Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic

Many functionally promiscuous plant 2,3-oxidosqualene cyclases (OSCs) have been found, but complete functional reshaping is rarely reported. In this study, we have identified two new plant OSCs: a unique protostadienol synthase (AoPDS) and a common cycloartenol synthase (AoCAS) from Alisma orientale (Sam.) Juzep. Multiscale simulations and mutagenesis experiments revealed that threonine-727 is an essential residue responsible for protosta-13 (17),24-dienol biosynthesis in AoPDS and that the F726T mutant completely reshapes the native function of AoCAS into a PDS function to yield almost exclusively protosta-13 (17),24-dienol. Unexpectedly, various native functions were uniformly reshaped into a PDS function by introducing the phenylalanine → threonine substitution at this conserved position in other plant and non-plant chair-boat-chair-type OSCs. Further computational modeling elaborated the trade-off mechanisms of the phenylalanine → threonine substitution that leads to the PDS activity. This study demonstrates a general strategy for functional reshaping by using a plastic residue based on the decipherment of the catalytic mechanism.

Computational studies on the sterol-like cyclization of a monodomain class II terpene cyclase

Recently the first example of a class II terpene cyclase comprised of only a single domain was reported. Class II synthases are a diverse group of enzymes that catalyze exceptionally complex reactions, including the remarkable cyclization of steroids. This discovery of a single-domain enzyme being able to catalyze a steroid-like product contradicted the long-held tenet that complex class II cyclizations required double-domain enzymes. The proposed mechanism for the sterol-like cyclization of a monodomain class II terpene cyclase was studied computationally by using density functional theory (DFT). The complete pathway for the conversion of 5-geranyl-3,4-dihydroxybenzoate to the steroid-like pentacyclic product merosterolic acid A was elucidated. The formation of a tricyclic carbocation intermediate with three cyclohexane rings was found to be a concerted, but asynchronous, cyclization. The formation of the fourth ring proceeds with a low energy activation Friedel-Crafts reaction. Subsequent deprotonation of this pentacyclic system gave as the final product merosterolic acid. The overall conversion was found to be highly exothermic due to the conversion of three C-C double bonds to C-C single bonds.

D-Meson Azimuthal Anisotropy in Midcentral Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV

The azimuthal anisotropy coefficient v_{2} of prompt D^{0}, D^{+}, D^{*+}, and D_{s}^{+} mesons was measured in midcentral (30%-50% centrality class) Pb-Pb collisions at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02  TeV, with the ALICE detector at the LHC. The D mesons were reconstructed via their hadronic decays at midrapidity, |y|<0.8, in the transverse momentum interval 1<p_{T}<24  GeV/c. The measured D-meson v_{2} has similar values as that of charged pions. The D_{s}^{+} v_{2}, measured for the first time, is found to be compatible with that of nonstrange D mesons. The measurements are compared with theoretical calculations of charm-quark transport in a hydrodynamically expanding medium and have the potential to constrain medium parameters.

J/ψ Elliptic Flow in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

We report a precise measurement of the J/ψ elliptic flow in Pb-Pb collisions at sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The J/ψ mesons are reconstructed at midrapidity (|y|<0.9) in the dielectron decay channel and at forward rapidity (2.5<y<4.0) in the dimuon channel, both down to zero transverse momentum. At forward rapidity, the elliptic flow v_{2} of the J/ψ is studied as a function of the transverse momentum and centrality. A positive v_{2} is observed in the transverse momentum range 2<p_{T}<8  GeV/c in the three centrality classes studied and confirms with higher statistics our earlier results at sqrt[s_{NN}]=2.76  TeV in semicentral collisions. At midrapidity, the J/ψ  v_{2} is investigated as a function of the transverse momentum in semicentral collisions and found to be in agreement with the measurements at forward rapidity. These results are compared to transport model calculations. The comparison supports the idea that at low p_{T} the elliptic flow of the J/ψ originates from the thermalization of charm quarks in the deconfined medium but suggests that additional mechanisms might be missing in the models.

Anomalous Evolution of the Near-Side Jet Peak Shape in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

The measurement of two-particle angular correlations is a powerful tool to study jet quenching in a p_{T} region inaccessible by direct jet identification. In these measurements pseudorapidity (Δη) and azimuthal (Δφ) differences are used to extract the shape of the near-side peak formed by particles associated with a higher p_{T} trigger particle (1<p_{T,trig}<8  GeV/c). A combined fit of the near-side peak and long-range correlations is applied to the data allowing the extraction of the centrality evolution of the peak shape in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. A significant broadening of the peak in the Δη direction at low p_{T} is found from peripheral to central collisions, which vanishes above 4  GeV/c, while in the Δφ direction the peak is almost independent of centrality. For the 10% most central collisions and 1<p_{T,assoc}<2  GeV/c, 1<p_{T,trig}<3  GeV/c a novel feature is observed: a depletion develops around the center of the peak. The results are compared to pp collisions at the same center of mass energy and ampt model simulations. The comparison to the investigated models suggests that the broadening and the development of the depletion is connected to the strength of radial and longitudinal flow.

