Cα Cβ Research Articles

Probing the range of applicability of structure- and energy-adjusted QM/MM link bonds II: Optimized link bond parameters for density functional tight binding approaches.

Optimized link bond parameters for the Cα—Cβ bond of 22 different capped amino acid model systems have been determined at SCC DFTB/mio (self‐consistent charge density functional tight‐binding), SCC DFTB/3ob and GFNn‐xTB (n = 0, 1, and 2) level in conjunction with the AMBER 99SB, 14SB, and 19B force fields. The resulting parameter sets have been compared to newly calculated reference data obtained via resolution‐of‐identity 2nd order Møller–Plesset perturbation theory. The data collected in this work suggests that the optimized values in this study provide a more suitable setup of the QM/MM link bonds compared to the use of a single global setting applied to every amino acid fragmented by the QM/MM interface. The results also imply that a transfer of the ideal link bond settings between different levels of theory is not advised. In contrast, virtually identical parameters were obtained in calculations employing different variants of the AMBER force field. Considering the increasing success of tight binding based approaches being inter alia a results of their exceptional accuracy/effort ratio the provided collection of link atoms parameters provides a valuable resource for QM/MM studies of biomacromolecular systems as demonstrated in an exemplary QM/MM MD simulation of the β‐amyloid/Zn2+ complex.

Exploration and structure-based engineering of alkenal double bond reductases catalyzing the Cα[sbnd]Cβ double bond reduction of coniferaldehyde

Lignin, a complex aromatic polymer, represents a significant obstacle in lignocellulosic biomass utilization. The polymerization of lignin occurs by radical couplings, which mainly form ether and C–C bonds between monolignol units. The chemical stability of these bonds between monolignol units causes the recalcitrant nature of lignin. Since the Cα–Cβ double bond in the monolignols is a crucial chemical feature for the radical coupling, reduction of the double bond would decrease the degree of lignin polymerization, avoiding the recalcitrance of lignin. To develop a method of lignin engineering, we have focused on alkenal double bond reductases (DBR), which can reduce the Cα–Cβ double bond of a monolignol precursor. Here, a novel bacterial DBR from Parvibaculum lavamentivorans DS-1 (PlDBR) was found. This enzyme can reduce the side-chain double bond of coniferaldehyde (CALD) and has a 41% amino-acid sequence identity with CALD DBR from Arabidopsis thaliana (AtDBR). The crystal structure of the PlDBR showed that it has a larger substrate-binding pocket than AtDBR, conferring broader substrate specificity on the former. Structural and mutation analyses of PlDBR and AtDBR suggested that Tyr51 and Try252 are critical residues for the catalytic activity of PlDBR. In addition, Tyr81 of AtDBR appears to cause substrate inhibition. Replacing Tyr81 of AtDBR with a smaller amino-acid residue, as in the AtDBR variants Tyr81Leu and Tyr81Ala, resulted in a substantially higher CALD-reducing activity compared to the wild type. These variants would be promising candidates for lignin manipulation to decrease the recalcitrance of lignocellulosic biomass.

Investigation into the Pyrolysis Bond Dissociation Enthalpies (BDEs) of a Model Lignin Oligomer Using Density Functional Theory (DFT)

Pyrolysis is a promising technology for converting lignocellulosic biomass into chemicals, materials, and fuels. Understanding the fundamental reactions and mechanisms during the fast pyrolysis of lignocellulosic biomass is essential for improving the efficiency of this technology. Investigations of lignin fast pyrolysis reactions and mechanisms have thus far lagged relative to cellulose and hemicellulose and have largely been focused on lignin model dimers and monomers. These studies provide valuable information about the reaction tendencies of individual linkages; however, the complex and varying nature of lignin interunit linkages does not allow direct extrapolation to larger lignin structures. In this study, we computationally investigate homolytic bond scission reactions of a larger, synthesizable model lignin oligomer, containing three major lignin linkages, using density functional theory. The bond dissociation enthalpies of the model oligomer showed the trend for the four lowest BDEs Cα–O (β-5) < Cα–Cβ (β-5) < Cα–O (α-O-4) < Cβ–O (β-O-4). Our results show that the general trends identified in smaller dimer molecules are maintained while the magnitude of the BDEs is increased in the model oligomer. This work is an important first step in developing a library of reaction information for various lignin substructures.

