Serendipity and four polymorphic structures of benzidine, C12H12N2

The search for a co-crystal of benzidine as a bifunctional hydrogen-bond donor with potential hydrogen-bond acceptors has instead revealed four polymorphs of the source material benzidine for which, somewhat surprisingly, no structure has been reported as of the November 2005 update of the CSD. All four structures are characterized by a rather unusual number of molecules in the asymmetric unit (Z' = 1.5, 3, and 4.5), which are found in only 0.25%, 0.4%, and 0.002% of structures in the CSD. Forms I and IV (Z' = 4.5) exhibit very similar crystal habits and are not distinguishable visually. In all forms except Form II (Z' = 3), one of the molecules lies on a crystallographic inversion center, requiring the molecule to be planar; other molecules are nonplanar. Spectroscopic and thermodynamic characterizations of the system, including at least two possible additional forms of benzidine obtained by HT polymorph screening are reported.     

NMR crystallography of oxybuprocaine hydrochloride, Modification II degrees

The (13)C CPMAS spectrum is presented for the polymorph of oxybuprocaine hydrochloride which is stable at room temperature, i.e. Mod. II degrees . It shows crystallographic splittings arising from the fact that there are two molecules, with substantially different conformations, in the asymmetric unit. An INADEQUATE two-dimensional experiment was used to link signals for the same independent molecule. The chemical shifts are discussed in relation to the crystal structure. Of the four ethyl groups attached to NH(+) nitrogens, one gives rise to unusually low chemical shifts, very different from those of the other three ethyl groups. This is attributed empirically to gamma-gauche conformational effects, as is confirmed by shielding computations. These considerations allow (13)C signals to be assigned to specific carbons in the two crystallographically inequivalent molecules in the crystal structure. Indeed, information about the conformations is inherent in the NMR spectrum, which thus provides data of crystallographic significance. A (13)C/(1)H HETCOR experiment enabled resolution to be obtained in the (1)H dimension and allowed (1)H and (13)C signals for the same independent molecule to be linked.     

Conformational, concomitant polymorphs of 4,4-diphenyl-2,5-cyclohexadienone: conformation and lattice energy compensation in the kinetic and thermodynamic forms

4,4-Diphenyl-2,5-cyclohexadienone (1) crystallized as four conformational polymorphs and a record number of 19 crystallographically independent molecules have been characterized by low-temperature X-ray diffraction: form A (P2(1), Z'=1), form B (P1, Z'=4), form C (P1, Z'=12), and form D (Pbca, Z'=2). We have now confirmed by variable-temperature powder X-ray diffraction that form A is the thermodynamic polymorph and B is the kinetic form of the enantiotropic system A-D. Differences in the packing of the molecules in these polymorphs result from different acidic C-H donors approaching the C=O acceptor in C-H...O chains and in synthons I-III, depending on the molecular conformation. The strength of the C-HO interaction in a particular structure correlates with the number of symmetry-independent conformations (Z') in that polymorph, that is, a short C-HO interaction leads to a high Z' value. Molecular conformation (Econf) and lattice energy (Ulatt) contributions compensate each other in crystal structures A, B, and D resulting in very similar total energies: Etotal of the stable form A=1.22 kcal mol(-1), the metastable form B=1.49 kcal mol(-1), and form D=1.98 kcal mol(-1). Disappeared polymorph C is postulated as a high-Z', high-energy precursor of kinetic form B. Thermodynamic form A matches with the third lowest energy frame based on the value of Ulatt determined in the crystal structure prediction (Cerius2, COMPASS) by full-body minimization. Re-ranking the calculated frames on consideration of both Econf (Spartan 04) and Ulatt energies gives a perfect match of frame #1 with stable structure A. Diphenylquinone 1 is an experimental benchmark used to validate accurate crystal structure energies of the kinetic and thermodynamic polymorphs separated by <0.3 kcal mol(-1) (approximately 1.3 kJ mol(-1)).     

Measurement of five dipolar couplings from a single 3D NMR multiplet applied to the study of RNA dynamics

A new three-dimensional NMR experiment is described that yields five scalar or dipolar couplings from a single cross-peak between three spins. The method is based on the E.COSY principle and is demonstrated for the H1'-C1'-C2' fragment of ribose sugars in a uniformly 13C-enriched 24-nucleotide RNA stem-loop structure, for which a complete set of couplings was obtained for all nonmodified nucleotides. The values of the isotropic J couplings and the 13C1' and 13C2' chemical shifts define the sugar pucker. Once the sugar pucker is known, the five dipolar couplings between C1'-H1', C2'-H2', H1'-H2', C1'-H2', and C2'-H1', together with C1'-C2', C3'-H3', and C4'-H4' available from standard experiments, can be used to derive the five unknowns that define the local alignment tensor, thereby simultaneously providing information on relative orientation and dynamics of the ribose units. Data indicate rather uniform alignment for all stem nucleotides in the 24-nt stem-loop structure, with only a modest reduction in order for the terminal basepair, but significantly increased mobility in part of the loop region. The method is applicable to proteins, nucleic acids, and carbohydrates, provided 13C enrichment is available.     

