Current Physical Chemistry - Volume 3, Issue 2, 2013

Gold nanorods absorb and scatter light strongly in the near-infrared portion of the electromagnetic spectrum, making them ideal tissue contrast agents for imaging techniques such as optical coherence tomography (OCT). Strong interactions occur at the nano-bio interface, such as proteins binding to gold nanorods forming a ‘corona.’ To fulfill the promise of nanorods for applications such as contrast agents, we must better understand the intrinsic interactions of these nanomaterials with biological systems at the molecular, cellular and tissue level. In this paper, we briefly review the nanorod-protein interface. We then present some new fast relaxation imaging (FReI) measurements of how the presence of strongly-absorbing gold nanorods affects protein binding and folding, taking into account inner filter effects and the strong quenching effect of nanorods on fluorescent-labeled proteins. Next we show that two-photon photoluminescence of the gold nanorods can be used to image the nanorods in tissue constructs, allowing us to independently study their tissue distribution so they can be used successfully as contrast agents in optical coherence microscopy.

Raman optical activity (ROA) results in small differences in the Raman spectra of chiral molecules depending on whether left-or right circularly polarized light has been used. Due to its origin in higher order effects ROA is an extremely weak phenomenon, usually 3-5 orders of magnitude smaller than Raman scattering. Here we combine Raman optical activity (ROA) and surface enhanced Raman scattering (SERS) and report ROA experiments performed on biologically relevant molecules on silver nanoparticles, such as adenosine and cytosine. Our studies show that adsorption and local optical field gradients may modify the ROA signature of a molecule: In the vicinity of plasmonic silver nanoparticles, adenosine and cytosine show a strong SEROA effect exhibiting circular induced differences (CIDs) on the order of ∼10-2 compared to 10-4 - 10-3 typically observed in ROA. The increase in CID in SEROA and the overall enhanced Raman signal allows improved experimental parameters in SEROA compared to ROA, such as dramatically shorter data acquisition times, reduced excitation power, and lower concentration of the target molecule.

In this mini-review, the rocky road of computational ROA, from a specialist novelty item to the front line of computational chemistry, is outlined. Particular attention is paid to the computational studies of large molecular systems and solvent effects, highlighting how computational ROA is becoming an important tool in structural biology and the detailed analysis of biomacromolecules in solution.

Studying membrane protein function using Xenopus laevis oocytes has been proven to be a successful tool since its introduction more than three decades ago. Due to their great availability, large size and ease of handling, X. laevis oocytes are often superior when compared to other expression systems such as Escherichia coli or eukaryote expression systems. The Xenopus laevis oocyte expression system is able to efficiently transcribe and translate injected genetic information and to assemble, process, and target protein products. Protein characterization studies in intact whole cell injected oocytes are done using established techniques such as electrophysiology, transport assays, and calcium imaging. Recently Xenopus oocytes have been analyzed using in-vivo NMR spectroscopy, and we wondered if it would be possible to use Raman spectroscopy for non-invasive analysis of single oocytes. We present here evidence that it is possible to identify Raman bands arising from heterologous expressed membrane proteins in stage VI oocytes. This opens the possibility for integrating the Raman analysis with already established protein expression methods in order to yield complementary information about membrane protein structure and function.

This study refers to the identification of cytocompatibility of vertically aligned carbon nanotubes, which are superhydrophobic or superhydrophilic. The identification of their thermodynamic aspects, for use as biomaterials, especially in the development of scaffolds and other devices for filing and tissue regeneration was also investigated.

Sugar puckering and hydrogen bond networks are the most important properties of nucleosides as either DNA functional moieties or antibiotics. This article studies such the relationship quantum mechanically for two cytidine nucleoside derivatives, 1’, 2’-didehydro-3’, 4’-deoxycytidine (I) and 2’-deoxycytidine (II) with respect to cytidine (III) in isolation. Vibrational infrared (IR) spectroscopy studied using density functional theory (DFT) models in addition to other properties such as potential energy surfaces (PES), geometries, molecular electrostatic potentials (MEP) and Fukui functions. The atomic site related Fukui function indicates that the sugar carbons are less chemically active in III but can be activated when losing the hydroxyl group at C(2’) as in II and can be significantly activated by forming a C=C double bond as in I. The simulated IR spectra indicate that the compounds are related structurally. Intramolecular hydrogen bond networks (as “spider webs”) of the biomolecules are revealed with IR red-shift and blue-shift. A detailed study in the region of C-H stretch in 2800-3300 cm-1 indicates that intramolecular H-bond networks cause IR spectral blue-shift.

