Coevolutionary Information Captures Catalytic Functions and Reveals Divergent Roles of Terpene Synthase Interdomain Connections

Inferring the historical and biophysical causes of diversity within protein families is a complex puzzle. A key to unraveling this problem is characterizing the rugged topography of sequence-function adaptive landscapes. Using biochemical data from a 29 = 512 combinatorial library of tobacco 5-epi-aristolochene synthase (TEAS) mutants engineered to make the native major product of Egyptian henbane premnaspirodiene synthase (HPS) and a complementary 512 mutant HPS library, we address the question of how product specificity is controlled. These data sets reveal that HPS is far more robust and resistant to mutations than TEAS, where most mutants are promiscuous. We also combine experimental data with a sequence Potts Hamiltonian model and direct coupling analysis to quantify mutant fitness. Our results demonstrate that the Hamiltonian captures variation in product outputs across both libraries, clusters native family members based on their substrate specificities, and exposes the divergent catalytic roles of couplings between the catalytic and noncatalytic domains of TEAS versus HPS. Specifically, we found that the role of the interdomain connectivities in specifying product output is more important in TEAS than connectivities within the catalytic domain. Despite being 75% identical, this property is not shared by HPS, where connectivities within the catalytic domain are more important for specificity. By solving the X-ray crystal structure of HPS, we assessed structural bases for their interdomain network differences. Last, we calculate the product profile Shannon entropies of the two libraries, which showcases that site-site connectivities also play divergent roles in catalytic accuracy.

Comparative transcriptome and metabolome analyses of four Panax species explore the dynamics of metabolite biosynthesis

Background

The genus Panax in the Araliaceae family has been used as traditional medicinal plants worldwide and is known to biosynthesize ginsenosides and phytosterols. However, genetic variation between Panax species has influenced their biosynthetic pathways is not fully understood.

Methods

Simultaneous analysis of transcriptomes and metabolomes obtained from adventitious roots of two tetraploid species (Panax ginseng and P. quinquefolius) and two diploid species (P. notoginseng and P. vietnamensis) revealed the diversity of their metabolites and related gene expression profiles.

Results

The transcriptome analysis showed that 2,3-OXIDOSQUALENE CYCLASEs (OSCs) involved in phytosterol biosynthesis are upregulated in the diploid species, while the expression of OSCs contributing to ginsenoside biosynthesis is higher in the tetraploid species. In agreement with these results, the contents of dammarenediol-type ginsenosides were higher in the tetraploid species relative to the diploid species.

Conclusion

These results suggest that a whole-genome duplication event has influenced the triterpene biosynthesis pathway in tetraploid Panax species during their evolution or ecological adaptation. This study provides a basis for further efforts to explore the genetic variation of the Panax genus.

High-throughput discovery of plastid genes causing albino phenotypes in ornamental chimeric plants

Chimeric plants composed of green and albino tissues have great ornamental value. To unveil the functional genes responsible for albino phenotypes in chimeric plants, we inspected the complete plastid genomes (plastomes) in green and albino leaf tissues from 23 ornamental chimeric plants belonging to 20 species, including monocots, dicots, and gymnosperms. In nine chimeric plants, plastomes were identical between green and albino tissues. Meanwhile, another 14 chimeric plants were heteroplasmic, showing a mutation between green and albino tissues. We identified 14 different point mutations in eight functional plastid genes related to plastid-encoded RNA polymerase (rpo) or photosystems which caused albinism in the chimeric plants. Among them, 12 were deleterious mutations in the target genes, in which early termination appeared due to small deletion-mediated frameshift or single nucleotide substitution. Another was single nucleotide substitution in an intron of the ycf3 and the other was a missense mutation in coding region of the rpoC2 gene. We inspected chlorophyll structure, protein functional model of the rpoC2, and expression levels of the related genes in green and albino tissues of Reynoutria japonica. A single amino acid change, histidine-to-proline substitution, in the rpoC2 protein may destabilize the peripheral helix of plastid-encoded RNA polymerase, impairing the biosynthesis of the photosynthesis system in the albino tissue of R. japonica chimera plant.

