NCIPLOT4: Fast, Robust, and Quantitative Analysis of Noncovalent Interactions

Discovering trends in the Lewis acidity of beryllium and magnesium hydrides and fluorides with increasing clusters size

We have reported in the last years the strong effect that Be- and Mg-containing Lewis acids have on the intrinsic properties of typical bases, which become acids upon complexation. In an effort to investigate these changes when the Be and Mg derivatives form clusters of increasing size, we have examined the behavior of the (MX2)n (M = Be, Mg; X = H, F; n = 1, 2, 3) clusters when they interact with ammonia, methanimine, hydrogen cyanide and pyridine, and with their corresponding deprotonated forms. The complexes obtained at the M06-2X/aug-cc-pVTZ level were analyzed using the MBIE energy decomposition formalism, in parallel with QTAIM, ELF, NCIPLOT and AdNDP analyses of their electron density. For n = 1 the interaction enthalpy for the different families of monomers, Be (Mg) hydrides and Be (Mg) fluorides, follows the same trend as the intrinsic basicity of the base that interacts with them. This interaction is greatly reinforced after the deprotonation of the base, resulting in a significant enhancement of the intrinsic acidity of the corresponding MX2-Base complex. For (MX2)2 clusters a further reinforcement of the interaction with the base is observed, this reinforcement being again larger for the deprotonated complexes. However, the concomitant increase of their intrinsic acidity is one order of magnitude larger for hydrides than for fluorides. Unexpectedly, the cyclic conformers (MX2)3, which are more unstable than the linear ones, become the global minima after association with the base and the same is true for the deprotonated complex. Accordingly, a further increase of the intrinsic acidity of the (MX2)3-Base complexes with respect to the (MX2)2-Base ones is observed. This effect is maximum for (MgF2)3 clusters, to the point that the (MgF2)3-Base complexes become more acidic than nitric acid, the extreme case being the cluster (MgF2)3-NCH, whose acidity is higher than that of perchloric acid.

Unusually Short H⋅⋅⋅H Contacts in Intramolecularly Cyclized Helically Fused Anthracenes

The intramolecular coupling of dichloro-substituted helically fused anthracenes using the Yamamoto coupling yielded cyclized products with sterically congested molecular structures. The X-ray analysis and DFT calculations showed that the aromatic framework adopted a nonplanar structure with a twisted conformation about the newly formed single bond, which acts as a chiral axis. Interestingly, the X-ray structure obtained through the Hirshfeld atom refinement revealed short interatomic distances between the inner hydrogen atoms (1.648-1.692 Å), much shorter than the sum of their van der Waals radii. Owing to these unusually short contacts, the 1H NMR spectrum exhibited a significant deshielding (12.5 ppm) and a large nuclear Overhauser effect (44 %). Additionally, the IR spectrum displayed a high-frequency shift of the C-H stretching vibration. These observations, along with the noncovalent interaction plot indicative of a characteristic steric environment, strongly support the presence of steric hindrance. Moreover, dynamic NMR measurement of the mesityl-substituted derivative yielded a barrier to helical inversion of 84 kJ mol-1. The optical properties and crystal packing of the cyclized products are also reported.

Molecular dynamics simulations in pre-polymerization mixtures for peptide recognition

CONTEXT

Molecularly imprinted polymers (MIPs) have promising applications as synthetic antibodies for protein and peptide recognition. A critical aspect of MIP design is the selection of functional monomers and their adequate proportions to achieve materials with high recognition capacity toward their targets. To contribute to this goal, we calibrated a molecular dynamics protocol to reproduce the experimental trends in peptide recognition of 13 pre-polymerization mixtures reported in the literature for the peptide toxin melittin.

METHODS

Three simulation conditions were tested for each mixture by changing the box size and the number of monomers and cross-linkers surrounding the template in a solvent-explicit environment. Fully atomistic MD simulations of 350 ns were conducted with the AMBER20 software, with ff19SB parameters for the peptide, gaff2 parameters for the monomers and cross-linkers, and the OPC water model. Template-monomer interaction energies under the LIE approach showed significant differences between high-affinity and low-affinity mixtures. Simulation systems containing 100 monomers plus cross-linkers in a cubic box of 90 Å3 successfully ranked the mixtures according to their experimental performance. Systems with higher monomer densities resulted in non-specific intermolecular contacts that could not account for the experimental trends in melittin recognition. The mixture with the best recognition capacity showed preferential binding to the 13-26-α-helix, suggesting a relevant role for this segment in melittin imprinting and recognition. Our findings provide insightful information to assist the computational design of molecularly imprinted materials with a validated protocol that can be easily extended to other templates.

Trans vs. cis: a computational study of enasidenib resistance due to IDH2 mutations

Isocitrate dehydrogenase 2 (IDH2) is a homodimeric enzyme that plays an important role in energy production. A mutation R140Q in one monomer makes the enzyme tumourigenic. Enasidenib is an effective inhibitor of IDH2/R140Q. A secondary mutation Q316E leads to enasidenib resistance. This mutation was hitherto only found in trans, i.e. where one monomer has the R140Q mutation and the other carries the Q316E mutation. It is not clear if the mutation only leads to resistance when in trans or if it has been discovered in trans only by chance, since it was only reported in two patients. Using molecular dynamics (MD) simulations we show that the binding of enasidenib to IDH2 is indeed much weaker when the Q316E mutation takes place in trans not in cis, which provides a molecular explanation for the clinical finding. This is corroborated by non-covalent interaction (NCI) analysis and DFT calculations. Whereas the MD simulations show a loss of one hydrogen bond upon the resistance mutation, NCI and energy decomposition analysis (EDA) reveal that a multitude of interactions are weakened.

In Silico Design and Characterization of a New Molecular Electride: Li@Calix[3]Pyrrole

Electrides, in which anionic electrons are localized independently of the atoms in the compound, have shown promise, especially as catalysts and optoelectronic materials. Here, we present a new computationally designed molecular electride, Li@calix[3]pyrrole (Li@C3P). Electron density and electron localization function analyses unequivocally confirm the existence of localized electride electron density, outside the system, independent of any specific atoms. Non-covalent interaction plots further validate the character of the isolated localized electron, suggesting that the system can be accurately represented by Li+@calix[3]pyrrole ⋅ e-, denoting its distinct charge separation. The remarkable non-linear optical properties of Li@C3P, including average polarizability,α ‾ ${\bar{\alpha }}$ =412.4 au, first hyperpolarizability, β=4.46×104 au, and second hyperpolarizability,γ ∥ ${{\gamma }_{\parallel }}$ =18.40×106 au, are unparalleled in the previously reported and similar Li@C4P molecular electride. Furthermore, energy decomposition analysis in combination with natural orbital for chemical valence theory sheds light on the mechanism of electron density transfer from Li to the C3P cage, yielding the charge-separated Li@C3P complex. In addition to the electron transfer, a key factor to its electride nature is the electronic structure of the CnP cage, which has its lowest unoccupied molecular orbital located in the void adjacent to the N-H groups at the back of the bowl-shaped CnP cage.

