BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. We observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

Targeted whole exome sequencing and Drosophila modelling to unveil the molecular basis of primary ovarian insufficiency

STUDY QUESTION

Can a targeted whole exome sequencing (WES) on a cohort of women showing a primary ovarian insufficiency (POI) phenotype at a young age, combined with a study of copy number variations, identify variants in candidate genes confirming their deleterious effect on ovarian function?

SUMMARY ANSWER

This integrated approach has proved effective in identifying novel candidate genes unveiling mechanisms involved in POI pathogenesis.

WHAT IS KNOWN ALREADY

POI, a condition occurring in 1% of women under 40 years of age, affects women’s fertility leading to a premature loss of ovarian reserve. The genetic causes of POI are highly heterogeneous and several determinants contributing to its prominent oligogenic inheritance pattern still need to be elucidated.

STUDY DESIGN, SIZE, DURATION

WES screening for pathogenic variants of 41 Italian women with non-syndromic primary and early secondary amenorrhoea occurring before age 25 was replicated on another 60 POI patients, including 35 French and 25 American women, to reveal statistically significant shared variants.

PARTICIPANTS/MATERIALS, SETTING, METHODS

The Italian POI patients’ DNA were processed by targeted WES including 542 RefSeq genes expressed or functioning during distinct reproductive or ovarian processes (e.g. DNA repair, meiosis, oocyte maturation, folliculogenesis and menopause). Extremely rare variants were filtered and selected by means of a Fisher Exact test using several publicly available datasets. A case-control Burden test was applied to highlight the most significant genes using two ad-hoc control female cohorts. To support the obtained data, the identified genes were screened on a novel cohort of 60 Caucasian POI patients and the same case-control analysis was carried out. Comparative analysis of the human identified genes was performed on mouse and Drosophila melanogaster by analysing the orthologous genes in their ovarian phenotype, and two of the selected genes were fruit fly modelled to explore their role in fertility.

MAIN RESULTS AND THE ROLE OF CHANCE

The filtering steps applied to search for extremely rare pathogenic variants in the Italian cohort revealed 64 validated single-nucleotide variants/Indels in 59 genes in 30 out of 41 screened women. Burden test analysis highlighted 13 ovarian genes as being the most enriched and significant. To validate these findings, filtering steps and Burden analysis on the second cohort of Caucasian patients yielded 11 significantly enriched genes. Among them, AFP, DMRT3, MOV10, FYN and MYC were significant in both patient cohorts and hence were considered strong candidates for POI. Mouse and Drosophila comparative analysis evaluated a conserved role through the evolution of several candidates, and functional studies using a Drosophila model, when applicable, supported the conserved role of the MOV10 armitage and DMRT3 dmrt93B orthologues in female fertility.

LARGE SCALE DATA

The datasets for the Italian cohort generated during the current study are publicly available at ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/): accession numbers SCV001364312 to SCV001364375.

LIMITATIONS, REASONS FOR CAUTION

This is a targeted WES analysis hunting variants in candidate genes previously identified by different genomic approaches. For most of the investigated sporadic cases, we could not track the parental inheritance, due to unavailability of the parents’ DNA samples; in addition, we might have overlooked additional rare variants in novel candidate POI genes extracted from the exome data. On the contrary, we might have considered some inherited variants whose clinical significance is uncertain and might not be causative for the patients’ phenotype. Additionally, as regards the Drosophila model, it will be extremely important in the future to have more mutants or RNAi strains available for each candidate gene in order to validate their role in POI pathogenesis.

WIDER IMPLICATIONS OF THE FINDINGS

The genomic, statistical, comparative and functional approaches integrated in our study convincingly support the extremely heterogeneous oligogenic nature of POI, and confirm the maintenance across the evolution of some key genes safeguarding fertility and successful reproduction. Two principal classes of genes were identified: (i) genes primarily involved in meiosis, namely in synaptonemal complex formation, asymmetric division and oocyte maturation and (ii) genes safeguarding cell maintenance (piRNA and DNA repair pathways).

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by Italian Ministry of Health grants ‘Ricerca Corrente’ (08C621_2016 and 08C924_2019) provided to IRCCS Istituto Auxologico Italiano, and by ‘Piano Sostegno alla Ricerca’ (PSR2020_FINELLI_LINEA_B) provided by the University of Milan; M.P.B. was supported by Telethon-Italy (grant number GG14181). There are no conflicts of interest.

