Electronic structure of the peptide linkage. I. Equilibrium geometry and electronic properties of formhydroxamic acid

The equilibrium geometry of formhydroxamic acid has been calculated within the framework of the INDO –MO formalism. Various structural factors are analyzed and discussed in terms of the calculated force constants and charge distribution. The possibility of internal rotation around the C? N bond of formhydroxamic acid has been examined. The potential energy surface for the amide-imide tautomerism is explored by calculating the geometries and characterizing saddle points on that surface. The cyclic and open dimers of formhydroxamic acid are examined and the hydrogenbond energy and length are calculated.     

Note on the Fermi–Amaldi correction for the Thomas–Fermi theory of atoms

The aim of this note is to ascertain the importance of the Fermi–Amaldi (FA ) correction for the Thomas–Fermi (TF ) theory of atoms. For this purpose, an analytic trial electron density has been chosen and the Thomas–Fermi–Amaldi (TFA ) energy expression has been minimized by the Ritz method for the closed-shell atoms Ne, Ar, Kr, Xe, and Rn. The variationally obtained electron densities have then been used for calculating the diamagnetic susceptibilities of these atoms. The calculated values show only a very small improvement over values calculated by Jensen by an analogous procedure from the TF energy expression.     

Thermal dissociation of 1,2-dioxethane. III. Localized molecular-orbital study

The localized MO 's (LMO 's) of 1,2-dioxethane in its ground state and along the dissociation reaction path (to formaldehyde products) are generated using Boys' criteria for localization. The total charge density in each LMO is partitioned into atomic and overlap densities and the binding or antibinding character of each LMO is discussed in terms of the forces exerted on the nuclei by these densities. The driving force for the dissociation reaction is shown to arise essentially from the atomic dipole forces exerted on the oxygen nuclei by their lone-pair LMO 's. The characterization of a saddle point on the potential energy surface has been discussed in terms of the electrostatic equilibrium between forces exerted by the electron clouds “incomplete following” and “preceding.” The differences between the LMO 's obtained from the two Hartree–Fock solutions to which the SCF procedure converges have been discussed.     

Electronic-structure studies of solides. V. Rigorous Hartree-Fock treatment of metallic hydrogen using a plane-wave basis

We have performed Hartree-Fock calculations for simple cubic metallic hydrogen crystals using Bloch functions expanded in plane waves, All integrals were evaluated accurately including exchangeterms. Increasingly larger basis sets were used, and the total Hartree-Fock energy obtained with the maximum number of plane waves (27) was ?0.4770 hartrees/atom. This total energy is believed to be within a few millihartress of the Hartree-Fock limit results. The deficiency of a plane-wave expansion to represent the atomic cusps, however, makes it difficult to obtain the exact Hartree-Fock limit with a plane-wave expansion. When the correlation energy (calculated in the random-phase approximation with Hartree-Fock bands and functions as zeroth order states) is added, and upper limit of ?0.501 hartrees/atom is found for the total energy of this system. The Fermi surface was found to touch the Brillouin zone boundaries around the X points due to an appreciable depression of the band energies in that part of the Brillouin zone. The equilibrium lattice spacing (a = 2.705 bohrs) was slightly smaller than that obtained earlier with an atomic orbital basis.     

Diffusion dynamics of the Li+ ion on a model surface of amorphous carbon: a direct molecular orbital dynamics study

Diffusion processes of the Li+ ion on a model surface of amorphous carbon (Li+C96H24 system) have been investigated by means of the direct molecular orbital (MO) dynamics method at the semiempirical AM1 level. The total energy and energy gradient on the full-dimensional AM1 potential energy surface were calculated at each time step in the dynamics calculation. The optimized structure, where Li+ is located in the center of the cluster, was used as the initial structure at time zero. The dynamics calculation was carried out in the temperature range 100-1000 K. The calculations showed that the Li+ ion vibrates around the equilibrium point below 200 K, while the Li+ ion moves on the surface above 250 K. At intermediate temperatures (300 K < T < 400 K), the ion moves on the surface and falls in the edge regions of the cluster. At higher temperatures (600 K < T), the Li+ ion transfers freely on the surface and edge regions. The diffusion pathway of the Li+ ion was discussed on the basis of theoretical results.     

