Metal-thiolate bonds in bioinorganic chemistry

Metal-thiolate active sites play major roles in bioinorganic chemistry. The M--S(thiolate) bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low-energy charge transfer transitions) reflect the high covalency of the M--S(thiolate) bonds. The energy of the metal-thiolate bond is fairly insensitive to its ionic/covalent and pi/sigma nature as increasing M--S covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving-Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the Cu(II) and Fe(III) ions, the cupric- and ferric-thiolate bonds are very covalent, with the former having strong pi and the latter having more sigma character. For the blue copper site, the high pi covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is pi in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H-bonding can significantly affect the covalency of the metal-thiolate bond and contribute to redox tuning by the protein environment.     

Low-Barrier Hydrogen Bonds in Negative Thermal Expansion Material H3[Co(CN)6]

The covalent nature of the low-barrier N−H−N hydrogen bonds in the negative thermal expansion material H₃[Co(CN)₆] has been established by using a combination of X-ray and neutron diffraction electron density analysis and theoretical calculations. This finding explains why negative thermal expansion can occur in a material not commonly considered to be built from rigid linkers. The pertinent hydrogen atom is located symmetrically between two nitrogen atoms in a double-well potential with hydrogen above the barrier for proton transfer, thus forming a low-barrier hydrogen bond. Hydrogen is covalently bonded to the two nitrogen atoms, which is the first experimentally confirmed covalent hydrogen bond in a network structure. Source function calculations established that the present N−H−N hydrogen bond follows the trends observed for negatively charge-assisted hydrogen bonds and low-barrier hydrogen bonds previously established for O−H−O hydrogen bonds. The bonding between the cobalt and cyanide ligands was found to be a typical donor–acceptor bond involving a high-field ligand and a transition metal in a low-spin configuration.     

Pyrazolate-bridging dinucleating ligands containing hydrogen-bond donors: synthesis and structure of their cobalt analogues

Convergent preparative routes to new urea-pyrazolate dinucleating ligands are described. Metal complexes of these ligands have hydrogen bond donors that are proximal to the metal centers that interact with other coordinated species. This is exemplified by Co(II) dimers with Co(II)-mu-Cl-Co(II) motifs, in which the chloro ligand is involved in four intramolecular hydrogen bonds. These noncovalent interactions appear to influence the Co(II)-Cl bonds, which are unusually long, having lengths greater than 2.5 A.     

First-second shell interactions in metal binding sites in proteins: a PDB survey and DFT/CDM calculations

The role of the second shell in the process of metal binding and selectivity in metalloproteins has been elucidated by combining Protein Data Bank (PDB) surveys of Mg, Mn, Ca, and Zn binding sites with density functional theory/continuum dielectric methods (DFT/CDM). Peptide backbone groups were found to be the most common second-shell ligand in Mg, Mn, Ca, and Zn binding sites, followed (in decreasing order) by Asp/Glu, Lys/Arg, Asn/Gln, and Ser/Thr side chains. Aromatic oxygen- or nitrogen-containing side chains (Tyr, His, and Trp) and sulfur-containing side chains (Cys and Met) are seldom found in the second coordination layer. The backbone and Asn/Gln side chain are ubiquitous in the metal second coordination layer as their carbonyl oxygen and amide hydrogen can act as a hydrogen-bond acceptor and donor, respectively, and can therefore partner practically every first-shell ligand. The second most common outer-shell ligand, Asp/Glu, predominantly hydrogen bonds to a metal-bound water or Zn-bound histidine and polarizes the H-O or H-N bond. In certain cases, a second-shell Asp/Glu could affect the protonation state of the metal ligand. It could also energetically stabilize a positively charged metal complex more than a neutral ligand such as the backbone and Asn/Gln side chain. As for the first shell, the second shell is predicted to contribute to the metal selectivity of the binding site by discriminating between metal cations of different ionic radii and coordination geometries. The first-shell-second-shell interaction energies decay rapidly with increasing solvent exposure of the metal binding site. They are less favorable but are of the same order of magnitude as compared to the respective metal-first-shell interaction energies. Altogether, the results indicate that the structure and properties of the second shell are dictated by those of the first layer. The outer shell is apparently designed to stabilize/protect the inner-shell and complement/enhance its properties.     

