Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions

The Role of Aromatic Alcohol Additives on Asymmetric Organocatalysis Reactions: Insights from Theory

The presence of an aromatic additive has been seen to enhance, often significantly, the enantioselectivity and yield in asymmetric organocatalysis. Considering their success across a dizzying range of organocatalysts and organic transformations, it would seem unlikely that a common principle exists for their functioning. However, the current investigations with DFT suggest a general principle: the phenolic additive sandwiches itself, through hydrogen bonding and π⋅⋅⋅π stacking, between the organocatalyst coordinated electrophile and nucleophile. This is seen for a wide range of experimentally reported systems. That such complex formation leads to enhanced stereoselectivity is then demonstrated for two cases: the cinchona alkaloid complex (BzCPD), catalysing thiocyanation (2-naphthol additive employed), as well as for L-pipecolicacid catalysing the asymmetric nitroaldol reaction with a range of nitro-substituted phenol additives. These findings, indicating that dual catalysis takes place when phenolic additives are employed, are likely to have a significant impact on the field of asymmetric organocatalysis.

Analyzing the cation-aromatic interactions in proteins: Cation-aromatic database V2.0

The cation-aromatic database (CAD) is a comprehensive repository of cation-aromatic motifs found in experimentally determined protein structures, first reported in 2007 [Proteins, 2007, 67, 1179]. The present article is an update of CAD that contains information of approximately 27.26 million cation-aromatic motifs. CAD uses three distance parameters (r, d1, and d2) to determine the position of the cation relative to the centroid of the aromatic residue and classifies the motifs as cation-π or cation-σ interactions. As of June 2023, about 193 936 protein structures were retrieved from Protein Data Bank, and this resulted in the identification of an impressive number of 27 255 817 cation-aromatic motifs. Among these motifs, spherical motifs constituted 94.09%, while cylindrical motifs made up the remaining 5.91%. When considering the interaction of metal ions with aromatic residues, 965 564 motifs are identified. Remarkably, 82.08% of these motifs involved the binding of metal ions to the amino acid HIS. Moreover, the analysis of binding preferences between cations and aromatic residues revealed that the HIS-HIS, PHE-ARG, and TRP-ARG pairs exhibited a preferential geometry. The motif pair HIS-HIS was the most prevalent, accounting for 19.87% of the total, closely followed by TYR-LYS at 10.17%. Conversely, the motif pair TRP-HIS had the lowest occurrence, representing only 4.20% of the total. The data generated help in revealing the characteristics and biological functions of cation-aromatic interactions in biological molecules. The updated version of CAD (Cation-Aromatic Database V2.0) can be accessed at https://acds.neist.res.in/cadv2.

Analyzing the aromatic-aromatic interactions in proteins: A2ID 2.0

The Aromatic-Aromatic Interactions Database (A2ID) is a comprehensive repository dedicated to documenting aromatic-aromatic (π-π) networks observed in experimentally determined protein structures. The first version of A2ID was reported in 2011 [Int J Biol Macromol, 2011, 48, 540]. It has undergone a series of significant updates, leading to its current version, which focuses on the identification and analysis of 3,444,619 π-π networks from proteins. The geometrical parameters such as centroid-centroid distances (r) and interplanar angles (ϕ) were used to identify and characterize π-π networks. It was observed that among the 84,500 proteins with at least one aromatic π-π network, about 92.50 % of the instances are found to be either 2π (77.34 %) or 3π (15.23 %) networks. The analysis of interacting amino acid pairs in 2π networks indicated a dominance of PHE residues followed by TYR. The updated version of A2ID incorporates analysis of π-π networks based on SCOP2 and ECOD classifiers, in addition to the existing SCOP, CATH, and EC classifications. This expanded scope allows researchers to explore the characteristics and functional implications of π-π networks in protein structures from multiple perspectives. The current version of A2ID along with its extensive dataset and detailed geometric information is publicly accessible using https://acds.neist.res.in/a2idv2.

