Noncovalent interactions: a challenge for experiment and theory

Computational Study of Complexation in LiH:nNH3 (n = 1-4) Clusters: An Interplay Among Hydrogen, Dihydrogen, and Lithium Bonds

Ab initio and density functional theory (DFT) calculations are employed to investigate LiH:nNH3 (n = 1-4) cluster complexes. The nature of the interactions is analyzed using molecular electrostatic potential maps, quantum theory of atoms in molecules, delocalization indices, and electron density difference maps. In the presence of LiH, NH3 molecules engage in several types of noncovalent interactions, namely, hydrogen bonding (HB), lithium bonding (LB), and dihydrogen bonding (DHB). The LiH:NH3 dimer is stabilized primarily through Li···N interactions. The role of these noncovalent interactions in complexes having more than one NH3 molecule, for example, hetero-trimer, tetramer, and pentamer structures, is also examined. Increasing the number of NH3 molecules enhances the number of HB sites. Additionally, the strengths of LB and DHB interactions associated with HB-bonded NH3 molecules increase. Interaction energy estimates and many-body energy decomposition analysis suggest that increasing NH3 molecules increases cooperativity, approaching ~10% of the total interaction's energy in the case of tetramers and pentamers.

Stabilization of α-Helical Folded Structures Retards Hydrophobic Zipping and Fibrillation of Bovine Insulin: A Key Signature from Raman Spectroscopic Analysis

Insulin is an α-helical-rich globular protein that is well-stabilized via several noncovalent forces including the inter-residue/intersubunit hydrophobic interactions. However, similar noncovalent forces, although of different degrees and orientations, effectuate many proteins to assemble and adapt thermodynamically stable β-sheet-rich fibrillar aggregates, causing a severe impact on their native structure and function. This fibrillation of proteins involves a key event, which is the zipping of hydrophobic amyloidogenic regions that are exposed intrinsically or become bared in the folded proteins under harsh conditions. This study has revealed that Coomassie Brilliant Blue G-250 (CBBG) can inhibit the essential zipping processes and stabilize the α-helical structure of bovine insulin (BI), resulting in a significant delay in the fibril formation. The interaction of CBBG with BI was found to be a thermodynamically favorable event, with it being an enthalpy-driven process (ΔH0 -88.04 kcal/mol), with the change in Gibb's free energy (ΔG0) observed to be ∼ -6.98 kcal/mol. Surface-enhanced Raman scattering measurements showed a characteristic α-helical signal of the protein at 1649 cm-1 in the presence of CBBG, suggesting the enhanced thermal stability of the hormone. Computational analysis further revealed that CBBG binds to both chains A and B of bovine insulin and boosts the folding stability in the monomeric state, causing a significant reduction in its structural fluctuation. The sulfonate moieties of CBBG showed significant intermolecular interactions with the B chain of N-terminal segments. Specifically, one sulfonate group formed multiple hydrogen bonds with both the backbone amide group and the terminal amine. Also, the N-terminal phenylalanine residue of BI (F1B) was found to have a significant contribution to the hydrophobic π-π stacking interactions with the CBBG aromatic phenyl ring.

Semiconductor Superstructures with Multiple Synergistic Resonances for SERS Exploring Multiplex Noncovalent Interactions

Noncovalent interactions (NCIs) are crucial for biological bond-forming events and have significant applications across various branches of chemistry. Here, we demonstrate for the first time the identification of multiple NCIs between two interacting species using semiconductor-based surface-enhanced Raman scattering (SERS) spectroscopy. This was accomplished by designing submicrometer-sized TiO2 superstructures with synergistic effects of Mie and charge-transfer resonances for SERS enhancement, enabling the TiO2/4-mercaptobenzoic acid (MBA) system to achieve both high SERS activity and interfacial charge-transfer sensitivity. The results clearly indicate that the vibrational frequencies of MBA shift in correlation with various intermolecular interactions from hydrogen-bonding to ionic interactions. Multiple SERS analyses of NCIs were conducted for both the four DNA bases and single-stranded DNA sequences. Additionally, we performed a proof-of-concept study utilizing the relative SERS intensity to detect the relative content of two bases in single-stranded DNA sequences. This study unlocks potential applications of semiconductor SERS for exploring intermolecular-specific interactions.

Box-like Molecules-Induced Discrete Ring-in-Rings Assembly of Hydrogen-Bonded Aramide Macrocycles

The controlled formation of ring-in-ring(s) assemblies is highly desirable as precursors for constructing higher order supramolecular architectures. We report our findings that this goal can be achieved by balancing molecular structures and conformational adaptivity through an interplay of multiple non-covalent bonding interactions. With hydrogen-bonded (H-bonded) aramide macrocycles and box-like molecules including naph-Box, m-Box and p4p-Box, ring-in-rings assembling systems with 4 : 1 stoichiometry are preferentially created. The formation of such assemblies with a defined number of rings threaded on a Box molecule is unprecedented using 2D shape-persistent macrocycles. The unusual assembly behaviors are rationalized by the aid of NMR spectroscopy, mass spectrometry, X-ray crystallography, and xTB computation. In sharp contrast to the use of o-Box and p-Box in forming ring-in-rings complexes where a distribution of various assembled species is observed, the box-like molecules all afford monodisperse compact assemblies. Conformational adaptivity is deemed as one of the major factors that is accountable for the selectivity observed, which is driven mainly by cooperative action of multiple non-covalent bonding interactions including H-bonding and π-π stacking interactions. Using pyrimidyl-incorporated H-bonded macrocycles and box-like molecules to form ring-in-rings assembling structures may provide opportunities for designing more sophisticated and topologically unique supramolecular systems with potential functions.

IR Spectroscopy of 4-Aminobenzonitrile+-Arn (n = 0-2): Determination of the Activation Barrier for the π → NH Site-Switching Reaction

Information about the intermolecular potential energy surface for the interaction between solute and solvent molecules is required to understand the impact of solvation on reaction mechanisms and dynamics. In this study, we measured vibrational-specific infrared (IR) spectra of 4-aminobenzonitrile-(argon)n cation clusters, 4ABN+-Arn (n = 1, 2), in the NH stretching range to elucidate the energetics of the photoionization-induced π → NH migration of Ar. The IR spectra of 4ABN+-Arn generated by resonant photoionization of neutral π-bonded clusters display the hydrogen-bonded NH2 stretching vibration (νNH2) only when intermolecular vibrational levels are excited. This is the first observation of Ar migration from the aromatic ring toward the NH2 group upon photoionization in the n = 1 cluster. From the vibrational-level dependence of the IR spectra, the activation barrier heights are determined to be 21-47 (34 ± 13) and <27 cm-1 for 4ABN+-Ar1 and 4ABN+-Ar2, respectively. The potential energy surfaces and mechanism of the Ar migration are discussed with the help of complementary density functional theory calculations.

