Regularized sequence-context mutational trees capture variation in mutation rates across the human genome.

Germline mutation is the mechanism by which genetic variation in a population is created. Inferences derived from mutation rate models are fundamental to many population genetics methods. Previous models have demonstrated that nucleotides flanking polymorphic sites-the local sequence context-explain variation in the probability that a site is polymorphic. However, limitations to these models exist as the size of the local sequence context window expands. These include a lack of robustness to data sparsity at typical sample sizes, lack of regularization to generate parsimonious models and lack of quantified uncertainty in estimated rates to facilitate comparison between models. To address these limitations, we developed Baymer, a regularized Bayesian hierarchical tree model that captures the heterogeneous effect of sequence contexts on polymorphism probabilities. Baymer implements an adaptive Metropolis-within-Gibbs Markov Chain Monte Carlo sampling scheme to estimate the posterior distributions of sequence-context based probabilities that a site is polymorphic. We show that Baymer accurately infers polymorphism probabilities and well-calibrated posterior distributions, robustly handles data sparsity, appropriately regularizes to return parsimonious models, and scales computationally at least up to 9-mer context windows. We demonstrate application of Baymer in three ways-first, identifying differences in polymorphism probabilities between continental populations in the 1000 Genomes Phase 3 dataset, second, in a sparse data setting to examine the use of polymorphism models as a proxy for de novo mutation probabilities as a function of variant age, sequence context window size, and demographic history, and third, comparing model concordance between different great ape species. We find a shared context-dependent mutation rate architecture underlying our models, enabling a transfer-learning inspired strategy for modeling germline mutations. In summary, Baymer is an accurate polymorphism probability estimation algorithm that automatically adapts to data sparsity at different sequence context levels, thereby making efficient use of the available data.

On-Demand Final State Control of a Surface-Bound Bistable Single Molecule Switch.

Modern electronic devices perform their defined action because of the complete reliability of their individual active components (transistors, switches, diodes, and so forth). For instance, to encode basic computer units (bits) an electrical switch can be used. The reliability of the switch ensures that the desired outcome (the component's final state, 0 or 1) can be selected with certainty. No practical data storage device would otherwise exist. This reliability criterion will necessarily need to hold true for future molecular electronics to have the opportunity to emerge as a viable miniaturization alternative to our current silicon-based technology. Molecular electronics target the use of single-molecules to perform the actions of individual electronic components. On-demand final state control over a bistable unimolecular component has therefore been one of the main challenges in the past decade (1-5) but has yet to be achieved. In this Letter, we demonstrate how control of the final state of a surface-supported bistable single molecule switch can be realized. On the basis of the observations and deductions presented here, we further suggest an alternative strategy to achieve final state control in unimolecular bistable switches.

New class of metal bound molecular switches involving H-tautomerism.

A potential end-point in the miniaturization of electronic devices lies in the field of molecular electronics, where molecules perform the function of single components. To date, hydrogen tautomerism in unimolecular switches has been restricted to the central macrocycle of porphyrin-type molecules. The present work reveals how H-tautomerism is the mechanism for switching in substituted quinone derivatives, a novel class of molecules with a different chemical structure. We hence reveal that the previous restrictions applying to tautomeric molecular switches bound to a surface are not valid in general. The activation energy of switching in a prototypical quinone derivative is determined using inelastic electron tunneling. Through computational modeling, we show that the mechanism underlying this process is tautomerization of protons belonging to two amino groups. This switching property is retained upon functionalization by the addition of side groups, meaning that the switch can be chemically modified to fit specific applications.

Crystal engineering of lattice metrics of perhalometallate salts and MOFs.

