Cγ Atom Research Articles

Crystal structure and conformation of methionyl dipeptides: Structure of L-methionyl-L-asparagine: Preferred conformations of peptides containing methionyl and asparaginyl residues

Crystals of L-methionyl-L-asparagines (C9N3H17O4S) are orthorhombic, space group P212121, with cell parameters at 294 K of a = 5.248(1), b = 13.251(2), c = 18.028(2) A, V = 1251.6(4) A3, Z = 4, Dm = 1.40 Mg/m3, and Dx = 1.397 Mg/m3. The crystal structure was solved by direct methods and refinded by full-matrix least-squares method to a final R value of 0.059 for 1804 reflections. The peptide is slightly nonpalnar [ω = 172.0(5)∘]; the other torsion angles ψ1, ϕ2, ψ21, and ψ22 are 155.6(5), −95.8(5), 152.5(5), and −29.4(6)∘ respectively. The methionyl side chain is disordered with two possible position for its Cγ, Sδ, and Ce atoms. The methionly side chain is twisted with χ1 = −86.4(7), χ2 = 177.5(9), and χ3 = 116.6(2)∘ for the major conformer A. The asparaginyl side chain is also twisted with χ1 = −76.3(5) and χ2 = 102.3(6)∘. The crystal structure is stabilized by an intermolecular network of hydrogen bonds involving the N-terminal amino group and the e-terminal amino group of asn residue as donors and the carboxyl oxygens of the C-terminal and the peptide carbonyl oxygens as acceptor atoms.

Localization of the N-terminal Domain in Light-harvesting Chlorophyll a/b Protein by EPR Measurements

The conformational distribution of the N-terminal domain of the major light-harvesting chlorophyll a/b protein (LHCIIb) has been characterized by electron-electron double resonance yielding distances between spin labels placed in various domains of the protein. Distance distributions involving residue 3 near the N terminus turned out to be bimodal, revealing that this domain, which is involved in regulatory functions such as balancing the energy flow through photosystems (PS) I and II, exists in at least two conformational states. Models of the conformational sub-ensembles were generated on the basis of experimental distance restraints from measurements on LHCIIb monomers and then checked for consistency with the experimental distance distribution between residues 3 in trimers. Only models where residue 3 is located above the core of the protein and extends into the aqueous phase on the stromal side fit the trimer data. In the other state, which consequently is populated only in monomers, the N-terminal domain extends sideways from the protein core. The two conformational states may correspond to two functional states of LHCIIb, namely trimeric LHCIIb associated with PSII in stacked thylakoid membranes and presumably monomeric LHCIIb associated with PSI in nonstacked thylakoids. The switch between these two is known to be triggered by phosphorylation of Thr-6. A similar phosphorylation-induced conformational change of the N-terminal domain has been observed by others in bovine annexin IV which, due to the conformational switch, also loses its membrane-aggregating property.

N-Amidino-4-hydroxy-L-proline monohydrate andN-amidino-L-methionine monohydrate

The title amidino-amino acids (a-Hpro), C6H11N3O3.H2O, (I), and a-Met, C6H13N3O2S.H2O, (II), respectively, exist in the form of zwitterions. The five-membered pyrrolidine ring in (I) adopts an envelope conformation, with the Cgamma atom out of the plane defined by the rest of the ring atoms, and with the hydroxyl and carboxylate groups in a trans configuration relative to the ring plane. The two crystallographically independent zwitterions in (II) reveal quite different conformations of their side chains and a slightly different orientation of the guanidine moiety with respect to the carboxylate group. The crystal structures of both (I) and (II) are stabilized by extensive networks of O-H...O, N-H...O and C-H...O hydrogen bonds, the network being three-dimensional in (I) and two-dimensional in (II).

Substituted 2-Azabicyclo[2.1.1]hexanes as Constrained Proline Analogues: Implications for Collagen Stability

Among the proteinogenic amino acids, only proline is a secondary amine and only proline has a saturated ring. Electronegative substituents on C-4 (that is, C(gamma)) have a substantial effect on the trans/cis ratio of the prolyl peptide bond and the pucker of the pyrrolidine ring. 2-Azabicyclo[2.1.1]hexane is, in essence, a proline analogue with two C(gamma) atoms, one in each of the two prevalent ring puckers of proline. Here, 2-azabicyclo[2.1.1]hexane analogues of 2S-proline, (2S,4S)-4-hydroxyproline, and (2S,4S)-4-fluoroproline residues were synthesized, and their trans/cis ratios were shown to be invariant in a particular solvent. Thus, the substitution of a proline residue on C-4 affects the trans/cis ratio by altering the pucker of its pyrrolidine ring. This finding has implications for the conformation of collagen, which has an abundance of 2S-proline and (2S,4R)-4-hydroxyproline residues, and can be stabilized by (2S,4R)-4-fluoroproline and (2S,4S)-4-fluoroproline residues.

