Unravelling ionic liquid solvent effects for a non-polar Cope rearrangement reaction.

The impact of ionic liquids (ILs) on polar reactions is well recognised, however the impact of ILs on non-polar reactions is less well understood or explored. Pericyclic Cope rearrangements are highly concerted, exhibit minimal charge localisation and pass through an uncharged but well-defined transition state, and thus provide a good mechanism for exploring the impact of IL polarizability on chemical reactivity. Recently, a 10× rate enhancement has been observed for the Cope rearrangement of 3-phenyl-1,5-hexadiene in the IL 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4C1im][NTf2] compared to benzene. In this work we undertake a DFT based computational study (B3LYP-D3BJ/6-311+G(d,p) and M06-2X-D3/6-311+G(d,p)) of the Cope rearrangement of 3-phenyl-1,5-hexadiene and 3-propyl-hexa-1,5-diene in molecular solvents (acetonitrile, benzene and ethanol) and the IL [C4C1im][NTf2] using the SMD solvation model. The impact of benzene and [C4C1im][NTf2] on the Cope rearrangement of 3-phenyl-1,5-hexadiene is studied in more detail and we provide insight into the reason for the rate enhancement in an IL. The volume of activation is evaluated and the potential impact of 'solvent pressure' is discussed. We identify two potential mechanisms for volume effects to contribute to the rate enhancement. Solvent association energies are evaluated at the DLNPO-CCSD(T) level. Specific solvent interactions are explored through atomic partial charge, molecular orbital and bond critical point analysis, as well as via non-colvalent interaction (NCI) plots, electrostatic potential (ESP) differences and density difference Δρ(r) plots. We find that the cation and anion together form an extensive van der Waals pocket in-which the transition state (TS) sits. Electron density within the TS is anisotropically polarised via a 'push-pull' effect due to the dual cation-anion nature of the IL, stabilising the TS relative to benzene. We also provide experimental evidence that these effects are generalisable to other ILs. Overall, our aim is to provide a deeper moleuclar level understanding of the impact of ILs on non-polar reactions.

Charge transfer and polarisability in ionic liquids: a case study.

The practical use of ionic liquids (ILs) is benefiting from a growing understanding of the underpinning structural and dynamic properties, facilitated through classical molecular dynamics (MD) simulations. The predictive and explanatory power of a classical MD simulation is inextricably linked to the underlying force field. A key aspect of the forcefield for ILs is the ability to recover charge based interactions. Our focus in this paper is on the description and recovery of charge transfer and polarisability effects, demonstrated through MD simulations of the widely used 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide [C4C1im][NTf2] IL. We study the charge distributions generated by a range of ab initio methods, and present an interpolation method for determining atom-wise scaled partial charges. Two novel methods for determining the mean field (total) charge transfer from anion to cation are presented. The impact of using different charge models and different partial charge scaling (unscaled, uniformly scaled, atom-wise scaled) are compared to fully polarisable simulations. We study a range of Drude particle explicitly polarisable potentials and shed light on the performance of current approaches to counter known problems. It is demonstrated that small changes in the charge description and MD methodology can have a significant impact; biasing some properties, while leaving others unaffected within the structural and dynamic domains.

Missed connections: recombination and human aneuploidy.

The physical exchange of DNA between homologs, crossing-over, is essential to orchestrate the unique, reductional first meiotic division (MI). In females, the events of meiotic recombination that serve to tether homologs and facilitate their disjunction at MI occur during fetal development, preceding the MI division by several decades in our species. Data from studies in humans and mice demonstrate that placement of recombination sites during fetal development influences the likelihood of an MI nondisjunction event that results in the production of an aneuploid egg. Here we briefly summarize what we know about the relationship between aneuploidy and meiotic recombination and important considerations for the future of human assisted reproduction.

Bi(III) halometallate ionic liquids: Interactions and speciation.

