Heats of formation of perchloric acid, HClO4_4, and perchloric anhydride, Cl2_2O7_7. Probing the limits of W1 and W2 theory

The heats of formation of HClO$_4$ and Cl$_2$O$_7$ have been determined to chemical accuracy for the first time by means of W1 and W2 theory. These molecules exhibit particularly severe degrees of inner polarization, and as such obtaining a basis-set limit SCF component to the total atomization energy becomes a challenge. (Adding high-exponent $d$ functions to a standard $spd$ basis set has an effect on the order of 100 kcal/mol for Cl$_2$O$_7$.) Wilson's aug-cc-pV(n+d)Z basis sets represent a dramatic improvement over the standard aug-cc-pVnZ basis sets, while the aug-cc-pVnZ+2d1f sequence converges still more rapidly. Jensen's polarization consistent basis sets still require additional high-exponent $d$ functions: for smooth convergence we suggest the \{aug-pc1+3d,aug-pc2+2d,aug-pc3+d,aug-pc4\} sequence. The role of the tight $d$ functions is shown to be an improved description of the Cl (3d) Rydberg orbital, enhancing its ability to receive back-bonding from the oxygen lone pairs. In problematic cases like this (or indeed in general), a single SCF/aug-cc-pV6Z+2d1f calculation may be preferable over empirically motivated extrapolations. Our best estimate heats of formation are $\Delta H^\circ_{f,298}[$HClO$_4$(g)$]=-0.6\pm$1 kcal/mol and $\Delta H^\circ_{f,298}[$Cl$_2$O$_7$(g)$]=65.9\pm$2 kcal/mol, the largest source of uncertainty being our inability to account for post-CCSD(T) correlation effects. While G2 and G3 theory have fairly large errors, G3X theory reproduces both values to within 2 kcal/mol.Comment: J. Mol. Struct. (THEOCHEM), in press (WATOC'05 special issue

Predictive response-relevant clustering of expression data provides insights into disease processes

This article describes and illustrates a novel method of microarray data analysis that couples model-based clustering and binary classification to form clusters of ;response-relevant' genes; that is, genes that are informative when discriminating between the different values of the response. Predictions are subsequently made using an appropriate statistical summary of each gene cluster, which we call the ;meta-covariate' representation of the cluster, in a probit regression model. We first illustrate this method by analysing a leukaemia expression dataset, before focusing closely on the meta-covariate analysis of a renal gene expression dataset in a rat model of salt-sensitive hypertension. We explore the biological insights provided by our analysis of these data. In particular, we identify a highly influential cluster of 13 genes-including three transcription factors (Arntl, Bhlhe41 and Npas2)-that is implicated as being protective against hypertension in response to increased dietary sodium. Functional and canonical pathway analysis of this cluster using Ingenuity Pathway Analysis implicated transcriptional activation and circadian rhythm signalling, respectively. Although we illustrate our method using only expression data, the method is applicable to any high-dimensional datasets

Modeling of the transient interstitial diffusion of implanted atoms during low-temperature annealing of silicon substrates

It has been shown that many of the phenomena related to the formation of "tails" in the low-concentration region of ion-implanted impurity distribution are due to the anomalous diffusion of nonequilibrium impurity interstitials. These phenomena include boron implantation in preamorphized silicon, a "hot" implantation of indium ions, annealing of ion-implanted layers et cetera. In particular, to verify this microscopic mechanism, a simulation of boron redistribution during low-temperature annealing of ion-implanted layers has been carried out under different conditions of transient enhanced diffusion suppression. Due to the good agreement with the experimental data, the values of the average migration length of nonequilibrium impurity interstitials have been obtained. It has been shown that for boron implanted into a silicon layer preamorphized by germanium ions the average migration length of impurity interstitials at the annealing temperature of 800 Celsius degrees be reduced from 11 nm to approximately 6 nm due to additional implantation of nitrogen. The further shortening of the average migration length is observed if the processing temperature is reduced to 750 Celsius degrees. It is also found that for implantation of BF2 ions into silicon crystal, the value of the average migration length of boron interstitials is equal to 7.2 nm for thermal treatment at a temperature of 800 Celsius degrees.Comment: 10 pages, 6 figures, RevTe

The rovibrational spectrum of BeH, MgH and CaH at high temperatures in the X 2Σ+X\,{}^2\Sigma^+ state: a theoretical study

