Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence

Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.Fil: Lara Popoca, Jesús. Universidad Nacional Autónoma de México; MéxicoFil: Thoke, Henrik S.. International and Interdisciplinary Research Network; DinamarcaFil: Stock, Roberto P.. Universidad Nacional Autónoma de México; MéxicoFil: Rudino Pinera, Enrique. Universidad Nacional Autónoma de México; MéxicoFil: Bagatolli, Luis Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra. Universidad Nacional de Córdoba. Instituto de Investigación Médica Mercedes y Martín Ferreyra; Argentin

Search for the Higgs boson in events with missing transverse energy and b quark jets produced in proton-antiproton collisions at s**(1/2)=1.96 TeV

We search for the standard model Higgs boson produced in association with an electroweak vector boson in events with no identified charged leptons, large imbalance in transverse momentum, and two jets where at least one contains a secondary vertex consistent with the decay of b hadrons. We use ~1 fb-1 integrated luminosity of proton-antiproton collisions at s**(1/2)=1.96 TeV recorded by the CDF II experiment at the Tevatron. We find 268 (16) single (double) b-tagged candidate events, where 248 +/- 43 (14.4 +/- 2.7) are expected from standard model background processes. We place 95% confidence level upper limits on the Higgs boson production cross section for several Higgs boson masses ranging from 110 GeV/c2 to 140 GeV/c2. For a mass of 115 GeV/c2 the observed (expected) limit is 20.4 (14.2) times the standard model prediction.Comment: 8 pages, 2 figures, submitted to Phys. Rev. Let

Measurement of the Helicity Fractions of W Bosons from Top Quark Decays Using Fully Reconstructed top-antitop Events with CDF II

We present a measurement of the fractions F_0 and F_+ of longitudinally polarized and right-handed W bosons in top quark decays using data collected with the CDF II detector. The data set used in the analysis corresponds to an integrated luminosity of approximately 318 pb -1. We select ttbar candidate events with one lepton, at least four jets, and missing transverse energy. Our helicity measurement uses the decay angle theta*, which is defined as the angle between the momentum of the charged lepton in the W boson rest frame and the W momentum in the top quark rest frame. The cos(theta*) distribution in the data is determined by full kinematic reconstruction of the ttbar candidates. We find F_0 = 0.85 +0.15 -0.22 (stat) +- 0.06 (syst) and F_+ = 0.05 +0.11 -0.05 (stat) +- 0.03 (syst), which is consistent with the standard model prediction. We set an upper limit on the fraction of right-handed W bosons of F_+ < 0.26 at the 95% confidence level.Comment: 11 pages, 2 figures, submitted to Phys. Rev.

Measurement of the ttbar Production Cross Section in ppbar Collisions at sqrt(s) = 1.96 TeV

We present a measurement of the top quark pair production cross section in ppbar collisions at sqrt(s)=1.96 TeV using 318 pb^{-1} of data collected with the Collider Detector at Fermilab. We select ttbar decays into the final states e nu + jets and mu nu + jets, in which at least one b quark from the t-quark decays is identified using a secondary vertex-finding algorithm. Assuming a top quark mass of 178 GeV/c^2, we measure a cross section of 8.7 +-0.9 (stat) +1.1-0.9 (syst) pb. We also report the first observation of ttbar with significance greater than 5 sigma in the subsample in which both b quarks are identified, corresponding to a cross section of 10.1 +1.6-1.4(stat)+2.0-1.3 (syst) pb.Comment: Accepted for publication in Physics Review Letters, 7 page

Observation and Mass Measurement of the Baryon Ξb−\Xi^-_b

We report the observation and measurement of the mass of the bottom, strange baryon $\Xi^-_b$ through the decay chain $\Xi^-_b \to J/\psi \Xi^-$, where $J/\psi \to \mu^+ \mu^-$, $\Xi^- \to \Lambda \pi^-$, and $\Lambda \to p \pi^-$. Evidence for observation is based on a signal whose probability of arising from the estimated background is 6.6 x 10^{-15}, or 7.7 Gaussian standard deviations. The $\Xi^-_b$ mass is measured to be $5792.9\pm 2.5$ (stat.) $\pm 1.7$ (syst.) MeV/$c^2$.Comment: Minor text changes for the second version. Accepted by Phys. Rev. Let

First Measurement of the W Boson Mass in Run II of the Tevatron

We present a measurement of the W boson mass using 200/pb of data collected in pbar p collisions at sqrt(s) = 1.96 TeV by the CDF II detector at Run II of the Fermilab Tevatron. With a sample of 63964 W -> e nu candidates and 51128 W -> mu nu candidates, we measure M_W = (80413 +- 34 (stat) +- 34 (syst) = 80413 +- 48) MeV/c^2. This is the most precise single measurement of the W boson mass to date.Comment: published version in PR

Search for New Particles Leading to Z+jets Final States in ppˉp\bar{p} Collisions at s=1.96\sqrt{s}=1.96 TeV

We present the results of a search for new particles that lead to a \Z boson plus jets in $p\bar{p}$ collisions at $\sqrt{s}=1.96$ TeV using the Collider Detector at Fermilab (CDF II). A data sample with a luminosity of 1.06 \ifb\ collected using \Z boson decays to $ee$ and $\mu\mu$ is used. We describe a completely data-based method to predict the dominant background from standard-model \Z+jet events. This method can be similarly applied to other analyses requiring background predictions in multi-jet environments, as shown when validating the method by predicting the background from $W$+jets in \ttbar production. No significant excess above the background prediction is observed, and a limit is set using a fourth generation quark model to quantify the acceptance. Assuming $BR(b' \to b\Z) = 100$ and using a leading-order calculation of the $b'$ cross section, $b'$ quark masses below 268 \gev/c^2 are excluded at 95% confidence level.Comment: To be submitted to PR

Precise measurement of the top quark mass in the lepton+jets topology at CDF II

We present a measurement of the mass of the top quark from proton-antiproton collisions recorded at the CDF experiment in Run II of the Fermilab Tevatron. We analyze events from the single lepton plus jets final state ($t\bar t\to W^+bW^-\bar b\to l\nu b q \bar q'\bar b$). The top quark mass is extracted using a direct calculation of the probability density that each event corresponds to the $t\bar t$ final state. The probability is a function of both the mass of the top quark and the energy scale of the calorimeter jets, which is constrained {\it in situ} by the hadronic $W$ boson mass. Using 167 events observed in 955 pb$^{{-}1}$ of integrated luminosity, we achieve the single most precise measurement of the top quark mass, 170.8 $\pm$ 2.2 (stat.) $\pm$ 1.4 (syst.) GeV/$c^2$.Comment: accepted by Phys. Rev. Let

Polarizations of J/psi and psi(2S) Mesons Produced in ppbar Collisions at 1.96 TeV

We have measured the polarizations of \jpsi and \psiprime mesons as functions of their transverse momentum \pt when they are produced promptly in the rapidity range $|y|<0.6$ with \pt \geq 5 \pgev. The analysis is performed using a data sample with an integrated luminosity of about 800 \ipb collected by the CDF II detector. For both vector mesons, we find that the polarizations become increasingly longitudinal as \pt increases from 5 to 30 \pgev. These results are compared to the predictions of nonrelativistic quantum chromodynamics and other contemporary models. The effective polarizations of \jpsi and \psiprime mesons from $B$-hadron decays are also reported.Comment: 8 pages, 7 figures, published in Physical Review Letter