X-ray structure of the curare alkaloid (+)-tubocurarine dibromide.

X-ray structure determination of the compound (C37H42N2O6)2+ .2Br-.4CH3OH, confirms that (+)-tubocurarine is a monoquaternary salt and has established that the molecule adopts different conformations in crystals of the dibromide and dichloride salts. The crystal structure is stabilised by a number of hydrogen bonds involving the two free hydroxyl groups and the tertiary nitrogen of the tubocurarine molecule, the bromide ions and the solvent molecules. The absolute configuration of the molecule, determined by X-ray anomalous scattering, confirms the configuration assigned earlier by chemical studies.     

Isolation of Festuclavine and Three New Indole Alkaloids,Roquefortine A,B and C from the Cultures of Penicillium roqueforti

The structure and absolute configuration of a metabolite isolated from Aspergillus silvaticus was studied by an X-ray diffraction method. Crystals were orthorhombic, with space group P2₁2₁2₁, and a=9.894 (5), b = 6.803 (4), c=22.519 (6) Å, and Z=4. The structure was solved by a direct method and refined by a block-diagonal least-square method to R=0.07 for 1143 non-zero reflections. The metabolite was identified as naphthalic anhydride obtained from atrovenetin. The absolute configuration determined by the Bijvoet method is consistent with that shown chemically. The molecule has two intramolecular hydrogen bonds.     

The effect of membrane stabilizers on phytochrome-controlled anthocyanin biosynthesis in Brassica oleracea

The promotion of anthocyanin synthesis in red-cabbage seedlings by 5 min exposure to R light is inhibited by subsequent application of CaCl₂. The stimulation of dark synthesis of anthocyanin by n-PrOH and by kinetin is also reduced by Ca²⁺ and by cholesterol, both of which are well known to stabilize cell membranes. By contrast, EDTA, which chelates Ca²⁺, promotes dark synthesis of anthocyanin. Assay of native Ca²⁺ extractable from seedlings immersed in EDTA demonstrates that R light exposure promotes a highly significant increase in extractable Ca²⁺. It is suggested that the molecular configuration of the phytochrome molecule affects the ability of a membrane to bind Ca²⁺ and that this in turn affects the permeability to substrates which are required for anthocyanin biosynthesis.     

Diaquabis(3,6-dioxaheptanoato)copper(II): crystal structure and EPR characteristics

The structure of the title compound has been determined by X-ray diffraction at 190 K. The complex has an all trans configuration with an elongated tetragonally distorted octahedral CuO6 chromophore. The elongated axis corresponding to the trans-Cu–O(ether) bonds. The ligand molecules are bidentate via the carboxyl and the 3-ether O atoms; the 6-ether O atoms are not coordinated and are remote from the Cu centres. The bond lengths to the Cu centres are Cu–O(ether) 2.355 Å, Cu–O(Carboxyl) 1.933 Å and Cu–OH2 1.995 Å.The EPR spectrum of both the powder and frozen solution forms is typical of a rhombic system with a dx2−y21 electronic configuration. There were no significant differences in spectra recorded over the temperature range 77 K to room temperature. These results are discussed in relation to earlier published results on closely related oxa-carboxyl complexes.     

Anionopentaaminecobalt(III) complexes with polyamine ligands. 24. The isolation and structure of mer-[CoCl(tn)(1,5, 9-triazanon-4-ene)]ZnCl4

The title complex is obtained as a by-product from the synthesis of trans-CoCl₂(tn)₂⁺ by dioxygen oxidation of Co(II) and the diamine in water at room temperature. A single crystal X-ray structure analysis shows that the tridentate Schiff's Base ligand adopts a meridional configuration and the remaining three octahedral sites are occupied by one bidentate tn ligand and one chloro ligand.     