The relative orientation of the Arg and Asp side chains defined by a pseudodihedral angle as a key criterion for evaluating the structure-activity relationship of RGD peptides.

The ability of an integrin to distinguish between the RGD-containing extracellular matrix proteins is thought to be due partially to the variety of RGD conformations. Three criteria have been proposed for the evaluation of the structure-activity relationship of RGD-containing peptides. These include: (i) the distance between the charged centres, (ii) the distance between the Arg Cbeta and Asp Cbeta atoms, and (iii) the pseudo-dihedral angle defining the Arg and Asp side-chain orientation formed by the Arg Czeta, Arg Calpha, Asp Calpha and Asp Cgamma atoms. A comparative conformation-activity study was performed between linear RGD peptides and strongly constrained cyclic (S,S) -CDC- bearing compounds, which cover a wide range of inhibition potency of platelet aggregation. It is concluded that the fulfilment of the -45 degrees < or = pseudo-dihedral angle < or = +45 degrees criterion is a prerequisite for an RGD compound to exhibit inhibitory activity. Once this criterion is accomplished, the longer the distance between the charged centres and/or between the Arg and Asp Cbeta atoms, the higher is the biological activity. In addition, the stronger the ionic interaction between Arg and Asp charged side chains, the lower the anti-aggregatory activity.

Living and non-living Ziegler–Natta catalysts: electronic properties of active site

Most of polymerization reactions with Ziegler catalysts operate through the ‘non-living’ mechanism, whereas lanthanide catalysts show a living-mechanism character. The degree of ‘livingness’ in a polymerization reaction is generally investigated through kinetics and the product analysis rather than by direct analysis of a catalyst. We have developed a new insight for judging the ‘livingness’ in polymerization reaction in aspect of electronical properties of the active chain ends of Li, Ni and Nd catalysts for 1,3-butadiene polymerization using the frontier orbital analysis. The frontier orbitals of the Ni catalyst are different from those of the Li and Nd based catalysts. The HOMO of the Ni catalyst has mostly the d-orbital (Ni) character while the LUMO has the p-orbital (Cα and Cγ atoms) as well as the d-orbital (Ni) character. The π-butenyl coordination at the Ni catalyst is η1-type but those of the Nd and Li catalysts are η3. The atomic charge (+0.003) on the Ni atom and the atomic charge (−0.14) on Cα of the Ni catalyst are much lower than those of the Nd catalyst (Nd +1.09, Cα −0.56).

DL-Threoninium dihydrogen phosphate

In the title compound, C4H10NO3+·H2PO4−, the threoninium residue forms strong O—H⋯O hydrogen bonds with the phosphate anion. A gauche I–gauche II conformation with respect to the Oγ and Cγ atoms is observed [the corresponding torsion angles are 59.5 (2) and −64.1 (3)°]. The adjacent threoninium cations, related by an a-glide plane normal to the c axis, are linked via N—H⋯O hydrogen bond involving ammonium and carboxyl­ic acid groups (dl2 head-to-tail sequence). The structure is stabilized by an extensive network of O—H⋯O and N—H⋯O hydrogen bonds, which form a three-dimensional hydrogen-bond system.

In Search of Optically Active γ-Keto Acetylenes via Regioselective Coupling of Allenylidene Groups and Cyclic Enolates

(Indenyl)ruthenium(II) allenylidene complexes [Ru{CCC(R)Ph}(η5-C9H7)(PPh3)2][PF6] (R = Ph (1), H (2)) regioselectively react with enolates derived from cyclopentanone and cyclohexanone at the Cγ atom to yield the σ-alkynyl derivatives (R = Ph, n = 1 (3a), 2 (3b); R = H, n = 1 (4a), 2 (4b)). Protonation of these species at Cβ of the alkynyl chain with HBF4 affords vinylidene complexes 5a,b and 6a,b, which can easily be demetalated with acetonitrile to yield the γ-keto acetylenes (7a,b and 8a,b). Compounds 4a,b, 6a,b and 8a,b, derived from the monosubstituted allenylidene complex 2, have been obtained as nonseparable mixtures of two diastereoisomers. The optically active allenylidene [Ru{CCC(C9H16)}(η5-C9H7)(PPh3)2][PF6] (10) (C(C9H16) = (1R)-1,3,3-trimethylbicyclo[2.2.1]hept-2-ylidene) undergoes a selective exo addition of the cyclopentanone enolate to afford the σ-alkynyl diastereoisomers (11a,b). Demetalation of 11a and 11b, via their corresponding vinylidenes, allows the preparation of optically pure te...

