Methylammonium Tetrel Halide Perovskite Ion Pairs and Their Dimers: The Interplay between the Hydrogen-, Pnictogen- and Tetrel-Bonding Interactions

The structural stability of the extensively studied organic-inorganic hybrid methylammonium tetrel halide perovskite semiconductors, MATtX₃ (MA = CH₃NH₃⁺; Tt = Ge, Sn, Pb; X = Cl, Br, I), arises as a result of non-covalent interactions between an organic cation (CH₃NH₃⁺) and an inorganic anion (TtX₃^-). However, the basic understanding of the underlying chemical bonding interactions in these systems that link the ionic moieties together in complex configurations is still limited. In this study, ion pair models constituting the organic and inorganic ions were regarded as the repeating units of periodic crystal systems and density functional theory simulations were performed to elucidate the nature of the non-covalent interactions between them. It is demonstrated that not only the charge-assisted N-H···X and C-H···X hydrogen bonds but also the C-N···X pnictogen bonds interact to stabilize the ion pairs and to define their geometries in the gas phase. Similar interactions are also responsible for the formation of crystalline MATtX₃ in the low-temperature phase, some of which have been delineated in previous studies. In contrast, the Tt···X tetrel bonding interactions, which are hidden as coordinate bonds in the crystals, play a vital role in holding the inorganic anionic moieties (TtX₃^-) together. We have demonstrated that each Tt in each [CH₃NH₃⁺•TtX₃^-] ion pair has the capacity to donate three tetrel (σ-hole) bonds to the halides of three nearest neighbor TtX₃^- units, thus causing the emergence of an infinite array of 3D TtX₆^4- octahedra in the crystalline phase. The TtX₄^4- octahedra are corner-shared to form cage-like inorganic frameworks that host the organic cation, leading to the formation of functional tetrel halide perovskite materials that have outstanding optoelectronic properties in the solid state. We harnessed the results using the quantum theory of atoms in molecules, natural bond orbital, molecular electrostatic surface potential and independent gradient models to validate these conclusions.

The inorganic chemistry of the cobalt corrinoids - an update

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B₁₂, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B₁₂-dependent enzymes is also given for the reader's convenience.

The Tetrel Bond and Tetrel Halide Perovskite Semiconductors

The ion pairs [Cs+•TtX3−] (Tt = Pb, Sn, Ge; X = I, Br, Cl) are the building blocks of all-inorganic cesium tetrel halide perovskites in 3D, CsTtX3, that are widely regarded as blockbuster materials for optoelectronic applications such as in solar cells. The 3D structures consist of an anionic inorganic tetrel halide framework stabilized by the cesium cations (Cs+). We use computational methods to show that the geometrical connectivity between the inorganic monoanions, [TtX3−]∞, that leads to the formation of the TtX64− octahedra and the 3D inorganic perovskite architecture is the result of the joint effect of polarization and coulombic forces driven by alkali and tetrel bonds. Depending on the nature and temperature phase of these perovskite systems, the Tt···X tetrel bonds are either indistinguishable or somehow distinguishable from Tt–X coordinate bonds. The calculation of the potential on the electrostatic surface of the Tt atom in molecular [Cs+•TtX3−] provides physical insight into why the negative anions [TtX3−] attract each other when in close proximity, leading to the formation of the CsTtX3 tetrel halide perovskites in the solid state. The inter-molecular (and inter-ionic) geometries, binding energies, and charge density-based topological properties of sixteen [Cs+•TtX3−] ion pairs, as well as some selected oligomers [Cs+•PbI3−]n (n = 2, 3, 4), are discussed.

The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond

The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX₆ (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials.

The Pnictogen Bond: The Covalently Bound Arsenic Atom in Molecular Entities in Crystals as a Pnictogen Bond Donor

In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity.

The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor

A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.

