Syntheses and Structures of Arenethiolato Cobalt(II) Complexes Containing Acylamino Groups: Steric Effects of Bulky Ligands on Coordination and Geometry.

Bulky thiolato ligands have been developed for creating biomimetic model complexes of active sites in metalloenzymes. Herein, we report a series of di-ortho-substituted arenethiolato ligands containing bulky acylamino groups (RCONH; R = t-Bu-, (4-t-BuC6H4)3C-,{3,5-(Me2CH)2C6H3}3C-, and {3,5-(Me3Si)2C6H3}3C-) that were developed for biomimetics. Bulky hydrophobic substituents generate a hydrophobic space around the coordinating sulfur atom through the NHCO bond. This steric environment induces the formation of low-coordinate mononuclear thiolato Co(II) complexes. The well-positioned NHCO moieties in the hydrophobic space coordinate to the vacant sites of the cobalt center with different coordination modes, viz., the S,O-chelate of the carbonyl C═O or the S,N-chelate of the acylamido CON-. The solid (crystalline) and solution structures of the complexes were investigated in detail using single-crystal X-ray crystallography, 1H NMR, and absorption spectroscopic analyses. The spontaneous deprotonation of NHCO, which is commonly observed in metalloenzymes but requires a strong base in artificial systems, was simulated by forming a hydrophobic space in the ligand. This new ligand design strategy is advantageous for creating model complexes that have never been constructed artificially.

Stability Enhancement of a π-Stacked Helical Structure Using Substituents of an Amino Acid Side Chain: Helix Formation via a Nucleation-Elongation Mechanism.

Molecular design involving the incorporation of an α-amino acid residue into the side chain or main chain of a polymer is often used to stabilize artificial molecular architectures through intramolecular hydrogen bonding. However, this molecular design strategy rarely considers the importance of interactions between substituents at the α-position of amino acid moieties, as found in nature. Herein, we report the synthesis of a novel series of π-stacked helical poly(quinolylene-2,3-methylene) with amino acid derivatives bearing different substituents at the α-position. We found that the thermal stability of π-stacked helical poly(quinolylene-2,3-methylene) is significantly improved by packing the substituents in the empty spaces between the side chains. In particular, when a bulky cyclohexyl alanine derivative was used as the side chain, the π-stacked helical structure maintained its stability even in dimethylsulfoxide, a hydrogen bond competitor. The stabilization of the π-stacked structure by the amino acid substituents resulted in a unique polymerization behavior involving nucleation-elongation steps. In the case of derivatives with leucine and cyclohexyl alanine, which form stable π-stacked helical structures, metastable structures with entangled main chains were formed in the initial polymerization stage. These structures subsequently underwent an irreversible structural change to achieve a thermodynamically stable helical π-stacked conformation as a nucleus for subsequent polymerization. Thereafter, the polymerization reaction proceeded with the elongation of the π-stacked helical structure. Differences in the stability of these systems indicated that the amino acid substituents on the side chains determine the most thermodynamically stable π-stacked helical structure.

Conformational Switch of Arylopeptide: Helix-Helix Transition Based on Side Chain Solvation.

Controlling the structural transition between well-defined architectures found in living system is essential in polymer chemistry as well as material science. Herein, the reversible conformational switch of a non-natural polypeptide with an aromatic ring (2,6-naphthalene spacer) on its peptide backbone, referred to as an arylopeptide, between two distinct well-defined helical structures (extended 31 -helix and contracted 41 -helix) using side chain solvation is demonstrated. The folding selectivity of the arylopeptide and found that the affinity between the solvent and side chains is an essential factor for determining the global structure is investigated. A thermoresponsive arylopeptide bearing oligoether groups (─(CH2 CH2 O)9 CH3 )) on the side chain is designed, which exhibited unique lower critical solution temperature behavior and converted from the 31 to the 41 -helix depending on the temperature. Furthermore, the solvent affinity of the entire polymer by combining substituents (─(CH2 CH2 O)3 CH3 and ─C12 H25 ) with different properties on the side chains to achieve a spring-like expansion-contraction system that allows interconversion between 31 - and 41 -helices is adjusted.

