Triazolyl- vs Pyridyl-Functionalized N-Heterocyclic Carbene Complexes: Impact of the Pendant N-Donor Ligand on Intramolecular C-C Bond Formation.

Organometallic Rh(Cp*) (Cp* = η5-pentamethylcyclopentadienyl) complexes with monodentate N-heterocyclic carbene (NHC) ligands bearing a pendant anthracenyl substituent have been shown to undergo intramolecular C-C coupling reactions. Herein, two bidentate NHC ligands substituted with pyridyl or triazolyl donor groups were prepared along with the corresponding MII/III (M = RuII, OsII, RhIII, IrIII) complexes. While the Rh(Cp*) complex featuring an NHC-triazole bidentate ligand underwent the equivalent reaction as the monodentate Rh(NHC) complex, i.e., it formed a polydentate ligand, the pyridyl-pendant derivative was unequivocally shown to be unreactive. This contrasting behavior was further investigated by density functional theory (DFT) calculations that highlighted significant differences between the two types of Rh(III) complexes with pendant pyridyl or triazolyl N-coordinating groups. Modeling of the reaction pathways suggests that the initial formation of a dicationic Rh(III) species is unfavorable and that the internal ligand transformation proceeds first by dissociation of the coordinated N atom of the pendant group from the Rh center. After the formation of a neutral η4-fulvene ligand via combined proton/single electron transfer, a cycloaddition occurs between the exo-ene bond of fulvene and the 9' and 10' positions on the pendant anthracenyl group. The resulting experimental UV-visible spectrum recorded in methanol of the polydentate triazolyl-based Rh species revealed the loss of the vibronic coupling typically associated with an anthracenyl functional group. Moreover, TD-DFT modeling indicates the presence of an equilibrium process whereby the N-coordination of the pendant triazolyl group to the RhIII center appears to be highly labile. Charge decomposition analysis (CDA) of the DFT-modeled species with the dissociated triazolyl group revealed a pseudo-η3-allylic interaction between the π-type MOs of the transformed anthracenyl group and the RhIII center; thus, the singly attached chelating ligand is classified as having rare nonadenticity.

Heptadentate, Octadentate, Or Even Nonadentate? Denticity in the Unexpected Formation of an All-Carbon Donor-Atom Ligand in RhIII(Cp*)(Anthracenyl-NHC) Complexes.

Investigations on incorporating an N-flanking anthracenyl moiety to [Rh(Cp*)(NHC)Cl2] complexes surprisingly led to the formation of an intramolecular C-C bond between the Cp* and anthracenyl moieties, with additional auxiliary interactions between the metal and the anthracenyl ring system. In silico modeling supports a reaction mechanism whereby Rh(η4-tetramethylfulvene) intermediates undergo metallocycloaddition and the abstraction of a chlorido ligand, affording unique cationic complexes that feature Rh centers coordinated by a nonadentate ligand with exclusively carbon donor atoms. Some Rh-C interactions were extremely weak but nevertheless exhibited covalent bonding character. These weak Rh-C interactions were readily displaced by stronger electron donors, and the nonadentate ligand reverted to the heptadentate coordination mode observed in the intermediate. As far as we are aware, this study provides the first conclusive evidence of complexes bearing a single nonadentate κ9-coordinating ligand that features only carbon donors bound to a metal center.

The Human Gene Mutation Database (HGMD®): optimizing its use in a clinical diagnostic or research setting.

The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that are thought to underlie, or are closely associated with human inherited disease. At the time of writing (June 2020), the database contains in excess of 289,000 different gene lesions identified in over 11,100 genes manually curated from 72,987 articles published in over 3100 peer-reviewed journals. There are primarily two main groups of users who utilise HGMD on a regular basis; research scientists and clinical diagnosticians. This review aims to highlight how to make the most out of HGMD data in each setting.

Water-Soluble Silver(I) Complexes Featuring the Hemilabile 3,7-Dimethyl-1,3,5-triaza-7-phosphabicyclo[3.3.1]nonane Ligand: Synthesis, Characterization, and Antimicrobial Activity.

