Molecular dynamics investigation of benzoic acid in confined spaces

Classical molecular dynamics simulations are carried out to investigate the aggregation of supercooled benzoic acid in confined spaces. Nanocavities, nanotubes and nanolayers are defined by restricting the periodicity of the simulation to zero, one or two dimensions, with boundaries set by adjustable, general, and computationally cheap van der Waals barriers. The effect of different confinement geometries is explored. It is found that the confinement impacts the liquid collective dynamics, strengthening the correlations that affect the motion of distant molecules. Overall, confinement determines up to a tenfold increase of the viscosity of the liquid and strongly slows down the rotational correlation times. Aggregation mediated by interactions with the walls and partial polarization of the liquid are observed. Additionally, transitions to high-density liquid states occur when stiffer barriers are used. In general, a reduced accessible amount of phase space fosters the struggle for a closer packing to relieve unfavorable atom-atom contacts, while maximizing the attractive ones. In benzoic acid, this implies that the hydrogen bond network is organized more efficiently in high density states.

Phosphine-Catalyzed Domino Regio- and Stereo-Selective Hexamerization of 2-(Bromomethyl)acrylates to 1,2-Bis(cyclohexenyl)ethenyl Derivatives

A phosphine-catalyzed domino assembly of six units of 2-bromomethyl acrylates afforded polyalkenyl adducts containing two cyclohexenyl rings. This reaction occurs under mild conditions providing the final product by formation of seven carbon-carbon bonds and four stereocenters. Experimental and computational studies support an initial dimerization of the substrate, which in turn trimerizes involving two totally regio- and stereocontrolled Diels-Alder cycloadditions. The yield of the hexamerization of the 2-bromomethyl acrylates depends on the size of the ester function. The protocol has also proved to be practicable on a gram scale.

Enantiopure β-isocyano-boronic esters: synthesis and exploitation in isocyanide-based multicomponent reactions

Various boron-containing isocyanides have been efficiently synthesized from the corresponding enantiopure β-substituted β-amino boronic acid pinacol esters, without need for protecting group interconversion, through a two-step, purification-free procedure. They were employed in a variety of isocyanide-based multicomponent reactions, proving to be reliable components for all of them and allowing the efficient synthesis of unprecedented, boron-containing peptidomimetics and heteroatom-rich small molecules, including biologically relevant cyclic boronates. Jointing together the β-amido boronic acid moiety, deriving from the isocyanide component, with prominent pharmacophoric rings emerging from the multicomponent process, a successful application of the molecular hybridization concept could be realized.

Non-Decarboxylative Ruthenium-Catalyzed Rearrangement of 4-Alkylidene-isoxazol-5-ones to Pyrazole- and Isoxazole-4-carboxylic Acids

Treatment of 4-(2-hydroaminoalkylidenyl)- and 4-(2-hydroxyalkylidenyl)-substituted isoxazol-5(4H)-ones with catalytic amounts of [RuCl2(p-cymene)]2, without any additive, afforded pyrazole- and isoxazole-4-carboxylic acids, respectively. The presence of an intramolecular H-bond in these substrates was the key to divert the classical mechanism toward a ring-opening non-decarboxylative path that is expected to generate a vinyl Ru-nitrenoid intermediate, the cyclization of which affords the rearranged products. A gram scale protocol demonstrated the synthetic applicability of this transformation.

Unexpected chiral vicinal tetrasubstituted diamines via borylcopper-mediated homocoupling of isatin imines

Addressing the asymmetric synthesis of oxindole-based α-aminoboronic acids, instead of the expected products we disclosed the efficient homocoupling of oxindole-based N-tert-butanesulfinyl imines, with the generation of chiral, quaternary 1,2-diamines in a mild and completely stereoselective way. The obtained 3,3′-bisoxindole derivatives were fully characterized by NMR and single-crystal X-ray diffraction analysis and proved to be single diastereoisomers and atropisomers. A plausible mechanism for the one-pot Cu(II)-catalyzed Bpin addition to the isatin-derived ketimine substrate and subsequent homocoupling is described.