The synthesis of the salt 3 and metallo-organic framework (MOF) [{(4,4(')-bipy)CoBr(2)}(n)] 4 by a range of solid state (mechanochemical and thermochemical) and solution methods is reported; they are isostructural with their respective chloride analogues 1 and 2. 3 and 4 can be interconverted by means of HBr elimination and absorption. Single phases of controlled composition and general formula [4,4(')-H(2)bipy][CoBr(4-x)Cl(x)] 5(x) may be prepared from 2 and 4 by solid--gas reactions involving HBr or HCl respectively. Crystalline single phase samples of 5(x) and [{(4,4(')-bipy)CoBr(2-x)Cl(x)}(n)] 6(x) were prepared by solid-state mechanochemical routes, allowing fine control over the composition and unit cell volume of the product. Collectively these methods enable continuous variation of the unit cell dimensions of the salts [4,4(')-H(2)bipy][CoBr(4-x)Cl(x)] (5(x)) and the MOFs [{(4,4(')-bipy)CoBr(2-x)Cl(x)}(n)] (6(x)) by varying the bromide to chloride ratio and establish a means of controlling MOF composition and the lattice metrics, and so the physical and chemical properties that derive from it.

Mechanochemistry: opportunities for new and cleaner synthesis.

The aim of this critical review is to provide a broad but digestible overview of mechanochemical synthesis, i.e. reactions conducted by grinding solid reactants together with no or minimal solvent. Although mechanochemistry has historically been a sideline approach to synthesis it may soon move into the mainstream because it is increasingly apparent that it can be practical, and even advantageous, and because of the opportunities it provides for developing more sustainable methods. Concentrating on recent advances, this article covers industrial aspects, inorganic materials, organic synthesis, cocrystallisation, pharmaceutical aspects, metal complexes (including metal-organic frameworks), supramolecular aspects and characterization methods. The historical development, mechanistic aspects, limitations and opportunities are also discussed (314 references).

Iron(I) in Negishi cross-coupling reactions.

Herein we demonstrate both the importance of Fe(I) in Negishi cross-coupling reactions with arylzinc reagents and the isolation of catalytically competent Fe(I) intermediates. These complexes, [FeX(dpbz)(2)] [X = 4-tolyl (7), Cl (8a), Br (8b); dpbz = 1,2-bis(diphenylphosphino)benzene], were characterized by crystallography and tested for activity in representative reactions. The complexes are low-spin with no significant spin density on the ligands. While complex 8b shows performance consistent with an on-cycle intermediate, it seems that 7 is an off-cycle species.

Identifying rare variants inconsistent with identity-by-descent in population-scale whole-genome sequencing data.

Analyses of genetic variation typically assume that rare variants within a population are inherited from a single common ancestral event identity-by-descent (IBD). However, there are genetic and technical processes through which rare variants in population genetic data may deviate from this simple evolutionary model, including recurrent mutations, gene conversions and genotyping error. All these processes can decrease the expected length of shared background haplotype surrounding a rare variant if that variant was inherited from a single event descending from a common ancestor. No method exists to computationally infer rare variants inconsistent with this simple model-denoted here as 'IBD-inconsistent'-using unphased population sequencing data.We hypothesized that the difference in shared haplotype background length can distinguish variants consistent and inconsistent with this simple IBD transmission population sequencing data without pedigree information. We implemented a Bayesian hierarchical model and used Gibbs sampling to estimate the posterior probability of IBD state for rare variants, using simulated recurrent mutations to demonstrate that our approach accurately distinguishes rare variants consistent and inconsistent with a simple IBD inheritance model.Applying our method to whole-genome sequencing data from 3,621 human individuals in the UK10K consortium, we found that IBD-inconsistent variants correlated with higher local mutation rates and genomic features like replication timing. Using a heuristic to categorize IBD-inconsistent variants as gene conversions, we found that potential gene conversions had expected properties such as enriched local GC content.By identifying IBD-inconsistent variants, we can better understand the spectrum of recent mutations in human populations, a source of genetic variation driving evolution and a key factor in understanding recent demographic history.

Syntheses of Group 4 ansa-trovacene complexes and conversion of [1]silatrovacenophanes into paramagnetic metallopolymers by ring-opening polymerization.

