QuickFF: A program for a quick and easy derivation of force fields for metal‐organic frameworks from ab initio input

QuickFF is a software package to derive accurate force fields for isolated and complex molecular systems in a quick and easy manner. Apart from its general applicability, the program has been designed to generate force fields for metal‐organic frameworks in an automated fashion. The force field parameters for the covalent interaction are derived from ab initio data. The mathematical expression of the covalent energy is kept simple to ensure robustness and to avoid fitting deficiencies as much as possible. The user needs to produce an equilibrium structure and a Hessian matrix for one or more building units. Afterward, a force field is generated for the system using a three‐step method implemented in QuickFF. The first two steps of the methodology are designed to minimize correlations among the force field parameters. In the last step, the parameters are refined by imposing the force field parameters to reproduce the ab initio Hessian matrix in Cartesian coordinate space as accurate as possible. The method is applied on a set of 1000 organic molecules to show the easiness of the software protocol. To illustrate its application to metal‐organic frameworks (MOFs), QuickFF is used to determine force fields for MIL‐53(Al) and MOF‐5. For both materials, accurate force fields were already generated in literature but they requested a lot of manual interventions. QuickFF is a tool that can easily be used by anyone with a basic knowledge of performing ab initio calculations. As a result, accurate force fields are generated with minimal effort. © 2015 Wiley Periodicals, Inc.     

Crassiflorone, a new naphthoquinone from Diospyros crassiflora (Hien)

A new naphthoquinone, 11-hydroxy-1,9-dimethyl-6H-naphtho[2′,3′:4,5]furo[3,2-c]chromene-6,7,12-trione, named crassiflorone, was isolated from the stem bark of Diospyros crassiflora together with the known compounds plumbagin, cyclocanaliculatin, gerberinol, lupeol, lupenone and betulinic acid. The structures of the compounds were established on the basis of 1D and 2D NMR spectroscopic data, as well as co-TLC with authentic samples. Some of the above compounds exhibited significant antimicrobial activity against bacteria and yeasts.     

Effect of temperature on carbon-black agglomeration in hydrocarbon liquid with adsorbed dispersant

Suspensions of carbon black in oil, stabilized with adsorbed polyisobutylene succinimide (PIBSI) dispersant, are commonly used as model systems for investigating the soot-handling characteristics of motor oils. The structure of the carbon-black agglomerates changes dramatically with temperature; this results in a concomitant change in the suspension rheology. Linear and nonlinear rheological experiments indicate a large increase of the interparticle attractions as the temperature is raised. To elucidate the origin of this behavior, we investigate the effect of temperature on the stabilizing effect of the dispersant. Measurements of adsorption isotherms of the dispersant on carbon black indicate that there is little variation of the binding energy with temperature. Intrinsic viscosity measurements of PIBSI dispersants in solution clearly exhibit an inverse dependence of the dispersant chain dimension with temperature. These results suggest that the temperature-dependent changes in the chain conformation of the PIBSI dispersant are primarily responsible for the changes in the dispersion rheology, and we propose a simple model to account for these data.     

Regio- and stereospecific ring opening of 1,1-dialkyl-2-(aryloxymethyl)aziridinium salts by bromide

Enantiomerically pure 2-(aryloxymethyl)aziridines are efficiently transformed into chiral N-(2-bromo-3-aryloxypropyl)amines via a regio- and stereospecific ring opening of the intermediate aziridinium salts, and the experimental results are rationalized on the basis of some high level ab initio calculations.     

Data-mining the diaryl(thio)urea conformational landscape: Understanding the contrasting behavior of ureas and thioureas with quantum chemistry

The conformations adopted by urea and thiourea functional groups influence catalysis and binding. We combine data-mining with quantum chemical calculations to understand the differences in conformational behavior for these two important structural motifs. We developed a Python tool to automate the compilation of X-ray structural information and perform conformational clustering and visualization, based on SMILES input. While diarylureas have an overwhelming preference for the anti,anti-conformer, diarylthioureas adopt a mixture of anti,anti- and anti,syn-conformers. Computations show the anti,anti-thiourea conformer is destabilized by out-of-plane rotations which avoid a steric clash with the sulfur atom. These conformational preferences were studied computationally under a variety of conditions, and apart from in the gas-phase, a preference for anti,anti-ureas was found. Consistent with experiments, this preference increases in more polar environments. Quantitative predicted ratios are sensitive to the computational treatment of solvation effects, with COSMO-RS giving more realistic amounts of the anti,anti-conformer in THF and DMSO.     