Direct Synthesis of Fluorescent Oxazolo-phenoxazines by Copper-Catalyzed/Hypervalent Iodine(III)-Mediated Dimerization/Cyclization of 2-Benzylamino-phenols

A dimerization/cyclization reaction of 2-benzylamino-phenols for the direct synthesis of the oxazolo-phenoxazine skeleton is reported. The reaction occurs under copper catalysis in the presence of hypervalent iodine(III), giving selectively the 5H-oxazolo[4,5-b]phenoxazine compounds. The cascade process, which allows the conversion of the substrates into the tetracyclic products, involves three C-H functionalization steps. Initial oxidation of electron-rich arenes by the hypervalent iodine is essential for the dimerization of substrates, whereas the formation of the five-membered rings is promoted by the copper species. 1-Benzyl-2-phenyl-6-(aryl-benzyl)amino-benzimidazoles are regioselectively obtained using N,N'-dibenzyl-phenylenediamines as starting substrates. The fluorescence emission properties of these classes of products have been evaluated.

Accurate experimental characterization of the labile N–Cl bond in N-chloro-N′-(p-fluorophenyl)-benzamidine crystal at 17.5 K

Very low temperature can preserve the photolabile N–Cl bond in a N-chloro-N-benzamidine derivative long enough to carry on an accurate experimental X-ray charge density study.

Molecular dynamics simulation of organic materials: structure, potentials and the MiCMoS computer platform

Molecular dynamics simulation shows atoms in action: liquids, crystals, mesophases, nanoparticles trace their paths in time, temperature and pressure in a computing platform designed for organic small molecules.

Switchable Oxidative Reactions of N-allyl-2-Aminophenols: Palladium-Catalyzed Alkoxyacyloxylation vs an Intramolecular Diels-Alder Reaction

The Pd(II)-catalyzed reaction of N-allyl-2-aminophenols in the presence of PhI(OCOR)₂ as the oxidant resulted in an alkoxyacyloxylation process, with the formation of functionalized dihydro-1,4-benzoxazines. The reaction performed in the absence of palladium catalyst switched to an intramolecular Diels–Alder reaction (IMDA) pathway, which was the result of an oxidative dearomatization of the 2-aminophenol, nucleophilic addition, and Diels–Alder reaction cascade, highlighting the role of the oxidant as both a nucleophilic donor and an oxidizing agent.

Enantio- and Regioselective Palladium(II)-Catalyzed Dioxygenation of (Aza-)Alkenols

An oxidative Pd-catalyzed intra-intermolecular dioxygenation of (aza-)alkenols has been reported, with total regioselectivity. To study the stereoselectivity, different chiral ligands as well as different hypervalent-iodine compounds have been compared. In particular, by using a C-6 modified pyridinyl-oxazoline (Pyox) ligand and hypervalent iodine bearing an aromatic ring, an excellent enantio- and diastereoselectivity has been achieved.

Highly diastereoselective entry to chiral oxindole-based β-amino boronic acids and spiro derivatives

We here describe the first Cu-catalysed, diastereoselective 1,2-addition of 1,1-diborylmethane to chiral ketimines for the synthesis of quaternary stereocenters and spiro compounds. The method provides easy access to a range of chiral, highly functionalized compounds, namely oxindole-based β,β'-disubstituted β-amino boronates, boron-containing peptidomimetics and six-, seven-membered spirocyclic hemiboronic esters. Such unprecedented compounds are mostly obtained in high yields and easily isolated as single diastereoisomers, paving the way to a more intense exploitation of boron-containing compounds in diversity-oriented chemistry and drug-discovery programs. Concerning stereochemistry, the application of Ellman's auxiliary strategy allows in principle to access both steric series of target compounds.

Crystal structure or chemical composition of salt–sugar-based metal–organic frameworks: what are the nonlinear optical properties due to?

Two new isomorphous metal–organic frameworks of formula [Ca(C₆H₁₂O₅)₂]X₂ have been synthesized and the parameters influencing their nonlinear optical response investigated.

