Analytical density-dependent representation of Hartree—Fock atomic potentials

A procedure to represent atomic electron charge densities [L. Fernandez Pacios, J. Phys. Chem., 95 , 10653 (1991); J. Phys. Chem., 96 , 7294 (1992)] is here generalized to obtain simple analytical functions for potential energy contributions. Based upon suitable functions to describe atomic electron densities in a physically meaningful form, the procedure is developed to define density-dependent analytical expressions for the electrostatic (classical) and exchange (quantum) potentials by means of proper approximate functionals. Calculations of correlation energies by using various density-functional approaches are also performed. The whole scheme is used to represent Hartree–Fock limit atomic wave functions by Clementi–Roetti. This way, a set of analytically simple, nonbasis set-dependent functions are defined with the aim to be further implemented in energy decomposition schemes for molecular interactions studies using atomic instead of electronic building blocks. © 1993 John Wiley & Sons, Inc.     

Effect of the crosslinking density and the method of sample preparation on the observed microstructure of macroporous and conventional poly(N,N-dimethylacrylamide) hydrogels

SEM micrographs of macroporous and conventional poly(N,N-dimethylacrylamide) hydrogels were obtained for specimens synthesized in different conditions and prepared for microscopy by different methods (freeze drying of different solvents and critical point drying). The crosslinking density of both types of samples was determined through T _g measurements. Open structures (honeycomb-like, fibrillar networks) were more frequently observed in specimens prepared by freeze drying of benzene, which was attributed to its large pressure and temperature at the triple point. In spite of the different structure in the millimeter scale, there is no significant difference in the mesh size of fibrillar networks observed for macroporous and conventional samples, and in both cases it decreases with increasing crosslinking density. Other effects of the crosslinking density are that only incomplete honeycomb-like structures were formed in low-crosslinking samples and that collapsed structures were developed by phase separation throughout polymerization in highly crosslinked samples. Fibrillar networks of 1-μm mesh size were observed for the uncrosslinked polymer.     

Theoretical Study of Stratospheric Relevant Anions: Nitrate—Nitric Acid Complexes

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.     

Compression elastic modulus of neutral and protonated poly(N-vinylimidazole) hydrogels

The compression modulus of poly(N-vinylimidazole) (PVI) hydrogels synthesized by cross-linking polymerization in aqueous solution, was measured at room temperature in several related systems: i) just after polymerization, ii) swollen at equilibrium in deionized water, iii) swollen in HCl (aq) (pH=2.5), iv) swollen in HCl (pH=2.5) and 1 M NaCl (aq) solution and v) swollen in H₂SO₄ (pH=2.5) (aq) solution. Samples of the first and second groups are neutral whereas hydrogels of the other three groups are ionic because of protonation of basic imidazole groups. The experimental results were fitted with the Erman-Monnerie theory, applied to compression measurements for the first time, to determine the phantom modulus, [f_ph*], and the parameter κ_G which measures the constraining role of entanglements on the fluctuations of chains between knots.     

Computational study of pH-dependent oligomerization and ligand binding in Alt a 1, a highly allergenic protein with a unique fold

Alt a 1 is a highly allergenic protein from Alternaria fungi responsible for several respiratory diseases. Its crystal structure revealed a unique β-barrel fold that defines a new family exclusive to fungi and forms a symmetrical dimer in a butterfly-like shape as well as tetramers. Its biological function is as yet unknown but its localization in cell wall of Alternaria spores and its interactions in the onset of allergy reactions point to a function to transport ligands. However, at odds with binding features in β-barrel proteins, monomeric Alt a 1 seems unable to harbor ligands because the barrel is too narrow. Tetrameric Alt a 1 is able to bind the flavonoid quercetin, yet the stability of the aggregate and the own ligand binding are pH-dependent. At pH 6.5, which Alt a 1 would meet when secreted by spores in bronchial epithelium, tetramer-quercetin complex is stable. At pH 5.5, which Alt a 1 would meet in apoplast when infecting plants, the complex breaks down. By means of a combined computational study that includes docking calculations, empirical pKa estimates, Poisson–Boltzmann electrostatic potentials, and Molecular Dynamics simulations, we identified a putative binding site at the dimeric interface between subunits in tetramer. We propose an explanation on the pH-dependence of both oligomerization states and protein–ligand affinity of Alt a 1 in terms of electrostatic variations associated to distinct protonation states at different pHs. The uniqueness of this singular protein can thus be tracked in the combination of all these features.     