An improved protocol for the selective dilithiation of [V(η(5)-C(5)H(5))(η(7)-C(7)H(7))] has been developed, which afforded [V(η(5)-C(5)H(4)Li)(η(7)-C(7)H(6)Li)]·PMDTA (5; PMDTA=N,N,N',N'',N''-pentamethyldiethylenetriamine) in almost quantitative yield (98%). In the solid state, the species features a dimeric structure with two terminal and two bridging lithium atoms, with the latter connecting both sandwich subunits. Reaction with suitable Group 4 dihalide compounds enabled the isolation of highly strained silicon- and germanium-bridged [1]trovacenophanes 6 and 7. Similarly, reaction of 5 with Cl(2)Sn(2)tBu(4) afforded the rather unstrained complex [V(η(5)-C(5)H(4))(η(7)-C(7)H(6))Sn(2)tBu(4)] (8), which together with 7 represent the first trovacenophanes to incorporate heavier analogues of silicon in the ansa-bridge. Ring-opening polymerization reactions of [V(η(5)-C(5)H(4))(η(7)-C(7)H(6))SiRR'] (2a: R=R'=Me; 6: R=Me, R'=iPr) were performed by heating in a solution of toluene in the presence of the Karstedt catalyst, which resulted in the formation of the corresponding soluble poly(trovacenylsilanes) in yields of 41 and 33%, respectively. As estimated by gel permeation chromatography (GPC), the macromolecules possess molecular weights of M(n)=10,010 and 5580 g mol(-1) with polydispersity indices of 2.31 and 1.64 for 9 and 10, respectively. ESR spectroscopic studies on 9 and 10 revealed only a single broad resonance in each case without any identifiable (51)V hyperfine coupling.

Cooperative spin transition in the two-dimensional coordination polymer [Fe(4,4'-bipyridine)2(NCX)2]·4CHCl3 (X = S, Se).

Two new isostructural two-dimensional (2D) coordination polymers exhibiting spin crossover (SCO) behavior of formulation [Fe(4,4'-bipy)(2)(NCX)(2)]·4CHCl(3) (4,4'-bipy = 4,4'-bipyridine; X = S [1·4CHCl(3)], Se [2·4CHCl(3)]) have been synthesized and characterized, and both undergo cooperative spin transitions (ST). For 1·4CHCl(3) the ST takes place in two steps with critical temperatures of T(c1)(down) = 143.1 K, T(c2)(down) = 91.2 K, T(c1)(up) = 150.7 K, and T(c2)(up) = 112.2 K. 2·4CHCl(3) displays half ST characterized by T(c)(down) = 161.7 K and T(c)(up) = 168.3 K. The average enthalpy and entropy variations and cooperativity parameters associated with the ST have been estimated to be ΔH(1)(av) = 5.18 kJ mol(-1), ΔS(1)(av) = 35 J K(-1) mol(-1), and Γ(1) = 2.8 kJ mol(-1) and ΔH(2)(av) = 3.55 kJ mol(-1), ΔS(2)(av) = 35 J K(-1) mol(-1), and Γ(2) = 2.6 kJ mol(-1) for 1·4CHCl(3), and ΔH(av) = 6.25 kJ mol(-1), ΔS(av) = 38.1 J K(-1) mol(-1), and Γ = 3.2 kJ mol(-1) for 2·4CHCl(3). At T > [T(c1) (1·4CHCl(3)); T(c) (2·4CHCl(3))], both compounds are in the space group P2/c while at T < [T(c1) (1·4CHCl(3)); T(c) (2·4CHCl(3))] they change to the C2/c space group and display an ordered checkerboard-like arrangement of iron(II) sites where the high- and low-spin states coexist at 50%.

On the causes of potential inversion in 1,2,4,5-tetrakis(amino)benzenes.