Synthesis of Aza[n]helicenes up to n = 19: Hydrogen-Bond-Assisted Solubility and Benzannulation Strategy

Synthetic challenges toward anomalous structures and electronic states often involve handling problems such as insolubility in common organic solvents and oxidative degradation under aerobic conditions. We designed benzo-annulated aza[n]helicenes, which benefit from both the suppressed elevation of highest occupied molecular orbital (HOMO) energies and high solubility due to hydrogen bonding with solvent molecules to overcome these challenges. This strategy enabled the synthesis of six new aza[n]helicenes ([n]AHs) of different lengths (n = 9-19) from acyclic precursors via one-pot intramolecular oxidative fusion reactions. The structures of all of the synthesized aza[n]helicenes were determined by X-ray diffraction (XRD) analysis, and their electrochemical potentials were measured by cyclic voltammetry. Among the synthesized aza[n]helicenes, [17]AH and [19]AH are the first heterohelicenes with a triple-layered helix. The noncovalent interaction (NCI) plots confirm the existence of an effective π-π interaction between the layers. The absorption and fluorescence spectra red-shifted as the helical lengths increased, without any distinct saturation points. The optical resolutions of N-butylated [9]AH, [11]AH, [13]AH, and [15]AH were accomplished, and their circular dichroism (CD) and circularly polarized luminescence (CPL) were measured. Thus, the structural, (chir)optical, and electrochemical properties of the aza[n]helicenes were comprehensively analyzed.

Unveiling structural and energetic characterization of the emissive RNA alphabet anchored in the methylthieno[3,4-d]pyrimidine heterocycle core

This study presents a comprehensive theoretical exploration of the fluorescent non-natural emissive nucleobases- mthA, mthG, mthC, and mthU derived from the methylthieno[3,4-d]pyrimidine heterocycle. Our calculations, aligning with experimental findings, reveal that these non-natural bases exert minimal influence on the geometry of classical Watson-Crick base pairs within an RNA duplex, maintaining H-bonding akin to natural bases. In terms of energy, the impact of the modified bases, but for mthG, is also found to be little significant. We delved into an in-depth analysis of the photophysical properties of these non-natural bases. This investigation unveiled a correlation between their absorption/emission peaks and the substantial impact of the modification on the energy levels of the highest unoccupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbital (LUMO). Notably, this alteration in energy levels resulted in a significant reduction of the HOMO-LUMO gap, from approximately 5.4-5.5 eV in the natural bases, to roughly 3.9-4.7 eV in the modified bases. This shift led to a consequential change in absorption and emission spectra towards longer wavelengths, elucidating their bathochromic shift.

Spontaneous Curvature Induction in an Artificial Bilayer Membrane

Maintaining lipid asymmetry across membrane leaflets is critical for functions like vesicular traffic and organelle homeostasis. However, a lack of molecular-level understanding of the mechanisms underlying membrane fission and fusion processes in synthetic systems precludes their development as artificial analogs. Here, we report asymmetry induction of a bilayer membrane formed by an extended π-conjugated molecule with oxyalkylene side chains bearing terminal tertiary amine moieties (BA1) in water. Autogenous protonation of the tertiary amines in the periphery of the bilayer by water induces anisotropic curvature, resulting in membrane fission to form vesicles and can be monitored using time-dependent spectroscopy and microscopy. Interestingly, upon loss of the induced asymmetry by extensive protonation using an organic acid restored bilayer membrane. The mechanism leading to the compositional asymmetry in the leaflet and curvature induction in the membrane is validated by density functional theory (DFT) calculations. Studies extended to control molecules having changes in hydrophilic (BA2) and hydrophobic (BA3) segments provide insight into the delicate nature of molecular scale interactions in the dynamic transformation of supramolecular structures. The synergic effect of hydrophobic interaction and the hydrated state of BA1 aggregates provide dynamicity and unusual stability. Our study unveils mechanistic insight into the dynamic transformation of bilayer membranes into vesicles.

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

In the current work, we analyzed the origin of difference in stabilities among the germacrene A and hedycaryol-derived carbocations. This study focused on twelve hydrocarbons derived from germacrene A and twelve from hedycaryol, which can be divided into three groups: four molecules containing 6-6 bicyclic rings, four 5-7 bicyclic compounds with the carbocation being on the seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (i.e., 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non-covalent interactions plots. Despite the structural similarities between germacrene A and hedycaryol cations, they possess a somewhat different stability trend. These differences are attributed to C+···OH intramolecular interactions present in some hedycaryol cations, which are absent in the carbocations derived from germecrene A.

A Pseudo-Surfactant Chemical Permeation Enhancer to Treat Otitis Media via Sustained Transtympanic Delivery of Antibiotics

Chemical permeation enhancers (CPEs) represent a prevalent and safe strategy to enable noninvasive drug delivery across skin-like biological barriers such as the tympanic membrane (TM). While most existing CPEs interact strongly with the lipid bilayers in the stratum corneum to create defects as diffusion paths, their interactions with the delivery system, such as polymers forming a hydrogel, can compromise gelation, formulation stability, and drug diffusion. To overcome this challenge, differing interactions between CPEs and the hydrogel system are explored, especially those with sodium dodecyl sulfate (SDS), an ionic surfactant and a common CPE, and those with methyl laurate (ML), a nonionic counterpart with a similar length alkyl chain. Notably, the use of ML effectively decouples permeation enhancement from gelation, enabling sustained delivery across TMs to treat acute otitis media (AOM), which is not possible with the use of SDS. Ciprofloxacin and ML are shown to form a pseudo-surfactant that significantly boosts transtympanic permeation. The middle ear ciprofloxacin concentration is increased by 70-fold in vivo in a chinchilla AOM model, yielding superior efficacy and biocompatibility than the previous highest-performing formulation. Beyond improved efficacy and biocompatibility, this single-CPE formulation significantly accelerates its progression toward clinical deployment.

