Study Of Noncovalent Interactions Research Articles

Why pay more? QTAIM descriptors of non-covalent interactions in S22 from promolecular electron density

Based on the comparative analysis of electron density topological features obtained by different methods for the model set of bimolecular associates it is shown that the simplest promolecule model can be an efficient tool in studies of non-covalent interactions

Absorption studies on serotonin neurotransmitter with the platinum metal cluster using the gas phase and different solvents, topological and non-covalent interaction: A DFT approach

The absorption studies on serotonin (STO) and platinum metal clusters were investigated. The STO-Pt3 (gas phase) cluster has the maximum adsorption energy, whereas the water medium has the lowest. The gas phase STO-Pt3 absorption energy is -19.18 kcal/mol, while the water solvent is -11.03. The electrophilicity index of all metal-drug systems is greater, indicating that metal clusters make the serotonin more electrophilic. The cluster's conductivity representation as energy gaps pointed, suggesting it could be a sensor. A more stable gas phase medium has more negative solvation energies than other media types. The metal clusters and molecules interacted substantially in non-covalent interaction studies. Electron localized function (ELF) and localized orbital locator (LOL) experiments proved electron delocalization energies and reduced density gradient (RDG) confirmed non-covalent interactions. Molecular electrostatic potential shows the electrophilic and nucleophilic attractions of STO with Pt3 metal clusters. Frontier molecular orbital (FMO) studies show very low energy gap values.

Ionic liquids as modifier for the oligomerization of α-olefins to reactive poly (α-olefins) via traditional AlCl3 catalyst

In the polymerization there are series of systems that are traditionally used because their procedures are well established, and it is not considered necessary to leave the comfort zone. Here, it is proposed to reevaluate the cationic initiator system with a trident of IL/AlCl3/H2O (IL: ionic liquid). Thus, different ILs comprising of similar anionic part, however various cationic moieties; based on triethanolamine (TEA), tributylamine (TBA), and pyridine (Pyr) precursors; were synthesized and evaluated together with AlCl3 in the cationic polymerization of 1-decene. According to the GPC results, while Pyr and TBA-based ILs suppressed molar mass of poly(α-olefins) (PAO), compared to PAO from neat AlCl3, TEA containing IL enhanced it. This affirms outstandingly higher performance of the IL/AlCl3 than AlCl3/H2O. According to the 13C NMR data, PAOs from IL containing initiators have higher content of long chain branching, which is beneficial to improved viscosity index characteristic. Kinematic viscosity results were in accordance with the molar mass and 13C NMR data. 1H NMR spectra point to the fact that PAOs derived from TEA and TBA-based ILs generate exo-olefins, a type of vinyl that leads to reactive oligomers with potential capacity for block copolymers. DFT theoretical calculations and studies of non-covalent interactions help to separate and understand how the nature of the IL translates into such different properties.

Interaction energy of Cl2 and Br2 with H2 O: Exchange, dispersion and density the crucial ingredients.

Modern Density Functional Theory models are now suitable for many molecular and condensed phase studies. The study of noncovalent interactions, a well-known drawback, is no longer an insurmountable obstacle through design and empirical corrections. However, using empirical corrections as in the DFT-D methods might not be an all-in-one solution. This work uses a simple system, X2 -H2 O with X=Cl or Br, with two different interactions, halogen-bonded (XB) and hydrogen-halogen (HX), to investigate the capability of current density functional approximations (DFA) in predicting interaction energies with eight different exchange-correlation functionals. SAPT(DFT) provides, for all the studied cases, better predictions than the widely used supermolecular approach. In addition, the components of the interaction energy suggest where some of the shortcomings originate in each DFA. The analysis of the functionals used confirms that PBE0 and ω-B97X-D have a physically correct behavior. Using SAPT(DFT) and PBE0, and ω-B97X-D, we obtained the interaction energy of Cl2 and Br2 inside different clathrate cages and satisfactorily compared with wavefunction results; hence, the lower and upper limits of this value are defined: Cl2 @512 , -5.3 ± 0.3kcal/mol; Cl2 @512 62 , -5.5 ± 0.1kcal/mol; Br2 @512 62 , -7.6 ± 1.0kcal/mol; Br2 @512 63 , -10.6 ± 1.0kcal/mol; Br2 @512 64 , -10.9 ± 0.8kcal/mol.