This paper describes the preparation and comprehensive characterization of a series of water-soluble cationic silver(I)-centered complexes featuring the hemilabile P, N-ligand known as 3,7-dimethyl-1,3,5-triaza-7-phosphabicyclo[3.3.1]nonane (herein abbreviated as PTN(Me)) and differing types of monoanionic counterions including known biologically active sulfadiazine and triclosan. The complexes primarily differed though the number of coordinating PTN(Me) ligands. The bis-substituted Ag(I) complexes revealed P, N bidentate coordination, while the only P-monocoordination of the metal center was observed for the tris-substituted systems. The bis-ligated silver compounds were observed to quickly degrade upon photoexposure or in contact with air. In contrast, the tris-ligated complexes demonstrated greater stability, in particular, a high resistance to photo-decomposition. Calculated geometry optimized models using the density functional theory method (BP86) revealed for the bis-substituted PTN(Me) Ag(I) species that the total enthalpy of the tetrahedral C2-symmetric structure is marginally lower by -0.6 kcal mol-1 compared to the planar C2 h structure, which is analogous for the corresponding [Au(PTN(Me))2]+ complex with Δ H = -0.5 kcal mol-1. Hence both types of complexes feature free rotation of the PTN ligand about the M-P bond axis. This series of Ag(I) and bis-PTN(Me) Au(I) complexes were evaluated using the agar well diffusion test for potential antimicrobial and antifungal activity. The nature of the counterion was found to have a strong correlation with the area of microbiological growth inhibition. Silver(I) complexes bearing the deprotonated triclosan as the counterion demonstrated the greatest activity, with large zones of growth inhibition, with the tris-ligated triclosan complex obtaining of a high clearance of 42 mm against the Gram-negative Escherichia coli. In contrast, the previously reported [Au(PTN(Me))2]Cl complex demonstrated activity only against E. coli, which is lower than that observed for the silver(I) PTN(Me) species.

The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies.

The Human Gene Mutation Database (HGMD®) constitutes a comprehensive collection of published germline mutations in nuclear genes that underlie, or are closely associated with human inherited disease. At the time of writing (March 2017), the database contained in excess of 203,000 different gene lesions identified in over 8000 genes manually curated from over 2600 journals. With new mutation entries currently accumulating at a rate exceeding 17,000 per annum, HGMD represents de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data. The public version of HGMD ( http://www.hgmd.org ) is freely available to registered users from academic institutions and non-profit organisations whilst the subscription version (HGMD Professional) is available to academic, clinical and commercial users under license via QIAGEN Inc.

Towards the design of novel boron- and nitrogen-substituted ammonia-borane and bifunctional arene ruthenium catalysts for hydrogen storage.

Electronic-structure density functional theory calculations have been performed to construct the potential energy surface for H2 release from ammonia-borane, with a novel bifunctional cationic ruthenium catalyst based on the sterically bulky ß-diketiminato ligand (Schreiber et al., ACS Catal. 2012, 2, 2505). The focus is on identifying both a suitable substitution pattern for ammonia-borane optimized for chemical hydrogen storage and allowing for low-energy dehydrogenation. The interaction of ammonia-borane, and related substituted ammonia-boranes, with a bifunctional η(6)-arene ruthenium catalyst and associated variants is investigated for dehydrogenation. Interestingly, in a number of cases, hydride-proton transfer from the substituted ammonia-borane to the catalyst undergoes a barrier-less process in the gas phase, with rapid formation of hydrogenated catalyst in the gas phase. Amongst the catalysts considered, N,N-difluoro ammonia-borane and N-phenyl ammonia-borane systems resulted in negative activation energy barriers. However, these types of ammonia-boranes are inherently thermodynamically unstable and undergo barrierless decay in the gas phase. Apart from N,N-difluoro ammonia-borane, the interaction between different types of catalyst and ammonia borane was modeled in the solvent phase, revealing free-energy barriers slightly higher than those in the gas phase. Amongst the various potential candidate Ru-complexes screened, few are found to differ in terms of efficiency for the dehydrogenation (rate-limiting) step. To model dehydrogenation more accurately, a selection of explicit protic solvent molecules was considered, with the goal of lowering energy barriers for H-H recombination. It was found that primary (1°), 2°, and 3° alcohols are the most suitable to enhance reaction rate.

Deleterious- and disease-allele prevalence in healthy individuals: insights from current predictions, mutation databases, and population-scale resequencing.

