Light-directed radial combinatorial chemistry: orthogonal safety-catch protecting groups for the synthesis of small molecule microarrays

We describe the development of photolabile protecting groups based on the 3,4,5-trimethoxyphenacyl group (TMP). Orthogonal safety-catches were created by introducing an acid-activatible dimethyl ketal (AA-TMP) and an oxidatively activatible 1,3-dithiane (OA-TMP) into the photolabile TMP group. We demonstrate the application of these protecting groups in light-directed synthesis of small molecule microarrays with diversity elements radially attached to a hydroxyproline scaffold.     

Nucleophilic Addition of CH, NH, and OH Bonds to the Phosphadiazonium Cation and Interpretation of (31)P Chemical Shifts at Dicoordinate Phosphorus Centers

The phosphadiazonium cation [MesNP](+) reacts quantitatively with the fluorenylide anion, MesNH(2), and MesOH (Mes = 2,4,6-tri-tert-butylphenyl), resulting in formal insertion of the N-P moiety into the H-Y (Y = C, N, O) bonds. Specifically, reaction of MesNPCl with fluorenyllithium gives the aminofluorenylidenephosphine [crystal data: C(31)H(38)NP, monoclinic, P2(1)/c, a = 9.568(8) ?, b = 24.25(2) ?, c = 11.77(1) ?, beta = 101.38(8) degrees, Z = 4]. Similarly, reaction of [MesNP][GaCl(4)] with MesNH(2) gives the diaminophosphenium salt [MesN(H)PN(H)Mes][GaCl(4)] [crystal data: C(36)H(60)Cl(4)GaN(2)P, monoclinic, C2/c, a = 24.921(2) ?, b = 10.198(4) ?, c = 16.445(2) ?, beta = 93.32(1) degrees, Z = 4], and reaction with MesOH gives the first example of an aminooxyphosphenium salt [MesN(H)POMes][GaCl(4)]. It is proposed that the reactions involve nucleophilic attack at phosphorus followed by a 1,3-hydrogen migration from Y to N. Experimental evidence for the formation of sigma-complex intermediates is provided by the isolation of [MesNP-PPh(3)][SO(3)CF(3)] [crystal data: C(37)H(44)F(3)NO(3)P(2)S, triclinic, P&onemacr;, a = 10.663(1) ?, b = 19.439(1) ?, c = 10.502(1) ?, alpha = 103.100(7) degrees, beta = 113.311(7) degrees, gamma = 93.401(7) degrees, Z = 2]. As part of the unequivocal characterization of the aminooxyphosphenium salt, detailed solid-state (31)P NMR studies and GIAO calculations on the phosphenium cations have been performed. Contrary to popular belief, the phosphorus shielding in dicoordinate cations is not caused by the positive charge but results from efficient mixing between the phosphorus lone pair and pi orbitals.     

Hydrogen migrations in mass spectrometry. VI—the chemical ionization mass spectra of substituted benzoic acids and benzyl alcohols

The H₂ and CH₄ chemical ionization mass spectra of a series of series of substituted benzoic acids and substituted benzyl alcohols have been determined. For the benzoic acids the major fragmentation reactions of the protonated molecule involve elimination of H₂O or elimination of CO₂, the latter reaction involving migration of the carboxylic hydrogen to the aromatic ring. For the benzyl alcohols the major fragmentation reactions of [MH]⁺ involve loss of H₂O or CH₂O, analogous to the CO₂ elimination reaction for the benzoic acids. It is shown that the CO₂ and CH₂O elimination reactions occur only when a conjugated aromatic ring system is present, and that for the carboxylic acid systems, methyl groups and, to a lesser extent, phenyl groups are capable of migrating. The only discernible effect of substituents on the fragmentation of [MH]⁺ is an enhancement of the H₂O loss reaction in the benzoic acid system when an amino, hydroxyl, or halogen substituent is ortho to the carboxyl function. This ‘ortho’ effect, which differs in scope from that observed in electron impact mass spectra, is attributed to an intramolecular catalysis by the ortho substituent of the 1,3 hydrogen migration in the carbonyl protonated acid followed by H₂O elimination. Apparently, this route is favoured over the direct elimination of H₂O from the carbonyl protonated acid, since the latter has a high activation energy barrier because of unfavourable orbital symmetry restrictions.     

