Study on the lignin-derived sp2-sp3 hybrid hard carbon materials and the feasibility for industrial production.

Hard carbon has been widely used in anode of lithium/sodium ion battery, electrode of supercapacitor, and carbon molecular sieve for CO2 capture and hydrogen storage. In this study the lignin derived hard carbon products are investigated, and the conclusions are abstracted as follows. (1) The lignin derived hard carbon products consist of microcrystal units of sp2 graphene fragments, jointed by sp3 carbon atoms and forming sp2-sp3 hybrid hard carbon family. (2) From the lignin precursors to the sp2-sp3 hybrid hard carbon products, most carbon atoms retain their original electron configurations (sp2 or sp3) and keep their composition in lignin. (3) The architectures of lignin-derived hard carbon materials are closely dependent on the forms of their lignin precursors, and could be preformed by different pretreatment techniques. (4) The carbonization of lignin precursors follows the mechanism "carbonization in situ and recombination nearby". (5) Due to the high carbon ratio and abundant active functional groups in lignin, new activation techniques could be developed for control of pore size and pore volume. In general lignin is an excellent raw material for sp2-sp3 hybrid hard carbon products, a green and sustainable alternative resource for phenolic resin, and industrial production for lignin derived hard carbon products would be feasible.

Study on the microcrystal cellulose and the derived 2D graphene and relative carbon materials.

Microcrystal cellulose (MCC) is a green and sustainable resource that widely exists in various lignocellulose species in percentage 10% to 30%. The fine powder of MCC is often discarded in industrial productions that use lignocellulose as feedstock. The crystal structure of two types of MCC (sugarcane pith and bamboo pith) and their derived carbon materials are studied, and the key findings are summarized as follows. (1) In the MCC refined from sugarcane pith, there are large amount of cellulose 2D crystal, which can be converted to valuable 2D graphene crystal. (2) In the MCC refined from bamboo pith there are large amount of cluster microcrystal cellulose, which can be converted to soft and elastic graphene microcrystal (GMC). (3) The 2D cellulose in MCC of sugarcane pith has large surface area and is easily to be degraded to sugars by acid-base hydrolysis reaction, which can be carbonized to Fullerenes-like carbon spheres. (4) The crystal structures of MCC derived carbon materials are strongly impacted by the crystal structures of MCC, and the carbonization reaction of MCC follows "in situ carbonization" and "nearby recombination" mechanism. In general, the results from this study may open a new way for value-added applications of microcrystal cellulose.

Simulated Protein Thermal Detection (SPTD) for Enzyme Thermostability Study and an Application Example for Pullulanase from Bacillus deramificans.

BACKGROUND: The relationship between protein structure and its bioactivity is one of the fundamental problems for protein engineering and pharmaceutical design. METHOD: A new method, called SPTD (Simulated Protein Thermal Detection), was proposed for studying and improving the thermal stability of enzymes. The method was based on the evidence observed by conducting the MD (Molecular Dynamics) simulation for all the atoms of an enzyme vibrating from the velocity at a room temperature (e.g., 25°C) to the desired working temperature (e.g., 65°C). According to the recorded MD trajectories and the coordinate deviations of the constituent residues under the two different temperatures, some new strategies have been found that are useful for both drug delivery and starch industry. CONCLUSION: The SPTD technique presented in this paper may become a very useful tool for pharmaceutical design and protein engineering.

Fabrication and Characterization of Graphene Microcrystal Prepared from Lignin Refined from Sugarcane Bagasse.

Graphene microcrystal (GMC) is a type of glassy carbon fabricated from lignin, in which the microcrystals of graphene are chemically bonded by sp³ carbon atoms, forming a glass-like microcrystal structure. The lignin is refined from sugarcane bagasse using an ethanol-based organosolv technique which is used for the fabrication of GMC by two technical schemes: The pyrolysis reaction of lignin in a tubular furnace at atmospheric pressure; and the hydrothermal carbonization (HTC) of lignin at lower temperature, followed by pyrolysis at higher temperature. The existence of graphene nanofragments in GMC is proven by Raman spectra and XRD patterns; the ratio of sp² carbon atoms to sp³ carbon atoms is demonstrated by XPS spectra; and the microcrystal structure is observed in the high-resolution transmission electron microscope (HRTEM) images. Temperature and pressure have an important impact on the quality of GMC samples. With the elevation of temperature, the fraction of carbon increases, while the fraction of oxygen decreases, and the ratio of sp² to sp³ carbon atoms increases. In contrast to the pyrolysis techniques, the HTC technique needs lower temperatures because of the high vapor pressure of water. In general, with the help of biorefinery, the biomass material, lignin, is found to be qualified and sustainable material for the manufacture of GMC. Lignin acts as a renewable substitute for the traditional raw materials of glassy carbon, copolymer resins of phenol formaldehyde, and furfuryl alcohol-phenol.