Solution Structures of α-Cyclodextrin Complexes with Propanol and Propanesulfonate Estimated from NMR and Molecular Surface Area

The complex formation of α-cyclodextrin (α-CD) with propanesulfonate (PS) and propanol (PrOH) was investigated by proton NMR spectroscopy and molecular surface area calculations. The 1:1 binding constant, K1, was determined from dependence of the chemical shift of the propyl β-methylene protons on the α-CD concentration to be 23.0 and 21.3 M-1 for PS and PrOH. Quantitative analysis of the ROESY spectra showed that the propyl groups of PS and PrOH penetrate from the secondary alcohol side of α-CD. This penetration side of PrOH is opposite to that in the crystal. The observed vicinal spin−spin coupling constant of the HC(5)−C(6)HR system of PS−α-CD indicated that the H5 and H6R atoms are in the gauche arrangement, though they are in the trans arrangement in the crystal. The observed vicinal coupling constant of the HCα−CβH system of PS−α-CD indicated that the sulfur and Cγ atoms are restricted around the trans arrangement because of the hindered rotation of the Cα−Cβ bond, although the Cα−Cβ bond of PrOH in...

Electronic excitation in anionic polymerization of butadiene: Nonempirical calculations of reaction complexes

AbstractA new mechanism of anionic polymerization of butadiene is proposed. In the elementary chemical act, the “living” polymer–monomer complex is excited into the low‐lying triplet state. This state has the character of charge (electron) and cation (Li+ or Na+) transfer from the terminal unit of the active center to the monomer molecule. In the framework of this concept, the probability of chemical bond formation is determined by spin density on radical centers of reagent molecules. Semiempirical and ab initio 6‐31G** quantum‐chemical calculations showed stable interaction between components of the complex in the ground electronic state (9–11 kcal/mol) and low energy levels of triplet excited states (&lt;14 kcal/mol). This new approach is shown to be useful in the analysis of polymerization kinetics and the microstructure of polybutadiene depending on the cation type and the ion pair state. The mechanism of cis‐trans isomerization in the terminal unit of the living polymer consists in concerted rotation about the CβCγ bond and the migration of Li between Cα and Cγ atoms. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002

Activation of Propargylic Alcohols Derived from Hormonal Steroids by the Indenyl−Ruthenium(II) Complex [RuCl(η5-C9H7)(PPh3)2]: Experimental and Theoretical Evidence of an Allenylidene−Vinylvinylidene Equilibrium

The indenyl−ruthenium(II) complex [RuCl(η5-C9H7)(PPh3)2] (1) reacts with ethisterone (2a), 17α-ethynylestradiol (2b), and mestranol (2c), in methanol and in the presence of NaPF6, to afford equilibrium mixtures containing the corresponding allenylidene 3a−c and vinylvinylidene 4a−c tautomers. Deprotonation of these mixtures with K2CO3 allows the preparation of σ-enynyl derivatives 5a−c, which can be selectively alkylated with MeOSO2CF3 to yield disubstituted vinylvinylidene complexes 6a−c. Displacement of these equilibriums can also be accomplished by treatment of the reaction mixtures with acetonitrile or PMe2Ph. Thus, while in the first case terminal 1,3-enynes 7a−c are selectively obtained by demetalation of vinylvinylidenes 4a−c, phosphonio-alkynyl complexes 9a−c are exclusively formed in the second case as the result of the nucleophilic addition of PMe2Ph on the electrophilic Cγ atom of allenylidenes 3a−c. Ab initio molecular orbital calculations on the models [Ru{CCC(H)CH3}(η5-C5H5)(PH3)2]+ and [Ru{CC(H)CHCH2}(η5-C5H5)(PH3)2]+ show that the vinylvinylidene tautomer is only 2.1 kcal/mol more stable than the allenylidene. The spontaneous tautomerization process between both complexes, which involves a [1,3]-hydrogen sigmatropic rearrangement, requires an activation energy of 66.5 kcal/mol.

