Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint

Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

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Revealing noncovalent interactions.

Solar photospheric and meteoritic CI chondrite abundance determinations for all elements are summarized and the best currently available photospheric abundances are selected. The meteoritic and solar abundances of a few elements (e.g., noble gases, beryllium, boron, phosphorous, sulfur) are discussed in detail. The photospheric abundances give mass fractions of hydrogen (X ¼ 0:7491), helium (Y ¼ 0:2377), and heavy elements (Z ¼ 0:0133), leading to Z=X ¼ 0:0177, which is lower than the widely used Z=X ¼ 0:0245 from previous compilations. Recent results from standard solar models considering helium and heavy-element settling imply that photospheric abundances and mass fractions are not equal to protosolar abundances (representative of solar system abundances). Protosolar elemental and isotopic abundances are derived from photospheric abundances by considering settling effects. Derived protosolar mass fractions are X0 ¼ 0:7110, Y0 ¼ 0:2741, and Z0 ¼ 0:0149. The solar system and photospheric abundance tables are used to compute self-consistent sets of condensation temperatures for all elements. Subject headings: astrochemistry — meteors, meteoroids — solar system: formation — Sun: abundances — Sun: photosphere

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Solar System Abundances and Condensation Temperatures of the Elements

Foundations of Confocal Scanned Imaging in Light Microscopy -- Fundamental Limits in Confocal Microscopy -- Special Optical Elements -- Points, Pixels, and Gray Levels: Digitizing Image Data -- Laser Sources for Confocal Microscopy -- Non-Laser Light Sources for Three-Dimensional Microscopy -- Objective Lenses for Confocal Microscopy -- The Contrast Formation in Optical Microscopy -- The Intermediate Optical System of Laser-Scanning Confocal Microscopes -- Disk-Scanning Confocal Microscopy -- Measuring the Real Point Spread Function of High Numerical Aperture Microscope Objective Lenses -- Photon Detectors for Confocal Microscopy -- Structured Illumination Methods -- Visualization Systems for Multi-Dimensional Microscopy Images -- Automated Three-Dimensional Image Analysis Methods for Confocal Microscopy -- Fluorophores for Confocal Microscopy: Photophysics and Photochemistry -- Practical Considerations in the Selection and Application of Fluorescent Probes -- Guiding Principles of Specimen Preservation for Confocal Fluorescence Microscopy -- Confocal Microscopy of Living Cells -- Aberrations in Confocal and Multi-Photon Fluorescence Microscopy Induced by Refractive Index Mismatch -- Interaction of Light with Botanical Specimens -- Signal-to-Noise Ratio in Confocal Microscopes -- Comparison of Widefield/Deconvolution and Confocal Microscopy for Three-Dimensional Imaging -- Blind Deconvolution -- Image Enhancement by Deconvolution -- Fiber-Optics in Scanning Optical Microscopy -- Fluorescence Lifetime Imaging in Scanning Microscopy -- Multi-Photon Molecular Excitation in Laser-Scanning Microscopy -- Multifocal Multi-Photon Microscopy -- 4Pi Microscopy -- Nanoscale Resolution with Focused Light: Stimulated Emission Depletion and Other Reversible Saturable Optical Fluorescence Transitions Microscopy Concepts -- Mass Storage, Display, and Hard Copy -- Coherent Anti-Stokes Raman Scattering Microscopy -- Related Methods for Three-Dimensional Imaging -- Tutorial on Practical Confocal Microscopy and Use of the Confocal Test Specimen -- Practical Confocal Microscopy -- Selective Plane Illumination Microscopy -- Cell Damage During Multi-Photon Microscopy -- Photobleaching -- Nonlinear (Harmonic Generation) Optical Microscopy -- Imaging Brain Slices -- Fluorescent Ion Measurement -- Confocal and Multi-Photon Imaging of Living Embryos -- Imaging Plant Cells -- Practical Fluorescence Resonance Energy Transfer or Molecular Nanobioscopy of Living Cells -- Automated Confocal Imaging and High-Content Screening for Cytomics -- Automated Interpretation of Subcellular Location Patterns from Three-Dimensional Confocal Microscopy -- Display and Presentation Software -- When Light Microscope Resolution Is Not Enough:Correlational Light Microscopy and Electron Microscopy -- Databases for Two- and Three-Dimensional Microscopical Images in Biology -- Confocal Microscopy of Biofilms — Spatiotemporal Approaches -- Bibliography of Confocal Microscopy.