Crystal-to-Crystal Isomerization via Drastic Intramolecular Ligand Exchange: Vapochromism of a Bis(arenethiolato)cobalt(II) Complex Containing Bulky Acylamino Groups.

Crystal-to-crystal transitions normally avoid drastic configurational changes that result in loss of crystallinity. A cobalt(II) complex, containing two unsymmetrically disubstituted arenethiolato ligands with bulky acylamino (Ar3CCONH, Ar = 4-t-BuC6H4) and t-BuCONH groups, showed crystal-to-crystal configurational isomerization accompanied by vapochromism. Recrystallization using THF/n-hexane afforded green crystals (isomer G) containing one n-hexane molecule per asymmetric unit. In contrast, blue crystals (isomer B), containing two toluene molecules per unit, were obtained using a toluene solution. Isomer G contained S,O-chelates involving Ar3CCO carbonyl groups, while isomer B contained chelates involving t-BuCO groups. Upon exposure to toluene vapor, crystal isomer G was gradually converted to crystal isomer B, maintaining its crystallinity despite the drastic intramolecular ligand exchange. Although the blue coloration was due to an unfavorable, distorted, and stretched chemical structure, formation of strong intermolecular NH···O═C hydrogen bond chains counteracted this disadvantage. Therefore, blue crystal formation as a whole was thermodynamically favorable. The release of n-hexane from the green crystals initiated the isomerization and resulted in tightly packed blue crystals. The tense conformation of the blue crystals was facilely relaxed by cleaving the hydrogen bond chains through grinding and resulted in a green powder that maintained the original coordination of isomer B, which reverted easily to blue crystals upon exposure to toluene vapor.

Construction of Helically Stacked π-Electron Systems in Poly(quinolylene-2,3-methylene) Stabilized by Intramolecular Hydrogen Bonds.

π-Stacked polymers, which consist of layered π-electron systems in a polymer, can be expected to be used in molecular electronic devices. However, the construction of a stable π-stacked structure in a polymer is considerably challenging because it requires sophisticated designs and precise synthetic methods. Herein, we present a novel π-stacked architecture based on poly(quinolylene-2,3-methylene) bearing alanine derivatives as the side chain, obtained through the living cyclo-copolymerization of an o-allenylaryl isocyanide. In the resulting polymer, the neighboring quinoline rings of the main chain form a layered structure with π-π interactions, which is stabilized by intramolecular hydrogen bonds. The vicinal quinoline units form two independent helices and the whole molecule is a twisted-tape structure. This structure is established on the basis of UV/CD spectra, theoretical calculations, and atomic-force microscopy.

Living Cyclocopolymerization through Alternating Insertion of Isocyanide and Allene via Controlling the Reactivity of the Propagation Species: Detailed Mechanistic Investigation.

Living cyclocopolymerization through the alternating insertion of an isocyanide and allene into palladium-carbon bond was developed based on the controlling the reactivity of the propagation species using bidentate ligands. We revealed that the rate of the presented cyclocopolymerization was depended on the ligands of Pd-initiator. When the palladium-methyl complexes having appropriate cis-chelating ligand, such as 1,3-bis(diphenylphosphino)propane (dppp), were used as initiator, the cyclocopolymerization of bifunctional aryl isocyanides (1) that contain both isocyano and allenyl moieties polymerized to afford poly(quinolylene-2,3-methylene)s with controlled molecular weight and narrow molecular weight distributions. The resulting polymer was characterized by 1H and 13C NMR analyses, which clearly showed that the terminal moiety of the polymer formed well-defined organopalladium complex as the resting state for the polymerization, which could undergo further polymerization; not only cyclocopolymerization with 1 but also homopolymerization of simple aryl isocyanide. In the analysis of the cyclocopolymerization mechanism, we conclusively demonstrated that the insertion reaction of isocyanide is the rate-determination step in the cyclocopolymerization, which proceeds via a five-coordinate intermediate with a geometrical change. The cis-chelating ligand controls the site interchange reaction, which dominates the reactivity of propagation species.

