Non-covalent Interaction Analysis Research Articles

Synthesis, Crystal Structure, and Theoretical Screening of Solvatochromism and Light-Harvesting Performance of Hexamine V-Substituted Lindqvist-Based Photosensitizer for Photovoltaic Solar Cells.

In this paper, we employ density functional theory (DFT) and time-dependent DFT (TD-DFT) approaches to predict the solvatochromism and light-harvesting properties of a newly synthesized hybrid hexamine (HMTA) vanadium-substituted Lindqvist-type (V 2 W 4 ) polyoxometalate (POM), (C7H15N4O)2(C6H13N4)2[V2W4O19]·6H2O, (HMTA-V 2 W 4 ) for application in dye-sensitized solar cells (DSSCs). Single crystal X-ray diffraction (XRD) and noncovalent interaction (NCI) analyses show a 3D-supramolecular packing stabilized by means of hydrogen bonds and van der Waals (vdW) and ionic interactions between highly nucleophilic cage-like HMTA surfactant, lattice water, and electrophilic V 2 W 4 polyanions. Experimental and theoretical UV/vis absorption spectra show large absorption in the visible region, which is strongly solvent polarity dependent. This solvatochromic behavior can be attributed to hydrogen bonding interactions between the V 2 W 4 polyanion and protic solvents. Furthermore, the energy level of semiconductor-like nature of HMTA-V 2 W 4 with high LUMO level matches well with the conduction band (CB) of TiO2, which is beneficial for the photovoltaic device performance. The photovoltaic empirical parameters are theoretically predicted to demonstrate a remarkably high open-circuit voltage (Voc) value (1.805 eV) and a photoelectric conversion efficiency (PCE) value up to 8.7% (FF = 0.88) along with superior light-harvesting efficiency (LHE) (0.7921), and therefore, the studied compound is expected to be a potential candidate as a photosensitizer dye for applications in DSSCs. The aim of this work was to broaden the range of applications of POMs, owing to their low-cost fabrication, leveraging and flourishing optoelectronic properties, and ever-improving efficiency and stability for use in future technology pointed to the development of clean and green renewable energy sources to solve the current energy crisis.

Exploring the Impact of Protein Chain Selection in Binding Energy Calculations with DFT.

Calculation of binding free energies between a protein and a ligand are highly desired for computer-aided drug design. Here we approximate the binding energies of ABL1, an enzyme which is the target for drugs used in the treatment of chronic myeloid leukaemia, with minimal models and density functional theory (DFT). Starting from the crystal structures of protein-drug complexes, we estimated the binding free energies having used all available individual molecules (protein chains) within each structure, not only a single one as commonly used, in order to see if the choice of the protein chain is important in such calculations. Differences were observed between chains in the same file. Energy decomposition analysis (EDA) revealed that the most important factors for binding were exchange, repulsion and electrostatics. The desolvation term varied dramatically between the inhibitors (between 4.2 and 92.3 kcal/mol). All functionals showed similar patterns in the EDA and in discriminating between the ligands. Non-covalent interactions (NCI) analysis was used to further explain the differences between protein chains and functionals. Overall, it is shown that small minimal models of a drug binding site can be useful to infer on the suitability of an initial crystal structure for further analysis such as EDA.

Vacancy defect in boron nitride nanotube improves CO2 uptake from the gaseous mixture

Boron Nitride Nanotubes (BNNTs), 1-D nanomaterials, having extraordinary mechanical properties, are similar to carbon nanotubes. The structure of BNNT consists of alternative boron and nitrogen atoms, arranged in hexagonal lattice. In the current study, we have investigated the defected boron nitride nanotube (defBNNT) capability to capture CO2 from a mixture of greenhouse gases such as CH4, CO2, CO, and H2. The deep understanding of analytes@defBNNT complexation is acquired by interaction energies, quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI), natural bond orbital (NBO), and frontier molecular orbital (FMO) analysis etc. It is evident from the results of interaction energies that all the analytes are physiosorbed over the defBNNT. The observed interaction energies are in the range of −2.09 to −6.43 kcal/mol. All the topological parameters, in QTAIM analysis, show that analyte@defBNNT complexes are stabilized through non-covalent interactions, particularly van der Waal's interactions. Results obtained from NCI analysis are strongly corroborated with the QTAIM analysis. The case of CO@defBNNT gives the highest charge transfer (0.031 e−), in natural bond orbital (NBO) analysis. Overall, there is a transfer of charge from analyte to the surface. Through electron density difference (EDD) analysis, the results of NBO charge transfer are also confirmed. We firmly believe that these findings could help experimentalists to design a well-suited surface for CO2 capture using defective boron nitride nanotubes (defBNNTs).