Systematic discrepancies between reference methods for noncovalent interactions within the S66 dataset

The accurate treatment of noncovalent interactions is necessary to model a wide range of applications, from molecular crystals to surface catalysts to aqueous solutions and many more. Quantum diffusion Monte Carlo (DMC) and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)] are considered two widely trusted methods for treating noncovalent interactions. However, while they have been well-validated for small molecules, recent work has indicated that these two methods can disagree by more than 7.5 kcal/mol for larger systems. The origin of this discrepancy remains unknown. Moreover, the lack of systematic comparisons, particularly for medium-sized complexes, has made it difficult to identify which systems may be prone to such disagreements and the potential scale of these differences. In this work, we leverage the latest developments in DMC to compute interaction energies for the entire S66 dataset, containing 66 medium-sized complexes with a balanced representation of dispersion and electrostatic interactions. Comparison to previous CCSD(T) references reveals systematic trends, with DMC predicting stronger binding than CCSD(T) for electrostatic-dominated systems, while the binding becomes weaker for dispersion-dominated systems. We show that the relative strength of this discrepancy is correlated to the ratio of electrostatic and dispersion interactions, as obtained from energy decomposition analysis methods. Finally, we have pinpointed model systems: the hydrogen-bonded acetic acid dimer (ID 20) and dispersion-dominated uracil-cyclopentane dimer (ID 42), where these discrepancies are particularly prominent. These systems offer cost-effective benchmarks to guide future developments in DMC, CCSD(T), as well as the wider electronic structure theory community.

Exploring coinage bonding interactions in [Au(CN)4]- assemblies with silver and zinc complexes: a structural and theoretical study

This study investigates the non-covalent interactions between [Au(CN)4]- anions and silver and zinc complexes, with a particular focus on coinage bonding interactions. Four new complexes, [Ag2(pyNP)2][Au(CN)4]2 (1) [Zn(bipy)3][Au(CN)4]2 (2), [Zn(phen)3][Au(CN)4]2 (3) and [Zn(terpy)(H2O)3][Au(CN)4]2 (4), were synthesized and spectroscopically characterized, including their X-ray solid-state structures, where pyNP is (2-(2-pyridyl)-1,8-naphthyridine, bipy is 2,2' bipyridine, phen is 1,10'-phenantroline and terpy is terpyridine. The [Au(CN)4]- anion exhibits unique anion⋯anion interactions, despite the electrostatic repulsion, forming stable 1D supramolecular polymers in the solid state. Using a combination of X-ray crystallography and DFT calculations, this work characterizes the coordination and non-covalent bonding modes, including Au⋯N coinage bonds. Energy decomposition analysis (EDA), QTAIM, and NCIplot methods were applied to understand the energetics and bonding nature. The study reveals that electrostatic and dispersion forces play critical roles in stabilizing these assemblies, especially in the formation of π-stacking and T-shaped dimers. These findings offer insights into the design of new materials leveraging coinage bonding in molecular architectures.

Nonbonded Force Field Parameters Derived from Atoms-in-Molecules Methods Reproduce Interactions in Proteins from First-Principles

Noncovalent interactions govern many chemical and biological phenomena and are crucial in protein-protein interactions, enzyme catalysis, and DNA folding. The size of these macromolecules and their various conformations demand computationally inexpensive force fields that can accurately mimic the quantum chemical nature of the atomic noncovalent interactions. Accurate force fields, coupled with increasingly longer molecular dynamics simulations, may empower us to predict conformational changes associated with the biochemical function of proteins. Here, we aim to derive nonbonded protein force field parameters from the partitioned electron density of amino acids, the fundamental units of proteins, via the atoms-in-molecules (AIM) approach. The AIM parameters are validated using a database of charged, aromatic, and hydrophilic side-chain interactions in 610 conformations, primarily involving π-π interactions, as recently reported by one of us (Carter-Fenk et al., 2023). Electrostatic and van der Waals interaction energies calculated with nonbonded force field parameters from different AIM methodologies were compared to first-principles interaction energies from absolute localized molecular orbital-energy decomposition analysis (ALMO-EDA) at the ωB97XV/def2-TZVPD level. Our findings show that electrostatic interactions between side chains are accurately reproduced by atomic charges from the minimal basis iterative stockholder (MBIS) scheme with mean absolute errors of 4-7 kJ/mol. Meanwhile, C6 coefficients from the MBIS AIM method effectively predict dispersion interactions with a mean error of -2 kJ/mol and a maximal error of -5 kJ/mol. As an outlook to use AIM methods in the development of protein force fields, we present the constrained AIM method that allows one to fix backbone parameters during the optimization of side-chain interactions. Backbone dihedral parameters have been optimized to reproduce secondary structure elements in proteins, and not altering them maintains compatibility with conventional protein force fields while improving the description of side-chain interactions. Our validated AIM methods allow for the depiction of noncovalent, long-range interactions in proteins using cost-effective force fields that achieve chemical precision.

The matere bond

This perpective delves into the emerging field of matere bonds, a novel type of noncovalent interaction involving group 7 elements such as manganese, technetium, and rhenium. Matere bonds, a new member of the σ-hole family where metal atoms act as electron acceptors, have been shown experimentally and theoretically to play significant roles in the self-assembly and stabilization of supramolecular structures both in solid-state and solution-phase environments. This perspective article explores the physical nature of these interactions, emphasizing their directionality and structural influence in various supramolecular architectures. Recent studies have expanded the understanding of matere bonds beyond classical metal-ligand coordination, highlighting their potential in crystal engineering and catalysis. This perspective article also examines the occurrence of matere bonds in biological systems, particularly within manganese-containing proteins, where they contribute to the structural integrity and catalytic activity. Theoretical and computational analyses, including molecular electrostatic potential surfaces and density functional theory, further elucidate the properties and applications of matere bonds, offering new insights for the design of advanced materials and biomimetic systems. This comprehensive overview underscores the versatility of matere bonds, paving the way for future innovations in supramolecular chemistry involving metals.

A General Nonbonded Force Field Based on Accurate Quantum Mechanics Calculations for Elements H-La and Hf-Rn

Noncovalent interactions (NCI) play a central role in numerous physical, chemical, and biological phenomena. An accurate description of NCI is the key to success for any theoretical study in such areas. Although quantum mechanics (QM) methods such as dispersion-corrected density functional theory are sufficiently accurate, their applications are practical only for <300 atoms and <100 ps of simulation time. Thus, empirical force fields (FF) have generally been the only choice for systems with thousands to millions of atoms and for nanoseconds and longer. We want to develop a FF that can be applied to applications of thousands to millions of atoms with an accuracy comparable to QM methods. As the first step, we develop here a new general nonbonded potential (GNB) based on a novel functional form with four adjustable parameters for each element. We report here parameters for elements H-La, Hf-Rn (excluding lanthanides and actinides) by fitting the interaction energy of molecular complexes to QM calculations using the accurate Head-Gordon ωB97M-V density functional. We performed extensive testing of GNB for organic molecules, organometallic molecules, and metal organic-framework (MOF) systems. The mean absolute errors of GNB are 0.37 kcal/mol for the dispersion and mixed groups of the S66 × 8 benchmark set, 0.35 kcal/mol for CO2 adsorption on MOF materials, and 4.53 kcal/mol for the XTMC43 benchmark. GNB outperforms existing FF and in many cases has accuracy comparable to that of QM methods such as PBE-D3. GNB can potentially replace the nonbonded part of existing FFs in a wide range of applications.

π-π stacking interactions in tryptophan-lumiflavin-tyrosine: a structural model for riboflavin insertion into riboflavin-binding protein

CONTEXT

Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions. Density functional theory (DFT) served as the computation framework for all calculations, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6-311+ +g** basis set. The solvation effects were incorporated through the implementation of the polarizable continuum model (PCM) simulating an aqueous solvent environment. The geometries of the five most stable complexes show exclusively p-p interactions among the aromatic moieties in a displaced parallel plane stacking arrangement with interplanar heights and displacements in the range of 3.22-3.62 Å and 0.50-0.63 Å, respectively, at ωB97XD level. The calculated total energies and binding energies indicate two stabilizing p-p interactions: lumiflavin-tyrosine and lumiflavin-tryptophan, with the later stronger for the more stable complexes by 2 kcal mol-1. The complexes are less entropically favored than the independent molecules as verified by the positive association free Gibbs energies with LC-ωPBE and nearly zero with ωB97XD. Orbital analysis indicates a smaller HOMO-LUMO gap for complexes compared to the individual compounds suggesting a charge transfer component to the interaction. Moreover, the HOMO is localized on tryptophan and HOMO-1 on tyrosine, consistent with the strength of the respective interactions with lumiflavin.

