Julia Contreras-García

Revealing Noncovalent Interactions

Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.

Are Bond Critical Points Really Critical for Hydrogen Bonding

Atoms in Molecules (AIM) theory is routinely used to assess hydrogen bond formation; however its stringent criteria controversially exclude some systems that otherwise appear to exhibit weak hydrogen bonds. We show that a regional analysis of the reduced density gradient, as provided by the recently introduced Non-Covalent Interactions (NCI) index, transcends AIM theory to deliver a chemically intuitive description of hydrogen bonding for a series of 1,n-alkanediols. This regional definition of interactions overcomes the known caveat of only analyzing electron density critical points. In other words, the NCI approach is a simple and elegant generalization of the bond critical point approach, which raises the title question. Namely, is it the presence of an electron density bond critical point that defines a hydrogen bond or the general topology in the region surrounding it?

Analysis of Hydrogen-Bond Interaction Potentials from the Electron Density: Integration of Noncovalent Interaction Regions

Hydrogen bonds are of crucial relevance to many problems in chemistry, biology, and materials science. The recently developed NCI (noncovalent interactions) index enables real-space visualization of both attractive (van der Waals and hydrogen-bonding) and repulsive (steric) interactions based on properties of the electron density. It is thus an optimal index to describe the interplay of stabilizing and destabilizing contributions that determine stable minima on hydrogen-bonding potential-energy surfaces (PESs). In the framework of density-functional theory, energetics are completely determined by the electron density. Consequently, NCI will be shown to allow quantitative treatment of hydrogen-bond energetics. The evolution of NCI regions along a PES follows a well-behaved pattern which, upon integration of the electron density, is capable of mimicking conventional hydrogen-bond interatomic potentials.

The Houk–List transition states for organocatalytic mechanisms revisited

The ten year old Houk–List model for rationalising the origin of stereoselectivity in the organocatalysed intermolecular aldol addition is revisited, using a variety of computational techniques that have been introduced or improved since the original study. Even for such a relatively small system, the role of dispersion interactions is shown to be crucial, along with the use of basis sets where the superposition errors are low. An NCI (non-covalent interactions) analysis of the transition states is able to identify the noncovalent interactions that influence the selectivity of the reaction, confirming the role of the electrostatic NCHδ+⋯Oδ− interactions. Simple visual inspection of the NCI surfaces is shown to be a useful tool for the design of alternative reactants. Alternative mechanisms, such as proton-relays involving a water molecule or the Hajos–Parrish alternative, are shown to be higher in energy and for which computed kinetic isotope effects are incompatible with experiment. The Amsterdam manifesto, which espouses the principle that scientific data should be citable, is followed here by using interactive data tables assembled via calls to the data DOI (digital-object-identifiers) for calculations held on a digital data repository and themselves assigned a DOI.

Revealing Non‐covalent Interactions in Molecular Crystals through Their Experimental Electron Densities

Non-covalent interactions (NCI) define the rules underlying crystallisation, self-assembly and drug-receptor docking processes. A novel NCI descriptor, based on the reduced electron density gradient (RDG), that enables easy visualisation of the zones of the electron density (ED) involved in either the supposedly attractive (dispersive, hydrogen bonding) or allegedly repulsive (steric) intermolecular interactions, was recently developed by Johnson et al. Here, it is applied for the first time to EDs derived from single-crystal X-ray diffraction data. A computer code handling both experimental and ab initio EDs in the RDG-NCI perspective was purposely written. Three cases spanning a wide range of NCI classes were analysed: 1) benzene, as the prototype of stacking and weak CH···π interactions; 2) austdiol, a heavily functionalised fungal metabolite with a complex hydrogen-bonding network; 3) two polymorphs of the heteroatom-rich anti-ulcer drug famotidine, with van der Waals and hydrogen-bond contacts between N- and S-containing groups. Even when applied to experimental EDs, the RDG index is a valuable NCI descriptor that can highlight their different nature and strength and provide results of comparable quality to ab initio approaches. Combining the RDG-NCI study with Baders ED approach was a key step forward, as the RDG index can depict inherently delocalised interactions in terms of extended and flat RDG isosurfaces, in contrast to the bond path analysis, which is often bounded to a too localised and possibly discontinuous (yes/no) description. Conversely, the topological tool can provide quantitative insight into the simple, qualitative NCI picture offered by the RDG index. Hopefully, this study may pave the way to a deeper analysis of weak interactions in proteins using structural and ED information from experiment.