Synthesis of Macrolactone Core of ent-Formosalide A via Regioselective Ether Cyclization

Formosalide A is a cytotoxic macrolide isolated from the dinoflagellate Prorocentrum sp, whose structure is characterized by functionalized 5- and 6-membered ether rings embedded in the macrolactone and an all cis-tetraene side chain. Here, we report the synthesis of the macrolactone core of ent-formosalide A. Our approach is highlighted by the Au-mediated 6-exo-dig cyclization for the synthesis of the 6-membered ether ring, which proceeded in a highly regioselective manner. Control experiments demonstrated that the acyclic protecting group of the C9,C10-diol was crucial for the desired 6-exo-dig cyclization. Theoretical studies were performed focusing on structural component analysis, which suggested that the C8-C9-C10-C11 dihedral angle induced by the protecting group controlled the regioselectivity. An additional 6 steps including Shiina macrolactone formation from the 6-membered ether ring completed the synthesis of the macrolactone core of ent-formosalide A.

Benzannulated Double Aza[9]helicenes: Synthesis, Structures, and (Chir)optical Properties

A benzannulated double aza[9]helicene 1 was successfully synthesized via a one-pot oxidative fusion reaction. 1 was derivatized to N-alkylated double aza[9]helicene 1-Et and 1-Bu, whose structures were determined by X-ray diffraction analysis. 1-Et and 1-Bu exhibited red-shifted absorption and fluorescence spectra compared to single aza[9]helicene. The double aza[9]helicenes were expected to have two different conformers. Consistent with solid-state structure, the chiral-isomer was estimated to be more stable by 16 kcal/mol relative to meso-isomer. Indeed, enantiomers of 1-Et and 1-Bu were optically resolved by HPLC and showed mirror-imaged CD and CPL spectra with the CPL brightness up to 19.2 M-1cm-1 for 1-Bu.

Reversible open-closed conformational switching of nano-size metalloporphyrin dimers triggered by light and temperature

The current work demonstrates the reversible control of substantial molecular motion in 'nano-sized' molecules, where two structural isomers can 'open' and 'close' their cavities in response to light or heat. The isomers differ widely in their photophysical properties, including colour, polarity, two-photon absorption and π-conjugation, and can easily be separated through column chromatography and thus have wide applicability.

Reinvigorating aza-Michael reactions under ionic liquid catalysis: a greener approach

Cholinium α-amino carboxylates, which debuted in the ionic liquid arena over a decade ago, exhibit superior stability and suitable physical properties relative to other RTILs. Although synthetic pursuits in such media, leveraging their dual role as solvents and catalysts, have been scarce so far, we herein illustrate their catalytic advantage in aza-Michael reactions in terms of low loading, acceleration and improved yields with respect to conventional conditions and other imidazolium-based ILs. These highly structured salts most likely act through multiple and cooperative non-covalent interactions. These mechanistic features have also been investigated through high-level computational analyses as well.

Photoswitchable imines: aryliminopyrazoles quantitatively convert to long-lived Z-isomers with visible light

Arylimines offer promise in dynamic-covalent materials due to their recyclability and ease of synthesis. However, their light-triggered E/Z isomerism has received little attention. This is attributed to challenges that include low thermal stability of their metastable state (<60 s at 20 °C), incomplete photoswitching (<50% to the metastable state), and the need for UV light (≤365 nm). We overcome these limitations with a novel class of imine photoswitch, the aryliminopyrazoles (AIPs). These AIPs can be switched using visible light (470 nm), attain photostationary states with over 95% of the Z-isomer, exhibit great resistance to fatigue, and have thermal half-lives up to 19.2 hours at room temperature. Additionally, they display T-type and negative photochromism under visible light irradiation-a useful property. The photochromic properties, quantitative assembly and accessibility of precursors set these photoswitches apart from their azo-based analogues. These findings open avenues for next-generation photoresponsive dynamic-covalent materials driven solely by these new photochromic linkages and further exploration of photocontrolled dynamic combinatorial chemistry.

Hierarchical Self-Assembly of Curved Aromatics: From Donor-Acceptor Porphyrins to Triply Periodic Minimal Surfaces

A saddle-shaped π-extended zinc porphyrin containing a peripheral pyridyl ligand undergoes quantitative self-assembly into a cyclic trimer. The trimer has a prismatic structure with negatively curved side walls, which promote the formation of supramolecular organic frameworks stabilized by dispersion interactions. The first framework type, UWr-1, has the npo topology, with a hexagonal structure analogous to the Schwartz H triply periodic minimal surface. Co-crystallization of the trimer with either C60 and C70 produces the isomorphous cubic UWr-2 and UWr-3 phases, characterized by the ctn network topology and a structural relationship to the Fischer-Koch minimal surface S. All three phases contain complex labyrinths of solvent-filled channels, corresponding to very large probe-accessible volumes (68 % to 76 %). The UWr-2 network could be partly desolvated while retaining its long range dimensional order, indicating remarkable strength of the dispersion interactions in the crystal. A theoretical analysis of noncovalent interactions shows the role of geometrical matching between the negatively curved porphyrin units and positively curved fullerenes.

Synthesis of Novel [{(2-Amino-5-Nitro-N-[(E)-Thiophen-2-yl-Methylidene]Aniline-κ3N1:N4:S)(Sulphato-κ2O1:O3)}Zinc(II)] Complex with Physico-Chemical and Biological Perspective Exploration: A Combined Experimental and Computational Studies

A novel metal complex was synthesized using freshly prepared 2-Amino-5-nitro-N-[(E)-thiophen-2-yl-methylidene]aniline ligand with Zn (II) sulphate heptahydrate in a 1:1 molar ratio. The ligand and the complex were characterized using different spectroscopic techniques, and the complex was assigned a distorted square pyramidal geometry. Additionally, DNA binding assays and antibacterial activity were used to assess the biological perspectives for the synthesized complex, including the ligand and complex which was further confirmed by molecular docking. Fluorescence Spectroscopy, viscosity measurement, and adsorption measurement were used to investigate the interaction of the Zn (II) complex with CT-DNA. A comparative in vitro antibacterial activity study against Escherichia coli, Klebsiella pneumoniae, Bacillus subtilis, and Staphylococcus aureus strains were studied with free ligand and Zn (II) metal complex. The stable geometry of the complex was additionally established through computational simulation utilizing density functional theory, which was followed by the calculation of several electronic properties. The ADMET characteristics of the complex and ligand were also assessed using ADMET analysis. The in-silico ADMET properties pointed to a significant drug-likeness feature in the synthesized compounds, based on the Lipinski criteria.