The Promiscuous Activity of the Radical SAM Enzyme NosL toward Two Unnatural Substrates

Main observation and conclusionThe radical S‐adenosylmethionine (SAM) enzyme NosL catalyzes the conversion of L‐tryptophan (L‐Trp, 1) to 3‐methyl‐2‐indolic acid (MIA, 2), a key intermediate in the biosynthesis of the peptide antibiotic nosiheptide. Previous study showed that this remarkable recombination reaction starts from the cleavage of the Cα—COO– bond to result in a •CO2− radical migration. In contrast to the radical SAM tyrosine lyases, NosL appears unable to cleave the Cα—Cβ bond, which is intrinsically more favorable to be cleaved than the Cα—COO– bond. In this study, we investigate the NosL activity with tryptamine (11) and tryptophol (12), two L‐Trp analogues lacking a carboxylate moiety. We showed that NosL cleaves the C1—C2 bond of these two substrates to produce 3‐methylindole (7), suggesting that the enzyme can still catalyze a β‐scission when the carboxyl group of Trp is absent. We also showed the enzyme exhibits a promiscuous activity, initiating the reaction by abstracting hydrogen atoms from two different sites to produce two sets of products.

Atomically Dispersed Pt-N3C1 Sites Enabling Efficient and Selective Electrocatalytic C-C Bond Cleavage in Lignin Models under Ambient Conditions.

Selective cleavage of C-C linkages is the key and a challenge for lignin degradation to harvest value-added aromatic compounds. To this end, electrocatalytic oxidation presents a promising technique by virtue of mild reaction conditions and strong sustainability. However, the existing electrocatalysts (traditional bulk metal and metal oxides) for C-C bond oxidative cleavage suffer from poor selectivity and low product yields. We show for the first time that atomically dispersed Pt-N3C1 sites planted on nitrogen-doped carbon nanotubes (Pt1/N-CNTs), constructed via a stepwise polymerization-carbonization-electrostatic adsorption strategy, are highly active and selective toward Cα-Cβ bond cleavage in β-O-4 model compounds under ambient conditions. Pt1/N-CNTs exhibits 99% substrate conversion with 81% yield of benzaldehyde, which is exceptional and unprecedented compared with previously reported electrocatalysts. Moreover, Pt1/N-CNTs using only 0.41 wt % Pt achieved a much higher benzaldehyde yield than those of the state-of-the-art bulk Pt electrode (100 wt % Pt) and commercial Pt/C catalyst (20 wt % Pt). Systematic experimental investigation together with density functional theory (DFT) calculation suggests that the superior performance of Pt1/N-CNTs arises from the atomically dispersed Pt-N3C1 sites facilitating the formation of a key Cβ radical intermediate, further inducing a radical/radical cross-coupling path to break the Cα-Cβ bond. This work opens up opportunities in lignin valorization via a green and sustainable electrochemical route with ultralow noble metal usage.

Mechanism of the Stereomutation of an Azaplatinacyclobutane Complex

The diastereomerically pure azaplatinacyclobutane complex , bearing a single deuterium atom at Cα, undergoes stereomutation about the Cα–Cβ bond of the azaplatinacyclobutane moiety at 30 °C with a ...

Metal-free and mild photo-thermal synergism in ionic liquids for lignin Cα–Cβ bond cleavage to provide aldehydes

Photo-thermal synergism of UV light and heating could excite lignin molecules and induce direct cleavage of the Cα–Cβ bond in lignin β-O-4 and β-1 interlinkages under metal-free and mild conditions with the assistance of ionic liquids.

Fluorine Effects for Tunable C–C and C–S Bond Cleavage in Fluoro-Julia–Kocienski Intermediates

Classical Julia–Kocienski fluoroolefination represents an indispensable platform for the construction of monofluoroalkenes. Nevertheless, its complex multistep mechanistic manifold along with the u...

