Noncovalent Interactions Reduced Density Gradient Research Articles

Investigations on Growth, Characterization, NCI-RDG, AIM, Molecular Docking and In-Silico ADME Properties of 1,2-Benzene Dicarboxylic Acid Anhydride

Superior single crystal of 1,2-benzene dicarboxylic acid anhydride additionally called Phthalic anhydride (PAN) was developed via solution growth at low temperatures. Single crystal X-ray diffraction investigation revealed the crystal system and unit cell characteristics. The phase stability and crystalline nature were uncovered by powder X-ray diffraction analysis. FT-IR examination was done for the titular material so as to survey the various functional groups. With the use of the VEDA program's relevant resources, vibrational assignments have been made on the concept of Potential Energy Distribution (PED). Density Functional Theory (DFT) was employed to smooth out the molecular structure of PAN and was additionally utilized to consider FT-IR spectrum at molecular level. Non covalent interactions reduced density gradient (NCI-RDG) analysis has been used for the prediction of the weak interaction in the actual space in terms of the electron density along with its derivatives for PAN. Atoms in Molecules (AIM) analysis was carried for out for PAN. The docking research of the small molecule (PAN) with target protein confirmed that this is a great molecule which docks nicely with numerous targets associated with Hypoxia Inducible Factor 1-α. The absorption, distribution, metabolism, excretion (ADME) characteristics have been calculated with the assist of online server preADMET.

Interactions between Diphenylamine with 2-Hydroxypropyl β-Cyclodextrin based on Spectral, Biological and Theoretical Investigations

The inclusion complex of diphenylamine (DPA) in 2-hydroxypropyl β-cyclodextrin (HP-β-CD) was synthesized by a co-precipitation method. The structure and molecular properties of the newly synthesized inclusion complex (DPA: HP-β-CD) were investigated along with a β-cyclodextrin (β-CD) inclusion complex (DPA: β-CD) using various analytical and theoretical methods. Phase solubility, absorption, fluorescence, Fourier transform-Infrared spectroscopy (FTIR), powder X-ray diffraction (PXRD) and scanning electron microscope (SEM) techniques were used to investigate the structural properties of the DPA before and after being encapsulated by the CDs (β-CD and HP-β-CD). Furthermore, the antioxidant and antibacterial activities were evaluated for DPA and the inclusion complexes (DPA: β-CD and DPA: HP-β-CD). The structure of the inclusion complexes was proposed based on the experimental results and their structural optimization was done using Becke’s three parameter density functional theory using Lee-Yang-Parr’s 3-21 G method in the gas phase. Then the various theoretical molecular properties, such as frontier molecular orbitals (FMO), molecular electrostatic potential map (MEP), Mulliken atomic charges, natural bond orbitals (NBO), electron localization function (ELF), localized orbital locator (LOL), quantum theory of atoms in a molecule (QTAIM) and noncovalent interactions—reduced density gradient (NCI-RDG) were studied for DPA and its inclusion complexes using the Gaussian 09 W software and Multiwfn 3.8 tool.

Triquinoxalinylene and benzoquinone based covalent organic framework as robust material for mitigation of environmental pollutants-A theoretical approach

The physisorption of pollutant gases (NH3, HCN, H2S and PH3) on TQBQ-COF has been explored using DFT calculations. The strength and nature of interactions were determined through interaction energy, non-Covalent interactions- Reduced Density Gradient (NCI-RDG) plots, Frontier Molecular Orbital (FMO), Natural bond orbital (NBO), Electron Density Difference (EDD) and Quantum Theory of Atoms In Molecule (QTAIM) analysis. The optimized geometries and interaction energy calculations revealed that the analytes interacted with Oxygen and Nitrogen atoms of TQBQ-COF leading to adsorption energy ranging from −10.66 to −5.85 kcal/mol. The values of recovery time were in agreement to that of interaction energy and decreased with the increase in temperature. The NCI-RDG plots and QTAIM analysis revealed the presence of weak van der Waals forces in all complexes and partial covalent character in H2S@TQBQ-COF. Charge transfer study (employing NBO and EDD analysis) depicted the transfer of charge from surface to analytes. The study of HOMO-LUMO energy gap in FMO analysis depicted the high sensitivity of TQBQ-COF for H2S and NH3 compared to HCN and PH3 due to significant lowering of HOMO-LUMO energy gap upon the adsorption of H2S and NH3 on TQBQ-COF.