Theoretical study of the interaction between the antibiotic linezolid and the active site of the 50S ribosomal subunit of the bacterium Haloarcula marismortui

First antibiotic in the oxazolidinone class, linezolid fights gram-positive multiresistant bacteria by inhibiting protein synthesis through its interaction with the 50S subunit of the functional bacterial ribosome. For its antimicrobial action, it is necessary that its chiral carbon located in the oxazolidinone ring is in the S-conformation. Computational calculation at time-dependent density functional theory methodology, ultraviolet-visible (UV-Vis), and electronic circular dichroism spectra was obtained for noncomplexed and complexed forms of linezolid to verify the possible chirality of nitrogen atom in the acetamide group of the molecule. The molecular system has two chiral centers. So, there are now four possible configurations: RR, RS, SR, and SS. For a better understanding of the system, the electronic spectra at the PBE0/6-311++G(3df,2p) level of theory were obtained. The complexed form was obtained from the crystallographic data of the ribosome, containing the S-linezolid molecular system. The computational results obtained for the electronic properties are in good agreement with the experimental crystallographic data and available theoretical results.

Molecular insight into endosulfan degradation by Ese protein from Arthrobacter: Evidence-based structural bioinformatics and quantum mechanical calculations

Endosulfan is an organochlorine insecticide widely used for agricultural pest control. Many nations worldwide have restricted or completely banned it due to its extreme toxicity to fish and aquatic invertebrates. Arthrobacter sp. strain KW has the ability to degrade α, β endosulfan and its intermediate metabolite endosulfate; this degradation is associated with Ese protein, a two-component flavin-dependent monooxygenase (TC-FDM). Employing in silico tools, we obtained the 3D model of Ese protein, and our results suggest that it belongs to the Luciferase Like Monooxygenase family (LLM). Docking studies showed that the residues V59, V315, D316, and T335 interact with α-endosulfan. The residues: V59, T60, V315, D316, and T335 are implicated in the interacting site with β-endosulfan, and the residues: H17, V315, D316, T335, N364, and Q363 participate in the interaction with endosulfate. Topological analysis of the electron density by means of the Quantum Theory of Atoms in Molecules (QTAIM) and the Non-Covalent Interaction (NCI) index reveals that the Ese-ligands complexes are formed mainly by dispersive forces, where Cl atoms have a predominant role. As Ese is a monooxygenase member, we predict the homodimer formation. However, enzymatic studies must be developed to investigate the Ese protein's enzymatic and catalytic activity.

Mutual induced fit transition structure stabilization of corannulene's bowl-to-bowl inversion in a perylene bisimide cyclophane

Corannulene is known to undergo a fast bowl-to-bowl inversion at r.t. via a planar transition structure (TS). Herein we present the catalysis of this process within a perylene bisimide (PBI) cyclophane composed of chirally twisted, non-planar chromophores, linked by para-xylylene spacers. Variable temperature NMR studies reveal that the bowl-to-bowl inversion is significantly accelerated within the cyclophane template despite the structural non-complementarity between the binding site of the host and the TS of the guest. The observed acceleration corresponds to a decrease in the bowl-to-bowl inversion barrier of 11.6 kJ mol-1 compared to the uncatalyzed process. Comparative binding studies for corannulene (20 π-electrons) and other planar polycyclic aromatic hydrocarbons (PAHs) with 14 to 24 π-electrons were applied to rationalize this barrier reduction. They revealed high binding constants that reach, in tetrachloromethane as a solvent, the picomolar range for the largest guest coronene. Computational models corroborate these experimental results and suggest that both TS stabilization and ground state destabilization contribute to the observed catalytic effect. Hereby, we find a "mutual induced fit" between host and guest in the TS complex, such that mutual geometric adaptation of the energetically favored planar TS and curved π-systems of the host results in an unprecedented non-planar TS of corannulene. Concomitant partial planarization of the PBI units optimizes noncovalent TS stabilization by π-π stacking interactions. This observation of a "mutual induced fit" in the TS of a host-guest complex was further validated experimentally by single crystal X-ray analysis of a host-guest complex with coronene as a qualitative transition state analogue.

Ligand 1 H NMR Chemical Shifts as Accurate Reporters for Protein-Ligand Binding Interfaces in Solution

The availability of high-resolution 3D structural information is crucial for investigating guest-host systems across a wide range of fields. In the context of drug discovery, the information is routinely used to establish and validate structure-activity relationships, grow initial hits from screening campaigns, and to guide molecular docking. For the generation of protein-ligand complex structural information, X-ray crystallography is the experimental method of choice, however, with limited information on protein flexibility. An experimentally verified structural model of the binding interface in the native solution-state would support medicinal chemists in their molecular design decisions. Here we demonstrate that protein-bound ligand 1 H NMR chemical shifts are highly sensitive and accurate probes for the immediate chemical environment of protein-ligand interfaces. By comparing the experimental ligand 1 H chemical shift values with those computed from the X-ray structure using quantum mechanics methodology, we identify significant disagreements for parts of the ligand between the two experimental techniques. We show that quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) ensembles can be used to refine initial X-ray co-crystal structures resulting in a better agreement with experimental 1 H ligand chemical shift values. Overall, our findings highlight the usefulness of ligand 1 H NMR chemical shift information in combination with a QM/MM MD workflow for generating protein-ligand ensembles that accurately reproduce solution structural data.

Synthesis of Closed-Heterohelicenes Interconvertible between Their Monomeric and Dimeric Forms

Oxidative fusion reaction of cyclic heteroaromatic pentads consisting of pyrrole and thiophene gave closed-heterohelicene monomers and dimers depending on the oxidation conditions. Specifically, oxidation with [bis(trifluoroacetoxy)iodo]benzene (PIFA) gave closed-[7]helicene dimers connected at the β-position of one of the pyrrole units with remarkably elongated C-C bonds of about 1.60 Å. Although this bond was intact against thermal and physical activations, homolytic bond dissociation took place in DMSO upon irradiation with UV light to give the corresponding monomers. Thus, interconversion between the closed-helicene monomer and dimer was achieved. The optically pure dimer was photo-dissociated into the monomers associated with a turn-on of circularly polarized luminescence (CPL).