2D hydrogen bonded organic framework (2D-HOF) in benzodioxane-coupled-pyridine as a charge carrier: Synthesis, structural, quantum computational investigation

This research presents a comprehensive investigation into the synthesis, structural features, and charge carrier properties of a novel 2D Hydrogen-Bonded Organic Framework (2D-HOF) formed by Benzodioxane-Coupled-Pyridine. The synthesis involves the reaction of 2,3-dihydrobenzo[b][1,4]dioxin-6-carbaldehyde with pyridine-2-carbohydrazide in the presence of acetic acid and ethanol solvent, leading to the formation of (E)-2-(2-((2,3-dihydrobenzo[b][1,4]dioxin-6-yl)methylene)hydrazinyl)pyridine (DDMP). Single crystal X-ray diffraction analysis reveals the monoclinic crystal system with the P21/n space group, showcasing a non-planar structure due to a distinctive twisting motion in the dioxane ring. The crystal packing is governed by a complex network of intermolecular interactions, including hydrogen bonds, short contacts, and π-stacking, ultimately forming a stable 2D-HOF. Hirshfeld Surface (HS) analysis provides insights into key interactions, emphasizing the significance of hydrogen bonding, short contacts, and stacking interactions in molecular packing. The 2D fingerprint (FP) plots quantitatively highlight crucial interatomic contacts, with hydrogen bonding, CH…H, and O…H interactions dominating. Molecular Electrostatic Potential (MEP) analysis reveals potential sites for electrophilic and nucleophilic attacks, aiding in predicting reactive sites and charge carrier behavior. Energy framework analysis sheds light on the pairwise interaction energies within the crystal structure, emphasizing the role of dispersive forces in stabilizing the crystal lattice. Density functional theory calculations indicate the molecule's charge transfer capabilities, suggesting its suitability for applications such as batteries, supercapacitors, and solar cells. Additionally, global reactivity parameters suggest that the 2D HOF material has electron and proton conduction capabilities, making it versatile for various applications. Atoms-in-molecules (AIM) topology analysis, particularly non-covalent interaction (NCI) analysis, provides a detailed understanding of intra and intermolecular interactions, highlighting hydrogen bonding and π…π interactions. H-bond binding energy analysis confirms the non-covalent nature of identified interactions, emphasizing their strength and significance.

Characterization and conformational analysis of a novel hydrazonoyltetrazole: Crystallographic and theoretical investigations of an unexpected reaction product

A new hydrazonoyltetrazole was isolated as a byproduct from a previously reported reaction, and characterized by 1H and 13C NMR spectroscopy, infrared spectroscopy, single-crystal X-ray diffraction, and high-resolution mass spectroscopy. Intermolecular interactions in the crystal state were examined by Hirshfeld surface analysis (HSA), 2D fingerprint plots, and noncovalent interaction analysis (NCI). Geometry optimization in the gaseous phase was executed at the ωB97X-D4/def2-TZVPP level of theory, and subsequent maps of molecular electrostatic potential (MEP) were generated and analyzed. The calculated MEP was in good agreement with the HSA and NCI results. Conformational analysis was performed using a CREST/CENSO protocol. Two low-energy solution conformers were obtained. To confirm the presence of the second conformer, 1H NMR spectra were calculated, the transition state connecting the two conformers was found, and their energies were obtained with the DLPNOCCSD(T) scheme. A barrier of only 4 kcal mol-1 was found between them, and their MEP maps were also created. The dispersion energies between fragments of the three structures were calculated using the local energy decomposition (LED) scheme.

