Search Results (18)

This study provides a comprehensive analysis of the interactions between dimethyl sulfoxide (DMSO) and two small peptides, diglycine and N-acetyl-glycine-methylamide (NAGMA), in aqueous solutions using FTIR spectroscopy and density functional theory (DFT) calculations. ATR-FTIR spectroscopy and DFT results revealed that DMSO does not form direct bonds with the peptides, suggesting that DMSO indirectly influences both peptides by modifying the surrounding water molecules. The analysis of HDO spectra allowed for the isolation of the contribution of water molecules that were simultaneously altered by the peptide and DMSO, and it also explained the changes in the hydration shells of the peptides in the presence of DMSO. In the DMSO–diglycine system, DMSO contributes to the additional strengthening of water hydrogen bonds in the reinforced hydration sphere of diglycine. In contrast, DMSO has a more moderate effect on the water molecules surrounding NAGMA due to the similarity of their hydration shells, leading to a slight weakening of the hydrogen bonds in the NAGMA hydration sphere. DFT/ONIOM calculations confirmed these observations. These findings demonstrated that DMSO influences peptide stability differentially based on their structural characteristics. Full article

In this work, an attempt is made to theoretically substantiate the experimentally known facts of the influence of halogen concentration on the catalytic properties of the neodymium-based Ziegler–Natta system. Based on the structural and thermochemical data obtained using modern methods of quantum chemistry, the process of the 1,3-butadiene cis-1,4-polymerization under the model active centers of the neodymium Ziegler–Natta catalysts with different contents of chloride ions was studied. Results are presented that explain the increase in the cis-stereospecificity and activity of the polymerization system with an increase in the content of the chloride ions in the neodymium catalytic system. Reasons were established for the decrease in the concentration of active centers relative to the introduced Nd(III) with an excess of chloride ions and the occurrence of the anti-syn isomerization as a source of the formation of the trans-1,4-structures in the cis-1,4-polybutadiene. Full article

The research on boron/nitrogen (B/N)-based multiresonance thermally activated delayed fluorescence (MR-TADF) emitters has been a prominent topic due to their narrowband emission and high luminous efficiency. However, devices derived from the common types of narrowband TADF materials often experience an efficiency roll-off, which could be ascribed to their relatively slow triplet–singlet exciton interconversion. Since inserting the heavy Se atom into the B/N scheme has been a proven strategy to address the abovementioned issues, herein, extensive density functional theory (DFT) and time-dependent DFT (TD-DFT) simulations have been employed to explore the effects of the structural modification on a series of structurally modified selenium-doped derivatives. Furthermore, the two-layered ONIOM (QM/MM) model has been employed to study the pressure effects on the crystal structure and photophysical properties of the pristine CzBSe. The theoretical results found that the introduced tert-butyl units in Cz-BSeN could result in a shorter charge transfer distance and smaller reorganization energy than the parent CzBSe. In contrast to directly incorporating the o-carborane (Cb) unit to CzBSe, incorporating the bridged phenyl units is important in order to achieve narrowband emissions and high luminous efficiency. The lowest three triplet excited states of CzBSe, Cz-BSeN and PhCb-BSeN all contribute to their triplet–singlet exciton conversions, resulting in a high utilization of triplet excitons. The pressure has an evident influence on the photophysical properties of the aggregated CzBSe and is favored for obtaining narrowband emissions. Our work is promised to provide a feasible strategy for designing selenium-doped derivatives with narrowband emissions and rapid triplet–singlet exciton interconversions. Full article