Binding propensity and selectivity of cationic, anionic, and neutral guests with model hydrophobic hosts: A first principles study

Computations play a critical role in deciphering the nature of host-guest interactions both at qualitative and quantitative levels. Reliable quantum chemical computations were employed to assess the nature, binding strength, and selectivity of ionic, and neutral guests with benzenoid hosts. Optimized complex structures reveal that alkali and ammonium ions are found to be in the hydrophobic cavity, while halide ions are outside, while both complexes elicit substantial binding energy. The origin of the selectivity of host toward the guest has been traced to the interaction and deformation energies, and the nature of associated interactions is quantified using energy decomposition and the Quantum Theory of Atoms in Molecules analyses. While the larger hosts lead to loosely bound complexes, as assessed by the longer intermolecular distances, the binding strengths are proportional to the size of the host systems. The binding of cationic complexes is electrostatic or polarization driven while exchange term dominates the anionic complexes. In contrast, dispersion contribution is a key in neutral complexes and plays a pivotal role in stabilizing the polyatomic complexes.

Real-time ultra-sensitive detection of SARS-CoV-2 by quasi-freestanding epitaxial graphene-based biosensor

We report the rapid detection of SARS-CoV-2 in infected patients (mid-turbinate swabs and exhaled breath aerosol samples) in concentrations as low as 60 copies/mL of the virus in seconds by electrical transduction of the SARS-CoV-2 S1 spike protein antigen via SARS-CoV-2 S1 spike protein antibodies immobilized on bilayer quasi-freestanding epitaxial graphene without gate or signal amplification. The sensor demonstrates the spike protein antigen detection in a concentration as low as 1 ag/mL. The heterostructure of the SARS-CoV-2 antibody/graphene-based sensor is developed through a simple and low-cost fabrication technique. Furthermore, sensors integrated into a portable testing unit distinguished B.1.1.7 variant positive samples from infected patients (mid-turbinate swabs and saliva samples, 4000-8000 copies/mL) with a response time of as fast as 0.6 s. The sensor is reusable, allowing for reimmobilization of the crosslinker and antibodies on the biosensor after desorption of biomarkers by NaCl solution or heat treatment above 40 °C.

Fate of Sc-Ion Interaction With Water: A Computational Study to Address Splitting Water Versus Solvating Sc Ion

An exhaustive study of Sc-ion interaction with water molecules in all its possible oxidation and spin states has been carried out to delineate the relative propensity of Sc ions toward solvation and water splitting. Potential energy surface analysis of the Sc-ion reaction with water molecules, topological analysis of bonds, and the effect of sequential solvation up to 6 water molecules have been examined. Calculated values showed good agreement with the available experimental results. Close-shell systems such as singlet mono- and tricationic Sc ions prefer to split the water molecules. In contrast, the open-shell systems such as triplet mono- and doublet dicationic Sc ions prefer to get solvated than split the water molecule. Topological analysis of electron density predicted the Sc^+/2+–water bond as a noncovalent bond while Sc³⁺–OH₂, Sc²⁺–OH, and Sc⁺–H bonds as partially covalent in nature. Energy decomposition analysis revealed that Sc ion–water interactions are driven by electrostatic energy followed by polarization energy. The current study reveals that transition metal catalysis can be one of the most effective tools to employ in water splitting, by properly tuning the electrons, spin, and ligands around the catalytic center.

Towards developing a criterion to characterize non-covalent bonds: a quantum mechanical study

Chemical bonds are central to chemistry, biology, and allied fields, but still, the criterion to characterize an interaction as a non-covalent bond has not been studied rigorously.