High-resolution array-CGH analysis on 46,XX patients affected by early onset primary ovarian insufficiency discloses new genes involved in ovarian function

STUDY QUESTION

Can high resolution array-CGH analysis on a cohort of women showing a primary ovarian insufficiency (POI) phenotype in young age identify copy number variants (CNVs) with a deleterious effect on ovarian function?

SUMMARY ANSWER

This approach has proved effective to clarify the role of CNVs in POI pathogenesis and to better unveil both novel candidate genes and pathogenic mechanisms.

WHAT IS KNOWN ALREADY

POI describes the progression toward the cessation of ovarian function before the age of 40 years. Genetic causes are highly heterogeneous and despite several genes being associated with ovarian failure, most of genetic basis of POI still needs to be elucidated.

STUDY DESIGN, SIZE, DURATION

The current study included 67 46,XX patients with early onset POI (<19 years) and 134 control females recruited between 2012 and 2016 at the Medical Cytogenetics and Molecular Genetics Lab, IRCCS Istituto Auxologico Italiano.

PARTICIPANTS/MATERIALS, SETTING, METHODS

High resolution array-CGH analysis was carried out on POI patients’ DNA. Results of patients and female controls were analyzed to search for rare CNVs. All variants were validated and subjected to a gene content analysis and disease gene prioritization based on the present literature to find out new ovary candidate genes. Case-control study with statistical analysis was carried out to validate our approach and evaluate any ovary CNVs/gene enrichment. Characterization of particular CNVs with molecular and functional studies was performed to assess their pathogenic involvement in POI.

MAIN RESULTS AND THE ROLE OF CHANCE

We identified 37 ovary-related CNVs involving 44 genes with a role in ovary in 32 patients. All except one of the selected CNVs were not observed in the control group. Possible involvement of the CNVs in POI pathogenesis was further corroborated by a case-control analysis that showed a significant enrichment of ovary-related CNVs/genes in patients (P = 0.0132; P = 0.0126). Disease gene prioritization identified both previously reported POI genes (e.g. BMP15, DIAPH2, CPEB1, BNC1) and new candidates supported by transcript and functional studies, such as TP63 with a role in oocyte genomic integrity and VLDLR which is involved in steroidogenesis.

LARGE SCALE DATA

ClinVar database (http://www.ncbi.nlm.nih.gov/clinvar/); accession numbers SCV000787656 to SCV000787743.

LIMITATIONS, REASONS FOR CAUTION

This is a descriptive analysis for almost all of the CNVs identified. Inheritance studies of CNVs in some non-familial sporadic cases was not performed as the parents’ DNA samples were not available. Addionally, RT-qPCR analyses were carried out in few cases as RNA samples were not always available and the genes were not expressed in blood.

WIDER IMPLICATIONS OF THE FINDINGS

Our array-CGH screening turned out to be efficient in identifying different CNVs possibly implicated in disease onset, thus supporting the extremely wide genetic heterogeneity of POI. Since almost 50% of cases are negative rare ovary-related CNVs, array-CGH together with next generation sequencing might represent the most suitable approach to obtain a comprehensive genetic characterization of POI patients.

STUDY FUNDING/COMPETING INTEREST(S)

Supported by Italian Ministry of Health grants ‘Ricerca Corrente’ (08C203_2012) and ‘Ricerca Finalizzata’ (GR-2011-02351636, BIOEFFECT) to IRCCS Istituto Auxologico Italiano.

Electron Density Analysis of Metal Clusters with Semi-Interstitial Main Group Atoms. Chemical Bonding in [Co6X(CO)16]- Species

In this work, we propose a careful and thorough analysis of the chemical bond nature in high nuclearity metal carbonyl clusters having semi-interstitial main group atoms. We investigated the species [Co₆X(CO)₁₆]^- (X = As, P), known for a rather interesting conformational flexibility of the cluster (leading to open or closed cages) and a corresponding polymorphism in the solid state (observed at least for X = As). The factors that trigger the molecular isomerism and the nature of X-Co and Co-Co interactions emerge from theoretical calculations and high resolution X-ray diffraction. Both energy and charge density atomic partitioning (QTAIM, EDA, IQA) are employed for this analysis, with the aim of revealing the stabilizing/destabilizing factors of the interaction between the cage and the semi-interstitial atoms in the various conformations.

