Is it True That the Normal Valence‐Length Correlation Is Irrelevant for Metal–Metal Bonds?

The most intriguing feature of metal–metal bonds in inorganic compounds is an apparent lack of correlation between the bond order and the bond length. In this study, we combine a variety of literature data obtained by quantum chemistry and our results based on the empirical bond valence model (BVM), to confirm for the first time the existence of a normal exponential correlation between the effective bond order (EBO) and the length of the metal–metal bonds. The difference between the EBO and the formal bond order is attributed to steric conflict between the (TM)_n cluster (TM=transition metal) and its environment. This conflict, affected mainly by structural type, should cause high lattice strains, but electron redistribution around TM atoms, evident from the BVM calculations, results in a full or partial strain relaxation.     

Redox Potential and Crystal Chemistry of Hexanuclear Cluster Compounds

Most of TM₆-cluster compounds (TM = transition metal) are soluble in polar solvents, in which the cluster units commonly remain intact, preserving the same atomic arrangement as in solids. Consequently, the redox potential is often used to characterize structural and electronic features of respective solids. Although a high lability and variety of ligands allow for tuning of redox potential and of the related spectroscopic properties in wide ranges, the mechanism of this tuning is still unclear. Crystal chemistry approach was applied for the first time to clarify this mechanism. It was shown that there are two factors affecting redox potential of a given metal couple: Lever’s electrochemical parameters of the ligands and the effective ionic charge of TM, which in cluster compounds differs effectively from the formal value due to the bond strains around TM atoms. Calculations of the effective ionic charge of TMs were performed in the framework of bond valence model, which relates the valence of a bond to its length by simple Pauling relationship. It was also shown that due to the bond strains the charge depends mainly on the atomic size of the inner ligands.     

Strength of the [Z–I···Hal]− and [Z–Hal···I]− Halogen Bonds: Electron Density Properties and Halogen Bond Length as Estimators of Interaction Energy

Bond energy is the main characteristic of chemical bonds in general and of non-covalent interactions in particular. Simple methods of express estimates of the interaction energy, E_int, using relationships between E_int and a property which is easily accessible from experiment is of great importance for the characterization of non-covalent interactions. In this work, practically important relationships between E_int and electron density, its Laplacian, curvature, potential, kinetic, and total energy densities at the bond critical point as well as bond length were derived for the structures of the [Z–I···Hal]⁻ and [Z–Hal···I]⁻ types bearing halogen bonds and involving iodine as interacting atom(s) (totally 412 structures). The mean absolute deviations for the correlations found were 2.06–4.76 kcal/mol.     

H2XP…SHY复合物中磷键与硫键的理论研究

用从头算量子化学方法MP2 与CCSD(T)研究了H₂XP和SHY (X, Y=H, F, Cl, Br)分子的P与S之间形成的磷键X―P…S与硫键Y―S…P的本质与规律以及取代基X与Y对成键的影响. 计算结果表明, 硫键比磷键强, 连接在Lewis 酸上的取代基的电负性增大导致形成的磷键或硫键增强, 键能增大, 对单体的结构和性质的影响也增大; 而连接在Lewis 碱上的取代基效应则相反. 硫键键能为8.37-23.45 kJ·mol^-1, 最强的硫键结构是Y 电负性最大而X 电负性最小的HFS…PH₃, CCSD(T)计算的键能是16.04 kJ·mol^-1; 磷键键能为7.54-14.65 kJ·mol^-1, 最强的磷键结构是X 电负性最大而Y 电负性最小的H₂FP…SH₂, CCSD(T)计算的键能是12.52 kJ·mol^-1. 对磷键与硫键能量贡献较大的是交换与静电作用. 分子间超共轭lp(S)-σ^*(PX)与lp(P)-σ^*(SY)对磷键与硫键的形成起着重要作用, 它导致单体的极化, 其中硫键的极化效应较大, 从而有一定的共价特征.     

Classification of So-Called Non-Covalent Interactions Based on VSEPR Model

The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.     

Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.     

Additive components of heteroatom influence in substituted alkanes. Polarization and depolarization of bonds

The general expression for the common one-electron density matrix (DM) of saturated organic molecules obtained previously in the framework of the Hückel type model (V. Gineityte, J. Mol. Struct. (Theochem) 343 (1995) 183) has been applied to reveal the additive components of the heteroatom influence in substituted alkanes. To this end, the occupation number of a basis orbital has been expressed as a sum of three terms describing the polarization and depolarization of bonds and the intramolecular charge transfer. These terms, in turn, have been related to certain types of direct (through-space) and indirect (through-bond) interactions of bond orbitals (BOs). In particular, changes in the secondary polarization of C-C and C-H bonds under the influence of a heteroatom giving rise to their induced dipole moments has been related to differences in the indirect interaction between the two BOs of the given bond before and after substitution. Additive quantum-chemical analogues of the classical inductive and electron-donating effects have been established. The above-mentioned expressions for the occupation numbers have been also applied to substantiate the implicit postulates of the classical chemistry about additivity of the heteroatom influence in substituted alkanes.     

Transition‐Metal‐Mediated and ‐Catalyzed C−F Bond Activation by Fluorine Elimination

The activation of carbon–fluorine (C?F) bonds is an important topic in synthetic organic chemistry. Metal‐mediated and ‐catalyzed elimination of β‐ or α‐fluorine proceeds under milder conditions than oxidative addition to C?F bonds. The β‐ or α‐fluorine elimination is initiated from organometallic intermediates having fluorine substituents on carbon atoms β or α to metal centers, respectively. Transformations through these elimination processes (C?F bond cleavage), which are typically preceded by carbon–carbon (or carbon–heteroatom) bond formation, have been increasingly developed in the past five years as C?F bond activation methods. In this Minireview, we summarize the applications of transition‐metal‐mediated and ‐catalyzed fluorine elimination to synthetic organic chemistry from a historical perspective with early studies and from a systematic perspective with recent studies.     

Selective cleavage of unactivated arene ring C–C bonds by iridium: key roles of benzylic C–H activation and metal–metal cooperativity

The cleavage of aromatic C–C bonds is central for conversion of fossil fuels into industrial chemicals and designing novel arene functionalisations through ring opening, expansion and contraction. However, the current progress is hampered by both the lack of experimental examples of selective oxidative addition of aromatic C–C bonds and limited understanding of the factors that favour insertion into the C–C rather than the C–H bonds. Here, we describe the comprehensive mechanism of the only reported chemo- and regioselective insertion of a transition metal into a range of substituted arene rings in simple iridium(i) complexes. The experimental and computational data reveal that this ring cleavage requires both reversible scission of a benzylic C–H bond and cooperativity of two Ir centres sandwiching the arene in the product-determining intermediate. The mechanism explains the chemoselectivity and scope of this unique C–C activation in industrially important methylarenes and provides a general insight into the role of metal–metal cooperativity in the cleavage of unsaturated C–C bonds.

The detailed mechanism of iridium-mediated C–C cleavage in unactivated arenes reveals the key factors enabling the process and helps predict the scope of the cleavage reaction.     

A–X⋯σ Interactions—Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.     

Recent Advances and Trends in Chemical CPP–Drug Conjugation Techniques

This review summarizes recent developments in conjugation techniques for the synthesis of cell-penetrating peptide (CPP)–drug conjugates targeting cancer cells. We will focus on small organic molecules as well as metal complexes that were used as cytostatic payloads. Moreover, two principle ways of coupling chemistry will be discussed direct conjugation as well as the use of bifunctional linkers. While direct conjugation of the drug to the CPP is still popular, the use of bifunctional linkers seems to gain increasing attention as it offers more advantages related to the linker chemistry. Thus, three main categories of linkers will be highlighted, forming either disulfide acid-sensitive or stimuli-sensitive bonds. All techniques will be thoroughly discussed by their pros and cons with the aim to help the reader in the choice of the optimal conjugation technique that might be used for the synthesis of a given CPP–drug conjugate     

