Conformation of tert‐butoxy­carbonyl­glycyl‐dehydro­alanyl‐glycine methyl ester in the crystalline state and calculated in the gas phase

tert‐Butoxy­carbonyl­glycyl‐dehydro­alanyl‐glycine methyl ester (systematic name: methyl {2‐[(tert‐butoxycarbonylamino)­acetamido]prop‐2‐enamido}acetate) (Boc⁰‐Gly¹‐ΔAla²‐Gly³‐OMe), C₁₃H₂₁N₃O₆, has been structurally characterized by single‐crystal X‐ray diffraction and by density functional theory (DFT) calculations at the B3LYP/6–311+G** level. The peptide chain in both the solid‐state and calculated structures adopts neither β nor γ turns. All amino acid residues in the tripeptide sequence are linked trans to each other. The bond lengths and valence angles of the amino acid units in the crystal structure and gas phase are comparable. However, the conformation of the third glycyl residue (Gly³) is different in the crystalline state and in the gas phase. It is stabilized in the calculated structure by an additional intra­molecular short contact between Gly³ NH and methyl ester COMe groups.     

Two stereoisomeric pentacyclic oxin­dole alkaloids from Uncaria tomentosa: uncarine C and uncarine E

The chloro­form solvate of uncarine C (pteropodine), (1′S,3R,4′aS,5′aS,10′aS)‐1,2,5′,5′a,7′,8′,10′,10′a‐octa­hydro‐1′‐methyl‐2‐oxospiro­[3H‐indole‐3,6′(4′aH)‐[1H]­pyrano­[3,4‐f]indolizine]‐4′‐carboxyl­ic acid methyl ester, C₂₁H₂₄N₂O₄·CHCl₃, has an absolute configuration with the spiro C atom in the R configuration. Its epimer at the spiro C atom, uncarine E (isopteropodine), (1′S,3S,4′aS,5′aS,10′aS)‐1,2,5′,5′a,7′,8′,10′,10′a‐octahydro‐1′‐methyl‐2‐oxospiro[3H‐indole‐3,6′(4′aH)‐[1H]pyrano[3,4‐f]indolizine]‐4′‐carboxylic acid methyl ester, C₂₁H₂₄N₂O₄, has Z′ = 3, with no solvent. Both form intermolecular hydrogen bonds involving only the ox­indole, with N?O distances in the range 2.759 (4)–2.894 (5) Å.     

The isomeric compounds nimbolide and isonimbolide

Nimbolide [systematic name: (4α,5α,6α,7α,15β,17α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,13,20,22‐tetraene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], C₂₇H₃₀O₇, was isolated from the leaves of Azadirachta indica, and its isomer, isonimbolide [systematic name: (4α,5α,6α,7α,15α)‐7,15:21,23‐diepoxy‐6‐hydroxy‐4,8‐dimethyl‐1‐oxo‐18,24‐dinor‐11,12‐secochola‐2,16,20,22‐tetra­ene‐4,11‐dicarboxylic acid γ‐lactone methyl ester], was prepared from a novel rearrangement reaction of nimbolide, using boron trifluoride etherate and tetra­butyl­ammonium bromide. The reaction conditions are probably responsible for the ether cleavage, double‐bond rearrangement and reformation of the ether linkage. As a result, there are conformational changes in two cyclo­pentane rings and the side‐chain –CH₂COOMe group. In isonimbolide, an (24) hydrogen‐bond motif is observed.     

Conformation of N‐methyl‐4‐piperidyl 2,4‐dinitrobenzoate

The crystal structure of N‐methyl‐4‐piperidyl 2,4‐di­nitro­benzoate, C₁₃H₁₅N₃O₆, (I), at 130 (2) K reveals that, in the solid state, the mol­ecule exists in the equatorial conformation, (Ieq). Thus, the through‐bond interaction present in the axial conformation, (Iax), is not strong enough to overcome the syn–diaxial interactions between the axial methyl substituent and the axial H atoms on the two piperidyl ring C atoms either side of the ester‐linked ring C atom. The carboxyl­ate group in (I) is orthogonal to the aromatic ring, in contrast with other 2,4‐di­nitro­benzoates, which are coplanar. The piperidyl–ester C—O bond distance is 1.467 (3) Å, which is actually shorter than other equatorial cyclo­hexyl–ester C—O distances. This shorter piperidyl–ester C—O bond distance is due to the reduced electron demand of the orthogonal ester group.     

