AssignFit: a program for simultaneous assignment and structure refinement from solid-state NMR spectra

AssignFit is a computer program developed within the XPLOR-NIH package for the assignment of dipolar coupling (DC) and chemical shift anisotropy (CSA) restraints derived from the solid-state NMR spectra of protein samples with uniaxial order. The method is based on minimizing the difference between experimentally observed solid-state NMR spectra and the frequencies back calculated from a structural model. Starting with a structural model and a set of DC and CSA restraints grouped only by amino acid type, as would be obtained by selective isotopic labeling, AssignFit generates all of the possible assignment permutations and calculates the corresponding atomic coordinates oriented in the alignment frame, together with the associated set of NMR frequencies, which are then compared with the experimental data for best fit. Incorporation of AssignFit in a simulated annealing refinement cycle provides an approach for simultaneous assignment and structure refinement (SASR) of proteins from solid-state NMR orientation restraints. The methods are demonstrated with data from two integral membrane proteins, one α-helical and one β-barrel, embedded in phospholipid bilayer membranes.     

Isospin splittings of doubly heavy baryons

The SELEX Collaboration has reported a very large isospin splitting of doubly charmed baryons. We show that this effect would imply that the doubly charmed baryons are very compact. One intriguing possibility is that such baryons have a linear geometry Q–q–Q$Q\text{–}q\text{–}Q$ where the light quark q oscillates between the two heavy quarks Q  , analogous to a linear molecule such as carbon dioxide. However, using conventional arguments, the size of a heavy-light hadron is expected to be around 0.5 fm, much larger than the size needed to explain the observed large isospin splitting. Assuming the distance between two heavy quarks is much smaller than that between the light quark and a heavy one, the doubly heavy baryons are related to the heavy mesons via heavy quark–diquark symmetry. Based on this symmetry, we predict the isospin splittings for doubly heavy baryons including Ξ_cc${\Xi }_{cc}$, Ξ_bb${\Xi }_{bb}$ and Ξ_bc${\Xi }_{bc}$. The prediction for the Ξ_cc${\Xi }_{cc}$ is much smaller than the SELEX value. On the other hand, the Ξ_bb${\Xi }_{bb}$ baryons are predicted to have an isospin splitting as large as (6.3±1.7) MeV$(6.3\pm 1.7)\text{MeV}$. An experimental study of doubly bottomed baryons is therefore very important to better understand the structure of baryons with heavy quarks.     

A generalized preferential attachment model for business firms growth rates

We present a preferential attachment growth model to obtain the distribution P(K) of number of units K in the classes which may represent business firms or other socio-economic entities. We found that P(K) is described in its central part by a power law with an exponent ϕ = 2+b/(1-b) which depends on the probability of entry of new classes, b. In a particular problem of city population this distribution is equivalent to the well known Zipf law. In the absence of the new classes entry, the distribution P(K) is exponential. Using analytical form of P(K) and assuming proportional growth for units, we derive P(g), the distribution of business firm growth rates. The model predicts that P(g) has a Laplacian cusp in the central part and asymptotic power-law tails with an exponent ζ = 3. We test the analytical expressions derived using heuristic arguments by simulations. The model might also explain the size-variance relationship of the firm growth rates.     

Light-Front Holography,Color Confinement,and Supersymmetric Features of QCD

Light-Front Quantization—Dirac’s “Front Form”—provides a physical, frame-independent formalism for hadron dynamics and structure. Observables such as structure functions, transverse momentum distributions, and distribution amplitudes are defined from the hadronic light-front wavefunctions. One obtains new insights into the hadronic spectrum, light-front wavefunctions, and the functional form of the QCD running coupling in the nonperturbative domain using light-front holography—the duality between the front form and AdS₅, the space of isometries of the conformal group. In addition, superconformal algebra leads to remarkable supersymmetric relations between mesons and baryons of the same parity. The mass scale \({\kappa}\) underlying confinement and hadron masses can be connected to the parameter \({\Lambda_{\overline {MS}}}\) in the QCD running coupling by matching the nonperturbative dynamics, as described by the effective conformal theory mapped to the light-front and its embedding in AdS space, to the perturbative QCD regime. The result is an effective coupling defined at all momenta. This matching of the high and low momentum transfer regimes determines a scale Q₀ which sets the interface between perturbative and nonperturbative hadron dynamics. The use of Q₀ to resolve the factorization scale uncertainty for structure functions and distribution amplitudes, in combination with the principle of maximal conformality for setting the renormalization scales, can greatly improve the precision of perturbative QCD predictions for collider phenomenology. The absence of vacuum excitations of the causal, frame-independent front form vacuum has important consequences for the cosmological constant. I also discuss evidence that the antishadowing of nuclear structure functions is non-universal; i.e., flavor dependent, and why shadowing and antishadowing phenomena may be incompatible with the momentum and other sum rules for nuclear parton distribution functions.     

