Increased Van Der Waals Interactions Research Articles

Characterization of DMPC bilayers and multilamellar islands on hydrophobic self-assembled monolayers of ODS/Si(100) and mixed ODS-DDS/Si(100)

We have examined the lamellar structure of l-α-dimyristoylphosphatidylcholine (DMPC) bilayers and multilamellar islands grown on monocomponent and bicomponent Self-Assembled Monolayers (SAM) of octadecylsiloxane (ODS), and mixed octadecylsiloxane/dodecylsiloxane (ODS/DDS), respectively. Electron density profiles revealed by hard X-ray reflectometry measurements show significant structural differences of the DMPC films on both surfaces. While DMPC grown on uniform ODS results in the formation of unilamellar and multilamellar islands of DMPC bilayers, DMPC growth on a mixed ODS/DDS-SAM results in the formation of a (almost) closed DMPC bilayer adsorbed onto the mixed SAM. The results are explained in terms of an increased van der Waals interaction of the DMPC alkyl chains with the SAM alkyl chains of the mixed ODS/DDS SAM. Swelling in water at increasing temperatures in between 50 °C and 95 °C, results in a reduced DMPC island height due to thermal unbinding of DMPC bilayers, in case of the DMPC/ODS system. Further, characterization by nc-AFM displays the lateral shape and size of the islands as well as the discrete height distribution of the islands, which is in good agreement with the X-ray reflectometry measurements.

The effect of the van der Waals interaction on the excited state for atom guiding in metal-coated, hollow-core optical fibers

The study of atom guiding in a metal-coated, hollow-core optical fiber has been extended to the case of moderate to strong coherent excitation. Significant populations of the upper level are produced and the effect of the increased van der Waals interaction of the excited state with the inner wall is represented as a multiplicative scaling factor of the ground state interaction. This scaling factor is justified by a simple, exact calculation for atomic hydrogen where the van der Waals interaction for H(4p) is a factor of 400 larger than that for the H(1s). By combining the optical dipole potential and the population-weighted van der Waals level shifts, an overall guiding barrier is obtained. The barrier functions are maximized in terms of both the detuning and the radial position to give the maximum barrier heights. For given laser field strengths at the inner wall, the resulting barriers depend strongly on the van der Waals scaling factors.

The interaction of polyphenols with bilayers: conditions for increasing bilayer adhesion

Because proteins and other molecules with a high polyphenol content are commonly involved in adhesion processes, we are investigating the interactions between polyphenols and biological materials. A naturally occurring polyphenol that binds a variety of proteins and lipids is tannic acid (TA), which contains five digallic acid residues covalently linked to a central D-glucose. A previous study has shown that TA increases the adhesion between apposing phosphatidylcholine (PC) bilayers and over a very narrow concentration range collapses the interbilayer fluid space from about 15 A to 5 A. To determine the chemical requirements a polyphenolic molecule must possess to increase bilayer adhesion, we have synthesized several simpler TA analogs that vary in their size, shape, and number of gallic acid and hydroxyl groups. X-ray diffraction, absorbance, binding, and differential scanning calorimetry measurements were used to investigate the interaction of these polyphenolic molecules with egg PC (EPC) and dipalmitoyl PC (DPPC) bilayers. Of these synthetic polyphenols, only penta-O-galloyl-alpha-D-glucose (PGG) was able to completely mimic the effects of TA by collapsing the interbilayer fluid space from 15 A to 5 A, decreasing the dipole potential by about 300 mV, increasing the transition enthalpy of DPPC liposomes, and inducing an interdigitated phase in DPPC. Binding studies indicated that the fluid space was reduced to 5 A at an EPC:PGG mole ratio of 5:1. We conclude that these polyphenols collapse the fluid space of PC bilayers because they 1) are amphipathic and partition into the bilayers interfacial region, 2) are long enough to span the interbilayer space, 3) contain several gallic acids distributed so that they can partition simultaneously into apposing bilayers, and 4) have sufficient gallic acid residues to interact with all lipid headgroups and cover the bilayer surface. Under these conditions we conclude that the polyphenols from interbilayer bridges. We argue that these bridges are stabilized by increased adhesion arising from an increased van der Waals interaction between apposing bilayers, electrostatic interactions between the pi electrons in the phenol ring and the -(N+CH3)3 groups on the PC headgroups, decreased hydration repulsion between bilayers, and hydrogen bonds between the H-bond-donating moieties on the polyphenols and H-bond-accepting groups in the bilayer.

Improved binding of cytochrome P450cam substrate analogues designed to fill extra space in the substrate binding pocket.

Cytochrome P450cam catalyzes the 5-exo-hydroxylation of camphor. Camphor analogues were designed to fill an empty region of the substrate binding pocket with the expectation that they would bind more tightly than camphor itself due to increased van der Waals interactions with the protein and the displacement of any solvent occupying this site. A series of compounds (endo-borneol methyl ether, endo-borneol propyl ether, endo-borneol allyl ether and endo-borneol dimethyl allyl ether) were synthesized with substituents at the camphor carbonyl oxygen. The spin conversion and thermodynamic properties of this series of compounds were measured for wild type and Y96F mutant cytochrome P450cam and were interpreted in the context of molecular dynamics simulations of the camphor analogues in the P450 binding site and in solution. Compounds with a 3-carbon chain substituent were predicted to match the size of the unoccupied region most optimally and thus bind best. Consistent with this prediction, the borneol allyl ether binds to cytochrome P450cam with highest affinity with a Kd = 0.6 +/- 0.1 microM (compared to a Kd = 1.7 +/- 0.2 microM for camphor under the same experimental conditions). Binding of the camphor analogues to the Y96F mutant is much enhanced over the binding of camphor, indicating that hydrogen bonding plays a less important role in binding of these analogues. Binding enthalpies calculated from the simulations, taking all solvent contributions into account, agree very well with experimental binding enthalpies. Binding affinity is not however correlated with the calculated binding enthalpy because the binding of the substrate analogues is characterized by enthalpy-entropy compensation. The new compounds are useful probes for further studies of the mechanism of cytochrome P450cam due to their high binding affinities and high spin properties.

Backbone conformations in nucleic acids: the occurrence of g+g+ internucleotide phosphodiester conformation.

AbstractSemiempirical conformational energy calculations have been performed on dinucleoside triphosphate models with and without base interactions to investigate the conformational requirement for the stereochemical and energetic feasibility of (gauche+,gauche+) phosphodiester conformation in a polynucleotide chain. Results show that the trans conformation of the C4′C5′ bond on the 5′‐sugar (either C3′‐endo or C2′‐endo) of a dinucleoside triphosphate renders the g+g+ phosphodiester energetically favorable. The degree of energetic preference shows a dependence on the C3′O3′ bond torsions (ϕ′); higher g+g+ conformation populations are correlated with higher values of ϕ′ ≃ 270° due to increased van der Waals interactions between adjacent sugar residues. For similar reasons, the g+g+ phosphodiester displays an energetic dependence on the nature and sequence of bases and their orientations. Other conformational combinations that also stereochemically permit the g+g+ phosphodiester are discussed along with base effects.