Flow Dominance and Factorization of Transverse Momentum Correlations in Pb-Pb Collisions at the LHC

We present the first measurement of the two-particle transverse momentum differential correlation function, P_{2}≡⟨Δp_{T}Δp_{T}⟩/⟨p_{T}⟩^{2}, in Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV. Results for P_{2} are reported as a function of the relative pseudorapidity (Δη) and azimuthal angle (Δφ) between two particles for different collision centralities. The Δϕ dependence is found to be largely independent of Δη for |Δη|≥0.9. In the 5% most central Pb-Pb collisions, the two-particle transverse momentum correlation function exhibits a clear double-hump structure around Δφ=π (i.e., on the away side), which is not observed in number correlations in the same centrality range, and thus provides an indication of the dominance of triangular flow in this collision centrality. Fourier decompositions of P_{2}, studied as a function of the collision centrality, show that correlations at |Δη|≥0.9 can be well reproduced by a flow ansatz based on the notion that measured transverse momentum correlations are strictly determined by the collective motion of the system.

Computational studies on the cyclization of squalene to the steroids and hopenes

A review of computational studies of the related biosyntheses of steroids and hopenes reported during the last two decades is presented.

Correlated Event-by-Event Fluctuations of Flow Harmonics in Pb-Pb Collisions at sqrt[s_{NN}]=2.76 TeV

We report the measurements of correlations between event-by-event fluctuations of amplitudes of anisotropic flow harmonics in nucleus-nucleus collisions, obtained for the first time using a new analysis method based on multiparticle cumulants in mixed harmonics. This novel method is robust against systematic biases originating from nonflow effects and by construction any dependence on symmetry planes is eliminated. We demonstrate that correlations of flow harmonics exhibit a better sensitivity to medium properties than the individual flow harmonics. The new measurements are performed in Pb-Pb collisions at the center-of-mass energy per nucleon pair of sqrt[s_{NN}]=2.76  TeV by the ALICE experiment at the Large Hadron Collider. The centrality dependence of correlation between event-by-event fluctuations of the elliptic v_{2} and quadrangular v_{4} flow harmonics, as well as of anticorrelation between v_{2} and triangular v_{3} flow harmonics are presented. The results cover two different regimes of the initial state configurations: geometry dominated (in midcentral collisions) and fluctuation dominated (in the most central collisions). Comparisons are made to predictions from Monte Carlo Glauber, viscous hydrodynamics, ampt, and hijing models. Together with the existing measurements of the individual flow harmonics the presented results provide further constraints on the initial conditions and the transport properties of the system produced in heavy-ion collisions.

Centrality Dependence of the Charged-Particle Multiplicity Density at Midrapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV

The pseudorapidity density of charged particles, dN_{ch}/dη, at midrapidity in Pb-Pb collisions has been measured at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV. For the 5% most central collisions, we measure a value of 1943±54. The rise in dN_{ch}/dη as a function of sqrt[s_{NN}] is steeper than that observed in proton-proton collisions and follows the trend established by measurements at lower energy. The increase of dN_{ch}/dη as a function of the average number of participant nucleons, ⟨N_{part}⟩, calculated in a Glauber model, is compared with the previous measurement at sqrt[s_{NN}]=2.76  TeV. A constant factor of about 1.2 describes the increase in dN_{ch}/dη from sqrt[s_{NN}]=2.76 to 5.02 TeV for all centrality classes, within the measured range of 0%-80% centrality. The results are also compared to models based on different mechanisms for particle production in nuclear collisions.

Measurement of an Excess in the Yield of J/ψ at Very Low p_{T} in Pb-Pb Collisions at sqrt[s]_{NN}=2.76 TeV

We report on the first measurement of an excess in the yield of J/ψ at very low transverse momentum (p_{T}<0.3  GeV/c) in peripheral hadronic Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV, performed by ALICE at the CERN LHC. Remarkably, the measured nuclear modification factor of J/ψ in the rapidity range 2.5<y<4 reaches about 7 (2) in the p_{T} range 0-0.3  GeV/c in the 70%-90% (50%-70%) centrality class. The J/ψ production cross section associated with the observed excess is obtained under the hypothesis that coherent photoproduction of J/ψ is the underlying physics mechanism. If confirmed, the observation of J/ψ coherent photoproduction in Pb-Pb collisions at impact parameters smaller than twice the nuclear radius opens new theoretical and experimental challenges and opportunities. In particular, coherent photoproduction accompanying hadronic collisions may provide insight into the dynamics of photoproduction and nuclear reactions, as well as become a novel probe of the quark-gluon plasma.

