A simple model for the scattering of electrons by a rotating dipole

The coupled equations describing the interaction of one electron with a dipole and hard sphere are shown to be exactly soluble, even when the energy levels of the dipole are taken into account. This model is used to discuss the critical moment for binding the electron in the dipole field. The condition for the existence of Feshbach resonances is similarly discussed. When the model is applied to calculate scattering phase shifts, shape resonances are found.     

Study of PEGylated lipid layers as a model for PEGylated liposome surfaces: molecular dynamics simulation and Langmuir monolayer studies

We have combined Langmuir monolayer film experiments and all-atom molecular dynamics (MD) simulation of a bilayer to study the surface structure of a PEGylated liposome and its interaction with the ionic environment present under physiological conditions. Lipids that form both gel and liquid-crystalline membranes have been used in our study. By varying the salt concentration in the Langmuir film experiment and including salt at the physiological level in the simulation, we have studied the effect of salt ions present in the blood plasma on the structure of the poly(ethylene glycol) (PEG) layer. We have also studied the interaction between the PEG layer and the lipid bilayer in both the liquid-crystalline and gel states. The MD simulation shows two clear results: (a) The Na(+) ions form close interactions with the PEG oxygens, with the PEG chains forming loops around them and (b) PEG penetrates the lipid core of the membrane for the case of a liquid-crystalline membrane but is excluded from the tighter structure of the gel membrane. The Langmuir monolayer results indicate that the salt concentration affects the PEGylated lipid system, and these results can be interpreted in a fashion that is in agreement with the results of our MD simulation. We conclude that the currently accepted picture of the PEG surface layer acting as a generic neutral hydrophilic polymer entirely outside the membrane, with its effect explained through steric interactions, is not sufficient. The phenomena we have observed may affect both the interaction between the liposome and bloodstream proteins and the liquid-crystalline-gel transition and is thus relevant to nanotechnological drug delivery device design.     

Incorporation of blood clotting factor X into phospholipid model membranes: fluorescence microscopy imaging and subphase effects surrounding the lipid phase transition region

Factor X is a blood clotting protein that associates at membrane surfaces to become activated during the coagulation cascade. A molecular level understanding of the protein-membrane phospholipid interactions has not been reached, although it is thought that the protein binds to phospholipids in the presence of calcium through a bridge with the Gla (gamma-carboxyglutamic acid) domain on the protein. In this work, phospholipid Langmuir monolayers have been utilized as model membranes to study factor X association with phospholipid membrane components. Surface pressure measurements indicate that subphase addition of sodium, magnesium, and calcium ions enhances protein penetration of the lipid monolayer, with the largest association found with calcium ions in the subphase. Fluorescence microscopy images collected after protein penetration of lipid monolayers indicate monolayer condensation in the presence of sodium and magnesium ions. Aggregation of lipid domains is induced when calcium is in the subphase, indicating binding-induced flocculation of surface lipid aggregates. Calcium binding to factor X likely causes a conformational change which allows protein-membrane interaction via hydrophobic association with lipid molecules.     

Self-assembled monolayers of Ru/Os dinuclear complexes: probing monolayer structure and interaction energies by electrochemical means

Monolayers of [Ru(bpy)2(micro-1)M2][PF6]4 salts (M = Os, Ru; bpy = 2,2'-bipyridine, 1 = 4'-(2,2'-bipyridin-4-yl)-2,2':6',2' '-terpyridine, tpy = 2,2':6',2' '-terpyridine, and 2 = 4'-(4-pyridyl)-2,2':6',2' '-terpyridine) were self-assembled on platinum and investigated by fast-scan electrochemistry. The electrochemistry of the complexes in solution and confined to the surface in self-assembled monolayers (SAMs) exhibited an almost ideal behavior. Scan-rate-dependent measurements of the peak current density (jp) were used to determine interaction energies within the monolayer. It is shown that the tpy coordination sites of the dinuclear complexes interact more strongly within the SAM than the bipyridine-coordinated fragments. This result was supported by peak potential shifts, which are due to interaction forces in SAMs. The alignment of the rodlike complexes relative to the surface is discussed, and the results of molecular mechanics calculations indicate that the species adopt a tilted orientation.     