Comparison between ocean-acoustic fluctuations in parabolic-equation simulations and estimates from integral approximations

Line-integral approximations to the acoustic path integral have been used to estimate the magnitude of the fluctuations in an acoustic signal traveling through an ocean filled with internal waves. These approximations for the root-mean-square (rms) fluctuation and the bias of travel time, rms fluctuation in a vertical arrival angle, and the spreading of the acoustic pulse are compared here to estimates from simulations that use the parabolic equation (PE). PE propagations at 250 Hz with a maximum range of 1000 km were performed. The model environment consisted of one of two sound-speed profiles perturbed by internal waves conforming to the Garrett-Munk (GM) spectral model with strengths of 0.5, 1, and 2 times the GM reference energy level. Integral-approximation (IA) estimates of rms travel-time fluctuations were within statistical uncertainty at 1000 km for the SLICE89 profile, and in disagreement by between 20% and 60% for the Canonical profile. Bias estimates were accurate for the first few hundred kilometers of propagation, but became a strong function of time front ID beyond, with some agreeing with the PE results and others very much larger. The IA structure functions of travel time with depth are predicted to be quadratic with the form theta(2)vc0(-2)deltaz(2), where deltaz is vertical separation, c0 is a reference sound speed, and thetav is the rms fluctuation in an arrival angle. At 1000 km, the PE results were close to quadratic at small deltaz, with values of thetav in disagreement with those of the integral approximation by factors of order 2. Pulse spreads in the PE results were much smaller than predicted by the IA estimates. Results imply that acoustic tomography of internal waves at ranges up to 1000 km can use the IA estimate of travel-time variance with reasonable reliability.     

Analysis of the urban atmosphere and air pollution source effluents for Phenalen-1-one and 7 H-benz(de)anthracen-7-one

Summary Through the use of one- and two-dimensional thin-layer chromatography and direct spectrophotofluorometric examination of thin-layer plates, two members of a new family of compounds have been found in the atmosphere. Phenalen-1-one and 7 H-benz(de)anthracen-7-one were identified and determined in particulates obtained from urban atmospheres and air pollution source effluents. Scanning techniques and other methods of analysis were also used in characterization and estimation. Two-dimensional thin-layer chromatography followed by direct spectrophotofluorometric analysis appears to be the most promising chromatographic method for the routine analysis of chemical compounds in complex mixtures. It approaches colorimetric analysis in simplicity and speed and surpasses it in sensitivity, selectivity and the amount of information that can be obtained from one analysis.

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Zusammenfassung Durch ein und zweidimensionale Dünnschichtchromatographie und direkte Spektralfluoreszenzanalyse der Dünnschichtplatten wurden zwei Vertreter einer neuen Verbindungsklasse in der Atmosphäre gefunden. Phenalen-1-on und 7 H-benz(de)anthracen-7-on wurden identifiziert und in Partikeln bestimmt, die aus Stadtatmosphäre bzw. aus Quellen der Luftverunreinigung gewonnen wurden. Scanning-Verfahren und andere Analysenmethoden wurden zur Charakterisierung und Bestimmung gleichfalls herangezogen. Die zweidimensionale Dünnschichtchromatographie mit nachfolgender direkter Fluoreszenzmessung scheint jedoch für Routine-untersuchungen das beste chromatographische Verfahren für komplexe Gemische zu sein. Es entspricht an Einfachheit und Schnelligkeit der Kolorimetrie und übertrifft diese an Empfindlichkeit, Selektivität und Aussagokraft bei Durchführung einer einzigen Bestimmung.

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Résumé On a découvert dans l'atmosphère une nouvelle famille de composés en utilisant la Chromatographie en couche mince, uni et bidimensionnelle et l'examen direct spectrofluorimétrique des plaques avec couches minces. On a identifié la phénalène one-1 et la benzo(de) anthracène-7 H one-7 et on en a fait le dosage dans les particules prélevées dans l'atmosphère urbaine et dans les effluents des sources de pollution de l'air. On a utilisé des techniques d'examen et d'autres méthodes d'analyse pour la caractérisation et l'estimation. La Chromatographie en couche mince bi-dimensionnelle suivie d'une analyse spectrofluorimétrique directe semble être la méthode chromatographique la plus prometteuse pour l'analyse en série de composés chimiques en mélanges complexes. Elle se rapproche de l'analyse colorimétrique par sa simplicité et sa vitesse et la dépasse en sensibilité, en sélectivité et par le nombre de renseignements que l'on peut tirer d'une seule analyse.

     

A Convenient Photocatalytic Fluorination of Unactivated CH Bonds

Fluorination reactions are essential to modern medicinal chemistry, thus providing a means to block site‐selective metabolic degradation of drugs and access radiotracers for positron emission tomography imaging. Despite current sophistication in fluorination reagents and processes, the fluorination of unactivated C? H bonds remains a significant challenge. Reported herein is a convenient and economic process for direct fluorination of unactivated C? H bonds that exploits the hydrogen abstracting ability of a decatungstate photocatalyst in combination with the mild fluorine atom transfer reagent N‐fluorobenzenesulfonimide. This operationally straightforward reaction provides direct access to a wide range of fluorinated organic molecules, including structurally complex natural products, acyl fluorides, and fluorinated amino acid derivatives.