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A static QM procedure for modeling solvated reaction mechanisms is calibrated using the Morita–Baylis–Hillman reaction., We report a static quantum chemistry modeling treatment to study how solvent molecules affect chemical reaction mechanisms without dynamics simulations. This modeling scheme uses a global optimization procedure to identify low energy intermediate states with different numbers of explicit solvent molecules and then the growing string method to locate sequential transition states along a reaction pathway. Testing this approach on the acid-catalyzed Morita–Baylis–Hillman (MBH) reaction in methanol, we found a reaction mechanism that is consistent with both recent experiments and computationally intensive dynamics simulations with explicit solvation. In doing so, we explain unphysical pitfalls that obfuscate computational modeling that uses microsolvated reaction intermediates. This new paramedic approach can promisingly capture essential physical chemistry of the complicated and multistep MBH reaction mechanism, and the energy profiles found with this model appear reasonably insensitive to the level of theory used for energy calculations. Thus, it should be a useful and computationally cost-effective approach for modeling solvent mediated reaction mechanisms when dynamics simulations are not possible.

A Comparative Molecular Similarity Indices Analysis (CoMSIA) was performed for 2,6-substituted-4-monosubstituted aminopyrimidine antagonists of prostaglandin D(2) receptor (DP). Both two-component (Q(2) = 0.63, R(2) = 0.82, SEE = 0.47 pIC(50)) and three-component (Q(2) = 0.70, R(2) = 0.91, SEE = 0.36 pIC(50)) CoMSIA models were established. Two hydrogen-bond acceptors with spatial separation of about 8Å are shown as optimal for binding. A large hydrophobic center that separates the two acceptors confers to the potency of the 2,6-substituted-4-monosubstituted aminopyrimidine. The models were used to predict IC(50) values for compounds which had functional groups different from those in the training set.

Pulmonary fibrosis is a debilitating disease affecting up to 2 million people worldwide, with a median survival rate of only 3 years after diagnosis. The aim of this study was to evaluate a potential protein biomarker (Cocoacrisp, CC) to identify the onset of pulmonary fibrosis. A model of fibrosis was induced via intratracheal instillation of bleomycin, and samples were collected during the early phase of the disease. Immunohistochemical identification of CC was carried out in lung tissue from the bleomycin model. Quantification by image analysis showed CC levels were doubled (p

Background Associations between smoking and the development of tobacco-related diseases in humans have historically been assessed by epidemiological studies. These studies are further complicated by the number of chemicals used in tobacco and individual smoking habits. An alternative approach is required to assess the biological responses. Objective Toxicogenomics was carried out to identify early molecular markers for events in pulmonary injury resulting from tobacco smoke components (TSC) exposure. Materials and methods EpiAirway-100 cells were exposed at the air/liquid interface to representative particle (nicotine; cadmium) and vapour phase [formaldehyde (FA) and ethyl carbamate] components of cigarette smoke. Microarray technology was used to compare expression profiles of human genes associated with toxicity and drug resistance, from control and TSC-treated respiratory epithelium (n=5/dose). Results Using the GEArray 'toxicology and drug resistance' microarray followed by significance analysis of microarray analysis, 42 mRNA transcripts were found to be significantly altered by the TSC exposure. The vapour [ethyl carbamate, FA and particle (nicotine, cadmium)] phase TSC exhibited differential transcriptional responses that could not be attributed to their chemical phase. The transcriptional changes could be classified according to a functional family, where ethyl carbamate, FA and cadmium classified as carcinogens, demonstrated the highest gene homology when compared with the noncarcinogen, nicotine. Discussion Analysis of the microarray data and further confirmation (reverse transcriptase-PCR) identified three potential biomarkers for TSC-induced injury. These three genes (CYP7A1, HMOX1 and PTGS1) are highly upregulated and have been linked with mechanistic pathways of disease.