2,3‐Diaryl‐3‐hydroxy­propionic acid inter­mediates in the synthesis of threo forms of 1,2‐diaryl‐1,3‐propane­diols

Racemic threo‐3‐hydroxy‐2,3‐diphenyl­propionic acid, C₁₅H₁₄O₃, (I), crystallizes from ethyl acetate as a conglomerate of separate (+)‐ and (−)‐crystals. The geometries of (I) and its methyl ester are compared. Reduction of (I) gives threo‐1,2‐diphenyl‐1,3‐propane­diol. The synthesis of threo forms of 1,2‐diaryl‐1,3‐propane­diols via 2,3‐diaryl‐3‐hydroxy­propionic acids is discussed.     

N‐(2‐Carboxy­benzoyl)‐l‐leucine methyl ester

The title compound (with the systematic name 2‐{[(1S)‐1‐(methoxy­carbonyl)‐3‐methyl­butyl]amino­carbonyl}benzoic acid), C₁₅H₁₉NO₅, crystallizes in the monoclinic space group P2₁, with two independent mol­ecules per asymmetric unit. The most notable difference between the two mol­ecules is in the dihedral angles between the planes of the carboxyl group and the benzene ring, which are 3.5 (3) and 25.7 (1)°. This difference may account for the fact that two competing reactions are observed in aqueous solution, namely cyclization to form the imide N‐phthaloyl­leucine and hydrolysis of N‐(2‐carboxy­benzoyl)‐l ‐leucine methyl ester to phthalic acid and leucine.     

Reactive intermediates in peptide synthesis. ortho‐Nitrophenyl Nα‐para‐toluenesulfonyl‐α‐aminoisobutyrate

The preparation, characterization, and molecular and crystal structures of the title compound [IUPAC name: 2‐nitro­phenyl 2‐methyl‐2‐(para‐toluene­sulfonyl­amino)­propanoate], C₁₇H₁₈­N₂O₆S, are reported. The phenyl group is almost perpendicular to the plane of the adjacent ester moiety. One O atom of the nitro group is wedged between the two ester O atoms. The implications of this peculiar conformation for the chemistry of ortho‐nitro­phenyl esters in peptide synthesis are discussed.     

cis,cis,cis‐Tetra­methyl 1,2,4,5‐cyclo­hexane­tetra­carboxyl­ate

The title compound, C₁₄H₂₀O₈, was synthesized from the hydrogenation of tetra­methyl 1,4‐cyclo­hexa­diene‐1,2,4,5‐tetra­carboxyl­ate with a catalytic amount of palladium/carbon. All four carbonyl moieties of the methyl ester groups are on the same face of the chair‐conformed ring. The substantial ring distortion associated with the 1,3‐diaxial methoxycarbonyl substituents is reflected in the large difference between bond angles as well as torsion angles, respectively, that in undistorted cyclo­hexanes would be approximately the same.     

Triterpenoide. XIX. 3β‐Hydroxy‐11‐oxo‐18α‐olean‐12‐en‐28‐säure‐methyl­ester und 3,11‐Dioxo‐18α‐olean‐12‐en‐28‐säure‐methyl­ester

The X‐ray crystal structure analyses of 3β‐hydroxy‐11‐oxo‐18α‐olean‐12‐en‐28‐oic acid methyl ester ethanol solvate, C₃₁H₄₈O₄·C₂H₆O, (I), and 3,11‐dioxo‐18α‐olean‐12‐en‐28‐oic acid methyl ester, C₃₁H₄₆O₄, (II), are described. These two compounds differ only in the structure of ring A. In (I), ring A has a chair conformation, while in (II), it has a twisted boat conformation. In both compounds, ring C has a slightly distorted sofa conformation, rings B, D and E are in chair conformations, and rings D and E are trans‐fused. The asymmetric unit of (I) contains one mol­ecule of ethanol linked by hydrogen bonds with two different mol­ecules of (I).     

The allyl complex di‐μ‐chloro‐bis­{[(1,2,3‐η)‐4‐oxo‐5,5‐di­methyl‐1‐(ethoxy­carbonyl)­hexenyl]palladium(II)}

The title compound, di‐μ‐chloro‐bis{[(2,3,4‐η)‐ethyl 6,6‐di­methyl‐5‐oxohept‐2‐enoato]­palladium(II)}, [Pd₂Cl₂(C₁₁­H₁₇­O₃)₂], is a binuclear chloro‐bridged palladium allyl complex that was obtained serendipitously From the reaction of 6,6‐di­methyl‐2‐hepten‐4‐ynoate with Na₂PdCl₄ in water‐containing alcohol. The allyl group is substituted with an ester and a tert‐butyl­carboxy group. The dimeric mol­ecules link via C—H?O contacts into a two‐dimensional network parallel to the bc plane.     

