Azido-mediated intermolecular interactions of transition metal complexes.

The coordinated azido ligand has a variety of ways to establish intermolecular contacts whose nature is computationally analysed in this work on dimers of the [N3-Hg(CF3)] complex with different interactions involving only N⋯N contacts, or with an additional Hg⋯N contact. The applied tools include the molecular electrostatic map of the monomer, an energy decomposition analysis (EDA), a topological AIM analysis of the electron density and the study of NCI (non-covalent interactions) isosurfaces. The interactions between two azido ligands are found to be weakly stabilizing (by 0.2 to 2.7 kcal mol-1), topology-dependent and require dispersion forces to complement orbital and electrostatic stabilization. Those interactions are supplemented by the formation of simultaneous Hg⋯N secondary interactions by about -1 kcal mol-1, and by the ability of the monomer to simultaneously interact with several neighbours in the crystal structure.

Performance of TDDFT Vertical Excitation Energies of Core-Substituted Naphthalene Diimides.

We have evaluated the performance of various density functionals, covering generalized gradient approximation (GGA), global hybrid (GH) and range-separated hybrid (RSH), using time dependent density functional theory (TDDFT) for computing vertical excitation energies against experimental absorption maximum (λmax ) for a set of 10 different core-substituted naphthalene diimides (cNDI) recorded in dichloromethane. The computed excitation in case of GH PBE0 is most accurate while the trend is most systematic with RSH LCY-BLYP compared to λmax . We highlight the importance of including solvent effects for optimal agreement with the λmax . Increasing the basis set size from TZ2P to QZ4P has a negligible influence on the computed excitation energies. Notably, RSH CAMY-B3LYP gave the least error for charge-transfer excitation. The poorest agreement with λmax is obtained with semi-local GGA functionals. Use of the optimally-tuned RSH LCY-BLYP* is not recommended because of the high computational cost and marginal improvement in results.

Correction: New light on an old debate: does the RCN-PtCl2 bond include any back-donation? RCN ← PtCl2 backbonding vs. the IR νC[triple bond, length as m-dash]N blue-shift dichotomy in organonitriles-platinum(ii) complexes. A thorough density functional theory - energy decomposition analysis study.

Correction for 'New light on an old debate: does the RCN-PtCl2 bond include any back-donation? RCN ← PtCl2 backbonding vs. the IR νC[triple bond, length as m-dash]N blue-shift dichotomy in organonitriles-platinum(ii) complexes. A thorough density functional theory - energy decomposition analysis study' by Girolamo Casella et al., Dalton Trans., 2019, DOI: 10.1039/c9dt02440a.

Efficient Copper-Catalyzed Multicomponent Synthesis of N-Acyl Amidines via Acyl Nitrenes.

Direct synthetic routes to amidines are desired, as they are widely present in many biologically active compounds and organometallic complexes. N-Acyl amidines in particular can be used as a starting material for the synthesis of heterocycles and have several other applications. Here, we describe a fast and practical copper-catalyzed three-component reaction of aryl acetylenes, amines, and easily accessible 1,4,2-dioxazol-5-ones to N-acyl amidines, generating CO2 as the only byproduct. Transformation of the dioxazolones on the Cu catalyst generates acyl nitrenes that rapidly insert into the copper acetylide Cu-C bond rather than undergoing an undesired Curtius rearrangement. For nonaromatic dioxazolones, [Cu(OAc)(Xantphos)] is a superior catalyst for this transformation, leading to full substrate conversion within 10 min. For the direct synthesis of N-benzoyl amidine derivatives from aromatic dioxazolones, [Cu(OAc)(Xantphos)] proved to be inactive, but moderate to good yields were obtained when using simple copper(I) iodide (CuI) as the catalyst. Mechanistic studies revealed the aerobic instability of one of the intermediates at low catalyst loadings, but the reaction could still be performed in air for most substrates when using catalyst loadings of 5 mol %. The herein reported procedure not only provides a new, practical, and direct route to N-acyl amidines but also represents a new type of C-N bond formation.

Secondary Electrostatic Interaction Model Revised: Prediction Comes Mainly from Measuring Charge Accumulation in Hydrogen-Bonded Monomers.