Mechanistic studies on an isothiourea-catalyzed reaction of an aromatic ester with an imine

Increasing attention is being paid to divergent chemical reactions as a strategy for synthesizing complex organic molecules simply by regulating and adjusting reaction conditions. However, the factors controlling this switchable transformation remain unclear. A systematic study was conducted using density functional theory (DFT) at the M06–2X level to determine the mechanism of an isothiourea-catalyzed divergent chemical reaction of an aryl acetic acid ester with an imine in different solvents (acetonitrile and ethanol). The origins of the stereoselectivity and chemoselectivity of the reaction were determined using noncovalent interaction (NCI) and electrostatic potential surface (EPS) analyses. Lactamization reaction occurs preferentially in acetonitrile, and esterification proceeds preferentially in ethanol. The reaction of an ammonium enolate intermediate with an alkynyl imine preferentially generates the SS-configured isomer. The results of this theoretical study provide insight into the general mechanism of isothiourea-catalyzed reactions in which the key intermediate is ammonium enolate.

Formulating Reduced Density Gradient Approaches for Noncovalent Interactions.

This work elucidates several forms of reduced electron density gradient (RDG) to describe noncovalent interactions (NCIs). By interpreting the RDG as a local moment function, we systematically leveraged Weizacker's and Fermi's local moments. This resulted in high-fidelity RDG representations consistent with the NCI analysis. In addition, the RDG version derived from the Lagrangian kinetic energy density is conveniently normalized. These results suggest the nonexistence of a particular RDG formulation when performing NCI analysis. Thus, an in-depth examination of the theoretical foundations connecting the RDG function with the nature of noncovalent interactions is necessary.

Efficient Self-Sorting Behaviours of Metallacages with Subtle Structural Differences.

Investigating the self-sorting behaviour of assemblies with subtle structural differences is a captivating yet challenging endeavour. Herein, we elucidate the unusual self-sorting behaviour of metallacages with subtle structural differences in batch reactors and microdroplets. Narcissistic self-sorting of metallacages has been observed for two ligands with identical sizes, shapes, and symmetries, with only minor differences in the substituted groups. In particular, the self-sorting process in microdroplets occurs within 1 min at room temperature, in stark contrast to batch reactors, which require equilibration for 30 min. To reveal the mechanism of self-sorting and the role of microdroplets, we conducted a series of experiments and theoretical calculations, including competitive self-assembly, cage-to-cage transformation, control experiments involving model metallacages with larger cavities, noncovalent interaction analysis, and root mean square deviation (RMSD) analysis. This research demonstrates an unusual case of self-sorting of very similar assemblies and provides a new strategy for facilitating the self-sorting efficiency of supramolecular systems.

Theoretical evaluation of C24 nanocage functionalization with protons for enhanced sulfacetamide drug delivery: A DFT study with non-covalent interaction analyses

In the realm of drug design, achieving precise and effective drug delivery poses a significant challenge. In this computational study, we explore the capacity of pristine C24 nanocages and those modified with 1H+ and 2H+ ions to serve as carriers for the sulfacetamide (SA) drug, employing density functional theory (DFT) calculations. Geometry optimizations of the SA&C24, SA&H+C24, and SA&2H+C24 complexes were conducted at the cam-B3LYP/6–31+G (d, p) level of theory. The optimized structures of all complexes exhibit local minima on the potential energy surface, indicated by the absence of imaginary frequencies, which confirms their thermodynamic stability. The negative values of adsorption energy (Eads) denote an exothermic and favorable adsorption process, with H+ ion functionalization enhancing the drug's binding affinity to the nanocages. Further analysis of the structural properties of the complexes was conducted through natural bond orbital (NBO) charge distribution, dipole moment calculations, and frontier molecular orbital analysis. Additionally, Atoms in Molecules (AIM), reduced density gradient (RDG), and electron localization function (ELF) analyses were employed to elucidate the nature of intermolecular interactions governing the drug-nanocage binding. UV-visible and nonlinear optical (NLO) response calculations reveal the potential of both pristine and functionalized C24 nanocages as optical sensors for SA drug detection. Our findings suggest that these nanocages hold promise for the development of sensitive drug delivery vehicles and targeted therapeutic agents.

