Extending conceptual DFT to include external variables: the influence of magnetic fields

An extension of conceptual DFT to include the influence of an external magnetic field is proposed in the context of a program set up to cope with the ever increasing variability of reaction conditions and concomitant reactivity. The two simplest global reactivity descriptors, the electronic chemical potential (μ) and the hardness (η), are considered for the main group atoms H-Kr using current density-functional theory. The magnetic field strength, |B|, is varied between 0.0 and 1.0 B0 = ħe−1a0−2 ≈ 2.3505 × 105 T, encompassing the Coulomb and intermediate regimes. The carbon atom is studied as an exemplar system to gain insight into the behaviour of the neutral, cationic and anionic species under these conditions. Their electronic configurations change with increasing |B|, leading to a piecewise behaviour of the ionization energy (I) and electron affinity (A) values as a function of |B|. This results in complex behaviour of properties such as the electronegativity χ = −1/2(I + A) = −μ and hardness η = 1/2(I − A). This raises an interesting question: to what extent are atomic properties periodic in the presence of a magnetic field? In the Coulomb regime, close to |B| = 0, we find the familiar periodicity of the atomic properties, and make the connections to response functions central to conceptual DFT. However, as the field increases in the intermediate regime configurational changes of the atomic species lead to discontinuous changes in their properties; fundamentally changing their behaviour, which is illustrated by constructing a periodic table of χ and η values at |B| = 0.5 B0. These values tend to increase for groups 1-2 and decrease for groups 16-18, leading to a narrower range overall and suggesting substantial changes in the chemistry of the main group elements. Changes within each group are also examined as a function of |B|. These are more complex to interpret due to the larger number of configurations accessible to heavier elements at high field. This is illustrated for group 17 where Cl and Br have qualitatively different configurations to their lighter cogener at |B| = 0.5 B0. The insight into periodic trends in strong magnetic fields may provide a crucial starting point for predicting chemical reactivity under these exotic conditions

Molecular charge distributions in strong magnetic fields: a conceptual and current DFT study

The effect of strong magnetic fields on the charge distribution of the hydrogen halides, H2O and NH3 is studied in the context of recent extensions of conceptual density functional theory to include additional variables such as external magnetic fields. From conceptual DFT studies on atoms in strong magnetic fields, changes in electronegativity and hardness suggest a reversal in polarity for all three diatomic molecules under these conditions. This is confirmed by current DFT calculations on these molecules in the presence of strong magnetic fields parallel and perpendicular to the internuclear axis; in the former case the electric dipole moment only undergoes small changes whereas in the latter case it changes significantly and also reverses in direction, doing so at lower field strength if the geometry is relaxed. The absence of a dipole moment induced perpendicular to the bond when a magnetic field is applied in this direction is understood by consideration of time reversal symmetry. Similar results are obtained for H2O and NH3; this may be an important point to consider in future studies focused on the unresolved question on the behaviour of hydrogen bonding in applied magnetic fields

Национально-психологические особенности иностранных учащихся начального этапа обучения

In recent years, a considerable interest has grown in the design of molecular nanowires with an increasing conductance with length. The development of such nanowires is highly desirable because they could play an important role in future molecular-scale circuitry. Whereas the first experimental observation of this nonclassical behavior still has to be realized, a growing number of candidate wires have been proposed theoretically. In this Letter, we point out that all the wires with an anti-Ohmic increasing conductance with length proposed so far share a common characteristic: their diradical character increases with length. The conceptual connection between diradical character and conductance enables a systematic design of such anti-Ohmic wires and explains the difficulty in their syntheses. A strategy is proposed to balance the stability and conductance so that this nonclassical phenomenon can be observed

Учебный план УВО

This review sets out to understand the reactivity of diradicals and how that may differ from monoradicals. In the first part of the review, we delineate the electronic structure of a diradical with its two degenerate or nearly degenerate molecular orbitals, occupied by two electrons. A classification of diradicals based on whether or not the two SOMOs can be located on different sites of the molecule is useful in determining the ground state spin. Important is a delocalized to localized orbital transformation that interchanges "closed-shell" to "open-shell" descriptions. The resulting duality is useful in understanding the dual reactivity of singlet diradicals. In the second part of the review, we examine, with a consistent level of theory, activation energies of prototypical radical reactions (dimerization, hydrogen abstraction, and addition to ethylene) for representative organic diradicals and diradicaloids in their two lowest spin states. Differences and similarities in reactivity of diradicals vs monoradicals, based on either a localized or delocalized view, whichever is suitable, are then discussed. The last part of this review begins with an extensive, comparative, and critical survey of available measures of diradical character and ends with an analysis of the consequences of diradical character for selected diradicaloids

A Micro-Costing Framework for Circulating Tumor DNA Testing in Dutch Clinical Practice