Cooperative Effect of a Classical and a Weak Hydrogen Bond for the Metal‐Induced Construction of a Self‐Assembled β‐Turn Mimic

A novel metal‐induced template for the self‐assembly of two independent phosphane ligands by means of unprecedented multiple noncovalent interactions (classical hydrogen bond, weak hydrogen bond, metal coordination, π‐stacking interaction) was developed and investigated. Our results address the importance and capability of weak hydrogen bonds (WHBs) as important attractive interactions in self‐assembling processes based on molecular recognition. Together with a classical hydrogen bond, WHBs may serve as promoters for the specific self‐assembly of complementary monomeric phosphane ligands into supramolecular hybrid structures. The formation of an intermolecular C? H???N hydrogen bond and its persistence in the solid state and in solution was studied by X‐ray crystal analysis, mass spectrometry and NMR spectroscopy analysis. Further evidence was demonstrated by DFT calculations, which gave specific geometric parameters for the proposed conformations and allowed us to estimate the energy involved in the hydrogen bonds that are responsible for the molecular recognition process. The presented template can be regarded as a new type of self‐assembled β‐turn mimic or supramolecular pseudo amino acid for the nucleation of β‐sheet structures when attached to oligopeptides.     

Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers

We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around C_amide C_aromatic (C_am C_ar) and N_amide C_aromtaic (N_am C_ar) bonds in arylamide‐foldamer building blocks. We found that differences of barrier height between models with different ortho‐aryl substituents stem from charge transfer and core interactions. In three‐center hydrogen‐bond (H‐bond) models with an NH proton donor H‐bound to two electronegative ortho‐aryl substituents, the interaction energy of the three‐center system is larger than in either of the two‐center H‐bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.     

Electron density distribution of an oxamato bridged Mn(II)-Cu(II) bimetallic chain and correlation to magnetic properties

The electron density distribution of the ferrimagnetic MnCu(pba)(H2O)3.2H2O chain compound, where pba stands for 1,3-propylenebis(oxamato), has been derived from high resolution X-ray diffraction measurements at 114 K using a multipolar model. The analysis of the chemical bonding has been carried out through the "Atoms in Molecules" formalism and thoroughly interpreted with regards to the strong intrachain and weak interchain magnetic couplings. The topological properties of the electron density on the oxamato bridge indicate large electron delocalization and conjugation effects, in addition to high charge transfer from both metals to the bridge. The resulting positive charges on Mn (+1.45 e) and Cu (+1.56 e) induce charge polarization of the bridge, leading to a shift of electron density from the central C atoms to the metal coordinating O and N atoms. The Mn-bridge interactions are mainly closed-shell interactions with low electron density at the corresponding bond critical points, whereas the Cu-bridge interactions exhibit significant covalent character. The Cu-N bonds are moreover stronger than the Cu-O bonds. The 3d Cu and Mn orbital populations are consistent with pyramidal and regular octahedral environments, respectively, in agreement with the loss of degeneracy due to ligand field effects. Interchain interaction pathways are evidenced by the existence of four bond critical points in hydrogen bond regions. Finally, these intrachain and interchain bonding features are correlated to the results of experimental and theoretical spin density distributions, as well as magnetic measurements.     

Water versus acetonitrile coordination to uranyl. Density functional study of cooperative polarization effects in solution

Optimizations at the BLYP and B3LYP levels are reported for mixed uranyl-water/acetonitrile complexes [UO(2)(H(2)O)(5-n)(MeCN)(n)](2+) (n = 0-5), in both the gas phase and a polarizable continuum modeling acetonitrile. Car-Parrinello molecular dynamics (CPMD) simulations have been performed for these complexes in the gas phase, and for selected species (n = 0, 1, 3, 5) in a periodic box of liquid acetonitrile. According to structural and energetic data, uranyl has a higher affinity for acetonitrile than for water in the gas phase, in keeping with the higher dipole moment and polarizability of acetonitrile. In acetonitrile solution, however, water is the better ligand because of specific solvation effects. Analysis of the dipole moment of the coordinated water molecule in [UO(2)(H(2)O)(MeCN)(4)](2+) reveals that the interaction with the second-shell solvent molecules (through fairly strong and persistent O-H···N hydrogen bonds) causes a significant increase of this dipole moment (by more than 1 D). This cooperative polarization of water reinforces the uranyl-water bond as well as the water solvation via strengthened (UO(2))OH(2)···NCMe hydrogen bonds. Such cooperativity is essentially absent in the acetonitrile ligands that make much weaker (UO(2))NCMe···NCMe hydrogen bonds. Beyond the uranyl case, this study points to the importance of cooperative polarization effects to enhance the M(n+) ion affinity for water in condensed phases involving M(n+)-OH(2)···A fragments, where A is a H-bond proton acceptor and M(n+) is a hard cation.     

