Linus Pauling

Evolutionary Divergence and Convergence in Proteins

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.

Molecules as documents of evolutionary history

Abstract Different types of molecules are discussed in relation to their fitness for providing the basis for a molecular phylogeny. Best fit are the “semantides”, i.e. the different types of macromolecules that carry the genetic information or a very extensive translation thereof. The fact that more than one coding triplet may code for a given amino acid residue in a polypeptide leads to the notion of “isosemantic substitutions” in genic and messenger polynucleotides. Such substitutions lead to differences in nucleotide sequence that are not expressed by differences in amino acid sequence. Some possible consequences of isosemanticism are discussed.

An investigation of the structure of silk fibroin

Abstract An investigation based on new X-ray diffraction data, including quantitative spectrometric measurements of X-ray intensities, has led to the derivation of the fundamental structural features of silk fibroin. The structure consists of extended polypeptide chains bonded together by lateral N—H…O hydrogen bonds to form antiparallel-chain pleated sheets. The sequence-G-X-G-X-G-X-in which G represents glycyl and X alanyl or seryl residues predominates throughout the structure, so that adjacent sheets pack together at distances of about 3.5 and 5.7 A. Longer inter-sheet distances are explained by the presence in the structure of the larger amino-acid residues, such as tyrosine.

The Diamagnetic Anisotropy of Aromatic Molecules

Values of the diamagnetic anisotropy of benzene and other aromatic hydrocarbon molecules are calculated on the basis of the assumption that the p_z electrons (one per aromatic carbon atom) are free to move from carbon atom to adjacent carbon atom under the influence of the impressed fields. When combined with the assumed values for the contributions of the other electrons (‐2.0×10^(‐6) for hydrogen, ‐4.5×10^(‐6) for aromatic carbon, ‐6.0×10^(‐6) for aliphatic carbon) these lead to principal diamagnetic susceptibilities of molecules in approximate agreement with the available experimental data. The diamagnetic anisotropy of graphite is also discussed.

The nature of the chemical bond. V. The quantum-mechanical calculation of the resonance energy of benzene and naphthalene and the hydrocarbon free radicals

The secular equations corresponding to the five canonical structures for benzene and the forty-two for naphthalene, considered as six and ten-electron systems, respectively, are set up and solved with certain simplifying assumptions, leading to energy values differing by 1.1055α and 2.0153α, respectively, from those corresponding to unexcited (Kekule-type) structures, α being a single exchange integral involving neighboring carbon atoms. Equating these values to the empirical values of the resonance energy, α is found to be about — 1.5 v.e.It is pointed out that the dissociation of certain substituted ethanes into free radicals is due not to weakness of the carbon-carbon bond in the ethane but to the stabilization of the free radicals resulting from resonance among the structures in which the unpaired electron is located on the methyl carbon and those in which it is on other atoms (ortho, para, etc., to the methyl carbon). The secular equations for a number of such radicals have been solved, neglecting excited structures. The experimentally determined heat of formation of hexaphenylethane from triphenylmethyl, 0.5 v.e., when equated to the calculated value C-C+2.2156α, with C-C = 3.65 v.e., leads to α = — 1.4 v.e. The calculated tendencies towards dissociation are in satisfactory agreement with observation, such features as the smaller dissociating power of β-naphthyl than of α-naphthyl and of biphenylene than of diphenyl being accounted for, so that resonance among the structures considered may be accepted as the principal effect causing the stability of the hydrocarbon free radicals.

The calculation of matrix elements for Lewis electronic structures of molecules

Starting from the discovery by Rumer that the eigen‐functions corresponding to different distributions of valence bonds in a molecule can be represented by plane diagrams which provide information regarding their mutual linear independence, a very simple graphical method is developed for calculating the coefficients of the integrals occurring in the matrix elements involved in Slaters treatment of the electronic structure of molecules.

Orthomolecular Psychiatry: Varying the concentrations of substances normally present in the human body may control mental disease

The functioning of the brain is affected by the molecular concentrations of many substances that are normally present in the brain. The optimum concentrations of these substances for a person may differ greatly from the concentrations provided by his normal diet and genetic machinery. Biochemical and genetic arguments support the idea that orthomolecular therapy, the provision for the individual person of the optimum concentrations of important normal constituents of the brain, may be the preferred treatment for many mentally ill patients. Mental symptoms of avitaminosis sometimes are observed long before any physical symptoms appear. It is likely that the brain is more sensitive to changes in concentration of vital substances than are other organs and tissues. Moreover, there is the possibility that for some persons the cerebrospinal concentration of a vital substance may be grossly low at the same time that the concentration in the blood and lymph is essentially normal. A physiological abnormality such as decreased permeability of the blood-brain barrier for the vital substance or increased rate of metabolism of the substance in the brain may lead to a cerebral deficiency and to a mental disease. Diseases of this sort may be called localized cerebral deficiency diseases. It is suggested that the genes responsible for abnormalities (deficiencies) in the concentration of vital substances in the brain may be responsible for increased penetrance of the postulated gene for schizophrenia, and that the so-called gene for schizophrenia may itself be a gene that leads to a localized cerebral deficiency in one or more vital substances.

