Accurate description of van der Waals complexes by density functional theory including empirical corrections

An empirical method to account for van der Waals interactions in practical calculations with the density functional theory (termed DFT-D) is tested for a wide variety of molecular complexes. As in previous schemes, the dispersive energy is described by damped interatomic potentials of the form C6R(-6). The use of pure, gradient-corrected density functionals (BLYP and PBE), together with the resolution-of-the-identity (RI) approximation for the Coulomb operator, allows very efficient computations for large systems. Opposed to previous work, extended AO basis sets of polarized TZV or QZV quality are employed, which reduces the basis set superposition error to a negligible extend. By using a global scaling factor for the atomic C6 coefficients, the functional dependence of the results could be strongly reduced. The "double counting" of correlation effects for strongly bound complexes is found to be insignificant if steep damping functions are employed. The method is applied to a total of 29 complexes of atoms and small molecules (Ne, CH4, NH3, H2O, CH3F, N2, F2, formic acid, ethene, and ethine) with each other and with benzene, to benzene, naphthalene, pyrene, and coronene dimers, the naphthalene trimer, coronene. H2O and four H-bonded and stacked DNA base pairs (AT and GC). In almost all cases, very good agreement with reliable theoretical or experimental results for binding energies and intermolecular distances is obtained. For stacked aromatic systems and the important base pairs, the DFT-D-BLYP model seems to be even superior to standard MP2 treatments that systematically overbind. The good results obtained suggest the approach as a practical tool to describe the properties of many important van der Waals systems in chemistry. Furthermore, the DFT-D data may either be used to calibrate much simpler (e.g., force-field) potentials or the optimized structures can be used as input for more accurate ab initio calculations of the interaction energies.     

NMR chemical shifts in the low–pH form of a-chymotrypsin. A QM/MM and ONIOM–NMR study

 The relationship between hydrogen bonding and NMR chemical shifts in the catalytic triad of low-pH α-chymotrypsin is investigated by combined use of the effective fragment potential [(2001) J Phys Chem A 105:293] and ONIOM–NMR [(2000) Chem Phys Lett 317:589] methods. Our study shows that while the His57 N^δ1−H bond is stretched by a relatively modest amount (to about 1.060 ?) this lengthening, combined with the polarization due to the molecular environment, is sufficient to explain the experimentally observed chemical shifts of 18.2 ppm. Furthermore, the unusual down-field shift of H^ɛ1 (9.2 ppm) observed experimentally is reproduced and shown to be induced by interactions with the C=O group of Ser214 as previously postulated. The free-energy cost of moving H^δ1 from His57 to Asp102 is predicted to be 5.5 kcal/mol. Received: 26 September 2001 / Accepted: 6 September 2002 / Published online: 21 January 2003 Contribution to the Proceedings of the Symposium on Combined QM/MM Methods at the 222nd National Meeting of the American Chemical Society, 2001 Correspondence to: J. H. Jensen e-mail: jan-jensen@uiowa.edu Acknowledgements. This work was supported by a Research Innovation Award from the Research Corporation and a type G starter grant from the Petroleum Research Fund. The calculations were performed on IBM RS/6000 workstations obtained through a CRIF grant from the NSF (CHE-9974502) and on supercomputers at the National Center for Supercomputer Applications at Urbana-Champaign. The authors are indebted to Visvaldas Kairys for help with the CHARMM program, and to Daniel Quinn for many helpful discussions.     

Concentrated reverse micelles in a random graft block copolymer system: structure and in-situ synthesis of silver nanoparticles

The structure and rheological properties of a poly(dimethylsiloxane)-graft-poly(oxyethylene) copolymer at high concentrations in block-selective solvents were studied by small-angle X-ray scattering (SAXS) and rheometry. Analysis of SAXS data indicates that quasispherical, reverse micellar aggregates (with no ordered packing) are present in concentrated solutions of the copolymer in nonpolar solvents, and that upon addition of water, the size of such aggregates increases due to the solubilization inside the micellar cores. The viscosity of concentrated polymer solutions increases exponentially as water is added, and finally, viscoelastic, gel-like behavior is found in the vicinity of the phase separation limit. It was found that small silver nanoparticles with an average diameter of ≈3 nm can be synthesized inside the copolymer aggregates without the need of a reducing agent; namely, particles embedded in a viscoelastic matrix are obtained. The synthesis seems to follow first-order kinetics. Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Palladium salicylaldimine complexes containing boronate esters