In the last few decades optical imaging techniques based on nonlinear optical properties have been of interest for biosensing applications. This work focuses on two isostructural and isomorphous sugar-derived metal–organic frameworks (MOFs) with second-harmonic generation (SHG) properties, in order to investigate their possible application as biosensors in view of their high biocompatibility. Combining 2-de­oxy-d-galactose with the metal halogenides CaX₂ (X = Br, I), two new isomorphous MOFs of formula [Ca(C₆H₁₂O₅)₂]X₂ were obtained and characterized through single-crystal X-ray diffraction. The first-order static hyperpolarizability and second-order susceptibility were estimated by in vacuo and in-crystal density functional theory calculations, and compared with the experimental SHG response of powdered samples. The parameters influencing the SHG response of these compounds were investigated by comparison with similar previously analysed MOFs, to understand how to design more efficient materials to be used as nanoprobes by exploiting crystal engineering techniques.

Anharmonic Thermal Motion Modelling in the Experimental XRD Charge Density Determination of 1-Methyluracil at T = 23 K

The experimental electron density distribution (EDD) of 1-methyluracil (1-MUR) was obtained by single crystal X-ray diffraction (XRD) experiments at 23 K. Four different structural models fitting an extensive set of XRD data to a resolution of (sinθ/λ)max = 1.143 Å-1 are compared. Two of the models include anharmonic temperature factors, whose inclusion is supported by the Hamilton test at a 99.95% level of confidence. Positive Fourier residuals up to 0.5 eÅ-3 in magnitude were found close to the methyl group and in the region of hydrogen bonds. Residual density analysis (RDA) and molecular dynamics simulations in the solid-state demonstrate that these residuals can be likely attributed to unresolved disorder, possibly dynamical and long-range in nature. Atomic volumes and charges, molecular moments up to hexadecapoles, as well as maps of the molecular electrostatic potential were obtained from distributed multipole analysis of the EDD. The derived electrostatic properties neither depend on the details of the multipole model, nor are significantly affected by the explicit inclusion of anharmonicity in the least-squares model. The distribution of atomic charges in 1-MUR is not affected by the crystal environment in a significant way. The quality of experimental findings is discussed in light of in-crystal and gas-phase quantum simulations.

Spin Density Topology

Despite its role in spin density functional theory and it being the basic observable for describing and understanding magnetic phenomena, few studies have appeared on the electron spin density subtleties thus far. A systematic full topological analysis of this function is lacking, seemingly in contrast to the blossoming in the last 20 years of many studies on the topological features of other scalar fields of chemical interest. We aim to fill this gap by unveiling the kind of information hidden in the spin density distribution that only its topology can disclose. The significance of the spin density critical points, the 18 different ways in which they can be realized and the peculiar topological constraints on their number and kind, arising from the presence of positive and negative spin density regions, is addressed. The notion of molecular spin graphs, spin maxima (minima) joining paths, spin basins and of their valence is introduced. We show that two kinds of structures are associated with a spin-polarized molecule: the usual one, defined through the electron density gradient, and the magnetic structure, defined through the spin density gradient and composed in general by at least two independent spin graphs, related to spin density maxima and minima. Several descriptors, such as the spin polarization index, are introduced to characterize the properties of spin density critical points and basins. The study on the general features of the spin density topology is followed by the specific example of the water molecule in the ³B₁ triplet state, using spin density distributions of increasing accuracy.

Isonitrile-Based Multicomponent Synthesis of β-Amino Boronic Acids as β-Lactamase Inhibitors

The application of various isonitrile-based multicomponent reactions to protected (2-oxoethyl)boronic acid (as the carbonyl component) is described. The Ugi reaction, both in the four components and in the four centers-three components versions, and the van Leusen reaction, proved effective at providing small libraries of MIDA-protected β-aminoboronic acids. The corresponding free β-aminoboronic acids, quantitatively recovered through basic mild deprotection, were found to be quite stable and were fully characterized, including by 11B-NMR spectroscopy. Single-crystal X-ray diffraction analysis, applied both to a MIDA-protected and a free β-aminoboronic acid derivative, provided evidence for different conformations in the solid-state. Finally, the antimicrobial activities of selected compounds were evaluated by measuring their minimal inhibitory concentration (MIC) values, and the binding mode of the most promising derivative on OXA-23 class D β-lactamase was predicted by a molecular modeling study.