Three 3,6-difluoro-1,2,4,5-tetrakis(amino)benzene compounds, bearing dimethylamino (1), piperidin-1-yl (3), or morpholin-1-yl (5) substituents, have been synthesized and subsequently defluorinated to give the corresponding 1,2,4,5-tetrakis(amino)benzene compounds 2, 4, and 6; the crystal structures of compounds 1, 4, and 6 have been obtained. Cyclic voltammetry shows that all six compounds will lose two electrons to form dications, and the use of suitable oxidizing agents has allowed isolation and crystallographic characterization of the dications 2(2+) and 6(2+) (as [PF(6)](2) salts) and 4(2+) (as a [I(5)][I(3)] salt). The separation DeltaE between the loss of the first electron and the second varies between compounds, from 0.23 V in 1 to 0.01 V in 6. Electrochemical studies involving the use of the noncoordinating electrolyte [Bu(4)N][B{C(6)H(3)(CF(3))(2)}(4)] show that it is possible to increase this separation, stabilizing the intermediate monocationic phase, and this has allowed the isolation and crystallographic characterization of the radical salts 2[B{C(6)H(3)(CF(3))(2)}(4)] and 4[B{C(6)H(3)(CF(3))(2)}(4)], the first radical cations of this family to be isolated. DFT studies of the ion pairing between oxidized forms of 1 and 2 and anions imply that the location of the ion pairing is different in the two species.

Coordination chemistry in the solid state: reactivity of manganese and cadmium chlorides with imidazole and pyrazole and their hydrochlorides.

Crystalline coordination compounds [MnCl(2)(Hpz)(2)] 3, [CdCl(2)(Hpz)(2)] 5, [MnCl(2)(Him)(2)] 9, and [CdCl(2)(Him)(2)] 13 (Him = imidazole; Hpz = pyrazole) can be synthesized in solid state reactions by grinding together the appropriate metal chloride and 2 equiv of the neutral ligand. Similarly, grinding together the metal chlorides with the ligand hydrochloride salts produces the halometallate salts [H(2)pz][MnCl(3)(OH(2))] 1, [H(2)pz][CdCl(4)] 4, [H(2)im](6)[MnCl(6)][MnCl(4)] 8, and [H(2)im](6)[CdCl(6)][CdCl(4)] 11. In contrast, reacting the metal chloride salt with the ligand in concentrated HCl solution yields a second set of salts [H(2)pz][MnCl(3)] 2, [H(2)im][MnCl(3)(OH(2))(2)] 7, and [H(2)im][CdCl(3)(OH(2))]·H(2)O 12. Compound 5 can be partly dehydrochlorinated by grinding with KOH to form an impure sample of the pyrazolate compound [Cd(pz)(2)] 6, while recrystallizing 9 from ethanol yielded crystals of solvated [Mn(4)Cl(8)(Him)(8)] 10. The crystal structure determinations of 1, 2, 4, 11, and 12 are reported.

Mechanism of Hsp70 specialized interactions in protein translocation and the unfolded protein response.

Hsp70 chaperones interact with substrate proteins in a coordinated fashion that is regulated by nucleotides and enhanced by assisting cochaperones. There are numerous homologues and isoforms of Hsp70 that participate in a wide variety of cellular functions. This diversity can facilitate adaption or specialization based on particular biological activity and location within the cell. In this review, we highlight two specialized binding partner proteins, Tim44 and IRE1, that interact with Hsp70 at the membrane in order to serve their respective roles in protein translocation and unfolded protein response signalling. Recent mechanistic data suggest analogy in the way the two Hsp70 homologues (BiP and mtHsp70) can bind and release from IRE1 and Tim44 upon substrate engagement. These shared mechanistic features may underlie how Hsp70 interacts with specialized binding partners and may extend our understanding of the mechanistic repertoire that Hsp70 chaperones possess.

UPR proteins IRE1 and PERK switch BiP from chaperone to ER stress sensor.

BiP is a major endoplasmic reticulum (ER) chaperone and is suggested to act as primary sensor in the activation of the unfolded protein response (UPR). How BiP operates as a molecular chaperone and as an ER stress sensor is unknown. Here, by reconstituting components of human UPR, ER stress and BiP chaperone systems, we discover that the interaction of BiP with the luminal domains of UPR proteins IRE1 and PERK switch BiP from its chaperone cycle into an ER stress sensor cycle by preventing the binding of its co-chaperones, with loss of ATPase stimulation. Furthermore, misfolded protein-dependent dissociation of BiP from IRE1 is primed by ATP but not ADP. Our data elucidate a previously unidentified mechanistic cycle of BiP function that explains its ability to act as an Hsp70 chaperone and ER stress sensor.