C-H Group as proton donor by formation of a weak hydrogen bond

A systematic CNDO/2 study has been carried out on the weak C-H...F, C-H...O, and C-H...N hydrogen bonds. An H-bond formation has been revealed for proton donors with negative excess charge on the hydrogen. The concept of the positive character of the hydrogen as well as some essential features of the hydrogen bond have been discussed. Some useful correlations have been found and the importance of the charge shifts has been emphasized.     

Theoretical study of formic acid-sulfur dioxide dimers

We report the first theoretical study of noncovalent and covalent interactions in formic acid (FA)-SO(2) complexes. Using ab initio and DFT model chemistries, five stable noncovalent complexes were identified, as well as a covalent adduct, formic sulfurous anhydride HOSO(2)CHO. syn-FA is predicted to form two nonplanar bidentate complexes with SO(2): the more stable one contains a normal hydrogen bond donated by OH, and the less stable one contains a blue-shifted hydrogen bond donated by CH. Both are stabilized by charge transfer from FA to SO(2). anti-FA forms three planar complexes of nearly equal energy containing OH-to-SO(2) hydrogen bonds. Formic sulfurous anhydride forms via an endothermic concerted cycloaddition. Natural bond orbital analysis showed that the bidentate SO(2)-FA complexes are stabilized by n → π* donation from FA to SO(2), and back-donation from SO(2) n and π* orbitals into FA σ(OH)* or σ(CH)* orbitals. The bidentate formic acid-SO(2) complex that contains an O-H···O hydrogen bond is more stable than the similar nitric acid-SO(2) complex. The latter contains a stronger hydrogen bond but shows no O→S charge transfer interaction.     

How resonance assists hydrogen bonding interactions: an energy decomposition analysis

Block-localized wave function (BLW) method, which is a variant of the ab initio valence bond (VB) theory, was employed to explore the nature of resonance-assisted hydrogen bonds (RAHBs) and to investigate the mechanism of synergistic interplay between pi delocalization and hydrogen-bonding interactions. We examined the dimers of formic acid, formamide, 4-pyrimidinone, 2-pyridinone, 2-hydroxpyridine, and 2-hydroxycyclopenta-2,4-dien-1-one. In addition, we studied the interactions in beta-diketone enols with a simplified model, namely the hydrogen bonds of 3-hydroxypropenal with both ethenol and formaldehyde. The intermolecular interaction energies, either with or without the involvement of pi resonance, were decomposed into the Hitler-London energy (DeltaEHL), polarization energy (DeltaEpol), charge transfer energy (DeltaECT), and electron correlation energy (DeltaEcor) terms. This allows for the examination of the character of hydrogen bonds and the impact of pi conjugation on hydrogen bonding interactions. Although it has been proposed that resonance-assisted hydrogen bonds are accompanied with an increasing of covalency character, our analyses showed that the enhanced interactions mostly originate from the classical dipole-dipole (i.e., electrostatic) attraction, as resonance redistributes the electron density and increases the dipole moments in monomers. The covalency of hydrogen bonds, however, changes very little. This disputes the belief that RAHB is primarily covalent in nature. Accordingly, we recommend the term "resonance-assisted binding (RAB)" instead of "resonance-assisted hydrogen bonding (RHAB)" to highlight the electrostatic, which is a long-range effect, rather than the electron transfer nature of the enhanced stabilization in RAHBs.     

Binding of the two-valence-electron metal ions Sc(+), Ti(2+), and V(3+) to the second-row hydrides BeH(2), BH(3), NH(3), OH(2), and FH: a computational study

We report results from a computational study of the binding in complexes formed from one of the transition-metal ions Sc(+), Ti(2+), or V(3+), each of which has two valence electrons outside an argon core, and one of the second-row hydrides FH, OH(2), NH(3), BH(3), or BeH(2). The complexes that involve the electron-rich ligands FH, OH(2), and NH(3) have strong ion-dipole components to their binding. There are large stabilization energies for sigma-interactions that transfer charge from occupied lone-pair natural bond orbitals on the F, O, or N atom of the (idealized) Lewis structure into empty non-Lewis orbitals on the metal ions; these interactions effectively increase electron density in the bonding region between the metal ion and liganded atom, and the metal ions in these complexes act in the capacity of Lewis acids. The complexes formed from the electron-poor hydrides BH(3) and BeH(2) consistently incorporate bridging hydrogen atoms to support binding, and there are large stabilization energies for interactions that transfer charge from the Be-H or B-H bonds into the region between the metal ion and liganded atom. The metal ions in Sc(+)-BeH(2), Ti(2+)-BeH(2), Ti(2+)-BH(3), and V(3+)-BH(3) act in the capacity of Lewis acids, whereas the scandium ion in Sc(+)-BH(3) acts as a Lewis base.     

Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: implications to reactivity and relevance to the nitrogenase problem

Dinitrogen complexes of transition metals exhibit different binding geometries of N2 (end-on terminal, end-on bridging, side-on bridging, side-on end-on bridging), which are investigated by spectroscopy and DFT calculations, analyzing their electronic structure and reactivity. For comparison, a bis(mu-nitrido) complex, where the N--N bond has been split, has been studied as well. Most of these systems are highly covalent, and have strong metal-nitrogen bonds. In the present review, particular emphasis is put on a consideration of the activation of the coordinated dinitrogen ligand, making it susceptible to protonation, reactions with electrophiles or cleavage. In this context, theoretical, structural, and spectroscopic data giving informations on the amount of charge on the N2 unit are presented. The orbital interactions leading to a charge transfer from the metals to the dinitrogen ligand and the charge distribution within the coordinated N2 group are analyzed. Correlations between the binding mode and the observed reactivity of N2 are discussed.     

Binding of genistein to the estrogen receptor based on an experimental electron density study

In a continuing effort to determine a relationship between the biological function and the electronic properties of steroidal and nonsteroidal estrogens by analysis of the submolecular properties, an experimental charge density study has been pursued on the nonsteroidal phytoestrogen, genistein. X-ray diffraction data were obtained using a Rigaku R-Axis Rapid high-power rotating anode diffractometer with a curved image plate detector at 20(1) K. The total electron density was modeled using the Hansen-Coppens multipole model. Genistein packs in puckered sheets characterized by intra- and intermolecular hydrogen bonds while weaker intermolecular hydrogen bonds (O...H-C) exist between the sheets. A topological analysis of the electron density of genistein was then completed to characterize all covalent bonds, three O...H-O and four O...H-C intermolecular hydrogen bonds. Two O...H-O hydrogen bonds are incipient (partially covalent) type bonds, while the other O...H-O hydrogen bond and O...H-C hydrogen bonds are of the pure closed-shell interaction type. In addition, two intermolecular H...H interactions have also been characterized from the topology of the electron density. The binding of genistein to the estrogen receptor is discussed in terms of the electrostatic potential derived from the electron density distribution.     

FALDI‐based decomposition of an atomic interaction line leads to 3D representation of the multicenter nature of interactions

Atomic interaction lines (AILs) and the QTAIM's molecular graphs provide a predominantly two‐center viewpoint of interatomic interactions. While such a bicentric interpretation is sufficient for most covalent bonds, it fails to adequately describe both formal multicenter bonds as well as many non‐covalent interactions with some multicenter character. We present an extension to our Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) electron density (ED) decomposition scheme, with which we can measure how any atom‐pair's delocalized density concentrates, depletes or reduces the electron density in the vicinity of a bond critical point. We apply our method on five classical bonds/interactions, ranging from formal either two‐ or three‐center bonds, a non‐covalent interaction (an intramolecular hydrogen bond) to organometallic bonds with partial multicenter character. By use of 3D representation of specific atom‐pairs contributions to the delocalized density we (i) fully recover previous notion of multicenter bonding in diborane and predominant bicentric character of a single covalent C C bond, (ii) reveal a multicenter character of an intramolecular H‐bond and (iii) illustrate, relative to a Schrock carbene, a larger degree of multicenter M C interaction in a Fischer carbene (due to a presence of a heteroatom), whilst revealing the holistic nature of AILs from multicenter ED decomposition. © 2018 Wiley Periodicals, Inc.     

