Ligand Lone-Pair Influence on Hydrocarbon C-H Activation: A Computational Perspective

Mid to late transition metal complexes that break hydrocarbon C-H bonds by transferring the hydrogen to a heteroatom ligand while forming a metal-alkyl bond offer a promising strategy for C-H activation. Here we report a density functional (B3LYP, M06, and X3LYP) analysis of cis-(acac)_2MX and TpM(L)X (M=Ir, Ru, Os, and Rh; acac=acetylacetonate, Tp=tris(pyrazolyl)-borate; X=CH_3, OH, OMe, NH_2, and NMe_2) systems for methane C-H bond activation reaction kinetics and thermodynamics.We address the importance of whether a ligand lone pair provides an intrinsic kinetic advantage through possible electronic d_π-p_π repulsions for M-OR and M-NR_2 systems versus M-CH_3 systems. This involves understanding the energetic impact of the X ligand group on ligand loss, C-H bond coordination, and C-H bond cleavage steps as well as understanding how the nucleophilicity of the ligand X group, the electrophilicity of the transition metal center, and cis-ligand stabilization effect influence each of these steps.We also explore how spectator ligands and second- versus third-row transition metal centers impact the energetics of each of these C-H activation steps

Amine, Amido, and Imido Complexes of Tantalum Supported by a Pyridine-Linked Bis(phenolate) Pincer Ligand: Ta−N π-Bonding Influences Pincer Ligand Geometry

A series of tantalum imido and amido complexes supported by a pyridine-linked bis(phenolate) ligand has been synthesized. Characterization of these complexes via X-ray crystallography reveals both C_s and C_2 binding modes of the bis(phenolate)pyridine ligand, with complexes containing two or fewer strong π-donor interactions from ancillary ligands giving C_s symmetry, whereas three strong π-donor interactions (e.g., three amido ligands or one amido ligand and one imido ligand) give C_2-symmetric binding of the bis(phenolate)pyridine ligand. DFT calculations and molecular orbital analyses of the complexes have revealed that the preference for C_s-symmetric ligand binding is a result of tantalum−phenolate π-bonding, whereas in cases where tantalum−phenolate π-bonding is overridden by stronger Ta−N π-bonding, C_2-symmetric ligand binding is preferred, likely because conformationally this is the lowest-energy arrangement. This electronically driven change in geometry indicates that, unlike analogous metallocene systems, the bis(phenolate)pyridine pincer ligand is not a strong enough π-donor to exert dominant control over the electronic and geometric properties of the complex

NMR Line Shapes and Multi-State Binding Equilibria

Biological function of proteins relies on conformational transitions and binding of specific ligands. Protein-ligand interactions are thermodynamically and kinetically coupled to conformational changes in protein structures as conceptualized by the models of pre-existing equilibria and induced fit. NMR spectroscopy is particularly sensitive to complex ligand-binding modes—NMR line-shape analysis can provide for thermodynamic and kinetic constants of ligand-binding equilibria with the site-specific resolution. However, broad use of line shape analysis is hampered by complexity of NMR line shapes in multi-state systems. To facilitate interpretation of such spectral patterns, I computationally explored systems where isomerization or dimerization of a protein (receptor) molecule is coupled to binding of a ligand. Through an extensive analysis of multiple exchange regimes for a family of three-state models, I identified signature features to guide an NMR experimentalist in recognizing specific interaction mechanisms. Results also show that distinct multistate models may produce very similar spectral patterns. I also discussed aggregation of a receptor as a possible source of spurious three-state line shapes and provided specific suggestions for complementary experiments that can ensure reliable mechanistic insight

Design of small molecule-responsive microRNAs based on structural requirements for Drosha processing

MicroRNAs (miRNAs) are prevalent regulatory RNAs that mediate gene silencing and play key roles in diverse cellular processes. While synthetic RNA-based regulatory systems that integrate regulatory and sensing functions have been demonstrated, the lack of detail on miRNA structure–function relationships has limited the development of integrated control systems based on miRNA silencing. Using an elucidated relationship between Drosha processing and the single-stranded nature of the miRNA basal segments, we developed a strategy for designing ligand-responsive miRNAs. We demonstrate that ligand binding to an aptamer integrated into the miRNA basal segments inhibits Drosha processing, resulting in titratable control over gene silencing. The generality of this control strategy was shown for three aptamer–small molecule ligand pairs. The platform can be extended to the design of synthetic miRNAs clusters, cis-acting miRNAs and self-targeting miRNAs that act both in cis and trans, enabling fine-tuning of the regulatory strength and dynamics. The ability of our ligand-responsive miRNA platform to respond to user-defined inputs, undergo regulatory performance tuning and display scalable combinatorial control schemes will help advance applications in biological research and applied medicine

The role of dynamical polarization of the ligand to metal charge transfer excitations in {\em ab initio} determination of effective exchange parameters

The role of the bridging ligand on the effective Heisenberg coupling parameters is analyzed in detail. This analysis strongly suggests that the ligand-to-metal charge transfer excitations are responsible for a large part of the final value of the magnetic coupling constant. This permits to suggest a new variant of the Difference Dedicated Configuration Interaction (DDCI) method, presently one of the most accurate and reliable for the evaluation of magnetic effective interactions. This new method treats the bridging ligand orbitals mediating the interaction at the same level than the magnetic orbitals and preserves the high quality of the DDCI results while being much less computationally demanding. The numerical accuracy of the new approach is illustrated on various systems with one or two magnetic electrons per magnetic center. The fact that accurate results can be obtained using a rather reduced configuration interaction space opens the possibility to study more complex systems with many magnetic centers and/or many electrons per center.Comment: 7 pages, 4 figure

Receptor crosstalk improves concentration sensing of multiple ligands

Cells need to reliably sense external ligand concentrations to achieve various biological functions such as chemotaxis or signaling. The molecular recognition of ligands by surface receptors is degenerate in many systems leading to crosstalk between different receptors. Crosstalk is often thought of as a deviation from optimal specific recognition, as the binding of non-cognate ligands can interfere with the detection of the receptor's cognate ligand, possibly leading to a false triggering of a downstream signaling pathway. Here we quantify the optimal precision of sensing the concentrations of multiple ligands by a collection of promiscuous receptors. We demonstrate that crosstalk can improve precision in concentration sensing and discrimination tasks. To achieve superior precision, the additional information about ligand concentrations contained in short binding events of the non-cognate ligand should be exploited. We present a proofreading scheme to realize an approximate estimation of multiple ligand concentrations that reaches a precision close to the derived optimal bounds. Our results help rationalize the observed ubiquity of receptor crosstalk in molecular sensing