Showing papers on "Molecule published in 1976"

Self‐consistent molecular orbital methods. XVII. Geometries and binding energies of second‐row molecules. A comparison of three basis sets

Abstract: Three basis sets (minimal s–p, extended s–p, and minimal s–p with d functions on second row atoms) are used to calculate geometries and binding energies of 24 molecules containing second row atoms. d functions are found to be essential in the description of both properties for hypervalent molecules and to be important in the calculations of two‐heavy‐atom bond lengths even for molecules of normal valence.

On the geometry of O–H⋯O hydrogen bonds

Abstract: The asymmetry of hydrogen bonds arises from the repulsion between the O atoms forming the bonds. A bond-valence analysis of the repulsion leads to the conclusion that strong and weak hydrogen bonds are different in kind, the stronger ones (O-O less than 2.7 A) involve strain and are linear while the weaker ones (O-O greater than 2.7 A) have an extra degree of freedom and are generally bent. The strength of the hydrogen bond is determined by a number of factors such as the requirement that the bond valences around each atom add up to the atomic valence, a tendency for the O-O distance to be close to 2.7 A, and by crystal-packing considerations which often lead to the formation of bent, and hence weaker, hydrogen bonds. The bond-valence analysis correctly predicts the observed correlations between H⋯O distance and O-H-O angle. The frequency with which various hydrogen-bond configurations are observed in crystals is used to propose a method for determining hydrogen-bond energies. This analysis of hydrogen bonding leads to an understanding of the lengthening of hydrogen bonds in high-pressure ices and to proposals for hydrated ion structures which can be used, for example, to predict the acid strengths of anions and to show that in neutral aqueous solutions the oxygen atoms of complex anions each hydrogen-bond to two or three water molecules.

Determination of the structure of cellulose II.

Abstract: The structure of regenerated cellulose is shown by x-ray diffraction to be comprised of an array of antiparallel chain molecules. The determination was based on the intensity data from rayon fibers and utilized rigid-body least-squares refinement techniques. The unit cell is monoclinic with space group P2(1) and dimensions a = 8.01 A, b = 9.04 A, c = 10.36 A (fiber axis), and gamma = 117.1 degrees. Models containing chains with the same sense (parallel) or alternating sense (antiparallel) were refined against the intensity data. The only acceptable model contains antiparallel chains. The -CH2OH groups of the corner chain are oriented near to the gt position while those of the center chain are near to the tg position. Both chains possess an O3-H-O5' intramolecular hydrogen bond, and the center chain also has an O2'-H-O6 intramolecular bond. Intermolecular hydrogen bonding occurs along the 020 planes (o6-h-o2 bonds for the corner chains and O6-H-O3 bonds for the center chains) and also along the 110 planes with a hydrogen bond between the O2-H of the corner chain and the O2' of the center chain. This center-corner chain hydrogen bonding is a major difference between the native and regenerated structures and may account for the stability of the latter form.

Partial molar volumes of organic compounds in water. III. Carbohydrates

Abstract: Partial molar volumes in water at 25°C have been determined for a number of carbohydrates, including mono-, di-, tri-, tetra-, penta-, hexa-, hepta-, and polysaccharides and their derivatives The experimental values can be calculated from the van der Waals volumes of the molecules if account is taken of the shrinkage in volume caused by hydrogen-bonding of solvent molecules to the hydroxyl groups of the sugars

Collisional Activation Mass Spectrometry—A New Probe for Determining the Structure of Ions in the Gas Phase

Abstract: Organic ions with high translational energy colliding inelastically with neutral atoms or molecules become excited electronically at the expense of their translational energy. The excitation energy enables a wide range of dissociation reactions to occur and the intensity relationships yield information about the structure of the ions concerned and also permit conclusions to be drawn about the mechanism of their formation.

Reactions of oriented molecules.

Abstract: Beams of oriented molecules have been used to directly study geometrical requirements in chemical reactions. These studies have shown that reactivity is much greater in some orientations than others and demonstrated the existence of steric effects. For some reactions portions of the orientation results are in good accord with traditional views of steric hindrance, but for others it is clear that our chemical intuition needs recalibrating. Indeed, the information gained from simultaneously orienting the reactants and observing the scattering angle of the products may lead to new insights about the detailed mechanism of certain reactions. Further work must be done to extend the scope and detail of the studies described here. More detailed information is needed on the CH(3)I reaction and the CF(3)I reaction. The effects of alkyl groups of various sizes and alkali metals of various sizes are of interest. In addition, reactions where a long-lived complex is formed should be studied to see if orientation is important. Finally, it would be of interest to apply the technique to the sort of reactions that led to our interest in the first place: the S(N)2 displacements in alkyl halides where the fascinating Walden inversion occurs.