Structural, optimization of and mechanistic insights into a new thiosemicarbazone derivative as a highly sensitive and selective chemosensor for Hg2+ recognition using DFT, COSMO-RS, RSM, and molecular dynamics simulation approaches

A new thiosemicarbazone derivative, N-(2-hydroxyphenyl)-2-[1-(pyridin-4-yl)ethylidene]hydrazinecarbothioamide (HPEH), has been synthesized, characterized, and further developed as a highly selective and sensitive colorimetric chemosensor for Hg2+ recognition in environmental water samples. Structural conformers of HPEH were successfully identified using a combination of the potential energy surface (PES) and time-dependent density functional theory (TD-DFT) methods. The synthesized HPEH was successfully characterized further and analyzed based on its harmonic vibrational frequencies, NMR spectra, and electronic transitions using the DFT approach. Sigma profiles were generated using the COSMO-RS approach to identify a compatible medium for HPEH to act as a chemosensor. The conditions for the highly sensitive and selective detection of Hg2+ by HPEH were successfully optimized using the statistical response surface methodology approach. The optimum sensing of HPEH occurred in an 8:2 v/v DMSO/pH 7.8 solution at a 20:60 μM HPEH/Hg2+ concentration and after a reaction time of 18 min, with statistically significant independent variables (p < 0.05) for all parameters. Under optimal conditions, the lowest Hg2+ concentration detected by HPEH was 3.56 µM, indicating that HPEH can serve as an alternative and comparable probe for the detection of Hg2+ in aqueous systems. Using the optimized results, the interaction between HPEH and Hg2+ in the chemosensor system was successfully modeled, and the model was subsequently used with the TD-DFT, non-covalent interaction-reduced density gradient (NCI-RDG), and molecular dynamics approaches to gain mechanistic insights into the interaction. The results showed that the newly synthesized HPEH, in addition to being cost-effective, could serve as a suitable alternative and comparable chemosensor for Hg2+ recognition in water samples, with the advantages of being efficient, portable, and eco-friendly, and offering rapid analysis without the need of specialized training.

Hirshfeld surface analyses, NCI–RDG and effect of surfactant on the size of Co3O4 nanostructures obtained from cobalt(II) nano-complex

Nanostructures of the compound [Co(O2CCH3)2(2-apy)2] (1) (2-apy = 2-Aminopyridine) have been synthesized by a sonochemical process at different of concentrations cobalt acetate tetrahydrate and 2-aminopyridine ligand. The smallest nanostructures of compound 1 are produced in low concentrations of initial reagents. Co3O4 nanoparticles were prepared from thermal decomposition in oleic acid as a surfactant and direct calcination of compound 1 at different temperatures. The effect of calcination temperature and oleic acid, as a surfactant, was investigated on the particle size distribution of the products. The compounds were studied by scanning electron microscopy (SEM), X-ray powder diffraction (XRD), UV–vis, FT-IR spectroscopy, thermal analyses (TGA and DTA) and elemental analyses. Hirshfeld surface analyses and Noncovalent interaction reduced density gradient (NCI-RDG) calculations of compound 1 were illustrated and discussed in order to quantify the order and nature of intermolecular interactions in the crystal network. Hirshfeld surface analysis indicated that there are other types of intermolecular contacts in Crystal, including H…H, H…O, C…H, H…N, C…C and C…N interactions, and the contributions of these interactions are 55.4%, 19.7%, 19.2%, 4.1%, 1.4% and 0.2%, respectively.

Synthesis, X-ray Crystal Structure, and Computational Characterization of Tetraphenylborate, 3-(5H-Dibenzo[a,d] cyclohepten-5-ylidene)-N, N-Dimethyl-1-propanamine

A cyclobenzaprine-tetraphenylborate (CBP-TPB) complex was synthesized, achieving a 78% yield through an anion exchange reaction. The white crystals of the complex were formed in acetonitrile and characterized using a variety of spectroscopic and analytical techniques, including ultraviolet, infrared, mass, elemental, and nuclear magnetic resonance (NMR) spectroscopy, as well as X-ray crystallography. The study employed a comprehensive approach to investigate the structural properties, stability, and behavior of the CBP-TPB complex. The use of crystallographic analysis, Hirshfeld surface analysis, quantum theory of atoms in molecules, noncovalent interaction reduced density gradient, global reactivity descriptors, frontier molecular orbitals, molecular electrostatic potential, and ultraviolet-visible spectroscopy provided valuable insights into the complex’s molecular geometries, supramolecular features, and intermolecular interactions. These findings contribute to a better understanding of the CBP-TPB complex’s potential applications in fields such as pharmaceuticals and materials science and emphasize the importance of combining theoretical predictions and experimental measurements in understanding molecular properties. The study also demonstrated the potential of density functional theory-based computational methods for predicting NMR spectroscopic parameters.