Furins are serine endoproteases that are involved in many biological processes, where they play important roles in normal metabolism, in the activation of various pathogens, while they are a target for therapeutic intervention. Dichlorophenyl-pyridine “BOS” compounds are well known drugs that are used as inhibitors of human furin by an induced-fit mechanism, in which tryptophan W254 in the furin catalytic cleft acts as a molecular transition energy gate. The binding of “BOS” drug into the active center of furin has been computationally studied using the density functional theory (DFT) and ONIOM multiscaling methodologies. The binding enthalpies of the W254 with the furin-BOS is −32.8 kcal/mol (“open”) and −18.8 kcal/mol (“closed”), while the calculated torsion barrier was found at 30 kcal/mol. It is significantly smaller than the value of previous MD calculations due to the relaxation of the environment, i.e., nearby groups of the W254, leading to the reduction of the energy demands. The significant lower barrier explains the experimental finding that the dihedral barrier of W254 is overcome. Furthermore, sartans were studied to evaluate their potential as furin inhibitors. Sartans are AT1 antagonists, and they effectively inhibit the hypertensive effects induced by the peptide hormone Angiotensin II. Here, they have been docked into the cavity to evaluate their effect on the BOS ligand via docking and molecular dynamics simulations. A consistent binding of sartans within the cavity during the simulation was found, suggesting that they could act as furin inhibitors. Finally, sartans interact with the same amino acids as W254, leading to a competitive binding that may influence the pharmacological efficacy and potential drug interactions of sartans. Full article

The computation of the rotation barriers of the methyl groups (Me) of tribromomesitylene (TBM) crystals has been carried out. Experimentally, the barriers of the three Me groups of TBM are found to be high and different. These groups do not experience the same hindering environment in the crystal state. For an isolated TBM molecule, the three barriers are equal and very low. We found that a cluster of 21 TBM molecules permits the reproduction of the crystal symmetry and structure of the bulk, with a central molecule surrounded by six molecules in the same plane and seven other molecules in two planes above and below. DFT computations including dispersion corrections have been carried out using the ONIOM procedure. The Me groups of the central TBM molecule were rotated step by step to determine the conformations of lowest and highest energy for each Me, thus allowing estimation of the rotation barriers as the difference between these energies. In doing so, we found the following barrier values, namely 105, 173, and 205 cm⁻¹, whereas the experimental values were 111, 180 and 200 cm⁻¹. Full article

Accurate thermochemical data are of great importance in developing quantitatively predictive reaction mechanisms for transportation fuels, such as diesel and jet fuels, which are primarily composed of large hydrocarbon molecules, especially large straight-chain alkanes containing more than 10 carbon atoms. This paper presents an ONIOM[QCISD(T)/CBS:DFT]-based theoretical thermochemistry study on the hydrogen abstraction reactions of straight-chain alkanes, n-C_nH_2n+2, (n = 1–16) by hydrogen (H), hydroxyl (OH), and hydroperoxyl (HO₂) radicals. These reactions, with n ≥ 10, pose significant computational challenges for prevalent high-level ab initio methods. However, they are effectively addressed using the ONIOM-based method. One notable aspect of this study is the consideration of the high symmetry of straight-chain alkanes. This symmetry allows us to study half of the reactions, employing a generalized approach. Therefore, a total of 216 reactions are systematically studied for the three reaction systems. Our results align very well with those from the widely accepted high-level QCISD(T)/CBS method, with discrepancies between the two generally less than 0.10 kcal/mol. Furthermore, we compared large straight-chain alkanes (n-C₁₆H₃₄ and n-C₁₈H₃₈) with large methyl ester molecules (C₁₅H₃₁COOCH₃ and C₁₇H₃₃COOCH₃) to elucidate the impact of functional groups (ester group and C=C double bond) on the reactivity of the long-chain structure. These findings underscore the accuracy and efficiency of the ONIOM-based method in computational thermochemistry, particularly for large straight-chain hydrocarbons in transportation fuels. Full article