Bismuth containing compounds are of particular interest for optical or photo-luminescent applications in sensing, bio-imaging, telecommunications, and opto-electronics and as components in non-toxic extremely dense liquids. Bismuth(III) halometallates form highly colored novel ionic liquid based solvents for which experimental characterization and fundamental understanding are limited. In this work, Bismuth(III) halometallates incorporating chloride, bromide, and iodide have been studied via density functional theory employing B3LYP-D3BJ/aug-cc-pVDZ. Lone anions, and anions in clusters with sufficient 1-ethyl-3-methyl-imidazolium [C2C1Im]+ counter-cations to balance the charge, have been investigated in the gas- phase, and with polarizable continuum solvation. Evaluation of speciation profiles indicates that dimeric or trimeric anions are prevalent. In contrast to analogous Al systems, anions of higher charge (-2, -3) are present. Speciation profiles are similar, but not identical with respect to the halide. The Bi based anions [BimXn]x- in the gas phase and generalized solvation environment produce multiple low energy conformers; moreover, key structural interaction patterns emerge from an analysis of ion-pair and neutral-cluster structures (BimXn)x-(C2C1Im)x + for x = 1, 2, and 3. Cation-anion interactions are weak; with Coulombic and dispersion forces predominating, anion-π structures are favored, while significant hydrogen bonding does not occur. Anion to cation charge transfer is minimal, but mutual polarization is significant, leading to local positive regions in the anion electrostatic potential surface. The key features of experimental x-ray photoelectron, UV-Vis spectra, and Raman spectra are reproduced, validating the computational results and facilitating rationalization of key features.

Ether functionalisation, ion conformation and the optimisation of macroscopic properties in ionic liquids.

Ionic liquids are an attractive material class due to their wide liquid range, intrinsic ionic conductivity, and high chemical as well as electrochemical stability. However, the widespread use of ionic liquids is hindered by significantly higher viscosities compared to conventional molecular solvents. In this work, we show how the transport properties of ionic liquids can be altered significantly, even for isostructural ions that have the same backbone. To this end, structure-property relationships have been determined for a set of 16 systematically varied representative ionic liquids. Variations in molecular structure include ammonium vs. phosphonium, ether vs. alkyl side chains, and rigid vs. flexible anions. Ab initio calculations are used to relate molecular structures to the thermal, structural and transport properties of the ionic liquids. We find that the differences in properties of ether and alkyl functionalised ionic liquids are primarily dependent on minimum energy geometries, with the conformational flexibility of ether side chains appearing to be of secondary importance. We also show unprecedented correlations between anion conformational flexibility and transport properties. Critically, increasing fluidity upon consecutive introduction of ether side chains and phosphonium centres into the cation is found to be dependent on whether the anion is flexible or rigid. We demonstrate that targeted design of functional groups based on structure-property relationships can yield ionic liquids of exceptionally high fluidity.

Correction: Germline and reproductive tract effects intensify in male mice with successive generations of estrogenic exposure.

[This corrects the article DOI: 10.1371/journal.pgen.1006885.].

Germline and reproductive tract effects intensify in male mice with successive generations of estrogenic exposure.

The hypothesis that developmental estrogenic exposure induces a constellation of male reproductive tract abnormalities is supported by experimental and human evidence. Experimental data also suggest that some induced effects persist in descendants of exposed males. These multi- and transgenerational effects are assumed to result from epigenetic changes to the germline, but few studies have directly analyzed germ cells. Typically, studies of transgenerational effects have involved exposing one generation and monitoring effects in subsequent unexposed generations. This approach, however, has limited human relevance, since both the number and volume of estrogenic contaminants has increased steadily over time, intensifying rather than reducing or eliminating exposure. Using an outbred CD-1 mouse model, and a sensitive and quantitative marker of germline development, meiotic recombination, we tested the effect of successive generations of exposure on the testis. We targeted the germline during a narrow, perinatal window using oral exposure to the synthetic estrogen, ethinyl estradiol. A complex three generation exposure protocol allowed us to compare the effects of individual, paternal, and grandpaternal (ancestral) exposure. Our data indicate that multiple generations of exposure not only exacerbate germ cell exposure effects, but also increase the incidence and severity of reproductive tract abnormalities. Taken together, our data suggest that male sensitivity to environmental estrogens is increased by successive generations of exposure.