A Resonating-Valence-Bond Theory of Metals and Intermetallic Compounds

The resonating-valence-bond theory of metals discussed in this paper differs from the older theory in making use of all nine stable outer orbitals of the transition metals, for occupancy by unshared electrons and for use in bond formation; the number of valency electrons is consequently considered to be much larger for these metals than has been hitherto accepted. The metallic orbital, an extra orbital necessary for unsynchronized resonance of valence bonds, is considered to be the characteristic structural feature of a metal. It has been found possible to develop a system of metallic radii that perm its a detailed discussion to be given of the observed interatomic distances of a metal in term s of its electronic structure. Some peculiar metallic structures can be understood by use of the postulate that the most simple fractional bond orders correspond to the most stable modes of resonance of bonds. The existence of Brillouin zones is compatible with the resonating-valence-bond theory, and the new metallic valencies for metals and alloys with filled-zone properties can be correlated with the electron numbers for important Brillouin polyhedra.

The Nature of the Chemical Bond. VI. The Calculation from Thermochemical Data of the Energy of Resonance of Molecules Among Several Electronic Structures

In the first part of this paper there is given a set of bond‐energy values for single, double, and triple bonds between atoms, obtained from thermochemical data, such that the total energy of formation from separate atoms of a molecule containing given bonds is equal to the sum of the energies for those bonds. In the derivation of these values data were used only for molecules for which it is probable that one electronic structure, corresponding to one distribution of valence bonds, represents the normal state to a satisfactory degree of approximation. For other molecules more than one electronic structure of this type contributes essentially to the normal state, the energy of formation of the molecule then being larger than that for any one of the contributing structures. On comparing the energies of formation given by thermochemical data with the values calculated for various structures, it is verified that this difference is always positive or zero (to within the limits of error involved). The difference in energy is interpreted as the resonance energy of the molecule among several electronic structures, and its existence in a given case provides strong evidence that more than one structure is contributing to the normal state of the molecule, the number and importance of the contributing structures being indicated by the magnitude of the resonance energy. In this way the existence of resonance is shown for many molecules, and values found for the resonance energy are tabulated. The substances discussed include carbon dioxide, carbon disulfide, alkyl isocyanates, carboxylic acids and esters, aliphatic amines, carbonic esters, urea and related substances, benzene and benzene derivatives, naphthalene and other condensed ring systems, pyridine and related heterocyclic compounds, biphenyl, fluorene, phenylethylene, dihydronaphthalene, quinone, some ureides and purines, etc.

The Crystal Structure of Bixbyite and the C-Modification of the Sesquioxides

It was discovered in 1925 by Goldschmidt that an extensive series of sesquioxides form cubic crystals with the unit of structure containing 16 M_2O_3, the value of a varying between 9.3 A and 10.9 A. An atomic arrangement based on the space group T^5 was assigned this C-modification of the sesquioxides by Zachariasen, who studied crystals of Sc_2O_3, Mn_2O_3, Y_2O_3, In_2O_3, Tl_2O_3, Sm_2O_3, Eu_2O_3, Gd_2O_3, Tb_2O_3, Dy_2O_3, Ho_2O_3, Er_2O_3, Tm_2O_3, Yb_2O_3, Lu_2O_3, and the mineral bixbyite, (Fe, Mn)_2O_3. Zachariasen’s procedure was the following. Using the data from powder and Laue photographs of Tl_2O_3, and neglecting the contribution of the oxygen atoms to the reflections, he decided that the space group is T^5, with the 32 Tl in 8b with parameter t = 0.25, in 12c with parameter u = 0.021, and in 12c with parameter v = 0.542. These parameter values were assumed to hold for all members of the series. The consideration of intensities of reflection of Sc_2O_3 then was found to indicate the 48 O to be in two groups of 24 in the general position of T^5, with parameters x_1 ~ 1/8, y_1 ~ 1/8, x_1 ~ 3/8 and x_2 ~ 1/8, y_2 ~ 3/8, x_2 ~ 3/8. The same structure was also assigned bixbyite, with 16(Mn, Fe)_2O_3 in a unit 9.35 ± 0.02 A on edge.