Modeling pi-pi interactions with the effective fragment potential method: the benzene dimer and substituents

This study compares the results of the general effective fragment potential (EFP2) method to the results of a previous combined coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] and symmetry-adapted perturbation theory (SAPT) study [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690] on substituent effects in pi-pi interactions. EFP2 is found to accurately model the binding energies of the benzene-benzene, benzene-phenol, benzene-toluene, benzene-fluorobenzene, and benzene-benzonitrile dimers, as compared with high-level methods [Sinnokrot and Sherrill, J. Am. Chem. Soc., 2004, 126, 7690], but at a fraction of the computational cost of CCSD(T). In addition, an EFP-based Monte Carlo/simulated annealing study was undertaken to examine the potential energy surface of the substituted dimers.     

Vibrational characterization of the 1:1 iodine-benzene complex isolated in solid krypton

The structure and properties of a 1:1 iodine-benzene complex isolated in an inert krypton matrix at low temperature have been studied with infrared and resonance Raman spectroscopy and with MP2 calculations. The structure of the ground-state complex is found to be unsymmetric, and the I-I vibrational frequency is found to be red-shifted by 3.94 cm(-1) upon complexation. The experimental data agree well with computational results, leading to the conclusion that the I2-Bz complex structure is not axial but of above-bond type, identically with other halogen-benzene complexes.     

Mechanism and stem-cell activity of 5-carboxycytosine decarboxylation determined by isotope tracing

Eraserhead: Stem cells seem to erase epigenetic information by decarboxylation of the newly discovered epigenetic base 5-carboxycytosine (caC; see picture). This reaction is likely to involve a nucleophilic attack of the C5-C6 double bond.     

Synthesis of Polycyclic Aromatic Hydrocarbon‐Based Nanovehicles Equipped with Triptycene Wheels

Two new nanovehicles that have extended aromatic platforms as the cargo zones have been obtained. Two strategies were considered for the formation of the perylene core from two naphthalene precursors. The first was based on a Scholl‐type reaction involving an oxidant, and the second used a brominated derivative to perform a homocoupling reaction. The first strategy failed under diverse coupling conditions in the presence of several strong oxidants. Nevertheless, the use of CoF₃ in trifluoroacetic acid triggered a dimerization reaction between two ester groups of one molecule and the naphthalene unit of another, thereby surprisingly yielding a ten‐membered carbon macrocycle. The second strategy encountered a lack of reactivity of the substrate under several homocoupling conditions. The dimerization was not easily performed but Ullmann‐type conditions ultimately gave the expected product. The low yield and low solubility of the product encouraged us to modify our initial design. The synthesis of a new chassis that incorporated additional tert‐butyl groups improved the solubility of the molecules and also prevented overcyclization of the aromatic platform by blocking these positions. Some p‐phenylene spacers were also intercalated between the iodine and perylene centers to increase the reactivity of the halide towards coupling reactions. Two new chassis were obtained by Scholl‐type oxidative coupling using FeCl₃ as the oxidant. The introduction of four triptycene wheels allowed the formation of the two corresponding nanovehicles.     

A convenient iodination of indoles and derivatives

We report a direct iodination of indole and derivative compounds with iodine monochloride (ICl) in the presence of Celite^®. This procedure has now been extended to the iodination of substituted indoles, azaindoles and pyrroles. The scope of this procedure is exemplified by the iodination of melatonin in 98% yield.     

A priori and a posteriori estimates for three‐dimensional Stokes equations with nonstandard boundary conditions

In this article, we study the Stokes problem with some nonstandard boundary conditions. The variational formulation decouples into a system for the velocity and a Poisson equation for the pressure. The corresponding discrete system do not need an inf‐sup condition. Hence, the velocity is approximated with “ curl ” conforming finite elements and the pressure with standard continuous elements. Next, we establish optimal a priori and a posteriori estimates and we finally concluded with numerical tests. © 2011 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2012     

Highly sensitive sensory materials for fluoride ions based on the dithieno[3,2-b:2',3'-d]phosphole system

[structure: see text]. The newly developed functionalization of an unsubstituted dithieno[3,2-b:2',3'-d]phosphole at the 5,5'-positions gives access to bis(pinacoleboryl) species that can be utilized as sensory materials for fluoride ions. The fluoride-triggered response of the air- and moisture-stable boryl-functionalized dithienophosphole oxide manifests itself in the generation of a new fluorescence emission that can be detected at very low analyte concentrations (ppm) or even with the naked eye upon irradiation with UV light (366 nm).     

Time-dependent alignment of molecules trapped in octahedral crystal fields

The hindered rotational states of molecules confined in crystal fields of octahedral symmetry, and their time-dependent alignment obtained by pulsed nonresonant laser fields, are studied computationally. The control over the molecular axis direction is discussed based on the evolution of the rotational wave packet generated in the cubic crystal-field potential. The alignment degree obtained in a cooperative case, where the alignment field is applied in a favorable crystal-field direction, or in a competitive direction, where the crystal field has a saddle point, is presented. The investigation is divided into two time regimes where the pulse duration is either ultrashort, leading to nonadiabatic dynamics, or long with respect to period of molecular libration, which leads to synchronous alignment due to nearly adiabatic following. The results are contrasted to existing gas phase studies. In particular, the irregularity of the crystal-field energies leads to persistent interference patterns in the alignment signals. The use of nonadiabatic alignment for interrogation of crystal-field energetics and the use of adiabatic alignment for directional control of molecular dynamics in solids are proposed as practical applications.     

Examining Supervised Machine Learning Methods for Integer Link Weight Prediction Using Node Metadata

With the goal of understanding if the information contained in node metadata can help in the task of link weight prediction, we investigate herein whether incorporating it as a similarity feature (referred to as metadata similarity) between end nodes of a link improves the prediction accuracy of common supervised machine learning methods. In contrast with previous works, instead of normalizing the link weights, we treat them as count variables representing the number of interactions between end nodes, as this is a natural representation for many datasets in the literature. In this preliminary study, we find no significant evidence that metadata similarity improved the prediction accuracy of the four empirical datasets studied. To further explore the role of node metadata in weight prediction, we synthesized weights to analyze the extreme case where the weights depend solely on the metadata of the end nodes, while encoding different relationships between them using logical operators in the generation process. Under these conditions, the random forest method performed significantly better than other methods in 99.07% of cases, though the prediction accuracy was significantly degraded for the methods analyzed in comparison to the experiments with the original weights.