Anisotropic Flow of Charged Particles in Pb-Pb Collisions at √[s{NN}]=5.02 TeV

We report the first results of elliptic (v_{2}), triangular (v_{3}), and quadrangular (v_{4}) flow of charged particles in Pb-Pb collisions at a center-of-mass energy per nucleon pair of sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the CERN Large Hadron Collider. The measurements are performed in the central pseudorapidity region |η|<0.8 and for the transverse momentum range 0.2<p_{T}<5  GeV/c. The anisotropic flow is measured using two-particle correlations with a pseudorapidity gap greater than one unit and with the multiparticle cumulant method. Compared to results from Pb-Pb collisions at sqrt[s_{NN}]=2.76  TeV, the anisotropic flow coefficients v_{2}, v_{3}, and v_{4} are found to increase by (3.0±0.6)%, (4.3±1.4)%, and (10.2±3.8)%, respectively, in the centrality range 0%-50%. This increase can be attributed mostly to an increase of the average transverse momentum between the two energies. The measurements are found to be compatible with hydrodynamic model calculations. This comparison provides a unique opportunity to test the validity of the hydrodynamic picture and the power to further discriminate between various possibilities for the temperature dependence of shear viscosity to entropy density ratio of the produced matter in heavy-ion collisions at the highest energies.

Measurement of pion, kaon and proton production in proton-proton collisions at [Formula: see text] TeV

The measurement of primary [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] production at mid-rapidity ([Formula: see text] 0.5) in proton-proton collisions at [Formula: see text][Formula: see text] 7 TeV performed with a large ion collider experiment at the large hadron collider (LHC) is reported. Particle identification is performed using the specific ionisation energy-loss and time-of-flight information, the ring-imaging Cherenkov technique and the kink-topology identification of weak decays of charged kaons. Transverse momentum spectra are measured from 0.1 up to 3 GeV/[Formula: see text] for pions, from 0.2 up to 6 GeV/[Formula: see text] for kaons and from 0.3 up to 6 GeV/[Formula: see text] for protons. The measured spectra and particle ratios are compared with quantum chromodynamics-inspired models, tuned to reproduce also the earlier measurements performed at the LHC. Furthermore, the integrated particle yields and ratios as well as the average transverse momenta are compared with results at lower collision energies.

Exclusive J/ψ photoproduction off protons in ultraperipheral p-Pb collisions at √(s(NN))=5.02 TeV

We present the first measurement at the LHC of exclusive J/ψ photoproduction off protons, in ultraperipheral proton-lead collisions at sqrt[s_{NN}]=5.02  TeV. Events are selected with a dimuon pair produced either in the rapidity interval, in the laboratory frame, 2.5<y<4 (p-Pb) or -3.6<y<-2.6 (Pb-p), and no other particles observed in the ALICE acceptance. The measured cross sections σ(γ+p→J/ψ+p) are 33.2±2.2(stat)±3.2(syst)±0.7(theor)  nb in p-Pb and 284±36(stat)_{-32}^{+27}(syst)±26(theor)  nb in Pb-p collisions. We measure this process up to about 700 GeV in the γp center of mass, which is a factor of two larger than the highest energy studied at HERA. The data are consistent with a power law dependence of the J/ψ photoproduction cross section in γp energies from about 20 to 700 GeV, or equivalently, from Bjorken x scaling variable between ∼2×10^{-2} and ∼2×10^{-5}, thus indicating no significant change in the gluon density behavior of the proton between HERA and LHC energies.

Measurement of prompt D-meson production in p-Pb collisions at √(s(NN))=5.02 TeV

The p_{T}-differential production cross sections of the prompt charmed mesons D^{0}, D^{+}, D^{*+}, and D_{s}^{+} and their charge conjugate in the rapidity interval -0.96<y_{cms}<0.04 were measured in p-Pb collisions at a center-of-mass energy sqrt[s_{NN}]=5.02  TeV with the ALICE detector at the LHC. The nuclear modification factor R_{pPb}, quantifying the D-meson yield in p-Pb collisions relative to the yield in pp collisions scaled by the number of binary nucleon-nucleon collisions, is compatible within the 15%-20% uncertainties with unity in the transverse momentum interval 1<p_{T}<24  GeV/c. No significant difference among the R_{pPb} of the four D-meson species is observed. The results are described within uncertainties by theoretical calculations that include initial-state effects. The measurement adds experimental evidence that the modification of the momentum spectrum of D mesons observed in Pb-Pb collisions with respect to pp collisions is due to strong final-state effects induced by hot partonic matter.