The secondary electrostatic interaction (SEI) model is often used to predict and explain relative hydrogen bond strengths of self-assembled systems. The SEI model oversimplifies the hydrogen-bonding mechanisms by viewing them as interacting point charges, but nevertheless experimental binding strengths are often in line with the model's predictions. To understand how this rudimentary model can be predictive, we computationally studied two tautomeric quadruple hydrogen-bonded systems, DDAA-AADD and DADA-ADAD. Our results reveal that when the proton donors D (which are electron-donating) and the proton acceptors A (which are electron-withdrawing) are grouped together as in DDAA, there is a larger accumulation of charge around the frontier atoms than when the proton donor and acceptor groups are alternating as in DADA. This accumulation of charge makes the proton donors more positive and the proton acceptors more negative, which enhances both the electrostatic and covalent interactions in the DDAA dimer. The SEI model is thus predictive because it provides a measure for the charge accumulation in hydrogen-bonded monomers. Our findings can be understood from simple physical organic chemistry principles and provide supramolecular chemists with meaningful understanding for tuning hydrogen bond strengths and thus for controlling the properties of self-assembled systems.

Comparison of the DFT-SAPT and Canonical EDA Schemes for the Energy Decomposition of Various Types of Noncovalent Interactions.

Interaction energies computed with density functional theory can be divided into physically meaningful components by symmetry-adapted perturbation theory (DFT-SAPT) or the canonical energy decomposition analysis (EDA). In this work, the decomposition results obtained by these schemes were compared for more than 200 hydrogen-, halogen-, and pnicogen-bonded, dispersion-bound, and mixed complexes to investigate their similarity in the evaluation of the nature of noncovalent interactions. BLYP functional with D3(BJ) correction was used for the EDA scheme, whereas asymptotically corrected PBE0 functional for DFT-SAPT provided some of the best combinations for description of noncovalent interactions. Both schemes provide similar results concerning total interaction energies and insight into the individual energy components. For most complexes, the dominant energetic term was identified equally by both decomposition schemes. Because the canonical EDA is computationally less demanding than the DFT-SAPT, the former can be especially used in cases where the systems investigated are very large.

Relevance of Orbital Interactions and Pauli Repulsion in the Metal-Metal Bond of Coinage Metals.

The importance of relativity and dispersion in metallophilicity has been discussed in numerous studies. The existence of hybridization in the bonding between closed shell d10-d10 metal atoms has also been speculated, but the presence of attractive MO interaction in the metal-metal bond is still a matter of an ongoing debate. In this comparative study, a quantitative molecular orbital analysis and energy decomposition is carried out on the metallophilic interaction in atomic dimers (M+···M+) and molecular perpendicular [H3P-M-X]2 (where M = Cu, Ag, and Au; X = F, Cl, Br, and I). Our computational studies prove that besides the commonly accepted dispersive interactions, orbital interactions and Pauli repulsion also play a crucial role in the strength and length of the metal-metal bond. Although for M+···M+ the orbital interaction is larger than the Pauli repulsion, leading to a net attractive MO interaction, the bonding mechanism in perpendicular [H3P-M-X] dimers is different due to the larger separation between the donor and acceptor orbitals. Thus, Pauli repulsion is much larger, and two-orbital, four-electron repulsion is dominant.

Reversible Self-Assembly of Water-Soluble Gold(I) Complexes.

The reaction of the gold polymers containing bipyridyl and terpyridyl units, [Au(C≡CC15H10N3)]n and [Au(C≡CC10H7N2)]n, with the water-soluble phosphines 1,3,5-triaza-7-phosphatricyclo[3.3.1.13.7]decane and 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane gives rise to the formation of four gold(I) alkynyl complexes that self-assemble in water (H2O) and dimethyl sulfoxide (DMSO), through different intermolecular interactions, with an impact on the observed luminescence displayed by the supramolecular assemblies. A detailed analysis carried out by NMR studies performed in different DMSO/deuterated H2O mixtures indicates the presence of two different assembly modes in the aggregates: (i) chain assemblies, which are based mainly on aurophilic interactions, and (ii) stacked assemblies, which are based on Au···π and π···π interactions. These different supramolecular environments can also be detected by their intrinsic optical properties (differences in absorption and emission spectra) and are predicted by the changes in the relative binding energy from density functional theory calculations carried out in DMSO and H2O. Small-angle X-ray scattering (SAXS) experiments performed in the same mixture of solvents are in agreement with the formation of aggregates in all cases. The aromatic units chosen, bipyridine and terpyridine, allow the use of external stimuli to reversibly change the aggregation state of the supramolecular assemblies. Interaction with the Zn2+ cation is observed to disassemble the aggregates, while encapsulating agents competing for Zn2+ complexation revert the process to the aggregation stage, as verified by SAXS and NMR. The adaptive nature of the supramolecular assemblies to the metal-ion content is accompanied by significant changes in the absorption and emission spectra, signaling the aggregation state and also the content on Zn2+.