Crura augmentation with Bio-A® mesh for laparoscopic repair of hiatal hernia: single-institution experience with 100 consecutive patients

BACKGROUND

The potential utility of both non-absorbable and absorbable meshes to reinforce the esophageal hiatus and prevent recurrent hernia has been investigated in observational studies and a few randomized clinical trials. Use of absorbable mesh has been associated with lesser side-effects, but the long-term safety and effectiveness are still debated. This rather scanty clinical evidence is due to heterogeneity and bias regarding the type of mesh and operation used, the modalities of follow-up, and the reporting of objective results.

OBJECTIVES

The aim of the study was to assess safety, quality of life, and recurrence-free probability after laparoscopic repair of hiatal hernia reinforced with a synthetic absorbable mesh.

METHODS

Observational, retrospective, single-center cohort study. All patients with hiatal hernia who underwent laparoscopic crura repair using a biosynthetic mesh (Gore Bio A^® tissue reinforcement, Flagstaff, AZ) were included. Pre- and post-operative symptoms were assessed with the GERD-HRQL questionnaire. Objective follow-up consisted of upper gastrointestinal endoscopy and barium swallow study.

RESULTS

From September 2011 to March 2016, a total of 100 patients underwent hiatal hernia repair using a Bio-A^® mesh. All surgical procedures were completed laparoscopically. Postoperative morbidity rate was 10%. All patients had a minimum follow-up of 6 months, and the median follow-up was 30 (IQR = 22) months. No mesh-related complications occurred. The incidence of recurrent hernia ≥2 cm was 9%, and eight of the nine patients had a preoperative type III hernia. The median GERD-HRQL score was significantly reduced after operation (p < 0.001). The recurrence-free probability at 1 and 5 years was, respectively, 0.99 (CI 0.97-1.00) and 0.84 (CI 0.74-0.97), and no reoperation was required. No association was found between age, BMI, hernia size, previously failed surgical repairs and hernia recurrence.

CONCLUSIONS

The use of a synthetic absorbable mesh to reinforce the esophageal hiatus is safe and appears to be effective and durable over a medium-term follow-up.

Multiscale Centerline Detection

Finding the centerline and estimating the radius of linear structures is a critical first step in many applications, ranging from road delineation in 2D aerial images to modeling blood vessels, lung bronchi, and dendritic arbors in 3D biomedical image stacks. Existing techniques rely either on filters designed to respond to ideal cylindrical structures or on classification techniques. The former tend to become unreliable when the linear structures are very irregular while the latter often has difficulties distinguishing centerline locations from neighboring ones, thus losing accuracy. We solve this problem by reformulating centerline detection in terms of a regression problem. We first train regressors to return the distances to the closest centerline in scale-space, and we apply them to the input images or volumes. The centerlines and the corresponding scale then correspond to the regressors local maxima, which can be easily identified. We show that our method outperforms state-of-the-art techniques for various 2D and 3D datasets. Moreover, our approach is very generic and also performs well on contour detection. We show an improvement above recent contour detection algorithms on the BSDS500 dataset.

Advances in Poly(4-aminodiphenylaniline) Nanofibers Preparation by Electrospinning Technique

Polyaniline (PANI) nanofibers are drawing a great deal of interest from academia and industry due to their multiple applications, especially in biomedical field. PANI nanofibers were successfully electrospun for the first time by MacDiarmid and co-workers at the beginning of the millennium and since then many efforts have been addressed to improve their quality. However, traditional PANI prepared from aniline monomer shows some drawbacks, such as presence of toxic (i.e., benzidine) and inorganic (salts and metals) co-products, that complicate polymer post-treatment, and low solubility in common organic solvents, making hard its processing by electrospinning technique. Some industrial sectors, such as medical and biomedical, need to employ materials free from toxic and polluting species. In this regard, the oxidative polymerization of N-(4-aminophenyl)aniline, aniline dimer, to produce poly(4-aminodiphenylaniline), P4ADA, a kind of PANI, represents an innovative alternative to the traditional synthesis because the obtained polymer results free from carcinogenic and/or polluting co-products, and, moreover, more soluble than traditional PANI. This latter feature can be exploited to obtain P4ADA nanofibers by electrospinning technique. In this paper we report the advances obtained in the P4ADA nanofibers electrospinnig. A comparison among polyethylene oxide (PEO), polymethyl methacrylate (PMMA) and polystyrene (PS), as the second polymer to facilitate the electrospinning process, is shown. In order to increase the conductivity of P4ADA nanofibers, two strategies were adopted and compared: selective insulating binder removal from electrospun nanofibers by a rinsing tratment, afterwards optimizing the minimum amount of binder necessary for the electrospinning process. Moreover, the effect of PEO/P4ADA weight ratio on the fibers morphology and conductivity was highlighted.