Correlations between Synaptic Initiation and Meiotic Recombination: A Study of Humans and Mice.

Meiotic recombination is initiated by programmed double strand breaks (DSBs), only a small subset of which are resolved into crossovers (COs). The mechanism determining the location of these COs is not well understood. Studies in plants, fungi, and insects indicate that the same genomic regions are involved in synaptic initiation and COs, suggesting that early homolog alignment is correlated with the eventual resolution of DSBs as COs. It is generally assumed that this relationship extends to mammals, but little effort has been made to test this idea. Accordingly, we conducted an analysis of synaptic initiation sites (SISs) and COs in human and mouse spermatocytes and oocytes. In contrast to our expectation, we observed remarkable sex- and species-specific differences, including pronounced differences between human males and females in both the number and chromosomal location of SISs. Further, the combined data from our studies in mice and humans suggest that the relationship between SISs and COs in mammals is a complex one that is not dictated by the sites of synaptic initiation as reported in other organisms, although it is clearly influenced by them.

WOMEN IN REPRODUCTIVE SCIENCE: Errors and insight: intentional and accidental studies of human chromosome abnormalities.

Perhaps every career makes sense in retrospect. I have spent mine facing a series of accidental environmental exposures that derailed our studies but provided new insight. Although at times I have felt more catalyst than scientist, the journey has been extraordinary, and the problem I have spent my career studying - human aneuploidy - has taken on new significance with growing evidence of the sensitivity of the germline to the environment.

Electron spectroscopy of ionic liquids: experimental identification of atomic orbital contributions to valence electronic structure.

The atomic contributions to valence electronic structure for 37 ionic liquids (ILs) are identified using a combination of variable photon energy XPS, resonant Auger electron spectroscopy (RAES) and a subtraction method. The ILs studied include a diverse range of cationic and anionic structural moieties. We introduce a new parameter for ILs, the energy difference between the energies of the cationic and anionic highest occupied fragment orbitals (HOFOs), which we use to identify the highest occupied molecular orbital (HOMO). The anion gave rise to the HOMO for 25 of the 37 ILs studied here. For 10 of the ILs, the energies of the cationic and anionic HOFOs were the same (within experimental error); therefore, it could not be determined whether the HOMO was from the cation or the anion. For two of the ILs, the HOMO was from the cation and not from the anion; consequently it is energetically more favourable to remove an electron from the cation than the anion for these two ILs. In addition, we used a combination of area normalisation and subtraction of XP spectra to produce what are effectively XP spectra for individual ions; this was achieved for 10 cations and 14 anions.

Human aneuploidy: mechanisms and new insights into an age-old problem.

Trisomic and monosomic (aneuploid) embryos account for at least 10% of human pregnancies and, for women nearing the end of their reproductive lifespan, the incidence may exceed 50%. The errors that lead to aneuploidy almost always occur in the oocyte but, despite intensive investigation, the underlying molecular basis has remained elusive. Recent studies of humans and model organisms have shed new light on the complexity of meiotic defects, providing evidence that the age-related increase in errors in the human female is not attributable to a single factor but to an interplay between unique features of oogenesis and a host of endogenous and exogenous factors.

Evaluating excited state atomic polarizabilities of chromophores.