Complete chloroplast genome of Gypsophila oldhamiana Miq. (Caryophyllales: Caryophyllaceae)

The complete chloroplast genome sequence of Gypsophila oldhamiana Miq., a species of the Caryophyllaceae family, was assembled and analyzed from the de novo assembly of Illumina paired-end sequencing data. The total length of the chloroplast genome of G. oldhamiana was 152,675 bp including a large single-copy (LSC) region of 83,552 bp, a small single-copy (SSC) region of 17,349 bp, and a pair of identical inverted repeat regions (IRs) of 25,887 bp. The genome possessed a total of 130 genes, including 85 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The phylogenetic analysis of G. oldhamiana with 14 related species discovered the closest taxonomical relationship with Gypsophila vaccaria voucher in the Caryophyllaceae family.

RNA editing may stabilize membrane-embedded proteins by increasing phydrophobicity: A study of Zanthoxylum piperitum and Z. schinifolium chloroplast NdhG

Most chloroplast genes in Zanthoxylum schinifolium (Korean pepper) and Z. piperitum (Japanese pepper) are subject to neutral or purifying selection (Ka/Ks values < 1); however, NAD(P)H dehydrogenase subunit G (ndhG) has a Ka/Ks value of 1.43, which may indicate positive selection. Here, we modeled the ZsNdhG and ZpNdhG structures by comparing them with the NuoJ subunit of respiratory complex I in Escherichia coli, revealing the locations of four amino acid differences between ZsNdhG and ZpNdhG. As these polymorphisms were located at the end of a membrane-spanning α-helix or in peptide loops external to the membrane, they are not expected to have major effects on the membrane-embedding properties of these proteins. However, we found that C-to-U RNA editing occurred at the ndhG-50 sites of ndhG (uCa to uUa, Ser to Leu) in both species, resulting in changes to an amino acid located in the middle of a membrane-spanning α-helix, which may maintain its hydrophobicity. RNA editing at the ndhG-50 site was conserved in many plant species, and the modeled structures of Anthoceros formosae NdhG and Spirodela polyrhiza NdhB provided further evidence that RNA editing increases the hydrophobicity of membrane-embedded proteins. We also speculate that the polar residues inside membrane-spanning α-helices serve to support the protein structure. This report represents the first RNA-editing site identified in Zanthoxylum and points to the importance of considering RNA editing when identifying positively selected genes based on Ka/Ks values.

Genome and evolution of the shade-requiring medicinal herb Panax ginseng

Panax ginseng C. A. Meyer, reputed as the king of medicinal herbs, has slow growth, long generation time, low seed production and complicated genome structure that hamper its study. Here, we unveil the genomic architecture of tetraploid P. ginseng by de novo genome assembly, representing 2.98 Gbp with 59 352 annotated genes. Resequencing data indicated that diploid Panax species diverged in association with global warming in Southern Asia, and two North American species evolved via two intercontinental migrations. Two whole genome duplications (WGD) occurred in the family Araliaceae (including Panax) after divergence with the Apiaceae, the more recent one contributing to the ability of P. ginseng to overwinter, enabling it to spread broadly through the Northern Hemisphere. Functional and evolutionary analyses suggest that production of pharmacologically important dammarane-type ginsenosides originated in Panax and are produced largely in shoot tissues and transported to roots; that newly evolved P. ginseng fatty acid desaturases increase freezing tolerance; and that unprecedented retention of chlorophyll a/b binding protein genes enables efficient photosynthesis under low light. A genome-scale metabolic network provides a holistic view of Panax ginsenoside biosynthesis. This study provides valuable resources for improving medicinal values of ginseng either through genomics-assisted breeding or metabolic engineering.

The complete chloroplast genome sequence of Korean Lonicera japonica and intra-species diversity

Lonicera japonica is a traditional medicinal plant well known for its anti-inflammatory effect. The complete chloroplast genome sequence of L. japonica collected from Korea was obtained by de novo assembly using whole genome sequence data. The chloroplast genome is 155,060 bp in length, containing 88,853 bp in a large single copy (LSC), 18,653 bp in a small single copy (SSC) and 23,777 bp in a pair of inverted repeats (IRs). A total of 112 genes including 78 protein-coding genes and 34 structural RNA genes were identified. The sequence comparison of two L. japonica collected from Korea and China revealed 48 single nucleotide polymorphisms (SNPs) and 45 insertions/deletions (InDels). In addition, phylogenetic analysis represented intraspecific diversity within L. japonica species collected in Korea and China.