The influence of substituents and the environment on the NMR shielding constants of supramolecular complexes based on A-T and A-U base pairs.

In the present study, we have theoretically analyzed supramolecular complexes based on the Watson-Crick A-T and A-U base pairs using dispersion-corrected density functional theory (DFT). Hydrogen atoms H8 and/or H6 in the natural adenine and thymine/uracil bases were replaced, respectively, by substituents X8, Y6 = NH-, NH2, NH3+ (N series), O-, OH, OH2+ (O series), F, Cl or Br (halogen series). We examined the effect of the substituents on the hydrogen-bond lengths, strength and bonding mechanism, and the NMR shielding constants of the C2-adenine and C2-thymine/uracil atoms in the base pairs. The general belief in the literature that there is a direct connection between changes in the hydrogen-bond strength and the C2-adenine shielding constant is conclusively rejected by our computations.

Substituent effects on the optical properties of naphthalenediimides: A frontier orbital analysis across the periodic table.

A comprehensive theoretical treatment is presented for the electronic excitation spectra of ca. 50 different mono-, di-, and tetrasubstituted naphthalenediimides (NDI) using time-dependent density functional theory (TDDFT) at ZORA-CAM-B3LYP/TZ2P//ZORA-BP86/TZ2P with COSMO for simulating the effect of dichloromethane (DCM) solution. The substituents -XHn are from groups 14-17 and rows 2-5 of the periodic table. The lowest dipole-allowed singlet excitation (S0 -S1 ) of the monosubstituted NDIs can be tuned from 3.39 eV for -F to 2.42 eV for -TeH, while the S0 -S2 transition is less sensitive to substitution with energies ranging between 3.67 eV for -CH3 and 3.44 eV for -SbH2 . In the case of NDIs with group-15 and -16 substituents, the optical transitions strongly depend on the extent to which -XHn is planar or pyramidal as well as on the possible formation of intramolecular hydrogen bonds. The accumulative effect of double and quadruple substitution leads in general to increasing bathochromic shifts, but the increased steric hindrance in tetrasubstituted NDIs can lead to deformations that diminish the effectiveness of the substituents. Detailed analyses of the Kohn-Sham orbital electronic structure in monosubstituted NDIs reveal the mesomeric destabilization of the HOMO as the primary cause of the bathochromic shift of the S0-S1 transition.

Computational (DFT) and Experimental (EXAFS) Study of the Interaction of [Ir(IMes)(H)2 (L)3 ] with Substrates and Co-substrates Relevant for SABRE in Dilute Systems.

Signal amplification by reversible exchange (SABRE) is an emerging hyperpolarization method in NMR spectroscopy, in which hyperpolarization is transferred through the scalar coupling network of para-hydrogen derived hydrides in a metal complex to a reversibly bound substrate. Substrates can even be hyperpolarized at concentrations below that of the metal complex by addition of a suitable co-substrate. Here we investigate the catalytic system used for trace detection in NMR spectroscopy with [Ir(IMes)(H)2 (L)3 ](+) (IMes=1,3-dimesitylimidazol-2-ylidene) as catalyst, pyridine as a substrate and 1-methyl-1,2,3-triazole as co-substrate in great detail. With density functional theory (DFT), validated by extended X-ray absorption fine structure (EXAFS) experiments, we provide explanations for the relative abundance of the observed metal complexes, as well as their contribution to SABRE. We have established that the interaction between iridium and ligands cis to IMes is weaker than that with the trans ligand, and that in mixed complexes with pyridine and triazole, the latter preferentially takes up the trans position.