Non-covalent interaction, topology, molecular properties, spectral and quantum chemical analysis of 2,5-dinitrophenol

Density functional theory (DFT) using the Becke-3-Parameter-Lee-Yang-Parr (B3LYP) functional and Ab-initio (HF) with the 6–311++G(d,p) basis set were employed to investigate the geometry, electronic structure, and absorption spectra of 2,5-Dinitrophenol(25DNP). The vibrational spectrum was utilized to identify functional groups. The ultraviolet–visible (UV–Vis) spectrum was simulated in the gas phase using TD-DFT to determine the range and percentage of transmission. The computed HOMO and LUMO energies indicate that charge transfer occurs within the molecule. The compound exhibits a molecular first hyperpolarizability (second-order optical nonlinearity) value of 1.690 × 10−30 esu, which is approximately five times greater than that of urea. For hyperpolarizability calculations, the hybrid Hartree-Fock exchange-correlation functional was used in conjunction with the 6–311++G(d,p) basis set. Fukui indices were employed to identify local reactive sites in the chemical system during electrophilic, nucleophilic, radical, and dual descriptor attacks. Docking simulations were performed using the Lamarckian Genetic Algorithm (LGA) and local search approach, ensuring proper establishment of the ligand molecules' starting position, orientation, and torsion. According to the molecular electrostatic potential (MEP) map, positive potential sites are found around hydrogen atoms, while negative potential sites are near electronegative atoms, providing insights into regions where the molecule may interact with other molecules, both internally and externally. Similarly, Mulliken charges and Fukui indices within the organic complex sustain the intermolecular hydrogen bonds.

Hydration effects on molecular structure, vibrational, electronic properties, drug-likeness analysis, molecular docking, and molecular dynamics studies of (Z)-3-(2-oxo-2-phenylethylidene)indolin-2-one

This study examines how solvation models, including COSMO, CPCM, PCM, and SMD, affect the conformations, molecular structure, vibrational behaviors, and electronic properties of the (Z)-3-(2-oxo-2-phenylethylidene)indolin-2-one (Z3-2O2PEI) molecule within the framework of the B3LYP/cc-pVTZ model chemistry, along with its potential effectiveness as a drug for treating COVID-19. The most stable molecular conformation of the studied coùpound was identified in the presence of the COSMO solvent. The theoretical vibrational frequencies matched the experimentally observed FT-IR and Raman data. Solvent influences on the UV–vis spectra of Z3-2O2PEI revealed electronic transitions from n to π* and π to π* orbitals, along with evidence of intermolecular charge transfer (ICT) supported by analyses of Frontier Molecular Orbitals (FMO) and Natural Bond Orbitals (NBO). The examinations of Mulliken atomic charge distributions and molecular electrostatic potential surfaces reveal the electrophilic and nucleophilic sites of the molecule under study. Non-covalent Interaction (NCI) analysis confirmed the presence of steric effects and Van der Waals interactions within the compound. According to molecular docking studies, the Z3-2O2PEI molecule exhibits significant binding affinity for PLpro, a protein targeted in COVID-19 treatment. This finding is supported by subsequent molecular dynamics analysis, validating the docking results.

Exploration of sensing behavior B3O3 quantum dot toward methyl halides; a quantum chemical approach

In this study, B3O3 quantum dot has been used for sensing of various methyl halides for the first time. The suitable cavity of B3O3 makes it more suitable for the sensing of variety of analytes. The three, very simple and most important methyl halides (CH3F, CH3Cl and CH3Br) are selected to adsorb on B3O3 surface. Density functional theory (DFT) method with appropriate basis set was implemented. Among the considered complexes, methyl bromide complex CH3Br@B3O3) showed higher interaction energy of −16.90 kcal mol−1. The noncovalent interaction (NCI) analysis identified the existence of van der Waals interactions among all analytes and adsorbent. The density of state (DOS) and natural bond orbital (NBO) charges analyses identified the charge transfer and conductive properties of B3O3 nanosheet after interaction with alkyl halides. Frontier molecular orbital study revealed the electronic attributes of considered complexes. It is revealed that B3O3 quantum dot can be a very good choice for sensing of methyl halides and could be helpful for monitoring and reducing the environmental pollution.

