Electron Density of Two Bioactive Oligocyclic Indole and Oxindole Derivatives Obtained from Low‐Order X‐Ray Data and Invariom Application

For two indole and oxindole bioactive molecules, low‐order room‐temperature X‐ray data were used to generate aspherical electron density (ED) distributions by application of the invariom formalism. An analysis of the ED using the quantum theory of atoms in molecules (QTAIM) was carried out, which allowed for quantitatively examining bond orders and charge separations in various parts of the molecules. The inspection of electrostatic potentials (ESPs) and Hirshfeld surfaces provided additional information on the intermolecular interactions. Thus, reactive regions of the molecules could be identified, covalent and electrostatic contributions to interactions could be visualized, and the forces causing the crystal packing scheme could be rationalized. As the used invariom formalism needs no extra experimental effort compared to routine X‐ray analysis, its wide application is recommended because it delivers information far beyond the normally obtained steric properties. In this way, complementary contributions to drug design can be given as is demonstrated for indoles in this study, which are involved in the metabolism of plants and animals as well as in cancer therapy.     

Invariom‐model refinement of l‐valinol

The structure of l ‐valinol [(S)‐(+)‐2‐amino‐3‐methyl­butan‐1‐ol or hydroxy­lated l ‐valine], C₅H₁₃NO, has been determined at 100 K by single‐crystal X‐ray diffraction. The independent atom model geometry, Flack parameter and figures of merit are compared with results from an invariom structure refinement. The latter provides H‐atom positions free of independent atom model bias and therefore yields a more accurate hydrogen‐bond pattern, and the geometry from invariom refinement shows an improved agreement with results from a quantum chemical geometry optimization.     

Invariom‐model refinement and Hirshfeld surface analysis of well‐ordered solvent‐free dibenzo‐21‐crown‐7

Crown ethers and their supramolecular derivatives are well‐known chelators and scavengers for a variety of cations, most notably heavier alkali and alkaline‐earth ions. Although they are widely used in synthetic chemistry, available crystal structures of uncoordinated and solvent‐free crown ethers regularly suffer from disorder. In this study, we present the X‐ray crystal structure analysis of well‐ordered solvent‐free crystals of dibenzo‐21‐crown‐7 (systematic name: dibenzo[b ,k ]‐1,4,7,10,13,16,19‐heptaoxacycloheneicosa‐2,11‐diene, C₂₂H₂₈O₇). Because of the quality of the crystal and diffraction data, we have chosen invarioms, in addition to standard independent spherical atoms, for modelling and briefly discuss the different refinement results. The electrostatic potential, which is directly deducible from the invariom model, and the Hirshfeld surface are analysed and complemented with interaction‐energy computations to characterize intermolecular contacts. The boat‐like molecules stack along the a axis and are arranged as dimers of chains, which assemble as rows to form a three‐dimensional structure. Dispersive C—H…H—C and C—H…π interactions dominate, but nonclassical hydrogen bonds are present and reflect the overall rather weak electrostatic influence. A fingerprint plot of the Hirshfeld surface summarizes and visualizes the intermolecular interactions. The insight gained into the crystal structure of dibenzo‐21‐crown‐7 not only demonstrates the power of invariom refinement, Hirshfeld surface analysis and interaction‐energy computation, but also hints at favourable conditions for crystallizing solvent‐free crown ethers.     

Application of the Molecular Invariom Model for the Study of Interactions Involving Fluorine Atoms in the { $${\text{Yb}}_{{\text{2}}}^{{{\text{II}}}}$$ (μ2-OCH(CF3)2)3(μ3-OCH(CF3)2)2YbIII(OCH(CF3)2)2(THF)(Et2O)} Complex

Russian Journal of Coordination Chemistry - The electron density distributions obtained by the quantum-chemical (density functional theory) calculations and molecular invariom model in the trimeric...     

molSimplify: A toolkit for automating discovery in inorganic chemistry

We present an automated, open source toolkit for the first‐principles screening and discovery of new inorganic molecules and intermolecular complexes. Challenges remain in the automatic generation of candidate inorganic molecule structures due to the high variability in coordination and bonding, which we overcome through a divide‐and‐conquer tactic that flexibly combines force‐field preoptimization of organic fragments with alignment to first‐principles‐trained metal‐ligand distances. Exploration of chemical space is enabled through random generation of ligands and intermolecular complexes from large chemical databases. We validate the generated structures with the root mean squared (RMS) gradients evaluated from density functional theory (DFT), which are around 0.02 Ha/au across a large 150 molecule test set. Comparison of molSimplify results to full optimization with the universal force field reveals that RMS DFT gradients are improved by 40%. Seamless generation of input files, preparation and execution of electronic structure calculations, and post‐processing for each generated structure aids interpretation of underlying chemical and energetic trends. © 2016 Wiley Periodicals, Inc.     

Comparison of Experimental and Experimental–Theoretical Topological Characteristics of the Electron Density in the Crystalline Complex η6-[3-Acetyltetrahydro-6-Phenyl-2Н-1,3-oxazine]tricarbonylchromium(0)

Russian Journal of Coordination Chemistry - Experimental and experimental–theoretical studies (using the molecular invariom) of the electron density distribution are performed for the...     