METHODS

The initial geometry was based on the atom coordinates of the bonding tryptophan-riboflavin-tyrosine region in the protein crystallographic data with the ribityl tail being discarded, leading to a model complex: tryptophan-lumiflavin-tyrosine. The initial conformational search using the Amber force field within the Gabedit led to 30 unique conformations. The subsequent calculations, energy optimization and orbital analysis, were performed in Guassian16 at density functional theory (DFT) level, utilizing long-range corrected hybrid functionals LC-ωPBE and ωB97XD in conjunction with the 6-311+ +g** basis set. The solvent, water, was accounted for using the polarized continuum model (PCM).

Electronic Desymmetrization of Cu3(μ3-E) Clusters (E = S, Se) Induced by Edge-to-Face π-Stacking Interactions in the Second Coordination Sphere

A pair of cyclophane-encapsulated [Cu3(μ3-E)]3+ complexes (E = S and Se) were characterized by resonant X-ray diffraction anomalous fine structure (DAFS), revealing unexpected polarization among the three Cu sites attributed to long-range effects of π-stacking interactions with cocrystallized benzene molecules. The resonant K-edge energies of individual Cu sites within the cluster molecules were found to vary as a function of distance from the cocrystallized benzene. This pattern was interpreted in the context of T-shaped, edge-to-face π-stacking with the assistance of theoretical charge density difference calculations.

Influence of Noncovalent Interaction on the Nucleophilicity and Electrophilicity of Metal Centers in [MII(S2CNEt2)2] (M = Ni, Pd, Pt)

A systematic theoretical study was performed on the electrophilic and nucleophilic properties of Group 10 square-planar metal compounds [MII(S2CNEt2)2] (M = Ni 1, Pd 2, and Pt 3) and their complexes. The nucleophilic metal center and coordinated sulfur atom in [M(S2CNEt2)2] facilitate the formation of metal-involving and conventional noncovalent bonds. The presence a heavier metal center results in a more negative electrostatic potential and a larger nucleophilicity, which in turn leads to the formation of stronger metal-involving noncovalent bonds than those formed by a lighter metal center. The NiII center was observed to display electrophilic-nucleophilic dualism with regard to noncovalent interactions, forming both a metal-involving halogen bond (Ni···I) with iodine chloride (ICl) and a semicoordination bond (Ni···N) with N-bases. The nucleophilicity and electrophilicity of the NiII center are enhanced in the ternary complexes LB···1···XCl (X = H, I; LB = NH3, NHCH2, pyridine) due to the push-pull mechanism. The N···Ni semicoordination bond exerts a push effect on the dz2 orbital of the NiII center, while the Ni···X noncovalent bond provides a symbiotic pull effect on this orbital. Furthermore, the formation of metal-involving noncovalent bonds may enhance the electrophilic ability of the PdII and PtII center, resulting in the formation of stable ternary complexes Py···2/3···XCl (X = H, I), which are characterized by M···N and M···X interactions.

Spin-Lifetime Probe for Detecting Intramolecular Noncovalent Interaction in Organic Semiconductors

Intramolecular noncovalent interaction (INCI), a crucial strategy for effectively enhancing molecular planarity and extending π-electron delocalization in organic semiconductors (OSCs), has played an increasingly important role in optoelectronic applications. However, though the INCI formation is regularly considered to improve the device performance by literature, there is no feasible approach to directly and reliably characterizing its formation in practical-OSC films thus far. Here in this study, by theoretical analysis and calculation, the generation of INCIs in OSCs is found, normally consisting of relatively heavy elements, such as O···Se, O···S, N···S interactions, etc., can induce enhanced strength of spin-orbit coupling, the primary factor dominating spin lifetime in OSCs. Based on this newly discovered theory, spin lifetime is creatively employed as a probe for sensitively detecting INCIs in OSC films via spin valves or field-induced electron paramagnetic resonance, respectively. This study will highly promote academic and applicable developments of the cross-cutting frontier research field between organic spintronics and electronics.

Unconventional C-Hlg···H-C (Hlg = Cl, Br, and I) Interactions Involving Organic Halides: A Theoretical Study

In this study, unconventional C-Hlg···H-C (Hlg = Cl, Br, and I) interactions involving sp, sp2, and sp3 organic halides were investigated at the RI-MP2/aug-cc-pVQZ level of theory. Energy Decomposition Analyses (EDA) and Natural Bonding Orbital (NBO) studies showed that these intermolecular contacts are mainly supported by orbital and dispersion contributions, which counteracted the unfavorable/slightly favorable electrostatics due to the halogen-hydrogen σ-hole facing. In addition, the Bader's Quantum Theory of Atoms in Molecules (QTAIM) and the Noncovalent Interaction plot (NCIplot) visual index methodologies were used to further characterize the interactions discussed herein. We expect that the results reported herein will be useful in the fields of supramolecular chemistry, crystal engineering, and rational drug design, where the fine tuning of noncovalent interactions is crucial to achieve molecular recognition or a specific solid-state architecture.

Probing Noncovalent Interaction Strengths of Host-Guest Complexes Using Negative Ion Photoelectron Spectroscopy

Noncovalent interactions (NCIs) are crucial for the formation and stability of host-guest complexes, which have wide-ranging implications across various fields, including biology, chemistry, materials science, pharmaceuticals, and environmental science. However, since NCIs are relatively weak and sensitive to bulk perturbation, direct and accurate measurement of their absolute strength has always been a significant challenge. This concept article aims to demonstrate the gas-phase electrospray ionization (ESI)-negative ion photoelectron spectroscopy (NIPES) as a direct and precise technique to measure the absolute interaction strength, probe nature of NCIs, and reveal the electronic structural information for host-guest complexes. Our recent studies in investigating various host-guest complexes that involve various types of NCIs such as anion-π, (di)hydrogen bonding, charge-separated ionic interactions, are overviewed. Finally, a summary and outlook are provided for this field.

Supramolecular Structure of Sulfonamide-Substituted Silatranes: Quantum Chemical DFT Calculations

The supramolecular structure of the crystal products-N-[2-chloro-2-(silatranyl)ethyl]-4-nitro-benzenesulfonamide 4d and N-chloro-N-[2-chloro-1-(silatran-1-yl-methyl)ethyl]benzene-sulfonamide 5a was established by X-ray diffraction analysis data, FTIR spectroscopy and DFT quantum chemical calculations. Their crystal lattice is formed by cyclic dimers with intermolecular hydrogen NH∙∙∙O-Si bonds and CH∙∙∙O=S short contacts. The distribution of electron density in the monomers was determined using quantum chemical calculations of their molecular electrostatic potential (MESP) in an isolated state (in gas) and in a polar medium. The transition from covalent N-Si bonds in crystal compounds and polar medium to non-covalent N∙∙∙Si bonds happened while performing the calculations on the monomer molecules and their dimers in gas. The effect of intermolecular interactions on the strength of the N-Si and N∙∙∙Si bonds in molecules was evaluated through calculations of their complexes with H2O and DMSO.