Directed flow of charged particles at midrapidity relative to the spectator plane in Pb-Pb collisions at √(s(NN))=2.76 TeV

The directed flow of charged particles at midrapidity is measured in Pb-Pb collisions at √(s(NN))=2.76 TeV relative to the collision symmetry plane defined by the spectator nucleons. A negative slope of the rapidity-odd directed flow component with approximately 3 times smaller magnitude than found at the highest RHIC energy is observed. This suggests a smaller longitudinal tilt of the initial system and disfavors the strong fireball rotation predicted for the LHC energies. The rapidity-even directed flow component is measured for the first time with spectators and found to be independent of pseudorapidity with a sign change at transverse momenta p(T) between 1.2 and 1.7  GeV/c. Combined with the observation of a vanishing rapidity-even p(T) shift along the spectator deflection this is strong evidence for dipolelike initial density fluctuations in the overlap zone of the nuclei. Similar trends in the rapidity-even directed flow and the estimate from two-particle correlations at midrapidity, which is larger by about a factor of 40, indicate a weak correlation between fluctuating participant and spectator symmetry planes. These observations open new possibilities for investigation of the initial conditions in heavy-ion collisions with spectator nucleons.

K(S)0 and Λ production in Pb-Pb collisions at √(s(NN))=2.76 TeV

The ALICE measurement of K(S)(0) and Λ production at midrapidity in Pb-Pb collisions at √(s(NN))=2.76 TeV is presented. The transverse momentum (p(T)) spectra are shown for several collision centrality intervals and in the p(T) range from 0.4 GeV/c (0.6 GeV/c for Λ) to 12 GeV/c. The p(T) dependence of the Λ/K(S)(0) ratios exhibits maxima in the vicinity of 3 GeV/c, and the positions of the maxima shift towards higher p(T) with increasing collision centrality. The magnitude of these maxima increases by almost a factor of three between most peripheral and most central Pb-Pb collisions. This baryon excess at intermediate p(T) is not observed in pp interactions at √s=0.9 TeV and at √s=7 TeV. Qualitatively, the baryon enhancement in heavy-ion collisions is expected from radial flow. However, the measured p(T) spectra above 2 GeV/c progressively decouple from hydrodynamical-model calculations. For higher values of p(T), models that incorporate the influence of the medium on the fragmentation and hadronization processes describe qualitatively the p(T) dependence of the Λ/K(S)(0) ratio.

J/ψ elliptic flow in Pb-Pb collisions at √(s(NN))=2.76 TeV

We report on the first measurement of inclusive J/ψ elliptic flow v2 in heavy-ion collisions at the LHC. The measurement is performed with the ALICE detector in Pb-Pb collisions at √(s(NN))=2.76 TeV in the rapidity range 2.5<y<4.0. The dependence of the J/ψ v2 on the collision centrality and on the J/ψ transverse momentum is studied in the range 0≤p(T)<10 GeV/c. For semicentral Pb-Pb collisions at √(s(NN))=2.76 TeV, an indication of nonzero v2 is observed with a largest measured value of v2=0.116±0.046(stat)±0.029(syst) for J/ψ in the transverse momentum range 2≤p(T)<4 GeV/c. The elliptic flow measurement complements the previously reported ALICE results on the inclusive J/ψ nuclear modification factor and favors the scenario of a significant fraction of J/ψ production from charm quarks in a deconfined partonic phase.

D meson elliptic flow in noncentral Pb-Pb collisions at sqrt[sNN]=2.76 Tev

Azimuthally anisotropic distributions of D0, D+, and D*+ mesons were studied in the central rapidity region (|y|<0.8) in Pb-Pb collisions at a center-of-mass energy sqrt[sNN]=2.76  TeV per nucleon-nucleon collision, with the ALICE detector at the LHC. The second Fourier coefficient v2 (commonly denoted elliptic flow) was measured in the centrality class 30%-50% as a function of the D meson transverse momentum pT, in the range 2-16  GeV/c. The measured v2 of D mesons is comparable in magnitude to that of light-flavor hadrons. It is positive in the range 2<pT<6  GeV/c with 5.7σ significance, based on the combination of statistical and systematic uncertainties.

The concerted nature of the cyclization of squalene oxide to the protosterol cation

Concerted A-C ring formation: A concerted, but highly asynchronous, pathway was identified for the formation of rings A-C in the biosynthetic conversion of squalene oxide to the prosterol cation, with ring B being formed in the required boat conformation.