Intermolecular interactions on amine‐cured epoxy matrices with different crosslink densities. Influence on the hole and specific volumes and the mechanical behavior

The architecture of an epoxy matrix was modified by curing the resin with mono‐/diamine mixtures having identical chemical structures. Both hole volume and specific volume variations were studied by positron annihilation lifetime spectroscopy and pressure‐volume‐temperature/density measurements, respectively. The average hole volume of the networks at room temperature slightly increased when the monoaminic chain extender content increased. The increment in the intermolecular interactions between functional groups of the networks chains, due to the less hindered nitrogen introduced by the monoamine, appears to be the responsible for the observed behavior. Besides, only small variations on the specific volume were observed on increasing the monoamine content, which points out that for a cured epoxy system, the chemical structure of the curing agent is mainly responsible for chain packing in the networks. On the other hand, intermolecular interactions between chains were considered as the key factor for fixing stiffness and strength. Thus, it was observed that the increase of the intermolecular interactions with the monoamine content produced a decrease in the sub‐T_g small‐range cooperative motions, which increased the low‐deformation mechanical properties at temperatures between β and α relaxations. This conclusion could be applied to previous investigations with epoxy matrices not fully crosslinked (nonstoichiometric or noncompletely cured formulations). Finally, it was found that fracture properties do not significantly depend either on the hole volume or on the intermolecular interactions. Fracture properties are more dependent on the crosslink density and the glass transition temperature. © 2009 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 47: 1240–1252, 2009     

Container Systems II: An Experimental Study of the High‐Pressure Intramolecular Cycloaddition of Tethered Furans and Anthracenes onto Norbornane Cyclobutene‐1,2‐diesters

A new class of container molecules is described and the first steps in producing protypes are reported. Central to the approach is the formation of polynorbornanes with cyclobutene‐1,2‐difurfuryl esters at the terminus or similar functionality at the bridgehead of a central norbornane subunit. The synthesis of the furfuryl starting materials is described as well as their anthracenyl counterparts. Conversion to the container systems involved the intermolecular linking of the furfuryl or anthracene by treatment with dimethyl acetylene dicarboxylate (DMAD) in a Diels–Alder (DA) protocol under thermal or high‐pressure (HP) conditions. In practice, no intermolecular linking occurred between the norbornane substrates and only products from DA 1:1‐addition with DMAD were produced. Intramolecular addition of one of the furfuryl units onto the cyclobutene π‐bond was detected under HP conditions, and this intermolecular product was capable of isolation and characterization by working at room temperature or below, but reverted to starting material above room temperature. When conducted in the presence of DMAD, a single 1:1‐adduct was obtained in which one furfuryl moiety was intramolecularly cyclized and the other present as the DMAD adduct; again this product underwent retro‐DA reaction at 40°C. Similar intermolecular cyclization was observed with the bis‐anthracenyl esters. The stereoselectivity of the intermolecular attack of the furfuryl diene with the dienophilic cyclobutene gave a single adduct by endo‐face attack in which the oxa‐bridge is endo‐positioned. Quantum chemical DFT calculations (B3LYP) predict that the formation of the endo‐isomer is kinetically favored and that relief of ring strain enhances the rate of retro‐Diels–Alder in the tethered system.     

Experimental and experimental-theoretical topological characteristics of the electron density distribution in the crystal of NCN-(2-pyridinecarbonitrile)-(3,6-di-tert-butylcatecholato)triphenylantimony(v)

Russian Chemical Bulletin - Experimental and experimental-theoretical studies (the invariom approach, whole-molecule aspherical scattering factors) of the electron density distribution were carried...     

Glycopeptide Mimetics Recapitulate High‐Mannose‐Type Oligosaccharide Binding and Function

High‐mannose‐type glycans (HMTGs) decorating viral spike proteins are targets for virus neutralization. For carbohydrate‐binding proteins, multivalency is important for high avidity binding and potent inhibition. To define the chemical determinants controlling multivalent interactions we designed glycopeptide HMTG mimetics with systematically varied mannose valency and spacing. Using the potent antiviral lectin griffithsin (GRFT) as a model, we identified by NMR spectroscopy, SPR, analytical ultracentrifugation, and microcalorimetry glycopeptides that fully recapitulate the specificity and kinetics of binding to Man₉GlcNAc₂Asn and a synthetic nonamannoside. We find that mannose spacing and valency dictate whether glycopeptides engage GRFT in a face‐to‐face or an intermolecular binding mode. Surprisingly, although face‐to‐face interactions are of higher affinity, intermolecular interactions are longer lived. These findings yield key insights into mechanisms involved in glycan‐mediated viral inhibition.     