Learning Separable Filters

Learning filters to produce sparse image representations in terms of over-complete dictionaries has emerged as a powerful way to create image features for many different purposes. Unfortunately, these filters are usually both numerous and non-separable, making their use computationally expensive. In this paper, we show that such filters can be computed as linear combinations of a smaller number of separable ones, thus greatly reducing the computational complexity at no cost in terms of performance. This makes filter learning approaches practical even for large images or 3D volumes, and we show that we significantly outperform state-of-the-art methods on the curvilinear structure extraction task, in terms of both accuracy and speed. Moreover, our approach is general and can be used on generic convolutional filter banks to reduce the complexity of the feature extraction step.

[Cu(imidazole)2(CO3)]⋅H2O: an intermediate in the formation of the copper bis-imidazolate polymer (blue phase)

The crystal structure of [Cu(Him)2(CO3)]·H2O, determined from conventional X-ray powder diffraction methods, allowed to clarify, on the basis of a structural interpretation of the chemical transformation, the role of the title compound in the formation of the blue phase of Cu(im)2 [Cu(Him)2(CO3)]·H2O is triclinic, P1̅; a = 8.8565(7), b = 8.9579(5), c = 8.3705(6) Å, α = 105.728(4)°, β = 105.318(3)°, γ = 114.369(4)°; final Rwp , Rp and RF agreement factors, for 4700 data collected in the 11–105° range, are 0.053, 0.036 and 0.078, respectively.

Multicystic peritoneal mesothelioma treated by surgical cytoreduction and hyperthermic intra-peritoneal chemotherapy (HIPEC)

BACKGROUND

Multicystic peritoneal mesothelioma (MPM) is an extremely uncommon lesion with uncertain malignant potential. Multiple recurrences after surgical interventions and transition to aggressive malignancies have been reported. Here, we review our experience with cytoreduction and hyperthermic intraperitoneal chemotherapy (HIPEC) in the management of MPM.

PATIENTS AND METHODS

Five women with MPM underwent 6 procedures of cytoreduction and close-abdomen HIPEC with cisplatin and doxorubicin. Three patients had recurrent disease after 1, 2 and 4 previous debulkings, respectively.

RESULTS

Optimal cytoreduction (residual tumor nodules < or =2.5 mm) was performed in all the procedures. One grade 4 postoperative complication (NCI/CTCAE v.3.0) and no operative mortality occurred. Median follow-up was 31 months (range 3-102). MPM recurred in two patients: one is presently disease-free after a second cytoreduction with HIPEC and the other is alive with minimal stable disease.

CONCLUSION

Definitive eradication by means of cytoreduction and HIPEC seems a safe and effective therapeutic option for MPM.

Improving the quality of diamond anvil cell data collected on an area detector by shading individual diamond overlaps

Crystallographic data collected on a CCD using a diamond anvil cell may present overlapping diamond and sample reflections. These false intensities may not be rejected by common data processing programs and may affect the finalhkllist. A utility was developed that shades these reflections during the integration, enabling their elimination before the solution or refinement. Moreover, this procedure avoids the error propagation to other reflections, caused by overlapping spots, through the profile fitting procedure of an integration run.

High-speed gas chromatography with direct resistively-heated column (ultra fast module-GC)-separation measure (S) and other chromatographic parameters under different analysis conditions for samples of different complexities and volatilities

The influence of GC speed on the separation capability of a chromatographic system is reported measuring a series of parameters including separation measure (S), peak capacity (n), peak width (w), analysis time, t(b) (determined on the last eluting compound) and separation measure/analysis time ratio (S/t(b)) determined by analyzing a bergamot essential oil sample and a standard mixture of pesticides. Conventional GC, fast GC (with 10 m (FGC10) and 5 m (FGC5) narrow-bore columns), and direct resistively-heated ultra fast module-GC (UFM-GC) were the GC speed approaches used. The influence of different heating rates with a constant flow for FGC5, FGC 10, and UFM-GC and with variable flows for UFM-GC on S, n, w, S/t(b), and t(b) was also studied. The results of this study show that: (a) separation capability of the chromatographic system (i.e. S and n) and analysis time depend on the GC approaches. Within each GC approach, S and n and analysis time depend on the heating rates, although to a different extent, and S and n decrease much less than the gain in analysis time, in particular when fast heating rates are applied; (b) in UFM-GC, the loss of separation capability with heating rate can also be partially compensated by the choice of an appropriate flow rate that, within each heating rate, may contribute to increase S while reducing t(b); (c) within a specific GC approach, the chromatographic system (column and stationary phase) and conditions (heating and flow rates) must be such to achieve a suitable S-value when two analytes must be separated with a given resolution in a minimum analysis time.