Insights into the structure of intrastrand cross-link DNA lesion-containing oligonucleotides: G[8-5m]T and G[8-5]C from molecular dynamics simulations.

Oxidatively generated complex DNA lesions occur more rarely than single-nucleotide defects, yet they play an important role in carcinogenesis and aging diseases because they have proved to be more mutagenic than simple lesions. Whereas their formation pathways are rather well understood, the field suffers from the absence of structural data that are crucial for interpreting the lack of repair. No experimental structures are available for oligonucleotides featuring such a lesion. Hence, the detailed structural basis of such damaged duplexes has remained elusive. We propose the use of explicit solvent molecular dynamics simulations to build up damaged oligonucleotides containing two intrastrand cross-link defects, namely, the guanine-thymine and guanine-cytosine defects. Each of these lesions, G[8-5m]T and G[8-5]C, is placed in the middle of a dodecameric sequence, which undergoes an important structural rearrangement that we monitor and analyze. In both duplexes, the structural evolution is dictated by the more favorable stacking of guanine G6, which aims to restore π-stacking with the 3' purine nucleobase. Subsequently, transient formation of hydrogen bonds with a strand shifting is observed. Our simulations are combined with density functional theory to rationalize the structural evolution. We report converging computational evidence that the G[8-5m]T- and G[8-5]C-containing structures evolve toward "abasic-like" duplexes, with a stabilization of the interstrand pairing noncovalent interactions. Meanwhile, both lesions restore B-helicity within tens of nanoseconds. The identification of plausible structures characterizes the last hydrogen abstraction step toward the formation of such defects as a non-innocent chemical reaction.

Covalency in resonance-assisted halogen bonds demonstrated with cooperativity in N-halo-guanine quartets.

Halogen bonds are shown to possess the same characteristics as hydrogen bonds: charge transfer, resonance assistance and cooperativity. This follows from the computational analyses of the structure and bonding in N-halo-base pairs and quartets. The objective was to achieve an understanding of the nature of resonance-assisted halogen bonds (RAXB): how they resemble or differ from the better understood resonance-assisted hydrogen bonds (RAHB) in DNA. We present an accurate physical model of the RAXB based on the molecular orbital theory, which is derived from the corresponding energy decomposition analyses and study of the charge distribution. We show that the RAXB arise from classical electrostatic interaction and also receive strengthening from donor-acceptor interactions within the σ-electron system. Similar to RAHB, there is also a small stabilization by π-electron delocalization. This resemblance leads to prove cooperativity in N-halo-guanine quartets, which originates from the charge separation that occurs with donor-acceptor orbital interactions in the σ-electron system.

Highly accelerated inverse electron-demand cycloaddition of electron-deficient azides with aliphatic cyclooctynes.

Strain-promoted azide-alkyne cycloaddition (SPAAC) as a conjugation tool has found broad application in material sciences, chemical biology and even in vivo use. However, despite tremendous effort, SPAAC remains fairly slow (0.2-0.5 M(-1) s(-1)) and efforts to increase reaction rates by tailoring of cyclooctyne structure have suffered from a poor trade-off between cyclooctyne reactivity and stability. We here wish to report tremendous acceleration of strain-promoted cycloaddition of an aliphatic cyclooctyne (bicyclo[6.1.0]non-4-yne, BCN) with electron-deficient aryl azides, with reaction rate constants reaching 2.0-2.9 M(-1) s(-1). A remarkable difference in rate constants of aliphatic cyclooctynes versus benzoannulated cyclooctynes is noted, enabling a next level of orthogonality by a judicious choice of azide-cyclooctyne combinations, which is inter alia applied in one-pot three-component protein labelling. The pivotal role of azide electronegativity is explained by density-functional theory calculations and electronic-structure analyses, which indicates an inverse electron-demand mechanism is operative with an aliphatic cyclooctyne.

Diastereoselective one-pot synthesis of tetrafunctionalized 2-imidazolines.

A convenient trans-selective one-pot synthesis of tetrafunctionalized 2-imidazolines is described. Our approach to these valuable heterocyclic scaffolds involves a formal 1,3-dipolar cycloaddition between nitrile ylides or nitrilium triflates and imines. A detailed experimental study in combination with a high-level computational exploration of reaction routes reveals a plausible reaction pathway that accounts for the observed diastereoselectivity.