In Situ Solid‐State Reactions Monitored by X‐ray Absorption Spectroscopy: Temperature‐Induced Proton Transfer Leads to Chemical Shifts

The dramatic colour and phase alteration with the solid‐state, temperature‐dependent reaction between squaric acid and 4,4′‐bipyridine has been probed in situ with X‐ray absorption spectroscopy. The electronic and chemical sensitivity to the local atomic environment through chemical shifts in the near‐edge X‐ray absorption fine structure (NEXAFS) revealed proton transfer from the acid to the bipyridine base through the change in nitrogen protonation state in the high‐temperature form. Direct detection of proton transfer coupled with structural analysis elucidates the nature of the solid‐state process, with intermolecular proton transfer occurring along an acid‐base chain followed by a domino effect to the subsequent acid‐base chains, leading to the rapid migration along the length of the crystal. NEXAFS thereby conveys the ability to monitor the nature of solid‐state chemical reactions in situ, without the need for a priori information or long‐range order.     

Weak Intermolecular Hydrogen Bonds with Fluorine: Detection and Implications for Enzymatic/Chemical Reactions,Chemical Properties,and Ligand/Protein Fluorine NMR Screening

It is known that strong hydrogen‐bonding interactions play an important role in many chemical and biological systems. However, weak or very weak hydrogen bonds, which are often difficult to detect and characterize, may also be relevant in many recognition and reaction processes. Fluorine serving as a hydrogen‐bond acceptor has been the subject of many controversial discussions and there are different opinions about it. It now appears that there is compelling experimental evidence for the involvement of fluorine in weak intramolecular or intermolecular hydrogen bonds. Using established NMR methods, we have previously characterized and measured the strengths of intermolecular hydrogen‐bond complexes involving the fluorine moieties CH₂F, CHF₂, and CF₃, and have compared them with the well‐known hydrogen‐bond complex formed between acetophenone and the strong hydrogen‐bond donor p‐fluorophenol. We now report evidence for the formation of hydrogen bonds involving fluorine with significantly weaker donors, namely 5‐fluoroindole and water. A simple NMR method is proposed for the simultaneous measurement of the strengths of hydrogen bonds between an acceptor and a donor or water. Important implications of these results for enzymatic/chemical reactions involving fluorine, for chemical and physical properties, and for ligand/protein ¹⁹F NMR screening are analyzed through experiments and theoretical simulations.     

ChemNetworks: A complex network analysis tool for chemical systems

Many intermolecular chemical interactions persist across length and timescales and can be considered to form a “network” or “graph.” Obvious examples include the hydrogen bond networks formed by polar solvents such as water or alcohols. In fact, there are many similarities between intermolecular chemical networks like those formed by hydrogen bonding and the complex and distributed networks found in computer science. Contemporary network analyses are able to dissect the complex local and global changes that occur within the network over multiple time and length scales. This work discusses the ChemNetworks software, whose purpose is to process Cartesian coordinates of chemical systems into a network/graph formalism and apply topological network analyses that include network neighborhood, the determination of geodesic paths, the degree census, direct structural searches, and the distribution of defect states of network. These properties can help to understand the network patterns and organization that may influence physical properties and chemical reactivity. The focus of ChemNetworks is to quantitatively describe intermolecular chemical networks of entire systems at both the local and global levels and as a function of time. The code is highly general, capable of converting a wide variety of systems into a chemical network formalism, including complex solutions, liquid interfaces, or even self‐assemblies. © 2013 Wiley Periodicals, Inc.     

Probing systematic errors in experimental charge density by multipole and invariom modeling: a twinned crystal of 1,10-phenanthroline hydrate

The modeling of experimental electron density in a twinned crystal of 1,10-phenanthroline hydrate within an invariom approach revealed its another advantage for charge density studies, which is assessing the reliability of chemically relevant information provided by a conventional multipole refinement against high-resolution X-ray diffraction data.     

BSSE‐corrected geometry and harmonic and anharmonic vibrational frequencies of formamide–water and formamide–formamide dimers

The basis set superposition error (BSSE) influence in the geometry structure, interaction energies, and intermolecular harmonic and anharmonic vibrational frequencies of cyclic formamide–formamide and formamide–water dimers have been studied using different basis sets (6‐31G, 6‐31G**, 6‐31++G**, D95V, D95V**, and D95V++**). The a posteriori “counterpoise” (CP) correction scheme has been compared with the a priori “chemical Hamiltonian approach” (CHA) both at the Hartree–Fock (HF) and second‐order Møller–Plesset many‐body perturbation (MP2) levels of theory. The effect of BSSE on geometrical parameters, interaction energies, and intermolecular harmonic vibrational frequencies are discussed and compared with the existing experimental data. As expected, the BSSE‐free CP and CHA interaction energies usually show less deep minima than those obtained from the uncorrected methods at both the HF and MP2 levels. Focusing on the correlated level, the amount of BSSE in the intermolecular interaction energies is much larger than that at the HF level, and this effect is also conserved in the values of the force constants and harmonic vibrational frequencies. All these results clearly indicate the importance of the proper BSSE‐free correlation treatment with the well‐defined basis functions. At the same time, the results show a good agreement between the a priori CHA and a posteriori CP correction scheme; this agreement is remarkable in the case of large and well‐balanced basis sets. The anharmonic frequency correction values also show an important BSSE dependence, especially for hydrogen bond stretching and for low frequencies belonging to the intermolecular normal modes. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005