Showing papers on "Molecule published in 1979"

Staphylococcal nuclease: proposed mechanism of action based on structure of enzyme-thymidine 3',5'-bisphosphate-calcium ion complex at 1.5-A resolution.

Abstract: The structure of the staphylococcal nuclease (EC 3.1.4.7)—thymidine 3′,5′-bisphosphate—Ca2+ (enzyme—inhibitor) complex has been extended to 1.5-A resolution by using much additional data and a phase refinement scheme based on an electron-density map modification procedure. By correlating this structure with the known properties of the enzyme, a mechanism of action is proposed that involves nucleophilic attack on phosphorus by a water molecule, which is bound to Glu-43, in line with the 5′-CH2O(H) leaving group. The carboxylate of Glu-43 promotes this attack by acting as a general base for the abstraction of a proton from the attacking water molecule. Nucleophilic attack is further facilitated by polarization of the phosphodiester by an ionic interaction between a Ca2+ ion and a phosphate oxygen atom and by four hydrogen bonds to phosphate oxygen atoms from guanidinium ions of Arg-35 and Arg-87. These interactions may also catalyze the reaction by lowering the energy of a trigonal bipyramidal transition state. The hydrolysis of nucleic acid substrate proceeds by cleavage of the 5′—P—O bond to yield a free 5′-hydroxyl group and a terminal, 3′-phosphate monoester group. In the inhibitor complex the only general acid group found in a position to donate a proton to the leaving 5′-oxygen is the guanidinium ion of Arg-87. Alternative proton donors, presently lacking direct structural support, could be the phenolic hydroxyl group of Tyr-113 or a water molecule. The precision and rigidity of the location of the reactants at the active site and the probable dual binding and catalytic roles of the guanidinium ions of Arg-35 and Arg-87 are especially noteworthy.

Experimental studies of molecular interactions between nitrogen bases of nucleic acids.

Abstract: New experimental results concerning molecular interactions between the nitrogen bases of nucleic acids in the crystalline phase and in vacuo are reported. The temperature dependence of the evaporation rate is measured for solid species. The sensitivity of conventional methods of sublimation heat measurements was improved essentially using a quartz resonator serving as a precise sensor of evaporation rate. Sublimation heats were found for both canonical bases and a number of their derivatives. The in vacuo formation of base associates interacting through hydrogen bonds was observed with a field mass spectrometer. The dimer formation enthalpies, which are indicative of a stronger attraction in complementary pairs compared with noncomplementary ones, were derived from the temperature dependence of ionic currents. Hydrogen-bound complexes of more intricate associates (base trimers and aqueous molecules associates) were studied. The energy gain in the formation of trimers of identical molecules was shown to be larger (per base molecule) than that for dimers.

Heats of Chemisorption of O2, H2, CO, CO2, and N2 on Polycrystalline and Single Crystal Transition Metal Surfaces

Abstract: One of the important physical-chemical properties that characterizes the interaction of solid surfaces with gases is the bond energy of the adsorbed species. The determination of the bond energy is usually performed indirectly by measuring the heat of adsorption (or heat of desorption) of the gas [1, 2], In order to define the heat of adsorption, let us consider the chemisorption of a diatomic molecule, X2, onto a site on a uniform solid surface, M. The molecule may adsorb without dissociation to form MX2. M represents the adsorption site where bonding occurs to a cluster of atoms or to a single atom. In this circumstance, the heat of adsorption, ΔHads, is defined as the energy needed to break the MX2 bond:

Molecular beam studies of benzene dimer, hexafluorobenzene dimer, and benzene–hexafluorobenzene

Abstract: A detailed study of the electric deflection of molecular beams of (C6H6)2, (C6F6)2, and C6H6–C6F6 is reported. Although no resolved microwave or radio frequency transitions were observable, examination of unresolved beam transitions at radio frequencies were useful in establishing that the homomolecular dimers (C6H6)2 and (C6F6)2 are asymmetric rotors while the heteromolecular dimer C6H6–C6F6 is a symmetric top. From analysis of the quantitative electric deflection the dipole moment of C6H6–C6F6 is 0.44±0.04 D.