Suppression of field emission from W(110) and W(111) by Cu overlayers

The total energy distribution and the Fowler-Nordheim preexponential factor have been measured for field emission from the (100) and (111) facets of tungsten in the absence and in the presence of overlayers of chemisorbed copper. It is found that at close to monolayer coverage on the (100) facet the adsorbate dramatically reduces the surface density of states at the Fermi energy, whereas on the (111) facet the surface density of states at the Fermi energy is little affected. Self-consistent, semirelativistic LMTO calculations of the k-resolved layer densities of states at the centre of the surface Brillouin zone have been carried out for a tungsten-vacuum interface with and without an ordered overlayer of copper. According to the calculations, a copper monolayer on W(100) strongly suppresses the surface density of states at the Fermi energy, whereas for a copper monolayer on W(111) no such suppression is predicted. The consistency of these results with the experimental data indicates the promise of the present method for calculating the electronic structures of metal-vacuum interfaces.     

Topological analysis of the electron density distribution in perturbed systems. I. Effect of charge on the bond properties of hydrogen fluoride

Within the framework of the molecular orbital (MO) theory, the addition of one electron to the 4sigma antibonding orbital of the neutral (F...H) system or the removal of one electron from its pi nonbonding orbitals, leading to (F...H)- and to (F...H)+, has permitted the investigation of these charge perturbations on the bond properties of the hydrogen fluoride molecule by using the topological analysis of rho(r). For (F...H), (F...H)-, and (F...H)+, the topological and energetic properties calculated at the F...H bond critical point (BCP) have been related to the 3sigma bonding molecular orbital (BMO) distribution, as this orbital is the main contributor to rho(r) at the interatomic surface. The analysis has been carried out at several F...H internuclear distances, ranging from 0.8 to 3.0 A. As far as the BMO distribution results from its interaction with the average Coulomb and exchange potential generated by the charge filling the other MOs, and in particular by the pi and 4sigma electrons, the comparison between the BCP properties calculated for the charged systems and those corresponding to the neutral one permits the interpretation of the differences in terms of the charge perturbation on BMO. Along with the BCP properties of (F...H), (F...H)-, and (F...H)+, the interaction energy magnitudes of these systems have been also calculated within the same range of internuclear distances, indicating that the applied perturbations do not break the F-H bond but soften it, giving rise to the stable species (F-H)- and (F-H)+. Comparing the three systems at their equilibrium geometries, the most stable configuration, which corresponds to the unperturbed (F...H) system, shows the highest quantity and the most locally concentrated charge density distribution, along with the largest total electron energy density magnitude, at the interatomic surface as a consequence of the BMO contraction toward the fluorine nucleus in (F...H)+ and of the BMO expansion toward both nuclei in (F...H)-. On the other hand, if the comparison is carried out at the equilibrium distance of (F...H) (d(eq)0), this one exhibits both the smallest total energy density magnitude and the largest quantity of bonding charge at the interatomic surface. Hence, being the signature of the most stable configuration, the characteristic magnitudes of the neutral system rho(d(eq)0), inverted triangle2 rho(d(eq)0), and H(d(eq)0) appear as boundary conditions at the interatomic surface of its unperturbed and relaxed electron distribution.     

Calculated anisotropies in the fermi surface of alkali metals

The densities of states and Fermi energies were accurately calculated from E(k) data obtained by the self-consistent-band Augmented Plane Wave (APW ) method, using a quadratic energy expansion. The reliability of the Monte Carlo integration was investigated. It was sufficiently good to determine the anisotropy of the Fermi surface of lithium, sodium, and potassium.     

