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HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade. [ABSTRACT FROM AUTHOR]

The influence of fluctuating charges or charge flow on the dynamic linear response properties of isolated molecules from the TS42 database is evaluated, with particular emphasis on dipole polarizability and C6 dispersion coefficients. Two new descriptors are defined to quantify the charge-flow contribution to response properties, making use of the recoupled dipole polarizability to separate isotropic and anisotropic components. Molecular polarizabilities are calculated using the "frequency-dependent atom-condensed Kohn–Sham density functional theory approximated to second order," i.e., the ACKS2ω model. With ACKS2ω, the charge-flow contribution can be constructed in two conceptually distinct ways that appear to yield compatible results. The charge-flow contribution is significantly affected by molecular geometry and the presence of polarizable bonds, in line with previous studies. We show that the charge-flow contribution qualitatively reproduces the polarizability anisotropy. The contribution to the anisotropic C6 coefficients is less pronounced but cannot be neglected. The effect of fluctuating charges is only negligible for small molecules with at most one non-hydrogen atom. They become important and sometimes dominant for larger molecules or when highly polarizable bonds are present, such as conjugated, double, or triple bonds. Charge flow contributions cannot be explained in terms of individual atomic properties because they are affected by non-local features such as chemical bonding and geometry. Therefore, polarizable force fields and dispersion models can benefit from the explicit modeling of charge flow. [ABSTRACT FROM AUTHOR]

A frequency-dependent extension of the polarizable force field "Atom-Condensed Kohn–Sham density functional theory approximated to the second-order" (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequency-dependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation is used. A numerical validation shows that accurate models can already be obtained with atomic monopoles and dipoles. Absorption spectra of 42 organic and inorganic molecular monomers are evaluated using ACKS2ω, and our results agree well with the time-dependent DFT calculations. Also for the calculation of C6 dispersion coefficients, ACKS2ω closely reproduces its TDDFT reference. When parameters for ACKS2ω are derived from a PBE/aug-cc-pVDZ ground state, it reproduces experimental values for 903 organic and inorganic intermolecular pairs with an MAPE of 3.84%. Our results confirm that ACKS2ω offers a solid connection between the quantum-mechanical description of frequency-dependent response and computationally efficient force-field models. [ABSTRACT FROM AUTHOR]

In this work we explore the properties which make many real-life global optimization problems extremely difficult to handle, and some of the common techniques used in literature to address them. We then introduce a general optimization management tool called GloMPO (Globally Managed Parallel Optimization) to help address some of the challenges faced by practitioners. GloMPO manages and shares information between traditional optimization algorithms run in parallel. We hope that GloMPO will be a flexible framework which allows for customization and hybridization of various optimization ideas, while also providing a substitute for human interventions and decisions which are a common feature of optimization processes of hard problems. GloMPO is shown to produce lower minima than traditional optimization approaches on global optimization test functions, the Lennard-Jones cluster problem, and ReaxFF reparameterizations. The novel feature of forced optimizer termination was shown to find better minima than normal optimization. GloMPO is also shown to provide qualitative benefits such a identifying degenerate minima, and providing a standardized interface and workflow manager. [ABSTRACT FROM AUTHOR]

We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields. [ABSTRACT FROM AUTHOR]

IOData is a free and open‐source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane‐wave density‐functional‐theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand‐alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third‐party) molecular quantum chemistry and solid‐state density‐functional‐theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library. [ABSTRACT FROM AUTHOR]

An efficient protocol is presented to compensate for the basis set superposition error (BSSE) in DFT molecular dynamics (MD) simulations using localized Gaussian basis sets. We propose a classical correction term that can be added a posteriori to account for BSSE. It is tested to what extension this term will improve radial distribution functions (RDFs). The proposed term is pairwise between certain atoms in different molecules and was calibrated by fitting reference BSSE data points computed with the counterpoise method. It is verified that the proposed exponential decaying functional form of the model is valid. This work focuses on hydrogen-bonded liquids, i.e., methanol, and more specific on the intermolecular hydrogen bond, but in principle the method is generally applicable on any type of interaction where BSSE is significant. We evaluated the relative importance of the Grimme-dispersion versus BSSE and found that they are of the same order of magnitude, but with an opposite sign. Upon introduction of the correction, the relevant RDFs, obtained from MD, have amplitudes equal to experiment. [ABSTRACT FROM AUTHOR]