Product-ion distributions for some ion-molecule reactions

Abstract: The reactions of He+ ions with N2, O2, CO2, and CH4, and of C+ and N+ ions with O2 are presented. The measurements were carried out in the SIFT apparatus (selected ion flow tube), which involves the injection of a mass-selected positive-ion beam into a flowing neutral gas into which a reactant gas is introduced at a position downstream in the flow. Data acquisition and analysis are made by the flowing afterglow technique. The results for the He++N2 reaction agree with the previously established branching ratio. For the other reactions, considerable differences are apparent between the product distributions obtained and those previously reported and an explanation is attempted. A brief discussion of the reaction mechanism is presented for each reaction in the light of the determined product distributions, and the anticipated development of the SIFT technique for ion-molecule reaction mechanisms is outlined.

Kinetic energy distributions from unimolecular decay: predictions of the Langevin model

Abstract: The kinetic energy released in a unimolecular decomposition is examined within the framework of quasiequilibrium theory. It is assumed that the motion is governed by the long‐range forces between the separating moieties. Explicit formulas are obtained for cases where the total angular momentum is either very low or very high. Comparison with experiment and with other formulations is made.

Principles and Synthetic Applications in Crown Ether Chemistry

Abstract: The principles involved in macroheterocycle chemistry are discussed. Classes and types of macroheterocycles, synthetic approaches (including the template effect), complexation and complexes are mentioned. The utilization of crown ethers in synthetic organic chemistry is also surveyed. 1. Introduction 1.1. History 1.2. Nomenclature and Characteristics 1.3. Classes of Crowns and Related Molecules 2. Synthetic Access 2.1. Templated Syntheses 2.2. Non-Williamson Syntheses 3. Complexation 3.1. The Complexation Phenomenon 3.2. Types of Complexes 4. Synthetic Utility 4.1. Solubilization and Phase Transfer 4.2. Cation Effects 4.3. Crowns as Reagents and Catalysts 4.4. Complexation Specificity 5. Toxicity 6. Conclusions

A van der Waals-type equation of state for fluids with associating molecules.

Abstract: The basic assumptions of van der Waals theory are contained in two well-known concepts: excluded volume (repulsive forces) and a homogeneous, isotropic field potential (attractive forces). We have superimposed on these, one more well-known concept: the existence of dimers, trimers, etc., at chemical equilibrium. With reasonable simplifying assumptions, we obtain a closed-form equation of state, applicable to all fluid densities, and potentially useful for fluids containing strongly polar or hydrogen-bonded molecules. At all temperatures and at high densities, the equation of state suggests a phase transition where, because of extensive association, a new (solid-like) phase is in equilibrium with a “normal” fluid phase. The boundary between these phases has no critical point.

The electronic structure of molecules by a many‐body approach. I. Ionization potentials and one‐electron properties of benzene

Abstract: The ionization potentials of benzene are studied by an ab initio many‐body approach which includes the effects of electron correlation and reorganization beyond the one‐particle approximation. The calculations confirm the assignment of the photoelectron spectrum experimentally proposed by Jonsson and Lindholm: 1e1g(π), 2e2g, 1a2u(π), 2e1u, 1b2u, 1b1u, 2a1g, 1e2g in order of increasing binding energy. To definitely establish the ordering of the ionization potentials in the second band, which has been very controversial, the corresponding vibrational structure has been calculated. A number of one‐electron properties are calculated in the one‐particle approximation and compared to experimental work and other theoretical calculations.

HF infrared chemiluminescence: Energy disposal and the role of the radical fragment in the abstraction of hydrogen from polyatomic molecules by F atoms

Abstract: HF infrared chemiluminescence has been utilized to study the energy disposal for the abstraction of hydrogen by fluorine atoms from polyatomic molecules which yield radical fragments with large stabilization energies. The prototype systems selected for study, methyl benzenes, phenol, and acetonitrile, are cases which yield resonance stabilized radicals as products. Comparison is made to the energy disposal from the reaction of F with the primary C–H bonds of aliphatic hydrocarbons, which have smaller radical stabilization energies. In general the radical stabilization energy, which is associated with major changes in geometry of the radical relative to the parent molecules, was not available to the HF product. The reactions of F + benzene and ethylene also were studied to provide reference data for different types of C–H bonds. The HF vibrational energy distributions have been interpreted using an extension of the information theory which previously has been applied to three body reactions. Vibrational surprisal analyses are developed and discussed for three models of the reference (prior) product distributions: (i) the polyatomic fragment product was treated as an atom, i.e., the three body case, (ii) the rotations of the radical fragment were added to the three body model, (iii) a complete model including all vibrational and rotational modes of the polyatomic radical fragment. For (iii) with the use of the full thermochemical exoergicity linear surprisal plots were found and these plots were used to assign relative populations to HF (v=0). The information‐theoretic parameters from the three reference models are compared for a series of F+HR reactions in which R increases in complexity from Cl to CH2C6H5. For reactions with large product stabilization energies, calculations for (i) and (ii) were done with a reduced ’’effective available’’ energy corresponding to the assumption that the energy available to HF was less than the full exoergicity. Some insight is gained into the role of the R fragment in the energy disposal.