The Phosphorus Bond, or the Phosphorus-Centered Pnictogen Bond: The Covalently Bound Phosphorus Atom in Molecular Entities and Crystals as a Pnictogen Bond Donor

The phosphorus bond in chemical systems, which is an inter- or intramolecular noncovalent interaction, occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a covalently or coordinately bonded phosphorus atom in a molecular entity and a nucleophile in another, or the same, molecular entity. It is the second member of the family of pnictogen bonds, formed by the second member of the pnictogen family of the periodic table. In this overview, we provide the reader with a snapshot of the nature, and possible occurrences, of phosphorus-centered pnictogen bonding in illustrative chemical crystal systems drawn from the ICSD (Inorganic Crystal Structure Database) and CSD (Cambridge Structural Database) databases, some of which date back to the latter part of the last century. The illustrative systems discussed are expected to assist as a guide to researchers in rationalizing phosphorus-centered pnictogen bonding in the rational design of molecular complexes, crystals, and materials and their subsequent characterization.

The Cs2AgRhCl6 Halide Double Perovskite: A Dynamically Stable Lead-Free Transition-Metal Driven Semiconducting Material for Optoelectronics

A-Site doping with alkali ions, and/or metal substitution at the B and B'-sites, are among the key strategies in the innovative development of A 2BB'X6 halide double perovskite semiconducting materials for application in energy and device technologies. To this end, we have investigated an intriguing series of five halide-based non-toxic systems, A 2AgRhCl6 (A = Li, Na, K, Rb, and Cs), using density functional theory at the SCAN-rVV10 level. The lattice stability and bonding properties emanating from this study of A 2AgRhCl6 matched well with those that have already been synthesized, characterized and discussed [viz. Cs2AgBiX6 (X = Cl, Br)]. Exploration of traditional and recently proposed tolerance factors has enabled us to identify A 2AgRhCl6 (A = K, Rb and Cs) as stable double perovskites. The band structure and density of states calculations suggested that the electronic transition from the top of the valence band [Cl(3p)+Rh(4d)] to the bottom of the conduction band [(Cl(3p)+Rh(4d)] is inherently direct at the X-point of the first Brillouin zone. The (non-spin polarized) bandgap of these materials was found in the range 0.57-0.65 eV with SCAN-rVV10, which were substantially smaller than those computed with hybrid HSE06 and PBE0, and quasi-particle GW methods. This, together with the appreciable refractive index and high absorption coefficient in the region covering the range 1.0-4.5 eV, enabled us to demonstrate that A 2AgRhCl6 (A = K, Rb, and Cs) are likely candidate materials for photoelectric applications. The results of our phonon calculations at the harmonic level suggested that the Cs2AgRhCl6 is the only system that is dynamically stable (no imaginary frequencies found around the high symmetry lines of the reciprocal lattice), although the elastic moduli properties suggested all five systems examined are mechanically stable.

C70 Fullerene Cage as a Novel Catalyst for Efficient Proton Transfer Reactions between Small Molecules: A Theoretical study

When acids are supplied with an excess electron (or placed in an Ar or the more polarizable N₂ matrix) in the presence of species such as NH₃, the formation of ion-pairs is a likely outcome. Using density functional theory and first-principles calculations, however, we show that, without supplying an external electron or an electric field, or introducing photo-excitation and -ionization, a single molecule of HCl or HBr in the presence of a single molecule of water inside a C₇₀ fullerene cage is susceptible to cleavage of the σ-bond of the Brønsted-Lowry acid into X⁻ and H⁺ ions, with concomitant transfer of the proton along the reaction coordinate. This leads to the formation of an X⁻···⁺HOH₂ (X = Cl, Br) conjugate acid-base ion-pair, similar to the structure in water of a Zundel ion. This process is unlikely to occur in other fullerene derivatives in the presence of H₂O without significantly affecting the geometry of the carbon cage, suggesting that the interior of C₇₀ is an ideal catalytic platform for proton transfer reactions and the design of related novel materials. By contrast, when a single molecule of HF is reacted with a single molecule of H₂O inside the C₇₀ cage, partial proton transfers from HF to H₂O is an immediate consequence, as recently observed experimentally. The geometrical, energetic, electron density, orbital, optoelectronic and vibrational characteristics supporting these observations are presented. In contrast with the views that have been advanced in several recent studies, we show that the encaged species experiences significant non-covalent interaction with the interior of the cage. We also show that the inability of current experiments to detect many infrared active vibrational bands of the endo species in these systems is likely to be a consequence of the substantial electrostatic screening effect of the cage.