Detailed Density Functional Theory Study of the Cationic Zirconocene Compound [Cp(C5H4CMe2C6H4F)ZrMe

Detailed density functional theory studies at the B3LYP and PBE-D3 levels of theory were performed on the cationic compound [Cp(C5H4CMe2C6H4F)ZrMe]+, with the F atom occupying either the ortho, meta, or para positions of the arene ring. In all cases, the arene ring coordinates with the cationic zirconium metal. The nature of this coordination is such that for the meta- or para-substituted arene ring, it is predominantly the ortho carbon atom of the C–H bond which interacts with the metal, as evident from noncovalent interaction studies. This is further corroborated by the natural bond orbital and quantum theory of atoms in molecular studies. In the case of the F atom being in the ortho position, we obtained clear-cut evidence for a Zr–F coordination.

Fabrication of Novel Potentiometric Sensor for Lead Ion Detection in Blood Samples: Experimental and Theoretical Approaches

One of the significant health problems in some developing countries such as Iran is lead toxicity. Potentiometric plasticizer-free Pb2+ selective electrode based on a simple and biocompatible ionophore, curcumin, for lead (II) detection in erythrocytes have been developed. Glassy carbon electrode modification was done with curcumin as an ionophore. Curcumin and its interaction with lead (II) were characterized using FT-IR, FE-SEM, and UV–Vis spectroscopic techniques. Match potential method (MPM) was applying for determining selectivity coefficients of the proposed sensor. Furthermore, the structures were optimized in various media for both tautomeric structures of curcumin, and then the binding mechanism was supported by DFT calculation, being in a high correlation and agreement by experiment. Also, noncovalent interaction studies were done to obtain a description of the sensing process. The fabricated ISE based on photocurable self-plasticizing (n-butylacrylate) membrane with curcumin shows a potentiometric response with a Nernstain slop of 28.348 ± 0.68 mV per decade in a linear range from 1.0 × 10-9 to 1.0 × 10-2 and detection limit of 3.98 × 10-10 M. The sensor' s response time was about 20 s at room temperature. The sensor shows a sensitive detection of Pb2+ in human erythrocytes and standard solutions.

Theoretical Investigation on Non-Covalent Interactions

This editorial is dedicated to announcing the Special Issue “Theoretical investigation on non-covalent interactions” of Crystals. The Special Issue covers the most recent progress in the rapidly growing fields of data science, artificial intelligence, and quantum and computational chemistry in topics relevant to the problem of theoretical investigation on non-covalent interactions (including, but not limited to, hydrogen, halogen, chalcogen, pnictogen, tetrel, and semi-coordination bonds; agosic and anagosic interactions; stacking, anion-/cation–π interactions; metallophilic interactions, etc.). The main successes of my colleagues and I in the field of fundamental theoretical studies of non-covalent interactions in various chemical compounds over the past year are briefly highlighted.

The study of noncovalent interactions between sevoflurane and acetone in liquefied Xe by the method of IR spectroscopy

The IR spectra of sevoflurane + acetone mixtures in liquefied Xe were studied at T ~ 165-190 K. Complex formation stabilized by noncovalent interactions of weak H-bond type has been identified on the basis of changes found at selected bands of both components. Quantum-chemical calculations made on MP2/6-311++G(d,p) level, show that the spectrum in the region of stretching vibrations of CH and CH2 groups is formed due to anharmonic effects, specifically Fermi resonances. Keywords: cryospectroscopy, sevoflurane, acetone, complex, noncovalent interactions, quantum-mechanical calculations.

Evidence of cluster formation of pyrrole with mixed silver metal clusters, Agx-My (x = 4,5, y = 2/1 and M = Au/Ni/Cu) using DFT/SERS analysis

Interaction between biologically active compounds and metal clusters are of immense theoretical and experimental interest due to its wide range of applications including drug delivery. We conducted a comprehensive analysis of the electronic characteristics of pyrrole interacting with metal atoms by combining DFT simulations with a literature review. Adsorption behavior of pyrrole (PYR) functionalized bimetallic clusters (PYR-Agx-My (x = 4/5, y = 2/1 and M = Au/Ni/Cu) is reported in the present study. In Ag4 and Ag5 systems, AgAu-PYR and AgNi-PYR systems have highest interaction energies. Mulliken charges and HOMO-LUMO energy can be utilized to determine the stability of molecule–metal interactions as well as the reactivity of PYR after they have interacted with metals. Study of noncovalent interactions indicates better interaction is between Ag4-Ni2 and PYR. It is found that electrons are localized over the PYR residue in the cluster.