A comparative study for the organic byproducts from hydrothermal carbonizations of sugarcane bagasse and its bio-refined components cellulose and lignin.

Sugarcane bagasse was refined into cellulose, hemicellulose, and lignin using an ethanol-based organosolv technique. The hydrothermal carbonization (HTC) reactions were applied for bagasse and its two components cellulose and lignin. Based on GC-MS analysis, 32 (13+19) organic byproducts were derived from cellulose and lignin, more than the 22 byproducts from bagasse. Particularly, more valuable catechol products were obtained from lignin with 56.8% share in the total GC-MS integral area, much higher than the 2.263% share in the GC-MS integral areas of bagasse. The organic byproducts from lignin make up more than half of the total mass of lignin, indicating that lignin is a chemical treasure storage. In general, bio-refinery and HTC are two effective techniques for the valorization of bagasse and other biomass materials from agriculture and forest industry. HTC could convert the inferior biomass to superior biofuel with higher energy quantity of combustion, at the same time many valuable organic byproducts are produced. Bio-refinery could promote the HTC reaction of biomass more effective. With the help of bio-refinery and HTC, bagasse and other biomass materials are not only the sustainable energy resource, but also the renewable and environment friendly chemical materials, the best alternatives for petroleum, coal and natural gas.

Enhanced production of optical (S)-acetoin by a recombinant Escherichia coli whole-cell biocatalyst with NADH regeneration.

Acetoin is an important platform chemical with a variety of applications in foods, cosmetics, chemical synthesis, and especially in the asymmetric synthesis of optically active pharmaceuticals. It is also a useful breath biomarker for early lung cancer diagnosis. In order to enhance production of optical (S)-acetoin and facilitate this building block for a series of chiral pharmaceuticals derivatives, we have developed a systematic approach using in situ-NADH regeneration systems and promising diacetyl reductase. Under optimal conditions, we have obtained 52.9 g L-1 of (S)-acetoin with an enantiomeric purity of 99.5% and a productivity of 6.2 g (L h)-1. The results reported in this study demonstrated that the production of (S)-acetoin could be effectively improved through the engineering of cofactor regeneration with promising diacetyl reductase. The systematic approach developed in this study could also be applied to synthesize other optically active α-hydroxy ketones, which may provide valuable benefits for the study of drug development.

2L-PCA: a two-level principal component analyzer for quantitative drug design and its applications.

A two-level principal component predictor (2L-PCA) was proposed based on the principal component analysis (PCA) approach. It can be used to quantitatively analyze various compounds and peptides about their functions or potentials to become useful drugs. One level is for dealing with the physicochemical properties of drug molecules, while the other level is for dealing with their structural fragments. The predictor has the self-learning and feedback features to automatically improve its accuracy. It is anticipated that 2L-PCA will become a very useful tool for timely providing various useful clues during the process of drug development.

Microbial Routes to (2R,3R)-2,3-Butanediol: Recent Advances and Future Prospects.

(2R,3R)-2,3-Butanediol has many industrial applications, such as it is used as an antifreeze agent and low freezing point fuel. In addition, it is particularly important to provide chiral groups in drugs. In recent years, this valuable bio-based chemical has attracted increasing attention, and significant progress has been made in the development of microbial cell factories for (2R,3R)-2,3-butanediol production. This article reviews recent advances and challenges in microbial routes to (2R,3R)-2,3- butanediol production, and highlights the metabolic engineering and synthetic biological approaches used to improve titers, yields, productivities, and optical purities. Finally, a systematic and integrative strategy for developing high-performance microbial cell factories is proposed.

Exploring the possibility to store the mixed oxygen-hydrogen cluster in clathrate hydrate in molar ratio 1:2 (O2+2H2).