We have assessed the numbers of potentially deleterious variants in the genomes of apparently healthy humans by using (1) low-coverage whole-genome sequence data from 179 individuals in the 1000 Genomes Pilot Project and (2) current predictions and databases of deleterious variants. Each individual carried 281-515 missense substitutions, 40-85 of which were homozygous, predicted to be highly damaging. They also carried 40-110 variants classified by the Human Gene Mutation Database (HGMD) as disease-causing mutations (DMs), 3-24 variants in the homozygous state, and many polymorphisms putatively associated with disease. Whereas many of these DMs are likely to represent disease-allele-annotation errors, between 0 and 8 DMs (0-1 homozygous) per individual are predicted to be highly damaging, and some of them provide information of medical relevance. These analyses emphasize the need for improved annotation of disease alleles both in mutation databases and in the primary literature; some HGMD mutation data have been recategorized on the basis of the present findings, an iterative process that is both necessary and ongoing. Our estimates of deleterious-allele numbers are likely to be subject to both overcounting and undercounting. However, our current best mean estimates of ~400 damaging variants and ~2 bona fide disease mutations per individual are likely to increase rather than decrease as sequencing studies ascertain rare variants more effectively and as additional disease alleles are discovered.

The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution.

The Human Gene Mutation Database (HGMD) constitutes a comprehensive core collection of data on germ-line mutations in nuclear genes underlying or associated with human inherited disease (http://www.hgmd.org). Data cataloged include single-base-pair substitutions in coding, regulatory, and splicing-relevant regions, micro-deletions and micro-insertions, indels, and triplet repeat expansions, as well as gross gene deletions, insertions, duplications, and complex rearrangements. Each mutation is entered into HGMD only once, in order to avoid confusion between recurrent and identical-by-descent lesions. By March 2012, the database contained in excess of 123,600 different lesions (HGMD Professional release 2012.1) detected in 4,514 different nuclear genes, with new entries currently accumulating at a rate in excess of 10,000 per annum. ∼6,000 of these entries constitute disease-associated and functional polymorphisms. HGMD also includes cDNA reference sequences for more than 98% of the listed genes.

Insights into hominid evolution from the gorilla genome sequence.

Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease.

Establishing the molecular basis of DNA mutations that cause inherited disease is of fundamental importance to understanding the origin, nature, and clinical sequelae of genetic disorders in humans. The majority of disease-associated mutations constitute single-base substitutions and short deletions and/or insertions resulting from DNA replication errors and the repair of damaged bases. However, pathological mutations can also be introduced by nonreciprocal recombination events between paralogous sequences, a phenomenon known as interlocus gene conversion (IGC). IGC events have thus far been linked to pathology in more than 20 human genes. However, the large number of duplicated gene sequences in the human genome implies that many more disease-associated mutations could originate via IGC. Here, we have used a genome-wide computational approach to identify disease-associated mutations derived from IGC events. Our approach revealed hundreds of known pathological mutations that could have been caused by IGC. Further, we identified several dozen high-confidence cases of inherited disease mutations resulting from IGC in ∼1% of all genes analyzed. About half of the donor sequences associated with such mutations are functional paralogous genes, suggesting that epistatic interactions or differential expression patterns will determine the impact upon fitness of specific substitutions between duplicated genes. In addition, we identified thousands of hitherto undescribed and potentially deleterious mutations that could arise via IGC. Our findings reveal the extent of the impact of interlocus gene conversion upon the spectrum of human inherited disease.

Polynuclear ruthenium, osmium and gold complexes. The quest for innovative anticancer chemotherapeutics.

Polynuclear compounds are a relatively new and successful approach in metal-based cancer chemotherapy as typified by the trinuclear Pt compound BBR3464 which was evaluated in clinical trials. In this review, we discuss newer developments of polynuclear ruthenium, osmium and gold complexes, focusing on their anticancer activity. The compounds presented are often supposed to exert their anticancer activity by different modes of action as compared to established drugs, including newly proposed mechanisms such as enzyme inhibition, crosslinking of biomacromolecules or through photo-activation, though many of the examples are also capable of binding to DNA nucleobases. Important metabolization and chemical characteristics of such compounds are discussed, and if the appropriate data is available, molecular modes of action are highlighted.