Reversible displacive phase transition in [Ni(en)3]2+(NO3−)2: a potential temperature calibrant for area-detector diffractometers

The coordination complex [Ni(en)3]2+(NO{}_{3}^{- })2(en = 1,2-diaminoethane) undergoes a sharp reversible displacive phase transition at ∼109 K, changing space group fromP6322 above the transition temperature toP6522 below. The phase change is accompanied by a tripling of thecaxis on cooling, resulting in an easy detection of the transition in images from area-detector diffractometers. The transition has been followed using a Nonius KappaCCD and a Bruker SMART APEX CCD. Data sets were collected over the temperature range 100–113 K and integrated using the low-temperature orientation matrix. Reflections withl≠ 3nshow a smooth and rapid decrease in intensity to zero on warming from 106.5 to 111 K. The results are reproducible to within ±2 K in two laboratories and suggest that this compound may be useful as a liquid-nitrogen cryo-calibrant for diffraction instruments equipped with area detectors.

Metal imidazolato complexes: synthesis, characterization, and X-ray powder diffraction studies of group 10 coordination polymers

Binary metal imidazolates of the group 10 metals have been prepared and typically found amorphous. However, the intermediacy of a number of (poly)crystalline species during their formation has been evidenced; their selective preparation and characterization, by chemical, spectroscopic, and thermal methods and their structure solution by the ab initio X-ray powder diffraction technique lead to the discovery of new interesting structural features, such as those of polymeric Ni(Him)(2)(im)(CH(3)COO) (Him = imidazole) and of the hydrogen-bonded polymers of general Pd(x)Pt(1-x)(Him)(2)(im)(2) formula (x = 0, 0.5, 1). The latter are built upon 2D frameworks of (pseudo)square meshes, which, in the pure Pd derivative, form an entangled structure based upon interpenetrating 2D layers, coupled in pairs. The different structures are discussed in terms of different conformations of the new "im-H-im" ligand, which acts as monoanionic exobidentate fragment, similar to im, pyrazolate (pz), "pz-H-pz", and pyrimidin-2-olate.

Group 4 dimethylmetallocenes: improved synthesis and reactivity studies

Group 4 dimethylmetallocenes are catalyst precursors for the methylmetallocenium/borate catalyst systems for olefin polymerization, and they are usually prepared by methylation (with MeMgCl or MeLi) of the parent metallocene dichlorides. We describe here a simpler preparation of a series of bisindenyldimethylmetallocenes carried out by reacting the pi-ligand with a 2-fold excess of MeLi, and then MtCl(4) (Mt = Ti, Zr, Hf). This simple, one-pot method produces the dimethylated complexes in higher overall yield, and saves on reaction time and solvents. Ind(2)MtMe(2) (1, Mt = Ti; 2a, Mt = Zr; 3, Mt = Hf), (4,7-Me(2)Ind)(2)ZrMe(2) (4), rac/meso-[C(2)H(4)(Ind)(2)]ZrMe(2) (5), meso-[C(2)H(4)(4,7-Me(2)Ind)(2)]ZrMe(2) (m-6a), and meso-[C(2)H(4)(4,7-Me(2)Ind)(2)]HfMe(2) (m-7a) have been prepared in 40-80% isolated yields. 2a reacts with 1-4 equiv of t-BuOH to give the mono-tert-butoxy derivative 2b, Ind(2)ZrMe(O-t-Bu), while reaction with 2 equiv of C(6)F(5)OH cleanly affords Ind(2)Zr(OC(6)F(5))(2) (2c). Analogously, in the presence of 2 equiv of t-BuOH, m-6a gives meso-[C(2)H(4)(4,7-Me(2)Ind)(2)]ZrMe(O-t-Bu) (m-6b) with replacement of the outward methyl group only, as established by NMR analysis; meso-[C(2)H(4)(4,7-Me(2)Ind)(2)]Zr(OC(6)F(5))(2) (m-6c) is obtained by reaction with 2 equiv of C(6)F(5)OH. The molecular structures of m-6a and m-6c are also described.

