Crystal Structure of the Native Chromoprotein from Provides Insights into the Pigmentation Mechanism.

The pink-colored protein from the fungus (PsPCP) possesses unusual primary sequences with little resemblance to those of known proteins and exhibits a red color in aqueous solution. To understand the pigmentation mechanism of PsPCP, we elucidated the X-ray crystal structure of the native PsPCP. We identified a highly conjugated polyene ligand 2-dehydro-3-deoxylaetiporic acid A as a chromophore ligand, whose solution exhibits yellow.

A DFT study of the active role of the phosphate group of an internal aldimine in a transamination reaction.

A transamination reaction from an internal aldimine ([PLP]) and ()-alanine to pyridoxamine phosphate (PMP) and pyruvic acid was investigated by DFT calculations. As [PLP], a model where the lysine (-Lys) part was approximated by -CH[-NH-C(O)-CH]-C(O)-NH-CH was adopted. (HO) was also included to trace reaction paths involving proton transfers.

A DFT study on the degradation mechanism of vitamin B2.

Degradation reaction paths starting from riboflavin (RF) were investigated using DFT (density functional theory) as the first attempt to reveal their elementary processes. Photochemical reactions were followed in the lowest triplet spin state, "(T)". Two intermediates [Int1(T) and Int2(T)] were found in the course, RF(T) → FMF (7,8-dimethyl-10-formylflavin, T).

Brønsted acid-induced transannulation of the phytochemical zerumbone.

The sesquiterpene zerumbone was treated with HCl in ethyl acetate under the light-protected condition, and the time-dependent conversions were analyzed by gas chromatography. Nine products were isolated, and their structures were revealed by several NMR measurements such as H NMR, C{H} NMR, distortionless enhancement by polarization transfer (DEPT)-135, H-H correlation spectroscopy (COSY), H-C heteronuclear multiple quantum coherence (HMQC), and H-C heteronuclear multiple bond coherence (HMBC). The X-ray crystallography determined the stereochemistries of the three products and the two derivatives.

How Is the Oxidation Related to the Tautomerization in Vitamin B9?

The relationship between the lactim-lactam tautomerization and the free-radical scavenging reaction in vitamin B9 [folic acid (FA)] was investigated by density functional theory calculations. 6-Methylpterin was also adopted for the detailed analyses of various reaction paths. For pterin, the transition state of the tautomerization with two water molecules ( = 2) was calculated to be of the lowest activation energy.

How is vitamin B1 oxidized to thiochrome? Elementary processes revealed by a DFT study.

The oxidation reaction of thiamine (vitamin B1) to thiochrome was investigated by DFT calculations. Three reaction systems, [A] thiamine + methyl peroxy radical + (H2O)8, [B] thiamine + cyanogen bromide + HO-(H2O)8 and [C] thiamine + mercury(ii) chloride + HO-(H2O)8, were investigated. wB97X-D/6-311+G** for [A] and [B] and wB97X-D/SDD&6-311(+)G** for [C] geometry optimizations were carried out with the solvent effect (water).

Remarkable Potential of Zerumbone to Generate a Library with Six Natural Product-like Skeletons by Natural Material-Related Diversity-Oriented Synthesis.

Diversity-oriented synthesis (DOS) is an effective strategy for the quick creation of diverse and high three-dimensional compounds from simple starting materials. The selection of a starting material is the key to constructing useful, chemically diverse compound libraries for the development of new drugs. Here, we report a novel, general, and facile strategy for the creation of diverse compounds with high structural diversity from readily available natural products, such as zerumbone, as the synthetic starting material.

DFT Study of the Hydroxyl Radical Addition to 2'-Deoxyguanosine and the Guanine Base in Four Double-Stranded B-Form Dimers.

Density functional theory (DFT) calculations of reactions between 2'-deoxyguanosine (dR-Gua) and hydroxyl radical (HO) with water molecules (HO), = 0, 1, and 2, were carried out. The HO addition to three carbon sites, C(4), C(5), and C(8), and the subsequent ring cleavage of the three HO adducts were investigated. The addition to C(5) is of the smallest activation energy according to the largest lobe of the dR-Gua highest occupied molecular orbital (HOMO) at C(5).

Synthesis and Systematic Structural Analysis of Cationic Half-Sandwich Ruthenium Chalcogenocarbonyl Complexes.

