An accurate comparative theoretical study of the interaction of furan,pyrrole, and thiophene with various gaseous analytes

An accurate comparison of the interaction of furan, pyrrole, and thiophene with different gaseous analytes is vital not only for understanding the sensing mechanism of corresponding polymers but also for rational design of new materials. In the present study, DFT calculations at (M05-2X/Aug-cc-PVDZ) have been performed to investigate the interaction behavior of furan, pyrrole, and thiophene (as models for their corresponding polymers) with different analytes (NH₃, CO₂, CO, N₂H₄, HCN, H₂O₂, H₂S, CH₄, CH₃OH, SO₂, SO₃, H₂O). The interaction of heterocycles with analytes is illustrated by changes in geometric, energetic, and electronic properties. SAPT calculations were performed for energy decomposition analysis to study the contribution of non-covalent components of the total interaction energy for each complex. Analysis of energetic and electronic properties reveals that all heterocycles are highly sensitive to SO₃. The results suggest that sensing ability of polypyrrole is higher than polyfuran and polythiophene for all analytes.

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Graphical abstract SAPT0 energies (kcal mol^-1) of furan, pyrrole, and thiophene with various gaseous analytes?

     

Insight into the interaction of benzothiazole tethered triazole analogues with human serum albumin: Spectroscopy and molecular docking approaches

The interaction of four benzothiazole tethered triazole analogues (MS43, MS70, MS71, and MS78) with human serum albumin (HSA) was investigated using various spectroscopic techniques (ultraviolet–visible (UV–vis) light absorption, fluorescence, circular dichroism (CD), molecular docking and density functional theory (DFT) studies). Fluorescence quenching constants (~10¹²) revealed a static mode of quenching and binding constants (K_b ~10⁴) indicating the strong affinity of these analogues for HSA. Further alteration in the secondary structure of HSA in the presence of these analogues was also confirmed by far UV–CD spectroscopy. The intensity loss in CD studied at 222 nm indicated an increase in random coil/β‐sheet conformations in the protein. Binding energy values (MS71 (?9.3 kcal mol^?1), MS78 (?8.02 kcal mol^?1), MS70 (?7.16 kcal mol^?1) and MS43 (?6.81 kcal mol^?1)) obtained from molecular docking revealed binding of these analogues with HSA. Molecular docking and DFT studies validated the experimental results, as these four analogues bind with HSA at site II through hydrogen bonding and hydrophobic interactions.     

Insight into the dynamic interaction between different flavonoids and bovine serum albumin using molecular dynamics simulations and free energy calculations

In this study, the binding of Bovine serum albumin (BSA) with three flavonoids, kaempferol-3-O-a-L-rhamnopyranosyl-(1–3)-a-L-rhamnopyranosyl-(1–6)-b-D-galacto- pyranoside (drug 1),kaempfol-7-O-rhamnosyl-3-O-rutinoside (drug 2)andkaempferide-7-O-(4”-O-acetylrhamnosyl)-3-O-ruti- noside (drug 3) is investigated by molecular docking, molecular dynamics (MD) simulation, and binding free energy calculation. The free energies are consistent with available experimental results and suggest that the binding site of BSA-drug1 is more stable than those of BSA-drug2 and BSA-drug3. The energy decomposition analysis is performed and reveals that the electrostatic interactions play an important role in the stabilization of the binding site of BSA-drug1 while the van der Waals interactions contribute largely to stabilization of the binding site of BSA-drug2 and BSA-drug3. The key residues stabilizing the binding sites of BSA-drug1, BSA-drug2 and BSA-drug3 are identified based on the residue decomposition analysis.     