One of the first lines of defence to inhaled toxins is the barrier formed by the tracheobronchial epithelium, making this the ideal region for studying the toxicity of inhaled substances. This study utilises a highly differentiated, three-dimensional, in vitro model of human upper respiratory tract epithelium (EpiAirway-100) to measure the acute toxicological responses to well-characterised tobacco smoke components. To determine the suitability of this model for screening inhaled toxicants, the EpiAirway tissue model (ETM) was treated apically with tobacco smoke components (nicotine, formaldehyde, cadmium, urethane) which are known to induce a variety of toxic effects (e.g. cytotoxic, thrombogenic, carcinogenic). A range of concentrations were used to model different mechanisms and severity of toxicity which were then compared to known in vivo responses. Similar trends in stress response occurred, with distinct alterations to the tissue in response to all four toxins. At high concentrations, cell viability decreased and tight junctions were degraded, but at sub-toxic concentrations epithelial resistance (indicating tissue integrity) increased 20–60% from control. This peak in resistance coincided with an increase in secreted protein levels, elevated cytokine release and goblet cell hyperplasia and hypertrophy. In conclusion, acute exposure to tobacco smoke components induces measurable toxic responses within human respiratory epithelium. Sub-toxic concentrations appear to illicit a protective response by increasing mucus secretion and mediating immune responses via cytokine release. These responses are comparable to human in vivo responses, indicating potential for the ETM as a tool for screening the toxicity of inhaled compounds.

A study was undertaken to determine the use of a plasmid DNA scission assay to evaluate the causal relationships between particle oxidative capacity and physico-chemistry. Field emission scanning electron microscopy (FESEM), image analysis (IA) and inductively coupled plasma-mass spectrometry (ICP-MS) were employed to investigate the physico-chemical characteristics of indoor PM10 (particulate matter with an aerodynamic diameter of 10 μm or less) in Beijing, China. Six PM10 samples (indoor smoker's living room; indoor non-smoker's living room and kitchen; and outdoor Beijing city; winter versus summer) were selected to represent typical indoor Beijing PM10 environments that contain high particle mass. The PM10 collected from a kitchen and two smoker's homes had the lowest TD50 (toxic dosage of PM10 causing 50% plasmid DNA damage), being as low as 45 μg ml−1 (kitchen) and 100 μg ml−1 (living room), which suggests a high oxidative capacity, with the PM10 generated in kitchens appearing to be the most toxic. The indoor PM10 from the non-smoker's home and outdoor PM10 samples demonstrated high TD50 values and were deemed less bioreactive (i.e. caused limited DNA damage). FESEM observations revealed that four types of particle species were prevalent in Beijing indoor PM10; soot aggregates, minerals, coal fly ash and unknown fine particles. IA showed that higher percentages of soot and unknown fine particles were associated with the lower TD50 values, suggesting that soot and the unknown fine particles may be important components responsible for the observed plasmid DNA damage. The water-soluble trace elements were negatively correlated with the TD50 values, implying that the DNA damage may be attributed to the water-soluble fraction of the PM10. Water-soluble zinc revealed the best relationship with the TD50 values than other analyzed elements, signifying it may play a role in driving the oxidative damage.

A series of 7-chloro-2,3-dihydro-2-[1-(pyridinyl)alkyl]-pyridazino[4,5-b]quinoline-1,4,10(5H)-triones were synthesized and found to have potent activity at the glycine site of the NMDA receptor. In some cases, these compounds possessed poor aqueous solubility that may have contributed to poor rat oral bioavailability. Subsequently, compounds have been identified with improved aqueous solubility and oral bioavailability. Several of these compounds were examined in a rat chronic constrictive injury (CCI) model of neuropathic pain and found to have potent activity when dosed orally.