High regioselectivity in the amination reaction of isoquinolinequinone derivatives using conceptual DFT and NCI analysis

DFT-derived reactivity descriptors and Non-Covalent interaction (NCI) analysis were performed to rationalize the regioselectivity in the amination reaction of some isoquinolinequinone derivatives. Statistical analysis was performed to assess robustness of atomic charges to the basis set. Various electronic population schemes including Mulliken population analysis (MPA), electrostatic method (ChelpG), Hirshfeld population analysis (HPA) and Natural population analysis (NPA) have been considered. The results revealed that NPA was the most efficient for this purpose. NCI study using the reduced density gradient (RDG) was performed for revealing weak interactions. Domains defined by isosurfaces of RDG have been integrated to quantitatively study the strength of weak interactions and their stabilities have also been examined. Steric hindrance caused by coordination of ethanol with the neighboring carbonyl prevents the nucleophilic attack on C-6 and therefore leads to preferential C-7 substitution. The quantitative study of NCI clearly demonstrates that the hydrogen bond of carbonyl (2) is more stabilizing. Consequently, the high polarity of hydrogen bond on this carbonyl may explain the high electrophilicity of C-5 compared to C-8. Our work proved that the difference in local reactivity, as well as the steric hindrance are the key elements explaining the high regioselectivity exhibited by the amination reaction.

Novel cis-[PdCl2(NHC)(PPh3)] complex: synthesis, crystal structure, spectral investigations, DFT and NCI studies, prediction of biological activity

This study contains the synthesis of a heteroleptic Pd(II) cis–[PdCl2(NHC)(PPh3)] complex containing an N-heterocyclic carbene (NHC) and a triphenylphosphine (PPh3) ligand. The complex was prepared from the related [PdCl2(NHC)(3–Clpy)] complex (PEPPSI), replacing the 3-chloropyridine ligand (3-Clpy) by the PPh3 ligand, and characterized by using 1H NMR, 31P NMR, 13C NMR, FT-IR, UV-vis spectroscopies and elemental analysis. The molecular and crystal structure of the complex was determined by single-crystal X-ray diffraction analysis. Comprehensive theoretical calculations including the optimized structural parameters, the HOMO–LUMO energy gap, vibrational frequencies, and chemical shifts were calculated using density functional theory (DFT) with the B3LYP/LanL2DZ//6–31G* level and compared with the experimental data. Natural population analysis (NPA), charge decomposition analysis (CDA) and natural bond analysis (NBO) were carried out. Non-covalent interaction (NCI) calculations were also performed to identify the weak non-covalent interactions from the topological analysis and the reduced gradient of the electron density of complex. Predictive study for the biological activities using PASS (prediction of activity spectra for biologically active substances) online software showed optimistic activities for the complex as an antineoplastic (melanoma) and nicotinic α6β3β4α5 receptor antagonist.

Local Energy Decomposition of Open-Shell Molecular Systems in the Domain-Based Local Pair Natural Orbital Coupled Cluster Framework.

Local energy decomposition (LED) analysis decomposes the interaction energy between two fragments calculated at the domain-based local pair natural orbital CCSD(T) (DLPNO-CCSD(T)) level of theory into a series of chemically meaningful contributions and has found widespread applications in the study of noncovalent interactions. Herein, an extension of this scheme that allows for the analysis of interaction energies of open-shell molecular systems calculated at the UHF-DLPNO-CCSD(T) level is presented. The new scheme is illustrated through applications to the CH2···X (X = He, Ne, Ar, Kr, and water) and heme···CO interactions in the low-lying singlet and triplet spin states. The results are used to discuss the mechanism that governs the change in the singlet–triplet energy gap of methylene and heme upon adduct formation.

Intramolecular Hydrogen Bonding Appetency for Conformational Penchants in Oxalohydrazide Fluoro Derivatives: NMR, MD, QTAIM, and NCI Studies.

The conformational stability of synthesized diphenyloxalohydrazide and dibenzoyloxalohydrazide fluoro derivatives has been investigated by extensive NMR studies that are ascertained by various levels of theoretical calculations. Two-dimensional 1H-19F HOESY NMR experiments revealed the close spatial proximity between two NMR-active nuclei, confirming the hydrogen bond (HB)-mediated interaction between them, further aiding in establishing the probable stable conformations of these molecules. The relaxed potential energy scan disclosed the energy-minimized most stable structure among the several possible multiple conformations, which is in concurrence with NMR interpretations. Atomistic molecular dynamics simulations have been employed to unequivocally establish the conformational stability and the nature of HB formation at varied temperatures. With the possibility of occurrence of a number of probable conformations, the percentage of occurrences of different types of HBs in them was determined by MD simulations. Their population analysis was carried out using a Boltzmann distribution, in addition to deriving their Gibbs free energies. The molecular interactions governing the stable conformations have not only been ascertained by experimental NMR interpretations but also corroborated by other theoretical computations, viz., quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI).

