Combining mistake-proofing and Jidoka to achieve world class quality in clinical chemistry

Presented at the 11th Conference Quality in the Spotlight, March 2006, Antwerp, Belgium.     

Avoiding pitfalls of a theoretical approach: the harmonic oscillator measure of aromaticity index from quantum chemistry calculations

The concept of the harmonic oscillator measure of aromaticity (HOMA) is based on comparing the geometrical parameters of a studied molecule with the parameters for an ideal aromatic system derived from bond lengths of the reference molecules. Nowadays, HOMA is routinely computed combining the geometries from quantum chemistry calculations with the experimentally based parameterization. Thus, obtained values of HOMA, however, are bound to suffer from inaccuracies of the theoretical methods and strongly depend on computational details. This could be avoided by obtaining both the input geometries and the parameters with the same theoretical method, but efficiency of the error compensation achieved in this way has not yet been probed. In our work, we have prepared a benchmark set of HOMA values for 25 cyclic hydrocarbons, based on the all core CCSD(T)/cc-pCVQ(T)Z geometries, and used it to investigate the impact of different choices of the exchange–correlation functionals and basis sets on HOMA, calculated against the experimentally based (HOMA^EP) or the consistently calculated (HOMA^CCP) parameters. We show that using HOMA^EP leads to large and unsystematic errors, and strong sensitivity to the choice of XC functional, basis set, and the experimental data for the reference geometry. This sensitivity is largely, although not completely attenuated in the consistent approach. We recommend the most suitable functionals for calculating HOMA in both approaches (HOMA^EP and HOMA^CCP), and provide the HOMA parameters for 25 studied exchange–correlation functionals and two popular basis sets.     

Electron transfer in environmental systems: a frontier for theoretical chemistry

The advances in understanding the kinetic behavior of certain environmental electron transfer (ET) systems are presented. Emphasis is placed on the homogeneous ET chemistry of transition metals, particularly the Fe^II/III system, in various relevant forms. In the context of modern ET theory, we examine the utility of computational chemistry methods for the calculation of ET quantities such as the reorganization energy and electronic coupling matrix element. We discuss successful application of the methods to topics of homogeneous oxidation of dissolved metal ions by molecular oxygen in aqueous solution, as well as the prediction of electron mobility in solid phase iron oxide crystals. The examples illustrate the significant potential for many more advances in understanding environmental ET systems through the combination of ET theory and computational chemistry.     

Analysis of a cycloheptenone derivative: an experimental and theoretical approach

A detailed analysis with total assignment of (1)H and (13)C NMR spectral data for a cycloheptenone derivative, a key intermediate for the synthesis of perhydroazulene terpenoids, is related. These assignments are based on 1D (1)H and (13)C NMR and on 2D NMR techniques including gCOSY, gHSQC, gHMBC, J-resolved and NOEDIF experiments. The unequivocal assignments were supported by theoretical chemical shifts and scalar coupling constant calculations at GIAO B3LYP/cc-pVDZ level from optimized structures at the same level of theory.     

Ion chemistry in germane/fluorocompounds gaseous mixtures: a mass spectrometric and theoretical study

The ion-molecule reactions occurring in GeH(4)/NF(3), GeH(4)/SF(6), and GeH(4)/SiF(4) gaseous mixtures have been investigated by ion trap mass spectrometry and ab initio calculations. While the NF(x)(+) (x=1-3) react with GeH(4) mainly by the exothermic charge transfer, the open-shell Ge(+) and GeH(2)(+) undergo the efficient F-atom abstraction from NF(3) and form GeF(+) and F-GeH(2)(+) as the only ionic products. The mechanisms of these two processes are quite similar and involve the formation of the fluorine-coordinated complexes Ge-F-NF(2)(+) and H(2)Ge-F-NF(2)(+), their subsequent crossing to the significantly more stable isomers FGe-NF(2)(+) and F-GeH(2)-NF(2)(+), and the eventual dissociation of these ions into GeF(+) (or F-GeH(2)(+)) and NF(2). The closed-shell GeH(+) and GeH(3)(+) are instead much less reactive towards NF(3), and the only observed process is the less efficient formation of GeF(+) from GeH(+). The theoretical investigation of this unusual H/F exchange reaction suggests the involvement of vibrationally-hot GeH(+). Passing from NF(3) to SF(6) and SiF(4), the average strength of the M-F bond increases from 70 to 79 and 142 kcal mol(-1), and in fact the only process observed by reacting GeH(n)(+) (n=0-3) with SF(6) and SiF(4) is the little efficient F-atom abstraction from SF(6) by Ge(+). Irrespective of the experimental conditions, we did not observe any ionic product of Ge-N, Ge-S, or Ge-Si connectivity. This is in line with the previously observed exclusive formation of GeF(+) from the reaction between Ge(+) and C-F compounds such as CH(3)F. Additionally observed processes include in particular the conceivable formation of the elusive thiohypofluorous acid FSH from the reaction between SF(+) and GeH(4).     