Structural study of pyrimidine nucleoside analogues. I: Molecular mechanics and semiempirical calculations of 2′-deoxy-2′-fluoroarabinofuranosyluracils

Molecular mechanics (MM) calculations have been performed on the title compounds. For the MM minimum energy conformation obtained by conformational analysis, molecular orbital (MO) calculations (MNDO and AM1) have also been performed. The geometries obtained have been compared with the experimental ones extracted from the Cambridge Structural Database (CSD). A qualitative structure-activity relationship has been pointed out based on the electrostatic potentials calculated at different positions on the electronic surface.     

Calculation of diamagnetic susceptibilities from the Thomas–Fermi–Amaldi theory for ions

The importance of the Fermi–Amaldi correction for the Thomas–Fermi theory for ions is analyzed. An analytical trial electron density with a proper limiting behavior has been chosen and the Thomas–Fermi–Amaldi energy expression is minimized in a variational way for several closed-shell ions. The obtained optimum electron densities have been used for calculating the diamagnetic susceptibilities, and a comparison with other theoretical results and available experimental data is performed.     

Hydrogen bond studies. 71. Ab initio calculation of the vibrational structure and equilibrium geometry in HF2 and DF2

MO LCAO SCF calculations have been performed to investigate the molecular astructure and vibrational spectrum of the bifluoride ion in its normal and deuterated form. The potential energy for nuclear motions has been evaluated as a function of the molecular degrees of freedom, taking only linear geometries into account. The vibrational Schrödinger equation has been solved by expanding the vibrational part of the total wavefunction as a sum of products of linear harmonic-oscillator eigenfunctions. The calculated properties are in good agreement with experiments, and even the minute effects of deuteration are well reproduced.     

ESCA applied to polymers. XXI. Investigation of sample-charging phenomena

Sample-charging phenomena arising in the ESCA experiment have been investigated for a series of polymers. For samples studied as films or powders mounted insulated from the spectrometer probe and for gold under similar conditions it is shown that over a wide range of operating conditions, equilibrium charging shifts are characteristic of the sample and show a strong dependence on the theoretically calculated total photoionization cross sections. The surface sensitivity of the phenomenon has been demonstrated by monitoring changes in charging shifts as a function of hydrocarbon contamination. For polymer films mounted directly in contact with the spectrometer, the charging shifts exhibit time-dependent behavior. The utility of studying sample-charging shifts as an interesting phenomenon in its own right is demonstrated by reference to changes which occur consequent upon surface modification of an ethylene–tetrafluoroethylene copolymer system in RF plasmas excited in inert gases.     

Wellenmechanische Absolutrechnung an einer intramolekularen Radikalreaktion an einem methyl– und hydroxylsubstituierten ungesättigten Kohlenwasserstoff

An energy surface for the intramolecular radical reaction oxygen radical ? methylene radical has been estimated on an important part of the α-Tocopherol molecule (Vitamin E), using the SCF –MO –LC (LCGO ) method. The total energy of the oxygen radical is greater than that of the methylene radical by about 49.6 kcal/Mol. The height of the potential barrier between the two tautomeric radicals was calculated to be 54.6 kcal/Mol. The calculated life time of the oxygen radical was 5.3 sec.     

The method of non-paired spatial orbitals

The calculation of non-paired spatial orbitals and alternant molecular orbital wavefunctions for the benzyl radical is described. The NPSO and AMO methods give comparable energy lowerings which indicate that they make substantial allowance for electron correlation. The calculated spin densities are not in very good accord with experiment and it is thought that this reflects inadequacies in the integral approximations used.     

Analysis of reduced density matrices in the co-ordinate representation. III. Electron density and correlation in the ground states of H2 and the H6 ring system within some approximations of the simple LCAO type

The electron density and spatial correlation as given by the MO , VB and AMO methods for H₂ and H₆ are studied by means of diagrams. For comparison, diagrams representing accurate wave functions for H₂ are also given. The study of model functions representing localized bonds leads to results concerning the nature of localized electron pairs in agreement with those of Lennard-Jones.     