Probing water interactions and vacancy production on gadolinia-doped ceria surfaces using electron stimulated desorption

Polycrystalline gadolinia-doped ceria (GDC) surfaces were studied using low-energy (5-400 eV) electron stimulated desorption (ESD). H(+), O(+), and H(3)O(+) were the primary cationic desorption products with H(+) as the dominant channel. H(+), H(3)O(+), and O(+) have a 22 eV threshold followed by a yield change around 40 eV. H(+) also has an additional yield change approximately 75 eV and O(+) has an additional change approximately 150 eV. The O(+) ESD yield change approximately 150 eV may indicate bond breaking of Gd-O and the involvement of oxygen vacancies. The H(+) and H(3)O(+) threshold data collectively indicate the presence of hydroxyl groups and chemisorbed water molecules on the GDC surfaces. ESD temperature dependence measurements show that the interaction of water with GDC surface defect sites, mainly oxygen vacancies, influences the desorption of H(+), O(+), and H(3)O(+). The temperature dependence of the O(+) ESD at 400 eV incident electron energy yields a 0.21 eV activation energy. This is close to the energy needed for oxygen vacancy production next to a pair of Ce(3+) on a CeO(2) surface. These results may indicate a correlation between the O(+) ESD yield and oxygen vacancy density on GDC surfaces and a potential correlation of O(+) ESD and GDC ionic conductivity.     

SOLAR SPECTRAL IRRADIANCE IN THE VISIBLE AND INFRARED REGIONS

Abstract— The analytical formulas previously developed for estimating the spectral irradiance reaching the ground in the ultraviolet are extended into the visible and infrared(350–3000 nm). This approach has two distinct features: (1) all physical inputs for calculating the direct irradiance are given in analytical form, and (2) the diffuse spectral irradiance (skylight) is calculated using dimensionless ratios which relate it to the direct irradiance. In common with other approaches, the global spectral irradiance for arbitrary ground reflectivity is calculated from the sum of the direct and diffuse spectral irradiances and a divisor which depends upon the ground and air spectral reflectivities. The global spectral irradiance on a tilted surface may also be calculated in terms of the above quantities and two angles. As in the case of the ultraviolet, the formulas presented are intended for photobiological applications.     

Short-chain reactive probes as tools to unravel the Pseudomonas aeruginosa quorum sensing regulon

In recent years, the world has seen a troubling increase in antibiotic resistance among bacterial pathogens. In order to provide alternative strategies to combat bacterial infections, it is crucial deepen our understanding into the mechanisms that pathogens use to thrive in complex environments. Most bacteria use sophisticated chemical communication systems to sense their population density and coordinate gene expression in a collective manner, a process that is termed “quorum sensing” (QS). The human pathogen Pseudomonas aeruginosa uses several small molecules to regulate QS, and one of them is N-butyryl-l-homoserine lactone (C₄-HSL). Using an activity-based protein profiling (ABPP) strategy, we designed biomimetic probes with a photoreactive group and a ‘click’ tag as an analytical handle. Using these probes, we have identified previously uncharacterized proteins that are part of the P. aeruginosa QS network, and we uncovered an additional role for this natural autoinducer in the virulence regulon of P. aeruginosa, through its interaction with PhzB1/2 that results in inhibition of pyocyanin production.

Short-chain reactive probes can be used as tools to shed new light on virulence mechanisms in bacterial pathogens.     

Transitions between disordered phases in supercooled liquid silicon

We have investigated the transitions between disordered phases in supercooled liquid silicon using computer simulations. The thermodynamic properties were directly obtained from the free energy, which was computed using the recently proposed reversible scaling method. The calculated free energies of the crystalline and liquid phases of silicon at zero pressure, obtained using the environment dependent interatomic potential, are in excellent agreement with the available experimental data. The results show that, at zero pressure, a weak first-order liquid-liquid transition occurs at 1135 K and a continuous liquid-amorphous transition takes place at 843 K. These results are consistent with the existence of a second critical point for the liquid-liquid transition at a negative pressure.     