Identification of candidate UDP-glycosyltransferases involved in protopanaxadiol-type ginsenoside biosynthesis in Panax ginseng

Ginsenosides are dammarane-type or triterpenoidal saponins that contribute to the various pharmacological activities of the medicinal herb Panax ginseng. The putative biosynthetic pathway for ginsenoside biosynthesis is known in P. ginseng, as are some of the transcripts and enzyme-encoding genes. However, few genes related to the UDP-glycosyltransferases (UGTs), enzymes that mediate glycosylation processes in final saponin biosynthesis, have been identified. Here, we generated three replicated Illumina RNA-Seq datasets from the adventitious roots of P. ginseng cultivar Cheongsun (CS) after 0, 12, 24, and 48 h of treatment with methyl jasmonate (MeJA). Using the same CS cultivar, metabolomic data were also generated at 0 h and every 12-24 h thereafter until 120 h of MeJA treatment. Differential gene expression, phylogenetic analysis, and metabolic profiling were used to identify candidate UGTs. Eleven candidate UGTs likely to be involved in ginsenoside glycosylation were identified. Eight of these were considered novel UGTs, newly identified in this study, and three were matched to previously characterized UGTs in P. ginseng. Phylogenetic analysis further asserted their association with ginsenoside biosynthesis. Additionally, metabolomic analysis revealed that the newly identified UGTs might be involved in the elongation of glycosyl chains of ginsenosides, especially of protopanaxadiol (PPD)-type ginsenosides.

Authentication of Zanthoxylum Species Based on Integrated Analysis of Complete Chloroplast Genome Sequences and Metabolite Profiles

We performed chloroplast genome sequencing and comparative analysis of two Rutaceae species, Zanthoxylum schinifolium (Korean pepper tree) and Z. piperitum (Japanese pepper tree), which are medicinal and culinary crops in Asia. We identified more than 837 single nucleotide polymorphisms and 103 insertions/deletions (InDels) based on a comparison of the two chloroplast genomes and developed seven DNA markers derived from five tandem repeats and two InDel variations that discriminated between Korean Zanthoxylum species. Metabolite profile analysis pointed to three metabolic groups, one with Korean Z. piperitum samples, one with Korean Z. schinifolium samples, and the last containing all the tested Chinese Zanthoxylum species samples, which are considered to be Z. bungeanum based on our results. Two markers were capable of distinguishing among these three groups. The chloroplast genome sequences identified in this study represent a valuable genomics resource for exploring diversity in Rutaceae, and the molecular markers will be useful for authenticating dried Zanthoxylum berries in the marketplace.

Integrated Transcriptomic and Metabolomic Analysis of Five Panax ginseng Cultivars Reveals the Dynamics of Ginsenoside Biosynthesis

Panax ginseng C.A. Meyer is a traditional medicinal herb that produces bioactive compounds such as ginsenosides. Here, we investigated the diversity of ginsenosides and related genes among five genetically fixed inbred ginseng cultivars (Chunpoong [CP], Cheongsun [CS], Gopoong [GO], Sunhyang [SH], and Sunun [SU]). To focus on the genetic diversity related to ginsenoside biosynthesis, we utilized in vitro cultured adventitious roots from the five cultivars grown under controlled environmental conditions. PCA loading plots based on secondary metabolite composition classified the five cultivars into three groups. We selected three cultivars (CS, SH, and SU) to represent the three groups and conducted further transcriptome and gas chromatography-mass spectrometry analyses to identify genes and intermediates corresponding to the variation in ginsenosides among cultivars. We quantified ginsenoside contents from the three cultivars. SH had more than 12 times the total ginsenoside content of CS, with especially large differences in the levels of panaxadiol-type ginsenosides. The expression levels of genes encoding squalene epoxidase (SQE) and dammarenediol synthase (DDS) were also significantly lower in CS than SH and SU, which is consistent with the low levels of ginsenoside produced in this cultivar. Methyl jasmonate (MeJA) treatment increased the levels of panaxadiol-type ginsenosides up to 4-, 13-, and 31-fold in SH, SU, and CS, respectively. MeJA treatment also greatly increased the quantity of major intermediates and the expression of the underlying genes in the ginsenoside biosynthesis pathway; these intermediates included squalene, 2,3-oxidosqualene, and dammarenediol II, especially in CS, which had the lowest ginsenoside content under normal culture conditions. We conclude that SQE and DDS are the most important genetic factors for ginsenoside biosynthesis with diversity among ginseng cultivars.