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes.

Mutations associated with tumorigenesis may either arise somatically or can be inherited through the germline. We performed a comparison of somatic, germline, shared (found in both soma and germline) and somatic recurrent mutational spectra for 17 human tumor suppressor genes, which focused upon missense single base-pair substitutions and microdeletions/microinsertions. Somatic and germline mutational spectra were similar in relation to C.G>T.A transitions but differed with respect to the frequency of A.T>G.C, A.T>T.A, and C.G>A.T substitutions. Shared missense mutations were characterized by higher mutability rates, greater physicochemical differences between wild-type and mutant residues, and a tendency to occur in evolutionarily conserved residues and within CpG/CpHpG oligonucleotides. Mononucleotide runs (≥4 bp) were identified as hotspots for shared microdeletions/microinsertions. Both germline and somatic microdeletions/microinsertions were found to be significantly overrepresented within the "indel-hotspot" motif, GTAAGT. Using a naïve Bayes' classifier trained to discriminate between five missense mutation groups, 63% of mutations in our dataset were on average correctly recognized. Applying this classifier to an independent dataset of probable driver mutations, we concluded that ∼50% of these somatic missense mutations possess features consistent with their being either shared or recurrent, suggesting that a disproportionate number of such lesions are likely to be drivers of tumorigenesis.

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics.

The number of reported germline mutations in human nuclear genes, either underlying or associated with inherited disease, has now exceeded 100,000 in more than 3,700 different genes. The availability of these data has both revolutionized the study of the morbid anatomy of the human genome and facilitated "personalized genomics." With approximately 300 new "inherited disease genes" (and approximately 10,000 new mutations) being identified annually, it is pertinent to ask how many "inherited disease genes" there are in the human genome, how many mutations reside within them, and where such lesions are likely to be located? To address these questions, it is necessary not only to reconsider how we define human genes but also to explore notions of gene "essentiality" and "dispensability."Answers to these questions are now emerging from recent novel insights into genome structure and function and through complete genome sequence information derived from multiple individual human genomes. However, a change in focus toward screening functional genomic elements as opposed to genes sensu stricto will be required if we are to capitalize fully on recent technical and conceptual advances and identify new types of disease-associated mutation within noncoding regions remote from the genes whose function they disrupt.

The Human Gene Mutation Database: 2008 update.

The Human Gene Mutation Database (HGMD((R))) is a comprehensive core collection of germline mutations in nuclear genes that underlie or are associated with human inherited disease. Here, we summarize the history of the database and its current resources. By December 2008, the database contained over 85,000 different lesions detected in 3,253 different genes, with new entries currently accumulating at a rate exceeding 9,000 per annum. Although originally established for the scientific study of mutational mechanisms in human genes, HGMD has since acquired a much broader utility for researchers, physicians, clinicians and genetic counselors as well as for companies specializing in biopharmaceuticals, bioinformatics and personalized genomics. HGMD was first made publicly available in April 1996, and a collaboration was initiated in 2006 between HGMD and BIOBASE GmbH. This cooperative agreement covers the exclusive worldwide marketing of the most up-to-date (subscription) version of HGMD, HGMD Professional, to academic, clinical and commercial users.

Development of ruthenium antitumor drugs that overcome multidrug resistance mechanisms.

Organometallic ruthenium(II) complexes of the general formula [Ru(eta6-p-cymene)Cl2(L)] and [Ru(eta6-p-cymene)Cl(L)2][BPh4] with modified phenoxazine- and anthracene-based multidrug resistance (MDR) modulator ligands (L) have been synthesized, spectroscopically characterized, and evaluated in vitro for their cytotoxic and MDR reverting properties in comparison with the free ligands. For an anthracene-based ligand, coordination to a ruthenium(II) arene fragment led to significant improvement of cytotoxicity as well as Pgp inhibition activity. A similar, but weaker effect was also observed when using a benzimidazole-phenoxazine derivative as Pgp inhibitor. The most active compound in terms of both Pgp inhibition and cytotoxicity is [Ru(eta6-p-cymene)Cl2(L)], where L is an anthracene-based ligand. Studies show that it induces cell death via inhibition of DNA synthesis. Moreover, because the complex is fluorescent, its uptake in cells was studied, and relative to the free anthracene-based ligand, uptake of the complex is accelerated and accumulation of the complex in the cell nucleus is observed.

