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Chemistry

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A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding

A protein determination method which involves the binding of Coomassie Brilliant Blue G-250 to protein is described. The binding of the dye to protein causes a shift in the absorption maximum of the dye from 465 to 595 nm, and it is the increase in absorption...

Density‐functional thermochemistry. III. The role of exact exchange

Despite the remarkable thermochemical accuracy of Kohn–Sham density‐functional theories with gradient corrections for exchange‐correlation [see, for example, A. D. Becke, J. Chem. Phys. 96, 2155 (1992)], we believe that further improvements are...

A short history of SHELX

An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis...

Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen

In the past, basis sets for use in correlated molecular calculations have largely been taken from single configuration calculations. Recently, Almlof, Taylor, and co‐workers have found that basis sets of natural orbitals derived from correlated atomic...

A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity

A technique for conveniently radiolabeling DNA restriction endonuclease fragments to high specific activity is described. DNA fragments are purified from agarose gels directly by ethanol precipitation and are then denatured and labeled with the large...

A new generation of Ca2+ indicators with greatly improved fluorescence properties.

A new family of highly fluorescent indicators has been synthesized for biochemical studies of the physiological role of cytosolic free Ca2+. The compounds combine an 8-coordinate tetracarboxylate chelating site with stilbene chromophores. Incorporation...

Estimation of the Concentration of Low-Density Lipoprotein Cholesterol in Plasma, Without Use of the Preparative Ultracentrifuge

A method for estimating the cholesterol content of the serum low-density lipoprotein fraction (Sf0-20) is presented. The method involves measurements of fasting plasma total cholesterol, triglyceride, and high-density lipoprotein cholesterol concentrations,...

The rise of graphene

: Graphene is a rapidly rising star on the horizon of materials science and condensed matter physics. This strictly two-dimensional material exhibits exceptionally high crystal and electronic quality and, despite its short history, has already revealed...

The CCP4 suite: programs for protein crystallography

Collaborative Computational, Number 4

Electric Field Effect in Atomically Thin Carbon Films

We describe monocrystalline graphitic films, which are a few atoms thick but are nonetheless stable under ambient conditions, metallic, and of remarkably high quality. The films are found to be a two-dimensional semimetal with a tiny overlap between valence...

Comparison of simple potential functions for simulating liquid water

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P....

PROCHECK-a program to check the stereochemical quality of protein structures

Roman A. Laskowski, Malcolm W. MacArthur, David S. Moss, Janet M. Thornton

Molecular dynamics with coupling to an external bath

In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to...

Crystallography & NMR system: A new software suite for macromolecular structure determination.

A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure determination...

Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar

Use of Dinitrosalicylic Acid Reagent for Determination of Reducing Sugar

A simple method for displaying the hydropathic character of a protein

A computer program that progressively evaluates the hydrophilicity and hydrophobicity of a protein along its amino acid sequence has been devised. For this purpose, a hydropathy scale has been composed wherein the hydrophilic and hydrophobic properties...

Advanced Inorganic Chemistry

Since the second edition of this text, the literature in inorganic chemistry has continued to grow at an extremely rapid rate. The work has been characterised by increasing sophistication in the use of physical methods as well as in concepts and insights....

Environmental Applications of Semiconductor Photocatalysis

Michael R. Hoffmann, Scot T. Martin, Wonyong Choi, D. Bahnemann

A new and rapid colorimetric determination of acetylcholinesterase activity.

A photometric method for determining acetylcholinesterase activity of tissue extracts, homogenates, cell suspensions, etc., has been described. The enzyme activity is measured by following the increase of yellow color produced from thiocholine when it...

Constitution of binary alloys

Kurt Anderko, H. W. Salzberg

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, Soumya Swaminathan, Martin Karplus

Phase Annealing in SHELX-90: Direct Methods for Larger Structures

A number of extensions to the multisolution approach to the crystallographic phase problem are discussed in which the negative quartet relations play an important role. A phase annealing method, related to the simulated annealing approach in other optimization...