Representative model compounds for understanding the pyrolytic behavior of pre-oxidized β-ether-type lignin

To achieve a better understanding of the pyrolysis behavior of pre-oxidized β-ether-type lignin, three Cα=O type dimers with different substituent groups on the aromatic ring were synthesized and analyzed by a simultaneous thermal analysis instrument (STA), in-situ Fourier transform infrared spectroscopy (in-situ FTIR), and pyrolysis-gas chromatography/ mass spectrometry (Py-GC/MS). The results showed that major primary pyrolysis reactions of Cα=O type models normally occurred at 200 to 400 °C, and connecting bridge structures of models were completely destroyed, causing the emission of abundant volatiles. Substituent groups of aromatic rings played direct roles in thermal stability of models, volatiles emission, product characteristics, and secondary reaction pathways of major primary products. Particularly, the aryl–OCH3 group clearly enhanced the reactivity of intramolecular linkages and was an important active functional group for secondary reactions. As major primary products and intermediates, guaiacol and 2-methoxy-benzaldehyde were formed via the cleavage of Cα–O and Cα–Cβ bonds and could also be converted into phenol, benzaldehyde, and 2-methylphenol via rearrangement of aryl–OCH3 into an aryl–CH3 group or –OCH3 group removal. Oxidization of benzylic alcohol to benzylic ketone not only simplified depolymerization pathways, but also resulted in better selectivity of phenolic monomers and a predictable product distribution.

Wavelength dependence of chiral recognition using ions between photoexcited tryptophan and sugars

The reactivity of cold gas-phase clusters was investigated as a model for chemical evolution in interstellar molecular clouds. Chiral recognition using ions between amino acids and sugars was examined by mass spectrometry and ultraviolet spectroscopy measurements of gas-phase tryptophan (Trp) enantiomers hydrogen bonded with methyl-α-d-glucoside in Na+-containing or protonated forms at 8 K. The chiral recognition mechanism between Trp and the glucoside changed depending on the photoexcitation wavelength: the enantiomer-selective reactions at 265–280 nm and the electronic structure of Trp at 280–290 nm. The attachment of Na+ to d-Trp and the Cα–Cβ bond cleavage of d-Trp were the enantiomer-selective reactions in the Na+-containing and protonated clusters, respectively. The wavelength dependences of the enantiomer-selective reactions were similar between the Na+-containing and protonated clusters. This is because the enantiomer-selective reactions were triggered by photoinduced electron transfer from the indole ring to the carboxyl group of Trp in the clusters.

Catalytic Carbon–Carbon Bond Activation of Saturated and Unsaturated Carbonyl Compounds via Chelate-Assisted Coupling Reaction with Indoles

The chelate assistance strategy was devised to promote a highly regioselective catalytic C–C bond activation reaction of saturated and unsaturated carbonyl compounds. The cationic Ru–H complex 1 was found to be an effective catalyst for mediating the coupling reaction of 1,2-disubstituted indoles with α,β-unsaturated aldehydes and ketones, in which the regioselective Cα–Cβ activation of the carbonyl substrates has been achieved in forming the 3-alkylindole products. The analogous coupling reaction of indoles with saturated aldehydes and ketones directly led to the Cα–Cβ cleavage of the carbonyl substrates in forming the 3-alkylindole products. The coupling reaction of 1,2-dimethylinole with (E)-3-nonen-2-one and 2-propanol-d8 showed 20–22% of deuterium incorporation to both α- and β-CH2 of the 3-alkylindole product. The coupling reaction of 1,2-dimethylinole with (E)-3-nonen-2-one exhibited the most significant carbon kinetic isotope effect on the α-carbon of the product (Cα = 1.046). The Hammett plot constructed from the reaction of 1,2-dimethylinole with a series of para-substituted enones p-X-C6H4CH═CHCOCH3 (X = OMe, Me, H, Cl, CF3) showed a modest promotional effect by an electron-donating group (ρ = −0.2 ± 0.1). Several catalytically relevant Ru–H species were detected by NMR from a stoichiometric reaction mixture of the Ru–H complex 1 with 1,2-dimethylindole and (E)-3-nonen-2-one in CD2Cl2. These results support a mechanism of the catalytic coupling reaction via conjugate addition of indoles to enones followed by the C–C bond activation and hydrogenolysis steps.