Synthesis, characterization, and in vitro evaluation of novel ruthenium(II) eta6-arene imidazole complexes.

Ten complexes of general formula [Ru(eta6-arene)Cl2(L)], [Ru(eta6-arene)Cl(L)2][X], and [Ru(eta6-arene)(L)3][X]2 (eta6-arene = benzene, p-cymene; L = imidazole, benzimidazole, N-methylimidazole, N-butylimidazole, N-vinylimidazole, N-benzoylimidazole; X = Cl, BF4, BPh4) have been prepared and characterized by spectroscopy. The structures of five representative compounds have been established in the solid state by single-crystal X-ray diffraction. All the new compounds were assessed by the same in vitro screening assays applied to [imidazole-H][trans-RuCl4(DMSO)(imidazole)] (NAMI-A) and [Ru(eta6-arene)Cl2(1,3,5-triaza-7-phosphaadamantane)] (RAPTA) compounds. It was found that the new compounds show essentially the same order of cytotoxicity as the RAPTA compounds toward cancer cells. Several of the compounds were selective toward cancer cells in that they were less (or not) cytotoxic toward nontumorigenic cells that are used to model healthy human cells. Thus, two of the compounds, [Ru(eta6-p-cymene)Cl(vinylimid)2][Cl] (vinylimid = N-vinylimidazole) and [Ru(eta6-benzene)(mimid)3][BF4]2 (mimid = N-methylimidazole), have been selected for a more detailed in vivo evaluation.

A counterintuitive structural effect of metal-metal bond protonation and its electronic underpinnings.

Protonation across the metal-metal bond in the complexes [(CO)(2)M(mu-dppm)(mu-PtBu(2))(mu-H)M(CO)(2)] (M=Fe or Ru, dppm=Ph(2)PCH(2)PPh(2)) induces M-M bond shortening of up to about 0.05 A. DFT calculations on simplified iron models reproduce this trend well. Conversely, the computations show that the M-M distance in the dimer [{Cp*Ir(CO)}(2)] lengthens with two consecutive protonations, but there are no crystal structure determinations to highlight the effects on the Ir-Ir bond. DFT calculations and the analogous cobalt system confirm that the transformation of a two-electron, two-center (2e-2c) bond into a 2e-3c bond is accompanied by the predicted elongation. An MO analysis indicated similar nature and evolution of the M-M bonding these cases. In particular, the HOMOs of the mono-hydrido cations [Cp(CO)M(mu-H)M(CO)Cp](+) (M=Ir, Co) have evident M-M bent-bond character, and hence subsequent protonation invariably causes a decrease in the bond index. The Fe(2) and Co(2) systems have also been analyzed with the quantum theory of atoms in molecules (QTAIM) method, but in no case was an M-M bond critical point located unless an artificially shorter M-M distance was imposed. However, the trends for the atoms-in-molecules (AIM) bond delocalization indexes delta(M-M) confirm the overall M-M bond weakening on protonation. In conclusion, all the computational results for the iron system indicate that the paradigm of a direct correlation between bond strength and distance is not always applicable. This is attributable to a very flat potential energy surface and various competing effects imposed by the bridging ligands.

Experimental and computational studies on the solvent-controlled cluster isomerism of Ru3(H)(CO)9(NPPh3) and related dynamics.

The species Ru3(H)(mu3-NPPh3)(CO)9 occurs in the solid state as two isomers, characterized either by one capping hydride and three CO bridges (1a) or by one bridging hydride and all terminals COs (1b); key intermediates for the formation, fluxionality and solvent-dependent interconversion of the isomers are highlighted through a DFT MO analysis.

A main-group donor-acceptor adduct: 1,3,4,5-tetramethylimidazol-2-ylidene-tris(pentafluorophenyl)borane.

The solid-state structural analysis of the title compound, Me4C2N2C-->B(C6F5)3 or C25H12BF15N2, provides useful metric parameters for the qualitative comparison of the donor strength with other mono- and dicoordinate main-group compounds which feature distinctive lone-pair character.