Reporting physisorption data for gas/solid systems with special reference to the determination of surface area and porosity (Recommendations 1984)

Reporting physisorption data for gas/solid systems with special reference to the determination of surface area and porosity (Recommendations 1984)

Analysis of nitrate, nitrite, and [15N]nitrate in biological fluids

A new automated system for the analysis of nitrate via reduction with a high-pressure cadmium column is described. Samples of urine, saliva, deproteinized plasma, gastric juice, and milk can be analyzed for nitrate, nitrite, or both with a lower limit...

Microsomal lipid peroxidation.

This chapter discusses microsomal lipid peroxidation. Lipid peroxidation is a complex process known to occur in both plants and animals. It involves the formation and propagation of lipid radicals, the uptake of oxygen, a rearrangement of the double bonds...

A New Family of Mesoporous Molecular Sieves Prepared with Liquid Crystal Templates

The synthesis, characterization, and proposed mechanism of formation of a new family of silicatelaluminosilicate mesoporous molecular sieves designated as M41S is described. MCM-41, one member of this family, exhibits a hexagonal arrangement of uniform...

Electron affinities of the first‐row atoms revisited. Systematic basis sets and wave functions

The calculation of accurate electron affinities (EAs) of atomic or molecular species is one of the most challenging tasks in quantum chemistry. We describe a reliable procedure for calculating the electron affinity of an atom and present results for hydrogen,...

The stopping and range of ions in solids

This chapter reviews the physics associated with the penetration of energetic ions into solids. It describes the quantitative evaluation of how the ions lose energy to the solid and the final distribution of these ions after they stop within the solid....

Self—Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian—Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules

Two extended basis sets (termed 5–31G and 6–31G) consisting of atomic orbitals expressed as fixed linear combinations of Gaussian functions are presented for the first row atoms carbon to fluorine. These basis functions are similar to the 4–31G...

Spectrometric identification of organic compounds

Robert M. Silverstein, G. Clayton Bassler

Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings

Experimental and computational approaches to estimate solubility and permeability in discovery and development settings are described. In the discovery setting ‘the rule of 5’ predicts that poor absorption or permeation is more likely when there are...

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body...

NMR of proteins and nucleic acids

NMR of proteins and nucleic acids

THE DISTRIBUTION AND CHEMICAL COMPOSITION OF ULTRACENTRIFUGALLY SEPARATED LIPOPROTEINS IN HUMAN SERUM

In the past few years several methods have been developed for the analysis of serum lipoproteins. Lindgren, Elliott, and Gofman (1) have utilized the relatively low density of the lipoproteins to separate them from the other serum proteins by ultracentrifugal...

Antioxidant activity applying an improved ABTS radical cation decolorization assay

A method for the screening of antioxidant activity is reported as a decolorization assay applicable to both lipophilic and hydrophilic antioxidants, including flavonoids, hydroxycinnamates, carotenoids, and plasma antioxidants. The pre-formed radical...

Ab initio effective core potentials for molecular calculations. Potentials for the transition metal atoms Sc to Hg

Ab initio effective core potentials (ECP’s) have been generated to replace the Coulomb, exchange, and core‐orthogonality effects of the chemically inert core electron in the transition metal atoms Sc to Hg. For the second and third transition series...

A New Mixing of Hartree-Fock and Local Density-Functional Theories

Previous attempts to combine Hartree–Fock theory with local density‐functional theory have been unsuccessful in applications to molecular bonding. We derive a new coupling of these two theories that maintains their simplicity and computational efficiency,...

Kinetics of Phase Change. I General Theory

The theory of the kinetics of phase change is developed with the experimentally supported assumptions that the new phase is nucleated by germ nuclei which already exist in the old phase, and whose number can be altered by previous treatment. The density...

Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction.

A theoretical analysis has been made of the relationship between the inhibition constant (KI) of a substance and the (I50) value which expresses the concentration of inhibitor required to produce 50 per cent inhibition of an enzymic reaction at a specific...

Solvent content of protein crystals.

An analysis has been made, from the data which are currently available, of the solvent content of 116 different crystal forms of globular proteins. The fraction of the crystal volume occupied by solvent is most commonly near 43 %, but has been observed...