Ethanol and/or radiofrequency ablation to treat venolymphatic malformations that manifest as a bulging mass in the head and neck

AIM

To evaluate the efficacy of ultrasound (US)-guided ethanol ablation (EA) and radiofrequency ablation (RFA) for treating venolymphatic malformations (VLM) of the head and neck.

MATERIALS AND METHODS

US-guided EA and/or RFA were performed on 17 patients with VLM of the head and neck. Computed tomography (CT) or magnetic resonance imaging (MRI) was used to locate the cranial nerves and salivary gland ducts that were close to targets, and these were avoided during the procedures. Treatment response was assessed using volume reduction and cosmetic grading scoring.

RESULTS

Nine VLMs were located close to the functional structures: Stensen's duct (n=3), cranial nerve branch (n=3), or both (n=3). All patients demonstrated >50% volume reduction, except one patient with a microcystic lymphatic malformation that was abutting the facial nerve. Median cosmetic grading scores improved from 4 to 1 (p<0.001).

CONCLUSION

US-guided EA and/or RFA are effective and safe treatment methods in patients with VLMs of the head and neck. Treatment selection of EA and/or RFA could be performed based on the composition of VLMs as assessed at CT and MRI.

Formation of a Novel Macrocyclic Alkaloid from the Unnatural Farnesyl Diphosphate Analogue Anilinogeranyl Diphosphate by 5-Epi-Aristolochene Synthase

As part of an effort to identify substrate analogs suitable for helping to resolve structural features important for terpene synthases, the inhibition of 5-epi-aristolochene biosynthesis from farnesyl diphosphate (FPP) by the tobacco 5-epi-aristolochene synthase incubated with anilinogeranyl diphosphate (AGPP) was examined. The apparent noncompetitive nature of the inhibition supported further assessment of how AGPP might be bound to crystallographic forms of the enzyme. Surprisingly, the bound form of the inhibitor appeared to have undergone a cyclization event consistent with the native mechanism associated with FPP catalysis. Biocatalytic formation of a novel 13-membered macrocyclic paracyclophane alkaloid was confirmed by high-resolution GC-MS and NMR analysis. This work provides insights into new biosynthetic means for generating novel, functionally diversified, medium-sized terpene alkaloids.

Tobacco class I cytosolic small heat shock proteins are under transcriptional and translational regulations in expression and heterocomplex prevails under the high-temperature stress condition in vitro

Seven genomic clones of tobacco (Nicotiana tabacum W38) cytosolic class I small heat shock proteins (sHSPs), probably representing all members in the class, were isolated and found to have 66 to 92% homology between their nucleotide sequences. Even though all seven sHSP genes showed heat shock-responsive accumulation of their transcripts and proteins, each member showed discrepancies in abundance and timing of expression upon high-temperature stress. This was mainly the result of transcriptional regulation during mild stress conditions and transcriptional and translational regulation during strong stress conditions. Open reading frames (ORFs) of these genomic clones were expressed in Escherichia coli and the sHSPs were purified from E. coli. The purified tobacco sHSPs rendered citrate synthase and luciferase soluble under high temperatures. At room temperature, non-denaturing pore exclusion polyacrylamide gel electrophoresis on three sHSPs demonstrated that the sHSPs spontaneously formed homo-oligomeric complexes of 200 ∼ 240 kDa. However, under elevated temperatures, hetero-oligomeric complexes between the sHSPs gradually prevailed. Atomic force microscopy showed that the hetero-oligomer of NtHSP18.2/NtHSP18.3 formed a stable oligomeric particle similar to that of the NtHSP18.2 homo-oligomer. These hetero-oligomers positively influenced the revival of thermally inactivated luciferase. Amino acid residues mainly in the N-terminus are suggested for the exchange of the component sHSPs and the formation of dominant hetero-oligomers under high temperatures.