Peptide fingerprinting of snake venoms by direct infusion nano-electrospray ionization mass spectrometry: potential use in venom identification and taxonomy

Fingerprinting by mass spectrometry has been increasingly used to study venom variations and for taxonomic analyses based on venom components. Most of these studies have concentrated on components heavier than 3 kDa, but Bothrops snake venoms contain many biologically active peptides, principally C-type natriuretic peptides and bradykinin-potentiating peptides (BPPs). In this work, we have examined the peptide profile of Bothrops venoms (B. alternatus, B. erythromelas, B. insularis, B. jararaca, B. jararacussu, B. leucurus and B. moojeni) using direct infusion nano-electrospray ionization mass spectrometry (nano-ESI-MS) subjecting the data further to principal components analysis (PCA) to assess whether the peptide distributions are reliable in distinguishing the venoms. ESI-MS of a low molar mass fraction obtained by ultrafiltration of each venom (5 kDa nominal cutoff filters) revealed that the venoms have a variety of peptides in common but that each venom also contains taxonomic marker peptides not shared with other venoms. One BPP peptide, QGGWPRPGPEIPP, was found to be common to the seven Bothrops species examined. This peptide may represent a specific marker for this genus since it was not found in the venom of the South American rattlesnake, Crotalus durissus terrificus. PCA on the ESI-MS data reveals a close relationship between B. jararaca, B. jararacussu and B. moojeni venoms, with B. leucurus and B. erythromelas being more distant from these three; B. alternatus and B. insularis were also located distant from these five species, as was C. d. terrificus. These results agree partially with established phylogenetic relationships among these species and suggest that ESI-MS peptide fingerprinting of snake venoms coupled with PCA is a useful tool for identifying venoms and for taxonomic analyses.     

Symmetry-adapted-cluster configuration interaction study of the doublet states of HCl+: potential energy curves, dipole moments, and transition dipole moments

The electronic structure of the HCl(+) molecular ion has been calculated using the general-R symmetry-adapted-cluster configuration interaction (SAC-CI) method. The authors present the potential energy curves, dipole moments, and transition dipole moments for a series of doublet states. The data are compared with the previous CASSCF and MCSCF calculations. The SAC-CI results reproduce quite well the data available in literature and extend the knowledge on the HCl(+) electronic structure for several higher states. The calculated R-dependent behavior of both dipole moments and transition dipole moments for a series of bound and unbound states reveals an intricate dissociation process at intermediate distances (R>R(e)). The pronounced maxima in transition dipole moment (TDM) describing transitions into high electronic states (X (2)Pi-->3 (2)Pi, X (2)Pi-->3 (2)Sigma, 2 (2)Pi-->3 (2)Pi, 3 (2)Pi-->4 (2)Pi) occur at different interatomic separations. Such TDM features are promising for selection of excitation pathways and, consequently, for an optimal control of the dissociation products.     

Rational tuning of the thiolate donor in model complexes of superoxide reductase: direct evidence for a trans influence in Fe(III)-OOR complexes