Structure of the concanavalin A-methyl alpha-D-mannopyranoside complex at 6-A resolution.

Abstract: The carbohydrate binding site of concanavalin A has been identified in crystals of the concanavalin A-methyl ..cap alpha..-D-mannopyranoside complex and is 35 A from the iodophenol binding site (K. D. Hardman and C. F. Ainsworth (1973), Biochemistry 12, 4442), which has been postulated to be adjacent to the carbohydrate-specific binding site (Edelman et al. (1972), Proc. Natl. Acad. Sci. U.S.A. 69, 2580). The crystals are orthorhombic in space group C222/sub l/ and crystal density measurements indicate a protein mass of four monomers (molecular weight of 104,000) per asymmetric unit. However, the electron density map contains eight monomers/asymmetric unit, revealing lattice disorder. The electron density map with a nominal resolution of 6 A has been solved using three heavy-atom derivatives and the position and orientation of each monomer established. Atomic coordinates of the native protein which has previously been determined (K. D. Hardman (1973), Adv. Exp. Med. Biol. 40, 103) were transposed into this new space group and the gross conformations of the monomers, dimers, and tetramers were found to be very similar to the previous structure. However, some minor differences were apparent even at this resolution. After crystal growth, the methyl ..cap alpha..-D-mannopyranoside was replaced by o-iodophenyl ..beta..-D-glucopyranoside or methylmore » 2-iodoacetimido-2-deoxy-..cap alpha..-D-glucopyranoside in separate experiments,and difference electron density maps were calculated. The highest peaks for both iodinated sugar derivatives associated with each monomer agreed within a few angstroms of each other and were found near side chains Tyr-12 and -100 and Asp-16 and -208. This region is 10 to 14 A from the manganese, in good agreement with nuclear magnetic resonance (NMR) studies in solution (C. F. Brewer et al. (1973), Biochemistry 12, 4448) and with the site predicted from cross-linked I222 crystal studies (K. D. Hardman (1973), Adv. Exp. Med. Biol. 40, 103). (auth)« less

Molecular Excitons in Small Aggregates

Abstract: The molecular exciton model, which deals with the excited state resonance interaction in weakly coupled electronic systems, is described as an interpretative tool for the study of the spectra and photochemistry of composite molecules. Under composite molecules are grouped loosely bound groups of light-absorbing units, held together by hydrogen bonds or by van der Waals forces. Another group of composite molecules included in the study consists of covalently bound light-absorbing units.

Semi-empirical calculations of π-electron affinities for some conjugated organic molecules

Abstract: Energy levels have been calculated for some conjugated systems containing C, N, and O atoms using a semi-empiricalmethod based upon a variableβ-γ modification of the Pariser-Parr-Pople approximation to the Hartree-Pock equation. Koopmans' theorem is used to relate the calculated energy of the lowest vacant molecular orbital, ɛLVMO, to the adiabatic electron affinity of a molecule. The approach is identical to that used previously by Kunii and Kuroda [13]. An excellent correlation is found between electron affinities deduced from recent beam experiments and ɛLVMO. This relationship is used to predict electron affinities for over 100 other organic molecules. In addition, excited state energies for negative ions are calculated, and good agreement is found with the available experimental data. Bound excited states are also predicted for some organics which contain the =C(CN)2 substructure. The additive contribution of group substitutions to the electron affinity is discussed for the case of CN substitutions to ethylene, benzene, and naphthalene.

Conformation of the cyclic tetrapeptide dihydrochlamydocin. Iabu-L-Phe-D-Pro-LX, and experimental values for 3 1 intramolecular hydrogen bonds by X-ray diffraction†

Abstract: Chlamydocin, Iabu-L-Phe-D-Pro-LX, is a naturally occurring cyclic tetrapeptide that exhibits high cytostatic activity. The conformation of the peptide ring, as well as the stereo configuration in the vicinity of the epoxide ring, have been established by a single-crystal X-ray study of dihydrochlamydocin: C28H40N4O6·H2O. It crystallizes in the monoclinic space group P21 with a = 12.616(6) A, b = 12.355(6) A, c = 9.442(5) A, and β = 99.5(1)°. The structure was solved by the symbolic addition procedure for phase determination followed by the tangent formula method of phase refinement. This structure represents the first cyclic tetrapeptide in which all four peptide units have been found in the trans conformation; however, each peptide unit is significantly nonplanar with ω angles deviating by 14–24° from the ideal value of 180°. This molecule contains two intramolecular 3 1 hydrogen bonds and experimentally determined parameters for these seven-membered turns are presented.