Intramolecular HB Interactions Evidenced in Dibenzoyl Oxalamide Derivatives: NMR, QTAIM, and NCI Studies.

Extensive NMR spectroscopic studies revealed information on the occurrence of bifurcated intramolecular hydrogen bond in the dibenzoyl oxalamide derivatives. One-dimensional NMR experiments, viz., solvent dilution, temperature perturbation, and two-dimensional experimental techniques, such as 15N-1H HSQC and 19F-1H HOESY, have been exploited to derive unambiguous confirmation of the participation of organic fluorine in the hydrogen-bonding interaction. The experimental NMR findings have been ratified by density functional theory based calculations, viz., NCI (noncovalent interaction) and QTAIM (quantum theory of atoms in molecules).

Study of non-covalent interactions on dendriplex formation: Influence of hydrophobic, electrostatic and hydrogen bonds interactions

The interaction of a double stranded small interference RNA (siRNA Nef) with cationic carbosilane dendrimers of generations 1–3 with two different ammonium functions at the periphery ([−NMe2R]+, R=Me, (CH2)2OH) has been studied by experimental techniques (zeta potential, electrophoresis, single molecule pulling experiments) and molecular dynamic calculations. These studies state the presence of different forces on dendriplex formation, depending on generation and type of ammonium group. Whilst for higher dendrimers electrostatic forces mainly drive the stability of dendriplexes, first generation compounds can penetrate into siRNA strands due to the establishment of hydrophobic interactions. Finally, in the particular case of first generation dendrimer [G1O3(NMe2(CH2)2OH))6]6+; the presence of hydroxyl groups reinforces dendriplex stability by hydrogen bonds formation. However, since these small dendrimers do not cover the RNA, only higher generation derivatives protect RNA from degradation.

Pemetrexed conjugated with gold nanoparticles – Synthesis, characterization and a study of noncovalent interactions

Gold nanoparticles (AuNPs) have been widely used as nanocarriers in drug delivery application. However, the binding mechanism between AuNPs and drug bases still remains a puzzle. Our study included: (i) optimization of three synthesis of the AuNPs-pemetrexed (PE) nanocomposites formation which was monitored by UV–Vis spectroscopy, (ii) identification of PE in gold nanocomposites and mechanism of PE interaction with gold nanoparticles by electrochemistry, NMR and Raman measurements, (iii) characterization of the three nanocomposites by TEM, DSL, ESL, zeta potential, XRPD and TGA analysis. The obtained nanocomposites are homogeneously shaped and have a maximum diameter of around 14nm and 88nm, as measured by the TEM and DSL techniques, respectively. The zeta potential of the nanocomposites is −43mV and suggests a high stability of the nanoparticles and lower toxicity for the normal cells. Quantum chemical calculations were also performed on model systems to estimate the strength of the AuNPs-PE interaction. Taking into account the experimental and theoretical data a mechanism of the nanocomposites' formation has been proposed in which PE interacts with the gold surface by the COOH/COO– group.

Theoretical analysis of the binding of iron(III) protoporphyrin IX to 4-methoxyacetophenone thiosemicarbazone via DFT-D3, MEP, QTAIM, NCI, ELF, and LOL studies.

Thiosemicarbazones display diverse pharmacological properties, including antimalarial activities. Their pharmacological activities have been studied in depth, but little of this research has focused on their antimalarial mode of action. To elucidate this antimalarial mechanism, we investigated the nature of the interactions between iron(III) protoporphyrin IX (Fe(III)PPIX) and the thione-thiol tautomers of 4-methoxyacetophenone thiosemicarbazone (MAPTSC). Dispersion-corrected density functional theory (DFT-D3), the quantum theory of atoms in molecules (QTAIM), the noncovalent interaction (NCI) index, the electron localization function (ELF), the localized orbital locator (LOL), and thermodynamic calculations were employed in this work. Fe(III)PPIX-MAPTSC binding is expected to inhibit hemozoin formation, thereby preventing Fe(III)PPIX detoxification in plasmodia. Preliminary studies geared toward the identification of atomic binding sites in the thione-thiol tautomers of MAPTSC were carried out using molecular electrostatic potential (MEP) maps and conceptual DFT-based local reactivity indices. The thionic sulfur and the 2 N-azomethine nitrogen/thiol sulfur of, respectively, the thione and thiol tautomers of MAPTSC were identified as the most favorable nucleophilic sites for electrophilic attack. The negative values of the computed Fe(III)PPIX-MAPTSC binding energies, enthalpies, and Gibbs free energies are indicative of the existence and stability of Fe(III)PPIX-MAPTSC complexes. MAPTSC-Fe(III) coordinate bonds and strong hydrogen bonds (N-H···O) between the NH2 group in MAPTSC and the C=O group in one propionate side chain of Fe(III)PPIX are crucial to Fe(III)PPIX-MAPTSC binding. QTAIM, NCI, ELF, and LOL analyses revealed a subtle interplay of weak noncovalent interactions dominated by dispersive-like van der Waals interactions between Fe(III)PPIX and MAPTSC that stabilize the Fe(III)PPIX-MAPTSC complexes.