Comparative study of the interaction mechanism of astilbin,isoastilbin, and neoastilbin with CYP3A4

The interactions of human CYP3A4 with three selected isomer flavonoids, such as astilbin, isoastilbin and neoastilbin, were clarified using spectral analysis, molecular docking, and molecular dynamics simulation. During binding with the three flavonoids, the intrinsic fluorescence of CYP3A4 was statically quenched in static mode with nonradiative energy conversion. The fluorescence and ultraviolet/visible (UV/vis) data revealed that the three flavonoids had a moderate and stronger binding affinity with CYP3A4 due to the order of the K_a1 and K_a2 values ranging from 10⁴ to 10⁵ L·mol⁻¹. In addition, astilbin had the highest affinity with CYP3A4, then isoastilbin and neoastilbin, at the three experimental temperatures. Multispectral analysis confirmed that binding of the three flavonoids resulted in clear changes in the secondary structure of CYP3A4. It was found from fluorescence, UV/vis and molecular docking analyses that these three flavonoids strongly bound to CYP3A4 by means of hydrogen bonds and van der Waals forces. The key amino acids around the binding site were also elucidated. Furthermore, the stabilities of the three CYP3A4 complexes were evaluated using molecular dynamics simulation.     

The elasticity of the potential of emission reduction to energy saving: Definition,measurement, and evidence from China

Based on energy and CO₂ emission efficiencies, this paper proposes a definition of the elasticity of the potential of emission reduction to energy saving (E_peres), and measures the elasticity in China’s 30 provincial regions. Although E_peres is a relative definition, it can be used (1) to measure the amount of reduced CO₂ emissions per unit fossil energy saving, (2) to reflect the effectiveness of fossil energy saving for CO₂ emission reduction in different regions, and (3) to provide decision-making criteria for selecting pathways for emission reductions in different regions. The results show that compared with energy saving, emission reduction is a more serious issue in China. This indicates that energy saving policies have been highly effective since their implementation during the 11th “Five-Year Plan”. With respect to provincial disparities, the emission reductions caused by fossil energy saving are not significant in Beijing, Shanghai, and Guangdong. Fujian province has significant E_peres, indicating that emission reduction causing by fossil energy saving is effective. E_peres has been increasing over time in Hunan and Hubei. Hainan’s E_peres has remained less than 1, indicating that its emission-reduction effect of fossil energy saving is worse than in other provinces. Moreover, the elasticity of Eastern China is greater than that of Central China and Western China. This finding sheds light on pathway selection for energy saving and emission reduction in China: it would be more appropriate to encourage fossil energy saving in Eastern China, and to promote clean energy use (e.g., water electricity and solar energy) in Central China and Western China.     

An assessment to evaluate the validity of different methods for the description of some corrosion inhibitors

New research and development efforts using computational chemistry in studying an assessment of the validity of different quantum chemical methods to describe the molecular and electronic structures of some corrosion inhibitors were introduced. The standard and the highly accurate CCSD method with 6-311++G(d,p), ab initio calculations using the HF/6-31G++(d,p) and MP2 with 6-311G(d,p), 6-31++G(d,p), and 6-311++G(2df,p) methods as well as DFT method at the B3LYP, BP86, B3LYP*, M06L, and M062x/6-31G++(d,p) basis set level were performed on some triazole derivatives and sulfur containing compounds used as corrosion inhibitors. Quantum chemical parameters, such as the energy of the highest occupied molecular orbital energy (E_HOMO), the energy of the lowest unoccupied molecular orbital energy (E_LUMO), energy gap (ΔE), dipole moment (μ), sum of total negative charges (TNC), chemical potential (Pi), electronegativity (χ), hardness (η), softness (σ), local softness (s), Fukui functions (f ⁺,f ^?), electrophilicity (ω), the total energy change (?E_T) and the solvation energy (S.E), were calculated. Furthermore, the accuracy and the applicability of these methods were estimated relative to the highest accuracy and standard CCSD with 6-311++G(d,p) method. Good correlations between the quantum chemical parameters and the corresponding inhibition efficiency (IE%) were found.     

The Spherical Expansion of H2 Dimer Interaction Energy by Double Symmetry-Adapted Perturbation Theory

Abstract

The weak interaction energy of H₂ dimer is studied by double symmetry-adapted perturbation theory (SAPT) within second-order of intermolecular and intramonomer perturbation for molecular simulations. The assumed orientations of H₂ dimer are linear, parallel, T type and X type. Among four orientations T orientation is the most stable, while linear orientation is the most repulsive. The second-order dispersion energy E _disp ⁽²⁾ is the most attractive contribution in all orientations. The interaction energy has the anisotropy, so we expressed our total interaction energy by the spherical expansion to compare with the experimental value. The isotropic interaction energy is about 85% of the experimental value.     