Although the chemistry of transition-metal complexes with carbonyl (CO) and thiocarbonyl (CS) ligands has been well developed, their heavier analogues, namely selenocarbonyl (CSe) and tellurocarbonyl (CTe) complexes remain scarce. The limited availability of such CSe and CTe complexes has so far hampered our understanding of the differences between such chalcogenocarbonyl (CE: E=O, S, Se, Te) ligands. Herein, we report the synthesis and properties of a series of cationic half-sandwich ruthenium CE complexes of the type [CpRu(CE)(H IMes)(CNCH Ts)][BAr ] (Cp=η -C H ; H IMes=1,3-dimesitylimidazolin-2-ylidene; Ar =3,5-(CF ) C H ).

Synthesis and properties of anionic ruthenium thionitrosyl and selenonitrosyl complexes that contain tetraanionic 2-hydroxybenzamidobenzene ligands.

Although transition-metal complexes that contain thiocarbonyl (CS) and selenocarbonyl (CSe) ligands have been well studied, only three neutral or cationic selenonitrosyl (NSe) complexes have been reported, while anionic NSe complexes remain elusive. Herein, we report the first examples of anionic NSe-ligated ruthenium complexes, which were obtained from the reaction of anionic ruthenium nitrido complexes, elemental selenium, and 4-(N,N-dimethylamino)pyridine (DMAP). The structures of one of these ruthenium NSe complexes, as well as of the corresponding thionitrosyl (NS) and nitrosyl (NO) complexes, were systematically examined by X-ray diffraction analyses and theoretical calculations.

P-C reductive elimination in Ru(ii) complexes to convert triarylphosphine ligands into five- or six-membered phosphacycles.

Rare examples of P-C reductive elimination in ruthenium complexes to generate phosphonium salts are presented. Triarylphosphines are converted into benzophospholium or phosphaphenalenium ligands via cyclometalation and 1,2-insertion of an alkyne followed by P-C reductive elimination. The intermediate in each step was successfully characterized using NMR and X-ray diffraction studies.

A ruthenium tellurocarbonyl (CTe) complex with a cyclopentadienyl ligand: systematic studies of a series of chalcogenocarbonyl complexes [CpRuCl(CE)(HIMes)] (E = O, S, Se, Te).

The first tellurocarbonyl complex with a half-sandwich structure [CpRuCl(CTe)(HIMes)] was synthesized by a ligand substitution reaction. The practically complete series of the CpCE complexes [CpRuCl(CE)(HIMes)] (E = O, S, Se, Te) were systematically explored. The tellurium atom in the CTe complex could be smoothly replaced with lighter chalcogen atoms.

R/X exchange reactions in cis-[M(R){P(X)(NMeCH)}] (M = Pd, Pt), via a phosphenium intermediate.

R/X exchange reactions in cis-[M(R){P(X)(NMeCH)}] (M = Pd, Pt; R = aryl, alkyl; X = Cl, Br) were achieved for the first time to give cis-[M(X){P(R)(NMeCH)}]. DFT calculations suggested that the exchange reaction proceeds via a phosphenium intermediate.

Competition between vinylidene rearrangement and 1,2-insertion of carbon-disubstituted internal alkynes at a Cp*Ir(III) complex.

Competition between vinylidene rearrangement/1,1-insertion and 1,2-alkyne insertion into the Ir-Ar bond of [Cp*Ir(ppy-F4)](+) was observed on reaction with diarylacetylenes. The former process afforded the iridacycle 2via the subsequent 1,4-Ir migration, whereas the latter led to the pyridoisoquinolinium complex 4. Detailed analysis revealed that 4 isomerizes to 2 by heating at 50 °C.

Frontier orbitals and transition states in the oxidation and degradation of L-ascorbic acid: a DFT study.

DFT calculations were carried out to investigate reaction paths of L-ascorbic acid (AAH2), hydroxyl radicals and water clusters. Frontier-orbital analyses were also performed to examine the regioselectivity of the OH˙ addition. Transition states of the electrolytic dissociation of AAH2 and intermediate carboxylic acids were found to have very small activation energies through proton transfers along hydrogen bonds.

DFT study of internal alkyne-to-disubstituted vinylidene isomerization in [CpRu(PhC≡CAr)(dppe)]+.

Internal alkyne-to-vinylidene isomerization in the Ru complexes ([CpRu(η(2)-PhC≡CC(6)H(4)R-p)(dppe)](+) (Cp = η(5)-C(5)H(5); dppe = Ph(2)PCH(2)CH(2)PPh(2); R = OMe, Cl, CO(2)Et)) has been investigated using a combination of quantum mechanics and molecular mechanics methods (QM/MM), such as ONIOM(B3PW91:UFF), and density functional theory (DFT) calculations. Three kinds of model systems (I-III), each having a different QM region for the ONIOM method, revealed that considering both the quantum effect of the substituent of the aryl group in the η(2)-alkyne ligand and that of the phenyl groups in the dppe ligand is essential for a correct understanding of this reaction. Several plausible mechanisms have been analyzed by using DFT calculations with the B3PW91 functional.