Circulating tumor DNA (ctDNA) is a promising new biomarker with multiple potential applications in cancer care. Estimating total cost of ctDNA testing is necessary for reimbursement and implementation, but challenging because of variations in workflow. We aimed to develop a micro-costing framework for consistent cost calculation of ctDNA testing. First, the foundation of the framework was built, based on the complete step-wise diagnostic workflow of ctDNA testing. Second, the costing method was set up, including costs for personnel, materials, equipment, overhead, and failures. Third, the framework was evaluated by experts and applied to six case studies, including PCR-, mass spectrometry–, and next-generation sequencing–based platforms, from three Dutch hospitals. The developed ctDNA micro-costing framework includes the diagnostic workflow from blood sample collection to diagnostic test result. The framework was developed from a Dutch perspective and takes testing volume into account. An open access tool is provided to allow for laboratory-specific calculations to explore the total costs of ctDNA testing specific workflow parameters matching the setting of interest. It also allows to straightforwardly assess the impact of alternative prices or assumptions on the cost per sample by simply varying the input parameters. The case studies showed a wide range of costs, from €168 to €7638 ($199 to$9124) per sample, and generated information. These costs are sensitive to the (coverage of) platform, setting, and testing volume

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

Asymptomatic bacteriuria may be considered a complication in women with diabetes

WSTĘP. Celem pracy jest ocena częstości występowania oraz czynników ryzyka bezobjawowej bakteriurii (ASB, asymptomatic bacteriuria) u kobiet bez cukrzycy i chorych na cukrzycę. MATERIAŁ I METODY. Do badania włączono 636 kobiet chorych na cukrzycę (typu 1 i 2) w wieku 18&#8211;75 lat, które w tym czasie nie były w ciąży i nie występowały u nich zaburzenia układu moczowego, oraz 153 kobiety bez cukrzycy, które zgłosiły się do okulisty lub do lekarza innej specjalności w celu leczenia urazów (jako grupa kontrolna). Bezobjawową bakteriurę zdefiniowano jako obecność co najmniej 105 bakterii na ml jednego lub dwóch rodzajów tworzących kolonie, wyhodowanych z czystego, środkowego strumienia moczu osoby bez objawów zakażenia dróg moczowych (UTI, urinary tract infection). WYNIKI. Bezobjawowa bakteriuria występowała u 26% kobiet chorych na cukrzycę i u 6% kobiet bez cukrzycy (p < 0,001). Częstość ASB u kobiet chorych na cukrzycę typu 1 wyniosła 21%. Czynniki ryzyka ASB w cukrzycy typu 1 to: dłuższy czas trwania choroby, neuropatia obwodowa i makroalbuminuria. U kobiet chorych na cukrzycę typu 2 ASB występowała w 29% przypadków. Czynniki ryzyka ASB w cukrzycy typu 2 to: wiek, makroalbuminuria, niższy wskaźnik BMI oraz przebyte w poprzednim roku zakażenie dróg moczowych. Nie stwierdzono związku między aktualnym poziomem HbA1c i obecnością ASB. WNIOSKI. Częstość ASB jest większa u kobiet chorych na cukrzycę niż bez cukrzycy i schorzenie to można uznać za jedno z powikłań cukrzycy u kobiet.OBJECTIVE. To study the prevalence of and risk factors for asymptomatic bacteriuria (ASB) in women with and without diabetes. RESEARCH DESIGN AND METHODS. A total of 636 nonpregnant women with diabetes (type 1 and type 2) who were 18&#150;75 years of age and had no abnormalities of the urinary tract, and 153 women without diabetes who were visiting the eye and trauma outpatient clinic (control subjects) were included. We defined ASB as the presence of at least 105 colony-forming units/ml of 1 or 2 bacterial species in a culture of clean-voided midstream urine from an individual without symptoms of a urinary tract infection (UTI). RESULTS. The prevalence of ASB was 26% in the diabetic women and 6% in the control subjects (P < 0.001). The prevalence of ASB in women with type 1 diabetes was 21%. Risk factors for ASB in type 1 diabetic women included a longer duration of diabetes, peripheral neuropathy, and macroalbuminuria. The prevalence of ASB was 29% in women with type 2 diabetes. Risk factors for ASB in type 2 diabetic women included age, macroalbuminuria, a lower BMI, and a UTI during the previous year. No association was evident between current HbA1c level and the presence of ASB. CONCLUSIONS. The prevalence of ASB is increased in women with diabetes and might be added to the list of diabetic complications in these women

Dutch National Round Robin Trial on Plasma-Derived Circulating Cell-Free DNA Extraction Methods Routinely Used in Clinical Pathology for Molecular Tumor Profiling