Reduced Model Captures Mg2+-RNA Interaction Free Energy of Riboswitches

The stability of RNA tertiary structures depends heavily on Mg²⁺. The Mg²⁺-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ₂₊, the number of excess Mg²⁺ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg²⁺ ions interact closely and strongly with the RNA, unlike monovalent ions such as K⁺, suggesting that an explicit treatment of Mg²⁺ is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg²⁺-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg²⁺ through the explicit representation of Mg²⁺ ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K⁺ and models its competition with condensed Mg²⁺. The model contains one fitted parameter, the number of condensed K⁺ ions in the absence of Mg²⁺. Values of Γ₂₊ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ₂₊ to the Mg²⁺-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg²⁺ and RNA dynamics.     

Reduced Model Captures Mg-RNA Interaction Free Energy of Riboswitches

The stability of RNA tertiary structures depends heavily on Mg²⁺. The Mg²⁺-RNA interaction free energy that stabilizes an RNA structure can be computed experimentally through fluorescence-based assays that measure Γ₂₊, the number of excess Mg²⁺ associated with an RNA molecule. Previous explicit-solvent simulations predict that the majority of excess Mg²⁺ ions interact closely and strongly with the RNA, unlike monovalent ions such as K⁺, suggesting that an explicit treatment of Mg²⁺ is important for capturing RNA dynamics. Here we present a reduced model that accurately reproduces the thermodynamics of Mg²⁺-RNA interactions. This model is able to characterize long-timescale RNA dynamics coupled to Mg²⁺ through the explicit representation of Mg²⁺ ions. KCl is described by Debye-Hückel screening and a Manning condensation parameter, which represents condensed K⁺ and models its competition with condensed Mg²⁺. The model contains one fitted parameter, the number of condensed K⁺ ions in the absence of Mg²⁺. Values of Γ₂₊ computed from molecular dynamics simulations using the model show excellent agreement with both experimental data on the adenine riboswitch and previous explicit-solvent simulations of the SAM-I riboswitch. This agreement confirms the thermodynamic accuracy of the model via the direct relation of Γ₂₊ to the Mg²⁺-RNA interaction free energy, and provides further support for the predictions from explicit-solvent calculations. This reduced model will be useful for future studies of the interplay between Mg²⁺ and RNA dynamics.     

Crystal and molecular structure of Δ-cis-α-ethylenebis-S-prolinato(1,2-diamino-ethane)cobalt(III) perchlorate dihydrate, Δ-cis-α-[Co(ss-EBP)(en)] ClO4·2H2O

The crystal and molecular structure of Δ- cis-α- ethylenebis-S-prolinato(1,2-diaminoethane)cobalt(III) perchlorate dihydrate, Δ-cis-α-[Co(SS-EBP)(en)] ClO₄· 2H₂O, was determined from three-dimensional X-ray diffractometer data. The complex crystallizes in the orthorhombic system, space group P2₁2₁2₁ with a = 7.879(4) Å, b = 13.738(9) Å, c = 19.445(2) Å, V = 2104(2) ų. With Z = 4, the observed and calculated densities are 1.60(2) and 1.605 g cm^?3, respectively. The structure was refined by the block- diagonal least-squares technique to a final R = 0.0560 for 1604 observed reflections. The geometry about the cobalt atom is roughly octahedral with the tetradentate SS-EBP (= ethylenebis-S-prolinate ion), assuming cis-α configuration in which the complex possesses two out-of-plane amino acidate (R) rings and the backbone ethylenediamine (E) ring. The E ring conformation is δ. On the other hand, the R rings have λ conformation as well as the en ring. Δ-R_NR_N?(δ_E  λ_R1  λ_R2)(λ_en)-cis-α-[Co(SS-EBP)(en)]⁺ is one of two possible isomers of this compound which have been isolated and whose absolute configurations have been tentatively assigned by spectroscopy. The crystal and molecular structure determination confirms these assignments.     