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

A comprehensive computer simulation insight into inhibitory mechanisms of EGCG and NQTrp ligands on amyloid-beta assemblies as the Alzheimer's disease insignia

Amyloid-β peptide with predominant presence in the senile plaques is the most common agent for Alzheimer's disease (AD) incidence. Assembly of the amyloid-β(1-42) (Aβ1-42) isoform is known as the main reason for the AD appearance. Epigallocatechin gallate (EGCG) and 1,4-naphthoquinone-2-yl-L-tryptophan (NQTrp) are two small molecules that inhibit the formation of the Aβ1-42 fibrils. The present study provides molecular insight to clarify the inhibitory mechanisms of the EGCG and NQTrp ligands on the Aβ1-42 assemblies by using molecular dynamics (MD) simulation. Hence, nine different Aβ1-42-containing systems including the monomer, dimer, and hexamer of Aβ1-42 considering each of them in a media with no ligands, in the presence of one EGCG ligand, and in the presence of one EGCG ligand were studied with a simulation time of 1 µs for each system. The precise investigation of the peptide-ligand distance, conformational factor (Pi), solvent accessible surface area (SASA), dictionary of secondary structure (DSSP), and Lys28-Ala42 salt bridge analyses confirmed that the hydroxyl-rich structure of the EGCG ligand applied its inhibitory effect on the aggregation of the peptides indirectly by involving water molecules. While the hydroxyl-free structure of the NQTrp ligand exposed its inhibitory effect through a direct interaction with the Aβ1-42 peptides. Besides, reduced density gradient (RDG) analysis clarified the hydrogen bonding interactions as the dominant ones for the peptide-EGCG systems, and also, steric and van der Waals interactions for the peptide-NQTrp systems.Communicated by Ramaswamy H. Sarma.

Atropisomerism about aryl-C(sp3) bonds: chemically driven rotational pathway in cannabidiol derivatives

The conformational behaviour arising from the restricted C(sp2)-C(sp3) axis in ortho O-substituted naphthylcyclohexane and naphthylcyclohexene oxide derivatives of cannabidiol was examined by means of VT-NMR experiments and DFT calculations. Atropisomeric compounds with barriers in the range of 91.1 to 95.1 kJ mol-1 were obtained at 298 K. Two possible transition states (TS1 and TS2) were located, one is more stable depending on the chemical modification made on the monoterpene ring close to the pivot bond. Extended analysis of TS structures to previously reported phenyl derivatives bearing the same O-substituent led to similar rotational pathways according to the series: through TS1 in arylcylohexenes and TS2 in arylcyclohexanes. Likewise, conversion of arylcyclohexenes into both series affects the rotation speed by decelerating it, and the nature of the aryl ring seems to have a very minor effect on this phenomenon.

A Holistic View of the Interactions between Electron-Deficient Systems: Clustering of Beryllium and Magnesium Hydrides and Halides

In the search for common bonding patterns in pure and mixed clusters of beryllium and magnesium derivatives, the most stable dimers and trimers involving BeX2 and MgX2 (X = H, F, Cl) have been studied in the gas phase using B3LYP and M06-2X DFT methods and the G4 ab initio composite procedure. To obtain some insight into their structure, stability, and bonding characteristics, we have used two different energy decomposition formalisms, namely MBIE and LMO-EDA, in parallel with the analysis of the electron density with the help of QTAIM, ELF, NCIPLOT, and AdNDP approaches. Some interesting differences are already observed in the dimers, where the stability sequence observed for the hydrides differs entirely from that of the fluorides and chlorides. Trimers also show some peculiarities associated with the presence of compact trigonal cyclic structures that compete in stability with the more conventional hexagonal and linear forms. As observed for dimers, the stability of the trimers changes significantly from hydrides to fluorides or chlorides. Although some of these clusters were previously explored in the literature, the novelty of this work is to provide a holistic approach to the entire series of compounds by using chemical bonding tools, allowing us to understand the stability trends in detail and providing insights for a significant number of new, unexplored structures.

Biological noncovalent N/O⋯V interactions: insights from theory and protein data bank analyses

Computations at the PBE0-D3/def2-TZVP level of theory in conjunction with a Protein Data Bank (PDB) survey have provided first time evidence of favorable noncovalent interactions between ADP metavanadate (VO4) and ADP orthovanadate (VO5) and electron rich atoms. These involve a σ-hole present in the V atom and the lone pairs belonging to (i) protein residues (e.g., serine (SER), glutamate (GLU) or histidine (HIS)), (ii) backbone carbonyl groups and (iii) water molecules. A computational study has been carried out to rationalize the physical nature and directionality of the interaction in addition to its plausible biological role. The results reported herein are expected to have an impact in the fields of medicinal chemistry, bioinorganic chemistry and chemical biology.

Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond

Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.

Molecular orbital and topological electron density study of n → π* interactions: amides and thioamides cases

The n → π* interactions were studied in amides and thioamides systems models, through the analysis of the electron density topology along with the Natural Bonding Orbital (NBO) approach. The effect of the dispersion terms was assessed using different DFT functionals. The NBO, independent gradient model (IGM), and the analysis of the reduced density gradient outcomes show that dispersion forces play a significant role in the strength of n → π* interactions. The IGM results indicate that δg height values for n → π* interactions do not extend beyond 0.025. All the methods used in this work predict that n → π* interaction between pairs of thioamides is stronger than those between amides. However, the electron density topology-based methods were not able to replicate the trends in the relative force of this interaction found in the experimental and NBO results.

Computational Study Focusing on a Comprehensive Conformational Analysis of Transition States for Aza-Spiro Ring Formations with N-Alkoxyamides

An accurate understanding of conformations in transition states is a critical piece in the theoretical analysis of complex molecular reactions. In this study, we investigated conformationally diverse transition states during intramolecular aza-spiro ring formation with an allylsilane moiety and N-alkoxy iminium ion, a key reaction in the synthesis of fasicularin by Sato and Chida et al., and identified the origins of stereoselectivity of the cyclization. A large number of conformational isomers with forming C-C bonds were comprehensively analyzed using Cremer-Pople puckering parameters. It was found that the conformations of the transition states had different puckering preferences depending on the reactant's double-bond geometry and the product's stereochemical configuration. Furthermore, an asymmetric aza-spiro cyclization with a tolyl group as a chiral auxiliary was investigated, showing that conformational anchoring by both a CH-O hydrogen bond and the CH-π interaction was critical for the asymmetric induction.

The Oxidation of Oxygen and Sulfur-Containing Heterocycles by Cytochrome P450 Enzymes

The cytochrome P450 (CYP) superfamily of monooxygenase enzymes play important roles in the metabolism of molecules which contain heterocyclic, aromatic functional groups. Here we study how oxygen- and sulfur-containing heterocyclic groups interact with and are oxidized using the bacterial enzyme CYP199A4. This enzyme oxidized both 4-(thiophen-2-yl)benzoic acid and 4-(thiophen-3-yl)benzoic acid almost exclusively via sulfoxidation. The thiophene oxides produced were activated towards Diels-Alder dimerization after sulfoxidation, forming dimeric metabolites. Despite X-ray crystal structures demonstrating that the aromatic carbon atoms of the thiophene ring were located closer to the heme than the sulfur, sulfoxidation was still favoured with 4-(thiophen-3-yl)benzoic acid. These results highlight a preference of this cytochrome P450 enzyme for sulfoxidation over aromatic hydroxylation. Calculations predict a strong preference for homodimerization of the enantiomers of the thiophene oxides and the formation of a single major product, in broad agreement with the experimental data. 4-(Furan-2-yl)benzoic acid was oxidized to 4-(4'-hydroxybutanoyl)benzoic acid using a whole-cell system. This reaction proceeded via a γ-keto-α,β-unsaturated aldehyde species which could be trapped in vitro using semicarbazide to generate a pyridazine species. The combination of the enzyme structures, the biochemical data and theoretical calculations provides detailed insight into the formation of the metabolites formed from these heterocyclic compounds.