Accurate line lists for three molecules, BeH, MgH and CaH, in their ground electronic states are presented. These line lists are suitable for temperatures relevant to exoplanetary atmospheres and cool stars (up to 2000K). A combination of empirical and \textit{ab initio} methods is used. The rovibrational energy levels of BeH, MgH and CaH are computed using the programs Level and DPotFit in conjunction with `spectroscopic' potential energy curves (PECs). The PEC of BeH is taken from the literature, while the PECs of CaH and MgH are generated by fitting to the experimental transition energy levels. Both spin-rotation interactions (except for BeH, for which it is negligible) and non-adiabatic corrections are explicitly taken into account. Accurate line intensities are generated using newly computed \textit{ab initio} dipole moment curves for each molecule using high levels of theory. Full line lists of rotation-vibration transitions for $^9$BeH, $^{24}$MgH, $^{25}$MgH, $^{26}$MgH and $^{40}$CaH are made available in an electronic form as supplementary data to this article and at \url{www.exomol.com}.Comment: MNRAS (in press

Electron affinities of the first- and second- row atoms: benchmark ab initio and density functional calculations

A benchmark ab initio and density functional (DFT) study has been carried out on the electron affinities of the first- and second-row atoms. The ab initio study involves basis sets of $spdfgh$ and $spdfghi$ quality, extrapolations to the 1-particle basis set limit, and a combination of the CCSD(T), CCSDT, and full CI electron correlation methods. Scalar relativistic and spin-orbit coupling effects were taken into account. On average, the best ab initio results agree to better than 0.001 eV with the most recent experimental results. Correcting for imperfections in the CCSD(T) method improves the mean absolute error by an order of magnitude, while for accurate results on the second-row atoms inclusion of relativistic corrections is essential. The latter are significantly overestimated at the SCF level; for accurate spin-orbit splitting constants of second-row atoms inclusion of (2s,2p) correlation is essential. In the DFT calculations it is found that results for the 1st-row atoms are very sensitive to the exchange functional, while those for second-row atoms are rather more sensitive to the correlation functional. While the LYP correlation functional works best for first-row atoms, its PW91 counterpart appears to be preferable for second-row atoms. Among ``pure DFT'' (nonhybrid) functionals, G96PW91 (Gill 1996 exchange combined with Perdew-Wang 1991 correlation) puts in the best overall performance. The best results overall are obtained with the 1-parameter hybrid modified Perdew-Wang (mPW1) exchange functionals of Adamo and Barone [J. Chem. Phys. {\bf 108}, 664 (1998)], with mPW1LYP yielding the best results for first-row, and mPW1PW91 for second-row atoms. Indications exist that a hybrid of the type $a$ mPW1LYP + $(1-a)$ mPW1PW91 yields better results than either of the constituent functionals.Comment: Phys. Rev. A, in press (revised version, review of issues concerning DFT and electron affinities added

Layered transition metal selenophosphites for visible light photoelectrochemical production of hydrogen

The growing consumption of global energy has posed serious challenges to environmental protection and energy supplies. A promising solution is via introducing clean and sustainable energy sources, including photo-electrochemical hydrogen fuel production. 2D materials, such as transition metal trichalcogenphosphites (MPCh(3)), are gaining more and more interest for their potential as photocatalysts. Crystals of transition metal selenophosphites, namely MnPSe3, FePSe3 and ZnPSe3, were tested as photocatalysts for the hydrogen evolution reaction (HER). ZnPSe3 is the one that exhibited the lowest overpotential and the higher response to the light during photocurrent experiments in acidic media. For this reason, among the crystals in this work, it is the most promising for the photocatalyzed production of hydrogen

Large-scale association analysis identifies new lung cancer susceptibility loci and heterogeneity in genetic susceptibility across histological subtypes.

Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis of lung cancer in 29,266 cases and 56,450 controls. We identified 18 susceptibility loci achieving genome-wide significance, including 10 new loci. The new loci highlight the striking heterogeneity in genetic susceptibility across the histological subtypes of lung cancer, with four loci associated with lung cancer overall and six loci associated with lung adenocarcinoma. Gene expression quantitative trait locus (eQTL) analysis in 1,425 normal lung tissue samples highlights RNASET2, SECISBP2L and NRG1 as candidate genes. Other loci include genes such as a cholinergic nicotinic receptor, CHRNA2, and the telomere-related genes OFBC1 and RTEL1. Further exploration of the target genes will continue to provide new insights into the etiology of lung cancer

Case Reports1. A Late Presentation of Loeys-Dietz Syndrome: Beware of TGFβ Receptor Mutations in Benign Joint Hypermobility

