Showing papers on "Molecule published in 1978"

Infrared and Raman Spectra of Inorganic and Coordination Compounds

Abstract: Inorganic molecules (ions) and ligands are classified into diatomic, triatomic, four-atomic, five-atomic, six-atomic, and seven-atomic types, and their normal modes of vibration are illustrated and the corresponding vibrational frequencies are listed for each type. Molecules of other types are grouped into compounds of boron, carbon, silicon, nitrogen, phosphorus, and sulfur, and the structures and infrared (IR)/Raman spectra of select examples are shown for each group. Group frequency charts including band assignments are shown for phosphorus and sulfur compounds. Other group frequency charts include hydrogen stretching frequencies, halogen stretching frequencies, oxygen stretching and bending frequencies, inorganic ions, and metal complexes containing simple coordinating ligands. Keywords: inorganic compounds; coordination compounds; diatomic molecules (ligands); triatomic molecules (ligands); four-atomic molecules (ligands); five-atomic molecules (ligands); six-atomic molecules (ligands); seven-atomic molecules (ligands); boron compounds; carbon compounds; silicon compounds; nitrogen compounds; phosphorus compounds; sulfur compounds; group frequency charts

Multiplicity of the ground state of large alternant organic molecules with conjugated bonds

Abstract: The multiplicity and the full spin of the ground state of large alternate molecules with conjugated bonds are considered. It is strictly shown that if the numbers of starred and unstarred atoms (say, carbon) differ from each other the full spin of the molecule is more than zero. Some possible planar and linear molecules having the full spin to be proportional to their sizes are presented. Particularly, they would be ferromagnets at infinite sizes.

The chemical bond

Abstract: Unlike many other books on chemical bonding, this introduction to the subject does not adopt the traditional historical treatment in which the two basic theories of valence, molecular orbital and valence bond, are introduced and applied to increasingly complex molecules. Instead it develops the subject area from fundamental concepts which are important in chemistry as a whole. The validity of these concepts is examined within both the older empirical models and within the more recent ab-initio calculations. In this second edition, the contents have been extended to cover the mathematical basis of ab-initio calculations and the structure of computer programs used to carry these out. The new edition has also allowed the authors to extend the coverage of group theory techniques and update aspects of transition metal chemistry.

Polarization model for water and its ionic dissociation products

Abstract: In order to achieve a simple description of aggregates of deformable water molecules, a new model has been constructed which treats H+ and O2− particles as the basic dynamical and structural elements. The H+ units are bare protons, while the O2− units possess a form of nonlocal polarizability consistent with their electronic structure. The model yields water molecules which have the correct geometry and dipole moment, and which engage in hydrogen bonding to one another. Minimum‐energy structures have been determined for the water dimer and trimer and for small hydrate clusters of H+ and OH−; comparison with relevant experiments and quantum–mechanical calculations is satisfactory.

Cryptates: inclusion complexes of macropolycyclic receptor molecules

Abstract: Molecular receptors use intermolecular interactions for the selective binding of substrates. Macropolycyclic molecules containing appropriate binding sites and cavities of suitable size and shape, may be designed so as to display molecular recognition in the formation of selective inclusion complexes, cryptates, with metal cations, anions and molecules. Macrocyclic receptors which form stable and selective complexes with primary ammonium and guanidinium groups are discussed; they display central and lateral discrimination. Enhanced rates of intramolecular thiolysis and hydrogen transfer have been observed when suitable reactive groups are attached to the receptor. Macrobicyclic ligands form very stable and selective cryptates with alkali and alkaline-earth cations; they may be modified so as to selectively complex toxic heavy metal cations. Binuclear cryptates of two types have been synthesized: macrobicyclic complexes of an ellipsoidal Bis-Tren ligand and cylindrical macrotricyclic complexes. They display interesting properties (like cation-cation interactions, copper protein type spectral parameters etc.) and are suitable for formation of “cascade complexes” by interaction of substrates with the bound cations. Spherical macrotricyclic receptors form cryptates with cations, anions and small inorganic species. They display tetrahedral recognition and may be considered as topologically optimal receptors for the ammonium ion, the water molecule, the halide ions, with which they form cryptates where the substrate is held in the intramolecular cavity by a tetrahedral array of hydrogen bonds. Finally, the macrobicyclic Bis-Tren system in its protonated form, complexes triatomic species like the azide anion. It represents a further step in the design of abiotic molecular receptors for polyatomic molecules or ions. The main lines of further developments in the chemistry of macropolycycles comprise the design of receptors for other important groups (carboxylate, phosphate), of polynuclear complexes and cascade complexes of potential use in polynuclear catalysis, of molecular catalysts as enzyme models and new chemical reagents.