Mining the Cambridge Database for theoretical chemistry. Mi-LJC: a new set of Lennard-Jones–Coulomb atom–atom potentials for the computer simulation of organic condensed matter

A novel, universal Lennard-Jones–Coulomb (LJC) atom–atom force field parametrization reproduces the experimental sublimation enthalpies of 377 molecular crystals drawn from the CSD.

Molecular dynamics simulation of organic crystals: introducing the CLP-dyncry environment

The CLP-dyncry molecular dynamics (MD) program suite and force field environment is introduced and validated with its ad hoc features for the treatment of organic crystalline matter. The package, stemming from a preliminary implementation on organic liquids (Gavezzotti & Lo Presti, 2019), includes modules for the preliminary generation of molecular force field files from ab initio derived force constants, and for the preparation of crystalline simulation boxes from general crystallographic information, including Cambridge Structural Database CIFs. The intermolecular potential is the atom–atom Coulomb–London–Pauli force field, well tested as calibrated on sublimation enthalpies of organic crystals. These products are then submitted to a main MD module that drives the time integration and produces dynamic information in the form of coordinate and energy trajectories, which are in turn processed by several kinds of crystal-oriented analytic modules. The whole setup is tested on a variety of bulk crystals of rigid, non-rigid and hydrogen-bonded compounds for the reproduction of radial distribution functions and of crystal-specific collective orientational variables against X-ray data. In a series of parallel tests, some advantages of a dedicated program as opposed to software more oriented to biomolecular simulation (Gromacs) are highlighted. The different and improved view of crystal packing that results from joining static structural information from X-ray analysis with dynamic upgrades is also pointed out. The package is available for free distribution with I/O examples and Fortran source codes.

Chemo- and Regioselective Palladium(II)-Catalyzed Aminoaryl­ation of N-Allylureas Providing 4-Arylmethyl Imidazolidinones

The aminoarylation reaction of N-allylureas under oxidative palladium catalysis, in the absence of ligands and by using inexpensive H2O2 as the sole oxidant, occurs in a chemo- and regioselective fashion. This intramolecular process takes place via a 5-exo-trig cyclization, and represents an easy approach to 4-arylmethyl imidazolidinones.

Developing new SrI2 and β-D-fructopyranose-based metal-organic frameworks with nonlinear optical properties

In the context of personalized medicine, there is a growing interest in materials bearing at the same time diagnostic and therapy functions. This article reports a cheap and easily reproducible procedure to obtain materials with a high potential for these applications. Three new strontium iodide-fructose-based metal-organic frameworks with formulae [Sr(C₆H₁₂O₆)₂]I₂, [Sr₂(C₆H₁₂O₆)₃(H₂O)₃]I₄·0.5H₂O and [Sr(C₆H₁₂O₆)(H₂O)₃I]I differing in stoichiometry, symmetry and crystal packing, were obtained and characterized by X-ray diffraction. Bulk quantum simulations show that both the ions and the sugar are crucial in determining the predicted nonlinear response; also, the relative arrangement of various functional groups in the unit cell plays a role in the computed optical properties. Small fragments of the three compounds were selected for in vacuo calculations, proving that the reduced dimensions of the particles have a great influence on the nonlinear optical response. Despite the similar chemical composition of the three compounds, second harmonic generation measurements and in crystal and in vacuo theoretical calculations agree that one of the compounds is a much more efficient second harmonic emitter than the other two, and is thus a suitable candidate for bio-sensor applications.

Dynamic simulation of liquid molecular nanoclusters: structure, stability and quantification of internal (pseudo)symmetries

In a few hours on a standard laptop, AA-CLP MD correctly reproduces the thermodynamic properties of bulk liquids and provides information on the nanoscale dynamics of liquid nanoclusters.

Allylation of isatin-derived N-Boc-hydrazones followed by Pd-catalyzed carboamination reaction: an entry to 3-spiro-pyrazolidyl-oxindoles

The indium-mediated allylation of novel 3-(2-Boc-hydrazono)indolin-2-one derivatives, followed by a palladium-catalysed carboamination reaction, is described to afford unprecedented spirocyclic oxindoles in good yields. The method provides an efficient access to both cis and trans diastereoisomers of highly functionalized compounds, bearing an N-Boc, 5-substituted pyrazolidine ring at the C3-oxindole spiro junction. The versatility of the method is fully demonstrated starting from a series of substituted isatins and employing a variety of aryl halides in the key cyclization step.