He adsorption and sensing properties of graphene nanoflakes doped with Mo and Nb

DFT calculations have been performed to study the He adsorption on the surface of Mo-doped graphene and Nb-doped graphene nanoflakes in order to evaluate the capability of studied doped graphene sheets as effective gas sensor materials. The ωB97XD (including dispersion)/6-311++G(d,p) (LanL2DZ for Mo and Nb) level of theory were utilized in this investigation. The HOMO-LUMO gap (Eg) of the Mo-doped and Nb-doped graphene structures decreased upon He adsorption on both sheets (−37.77% and −8.33%, respectively). Therefore, the electrical conductivity of both surfaces have increased. However, alteration of the Eg value in Mo-doped graphene is very higher than that of Nb-doped graphene. So, the Mo-doped graphene is more sensitive to He molecule in comparison with Nb-doped graphene and it could be used as a gas sensor material to detect He gas. Variety analyses such as natural bond orbital (NBO), density of states (DOS), electron density distribution (ED), electron localization function (ELF) and non-covalent interaction-reduced density gradient (NCI-RDG) have been carried-out in order to better evaluate the He adsorption nature on the investigated surfaces.

Sulfido-bridged 1,2-bis(diphenylphosphino)ethane (dppe) appended trinuclear nickel(II) clusters: Crystallographic and computational analyses

The cluster compounds are still gaining considerable attention due to their peculiar behaviour and M−M bonding or M···M interactions. In this report, two sufido-bridged, 1,2-bis-(diphenylphosphino)ethane (dppe) appended trinuclear Ni(II) clusters having formula [Ni3S2(dppe)3].2BPh4 (Ni3S2-1) and [Ni3S2(dppe)2(4-pyCH2OH)2].2PF6 (Ni3S2-2) are reported. These clusters are synthesized from the same starting reactants the xanthate ligand 4-PyCH2OCS2Na, Ni(II) and dppe employing two different reaction pathways. The obtained compounds have been characterized by microanalyses, FTIR, UV–Vis, 1H, 13C and 31P NMR spectroscopy as well as by single crystal X-ray diffraction technique. The X-ray analyses revealed that in both compounds three Ni(II) centers are coordinated to two sulfido and dppe ligands. In Ni3S2-1 three dppe and two sulfido ligands are stabilising the trinuclar cluster cation while in Ni3S2-2 along with two sulfido and two dppe ligands, two 4-pyCH2OH are also coordinating with one of the Ni(II) center. Both Ni3S2-1 and Ni3S2-2 display different non-covalent interactions along with the Ni···Ni interactions. The nature of these interactions has been addressed with the aid of Hirshfeld surface analysis, density functional theory and quantum theory of atoms-in-molecules (QTAIM) analyses. The occurrence of such non-covalent intermolecular interactions is also well supported by the non-covalent interactions reduced density gradient (NCI-RDG) approaches. Also, the Wiberg bond index, Mayer bond order and delocalization indices have been calculated to assess the nature of Ni···Ni interactions.

Characterization of non-covalent contacts in mono- and di-halo substituted acetaldehydes: probing the substitution effects of electron donating and withdrawing groups.