Bis(L-histidinium sulfate) trihydrate

In the title compound, 2C6H11N3O22+·2SO42−·3H2O, both diprotonated histidinium cations are linked by strong hydrogen bonds by water mol­ecules and normal hydrogen bonds by sulfate anions. The Cγ atom has a gauche II conformation with respect to the amino N atom and it is trans to the C′ atom for both mol­ecules. The imidazolinium rings are normal to the carbon skeletal plane, as expected.

Efficient Synthetic Routes to Terminal γ-Keto−Alkynes and Unsaturated Cyclic Carbene Complexes Based on Regio- and Diastereoselective Nucleophilic Additions of Enolates on Ruthenium(II) Indenyl Allenylidenes

Ruthenium(II) indenyl allenylidene complexes [Ru{CCC(R1)Ph}(η5-C9H7)(PPh3)2][PF6] (R1 = Ph (1), H (2)) regioselectively react with lithium enolates LiCH2COR2 (R2 = Ph, iPr, Me, Fc, (E)-CHCHPh) at the Cγ atom to yield the neutral σ-alkynyl derivatives [Ru{C⋮CC(R1)Ph(CH2COR2)}(η5-C9H7)(PPh3)2] (3a−e, 4a−d). Protonation of 3a−e and 4a−d with HBF4·Et2O affords the cationic vinylidene derivatives [Ru{CC(H)C(R1)Ph(CH2COR2)}(η5-C9H7)(PPh3)2][BF4] (5a−e, 6a−d), which can be easily demetalated, by treatment with acetonitrile, to yield the terminal γ-keto-substituted alkynes HC⋮CC(R1)Ph(CH2COR2) (7a−e, 8a−d) and the nitrile complex [Ru(N⋮CMe)(η5-C9H7)(PPh3)2][BF4] (9). The addition of lithium enolates LiCH2COR (R = Ph, iPr, Me) on the optically active allenylidene complex [Ru{CCC(C9H16)}(η5-C9H7)(PPh3)2][PF6] (12; C(C9H16) = (1R)-1,3,3-trimethylbicyclo[2.2.1]hept-2-ylidene) proceeds in a regio- and diastereoselective manner, affording σ-alkynyl derivatives [Ru{C⋮CC(C9H16)(CH2COR)}(η5-C9H7)(PPh3)2] (13a−c). The X-ra...

Quantum-Chemical Calculations of the Structure of the Triplet Reaction Complexes in Anionic Polymerization of Butadiene

A new mechanism of anionic polymerization of butadiene, radically changing the existing concepts on the structure and properties of the reaction complex, is suggested. It is stated that an elementary chemical process involves excitation into the low-lying triplet state of the “living” polymer–monomer complex, characterized as a transfer of a charge (electron) and cation (Li+ or Na+) from the terminal unit to the monomer molecule. In the framework of this concept, the probability of chemical bonding is determined by the spin density on the radical centers of reagent molecules. The semiempirical and ab initio 6-31G** calculations have revealed a strong interaction in the ground electronic state of the complex (5-10 kcal/mole) and low energies of the excited triplet levels (< 10 kcal/mole). A mechanism of cis-trans-isomerization in the terminal unit of the “living” polymer is suggested. The mechanism involves concerted rotation around the Cβ - Cβ bond and migration of Li between the Cα and Cγ atoms. The new approach is shown to be fruitful for microstructure analysis of polybutadiene in relation to the type of cation and the state of the terminal unit of the “living” polymer.

Intramolecular carbon–carbon coupling reactions of a κ2(P,P)-bis(diphenylphosphino)methanide ligand with unsaturated carbene moieties in indenyl–ruthenium(II) complexes