Nature of halogen-centered intermolecular interactions in crystal growth and design: Fluorine-centered interactions in dimers in crystalline hexafluoropropylene as a prototype

The wide occurrence of halogen-centered noncovalent interactions in crystal growth and design prompted this study, which includes a mini review of recent advances in the field. Particular emphasis is placed on providing compelling theoretical evidence of the formation of these interactions between sites of positive electrostatic potential, as well as between sites of negative electrostatic potential, localized on the electrostatic surfaces of the bound fluorine atoms in a prototypical system, hexafluoropropylene (C₃ F₆ ), upon its interaction with another same molecule to form (C₃ F₆ )₂ dimers. The existence of σ- and π-hole interactions is shown for the stable dimers. Even so, weakly bound interactions locally responsible in holding the molecular fragments together cannot and should not be overlooked since they are partly responsible for determining the overall geometry of the crystal. The results of combined quantum theory of atoms in molecules, molecular electrostatic surface potential, and reduced density gradient noncovalent interaction analyses showed that these latter interactions do indeed play a role in the stability and growth of crystalline C₃ F₆ itself and the (C₃ F₆ )₂ dimers. A symmetry adapted perturbation theory energy decomposition analysis leads to the conclusion that a great majority of the (C₃ F₆ )₂ dimers examined are the consequence of dispersion (and electrostatics), with nonnegligible contribution from polarization, which together competes with an exchange repulsion component to determine the equilibrium geometries. In a few structures of the (C₃ F₆ )₂ dimer, the fluorine is found to serve as a six-center five-bond donor/acceptor, as found for carbon in other systems (Malischewski and Seppelt, Angew. Chem. Int. Ed. 2017, 56, 368). © 2019 Wiley Periodicals, Inc.

Significance of hydrogen bonding and other noncovalent interactions in determining octahedral tilting in the CH3NH3PbI3 hybrid organic-inorganic halide perovskite solar cell semiconductor

The CH₃NH₃PbI₃ (methylammonium lead triiodide) perovskite semiconductor system has been viewed as a blockbuster research material during the last five years. Because of its complicated architecture, several of its technological, physical and geometrical issues have been examined many times. Yet this has not assisted in overcoming a number of problems in the field nor in enabling the material to be marketed. For instance, these studies have not clarified the nature and type of hydrogen bonding and other noncovalent interactions involved; the origin of hysteresis; the actual role of the methylammonium cation; the nature of polarity associated with the tetragonal geometry; the unusual origin of various frontier orbital contributions to the conduction band minimum; the underlying phenomena of spin-orbit coupling that causes significant bandgap reduction; and the nature of direct-to-indirect bandgap transition features. Arising from many recent reports, it is now a common belief that the I···H–N interaction formed between the inorganic framework and the ammonium group of CH₃NH₃⁺ is the only hydrogen bonded interaction responsible for all temperature-dependent geometrical polymorphs of the system, including the most stable one that persists at low-temperatures, and the significance of all other noncovalent interactions has been overlooked. This study focussed only on the low temperature orthorhombic polymorph of CH₃NH₃PbI₃ and CD₃ND₃PbI₃, where D refers deuterium. Together with QTAIM, DORI and RDG based charge density analyses, the results of density functional theory calculations with PBE with and without van der Waals corrections demonstrate that the prevailing view of hydrogen bonding in CH₃NH₃PbI₃ is misleading as it does not alone determine the a⁻b⁺a⁻ tilting pattern of the PbI₆⁴⁻ octahedra. This study suggests that it is not only the I···H/D–N, but also the I···H/D–C hydrogen/deuterium bonding and other noncovalent interactions (viz. tetrel-, pnictogen- and lump-hole bonding interactions) that are ubiquitous in the orthorhombic CH₃NH₃PbI₃/CD₃ND₃PbI₃ perovskite geometry. Their interplay determines the overall geometry of the polymorph, and are therefore responsible in part for the emergence of the functional optical properties of this material. This study also suggests that these interactions should not be regarded as the sole determinants of octahedral tilting since lattice dynamics is known to play a critical role as well, a common feature in many inorganic perovskites both in the presence and the absence of the encaged cation, as in CsPbI₃/WO₃ perovskites, for example.