Predicted Loop Regions Promote Aggregation: A Study of Amyloidogenic Domains in the Functional Amyloid FapC

Protein fibrillation is traditionally associated with misfolding, loss of functional phenotype, and gain of toxicity in neurodegenerative diseases. However, many organisms exploit fibrils in the form of functional amyloids (FA), as seen in bacteria, such as E. coli, Salmonella, Bacillus, and Pseudomonas. Here, we provide structural information and mechanistic data for fibrillation of the smallest amyloidogenic truncation unit along with the full-length version (FL) of the major amyloid protein FapC from Pseudomonas, predicted to consist of three β-hairpin-forming imperfect repeats separated by disordered regions. Using a series of truncation mutants, we establish that the putative loops (linkers) increase the rate of aggregation. The minimal aggregation unit consisting of a single repeat with flanking disordered regions (R3C) aggregates in a pathway dominated by secondary nucleation, in contrast to the primary nucleation favored by full-length (FL) FapC. SAXS on FapC FL, R3C, and remaining truncation constructs resolves two major coexisting species in the fibrillation process, namely pre-fibrillar loosely aggregated monomers, and cylindrical, elliptical cross-section fibrils. Solid-state NMR spectra identified rigid parts of the FapC fibril. We assigned Cα–Cβ chemical shifts, indicative of a predominant β-sheet topology with some α-helix or loop chemical shifts. Our work emphasizes the complex nature of FapC fibrillation. In addition, we are able to deduce the importance of non-repeat regions (i.e., predicted loops), which enhance the amyloid protein aggregation and their influence on the polymorphism of the fibril architecture.

Base-Promoted C-C Bond Activation Enables Radical Allylation with Homoallylic Alcohols.

The Cα–Cβ bond in homoallylic alcohols can be activated under basic conditions, qualifying these nonstrained acyclic systems as radical allylation reagents. This reactivity is exemplified by photoinitiated (with visible light and/or blue LEDs) allylation of perfluoroalkyl and alkyl radicals generated from perfluoroalkyl iodides and alkylpyridinium salts, respectively, with homoallylic alcohols. C-radical addition to the double bond of the title reagents and subsequent base-promoted homolytic Cα–Cβ cleavage leads to the formation of the corresponding allylated products along with ketyl radicals that act as single electron reductants to sustain the chain reactions. Substrate scope is documented and the role of base in the C–C bond activation is studied by computation.

Redox-neutral photocatalytic strategy for selective C–C bond cleavage of lignin and lignin models via PCET process

It remains challenging to achieve the selective cleavage of C–C bonds in lignin or lignin model compounds to produce aromatic products in high yield and selectivity. We have developed a redox-neutral photocatalytic strategy to accomplish this goal in both β-O-4 and β-1 lignin models at room temperature (RT) via proton-coupled electron transfer (PCET) process without any pretreatments of substrate, by adjusting the alkalinity of base to obtain a lignin models/base PCET pair with a bond dissociation free energy close to 102 kcal/mol. Without breaking down Cβ–Cγ bond and any C–O bonds, this PCET method is 100% atom economy and produces exclusive Cα–Cβ bond cleavage products, such as benzaldehydes (up to 97%) and phenyl ethers (up to 96%), in high to excellent yields and selectivities. Preliminary studies indicated that the PCET strategy is also effective for the depolymerization of native lignin at RT, thus providing significantly important foundation to the depolymerization of lignin.

Copper Catalyzed Alcohol Oxidation and Cleavage of β‐O‐4 Lignin Model Systems: From Development to Mechanistic Examination

AbstractLignin, an abundant natural polymer with high aromaticity, is a potential source of renewable chemicals and fuels among other biomaterials. Herein, a study on copper catalyzed alcohol oxidation and cleavage of lignin β‐O‐4 model substrates is reported. The potential of CuX/BiPy/TEMPO(/additive) systems (X=halide or triflate, BiPy=2,2’‐bipyridine; TEMPO=2,2,6,6‐tetramethylpiperidine‐N‐oxyl) was explored and the optimized protocol was studied with several type of model compounds. Mechanistic studies elucidated two types of cascade reactions: Both involve a cleavage of Cα–Cβ bond, which is most likely activated by 1) primary alcohol oxidation in β‐O‐4 glycerolaryl ethers resulting in retro‐aldol cleavage and 2) Cβ–H oxidation after secondary alcohol oxidation in β‐O‐4 ethanolaryl ethers leading to oxidative radical cleavage. The first process affords aromatic aldehydes while the latter delivers aryl acids.