Computational study on the structural and optoelectronic properties of a carbazole-benzothiadiazole based conjugated oligomer with various alkyl side-chain lengths

The effect of the alkyl side-chain length on the structural and optoelectronic properties of poly[N-9′-heptadecanyl-27-carbazole-alt-55-(4′,7′-di-2-thienyl-2′,1′,3′-benzothiadiazole)] (PCDTBT) conjugated oligomers have been studied by density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The study was carried out by varying the length of alkyl side-chain attached to the nitrogen atom of the carbazole unit of the PCDTBT oligomers. The structural properties of the optimised oligomers were then studied by determining the bond-length alternation and dihedral angles (Φ) for various side-chain lengths. Total energy calculations for the determination of HOMO energy (E_HOMO), LUMO energy (E_LUMO), and fundamental energy gap (E_Gap) were performed using DFT at the B3LYP/6-31G(d), while the first singlet excitation energies (E_Opt) were calculated by TD-DFT also at the same level of theory. It was observed that there are no significant structural changes occurring as the alkyl chain lengths are varied. For the electronic properties, very small differences (i.e. ~0.01 eV) were observed for E_Gap and E_Opt while the exciton binding energies (E_B) were virtually the same. The results suggest that using shorter alkyl side-chains do not significantly affect the structural and optoelectronic properties of the carbazole-benzothiadiazole based polymer. The observations can aid future computational design studies of analogous systems by reducing large structures thus decreasing computational costs.     

Mechanism of inhibition of arginine kinase by flavonoids consistent with thermodynamics of docking simulation

Arginine kinase plays a vital role in invertebrate homeostasis by buffering ATP concentrations. Arginine kinase might serve as a target for environmentally friendly insect-selective pesticides, because it differs notably from its counterpart in vertebrates, creatine kinase. In this study, two members of the flavonoid family, quercetin (QU) and luteolin (LU), were identified as novel noncompetitive inhibitors of locust arginine kinase. They were found to have inhibition parameters (K_i) of 11.2 and 23.9 μM, respectively. By comparing changes in the activity and intrinsic fluorescence of AK, the inhibition mechanisms of these flavonoids were found to involve binding to Trp residues in the active site. This was determined by examination of the static quenching parameter K_sv. The main binding forces between flavonoids and AK were found to be hydrophobic based on the thermodynamic parameters of changes in enthalpy (ΔH), entropy (ΔS), and free energy (ΔG) and on docking simulation results. Molecular docking analyses also suggested that flavonoids could bind to the active site of AK and were close to the Trp 221 in active site. Molecular simulation results mimic the experimental results, indicated that QU had a lower binding energy and a stronger inhibitory effect on AK than LU, suggesting that the extra hydroxyl group in QU might increase binding ability.     

Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: A molecular docking analysis

A molecular docking investigation has been carried out on cytotoxic prenylated flavonoids from Lonchocarpus haberi with cancer-relevant chemotherapeutic targets known to be inhibited by flavonoids. Two molecular docking programs, Molegro and ArgusDock, were used to compare the binding energies of Lonchocarpus flavonoids with other flavonoids, inhibitors, or known ligands, to aromatase (CYP 19), fatty acid synthase (FAS), xanthine oxidase (XO), cyclooxygenases (COX-1 and COX-2), lipoxygenase (LOX-3), ornithine decarboxylase (ODC), protein tyrosine kinase (PTK), phosphoinositide 3-kinase (PI3K), protein kinase C (PKC), topoisomerase II (ATP binding site), ATP binding cassette (ABC) transporter, and phospholipase A₂ (PLA). The Lonchocarpus flavonoids examined in this study exhibited docking energies comparable to or stronger than other flavonoids that had been previously shown to be effective inhibitors of these enzymes. Furthermore, prenylated flavonoids, such as the Lonchocarpus flavonoids and xanthohumol, generally showed greater binding energies than the non-prenylated flavonoids. We conclude, therefore, that the Lonchocarpus flavonoids possibly owe their cytotoxic activity by inhibition of one or more of these enzymes.      