Measurement of inelastic, single- and double-diffraction cross sections in proton-proton collisions at the LHC with ALICE

Measurements of cross sections of inelastic and diffractive processes in proton-proton collisions at LHC energies were carried out with the ALICE detector. The fractions of diffractive processes in inelastic collisions were determined from a study of gaps in charged particle pseudorapidity distributions: for single diffraction (diffractive mass MX <200 GeV/c2) [Formula: see text], and [Formula: see text], respectively at centre-of-mass energies [Formula: see text]; for double diffraction (for a pseudorapidity gap Δη>3) σDD/σINEL=0.11±0.03,0.12±0.05, and [Formula: see text], respectively at [Formula: see text]. To measure the inelastic cross section, beam properties were determined with van der Meer scans, and, using a simulation of diffraction adjusted to data, the following values were obtained: [Formula: see text] mb at [Formula: see text] and [Formula: see text] at [Formula: see text]. The single- and double-diffractive cross sections were calculated combining relative rates of diffraction with inelastic cross sections. The results are compared to previous measurements at proton-antiproton and proton-proton colliders at lower energies, to measurements by other experiments at the LHC, and to theoretical models.

Net-charge fluctuations in Pb-Pb collisions at sqrt[sNN]=2.76 TeV

We report the first measurement of the net-charge fluctuations in Pb-Pb collisions at sqrt[sNN]=2.76  TeV, measured with the ALICE detector at the CERN Large Hadron Collider. The dynamical fluctuations per unit entropy are observed to decrease when going from peripheral to central collisions. An additional reduction in the amount of fluctuations is seen in comparison to the results from lower energies. We examine the dependence of fluctuations on the pseudorapidity interval, which may account for the dilution of fluctuations during the evolution of the system. We find that the fluctuations at the LHC are smaller compared to the measurements at the BNL Relativistic Heavy Ion Collider, and as such, closer to what has been theoretically predicted for the formation of a quark-gluon plasma.

Concerted, highly asynchronous, enzyme-catalyzed [4 + 2] cycloaddition in the biosynthesis of spinosyn A; computational evidence

A theoretical study has been carried out on model systems to study a recently reported, (Nature, 2011, 473, 109) biosynthetic, [4 + 2] cycloaddition catalyzed by a stand-alone enzyme (the cyclase SpnF). It was suggested in this paper that SpnF is the first known example of a Diels-Alderase (DA). In the present study, for a model system of the substrate a transition structure was found with density functional calculations (DFT). In addition, the intrinsic reaction coordinate calculations indicated that the transition structure is that of a concerted, but highly asynchronous, DA reaction. Based on the DFT and Møller-Plesset second order calculations the activation energy was estimated to be about 15 kcal mol(-1). The results of a natural population analysis indicated that there is significant charge transfer in the transition state, and it is proposed that possibly the enzyme plays a dual role of not only folding the substrate into the proper conformation for the DA reaction to occur, but also lowering its activation energy by stabilization of the highly polarized transition structure.

Transverse momentum distribution and nuclear modification factor of charged particles in p+Pb collisions at sqrt[s(NN)] = 5.02 TeV

The transverse momentum (p(T)) distribution of primary charged particles is measured in minimum bias (non-single-diffractive) p+Pb collisions at sqrt[s(NN)]=5.02 TeV with the ALICE detector at the LHC. The p(T) spectra measured near central rapidity in the range 0.5<p(T) <20 GeV/c exhibit a weak pseudorapidity dependence. The nuclear modification factor R(pPb) is consistent with unity for p(T) above 2 GeV/c. This measurement indicates that the strong suppression of hadron production at high p(T) observed in Pb+Pb collisions at the LHC is not due to an initial-state effect. The measurement is compared to theoretical calculations.

Pseudorapidity density of charged particles in p+Pb collisions at √(s(NN))=5.02 TeV

The charged-particle pseudorapidity density measured over four units of pseudorapidity in nonsingle-diffractive p+Pb collisions at a center-of-mass energy per nucleon pair √(s(NN))=5.02 TeV is presented. The average value at midrapidity is measured to be 16.81±0.71 (syst), which corresponds to 2.14±0.17 (syst) per participating nucleon, calculated with the Glauber model. This is 16% lower than in nonsingle-diffractive pp collisions interpolated to the same collision energy and 84% higher than in d+Au collisions at s√(s(NN))=0.2 TeV. The measured pseudorapidity density in p+Pb collisions is compared to model predictions and provides new constraints on the description of particle production in high-energy nuclear collisions.

Charge separation relative to the reaction plane in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

Measurements of charge-dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudorapidity range |η| < 0.8 are presented as a function of the collision centrality, particle separation in pseudorapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge-dependent azimuthal correlations observed at RHIC and LHC energies.