The indium-mediated allylation of novel 3-(2-Boc-hydrazono)indolin-2-one derivatives, followed by a palladium-catalysed carboamination reaction, is described to afford unprecedented spirocyclic oxindoles in good yields.

Design and synthesis of constrained bicyclic molecules as candidate inhibitors of influenza A neuraminidase

The rise of drug-resistant influenza A virus strains motivates the development of new antiviral drugs, with different structural motifs and substitution. Recently, we explored the use of a bicyclic (bicyclo[3.1.0]hexane) analogue of sialic acid that was designed to mimic the conformation adopted during enzymatic cleavage within the neuraminidase (NA; sialidase) active site. Given that our first series of compounds were at least four orders of magnitude less active than available drugs, we hypothesized that the new carbon skeleton did not elicit the same interactions as the cyclohexene frameworks used previously. Herein, we tried to address this critical point with the aid of molecular modeling and we proposed new structures with different functionalization, such as the introduction of free ammonium and guanidinium groups and ether side chains other than the 3-pentyl side chain, the characteristic side chain in Oseltamivir. A highly simplified synthetic route was developed, starting from the cyclopropanation of cyclopentenone and followed by an aziridination and further functionalization of the five-member ring. This allowed the efficient preparation of a small library of new bicyclic ligands that were characterized by enzyme inhibition assays against influenza A neuraminidases N1, its H274Y mutant, and N2. The results show that none of the new structural variants synthesized, including those containing guanidinium groups rather than free ammonium ions, displayed activity against influenza A neuraminidases at concentrations less than 2 mM. We conclude that the choice and positioning of functional groups on the bicyclo[3.1.0]hexyl system still need to be properly tuned for producing complementary interactions within the catalytic site.

Sequential Multicomponent Strategy for the Diastereoselective Synthesis of Densely Functionalized Spirooxindole-Fused Thiazolidines

We developed two Ugi-type three-component reactions of spirooxindole-fused 3-thiazolines, isocyanides, and either carboxylic acids or trimethylsilyl azide, to give highly functionalized spirooxindole-fused thiazolidines. Two diverse libraries were generated using practical and robust procedures affording the products in typically good yields. The obtained thiazolidines proved to be suitable substrates for further transformations. Notably, both the Ugi-Joullié and the azido-Ugi reactions resulted highly diastereoselective, affording predominantly the trans-configured products, as confirmed by X-ray crystallographic analysis.

Crystallization and structural properties of a family of isotopological 3D-networks: the case of a 4,4′-bipy ligand–M2+ triflate system

Desolvation process characterization of a flexible coordination network performed by time-resolved single-crystal X-ray diffraction. Influence of the metal centre on the network stability.

A variable-temperature X-ray diffraction and theoretical study of conformational polymorphism in a complex organic molecule (DTC)

Two conformational crystal polymorphs of 3-diethylamino-4-(4-methoxyphenyl)-1,1-dioxo-4H-1λ⁶,2-thiazete-4-carbonitrile (DTC) have been analyzed in the 100 K-room temperature range by single crystal X-ray diffraction and high quality DFT calculations. DTC has strongly polar as well as aliphatic substituents but no hydrogen bonding groups, and thus qualifies as a test molecule for the relative importance of electrostatic vs. dispersion–repulsion terms. The two polymorphs have the same P2₁/n space group and differ by a flipping of the –OCH₃ group, the two conformations being almost equi-energetic and separated by a low barrier. The system is monotropic in the observed temperature range with nearly identical thermal expansion coefficients and energy–temperature slopes, one phase consistently predicted to be more stable in agreement with the relative ease of appearance. Energy decompositions show that the electrostatic term is dominant and stabilizes with decreasing temperature. Dispersion and repulsion show the expected behavior, the former becoming more stabilizing at lower temperature in contrast with increasing repulsion at higher density. Absolute values and trends are very similar in the two phases, explaining the small total energy difference. Geometrical analyses of intermolecular contacts using fingerprint plots, as well as the study of molecular dipole moments as a function of T in the framework of the Quantum Theory of Atoms in Molecules, reveal more details of phase stability.