Iron peroxide species have been identified as important intermediates in a number of nonheme iron as well as heme-containing enzymes, yet there are only a few examples of such species either synthetic or biological that have been well characterized. We describe the synthesis and structural characterization of a new series of five-coordinate (N4S(thiolate))Fe(II) complexes that react with tert-butyl hydroperoxide ((t)BuOOH) or cumenyl hydroperoxide (CmOOH) to give metastable alkylperoxo-iron(III) species (N4S(thiolate)Fe(III)-OOR) at low temperature. These complexes were designed specifically to mimic the nonheme iron active site of superoxide reductase, which contains a five-coordinate iron(II) center bound by one Cys and four His residues in the active form of the protein. The structures of the Fe(II) complexes are analyzed by X-ray crystallography, and their electrochemical properties are assessed by cyclic voltammetry. For the Fe(III)-OOR species, low-temperature UV-vis spectra reveal intense peaks between 500-550 nm that are typical of peroxide to iron(III) ligand-to-metal charge-transfer (LMCT) transitions, and EPR spectroscopy shows that these alkylperoxo species are all low-spin iron(III) complexes. Identification of the vibrational modes of the Fe(III)-OOR unit comes from resonance Raman (RR) spectroscopy, which shows nu(Fe-O) modes between 600-635 cm(-1) and nu(O-O) bands near 800 cm(-1). These Fe-O stretching frequencies are significantly lower than those found in other low-spin Fe(III)-OOR complexes. Trends in the data conclusively show that this weakening of the Fe-O bond arises from a trans influence of the thiolate donor, and density functional theory (DFT) calculations support these findings. These results suggest a role for the cysteine ligand in SOR, and are discussed in light of the recent assessments of the function of the cysteine ligand in this enzyme.     

Porphyrin nanofiber patterning by air/water interfacial assembly: effect of molecular structure, surface pressure, and ionic liquid doped subphase

Porphyrin nanofiber patterning was generated by air/water interfacial assembly. The air/water interfacial aggregation behavior of two prophyrins, both of which contain two hydrophobic alkyl chains and two carboxylic acid substituent groups at different positions, was investigated using UV spectra, FT-IR spectra, and AFM measurements on the corresponding transferred films. The porphyrin nanofiber patterning can only be produced on ionic liquid (IL) doped water subphases by the assembly of the building blocks with two carboxylic acids located at the para-position (TPPA2b-A). The results suggest that the bulky cations of ionic liquids (ILs) can interact with the carboxylate of porphyrin electrostatically. The appropriate molecular geometries, ionic liquid (IL) doped water subphases, and relatively high surface pressures help the TPPA2b-A to form nanofiber patterns.     

The interaction between an oscillating dipole and a metal surface described by a jellium model and the random phase approximation

The electric field acting on an oscillating dipole located near a metal surface is computed. The latter is described by a jellium model and the random phase approximation. The aim is ascertaining to what extent spatial dispersion and variation of the dielectric properties across the interface modify the image dipole. Implications for surface Raman and fluorescence spectroscopy are discussed.     

Characterization of the nanostructure of complexes formed by a redox-active cationic lipid and DNA

We report characterization of the nanostructures of complexes formed between the redox-active lipid bis(n-ferrocenylundecyl)dimethylammonium bromide (BFDMA) and DNA using small-angle neutron scattering (SANS) and cryogenic transmission electron microscopy (cryo-TEM). A particular focus was directed to the influence of lipid oxidation state (where reduced BFDMA has a net charge of +1 and oxidized BFDMA has a charge of +3) on the nanostructures of the solution aggregates formed. Complexes were characterized over a range of charge ratios of reduced BFDMA to DNA (1.1:1, 2.75:1, and 4:1) in solutions of 1 mM Li2SO4. For these complexes, a single peak in the SANS data at 1.2 nm(-1) indicated that a nanostructure with a periodicity of 5.2 nm was present, similar to that observed with complexes of the classical lipids DODAB/DOPE and DNA (multilamellar spacing of 7.0 nm). The absence of additional Bragg peaks in all the SANS data indicated that the periodicity did not extend over large distances. Both inverse Fourier transform analysis and form factor fitting suggested formation of a multilamellar vesicle. These results were confirmed by cryo-TEM images in which multilamellar complexes with diameters between 50 and 150 nm were observed with no more than seven lamellae per aggregate. In contrast to complexes of reduced BFDMA and DNA, Bragg peaks were absent in SANS spectra of complexes formed by oxidized BFDMA and DNA at all charge ratios investigated. The low-q behavior of the SANS data obtained using oxidized BFDMA and DNA complexes suggested that large, loose aggregates were formed, consistent with complementary cryo-TEM images showing predominantly loose disordered aggregates. Some highly ordered spongelike and cubic phase nanostructures were also detected in cryo-TEM images. We conclude that control of BFDMA oxidation state can be used to manipulate the nanostructures of lipid-DNA complexes formed using BFDMA.     