Extended polymorphism in copper(II) imidazolate polymers: a spectroscopic and XRPD structural study

Copper(II) bisimidazolate affords five different polymorphs; of these, one was structurally characterized 40 years ago by standard single-crystal X-ray diffraction (Jarvis, J. A. J.; Wells, A. F. Acta Crystallogr. 1960, 13, 1027), while the remaining four, selectively prepared as pure polycrystalline phases, have been now studied by X-ray powder diffraction (XRPD) methods. Of the four new (blue, green, olive-green, and pink) phases, three were solved by the ab initio XRPD technique and refined by the Rietveld method, and the fourth phase (pink) could not be structurally characterized. Crystal data for [Cu(imidazolate)(2)](n): blue phase, a = 27.559(3) A, c = 5.3870(9) A, trigonal, R3 macro, Z = 54; green phase, a = 21.139(1) A, b = 19.080(1) A, c = 9.2842(8) A, orthorhombic, Ccca, Z = 20; olive-green phase, a = 11.7556(8) A, b = 23.422(2) A, c = 9.0727(9) A, beta = 104.993(5) degrees, monoclinic, C2/c, Z = 12. All polymorphs contain four-coordinate CuN(4) chromophores and (N,N')-exobidentate imidazolate ligands, but show different spectroscopic and structural properties, the latter ranging from 2D to different 3D networks of the PtS, sodalite, and moganite archetypes. The intermediacy of the [Cu(imidazole)(2)CO(3)]-H(2)O species in the synthesis of the blue polymorph has been confirmed by spectroscopic and thermal analyses. FTIR, Raman, and electronic spectra were correlated with the structural features revealed in the present work, and used to gain insight into the coordination geometry of copper(II) ions of the pink polymorph. In addition, the correct Raman spectrum for copper(II) bisimidazolate, common for all polymorphs, has been definitely determined.

Extended polymorphism in copper(II) imidazolate polymers: a spectroscopic and XRPD structural study

Copper(II) bisimidazolate affords five different polymorphs; of these, one was structurally characterized 40 years ago by standard single-crystal X-ray diffraction (Jarvis, J. A. J.; Wells, A. F. Acta Crystallogr. 1960, 13, 1027), while the remaining four, selectively prepared as pure polycrystalline phases, have been now studied by X-ray powder diffraction (XRPD) methods. Of the four new (blue, green, olive-green, and pink) phases, three were solved by the ab initio XRPD technique and refined by the Rietveld method, and the fourth phase (pink) could not be structurally characterized. Crystal data for [Cu(imidazolate)(2)](n): blue phase, a = 27.559(3) A, c = 5.3870(9) A, trigonal, R3 macro, Z = 54; green phase, a = 21.139(1) A, b = 19.080(1) A, c = 9.2842(8) A, orthorhombic, Ccca, Z = 20; olive-green phase, a = 11.7556(8) A, b = 23.422(2) A, c = 9.0727(9) A, beta = 104.993(5) degrees, monoclinic, C2/c, Z = 12. All polymorphs contain four-coordinate CuN(4) chromophores and (N,N')-exobidentate imidazolate ligands, but show different spectroscopic and structural properties, the latter ranging from 2D to different 3D networks of the PtS, sodalite, and moganite archetypes. The intermediacy of the [Cu(imidazole)(2)CO(3)]-H(2)O species in the synthesis of the blue polymorph has been confirmed by spectroscopic and thermal analyses. FTIR, Raman, and electronic spectra were correlated with the structural features revealed in the present work, and used to gain insight into the coordination geometry of copper(II) ions of the pink polymorph. In addition, the correct Raman spectrum for copper(II) bisimidazolate, common for all polymorphs, has been definitely determined.