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

Abstract: Refinement of the diffraction data at 2.5-A resolution from orthorhombic crystals of yeast tRNAPhe has proceeded to the point where spermine and magnesium ions can be located in the difference electron density map. Two spermine molecules are found: one is located in the major groove at one end of the anticodon stem; the other is near the variable loop and curls around phosphate 10 in a region where the polynucleotide chain takes a sharp turn. Four distinct magnesium ions have been identified: one in the anticodon loop, two in the D loop, and one coordinated with phosphates 8, 9, 11, and 12, where the polynucleotide chain is coiled. The conformation of the anticodon stem and loop is stabilized by the cations at the end of the molecule. The positions of these ions may be related to aspects of the biological activity of tRNA. The spermine and magnesium ions appear to be important in maintaining the overall folding of the tRNA molecule.

A laboratory study of the reactions of N+, N2+, N3+, N4+, O+, O2+, and NO+ ions with several molecules at 300 K

Abstract: A study has been made of the rate coefficients and product ion distributions for the reactions at 300 K of the ions N+, N2+, N3+, N4+, O+, O2+, and NO+ with CH3NH2, NH3, H2S, CH3OH, H2CO, COS, O2, H2O, CH4, CO2, CO, H2, and N2 molecules listed in increasing order of their ionization energies. These measurements are intended as a contribution to stratospheric chemistry. In the binary reactions of the ions of large recombination energy with molecules of low ionization energy, multiple ion products generally result and the rate coefficients are close to gas kinetic. Conversely, the low recombination energy ions NO+ and O2+ generally undergo ternary association reactions with the large ionization energy molecules. The reactions of N2+ and N4+ are very similar, the most common mechanism apparently being direct charge transfer usually followed by fragmentation, the nitrogen–nitrogen bonds in the reacting ions remaining intact. The N+ and N3+ reactions differ from the N2+ and N4+ reactions in that they show a gr...

Atkins' Physical Chemistry

Abstract: PART 1. EQUILIBRIUM 1. The properties of gases 2. The first law 3. The second law 4. Physical transformations of pure substances 5. Simple mixtures 6. Phase diagrams 7. Chemical equilibrium PART 2. STRUCTURE 8. Quantum theory: introduction and principles 9. Quantum theory: techniques and applications 10. Atomic structure and atomic spectra 11. Molecular orbitals for polyatomic systems 12. Molecular symmetry 13. Spectroscopy 1: rotational and vibrational spectra 14. Spectroscopy 2: electronic transitions 15. Spectroscopy 3: magnetic resonance 16. Statistical thermodynamics: the concepts 17. Statistical thermodynamics: the machinery 18. Molecular interactions 19. Materials 1: Macromolecules and aggregates 20. Materials 2: The solid state PART 3. CHANGE 21. Molecules in motion 22. The rates of chemical reactions 23. The kinetics of complex reactions 24. Molecular reaction dynamics 25. Processes at solid surfaces DATA SECTION ANSWERS TO EXERCISES ANSWERS TO PROBLEMS INDEX

Interaction of the peptide bond with solvent water: a vapor phase analysis.