Life in Its Uniqueness Remains Difficult to Define in Scientific Terms

Abstract

The crystal structure of the dehydro octapeptide Boc-Val-ΔPhe-Phe-Ala-Leu-Ala-ΔPhe-Leu-OH has been determined to atomic resolution by X-ray crystallographic methods. The crystals grown by slow evaporation of peptide solution in methanol/water are orthorhombic, space group P2₁2₁2₁. The unit cell parameters are a= 8.404 (3), b= 25.598(2) and c = 27.946(3) Å, Z=4. The agreement factor is R= 7.58% for 3636 reflections having (IF₀I) ≥ 3σ (IF₀I). The peptide molecule is characterised by a 3₁₀-helix at the N-terminus and a π-turn at the C-terminus. This conformation is exactly similar to the helix termination features observed in proteins. The π-turn conformation observed in the octapeptide is in good agreement with the conformational features of π-turns seen in some proteins. The α_L-position in the π-turn of the octapeptide is occupied by ΔPhe⁷, which shows that even bulky residues can be accommodated in this position of the π-turns. In proteins, it is generally seen that aL- position is occupied by glycine residue. No intermolecular head-to-tail hydrogen bonds are observed in solid state structure of the octapeptide. A water molecule located in the unit cell of the peptide molecule is mainly used to hold the peptide molecule together in the crystal. The conformation observed for the octapeptide might be useful to understand the helix termination and chain reversal in proteins and to construct helix terminators for denovo protein design.     

Ortho/para spin-isomers of H2O molecules as a factor responsible for formation of two structural motifs in water

According to the latest results obtained by small-angle X-ray scattering and X-ray spectroscopy, it was suggested that water on a nanometer scale represents a fluctuating mixture of clusters with tetrahedral structure and a subphase with partially broken hydrogen bonds, whereas the nuclear configuration of the H₂O molecule corresponds to single tetrahedral coordination. The basic reason of such structural partition is not clear until now. Here we show that it can be associated with existence of two nuclear H₂O spin isomers that have different probability to be in one or the other subphase. The para molecule can transfer an excess of its rotational energy to the environment, up to complete stopping of rotation because its rotational quantum number J = 0 in the basic state. This property is favorable for formation of clusters with closed H-bonds. Ortho molecules with odd-numbered J states lack this property and thus should be predominantly present in the locations with impaired bonds.     

Adsorption and decomposition mechanism of hexogen (RDX) on Al(111) surface by periodic DFT calculations

The adsorption of hexogen (RDX) molecule on the Al(111) surface was investigated by the generalized gradient approximation (GGA) of density functional theory (DFT). The calculations employ a supercell (4×4×3) slab model and three-dimensional periodic boundary conditions. The strong attractive forces between RDX molecule and aluminum atoms induce the N?O and N?N bond breaking of the RDX. Subsequently, the dissociated oxygen atoms, NO₂ group and radical fragment of RDX oxidize the Al surface. The largest adsorption energy is ?835.7 kJ mol^–1. We also investigated the adsorption and decomposition mechanism of RDX molecule on the Al(111) surface. The activation energy for the dissociation steps of V4 configuration is as large as 353.1 kJ mol^–1, while activation energies of other configurations are much smaller, in the range of 70.5–202.9 kJ mol^–1. The N?O is even easier than the N?NO₂ bond to decompose on the Al(111) surface.     

The "prismane" protein resolved: X-ray structure at 1.7 Å and multiple spectroscopy of two novel 4Fe clusters