Computational insights into the binding pattern of mitochondrial calcium uniporter inhibitor through homology modeling,molecular dynamics simulation,binding free energy prediction and density functional theory calculation

Abstract

The mitochondrial calcium uniporter (MCU) is the critical protein of the inner mitochondrial membrane that is the primary mediator for calcium uptake into the mitochondrial matrix. Herein we built the optimal homology model of human MCU which was refined through all-atom molecular dynamics simulation. Then, the binding mode of known inhibitor was predicted through molecular docking method, along with molecular dynamics simulation and binding free energy calculation to verify the docking result and stability of the protein-inhibitor complex. Finally, density functional theory (DFT) calculation enhanced our understanding of the molecular interaction of MCU inhibitor. Our research would provide a deeper insight into the interactions between human MCU and its inhibitor, which boosts to develop novel therapy against MCU related disease.

Communicated by Ramaswamy H. Sarma     

Multi-spectroscopic studies on the interaction between traditional Chinese herb,helicid with pepsin

Study on the binding properties of helicid by pepsin systematically using multi-spectroscopic techniques and molecular docking method, and these interactions comprise biological recognition at molecular level and backbone of biological significance in medicine concerned with the uses, effects, and modes of action of drugs. We investigated the mechanism of interaction between helicid and pepsin by using various spectroscopic techniques viz., fluorescence spectra, UV–Vis absorption spectra, circular dichroism (CD), 3D spectra, synchronous fluorescence spectra and molecular docking methods. The quenching mechanism associated with the helicid–pepsin interaction was determined by performing fluorescence measurements at different temperatures. From the experimental results show that helicid quenched the fluorescence intensity of pepsin via a combination of static and dynamic quenching process. The binding constants (K_a) at three temperatures (288, 298, and 308 K) were 7.940?×?10⁷, 2.082?×?10⁵ and 3.199?×?10⁵ L mol^?1, respectively, and the number of binding sites (n) were 1.44, 1.14, and 1.18, respectively. The n value is close to unity, which means that there is only one independent class of binding site on pepsin for helicid. Thermodynamic parameters at 298 K were calculated as follows: ΔH^o (??83.85 kJ mol^?1), ΔG^o (??33.279 kJ mol^?1), and ΔS^o (??169.72 J K^?1 mol^?1). Based on thermodynamic analysis, the interaction of helicid with pepsin is driven by enthalpy, and Van der Waals’ forces and hydrogen bonds are the main forces between helicid and pepsin. A molecular docking study further confirmed the binding mode obtained by the experimental studies. The conformational changes in the structure of pepsin was confirmed by 3D fluorescence spectra and circular dichroism.     

Comparative theoretical study of the structures and stabilities of four typical gadolinium carboxylates in different scintillator solvents

The structural properties and stabilities of four typical gadolinium carboxylates (Gd-CBX) in toluene, linear alkyl benzene (LAB), and phenyl xylyl ethane (PXE) solvents were theoretically studied using density functional theory (DFT/B3LYP with the basis sets 6-311G(d) and MWB54) and the polarizable continuum model (PCM). The average Gd–ligand interaction energies (E _int, corrected for dispersion) and the values of the energy gap between the highest occupied molecular orbital and lowest unoccupied molecular orbital (\( \varDelta \) _HL) for the gadolinium complexes were calculated to compare the relative stabilities of the four Gd-CBX molecules in the three liquid scintillator solvents. According to the calculations, the values of E _int and \( \varDelta \) _HL for Gd-CBX in LAB are larger than the corresponding values in PXE and toluene. Gd-CBX may therefore be more compatible with LAB than with PXE and toluene. It was also found that, in the three scintillator solvents, the stabilities of the four Gd-CBX molecules increase in the order Gd-2EHA?<?Gd-2MVA?<?Gd-pivalate?<?Gd-TMHA.     

