Ultrasensitive detection of malondialdehyde with surface-enhanced Raman spectroscopy.

Malondialdehyde (MDA) is a biomarker of lipid peroxidation that has been widely associated with food rancidity as well as many human diseases. Most current MDA detection methods involve MDA reaction with thiobarbituric acid (TBA), followed by UV-visible and/or fluorescence detection of high-performance liquid chromatography (HPLC)-separated TBA-MDA. Herein, we report the first proof-of-concept study of surface-enhanced Raman detection of a TBA-MDA adduct using silver nanoparticles as the SERS substrate and the 632.8 nm HeNe laser as a Raman excitation source. Current SERS detection limit of TBA-MDA is 0.45 nM, ~100 times higher than the 36 nM fluorescence sensitivity recently reported with the HPLC-purified TBA-MDA. Molecular specificity of the SERS technique was studied by comparing the SERS spectrum of TBA-MDA with those acquired with TBA adducts of other TBA-reactive compounds (TBARCs) that includes formaldehyde, acetaldehyde, butyraldehyde, trans-2-hexenal, and pyrimidine. Compared to TBA and TBA adducts with those TBARCs, the SERS activity of TBA-MDA adduct is significantly higher. The possibility of direct SERS detection of TBA-MDA in a reaction mixture (without HPLC separation) has also been investigated.

Quantum chemistry in parallel with PQS.

This article describes the capabilities and performance of the latest release (version 4.0) of the Parallel Quantum Solutions (PQS) ab initio program package. The program was first released in 1998 and evolved from the TEXAS program package developed by Pulay and coworkers in the late 1970s. PQS was designed from the start to run on Linux-based clusters (which at the time were just becoming popular) with all major functionality being (a) fully parallel; and (b) capable of carrying out calculations on large-by ab initio standards-molecules, our initial aim being at least 100 atoms and 1000 basis functions with only modest memory requirements. With modern hardware and recent algorithmic developments, full accuracy, high-level calculations (DFT, MP2, CI, and Coupled-Cluster) can be performed on systems with up to several thousand basis functions on small (4-32 node) Linux clusters. We have also developed a graphical user interface with a model builder, job input preparation, parallel job submission, and post-job visualization and display.

Accuracy and efficiency of atomic basis set methods versus plane wave calculations with ultrasoft pseudopotentials for DNA base molecules.

Recent results from Preuss et al. (J Comput Chem 2004, 25, 112) on DNA base molecules, obtained by plane wave density functional calculations using ultrasoft pseudopotentials, are compared with calculations using Gaussian basis sets. Bond lengths and angles agree closely, but dihedral angles and vibrational frequencies show significant differences. The Gaussian basis calculations are at least an order of magnitude more efficient than the plane wave/ultrasoft pseudopotential calculations at a similar level of accuracy; the advantage is even larger if the Fourier Transform Coulomb method is used. To obtain definite benchmark values, the geometries of the four DNA bases were optimized at the MP2 level with large basis sets, up to cc-pVQZ and aug-cc-pVTZ.

An efficient atomic orbital based second-order Møller-Plesset gradient program.

Based on the orbital-invariant atomic orbital formulation of the MP2 (Møller-Plesset second-order perturbation theory) energy and gradient [P. Pulay and S. Saebø, Theor. Chim. Acta 69, 357 (1986)], we have derived and programmed detailed working equations for closed-shell MP2 gradients. The orbital-invariant form avoids the difficulties of other formulations with frozen orbitals, and allows the use of arbitrary occupied orbitals, an important consideration for local correlation theories, although the present program uses canonical molecular orbitals. The atomic orbital formulation offers savings both in storage and computer time. Test calculations on systems containing up to approximately 100 atoms and approximately 1000 basis functions, performed on a single personal computer, are reported. Parallelization of the code is underway.