The debromination of deca-bromodiphenyl ester (BDE209) is one of the most important processes in its removal from the environment. Despite numerous experimental studies improved the efficiency of poly brominated diphenyl ethers (PBDEs’) debromination, few studies focused on the mechanism. This work provides a preliminary investigation on studying the debromination mechanism of BDE209 with density functional theory (DFT). Experimental results suggest a stepwise process catalyzed by Ni-Fe bimetallic nano particles. So, a potential debromination mechanism of BDE209 via a four-membered ring transition state has been proposed. The B3LYP calculations indicate lower activation energies catalyzed by Ni relative to Fe, which agrees with the experimental result that a much higher debromination efficiency with Ni-Fe bimetallic nano particles than nano zero-valent iron. Also water has small solvent effect on the activation energies of debromination. The efficiency of debromination improves greatly in solvent mixture with higher ratio of water in experiment probably because of more protons provided by more water for the corrosion and debromination. Finally, the meta-bromine atoms are the most susceptible to be debrominated.

In the present study, the binding of the cationic MnIIITMPyP [meso-tetrakis (4-N-methyl pyridinium) porphyrin] to negatively charged membrane models containing phosphatidylcholine (PC)/ phosphatidylserine (PS) and the porphyrin reactivity with PS-derived peroxides (LOOH) were evaluated. This investigation is relevant due to the participation of PS in cell signaling and apoptosis. Addition of PC/PS liposomes to MnIIITMPyP solutions led to spectral changes of the porphyrin electronic absorption spectrum suggestive of electrostatic interactions with the negatively charged interface provided by PS. The binding of MnIIITMPyP to PC/PS liposomes was corroborated by the quenching of the fluorophore merocyanine 540. In addition total energy calculations of saturated and unsaturated PS based on the spinpolarized variant of KS-DFT were used to support some experimental data. Cyclic voltammetry analysis revealed that the association to PC/PS liposomes shifted the redox potential of the MnII/MnIII (+87 mV vs NHE, in aqueous buffered solution) couple to a more positive value to (+110 mV vs NHE). This event favors the oxidation of O2-• to O2 by the porphyrin. MnIIITMPyP was able to react with the lipid-derived peroxides as evidenced by spectral changes of the porphyrin consistent with the generation of a high valence state (MnIV=O) of the catalyst. The spectral changes were not observed when biological lipids containing unsaturated PC and PS were replaced by the corresponding dipalmitoyl (DP)- derived: DPPC/DPPS.

To the best of our knowledge we here for the first time demonstrate surface enhanced Raman spectroscopy (SERS) to detect a quorum sensing (QS) signal molecule below 1 nM concentration in both ultrapure water and under physiological conditions. Based on our results, SERS shows promise as a highly suitable tool for in situ measurements of low Acyl-Homoserine Lactone (AHL) concentrations in biofilms containing QS bacteria. Signal molecules communicate information about their environment and coordinate certain physiological activities in QS systems that exist in many bacteria. SERS enables detection of different AHLs at low concentrations due to structural differences observed in the corresponding SERS spectra. Ag colloidal nanoparticles, produced by the hydroxylamine reducing method, were used for the SERS measurements. SERS spectra of C12-HSL suspended in ultrapure water and in supplemented minimal medium were collected for 5 concentrations ranging from 2 μM to 0.2 nM, and a comparison between the spectra from these two media is also presented. We have been able to detect biologically relevant concentrations of AHL molecules ranging from 1 nM to 1 μM using SERS.

The light-induced isomerization of the retinal chromophore starts the reaction cycles of retinal proteins. We review and discuss some new computations on the role of the retinal methyl groups in determining the structure, dynamics, and protein interactions of the retinal. The torsional potential of the C11=C12 bond suggests that moderate twisting of this bond can be achieved without a significant energetic cost, allowing for twisted 11-cis geometries to be sampled within the protein environment. The 9- and 13-methyl groups contribute significantly to the geometry and the ground-state torsional properties of the retinal chromophore, but the relative importance of these two methyl groups appears to be different in the dark- vs. the batho-intermediates of visual rhodopsins.

In this paper, the Enhanced Homotopy Perturbation Method (EHPM) has been applied along with the Boubaker polynomials Expansion Scheme (BPES) to a system of nonlinear partial differential equations which governs non-isothermal tubular chemical reactors. Theoretical considerations have been discussed in order to illustrate the reliability of the methods. Comparison of EHPM results with those of BPES showed that both techniques are effective and convenient.

The structures and rheological properties of Span 80/PEG 400/H2O niosomes are studied by using atomic force microscopy, dynamic light scattering and rheology techniques. The niosome system at high frequency region is a Newtonian fluid with linear viscoelasticity. The cole-cole plots at low frequency region are not semicircular and the system is not linear viscoelastic. At a mass ratio of Span 80-PEG 400, the viscosity, relaxation time, elastic and loss moduli of the system decrease with water content but increase with PEG 400 content. With the increase of oscillatory shear frequency, the storage modulus increases but the loss modulus first increases and then decreases.