Background: Thoracic aortic aneurysms (TAA) and dissections are not uncommon causes of sudden death in young adults. Loeys-Dietz syndrome (LDS) is a rare, recently described, autosomal dominant, connective tissue disease characterized by aggressive arterial aneurysms, resulting from mutations in the transforming growth factor beta (TGFβ) receptor genes TGFBR1 and TGFBR2. Mean age at death is 26.1 years, most often due to aortic dissection. We report an unusually late presentation of LDS, diagnosed following elective surgery in a female with a long history of joint hypermobility. Methods: A 51-year-old Caucasian lady complained of chest pain and headache following a dural leak from spinal anaesthesia for an elective ankle arthroscopy. CT scan and echocardiography demonstrated a dilated aortic root and significant aortic regurgitation. MRA demonstrated aortic tortuosity, an infrarenal aortic aneurysm and aneurysms in the left renal and right internal mammary arteries. She underwent aortic root repair and aortic valve replacement. She had a background of long-standing joint pains secondary to hypermobility, easy bruising, unusual fracture susceptibility and mild bronchiectasis. She had one healthy child age 32, after which she suffered a uterine prolapse. Examination revealed mild Marfanoid features. Uvula, skin and ophthalmological examination was normal. Results: Fibrillin-1 testing for Marfan syndrome (MFS) was negative. Detection of a c.1270G > C (p.Gly424Arg) TGFBR2 mutation confirmed the diagnosis of LDS. Losartan was started for vascular protection. Conclusions: LDS is a severe inherited vasculopathy that usually presents in childhood. It is characterized by aortic root dilatation and ascending aneurysms. There is a higher risk of aortic dissection compared with MFS. Clinical features overlap with MFS and Ehlers Danlos syndrome Type IV, but differentiating dysmorphogenic features include ocular hypertelorism, bifid uvula and cleft palate. Echocardiography and MRA or CT scanning from head to pelvis is recommended to establish the extent of vascular involvement. Management involves early surgical intervention, including early valve-sparing aortic root replacement, genetic counselling and close monitoring in pregnancy. Despite being caused by loss of function mutations in either TGFβ receptor, paradoxical activation of TGFβ signalling is seen, suggesting that TGFβ antagonism may confer disease modifying effects similar to those observed in MFS. TGFβ antagonism can be achieved with angiotensin antagonists, such as Losartan, which is able to delay aortic aneurysm development in preclinical models and in patients with MFS. Our case emphasizes the importance of timely recognition of vasculopathy syndromes in patients with hypermobility and the need for early surgical intervention. It also highlights their heterogeneity and the potential for late presentation. Disclosures: The authors have declared no conflicts of interes

The empirical equilibrium structure of diacetylene

High-level quantum-chemical calculations are reported at the MP2 and CCSD(T) levels of theory for the equilibrium structure and the harmonic and anharmonic force fields of diacetylene, HCCCCH. The calculations were performed employing Dunning's hierarchy of correlation-consistent basis sets cc-pVXZ, cc-pCVXZ, and cc-pwCVXZ, as well as the ANO2 basis set of Almloef and Taylor. An empirical equilibrium structure based on experimental rotational constants for thirteen isotopic species of diacetylene and computed zero-point vibrational corrections is determined (r_e^emp: rC-H=1.0615 A, rCtripleC=1.2085 A, rC-C = 1.3727 A) and in good agreement with the best theoretical structure (CCSD(T)/cc-pCV5Z: rC-H=1.0617 Angstrom, rCtripleC=1.2083 A, rC-C=1.3737 A). In addition, the computed fundamental vibrational frequencies are compared with the available experimental data and found in satisfactory agreement.Comment: 12 pages, accepted for publication in J. Mol. Spectros

Paleozoic to Cenozoic sedimentary bedrock geology and lithostratigraphy of Singapore

A new lithostratigraphical framework for Singapore is proposed, based on the analysis of c. 20,000 m of core recovered from 121 c. 205 m deep boreholes and augmented with 218 field localities from across Singapore. The new framework describes a succession dating from the Carboniferous to the Quaternary. New U-Pb detrital zircon dates and fossil analysis were used to constrain the ages of key sedimentary units. The oldest known sedimentary rocks in Singapore are found to be the deformed Carboniferous (Mississippian) Sajahat Formation. These are succeeded by the newly erected, Middle and Upper Triassic, marine to continental Jurong Group and Sentosa Group successions that accumulated in the southern part of the Semantan Basin. The Jurong Group comprises four formations: the Tuas Formation, the Pulau Ayer Chawan Formation, the Pandan Formation and the Boon Lay Formation. The Sentosa Group contains two formations: the Tanjong Rimau Formation and the Fort Siloso Formation. In Singapore, the depositional record during this time is related to late Permian to Triassic arc magmatism in the southern part of the forearc basin to the Sukhothai Arc. The Jurong and Sentosa groups were deformed and weakly metamorphosed during the final stages of the Late Triassic to Early Jurassic orogenic event, deformation that led to the formation of the syn-orogenic conglomerates of the Buona Vista Formation. Following this, two distinct Lower Cretaceous sedimentary successions overstepped the Jurong and Sentosa group strata, including the Kusu Formation and the Bukit Batok Formation, both deposited in the southern part of the Tembeling Basin. A series of Neogene to Quaternary formations overly the Mesozoic and Palaeozoic stratigraphy, including the Fort Canning Formation, Bedok Formation and the Kallang Group