BACKGROUND: Efficient recovery of circulating tumor DNA (ctDNA) depends on the quantity and quality of circulating cell-free DNA (ccfDNA). Here, we evaluated whether various ccfDNA extraction methods routinely applied in Dutch laboratories affect ccfDNA yield, ccfDNA integrity, and mutant ctDNA detection, using identical lung cancer patient-derived plasma samples. METHODS: Aliquots of 4 high-volume diagnostic leukapheresis plasma samples and one artificial reference plasma sample with predetermined tumor-derived mutations were distributed among 14 Dutch laboratories. Extractions of ccfDNA were performed according to local routine standard operating procedures and were analyzed at a central reference laboratory for mutant detection and assessment of ccfDNA quantity and integrity. RESULTS: Mutant molecule levels in extracted ccfDNA samples varied considerably between laboratories, but there was no indication of consistent above or below average performance. Compared to silica membrane-based methods, samples extracted with magnetic beads-based kits revealed an overall lower total ccfDNA yield (-29%; P < 0.0001) and recovered fewer mutant molecules (-41%; P < 0.01). The variant allelic frequency and sample integrity were similar. In samples with a higher-than-average total ccfDNA yield, an augmented recovery of mutant molecules was observed. CONCLUSIONS: In the Netherlands, we encountered diversity in preanalytical workflows with potential consequences on mutant ctDNA detection in clinical practice. Silica membrane-based methodologies resulted in the highest total ccfDNA yield and are therefore preferred to detect low copy numbers of relevant mutations. Harmonization of the extraction workflow for accurate quantification and sensitive detection is required to prevent introduction of technical divergence in the preanalytical phase and reduce interlaboratory discrepancies

How Thioredoxin Dissociates Its Mixed Disulfide

The dissociation mechanism of the thioredoxin (Trx) mixed disulfide complexes is unknown and has been debated for more than twenty years. Specifically, opposing arguments for the activation of the nucleophilic cysteine as a thiolate during the dissociation of the complex have been put forward. As a key model, the complex between Trx and its endogenous substrate, arsenate reductase (ArsC), was used. In this structure, a Cys29Trx-Cys89ArsC intermediate disulfide is formed by the nucleophilic attack of Cys29Trx on the exposed Cys82ArsC-Cys89ArsC in oxidized ArsC. With theoretical reactivity analysis, molecular dynamics simulations, and biochemical complex formation experiments with Cys-mutants, Trx mixed disulfide dissociation was studied. We observed that the conformational changes around the intermediate disulfide bring Cys32Trx in contact with Cys29Trx. Cys32Trx is activated for its nucleophilic attack by hydrogen bonds, and Cys32Trx is found to be more reactive than Cys82ArsC. Additionally, Cys32Trx directs its nucleophilic attack on the more susceptible Cys29Trx and not on Cys89ArsC. This multidisciplinary approach provides fresh insights into a universal thiol/disulfide exchange reaction mechanism that results in reduced substrate and oxidized Trx

Why Are Outcomes Different for Registry Patients Enrolled Prospectively and Retrospectively? Insights from the Global Anticoagulant Registry in the FIELD-Atrial Fibrillation (GARFIELD-AF).

Background: Retrospective and prospective observational studies are designed to reflect real-world evidence on clinical practice, but can yield conflicting results. The GARFIELD-AF Registry includes both methods of enrolment and allows analysis of differences in patient characteristics and outcomes that may result. Methods and Results: Patients with atrial fibrillation (AF) and ≥1 risk factor for stroke at diagnosis of AF were recruited either retrospectively (n = 5069) or prospectively (n = 5501) from 19 countries and then followed prospectively. The retrospectively enrolled cohort comprised patients with established AF (for a least 6, and up to 24 months before enrolment), who were identified retrospectively (and baseline and partial follow-up data were collected from the emedical records) and then followed prospectively between 0-18 months (such that the total time of follow-up was 24 months; data collection Dec-2009 and Oct-2010). In the prospectively enrolled cohort, patients with newly diagnosed AF (≤6 weeks after diagnosis) were recruited between Mar-2010 and Oct-2011 and were followed for 24 months after enrolment. Differences between the cohorts were observed in clinical characteristics, including type of AF, stroke prevention strategies, and event rates. More patients in the retrospectively identified cohort received vitamin K antagonists (62.1% vs. 53.2%) and fewer received non-vitamin K oral anticoagulants (1.8% vs . 4.2%). All-cause mortality rates per 100 person-years during the prospective follow-up (starting the first study visit up to 1 year) were significantly lower in the retrospective than prospectively identified cohort (3.04 [95% CI 2.51 to 3.67] vs . 4.05 [95% CI 3.53 to 4.63]; p = 0.016). Conclusions: Interpretations of data from registries that aim to evaluate the characteristics and outcomes of patients with AF must take account of differences in registry design and the impact of recall bias and survivorship bias that is incurred with retrospective enrolment. Clinical Trial Registration: - URL: http://www.clinicaltrials.gov . Unique identifier for GARFIELD-AF (NCT01090362)