Influence of ligand shape and steric hindrance on the composition of the nanocrystal ligand shell

Organic ligands play a key role in the synthesis of colloidal semiconductor nanocrystals or quantum dots. Generally they consist of a functional group and an aliphatic chain, with carboxylic acids, thiols and phosphonic acids as typical examples. The functional group ensures the binding to the nanocrystal surface, while the stability of the dispersion strongly depends on the interactions between the organic chains of the adjacent ligands. A number of studies already addressed the binding strength and the type of binding between the nanocrystal surface and the ligand yet none discuss the effect of the organic chain on the ligand exchange. By means of NMR spectroscopy, we examine the ligand shell composition of CdSe nanocrystals originally capped with oleic acid (OA), when exposed to a linear carboxylic acid. Regardless of chain length, we see a one-to-one exchange between the carboxylic acids. The composition of the ligand shell closely matches that of the ligand mixture in solution, indicating that the ligand shell can be seen as an ideal mixture of both ligands. As a consequence, a mixed ligand shell can easily be prepared by adding a ligand mixture with desired composition to the nanocrystal dispersion. On the other hand, when the CdSe nanocrystals are exposed to a branched carboxylic acid with two long aliphatic chains, like 2-hexyldecanoic acid, the ligand shell mainly consists of OA moieties. We interpret these results using an exchange process where the incoming ligand not only displaces oleic acid but also occupies additional space in the ligand shell to accommodate both aliphatic chains. Hence, given a one-for-one exchange reaction, steric hindrance in a fully packed ligand shell will prevent complete ligand exchange. These results can be very useful in view of producing nanocrystals with lower ligand densities by means of synthesis with these branched carboxylic acids

Morphology of passivating organic ligands around a nanocrystal

Semiconductor nanocrystals are a promising class of materials for a variety of novel optoelectronic devices, since many of their properties, such as the electronic gap and conductivity, can be controlled. Much of this control is achieved via the organic ligand shell, through control of the size of the nanocrystal and the distance to other objects. We here simulate ligand-coated CdSe nanocrystals using atomistic molecular dynamics, allowing for the resolution of novel structural details about the ligand shell. We show that the ligands on the surface can lie flat to form a highly anisotropic 'wet hair' layer as opposed to the 'spiky ball' appearance typically considered. We discuss how this can give rise to a dot-to-dot packing distance of one ligand length since the thickness of the ligand shell is reduced to approximately one-half of the ligand length for the system sizes considered here; these distances imply that energy and charge transfer rates between dots and nearby objects will be enhanced due to the thinner than expected ligand shell. Our model predicts a non-linear scaling of ligand shell thickness as the ligands transition from 'spiky' to 'wet hair'. We verify this scaling using TEM on a PbS nanoarray, confirming that this theory gives a qualitatively correct picture of the ligand shell thickness of colloidal quantum dots.Comment: 17 Pages, 9 Figure

Seven coordinate molybdenum and tungsten complexes containing Tpm and Tpm derivatives and the impact of ligand substitution on NMR chemical shifts

A series of known and new seven coordinate molybdenum and tungsten complexes of tris(pyrazolyl)methane (Tpm) and substituted Tpm, [TpmM(CO)3X]+, have been synthesized. Depending on the identity of X, (bromo, iodo, hydrido) and the substitution of the Tpm ligand, substantial chemical shift differences are observed for the hydrogen on the central carbon of the Tpm ligand. Factors impacting the chemical shift of the hydrogen on the central carbon of the Tpm ligand, such as the electron donating ability of the Tpm ligand and the electronegativity of the additional ligand on the metal, will be discussed

Ligand-Receptor Interactions

The formation and dissociation of specific noncovalent interactions between a variety of macromolecules play a crucial role in the function of biological systems. During the last few years, three main lines of research led to a dramatic improvement of our understanding of these important phenomena. First, combination of genetic engineering and X ray cristallography made available a simultaneous knowledg of the precise structure and affinity of series or related ligand-receptor systems differing by a few well-defined atoms. Second, improvement of computer power and simulation techniques allowed extended exploration of the interaction of realistic macromolecules. Third, simultaneous development of a variety of techniques based on atomic force microscopy, hydrodynamic flow, biomembrane probes, optical tweezers, magnetic fields or flexible transducers yielded direct experimental information of the behavior of single ligand receptor bonds. At the same time, investigation of well defined cellular models raised the interest of biologists to the kinetic and mechanical properties of cell membrane receptors. The aim of this review is to give a description of these advances that benefitted from a largely multidisciplinar approach

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

Ligand Substitution Dynamics

Substitution of a ligand in an inner sphere complex by an outside group is the most fundamental reaction in metal ion chemistr

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

Two Rules on the Protein-Ligand Interaction

So far, we still lack a clear molecular mechanism to explain the protein-ligand interaction on the basis of electronic structure of a protein. By combining the calculation of the full electronic structure of a protein along with its hydrophobic pocket and the perturbation theory, we found out two rules on the protein-ligand interaction. One rule is the interaction only occurs between the lowest unoccupied molecular orbitals (LUMOs) of a protein and the highest occupied molecular orbital (HOMO) of its ligand, not between the HOMOs of a protein and the LUMO of its ligand. The other rule is only those residues or atoms located both on the LUMOs of a protein and in a surface pocket of a protein are activity residues or activity atoms of the protein and the corresponding pocket is the ligand binding site. These two rules are derived from the characteristics of energy levels of a protein and might be an important criterion of drug design

Dewetting-controlled binding of ligands to hydrophobic pockets

We report on a combined atomistic molecular dynamics simulation and implicit solvent analysis of a generic hydrophobic pocket-ligand (host-guest) system. The approaching ligand induces complex wetting/dewetting transitions in the weakly solvated pocket. The transitions lead to bimodal solvent fluctuations which govern magnitude and range of the pocket-ligand attraction. A recently developed implicit water model, based on the minimization of a geometric functional, captures the sensitive aqueous interface response to the concave-convex pocket-ligand configuration semi-quantitatively

Crystal field, ligand field, and interorbital effects in two-dimensional transition metal dichalcogenides across the periodic table

Two-dimensional transition metal dichalcogenides (TMDs) exist in two polymorphs, referred to as $1T$ and $1H$, depending on the coordination sphere of the transition metal atom. The broken octahedral and trigonal prismatic symmetries lead to different crystal and ligand field splittings of the $d$ electron states, resulting in distinct electronic properties. In this work, we quantify the crystal and ligand field parameters of two-dimensional TMDs using a Wannier-function approach. We adopt the methodology proposed by Scaramucci et al. [A. Scaramucci et al., J. Phys.: Condens. Matter 27, 175503 (2015)]. that allows to separate various contributions to the ligand field by choosing different manifolds in the construction of the Wannier functions. We discuss the relevance of the crystal and ligand fields in determining the relative stability of the two polymorphs as a function of the filling of the $d$-shell. Based on the calculated parameters, we conclude that the ligand field, while leading to a small stabilizing factor for the $1H$ polymorph in the $d^1$ and $d^2$ TMDs, plays mostly an indirect role and that hybridization between different $d$ orbitals is the dominant feature. We investigate trends across the periodic table and interpret the variations of the calculated crystal and ligand fields in terms of the change of charge-transfer energy, which allows developing simple chemical intuition.Comment: 16 pages, 14 figure