Understanding the Fundamental Role of π/π, σ/σ, and σ/π Dispersion Interactions in Shaping Carbon‐Based Materials

Noncovalent interactions involving aromatic rings, such as π-stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion-corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene⋅⋅⋅methane and cyclohexane⋅⋅⋅methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel-displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non-additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.

Silver‐Catalysed Enantioselective Addition of OH and NH Bonds to Allenes: A New Model for Stereoselectivity Based on Noncovalent Interactions

The ability of silver complexes to catalyse the enantioselective addition of O-H and N-H bonds to allenes is demonstrated for the first time by using optically active anionic ligands that were derived from oxophosphorus(V) acids as the sources of chirality. The intramolecular addition of acids, alcohols, and amines to allenes can be achieved with up to 73% ee. The exploitation of a C-H anomeric effect allowed the absolute configuration of a sample of 2-substituted tetrahydrofuran of low ee to be unambiguously assigned by comparison of the chiroptical ORD and VCD measurements with calculated spectra. In the second part of the work, the origin of the stereoselectivity was probed by DFT free-energy calculations of the transition states. A new model of enantiomeric differentiation was developed that was based on noncovalent interactions. This model allowed us to identify the source of stereoselectivity as weak attractive interactions; such dispersive forces are often overlooked in asymmetric catalysis. A new computational approach was developed that represents these interactions as colour-coded isosurfaces that are characterised by the reduced density-gradient profile.

Delocalization error of density-functional approximations: A distinct manifestation in hydrogen molecular chains

Delocalization error is one of the major sources of inaccuracy for mainstream density functional approximations and it is responsible for many of the most glaring failures. Quantitative identification of delocalization error in chemical species and analysis of its influence on calculated thermodynamic properties have remained scarce. In this work we demonstrate unambiguously the effect of delocalization error on a series of hydrogen molecular chains and elucidate the underlying relationship between the error magnitude and system geometry. This work stresses the necessity of minimizing delocalization error associated with density functional approximations.

Following the Molecular Mechanism for the NH3 + LiH → LiNH2 + H2 Chemical Reaction: A Study Based on the Joint Use of the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interaction (NCI) Index

The molecular mechanism for the NH3 + LiH → LiNH2 + H2 reaction has been elucidated by the combined use of quantum theory of atoms in molecules (QTAIM) and noncovalent interactions (NCI) index. The topology of the electron density, obtained by QTAIM/NCI, is able to identify the evolution of strong and weak interactions, recovering the bonding patterns along the reaction pathway. Thus, the combination of these two techniques is a useful and powerful tool in the study of chemical events, providing new strategies to understand and visualize the molecular mechanisms of chemical rearrangements. Also, for the first time, the topology of the reduced density gradient has been analyzed, taking into account saddle points for the construction of bifurcation trees. This approach has demonstrated the ability of NCI to account for delocalized interactions, very often characteristic of transitions states.

Highly selective mercury(II) cations detection in mixed-aqueous media by a ferrocene-based fluorescent receptor.

A new chemosensor molecule 3 based on a ferrocene-imidazophenanthrophenazine dyad effectively recognizes Hg(2+) in an aqueous environment through three different channels. Upon recognition, an anodic shift of the ferrocene-ferrocenium oxidation potential (ΔE(1/2) = 240 mV) and a progressive red shift (Δλ = 17 nm) of the low energy band in its absorption spectrum is produced. The emission spectrum of 3 in an aqueous environment, CH(3)CN-EtOH-H(2)O (65:25:10), and conducted at pH = 7.4 (20 × 10(-3) M HEPES) (Φ = 0.003), is perturbed after addition of Hg(2+) cations and an intense and structureless red shift emission band at 494 nm (Δλ = 92 nm) appeared along with an increase of the intensity of the emission band (CHEF = 77), the quantum yield (Φ = 0.054) resulted in a 18-fold increase. The combined (1)H NMR data of the complex and the theoretical calculations suggest the proposed bridging coordination mode.