Small heat shock proteins can release light dependence of tobacco seed during germination

Small heat shock proteins (sHSPs) function as ATP-independent molecular chaperones, and although the production and function of sHSPs have often been described under heat stress, the expression and function of sHSPs in fundamental developmental processes, such as pollen and seed development, have also been confirmed. Seed germination involves the breaking of dormancy and the resumption of embryo growth that accompany global changes in transcription, translation, and metabolism. In many plants, germination is triggered simply by imbibition of water; however, different seeds require different conditions in addition to water. For small-seeded plants, like Arabidopsis (Arabidopsis thaliana), lettuce (Lactuca sativa), tomato (Solanum lycopersicum), and tobacco (Nicotiana tabacum), light is an important regulator of seed germination. The facts that sHSPs accumulate during seed development, sHSPs interact with various client proteins, and seed germination accompanies synthesis and/or activation of diverse proteins led us to investigate the role of sHSPs in seed germination, especially in the context of light dependence. In this study, we have built transgenic tobacco plants that ectopically express sHSP, and the effect was germination of the seeds in the dark. Administering heat shock to the seeds also resulted in the alleviation of light dependence during seed germination. Subcellular localization of ectopically expressed sHSP was mainly observed in the cytoplasm, whereas heat shock-induced sHSPs were transported to the nucleus. We hypothesize that ectopically expressed sHSPs in the cytoplasm led the status of cytoplasmic proteins involved in seed germination to function during germination without additional stimulus and that heat shock can be another signal that induces seed germination.

Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

BACKGROUND

Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric.

RESULTS

In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols.

CONCLUSION

A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific transcription factors and other regulatory genes were found that were common to the two species and that are excellent candidates for involvement in rhizome growth, differentiation and development. Large classes of enzymes involved in specialized metabolism were also found to have apparent tissue-specific expression, suggesting that gene expression itself may play an important role in regulating metabolite production in these plants.

Suites of terpene synthases explain differential terpenoid production in ginger and turmeric tissues

The essential oils of ginger (Zingiber officinale) and turmeric (Curcuma longa) contain a large variety of terpenoids, some of which possess anticancer, antiulcer, and antioxidant properties. Despite their importance, only four terpene synthases have been identified from the Zingiberaceae family: (+)-germacrene D synthase and (S)-β-bisabolene synthase from ginger rhizome, and α-humulene synthase and β-eudesmol synthase from shampoo ginger (Zingiber zerumbet) rhizome. We report the identification of 25 mono- and 18 sesquiterpene synthases from ginger and turmeric, with 13 and 11, respectively, being functionally characterized. Novel terpene synthases, (-)-caryolan-1-ol synthase and α-zingiberene/β-sesquiphellandrene synthase, which is responsible for formation of the major sesquiterpenoids in ginger and turmeric rhizomes, were also discovered. These suites of enzymes are responsible for formation of the majority of the terpenoids present in these two plants. Structures of several were modeled, and a comparison of sets of paralogs suggests how the terpene synthases in ginger and turmeric evolved. The most abundant and most important sesquiterpenoids in turmeric rhizomes, (+)-α-turmerone and (+)-β-turmerone, are produced from (-)-α-zingiberene and (-)-β-sesquiphellandrene, respectively, via α-zingiberene/β-sesquiphellandrene oxidase and a still unidentified dehydrogenase.