A polarizable dipole–dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen‐bonded complexes

In this article, a polarizable dipole–dipole interaction model is established to estimate the equilibrium hydrogen bond distances and the interaction energies for hydrogen‐bonded complexes containing peptide amides and nucleic acid bases. We regard the chemical bonds N? H, C?O, and C? H as bond dipoles. The magnitude of the bond dipole moment varies according to its environment. We apply this polarizable dipole–dipole interaction model to a series of hydrogen‐bonded complexes containing the N? H···O?C and C? H···O?C hydrogen bonds, such as simple amide‐amide dimers, base‐base dimers, peptide‐base dimers, and β‐sheet models. We find that a simple two‐term function, only containing the permanent dipole–dipole interactions and the van der Waals interactions, can produce the equilibrium hydrogen bond distances compared favorably with those produced by the MP2/6‐31G(d) method, whereas the high‐quality counterpoise‐corrected (CP‐corrected) MP2/aug‐cc‐pVTZ interaction energies for the hydrogen‐bonded complexes can be well‐reproduced by a four‐term function which involves the permanent dipole–dipole interactions, the van der Waals interactions, the polarization contributions, and a corrected term. Based on the calculation results obtained from this polarizable dipole–dipole interaction model, the natures of the hydrogen bonding interactions in these hydrogen‐bonded complexes are further discussed. © 2013 Wiley Periodicals, Inc.     

Trajectory of Approach of a Zinc–Hydrogen Bond to Transition Metals

Through a dramatic advance in the coordination chemistry of the zinc–hydride bond, we describe the trajectory for the approach of this bond to transition metals. The dynamic reaction coordinate was interrogated through analysis of a series of solid state structures and is one in which the TM‐H‐Zn angle becomes increasingly acute as the TM–Zn distance decreases. Parallels may be drawn with the oxidative addition of boron–hydrogen and silicon–hydrogen bonds to transition metal centers.     

Metal complexes of a phenol-tailed porphyrin with different hydrogen bonds

Hydrogen bonds are very common and important interactions in biological systems, they are used to control the microenvironment around metal centers. It is a challenge to develop appropriate models for studying hydrogen bonds. We have synthesized two metal complexes of the phenol-tailed porphyrin, [Zn(HL)] and [Fe(HL)(C₆H₄(OH)(O))]. X-ray crystallography reveals that the porphyrin functions as a dianion HL^2? and the phenol OH is involved in hydrogen bonds in both structures. In [Zn(HL)], an intramolecular hydrogen bond is formed between the carbonyl oxygen and OH. In [Fe(HL)(C₆H₄(OH)(O))], the unligated O(5) of the ligand is involved in two hydrogen bonds, as a hydrogen bond donor and a hydrogen bond acceptor. The overall electronic effect on the ligand could be very small, with negligible impact on the structure and the spin state of iron(III). The structural differences caused by the hydrogen bonds are also discussed.     

Saturated Heavier Group 14 Compounds as ‐Electron‐Acceptor (Z‐Type) Ligands

This review article describes the chemistry of transition‐metal complexes containing heavier group 14 elements (Si, Ge, and Sn) as the σ‐electron‐acceptor (Z‐type) ligands and discusses the characteristics of bonds between the transition metal and Z‐type ligand. Moreover, we review the iridium hydride mediated cleavage of E–X bonds (E=Si, Ge; X=F, Cl), where the key intermediates are pentacoordinate silicon or germanium compounds bearing a dative M→E bond.     