In the current work, a systematic evaluation of the different types of non-covalent interactions (NCIs) in acetaldehyde dimers, including dimers of mono-halo (XCH2CHO)2, di-halo (X2CHCHO)2 and tri-halo substituted (X3CCHO)2 acetaldehydes via the associated stabilization energy of these dimers has been performed. Furthermore, a topological analysis of the electron density based on the quantum theory of atoms in molecules (QTAIM) and non-covalent interaction reduced density gradient (NCI-RDG) isosurfaces has also been performed to evaluate the nature of these NCIs. The geometrical and electronic characteristics have been evaluated via the presence of different electron-donating groups (EDGs) and electron-withdrawing groups (EWGs) or substituents in dimers of these molecules, namely, XCH(Y)CHO and X2C(Y)CHO (wherein X = -F, -Cl, and -Br and Y = -SO3H, -CN, -NO2, -NH2, -CH3, -OCH3, and -SMe3). The C-H⋯O, C-H⋯X, X⋯X, X⋯O and C⋯O tetrel bonded contacts have been recognized to play an important role in the stabilization of the formed dimers. This study also establishes the fact that the overall stability of the dimeric assemblies is governed by the contributions from the mutual and complex interplay of a variety of interactions in the investigated dimers. Hence considerations based on strong H-bond donor-acceptor characteristics hold relevance for simple systems only, but slight alteration in the electronic environment can affect the overall stabilization energies of the system being investigated and the nature of the interactions that contribute towards the same.

Experimental and computational investigation of a novel organic cation hexachlorostannate (IV) material (C7H9N2O)2(SnCl6)

A novel organic–inorganic hybrid material (C7H9N2O)2(SnCl6) was obtained by synthetic reaction in aqueous solution. The crystallographic study shows that the investigated compound crystallizes in the triclinic system with P-1 space group. Its unit cell dimensions are a = 7.0859 (7) Å, b = 9.0553 (9) Å, c = 9.1442 (8) Å, a = 81.152(8) Å3, b = 87.126 (8) Å3, c = 67.977 (10) Å3 with V = 537, 43(25) and Z = 2.The three-dimensional framework and the stability of the crystal are insured by N−H⋯Cl, N−H⋯O and C−H⋯O hydrogen bonds and Cg⋯Cg (π⋯π) stacking. The vibrational absorption bands were recorded by IR spectroscopy and have been identified in relation to the crystal structure of a made-up (C7H9N2O)2(SnCl6) sample. The optical properties of the crystal were studied by using UV–visible absorption spectroscopy. The intermolecular interactions occurring in the crystal and their relative contributions in building the solid-state architecture, were quantified by using the three-dimensional Hirshfeld surfaces and two-dimensional fingerprint plots. In addition, the molecular geometries, vibrational frequencies of the compounds in the ground state have been performed using density functional theory (DFT) method, at B3LYP with 6-311g+(2d,2p) set for C, H, N, O, Cl atoms and LANL2DZ basis set for Sn atom.Topological AIM approaches and noncovalent interaction reduced density gradient (NCI-RDG) analyses and were pursued to generate a profound understanding of the structure-directing interactions in the compound. The NBO analysis was carried out to provide information about the delocalization of charge and energy density of atoms.

Mechanically Strong, Hydrostable, and Biodegradable Starch–Cellulose Composite Materials for Tableware

AbstractThe extensive use of nondegradable plastic tableware has brought serious environmental problems. Starch‐based materials are good alternatives to plastics, but poor mechanical properties and intrinsic hydrophilicity limit their utilizations. In order to address this issue, naturally abundant bagasse pulp fiber is used as the reinforcing agent to improve the mechanical properties of starch and polydimethylsiloxane coating (CSB35‐PDMS50) to improve their hydrophobicity and hydrostability. CSB35‐PDMS50 reaches the tensile strength of 21.2 MPa and contact angle of 121°. The enhancement of the mechanical strength can be explained by strong hydrogen bonding between starch and cellulose, as indicated by noncovalent interaction‐reduced density gradient (NCI‐RDG) analysis. CSB35‐PDMS50 retains the low water adsorption rate within 60 h, remains stable in water for 24 h without morphology change, and maintains initial hydrophobicity after continuous abrasion in sandpaper and high‐pressure water spraying due to the formation of Si─O–C bonds. The water absorption capacity of CSB35‐PDMS50 is less than 10% when used as the cap materials for Eppendorf tube for 30 days. Furthermore, CSB35‐PDMS50 demonstrates good biodegradability in the soil with 74% in 100 days. The tableware prepared from ther composites demonstrates good potentials as the competitive substitute for plastics with easy production, high strength, and biodegradability.