Pion, kaon, and proton production in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

In this Letter we report the first results on π(±), K(±), p, and p production at midrapidity (|y|<0.5) in central Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV, measured by the ALICE experiment at the LHC. The p(T) distributions and yields are compared to previous results at sqrt[s(NN)] = 200 GeV and expectations from hydrodynamic and thermal models. The spectral shapes indicate a strong increase of the radial flow velocity with sqrt[s(NN)], which in hydrodynamic models is expected as a consequence of the increasing particle density. While the K/π ratio is in line with predictions from the thermal model, the p/π ratio is found to be lower by a factor of about 1.5. This deviation from thermal model expectations is still to be understood.

Measurement of the cross section for electromagnetic dissociation with neutron emission in Pb-Pb collisions at sqrt[s(NN)] = 2.76 TeV

The first measurement of neutron emission in electromagnetic dissociation of ^{208}Pb nuclei at the LHC is presented. The measurement is performed using the neutron zero degree calorimeters of the ALICE experiment, which detect neutral particles close to beam rapidity. The measured cross sections of single and mutual electromagnetic dissociation of Pb nuclei at sqrt[s(NN)]=2.76 TeV with neutron emission are σ(singleEMD)=187.4 ± 0.2(stat)(-11.2)(+13.2) (syst) b and σ(mutualEMD) = 5.7 ± 0.1(stat) ± 0.4(syst) b, respectively. The experimental results are compared to the predictions from a relativistic electromagnetic dissociation model.

Production of muons from heavy flavor decays at forward rapidity in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76 TeV

The ALICE Collaboration has measured the inclusive production of muons from heavy-flavor decays at forward rapidity, 2.5<y<4, in pp and Pb-Pb collisions at sqrt[s(NN)]=2.76  TeV. The p(t)-differential inclusive cross section of muons from heavy-flavor decays in pp collisions is compared to perturbative QCD calculations. The nuclear modification factor is studied as a function of p(t) and collision centrality. A weak suppression is measured in peripheral collisions. In the most central collisions, a suppression of a factor of about 3-4 is observed in 6<p(t)<10  GeV/c. The suppression shows no significant p(t) dependence.

Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates

Sesquiterpene skeletal complexity in nature originates from the enzyme-catalyzed ionization of (trans,trans)-farnesyl diphosphate (FPP) (1a) and subsequent cyclization along either 2,3-transoid or 2,3-cisoid farnesyl cation pathways. Tobacco 5-epi-aristolochene synthase (TEAS), a transoid synthase, produces cisoid products as a component of its minor product spectrum. To investigate the cryptic cisoid cyclization pathway in TEAS, we employed (cis,trans)-FPP (1b) as an alternative substrate. Strikingly, TEAS was catalytically robust in the enzymatic conversion of (cis,trans)-FPP (1b) to exclusively (>/=99.5%) cisoid products. Further, crystallographic characterization of wild-type TEAS and a catalytically promiscuous mutant (M4 TEAS) with 2-fluoro analogues of both all-trans FPP (1a) and (cis,trans)-FPP (1b) revealed binding modes consistent with preorganization of the farnesyl chain. These results provide a structural glimpse into both cisoid and transoid cyclization pathways efficiently templated by a single enzyme active site, consistent with the recently elucidated stereochemistry of the cisoid products. Further, computational studies using density functional theory calculations reveal concerted, highly asynchronous cyclization pathways leading to the major cisoid cyclization products. The implications of these discoveries for expanded sesquiterpene diversity in nature are discussed.

Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

Throughout molecular evolution, organisms create assorted chemicals in response to varying ecological niches. Catalytic landscapes underlie metabolic evolution, wherein mutational steps alter the biosynthetic properties of enzymes. Here we report the first systematic quantitative characterization of the catalytic landscape underlying the evolution of sesquiterpene chemical diversity. On the basis of our previous discovery of a set of nine naturally occurring amino acid substitutions that functionally interconverted orthologous sesquiterpene synthases from Nicotiana tabacum and Hyoscyamus muticus, we created a library of all possible residue combinations (2(9) = 512) in the N. tabacum enzyme. The product spectra of 418 active enzymes revealed a rugged landscape where several minimal combinations of the nine mutations encode convergent solutions to the interconversions of parental activities. Quantitative comparisons indicated context dependence for mutational effects--epistasis--in product specificity and promiscuity. These results provide a measure of the mutational accessibility of phenotypic variability in a diverging lineage of terpene synthases.

