The effective ionic radii of Shannon & Prewitt [Acta Cryst. (1969), B25, 925-945] are revised to include more unusual oxidation states and coordinations. Revisions are based on new structural data, empirical bond strength-bond length relationships, and plots of (1) radii vs volume, (2) radii vs coordination number, and (3) radii vs oxidation state. Factors which affect radii additivity are polyhedral distortion, partial occupancy of cation sites, covalence, and metallic character. Mean Nb5+-O and Mo6+-O octahedral distances are linearly dependent on distortion. A decrease in cation occupancy increases mean Li+-O, Na+-O, and Ag+-O distances in a predictable manner. Covalence strongly shortens Fe2+-X, Co2+-X, Ni2+-X, Mn2+-X, Cu+-X, Ag+-X, and M-H- bonds as the electronegativity of X or M decreases. Smaller effects are seen for Zn2+-X, Cd2+-X, In2+-X, pb2+-X, and TI+-X. Bonds with delocalized electrons and therefore metallic character, e.g. Sm-S, V-S, and Re-O, are significantly shorter than similar bonds with localized electrons.

Revised effective ionic radii and systematic studies of interatomic distances in halides and chalcogenides

This article reviews the basic theoretical aspects of graphene, a one-atom-thick allotrope of carbon, with unusual two-dimensional Dirac-like electronic excitations. The Dirac electrons can be controlled by application of external electric and magnetic fields, or by altering sample geometry and/or topology. The Dirac electrons behave in unusual ways in tunneling, confinement, and the integer quantum Hall effect. The electronic properties of graphene stacks are discussed and vary with stacking order and number of layers. Edge (surface) states in graphene depend on the edge termination (zigzag or armchair) and affect the physical properties of nanoribbons. Different types of disorder modify the Dirac equation leading to unusual spectroscopic and transport properties. The effects of electron-electron and electron-phonon interactions in single layer and multilayer graphene are also presented.

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The electronic properties of graphene

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

For a successful analysis of the relation between amino acid sequence and protein structure, an unambiguous and physically meaningful definition of secondary structure is essential. We have developed a set of simple and physically motivated criteria for secondary structure, programmed as a pattern-recognition process of hydrogen-bonded and geometrical features extracted from x-ray coordinates. Cooperative secondary structure is recognized as repeats of the elementary hydrogen-bonding patterns “turn” and “bridge.” Repeating turns are “helices,” repeating bridges are “ladders,” connected ladders are “sheets.” Geometric structure is defined in terms of the concepts torsion and curvature of differential geometry. Local chain “chirality” is the torsional handedness of four consecutive Cα positions and is positive for right-handed helices and negative for ideal twisted β-sheets. Curved pieces are defined as “bends.” Solvent “exposure” is given as the number of water molecules in possible contact with a residue. The end result is a compilation of the primary structure, including SS bonds, secondary structure, and solvent exposure of 62 different globular proteins. The presentation is in linear form: strip graphs for an overall view and strip tables for the details of each of 10.925 residues. The dictionary is also available in computer-readable form for protein structure prediction work.

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

https://staff.blog.ui.ac.id/hsuryadi/files/2012/02/ROS_RNS.pdf

Free radicals and antioxidants in normal physiological functions and human disease

The Nature of the Chemical Bond

Publisher Summary Informational macromolecules, or semantides, play a unique role in determining the properties of living matter in the perspectives that differ by the magnitude of time required for the processes involved—the short-timed biochemical reaction, the medium-timed ontogenetic event, and the long-timed evolutionary event. Although the slower processes should be broken down into linked faster processes, if one loses sight of the slower processes one also loses the links between the component faster processes. The relative importance of the contributions to evolution of changes in functional properties of polypeptides through their structural modification on the one hand, and of changes in the timing and the rate of synthesis of these polypeptides on the other hand, constitutes a problem that justifies the study of evolution at the level of informational macromolecules. The evaluation of the amount of differences between two organisms as derived from sequences in structural genes or in their polypeptide translation is likely to lead to quantities different from those obtained on the basis of observations made at any other, higher level of biological integration.

Evolutionary Divergence and Convergence in Proteins

During the past fifteen years we have been attacking the problem of the structure of proteins in several ways. One of these ways is the complete and accurate determination of the crystal structure of amino acids, peptides, and other simple substances related to proteins, in order that information about interatomic distances, bond angles, and other configurational parameters might be obtained that would permit the reliable prediction of reasonable configurations for the polypeptide chain. We have now used this information to construct two reasonable hydrogen-bonded helical configurations for the polypeptide chain; we think that it is likely that these configurations constitute an important part of the structure of both fibrous and globular proteins, as well as of synthetic polypeptides. A letter announcing their discovery was published last year [1]. 

The problem that we have set ourselves is that of finding all hydrogen-bonded structures for a single polypeptide chain, in which the residues are equivalent (except for the differences in the side chain R). An amino acid residue (other than glycine) has no symmetry elements. The general operation of conversion of one residue of a single chain into a second residue equivalent to the first is accordingly a rotation about an axis accompanied by translation along the axis. Hence the only configurations for a chain compatible with our postulate of equivalence of the residues are helical configurations. For rotational angle 180° the helical configurations may degenerate to a simple chain with all of the principal atoms, C, C' (the carbonyl carbon), N, and O, in the same plane.

https://www.pnas.org/content/pnas/37/4/205.full.pdf

The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.

The erythrocytes of certain individuals possess the capacity to undergo reversible changes in shape in response to changes in the partial pressure of oxygen. When the oxygen pressure is lowered, these cells change their forms from the normal biconcave disk to crescent, holly wreath, and other forms. This process is known as sickling. About 8 percent of American Negroes possess this characteristic; usually they exhibit no pathological consequences ascribable to it. These people are said to have sicklemia, or sickle cell trait. However, about 1 in 40 (4) of these individuals whose cells are capable of sickling suffer from a severe chronic anemia resulting from excessive destruction of their erythrocytes; the term sickle cell anemia is applied to their condition.

https://science.sciencemag.org/content/sci/110/2865/543.full.pdf

Linus Pauling

Papers

The Nature of the Chemical Bond

Evolutionary Divergence and Convergence in Proteins

The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain.

Sickle Cell Anemia, a Molecular Disease

The principles determining the structure of complex ionic crystals