The three-dimensional structure of the native "putative prismane" protein from Desulfovibrio vulgaris (Hildenborough) has been solved by X-ray crystallography to a resolution of 1.72?Å. The molecule does not contain a [6Fe-6S] prismane cluster, but rather two 4Fe clusters some 12?Å apart and situated close to the interfaces formed by the three domains of the protein. Cluster 1 is a conventional [4Fe-4S] cubane bound, however, near the N-terminus by an unusual, sequential arrangement of four cysteine residues (Cys 3, 6, 15, 21). Cluster 2 is a novel 4Fe structure with two μ₂-sulfido bridges, two μ₂-oxo bridges, and a partially occupied, unidentified μ₂ bridge X. The protein ligands of cluster 2 are widely scattered through the second half of the sequence and include three cysteine residues (Cys 312, 434, 459), one persulfido-cysteine (Cys 406), two glutamates (Glu 268, 494), and one histidine (His 244). With this unusual mixture of bridging and external type of ligands, cluster 2 is named the "hybrid" cluster, and its asymmetric, open structure suggests that it could be the site of a catalytic activity. X-ray absorption spectroscopy at the Fe K-edge is readily interpretable in terms of the crystallographic model when allowance is made for volume contraction at 10?K; no Fe··Fe distances beyond 3.1?Å could be identified. EPR, Mössbauer and MCD spectroscopy have been used to define the oxidation states and the magnetism of the clusters in relation to the crystallographic structure. Reduced cluster 1 is a [4Fe-4S]¹⁺ cubane with S?=?3/2; it is the first biological example of a "spin-admixed" iron-sulfur cluster. The hybrid cluster 2 has four oxidation states from (formally) all Fe^III to three Fe^II plus one Fe^III. The four iron ions are exchange coupled resulting in the system spins S?=?0, 9/2, 0 (and 4), 1/2, respectively, for the four redox states. Resonance Raman spectroscopy suggests that the bridging ligand X which could not be identified unambiguously in the crystal structure is a solvent-exchangeable oxygen.     

Tautomeric changes in guanfacine and its copper(II) complex as revealed by X-ray crystallography; synthesis and EPR

Obtention and crystal structure of guanfacine (guaH) together with synthesis and crystal structure of its copper complex [Cu^II(gua)₂] · DMF were reported. The free molecule guaH exhibits one tautomeric form (B) in contrast to the form (A) which was reported in the Merck index. In the copper(II) complex, the anionic form gua⁻ exhibits the third tautomeric form (C). This complex is characterized by a CuN₂O₂ coordination. The EPR spectrum is in agreement with a Cu(II) ion in a square planar configuration.     

Spatial structure of dimeric a genetically engineered variant of green fluorescent protein EGFP-K162Q in the P61 crystal space group

The spatial structure of dimeric green fluorescent protein EGFP-K162Q with MDELYK (EGFPv) C-terminal deletion has been assigned in the P6₁ space group with resolution 1.34 Å by X-ray diffraction analysis. The results have been compared with X-ray diffraction data of monomeric EGFP (green biomarker with enhanced photophysical properties) assigned in another crystal space group, P2₁2₁2₁, with resolution 1.50 and 1.35 Å. Subunits in the EGFPv dimeric structure are located at 75° angle with the contact area ～800 Ų. The dimeric framework is stabilized by the six hydrogen bonds and central hydrophobic core of six residues. The root-mean-square deviation value for C^α atoms in 3–230 residues of the P6₁ and P2₁2₁2₁ crystal structures is 0.55 Å. The differential characteristics of EGFPv-P6₁ structure, compared to that of P2₁2₁2₁, is a noticeably different orientation of the Glu222 side chain, and a new conformation of the 155–159 loop fragment, characterized by deviations among the C^α atoms of superimposed structures reaching 4.6 Å for Lys156 and 5.5 Å for Lys158.     

Design of peptides using α,β-dehydro-residues: Synthesis,crystal structure and molecular conformation of Boc-L-Val- ΔPhe-ΔPhe-L-Val-OCH3