Characterization of two types of intermolecular interactions on halogen monoxide monohydrates

Monohydrates of halogen monoxides ClO·H₂O and BrO·H₂O have been studied by means of DFT (B3LYP) and ab initio (MP2) correlated calculations with aug‐cc‐pVnZ basis sets ranging from triple‐ up to quintuple‐ζ. These complexes might be formed in the troposphere and stratosphere and participate in chemical reactions involved in ozone depletion. Two stable structures are found that differ in the intermolecular interaction which takes place, namely: conventional XO…HOH hydrogen bond and OX…OH₂ halogen bond. We demonstrate that both types of interactions participate in the formation of these complexes yet all the computational methods tested predict a slightly greater stability for the latter OX…O link. Both intermolecular interactions are characterized upon analyzing electron density distribution, charge transfer effects, and electron localization domains. These analyses reveal the central role played by electron redistribution. Because of this, the greater spatial extent of the electron density in Cl or Br as compared to H could be the main cause to yield a slightly greater stability for the O? X…O halogen bond with respect to the O…H? O hydrogen bond. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

A theoretical study of the intramolecular interaction between proximal atoms in planar conformations of biphenyl and related systems

The nature of the interaction between proximal hydrogens in planar biphenyl has been recently a matter of debate as arguments in favor of and against the existence of “H–H” bonding have been recently put forward. This issue is addressed here through the study of both the electron density ρ(r) and the electron localization function (ELF) η(r) obtained in quantum calculations on molecular systems with F atoms replacing hydrogens in the moiety that presents this interaction. The analysis of geometries and properties of ρ(r) and η(r) at both planar and twisted equilibrium conformations of those systems along with biphenyl, permits to get information on this intramolecular interaction that is compared with the use of the traditional chemical concepts (steric hindrance and π-resonance effects) involved. It is shown that although the ELF gives information compatible with these classical terms, this does not preclude the existence of bonds between proximal atoms with features rather similar to those of well-established intramolecular hydrogen bonds.     

CHECKDEN: a computer program to generate 1D, 2D and 3D grids of functions dependent on the molecular ab initio electron density

A program to compute many functions dependent on the electron density rho(r) from the results of ab initio molecular calculations is presented. The program allows the generation of different one-, two-, and three-dimensional grids for further graphical representation or numerical analysis. Other options like extracting separate atom contributions to the function computed or locating maximum and minimum values are also implemented. A number of illustrative applications regarding different rho(r)-dependent functions are presented and the performance and portability of the program is discussed.     

Ab initio study of hydroxyl torsional barriers and molecular properties of mono- and di-iodotyrosine

Phenol rings with one or two iodine atoms bonded to ortho carbons are the essential organic source of iodine for living organisms. The salvage of this halogen fundamental for a variety of biological functions is accomplished through enzymatic processes that rely on recognition of mono- and di-iodotyrosine (MIT and DIT, respectively). Ab initio quantum calculations are used to investigate molecular properties of MIT and DIT associated with their recognition by cognate proteins. Energies, electron density properties, atomic charges, and electrostatic potentials are analyzed in relation with the presence of one or two iodine atoms and internal rotation of hydroxyl hydrogen. The formation of an intramolecular hydrogen bond at some conformations has little effect on the properties that might affect the recognition and further deiodination of MIT and DIT. Polarizability of iodine and the reactive nature of iodinated tyrosines as nucleophilic targets are the essential features revealed in this work.