Gas-phase chemistry of ionized and protonated GeF4: a joint experimental and theoretical study

The gas-phase ion chemistry of GeF(4) and of its mixtures with water, ammonia and hydrocarbons was investigated by ion trap mass spectrometry (ITMS) and ab initio calculations. Under ITMS conditions, the only fragment detected from ionized GeF(4) is GeF(3)(+). This cation is a strong Lewis acid, able to react with H(2)O, NH(3) and the unsaturated C(2)H(2), C(2)H(4) and C(6)H(6) by addition-HF elimination reactions to form F(2)Ge(XH)(+), FGe(XH)(2)(+), Ge(XH)(3)(+) (X = OH or NH(2)), F(2)GeC(2)H(+), F(2)GeC(2)H(3)(+) and F(2)GeC(6)H(5)(+). The structure, stability and thermochemistry of these products and the mechanistic aspects of the exemplary reactions of GeF(3)(+) with H(2)O, NH(3) and C(6)H(6) were investigated by MP2 and coupled cluster calculations. The experimental proton affinity (PA) and gas basicity (GB) of GeF(4) were estimated as 121.5 ± 6.0 and 117.1 ± 6.0 kcal mol(-1), respectively, and GeF(4)H(+) was theoretically characterized as an ion-dipole complex between GeF(3)(+) and HF. Consistently, it reacts with simple inorganic and organic molecules to form GeF(3)(+)-L complexes (L = H(2)O, NH(3), C(2)H(2), C(2)H(4), C(6)H(6), CO(2), SO(2) and GeF(4)). The theoretical investigation of the stability of these ions with respect to GeF(3)(+) and L disclosed nearly linear correlations between their dissociation enthalpies and free energies and the PA and GB of L. Comparing the behavior of GeF(3)(+) with the previously investigated CF(3)(+) and SiF(3)(+) revealed a periodically reversed order of reactivity CF(3)(+) < GeF(3)(+) < SiF(3)(+). This parallels the order of the Lewis acidities of the three cations.     

Spin-spin and spin-orbit interactions in nanographene fragments: a quantum chemistry approach

The relativistic behavior of graphene structures, starting from the fundamental building blocks--the poly-aromatic hydrocarbons (PAHs) along with other PAH nanographenes--is studied to quantify any associated intrinsic magnetism in the triplet (T) state and subsequently in the ground singlet (S) state with account of possible S-T mixture induced by spin-orbit coupling (SOC). We employ a first principle quantum chemical-based approach and density functional theory (DFT) for a systematic treatment of the spin-Hamiltonian by considering both the spin-orbit and spin-spin interactions as dependent on different numbers of benzene rings. We assess these relativistic spin-coupling phenomena in terms of splitting parameters which cause magnetic anisotropy in absence of external perturbations. Possible routes for changes in the couplings in terms of doping and defects are also simulated and discussed. Accounting for the artificial character of the broken-symmetry solutions for strong spin polarization of the so-called "singlet open-shell" ground state in zigzag graphene nanoribbons predicted by spin-unrestricted DFT approaches, we interpolate results from more sophisticated methods for the S-T gaps and spin-orbit coupling (SOC) integrals and find that these spin interactions become weak as function of size and increasing decoupling of electrons at the edges. This leads to reduced electron spin-spin interaction and hence almost negligible intrinsic magnetism in the carbon-based PAHs and carbon nanographene fragments. Our results are in agreement with the fact that direct experimental evidence of edge magnetism in pristine graphene has been reported so far. We support the notion that magnetism in graphene only can be ascribed to structural defects or impurities.     