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomic charge transfer and polarizability terms, and variation in the presence of an electric field has been used to evaluate atomic polarizabilities. On excitation, MQ undergoes very site-specific changes in polarizability while C153 shows significantly less variation. We also conclude that MQ cannot be adequately described by standard atomic polarizabilities based on atomic number and hybridization state. Changes in the molecular polarizability of MQ (on excitation) are not representative of the local site-specific changes in atomic polarizability, thus the overall molecular polarizability ratio does not provide a good approximation for local atom-specific polarizability changes on excitation. Accurate excited state force fields are needed for computer simulation of solvation dynamics. The chromophores considered in this study are often used as molecular probes. The methods and data reported here can be used for the construction of polarizable ground and excited state force fields. Atomic and molecular polarizabilities (ground and excited states) have been evaluated over a range of functionals and basis sets. Different mechanisms for including solvation effects have been examined; using a polarizable continuum model, explicit solvation and via sampling of clusters extracted from a MD simulation. A range of different solvents have also been considered.

Experimental validation of calculated atomic charges in ionic liquids.

A combination of X-ray photoelectron spectroscopy and near edge X-ray absorption fine structure spectroscopy has been used to provide an experimental measure of nitrogen atomic charges in nine ionic liquids (ILs). These experimental results are used to validate charges calculated with three computational methods: charges from electrostatic potentials using a grid-based method (ChelpG), natural bond orbital population analysis, and the atoms in molecules approach. By combining these results with those from a previous study on sulfur, we find that ChelpG charges provide the best description of the charge distribution in ILs. However, we find that ChelpG charges can lead to significant conformational dependence and therefore advise that small differences in ChelpG charges (<0.3 e) should be interpreted with care. We use these validated charges to provide physical insight into nitrogen atomic charges for the ILs probed.

Inactivation of Retinoblastoma Protein (Rb1) in the Oocyte: Evidence That Dysregulated Follicle Growth Drives Ovarian Teratoma Formation in Mice.

The origin of most ovarian tumors is undefined. Here, we report development of a novel mouse model in which conditional inactivation of the tumor suppressor gene Rb1 in oocytes leads to the formation of ovarian teratomas (OTs). While parthenogenetically activated ooctyes are a known source of OT in some mutant mouse models, enhanced parthenogenetic propensity in vitro was not observed for Rb1-deficient oocytes. Further analyses revealed that follicle recruitment and growth is disrupted in ovaries of mice with conditional inactivation of Rb1, leading to abnormal accumulation of secondary/preantral follicles. These findings underpin the concept that miscues between the germ cell and somatic compartments cause premature oocyte activation and the formation of OTs. Furthermore, these results suggest that defects in folliculogenesis and a permissive genetic background are sufficient to drive OT development, even in the absence of enhanced parthenogenetic activation. Thus, we have discovered a novel role of Rb1 in regulating the entry of primordial oocytes into the pool of growing follicles and signaling between the oocyte and granulosa cells during the protracted process of oocyte growth. Our findings, coupled with data from studies of other OT models, suggest that defects in the coordinated regulation between growth of the oocyte and somatic components in follicles are an underlying cause of OT formation.

Estrogenic exposure alters the spermatogonial stem cells in the developing testis, permanently reducing crossover levels in the adult.

Bisphenol A (BPA) and other endocrine disrupting chemicals have been reported to induce negative effects on a wide range of physiological processes, including reproduction. In the female, BPA exposure increases meiotic errors, resulting in the production of chromosomally abnormal eggs. Although numerous studies have reported that estrogenic exposures negatively impact spermatogenesis, a direct link between exposures and meiotic errors in males has not been evaluated. To test the effect of estrogenic chemicals on meiotic chromosome dynamics, we exposed male mice to either BPA or to the strong synthetic estrogen, ethinyl estradiol during neonatal development when the first cells initiate meiosis. Although chromosome pairing and synapsis were unperturbed, exposed outbred CD-1 and inbred C3H/HeJ males had significantly reduced levels of crossovers, or meiotic recombination (as defined by the number of MLH1 foci in pachytene cells) by comparison with placebo. Unexpectedly, the effect was not limited to cells exposed at the time of meiotic entry but was evident in all subsequent waves of meiosis. To determine if the meiotic effects induced by estrogen result from changes to the soma or germline of the testis, we transplanted spermatogonial stem cells from exposed males into the testes of unexposed males. Reduced recombination was evident in meiocytes derived from colonies of transplanted cells. Taken together, our results suggest that brief exogenous estrogenic exposure causes subtle changes to the stem cell pool that result in permanent alterations in spermatogenesis (i.e., reduced recombination in descendent meiocytes) in the adult male.