Electroclinic effect at the A-C phase change in a chiral smectic liquid crystal

Abstract: When a smectic-$A$ phase is composed of chiral molecules, it exhibits an electroclinic effect, i.e., a direct coupling of molecular tilt to applied field. The pretransitional behavior of the electroclinic effect in the $A$ phase is used to study the critical behavior near the second-order, smectic-$A$---smectic-$C$ phase transition. This behavior is measured by monitoring the change in birefringence of a sample as the electroclinic effect causes a tilt of the molecules. A large pretransitional effect is measured, and constants describing the critical behavior are determined.

An efficient ab initio method for computing infrared and Raman intensities: Application to ethylene

Abstract: A new and very efficient method for the calculation of the infrared and Raman spectral intensities of polyatomic molecules using ab initio Hartree–Fock theory is described. The utility of the method is exemplified by an evaluation of the dipole and polarizability derivatives of the ethylene molecule employing a Gaussian basis set of double zeta quality, augmented by two sets of polarization functions. The predicted values of the vibrational intensities and the depolarization ratios are nearly within the experimental uncertainty which indicates that Hartree–Fock theory is capable of correctly describing these phenomena. The new method enables the efficient calculation of these properties by evaluating the dipole and polarizability derivatives as the first and second order contributions to the potential energy gradient of a molecule in the presence of a finite perturbing electric field. The calculations are thus performed at a single nuclear geometry and the molecular integrals are evaluated only once. The ...

Circular hydrogen bonds

Abstract: CIRCULAR hydrogen bonds present a new, experimentally demonstrated principle showing how hydration water molecules and hydroxyl groups of macromolecules can cooperate to form a network-like pattern. Quantum chemical calculations show that chain-like H-bonds in the crystal lattice1 are energetically favoured above individual ones2,3. This is due to the cooperative effect, which leads to increased H-bonding activity of an OH-group if it is already accepting or donating an H-bond. These linear structures can close up to form circular arrangements comprising four and more OH-groups4–6. Such circles have actually been described for crystal structures of ice7 and of ice clathrates8, but in these cases the water molecules within the circles are related by crystallographic symmetry elements and are therefore not independent of each other. One should expect to find lattice-independent circular H-bonds in crystal structures of large O—H-rich molecules which co-crystallise with water of hydration, conditions which are satisfied by the cyclodextrin family. The smallest member, α-cyclodextrin (α-CD; cyclohexaamylose), consists of six α(1, 4)-linked glucose molecules and contains six primary and 12 secondary hydroxyl groups ((C6H10O5)6, molecular weight 973). From aqueous solution, α-CD crystallises as hexahydrate, α-CD·6H2O, and this complex, with a total of 120 hydroxyl groups (4 × 18 from α-CD and 4 × 12 from the six H2O) in one unit cell has been studied by X-ray and neutron diffraction methods (ref. 9, and Klar, Hingerty and W.S., unpublished). Two other complexes, a second modification of the hexahydrate (K. Lindner and W.S., unpublished) and α-CD·methanol·4H2O (ref. 10) have been investigated by X rays. As refinement in all cases is around R = 4% for data extending to 0.89 A resolution, hydrogen atom positions could be assigned. I discuss here results obtained from the X-ray/neutron study of α-CD·6H2O.

First observation of the coil–globule transition in a single polymer chain

Abstract: The conformations of single polymer chains in solution have been studied extensively since the 1940s. At high temperatures and in good solvents, a polymer has an extended coil configuration, while at low temperatures and in poor solvents a polymer is in a collapsed globule state. The transition between the extended and collapsed state as the temperature or solvent composition is varied was thought to be smooth and continuous, and experiments supported this idea1. However, in the 1960s it was suggested2–4 that the transition between the two configurations, the coil–globule transition, was discrete. We now report the first observations of the single polymer coil–globule transition. The observations were made on polyacrylamide molecules dissolved in acetone–water mixtures.

Spherands-ligands whose binding of cations relieves enforced electron-electron repulsions

Abstract: A new series of ligands called spherands are similar to the crowns and cryptands However, the cavity formed by the oxygen shell can be occupied only by spherical entities such as single atoms or monatomic ions A cyclohexamato phenylene system provides a framework which holds the oxygen of 6 methoxyl groups in a perfect octahedral arrangement by their attachment to the six convergent positions of the aryl groups Ligand complexes with lithium and sodium as cations and FeCl/sub 4/, chlorides, perchlorates and bromides as anions were prepared; their thermal stabilities were examined; and their NMR spectra were analyzed The structures of the compounds are discussed

Local density functional theory of atoms and molecules.