An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules. (3) The dimension of O2-2H2 interaction structure is smaller than the dimension of CO2-2H2 interaction structure. (4) The escaping energy of oxygen molecules from the hydrate cell is larger than that of the hydrogen molecules. (5) The high affinity of the oxygen molecules with both the water molecules and the hydrogen molecules may promote the stability of oxygen-hydrogen mixture in the clathrate hydrate. Therefore it is possible to store the mixed (O2+2H2) cluster in clathrate hydrate.

Active Hydrogen Bond Network (AHBN) and Applications for Improvement of Thermal Stability and pH-Sensitivity of Pullulanase from Bacillus naganoensis.

A method, so called "active hydrogen bond network" (AHBN), is proposed for site-directed mutations of hydrolytic enzymes. In an enzyme the AHBN consists of the active residues, functional residues, and conservative water molecules, which are connected by hydrogen bonds, forming a three dimensional network. In the catalysis hydrolytic reactions of hydrolytic enzymes AHBN is responsible for the transportation of protons and water molecules, and maintaining the active and dynamic structures of enzymes. The AHBN of pullulanase BNPulA324 from Bacillus naganoensis was constructed based on a homologous model structure using Swiss Model Protein-modeling Server according to the template structure of pullulanase BAPulA (2WAN). The pullulanase BNPulA324 are mutated at the mutation sites selected by means of the AHBN method. Both thermal stability and pH-sensitivity of pullulanase BNPulA324 were successfully improved. The mutations at the residues located at the out edge of AHBN may yield positive effects. On the other hand the mutations at the residues inside the AHBN may deprive the bioactivity of enzymes. The AHBN method, proposed in this study, may provide an assistant and alternate tool for protein rational design and protein engineering.

A new type of two-dimensional carbon crystal prepared from 1,3,5-trihydroxybenzene.

A new two-dimensional (2D) carbon crystal, different from graphene, has been prepared from 1,3,5-trihydroxybenzene, consisting of 4-carbon and 6-carbon rings in 1:1 ratio, named 4-6 carbophene by authors, in which all carbon atoms possess sp2 hybrid orbitals with some distortion, forming an extensive conjugated π-bonding planar structure. The angles between the three σ-bonds of the carbon sp2 orbitals are roughly 120°, 90°, and 150°. Each of the three non-adjacent sides of a 6C-ring is shared with a 4C-ring; and each of the two opposite sides of a 4C-ring is shared with a 6C-ring. Dodecagonal holes with a diameter of approximate 5.8 Å are regularly located throughout the 2D carbon crystal. Even though the bond energies in 4-6 carbophene are weaker than those in the graphene, the new planar crystal is quite stable in ambient conditions. The 4-6 carbophene can be synthetized from 1,3,5-trihydroxybenzene or other benzene derivatives through dehydration and polymerization reactions, and may possess several possible patterns that form a family of 2D carbon crystals. A possible side reaction involving 1,3,5-trihydroxybenzene is also discussed, which may produce a carbon-oxygen two dimensional crystal.

Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design.

OBJECTIVES: Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. METHODS: Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. RESULTS: The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. CONCLUSION: (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions.

Recent development of peptide drugs and advance on theory and methodology of peptide inhibitor design.

Due to the low toxicity, easy synthesis, rapid elimination, and less side effect, more and more peptide inhibitors are emerging as the effective drugs that are clinically used in therapies of a number of diseases. At the same time the computer-aided drug design (CADD) methods have remarkably developed. In this mini review the newly developed peptide inhibitors and drugs are introduced, including peptide vaccines for cancers, peptide inhibitors for HIV, Alzheimer's disease and related diseases, and the peptides as the leading compounds of drugs. The recent progress in the theory and methodology of peptide inhibitor design is reviewed. (1) The flexible protein-peptide docking model is introduced, in which the peptide structures are treated as segment-flexible chains using genetic algorithm and special force field parameters. (2) The "Wenxiang diagram" is illustrated for protein-peptide interaction analysis that has been successfully used in the coiled-coil interaction analysis. (3) The "Distorted key" theory is reviewed, which is an effective method to convert the peptide inhibitors to the small chemical drugs. (4) The amino acid property-based peptide prediction method (AABPP) is described that is a twolevel QSAR prediction network for the bioactivity prediction of peptide inhibitors. (5) Finally, several types of molecular interactions between protein and peptide ligands are summarized, including cation-π interactions; polar hydrogen-π interactions; and π-π stocking interactions.

Insight into a molecular interaction force supporting peptide backbones and its implication to protein loops and folding.