Tobacco mitochondrial small heat shock protein NtHSP24.6 adopts a dimeric configuration and has a broad range of substrates

There is a broad range of different small heat shock proteins (sHSPs) that have diverse structural and functional characteristics. To better understand the functional role of mitochondrial sHSP, NtHSP24.6 was expressed in Escherichia coli with a hexahistidine tag and purified. The protein was analyzed by non-denaturing PAGE, chemical cross-linking and size exclusion chromatography and the H6NtHSP24.6 protein was found to form a dimer in solution. The in vitro functional analysis of H6NtHSP24.6 using firefly luciferase and citrate synthase demonstrated that this protein displays typical molecular chaperone activity. When cell lysates of E. coli were heated after the addition of H6NtHSP24.6, a broad range of proteins from 10 to 160 kD in size remained in the soluble state. These results suggest that NtHSP24.6 forms a dimer and can function as a molecular chaperone to protect a diverse range of proteins from thermal aggregation.

Metabolic profiling and phylogenetic analysis of medicinal Zingiber species: Tools for authentication of ginger (Zingiber officinale Rosc)

Phylogenetic analysis and metabolic profiling were used to investigate the diversity of plant material within the ginger species and between ginger and closely related species in the genus Zingiber (Zingiberaceae). In addition, anti-inflammatory data were obtained for the investigated species. Phylogenetic analysis demonstrated that all Zingiber officinale samples from different geographical origins were genetically indistinguishable. In contrast, other Zingiber species were significantly divergent, allowing all species to be clearly distinguished using this analysis. In the metabolic profiling analysis, the Z. officinale samples derived from different origins showed no qualitative differences in major volatile compounds, although they did show some significant quantitative differences in non-volatile composition, particularly regarding the content of [6]-, [8]-, and [10]-gingerols, the most active anti-inflammatory components in this species. The differences in gingerol content were verified by HPLC. The metabolic profiles of other Zingiber species were very different, both qualitatively and quantitatively, when compared to Z. officinale and to each other. Comparative DNA sequence/chemotaxonomic phylogenetic trees showed that the chemical characters of the investigated species were able to generate essentially the same phylogenetic relationships as the DNA sequences. This supports the contention that chemical characters can be used effectively to identify relationships between plant species. Anti-inflammatory in vitro assays to evaluate the ability of all extracts from the Zingiber species examined to inhibit LPS-induced PGE(2) and TNF-alpha production suggested that bioactivity may not be easily predicted by either phylogenetic analysis or gross metabolic profiling. Therefore, identification and quantification of the actual bioactive compounds are required to guarantee the bioactivity of a particular Zingiber sample even after performing authentication by molecular and/or chemical markers.

Magnetic superstructures of cupric oxide CuO as ordered arrangements of one-dimensional antiferromagnetic chains

In cupric oxide CuO, each Cu(2+) ion has 12 nearest-neighbor Cu(2+) ions grouped into six pairs related by inversion symmetry. The relative strengths of the Cu-O-Cu superexchange interactions in cupric oxide CuO were estimated by spin dimer analysis to confirm that the strongest superexchange interactions form one-dimensional antiferromagnetic chains along the [101] direction, and the remaining interactions are weak. We analyzed ordered arrangements of these one-dimensional antiferromagnetic chains to examine why the antiferromagnetic phase transition of CuO below 212.5 K adopts a (2a, b, 2c) superstructure. The local spin arrangement around each Cu(2+) ion is more balanced in the ordered spin structures leading to a (2a, b, 2c) supercell than in any other ordered spin structures.

On the Origin of the × Superstructure and the Anomalous Magnetic and Transport Properties of the Layered Compound Sr6V9S22O2

We examined why the 1T-VS(2) layer of the layered compound Sr(6)V(9)S(22)O(2) has the x superstructure in terms of electronic band structure calculations and metal-metal bonding across the shared edges of adjacent VS(6) octahedra. On the basis of this analysis we explored how the anomalous magnetic and transport properties of Sr(6)V(9)S(22)O(2) can be explained. Our work shows that the x superstructure is not caused by a charge density wave instability associated with Fermi surface nesting but by the metal-metal bonding through the shared edges of adjacent VS(6) octahedra. The weak and strong electron localizations observed for Sr(6)V(9)S(22)O(2) were discussed in terms of three-center two-electron and two-center two-electron V-V bonds in the 1T-VS(2) layers.