Unraveling the Geometry-Driven C═C Epoxidation and C-H Hydroxylation Reactivity of Tetra-Coordinated Nonheme Iron(IV)-Oxo Complexes.

The electronic structure and reactivity of tetra-coordinated nonheme iron(IV)-oxo complexes have remained unexplored for years. The recent synthesis of a closed-shell iron(IV)-oxo complex [(quinisox)FeIV(O)]+ (1) has set up a platform to understand how such complexes compare with the celebrated open-shell iron-oxo chemistry. Herein, using density functional theory and ab initio calculations, we present an in-depth electronic structure investigation of the C═C epoxidation [oxygen atom transfer (OAT)] and C-H hydroxylation [hydrogen atom transfer (HAT)] reactivity of 1. Using a solvent-coordinated geometry of 1 (1') and other potential tetra-coordinated iron(IV)-oxo complexes bearing rigid ligands (2 and 3), we established the geometric origin of spin-state energetics and reactivity of 1. Complex 1 featuring a strong Fe-O bond exhibits OAT and HAT reactivity in its quintet state. The lowest quintet OAT pathway has a lower barrier by ∼4 kcal/mol than the quintet HAT pathway, corroborating the experimentally observed gas-phase OAT reactivity preference. A conventional HAT reactivity preference for 2 and a comparable OAT and HAT reactivity for 3 are observed. This further supports the geometry-driven reactivity preference for 1. Noncovalent interaction analyses reveal a pronounced π-π interaction between the substrate and ligand in the OAT transition state, rationalizing the origin of the observed reactivity preference for 1.

Theoretical insights into enantioselective [2 + 1] cyclopropanation reactions of diazo compounds with electron-deficient olefins.

The cyclopropane skeleton plays a significant role in bioactive molecules due to its distinctive structural properties. This has sparked keen interest and in-depth exploration in the field of stereoselective synthesis of cyclopropane derivatives. In the present study, the mechanism and the origin of stereoselectivity of diastereodivergent synthesis of cyclopropane derivatives via the catalyst-free [2 + 1]-cyclopropanation reactions of 3-diazo-N-methylindole (R1) with two types of electron-deficient olefins (R2 and R3) in both aqueous and toluene media have been studied using the DFT calculations. The findings indicate that these [2 + 1] cycloaddition reactions proceed in two stages, where the first step is not only the rate-determining step but also critically dictates the stereoselectivity of the product. The calculated diastereomeric ratios are in agreement with the experimental results. Furthermore, by utilizing non-covalent interaction (NCI) analysis and energy decomposition analysis based on molecular force fields (EDA-FF), we elucidated that the electrostatic interactions between reactant fragments in the transition state TS1s for the first step are the predominant factors determining the stereoselectivity, as opposed to the experimentally hypothesized steric hindrance and π-π stacking interactions. The geometrical structures of all minima and transition states on the potential energy surface (PES) in solvents water and toluene were fully optimized using the DFT method at the M06-2X(D3)/SMD/6-31 + G(d,p) level of theory. Single-point energy calculations were carried out based on the optimized geometries in the solution at the M06-2X(D3)/6-311 + G(d,p) level. All the DFT calculations were performed using the Gaussian 09 software. The optimized molecular structures were visualized using CYLview software. NCI analysis was performed using the Multiwfn and VMD softwares. The Multiwfn program was also used for CDFT and EDA-FF analyses.

Computational Study of Molecular Interactions in ZnCl2(urea)2 Crystals as Precursors for Deep Eutectic Solvents

Deep eutectic solvents (DESs) are now enjoying an increased scientific interest due to their interesting properties and growing range of possible applications. Computational methods are at the forefront of deciphering their structure and dynamics. Type IV DESs, composed of metal chloride and a hydrogen bond donor, are among the less studied systems when it comes to their understanding at a molecular level. An important example of such systems is the zinc chloride–urea DES, already used in chemical synthesis, among others. In this paper, the ZnCl2(urea)2 crystal is studied from the point of view of its structure, infrared spectrum, and intermolecular interactions using periodic density functional theory and non-covalent interactions analysis. The two main structural motifs found in the crystal are a strongly hydrogen-bonded urea dimer assisted by chloride anions and a tetrahedral Zn(II) coordination complex. The crystal is composed of two interlocking parallel planes connected via the zinc cations. The infrared spectrum and bond lengths suggest a partially covalent character of the Zn−Cl bonds. The present analysis has far-reaching implications for the liquid ZnCl2–urea DES, explaining its fluidity, expected microstructure, and low conductivity, among others.