Although not being classified as the most fundamental protein structural elements like α-helices and ß-strands, the loop segment may play considerable roles for protein stability, flexibility, and dynamic activity. Meanwhile, the protein loop is also quite elusive; i.e. its interactions with the other parts of protein as well as its own shape-maintaining forces have still remained as a puzzle or at least not quite clear yet. Here, we report a molecular force, the so-called polar hydrogen-π interaction (Hp-π), which may play an important role in supporting the backbones of protein loops. By conducting the potential energy surface scanning calculations on the quasi π-plane of peptide bond unit, we have observed the following intriguing phenomena: (1) when the polar hydrogen atom of a peptide unit is perpendicularly pointing to the π-plane of other peptide bond units, a remarkable Hp-π interaction occurs; (2) the interaction is distance and orientation dependent, acting in a broad space, and belonging to the 'point-to-plane' one. The molecular force reported here may provide useful interaction concepts and insights into better understanding the loop's unique stability and flexibility feature, as well as the driving force of the protein global folding.

Genome sequence of type strain Paenibacillus polymyxa DSM 365, a highly efficient producer of optically active (R,R)-2,3-butanediol.

Paenibacillus polymyxa DSM 365, an efficient producer of (R,R)-2,3-butanediol, is known to show the highest production titer and productivity reported to date. Here, the first draft genome sequence of this promising strain may provide the genetic basis for further insights into the molecular mechanisms underlying the production of (R,R)-2,3-butanediol with high optical purity and at a high titer. It will also facilitate the design of rational strategies for further strain improvements, as well as construction of artificial biosynthetic pathways through synthetic biology for asymmetric synthesis of chiral 2,3-butanediol or acetoin in common microbial hosts.

Genome Sequence of Tumebacillus flagellatus GST4, the First Genome Sequence of a Species in the Genus Tumebacillus.

We present here the first genome sequence of a species in the genus Tumebacillus. The draft genome sequence of Tumebacillus flagellatus GST4 provides a genetic basis for future studies addressing the origins, evolution, and ecological role of Tumebacillus organisms, as well as a source of acid-resistant amylase-encoding genes for further studies.

In depth analysis on the binding sites of adamantane derivatives in HCV (hepatitis C virus) p7 channel based on the NMR structure.

BACKGROUND: The recently solved solution structure of HCV (hepatitis C virus) p7 ion channel provides a solid structure basis for drug design against HCV infection. In the p7 channel the ligand amantadine (or rimantadine) was determined in a hydrophobic pocket. However the pharmocophore (-NH2) of the ligand was not assigned a specific binding site. RESULTS: The possible binding sites for amino group of adamantane derivatives is studied based on the NMR structure of p7 channel using QM calculation and molecular modeling. In the hydrophobic cavity and nearby three possible binding sites are proposed: His17, Phe20, and Trp21. The ligand binding energies at the three binding sites are studied using high level QM method CCSD(T)/6-311+G(d,p) and AutoDock calculations, and the interaction details are analyzed. The potential application of the binding sites for rational inhibitor design are discussed. CONCLUSIONS: Some useful viewpoints are concluded as follows. (1) The amino group (-NH2) of adamantane derivatives is protonated (-NH3+), and the positively charged cation may form cation-π interactions with aromatic amino acids. (2) The aromatic amino acids (His17, Phe20, and Trp21) are the possible binding sites for the protonated amino group (-NH3+) of adamantane derivatives, and the cation-π bond energies are 3 to 5 times stronger than the energies of common hydrogen bonds. (3) The higher inhibition potent of rimantadine than amantadine probably because of its higher pKa value (pKa = 10.40) and the higher positive charge in the amino group. The potential application of p7 channel structure for inhibitor design is discussed.

Unconventional interaction forces in protein and protein-ligand systems and their impacts to drug design.