CH3 CN@open-C60 : An Effective Inner-Space Modification and Isotope Effect Inside a Nano-Sized Flask

Despite several small molecules being encapsulated inside cage-opened fullerene derivatives, such species have not considerably affected the structures and properties of the outer carbon cages. Herein, we achieved an effective inner-space modification for an open-cage C60 derivative by insertion of a neutral CH3 CN molecule into the cavity. The CH3 CN@open-C60 thus obtained showed an enhanced polarity, thus affording an easy separation from a mixture containing the empty cage by column chromatography on silica gel, without the preparative HPLC that was needed for previous cases. The less negative reduction potentials with respect to those of empty cage reflect the decreased energy level of the LUMO, which is supported by the DFT calculations. NMR spectroscopy, single-crystal X-ray analysis, and theoretical calculations revealed that both the presence of the encapsulated CH3 CN and cage deformation caused by the CH3 CN play an essential role in the change of the electronic properties. Furthermore, the favored binding affinity of deuterated acetonitrile CD3 CN with internal C60 surface is discussed.

The NCIWEB Server: A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems

It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions. Structure preparation is automated and allows direct importing from the PDB database, making this server (https://nciweb.dsi.upmc.fr) accessible to scientists with limited experience in bioinformatics. A quick overview of this tool and concise instructions are presented, together with an illustrative application.

H-Bonding leading to latent initiators for olefin metathesis polymerization

Ruthenium-NHC based catalysts, with a chelated iminium ligand trans to the N-heterocyclic carbene (NHC) ligand, that polymerize dicyclopentadiene (DCPD) at different temperatures are monitored using Density Functional Theory calculations to unveil the reaction mechanism, and subsequently how important are the geometrical and electronic features vs. the non-covalent interactions in between. The balance is very fragile and H-bonds are fundamental to explain the different behaviour of latent catalysts. This computational study aims to facilitate future studies of new generations of latent initiators for olefin metathesis polymerization, with the 3D and mainly the 2D Non-Covalent Interaction plots the characterization tool for H-bonds.

Calcium-Alginate-Chitosan Nanoparticle as a Potential Solution for Pesticide Removal, a Computational Approach

Pesticides have a significant negative impact on the environment, non-target organisms, and human health. To address these issues, sustainable pest management practices and government regulations are necessary. However, biotechnology can provide additional solutions, such as the use of polyelectrolyte complexes to encapsulate and remove pesticides from water sources. We introduce a computational methodology to evaluate the capture capabilities of Calcium-Alginate-Chitosan (CAC) nanoparticles for a broad range of pesticides. By employing ensemble-docking and molecular dynamics simulations, we investigate the intermolecular interactions and absorption/adsorption characteristics between the CAC nanoparticles and selected pesticides. Our findings reveal that charged pesticide molecules exhibit more than double capture rates compared to neutral counterparts, owing to their stronger affinity for the CAC nanoparticles. Non-covalent interactions, such as van der Waals forces, π-π stacking, and hydrogen bonds, are identified as key factors which stabilized the capture and physisorption of pesticides. Density profile analysis confirms the localization of pesticides adsorbed onto the surface or absorbed into the polymer matrix, depending on their chemical nature. The mobility and diffusion behavior of captured compounds within the nanoparticle matrix is assessed using mean square displacement and diffusion coefficients. Compounds with high capture levels exhibit limited mobility, indicative of effective absorption and adsorption. Intermolecular interaction analysis highlights the significance of hydrogen bonds and electrostatic interactions in the pesticide-polymer association. Notably, two promising candidates, an antibiotic derived from tetracycline and a rodenticide, demonstrate a strong affinity for CAC nanoparticles. This computational methodology offers a reliable and efficient screening approach for identifying effective pesticide capture agents, contributing to the development of eco-friendly strategies for pesticide removal.

Dispersion, Rehybridization, and Pentacoordination: Keys to Understand Clustering of Boron and Aluminum Hydrides and Halides

The structure, stability, and bonding characteristics of dimers and trimers involving BX₃ and AlX₃ (X = H, F, Cl) in the gas phase, many of them explored for the first time, were investigated using different DFT (B3LYP, B3LYP/D3BJ, and M06-2X) and ab initio (MP2 and G4) methods together with different energy decomposition formalisms, namely, many-body interaction-energy and localized molecular orbital energy decomposition analysis. The electron density of the clusters investigated was analyzed with QTAIM, electron localization function, NCIPLOT, and adaptive natural density partitioning approaches. Our results for triel hydride dimers and Al₂X₆ (X = F, Cl) clusters are in good agreement with previous studies in the literature, but in contrast with the general accepted idea that B₂F₆ and B₂Cl₆ do not exist, we have found that they are predicted to be weakly bound systems if dispersion interactions are conveniently accounted for in the theoretical schemes used. Dispersion interactions are also dominant in both homo- and heterotrimers involving boron halide monomers. Surprisingly, B₃F₉ and B₃Cl₉ C_3v cyclic trimers, in spite of exhibiting rather strong B-X (X = F, Cl) interactions, were found to be unstable with respect to the isolated monomers due to the high energetic cost of the rehybridization of the B atom, which is larger than the two- and three-body stabilization contributions when the cyclic is formed. Another important feature is the enhanced stability of both homo- and heterotrimers in which Al is the central atom because Al is systematically pentacoordinated, whereas this is not the case when the central atom is B, which is only tri- or tetra-coordinated.