3‐Germyl‐3,3‐di­methyl­propionic acid derivatives

The crystal structures of 3,3‐di­methyl‐3‐(tri­chloro­germyl)­propionic acid, [Ge(C₅H₉O₂)Cl₃], 3,3‐di­methyl‐3‐(tri­phenyl­germyl)­propionic acid, [Ge(C₆H₅)₃(C₅H₉O₂)], and 3,3‐di­methyl‐3‐(tri‐p‐toly­lgermyl)­propionic acid, [Ge(C₇H₇)₃(C₅H₉O₂)], have slightly distorted tetrahedral geometries about the Ge atoms. All the structures form dimers via strong O—H·O hydrogen bonds, resulting in eight‐membered rings that can be best described in terms of graph‐set notation (8).     

Hamigerin A and a hamigerin D decomposition product

The sponge Hamigera tarangaensis has yielded eight new compounds and we report here the structure of one of these compounds, hamigeran A, C₂₀H₂₅BrO₅, or methyl 7‐bromo‐4β,6‐di­hydroxy‐1β‐iso­propyl‐3aα,8‐di­methyl‐5‐oxo‐1a,3a,4,5‐tetra­hydro­cyclo­penta­[a]­naphthalene‐4‐carboxyl­ate, and the decomposition product of hamigeran D, C₂₁H₂₈BrNO₄, namely 2‐(8‐bromo‐2β,7‐di­methyl‐4‐oxo‐1,3α‐benzox­aza­n‐5‐yl)‐3‐iso­propylcyclo­pentyl­acetic acid.     

2‐(6‐Bromopyridin‐3‐yl)‐4,4,5,5‐tetramethyl‐1,3,2‐dioxaborolane and (6‐bromopyridin‐3‐yl)boronic acid,new bifunctional building blocks for combinatorial chemistry

The first comparative study between two new heterocyclic boron derivatives, viz. a (6‐bromo­pyridin‐3‐yl)­boronic ester, C₁₁H₁₅BBrNO₂, and (6‐bromo­pyridin‐3‐yl)­boronic acid, C₅H₅BBrNO₂, shows a small but not significant difference in their C—B bond lengths, which cannot explain the experimentally observed difference in their stabilities. The crystal packing of the boronic ester consists principally of van der Waals interactions, while the boronic acid mol­ecules interact in their crystal through hydrogen bonds.     

Cyano‐stabilized triphenyl­phospho­nium ylids

Crystalline cyano‐stabilized triphenyl­phospho­nium ylids with keto or ester groups give rise to an extended electronic delocalization. In methyl 2‐cyano‐2‐(trimethyl­phospho­nio)­ethenoate, Ph₃P=C(CN)CO₂CH₃ or C₂₂H₁₈NO₂P, (I), and 1‐cyano‐1‐(trimethyl­phospho­nio)prop‐1‐en‐2‐olate, Ph₃P=C(CN)CO—CH₃ or C₂₂H₁₈NOP, (II), the carbonyl groups are oriented toward the cationoid P atom. Bond lengths and angles, torsion angles and P⋯O contact distances are consistent with a dominant coplanar conformation where the mol­ecular structures are the result of a balance between intra‐ and inter­molecular inter­actions. The main inter­actions presented by cyano‐ester (I) and cyano‐keto (II) are intra­molecular inter­actions between the carbonyl O and the P atoms. In addition, both compounds show other less important intra­molecular inter­actions between the carbonyl O and phenyl H atoms, which could contribute to form a preferred conformation in the crystal structure.     

Ribbons of hydrogen‐bonded rings in the 1:2 complex of pyromellitic acid and di­methyl sulfoxide

In the title complex, pyromellitic acid–di­methyl sulfoxide (1/­2), C₁₀H₆O₈·2C₂H₆OS, mol­ecules of pyromellitic acid (1,2,4,5‐benzene­tetra­car­box­ylic acid) and di­methyl sulfoxide, the latter being well ordered, are linked to each other by O—­H⃛O hydrogen bonds. The formula unit displays crystallographic inversion symmetry. The packing consists of ribbons of hydrogen‐bonded rings that can be described by graph set C(10)R(18).     