Examining variation in recombination levels in the human female: a test of the production-line hypothesis.

The most important risk factor for human aneuploidy is increasing maternal age, but the basis of this association remains unknown. Indeed, one of the earliest models of the maternal-age effect--the "production-line model" proposed by Henderson and Edwards in 1968--remains one of the most-cited explanations. The model has two key components: (1) that the first oocytes to enter meiosis are the first ovulated and (2) that the first to enter meiosis have more recombination events (crossovers) than those that enter meiosis later in fetal life. Studies in rodents have demonstrated that the first oocytes to enter meiosis are indeed the first to be ovulated, but the association between the timing of meiotic entry and recombination levels has not been tested. We recently initiated molecular cytogenetic studies of second-trimester human fetal ovaries, allowing us to directly examine the number and distribution of crossover-associated proteins in prophase-stage oocytes. Our observations on over 8,000 oocytes from 191 ovarian samples demonstrate extraordinary variation in recombination within and among individuals but provide no evidence of a difference in recombination levels between oocytes entering meiosis early in fetal life and those entering late in fetal life. Thus, our data provide a direct test of the second tenet of the production-line model and suggest that it does not provide a plausible explanation for the human maternal-age effect, meaning that-45 years after its introduction-we can finally conclude that the production-line model is not the basis for the maternal-age effect on trisomy.

Atomic charges of sulfur in ionic liquids: experiments and calculations.

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra, X-ray photoelectron (XP) spectra and Auger electron spectra are reported for sulfur in ionic liquids (ILs) with a range of chemical structures. These values provide experimental measures of the atomic charge in each IL and enable the evaluation of the suitability of NEXAFS spectroscopy and XPS for probing the relative atomic charge of sulfur. In addition, we use Auger electron spectroscopy to show that when XPS binding energies differ by less than 0.5 eV, conclusions on atomic charge should be treated with caution. Our experimental data provides a benchmark for calculations of the atomic charge of sulfur obtained using different methods. Atomic charges were computed for lone ions and ion pairs, both in the gas phase (GP) and in a solvation model (SMD), with a wide range of ion pair conformers considered. Three methods were used to compute the atomic charges: charges from the electrostatic potential using a grid based method (ChelpG), natural bond orbital (NBO) population analysis and Bader's atoms in molecules (AIM) approach. By comparing the experimental and calculated measures of the atomic charge of sulfur, we provide an order for the sulfur atoms, ranging from the most negative to the most positive atomic charge. Furthermore, we show that both ChelpG and NBO are reasonable methods for calculating the atomic charge of sulfur in ILs, based on the agreement with both the XPS and NEXAFS spectroscopy results. However, the atomic charges of sulfur derived from ChelpG are found to display significant, non-physical conformational dependence. Only small differences in individual atomic charge of sulfur were observed between lone ion (GP) and ion pair IL(SMD) model systems, indicating that ion-ion interactions do not strongly influence individual atomic charges.

NEXAFS spectroscopy of ionic liquids: experiments versus calculations.