Probing Noncovalent Interactions by Fast Magic-Angle Spinning NMR at 100 kHz and More

Noncovalent interactions are the basis for a large number of chemical and biological molecular-recognition processes, such as those occurring in supramolecular chemistry, catalysis, solid-state reactions in mechanochemistry, protein folding, protein-nucleic acid binding, and biomolecular phase separation processes. In this perspective article, some recent developments in probing noncovalent interactions by proton-detected solid-state Nuclear Magnetic Resonance (NMR) spectroscopy at Magic-Angle Spinning (MAS) frequencies of 100 kHz and more are reviewed. The development of MAS rotors with decreasing outer diameters, combined with the development of superconducting magnets operating at high static magnetic-field strengths up to 28.2 T (1200 MHz proton Larmor frequency) improves resolution and sensitivity in proton-detected solid-state NMR, which is the fundamental requirement for shedding light on noncovalent interactions in solids. The examples reported in this article range from protein-nucleic acid binding in large ATP-fueled motor proteins to a hydrogen-π interaction in a calixarene-lanthanide complex.

A Nanosized Porous Supramolecular Lead(II)-N'-phenyl(pyridin-2-yl)methylene-N-phenylthiosemicarbazide Aggregate, Obtained Under Electrochemical Conditions

A novel nanosized porous supramolecular nonanuclear complex [Pb9(HL)12Cl2(ClO4)](ClO4)3·15H2O·a(solvent) (1·15H2O·a(solvent)) is reported that was synthesized by electrochemical oxidation of a Pb anode under the ambient conditions in a CH3CN:MeOH solution of N'-phenyl(pyridin-2-yl)methylene-N-phenylthiosemicarbazide (H2L), containing [N(CH3)4]ClO4 as a current carrier. The supramolecular aggregate of 1 is enforced by a myriad of Pb···S tetrel bonds (TtBs) established with the thiocarbonyl sulfur atoms of adjacent species, which have been also analyzed by DFT calculations via 2D maps of ELF, Laplacian and RDG properties. Moreover, Pb···Cl TtBs with the central Cl- anion, and Pb···O TtBs with the three oxygen atoms of the ClO4- anion, were revealed. Notably, the molecular structure of 1 differs significantly from that recently reported by us [Pb2(HL)2(CH3CN)(ClO4)2]·2H2O (2·2H2O), which was obtained using a conventional synthetic procedure by reacting Pb(ClO4)2 with H2L in the same CH3CN:MeOH solution, thus highlighting a crucial role of the electrochemical conditions. The optical characteristics of the complex were investigated using UV-vis spectroscopy and spectrofluorimetry in methanol. The complex was found to be emissive when excited at 304 nm, producing a broad emission band ranging from approximately 420 to 600 nm with multiple peaks. The CIE-1931 chromaticity coordinates, calculated as (0.33, 0.24), suggest that the emission lies in the white region of the chromaticity diagram. Further investigation is needed to fully characterize the origin of this emission.

Effects of Acid Dissociation and Ionic Solutions on the Aggregation of 2-Pyrone-4,6-dicarboxylic Acid

The conversion of lignin can produce biomass-derived aromatic compounds such as 2-pyrone-4,6-dicarboxylic acid (PDC), which is a potential sustainable precursor of bioplastics. PDC is a pseudoaromatic dicarboxylic acid that can aggregate in aqueous solution. Aggregation depends upon PDC-PDC, PDC-water, and PDC-ion interactions that are representative of interactions in similar charged, aromatic compounds. These interactions both dictate PDC aggregation and the likelihood that PDC aggregates exhibit parallel stacking configurations that may promote PDC crystallization, which can be leveraged to separate PDC from solution. However, the interplay of interactions that drive aggregation and structure formation, and how these depend upon the charge of PDC and ionic species present in solution, remains unclear. In this work, we investigate PDC aggregation in diverse ionic solutions using all-atom molecular dynamics simulations and molecular clustering analysis. We consider ion-induced dipole interactions by using a modified Lennard-Jones nonbonded model for divalent ions in solutions. From molecular clustering analysis, we derive characteristic parameters to quantify aggregate sizes and parallel stacking configurations. We show that acid dissociation facilitates PDC aggregation in ionic solutions via ion-mediated interactions, and different ionic solutions influence both the likelihood of aggregation and the formation of parallel aggregates. In particular, we find that parallel stacking is primarily found in solutions with monovalent ions, whereas divalent ions promote larger, but less structured, aggregates. These results provide molecular-scale insight into the effects of specific ions on the aggregation of like-charged PDC molecules to inform understanding of related separation processes.

Interacted Ternary Component Ensuring High-Security Eutectic Electrolyte for High Performance Sodium-Metal Batteries

Due to the intrinsic flame-retardant, eutectic electrolytes are considered a promising candidate for sodium-metal batteries (SMBs). However, the high viscosity and ruinous side reaction with Na metal anode greatly hinder their further development. Herein, based on the Lewis acid-base theory, a new eutectic electrolyte (EE) composed of sodium bis(trifluoromethanesulfonyl)imide (NaTFSI), succinonitrile (SN), and fluoroethylene carbonate (FEC) is reported. As a strong Lewis base, the ─C≡N group of SN can effectively weaken the interaction between Na+ and TFSI-, achieving the dynamic equilibrium and reducing the viscosity of EE. Moreover, the FEC additive shows a low energy level to construct thicker and denser solid electrolyte interphase (SEI) on the Na metal surface, which can effectively eliminate the side reaction between EE and Na metal anode. Therefore, EE-1:6 + 5% FEC shows high ionic conductivity (2.62 mS cm-1) and ultra-high transference number of Na+ (0.96). The Na||Na symmetric cell achieves stable Na plating/stripping for 1100 h and Na||Na3V2(PO4)3/C cell shows superior long-term cycling stability over 2000 cycles (99.1% retention) at 5 C. More importantly, the Na||NVP/C pouch cell demonstrates good cycling performance of 102.1 mAh g-1 after 135 cycles at 0.5 C with an average coulombic efficiency of 99.63%.

The Rivalry between Intramolecular Tetrel Bonds and Intermolecular Hydrogen Bonds in (O-Si) Chelates of N-Silylmethylamides and -ureas. A Theoretical Study

The comparison of the results of theoretical calculations of (O-Si) chelates of N-silylmethylated amides and ureas with the axial chlorine or fluorine atom at silicon to the data of X-ray analysis of related compounds revealed the formation of covalent O-Si tetrel bonds (TB) or noncovalent O⋅⋅⋅Si tetrel bonds (NTB). The nature of the formed tetrel bond depends on the substituents at silicon and the polarity of the medium. The competition between the intramolecular TB and intermolecular hydrogen bonds (HB) with proton donors depends on the center of basicity involved in the formation of HB, which could be either oxygen or halogen. The hydrogen bonding can result in changing the nature of the tetrel bonds from covalent to noncovalent and vice versa by varying their lengths and energies. The O-Si bond energies estimated by QTAIM analysis of N-[(chlorodimethylsilyl)methyl]-N-methylacetamide and its H-complexes vary within the range of 7.2 and 12 kcal/mol in gas and solution, respectively, and correlate with the O-Si bond lengths.