Crystal Structures of Expanded Poly(l-leucine) Isomers Containing Bis(pyridine)silver(I) Moieties: Precise Formation of Secondary Structure Depending on the Side Chain.

Precise construction of a three-dimensional molecular structure is key for functional macromolecules, such as enzymes or proteins. Previously, a new concept, "expanded poly(α-amino acid)s" containing rigid spacers, was proposed for strategic construction of chiral helices. Herein, expanded poly(l-leucine) isomers containing bis(pyridine)silver(I) moieties were synthesized, and their crystal structures were determined by X-ray analysis. Each expanded polypeptide forms a unique secondary structure, a left-handed 61 helix or zigzag chain (21 helix), precisely depending on the chemical structure of the side chain, that is, slight branching. Distinct conformations were indicated by two main areas in the Ramachandran plot. These results suggest that the appropriate selection of the amino acid sequence and rigid spacers will lead to a new expanded protein with a tailor-made three-dimensional structure and desired functions.

Snapshot of Oxidation of Thiolate by Diiodine: Stabilization of Intermediate by NH···S Hydrogen Bonds.

Ordinary thiolate (RS-) reacts with diiodine (I2) to afford an intermediate sulfenyl iodide (RSI) by releasing I-; RSI is readily converted to disulfide (RSSR) by a disproportionation reaction. In the case of thiolate Ar1S- containing very bulky acylamino groups forming NH···S hydrogen bonds, the crystal of the intermediate, [Ar1S-I-I]-, was obtained under usual conditions, and the structure was determined by X-ray diffraction analysis. The results show that the intramolecular NH···S hydrogen bonds stabilized the intermediate [Ar1S-I-I]-, consistent with theoretical calculations.

Regulation of the hydrolytic activity of Mg²âº-dependent phosphatase models by intramolecular NH···O hydrogen bonds.

Magnesium-dependent phosphatase models containing intramolecular NH···O hydrogen bonds were synthesized and structurally characterized by X-ray analysis. The Mg-O bond distances varied with the mode of the hydrogen bonds. (1)H NMR spectra in nonpolar solvents revealed that the acidity of the coordinated water molecule was regulated by the hydrogen bonds. Further, stoichiometric hydrolysis of phosphoric ester significantly depended on the hydrogen bonds. Zinc analogues showed similar but smaller dependencies, which suggest the indispensable role of Mg(2+) ion in the activation of the enzymes.

Contribution of intramolecular NH···O hydrogen bonds to magnesium-carboxylate bonds.

A series of magnesium carboxylate complexes containing intramolecular NH···O hydrogen bonds were synthesized. Their molecular structures were determined by X-ray analysis. A direct NH···O hydrogen bond to the coordinated oxygen atom elongated the Mg-O bond, while a hydrogen bond to the carbonyl group shortened the Mg-O bond. Double NH···O hydrogen bonds significantly lowered the basicity of the carboxylate anion and prevented coordination to the Mg ion in a trans configuration; however, a cis-dicarboxylate complex was successfully obtained. Strong coordination of water to the Mg(2+) ion stabilizes the weak Mg-carboxylate bond at the trans position. In contrast, a weak Mg-carboxylate bond strengthens the Mg-O(water) bond, probably increasing the acidity. Based on the experimental results and theoretical calculations, a new switching mechanism is proposed. In the proposed mechanism, the acidity of the coordinated water on magnesium is controlled during catalytic hydrolysis in endonuclease.

Systematic investigation of relationship between strength of NH···S hydrogen bond and reactivity of molybdoenzyme models.