Absolute configuration of scyphostatin

[reaction: see text] The absolute configuration of the side chain of scyphostatin (1) has been established. The chemical degradation of 1 gave 4 and 9, which correspond to the C7'-C12' and C13'-C16' fragments of the natural products, respectively. The spectroscopic data and [alpha]D values of both compounds were compared to those of authentic samples. The results show that the absolute configuration of 1 is 8'R,10'S,14'R.     

Application of solid-state 35Cl NMR to the structural characterization of hydrochloride pharmaceuticals and their polymorphs

Solid-state (35)Cl NMR (SSNMR) spectroscopy is shown to be a useful probe of structure and polymorphism in HCl pharmaceuticals, which constitute ca. 50% of known pharmaceutical salts. Chlorine NMR spectra, single-crystal and powder X-ray diffraction data, and complementary ab initio calculations are presented for a series of HCl local anesthetic (LA) pharmaceuticals and some of their polymorphs. (35)Cl MAS SSNMR spectra acquired at 21.1 T and spectra of stationary samples at 9.4 and 21.1 T allow for extraction of chlorine electric field gradient (EFG) and chemical shift (CS) parameters. The sensitivity of the (35)Cl EFG and CS tensors to subtle changes in the chlorine environments is reflected in the (35)Cl SSNMR powder patterns. The (35)Cl SSNMR spectra are shown to serve as a rapid fingerprint for identifying and distinguishing polymorphs, as well as a useful tool for structural interpretation. First principles calculations of (35)Cl EFG and CS tensor parameters are in good agreement with the experimental values. The sensitivity of the chlorine NMR interaction tensor parameters to the chlorine chemical environment and the potential for modeling these sites with ab initio calculations hold much promise for application to polymorph screening for a wide variety of HCl pharmaceuticals.     

Toward the total synthesis of disorazole A(1) and C(1): asymmetric synthesis of a masked southern segment

[reaction: see text] A highly convergent asymmetric synthesis of the masked southern segment of the antimitotic agent disorazole A(1) involves a Sonogashira coupling between a C1'-C10' enyne and a suitably protected C11'-C19' vinyl iodide. The central E,Z,Z-triene moiety is masked as a more stable ynediene.     

Twinning in 5‐fluorosalicylic acid: description of a new polymorph

The crystal structure of 5‐fluorosalicylic acid is known from the literature [Choudhury & Guru Row (2004). Acta Cryst. E 60 , o1595–o1597] as crystallizing in the monoclinic crystal system with space‐group setting P2₁/n and with one molecule in the asymmetric unit (polymorph I). We describe here a new polymorph which is again monoclinic but with different unit‐cell parameters (polymorph II). Polymorph II has two molecules in the asymmetric unit. Its structure was modelled as a twin, with a pseudo‐orthorhombic C‐centred twin cell.     

Total synthesis of (-)-sarain A

This article describes the details of our synthetic studies toward the complex marine alkaloid sarain A. Various strategies were conceived, setbacks encountered, and solutions developed, ultimately leading to a successful enantioselective total synthesis. Our route to (-)-sarain A features a number of key steps, including an asymmetric Michael addition to install the C4'-C3'-C7' stereotriad, an enoxysilane-N-sulfonyliminium ion cyclization to set the C3 quaternary carbon stereocenter, and assemble the diazatricycloundecane core, a ring-closing metathesis to construct the 13-membered ring, an intramolecular Stille coupling to fashion the unsaturated 14-membered macrocycle, and a late-stage installation of the tertiary amine-aldehyde proximity interaction.     