Abstract: A dynamic technique, using radioactivity as a means of detection, makes it possible to measure the partial pressures of highly polar compounds in dilute aqueous solution. The results can be expressed in terms of the dimensionless distribution coefficient for transfer of a compound from dilute aqueous solution to the vapor phase. For acetic acid this coefficient is 1.1 X 10(-5), for acetamide 7.6 X 10(-8), for N-methylacetamide 4.1 X 10(-8), and for N,N-dimethylacetamide 5.4 X 10(-7). Thus acetamide is much more strongly solvated than the uncharged acetic acid molecule. The results suggest: (1) that the peptide bond represents an extreme among uncharged functional groups in the degree to which it is stabilized by solvent water; (2) that the very great hydrophilic character of the peptide bond may be associated mainly with hydrogen bonding of the solvent to the carbonyl oxygen atom (rather than the N-H group); and (3) that the observed equilibria of biosynthesis and hydrolysis of peptide bonds in aqueous solution are largely determined by differences between reactants and products in their free energies of solvation. It is anticipated that where "bound" water is found in proteins, it will often be found to be associated with peptide bonds, and will tend to be associated with the C-O group rather than with the N-H group.

The formation of the γ phase from the α and β polymorphs of polyvinylidene fluoride

Abstract: Thermal, optical, infrared, and x‐ray techniques are used to demonstrate that the γ phase of polyvinylidene fluoride can be obtained from existing α‐ and/or β‐phase crystallites by either an annealing‐induced solid state α→γ phase transformation or as the result of a slow melting and recrystallization process. It is shown that certain surfactants modify the melting behavior of the α and β phases in a manner that accelerates the rapid recrystallization of the γ form. PVF2 samples that contain only the γ polymorph can be produced by this surfactant‐controlled technique. It is postulated that the surfactant delays the diffusion of molecules freed in the melting process and thus increases the probability of the stabilization of conformational fluctuations that result in the γ phase.

Chemical‐state effects in Auger electron spectroscopy

Abstract: We have used Auger spectroscopy as a probe of local chemical environment both in the gas and condensed phases using a systematically chosen series of molecules [H2O, CH3OH, (CH3)2O, CH4, C2H4, and C2H2]. For the series of gas phase molecules, H2O, CH3OH, (CH3)2O, and CH4, where oxygen and carbon are, respectively, in similar bonding arrangements, characteristic fingerprint spectra (methanelike for C and waterlike for O) are shown to result. Additional fine structure, which is dependent on the specific molecular environment, appears on the spectra. In contrast, dramatic differences are observed for the series CH4, C2H2, and C2H4 in which major differences in hybridization exist at the carbon site. H2O, CH3OH, and (CH3)2O were studied both in the gas phase (electron excited) and in the condensed phase (x‐ray excited). The O(KVV) (K level–valence–valence transition) and C(KVV) spectra are shown to be similar when comparing the gas–solid results only if the multilayer spectra are properly corrected for electr...

Hydrogen-bond structure in carbohydrate crystals

Abstract: So that possible relationships between hydrogen-bond lengths and hydrogen-bond types could be investigated, it was decided to study by neutron diffraction the crystal structures of several molecules having nearly the same size and shape. Feasibility of crystallization of a homogeneous species was a prime criterion. The three methyl pyranosides selected for the studies had been previously investigated by X-ray diffraction. These were the crystals of methyl ..cap alpha..-glucopyranoside, methyl ..cap alpha..-mannopyranoside, and methyl ..cap alpha..-altopyranoside. Hydrogen bonding in these three structures is especially significant because they contain examples of five of the ten possible types of O-H-O interactions shown in Table I. The results of these neutron diffraction studies provided a systematic relationship between hydrogen-bond length and hydrogen-bond type in the three structures. Not all crystalline carbohydrates fall into their classifications as ''neatly'' as did those from the first three pyranosides. Complicating factors include the competitive effects of hydrogen bonds, polar and dipolar interactions, and van der Waals forces. Most noticeable feature of Table I is the predominance of the bonds of the donor-acceptor type which correspond to the shorter, stronger bonds and are part of the infinite chains or are the inner bonds of finite chains, a consequence ofmore » the ''cooperative effect'' which is also discussed. The anomeric effect of hydrogen bonding is also evaluated and the results are tabulated. Table II illustrates comparative X-ray data and neutron diffraction data on H--O bond lengths. Authors believe that the systematics of the hydrogen-bond data presented will form a useful framework with which to compare future experimental measurements and theoretical calculations.« less