Structure and Molecular Mechanism of ER Stress Signaling by the Unfolded Protein Response Signal Activator IRE1.

The endoplasmic reticulum (ER) is an important site for protein folding and maturation in eukaryotes. The cellular requirement to synthesize proteins within the ER is matched by its folding capacity. However, the physiological demands or aberrations in folding may result in an imbalance which can lead to the accumulation of misfolded protein, also known as "ER stress." The unfolded protein response (UPR) is a cell-signaling system that readjusts ER folding capacity to restore protein homeostasis. The key UPR signal activator, IRE1, responds to stress by propagating the UPR signal from the ER to the cytosol. Here, we discuss the structural and molecular basis of IRE1 stress signaling, with particular focus on novel mechanistic advances. We draw a comparison between the recently proposed allosteric model for UPR induction and the role of Hsp70 during polypeptide import to the mitochondrial matrix.

Synthesis, reactivity, and electronic structure of [n]vanadoarenophanes: an experimental and theoretical study.

An optimized procedure for the selective dimetalation of [V(eta (6)-C 6H 6) 2] by BuLi/tmeda allowed for the isolation and characterization of [V(eta (6)-C 6H 5Li) 2].tmeda. X-ray diffraction of its thf solvate [V(eta (6)-C 6H 5Li) 2].(thf) 7 revealed an unsymmetrical, dimeric composition in the solid state, in which both subunits are connected by three bridging lithium atoms. Treatment with several element dihalides facilitated the isolation of [ n]vanadoarenophanes ( n = 1, 2) with boron and silicon in the bridging positions. In agreement with the number and covalent radii of the bridging elements, these derivatives exhibit molecular ring strain to a greater or lesser extent. The B-B bond of the [2]bora species [V(eta (6)-C 6H 5) 2B 2(NMe 2) 2] was readily cleaved by [Pt(PEt 3) 3] to afford the corresponding oxidative addition product. Subsequently, [V(eta (6)-C 6H 5) 2B 2(NMe 2) 2] was employed as a diborane(4) precursor in the diboration of 2-butyne under stoichiometric, homogeneous, and heterogeneous catalysis conditions. This transformation is facilitated by the reduction of molecular ring strain, which was confirmed by a decrease of the tilt angle alpha observed in the corresponding solid-state structures. EPR spectroscopy was used to probe the electronic structure of strained [ n]vanadoarenophanes and revealed an obvious correlation between the degree of molecular distortion and the observed hyperfine coupling constant a iso. State-of-the-art DFT calculations were able to reproduce the measured isotropic vanadium hyperfine couplings and the coupling anisotropies. The calculations confirmed the decrease of the absolute isotropic hyperfine couplings with increasing tilt angle. Closer analysis showed that this is mainly due to increased positive contributions to the spin density at the vanadium nucleus from the spin polarization of doubly occupied valence orbitals of vanadium-ligand sigma-antibonding character. The latter are destabilized and thus made more polarizable in the bent structures.

Photophysical properties of platinum(II)-acetylide complexes: the effect of a strongly electron-accepting diimine ligand on excited-state structure.