A low‐temperature polymorph of m‐quinquephenyl

A low‐temperature polymorph of 1,1′:3′,1′′:3′′,1′′′:3′′′,1′′′′‐quinquephenyl (m‐quinquephenyl), C₃₀H₂₂, crystallizes in the space group P2₁/c with two molecules in the asymmetric unit. The crystal is a three‐component nonmerohedral twin. A previously reported room‐temperature polymorph [Rabideau, Sygula, Dhar & Fronczek (1993). Chem. Commun. pp. 1795–1797] also crystallizes with two molecules in the asymmetric unit in the space group P. The unit‐cell volume for the low‐temperature polymorph is 4120.5 (4) ų, almost twice that of the room‐temperature polymorph which is 2102.3 (6) ų. The molecules in both structures adopt a U‐shaped conformation with similar geometric parameters. The structural packing is similar in both compounds, with the molecules lying in layers which stack perpendicular to the longest unit‐cell axis. The molecules pack alternately in the layers and in the stacked columns. In both polymorphs, the only interactions between the molecules which can stabilize the packing are very weak C—H...π interactions.     

ss‐NMR and single‐crystal X‐ray diffraction in the elucidation of a new polymorph of bischalcone (1E,4E)‐1,5‐bis(4‐fluorophenyl)penta‐1,4‐dien‐3‐one

We report a new polymorph of (1E,4E)‐1,5‐bis(4‐fluorophenyl)penta‐1,4‐dien‐3‐one, C₁₇H₁₂F₂O. Contrary to the precedent literature polymorph with Z′ = 3, our polymorph has one half molecule in the asymmetric unit disordered over two 50% occupancy sites. Each site corresponds to one conformation around the single bond vicinal to the carbonyl group (so‐called anti or syn). The other half of the bischalcone is generated by twofold rotation symmetry, giving rise to two half‐occupied and overlapping molecules presenting both anti and syn conformations in their open chain. Such a disorder allows for distinct patterns of intermolecular C—H…O contacts involving the carbonyl and anti‐oriented β‐C—H groups, which is reflected in three ¹³C NMR chemical shifts for the carbonyl C atom. Here, we have also assessed the cytotoxicity of three symmetric bischalcones through their in vitro antitumour potential against three cancer cell lines. Cytotoxicity assays revealed that this biological property increases as halogen electronegativity increases.     

A centrosymmetric polymorph of chloridotris(triphenylphosphine‐κP)copper(I) at 150 K

This study characterizes a new polymorph of the title compound, [CuCl(C₁₈H₁₅P)₃], and analyses the influence of the extensive network of weak hydrogen‐bonding interactions in the generation of this different crystal structure. The compound crystallizes in the centrosymmetric space group C2/c with two crystallographically independent molecules per asymmetric unit, in contrast with the previously determined polymorph which crystallizes in the noncentrosymmetric space group P3 with three crystallographically independent molecules in the asymmetric unit, each with crystallographically imposed C3 symmetry [Gill, Mayerle, Welcker, Lewis, Ucko, Barton, Stowens & Lippard (1976). Inorg. Chem. 15 , 1155–1168]. The geometries of the two molecules of the title compound are very similar, with each having an approximately tetrahedral coordination around the central Cu atom and approximate C_s molecular symmetry. The molecules pack in chains parallel to the crystallographic b axis, connected by C—H...Cl and C—H...π(phenyl) hydrogen bonds.     

The Polymorphs of L‐Phenylalanine

The solid‐state structure of the amino acid phenylalanine (Phe) offers a potential key to understanding the behavior of a large class of important aromatic compounds. Obtaining good single crystals is, however, notoriously difficult. The structure of the common polymorph of Phe, form I, was first reported by Weissbuch et al. (as D ‐Phe) in 1990, but the correctness of the published C2 unit cell with two disordered molecules in the asymmetric unit was later questioned and other space groups suggested. The identity of form I of L ‐Phe is here established to be P2₁ with Z′=4, based on data from a well‐diffracting single crystal grown from an acetic acid solution of the amino acid. A second new polymorph, form IV, together with the two recently described forms II and III provide unprecedented information on the structural complexity of this essential amino acid. It is furthermore documented that the racemate, dl ‐Phe, does not grow proper single crystals.     

Atropisomerism observed in indometacin derivatives

To elucidate the active conformation of indometacin that differentiates between cyclooxygenase-1 (COX-1) and cyclooxygenase-2 (COX-2), the stereochemistry around the N-benzoylated indole moiety of indometacin was studied. Resolution of stable atropisomers as representative conformations was found to be possible by restricting rotation about the N-C7' and/or C7'-C1' bond. Only the aR-isomer showed specific inhibition of COX-1, and COX-2 was not inhibited by either atropisomer.     