Spin dimer analysis of the anisotropic spin exchange interactions in the distorted wolframite-type oxides CuWO4, CuMoO4-III, and Cu(Mo(0.25)W0.75)O4

The distorted wolframite-type oxides CuWO4 and CuMoO4-III have a structure in which CuO4 zigzag chains, made up of cis-edge-sharing CuO6 octahedra, run along the c-direction and hence exhibit low-dimensional magnetic properties. We examined the magnetic structures of these compounds and their isostructural analogue Cu(Mo(0.25)W0.75)O4 on the basis of the spin-orbital interaction energies calculated for their spin dimers. Our study shows that these compounds consist of two-dimensional (2D) magnetic sheets defined by one superexchange (intrachain Cu-O-Cu) and three super-superexchange (interchain Cu-O.O-Cu) paths, the strongly interacting spin units of these 2D magnetic sheets are the two-leg antiferromagnetic (AFM) ladder chains running along the (a + c)-direction, and the spin arrangement between adjacent AFM ladder chains leads to spin frustration. The similarities and differences in the magnetic structures of CuWO4, CuMoO4-III, and Cu(Mo(0.25)W0.75)O4 were discussed by examining how adjacent AFM ladder chains are coupled via the superexchange paths in the 2D magnetic sheets and how adjacent 2D magnetic sheets are coupled via another superexchange paths along the c-direction. Our study reproduces the experimental finding that the magnetic unit cell is doubled along the a-axis in CuWO(4) and along the c-axis in CuMoO4-III and predicts that the magnetic unit cell should be doubled along the a- and b-axes in Cu(Mo(0.25)W0.75)O4. In the understanding of the strength of a super-superexchange interaction, the importance of the geometrical factors controlling the overlap between the tails of magnetic orbitals was pointed out.

Long-range magnetic order in Mn[N(CN)2]2(pyz) (pyz = pyrazine). Susceptibility, magnetization, specific heat, and neutron diffraction measurements and electronic structure calculations

Using dc magnetization, ac susceptibility, specific heat, and neutron diffraction, we have studied the magnetic properties of Mn[N(CN)2]2(pyz) (pyz = pyrazine) in detail. The material crystallizes in the monoclinic space group P2(1)/n with a = 7.3248(2), b = 16.7369(4), and c = 8.7905 (2) A, beta = 89.596 (2) degrees, V = 1077.65(7) A(3), and Z = 4, as determined by Rietveld refinement of neutron powder diffraction data at 1.35 K. The 5 K neutron powder diffraction data reflect very little variation in the crystal structure. Interpenetrating ReO3-like networks are formed from axially elongated Mn(2+) octahedra and edges made up of mu-bonded [N(CN)2](-) anions and neutral pyz ligands. A three-dimensional antiferromagnetic ordering occurs below T(N) = 2.53(2) K. The magnetic unit cell is double the nuclear one along the a- and c-axes, giving the (1/2, 0, 1/2) superstructure. The crystallographic and antiferromagnetic structures are commensurate and consist of collinear Mn(2+) moments, each with a magnitude of 4.15(6) mu(B) aligned parallel to the a-direction (Mn-pyz-Mn chains). Electronic structure calculations indicate that the exchange interaction is much stronger along the Mn-pyz-Mn chain axis than along the Mn-NCNCN-Mn axes by a factor of approximately 40, giving rise to a predominantly one-dimensional magnetic system. Thus, the variable-temperature magnetic susceptibility data are well described by a Heisenberg antiferromagnetic chain model, giving g = 2.01(1) and J/k(B) = -0.27(1) K. Owing to single-ion anisotropy of the Mn(2+) ion, field-induced phenomena ascribed to spin-flop and paramagnetic transitions are observed at 0.43 and 2.83 T, respectively.

Effect of the double bond pi-conjugation of the aromatic group of racemic analytes on the liquid chromatographic separation of enantiomers

Various arylcarbinol esters were resolved on a commercial chiral column, (S, S) Whelk-O1. Among others, the analytes in which the aryl group is in conjugation with the double bond(s) to the chiral center were resolved much better on (S, S) Whelk-O1 than the corresponding non-double bonded analytes. From these results, it was proposed that the double bond pi-conjugation of the aromatic group of racemic analytes is very important for the chiral recognition. In addition, the size of the acyl group of arylcarbinol esters has been demonstrated to be important for the chiral recognition. In general, the large acyl group such as pivaloyl group was very effective for the chiral recognition of arylcarbinol esters on (S, S) Whelk-O1.