The compounds [Pt(MesBIAN)(C[triple bond]CR)2] (R = C6H4-CN-p, 1; SiMe3, 2; C6H4-CF3-p, 3; C6H5, 4; C6H4-CH3-p 5) {MesBIAN = bis(mesitylimino)acenaphthene} have been synthesized; the X-ray crystal structure determinations of 4 and 5 and the starting material [Pt(MesBIAN)Cl2] are reported. Chemical oxidation of 4 with diiodine leads to generation of an intermediate platinum(IV) bis(acetylide) diiodide complex, which then couples and reductively eliminates the acetylide ligands as a diyne, leading to the generation of [Pt(MesBIAN)I2] 6. Compound 2 readily forms an adduct 2a with copper(I) chloride, in which the copper atom is bonded to the two acetylide triple bonds. 1-5 each undergo an irreversible oxidation, and a reversible one-electron reduction to generate a stable anion. ESR studies of 1(-)-5(-) show that the unpaired electron is localized mainly on the pi* orbital of the coordinated MesBIAN ligand, with about 10% platinum contribution to the singly occupied molecular orbital (SOMO). The compounds show a strong absorption at around 500 nm in the UV/visible spectrum, which is assigned to a "mixed metal-ligand to ligand charge transfer" (MMLL'CT) transition; this assignment is supported by time-dependent density-functional theory (TD-DFT) calculations on 5. 1-5 emit in the near-infrared region from a (3)MMLL'CT excited state, with lifetimes ranging from 8 to 36 ns. Picosecond and nanosecond time-resolved infrared (TRIR) spectroscopy has been used to probe directly the nature and dynamics of the excited state of 5. The TRIR data show a decrease of the energy of the C[triple bond]C vibration upon excitation, by about 90 cm(-1) in comparison to the ground state, and formation of a new, very intense, and very broad band at 1820 cm(-1). We propose that the excited-state structure contains some contribution from a pseudo-cumulenic form of the platinum-acetylide moiety, which is supported by TD-DFT calculations. Picosecond TRIR allowed determination of the rate of vibrational relaxation (14 ps) of the vibrationally "hot" electronic excited state of 5 formed upon initial laser excitation.

Isolation by HPLC and characterisation of the bioactive fraction of New Zealand manuka (Leptospermum scoparium) honey.

Using HPLC a fraction of New Zealand manuka honey has been isolated, which gives rise to the non-peroxide antibacterial activity. This fraction proved to be methylglyoxal, a highly reactive precursor in the formation of advanced glycation endproducts (AGEs). Methylglyoxal concentrations in 49 manuka and 34 non-manuka honey samples were determined using a direct detection method and compared with values obtained using standard o-phenylenediamine derivatisation. Concentrations obtained using both the methods were similar and varied from 38 to 828 mg/kg.

A tetra-nuclear chlorido-bridged manganese(II) cluster with imidazole ligands.

The crystal structure of di-µ(3)-chlorido-tetra-µ(2)-chlorido-dichloridoocta-(imidazole-κN)tetra-manganese(II) ethanol 1.234 solvate, [Mn(4)Cl(8)(C(3)H(4)N(2))(8)]·1.234C(2)H(5)O or [Mn(4)Cl(8)(Him)(8)]·1.234EtOH, where Him is imidazole (C(3)H(4)N(2)), is based upon two Mn(4)Cl(4) cubes which share one face, and which each lack one manganese vertex, giving a Mn(4)Cl(6) unit. This contains two different octa-hedral coordination environments for the Mn atoms. Mn1 is coordinated by four bridging chlorido ligands and two imidazole N atoms, whereas Mn2 is coordinated by three bridging and one terminal Cl and two imidazole N atoms. The remaining two Mn centres are generated by inversion symmetry. A partial occupancy solvent mol-ecule (ethanol) is present. The crystal structure displays several N-H⋯Cl and N-H⋯O hydrogen bonds.

2-Oxo-1,2-dihydro-pyrimidin-3-ium di-µ-chlorido-bis-{dichloridobis[pyrimidin-2(1H)-one-κN]cuprate(II)} dihydrate.

The asymmetric unit of the title compound, (C(4)H(5)N(2)O)(2)[Cu(2)Cl(6)(C(4)H(4)N(2)O)(2)]·2H(2)O, consists of one cation, one half of a centrosymmetric dianion and one water mol-ecule. The centrosymmetric dianion formed by dimerization in the crystal structure has neutral pyrimidin-2-one ligands coordinated to each copper(II) centre through Cu-N bonds. The Cu atoms each have a distorted trigonal bipyramidal geometry, with the N atom of the pyrimidin-2-one ligand in an axial position, and dimerize by sharing two equatorial Cl atoms. N-H⋯Cl, O-H⋯Cl and N-H⋯O hydrogen bonds connect the anions, cations and water mol-ecules, forming a three-dimensional network.