Kobalt(III)ammin-derivate einiger Reineckesalz-Analoga mit Xylidinen

Zusammenfassung Es wurden 34 neue Komplexsalze durch doppelte Umsetzung aus wäßr.-alkohol. Lösungen der folgenden Reineckeat-Analoga: [Cr(NCS)₄(m-xylidin)₂]^–, [Cr(NCS)₄(p-xyl)₂]^– und Hexammin-, Monoacido-pentammin- und Diacido-tetramminkobalt(III)-komplexsalze erhalten. Es wurden in einigen Fällen Unterschiede in physiko-chemischen Eigenschaften, wie Farbtönung, Kristallform, Löslichkeit und papierchromatographischeR _f-Werte, bei den stellungsisomeren Salzen vom Typus: Kation · [Cr(NCS)₄(xyl)₂] und auch bei den Koordinationsisomerpaaren: [Co(DH)₂(m-xyl)₂] [Cr(NCS)₄(p-xyl)₂] und [Co(DH)₂(p-xyl)₂] [Cr(NCS)₄(m-xyl)₂] usw. beobachtet.

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Cobalt(III)ammine derivatives of some reineckate analogues with xylidines

34 new complex salts were prepared by double conversion of the reineckate analogues [Cr(NCS)₄(m-xylidine)₂]^–, [Cr(NCS)₄(p-xyl)₂]^–, with the hexammine-, monoacido-pentammine- and diacidotetrammine-complexes of Co(III). In some of the position and coordination isomeres differences of the standard physico-chemical properties, i.e. color, crystal form, solubility and paper chromatographyR _f-values were observed.

     

Bispectral KP solutions and linearization of Calogero-Moser particle systems

Rational and soliton solutions of the KP hierarchy in the subgrassmannianGr ₁ are studied within the context of finite dimensional dual grassmannians. In the rational case, properties of the tau function, , which are equivalent to bispectrality of the associated wave function, , are identified. In particular, it is shown that there exists a bound on the degree of all time, variables in if and only if is a rank one bispectral wave function. The action of the bispectral involution, , in the generic rational case is determined explicitly in terms of dual grassmannian parameters. Using the correspondence between rational solutions, and particle systems, it is demonstrated that is a linearizing map of the Calogero-Moser particle system and is essentially the map introduced by Airault, McKean and Moser in 1977 [2].Research supported by NSA Grant MDA904-92-H-3032     

Inclusion-exclusion: Exact and approximate

It is often required to find the probability of the union of givenn eventsA ₁ ,...,A _n . The answer is provided, of course, by the inclusion-exclusion formula: Pr(A _i )= _i – _i<j Pr(A _i A _j )±.... Unfortunately, this formula has exponentially many terms, and only rarely does one manage to carry out the exact calculation. From a computational point of view, finding the probability of the union is an intractable, #P-hard problem, even in very restricted cases. This state of affairs makes it reasonable to seek approximate solutions that are computationally feasible. Attempts to find such approximate solutions have a long history starting already with Boole [1]. A recent step in this direction was taken by Linial and Nisan [4] who sought approximations to the probability of the union, given the probabilities of allj-wise intersections of the events forj=1,...k. The developed a method to approximate Pr(A _i ), from the above data with an additive error of exp . In the present article we develop an expression that can be computed in polynomial time, that, given the sums _|S|=j Pr( _iS A _i ) forj=1,...k, approximates Pr(A _i ) with an additive error of exp . This error is optimal, up to the logarithmic factor implicit in the notation.The problem of enumerating satisfying assignments of a boolean formula in DNF formF=v _l ^m C _i is an instance of the general problem that had been extensively studied [7]. HereA _i is the set of assignments that satisfyC _i , and Pr( _iS A _i )=a _S /2ⁿ where _iS C _i is satisfied bya _S assignments. Judging from the general results, it is hard to expect a decent approximation ofF's number of satisfying assignments, without knowledge of the numbersa _S for, say, all cardinalities . Quite surprisingly, already the numbersa _S over |S|log(n+1)uniquely determine the number of satisfying assignments for F.We point out a connection between our work and the edge-reconstruction conjecture. Finally we discuss other special instances of the problem, e.g., computing permanents of 0,1 matrices, evaluating chromatic polynomials of graphs and for families of events whose VC dimension is bounded.Work supported in part by a grant of the Binational Israel-US Science Foundation.Work supported in part by a grant of the Binational Israel-US Science Foundation and by the Israel Science Foundation.