Automatic recording apparatus for use in the chromatography of amino acids.

Darrel H. Spackman, William H. Stein, Stanford Moore

Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set

We present a detailed description and comparison of algorithms for performing ab-initio quantum-mechanical calculations using pseudopotentials and a plane-wave basis set. We will discuss: (a) partial occupancies within the framework of the linear tetrahedron...

Adsorption Surface Area and Porosity

S. J. Gregg, K. S. W. Sing, H. W. Salzberg

A Film Detection Method for Tritium‐Labelled Proteins and Nucleic Acids in Polyacrylamide Gels

A simple method is described for detecting 3H in polyacrylamide gels by scintillation autography (fluorography) using X-ray film. The gel is dehydrated in dimethyl sulphoxide, soaked in a solution of 2,5-diphenyloxazole (PPO) in dimethylsulphoxide, dried...

THE FERRIC REDUCING ABILITY OF PLASMA (FRAP) AS A MEASURE OF “ANTIOXIDANT POWER”: THE FRAP ASSAY

A simple, automated test measuring the ferric reducing ability of plasma, the FRAP assay, is presented as a novel method for assessing `'antioxidant power.'' Ferric to ferrous ion reduction at low pH causes a colored ferrous-tripyridyltriazine complex...

Spin diffusion measurements : spin echoes in the presence of a time-dependent field gradient

A derivation is given of the effect of a time‐dependent magnetic field gradient on the spin‐echo experiment, particularly in the presence of spin diffusion. There are several reasons for preferring certain kinds of time‐dependent magnetic field...

Enzymic method for quantitative determination of nanogram amounts of total and oxidized glutathione: Applications to mammalian blood and other tissues

A method for the analysis of nanogram quantities of glutathione has been developed which is based on the catalytic action of GSH or GSSG in the reduction of Ellman reagent (DTNB) by a mixture of TPNH and yeast glutathione reductase. Unlike previous methods...

Probability-based protein identification by searching sequence databases using mass spectrometry data

Several algorithms have been described in the literature for protein identification by searching a sequence database using mass spectrometry data. In some approaches, the experimental data are peptide molecular weights from the digestion of a protein...

MOLMOL: a program for display and analysis of macromolecular structures.

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL...

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins

New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding)...

An extraction method for measuring soil microbial biomass C

E. D. Vance, P. C. Brookes, D. S. Jenkinson

Ligand: a versatile computerized approach for characterization of ligand-binding systems.

We have developed a general strategy and a versatile computer program for analysis of data from ligand-binding experiments (e.g., radioreceptor assay systems for hormones, neurotransmitters, drugs). This method provides optimal (weighted least squares)...

Click Chemistry: Diverse Chemical Function from a Few Good Reactions

Examination of natures favorite molecules reveals a striking preference for making carbon ‐ heteroatom bonds over carbon ‐ carbon bonds—surely no surprise given that carbon dioxide is natures starting material and that most reactions are performed...

PSEUDO-SECOND ORDER MODEL FOR SORPTION PROCESSES

A literature review of the use of sorbents and biosorbents to treat polluted aqueous effluents containing dyes:organics or metal ions has been conducted. Over 70 systems have been reported since 1984 and over 43 of these reported the mechanism as being...

Nonionic Triblock and Star Diblock Copolymer and Oligomeric Surfactant Syntheses of Highly Ordered, Hydrothermally Stable, Mesoporous Silica Structures

A family of highly ordered mesoporous (20−300 A) silica structures have been synthesized by the use of commercially available nonionic alkyl poly(ethylene oxide) (PEO) oligomeric surfactants and poly(alkylene oxide) block copolymers in acid media. Periodic...

Crystal Structure of Rhodopsin: A G Protein-Coupled Receptor

Heterotrimeric guanine nucleotide–binding protein (G protein)–coupled receptors (GPCRs) respond to a variety of different external stimuli and activate G proteins. GPCRs share many structural features, including a bundle of seven transmembrane α...

Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions

A contracted Gaussian basis set (6‐311G**) is developed by optimizing exponents and coefficients at the Mo/ller–Plesset (MP) second‐order level for the ground states of first‐row atoms. This has a triple split in the valence s and p shells together...