Several members of the 7-chloro-2,3-dihydro-2-[1-(pyridinyl)alkyl]-pyridazino[4,5-b]quinoline-1,4,10(5H)-triones (2) have been identified as being potent and selective NMDA glycine-site antagonists. Increasing size of the alkyl substituent on the alpha-carbon led to a progressive decrease in binding affinity. Some of these analogues possess improved drug-like properties such as cellular permeability, solubility and oral absorption.

Historically, it has been challenging to go beyond epidemiology to investigate the pathogenic changes caused by tobacco smoking. The EpiAirway-100 (MatTek Corp., Ashland, MA) was employed to investigate the effects of cigarette smoke components. Exposure at the air-liquid-interface represented particle and vapour phase components of cigarette smoke. A proteomic study utilising iTRAQ labelling compared expression profiles. The correlative histopathology revealed focal regions of hyperplasia, hypertrophy, cytolysis and necrosis. We identified 466 proteins, 250 with a parameter of two or more peptides. Four of these proteins are potential markers of lung injury and three are related to mechanistic pathways of disease.

An investigation of modern computational simulation techniques and their results in describing two notable organopalladium reactions are discussed. First, a methodology for computational quantum chemistry simulations of homogeneous catalysis is presented. We find that through careful consideration of electronic and thermodynamic energy contributions, practical methods are available to accurately study complicated reaction mechanisms and to make educated predictions about their chemistry. We apply this technique to develop the first full analysis of the Wacker Process, olefin oxidation by PdCl2 catalysts, effectively uniting nearly 50 years of research into one mechanistic model. Key findings include the identification of competitive rate determining steps that are dependent on ion concentrations and the inaccessibility of [beta]-hydride elimination during product formation. The second analysis addresses the unique performance of the enantioselective Tsuji-allylation reaction, a reaction the great potential in the fields of asymmetric catalysis and natural product synthesis. In this reaction, calculations point towards enantioselectivity determined after the rate determining step. Intriguingly, we find that C-C coupling is facile in a variant to canonical reductive elimination containing characteristics of both reductive cheletropic and Claisen rearrangements. Lastly, a model is presented to direct improved catalyst design. In total, this dissertation presents an outline for practical quantum chemical simulation of complicated and elaborate organopalladium reactions.

The interrelationships between cigarette, alcohol, and coffee use were examined in 307 U.S. army trainees and 304 U.S. enlisted army personnel. Usage patterns indicated distinct gender differences in this occupational setting. Among women, cigarette use and alcohol consumption were positively correlated; whereas for men, cigarette and coffee use were positively related. For both males and females, alcohol and coffee use were only weakly correlated. As demonstrated in other studies, nonsmokers showed a consistent pattern of abstention from coffee and alcohol or moderate alcohol use.

1. The general term ‘nanoparticle’ (NP) is used to define any particle less than 100 nm in at least one dimension and NPs are generally classified as natural, anthropogenic or engineered in origin. Anthropogenic, also referred to as ‘ultrafine’ particles (UFPs), are predominately combustion derived and are characterized by having an equivalent spherical diameter less than 100 nm. 2. These particles, considered to be ‘combustion-derived nanoparticles’ (CDNPs), are of toxicological interest given their nanosized dimensions, with properties not displayed by their macroscopic counterparts. 3. The pulmonary deposition efficiency of inhaled UFPs, along with their large surface areas and bound transition metals, is considered important in driving the emerging health effects linked to respiratory toxicity. 4. The toxicology of CDNPs is currently used to predict the health outcomes in humans following exposure to manufactured NPs. Their similar physicochemistry would suggest similar adverse health effects (i.e. pulmonary (and perhaps cardiac) toxicity). As such, it is essential to fully understand CDNP nanotoxicology in order to minimize occupational and environmental exposure. Key words: carbon black, combustion-derived particles, diesel exhaust, fly ash, nanoparticles, pulmonary toxicity.