Rational modulation of N and O binding in Fe(III) complex formation derived from hydroxychloroquine: Synthesis, spectroscopic, computational, and docking simulation with human thrombin plasma

Hydroxychloroquine (HCQ) can bind with Fe(III) by both N and O atoms to form either [Fe-HCQ] or [Fe-(HCQ)2] complex. The characterization of the product developed as a result of the reaction between HCQ and Fe(III) salt suggested the formation of [Fe-HCQ] complex. Rational studies characterized the synthesized complex with several types of spectroscopic analysis such FT-IR, UV-Visible and mass spectra and XRD evaluation. The computational analysis involved in this study view an investigation about the electronic behavior around the central metal atom coordinated to the donor ligand atoms. The postulation discussed the formation of [Fe-HCQ] complex rather than [Fe-(HCQ)2] complex. Quantum reactivity parameters (Physiochemical properties) and FMOs analysis were studied. Important topological parameters such as electronic localization function (ElF), average local ionization energy (ALIE), and molecular electrostatic potential (MEP) analyses were studied; also, non-covalent interaction- reduced density gradient (NCI-RDG) analysis illustrated the type of interactions in HCQ and [Fe-HCQ]. Molecular docking of the ligand and its synthesized complex was performed on the protein crystal structure (5TO3) of human thrombin plasma, and a good predicted result was obtained in inhibiting thrombosis acceleration with the synthesized Fe-complex. Molecular dynamic simulation analysis was applied to predict the stability of the studied compounds based on energetic variables and RMSD values.

Hydroxycoumarin encapsulated sulfonatothiacalix[4]arene: 1H NMR, steady state fluorescence and theory

Encapsulation of 4-hydroxy coumarin (4HC) within the p-sulfonatothiacalix[4]arene has been investigated employing the steady state fluorescence, 1H NMR titration experiments combined with ωB97x-D based density function theory. Theoretical calculations have shown that in the 4HC⊂TSCX4 complex the guest encapsulates partially within the cavity of the macrocycle via CH⋅⋅⋅π interactions while the lactone ring excludes the cavity binds to sulfonate portals of the host by hydrogen bonding interactions. Natural transition orbital analyses were used to assign electronic transitions in 4HC⊂TSCX4 complex and its 7HC analogue. The first allowed vertical excitation at 266 nm in the complex arises from a transfer of electron density on the lactone ring of 4HC to aromatic ring of the macrocycle. Further the C=O vibration at 1791 cm−1 in the infrared spectra of 4HC downshifts to 1724 cm−1 upon complexation with the TSCX4. The noncovalent interactions reduced density gradient method was employed to characterize non-bonding interactions in the complex in conjunction with quantum theory of atoms in molecules. Steady state fluorescence measurements reveal that addition of TSCX4 in DMSO to 4HC results in quenching of the 397 nm band. Furthermore, the Stern-Volmer quenching constant of the complex determined to be Ksv = 2.19 × 104 M−1 has static and the upward curvature concave towards the I0/I axis in Stern-Volmer plots thus was noticed. The recorded excited state lifetime of complex led to the bimolecular quenching constant kq to be 1.98 × 104 M−1 s-1. Upon complexation the hydroxyl protons (Hb) in 4HC engender large deshielding as opposed to aromatic protons of TSCX4 macrocycle which emerge with up-field signals in the measured 1H NMR spectra. The noncovalent binding manifests in NOESY spectrum of the 4HC⊂TSCX4 complex. The association constant of the complex obtained from the UV–Vis and steady state fluorescence correlate well with those from 1H NMR titration experiments which establish that the inclusion complex is stable.

Insights into theoretical detection of CO2, NO, CO, O2, and O3 gases molecules using Zinc phthalocyanine with peripheral mono and tetra quinoleinoxy substituents: Molecular geometries, Electronic properties, and Vibrational analysis

In this paper, Zn-phthalocyanine (ZnPc) with peripheral mono (ZnPcR 1 ) and tetra quinoleinoxy (ZnPcR 4 ) substituents of the phtalocyanine ring were theoretically studied for the adsorption of NO, CO 2 , CO, O 2 and O 3 gases using DFT/B3LYP-D3/6–311++ G (d, p) method. Data displayed a strong interaction between ZnPc, ZnPcR 1 and ZnPcR 4 and the studied gases. The calculated adsorption energies were - 19.509, - 13.175, - 7.538, - 5.359, and - 5.280 k c a l ∙ m o l - 1 for ZnPcR 4 /O 3 , ZnPcR 4 /O 2 , ZnPcR 4 /CO 2 , ZnPcR 4 /NO, and ZnPcR 4 /CO, respectively. The absorption spectra of the studied complexes were determined using time-dependent density functional theory (TD-DFT). The blue shifted λ max values confirmed the interaction between the complexes and the gases. The electronic properties, geometries, stabilities, noncovalent interactions reduced density gradient (NCI-RDG) and natural population analysis (NPA) have been carried out. FT-IR spectra of all studied complexes displayed a major change in the vibrational frequency and signal strength after gases adsorption. In brief, the optical spectra, the change in the energy gap and the vibrational spectra showed that the studied gases mainly O 3 and O 2 were very sensitive to ZnPc, ZnPcR 1 , and ZnPcR 4 and hence could be used in sensors.