The chalcogen bond: can it be formed by oxygen?

This study theoretically investigates the possibility of oxygen-centered chalcogen bonding in several complexes. Shown in the graph is such a bonding scenario formed between the electrophile on O in OF₂ and the nucleophile on O in H₂CO.

Halogen in materials design: Chloroammonium lead triiodide perovskite (ClNH3 PbI3 ) a dynamical bandgap semiconductor in 3D for photovoltaics

Methylammonium lead trihalides and their derivatives are photovoltaic materials. CH₃ NH₃ PbI₃ is the most efficient light harvester among all the known halide perovskites (PSCs). It is regarded as unsuitable for long-term stable solar cells, thus it is necessary to develop other types of PSC materials to achieve stable PSCs (Wang et al., Nat. Energy 2016, 2, 16195). Because of this, various research efforts are on-going to discover novel lead-based or lead-free single/double PSCs, which can be stable, synthesizable, transportable, abundant and efficient in solar energy conversion. Keeping these factors in mind, we report here the electronic structures, energetic stabilities and some materials properties (viz. band structures, density of states spectra and photo-carrier masses) of the PSC chloroammonium lead triiodide (ClNH₃ PbI₃ ). This emerges through compositional engineering that often focuses on B- and Y-site substitutions within the domain of the BMY₃ PSC stoichiometry. ClNH₃ PbI₃ is found to be stable as orthorhombic and pseudocubic polymorphs, which are analogous with the low and high temperature polymorphs of CH₃ NH₃ PbI₃ . The bandgap of ClNH₃ PbI₃ (values between 1.28 and 1.60 eV) is found to be comparable with that of CH₃ NH₃ PbI₃ , (1.58 eV), both obtained with periodic DFT at the PBE level of theory. Spin orbit coupling is shown to have a pronounced effect on both the magnitude and character of the bandgap. The computed results show that ClNH₃ PbI₃ may act as a competitor for CH₃ NH₃ PbI₃ for photovoltaics. © 2018 Wiley Periodicals, Inc.

A DFT assessment of some physical properties of iodine-centered halogen bonding and other non-covalent interactions in some experimentally reported crystal geometries

A set of six binary complexes that feature iodine-centered halogen bonding, extracted from structures deposited in the Cambridge Structure Database, has been examined computationally using density functional theory calculations with the M06-2X global hybrid, and dispersion corrected B3LYP-D3 and B97-D3, to determine their equilibrium geometries, binding energies and electronic properties. The results show that gas phase calculations are very informative in evaluating what occurs in the solid state, even though these calculations ignore the importance of lattice packing and counter ion effects. The calculated binding energies for the non-covalent interactions responsible for these complexes lie between -4.15 and -7.48 kcal mol-1 (M06-2X), which enables us to characterize them as weak-to-moderate in strength. The basis set superposition error energies are calculated to vary between 0.60 and 2.42 kcal mol-1 for all the complexes examined, even though an all-electron QZP basis set used in the analysis was of quadrupole-ζ (plus polarization) quality. Dispersion is found to have a profound effect on the binding energy of some of these complexes, and was estimated to be as large as 5.0 kcal mol-1. For one complex, the crystal geometry could not be precisely reproduced using a gas phase calculation. While both halogen- and hydrogen-bonding interactions were found competitive, they cooperate with each other to determine the stable configuration of the binary complex. The molecular electrostatic surface potential, quantum theory of atoms in molecules, and reduced density gradient non-covalent Interaction models were utilized to arrive at a fundamental understanding of the various inter- and intra-molecular molecular interactions involved, as well as some other previously-overlooked non-covalent interactions that emerge in the modelling.