Handbook of biological confocal microscopy

THE definitions currently used to classify chemical bonds (in terms of bond order, covalency versus ionicity and so forth) are derived from approximate theories1–3 and are often imprecise. Here we outline a first step towards a more rigorous means of classification based on topological analysis of local quantum-mechanical functions related to the Pauli exclusion principle. The local maxima of these functions define 'localization attractors', of which there are only three basic types: bonding, non-bonding and core. Bonding attractors lie between the core attractors (which themselves surround the atomic nuclei) and characterize the shared-electron interactions. The number of bond attractors is related to the bond multiplicity. The spatial organization of localization attractors provides a basis for a well-defined classification of bonds, allowing an absolute characterization of covalency versus ionicity to be obtained from observable properties such as electron densities.

Classification of chemical bonds based on topological analysis of electron localization functions

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The Atom and the Molecule

hours the rotation was again taken: [ C ~ ] ~ D +77.2 * 5\" (a% +1.75 * 0.1'; 1 = 2 dm.). Treatment of 17-Isopregnan-3( a)-ol-20-one with Hydrogen chloride.-In a manner similar to the above a solution of 44.7 mg. of 17-isopregnan-3(a)-ol-20-one made up to 5 ml. with 4.3% methanolic hydrogen chloride was refluxed for four hours and then the rotation was taken: [ a I s 1 ~ $75.6 * 5\" ( C Y ~ ~ D $1.35 * 0.1\"; 1 = 2 dm.). Acetate of 17-bopregnan-3( ~~)-ol-2O-one.-A solution of 100 mg. of 17-isopregnan-3(a)-oI-20-one in 1 ml. of acetic anhydride and 0.66 ml. of acetic acid was refluxed for twenty minutes. After standing for three hours the solution was diluted to turbidity with water. The acetate separated in fine needles and was collected, weight 95 mg. After one recrystallization from methanol it melted a t 157-159' and mixed melting points with b:th the normal and 17-isopregnanolones gave about 30 depressions: [a]*'D -28.2 * 8' (24.16 mg. made up to 2 cc. with methanol; 1 = 1 dm.; a a 4 ~ -0.34 * 0.1'). Anal. Calcd. for CzzH380~: C, 76.61; H, 10.07. Found: C, 76.82; H, 10.32. Oxime of 17-Isopregnan-3(a)-oI-20-one.-A solution of 100 mg. of 17-isopregnan-3(a)-oI-20-one, 100 mg. of hydroxylammonium chloride, and 150 mg. of sodium acetate (trihydrate) in 2 ml. of methanol and 0.5 d. of water was refluxed for two hours. After cooling the solution was poured into water, extracted with ether, and the ether solution was dried over anhydrous sodium sulfate. The ether was removed and the residue was crystallized first from dilute acetone and then from methanol giving a white crystalline oxime melting at 192-197\" (with decomposition). A mixed melting point with a sample of the oxime of the normal pregnan-3(~~)-01-20-one@ gave a depression of about 20\". Anal. Calcd. for ColHssOzN: N, 4.20. Found: N, 4.57. Test with Digitonin.-To about 1 mg. of 17-isopregnan3(a)-ol-20-one in a few drops of 90% methanol was added an equal volume of a saturated solution of digitonin in 90% methanol. No precipitate was obtained even after standing for several hours.

Gilbert N. Lewis

Papers

The Atom and the Molecule

Phosphorescence and the Triplet State

Valence and the structure of atoms and molecules

Thermodynamics and the free energy of chemical substances

The Color of Organic Substances.