A small conformational change in the asymmetric unit has a significant effect on how non-covalent interactions determine (i) the crystal packing and (ii) the effect of T on the relative balance of electrostatics and dispersion–repulsions.

One step access to oxindole-based β-lactams through Ugi four-center three-component reaction

A multicomponent Ugi reaction involving isatin, isocyanide and β-amino acid components has been developed. The reactions proceeded smoothly to give β-lactam-containing 3,3-disubstituted oxindoles in only one step and generally high yields. When chiral, non racemic, β-amino acids were used, products were obtained as enantiomerically pure β-lactams diastereoisomers, whose relative stereochemistry was determined by X-ray analysis. For one compound, a weak antibacterial activity has been preliminarily highlighted.

A multicomponent Ugi reaction involving isatin, isocyanide and β-amino acid components has been developed.

On the significance of weak hydrogen bonds in crystal packing: a large databank comparison of polymorphic structures

Weak hydrogen bonds control initial molecular recognition modes, but the structure is determined by the interactions among larger supramolecular assemblies.

Atomistic Explanation for Interlayer Charge Transfer in Metal-Semiconductor Nanocomposites: The Case of Silver and Anatase

A concerted theoretical and experimental investigation of the silver/anatase hybrid nanocomposite, a very promising material for advanced sensing applications, is presented. We measure its exceptional electrochemical virtues in terms of current densities and reproducibility, providing their explanation at the atomic-scale level and demonstrating how and why silver acts as a positive electrode. Using periodic plane-wave DFT calculations, we estimate the overall amount of electron transfer toward the semiconductor side of the interface at equilibrium. Suitably designed (photo)electrochemical experiments strictly agree, both qualitatively and quantitatively, with the theoretical charge transfer estimates. The unique permanent charge separation occurring in the device is possible because of the favorable synergy of Ag and TiO₂, which exploits in a favorable band alignment, while the electron-hole recombination rate and carrier mobility decrease when electrons cross the metal-semiconductor interface. Finally, the hybrid material is proven to be extremely robust against aging, showing complete regeneration, even after 1 year.

Anharmonic motions versus dynamic disorder at the Mg ion from the charge densities in pyrope (Mg3Al2Si3O12) crystals at 30 K: six of one, half a dozen of the other

The possible occurrence of static/dynamic disorder at the Mg site in pyrope (Mg₃Al₂Si₃O₁₂), with or without anharmonic contribution to the thermal vibrations even at low temperatures, has been largely debated but conclusions were contrasting. Here a report is given on the experimental charge density distribution, ρ_EXP, of synthetic pyrope at T = 30 K, built through a Stewart multipolar expansion up to l = 5 and based on a very precise and accurate set of in-home measured single-crystal X-ray diffraction amplitudes with a maximum resolution of 0.44 Å. Local and integral topological properties of ρ_EXP are in substantial agreement with those of ρ_THEO, the corresponding DFT-grade quantum charge density of an ideal pyrope crystal, and those derived from synchrotron investigations of chemical bonding in olivines. Relevant thermal atomic displacements, probably anharmonic in nature, clearly affect the whole structure down to 30 K. No significant (> 2.5σ) residual Fourier peaks are detectable from the ρ_EXP distribution around Mg, after least-squares refinement of a multipole model with anharmonic thermal motion at the Mg site. Experimental findings were confirmed by a full analysis of normal vibration modes of the DFT-optimized structure of the perfect pyrope crystal. Mg undergoes wide displacements from its equilibrium position even at very low temperatures, as it is allocated in a ∼ 4.5 Å large dodecahedral cavity and involved in several soft phonon modes. Implications on the interplay among static/dynamic disorder of Mg and lattice vibrational degrees of freedom are discussed.