Reactions of salicylaldehydes with boronate ester derivatives of aniline have been examined. Addition of these Schiff base ligands to palladium acetate or Na₂PdCl₄ afforded novel boron-containing trans-bis(N-arylsalicylaldiminato) palladium complexes.Condensation of salicylaldehyde (2-HOC₆H₄C(O)H) with H₂NC₆H₄Bpin (pin=1,2-O₂C₂Me₄) afforded the boron-containing Schiff bases, 2-HOC₆H₄C(H)=NC₆H₄Bpin (1–3a). Similar reactivity with 2-hydroxy-5-nitrobenzaldehyde and 2-hydroxy-1-naphthaldehyde gave the corresponding Schiff bases (1-3b) and (1-3c), respectively. Reaction of Schiff bases (2) and (3) with palladium acetate or Na₂PdCl₄ afforded complexes of the type PdL₂ (4,5), where L=deprotonated Schiff base. The molecular structure of the nitro-salicylaldehyde 4-Bpin palladium complex (5b) was characterized by an X-ray diffraction study. All new palladium compounds have been characterized fully and tested for their antifungal activity against Aspergillus niger and Aspergillus flavus.     

The self-organization properties of <Emphasis Type="Italic">n</Emphasis>-dodecylammonium α-glutamate/<Emphasis Type="Italic">n</Emphasis>-C<Subscript>5</Subscript>H<Subscript>11</Subscript>OH/water system

A biocompatible surfactant-n-dodecylammonium α-glutamate (GDA) with biodegradable and biocompatible properties was synthesized, and the phase behavior and the structural properties of GDA/n-pentanol/water system was studied by small-angle X-ray diffraction, electron spin resonance, and freeze-fracture transmission electron microscopy (FF-TEM). In the ternary phase diagram of GDA/n-pentanol/water system, there exist three isotropic regions—O/W, bicontinuous, and W/O structures, and two anisotropic regions—hexagonal liquid crystal (HEX), and lamellar liquid crystal (LLC) regions. UV irradiation causes the decrease in the interlayer space, d, of lamellar liquid crystal and in the radius, r, of column aggregates of hexagonal liquid crystal, but it has little effect on the structure of O/W and W/O microemulsions.     

Immobilization and direct electrochemistry of cytochrome <Emphasis Type="BoldItalic">c</Emphasis> at a single-walled carbon nanotube-modified electrode

A single-walled carbon nanotube (SWNT)-modified electrode was fabricated and characterized by SEM and ac impedance techniques. The direct electrochemistry of cytochrome c (Cyt c), which was adsorbed on the surface of the SWNT, was studied by cyclic voltammetry. The results from cyclic voltammetry and infrared spectroscopy indicated that Cyt c remained in its original structure and did not undergo structural change after its immobilization on the SWNT. Further results demonstrated that the SWNT had promotional effects on the direct electron transfer of Cyt c and also indicated that the immobilized Cyt c retained its electrocatalytic activity to the reduction of H₂O₂. This modified electrode might be used in development of new biosensors and the biofuel cells.     

The W algorithm and the D transformation for the numerical evaluation of three‐center nuclear attraction integrals

Three‐center nuclear attraction integrals over exponential‐type functions are required for ab initio molecular structure calculations and density functional theory (DFT). These integrals occur in many millions of terms, even for small molecules, and they require rapid and accurate numerical evaluation. The use of a basis set of B functions to represent atomic orbitals, combined with the Fourier transform method, led to the development of analytic expressions for these molecular integrals. Unfortunately, the numerical evaluation of the analytic expressions obtained turned out to be extremely difficult due to the presence of two‐dimensional integral representations, involving spherical Bessel integral functions. % The present work concerns the development of an extremely accurate and rapid algorithm for the numerical evaluation of these spherical Bessel integrals. This algorithm, which is based on the nonlinear D transformation and the W algorithm of Sidi, can be computed recursively, allowing the control of the degree of accuracy. Numerical analysis tests were performed to further improve the efficiency of our algorithm. The numerical results section demonstrates the efficiency of this new algorithm for the numerical evaluation of three‐center nuclear attraction integrals. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Identification of anhydroecgonine methyl ester N-oxide,a new metabolite of anhydroecgonine methyl ester,using electrospray mass spectrometry

Cocaine is transformed into hepatotoxic metabolites through oxidative pathways. For anhydroecgonine methyl ester (AEME), the main constituent in crack smoke, the oxidative metabolism has not been studied. Therefore, incubation of AEME with rat liver microsomes was performed and a metabolite of AEME, anhydroecgonine methyl ester N-oxide (AEMENO), was identified. The chemical structure of this new metabolite was confirmed by synthesis and by comparative interpretation of electrospray multiple-stage mass spectra, which were obtained in the positive ion mode. This metabolite was also detected in whole blood, serum and urine samples from crack users. The application of liquid chromatography/electrospray mass spectrometry or nanoelectrospray mass spectrometry was necessary because AEMENO is susceptible to thermal degradation during gas chromatographic/mass spectrometric analysis. This study demonstrated that AEMENO is produced by rat hepatic microsomal metabolism in vitro and is present in body fluids from crack users.