On the existence of MHn species with M=Al, Ga and n=4, 5, 6. Computational study of structures, stabilities and bonding

Based on second-order perturbation theory (MP2) predictions with large 6-311++G(3df, 3pd) basis set we have reviewed the possible structures and stabilities of a series of neutral MH_n(M=Al, Ga; n=4, 5, 6) species. For AlH₄ and AlH₅, our results confirm the previous theoretical findings, which indicate the dihydrogen C_s complexes (²A′) AlH₂(H₂) and (¹A′) AlH₃(H₂), respectively, as the lowest energy isomers. We found, similarly, C_s (²A′) GaH₂(H₂) and (¹A′) GaH₃(H₂) van der Waals complexes as the most stable species of the gallium analogues GaH₄ and GaH₅. The calculated H₂ dissociation energies (D_e) for AlH₂(H₂) and AlH₃(H₂) are of the order 1.8–2.5 kcalmol¹, whereas this range of values for GaH₂(H₂) and GaH₃(H₂) is 1.4–1.8 kcalmol¹ . Symmetry-adapted perturbation theory (SAPT) was used to analyze the interaction energies of these dihydrogen complexes (for n=5) to determine why the Ga species show a smaller binding energy than the Al species. The SAPT partitioning of the interaction energy showed significant differences between AlH₃(H₂) and GaH₃(H₂), resulting from the much stronger “hydride” character of the aluminum species. The experimental observation of AlH₂(H₂) and AlH₃(H₂), and likely GaH₃(H₂), via low-temperature matrix isolation has been reported recently by Pullumbi et al. and Andrews et al., supporting the theoretical predictions. For n=6, we found the degenerate C₂(²A) and C_s(²A′) MH₂(H₂)₂ “double H₂” type van der Waals complexes as the lowest energy species for both M=Al and Ga.Electronic Supplementary Material Supplementary material is available for this article at     

The molecular basis for the inhibition of phosphodiesterase-4D by three natural resveratrol analogs. Isolation,molecular docking,molecular dynamics simulations,binding free energy,and bioassay

The phosphodiesterase-4 (PDE4) enzyme is a promising therapeutic target for several diseases. Our previous studies found resveratrol and moracin M to be natural PDE4 inhibitors. In the present study, three natural resveratrol analogs [pterostilbene, (E)-2′,3,5′,5-tetrahydroxystilbene (THSB), and oxyresveratrol] are structurally related to resveratrol and moracin M, but their inhibition and mechanism against PDE4 are still unclear. A combined method consisting of molecular docking, molecular dynamics (MD) simulations, binding free energy, and bioassay was performed to better understand their inhibitory mechanism. The binding pattern of pterostilbene demonstrates that it involves hydrophobic/aromatic interactions with Phe340 and Phe372, and forms hydrogen bond(s) with His160 and Gln369 in the active site pocket. The present work also reveals that oxyresveratrol and THSB can bind to PDE4D and exhibits less negative predicted binding free energies than pterostilbene, which was qualitatively validated by bioassay (IC₅₀ = 96.6, 36.1, and 27.0 μM, respectively). Additionally, a linear correlation (R² = 0.953) is achieved for five PDE4D/ligand complexes between the predicted binding free energies and the experimental counterparts approximately estimated from their IC₅₀ values (≈RT ln IC₅₀). Our results imply that hydrophobic/aromatic forces are the primary factors in explaining the mechanism of inhibition by the three products. Results of the study help to understand the inhibitory mechanism of the three natural products, and thus help the discovery of novel PDE4 inhibitors from resveratrol, moracin M, and other natural products.     

Quantitative structure-activity relationship analysis of phenolic antioxidants

In this report, the quantitative structure-activity relationship (QSAR) analyses of substituted phenols, vitamin E derivatives and flavonoids are presented. Two models have been derived using calculated parameters such as the heat of formation (H_f), the energy of the lowest unoccupied molecular orbital of radicals (E_lumo-r), the energy of the highest occupied molecular orbital of the parent compounds (E_homo) and the number of hydroxyl groups (OH). These models can be used to estimate the redox potentials or antioxidant activities of new substituted phenolic compounds or vitamin E derivatives. The Trolox equivalent antioxidant capacities (TEACs) of 42 different flavonoids are found to be mainly governed by the number and location of hydroxyl groups on the flavonoid ring system.     

Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium

Quantum chemical calculations using the density functional theory (B3LYP/6-31G* DFT) and semi-empirical AM1 methods were performed on ten pyridine derivatives used as corrosion inhibitors for mild steel in acidic medium to determine the relationship between molecular structure and their inhibition efficiencies. Quantum chemical parameters such as total negative charge (TNC) on the molecule, energy of highest occupied molecular orbital (E _HOMO), energy of lowest unoccupied molecular orbital (E _LUMO) and dipole moment (μ) as well as linear solvation energy terms, molecular volume (Vi) and dipolar-polarization (π*) were correlated to corrosion inhibition efficiency of ten pyridine derivatives. A possible correlation between corrosion inhibition efficiencies and structural properties was searched to reduce the number of compounds to be selected for testing from a library of compounds. It was found that theoretical data support the experimental results. The results were used to predict the corrosion inhibition of 24 related pyridine derivatives.     

Characteristics and nature of the intermolecular interactions in boron-bonded complexes with carbene as electron donor: an <Emphasis Type="Italic">ab initio</Emphasis>, SAPT and QTAIM study

We report geometries, stabilization energies, symmetry adapted perturbation theory (SAPT) and quantum theory of atoms in molecules (QTAIM) analyses of a series of carbene–BX₃ complexes, where X = H, OH, NH₂, CH₃, CN, NC, F, Cl, and Br. The stabilization energies were calculated at HF, B3LYP, MP2, MP4 and CCSD(T)/aug-cc-pVDZ levels of theory using optimized geometries of all the complexes obtained from B3LYP/aug-cc-pVTZ. Quantitatively, all the complexes indicate the presence of B–C_carbene interaction due to the short B–C_carbene distances. Inspection of stabilization energies reveals that the interaction energies increase in the order NH₂ > OH > CH₃ > F > H > Cl > Br > NC > CN, which is the opposite trend shown in the binding distances. Considering the SAPT results, it is found that electrostatic effects account for about 50% of the overall attraction of the studied complexes. By comparison, the induction components of these interactions represent about 40% of the total attractive forces. Despite falling in a region of charge depletion with ∇² ρ _BCP >0, the B–C_carbene bond critical points (BCPs) are characterized by a reasonably large value of the electron density (ρ _BCP) and H_BCP <0, indicating that the potential energy overcomes the kinetic energy density at BCP and the B–C_carbene bond is a polar covalent bond.     

How Does (E)-2-(Acetamidomethylene)succinate Bind to Its Hydrolase? From the Binding Process to the Final Result

The binding of (E)-2-(acetamidomethylene)succinate (E-2AMS) to E-2AMS hydrolase is crucial for biological function of the enzyme and the last step reaction of vitamin B₆ biological degradation. In the present study, several molecular simulation methods, including molecular docking, conventional molecular dynamics (MD), steered MD (SMD), and free energy calculation methods, were properly integrated to investigate the detailed binding process of E-2AMS to its hydrolase and to assign the optimal enzyme-substrate complex conformation. It was demonstrated that the substrate binding conformation with trans-form amide bond is energetically preferred conformation, in which E-2AMS''s pose not only ensures hydrogen bond formation of its amide oxygen atom with the vicinal oxyanion hole but also provides probability of the hydrophobic interaction between its methyl moiety and the related enzyme''s hydrophobic cavity. Several key residues, Arg146, Arg167, Tyr168, Arg179, and Tyr259, orientate the E-2AMS''s pose and stabilize its conformation in the active site via the hydrogen bond interaction with E-2AMS. Sequentially, the binding process of E-2AMS to E-2AMS hydrolase was studied by SMD simulation, which shows the surprising conformational reversal of E-2AMS. Several important intermediate structures and some significant residues were identified in the simulation. It is stressed that Arg146 and Arg167 are two pivotal residues responsible for the conformational reversal of E-2AMS in the binding or unbinding. Our research has shed light onto the full binding process of the substrate to E-2AMS hydrolase, which could provide more penetrating insight into the interaction of E-2AMS with the enzyme and would help in the further exploration on the catalysis mechanism.