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra are reported for 12 ionic liquids (ILs) encompassing a range of chemical structures for both the sulfur 1s and nitrogen 1s edges and compared with time-dependent density functional theory (TD-DFT) calculations. The energy scales for the experimental data were carefully calibrated against literature data. Gas phase calculations were performed on lone ions, ion pairs and ion pair dimers, with a wide range of ion pair conformers considered. For the first time, it is demonstrated that TD-DFT is a suitable method for simulating NEXAFS spectra of ILs, although the number of ions included in the calculations and their conformations are important considerations. For most of the ILs studied, calculations on lone ions in the gas phase were sufficient to successfully reproduce the experimental NEXAFS spectra. However, for certain ILs - for example, those containing a protic ammonium cation - calculations on ion pairs were required to obtain a good agreement with experimental spectra. Furthermore, significant conformational dependence was observed for the protic ammonium ILs, providing insight into the predominant liquid phase cation-anion interactions. Among the 12 investigated ILs, we find that four have an excited state that is delocalised across both the cation and the anion, which has implications for any process that depends on the excited state, for example, radiolysis. Considering the collective experimental and theoretical data, we recommend that ion pairs should be the minimum number of ions used for the calculation of NEXAFS spectra of ILs.

Doubly ionic hydrogen bond interactions within the choline chloride-urea deep eutectic solvent.

Deep eutectic solvents (DESs) are exemplars of systems with the ability to form neutral, ionic and doubly ionic H-bonds. Herein, the pairwise interactions of the constituent components of the choline chloride-urea DES are examined. Evidence is found for a tripodal CHCl doubly ionic H-bond motif. Moreover it is found that the covalency of doubly ionic H-bonds can be greater than, or comparable with, neutral and ionic examples. In contrast to many traditional solvents, an "alphabet soup" of many different types of H-bond (OHO[double bond, length as m-dash]C, NHO[double bond, length as m-dash]C, OHCl, NHCl, OHNH, CHCl, CHO[double bond, length as m-dash]C, NHOH and NHNH) can form. These H-bonds exhibit substantial flexibility in terms of number and strength. It is anticipated that H-bonding will have a significant impact on the entropy of the system and thus could play an important role in the formation of the eutectic. The 2 : 1 urea : choline-chloride eutectic point of this DES is often associated with the formation of a [Cl(urea)2](-) complexed anion. However, urea is found to form a H-bonded urea[choline](+) complexed cation that is energetically competitive with [Cl(urea)2](-). The negative charge on [Cl(urea)2](-) is found to remain localised on the chloride, moreover, the urea[choline](+) complexed cation forms the strongest H-bond studied here. Thus, there is potential to consider a urea[choline](+)·urea[Cl](-) interaction.

A structural investigation of ionic liquid mixtures.

The structures of mixtures of ionic liquids (ILs) featuring a common 1-butyl-3-methylimidazolium ([C4C1im](+)) cation but different anions have been investigated both experimentally and computationally. (1)H and (13)C NMR of the ILs and their mixtures has been performed both on the undiluted liquids and those diluted by CD2Cl2. These experiments have been complemented by quantum chemical density functional theory calculations and molecular dynamics simulations. These techniques have identified the formation of preferential interactions between H(2) of the imidazolium cation and the most strongly hydrogen bond (H-bond) accepting anion. In addition, a preference for the more weakly H-bond accepting anion to interact above the imidazolium ring through anion-π(+) interactions has been identified. The modelling of these data has identified that the magnitude of these preferences are small, of the order of only a few kJ mol(-1), for all IL mixtures. No clustering of the anions around a specific cation could be observed, indicating that these interactions arise from the reorientation of the cation within a randomly assigned network of anions. π(+)-π(+) stacking of the imidazolium cations was also studied and found to be promoted by ILs with a strong H-bond accepting anion. Stacking interactions are easily disrupted by the introduction of small proportions (<50 mol%) of a weakly coordinating anion due to their propensity to form anion-π(+) interactions. These results suggest that the formation of IL mixtures with different anions leads to subtle structural changes of much lower energy than the Coulombic ordering of ions, accounting for why most IL mixtures exhibit ideal, or nearly ideal, behaviour.