HPLC in clinical chemistry: Selected topics and clinical applications

Nowadays, HPLC is a very valuable tool in the clinical laboratory. In the future more and more HPLC methods will replace old photometric assays and also immunoassays, since these methods fulfill the claims in clinical chemistry: high precision, accuracy, sensitivity and specificity.     

O-H bond dissociation enthalpies of oximes: a theoretical assessment and experimental implications

By using a multilayer composite ab initio method ONION-G3B3, we calculated O-H bond dissociation enthalpies (BDEs) of 58 oximes that were measured experimentally. Experimental BDEs derived from thermal decomposition kinetics and calorimetric measurements were found to be consistent with the theory. However, the electrochemical method was found to give questionably high BDEs possibly due to errors in the measurement of pKa's or redox potentials. Subsequently, the performances of a variety of DFT functionals including B3LYP, B3P86, B3PW91, BHandH, BHandHLYP, BMK, PBE1PBE, MPW1KCIS, mPWPW91, MPW1B95, and MPW1K were tested to calculate oxime O-H BDEs, where ROBHandHLYP was found to be the most accurate. By using this method, we calculated O-H BDEs of over 140 oximes in a systematic fashion. All of the calculated O-H BDEs fell in the range from 76.8 to 89.8 kcal/mol. An amino group on the azomethine carbon was found to strengthen the O-H bond, whereas bulky alkyl substituents on oximes decreased O-H BDEs due to their large steric-strain-relieving effects in the process of O-H bond cleavage. Para substituents had little effect on the BDEs of benzaldoximes and phenyl methyl ketoximes. Finally, on the basis of a spin distribution calculation, aryl-, alkyl-, and carbonyl-substituted iminoxyl radicals were found to be sigma-radicals, whereas amino-substituted iminoxyl radicals were of pi-structure.     

On the influence of diameter and length on the properties of armchair single-walled carbon nanotubes: A theoretical chemistry approach

Open-ended fragments of armchair single-walled carbon nanotubes (n, n) with n = 3, 4, 5, and 6, have been modeled, with increasing lengths from 0.6 to 3 nm long. The geometries of all the studied fragments have been fully optimized. The influence of diameter and length on different electronic properties has been analyzed. These properties are electronegativity, ionization potential, electron affinities, and hardness, and all of them have been expressed as functions of the frontier orbitals. The binding energies per C atom have been calculated, using an expression that improves the previously reported ones. Their absolute values were found to steadily increase with tubes length and diameter, which allows extrapolations to obtain BE_/C atom for tubes of infinite length. The extrapolated values are 8.45, 8.65, 8.74, and 8.79 eV for armchair nanotubes with n = 3, 4, 5, and 6, respectively.     

Theoretical group 14 chemistry. Part 2. Si4R6: a theoretical approach

The relative energies of the isomeric compounds of Si₄R₆ (R=H, Me, Ph, 2,6-dimethylphenyl, 2,6-diisopropylphenyl) were explored with different theoretical methods including semiempirical, DFT and perturbation theory calculations. The results are compared with previous calculations and with experimental findings. On going from small substituents to bulky aryl groups the stability of the isomers is reversed from tetrasilabicyclo[1.1.0]butane (1) and tetrasilacyclobutene derivatives to the s-cis and s-trans conformers of tetrasilabuta-1,3-dienes. The concept of bond stretch isomerism of 1 and its dependence on the substituents at the central silicon atoms is also discussed.     

Machine learning simulation of pharmaceutical solubility in supercritical carbon dioxide: Prediction and experimental validation for busulfan drug

An artificial intelligence-based predictive model was developed using a support vector machine to investigate the solubility data of the drug Busulfan drug in supercritical carbon dioxide. The data for simulations were collected from literature. The model was trained and implemented in order to determine the correlation between the solubility values and the input parameters, namely, temperature and pressure. These parameters were used as the inputs as they are known to have a significant effect on the solubility of Busulfan in supercritical carbon dioxide. In the artificial intelligence model, a polynomial model with kernel function was applied to the data, and the model’s findings were compared with measured data for fitting. Good agreement was observed between the model’s outputs and the measured data with coefficient of determination greater than 0.99.     