An extensive benchmark of the electronegativity equalization method (EEM) and the split charge equilibration (SQE) model on a very diverse set of organic molecules is presented. These models efficiently compute atomic partial charges and are used in the development of polarizable force fields. The predicted partial charges that depend on empirical parameters are calibrated to reproduce results from quantum mechanical calculations. Recently, SQE is presented as an extension of the EEM to obtain the correct size dependence of the molecular polarizability. In this work, 12 parametrization protocols are applied to each model and the optimal parameters are benchmarked systematically. The training data for the empirical parameters comprise of MP2/Aug-CC-pVDZ calculations on 500 organic molecules containing the elements H, C, N, O, F, S, Cl, and Br. These molecules have been selected by an ingenious and autonomous protocol from an initial set of almost 500 000 small organic molecules. It is clear that the SQE model outperforms the EEM in all benchmark assessments. When using Hirshfeld-I charges for the calibration, the SQE model optimally reproduces the molecular electrostatic potential from the ab initio calculations. Applications on chain molecules, i.e., alkanes, alkenes, and alpha alanine helices, confirm that the EEM gives rise to a divergent behavior for the polarizability, while the SQE model shows the correct trends. We conclude that the SQE model is an essential component of a polarizable force field, showing several advantages over the original EEM. [ABSTRACT FROM AUTHOR]

Grid is a free and open-source Python library for constructing numerical grids to integrate, interpolate, and differentiate functions (e.g., molecular properties), with a strong emphasis on facilitating these operations in computational chemistry and conceptual density functional theory. Although designed, maintained, and released as a stand-alone Python library, Grid was originally developed for molecular integration, interpolation, and solving the Poisson equation in the HORTON and ChemTools packages. Grid is designed to be easy to use, extend, and maintain; this is why we use Python and adopt many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. We leverage popular scientific packages, such as NumPy and SciPy, to ensure high efficiency and optimized performance in grid development. This article is the official release note of the Grid library showcasing its unique functionality and scope. [ABSTRACT FROM AUTHOR]

Pin1 is an enzyme that specificallycatalyzes the cis–transisomerization of prolineamide bonds in peptides that contain aphosphorylated threonine or serine residue in the position precedingproline. In the cell, the isomerization reaction is associated withcellular signaling and has been related to diseases such as Alzheimerand cancer. The catalytic mechanism by which Pin1 accelerates theisomerization reaction, however, is still unknown. In this study,we use molecular dynamics simulation in combination with the QM/MMmethodology to disclose the influence of the residues Ser-154 andCys-113 in the enzyme and the phosphorylated threonine residue inthe peptide on the reaction mechanism. To account for the correctelectrostatic interaction between the three residues and the reactivecenter, we derive atomic charges that account for the varying electrostaticfield in the catalytic cavity. Different methods based on reproducingthe molecular electrostatic potential or an atoms in molecules approachwere investigated. Finally, the reaction mechanism is analyzed withthe mean reaction force and the influence of the three residues isdisclosed. Our results show that Pin1 specifically catalyzes the isomerizationof the transconformer in a jump-rope type of motion,as suggested by us and confirmed experimentally by others. This isaccomplished by anchoring the threonine phosphate residue on one endof the peptide through electrostatic interactions with the basic triadof the enzyme and at the other end through specific enzyme–peptidehydrogen bonds. Cys-113 reduces the structural contribution to theactivation free energy through the stabilization of the cisconformer, and Ser-154 in combination with Gln-131 assist in theisomerization reaction of the transisomer. [ABSTRACT FROM AUTHOR]

Zeolite synthesis is driven by structure-directing agents, such as tetrapropyl ammonium ions (TPA+) for Silicalite-1 and ZSM-5. However, the guiding role of these organic templates in the complex assembly to highly ordered frameworks remains unclear, limiting the prospects for advanced material synthesis. In this work, both static ab initio and dynamic classical modeling techniques are employed to provide insight into the interactions between TPA+ and Silicalite-1 precursors. We find that as soon as the typical straight 10-ring channel of Silicalite-1 or ZSM-5 is formed from smaller oligomers, the TPA+ template is partially squeezed out of the resulting cavity. Partial retention of the template in the cavity is, however, indispensable to prevent collapse of the channel and subsequent hydrolysis. [ABSTRACT FROM AUTHOR]