Mussel-Inspired Injectable Adhesive Hydrogels for Biomedical Applications

The impressive adhesive capacity of marine mussels has inspired various fascinating designs in biomedical fields. Mussel-inspired injectable adhesive hydrogels, as a type of promising mussel-inspired material, have attracted much attention due to their minimally invasive property and desirable functions provided by mussel-inspired components. In recent decades, various mussel-inspired injectable adhesive hydrogels have been designed and widely applied in numerous biomedical fields. The rational incorporation of mussel-inspired catechol groups endows the injectable hydrogels with the potential to exhibit many properties, including tissue adhesiveness and self-healing, antimicrobial, and antioxidant capabilities, broadening the applications of injectable hydrogels in biomedical fields. In this review, we first give a brief introduction to the adhesion mechanism of mussels and the characteristics of injectable hydrogels. Further, the typical design strategies of mussel-inspired injectable adhesive hydrogels are summarized. The methodologies for integrating catechol groups into polymers and the crosslinking methods of mussel-inspired hydrogels are discussed in this section. In addition, we systematically overview recent mussel-inspired injectable adhesive hydrogels for biomedical applications, with a focus on how the unique properties of these hydrogels benefit their applications in these fields. The challenges and perspectives of mussel-inspired injectable hydrogels are discussed in the last section. This review may provide new inspiration for the design of novel bioinspired injectable hydrogels and facilitate their application in various biomedical fields.

Growth mechanism of aromatic prebiotic molecules: insights from different processes of ion-molecule reactions in benzonitrile-ammonia and benzonitrile-methylamine clusters

Benzonitrile (BN, C6H5CN) has been detected in the cold molecular cloud Taurus molecular cloud-1 (TMC-1) in 2018, which is suggested to be a precursor in the formation of more complex nitrogen-containing aromatic interstellar compounds. In this study, we utilized mass-selected infrared (IR) photodissociation spectroscopy and quantum chemical calculations to investigate the structures and gaseous ion-molecule reactions of benzonitrile-ammonia (BN-NH3) and benzonitrile-methylamine (BN-MA) clusters. The spectral observations indicate that the cyclic hydrogen bonding structure predominates in both neutral clusters. After VUV (118 nm) single-photon ionization, a new C-N covalent bond formed between BN and NH3 in the (BN-NH3)+ cluster. However, proton sharing constitutes the primary structure of the (BN-MA)+ cluster. The two nitrogen-containing interstellar molecules react with BN to yield distinct products due to difference in charge distribution and molecular polarity in the ionized clusters. The reactions of BN with other molecules contribute to our understanding of the growth mechanisms of complex interstellar molecules.

Do electrostatic interactions make a difference in physics-based AutoDock4 scoring function?

Physics-based scoring function AutoDock4 is one of the most successfully applied tools in the area of structure-based drug design. However, current scoring functions are still far from being perfect. In a recent work highlighting the strengths and deficiencies of current scoring functions, we discovered that the residual error of ΔGbind predictions made by AutoDock4 is highly correlated to the presence of formally charged fragments in a ligand. In this work, we study how the use of the high-quality atomic charges, applied for contemporary force fields calculation, affects the quality of the experimental ΔGbind prediction by means of AutoDock4. We initially expected that the previously found discrepancy could be attributed to the Gasteiger charges used within AutoDock4. We show that AutoDock4 is, surprisingly, not sensitive to the charges used, and the use of QC-derived atomic charges does not lead to any statistical improvements. We also briefly discuss the role of the explicit empirical hydrogen bond term along with the electrostatic term.

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.

Evaluating Noncovalent Interactions in Halogenated Molecules with Double-Hybrid Functionals and a Dedicated Small Basis Set

We present here an extension of our recently developed PBE-QIDH/DH-SVPD basis set to halogen atoms, with the aim of obtaining, for weakly interacting halogenated molecules, interaction energies close to those provided by a large basis set (def2-TZVPP) coupled to empirical dispersion potential. The core of our approach is the split-valence basis set, DH-SVPD, that has been developed for F, Cl, Br, and I atoms using a self-consistent formula, containing only energy terms computed for dimers and the corresponding monomers at the same level of theory. The basis set developed considering four systems, one for each halogen atoms, has been then tested on the X40, X4 × 10 benchmarks as well as on other two, less standard, data sets. Finally, a large system (380 atoms) has been also considered as a "crash" test. Our results show that the simple and nonempirical PBE-QIDH/DH-SVPD approach is able to provide accurate results for interaction energies of all the considered systems and can thus be considered as a cheaper alternative to DH functionals paired with empirical dispersion corrections and a large basis set of triple-ζ quality.

Dual Dynamic Cross-Linked Epoxy Vitrimers Used for Strong, Detachable, and Reworkable Adhesives

Novel reprocessable thermosetting adhesives (RTAs), which combine high adhesive strength, reusability, disassembly, and recyclability features, have attracted increasing attention. However, developing RTAs with a rapidly adhesive rate while ensuring high adhesive strength and self-healing ability is still a significant challenge. Here, we prepared a novel vitrimer called DAx-DTSAy, which can be used as an RTA. First, by adjusting the ratio of rigid and flexible segments, maximum tensile strength reached 35.92 MPa. Second, the combined effect of dynamic hydroxyl ester bonds and dynamic disulfide bonds resulted in a rapid stress relaxation behavior, with a complete relaxation time 13.6 times shorter than a vitrimer only cross-linked with hydroxy ester bonds. This feature endowed its good self-healing and reprocessing capabilities. After self-healing at 180 °C, the maximum healing rate of mechanical properties was 91.8%. After three reprocesses, the maximum recovery rate of tensile strength was 120.2%. Furthermore, the combination of rigid and flexible segments and the synergistic effect of dual dynamic covalent bonds made DAx-DTSAy capable of use as a high-performance RTA. The lap shear strength of a DAx-DTSAy film on stainless steel reached 18.18 MPa after 15 min, with a recovery rate of 91.9% after 5 rebonding cycles. Additionally, DAx-DTSAy can be disassembled in chemical agents and exhibited better insulation properties compared to traditional epoxy resins. DAx-DTSAy can be employed as a novel high-performance adhesive in applications such as electronic devices and transportation, contributing to the development of thermosetting adhesives toward recyclability and sustainability.

σ-Hole, lone-pair-hole, and π-hole site-based interactions in aerogen-comprising complexes: a comparative study

Herein, the potential of ZO3 and ZF2 aerogen-comprising molecules (where Z = Ar, Kr, and Xe) to engage in σ-, lp-, and π-hole site-based interactions was comparatively studied using various ab initio computations. For the first time, a premier in-depth elucidation of the external electric field (EEF) influence on the strength of the σ-, lp-, and π-hole site-based interactions within the ZO3/ZF2⋯NH3 and ⋯NCH complexes was addressed using oriented EEF with disparate magnitude. Upon the energetic features, σ-hole site-based interactions were noticed with the most prominent preferability in comparison to lp- and π-hole analogs. This finding was ensured by the negative interaction energy values of -11.65, -3.50, and -2.74 kcal mol-1 in the case of σ-, lp-, and π-hole site-based interactions within the XeO3⋯ and XeF2⋯NH3 complexes, respectively. Detailedly, the strength of the σ- and lp-hole site-based interactions directly correlated with the atomic size of the aerogen atoms and the magnitude of the positively oriented EEF. Unexpectedly, an irregular correlation was noticed for the interaction energies of the π-hole site-based interactions with the size of the π-hole. Interestingly, the π-hole site-based interactions within Kr-comprising complexes exhibited higher negative interaction energies than the Ar- and Xe-comprising counterparts. Notwithstanding, a direct proportion between the interaction energies of the π-hole site-based interactions and π-hole size was obtained by employing EEF along the positive orientation with high strength. The present outcomes would be a fundamental basis for forthcoming progress in studying the σ-, lp-, and π-hole site-based interactions within aerogen-comprising complexes and their pertinent applications in materials science and crystal engineering.