Abstract Treatment of disubstituted indenyl–ruthenium(II) vinylidene complexes [Ru{CC(Me)R}(η5-C9H7)(dppm)][CF3SO3] (R=tBu (4a), Ph (4b); dppm=bis(diphenylphosphino)methane) with NaOMe results in the deprotonation of the coordinated dppm ligand to give a κ2(P,P)-(Ph2P)2CH ligand. Subsequent intramolecular nucleophilic attack of the methanide group on the electrophilic vinylidene α-carbon gives the alkenyl metallacycles (Z)-[Ru{κ3(C,P,P)-C C (Me)R(Ph 2 PC HPPh2)}(η5-C9H7)] (R=tBu (6a), Ph (6b)). The related metallacycle species [Ru{κ3(C,P,P)-C(OMe)C(H) C(H)R(Ph 2 PC HPPh2)}(η5-C9H7)] (R=H (11a), Ph (11b)) have also been prepared. They have been obtained through an analogous carbon–carbon coupling process involving the bis(phenyl-phosphino)methanide anion, generated by the treatment of the α,β-unsaturated methoxy–carbene derivatives [Ru{C(OMe)C(H)C(H)R}(η5-C9H7)(dppm)][PF6] (R=H (9a), Ph (9b)) and LitBu, and the Cγ atom of the unsaturated carbene ligand.

Very short F-H...F hydrogen bond in L-argininium fluoride hydrogen fluoride

There are two symmetry-independent formula units of the title compound, C6H15N4O2+·F−·HF, per cell. Both cations have a zwitterionic form, protonated at both the guanidyl and amino groups. The two symmetry-independent cations differ in their conformation. In one of them the Cγ atom is in a gauche position to both the amino and carboxyl groups, while in the other this atom is trans to the amino group. The two anions have very similar geometry. The F− ions are strongly hydrogen bonded to an HF molecule [F—H⋯F 2.233 (2) and 2.248 (3) Å], thereby forming an asymmetric non-linear bifluoride anion. These F⋯F distances are the shortest reported for an asymmetric HF2− anion.

Crystal structure of the nonlinear optical compound L-arginine fluoride

L-arginine fluoride is a promising compound that exhibits nonlinear optical properties. It efficiently converts two single photons of the same polarization and frequency ω to one photon of frequency 2ω (type I phase matching). C6H15N4O2 +F− is monoclinic, space group P21, a = 5.4475(4) Å, b = 8.5133(6) Å, c = 10.2195(7) Å, β = 93.475(6)°. The cation has a zwitterionic form, protonated at both the guanidyl and amino groups. The arginine Cγ atom is in a trans position to the carboxyl group. A complex three-dimensional hydrogen bond network links the anions and cations together.

Regioselective Addition of PRPh2 to the Cα Atom of the Diphenylallenylidene Ligand of [Ru(η5-C5H5)(CCCPh2)(CO)(PPri3)]BF4

The allenylidene ligand of [Ru(η5-C5H5){CCCPh2}(CO)(PPri3)]BF4 adds PHPh2, PMePh2, and PPh3 selectively at the Cα atom, whereas OH- and [OMe]- are added at the Cγ atom.

Regio- and Diastereoselective Nucleophilic Additions of Lithium Enolates on the Allenylidene Complexes [Ru{CCC(R)Ph}(η5-C9H7)(PPh3)2][PF6] (R = H, Ph): Synthesis of the First Chiral Keto-Functionalized (σ-Alkynyl)ruthenium(II) Complexes

Indenylruthenium(II) allenylidene complexes undergo regioselective nucleophilic additions of lithium enolates at the Cγ atom of the unsaturated chain to afford keto-functionalized σ-alkynyl derivatives. Enolates derived from the chiral ketones (−)-carvone and (+)-pulegone are added regio- and diastereoselectively to give the first chiral keto-functionalized (σ-alkynyl)ruthenium(II) complexes.

Crystal structure of platinum(II) chloro(1,1,1-trifluoro-4-imino-2-pentanononate(Hydrate)) [PtCl(ktf)H2O

This paper reports on our study of the mixedligand βiminoketonate complex [PtCl(ktf)H2O] including 1,1,1-trifluoro-4-imino-2-pentanone as a ligand. An X-ray diffraction analysis was performed on a CAD-4 diffractometer (MoKα radiation, ω/2θ scan mode). Crystal data ofPtClF3O2NC5H7: a = 26.264(5), b = 4.750(1), c = 15.955(3) A, β = 108.16(3)°, V = 1891.3A3, space group C2/c, Z = 8, dcalc = 2.82 g/cm3. The Pt atom has a distorted square planar environment. The Pt-Cl, Pt-O(H2O), Pt-N, and Pt-O bonds are 2.29, 2.07, 1.97, and 1.98 A in length, respectively. The chelate angle is 93.7°. The environment of Pt is completed to pyramidal due to interactions with the Cγ atom of the neighboring molecule at a distance of 3.57 A. The compound has a molecular structure. The molecules of the complex are stacked along the Y direction.