COLORIMETRY OF TOTAL PHENOLICS WITH PHOSPHOMOLYBDIC-PHOSPHOTUNGSTIC ACID REAGENTS

Several details of the assay of total phenolic substances have been investigated and an improved procedure developed. The improvements include the use of Folin-Ciocalteu reagent rather than the Folin-Denis reagent, gallic acid as a reference standard,...

Mass Spectrometric Sequencing of Proteins from Silver-Stained Polyacrylamide Gels

Proteins from silver-stained gels can be digested enzymatically and the resulting peptides analyzed and sequenced by mass spectrometry. Standard proteins yield the same peptide maps when extracted from Coomassie- and silver-stained gels, as judged by...

Quantum dot bioconjugates for ultrasensitive nonisotopic detection

Highly luminescent semiconductor quantum dots (zinc sulfide—capped cadmium selenide) have been covalently coupled to biomolecules for use in ultrasensitive biological detection. In comparison with organic dyes such as rhodamine, this class of luminescent...

Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi

A consistent set of ab initio effective core potentials (ECP) has been generated for the main group elements from Na to Bi using the procedure originally developed by Kahn. The ECP’s are derived from all‐electron numerical Hartree–Fock atomic wave...

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

We present two new hybrid meta exchange-correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount...

Microdetermination of Phosphorus

P. S. Chen, T. Y. Toribara, Huber R. Warner

Self‐Consistent Molecular‐Orbital Methods. IX. An Extended Gaussian‐Type Basis for Molecular‐Orbital Studies of Organic Molecules

An extended basis set of atomic functions expressed as fixed linear combinations of Gaussian functions is presented for hydrogen and the first‐row atoms carbon to fluorine. In this set, described as 4–31 G, each inner shell is represented by a single...

Two-photon laser scanning fluorescence microscopy.

Molecular excitation by the simultaneous absorption of two photons provides intrinsic three-dimensional resolution in laser scanning fluorescence microscopy. The excitation of fluorophores having single-photon absorption in the ultraviolet with a stream...

Functional Porous Coordination Polymers

Susumu Kitagawa, Ryo Kitaura, Shin-ichiro Noro

A simplification of the protein assay method of Lowry et al. Which is more generally applicable

Some recent modifications of the protein assay by the method of Lowry, Rosebrough, Farr, and Randall (1951, J. Biol. Chem. 193, 265-275) have been reexamined and altered to provide a consolidated method which is simple, rapid, objective, and more generally...

Apparent hydroxyl radical production by peroxynitrite: implications for endothelial injury from nitric oxide and superoxide.

Superoxide dismutase reduces injury in many disease processes, implicating superoxide anion radical (O2-.) as a toxic species in vivo. A critical target of superoxide may be nitric oxide (NO.) produced by endothelium, macrophages, neutrophils, and brain...

Natural population analysis 8 )

A method of ‘‘natural population analysis’’ has been developed to calculate atomic charges and orbital populations of molecular wave functions in general atomic orbital basis sets. The natural analysis is an alternative to conventional Mulliken...

Probing Single Molecules and Single Nanoparticles by Surface-Enhanced Raman Scattering

Optical detection and spectroscopy of single molecules and single nanoparticles have been achieved at room temperature with the use of surface-enhanced Raman scattering. Individual silver colloidal nanoparticles were screened from a large heterogeneous...

A consistent and accurate ab initio parametrization of density functional dispersion correction "DFT-D… for the 94 elements H-Pu

The method of dispersion correction as an add-on to standard Kohn–Sham density functional theory DFT-D has been refined regarding higher accuracy, broader range of applicability, and less empiricism. The main new ingredients are atom-pairwise specific...

THE [14C]DEOXYGLUCOSE METHOD FOR THE MEASUREMENT OF LOCAL CEREBRAL GLUCOSE UTILIZATION: THEORY, PROCEDURE, AND NORMAL VALUES IN THE CONSCIOUS AND ANESTHETIZED ALBINO RAT1

— A method has been developed for the simultaneous measurement of the rates of glucose consumption in the various structural and functional components of the brain in vivo. The method can be applied to most laboratory animals in the conscious state....