Abstract: A local density functional theory of the ground electronic states of atoms and molecules is generated from three assumptions: (i) The energy functional is local. (ii) The chemical potential of a neutral atom is zero. (iii) The energy of a neutral atom of atomic number Z is -0.6127 Z7/3. The energy functional is shown to have the form [Formula: see text] where A0=6.4563 and B0=1.0058. The first term represents the electronic kinetic energy, the second term represents the electron—electron repulsion energy for N electrons, and the third term is the nucleus—electron attraction energy. The energy E and the electron density ρ are obtained and discussed in detail for atoms; their general properties are described for molecules. For any system the density becomes zero continuously at a finite distance from nuclei, and contours of the density are contours of the bare-nuclear potential v. For an atomic species of fractional charge q = 1 - (N/Z), an energy formula is obtained, [Formula: see text] which fits Hartree—Fock energies of 625 atoms and ions with root-mean-square error of 0.0270. A more general local density functional involving a coefficient B(N) = B0N2/3 + B1 is briefly considered.

Creation and Disposal of Vibration Energy in Polyatomic Molecules

Abstract: The importance of vibrational excitation in chemical reactions has been known for many years, having been recognized first in the study of the unimolecular reactions of polyatomic molecules. Because a nonlinear polyatomic molecule of N atoms has 3N 6 vibrational degrees of freedom (compared to three rotations and three translations), it is clear that much of the phenomenology of excited molecules must reside in vibration. As in most fields of chemical physics the study of vibrational excitation has grown together from two widely separated areas. Bulk kinetic data (thermal unimolecular reaction rates and sound dispersion) and static spectroscopic energy level experiments are now combined into a large area of interest dominated by spectroscopic measurements of dynamic processes. A knowledge of the chemical, energetic, and spectral properties of poly atomic molecules is important for studies of chemical reactivity, isotope separation, combustion processes, chemical lasers and other technologies, as well as being a splendid stimulus to the ever expanding predictive abilities of chemical theorists. The importance of a knowledge of vibrational processes has increased rapidly with the possibility of using lasers to induce state-specific chemical reactions. Such excitation can result in interesting selectivity only if the resulting molecules retain their state-specific excitation long enough to react. In contrast to the extremely large number of highly selective electronic photochemical reactions, the only comparably selec­ tive effect for vibrational excitation is the isotope selectivity of infrared multiphoton dissociation. Although vibrational excitation is known to enhance strongly the rate of a few bimolecular reactions, there are to date no data showing chemical selectivity based on state-specific excita-

A relationship between the retention indices on nematic and isotropic phases and the shape of polycyclic aromatic hydrocarbons

Abstract: An equation has been derived allowing to predict retention index values on nematic phases from computable parameters and sizes of the molecules of polycyclic aromatic hydrocarbons. Another equation, which has also been derived, allows to determine the shape parameter of a molecule from chromatographic data.

Photoelectron spectra of AsF5‐doped polyacetylenes

Abstract: The x‐ray and ultraviolet photoemission spectra of undoped polyacetylene, AsF5‐doped polyacetylene, AsF5, and AsF3 are reported and compared. At a doping level near where the electrical conductivity saturates (∼11% AsF5), the As:F ratio is 1:5 and a large fraction of the arsenic–fluoride moieties are localized near the surface of the polyacetylene fibrils. The C (1s) core‐level spectra indicate a charge transfer of about one electron per AsF5 molecule. The UPS spectra, the x‐ray induced Auger spectra and CNDO calculations suggest, however, that the arsenic pentafluoride moieties are not simple AsF5‐radical anions. At lower doping levels (0.1 to 1%) very different results are obtained.

Calculation of molecular parameters for stepwise polyfunctional polymerization

Abstract: Our recursive method is extended to calculate several new parameters for stepwise polyfunctional polymerization. In the pregel region we calculate weight average molecular weight, Mw, for polydisperse reactants and effective average functionality, fe, of a reacting mixture. These quantities are useful for systems employing reactive oligomers. We also calculate weight average number of branches per molecule, Bw, and the weight average of a longest chain. These should be useful for viscosity relations. In the postgel region we give relations for the extent of reaction in the soluble fraction. This result can be used to calculate sol properties directly from existing pregel relations. We also calculate the weight fraction of pendant chains on the gel, wp, and the average molecular weight of the elastically effective network chains, Mc,w.