A series of monooxomolybdenum(IV) and dioxomolybdenum(VI) complexes containing two intramolecular NH···S hydrogen bonds were synthesized and characterized by (1)H NMR, UV-visible, IR, and Raman spectroscopies, and electrochemical measurements. Elimination of the steric effects enabled the accurate and quantitative evaluation of NH···S hydrogen bonds. Strong correlations among the strength of the hydrogen bond, the strength of the Mo(VI)═O bond, and the redox potential were clearly shown. The hydrogen bonds stabilize the intermediate in the reaction between the monooxomolybdenum(IV) and Me(3)NO, resulting in acceleration of the reaction or retardation of trans-cis rearrangement. The proposed intermediate and the reaction mechanism, discussed on the basis of theoretical calculations, provided a unified explanation of the reaction.

Selective and effective stabilization of Mo(VI)═O bonds by NH···S hydrogen bonds via trans influence.

A monooxomolybdenum(IV) complex containing two intramolecular NH···S hydrogen bonds, (NEt(4))(2)[Mo(IV)O(1,2-S(2)-3-t-BuNHCOC(6)H(3))(2)], was synthesized. The trans isomer was crystallized as the major product, and the molecular structure was determined by X-ray analysis. The trans isomer was isomerized by heating in solution to give a 1:1 mixture of trans and cis isomers. Oxidation of these isomers by Me(3)NO afforded (NEt(4))(2)[Mo(VI)O(2)(1,2-S(2)-3-t-BuNHCOC(6)H(3))(2)]. (1)H NMR analysis revealed that the dioxomolybdenum(VI) complex existed as a single isomer where both oxo ligands were trans to each of the two hydrogen-bonded thiolate ligands. The Mo(VI)═O bond was effectively stabilized by the NH···S hydrogen bond via trans influence, which was determined using resonance Raman spectroscopy. These results were supported by preliminary density functional theory calculations.

Reversible single-crystal-to-single-crystal transformation and highly selective adsorption property of three-dimensional cobalt(II) frameworks.

A three-dimensional (3D) coordination polymer, [Co(3)(L)(2)(BTEC)(H(2)O)(2)]·2H(2)O [1, HL = 3,5-di(imidazol-1-yl)benzoic acid, H(4)BTEC = 1,2,4,5-benzenetetracarboxylic acid], with tfz-d topology has been hydrothermally synthesized. The framework of 1 has high thermal stability and exhibits single-crystal-to-single-crystal (SCSC) transformations upon removing and rebinding the noncoordinated and coordinated water molecules. X-ray crystallographic analyses revealed that the coordination geometry of Co(II) changes from octahedral to square pyramid upon dehydration, accompanying the appearance of one-dimensional (1D) open channels with dimensions of 2.0 × 2.8 Å. The dehydrated form [Co(3)(L)(2)(BTEC)] (2) exhibits highly selective adsorption of water molecules over N(2), CH(3)OH, and CH(3)CH(2)OH, which could be used as sensors for water molecules. Furthermore, the magnetic properties of 1 and 2 were investigated, showing the existence of ferromagnetic interaction between the Co(II) atoms within the trinuclear subunit.

Folding control of a non-natural glycopeptide using saccharide-coded structural information for polypeptides.

We synthesized "glyco-arylopeptides", whose folding structure significantly changes depending on the kind of saccharide in their side chain. The saccharide moiety interacts with the main chain via hydrogen bonding, and the non-natural polypeptides form two well-defined architectures-(P)-31- and (M)-41-helices-depending on the length of the saccharide chains and even the configuration of a single stereo-genic center in the epimers.

Color regulation and stabilization of chromophore by Cys69 in photoactive yellow protein active center.

Model compounds of PYP chromophore were synthesized and characterized to investigate the role of the Cys69 residue in the active center, which has the intramolecular NHOC hydrogen bond to the conjugated carbonyl oxygen and thioester linkage of the chromophore. The results of UV-vis and (13)C NMR spectroscopy of the model compounds indicated that they delocalized the negative charge of the chromophore and increased the contribution of the quinoid-like resonance structure in the phenolate anion state. Thus, the Cys69 residue plays an important role in the regulation of the color and the stabilization of the chromophore anion in the active center.

Mass spectrometric analysis using ruthenium (II)-labeling for identification of glycosyl hydrolase product.