Cylindrical cell model for the electrostatic free energy of polyelectrolyte complexes

Associative phase separation (complex coacervation) in a mixture of oppositely charged polyelectrolytes can lead to different types of (inter-)polyelectrolyte complexes (soluble micelles, macroscopic precipitation). In a previous report [Langmuir 2004, 20, 2785-2791], we presented a model for the electrostatic free energy change when (weakly charged) polyelectrolyte forms a homogeneous complex phase. The influence of ionization of the polymer on the electrostatic free energy of the complex was incorporated but the influence of complex density neglected. In the present effort, cylindrical cells are assumed around each polyelectrolyte chain in the complex, and on the basis of the Poisson-Boltzmann equation, the electrostatic free energy is calculated as a function of the complex density. After combination with Flory-Huggins mixing free energy terms and minimization of the total free energy, the equilibrium complex density is obtained, for a given ratio of polycations to polyanions in the complex. The analysis is used in an example calculation ofpolyelectrolyte film formation by alternatingly applying a polycation and a polyanion solution. The calculation suggests that the often observed exponential growth of a polyelectrolyte film when the polymer is weakly charged has a thermodynamic origin: the polyelectrolyte complex shifts repeatedly between two equilibrium states of different densities and compositions. However, when the polyelectrolytes are strongly charged the difference in the compositions between the two equilibrium states is very small, and exponential growth by an absorption mechanism is no longer possible.     

Adsorption modes of cysteine on Au(111): thiolate, amino-thiolate, disulfide

The adsorption of cysteine on the (111) surface of gold has been studied by means of periodic supercell density-functional theory calculations. A number of different adsorption modes are examined, including adsorption through the thiol group in either thiolate or disulfide form, and adsorption through both the thiol and amino functional groups. We find that at intermediate coverage densities the latter mode of adsorption is favored, followed by thiolate adsorption at the bridge (slightly displace toward fcc) site. The N-Au and S-Au bond strengths in the amino-thiolate adsorption are estimated to be of the order of 6 and 47 kcal/mol, respectively. The electronic structure of the different systems is analyzed, with focus on the total and projected density of states, as well as on the detailed character of the electronic states at the interface. States near the Fermi energy are found to have a metal-molecule antibonding character, whereas metal-molecule bonding states mostly occur near the lower edge of the Au-d band.     

A study on the electronic spectra of vinylpyridines and 1,2-(dipyridyl)ethylenes. Molecular orbital calculations

The electronic absorption spectra of 2-, 3-, and 4-vinylpyridines and 1,2-(2,3-dipyridyl), 1,2-(2,4-dipyridyl), 1,2-(3,4-dipyridyl), and 1,2-(4,4-dipyridyl) ethylenes have been investigated in polar and nonpolar solvents. A correlation has been made between the geometry of the molecule and the observed spectrum. Molecular orbital calculations have been carried out using the INDO/S? CI procedure and a limited geometry optimization. The solvent effect at the MO level has been calculated. MO calculations predicted the existence of nπ* transitions that were not observed experimentally. The wave functions of the different CI states were calculated. The experimental transition energy as well as oscillator strength corresponded satisfactorily with the calculated ones. The observed transitions were assigned according to the results of MO calculations.     

Bond length alternation in cyclic polyenes. III. Alternant molecular orbital method

The bond length alternation problem in cyclic polyene models as described by the Pariser–Parr–Pople Hamiltonian and an empirical quasiharmonic π-core potential is investigated using the one-parameter alternant molecular orbital (AMO) method. It is shown that in contrast to the unrestricted Hartree–Fock (UHF) results, which lead to symmetric equidistant structures, the one-parameter AMO results yield bond length alternating structures similar to those obtained with the restricted HF approach. The correlation energy recovered by the AMO method is examined for the symmetric polyenes in the whole range of coupling constants for both the Pariser–Parr–Pople and Hubbard Hamiltonians and compared with exact full configuration interaction (FCI) results. For the first member of the cyclic polyene series we also compared the FCI and AMO correlation energies for different nuclear framework distortions. This comparison indicates that in contrast to the UHF results the fraction of the correlation energy recovered by the AMO approach is very uniform over the range of nuclear distortions considered. The AMO results thus strongly indicate the dimerization in the polyenic chains.