Revealing protein structures in solid-phase peptide synthesis by 13C solid-state NMR: evidence of excessive misfolding for Alzheimer's β

Solid-phase peptide synthesis (SPPS) is a widely used technique in biology and chemistry. However, the synthesis yield in SPPS often drops drastically for longer amino acid sequences, presumably because of the occurrence of incomplete coupling reactions. The underlying cause for this problem is hypothesized to be a sequence-dependent propensity to form secondary structures through protein aggregation. However, few methods are available to study the site-specific structure of proteins or long peptides that are anchored to the solid support used in SPPS. This study presents a novel solid-state NMR (SSNMR) approach to examine protein structure in the course of SPPS. As a useful benchmark, we describe the site-specific SSNMR structural characterization of the 40-residue Alzheimer's β-amyloid (Aβ) peptide during SPPS. Our 2D (13)C/(13)C correlation SSNMR data on Aβ(1-40) bound to a resin support demonstrated that Aβ underwent excessive misfolding into a highly ordered β-strand structure across the entire amino acid sequence during SPPS. This approach is likely to be applicable to a wide range of peptides/proteins bound to the solid support that are synthesized through SPPS.     

Two polymorphs of N‐(2‐methoxyphenyl)‐4‐oxo‐4H‐chromone‐3‐carboxamide

The title compound, C₁₇H₁₃NO₄, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space group P2₁/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three‐dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings.     

Packing considerations of 10‐oxa‐9‐boraphenanthrene derivatives

The crystal structures of three products of the reaction of 2‐phenylphenol and BCl₃ have been determined. The structures show intriguing packing patterns and an interesting case of pseudosymmetry. In addition, one of the two polymorphs has a primitive monoclinic crystal system, but it is twinned and emulates an orthorhombic C‐centred structure. Tris(biphenyl‐2‐yl) borate, C₃₆H₂₇BO₃, ( III ), crystallizes with only one molecule in the asymmetric unit. The dihedral angles between the planes of the aromatic rings in the biphenyl moieties are 50.47 (13), 44.95 (13) and 42.60 (13)°. The boron centre is in a trigonal planar coordination with two of the biphenyl residues on one side of the BO₃ plane and the remaining biphenyl residue on the other side. One polymorph of 10‐oxa‐9‐boraphenanthren‐9‐ol, C₁₂H₉BO₂, ( V a ), crystallizes with two almost identical molecules (r.m.s. deviation of all non‐H atoms = 0.039 Å) in the asymmetric unit. All non‐H atoms lie in a common plane (r.m.s. deviation = 0.015 Å for both molecules in the asymmetric unit). The two molecules in the asymmetric unit are connected into dimers via O—H...O hydrogen bonds. A second polymorph of 10‐oxa‐9‐boraphenanthren‐9‐ol, ( V b ), crystallizes as a pseudo‐merohedral twin with two almost identical molecules (r.m.s. deviation of all non‐H atoms = 0.035 Å) in the asymmetric unit. All non‐H atoms lie in a common plane (r.m.s. deviation = 0.012 Å for molecule 1 and 0.014 Å for molecule A). Each of the two molecules in the asymmetric unit is connected into a centrosymmetric dimer via O—H...O hydrogen bonds. The main difference between the two polymorphic structures is that in ( V a ) the two molecules in the asymmetric unit are hydrogen bonded to each other, whereas in ( V b ), each molecule in the asymmetric unit forms a hydrogen‐bonded dimer with its centrosymmetric equivalent. 9‐[(Biphenyl‐2‐yl)oxy]‐10‐oxa‐9‐boraphenanthrene, C₂₄H₁₇BO₂, ( VI ), crystallizes with four molecules in the asymmetric unit. The main differences between them are the dihedral angles between the ring planes. Apart from the biphenyl moiety, all non‐H atoms lie in a common plane (r.m.s. deviations = 0.026, 0.0231, 0.019 and 0.033 Å for molecules 1, A, B and C, respectively). This structure shows pseudosymmetry; molecules 1 and A, as well as molecules B and C, are related by a pseudo‐translation of about in the direction of the b axis. Molecules 1 and B, as well as molecules A and C, are related by a pseudo‐inversion centre at ,,. Neither between molecules 1 and C nor between molecules A and B can pseudosymmetry be found.     

