structures of binary crystals of dl ‐tartaric acid with glycine, (I), β‐alanine, (II) and (III), GABA, (IV), and dl ‐AABA, (V), have similar molecular packing and crystallographic motifs. The shortest amino acid (i.e. glycine) forms a cocrystal, (I), with dl ‐tartaric acid, whereas the larger amino acids form molecular salts, viz. (IV) and (V). β‐Alanine is the only amino acid capable of forming both a cocrystal [i.e. (II)] and a molecular salt [i.e. (III)] with dl ‐tartaric acid. The cocrystals of glycine and β‐alanine with dl ‐tartaric acid, i.e. (I) and (II), respectively, contain chains of amino acid zwitterions, similar to the structure of pure glycine. In the structures of the molecular salts of amino acids, the amino acid cations form isolated dimers [of β‐alanine in (III), GABA in (IV) and dl ‐AABA in (V)], which are linked by strong O—H…O hydrogen bonds. Moreover, the three crystal structures comprise different types of dimeric cations, i.e. (A…A)⁺ in (III) and (V), and A⁺…A⁺ in (IV). Molecular salts (IV) and (V) are the first examples of molecular salts of GABA and dl ‐AABA that contain dimers of amino acid cations. The geometry of each investigated amino acid (except dl ‐AABA) correlates with the melting point of its mixed crystal.     

Specificity and versatility of nucleating agents toward isotactic polypropylene crystal phases

Nucleating agents with an ≈6.5 Å lattice parameter induced the α phase of isotactic polypropylene (iPP, α‐iPP). A 6.5 Å periodicity is also involved in the nucleating agents for the β phase of iPP (β‐iPP). The similarity in substrate periodicities suggests that some nucleating agents may induce either the α or β phase under different crystallization conditions. 4‐Fluorobenzoic acid, dicyclohexylterephthalamide, and γ‐quinacridone (the latter two are known as β‐iPP nucleators) were tested over a wide range of crystallization temperatures [up to crystallization temperature (T_c) > 145 °C]. The two former nucleating agents induce exclusively α‐iPP and β‐iPP, respectively. γ‐Quinacridone on the contrary is a versatile agent with respect to the crystal phase generated. More specifically, the same crystal face of γ‐quinacridone induces either β‐iPP or α‐iPP when T_c is below or above ≈140 °C. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2504–2515, 2002     

Benzyl tert‐but­oxy­carbonyl‐α‐amino­isobutyrate

The small synthetic peptide, benzyl 2‐(tert‐but­oxy­carbonyl‐amino)­isobutyrate, C₁₆H₂₃NO₄, has the α‐helical conformation [|?| = 55.8 (2)° and |ψ| = 37.9 (2)°] observed in peptide fragments of peptaibols containing the α‐amino­isobutyric acid (Aib) residue. The structure shows no intramolecular hydrogen bonding, which would disrupt the limited conformational freedom associated with this amino acid. Two weak intermolecular hydrogen contacts are observed.     

Differentiation of α‐COOH from β‐COOH in aspartic acids by N‐phosphorylation

The biomimic reactions of N‐phosphoryl amino acids, which involved intramolecular penta‐coordinate phosphoric‐carboxylic mixed anhydrides, are very important in the study of many biochemical processes. The reactivity difference between the α‐COOH group and β‐COOH in phosphoryl amino acids was studied by experiments and theoretical calculations. It was found that the α‐COOH group, and not β‐COOH, was involved in the ester exchange on phosphorus in experiment. From MNDO calculations, the energy of the penta‐coordinate phosphoric intermediate containing five‐member ring from α‐COOH was 35 kJ/mol lower than that of the six‐member one from β‐COOH. This result was in agreement with that predicted by HF/6‐31G** and B3LYP/6‐31G** calculations. Theoretical three‐dimensional potential energy surface for the intermediates predicted that the transition states 4 and 5 involving α‐COOH or β‐COOH group had energy barriers of ΔE=175.8 kJ?mol^?1 and 210.4 kJ?mol^?1, respectively. So the α‐COOH could be differentiated from β‐COOH intramolecularly in aspartic acids by N‐phosphorylation. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 83: 41–51, 2001     

An oxazol‐5(4H)‐one from benzyloxy­carbonyl‐(Aib)4‐OH

Benzyl N‐[8‐(4,4‐dimethyl‐5‐oxo‐4,5‐dihydrooxazol‐2‐yl)‐2,5,5,8‐tetra­methyl‐3,6‐dioxo‐4,7‐diazanon‐2‐yl]­carbamate, C₂₄H₃₄N₄O₆, an oxazol‐5(4H)‐one from N‐α‐benzyloxycarbonyl‐(Aib)₄‐OH (Aib = α‐amino­isobutyryl) represents the longest peptide oxazolone so far characterized by X‐ray diffraction. The overall geometry of the oxazolone ring compares well with literature data. The Aib(1) and Aib(2) residues are folded into a type III β‐bend, while the conformation adopted by Aib(3), preceding the oxazolone moiety, is semi‐extended. The disposition of the oxazolone ring relative to the preceding residue is stabilized by C—­H?N and C—H?O intramolecular interactions.     

Stereochemistry and Conformation of Skyllamycin,a Non‐Ribosomally Synthesized Peptide from Streptomyces sp. Acta 2897

Skyllamycin is a non‐ribosomally synthesized cyclic depsipeptide from Streptomyces sp. Acta 2897 that inhibits PDGF‐signaling. The peptide scaffold contains an N‐terminal cinnamoyl moiety, a β‐methylation of aspartic acid, three β‐hydroxylated amino acids and one rarely occurring α‐hydroxy glycine. With the exception of α‐hydroxy glycine, the stereochemistry of the amino acids was assigned by comparison to synthetic reference amino acids applying chiral GC‐MS and Marfey‐HPLC analysis. The stereochemistry of α‐hydroxy glycine, which is unstable under basic and acidic conditions, was determined by conformational analysis, employing a combination of data from NOESY‐NMR spectroscopy, simulated annealing and free MD simulations. The simulation procedures were applied for both R‐ and S‐configured α‐hydroxy glycine of the skyllamycin structure and compared to the NOESY data. Both methods, simulated annealing and free MD simulations independently support S‐configured α‐hydroxy glycine thus enabling the assignment of all stereocenters in the structure of skyllamycin and devising the role of two‐component flavin dependent monooxygenase (Sky39) as S‐selective.     

Highly E‐Selective and Enantioselective Michael Addition to Electron‐Deficient Internal Alkynes Under Chiral Iminophosphorane Catalysis

A highly E‐selective and enantioselective conjugate addition of 2‐benzyloxythiazol‐5(4H)‐ones to β‐substituted alkynyl N‐acyl pyrazoles is achieved under the catalysis of a P‐spiro chiral iminophosphorane. Simultaneous control of the newly generated central chirality and olefin geometry is possible with a wide array of the alkynyl Michael acceptors possessing different aromatic and aliphatic β‐substituents, as well as the various α‐amino acid‐derived thiazolone nucleophiles. This protocol provides access to structurally diverse, optically active α‐amino acids bearing a geometrically defined trisubstituted olefinic component at the α‐position.