In drug design and enzyme engineering, the information of interactions between receptors and ligands is crucially important. In many cases, the protein structures and drug-target complex structures are determined by a delicate balance of several weak molecular interaction types. Among these interaction forces several unconventional interactions play important roles, however, less familiar for researchers. The cation-π interaction is a unique noncovalent interaction only acting between aromatic amino acids and organic cations (protonated amino acids) and inorganic cations (proton and metallic). This article reports new study results in the interaction strength, the behaviors and the structural characters of cation-π interactions between aromatic amino acids (Phe, Tyr, and Trp) and organic and inorganic cations (Lys(+), Arg(+), H(+), H3O(+), Li(+), Na(+), K(+), Ca(2+), and Zn(2+)) in gas phase and in solutions (water, acetonitrile, and cyclohexane). Systematical research revealed that the cation-π interactions are point-to-plane (aromatic group) interactions, distance and orientationdependent, and the interaction energies change in a broad range. In gas phase the cation-π interaction energies between aromatic amino acids (Phe, Tyr, and Trp) and metallic cations (Li(+), Na(+), K(+), Ca(2+), and Zn(2+)) are in the range -12 to -160 kcal/mol, and the interaction energies of protonated amino acids (Arg(+) and Lys(+)) are in the range from -9 to -18 kcal/mol. In solutions the cation-π energies decrease with the dielectric constant ε of solvents. However, in aqueous solution the cation-π energies of H3O(+) and protonated amino acids are less affected by solvation effects. The applications of unconventional interaction forces in drug design and in protein engineering are introduced.

Theoretical study on the polar hydrogen-π (Hp-π) interactions between protein side chains.

BACKGROUND: In the study of biomolecular structures and interactions the polar hydrogen-π bonds (Hp-π) are an extensive molecular interaction type. In proteins 11 of 20 natural amino acids and in DNA (or RNA) all four nucleic acids are involved in this type interaction. RESULTS: The Hp-π in proteins are studied using high level QM method CCSD/6-311 + G(d,p) + H-Bq (ghost hydrogen basis functions) in vacuum and in solutions (water, acetonitrile, and cyclohexane). Three quantum chemical methods (B3LYP, CCSD, and CCSD(T)) and three basis sets (6-311 + G(d,p), TZVP, and cc-pVTZ) are compared. The Hp-π donors include R2NH, RNH2, ROH, and C6H5OH; and the acceptors are aromatic amino acids, peptide bond unit, and small conjugate π-groups. The Hp-π interaction energies of four amino acid pairs (Ser-Phe, Lys-Phe, His-Phe, and Tyr-Phe) are quantitatively calculated. CONCLUSIONS: Five conclusion points are abstracted from the calculation results. (1) The common DFT method B3LYP fails in describing the Hp-π interactions. On the other hand, CCSD/6-311 + G(d,p) plus ghost atom H-Bq can yield better results, very close to the state-of-the-art method CCSD(T)/cc-pVTZ. (2) The Hp-π interactions are point to π-plane interactions, possessing much more interaction conformations and broader energy range than other interaction types, such as common hydrogen bond and electrostatic interactions. (3) In proteins the Hp-π interaction energies are in the range 10 to 30 kJ/mol, comparable or even larger than common hydrogen bond interactions. (4) The bond length of Hp-π interactions are in the region from 2.30 to 3.00 Å at the perpendicular direction to the π-plane, much longer than the common hydrogen bonds (~1.9 Å). (5) Like common hydrogen bond interactions, the Hp-π interactions are less affected by solvation effects.

The multiple roles of histidine in protein interactions.

BACKGROUND: Among the 20 natural amino acids histidine is the most active and versatile member that plays the multiple roles in protein interactions, often the key residue in enzyme catalytic reactions. A theoretical and comprehensive study on the structural features and interaction properties of histidine is certainly helpful. RESULTS: Four interaction types of histidine are quantitatively calculated, including: (1) Cation-π interactions, in which the histidine acts as the aromatic π-motif in neutral form (His), or plays the cation role in protonated form (His+); (2) π-π stacking interactions between histidine and other aromatic amino acids; (3) Hydrogen-π interactions between histidine and other aromatic amino acids; (4) Coordinate interactions between histidine and metallic cations. The energies of π-π stacking interactions and hydrogen-π interactions are calculated using CCSD/6-31+G(d,p). The energies of cation-π interactions and coordinate interactions are calculated using B3LYP/6-31+G(d,p) method and adjusted by empirical method for dispersion energy. CONCLUSIONS: The coordinate interactions between histidine and metallic cations are the strongest one acting in broad range, followed by the cation-π, hydrogen-π, and π-π stacking interactions. When the histidine is in neutral form, the cation-π interactions are attractive; when it is protonated (His+), the interactions turn to repulsive. The two protonation forms (and pKa values) of histidine are reversibly switched by the attractive and repulsive cation-π interactions. In proteins the π-π stacking interaction between neutral histidine and aromatic amino acids (Phe, Tyr, Trp) are in the range from -3.0 to -4.0 kcal/mol, significantly larger than the van der Waals energies.