Design of Peptides with α,β-Dehydro Residues: Synthesis,Crystal Structure and Molecular Conformation of a Peptide N-Boc-Phe-ΔPhe-Ile-OCH<Subscript>3</Subscript>

To develop a complete set of design rules with α,β-dehydro residues, a tripeptide N-Boc-Phe-ΔPhe-Ile-OCH₃ was synthesized. The synthesis was carried out in solution phase using azlactone procedure. The three-dimensional structure of the peptide was determined by X-ray diffraction method and refined to an R-factor of 0.085. The structure contains three peptide molecules in the asymmetric unit. In all the three crystallographically independent molecules ΔPhe residue adopts one of the three conformations that have been reported for a ΔPhe residue. The overall conformations of three peptide molecules in the asymmetric unit are not similar. Two out of three crystallographically independent molecules adopt type II β-turn conformations whereas the third molecule is found having the characteristic S-shaped conformation in which the values of dihedral angles φ, ψ have opposite signs alternately. One of these two types of conformations has been observed when a ΔPhe is introduced at (i+2) position of a tetrapeptide. The β-turn conformation is stabilized by a 4→1 hydrogen bond where the hydrophobic side chains of residues at (i+1) and (i+3) positions stabilized the unfolded conformation with van der Waals interactions. The three independent molecules are locked together by three hydrogen bonds between molecules A and B and two hydrogen bonds between molecules B and C.     

Structure and dynamics of L-selenomethionine in the solid state

L-selenomethionine 1 crystallizes in P2(1) space group with two molecules in the asymmetric unit. Solid-state NMR spectroscopy is used for searching of structure and dynamics of 1 in the crystal lattice. The distinct molecular motion of side chains for A and B molecules of 1 is apparent from measurements of relaxation parameters (1H 1rho, 13C T1) and analysis of CSA data (2D-PASS experiment). The 13C delta(ii) and 77Se delta(ii) parameters are correlated with theoretical shielding parameters obtained by means DFT GIAO calculations. Attempt to explain the mechanism of phase transition of crystals of 1 at 313K is presented.     

Progress in 13C and 1H solid-state nuclear magnetic resonance for paramagnetic systems under very fast magic angle spinning

High-resolution solid-state NMR (SSNMR) of paramagnetic systems has been largely unexplored because of various technical difficulties due to large hyperfine shifts, which have limited the success of previous studies through depressed sensitivity/resolution and lack of suitable assignment methods. Our group recently introduced an approach using "very fast" magic angle spinning (VFMAS) for SSNMR of paramagnetic systems, which opened an avenue toward routine analyses of small paramagnetic systems by (13)C and (1)H SSNMR [Y. Ishii et al., J. Am. Chem. Soc. 125, 3438 (2003); N. P. Wickramasinghe et al., ibid. 127, 5796 (2005)]. In this review, we discuss our recent progress in establishing this approach, which offers solutions to a series of problems associated with large hyperfine shifts. First, we demonstrate that MAS at a spinning speed of 20 kHz or higher greatly improves sensitivity and resolution in both (1)H and (13)C SSNMR for paramagnetic systems such as Cu(II)(DL-alanine)(2)H(2)O (Cu(DL-Ala)(2)) and Mn(acac)(3), for which the spectral dispersions due to (1)H hyperfine shifts reach 200 and 700 ppm, respectively. Then, we introduce polarization transfer methods from (1)H spins to (13)C spins with high-power cross polarization and dipolar insensitive nuclei enhanced by polarization transfer (INEPT) in order to attain further sensitivity enhancement and to correlate (1)H and (13)C spins in two-dimensional (2D) SSNMR for the paramagnetic systems. Comparison of (13)C VFMAS SSNMR spectra with (13)C solution NMR spectra revealed superior sensitivity in SSNMR for Cu(DL-Ala)(2), Cu(Gly)(2), and V(acac)(3). We discuss signal assignment methods using one-dimensional (1D) (13)C SSNMR (13)C-(1)H rotational echo double resonance (REDOR) and dipolar INEPT methods and 2D (13)C(1)H correlation SSNMR under VFMAS, which yield reliable assignments of (1)H and (13)C resonances for Cu(Ala-Thr). Based on the excellent sensitivity/resolution and signal assignments attained in the VFMAS approach, we discuss methods of elucidating multiple distance constraints in unlabeled paramagnetic systems by combing simple measurements of (13)C T(1) values and anisotropic hyperfine shifts. Comparison of experimental (13)C hyperfine shifts and ab initio calculated shifts for alpha- and beta-forms of Cu(8-quinolinol)(2) demonstrates that (13)C hyperfine shifts are parameters exceptionally sensitive to small structural difference between the two polymorphs. Finally, we discuss sensitivity enhancement with paramagnetic ion doping in (13)C SSNMR of nonparamagnetic proteins in microcrystals. Fast recycling with exceptionally short recycle delays matched to short (1)H T(1) of approximately 60 ms in the presence of Cu(II) doping accelerated 1D (13)C SSNMR for ubiquitin and lysozyme by a factor of 7.3-8.4 under fast MAS at a spinning speed of 40 kHz. It is likely that the VFMAS approach and use of paramagnetic interactions are applicable to a variety of paramagnetic systems and nonparamagnetic biomolecules.