Analysis of products digested by glycosyl hydrolases helps understanding of the hydrolysis mechanism and the substrate recognition in the enzymes. We developed a new universal technique, which consists of ruthenium (II) complex labeling and mass spectrometry analysis, to identify the reducing sugars released from oligosaccharides by enzymatic digestion. This method was applied to enzymatic digestion by chitinase and cellulase of the hyperthermophilic archaea Pyrococcus fusiosus and Pyrococcus horikoshii respectively.

Zigzag-Helix Transformation of Expanded Polyvaline Induced by Racemization.

Biological macromolecules are essentially homochiral. For example, proteins mostly consist of l-amino acids. What happens when a chiral molecule meets itself in a mirror? For expanded polyvaline, zigzag-helix transformation occurs. In this study, expanded polyvalines containing bis(pyridine)silver(I) moieties were synthesized and isolated as single crystals. The molecular structures were determined by X-ray analysis, which revealed that chiral expanded poly(l-valine) and poly(d-valine) form zigzag chains. However, racemic mixture of these molecules form left- and right-handed 41 helices that retain the original sequences. These secondary structures can be transformed by only flipping the C-terminal amide plane for each unit, which is reminiscent of the relationship between an α-helix and a ß-strand. Such expanded polypeptides can be built up into expanded protein, forming a tailor-made three-dimensional structure, which will lead to new functions.

Side-Chain-Driven Dual Structural System of Poly-Arylopeptide: Selective Helical Formation Derived from Aromatic Ring Flips on the Backbone.

A methodology for producing dual structural systems of macromolecules, which involves flipping the unsymmetrical aromatic rings on the main chain is presented. Previously, we reported a non-natural polypeptide containing an aromatic ring on the peptide backbone, called a poly "arylopeptide". Herein, we used 2,6-naphthalene rings as axially unsymmetrical spacers, which has two geometrical isomers, anti and syn, to create dual structural properties. The miniscule energy difference between the two geometrical isomers can be amplified by incorporating the 2,6-naphthylene units into the polypeptide backbone, which creates a thermodynamic driving force for the formation of two specific global structures (i.e., 31-helix or 41-helix) biased toward one side geometrical isomer depending on the side chain. Additionally, the 31-helix can be switched to the 41-helix upon addition of a small amount of additives, indicating a conformational conversion from an identical sequence. The developmental dual helical systems exploit basic molecular geometry and can serve as a design platform for synthetic polymers.

Terminal proteomics: N- and C-terminal analyses for high-fidelity identification of proteins using MS.

In proteomics, MS plays an essential role in identifying and quantifying proteins. To characterize mature target proteins from living cells, candidate proteins are often analyzed with PMF and MS/MS ion search methods in combination with computational search routines based on bioinformatics. In contrast to shotgun proteomics, which is widely used to identify proteins, proteomics based on the analysis of N- and C-terminal amino acid sequences (terminal proteomics) should render higher fidelity results because of the high information content of terminal sequence and potentially high throughput of the method not requiring very high sequence coverage to be achieved by extensive sequencing. In line with this expectation, we review recent advances in methods for N- and C-terminal amino acid sequencing of proteins. This review focuses mainly on the methods of N- and C-terminal analyses based on MALDI-TOF MS for its easy accessibility, with several complementary approaches using LC/MS/MS. We also describe problems associated with MS and possible remedies, including chemical and enzymatic procedures to enhance the fidelity of these methods.

Novel photosystem involving protonation and deprotonation processes modelled on a PYP photocycle.

The synthesis of novel ortho-coumaric acid derivatives, with an amide group linked with an olefin moiety, which introduced photoinduced switching of the intramolecular hydrogen bonds is presented. An intramolecular OH...O=C hydrogen bond formed in a Z-phenol compound was switched to an intramolecular NH...O hydrogen bond in Z phenolate state via deprotonation. The pK(a) value of the Z-phenol derivative was lower than that of E-phenol, and a novel photocycle system involving protonation and deprotonation processes was achieved.