Influence of 2'-Modifications (O-Methylation, Fluorination, and Stereochemical Inversion) on the Base Pairing Energies of Protonated Cytidine Nucleoside Analogue Base Pairs: Implications for the Stabilities of i-Motif Structures

Naturally occurring and chemically engineered modifications are among the most powerful strategies explored for fine-tuning the conformational characteristics and intrinsic stability of nucleic acids topologies. Modifications at the 2'-position of the ribose or 2'-deoxyribose moieties differentiate nucleic acid structures and have a significant impact on their electronic properties and base-pairing interactions. 2'-O-Methylation, a common post-transcriptional modification of tRNA, is directly involved in modulating specific anticodon-codon base-pairing interactions. 2'-Fluorinated and arabino nucleosides possess novel and beneficial medicinal properties and find use as therapeutics for treating viral diseases and cancer. However, the potential to deploy 2'-modified cytidine chemistries for tuning i-motif stability is largely unknown. To address this knowledge gap, the effects of 2'-modifications including O-methylation, fluorination, and stereochemical inversion on the base-pairing interactions of protonated cytidine nucleoside analogue base pairs, the core stabilizing interactions of i-motif structures, are examined using complementary threshold collision-induced dissociation techniques and computational methods. The 2'-modified cytidine nucleoside analogues investigated here include 2'-O-methylcytidine, 2'-fluoro-2'-deoxycytidine, arabinofuranosylcytosine, 2'-fluoro-arabinofuranosylcytosine, and 2',2'-difluoro-2'-deoxycytidine. All five 2'-modifications examined here are found to enhance the base-pairing interactions relative to the canonical DNA and RNA cytidine nucleosides with the greatest enhancements arising from 2'-O-methylation and 2',2'-difluorination, suggesting that these modifications should well be tolerated in the narrow grooves of i-motif conformations.

IGMPlot: A program to identify, characterize, and quantify molecular interactions

We describe the development and features of a program called IGMPlot, which is based on the independent gradient model (IGM) and its local descriptor δ g $$ \delta g $$ . The IGM approach analyzes the gradient of the electron density (ED) in a molecular system to identify regions of space where chemical interactions take place. IGMPlot is intended for use by both experimental scientists and theoretical chemists. It is standalone software written in C++, with versions available for multiple platforms. Some key features are: probing and quantifying interactions between two given molecular fragments, determining bond strength (IBSI), estimating the atomic contributions to an intermolecular interaction and preparing data to build 2D and 3D representations of interaction regions. The software has been updated to include new features: critical point analysis of the ED, assessing ED asymmetry of a given bond (PDA) and a new descriptor called q g $$ qg $$ designed to enhance the IGM- δ g $$ \delta g $$ analysis. The program can be found at: http://igmplot.univ-reims.fr.

Catalytic enantioselective nucleophilic desymmetrization of phosphonate esters

Molecules that contain a stereogenic phosphorus atom are crucial to medicine, agrochemistry and catalysis. While methods are available for the selective construction of various chiral organophosphorus compounds, catalytic enantioselective approaches for their synthesis are far less common. Given the vastness of possible substituent combinations around a phosphorus atom, protocols for their preparation should also be divergent, providing facile access not only to one but to many classes of phosphorus compounds. Here we introduce a catalytic and enantioselective strategy for the preparation of an enantioenriched phosphorus(V) centre that can be diversified enantiospecifically to a wide range of biologically relevant phosphorus(V) compounds. The process, which involves an enantioselective nucleophilic substitution catalysed by a superbasic bifunctional iminophosphorane catalyst, can accommodate a wide range of carbon substituents at phosphorus. The resulting stable, yet versatile, synthetic intermediates can be combined with a multitude of medicinally relevant O-, N- and S-based nucleophiles.

Lithium-Mediated Mechanochemical Cyclodehydrogenation

Cyclodehydrogenation is an essential synthetic method for the preparation of polycyclic aromatic hydrocarbons, polycyclic heteroaromatic compounds, and nanographenes. Among the many examples, anionic cyclodehydrogenation using potassium(0) has attracted synthetic chemists because of its irreplaceable reactivity and utility in obtaining rylene structures from binaphthyl derivatives. However, existing methods are difficult to use in terms of practicality, pyrophoricity, and lack of scalability and applicability. Herein, we report the development of a lithium(0)-mediated mechanochemical anionic cyclodehydrogenation reaction for the first time. This reaction could be easily performed using a conventional and easy-to-handle lithium(0) wire at room temperature, even under air, and the reaction of 1,1'-binaphthyl is complete within 30 min to afford perylene in 94% yield. Using this novel and user-friendly protocol, we investigated substrate scope, reaction mechanism, and gram-scale synthesis. As a result, remarkable applicability and practicality over previous methods, as well as limitations, were comprehensively studied by computational studies and nuclear magnetic resonance analysis. Furthermore, we demonstrated two-, three-, and five-fold cyclodehydrogenations for the synthesis of novel nanographenes. In particular, quinterrylene ([5]rylene or pentarylene), the longest nonsubstituted molecular rylene, was synthesized for the first time.

Comprehensive Mechanistic Scenario for the Cu-Mediated Asymmetric Propargylic Sulfonylation Forging Tertiary Carbon Stereocenters

Metal-catalyzed propargylic transformations represent a powerful tool in organic synthesis to achieve new carbon-carbon and carbon-heteroatom bonds. However, detailed knowledge about the mechanistic intricacies related to the asymmetric formation of propargylic products featuring challenging heteroatom-substituted tertiary stereocenters is scarce and therefore provides an inspiring challenge. Here, we present a meticulous mechanistic analysis of a propargylic sulfonylation reaction promoted by a chiral Cu catalyst through a combination of experimental techniques and computational studies. Surprisingly, the enantio-discriminating step is not the coupling between the nucleophile and the propargylic precursor but rather the following proto-demetalation step, a scenario further validated by computing enantio-induction levels under other previously reported experimental conditions. A full mechanistic scenario for this propargylic substitution reaction is provided, including a catalyst pre-activation stage, a productive catalytic cycle, and an unanticipated non-linear effect at the Cu(I) oxidation level.

Infrared Spectroscopy Evidence of Weak Interactions in Frustrated Lewis Pairs Formed by Tris(pentafluorophenyl)borane

Frustrated Lewis pairs (FLPs) have been widely investigated as promising catalysts due to their metal-free feature and ability to activate small molecules. Since their discovery, many works have been investigating how these Lewis pairs (intermolecular pairs) are held together in an encounter complex. This prompted several studies based on theoretical investigations, but experimental ones are limited yet. In this communication we show evidence of weak intermolecular interactions between Lewis acids and Lewis bases, distinguishing the Lewis adduct from FLPs, by probing fluorine-carbon vibrational modes using infrared spectroscopy. The main evidence is based on the band shifts occurring in FLPs due to weak hydrogen bonds between the hydrogen atoms of the Lewis base and the fluorine atoms of Lewis acid.

