Cellular logic with orthogonal ribosomes

The creation and use of unnatural molecules to control cellular function is a long standing goal of the chemical community, but in general, these efforts have been directed at finding molecules to inhibit or activate a particular molecular target or function, or to elicit a particular phenotype. Here we show that multiple unnatural molecules (orthogonal ribosomes) can be used combinatorially, in a single cell, to program Boolean logic functions. These experiments show how attention to the molecular specificity of noncovalent interactions between unnatural macromolecules allows the synthesis of complex function from the "bottom-up" in living matter.     

Gradient corrections in density functional theory calculations for surfaces: Co on Pd{110}

Ab initio total energy calculations have been performed for CO chemisorption on Pd{110}. Local density approximation (LDA) calculations yield chemisorption energies which are significantly higher than experimental values but inclusion of the generalised gradient approximation (GGA) gives better agreement. In general, sites with higher coordination of the adsorbate to surface atoms lead to a larger degree of overbinding with LDA, and give larger corrections with GGA. The reason is discussed using a first-order perturbation approximation. It is concluded that this may be a general failure of LDA for chemisorption energy calculations. This conclusion may be extended to many surface calculations, such as potential energy surfaces for diffusion.     

Absorption,fluorescence and phosphorescence spectra of the singlet and triplet states of s-tetrazine in the crystal and in mixed crystals at low temperatures

The electronic absorption, fluorescence and phosphorescence spectra of s-tetrazine at low temperatures (4.2-1.5 K) are reported and analyzed in the neat crystal and in several mixed crystals. The ³B_3u-¹A_g (nπ^*) origin is at 18414 ± 5 cm^?1 for neat tetrazine. In the mixed crystal several sites identified. The lowest energy origin is at 17453 cm^?1 for tetrazine in pyrazine; 17 701 cm^?1 in pyrimidine; and 17 676 cm^?1 in pyridazine. The ^eB_3u-¹A_g (nπ^*) origin is at 14 096 ± 2 cm^?1 for the neat crystal. The phosphorescence lifetime of neat tetrazine is measured to be 96.8 ± 2.1 μs at 4.2 and 1.8 K. All the spectra are predominately composed of members of progressions in a single totally symmetric mode (ν_6a) built upon site origins and vibrational fundamentals. The ν_6a interval is: 743 (¹A_g), 715 (³B_3u), and 709 cm^?1 (¹B_3u) in the neat tetrazine crystal; 732 (¹A_g) and 705 cm^?1 (¹B_3u in pyrazine host, 737 (¹A_g) and 701 cm^?1 (¹B_3u) in pyrimidine host, and 732 (¹A_g) and 703 cm^?1 (¹B_3u) in pyridazine host mixed crystals. All emission spectra may be analyzed by Oi → (ν″_6a)^o_n (i), i indicating the observed s     

Computation of electron repulsion integrals using the rys quadrature method

Following an earlier proposal to evaluate electron repulsion integrals over Gaussian basis functions by a numerical quadrature based on a set of orthogonal polynomials (Rys polynomials), a computational procedure is outlined for efficient evaluation of the two-dimensional integrals I_x, I_y, and I_z. Compact recurrence formulas for the integrals make the method particularly fitted to handle high-angular-momentum basis functions. The technique has been implemented in the HONDO molecular orbital program.     

Optimization of the extraction and fractionation of corn bran oil using analytical supercritical fluid instrumentation

Supercritical fluid extraction (SFE) is combined with supercritical fluid chromatography (SFC) in an analytical mode to develop a system for fractionating and enriching high value ferulate-phytosterol esters (FPE) contained in corn bran oil. Corn bran is initially extracted with neat supercritical carbon dioxide (SC-CO2) at various pressures (13.8, 34.5, and 69 MPa) and temperatures (40, 60, and 80 degrees C) to see if the FPE can be enriched in the extracts. These initial studies show the greatest percentage of FPE could be extracted under two sets of conditions: 69 MPa at 80 degrees C and 34.5 MPa at 40 degrees C. Both sets of parameters yield an extract containing approximately 1.25% FPE. A stock supply of corn bran oil is then produced by scaled-up SFE at 34.5 MPa and 40 degrees C for subsequent chromatographic fractionation. The SFE-obtained corn bran oil is then applied to the head of a minichromatographic column containing an amino-propyl sorbent. SFC is than commenced using neat SC-CO2 at 69 MPa and 80 degrees C to remove the majority of the triglyceride-based oil. Pressure and temperature are then lowered to 34.5 MPa and 40 degrees C, respectively, and ethanol is added as a modifier. The modifier is added in an increasing stepwise gradient program, and fractions are collected at equal volume intervals. The resultant fractions are analyzed by analytical high-performance liquid chromatography with evaporative light-scattering detection and show that FPE could be enriched to a 14.5% (w) level.     