Differences in the crystal structures of two dialkyl diester triphenyl­phospho­nium ylids

Hydrogen bonding and crystal packing play major roles in determining the conformations of ethyl methyl 2‐(triphenyl­phospho­ranyl­idene)malonate, Ph₃P=C(CO₂CH₃)CO₂CH₂CH₃ or C₂₄H₂₃O₄P, (I), and dimethyl 2‐(triphenyl­phosphor­anyl­idene)malonate, Ph₃P=C(CO₂CH₃)₂ or C₂₃H₂₁O₄P, (II). In (I), the acyl O atom of the ethyl ester group is anti to the P atom, while the O atom of the methyl ester group is syn. In (II), the dimethyl diester is a 1:1 mixture of anti–anti and syn–anti conformers.     

cis‐(6RS,13RS)‐3,3,10,10‐Tetra­methyl‐6,13‐diphenyl‐1,8‐dioxa‐4,11‐diaza­cyclo­tetra­decane‐2,5,9,12‐tetra­one and two of its precursors

The title macrocycle, C₂₆H₃₀N₂O₆, (VI), was obtained by `direct amide cyclization' from the linear precursor 3‐hydr­oxy‐N‐[1‐methyl‐1‐(N‐methyl‐N‐phenyl­carbamoyl)ethyl]‐2‐phenylpropanamide, the N‐methyl­anilide of rac‐2‐methyl‐2‐[(3‐hydroxy‐2‐phenyl­propanoyl)­amino]­propanoic acid, C₁₃H₁₇NO₄, (IV). The reaction proceeds via the inter­mediate rac‐2‐(2‐hydroxy‐1‐phenyl­ethyl)‐4,4‐dimethyl‐1,3‐oxazol‐5(4H)‐one, C₁₃H₁₅NO₃, (V), which was synthesized independently and whose structure was also established. Unlike all previously described analogues, the title macrocycle has the cis‐diphenyl configuration. The 14‐membered ring has a distorted rect­angular diamond‐based [3434] configuration and inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into a three‐dimensional framework. The propanoic acid precursor forms a complex series of inter­molecular hydrogen bonds, each of which involves pairwise association of mol­ecules and which together result in the formation of extended two‐dimensional sheets. The oxazole inter­mediate forms centrosymmetric hydrogen‐bonded dimers in the solid state.     

Gabapentin and gabapentin monohydrate

Gabapentin [1‐(amino­methyl)­cyclo­hexane­acetic acid, C₉H₁₇NO₂] is a zwitterion in the solid state. Its crystal structure involves extensive hydrogen bonding between the NH₃⁺ and COO^? groups of neighboring mol­ecules. The structure of gabapentin monohydrate [1‐(amino­methyl)­cyclo­hexane­acetic acid monohydrate, C₉H₁₇NO₂·H₂O] also involves such hydrogen bonding and, in addition, has a hydrogen‐bonding network comprising the water mol­ecules and both the NH₃⁺ and COO^? groups.     

Model porphyrin precursors: 1,2,4,5‐tetrakis(cyanomethyl)­benzene,methyl 3,4,5‐triacetoxy­benzoate and 2‐(N‐phthalimidomethyl)benzoic acid

In the crystalline state, the centrosymmetric mol­ecule 1,2,4,5‐tetrakis­(cyano­methyl)­benzene, C₁₄H₁₀N₄, has one cyano­methyl group in the benzene plane and one cyano­methyl group rotated 67.2 (2)° out of the benzene plane. Molecules of methyl 3,4,5‐tri­acetoxy­benzoate, C₁₄H₁₄O₈, form chains with each mol­ecule twisted 89.6 (1)° from the preceding mol­ecule. In this orientation, a close C—H?O contact is formed, with an H?O distance of 2.34 Å. The structure of 2‐(N‐phthalimido­methyl)­benzoic acid, C₁₆H₁₁NO₄, reveals hydrogen‐bonded dimers linked by the carboxyl groups of adjacent mol­ecules. The O4?O3 distance is 2.636 (2) Å and the O4—H?O3 angle is 171 (2)°.     

Hydro­gen‐bonded assemblages in 2,6‐bis­(hydroxy­methyl)‐4‐R‐phenol,with R = methyl,methoxy, phenoxy and 1‐(4‐methoxy­phenyl)‐1‐methyl­ethyl

Four derivatives of 2,6‐bis­(hydroxy­methyl)­phenol, with various para substituents, have been investigated; these are 2,6‐bis­(hydroxy­methyl)‐4‐methyl­phenol, C₉H₁₂O₃, (I), 2,6‐bis­(hydroxy­methyl)‐4‐methoxy­phenol, C₉H₁₂O₄, (II), 2,6‐bis­(hydroxy­methyl)‐4‐phenoxy­phenol, C₁₄H₁₄O₄, (III), and 2,6‐bis­(hydroxy­methyl)‐4‐[1‐(4‐methoxy­phenyl)‐1‐methyl­ethyl]­phenol, C₁₈H₂₂O₄, (IV). All four structures display hydrogen‐bonding networks resulting in sheets, with possible weak inter‐sheet π–π interactions in one case. In all the structures but one, the mol­ecules form centrosymmetric dimeric subunits held together by two hydrogen bonds between the hydroxy­methyl groups and, in two cases, by probable π–π interactions.