Revealing Factors Influencing the Fluorine-Centered Non-Covalent Interactions in Some Fluorine-Substituted Molecular Complexes: Insights from First-Principles Studies

We examine the equilibrium structure and properties of six fully or partially fluorinated hydrocarbons and several of their binary complexes using computational methods. In the monomers, the electrostatic surface of the fluorine is predicted to be either entirely negative or weakly positive. However, its lateral sites are always negative. This enables the fluorine to display an anisotropic distribution of charge density on its electrostatic surface. While this is the electrostatic surface scenario of the fluorine atom, its negative sites in some of these monomers are shown to have the potential to engage in attractive engagements with the negative site(s) on the same atom in another molecule of the same type, or a molecule of a different type, to form bimolecular complexes. This is revealed by analyzing the results of current state-of-the-art computational approaches such as DFT, together with those obtained from the quantum theory of atoms in molecules, molecular electrostatic surface potential and symmetry adapted perturbation theories. We demonstrate that the intermolecular interaction energy arising in part from the universal London dispersion, which has been underappreciated for decades, is an essential factor in explaining the attraction between the negative sites, although energy arising from polarization strengthens the extent of the intermolecular interactions in these complexes.

Synthesis of copper and zinc 2-(pyridin-2-yl)imidazo[1,2-a]pyridine complexes and their potential anticancer activity

A small library of novel copper and zinc imidazo[1,2-a]pyridine complexes have been synthesized. Their structures were confirmed by X-ray diffraction crystallography and a selection of these compounds was tested against five cancer cell lines originating from breast cancer (MCF-7 and MDA-MB-231), leukemia (K562 and HL-60) and colorectal cancer (HT-29). The imidazo[1,2-a]pyridines and their zinc complexes showed poor anticancer activity, while the copper complexes were active against the cancer cell lines with IC₅₀ values comparable to and lower than camptothecin. For example, copper 6-bromo-N-cyclohexyl-2-(pyridin-2-yl)imidazo[1,2-a]pyridin-3-amine acetate 21 had an IC₅₀ value lower than 1 μM against the HT-29 cells. Fluorescence microscopy with acridine orange, Hoechst 33342 and ethidium bromide, used in a preliminary investigation to evaluate morphological changes showed that copper 6-bromo-N-cyclohexyl-2-(pyridin-2-yl)imidazo[1,2-a]pyridin-3-amine acetate 21 caused both apoptosis, necrosis and paraptosis in the MCF-7 and HL-60 cells. A select group of copper N-cyclohexyl-2-(pyridin-2-yl)imidazo[1,2-a]pyridin-3-amines (26, 27, 29 and 31) induced apoptosis, paraptosis and deformed nuclei in MCF-7 cells.

Phenylvinylcobalamin: an alkenylcobalamin featuring a ligand with a large trans influence

Cob(I)alamin reacts with phenylacetylene to produce two diastereomers in which the organic ligand is coordinated to the upper (β) and lower (α) face of the corrin ring, respectively. The isomers were separated chromatographically and characterised by ESI-MS and, in the case of the β isomer, by (1)H and (13)C NMR. Only the β isomer crystallised and its molecular structure, determined by X-ray diffraction, shows that the organic ligand coordinates Co(III) through the β carbon of the phenylvinyl ligand. The Co-C bond length is 2.004(8) Å while the Co-N bond length to the trans 5,6-dimethylbenzimidazole (dmbzm) base is 2.217(8) Å, one of the longest Co-Ndmbzm bond lengths known in an organocobalamin. Unlike benzylcobalamin (BzCbl), phenylvinylcobalamin (PhVnCbl) is stable towards homolysis. DFT calculations (BP86/TZVP) on model compounds of BzCbl and PhVnCbl show that the Co-C bond dissociation energy for homolysis to Co(II) and an organic radical in the former is 8 kcal mol(-1) lower than in the latter. An analysis of the electron density at the Co-C bond critical point using Bader's QTAIM approach shows that the Co-C bond in PhVnCbl is shorter, stronger and somewhat more covalent than that in BzCbl, and has some multiple bond character. Together with calculations that show that the benzyl radical is more stable than the phenylvinyl radical, this rationalises the stability of PhVnCbl compared to BzCbl. The phenylvinyl ligand has a large trans influence. The pKa for deprotonation of dmbzm and its coordination by the metal in β-PhVnCbl is 4.60 ± 0.01, one of the highest values reported to date in cobalamin chemistry. The displacement of dmbzm ligand by CN(-) in β-PhVnCbl occurs with log K = 0.7 ± 0.1; the trans influence order of C-donor ligands is therefore CN(-) < CCH < CHCH2 = PhVn < Me < Et.