Abstract: It has been shown previously that two distinctive variants (called RHop and RO4) exist of the radiation-induced rhamnose alkoxy radical. Density functional theory (DFT) calculations of the electron paramagnetic resonance (EPR) properties were found to be consistent with two separate measurements at different temperatures [E. Pauwels, R. Declerck, V. Van Speybroeck, M. Waroquier, Radiat. Res., in press]. However, the agreement between theory and experiment was only of a qualitative nature, especially for the latter radical. In the present work, it is examined whether this residual difference between theoretical and experimental spectroscopic properties can be explained by explicitly accounting for temperature in DFT calculations. With the aid of ab-initio molecular dynamics, a temperature simulation was conducted of the RO4 variant of the rhamnose alkoxy radical. At several points along the MD trajectory, g and hyperfine tensors were calculated, yielding time (and temperature) dependent mean spectroscopic properties. The effect of including temperature is evaluated but found to be within computational error. [Copyright &y& Elsevier]

We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties. [ABSTRACT FROM AUTHOR]

The numerical ill‐conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater‐type functions is overcome by using the (extended) Kullback–Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non‐negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non‐negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non‐negative basis functions. We present a fixed‐point iteration method for optimizing the Kullback–Leibler divergence and compare it to conventional gradient‐based optimization methods. These algorithms are released through the free and open‐source BFit package, which also includes a L2‐norm squared optimization routine applicable to any square‐integrable scalar function. [ABSTRACT FROM AUTHOR]

Many population analysis methods are based on the precept that molecules should be built from fragments (typically atoms) that maximally resemble the isolated fragment. The resulting molecular building blocks are intuitive (because they maximally resemble well-understood systems) and transferable (because if two molecular fragments both resemble an isolated fragment, they necessarily resemble each other). Information theory is one way to measure the deviation between molecular fragments and their isolated counterparts, and it is a way that lends itself to interpretation. For example, one can analyze the relative importance of electron transfer and polarization of the fragments. We present key features, advantages, and disadvantages of the information-theoretic approach. We also codify existing information-theoretic partitioning methods in a way that clarifies the enormous freedom one has within the information-theoretic ansatz. [ABSTRACT FROM AUTHOR]

Fanpy is a free and open‐source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N‐electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin‐orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library. [ABSTRACT FROM AUTHOR]

Many benchmarks of density-functional theory with respect to experiment suggest the error on predicted equilibrium volumes to scale with the volume. Relative volume errors are therefore often used as a decisive argument to select one exchange–correlation functional over another. We show that the error on the volume (after correcting for systematic deviations) is only approximately relative. A simple analytic model, validated by rigorous Monte Carlo simulations, reveals that a more accurate error estimate can be derived from the inverse of the bulk modulus. This insight is not only instrumental for the selection or design of suitable functionals. It also calls for a new attitude towards computational errors: to report computational errors on electronic-structure calculations, identify systematic deviations and distinguish between relative and absolute effects. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

This work aims at a critical assessmentof properties predictingor extracting information on the density and structure of liquids.State-of-the-art NVT and NpT molecular dynamics (MD) simulations havebeen performed on five liquids: methanol, chloroform, acetonitrile,tetrahydrofuran, and ethanol. These simulations allow the computationof properties based on first principles, including the equilibriumdensity and radial distribution functions (RDFs), characterizing theliquid structure. Refinements have been incorporated in the MD simulationsby taking into account basis set superposition errors (BSSE). An extendedBSSE model for an instantaneous evaluation of the BSSE correctionshas been proposed, and their impact on the liquid properties has beenassessed. If available, the theoretical RDFs have been compared withthe experimentally derived RDFs. For some liquids, significant discrepancieshave been observed, and a profound but critical investigation is presentedto unravel the origin of these deficiencies. This discussion is focusedon tetrahydrofuran where the experiment reveals some prominent peakscompletely missing in any MD simulation. Experiments providing informationon liquid structure consist mainly of neutron diffraction measurementsoffering total structure factors as the primary observables. The splittingof these factors in reciprocal space into intra- and intermolecularcontributions is extensively discussed, together with their sensitivityin reproducing correct RDFs in coordinate space. [ABSTRACT FROM AUTHOR]