Carbon‐Centered Radical Addition and β‐Scission Reactions: Modeling of Activation Energies and Pre‐exponential Factors

A consistent set of group additive values ΔGAV° for 46 groups is derived, allowing the calculation of rate coefficients for hydrocarbon radical additions and β-scission reactions. A database of 51 rate coefficients based on CBS-QB3 calculations with corrections for hindered internal rotation was used as training set. The results of this computational method agree well with experimentally observed rate coefficients with a mean factor of deviation of 3, as benchmarked on a set of nine reactions. The temperature dependence on the resulting ΔGAV°s in the broad range of 300–1300 K is limited to ±4.5 kJ mol⁻¹ on activation energies and to ±0.4 on logA (A: pre-exponential factor) for 90 % of the groups. Validation of the ΔGAV°s was performed for a test set of 13 reactions. In the absence of severe steric hindrance and resonance effects in the transition state, the rate coefficients predicted by group additivity are within a factor of 3 of the CBS-QB3 ab initio rate coefficients for more than 90 % of the reactions in the test set. It can thus be expected that in most cases the GA method performs even better than standard DFT calculations for which a deviation factor of 10 is generally considered to be acceptable.     

A DFT‐Based Investigation of Hydrogen Abstraction Reactions from Methylated Polycyclic Aromatic Hydrocarbons

The growth of polycyclic aromatic hydrocarbons (PAHs) is in many areas of combustion and pyrolysis of hydrocarbons an inconvenient side effect that warrants an extensive investigation of the underlying reaction mechanism, which is known to be a cascade of radical reactions. Herein, the focus lies on one of the key reaction classes within the coke formation process: hydrogen abstraction reactions induced by a methyl radical from methylated benzenoid species. It has been shown previously that hydrogen abstractions determine the global PAH formation rate. In particular, the influence of the polyaromatic environment on the thermodynamic and kinetic properties is the subject of a thorough exploration. Reaction enthalpies at 298 K, reaction barriers at 0 K, rate constants, and kinetic parameters (within the temperature interval 700–1100 K) are calculated by using B3LYP/6‐31+G(d,p) geometries and BMK/6‐311+G(3df,2p) single‐point energies. This level of theory has been validated with available experimental data for the abstraction at toluene. The enhanced stability of the product benzylic radicals and its influence on the reaction enthalpies is highlighted. Corrections for tunneling effects and hindered (or free) rotations of the methyl group are taken into account. The largest spreading in thermochemical and kinetic data is observed in the series of linear acenes, and a normal reactivity–enthalpy relationship is obtained. The abstraction of a methyl hydrogen atom at one of the center rings of large methylated acenes is largely preferred. Geometrical and electronic aspects lie at the basis of this striking feature. Comparison with hydrogen abstractions leading to arylic radicals is also made.     

Experimental and computational study of the conrotatory ring opening of various 3-chloro-2-azetines

A combined experimental and theoretical study is presented on 2-azetines, a class of azaheterocyclic compounds, which are difficult to access but have shown a unique reactivity as strained cyclic enamines. New highly substituted 2-azetines bearing aryl substituents at the 2- and 4-position were synthesized from 3,3-dichloroazetidines. Whereas 2-aryl-3,3-dichloroazetidines gave stable 2-aryl-3-chloro-2-azetines upon treatment with sodium hydride in DMSO, 2,4-diaryl-3,3-dichloroazetidines showed a remarkably different reactivity in that they afforded benzimidoyl-substituted alkynes under similar mild treatment with base. The formation of the alkynes involves electrocyclic ring opening of intermediate 2,4-diaryl-3-chloro-2-azetines and elimination of hydrogen chloride. Ab initio theoretical calculations confirmed the experimental findings and demonstrated that the 4-aryl substituent is responsible for this remarkably enhanced reactivity of 2-azetines toward electrocyclic conrotatory ring opening by a significant decrease in reaction barrier of about 30 kJ/mol. This activation effect by an aryl group in the allylic position toward electrocyclic ring opening of unsaturated four-membered rings is of general importance since a similar increased reactivity of 4-aryloxetes, 4-arylthiete-1,1-dioxides, and 3-arylcyclobutenes has been reported in literature as well.     

SU-8 as a structural material for labs-on-chips and microelectromechanical systems

Since its introduction in the nineties, the negative resist SU-8 has been increasingly used in micro- and nanotechnologies. SU-8 has made the fabrication of high-aspect ratio structures accessible to labs with no high-end facilities such as X-ray lithography systems or deep reactive ion etching systems. These low-cost techniques have been applied not only in the fabrication of metallic parts or molds, but also in numerous other micromachining processes. Its ease of use has made SU-8 to be used in many applications, even when high-aspect ratios are not required. Beyond these pattern transfer applications, SU-8 has been used directly as a structural material for microelectromechanical systems and microfluidics due to its properties such as its excellent chemical resistance or the low Young modulus. In contrast to conventional resists, which are used temporally, SU-8 has been used as a permanent building material to fabricate microcomponents such as cantilevers, membranes, and microchannels. SU-8-based techniques have led to new low-temperature processes suitable for the fabrication of a wide range of objects, from the single component to the complete lab-on-chip. First, this article aims to review the different techniques and provides guidelines to the use of SU-8 as a structural material. Second, practical examples from our respective labs are presented.