Insights on spin delocalization and spin polarization mechanisms in crystals of azido copper(II) dinuclear complexes through the electron spin density Source Function

The Source Function (SF) tool was applied to the analysis of thetheoreticalspin density in azido CuIIdinuclear complexes, where the azido group, acting as a coupler between the CuIIcations, is linked to the metal centres either in an end-on or in an end–end fashion. Results for only the former structural arrangement are reported in the present paper. The SF highlights to which extent the magnetic centres contribute to determine the local spin delocalization and polarization at any point in the dimetallic complex and whether an atom or group of atoms of the ligands act in favour or against a given local spin delocalization/polarization. Ball-and-stick atomic SF percentage representations allow for a visualization of the magnetic pathways and of the specific role played by each atom along these paths, at given reference points. Decomposition of SF contributions in terms of a magnetic and of a relaxation component provides further insight. Reconstruction of partial spin densities by means of the Source Function has for the first time been introduced. At variance with the standard SF percentage representations, such reconstructions offer a simultaneous view of the sources originating from specific subsets of contributing atoms, in a selected molecular plane or in the whole space, and are therefore particularly informative. The SF tool is also used to evaluate the accuracy of the analysed spin densities. It is found that those obtained at the unrestricted B3LYP DFT level, relative to those computed at the CASSCF(6,6) level, greatly overestimate spin delocalization to the ligands, but comparatively underestimate magnetic connection (spin transmission) among atoms, along the magnetic pathways. As a consequence of its excessive spin delocalization, the UB3LYP method also overestimates spin polarization mechanisms between the paramagnetic centres and the ligands. Spin delocalization measures derived from the refinement of Polarized Neutron Diffraction data seem in general superior to those obtained through the DFT UB3LYP approach and closer to the far more accurate CASSCF results. It is also shown that a visual agreement on the spin-resolved electron densities ραand ρβderived from different approaches does not warrant a corresponding agreement between their associated spin densities.

A Close Look at the Structure of the TiO2-APTES Interface in Hybrid Nanomaterials and Its Degradation Pathway: An Experimental and Theoretical Study

The surface functionalization of TiO₂-based materials with alkylsilanes is attractive in several cutting-edge applications, such as photovoltaics, sensors, and nanocarriers for the controlled release of bioactive molecules. (3-Aminopropyl)triethoxysilane (APTES) is able to self-assemble to form monolayers on TiO₂ surfaces, but its adsorption geometry and solar-induced photodegradation pathways are not well understood. We here employ advanced experimental (XPS, NEXAFS, AFM, HR-TEM, and FT-IR) and theoretical (plane-wave DFT) tools to investigate the preferential interaction mode of APTES on anatase TiO₂. We demonstrate that monomeric APTES chemisorption should proceed through covalent Si-O-Ti bonds. Although dimerization of the silane through Si-O-Si bonds is possible, further polymerization on the surface is scarcely probable. Terminal amino groups are expected to be partially involved in strong charge-assisted hydrogen bonds with surface hydroxyl groups of TiO₂, resulting in a reduced propensity to react with other species. Solar-induced mineralization proceeds through preferential cleavage of the alkyl groups, leading to the rapid loss of the terminal NH₂ moieties, whereas the Si-bearing head of APTES undergoes slower oxidation and remains bound to the surface. The suitability of employing the silane as a linker with other chemical species is discussed in the context of controlled degradation of APTES monolayers for drug release and surface patterning.

Source Function applied to experimental densities reveals subtle electron-delocalization effects and appraises their transferability properties in crystals