A Geometric Definition of Short to Medium Range Hydrogen-Mediated Interactions in Proteins

We present a method to rapidly identify hydrogen-mediated interactions in proteins (e.g., hydrogen bonds, hydrogen bonds, water-mediated hydrogen bonds, salt bridges, and aromatic π-hydrogen interactions) through heavy atom geometry alone, that is, without needing to explicitly determine hydrogen atom positions using either experimental or theoretical methods. By including specific real (or virtual) partner atoms as defined by the atom type of both the donor and acceptor heavy atoms, a set of unique angles can be rapidly calculated. By comparing the distance between the donor and the acceptor and these unique angles to the statistical preferences observed in the Protein Data Bank (PDB), we were able to identify a set of conserved geometries (15 for donor atoms and 7 for acceptor atoms) for hydrogen-mediated interactions in proteins. This set of identified interactions includes every polar atom type present in the Protein Data Bank except OE1 (glutamate/glutamine sidechain) and a clear geometric preference for the methionine sulfur atom (SD) to act as a hydrogen bond acceptor. This method could be readily applied to protein design efforts.     

The Exchange of Cyclometalated Ligands

Reactions of cyclometalated compounds are numerous. This account is focused on one of such reactions, the exchange of cyclometalated ligands, a reaction between a cyclometalated compound and an incoming ligand that replaces a previously cyclometalated ligand to form a new metalacycle: + H-C*~Z ⇄ + H-C~Y. Originally discovered for Pd^II complexes with Y/Z = N, P, S, the exchange appeared to be a mechanistically challenging, simple, and convenient routine for the synthesis of cyclopalladated complexes. Over four decades it was expanded to cyclometalated derivatives of platinum, ruthenium, manganese, rhodium, and iridium. The exchange, which is also questionably referred to as transcyclometalation, offers attractive synthetic possibilities and assists in disclosing key mechanistic pathways associated with the C–H bond activation by transition metal complexes and C–M bond cleavage. Both synthetic and mechanistic aspects of the exchange are reviewed and discussed.     

Observing the 3D Chemical Bond and its Energy Distribution in a Projected Space

Our curiosity-driven desire to “see” chemical bonds dates back at least one-hundred years, perhaps to antiquity. Sweeping improvements in the accuracy of measured and predicted electron charge densities, alongside our largely bondcentric understanding of molecules and materials, heighten this desire with means and significance. Here we present a method for analyzing chemical bonds and their energy distributions in a two-dimensional projected space called the condensed charge density. Bond “silhouettes” in the condensed charge density can be reverse-projected to reveal precise three-dimensional bonding regions we call bond bundles. We show that delocalized metallic bonds and organic covalent bonds alike can be objectively analyzed, the formation of bonds observed, and that the crystallographic structure of simple metals can be rationalized in terms of bond bundle structure. Our method also reproduces the expected results of organic chemistry, enabling the recontextualization of existing bond models from a charge density perspective.     

Dual XH–π Interaction of Hexafluoroisopropanol with Arenes

The dual XH (OH and CH) hydrogen-bond-donating property of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and the strong dual XH–π interaction with arenes were firstly disclosed by theoretical studies. Here, the high accuracy post-Hartree–Fock methods, CCSD(T)/CBS, reveal the interaction energy of HFIP/benzene complex (−7.22 kcal/mol) and the contribution of the electronic correlation energy in the total interaction energy. Strong orbital interaction between HFIP and benzene was found by using the DFT method in this work to disclose the dual XH–π intermolecular orbital interaction of HFIP with benzene-forming bonding and antibonding orbitals resulting from the orbital symmetry of HFIP. The density of states and charge decomposition analyses were used to investigate the orbital interactions. Isopropanol (IP), an analogue of HFIP, and chloroform (CHCl₃) were studied to compare them with the classical OH–π, and non-classical CH–π interactions. In addition, the influence of the aggregating effect of HFIP, and the numbers of substituted methyl groups in benzene rings were also studied. The interaction energies of HFIP with the selected 24 common organic compounds were calculated to understand the role of HFIP as solvent or additive in organic transformation in a more detailed manner. A single-crystal X-ray diffraction study of hexafluoroisopropyl benzoate further disclosed and confirmed that the CH of HFIP shows the non-classical hydrogen-bond-donating behavior.