Conventional inner diameter short capillary columns: an approach to speeding up gas chromatographic analysis of medium complexity samples

Short capillary columns (5 m) with 0.25 mm inner diameter (I.D.) are applied to the GC analysis of medium complexity samples (up to 30 components) with the aim of shortening analysis time. This approach is complementary to fast GC with narrow-bore columns and is based on compensating the lower efficiency of short columns with conventional I.D.'s (0.25-0.32 mm) by using a stationary phase selectivity suitable to separate the components of the sample under investigation, so that the required resolution power is achieved but, at the same time, the analysis time is shortened. The qualitative and quantitative effectiveness of this approach is demonstrated through the analysis of: essential oils with different compositions (chamomile and rosemary), low-volatility triterpenes in a plant extract (Maytenus aquifolium and M. ilicfolium), thermolabile pyrethrins in a Pyrethrum extract, and a mixture of pesticides applied to protect medicinal plant crops. In all examples, GC analysis was five to ten times faster than with conventional columns.

Synthesis and X-ray characterization of the phosphido-carbonyl cluster anions

The [Co(9)P(CO)(21)](2)(-) anion has been isolated from the products of the reaction between Na[Co(CO)(4)] and PCl(5) in tetrahydrofuran at reflux. The structure of the cluster anion [Co(9)P(CO)(21)](2)(-) in its tetraphenylphosphonium salt has been elucidated by X-ray analysis. The crystals are monoclinic, space group P2(1)/n, a = 12.528(3), b = 14.711(5), c = 19.312(6) A, beta = 93.68(2) degrees, Z = 2. Final R = 0.065 for 2300 unique reflections having I > 3sigma(I). The anion, which is disordered about an inversion center, consists of a monocapped square antiprismatic cluster containing an interstitial phosphide and surrounded by 13 terminal and 8 edge-bridging carbonyl ligands. Average values are: Co-Co 2.685 A, and Co-P 2.256 A. The [Co(10)P(CO)(22)](3)(-) anion has been obtained by condensation of the [Co(9)P(CO)(21)](2)(-) anion with [Co(CO)(4)](-) in tetrahydrofuran at reflux. While the [Co(9)P(CO)(21)](2)(-) anion is stable under CO, the [Co(10)P(CO)(22)](3)(-) anion is decomposed to [Co(9)P(CO)(21)](2)(-) and [Co(CO)(4)](-). The benzyltrimethylammonium salt of the [Co(10)P(CO)(22)](3)(-) anion has been studied by X-ray analysis. It gives triclinic crystals, space group P_1, a = 11.452(3), b = 23.510(6), c = 25.606(4) A, alpha = 112.46(1), beta = 95.79(1), gamma = 73.548(2) degrees, Z = 4. Final R = 0.041 for 8600 unique reflections having I > 3sigma(I). There are two independent trianions in the asymmetric unit, both showing similar geometries, consisting of bicapped square antiprismatic clusters with a central P atom, each bearing 10 terminal and 12 edge-bridging carbonyl ligands, 8 of which, bound to the capping metals, are markedly asymmetric. Average values are: Co-Co 2.678 A, and Co-P 2.262 A. Electrochemistry shows that [Co(9)P(CO)(21)](2)(-) and [Co(10)P(CO)(22)](3)(-) in acetonitrile solution undergo either a one-electron oxidation or a two-electron reduction. This latter process appears as a single step in the case of the dianion and as two separated one-electron steps in the case of the trianion. All the processes are accompanied by slow chemical complications, thus testifying that no stable redox congeners exist for these phosphide clusters.

[Re]

A chair conformation comparable to that observed for six-membered rings composed of tetrahedral carbon atoms is found for the cluster anion [Re(6)(µ-H)(5)(CO)(24)](-) (see picture; black spheres: Re, white spheres: µ-H; CO ligands omitted for clarity) in spite of the octahedral coordination at the Re centers. This is the first example of a carbonyl cluster exhibiting a cyclohexane-like geometry of the metallic framework.

SMILE--shaded molecular imaging on low-cost equipment

The SMILE program runs under MS-DOS on IBM PC AT-compatible computers equipped with the SM640 or the PG640 Matrox graphic board. The program allows real-time three-dimensional (3D) animation and modeling of several isolated molecules that can be built from scratch, manipulated interactively and compared by superimposition. SMILE enables users to compute atomic partial charges, molecular surface area, molecular volume, electrostatic and nonbonded potential energies. PLUTO, ORTEP, and MMP2 input files are set up automatically. The program also provides simple access to crystal packing by real-time animation of the unit cell contents, interactive inspection of the relevant stereochemical parameters and fragment manipulation within the unit cell. SMILE animates stereo views and produces beautiful shaded 3D images (8 colors, 32 shades each) of molecules in many different styles--stick, ball-and-stick, CPK (space filling), and transparent CPK with backbone.