Mixed hydrazido amido/imido complexes of tantalum, hafnium and zirconium: potential precursors for metal nitride MOCVD

The coordination chemistry of the hydrazine derivatives dimethylhydrazine (Hdmh) and N-trimethylsilyl-N'N'-dimethylhydrazine (Htdmh) at Ta, Zr and Hf was investigated aiming at volatile mixed ligand all-nitrogen coordinated compounds. The hydrazido ligands were introduced either by salt metathesis employing the Li salts of the hydrazines and the tetrachlorides MCl(4) (M = Zr, Hf) or by amine substitution using M(NR(2))(4) (R = Me, Et) and [(t-BuN)Ta(NR(2))(3)]. The new complexes were fully characterised including (1)H/(13)C NMR, mass spectrometry and a study of their thermal behaviour. The crystal structures of [ZrCl(tdmh)(3)] and the all-nitrogen coordinated complex [Ta(N-t-Bu)(NMe(2))(2)(tdmh)] are discussed as well as the structure of the by-product [Li(tdmh)(py)](2). Preliminary MOCVD experiments of the liquid compound [Ta(NEt(2))(2)(N-t-Bu)(tdmh)] were performed and the deposited TaN(Si) films were analysed by RBS and SEM.     

Calculation of the structure, potential energy surface, vibrational dynamics, and electric dipole properties for the Xe:HI van der Waals complex

We report the structure and spectroscopic characteristics for the Xe:HI van der Waals binary isomers determined from variational solutions of two-dimensional and three-dimensional (3D) vibrational Schro?dinger equations. The solutions are based on a potential energy surface computed at the coupled-cluster level of theory including single and double excitations and a non-iterative perturbation treatment of triple excitations [CCSD(T)]. The dipole moment surface was calculated using quadratic configuration interaction (QCISD). The global potential minimum is shown to be located at the anti-hydrogen-bonded Xe-IH isomer, 21 cm(-1) below the secondary local minimum associated with the hydrogen-bonded Xe-HI isomeric form. The dissociation energy from the global minimum is 245.9 cm(-1). 3D Schro?dinger equations are solved for the rotational quantum numbers J = k = 0, 1, and 2, without invoking an adiabatic separation of high- and low-frequency degrees of freedom. The vibrational ground state resides in the Xe-HI potential well, while the first excited state, 8.59 cm(-1) above the ground, occupies the Xe-IH well. We find that intra-complex dynamics exhibits a sudden transformation upon increase of the r(HI) bond length, accompanied by abrupt changes in the geometric and dipole parameters. A similar chaotic behavior is predicted to occur for Xe:DI at a shorter r(DI) bond length, which implies stronger coupling between low- and high-frequency motions in the heavier complex. Our calculations confirm a strong enhancement for the r(HI) stretch fundamental and a significant weakening for the first overtone vibrational transitions in Xe:HI, as compared to those in the free HI molecule. A qualitative explanation of this, earlier experimentally detected effect is suggested.     