Correlation between the rate order and the number of molecules in the reaction of trimethyl phosphite with water in acetonitrile solvent.

Density functional theory calculations of the title reaction, P(OCH₃)₃ + (H₂O)(n) in CH₃CN, were conducted, where n is the number of water molecules. Two routes, the routes suggested by (A) Aksnes and (B) Arbuzov, were traced with various n values. Both routes consist of two transition states (TSs) and one intermediate.

A new mechanism for the Favorskii rearrangement.

The title reaction was investigated by the use of ONIOM-RB3LYP calculations. A reaction system composed of alpha-chlorocyclohexanone, a methoxide ion and 8 MeOH solvent molecules was adopted. Two reaction channels, the semibenzilic acid mechanism (A) and cyclopropanone mechanism (B), were compared.

Reaction paths of the water-assisted solvolysis of N,N-dimethylformamide.

Density functional theory calculations were conducted on the title reactions with explicit inclusion of a variety of water molecules, H-CO-NMe2+MeOH+(H2O)n-->H-CO-OMe+HNMe2+(H2O)n. Geometries of transition states, reactant-like complexes and product-like ones were determined by the use of RB3LYP/6-31G(d) SCRF=dipole. Concerted paths were examined with n=0-3.

Theoretical study of the role of solvent H2O in neopentyl and pinacol rearrangements.

The neopentyl and the pinacol rearrangements as examples of Wagner-Meerwein rearrangements were investigated by the use of DFT calculations. As the first reaction, a model of neopentyl chloride (1b) and (H2O)12 was employed. In the reaction, the patterns of C--Cl scission, methyl migration, and C--OH formation were analyzed.

Active Role of Hydrogen Bonds in Rupe and Meyer-Schuster Rearrangements.

Rupe and Meyer-Schuster rearrangements for the R2C(OH) [Formula: see text] C⋮C [Formula: see text] H + H3O(+) and (H2O)9 model (R = methyl and phenyl groups) have been investigated by the use of density functional theory calculations. In the substrate R2C(OH) [Formula: see text] C⋮CH catalyzed by H3O(+)(H2O), three reaction channels, the two rearrangements and SN (nucleophilic substitution), were predicted by the frontier molecular orbital theory. The SN (the OH-group exchange) path was found to have a large activation energy.

Reaction paths of the water-assisted neutral hydrolysis of ethyl acetate.

Density functional theory calculations were conducted on the title reactions with explicit inclusion of a variety of water molecules. Concerted reaction paths were examined first in the reaction model, ester(H2O)n --> MeCOOH(H2O)(n-1)EtOH, with n = 1-4. Their Gibbs activation energies are much larger than the experimental value, and the concerted paths are unfavorable.

Reaction paths of tautomerization between hydroxypyridines and pyridones.

Tautomerization paths of 2(and 4)-hydroxypyridine (called here HP) to 2(and 4)-pyridone (called here PY) with water molecules were investigated by the use of density functional theory calculations. Potential energies were compared for a number of water molecules. The 2-HP molecule was found to be isomerized most readily and concertedly to the 2-PY one via proton relays with two water molecules.

A FMO-controlled reaction path in the benzil-benzilic acid rearrangement.

Reaction paths for the title rearrangement along with its methyl analogue were investigated by density functional theory calculations. The reaction model is R-CO-CO-R + OH(-)(H2O)4 --> R2C(OH)-COO- + (H2O)4 (R = Me and Ph), where the water tetramer is employed both for solvation to OH- and for the proton relay along hydrogen bonds. The reaction is composed of OH- addition, C-C rotation, carbanion [1,2] migration, and proton relay toward the product anions.

Is the Beckmann rearrangement a concerted or stepwise reaction? A computational study.

[reaction: see text] RB3LYP calculations were performed on the Beckman rearrangement by the use of three substrates, acetone oxime (1), acetophenone oxime (2), and cyclohexanone oxime (3). Acidic solvents were modeled by H+ (CH3COOH)3 and H3O+ (H2O)6, and reaction paths were determined precisely. For 1, a two-step process involving a sigma-type cationic complex was obtained.