The Surprising Importance of Peptide Bond Contacts in Drug-Protein Interactions.

The study of noncovalent interactions, notably including drug-protein binding, relies heavily on the language of localized functional group contacts: hydrogen bonding, π-π interactions, CH-π contacts, halogen bonding, etc. Applying the state-of-the-art functional group symmetry-adapted perturbation theory (F-SAPT) to an important question of chloro versus methyl aryl substitution in factor Xa inhibitor drugs, we find that a localized contact model provides an incorrect picture for the origin of the enhancement of chloro-containing ligands. Instead, the enhancement is found to originate from many intermediate-range contacts distributed throughout the binding pocket, particularly including the peptide bonds in the protein backbone. The contributions from these contacts are primarily electrostatic in nature, but require ab initio computations involving nearly the full drug-protein pocket system to be accurately quantified.

Synthesis and theoretical studies of non‒covalent interactions within a newly synthesized chiral 1,2,4-triazolo[3,4-b][1,3,4]thiadiazine

In this work the synthesis of a new compound formulated as C12H12N4OS, ((S)-1-(6-Phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-3-yl)ethanol) (5) reported and theoretical studies of the non‒covalent interactions constructed the related crystalline network described. It has been characterized by IR, Mass, and 1H, 13C NMR spectroscopy and single crystal X‒ray diffraction analysis. The binding energy of the non‒covalent interactions constructing the network of 5 have been calculated by dispersion corrected density functional theory (DFT‒D). The optimization of the formed network using H‒bonding and π‒stacking revealed that 1‒D coordination chain has been composed of neutral monomeric compound. For this purpose, the independent smallest fragment (monomer) and subsequently the related network, including seven monomers, having all non‒covalent interactions have been optimized. The results demonstrate that hydrogen bonds, especially OH⋯N, CH⋯O, CH⋯N, and CH⋯S interactions, govern the network formation. The calculated results of electronic transition in agreement with the experiment ones show eleven major bands derived from σ → π, n → n/σ*/π* aromatic rings to hydroxyl, inter‒atomic of oxygen, and thiadiazine to phenyl ring charge transfer transitions.

Does borazine-water behave like benzene-water? A matrix isolation infrared and ab initio study.

Borazine is isoelectronic with benzene and is popularly referred to as inorganic benzene. The study of non-covalent interactions with borazine and comparison with its organic counterpart promises to show interesting similarities and differences. The motivation of the present study of the borazine-water interaction, for the first time, stems from such interesting possibilities. Hydrogen-bonded complexes of borazine and water were studied using matrix isolation infrared spectroscopy and quantum chemical calculations. Computations were performed at M06-2X and MP2 levels of theory using 6-311++G(d,p) and aug-cc-pVDZ basis sets. At both the levels of theory, the complex involving an N-H⋯O interaction, where the N-H of borazine serves as the proton donor to the oxygen of water was found to be the global minimum, in contrast to the benzene-water system, which showed an H-π interaction. The experimentally observed infrared spectra of the complexes corroborated well with our computations for the complex corresponding to the global minimum. In addition to the global minimum, our computations also located two local minima on the borazine-water potential energy surface. Of the two local minima, one corresponded to a structure where the water was the proton donor to the nitrogen of borazine, approaching the borazine ring from above the plane of the ring; a structure that resembled the global minimum in the benzene-water H-π complex. The second local minimum corresponded to an interaction of the oxygen of water with the boron of borazine, which can be termed as the boron bond. Clearly the borazine-water system presents a richer landscape than the benzene-water system.