Fourier transform infrared spectroscopic study of the structure of silane coupling agent on E-glass fiber

Abstract: Infrared spectra of silane coupling agents deposited on E-glass fiber were obtained by Fourier transform infrared spectroscopy (FT-IR). A spectral subtraction technique resolved all vibrational modes of the coupling agent deposited from various concentrations of treating solutions. The amount of vinyl functional coupling agent was determined by measuring the integrated peak intensities of the organic functional group. It revealed that the thickness of the coupling agent layer on the glass fiber depended on the concentrations of the treating solution. The rates of condensation reaction of polysiloxanol with and without glass fiber were followed. The coupling agent on the glass fiber reacted much faster than without glass at room temperature. It was concluded that the coupling agent molecules near the glass fiber surface have some order and can easily participate in the condensation reaction. The carbonyl group of a methacryl functional silane hydrogen bonds with hydroxyl groups. The methacryl functional silane on the glass fiber showed less hydrogen bonded groups than the precipitated polysiloxanol suggesting a mechanism of predominant head-to-head adsorption.

Role of hydrophobicity in the binding of coenzymes

Abstract: We calculate the loss of surface area accessible to solvent associated with coenzyme binding in Clostridium flavodoxin, in dogfish lactate dehydrogenase, and in lobster glyceraldehyde-3-phosphate dehydrogenase. The coenzymes are nearly buried in the complexes and lose on the order of 600 A*, while the proteins lose a similar amount of accessible surface area. Some of the loss can be attributed to conforma- tion changes in the protein, at least in the case of lactate de- hydrogenase, where we show that the apoenzyme has a larger Hydrophobic, electrostatic, and van der Waals forces are involved in all the various types of interactions made by the polypeptide chain of a protein: interactions with itself to fold into a globular structure; association with other chains to form multisubunit complexes; and the binding of small ligands. Thus when structural data are available from x-ray crystallography, the geometrical arrangement of polar atoms shows the presence of intra- and intermolecular hydrogen bonds and charge in- teractions and the volume of the Voronoi polyhedron around each atom describes the atomic packing (Richards, 1974; Chothia & Janin, 1975). The role of hydrophobicity can be assessed using the concept of accessible surface area (Lee & Richards, 1971). For a given protein atom this is the area of the surface over which the center of a water molecule can be placed while it is in van der Waals contact with the atom and not penetrating any other protein atom. Each square angstrom of protein accessible surface that is removed from contact with the solvent gives a hydrophobic free energy of 25 cal (Chothia, 1974). How do these different forces create the specific strong bonds that are essential for biological systems? From an analysis of the structure of the interfaces that occur between protein monomers, we concluded that hydrophobicity is the major force stabilizing protein-protein association; van der Waals forces and hydrogen bonds (i.e., complementarity) play

Interaction of ribonuclease A with aqueous 2-methyl-2,4-pentanediol at pH 5.8

Abstract: The interactions between ribonuclease A and solvent components in aqueous 2-methyl-2,4-pentanediol (MPD) have been investigated by differential refractometry and light scattering at pH 5.8, i.e., conditions similar to those used to crystallize the protein from this solvent system. Application of multicomponent thermodynamic theory shows that, at all solvent compositions up to 50% (v/v) MPD, the protein is preferentially hydrated; i.e., addition of ribonuclease to the mixed solvent leads to an increase in the chemical potential of MPD. This unfavorable thermodynamic interaction leads to phase separation, probably caused by local salting out of the MPD by the charges on the surface of the protein molecule. A parallel examination by circular dichroism (CD) has shown that the CD spectrum of ribonuclease in 50% MPD is indistinguishable from that in dilute buffer.