Probing the nature of the Co(III) ion in corrins: comparison of reactions of aquacyanocobyrinic acid heptamethyl ester and aquacyano-stable yellow cobyrinic acid hexamethyl ester with neutral N-donor ligands

Equilibrium constants (log K) for substitution of coordinated H(2)O in aquacyanocobyrinic acid heptamethyl ester (aquacyanocobester, ACCbs) and aquacyano-stable yellow cobyrinic acid hexamethyl ester (aquacyano-stable yellow cobester, ACSYCbs), in which oxidation of the C5 carbon of the corrin interrupts the normal delocalized system of corrins, by neutral N-donor ligands (ammonia, ethanolamine, 2-methoxyethylamine, N-methylimidazole, and 4-methylpyridine) have been determined spectrophotometrically as a function of temperature. Log K values increase with the basicity of the ligand, but a strong compensation effect between ΔH and ΔS values causes a leveling effect. The aliphatic amines with a harder donor atom produce ΔH values that are more negative in their reactions with ACSYCbs than with ACCbs, while the softer, aromatic N donors produce more negative ΔH values with ACCbs than with ACSYCbs. Molecular modeling (DFT, M06L/SVP, and a quantum theory of atoms in molecules analysis of the electron density) shows that complexes of the aliphatic amines with SYCbs produce shorter and stronger Co-N bonds with less ionic character than the Co-N bonds of these ligands with the cobester. Conversely, the Co-N bond to the aromatic N donors is shorter, stronger, and somewhat less ionic in the complexes of the cobester than in those of the SYCbs. Therefore, the distinction between the harder Co(III) in ACSYCbs and softer Co(III) in ACCbs, reported previously for anionic ligands, is maintained for neutral N-donor ligands.

Helical self-assembly of 2-(1,4,7,10-tetraazacyclododecan-1-yl)cyclohexan-1-ol (cycyclen)

The title macrocyclic amino alcohol compound, C(14)H(30)N(4)O, is investigated as a solid-state synthon for the design of a self-assembled tubular structure. It crystallizes in a helical column constructed by stereospecific O-H···N and N-H···N interactions. The hydrogen-bonding interactions, dependent upon macrocyclic ring helicity and molecular conformation, link R,R and S,S enantiomers in a head-to-tail fashion, forming a continuous hydrophilic inner core.

Bis(2-hydroxyethyl)ammonium 2-bromophenolate

In the crystal structure of the 1:1 title salt, C₄H₁₂NO₂⁺·C₆H₄BrO⁻, hydrogen-bonding inter­actions originate from the ammonium cation, which adopts a syn conformation. A gauche relationship between the C—O and C—N bonds of the 2-hy­droxy­ethyl fragments also facilitates O—H⋯O inter­actions of bis­(2-hy­droxy­eth­yl)ammonium cation chains to phenolate O atoms. The resulting double-ion chains along [100] are further linked by N—H⋯O inter­actions, forming chains parallel to [110].

Bis(2-bromoethyl)ammonium bromide

The title salt, C₄H₁₀Br₂N⁺·Br⁻, crystallizes with four cations and four anions in the asymmetric unit. In the crystal, the bis­(2-bromo­eth­yl)ammonium cations and bromide anions are linked into chains by N—H⋯Br hydrogen bonds describing a binary C₂¹(4) motif along [010]. Each of these chains is formed by a unique cation and anion pair. The ammonium cations occur in the less preferred anti conformation, characterized by different NCCBr torsion angles. Adjacent chains are linked by weak C—H⋯Br inter­actions, forming a three-dimensional network. The crystal studied was a pseudo-merohedral twin with twin ratio 0.640 (2):0.360 (2).

4-(Dimethoxymethyl)phenyl 2,3,4,6-tetra-O-acetyl-β-D-glucopyranoside

The enanti­omerically pure title compound, C₂₃H₃₀O₁₂, crystallizes in the chiral space group P2₁2₁2₁. The O-acetyl­ated-glucopyran­oside moiety adopts a chair conformation. Numerous C—H⋯O inter­actions as well as a C—H⋯π inter­action are present in the crystal structure.