Ligand influences of the structures of molybdenum oxide networks

The influence of organonitrogen ligands on the network structure of molybdenum oxides was examined by preparing three new molybdenum oxide phases [MoO3(4,4'-bpy)0.5] (MOXI-8), [HxMoO3(4,4'-bpy)0.5] (MOXI-9), and [MoO3(triazole)0.5] (MOXI-32). The structure of [MoO3(4,4'-bpy)0.5) consists of layers of corner-sharing MoO5N octahedra, buttressed by bridging 4,4'-bipyridyl ligands into a three-dimensional covalently bonded organic-inorganic composite material. Partial reduction of [MoO3(4,4'-bpy)0.5] yields the mixed-valence material [HxMoO3(4,4'-bpy)0.5] (x approximately 0.5). The most apparent structural change upon reduction is found in the Mo-ligand bond lengths of the MoO5N octahedra, which exhibit the usual (2 + 2 + 2) pattern in [MoO3(4,4'-bpy)0.5] and a more regular (5 + 1) pattern in [HxMoO3(4,4'-bpy)0.5]. Substitution of triazole for 4,4'-bipyridine yields [MoO3(triazole)0.5], which retains the layer motif of corner-sharing MoO5N octahedra but with distinct sinusoidal ruffling in contrast to planar layers of [MoO3(4,4'-bpy)0.5] and [HxMoO3(4,4'-bpy)0.5]. The folding reflects the ligand constraints imposed by the triazole ligand that bridges adjacent Mo sites within a layer. MOXI-8, C5H4NMoO3: monoclinic P2(1)/c, a = 7.5727(6) A, b = 7.3675(7) A, c = 22.433(3) A, beta = 90.396(8) degrees, Z = 8. MOXI-9, C5H4.5NMoO3: monoclinic I2/m, a = 5.2644(4) A, b = 5.2642(4) A, c = 22.730(2) A, beta = 90.035(1) degrees, Z = 4. MOXI-32, C2H3N3Mo2O6: orthorhombic Pbcm, a = 3.9289(5) A, b = 13.850(2) A, c = 13.366(2) A, Z = 4.

Synthesis and crystal structure determination of a new pressure-induced iridium ditelluride phase, m-IrTe2, and comparison of the crystal structures and relative stabilities of various IrTe2 polymorphs

The new monoclinic IrTe2 phase m-IrTe2 was synthesized under pressure, and its structure was determined by X-ray powder diffraction. The relative stabilities of the three known and three hypothetical IrTe2 polymorphs were discussed on the basis of tight binding electronic band structure calculations. m-IrTe2 exhibits structural features of both CdI2- and pyrite-type IrTe2 phases and is expected to be nearly as stable as that of the CdI2-type IrTe2. The hypothetical IrS2- and ramsdellite-type IrTe2 phases are predicted to be more stable than the CdI2-type IrTe2.

Analysis of the spin exchange interactions in the three phases of vanadium pyrophosphate, (VO)2P2O7, in terms of spin-orbital interaction energy

The spin exchange interactions in the ambient-pressure orthorhombic (APO), high-pressure orthorhombic (HPO), and ambient-pressure monoclinic (APM) phases of the vanadium pyrophosphate, (VO)2P2O7, were analyzed by calculating the spin-orbital interaction energies delta e-delta e0 of their spin dimers. The anisotropy of the spin exchange interactions in the HPO phase is well explained by the delta e-delta e0 values. For the APO phase, the reported crystal structure does not provide accurate enough delta e-delta e0 values to conclude unambiguously which of the V1-V2 and V3-V4 chains has a larger spin gap and which of the bridged and edge-sharing spin dimers has a stronger spin exchange interaction in the V1-V2 and V3-V4 chains. The APM phase is predicted to exhibit essentially two spin gaps, with a large spin gap for the V8-V5-V7-V6 chain and a very small one for the V4-V2-V3-V1 chain.