Lewis acid-catalyzed one-pot, three-component route to chiral 3,3'-bipyrroles

3,3'-Bipyrroles 3 could be synthesized using a double Michael addition reaction involving diaroyl acetylene 1 and the appropriate 1,3-dicarbonyls 2 using ammonium acetate as a nitrogen source. The axial chirality of bipyrrole was anticipated from the X-ray crystal structure and DFT calculations and confirmed by separating the racemates on a chiral column and subsequent CD spectra of the enantiomers. The absolute configuration of the enantiomers was achieved by theoretical CD spectra calculation using the ZINDO method.

The Concerted Nature of the Enzymatic Cyclization of Rings A-D of Squalene to Hopene

A conformational analysis of squalene encapsulated in squalene-hopene cyclase has been performed based on Schulz's X-ray structure and our DFT calculations. Based on this analysis it is concluded that the formation of rings A-D in the cyclization of squalene are likely to be a concerted but highly asynchronous reaction.

Thermal [1,5] Hydrogen Sigmatropic Shifts in cis,cis-1,3-Cyclononadienes Probed by Gas-Phase Kinetic Studies and Density Functional Theory Calculations

The kinetics of gas-phase thermal [1,5] hydrogen shifts interconverting the five isomeric mono-deuterium-labeled cis,cis-1,3-cyclononadienes have been followed at four temperatures from 240 to 287 degrees C. The activation parameters found were Ea = 37.1 +/- 0.8 kcal/mol, log A = 11.6 +/- 0.3, DeltaH++ = 36.0 +/- 0.8 kcal/mol, and DeltaS++ = -9.0 +/- 0.3 eu. Density functional theory based calculations have provided geometries and energies for the ground-state cyclononadiene conformational isomers, for the transition states linking one to another, and for the transition states for [1,5] hydrogen shifts responsible for isomerizations among the five labeled dienes. A generalized formulation of the Winstein-Holness equation is presented and applied to the complex system, one that involves 11 ground-state conformers, 10 transition states separating them, and five transition states for [1,5] hydrogen shifts. The value for the empirical Ea derived from calculated mole fractions of ground-state conformers and calculated energies for specific ground-state conformers and [1,5] hydrogen shift transition structures was 37.5 kcal/mol, in excellent agreement with the experimentally obtained activation energy. The significance of conformational options in various ground states and transition structures for the [1,5] hydrogen shifts is considerable, an inference that may well have general applicability.

Density-functional theory structures of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid complexes for ions across the lanthanide series

The use of organically chelated lanthanides in diagnosis and treatment is a rapidly growing field in medicine. In order to gain a deeper understanding into the properties of these chelates, particularly spectroscopic, density-functional calculations have been performed on a series of lanthanide ions chelated with 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid. Based on the results of these calculations, it has been concluded that the local symmetry experienced by the chelated lanthanide ion may be treated as being axial, which will make the interpretation of their spectroscopic properties greatly simplified. It has also been suggested that the so-called "capping" water molecule at the ninth coordination position of the lanthanide is hydrogen bonded to the acetate oxygens of the sidearms, rather than coordinated as the ninth ligand of the lanthanide.

Binding H2, N2, H−, and BH3 to Transition-Metal Sulfur Sites: Synthesis and Properties of[Ru(L)(PR3)(‘N2Me2S2’)] Complexes (L=η2-H2, H−, BH3; R=Cy,iPr)