Exploring the interaction between graphyne and Purinethol: A DFT study of drug loading capacity

Within this piece of research, DFT calculations were undertaken in order to investigate the drug-loading performance of graphyne for Purinethol. In order to evaluate the possibility of using graphyne as a carrier, the energetic, geometrical and optimized attributes of graphyne, Purinethol, and the complex of graphyne and Purinethol were investigated. We investigated three sites, namely a, b and c, in the structures of Purinethol for its interaction with graphyne. The most suitable interaction was the one in which sulfur and nitrogen atoms were involved. Purinethol had an interaction with graphyne with the adhesion-energy of −1.87 eV in the gaseous phase. The non-covalent interaction analysis was performed to explore the interaction of graphyne with Purinethol. Based on the analysis results, the interaction forces of the complex of graphyne and Purinethol were weak. The HOMO-LUMO analysis and charge-decomposition analysis were performed to describe the charge transported from Purinethol to graphyne during the formation of graphyne and Purinethol. The results demonstrated the possibility of using graphyne as a suitable carrier for Purinethol. The theoretical results obtained within this work can inspire researchers to find novel 2D nanomaterials for drug delivery purposes.

Synthesis, single crystal X-ray, and DFT study of new hybrid-ligand complex [Cu(hfac)2(Me3TTF-CH=CH-Pyr)] and new mixed-valence radical ion salt (Me3TTF-CH=CH-Pyr)2(PF6)3

This paper presents a comprehensive study that combines experimental techniques and Density Functional Theory (DFT) to investigate a newly synthesized mixed-ligand complex, [Cu(hfac)2(Me3TTF-CH=CH-Pyr)] (where hfac is hexafluoroacetylacetonate), and a novel mixed-valence radical ion salt (Me3TTF-CH=CH-Pyr)2(PF6)3. Both are constructed using ligands derived from the tetrathiafulvalene (TTF) donor molecule. These materials are meticulously characterized through single-crystal X-ray diffraction analysis. The complex crystallizes in the monoclinic system, specifically in the C2/c space group, with the following lattice parameters: a = 24.583(2) Å, b = 21.613(2) Å, c = 14.2066(13) Å, β = 99.789(5)°, and a volume of V = 7438.3(12) Å3. It exhibits five-coordinate behavior, forming a slightly distorted pyramid with a square base. The paper also provides a detailed account of the crystal structures and reports spectroscopic study results. Electrochemical behavior is explored through cyclic voltammetry in CH2Cl2 as the solvent. Additionally, the reactivity of these compounds is predicted using various theoretical tools, such as Local and Global reactivity descriptors, Hirshfeld charge analyses, and Molecular Electrostatic Potential. To elucidate charge transfer processes, Time-Dependent Density Functional Theory is utilized. Various types of interactions are analyzed through the Quantum Theory of Atoms in Molecules and Non-Covalent Interaction analyses. Finally, conductivity is estimated using frontier molecular orbitals (FMO) and gap energies as crucial parameters.

Carbene-catalyzed and Pnictogen Bond-assisted Access to PIII-Stereogenic Compounds.

Intermolecular pnictogen bonding (PnB) catalysis has received increased interest in non-covalent organocatalysis. It has been demonstrated that organic electron-deficient pnictogen atoms can act as prospective Lewis acids. Here, we present a catalytic approach for the asymmetric synthesis of chiral PIII compounds by combining intramolecular PnB interactions and carbene catalysis. Our design features a pre-chiral phosphorus molecules bearing two electron-withdrawing benzoyl groups, resulting in the formation of a σ-hole at the P atom. X-ray and non-covalent interaction (NCI) analysis indicate that these phosphorus substrates exhibit intrinsic PnB interactions between the oxygen atom of the formyl group and the phosphorus atom. This induces a conformational locking effect, leading to the crystallization of the phosphorus substrates in a preferred conformation (P212121 chiral group). Under the catalysis of N-heterocyclic carbene, the aldehyde moiety activated by the pnictogen bond selectively reacts with an alcohol to yield the corresponding chiral monoester/phosphorus products with excellent enantioselectivity. This Lewis acidic phosphorus center, aroused by the non-polarized intramolecular pnictogen bond interaction, assists in conformational and selective regulations, providing unique opportunities for catalysis and beyond.