Stability of cis, trans, and nonplanar peptide groups.

Abstract: Conformational energy calculations using ECEPP (Empirical Conformational Energy Program for Peptides) were performed on the molecular fragment Calpha1C'ONHCalpha2, on N-methylacetamide, and on several peptide molecules including N-acetyl-N'-methylglycineamide (Gly single residue), N-acetyl-N',N'-dimethylglycine-amide, and N-acetyl-N'-methylamide dipeptides of Gly-Gly and Gly-Pro. Energy minimization was carried out with peptide groups taken in both the cis and trans conformations, and the librational entropy and conformational free energy were determined at each minimum. It was found that the instability of cis in Gly-Gly comes primarily from interactions of the Calpha1 and HCalpha1 atoms with the Calpha2 and HCalpha2 atoms, and also from avorable interactions present in the trans form which are disallowed in the cis form, and from conformational entropy. The instability of cis in Gly-Pro is much less than in Gly-Gly because unfavorable interactions of the type CalphaH-CalphaH present in the cis conformation of Gly-Gly are present in both the cis and trans forms of Gly-Pro. The instability of cis in Gly-Pro arises mainly from the change in electrostatic energy caused by the restricted rotation about the N-Calpha bond of Pro. Entropy accounts for about 0.5 kcal/mol of the instability of cis in Gly-Pro compared with about 1.5 kcal/mol in Gly-Gly. The calculated fraction (4%) of cis in Gly-pro is in good agreement with the experimental value (5%) for related peptides in nonpolar solvents. When the dihedral angle omega of the central peptide bond in these dipeptides is allowed to vary during energy minimization, the deviations from planarity are only 1-3 degrees in low-energy minima of Gly-Gly but as much as 10 degrees in Gly-Pro. A comparison of these results with calculations in which the peptide bond was held fixed in the planar trans conformation shows that conformation-dependent properties of blocked dipeptides can be represented adequately without allowing omega to vary.

HFClF: Structure and bonding

Abstract: The structure of the complex formed between HF and ClF has been determined by molecular beam electric resonance spectroscopy. The molecule HFClF is a slightly asymmetric prolate top. The spectroscopic constants determined from K=0 spectra of several isotopic species are as follows: The atomic arrangement in the complex is HFClF with the three heavy atoms collinear. The proton is off axis by 55°. The FCl van der Waals bond length is 2.76 A. Comparison of the structure of HFClF with that of (HF)2 shows striking similarities. It appears that the bonding in both complexes is quite similar.

E.S.R. spectra of matrix isolated alkali atom clusters

Abstract: E.S.R. spectra assigned to Na3 molecules have been obtained by codepositing sodium atoms and diluent argon on a sapphire surface loosely coupled to a liquid helium cryostat and warmed by a heat leak, to allow aggregation before the alkali atoms are frozen into the argon matrix. The trimer spectra under these conditions were much more intense than the residual atom spectra. The trimer spectra indicate the unpaired electron in these molecules has predominantly s rather than p character. Approximately 95 per cent of the 3s spin density is equally distributed between two of the alkali atoms, with only about 7 per cent of the spin density on the third atom. The trimers thus are not merely van der Waals adducts but involve chemical bonding. Both a covalent molecular orbital model for linear or obtuse isosceles geometry and an ionic charge-transfer model giving M2 +M- or M+M2 - appear qualitatively consistent with the spectra.

Characterization of the methylene 13C chemical shift tensor in the normal alkane n‐C20H42

Abstract: 13C NMR chemical shifts in a single crystal of n‐eicosane (n‐C20H42) have been measured using the method of high power proton decoupling and the chemical shift tensors were characterized. Principal values in ppm relative to CS2 are: (a) For CH3: σ11=166.7±2, <22=171.2±2.0, σ33=189.8±2; (b) For the α‐methylene: σ11=156.0±2.5, σ22=163.1±2.5, σ33=178.0±2.5; and (c) For the interior methylenes: σ11=142.6±2.0, σ22= 154.6±2.0, σ33=175.6±2.0. From x‐ray studies, only the unit cell parameters are known. On the basis of isolated molecule symmetry considerations, cross‐polarization rate studies, and oriented polyethylene spectra, the interior methylene chemical shift tensor is assigned with respect to molecular orientation. The crystallographic axes are also related to the interior methylene chemical shift tensor and a prediction is made for the C–CH3 bond direction relative to these crystallographic axes. The principal axes of the α‐CH2 and the CH3 chemical shift tensors do not coincide with any bond directions. T...