Metal ion-decorated hexasilaprismane and its derivative as a molecular container for the separation of CO2 from flue gas molecules: a computational study

The electronic structure of hexasilaprismane (HSP) was examined with different computational techniques to elucidate the bonding features and the electrostatic surface potential of HSP. The carbon dioxide adsorption and separation capacities of metal-ion-decorated hexasilaprismane (HSP) were examined with DFT and CBS-QB3. Furthermore, the 1,2,3,4,5,6-hexaphenylprismasilane (HPPS) molecule was examined for its binding with metal ions and gas adsorption capacity. The Mg²⁺ ion complexed HPPS molecule adsorbs 15CO₂ molecules with an average binding free energy of -0.98 eV per molecule. The calculated gravimetric densities of 45.1 and 48.4 wt% show that these systems can be employed for CO₂ capture. The substantial difference in the affinity of the designed systems for CO₂ gas molecules compared to N₂ and CH₄ molecules show the potential of the systems for CO₂ separation from N₂ and CH₄ gas molecules.

Structures and Supramolecular Properties of Inclusion Complexes of Anthracene-Triptycene Nanocages with Fullerene Guests and Their Dynamic Motion as Molecular Gyroscopes

Three derivatives of macrocyclic cage compounds consisting of diarylanthracene and triptycene units were synthesized. These nanocages formed host-guest complexes with C₆₀ and other fullerene guests as confirmed by ¹ H NMR and fluorescence spectroscopy. The association constant of the mesityl and 2,4,6-tributoxyphenyl derivatives with C₆₀ was determined to be 2.2 × 10⁴  L mol^-1 , which was larger than that of the pentafluorophenyl derivative. Direct experimental evidence of the complexation was obtained by X-ray diffraction analysis: the guest C₆₀ molecule was included in the cavity via multipoint CH⋅⋅⋅π interactions. Dynamic disorders of the included C₆₀ molecule in variable-temperature X-ray analysis indicated uniaxial motion, such as gyroscopic motion. The unique dynamic behavior of the spherical C₆₀ rotor anchored by the cage stator via CH⋅⋅⋅π interactions in the crystal, as well as substituent effects on the association properties, are discussed with the aid of DFT calculations.

Anion and ether group influence in protic guanidinium ionic liquids

Ionic liquids are attractive liquid materials for many advanced applications. For targeted design, in-depth knowledge about their structure-property-relations is urgently needed. We prepared a set of novel protic ionic liquids (PILs) with a guanidinium cation with either an ether or alkyl side chain and different anions. While being a promising cation class, the available data is insufficient to guide design. We measured thermal and transport properties, nuclear magnetic resonance (NMR) spectra as well as liquid and crystalline structures supported by ab initio computations and were able to obtain a detailed insight into the influence of the anion and the ether substitution on the physical and spectroscopic properties. For the PILs, hydrogen bonding is the main interaction between cation and anion and the H-bond strength is inversely related to the proton affinity of the constituting acid and correlated to the increase of ¹H and ¹⁵N chemical shifts. Using anions from acids with lower proton affinity leads to proton localization on the cation as evident from NMR spectra and self-diffusion coefficients. In contrast, proton exchange was evident in ionic liquids with triflate and trifluoroacetate anions. Using imide-type anions and ether side groups decreases glass transitions as well as fragility, and accelerated dynamics significantly. In case of the ether guanidinium ionic liquids, the conformation of the side chain adopts a curled structure as the result of dispersion interactions, while the alkyl chains prefer a linear arrangement.

i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds

G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC₅ normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC₅ to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.

Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity

DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is composed of over 10 proteins. A subset of these proteins (Pol III*) includes the polymerase (α), exonuclease (ϵ), clamp (β), and accessory protein (θ). Mutations of residues in, or around the active site of the catalytic subunits (α and ϵ), can have a significant impact on catalysis. However, the effects of distal mutations in noncatalytic subunits on the activity of catalytic subunits are less well-characterized. Here, we investigate the effects of two Pol III* variants, β-L82E/L82'E and β-L82D/L82'D, on the proofreading reaction catalyzed by ϵ. MD simulations reveal major changes in the dynamics of Pol III*, which extend throughout the complex. These changes are mostly induced by a shift in the position of the DNA substrate inside the β-clamp, although no major structural changes are observed in the protein complex. Quantum mechanics/molecular mechanics (QM/MM) calculations indicate that the β-L82D/L82'D variant has reduced catalytic proficiency due to highly endoergic reaction energies resulting from structural changes in the active site and differences in the electric field at the active site arising from the protein and substrate. Conversely, the β-L82E/L82'E variant is predicted to maintain proofreading activity, exhibiting a similar reaction barrier for nucleotide excision compared with the WT system. However, significant differences in the reaction mechanism are obtained due to the changes induced by the mutations on the β-clamp.

Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses

The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.

TFRegNCI: Interpretable Noncovalent Interaction Correction Multimodal Based on Transformer Encoder Fusion

The interpretability is an important issue for end-to-end learning models. Motivated by computer vision algorithms, an interpretable noncovalent interaction (NCI) correction multimodal (TFRegNCI) is proposed for NCI prediction. TFRegNCI is based on RegNet feature extraction and a transformer encoder fusion strategy. RegNet is a network design paradigm that mainly focuses on local features. Meanwhile, the Vision Transformer is also leveraged for feature extraction, because it can capture global features better than RegNet while lowering the computational cost. Using a transformer encoder as the fusion strategy rather than multilayer perceptron can enhance model performance, due to its emphasis on important features with less parameters. Therefore, the proposed TFRegNCI achieved high accurate prediction (mean absolute error of ∼0.1 kcal/mol) comparing with the coupled cluster single double (triple) (CCSD(T)) benchmark. To further improve the model efficiency, TFRegNCI applies two-dimensional (2D) inputs transformed from three-dimensional (3D) electron density cubes, which saves time (30%), while the model accuracy remains. To improve model interpretability, a visualization module, Gradient-weighted Regression Activation Mapping (Grad-RAM) has been embedded. Grad-RAM is promoted from the classification algorithm, Gradient-weighted Class Activation Mapping, to perform feature visualization for the regression task. With Grad-RAM, the visual location map for features in deep learning models can be displayed. The feature map visualizations suggest that the 2D model has the similar performance as the 3D model, because of equally effective feature extractions from electron density. Moreover, the valid feature region on the location map by the 3D model is consistent with the NCIPLOT NCI isosurface. It is confirmed that the model does extract significant features related to the NCI interaction. The interpretable analyses are carried out through molecular orbital contribution on effective features. Thereby, the proposed model is likely to be a promising tool to reveal some essential information on NCIs, with regard to the level of electronic theory.