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. (c) 2008 Wiley Periodicals, Inc. J Comput Chem, 2008.
"During the optimization, the atoms in the second shell were fixed at their 6-31G * -optimized positions. Both the NWChem (Valiev et al., 2010) and PQS (Baker et al., 2009) quantum chemistry codes were used. All clusters were optimized with " tight " settings and 'fine' integration grids in NWChem. "
[Show abstract][Hide abstract] ABSTRACT: The aqueous-mineral Δ44/40Ca solid–solution fractionation factors were measured for equilibrating solutions and a set of inorganic solids that trap solvated calcium in six, seven and eight coordination as an intact solvated ion in the lattice. The measured values were then compared to Δ44/40Casolid–solution values predicted from electronic-structure calculations and vibrational frequencies of molecular models of the solvated ions and their solid hydrates. Experimentally, the Δ44/40Casolid–solution values differed by ∼2‰ for crystals of six- and seven-hydrated calcium, and by about ∼2‰ between crystals having seven- and eight-hydrated calcium. In comparison, the calculations predict Δ44/40Casolid–solution values between the sixfold- and eightfold-coordinated aquo ions of 5.4‰. Calculations predict 2.6‰ fractionation between the sixfold- and sevenfold-coordinated aquo ions. Stirred and unstirred experiments gave similar results in most, but not all cases. In general, measured isotopic fractionations compare well with the predictions from quantum mechanics and vibrational analysis. Isotopic fractionation is directly correlated with coordination number. We consider this to be a well-poised test of predictions.
[Show abstract][Hide abstract] ABSTRACT: During their lifetime, humans are exposed to physical, chemical, and biological agents. Among the physical agents, ionizing radiations can produce damage to molecular systems. Ionizing radiations have been known to induce a broad spectrum of genetic effects, including gene, minisatellite mutations, micronucleus formation, chromosome aberrations, ploidy changes DNA (deoxyribonucleic acid) strand breaks and chromosome instability. It has long been known to be deleterious after high dose exposure (>100mSv), predominantly inducing cancer although very high dose exposures yield to tissue damage and ultimately death. Furthermore, ionizing radiation has been called the "universal carcinogen" in that it might induce cancer in most tissues of most species at all ages, including fetus. The hazards of exposure to ionizing radiation were recognized shortly after Roentgen's discovery of the x-ray in 1895. Acute skin reactions were observed in many individuals working with early x-ray generators, and by 1902 the first radiation-induced cancer was reported arising in an ulcerated area of the skin. Then, a few years later, a large number of cancers were 2 observed, and the first report of leukemia in five radiation workers appeared in 1911. Indeed, Marie Curie and her daughter Irene are both thought to have died of radiation-induced leukemia.
[Show abstract][Hide abstract] ABSTRACT: The predictive capabilities of the newly proposed effective scaling frequency factor (ESFF) method and transferability of scaling factors are checked. A set of three related but with different structural motifs molecules, i.e. toluene, styrene and 4-methylstyrene, was used. Four sets of optimized local scaling factors were generated on the basis of different choices of bands from the experimental IR spectra. In all cases the spectral range was 3000–400cm−1. The best fitting was obtained with the so-called Set A (66 experimental bands and 14 optimized local scaling factors). Only slightly worse results were obtained with the Set B containing merely eight local scaling factors. Different statistical tests demonstrate good transferability of local scaling factors as well as better performance of the ESFF approach than Pulay’s SQM method. In particular, the RMS deviation calculated for 66 vibrational modes with ESFF is 28% lower than that obtained with SQM method.
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