Influence of inherent alkali metal chlorides on pyrolysis mechanism of a lignin model dimer based on DFT study

In order to understand the catalytic effects of inherent inorganic elements in biomass on the pyrolysis mechanism of lignin, density functional theory with a Gaussian method of M06-2X and basic set of 6-31 + G(d,p) was employed to simulate the pyrolysis pathways of a β-O-4 type lignin dimer model compound (1-methoxy-2-(4-methoxyphenethoxy)benzene) catalyzed by NaCl and KCl which are major inorganic constituents of biomass at microscale level. The calculation results indicate that cations (Na+ and K+) in alkali metal chlorides are facile to combine with the oxygen-containing functional groups in the lignin dimer model compound. Both cations increase the Cβ−O bond length and shorten the Cα–Cβ bond length, which will further affect their bond dissociation energies. In the initial pyrolysis process of the lignin dimer model compound, NaCl and KCl can promote the Cβ–O homolytic reaction and concerted decomposition reaction, while restrain the Cα–Cβ homolytic reaction. Therefore, the lignin dimer model compound decomposes mainly through the concerted decomposition and Cβ–O homolytic mechanisms under NaCl and KCl catalytic pyrolysis conditions, producing 1-methoxy-4-vinylbenzene, 1-ethyl-4-methoxybenzene, 2-methoxyphenol, catechol and 2-hydroxybenzaldehyde, among which NaCl and KCl have inhibitory effect on 2-hydroxybenzaldehyde, but have promoting effect on the other pyrolytic products.

Cα–Cβ bond cleavage occurs at the side chain of the N-terminal phenylalanine residue during CID of tyrosine-containing peptide radical cations

Molecular radical cationic peptides (M+) display rich and diverse gas-phase ion chemistry that can differ substantially from that of their protonated counterparts. Dissociation of M+ radical cations can provide relevant structural information for protein sequencing, often complementary to that obtained using traditional approaches. In this study, low-energy collision-induced dissociation (CID) of a series of tyrosine-containing peptide molecular radical cations having an N-terminal phenylalanine residue led to new products resulting from radical-mediated Cα–Cβ bond cleavage at the side chain of the phenylalanine residue. The chemical identity of the species formed through side chain loss (91 Da) occurring via N-terminal Cα–Cβ bond cleavage was examined using a combination of low-energy CID experiments, isotopic labeling mass spectrometric experiments, and density functional theory calculations. This unusual dissociation process occurs with fascinating unimolecular gas phase ion chemistry and requires a π-radical cationic tyrosine residue with significant spin density delocalized into the N-terminal amino group. The radical character at the resulting –NH2+ moiety then induces β-scission at the side chain Cα–Cβ bond of the phenylalanine residue. This discovery also demonstrates the role of the NH2 group in facilitating Cα–Cβ bond cleavage of the phenylalanine residue by the proximal tyrosine π-radical cation, probably involving a through-space electron transfer process.

Mechanistic insight in the selective delignification of wheat straw by three white-rot fungal species through quantitative 13C-IS py-GC\u2013MS and whole cell wall HSQC NMR

