Model management systems: A survey

This paper provides a survey of model management literature within the mathematical modeling domain. The first part of the survey is a review and a summary of the literature. After giving some basic definitions of modeling, modeling life cycle, and model management, two representative algebraic modeling languages followed by three approaches to modeling are introduced. These approaches are database, graph-based, and knowledge-based. The discussion is followed by a review of two specialized model management systems. The second part of the survey is a categorization of various modeling systems based on the modeling functions they provide and some of their features. These functions include life cycle support and model base administration. The degree of model independence provided by model management systems and the implemented environment systems is also summarized. The last part of the paper provides directions for future research.     

Hierarchical equations of motion in the Libra software package

We report the implementation of a hierarchical equations of motion (HEOM) module within the open-source Libra software. It includes the standard and scaled HEOM algorithms for computing the dynamics of open quantum systems interacting with a harmonic bath. The module allows the computing of the evolution of the reduced density matrix, as well as spectral lineshapes. The truncation, filtering, and “update list” schemes, as well as OpenMP parallelization, allow for further computational saving. The package is written in a mix of C++ and Python languages, delivering the best compromise between user friendliness and efficiency. The Python layer of the package takes advantage of standard Python libraries, such as h5py, which allows efficient storage and retrieval of the generated results. The package can be seamlessly used within Jupyter notebooks; its careful design shall provide the maximal convenience and intuitiveness to its users.     

Chloride anion triggered motion in a bis-imidazolium rotaxane

We report the first bis-imidazolium-containing rotaxane, synthesised via anion templated self-assembly. Its co-conformation is controlled by a chloride anion recognition mechanism, thus demonstrating the viability of this protocol as a stimulus for shuttling molecular motion.     

Development and optimization of an LC-MS/MS-based method for simultaneous quantification of vitamin D2 , vitamin D3 , 25-hydroxyvitamin D2 and 25-hydroxyvitamin D3

Simultaneous and accurate measurement of vitamin D and 25-hydroxyvitamin D in biological samples is a barrier limiting our ability to define "optimal" vitamin D status. Thus, our goal was to optimize conditions and evaluate an LC-MS method for simultaneous detection and quantification of vitamin D(2) , vitamin D(3) , 25-hydroxyvitamin D(2) and 25-hydroxyvitamin D(3) in serum. Extraction and separation of vitamin D forms were achieved using acetone liquid-liquid extraction and by a reversed phase C8 column, respectively. Detection was performed on a triple quadrupole tandem mass spectrometer (QQQ-MS/MS) equipped with atmospheric pressure photo ionization source. The LOQs for all analytes tested were 1 ng/mL for hydroxylated molecules and 2 ng/mL for the parent vitamin Ds. RSD at lower LOQ (2 ng/mL) and in medium (80 ng/mL) and high (200 ng/mL) quality control samples did not exceed 20 and 15% CV, respectively. Accuracy of the method for determination of hydroxylated molecules was also validated using National Institutes of Standards and Technology standard samples and found to be in the range of 90.9-111.2%. In summary, a sensitive and reproducible method is reported for simultaneous quantification of vitamin D(2) , vitamin D(3) , 25-hydroxyvitamin D(2) and 25-hydroxyvitamin D(3) molecules in biological samples.     

Organocatalyzed enantioselective fluorocyclizations

Enantioenriched fluorinated heterocycles can be prepared through fluorocyclizations of prochiral indoles (see scheme; Ts=tosyl, Bn=benzyl, Boc=tert-butoxycarbonyl). More than twenty examples for this cascade fluorination-cyclization, which is catalyzed by cinchona alkaloids and employs N-fluorobenzenesulfonimide as the electrophilic fluorine source have been explored, and an unprecedented catalytic asymmetric difluorocyclization has also been identified.     

Responses to unsaturation in iridium mono(N-heterocyclic carbene) complexes: synthesis and oligomerization of [LIr(H)2Cl] and [LIr(H)2]+

Highly unsaturated mono(N-heterocyclic carbene) Ir(iii) systems have been targeted via ligand abstraction protocols. Hydrogenation of Ir(IPr)(cod)Cl (1a) leads to the formation of the highly reactive (fluxional) trimer [Ir(IPr)(H)(2)Cl](3), while the related IMes system undergoes further C-H bond activation. Chloride abstraction from 1a prior to hydrogenation allows access to sources of the 12-electron [Ir(IPr)(H)(2)](+) fragment, which, in the absence of a suitable donor, dimerizes to give [{Ir(IPr)(H)(μ-H)}(2)](2+).     

Steric effects control self-sorting in self-assembled clusters

Endohedrally functionalized bis(pyridine) ligands show the ability to self-discriminate when treated with coordinating metals to form self-assembled clusters. Self-sorting between components is controlled by substitution on the interior of the complex. Tuning the size of the internal substituent allows selective heterocluster formation, determined by noncovalent and space-filling interactions. This novel method of self-sorting allows discrimination between ligands of identical geometry and donor type.