The porous MIL-47 material shows a selective adsorption behavior for para-, ortho-, and meta-isomers of xylenes, making the material a serious candidate for separation applications. The origin of the selectivity lies in the differences in interactions (energetic) and confining (entropic). This paper investigates the xylene-framework interactions and the xylene-xylene interactions with quantum mechanical calculations, using a dispersion-corrected density functional and periodic boundary conditions to describe the crystal. First, the strength and geometrical characteristics of the optimal xylene-xylene interactions are quantified by studying the pure and mixed pairs in gas phase. An extended set of initial structures is created and optimized to sample as many relative orientations and distances as possible. Next, the pairs are brought in the pores of MIL-47. The interaction with the terephthalic linkers and other xylenes increases the stacking energy in gas phase (−31.7 kJ/mol per pair) by roughly a factor four in the fully loaded state (−58.3 kJ/mol per xylene). Our decomposition of the adsorption energy shows various trends in the contributing xylene-xylene interactions. The absence of a significant difference in energetics between the isomers indicates that entropic effects must be mainly responsible for the separation behavior. [ABSTRACT FROM AUTHOR]

QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal–organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparent workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster‐based models. This is essential for an accurate description of MOFs with one‐dimensional metal‐oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL‐53(Al), MOF‐5, CAU‐13 and NOTT‐300. As expected, periodic input data are proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL‐53(Al). Bulk moduli and thermal expansion coefficients of MOF‐5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU‐13 and NOTT‐300, the transition pressure is accurately predicted provided cross terms are taken into account. © 2018 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

The mechanisms of human soluble epoxide hydrolase (sEH) and the corresponding epoxide hydrolase enzyme from Mycobacterium tuberculosis (EHB) are studied computationally, using the quantum mechanics/molecular mechanics (QM/MM) method. To do this, we modeled the alkylation and the hydrolysis steps of three substrates: trans-1,3-diphenylpropene oxide, trans-stilbene oxide and cis-stilbene oxide. Studying the regioselectivity for trans-1,3-diphenylpropene oxide, we determined that both enzymes prefer ring opening via attack on the benzylic carbon. In agreement with experimental studies, our computations show that the rate-limiting step is hydrolysis of the ester intermediate, with reaction barriers of approximately 13 to 18 kcal/mol. Using the barrier energies of this rate-limiting step, the three epoxides were ranked in order of reactivity. Though the reactivity order was correctly predicted for sEH, the predicted order for EHB did not correspond to experimental observations. Next, the electrostatic contributions of individual residues on the barrier height of the rate-limiting step were also studied. This revealed several residues important for catalysis. The secondary tritium kinetic isotope effect for the alkylation step was determined using a cluster model for the active site of sEH. The calculated value was 1.27, suggesting a late transition state for the rate-limiting step. Finally, we analyzed the reactivity trends using reactivity indicators from conceptual density functional theory, allowing us to identify ease of electron transfer as the primary driving force for the reaction. [ABSTRACT FROM AUTHOR]

We consider the problem of defining an appropriate local descriptor corresponding to an arbitrary global descriptor. Although it does not seem easy to rigorously and uniquely define local analogues of derived global descriptors (e.g., the electrophilicity) or the fundamental global descriptors associated with the canonical ensemble (e.g., the hardness), the local response of these global descriptors can be defined unambiguously. We look at the local response of the global electrophilicity and compare it to the conventional, ad hoc, definition of the local electrophilicity. The local response of global nucleofugality and electrofugality is also discussed. [ABSTRACT FROM AUTHOR]

We present explicit formulas for arbitrary-order derivatives of the energy, grand potential, electron density, and higher-order response functions with respect to the number of electrons, and the chemical potential for any smooth and differentiable model of the energy versus the number of electrons. The resulting expressions for global reactivity descriptors (hyperhardnesses and hypersoftnesses), local reactivity descriptors (hyperFukui functions and local hypersoftnesses), and nonlocal response functions are easy to evaluate computationally. Specifically, the explicit formulas for global/local/nonlocal hypersoftnesses of arbitrary order are derived using Bell polynomials. Explicit expressions for global and local hypersoftness indicators up to fifth order are presented. [ABSTRACT FROM AUTHOR]

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal-organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials. [ABSTRACT FROM AUTHOR]

We present a systematic theoreticalstudy on the dissociation ofdiatomic molecules and their spectroscopic constants using our recentlypresented geminal-based wave function ansätze. Specifically,the performance of the antisymmetric product of rank two geminals(APr2G), the antisymmetric product of 1-reference-orbital geminals(AP1roG) and its orbital-optimized variant (OO-AP1roG) are assessedagainst standard quantum chemistry methods. Our study indicates thatthese new geminal-based approaches provide a cheap, robust, and accuratealternative for the description of bond-breaking processes in closed-shellsystems requiring only mean-field-like computational cost. In particular,the spectroscopic constants obtained from OO-AP1roG are in very goodagreement with reference theoretical and experimental data. [ABSTRACT FROM AUTHOR]