BackgroundThe white-rot fungi Ceriporiopsis subvermispora (Cs), Pleurotus eryngii (Pe), and Lentinula edodes (Le) have been shown to be high-potential species for selective delignification of plant biomass. This delignification improves polysaccharide degradability, which currently limits the efficient lignocellulose conversion into biochemicals, biofuels, and animal feed. Since selectivity and time efficiency of fungal delignification still need optimization, detailed understanding of the underlying mechanisms at molecular level is required. The recently developed methodologies for lignin quantification and characterization now allow for the in-depth mapping of fungal modification and degradation of lignin and, thereby, enable resolving underlying mechanisms.ResultsWheat straw treated by two strains of Cs (Cs1 and Cs12), Pe (Pe3 and Pe6) and Le (Le8 and Le10) was characterized using semi-quantitative py-GC–MS during fungal growth (1, 3, and 7 weeks). The remaining lignin after 7 weeks was quantified and characterized using 13C lignin internal standard based py-GC–MS and whole cell wall HSQC NMR. Strains of the same species showed similar patterns of lignin removal and degradation. Cs and Le outperformed Pe in terms of extent and selectivity of delignification (Cs ≥ Le >> Pe). The highest lignin removal [66% (w/w); Cs1] was obtained after 7 weeks, without extensive carbohydrate degradation (factor 3 increased carbohydrate-to-lignin ratio). Furthermore, though after treatment with Cs and Le comparable amounts of lignin remained, the structure of the residual lignin vastly differed. For example, Cα-oxidized substructures accumulated in Cs treated lignin up to 24% of the total aromatic lignin, a factor two higher than in Le-treated lignin. Contrarily, ferulic acid substructures were preferentially targeted by Le (and Pe). Interestingly, Pe-spent lignin was specifically depleted of tricin (40% reduction). The overall subunit composition (H:G:S) was not affected by fungal treatment.ConclusionsCs and Le are both able to effectively and selectively delignify wheat straw, though the underlying mechanisms are fundamentally different. We are the first to identify that Cs degrades the major β-O-4 ether linkage in grass lignin mainly via Cβ–O–aryl cleavage, while Cα–Cβ cleavage of inter-unit linkages predominated for Le. Our research provides a new insight on how fungi degrade lignin, which contributes to further optimizing the biological upgrading of lignocellulose.

T cell receptor (TCR) α and β genes of loach (Misgurnus anguillicaudatus): Molecular cloning and expression analysis in response to bacterial, parasitic and fungal challenges

In vertebrates, the T cell receptor (TCR) plays a crucial role in immune system. To date, the roles of fish TCRs in response to pathogen infection are still poorly understood. In the present study, we firstly cloned and identified the TCRα and TCRβ from dojo loach (Misgurnus anguillicaudatus) by RACE approaches. The full-length cDNAs of Ma-TCRα and Ma-TCRβ include an open reading frame (ORF) of 723 and 879 bp encoding a polypeptide of 241 and 293 amino acids, respectively. Structural analysis indicated that Ma-TCRα and Ma-TCRβ had a signal peptide, IgV domain, IgC domain, a connecting peptide (CPS), a transmembrane region (TM) and a cytoplasmic (CYT), which are similar to their counterparts described in other teleost. Phylogenetic analysis supported that Ma-TCR Cα and Ma-TCR Cβ were closely related to the Cα and Cβ region of Cyprinidae family, respectively. Transcriptional expression analysis indicated that Ma-TCRα and Ma-TCRβ mRNAs were ubiquitously expressed in a wide array of tissues and most abundantly found in skin, brain, kidney, gill and spleen. The expression patterns of Ma-TCRα and Ma-TCRβ after bacteria (F. columnare G4), parasite (Ichthyophthirius multifiliis) and fungus (Saprolegnia) infection were detected by qRT-PCR. Additionally, the morphological changes of gill and skin following the three infection models were investigated. The results clearly indicated that Ma-TCRα and Ma-TCRβ was significant up-regulated not only in spleen and kidney, but also in skin and gill. In summary, our present findings suggested that Ma-TCRα and Ma-TCRβ might play significantly roles in the modulation of immune response and protect loach from different pathogens infection.

Correlated motions of C'-N and Cα-Cβ pairs in protonated and per-deuterated GB3.

We investigated correlated µs-ms time scale motions of neighboring 13C'-15N and 13Cα-13Cβ nuclei in both protonated and perdeuterated samples of GB3. The techniques employed, NMR relaxation due to cross-correlated chemical shift modulations, specifically target concerted changes in the isotropic chemical shifts of the two nuclei associated with spatial fluctuations. Field-dependence of the relaxation rates permits identification of the parameters defining the chemical exchange rate constant under the assumption of a two-site exchange. The time scale of motions falls into the intermediate to fast regime (with respect to the chemical shift time scale, 100-400s-1 range) for the 13C'-15N pairs and into the slow to intermediate regime for the 13Cα-13Cβ pairs (about 150s-1). Comparison of the results obtained for protonated and deuterated GB3 suggests that deuteration has a tendency to reduce these slow scale correlated motions, especially for the 13Cα-13Cβ pairs.