How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

This study examines the accuracy of molecular dynamics-linear response (MD/LR) and Poisson–Boltzmann/solvent accessible surface (PB/SAS) calculations to predict relative binding affinities. A series of acetylcholinesterase (AChE) huprine inhibitors has been chosen as a test system owing to the availability of free-energy (thermodynamic integration) calculations. The results obtained with the MD/LR approach point out a clear relationship between the experimental affinity and the electrostatic interaction energy alone for a subset of huprines, but the suitability of the MD/LR approach to predict the binding affinity of the whole series of compounds is limited. On the other hand, PB/SAS calculations show a marked dependence on both the computational protocol and the nature of the inhibitor–enzyme complex. Received: 2 August 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000     

Increased covalent conjugation of a model antigen to poly(lactic acid)-g-maleic anhydride nanoparticles compared to bare poly(lactic acid) nanoparticles

Maleic anhydride (MA) grafted poly(lactic acid) (PLA) (PLA-g-MA) was synthesized from PLA. Proton nuclear magnetic resonance confirmed the grafting of the MA. PLA-g-MA and PLA were used to prepare polymeric nanoparticles. Particle size distributions were measured by dynamic light scattering, and colloidal stability was determined by (zeta) ζ-potential. The ζ-potential becomes more negative for PLA-g-MA than PLA nanoparticle dispersions, due to the presence of deprotonated carboxylic acid groups on the backbone of the PLA and confirms the MA grafting results. Maleic anhydride grafted on PLA backbone improves the covalent conjugation with ovalbumin (OVA) compared to OVA physically adsorbed on the particles. The chemical conjugation was carried out via amide linkages between the carboxylic groups of the nanoparticles, activated with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide, and the amino groups of the protein. The amount of protein conjugated was measured by using the bicinchoninic acid method and is threefold higher compared to the adsorbed OVA. Moreover, the PLA-g-MA nanoparticles increased the amount of conjugated OVA by 36 wt% compared to PLA nanoparticles. OVA adsorption and OVA conjugation provided colloidal dispersions with excellent stability.     

Molecular interaction potential: A new tool for the theoretical study of molecular reactivity

A new methodology to compute molecular interaction potentials (MIPs) is developed and tested. The calculation of the MIP is based upon the generalization of the rigorous quantum mechanical molecular electrostatic potential (MEP) and further addition of a classical repulsion-dispersion term. As a result, the MIP is able to represent not only with high accuracy electrostatic interactions but also represent in a suitable way steric effects. The analysis of the results obtained for different molecules demonstrates the superiority of the MIP with regard to the standard MEP to describe nonbonded interactions, in particular hydrogen bonds. The comparison of results calculated at the ab initio I 6-31G* and semiempirical AM1 levels points out the suitability of semiempirical calculations to qualitatively reproduce the most relevant reactive features of the molecules. Finally, possible applications of the MIP in different fields are discussed. © 1993 John Wiley & Sons, Inc.     

Motion-driven sensing and biosensing using electrochemically propelled nanomotors

Electrochemically-propelled nanomotors offer considerable promise for developing new and novel bioanalytical and biosensing strategies based on the direct isolation of target biomolecules or changes in their movement in the presence of target analytes. For example, receptor-functionalized nanomotors offer direct and rapid target isolation from raw biological samples without preparatory and washing steps. Microtube engines functionalized with ss-DNA, aptamer or antibody receptors are particularly useful for the direct isolation of nucleic acids, proteins or cancer cells, respectively. A new nanomotor-based signal transduction involving measurement of speed and distance travelled by nanomotors, offers highly sensitive, rapid, simple and low cost detection of target biomarkers, and a new dimension of analytical information based on motion. The resulting distance signals can be easily visualized by optical microscope (without any sophisticated analytical instrument) to reveal the target presence and concentration. The attractive features of the new micromachine-based target isolation and signal transduction protocols reviewed in this article offer numerous potential applications in biomedical diagnostics, environmental monitoring, and forensic analysis.     

NMR and Raman Spectroscopic Studies of 4-Phenyl-3-buten-2-one Dissolved in an Electroplating Zinc Bath

Raman, IR and NMR spectra were measured in order to elucidate the role of 4-phenyl-3-buten-2-one in zinc electroplating. First, solutions of this compound dissolved in methanol and methanol/water mixtures were studied. NMR data show that the solvation was caused by Van der Waals forces. Density functional theory calculations were performed to support vibrational wavenumber assignments of the observed bands. The studied SVWN/DN** basis set shows good agreement with the experimental results. Additionally, Raman spectra of 4-phenyl-3-buten-2-one dissolved in an electroplating bath were obtained and a red shift was observed of the carbonyl group. This effect was explained as a result of the packing density of the investigated molecule modified in the electroplating bath. No complex was detected between zinc and 4-phenyl-3-buten-2-one.     

In1.06Ho0.94Ge2O7: a thortveitite‐type compound

A new indium holmium digermanate, In_1.06Ho_0.94Ge₂O₇, with a thortveitite‐type structure, has been prepared as a polycrystalline powder material by high‐temperature solid‐state reaction. This new compound crystallizes in the monoclinic system (space group C2/c, No. 15). The structure was characterized by Rietveld refinement of powder laboratory X‐ray diffraction data. The In³⁺ and Ho³⁺ cations occupy the same octahedral site, forming a hexagonal arrangement on the ab plane. In their turn, the hexagonal arrangements of (In/Ho)O₆ octahedral layers are held together by sheets of isolated diortho groups comprised of double tetrahedra sharing a common vertex. In this compound, the Ge₂O₇ diortho groups lose the ideal D_3d point symmetry and also the C_2h point symmetry present in the thortveitite diortho groups. The Ge—O—Ge angle bridging the diortho groups is 160.2 (3)°, compared with 180.0° for Si—O—Si in thortveitite (Sc₂Si₂O₇). The characteristic mirror plane in the thortveitite space group (C2/m, No. 12) is not present in this new thortveitite‐type compound and the diortho groups lose the C_2h point symmetry, reducing to C₂.     

Lévy processes and Schrödinger equation

We analyze the extension of the well known relation between Brownian motion and the Schrödinger equation to the family of the Lévy processes. We consider a Lévy-Schrödinger equation where the usual kinetic energy operator-the Laplacian-is generalized by means of a selfadjoint, pseudodifferential operator whose symbol is the logarithmic characteristic of an infinitely divisible law. The Lévy-Khintchin formula shows then how to write down this operator in an integro-differential form. When the underlying Lévy process is stable we recover as a particular case the fractional Schrödinger equation. A few examples are finally given and we find that there are physically relevant models-such as a form of the relativistic Schrödinger equation-that are in the domain of the non stable Lévy-Schrödinger equations.     

Gravitational Collapse in Loop Quantum Gravity

In this paper we study the gravitational collapse applying methods of loop quantum gravity to a minisuperspace model. We consider the space-time region inside the Schwarzschild black hole event horizon and we divide this region in two parts, the first one where the matter (dust matter) is localized and the other (outside) where the metric is Kantowski–Sachs type. We study the Hamiltonian constraint obtaining a set of three difference equations that give a regular and natural evolution beyond the classical singularity point in “r=0” localized.