The reactions of [Ru(N(2))(PR(3))('N(2)Me(2)S(2)')] ['N(2)Me(2)S(2)'=1,2-ethanediamine-N,N'-dimethyl-N,N'-bis(2-benzenethiolate)(2-)] [1 a (R=iPr), 1 b (R=Cy)] and [micro-N(2)[Ru(N(2))(PiPr(3))('N(2)Me(2)S(2)')](2)] (1 c) with H(2), NaBH(4), and NBu(4)BH(4), intended to reduce the N(2) ligands, led to substitution of N(2) and formation of the new complexes [Ru(H(2))(PR(3))('N(2)Me(2)S(2)')] [2 a (R=iPr), 2 b (R=Cy)], [Ru(BH(3))(PR(3))('N(2)Me(2)S(2)')] [3 a (R=iPr), 3 b (R=Cy)], and [Ru(H)(PR(3))('N(2)Me(2)S(2)')](-) [4 a (R=iPr), 4 b (R=Cy)]. The BH(3) and hydride complexes 3 a, 3 b, 4 a, and 4 b were obtained subsequently by rational synthesis from 1 a or 1 b and BH(3).THF or LiBEt(3)H. The primary step in all reactions probably is the dissociation of N(2) from the N(2) complexes to give coordinatively unsaturated [Ru(PR(3))('N(2)Me(2)S(2)')] fragments that add H(2), BH(4) (-), BH(3), or H(-). All complexes were completely characterized by elemental analysis and common spectroscopic methods. The molecular structures of [Ru(H(2))(PR(3))('N(2)Me(2)S(2)')] [2 a (R=iPr), 2 b (R=Cy)], [Ru(BH(3))(PiPr(3))('N(2)Me(2)S(2)')] (3 a), [Li(THF)(2)][Ru(H)(PiPr(3))('N(2)Me(2)S(2)')] ([Li(THF)(2)]-4 a), and NBu(4)[Ru(H)(PCy(3))('N(2)Me(2)S(2)')] (NBu(4)-4 b) were determined by X-ray crystal structure analysis. Measurements of the NMR relaxation time T(1) corroborated the eta(2) bonding mode of the H(2) ligands in 2 a (T(1)=35 ms) and 2 b (T(1)=21 ms). The H,D coupling constants of the analogous HD complexes HD-2 a ((1)J(H,D)=26.0 Hz) and HD-2 b ((1)J(H,D)=25.9 Hz) enabled calculation of the H--D distances, which agreed with the values found by X-ray crystal structure analysis (2 a: 92 pm (X-ray) versus 98 pm (calculated), 2 b: 99 versus 98 pm). The BH(3) entities in 3 a and 3 b bind to one thiolate donor of the [Ru(PR(3))('N(2)Me(2)S(2)')] fragment and through a B-H-Ru bond to the Ru center. The hydride complex anions 4 a and 4 b are extremely Brønsted basic and are instantaneously protonated to give the eta(2)-H(2) complexes 2 a and 2 b.

Binding N2, N2H2, N2H4, and NH3 to transition-metal sulfur sites: modeling potential intermediates of biological N2 fixation

In the quest for low-molecular-weight metal sulfur complexes that bind nitrogenase-relevant small molecules and can serve as model complexes for nitrogenase, compounds with the [Ru(PiPr(3))('N(2)Me(2)S(2)')] fragment were found ('N(2)Me(2)S(2)'(2-)=1,2-ethanediamine-N,N'-dimethyl-N,N'-bis(2-benzenethiolate)(2-)). This fragment enabled the synthesis of a first series of chiral metal sulfur complexes, [Ru(L)(PiPr(3))('N(2)Me(2)S(2)')] with L=N(2), N(2)H(2), N(2)H(4), and NH(3), that meet the biological constraint of forming under mild conditions. The reaction of [Ru(NCCH(3))(PiPr(3))('N(2)Me(2)S(2)')] (1) with NH(3) gave the ammonia complex [Ru(NH(3))(PiPr(3))('N(2)Me(2)S(2)')] (4), which readily exchanged NH(3) for N(2) to yield the mononuclear dinitrogen complex [Ru(N(2))(PiPr(3))('N(2)Me(2)S(2)')] (2) in almost quantitative yield. Complex 2, obtained by this new efficient synthesis, was the starting material for the synthesis of dinuclear (R,R)- and (S,S)-[micro-N(2)[Ru(PiPr(3))('N(2)Me(2)S(2)')](2)] ((R,R)-/(S,S)-3). (Both 2 and 3 have been reported previously.) The as-yet inexplicable behavior of complex 3 to form also the R,S isomer in solution has been revealed by DFT calculations and (2)D NMR spectroscopy studies. The reaction of 1 or 2 with anhydrous hydrazine yielded the hydrazine complex [Ru(N(2)H(4))(PiPr(3))('N(2)Me(2)S(2)')] (6), which is a highly reactive intermediate. Disproportionation of 6 resulted in the formation of mononuclear diazene complexes, the ammonia complex 4, and finally the dinuclear diazene complex [micro-N(2)H(2)[Ru(PiPr(3))('N(2)Me(2)S(2)')](2)] (5). Dinuclear complex 5 could also be obtained directly in an independent synthesis from 1 and N(2)H(2), which was generated in situ by acidolysis of K(2)N(2)(CO(2))(2). Treatment of 6 with CH(2)Cl(2), however, formed a chloromethylated diazene species [[Ru(PiPr(3))('N(2)Me(2)S(2)')]-micro-N(2)H(2)[Ru(Cl)('N(2)Me(2)S(2)CH(2)Cl')]] (9) ('N(2)Me(2)S(2)CH(2)Cl'(2-) =1,2-ethanediamine-N,N'-dimethyl-N-(2-benzenethiolate)(1-)-N'-(2-benzenechloromethylthioether)(1-)]. The molecular structures of 4, 5, and 9 were determined by X-ray crystal structure analysis, and the labile N(2)H(4) complex 6 was characterized by NMR spectroscopy.