Neutral six-coordinate and cationic five-coordinate silicon(IV) complexes with two bidentate monoanionic N,S-pyridine-2-thiolato(-) ligands.

A series of neutral six-coordinate silicon(IV) complexes (4-11) with two bidentate monoanionic N,S-pyridine-2-thiolato ligands and two monodentate ligands R(1) and R(2) was synthesized (4, R(1) = R(2) = Cl; 5, R(1) = Ph, R(2) = Cl; 6, R(1) = Ph, R(2) = F; 7, R(1) = Ph, R(2) = Br; 8, R(1) = Ph, R(2) = N3; 9, R(1) = Ph, R(2) = NCO; 10, R(1) = Ph, R(2) = NCS; 11, R(1) = Me, R(2) = Cl). In addition, the related ionic compound 12 was synthesized, which contains a cationic five-coordinate silicon(IV) complex with two bidentate monoanionic N,S-pyridine-2-thiolato ligands and one phenyl group (counterion: I(-)). Compounds 4-12 were characterized by elemental analyses, NMR spectroscopic studies in the solid state and in solution, and crystal structure analyses (except 7). These structural investigations were performed with a special emphasis on the sophisticated stereochemistry of these compounds. These experimental investigations were complemented by computational studies, including bonding analyses based on relativistic density functional theory.

Normal-to-abnormal rearrangement and NHC activation in three-coordinate iron(II) carbene complexes.

The 'normal' three-coordinate iron-NHC complex [(IPr)Fe(N'')2] (N″ = N(SiMe3)2) rearranges to its abnormal NHC analogue [(aIPr)Fe(N″)2] (6) on heating, providing a rare abnormal iron-aNHC complex, and the first such three-coordinate complex. The tert-butyl-substituted complex [(I(t)Bu)Fe(N″)2] (4) undergoes a thermal decomposition that has not previously been observed in iron-NHC chemistry, resulting in the bis(imidazole) complex [((t)BuIm)2Fe(N″)2] (7). A mechanism that involves consecutive C-H and C-N activation is proposed to account for the formation of 7.

Supramolecular H-bonded porous networks at surfaces: exploiting primary and secondary interactions in a bi-component melamine-xanthine system.

The control over the formation of a bi-component porous network was attained by the self-assembly at a solid-liquid interface by exploiting both primary and secondary non-covalent interactions between melamine and N(3)-alkylated xanthine modules.

Self-assembly of N3-substituted xanthines in the solid state and at the solid-liquid interface.

The self-assembly of small molecular modules interacting through noncovalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic, and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by exploiting the rich programmability of artificial nucleobases undergoing self-assembly through strong H bonds. Here N(3)-functionalized xanthine modules are described, which are capable of self-associating through self-complementary H-bonding patterns to form H-bonded supramolecular ribbons. The self-association of xanthines through directional H bonding between neighboring molecules allows the controlled generation of highly compact 1D supramolecular polymeric ribbons on graphite. These architectures have been characterized by scanning tunneling microscopy at the solid-liquid interface, corroborated by dispersion-corrected density functional theory (DFT) studies and X-ray diffraction.

Complexes of 4-substituted phenolates with HF and HCN: energy decomposition and electronic structure analyses of hydrogen bonding.

We have computationally studied para-X-substituted phenols and phenolates (X = NO, NO(2), CHO, COMe, COOH, CONH(2), Cl, F, H, Me, OMe, and OH) and their hydrogen-bonded complexes with B(-) and HB (B = F and CN), respectively, at B3LYP/6-311++G** and BLYP-D/QZ4P levels of theory. Our purpose is to explore the structures and stabilities of these complexes. Moreover, to understand the emerging trends, we have analyzed the bonding mechanisms using the natural bond orbital scheme as well as Kohn-Sham molecular orbital (MO) theory in combination with quantitative energy decomposition analyses [energy decomposition analysis (EDA), extended transition state-natural orbitals for chemical valence (ETS-NOCV)]. These quantitative analyses allow for the construction of a simple physical model that explains all computational observations.