Molecular dynamics simulations reliably identify vibrational modes in far-IR spectra of phospholipids

The properties of self-assembled phospholipid membranes are of essential importance in biochemistry and physical chemistry, providing a platform for many cellular life functions. Far-infrared (far-IR) vibrational spectroscopy, on the other hand, is a highly information-rich method to characterize intermolecular interactions and collective behaviour of lipids that can help explain, e.g., chain packing, thermodynamic phase behaviour, and sequestration. However, reliable interpretation of the far-IR spectra is still lacking. Here we present a molecular dynamics (MD) based approach to simulate vibrational modes of individual lipids and in an ensemble. The results are a good match to synchrotron far-IR measurements and enable identification of the molecular motions corresponding to each vibrational mode, thus allowing the correct interpretation of membrane spectra with high accuracy and resolving the longstanding ambiguities in the literature in this regard. Our results demonstrate the feasibility of using MD simulations for interpreting far-IR spectra broadly, opening new avenues for practical use of this powerful method.

Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains

The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.

Cooperativity between Intermolecular Hydrogen and Carbon Bonds in ZY···CH3CN/CH3NC···HX Trimers (ZY = H2O, H2S, HF, HCl, HBr, NH3, and H2CO; HX = HF, HCl, and HBr)

Hydrogen-bonding and carbon-bonding interactions are widespread in nature. We studied the cooperativity between these interactions in 42 trimeric complexes ZY···CH3CN/CH3NC···HX, where ZY molecules are H2O, H2S, HF, HCl, HBr, NH3, and H2CO, and HX molecules are HF, HCl, and HBr. Acetonitrile (CH3CN) and isoacetonitrile (CH3NC) act as hydrogen bond acceptors as well as carbon bond donors in these trimers. Various theoretical methods, such as electronic structure calculations, quantum theory of atoms in molecule (QTAIM), natural bond orbital (NBO), and reduced density gradient analysis, are employed to study these trimers, and the results are compared with the corresponding ZY···CH3CN/CH3NC and CH3CN/CH3NC···HX dimers. Electronic structure calculations are performed at the second-order Mo̷ller-Plesset perturbation theory using the 6-311++G(2d,2p) basis set. We show that both the interactions act synergistically in these trimers leading to an increase in their bond strength as compared to the strength in the individual dimers. The cooperative energies for these trimers are in the range of 0.69 to 3.22 kJ/mol. It is seen that the carbon bonds benefit more from the cooperativity than the hydrogen bonds. The trends of cooperativity and correlations of interaction energies and cooperative energies with relevant QTAIM and NBO parameters are reported.

Synthesis of organic solvent-free nitrogen-doped carbon quantum dots as unique green fluorimetric probes for analysis of abrocitinib in human plasma

Atopic dermatitis (AD) is a persistent, inflammatory skin condition that impacts approximately 15 to 20% of children and 1 to 3% of adults globally. Common skin manifestations include papules, papulovesicular, and brown or red patches with swelling, crusting, and flaking. Therefore, the drug abrocitinib (ABR) was approved by the US FDA as an oral treatment for atopic dermatitis. The present study outlines the development of innovative, thermostable, and pH-stable organic solvent-free nitrogen-doped carbon dots (N@CQDs) synthesized through a one-step method for evaluating ABR with a notable quantum yield of 33.84% to minimize the use of organic solvents. Their cost-effectiveness, eco-friendly characteristics, and outstanding photocatalytic properties have established them as a promising alternative to conventional luminescent techniques like fluorescent dyes and luminous derivatization technique. The reaction of ABR with N@CQDs led to a significant decrease in the luminescent response of the produced green and stable carbon quantum dots at 513 nm. The detection range was determined to be 1.0-150.0 ng mL-1, with a lower limit of quantitation (LOQ) equal to 0.52 ng mL-1 based on the linear graph. The green method effectively used for analysis of ABR in pharmaceutical tablets and pharmacokinetic study with high sensitivity.

Biochar-derived dissolved organic matter enhanced the release of residual ciprofloxacin from the soil solid phase

Biochar has been utilized to reduce ciprofloxacin (CIP) residues in soil. However, little is known about the effect of biochar-derived dissolved organic matter (DOM) on residual CIP transformation. Thus, we analyzed the residual soil CIP as influenced by biochar generated from rice straw (RS3 and RS6), pig manure (PM3 and PM6), and cockroach shell (CS3 and CS6) at 300 °C and 600 °C. The three-dimensional excitation-emission matrix (3D-EEM), parallel factor analysis (PARAFAC) and two-dimensional correlation spectral analysis (2D-COS) were used to describe the potential variation in the DOM-CIP interaction. Compared with CK, biochar amendment increased the water-soluble CIP content by 160.7% (RS3), 55.2% (RS6), 534.1% (PM3), 277.5% (PM6), 1160.6% (CS3) and 703.9% (CS6), indicating that the biochar feedstock controlled the soil CIP release. The content of water-soluble CIP was positively correlated with the content of dissolved organic carbon (r = 0.922, p < 0.01) and dissolved organic nitrogen (r = 0.898, p < 0.01), suggesting that the major influence of the water-soluble CIP increase was DOM. The fluorescence quenching experiment showed that the interaction between DOM and CIP triggered static quenching and the creation of a DOM complex. The mean log K of protein-like material (4.977) was higher than that of terrestrial humus-like material (3.491), suggesting that the protein-like material complexed CIP was more stable than the humus-like material. Compared with pyrolysis at 300 °C, pyrolysis at 600 °C decreased the stability of the complex of protein-like material and CIP by 0.44 (RS), 1.689 (PM) and 0.548 (CS). This result suggested that the influence of temperature change was more profound on PM biochar-derived DOM than on RS and CS. These insights are essential for understanding CIP transportation in soil and controlling CIP contamination with biochar.

Intermolecular interactions probed by rotational dynamics in gas-phase clusters

The rotational dynamics of a molecule is sensitive to neighboring atoms or molecules, which can be used to probe the intermolecular interactions in the gas phase. Here, we real-time track the laser-driven rotational dynamics of a single N2 molecule affected by neighboring Ar atoms using coincident Coulomb explosion imaging. We find that the alignment trace of N-N axis decays fast and only persists for a few picoseconds when an Ar atom is nearby. We show that the decay rate depends on the rotational geometry of whether the Ar atom stays in or out of the rotational plane of the N2 molecule. Additionally, the vibration of the van der Waals bond is found to be excited through coupling with the rotational N-N axis. The observations are well reproduced by solving the time-dependent Schrödinger equation after taking the interaction potential between the N2 and Ar into consideration. Our results demonstrate that environmental effects on a molecular level can be probed by directly visualizing the rotational dynamics.

7Li NMR Spectroscopy: A Tool for Determining Dimerization Constants and Averaged Dimerization Constants of the Monomer/Dimer Equilibrium of Hierarchical Helicates

7Li nuclear magnetic resonance (NMR) spectroscopy is an ideal tool to study hierarchically assembled helicates of the form Li[Li3L6Ti2]. Internally bound and external lithium ions can be well distinguished by solution- or solid-state NMR spectroscopy and dimerization constants of the monomer/dimer equilibrium can be easily determined in solution. Averaged dimerization constants can be estimated in case of statistical mixtures of helicates formed from mixtures of ligands.