(2-Amino-phen-yl)methanol

The crystal strucure of the title compound, C₇H₉NO, displays N—H⋯O hydrogen bonds which link mol­ecules related by translation along the b axis, and O—H⋯N and further N—H⋯O hydrogen bonds which link mol­ecules related by the 2₁ screw axis along the c axis. The resulting combination is a hydrogen-bonded layer of mol­ecules parallel to (011).

Hydrogen-bond inter-actions in morpholinium bromide

In the title compound, C₄H₁₀NO⁺·Br⁻, which was synthesized by dehydration of diethano­lamine with HBr, morpholinium and bromide ions are linked into chains by N—H⋯Br hydrogen bonds describing a C₂¹(4) graph-set motif. Weaker bifurcated N—H⋯Br inter­actions join centrosymmetrically related chains through alternating binary graph-set R₄²(8) and R₂²(4) motifs, to form ladders along [100]. In addition, C—H⋯O inter­actions between centrosymmetric morpholinium cations link ladders, via(8) motifs, to yield sheets parallel to (101), which in turn are crosslinked by weak C—H⋯O inter­actions, related across a glide plane, to form a three-dimensional network.

NMR spectroscopy and molecular modelling studies of nitrosylcobalamin: further evidence that the deprotonated, base-off form is important for nitrosylcobalamin in solution

The structure of nitrosylcobalamin (NOCbl) in solution has been studied by NMR spectroscopy and the 1H and 13C NMR spectra have been assigned. 13C and 31P NMR chemical shifts, the UV-vis spectrum of NOCbl and the observed pKbase-off value of approximately 5.1 for NOCbl provide evidence that a significant fraction of NOCbl is present in the base-off, 5,6-dimethylbenzimidazole (DMB) deprotonated, form in solution. NOE-restrained molecular mechanics modelling of base-on NOCbl gave annealed structures with minor conformational differences in the flexible side chains and the nucleotide loop position compared with the X-ray structure. A molecular dynamics simulation at 300 K showed that DMB remains in close proximity to the alpha face of the corrin in the base-off form of NOCbl. Simulated annealing calculations produced two major conformations of base-off NOCbl. In the first, the DMB is perpendicular to the corrin and its B3 nitrogen is about 3.1 A away from and pointing directly at the metal ion; in the second the DMB is parallel to and tucked beneath the D ring of the corrin.

The crystal structure of halofantrine-ferriprotoporphyrin IX and the mechanism of action of arylmethanol antimalarials

The crystal structure of the complex formed between the antimalarial drug halofantrine and ferriprotoporphyrin IX (Fe(III)PPIX) has been determined by single crystal X-ray diffraction. The structure shows that halofantrine coordinates to the Fe(III) center through its alcohol functionality in addition to pi-stacking of the phenanthrene ring over the porphyrin. The length of the Fe(III)-O bond is consistent with an alkoxide and not an alcohol coordinating group. The iron porphyrin is five coordinate and monomeric. Changes in the electronic spectrum of Fe(III)PPIX upon addition of halofantrine base in acetonitrile solution are almost identical to those observed upon addition of quinidine free base in the same solvent. This suggests homologous binding. Molecular mechanics modeling of Fe(III)PPIX complexes of quinidine, quinine, 9-epiquinine and 9-epiquinidine based on this homology suggests that the antimalarially active quinidine and quinine can readily adopt conformations that permit formation of an intramolecular salt bridge between the protonated quinuclidine tertiary amino group and unprotonated heme propionate group, while the inactive epimers 9-epiquinidine and 9-epiquinine have to adopt high energy conformations in order to accommodate such salt bridge formation. We propose that salt bridge formation may interrupt formation of the hemozoin precursor dimer formed during the heme detoxification pathway and so account for the strong activity of the two active isomers.

Insights into porphyrin chemistry provided by the microperoxidases, the haempeptides derived from cytochrome c

The water-soluble haem-containing peptides obtained by proteolytic digestion of cytochrome c, the microperoxidases, have been used to explore aspects of the chemistry of iron porphyrins, and as mimics for some reactions catalysed by the haemoproteins, including the reactions catalysed by the peroxidases and the cytochromes P450. The preparation of the microperoxidases, their physical and chemical properties including their electronic structure, the kinetics and thermodynamics of their reactions with ligands, electrochemical studies and examples of their uses as haemoproteins mimics, is reviewed.