The epoxidation of cyclohexene has been investigated on a metal-organic framework MIL-47 containing saturated V+IV sites linked with functionalized terephthalate linkers (MIL-47-X, X=OH, F, Cl, Br, CH3, NH2). Experimental catalytic tests have been performed on the MIL-47-X materials to elucidate the effect of linker substitution on the conversion. Notwithstanding the fact that these substituted materials are prone to leaching in the performed catalytic tests, the initial catalytic activity of these materials correlates with the Hammett substituent constants. In general, substituents led to an increased activity relative to the parent MIL-47. To rationalize the experimental findings, first-principles kinetic calculations were performed on periodic models of MIL-47 to determine the most important active sites by creating defect structures in the interior of the crystalline material. In a next step these defect structures were used to propose extended cluster models, which are able to reproduce in an adequate way the direct environment of the active metal site. An alkylperoxo species V+VO(OO tBu) was identified as the most abundant and therefore the most active epoxidation site. The structure of the most active site was a starting basis for the construction of extended cluster models including substituents. They were used for quantifying the effect of functionalization of the linkers on the catalytic performance of the heterogeneous catalyst MIL-47-X. Electron-withdrawing as well as electron-donating groups have been considered. The epoxidation activity of the functionalized models has been compared with the measured experimental conversion of cyclohexene. The agreement is fairly good. This combined experimental-theoretical study makes it possible to elucidate the structure of the most active site and to quantify the electronic modulating effects of linker substituents on the catalytic activity. [ABSTRACT FROM AUTHOR]

Mycobacterium tuberculosis thymidylate kinase (Mt TMPK) has emerged as an attractive target for rational drug design. We recently investigated new families of non-nucleoside Mt TMPK inhibitors in an effort to diversify Mt TMPK inhibitor chemical space. We here report a new series of Mt TMPK inhibitors by combining the Topliss scheme with rational drug design approaches, fueled by two co-crystal structures of Mt TMPK in complex with developed inhibitors. These efforts furnished the most potent Mt TMPK inhibitors in our assay, with two analogues displaying low micromolar MIC values against H37Rv Mtb. Prepared inhibitors address new sub-sites in the Mt TMPK nucleotide binding pocket, thereby offering new insights into its druggability. We studied the role of efflux pumps as well as the impact of cell wall permeabilizers for selected compounds to potentially provide an explanation for the lack of correlation between potent enzyme inhibition and whole-cell activity. [Display omitted] • Structure-based design and synthesis of new Mt TMPK inhibitors, e.g. featuring a pyridine C-ring. • D-ring substitution afforded potent Mt TMPK inhibitors with submicromolar IC 50 -values. • A co-crystal structure indicates that inhibitor 3 addresses a new subsite in the Mt TMPK nucleotide binding pocket. [ABSTRACT FROM AUTHOR]

Diphosphonylated diazaheterocyclic compounds were synthesized in a one-step reaction by using dimethyl trimethylsilyl phosphite (DMPTMS) under acidic conditions. The reaction of DMPTMS with 1,5-naphthyridine yielded the corresponding diphosphonylated product through a tandem 1,4-1,2 addition under microwave conditions. This tandem 1,4-1,2 addition was also evaluated for other substrates, namely, 1,10-phenanthroline, 1,7-phenanthroline and 4,7-phenanthroline. Reactions under reflux and microwave conditions were compared. 1,5-Naphthyridine and the phenanthroline derived substrates are less reactive than previously investigated quinolines. The experimental trends in reactivity were rationalized by means of theoretical calculations. The intrinsic properties, such as aromaticity and proton affinities, showed distinct differences for the various substrates. Furthermore, the calculated free energies of activation for the rate-determining step of the tandem addition reaction enabled us to rationalize the differences in product yields. Both the theoretical and the experimental results show the substantial influence of the position of the nitrogen atoms in the (poly)aromatic compounds on the reaction outcome. [ABSTRACT FROM AUTHOR]

The mechanical energy absorption ability of the highly flexible MIL-53(Al) MOF material was explored using a combination of experiments and molecular simulations. A pressure-induced transition between the large pore and the closed pore forms of this solid was revealed to be irreversible and associated with a relatively large energy absorption capacity. Both features make MIL-53(Al) the first potential MOF candidate for further use as a shock absorber. [ABSTRACT FROM AUTHOR]

A correction to the article "Diphosphonylation of Aromatic Diazaheterocycles and Theoretical Rationalization of Product Yields," that was published in a previous issue is presented.