Effect of functionalization on the adsorption performance of carbon nanotube as a drug delivery system for imatinib: molecular simulation study

In this study, efficiency of functionalized carbon nanotube as a potential delivery system for imatinib anti-cancer drug was investigated. Accordingly, carboxyl and hydroxyl functionalized carbon nanotube were inspected as a notable candidate for the carriage of this drug in aqueous media. For this purpose, possible interactions of imatinib with pure and functionalized carbon nanotube were considered in aqueous media. The compounds were optimized in gas phase using density functional calculations. Solvation free energies and association free energies of the optimized structures were then studied by Monte Carlo simulation and perturbation method in water environment. Outcomes of quantum mechanical calculations presented that pure and functionalized carbon nanotubes can act as imatinib drug adsorbents in gas phase. However, results of association free energy calculations in aqueous solution indicated that only carboxyl and hydroxyl functionalized carbon nanotubes could interact with imatinib. Monte Carlo simulation results revealed that electrostatic interactions play a vital role in the intermolecular interaction energies after binding of drug and nanotube in aqueous solution. Computed solvation free energies in water showed that the interactions with functionalized carbon nanotubes significantly enhance the solubility of imatinib, which could improve its in vivo bioavailability.

Hydrogen Bonds Are Never of an "Anti-electrostatic" Nature: A Brief Tour of a Misleading Nomenclature

A large amount of scientific works have contributed through the years to rigorously reflect the different forces leading to the formation of hydrogen bonds, the electrostatic and polarization ones being the most important among them. However, we have witnessed lately with the emergence of a new terminology, anti-electrostatic hydrogen bonds (AEHBs), that seems to contradict this reality. This nomenclature is used in the literature to describe hydrogen bonds between equally charged systems to justify the existence of these species, despite numerous proofs showing that AEHBs are, as any other hydrogen bond between neutral species, mostly due to electrostatic forces. In this Viewpoint, we summarize the state of the art regarding this issue, try to explain why this terminology is very misleading, and strongly recommend avoiding its use based on the hydrogen bond physical grounds.

Metamagnetism and canted antiferromagnetic ordering in two monomeric CoII complexes with 1-(2-pyrimidyl)piperazine. Hirshfeld surface analysis and theoretical studies

Here we present the magnetic properties of two cobalt complexes formulated as: [Co(SCN)2(L)2] (1) and (H2L)2[Co(SCN)4]·H2O (2) (L = 1-(2-pyrimidyl)piperazine). The two compounds contain isolated tetrahedral CoII complexes with important intermolecular interactions that lead to the presence of a canted antiferromagnetic order below 11.5 and 10.0 K, with coercive fields at 2 K of 38 and 68 mT, respectively. Theoretical calculations have been used to explain this behaviour. Hirshfeld surface analysis shows the presence of strong intermolecular interactions in both compounds. The crystal geometries were used for geometry optimization using the DFT method. From the topological properties, electrostatic potential maps and molecular orbital analysis, information about the noncovalent interaction and chemical reactivity was obtained.

Unraveling pnicogen bonding cooperativity: Insights from molecular electrostatic potential analysis

A theoretical investigation on the cooperativity of a series of binary, ternary, and quaternary complexes interconnected by pnicogen bonds has been conducted using calculations at the M06-2X/aug-cc-pVTZ level of density functional theory. By measuring changes in the molecular electrostatic potential (MESP) at the nucleus of interacting atoms in all of the complexes, it is possible to quantify the substantial reorganization of the electron density triggered by the formation of pnicogen bonds. The positive change in MESP, indicating a loss of electron density from the donor molecule in a dimer, facilitates the acceptance of electron density from a third molecule, resulting in the formation of a ternary complex with a stronger pnicogen bond compared to the one present in the binary complex. Similarly, the acceptor molecule in a dimer with a negative change in MESP showed an enhanced tendency to donate electron density to an electron-deficient third molecule. The MESP analysis provided valuable insights into the donor/acceptor characteristics of pnicogen bonds within the quaternary complexes. The proposed MESP hypotheses are consistent with the positive cooperativity observed in the pnicogen-bonded clusters. To quantify the changes in MESP, both at the donor atom (ΔVdonor ) and the acceptor atom (ΔVacceptor ), for all pnicogen bonds in the cluster, the total change in MESP (ΔΔVn ) was measured as ΔΔVn  = ∑(ΔVdonor )-∑(ΔVacceptor ). Remarkably, ΔΔVn exhibited a strong linear relationship with the sum of the bond energies of the pnicogen bonds in the cluster. This establishes the MESP analysis as a robust approach for understanding the strength and cooperative behavior of pnicogen-bonded clusters. Additionally, the MESP features provided clear evidence of pnicogen bond formation, further supporting the reliability of this approach.

Exploring the Reactivity of Donor-Acceptor Systems through a Combined Conceptual and Constrained DFT Approach

In the context of the conceptual density functional theory (cDFT) and based on the computational efficiency of the constrained DFT (CDFT), we demonstrate that chemical reactivity can be governed by the difference between the local interacting chemical potentials of the reactants (referred as Edual), in agreement with Sanderson's equalization principle. In a proof-of-concept study, we investigated illustrative examples involving typical non-covalent donor-acceptor systems and reactive systems are provided. For the selected systems, our approach reveals significant mimicking between Edual and the DFT-computed intermolecular interaction energy profiles. We further evaluate the influence of the Coulomb and exchange-correlation contributions in Edual. These latter results suggest that numerous potential energy surfaces of clusters can be explored using a Sanderson-like model only based on classical interactions between molecular orbitals domains. To conclude, this study achieved a deeper understanding of the principles of cDFT and assessed, in a wider context, its efficiency in predicting the chemical reactivity.

Spodium bonding with noble gas atoms

The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.

Effect of electronegative atoms on π - π stacking and hydrogen bonding behavior in simple aromatic molecules - An Ab initio MD study

Ab initio molecular dynamics studies have been performed on fluorobenzene, phenol, and aniline, which have the three most electronegative atoms, fluorine, oxygen, and nitrogen, respectively. Radial distribution functions show strong hydrogen bonding in the phenolic -OH group, whereas it is less prominent in the -NH2 group of aniline. Fluorobenzene does not show strong hydrogen bonds as no solvation shell is found between the fluorine atom and different aromatic hydrogens of the molecule. Spatial distribution functions show that the nitrogen atom of aniline interacts with the aromatic plane, the oxygen atom of phenol is concentrated near the -OH group and fluorobenzene's fluorine atom interacts with the para hydrogen. Liquid phase dimer structures of these systems reveal that perpendicular orientation (Y-shaped) is preferred over parallel ones. Almost half of the total dimer population tends to prefer 90∘±30° angle. H-bond analyses show that fluorobenzene has the longest mean H-bond lifetime for the H-bond between the aromatic hydrogens and the fluorine atoms, whereas the aniline has the least. The mean lifetime between aromatic hydrogens and electronegative atoms increases steadily from aniline to fluorobenzene. Phenolic -OH and amino -NH2 groups show considerably longer mean H-bond lifetime than the aromatic hydrogens. Gas-phase binding energies obtained from quantum chemical calculations show that aniline and phenol dimers have higher binding energy values than the fluorobenzene dimer. Only the phenol dimer shows a perpendicular structure as a stable one, while aniline and fluorobenzene prefer the parallel orientation.