Analyzing noncovalent interactions between notoginseng saponins and lysozyme by deposition scanning intensity fading MALDI-TOF mass spectrometry.

Analysis of noncovalent interactions between natural products and proteins is important for rapid screening of active ingredients and understanding their pharmacological activities. In this work, the intensity fading MALDI-TOF mass spectrometry (IF-MALDI-MS) method with improved reproducibility was implemented to investigate the binding interactions between saponins from Panax notoginseng and lysozyme. The benchmark IF-MALDI-MS experiment was established using N,N',N″-triacetylchitotriose-lysozyme as a model system. The reproducibility of ion intensities in IF-MALDI-MS was improved by scanning the whole sample deposition with a focused laser beam. The relative standard deviation (RSD) of deposition scanning IF-MALDI-MS is 5.7%. Similar decay trends of the relative intensities of notoginseng saponins against increasing amounts of lysozyme were observed for all six notoginseng saponins. The half-maximal fading concentration (FC50) was calculated to quantitatively characterize the binding affinity of each ligand based on the decay curve. According to the FC50 values obtained, the binding affinities of the six notoginseng saponins were evaluated in the following order: notoginsenoside S > notoginsenoside Fc > ginsenoside Rb1 > ginsenoside Rd > notoginsenoside Ft1 > ginsenoside Rg1. The binding order was in accordance with molecular docking studies, which showed hydrogen bonding might play a key role in stabilizing the binding interaction. Our results demonstrated that deposition scanning IF-MALDI-MS can provide valuable information on the noncovalent interactions between ligands and proteins.

Frustrated Lewis pair-mediated hydro-dehalogenation: crucial role of non-covalent interactions.

Organic halides stand as invaluable reagents with diverse applications in synthetic chemistry and various industrial processes. Despite their utility, concerns arise due to their inherent toxicity. Addressing these apprehensions, hydro-dehalogenation has emerged as a promising strategy involving the replacement of halogen atoms with hydrogen atoms to transform toxic organic halides into hydrocarbons. This study delves into the computational exploration of hydro-dehalogenation reactions of benzyl halide, mediated by frustrated Lewis pairs (FLPs), using density functional theory (DFT). The reactions entail the formation of FLP1 or FLP2 in the presence of TMP or lutidine with B(C6F5)3, respectively. This is followed by heterolytic cleavage of dihydrogen and subsequent reaction with benzyl halides. Non-covalent interaction analysis underscores the significance of π-π stacking and CH-π interactions in stabilizing transition states. Additionally, the activation strain model (ASM) dissects activation energies, revealing the substantial impact of strain energy on reaction barriers. Energy decomposition analysis (EDA) offers insights into the contributions of electrostatic, orbital, and dispersion energies to the overall attractive interaction energy. The investigation extends to hydro-dehalogenation reactions of ethyl halides, uncovering distinct mechanisms and activation barriers. This comprehensive analysis illuminates the intricacies of hydro-dehalogenation reactions, providing valuable insights into their mechanisms and paving the way for future studies in this field. Geometry optimizations were carried out at the M06-2X/def2-SVP level of theory, which was performed using the Gaussian 16 program. Solvent-corrected single-point energies were also calculated using the polarizable continuum model (PCM) at the PCM(chloroform)-M06-2X/def2-TZVP//M06-2X/def2-SVP level of theory. The Gibbs free energy correction was determined from computations performed at the M06-2X/def2-SVP level of theory. Principal interacting orbital (PIO) analysis was conducted using the NBO 6.0 software. The nature of bonding in the respective transition state (TS) structures was analyzed using atoms-in-molecules (AIM) analyses. Additionally, the presence of non-covalent interactions (NCI) was exemplified using Multiwfn software.