Electrospray ionization for mass spectrometry of large biomolecules

Electrospray ionization has recently emerged as a powerful technique for producing intact ions in vacuo from large and complex species in solution. To an extent greater than has previously been possible with the more familiar "soft" ionization methods,...

Pharmaceuticals, hormones, and other organic wastewater contaminants in U.S. streams, 1999-2000: A national reconnaissance

To provide the first nationwide reconnaissance of the occurrence of pharmaceuticals, hormones, and other organic wastewater contaminants (OWCs) in water resources, the U.S. Geological Survey used five newly developed analytical methods to measure concentrations...

Atom Transfer Radical Polymerization

Krzysztof Matyjaszewski, Jianhui Xia

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely...

Use of a Free Radical Method to Evaluate Antioxidant Activity

Tile antiradical activities of various antioxidants were determined using the free radical, 2.2-Diphenyl-l-pict3,1hydrazyl (DPPI-I°). In its radical form, DPPI-I ° has an absorption band at 515 nm which disappears upon reduction by an antiradical compound....

The Surface Science of Titanium Dioxide

Titanium dioxide is the most investigated single-crystalline system in the surface science of metal oxides, and the literature on rutile (1 1 0), (1 0 0), (0 0 1),...

Abundances of the elements: Meteoritic and solar

New abundance tables have been compiled for Cl chondrites and the solar photosphere and corona, based on a critical review of the literature to mid-1988. The meteorite data are generally accurate to ± 5–10%. Significant discrepancies between Sun and...

Synthesis of graphene-based nanosheets via chemical reduction of exfoliated graphite oxide

Reduction of a colloidal suspension of exfoliated graphene oxide sheets in water with hydrazine hydrate results in their aggregation and subsequent formation of a high-surface-area carbon material which consists of thin graphene-based sheets. The reduced...

The SIESTA method for ab initio order-N materials simulation

We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals....

A modification of the Lowry procedure to simplify protein determination in membrane and lipoprotein samples.

The original Lowry method of protein determination has been modified by the addition of sodium dodecyl sulfate in the alkali reagent and an increase in the amount of copper tartrate reagent. These alterations allowed the method to be used with membrane...

Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals (・OH/・O[-]) in aqueous solution

Kinetic data for the radicals H⋅ and ⋅OH in aqueous solution,and the corresponding radical anions, ⋅O− and e aq− , have been critically pulse radiolysis, flash photolysis and other methods. Rate constants for over 3500 reaction are tabulated,...

Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects

A method is presented which utilizes the calculation of the molecular electrostatic potential or the electric field at a discrete number of preselected points to evaluate the environmental effects of a solvent on the properties of a molecular system....

Exact Stochastic Simulation of Coupled Chemical Reactions

Daniel T. Gillesple, Danlel T. Gillespie

Gaussian‐Type Functions for Polyatomic Systems. III

The use of a linear combination of Gaussian‐type orbitals (CGTO), instead of an individual Gaussian‐type orbital (GTO), as a unit of basis functions for large‐scale molecular calculations, is discussed. A systematic construction of the CGTO basis...

Quantitative estimation of proteins by electrophoresis in agarose gel containing antibodies

A method is deseribed for quantitative analysis of proteins with a charge differing from that of the bulk of the immunoglobulins. The method utilizes the difference between the rate of electrophoretic migration of proteins and of their antibody complexes...

Mechanical alloying and milling

Mechanical alloying (MA) is a solid-state powder processng technique involving repeated welding, fracturing, and rewelding of powder particles in a high-energy ball mill. Originally developed to produce oxide-dispersion strengthened (ODS) nickel- and...

Iron-based layered superconductor La[O(1-x)F(x)]FeAs (x = 0.05-0.12) with T(c) = 26 K.

We report that a layered iron-based compound LaOFeAs undergoes superconducting transition under doping with F- ions at the O2- site. The transition temperature (Tc) exhibits a trapezoid shape dependence on the F- content, with the highest Tc of ∼26...

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