High accuracy analysis by isotope dilution mass spectrometry using an iterative exact matching technique

The selection of an appropriate isotope dilution mass spectrometry technique for the practical application of this potentially primary method of analysis is highly important. The NARL approach for the application of the exact matching double isotope dilution mass spectrometry technique developed by Henrion is presented. NARL's approach utilises exact matching to minimise the effect of measurement biases within the method but also includes the thorough examination of all other biasing factors. The approach has been successfully tested in international CCQM intercomparisons with other national metrology institutes.     

Metal triangles as building blocks in metal cluster chemistry

Many trinuclear metal clusters have structures based on isolated metal triangles with either single bonds (e.g.,M ₃(CO)₁₂ whereM = Fe, Ru, Os) or double bonds (e.g., Re₃ Cl ₁₂ ^3– ) along each edge of the triangle. Individual metal triangles can be joined in the following ways to form more complicated triangulated networks: (1) Bridging an edge of a triangle with a new vertex to give rafts in which adjacent triangles share edges; (2) Bridging a vertex of a triangle with a new edge to give bowties in which adjacent triangles share vertices; (3) Capping a triangular face with a new vertex to give a chain of tetrahedra in which adjacent tetrahedra share faces. Such triangulated metal networks are particularly common in osmium carbonyl chemistry and in mixed osmium/platinum carbonyl derivatives. Platinum triangles of the type Pt₃L₆ are analogous to cyclopropenyl rings and can form sandwiches with one or two mercury atoms in the center such as the mercuric derivative Hg[Pt.₃(µ₂-2,6-Me₂C₆H₃NC)₃] (2,6-Me₂C₆H₃NC)₃]₂ and the mercurous derivative Hg₂[Pt₃(µ₂-CO)₃L₃]₂. Platinum triangles can also be stacked in the absence of filling to give [Pt₃(µ₂-CO)₃(CO)₃] _n ^2– (n=2, 3, 4, 5, 6, 10). Metal triangles also form the faces of metal deltahera of which the octahedron, bicapped square antiprism, and icosahedron are found in globally delocalized transition metal clusters.This article is dedicated to Prof. L. F. Dahl in recognition of his many seminal contributions to metal cluster chemistry.     

Use of U-shaped donor-bridge-acceptor molecules to study electron tunneling through nonbonded contacts

A systematic determination of electronic coupling matrix elements in U-shaped molecules is demonstrated. The unique architecture of these systems allows for the determination of the electronic coupling through a pendant molecular moiety that resides between the donor and acceptor groups; this moiety quantifies the efficiency of electron tunneling through nonbonded contacts. Experimental electron-transfer rate constants and reaction free energies are used to calibrate a molecular-based model that describes the solvation energy. This approach makes it possible to experimentally determine electronic couplings and compare them with computational values.     

Radium-224 in natural waters measured by γ-ray spectrometry

A method based on Ge(Li) γ-ray spectrométry is applied to the determination of ²²⁴Ra (t_{$\text{1}\text{2}$}= 3.64 days) in natural waters. The ²²⁴Ra is first removed from several hundred liters of water by preconcentration onto manganese dioxide-impregnated acrylic fibers. The fibers are leached, radium is coprecipitated with barium sulfate, and the γ-ray activity is counted so that activity ratios among ²²⁴Ra, ²²⁵Ra and ²²⁶Ra can be calculated. Concentrations are determined by using the ²²⁶Ra concentration determined on a small separate sample. Results from samples collected from ground water, estuarine, and continental shelf environments are presented.     

Three-dimensional aromaticity in deltahedral boranes and carboranes

Methods derived from topology and graph theory indicate that the deltahedral boranes B _n H _n ^2– and the corresponding carboranes C₂B_n–2H _n (6 n 12) may be regarded as three-dimensional delocalized aromatic systems in which surface bonding and core bonding correspond to -bonding and -bonding, respectively, in planar polygonal two-dimensional hydrocarbons CinnH _n ^(n–6)+ (n=5/7). The two extreme types of topologies which may be used to model core bonding in deltahedral boranes and carboranes are the deltahedral (D _n ) topology based on the skeleton of the underlying deltahedron and the complete (K _n ) topology based on the corresponding complete graph. Analyses of the Hoffmann-Lipscomb LCAO extended Hückel computations, the Armstrong—Perkins—Stewart self-consistent molecular orbital computations, and SCF MOab initio GAUSSIAN-82 computations on B₆H₆ ^2– indicate that the approximation of the atomic orbitals by the sum of the molecular orbitals, as is typical in modernab initio computations, leads to significantly weaker apparent core bonding approximated more closely by deltahedral (D _n ) topology than by complete (K _n ) topology.This work was presented at the Workshop The Modern Problems of Heteroorganic Chemistry sponsored by the A. N. Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences (May 8–13, 1993).Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1353–1360, August, 1993.