Temozolomide binding to Cucurbit[7]uril: QTAIM, NCI-RDG and NBO analyses

The inclusion behavior of antineoplastic Temozolomide (TMZ) in the cavitand host Cucurbit[7]uril (CB[7]), with 1:1 stoichiometry, was investigated in this research work. Structural and electronic studies were conducted in vacuum and water. We used the DFT/B3LYP and the dispersion corrected DFT-D/wB97X-D functionals with 6-31G(d), 6–31 + G(d) and 6-31 + G(d,p) basis sets. All methods agree on the 3D optimum structure, in which a total inclusion of TMZ in CB[7] cavity is observed. A destabilizing effect of solvation was highlighted and confirmed from Frontier Molecular Orbital and global reactivity descriptors analyses. Furthermore, The nature and strength of intermolecular interactions were studied using Natural Bond Orbital (NBO) and Quantum Theory of Atoms In Molecule (QTAIM) analyses. Both models corroborate on the overall conclusion revealing that the conventional N–H⋯O and improper C–H⋯O H-bonds are mainly the driving forces stabilizing TMZ@CB[7] complex. Also, in the framework of the topological QTAIM analysis, we classified these closed shell interactions and distinguished two kinds of H-bonds: with electrostatic character or partially covalent in nature. The analysis of Espinosa energies unveils a good correlation with the intermolecular bond distance and electron density. Moreover, The Non-Covalent Interactions Reduced Density Gradient (NCI-RDG) method was used to reveal and distinguish between weak interaction regions; in fact it segregates attractive (H-bonding), dispersive (VdW) and repulsive interactions. Finally, from 1H NMR and TD-DFT computations, we identified, the interaction sites and the electronic transitions responsible of UV–Vis absorption bands, respectively. The best reproduction of experimental spectra is achieved with the dispersion corrected wB97X-D and extended basis sets.

Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers.

Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP–MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.

Investigation of intermolecular interactions in inclusion complexes of pyroquilon with cucurbit[n]urils (n = 7,8) using DFT-D3 correction dispersion

In this work, the host-guest inclusion complexes of pyroquilon (Pyn) with two cucurbit[ n ]urils (CB[7] and CB[8]) were investigated by the density functional theory including dispersion correction (DFT-D3) method using the following functional, B3LYP and M06-2X with the split valence double zeta 6-31G(d) basis set in both gas and aqueous phases. The geometries of these complexes were optimized and the results were analyzed and compared. To provide insights into the contributions of different components of interaction energy of studied complexes, we used the energy decomposition analysis (EDA) which provides quantitative interpretation of chemical bonds. HOMO and LUMO energies, the global chemical reactivity descriptors and Fukui function were computed. The absorption spectra of the complexes have been calculated using TD-DFT method. Molecular electrostatic potential was calculated to predict the reactive sites for electrophilic and nucleophilic attack. The study of the type of the interaction between the pyroquilon molecule and the two hosts is better explained using the non-covalent interaction-reduced density gradient (NCI-RDG). AIM analyses demonstrate the establishment of conventional H-bond interaction. The 1 H nuclear magnetic resonance ( 1 H NMR) chemical shift of the complexes was studied using the Gauge-Including Atomic Orbital (GIAO) method and compared with experimental data. It has been shown that hydrogen bond energies from the QTAIM theory correlate well with the 1 H NMR chemical shifts calculated. • Density functional calculation was applied to study the complexes of pyroquilon/CB[7, 8]. • Energies analysis shows that dispersion has the main role in complexes formation. • EDA and chemical reactivity have been investigated. • AIM analyses demonstrate the establishment of H-bond interaction. • Excellent correlation between E HB and δ H .