Development of a Gas-Tight Syringe Headspace GC-FID Method for the Detection of Ethanol,and a Description of the Legal and Practical Framework for Its Analysis,in Samples of English and Welsh Motorists’ Blood and Urine

Ethanol is the most commonly used recreational drug worldwide. This study describes the development and validation of a headspace gas chromatography flame ionisation detection (HS-GC-FID) method using dual columns and detectors for simultaneous separation and quantitation. The use of a dual-column, dual-detector HS-GC-FID to quantitate ethanol is a common analytical technique in forensic toxicology; however, most analytical systems utilise pressure-balance injection rather than a simplified gas-tight syringe, as per this technique. This study is the first to develop and validate a technique that meets the specifications of the United Kingdom’s requirements for road traffic toxicology testing using a Shimadzu GC-2014 gas-tight syringe. The calibration ranged from 10 to 400 mg/100 mL, with a target minimum linearity of r2 > 0.999, using tertiary butanol as the internal standard marker. The method has an expanded uncertainty at 99.73% confidence of 3.64% at 80 mg/100 mL, which is the blood alcohol limit for drink driving in England and Wales. In addition, at 200 mg%—the limit at which a custodial sentence may be imposed on the defendant—the expanded uncertainty was 1.95%. For both the 80 mg% and 200 mg% concentrations, no bias was present in the analytical method. This method displays sufficient separation for other alcohols, such as methanol, isopropanol, acetaldehyde, and acetone. The validation of this technique complies with the recommended laboratory guidelines set out by United Kingdom and Ireland Association of Forensic Toxicologists (UKIAFT), the recently issued Laboratory 51 guidelines by the United Kingdom Accreditation Service (UKAS), and the criteria set out by the California Code of Regulations (CCR), 17 CCR § 1220.1.     

Binding of antitumor ruthenium complexes to DNA and proteins: a theoretical approach

The thermodynamics of the binding of the antitumor ammine, amine, and immine complexes of ruthenium(II) and ruthenium(III) to DNA and peptides was studied computationally using model molecules. We performed density functional calculations on several monofunctional ruthenium complexes of the formula [Ru(NH3)5B]z+, where B is an adenine, guanine, or cytosine nucleobase or an 4-methylimidazole, a dimethylthioether, or a dimethylphosphate anion and z = 2 and 3. The pentammineruthenium fragment has been intensively studied and also constitutes a good model for a wide class of antitumor ammine, amine, and imine complexes of Ru(II) and Ru(III), while the considered bases/ligands have been chosen as models for the main binding sites of DNA, nucleobases, and phosphate backbone and proteins, histidyl, and sulfur-containing residue such as methionine or cysteine. Bond dissociation enthalpies and free energies have been calculated for all the considered metal binding sites both in the gas phase and in solution and allow building a binding affinity order for the considered nucleic acid or protein binding sites. The binding of guanine to some bifunctional complexes, [Ru(NH3)(4)Cl2], [cis-RuCl(2)(bpy)2], and [cis-RuCl(2)(azpy)2], has also been considered to evaluate the effect of a second labile chloro or aquo ligand and more realistic polypyridyl and arylazopyridine ligands.     

Kinetic Modeling and Parameter Estimation in a Tower Bioreactor for Bioethanol Production

In this work, a systematic method to support the building of bioprocess models through the use of different optimization techniques is presented. The method was applied to a tower bioreactor for bioethanol production with immobilized cells of Saccharomyces cerevisiae. Specifically, a step-by-step procedure to the estimation problem is proposed. As the first step, the potential of global searching of real-coded genetic algorithm (RGA) was applied for simultaneous estimation of the parameters. Subsequently, the most significant parameters were identified using the Placket–Burman (PB) design. Finally, the quasi-Newton algorithm (QN) was used for optimization of the most significant parameters, near the global optimum region, as the initial values were already determined by the RGA global-searching algorithm. The results have shown that the performance of the estimation procedure applied in a deterministic detailed model to describe the experimental data is improved using the proposed method (RGA–PB–QN) in comparison with a model whose parameters were only optimized by RGA.