Photoelectric response of purple membrane fragments adsorbed on a lipid monolayer supported by mercury and characterization of the resulting interphase

Purple membrane (PM) fragments were adsorbed on a dioleoylphosphatidylcholine (DOPC) monolayer supported by mercury to investigate the kinetics of light-driven proton transport by bacteriorhodopsin (bR). PM fragments were also adsorbed on a mercury-supported triethyleneoxythiol (TET) monolayer. On both monolayers, the light-on current exhibits a finite, potential dependent stationary component that decreases linearly with a positive shift in the applied potential. The light-on and light-off capacitive photocurrents were interpreted on the basis of a simple equivalent circuit, which accounts for the potential dependence of the stationary light-on current. The potential of zero stationary current is about equal to +0.010 V vs. saturated calomel electrode (SCE) on DOPC-coated mercury. The absolute potential difference across the PM fragments adsorbed at this applied potential was estimated on the basis of extrathermodynamic considerations and amounts to about +260 mV; it compares favorably with the value, +250 mV, of the transmembrane potential of zero stationary current across an oocyte plasma membrane incorporating bR [Biophys. J. 74 (1998) 403.]. The effect of the proton pumping activity of photoexcited PM fragments on the electroreduction kinetics of ubiquinone-10 incorporated in the DOPC monolayer underlying the PM fragments was investigated.     

Calculating the electrostatic potential of molecular models with separate evaluations by conventional, vector, and array processors

A simple computational scheme for estimating the electrostatic potential about molecular models of moderate size is given. The large amount of calculations required for the evaluation of the hypersurface lends itself to treatment by high speed, unconventional computing machines. The essence of these calculations lies in Coulombic interactions that are computed between hypothetical proton test probes positioned in a gridded region surrounding the model and the partial electrostatic charges (CNDO/2) of each atom in the model. A specific scientific application is discussed which involves the recognition of amino acids and nucleotide bases. Three different evaluations of the potential hypersurface within the context of this approach were made. The first was performed on a VAX 11/780 which is a general purpose machine widely used in the scientific community; the second was performed using a pipelined Vector Processor, the FPS AP-120B; and the third by a processor array, the ILLIAC-IV. A comparison of the architectures and processing speeds of each class of machines is made. The computing power observed is consistent with the design and purpose of each machine. Also discussed are methods for displaying the vast amount of data that result from such calculations. It is determined that computer graphics offers an effective means for extracting information from large amounts of data. Finally, the scientific value of the calculations are briefly discussed. If caution is applied to interpreting the results, then the electrostatic potential (EP) mappings can be useful in identifying sites of potential chemical interactions.     

Comparison of direct infusion and on-line liquid chromatography/electrospray ionization mass spectrometry for the analysis of nucleic acids

The applicability of ion-pair reversed-phase high-performance liquid chromatography/electrospray ionization mass spectrometry (IP-RP-HPLC/ESI-MS) and direct infusion/ESI-MS to the characterization of nucleic acid mixtures was evaluated by the analysis of the reaction products obtained from solid-phase synthesis of a 39-mer oligonucleotide. IP-RP-HPLC/ESI-MS was performed using 200 microm i.d. capillary columns packed with octadecylated, micropellicular poly(styrene-divinylbenzene) particles and applying gradients of acetonitrile in 50 mM triethylammonium bicarbonate (TEAB). Three different solvent systems were utilized for direct infusion/ESI-MS with removal of metal cations by on-line cation exchange: (1) 10 mM triethylamine (TEA) in 50% aqueous acetonitrile, (2) 2.2 mM TEA, 400 mM hexafluoro-2-propanol (HFIP) in 20% aqueous methanol and (3) 50 mM TEAB in 10% aqueous acetonitrile. Owing to its separation capability, the highest selectivity and specificity were achieved with IP-RP-HPLC/ESI-MS, which, apart form the 39-mer target sequence, allowed the identification of two isobutyryl-protected target sequences and a 10-mer and 20-mer failure sequence. Direct infusion/ESI-MS with TEA-acetonitrile or TEA-HFIP-methanol as solvent revealed signals for the 39-mer in the m/z range 700-1600. The presence of derivatives containing one, two, three and four isobutyryl groups indicated that the hydrolysis of the protecting groups after solid-phase synthesis was not complete. Failure sequences could not be identified by direct infusion/ESI-MS under conditions favoring multiple charging of the analytes owing to the high chemical background and coincidental overlapping of m/z signals. However, efficient charge state reduction upon addition of carbonic acid to the electrosprayed solvent shifted the signals of the 39-mer and derivatives to m/z values >2400 and allowed the detection of seven different failure sequences, ranging from the 8-mer to the 23-mer, in the mixture.     