Structural Patterns and Stabilities of Hydrogen-Bonded Pairs Involving Ribonucleotide Bases and Arginine, Glutamic Acid, or Glutamine Residues of Proteins from Quantum Mechanical Calculations.

Ribonucleotide:protein interactions play crucial roles in a number of biological processes. Unlike the RNA:protein interface where van der Waals contacts are prevalent, the recognition of a single ribonucleotide such as ATP by a protein occurs predominantly through hydrogen-bonding interactions. As a first step toward understanding the role of hydrogen bonding in ribonucleotide:protein recognition, the present work employs density functional theory to provide a detailed quantum-mechanical analysis of the structural and energetic characteristics of 18 unique hydrogen-bonded pairs involving the nucleobase/nucleoside moiety of four canonical ribonucleotides and the side chains of three polar amino-acid residues (arginine, glutamine, and glutamic acid) of proteins. In addition, we model five new pairs that are till now not observed in crystallographically identified ribonucleotide:protein complexes but may be identified in complexes crystallized in the future. We critically examine the characteristics of each pair in its ribonucleotide:protein crystal structure occurrence and (gas phase and water phase) optimized intrinsic structure. We further evaluated the interaction energy of each pair and characterized the associated hydrogen bonds using a number of quantum mechanics-based relationships including natural bond orbital analysis, quantum theory atoms in molecules analysis, Iogansen relationships, Nikolaienko–Bulavin–Hovorun relationships, and noncovalent interaction–reduced density gradient analysis. Our analyses reveal rich variability in hydrogen bonds in the crystallographic as well as intrinsic structure of each pair, which includes conventional O/N–H···N/O and C–H···O hydrogen bonds as well as donor/acceptor-bifurcated hydrogen bonds. Further, we identify five combinations of nucleobase and amino acid moieties; each of which exhibits at least two alternate (i.e., multimodal) structures that interact through the same nucleobase edge. In fact, one such pair exhibits four multimodal structures; one of which possesses unconventional “amino–acceptor” hydrogen bonding with comparable (−9.4 kcal mol–1) strength to the corresponding conventional (i.e., amino:donor) structure (−9.2 kcal mol–1). This points to the importance of amino–acceptor hydrogen bonds in RNA:protein interactions and suggests that such interactions must be considered in the future while studying the dynamics in the context of molecular recognition. Overall, our study provides preliminary insights into the intrinsic features of ribonucleotide:amino acid interactions, which may help frame a clearer picture of the molecular basis of RNA:protein recognition and further appreciate the role of such contacts in biology.

Trimerization of Vitamin K3: Molecular structure and density functional theoretic investigations

We demonstrate the unusual reactivity of Vitamin K3 with sodium ethoxide accompanying its trimerization which gave 6-(3-methyl-1,4-dioxo-1,4-dihydronaphthalen-2-yl) pentaphene-5,8,13,14-tetraone (1) as the product made up of substituted naphthoquinone and anthraquinone core. X-ray structure of the product revealed CH⋯O interaction; π-π stacking and C⋯O close contacts in its crystal. Electronic structure of 1 obtained from the M06-2X/6-311++G (d, p) theory is in consonance with the experiment. Besides the π-π stacking in its dimer are probed through the noncovalent interactions reduced density gradient analysis within the quantum theory of atoms in molecules.

Influence of remote intramolecular hydrogen bonding on the acidity of hydroxy‐1,4‐benzoquinonederivatives: A DFT study

AbstractIn this study, the effects of the remote intramolecular hydrogen bonding on the acidity of hydroxy‐1,4‐benzoquinone derivatives have been investigated ab initio by employing density functional theory (DFT) methods. The computational studies were performed for both gas and solution (H2O, DMSO, and MeCN solutions) phases. Our results indicated that remote hydrogen bonding could play an important role in increasing the acidity of hydroxy‐1,4‐benzoquinone. Noncovalent interaction reduced density gradient (NCI‐RDG) methods were used to visualize the attractive and repulsive interactions in the studied acids and their conjugate bases. Natural bond orbital (NBO) analysis was performed to confirm intramolecular hydrogen bonding effect on acidity. Quantum theory of atoms in molecules (QTAIM) was also used to study the nature of hydrogen bonds. QTAIM results showed that the intramolecular hydrogen bonds in these structures are electrostatic (closed‐shell) interactions in nature.