The peptide Boc-L-Val-ΔPhe-ΔPhe-L-Val-OCH₃ was synthesized by the azlactone method in solution phase, and its crystal and molecular structures were determined by x-ray diffraction method. Single crystals were grown by slow evaporation from a methanol/water solution at 6°C. The crystals belong to an orthorhombic space group P2₁2₁2₁ with a = 10.478 (6) Å, b = 13.953 (1), c = 24.347 (2) and Z = 4. The structure was determined by direct methods and refined by least squares procedure to an R value of 0.052. The structure consists of a peptide and a water molecule. The peptide adopts two overlapping β-turn conformations of Types II and I′ with torsion angles: ϕ₁ = -54.8 (6), ψ₁ = 130.5 (4), ϕ₂ = 65.8 (5), ψ₂ = 12.8 (6), ϕ₃ = 79.4 (5), ψ₃ = 3.9 (7)°. The conformation is stabilized by intramolecular hydrogen bonds involving Boc CO and NH of ΔPhe³ and CO of Val¹ and NH of Val⁴. The molecules are tightly packed in the unit cell. The crystal structure is stabilized by hydrogen bonds involving NH of ΔPhe² and CO of a symmetry related (x-½, ½ -y, -z) ΔPhe². The solvent-water molecule forms two hydrogen bonds with peptide molecule involving NH of Val¹ as an acceptor and another with CO of a symmetry related (1 -x, y-½, ½ -z) ΔPhe³ as a donor. These studies indicate that a tetrapeptide with two consecutive ΔPhe residues sequenced with valines on both ends adopts two overlapping β-turns of Types II and I′. © 1996 John Wiley & Sons, Inc.     

Concentration-dependent palladium(II)-indole bond formation in complexes with a 2N-donor ligand containing an indole moiety: Synthesis, characterization, and reaction analysis

The Pd(II) complexes of a 2N-donor ligand containing a pendent indole, 3-(2-pyridylmethylamino)ethylindole (L), were synthesized and characterized. Reaction of the ligand with [PdCl₂(CH₃CN)₂] at room temperature gave [Pd(L)Cl₂] (1) as pale yellow crystals. The X-ray crystal structure analysis and ¹H NMR spectrum of 1 revealed that the complex has a 2N2Cl-donor set in a square-planar geometry and that the pendent indole ring has no characteristic intramolecular interaction with the Pd(II) ion and the coordinated pyridine moiety. Refluxing a solution of 1 in CH₂Cl₂/DMF for a few hours under basic conditions gave yellow crystals, which were shown to be an indole-C2 binding complex [Pd(L)Cl] (2) by X-ray analysis. Conversion of complex 1 to 2 in DMSO was observed upon dilution of the solution of complex 1. From solution equilibrium and kinetic studies the initial step of the conversion by dilution has been assigned to the replacement of a coordinated Cl⁻ ion with the DMSO molecule. The ligand replacement easily occurred at low concentrations of 1. The complex with a coordinated solvent molecule exhibited a high reactivity and formed a stable Pd-C bond with the indole ring located close to the Pd(II) center. We discussed the concentration dependent formation of the indole-C2 binding complex 2 and its detailed mechanism.     

Structural Features of 2′,3′-Dideoxy-2′,3′-Didehydrocytidine,A Potent Inhibitor of the HIV (AIDS) Virus

Abstract

The structure and conformation of 2′,3′-dideoxy-2′,3′-didehydrocytidine (2′,3′-dideoxycytidin-2′-ene, d4C), a potent inhibitor of the human immunodeficiency virus, was determined by X-ray crystallography. The nucleoside crystallizes in the orthorhombic space group P2₁2₁2₁ with cell dimensions a = 8.603(1), b = 9.038(1), c = 25.831(2) A and with two independent molecules in the asymmetric unit (Z = 8). Atomic parameters were refined by full-matrix least squares to a final value of R = 0.033 for 2258 observed reflections. The molecules are quite flexible: in molecule A the glycosyl torsion angle (X_CN) is 61.3° and the -CH₂OH side chain is in the gauche ⁺ orientation while in molecule B X_CN = 19.8° and the side chain is trans. The five-membered rings are slightly puckered (～0.1 Å), 04′ being endo in molecule A and exo in molecule B. A mechanism is proposed for the known instability of 2′,3′-unsaturated nucleosides.     

Conformation of the cyclic tetrapeptide dihydrochlamydocin. Iabu-L-Phe D-Pro-LX, and experimental values for 3 leads to 1 intramolecular hydrogen bonds by X-ray diffraction.