An Innovative Selective Fluorescence Sensor for Quantification of Hazardous Food Colorant Allura Red in Beverages Using Nitrogen-Doped Carbon Quantum Dots

An innovative simple, sensitive, and selective method has been developed and validated for quantification of hazardous Allura red (AR, E129) dye in beverages. Allura red (AR) is a synthetic dye that is commonly used in the food industry to give foods a bright and appealing color. The method is based on microwave-assistant nitrogen-doped carbon quantum dots (N@CQDs) from a very cheap source with a high quantum yield equal to (36.60%). The mechanism of the reaction is based on an ion-pair association complex between AR and nitrogen-doped carbon quantum dots (N@CQDs) at pH 3.2. The reaction between AR and N@CQDs led to a quenching effect of the fluorescence intensity of N@CQDs at 445 nm after excitation at 350 nm. Moreover, the quantum method's linearity covered the range between 0.07 and 10.0 µg mL- 1 with a regression coefficient is 0.9992. The presented work has been validated by ICH criteria. High-resolution transmission electron microscopy (HR-TEM), X-ray photon spectroscopy (XPS), Zeta potential measurements, fluorescence, UV-VIS, and FTIR spectroscopy have all been used to fully characterize of the N@CQDs. The N@CQDs were successfully utilized in different applications (beverages) with high accuracy.

Probing Non-Covalent Interactions through Molecular Balances: A REG-IQA Study

The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe2 and 2-Y with Y = H, CN, NO2, OMe, NMe2) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional "back-of-the-envelope" open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe2 balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange-correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe2. REG-IQF also shows that exchange-correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved.

Insights into non-covalent interactions in dicopper(II,II) complexes bearing a naphthyridine scaffold: anion-dictated electrochemistry

A family of bis(μ-hydroxido)dicopper(II,II) complexes bearing a naphthyridine-based scaffold has been synthesized and characterized. Cyclic voltammetry reveals that the nature of the anions present in the complexes plays a pivotal role in their electrochemical properties. X-ray diffraction, spectroscopic and electrochemical analysis data support the formation of intimate ion pairs by non-covalent interactions driving to a ca. 270 mV difference for the potential required to monooxidize the CuIICuII species.

Correlation of the Charge Resonance Interaction with Cluster Conformations Probed by Electronic Spectroscopy of Dimer Radical Cations of CO2 and CS2 in a Cryogenic Ion Trap

Radical cations of dimeric clusters of carbon dioxide/disulfide, [(CX2)2]+• (X = O and S), form strong intracluster bonds through charge resonance (CR) interactions. We herein performed electronic photodissociation spectroscopy of [(CX2)2]+• while regulating the temperature under ambient and cryogenic conditions using a quadrupole ion trap. Both ions exhibited broad band absorption in the near-infrared-visible light region; it is called the "CR band", as a measure of the strength of the CR interaction. Strikingly, this band underwent a noticeable blue shift upon cryogenic cooling for [(CS2)2]+• while not for [(CO2)2]+•. On the basis of quantum chemical calculations with a coupled cluster method, the band shift was attributed to the variations in the relative population of two energetically close conformers found for [(CS2)2]+•. This study highlights a strong correlation between CR interactions and conformation of the radical dimer cations, demonstrating the exceptional significance of cryogenic cooling in the chemistry of ionic molecular clusters.

Experimental and Theoretical Survey of Intramolecular Spodium Bonds/σ/π-Holes and Noncovalent Interactions in Trinuclear Zn(II)-Salen Type Complex with OCN- Ions: A Holistic View in Crystal Engineering

In this work, one new centrosymmetric trinuclear Zn(II) complex 1, [{(OCN)Zn(L)}2Zn], using a salen-type ligand (H2L) in the presence of OCN- was synthesized and characterized via elemental, spectral, SEM-EDX, and single-crystal X-ray diffraction (SCXRD) study. In 1, SCXRD reveals two different stereochemical environments of zinc metal ions; one terminal Zn(II) center adopts square pyramidal geometries with the Addison parameter (τ) 0.095, and the central Zn(II) is tetracoordinated tetrahedral geometry. This article provides evidence of the significance and presence of spodium bonds (SpBs) in solid-state crystal structures involving a pseudotetrahedral environment of the central Zn-atom. X-ray structures reveal intramolecular Zn···O SpBs caused by the methoxy (-OCH3) substituent O-atom adjacent to the coordinated phenoxy O-atom. These noncovalent interactions have been thoroughly studied using density functional theory calculations at the RI-BP86[2]-D3[3]/def2-TZVP level of theory that characterizes the nature of SpBs, including the Baders quantum theory of atoms-in-molecules "QTAIM", molecular electrostatic potential (MEP) surface, and noncovalent index plot (NCI). In addition, a unique complex-isomer-based theoretical model has been vividly employed to estimate the SpBs energy in the complex. Natural bond orbital (NBO) analysis also tries to establish the differentiation between σ-hole and π-hole SpBs' natures more authentically. The complex energy frameworks were used to investigate noncovalent interactions. To better understand the different intermolecular interactions, we conducted a Hirshfeld surface, which revealed N···H (15.4%) and O···H (9.1%) contacts and Zn···O (5.1%) (SpBs).

Benchmarking Swaths of Intermolecular Interaction Components with Symmetry-Adapted Perturbation Theory

A benchmark database for interaction energy components of various noncovalent interactions (NCIs) along their dissociation curve is one of the essential needs in theoretical chemistry, especially for the development of force fields and machine-learning methods. We utilize DFT-SAPT or SAPT(DFT) as one of the most accurate methods to generate an extensive stock of the energy components, including dispersion energies extrapolated to the complete basis set limit (CBS). Precise analyses of the created data, and benchmarking the total interaction energies against the best available CCSD(T)/CBS values, reveal different aspects of the methodology and the nature of NCIs. For example, error cancellation effects between the S2 approximation and nonexact xc-potentials occur, and large charge transfer energies in some systems, including heavy atoms, can explain the lower accuracy of DFT-SAPT. This method is perfect for neutral complexes containing light nonmetals, while other systems with heavier atoms should be treated carefully. In the last part, a representative data set for all NCIs is extracted from the original data.

An atomic surface site interaction point description of non-covalent interactions

Molecular electrostatic potential surfaces (MEPS) calculated using density functional theory have been used to develop a simplified description of the non-covalent interaction properties of organic molecules. The Atomic Interaction Point (AIP) model introduced here represents an evolution of the Surface Site Interaction Point (SSIP) model described previously, in which a molecule is represented by a discrete set of interaction points that define sites of interaction with other molecules. The interaction sites are described by interaction parameters that are equivalent to the experimentally determined H-bond donor and acceptor parameters α and β. By using high electron density MEPS that lie inside the van der Waals surface, it is possible to obtain accurate interaction parameters and locations for polar sites (s-holes, H-bond donors and acceptors), which are identified as local maxima and minima on the MEPS. For non-polar sites that represent π-systems and halogens, an approach based on molecular orbitals was used to assign the locations of the AIPs, and the interaction parameters were obtained using a lower electron density MEPS that lies close to the van der Waals surface. The AIP descriptions can be implemented directly in the Surface Site Interaction Point Model for Liquids at Equilibrium (SSIMPLE) to calculate solvation free energies, and the free energy of transfer of 1504 compounds from n-hexadecane to water was predicted with a root mean square error of 5 kJ mol-1. AIPs also provide a useful tool for mapping non-covalent interactions in intermolecular complexes, and examples are provided showing how X-ray crystal structures can be converted into AIP interaction maps that allow quantification of the free energy contributions of both polar and non-polar interactions to the stabilities of complexes in solution.