A discussion on the energies involved in specific adsorption of ions

The change in specific adsorption of I^? ions on the series of metals Au, Hg, Bi, Pb, Cd, and Ga is analyzed using data of specifically adsorbed charge and shift in potential of zero charge. Factors determining the change in adsorbability are discussed in the light of previous formulations. It is shown that the work connected with water desorption as an ion becomes adsorbed, usually neglected or underestimated in previous discussions, is very likely to be the main factor determining the change in adsorbability along the series of metals. A rough estimation of energies involved in water desorption suggests that metal—water surface bonds are probably weak on sp-metals so that they are unable to affect the reactivity of metal surfaces with respect to the gas phase as strong covalent surface bonds are involved, for instance in the hydrogen evolution reaction. Conversely, the strong effect of water desorption on the specific adsorption of ions may be an indication of ion—metal interactions to be substantially independent of the nature of the metal. This suggests that covalent contributions to the surface bond are apparently minor for metals more electropositive than Au.     

Effects induced by axial ligands binding to tetrapyrrole-based aromatic metallomacrocycles

The axial positions of planar metallomacrocycles are unoccupied. The positively charged metal is thus a potential binding site for electron-donating groups. The binding strength is affected by the central metal, the ligand, and the macrocycle. One ligand leads to the out-of-plane displacement of the central metal, whereas two ligands from two sides structurally neutralize each other. The axial ligand donates charge to the central metal and the macrocycle when the lone pair orients along the interaction axis. The frontier orbital levels are elevated because of the charge donated to the macrocycle. Even though the singlet-triplet gap and the absorption maximum do not change significantly upon binding, the redox chemistry is considerably affected by the shifts of orbital levels. The macrocyclic M-N bonds are weakened by the binding, but their natures remain almost unchanged. Calcium phthalocyanine is a special case, as the central calcium is too large to fit the cavity. Accordingly, multiple ligands facilely bind to the calcium from one side. The aluminum phthalocyanine halogen is another special case, as it has a halogen ligand coordinating to the aluminum through a nondative bond. This leads to some effects different from those caused by dative binding. When there is no considerable steric demand, the lone pair points along the interaction axis to facilitate the donation. When in a stacked dimer, the electron-rich group is part of a large molecule, and the orientation of the lone pair is approximately perpendicular to the interaction axis. This induces the charge loss of the central metal. Because metallomacrocycles are widespread in the biological, medical, and material sciences, the results from this study are expected to bring useful insights to these fields.     

SH···N and SH···P blue-shifting H-bonds and N···P interactions in complexes pairing HSN with amines and phosphines

Quantum calculations at the MP2/aug-cc-pVDZ level examine complexes pairing HSN with aliphatic amines and phosphines. Complexes are cyclic and contain two attractive interactions. The first is a SH···N/P H-bond in which the S-H covalent bond contracts and shifts its stretching frequency to the blue, more so for amines than for phosphines. The second interaction is different for the amines and phosphines. The amines engage in a NH···N H-bond comparable in strength to the aforementioned SH···N interaction. In contrast, the second interaction in the phosphine complexes is a direct N···P attraction without an intervening H. This interaction is due in part to opposite partial charges on the N and P atoms, as well as covalent forces generated by charge transfer effects.     

Ligands Based on Phosphine-Stabilized Aluminum(I), Boron(I), and Carbon(0)

A systematic quantum chemical study of the bonding in d⁶-transition-metal complexes, containing phosphine-stabilized, main-group-element fragments, (R₃P)₂E, as ligands (E=AlH, BH, CH⁺, C), is reported. By using energy decomposition analysis, it is demonstrated that a strong M−E bond is accompanied by weak P−E bonds, and vice versa. Although the Al−M bond is, for example, found to be very strong, the weak Al−P bond suggests that the corresponding metal complexes will not be stable towards phosphine dissociation. The interaction energies for the boron(I)-based ligand are lower, but still higher than those for two-carbon-based ligands. For neutral ligands, electrostatic interactions are the dominating contributions to metal–ligand bonding, whereas for the cationic ligand a significant destabilization, with weak orbital and even weaker electrostatic metal–ligand interactions, is observed. Finally, for iron(II) complexes, it is demonstrated that different reactivity patterns are expected for the four donor groups: the experimentally observed reversible E−H reductive elimination of the borylene-based ligand (E=BH) exhibits significantly higher barriers for the protonated carbodiphosphorane (CDP) ligand (E=CH) and would proceed through different intermediates and transition states. For aluminum, such reaction pathways are not feasible (E=AlH). Moreover, it is demonstrated that the metal hydrido complexes with CDP ligands might not be stable towards reduction and isomerization to a protonated CDP ligand and a reduced metal center.