Chlamydocin, Iabu-L -Phe-D -Pro-L X, is a naturally occurring cyclic tetrapeptide that exhibits high cytostatic activity. The conformation of the peptide ring, as well as the stereo configuration in the vicinity of the epoxide ring, have been established by a single-crystal X-ray study of dihydrochlamydocin: C₂₈H₄₀N₄O₆·H₂O. It crystallizes in the monoclinic space group P2₁ with a = 12.616(6) Å, b = 12.355(6) Å, c = 9.442(5) Å, and β = 99.5(1)°. The structure was solved by the symbolic addition procedure for phase determination followed by the tangent formula method of phase refinement. This structure represents the first cyclic tetrapeptide in which all four peptide units have been found in the trans conformation; however, each peptide unit is significantly nonplanar with ω angles deviating by 14–24° from the ideal value of 180°. This molecule contains two intramolecular 3 → 1 hydrogen bonds and experimentally determined parameters for these seven-membered turns are presented.     

Understanding substrate misrecognition of hydrogen peroxide dependent cytochrome P450 from Bacillus subtilis

Cytochrome P450_BSβ, a H₂O₂-dependent cytochrome P450 catalyzing the hydroxylation of long-alkyl-chain fatty acids, lacks the general acid–base residue around the heme, which is indispensable for the efficient generation of the active species using H₂O₂. On the basis of the crystal structure of the palmitic acid bound form of cytochrome P450_BSβ, it was suggested that the role of the general acid–base function was provided by the carboxylate group of fatty acids. The participation of the carboxylate group of the substrate was supported by the fact that cytochrome P450_BSβ can catalyze oxidations of nonnatural substrates such as styrene and ethylbenzene in the presence of a series of short-alkyl-chain carboxylic acids as a dummy molecule of fatty acid. We refer to a series of short-alkyl-chain carboxylic acids as a “decoy molecule”. As shown here, we have clarified the crystal structure of the decoy-molecule-bound form and elucidated that the location of its carboxylate group is virtually the same as that of palmitic acid in the heme cavity, indicating that the carboxylate group of the decoy molecule serves as the general acid–base catalyst. This result further confirms that the role of the acid–base function is satisfied by the carboxylate group of the substrates. In addition, the structure analysis of the substrate-free form has clarified that no remarkable structural change is induced by the binding of the decoy molecule as well as fatty acid. Consequently, whether the carboxylate group is positioned in the active site provides the switching mechanism of the catalytic cycle of cytochrome P450_BSβ.     

Synthesis, characterization, crystal structures and magnetic properties of dissymmetrical double schiff base heterotrinuclear complexes: [CuL(H2O)CoCuL] · H2O · CH3OH and [(CuL)2Ni] · 2H2O

A dissymmetrical double Schiff base Cu(II) mononuclear complex: CuHL (1) (where H₃L is N-3-carboxylsalicylidene-N^′-salicylaldehyde-1,2-diaminoethane) and two trinuclear complexes: [CuL(H₂O)CoCuL] · H₂O · CH₃OH (2) and [(CuL)₂Ni] · 2H₂O (3) have been synthesized and characterized by means of elemental analyses, IR and electronic spectra. The crystal structures of two heterotrinucler complexes were determined by X-ray analysis. Each dissymmetrical cell unit of the complex 2 contains two heterotrinucler neutral molecules. In each neutral molecule, the central Co²⁺ ion is located at the site of O₆ with a distorted octahedral geometry and one terminal Cu²⁺ ion at the four-coordination site of N₂O₂, but the other one at the square-pyramidal environment of N₂O₃. Each dissymmetrical unit of the complex 3 contains a heterotrinucler neutral molecule, whose structure is similar to that of 2 except two terminal Cu²⁺ ions both at the inner site of N₂O₂. The magnetic properties of two heterotrinucler complexes have been determined in the temperature range of 5-300 K, which indicate that the interaction between the central Co²⁺ ion or Ni²⁺ ion and the outer Cu²⁺ ions is antiferromagnetic. The exchange integrals are equal to −26.2 cm⁻¹ for 2 and −50.6 cm⁻¹ for 3.