Structure and bonding in triorganotin chlorides: a perspective from energy decomposition analysis

The Sn-Cl chemical bond of four organotin halides (Me₃SnCl, Et₃SnCl, Bu₃SnCl, and Ph₃SnCl) was studied by using relativistic density functional theory in combination with a quantitative energy decomposition analysis to explain the formation of charged species. The σ orbital is the dominant contributor to the stabilization of the Sn-Cl bond, and the π-orbital interactions also have a significant contribution to the stabilization of Ph₃Sn⁺ cation when the aromatic groups are bonded to the tin atom. The aromaticity of the phenyl groups delocalizes the positive charge, donating electrons to tin atom by conjugation. Although Me₃SnCl and Ph₃SnCl are constituted by groups which the size of the substituents is different, the interaction energies obtained with the energy decomposition analysis present similar values, which also occur with the thermodynamic parameters. Graphical abstract Organotin compounds have widely studied as a potential antitumoral agent. The mechanism in triorganotin compounds includes the formation of cation species, R₃Sn⁺. This article studies the influence of the R groups on the rupture of Sn-Cl bond using the fragment analysis and quantitative energy decomposition analysis.

Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions?

Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.

Antiproliferative activity of (η6-arene)ruthenacarborane sandwich complexes against HCT116 and MCF7 cell lines

Three [(η⁶-arene)RuC₂B₉H₁₁] complexes (arene = p-cymene (2), biphenyl (3) and 1-Me-4-COOEt-C₆H₄ (4)) were synthesised according to modified literature procedures and fully characterised. 2-4 were found to be moderately active against two types of tumour cell lines (HCT116 and MCF7), with IC₅₀ values in the low micromolar range. However, viability of normal, healthy cells (MRC-5 cell line, MLEC and mouse macrophages) was not affected by treatment with 2-4, indicating high selectivity of the metallacarborane complexes towards tumour cell lines, compared to the unselective antitumour agent cisplatin and other potential Ru^II drugs. Moreover, flow cytometric analysis suggested that 4 induces cell death via a caspase-dependent apoptotic mechanism. DFT calculations of the frontier molecular orbitals showed that the HOMO-LUMO gap in 2-4 is smaller than in the corresponding cyclopentadienyl complexes 2-Cp-4-Cp (e.g. 5.47 (2) vs. 6.31 eV (2-Cp)). In order to assess the stability of 2-4, particularly the ruthenium-dicarbollide bond, energy decomposition analysis (EDA) of 2-4, together with the respective cyclopentadienyl analogues 2-Cp-4-Cp, was performed. EDA suggests that the ruthenium(ii)-dicarbollide bond in the three complexes is mostly ionic and far stronger than the ruthenium(ii)-arene bond.

Preponderant adsorption for chlorpyrifos over atrazine by wheat straw-derived biochar: experimental and theoretical studies

In competitive sorption, WS750 prefers to adsorb chlorpyrifos over atrazine since that chlorpyrifos has stronger pi–pi interaction with WS750 (23.68 kcal mol⁻¹) and larger lipophilicity (log P= 4.7) than that (22.70 kcal mol⁻¹, log P= 2.7) of atrazine.

Two-State or Non-Two-State? An Excess Spectroscopy-based Approach to Differentiate the Existing Forms of Molecules in Liquids Mixtures

Characterization/identification of the clusters/associates in liquids has long been a challenging topic. In this paper, we report a method to identify molecules with two different existing forms in a binary liquid solution. In this so-called two-state situation, the excess infrared spectra of a vibration mode of the respective molecule will show identical band shape if the other component is transparent in the region. More conveniently, the positions of the positive peak, negative peak, and zero-value will be seen to be fixed with varying compositions of the binary system. In the case of non-two-state mixtures, for example the mere solvation of solute by solvent, those positions will be variable. The conclusions are supported/demonstrated by computational simulation and experiments on two binary systems, D2O-H2O and C6F5I-cyclo-C6H12.

Removal of chlorpyrifos from waste water by wheat straw-derived biochar synthesized through oxygen-limited method

Wheat straw-derived biochar at 750 °C (WS750) can effectively adsorb chlorpyrifos and the driving force is most likely attributed to the π⋯π stack between the aromatic ring of chlorpyrifos and these aromatic areas on WS750 surface.