Prostanoids play important physiological roles in the cardiovascular and immune systems and in pain sensation in peripheral systems through their interactions with eight G-protein coupled receptors. These receptors are important drug targets, but development of subtype specific agonists and antagonists has been hampered by the lack of 3D structures for these receptors. We report here the 3D structure for the human DP G-protein coupled receptor (GPCR) predicted by the MembStruk computational method. To validate this structure, we use the HierDock computational method to predict the binding mode for the endogenous agonist (PGD2) to DP. Based on our structure, we predicted the binding of different antagonists and optimized them. We find that PGD2 binds vertically to DP in the TM1237 region with the alpha chain toward the extracellular (EC) region and the omega chain toward the middle of the membrane. This structure explains the selectivity of the DP receptor and the residues involved in the predicted binding site correlate very well with available mutation experiments on DP, IP, TP, FP, and EP subtypes. We report molecular dynamics of DP in explicit lipid and water and find that the binding of the PGD2 agonist leads to correlated rotations of helices of TM3 and TM7, whereas binding of antagonist leads to no such rotations. Thus, these motions may be related to the mechanism of activation.

The physiological role of the duodenal peptide secretin is as a potent stimulant of electrolyte and water movement in pancreatic and biliary epithelium, via activation of G protein-coupled secretin receptors (hSCTR). However, the distribution and potential function of hSCTR in human lung has not previously been addressed. Using real-time quantitative reverse transcriptase-polymerase chain reaction profiling, in situ hybridization, and immunohistochemistry, we demonstrated that the hSCTR is abundantly expressed within the distal regions of human lung (tertiary bronchus and parenchyma), with negligible expression detected in more proximal regions (trachea, primary, and secondary bronchus). Expression was observed predominantly on the basolateral membrane of the bronchial epithelial layer, with some expression also observed in bronchial smooth muscle. In primary cultures of human tertiary bronchial epithelial cells, secretin was demonstrated to potently stimulate channel-mediated Cl- efflux in a concentration-dependent manner. Secretin was also shown to cause concentration-dependent relaxation of human tertiary bronchial smooth muscle. In summary, these data demonstrate that secretin receptors are present in human lung, and that activation of these receptors with human secretin potently stimulates concentration-dependent Cl- efflux from bronchial epithelial cells and bronchorelaxation.

In the analytical method outlined in this paper airborne methyl tert-butyl ether (MTBE) and other hydrocarbon vapours are sampled by drawing the atmosphere through a primary sorption tube containing a porous polymer sorbent. A known volume of air is drawn by a suitable sampling pump, which may be worn by an operator or remain static at a specified location. Factors influencing the choice of sorbent are discussed. After sampling, the primary sorption tube is capped and returned to the laboratory for analysis. Sampled vapours are desorbed from the primary trap by thermal desorption. The desorbed sample is re-concentrated on a small secondary cold trap containing a solid sorbent. When desorption from the primary trap is complete, the secondary trap is heated rapidly and the sample (now in a very narrow plug) is swept on to a fused-silica capillary column that is located only a few millimetres from the sorbent bed of the secondary trap. MTBE is separated from gasoline hydrocarbons on an OV-1701 capillary column and quantified by a calibrated flame-ionisation detector.

Sunlight-powered CO2-photoelectroreduction is a promising and potentially sustainable route to recycle CO2 byproducts back into energy-dense liquid fuels. One of the most intriguing processes known to date is the pyridinium-catalyzed CO2 reduction on p-type GaP photoelectrodes, where conversion to methanol has reported faradaic efficiencies nearing 100 %. Modeling this reactive environment requires understanding energetics of differently charged species at semiconductor electrodes, so we develop a cluster model and benchmark binding energies from it to those from Kohn–Sham density functional theory calculations that employ periodic boundary conditions. We then use this cluster model to theoretically predict structures and binding energies for charged and neutral adsorbates on the GaP(110) surface with and without the presence of van der Waals interactions and implicit solvation. We discuss the relative magnitudes of binding energy contributions for different adsorbates considered relevant in this CO2 reduction process and provide details showing pitfalls when using cluster models.