Crystal structures of sodium sulfate decahydrate (Glauber's salt) and sodium tetraborate decahydrate (borax). Redetermination by neutron diffraction

Abstract: Single-crystal neutron-diffraction data with full-matrix least-squares refinements have yielded precise locations for all atoms (for the H atoms in particular), in both compounds. Hydrogen bonding with H atom sites disordered with equal occupancy, as previously postulated to be the source of zero-point entropy in the sulfate, is quantitatively verified. A thermally excited librational mode of the sulfate ion involving a rearrangement of hydrogen bonding has been found. The two structures, which have closely similar chains of Na ions with coordinated water molecules, are compared in detail. Measures of disagreement are: for the sulfate, R(F 2) = 0.082 for 1750 F 2 > a(F2); for the borate, R(F 2) = 0.060 for 1837 F 2 > o(F2).

Graphite intercalation compounds

Abstract: Solid‐state physicists are turning more and more to complex synthetic materials in their search for novel phenomena and potentially useful properties. Many of these materials are highly anisotropic, so that interatomic interactions can for all practical purposes be neglected along one or two crystal axes. One of the oldest classes of prototype systems for exploring phenomena predicted to occur in two‐dimensional systems are graphite intercalation compounds. These consist of stacks of one or more layers of hexagonally arrayed carbon atoms, alternating with monolayers of guest atoms or molecules. Striking changes in the properties of both host and guest result from intercalation. In addition to their quasi‐two‐dimensional behavior, fundamental interest centers on their variable anisotropy, which results from the fact that the strength of the interlayer interactions depends on the nature of the intercalated species.

Exchange in low-energy electron-molecule scattering: Free-electron-gas model exchange potentials and applications to e - H 2 and e - N 2 collisions

Abstract: Calculations of cross sections for elastic $e$-${\mathrm{N}}_{2}$ collisions have been performed for impact energies from 0.01 to 1.0 Ry using model exchange potentials based on a free-electron-gas approximation in order to evaluate the utility of such local potentials in low-energy electron-molecule scattering. A body-frame fixed-nuclei formulation of the collision problem is used which treats the molecule as rigid and does not allow for electronic or vibrational excitation. Coupled integro-differential scattering equations which incorporate exchange rigorously are derived and the simplification of the nonlocal exchange potential to an approximate energy-dependent local potential is described. An initial study of $e$-${\mathrm{H}}_{2}$ collisions is reported in which results obtained with various model excahnge potentials are compared to those of exact static-exchange calculations. Cross sections for the $e$-${\mathrm{N}}_{2}$ system obtained using the model exchange potentials (with and without polarization) are reported and compared with measured cross sections and the results of other theoretical studies. For both systems, good agreement with more rigorous treatments of the exchange can be obtained.

Effects of hydrogen bonding on the Raman intensities of methanol, ethanol and water

Abstract: The absolute Raman intensities of methanol, ethanol and water in the gas and liquid phases have been measured using 514.5 and 337.1 nm excitation. Large intensity changes were observed for the Raman lines of the OH stretching vibrations in changing from gas to liquid. The observed intensity changes are interpreted as due to the additional contribution of the charge transfer electronic excited state arising from hydrogen bond formation. The Raman intensities of methanol, ethanol and water in alkali halide solutions were also studied. The observed effects of halide ions on the intensities and their excitation wavelength dependences were found to be well correlated with the known charge transfer states resulting from electron transfer from the halide ion to the surrounding solvent molecules.

The structure of the HeI2 van der Waals molecule

Abstract: The rotational structure of the fluorescence excitation spectrum of the B (v′=10) ←X (v″=0) transition of the van der Waals molecule HeI2 has been measured and analyzed. The analysis indicates that the molecule has a nonlinear equilibrium structure with R′=4.79±0.22 A and R″=4.47±0.13 A, where R is the perpendicular distance from the helium atom to a line drawn through the iodine atoms.