The Source Function (SF), introduced in 1998 by Richard Bader and Carlo Gatti, is succinctly reviewed and a number of paradigmatic applications to in vacuo and crystal systems are illustrated to exemplify how the SF may be used to discuss chemical bonding in both conventional and highly challenging cases. The SF enables the electron density to be seen at a point determined by source contributions from the atoms or a group of atoms of a system, and it is therefore well linked to the chemist's awareness that any local property and chemical behaviour is to some degree influenced by all the remaining parts of a system. The key and captivating feature of the SF is that its evaluation requires only knowledge of the electron density (ED) of a system, thereby enabling a comparison of ab initio and X-ray diffraction derived electron density properties on a common and rigorous basis. The capability of the SF to detect electron-delocalization effects and to quantify their degree of transferability is systematically explored in this paper through the analysis and comparison of experimentally X-ray derived Source Function patterns in benzene, naphthalene and (±)-8'-benzhydrylideneamino-1,1'-binaphthyl-2-ol (BAB) molecular crystals. It is shown that the SF tool recovers the characteristic SF percentage patterns caused by π-electron conjugation in the first two paradigmatic aromatic molecules in almost perfect quantitative agreement with those obtained from ab initio periodic calculations. Moreover, the effect of chemical substitution on the degree of transferability of such patterns to the benzene- and naphthalene-like moieties of BAB is neatly shown and quantified by the observed systematic deviations, relative to benzene and naphthalene, of only those SF contributions from the substituted C atoms. Finally, the capability of the SF to reveal electron-delocalization effects is challenged by using a promolecule density, rather than the proper quantum mechanical density, to determine the changes in SF patterns along the cyclohexene, 1,3-cyclohexadiene and benzene molecule series. It is shown that, differently from the proper quantum density, the promolecular density is unable to reproduce the SF trends anticipated by the increase of electron delocalization along the series, therefore ruling out the geometrical effect as being the only cause for the observed SF patterns changes.

Characterization of 2,4-Diamino-6-oxo-1,6-dihydropyrimidin-5-yl Ureido Based Inhibitors of Trypanosoma brucei FolD and Testing for Antiparasitic Activity

The bifunctional enzyme N⁵,N¹⁰-methylenetetrahydrofolate dehydrogenase/cyclo hydrolase (FolD) is essential for growth in Trypanosomatidae. We sought to develop inhibitors of Trypanosoma brucei FolD (TbFolD) as potential antiparasitic agents. Compound 2 was synthesized, and the molecular structure was unequivocally assigned through X-ray crystallography of the intermediate compound 3. Compound 2 showed an IC₅₀ of 2.2 μM, against TbFolD and displayed antiparasitic activity against T. brucei (IC₅₀ 49 μM). Using compound 2, we were able to obtain the first X-ray structure of TbFolD in the presence of NADP⁺ and the inhibitor, which then guided the rational design of a new series of potent TbFolD inhibitors.

Insights on spin polarization through the spin density source function

The source function for the spin density s(r) is introduced, allowing the H and O influence on s(r) to be disentangled.

Understanding how spin information is transmitted from paramagnetic to non-magnetic centers is crucial in advanced materials research and calls for novel interpretive tools. Herein, we show that the spin density at a point may be seen as determined by a local source function for such density, operating at all other points of space. Integration of the local source over Bader's quantum atoms measures their contribution in determining the spin polarization at any system's location. Each contribution may be then conveniently decomposed in a magnetic term due to the magnetic natural orbital(s) density and in a reaction or relaxation term due to the remaining orbitals density. A simple test case, ³B₁ water, is chosen to exemplify whether an atom or group of atoms concur or oppose the paramagnetic center in determining a given local spin polarization. Discriminating magnetic from reaction or relaxation contributions to such behaviour strongly enhances chemical insight, though care needs to be paid to the large sensitivity of the latter contributions to the level of the computational approach and to the difficulty of singling out the magnetic orbitals in the case of highly correlated systems. Comparison of source function atomic contributions to the spin density with those reconstructing the electron density at a system's position, enlightens how the mechanisms which determine the two densities may in general differ and how diverse may be the role played by each system's atom in determining each of the two densities. These mechanisms reflect the quite diverse portraits of the electron density and electron spin density Laplacians, hence the different local concentration/dilution of the total and (α–β) electron densities throughout the system. Being defined in terms of an observable, the source function for the spin density is also potentially amenable to experimental determination, as customarily performed for its electron density analogue.

Model peptides containing the 3-sulfanyl-norbornene amino acid, a conformationally constrained cysteine analogue effective inducer of 310-helix secondary structures

Two model peptides containing the 3-benzylsulfanylnorbornene amino acid (NRB) was prepared. Theoretical calculations, spectroscopic and X-ray analyses confirmed that both NRB enantiomers possess a strong right-handed helicogenic effect.

Synthesis of unusual isoxazoline containing and -dipeptides as potential glutamate receptor ligands

Unconventional beta and gamma dipeptides as tools to investigate the iGluR binding domain.