Derivatization-independent cholesterol analysis in crude lipid extracts by liquid chromatography/mass spectrometry: applications to a rabbit model for atherosclerosis

Direct measurement of various sterols in crude lipid extracts in a single experiment from limited biological samples is challenging. Current mass spectrometry (MS) based approaches usually require chemical derivatization before subjecting to MS analysis. Here, we present a derivatization-independent method for analyzing various sterols, including cholesterol and its congeners, using liquid chromatography and atmospheric pressure chemical ionization mass spectrometry. Based on the specific tandem mass spectrometry pattern of cholesterol, multiple reaction monitoring (MRM) transitions were used to quantify free cholesterol and its fatty acyl esters. Several cholesterol oxidation products could also be measured using the upfront liquid chromatography separation and specific MRM transitions. The method was validated alongside established enzymatic assays in measuring total cholesterol. As a proof of concept, we analyzed plasma sterols in rabbits administrated with a high cholesterol diet (HCD) which is a classical atherosclerotic model. Free cholesterol, cholesterol esters, 7-hydroxycholesterol, and 7-ketocholesterol were elevated in plasma of rabbits on HCD. This method could also serve as an excellent tool for quantitative analysis of other sterols such as ergosterol and sitosterol in other organisms beside mammalian. In Saccharomyces cerevisiae, our results indicated dramatic increases of the ratio of ergosterol esters to free ergosterol in both yeh2Δ and tgl1Δ cells, which are consistent with the function of the respective enzymes.     

A two-state model for the multilamellar structure of a DNA/cationic lipid complex in the bulk

Polyanionic DNA can bind electrostatically with cationic lipids to form a complex used for gene delivery and nanostructure construction. Here, we reveal two multilamellar phases, L(I) and L(II), characterized by distinct states of lipid packing and DNA conformation in a DNA/cationic lipid complex in the bulk state. The L(II) phase, formed when the lipids are in excess of DNA in terms of overall ionic charge, is composed of B-DNA confined between the bilayers with the lipid tails aligning normal to the lamellar interface. When DNA becomes in excess of the lipids, the L(I) phase in which the DNA is bound with the tilted lipid chains adopting the A conformation is favored because this configuration offers more economical electrostatic binding between these two components.     

A statistical mechanical model of cholesterol/phospholipid mixtures: linking condensed complexes, superlattices, and the phase diagram

Despite extensive studies for nearly three decades, lateral distribution of molecules in cholesterol/phospholipid bilayers remains elusive. Here we present a statistical mechanical model of cholesterol/phospholipid mixtures that is able to rationalize almost every critical mole fraction (X(cr)) value previously reported for sterol superlattice formation as well as the observed biphasic changes in membrane properties at X(cr). This model is able to explain how cholesterol superlattices and cholesterol/phospholipid condensed complexes are interrelated. It gives a more detailed characterization of the LG(I)region (a broader region than the liquid disordered-liquid ordered mixed-phase region), which is considered to be a sludgelike mixture of fluid phase and aggregates of rigid clusters. A rigid cluster is formed by a cholesterol molecule and phospholipid molecules that are condensed to the cholesterol. Rigid clusters of similar size tend to form aggregates, in which cholesterol molecules are regularly distributed into superlattices. According to this model, the extent and type of sterol superlattices, thus the lateral distribution of the entire membrane, should vary with cholesterol mole fraction in a delicate, predictable, and nonmonotonic manner, which should have profound functional implications.