In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol with biological activity. Acylphloroglucinols have attracted attention for treating tuberculosis due to their structural characteristics, highlighting the stabilizing effect of their intramolecular hydrogen bonds (IHBs). In this work, a conformational search for the caespitate was performed using the MM method. Posteriorly, DFT calculations with the APFD functional were used for full optimization and vibrational frequencies, obtaining stable structures. A population analysis was performed to predict the distribution of the most probable conformers. The calculations were performed in the gas phase and solution using the implicit SMD model for water, chloroform, acetonitrile, and DMSO solvents. Additionally, the multiscale ONIOM QM1/QM2 model was used to simulate the explicit solvent. The implicit and explicit solvent effects were evaluated on the global reactivity indexes using the conceptual-DFT approach. In addition, the QTAIM approach was applied to analyze the properties of the IHBs of the most energetically and populated conformers. The obtained results indicated that the most stable and populated conformer is in the gas phase, and chloroform has an extended conformation. However, water, acetonitrile, and DMSO have a hairpin shape. The optimized structures are well preserved in explicit solvent and the interaction energies for the IHBs were lower in explicit than implicit solvents due to non-covalent interactions formed between the solvent molecules. Finally, both methodologies, with implicit and explicit solvents, were validated with ¹H and ¹³C NMR experimental data. In both cases, the results agreed with the experimental data reported in the CDCl₃ solvent. Full article

In this study, we investigated the abilities of nitrogen and sulfur heterocyclic carbenes of benzotriazole, 2-mercaptobenzothiazole, 8-hydroxyquinoline, and 3-amino-1,2,4-triazole-5-thiol regarding adsorption on an Al-Mg-Si alloy toward corrosion inhibition of the surface. Al-Si(14), Al-Si(19), and Al-Si(21) in the Al-Mg-Si alloy surface with the highest fluctuation in the shielding tensors of the “NMR” spectrum generated by intra-atomic interaction directed us to the most influence in the neighbor atoms generated by interatomic reactions of N → Al, O → Al, and S → Al through the coating and adsorbing process of Langmuir adsorption. The values of various thermodynamic properties and dipole moments of benzotriazole, 2-mercaptobenzothiazole, 8-hydroxyquinoline, and 3-amino-1,2,4-triazole-5-thiol adsorbed on the Al-Mg-Si increased by enhancing the molecular weight of these compounds as well as the charge distribution between organic compounds (electron donor) and the alloy surface (electron acceptor). Finally, this research can build up our knowledge of the electronic structure, relative stability, and surface bonding of various metal alloy surfaces, metal-doped alloy nanosheets, and other dependent mechanisms such as heterogeneous catalysis, friction lubrication, and biological systems. Full article

Using modern methods of quantum chemistry, a theoretical substantiation of the high cis-stereospecificity of 1,3-butadiene polymerization catalyzed by the neodymium-based Ziegler–Natta system was carried out. For DFT and ONIOM simulation, the most cis-stereospecific active site of the catalytic system was used. By analyzing the total energy, as well as the enthalpy and Gibbs free energy of the simulated catalytically active centers, it was found that the coordination of 1,3-butadiene in the trans-form was more favorable than in the cis-form by 11 kJ/mol. However, as a result of π-allylic insertion mechanism modeling, it was found that the activation energy of cis-1,3-butadiene insertion into the π-allylic neodymium–carbon bond of the terminal group on the reactive growing chain was 10–15 kJ/mol lower than the activation energy of trans-1,3-butadiene insertion. The activation energies did not change when both trans-1,4-butadiene and cis-1,4-butadiene were used for modeling. That is, 1,4-cis-regulation was due not to the primary coordination of 1,3-butadiene in its cis-configuration, but to its lower energy of attachment to the active site. The obtained results allowed us to clarify the mechanism of the high cis-stereospecificity of 1,3-butadiene polymerization by the neodymium-based Ziegler–Natta system. Full article

In this research, the ability of transition metals (TM)-doped graphene nanosheets to adsorb the toxic gas CO has been investigated. The Langmuir adsorption model was used, with a three-layered ONIOM, using the CAM-B3LYP functional accompanying the LANL2DZ and 6-31+G (d,p) basis sets, and using the Gaussian 16 revision C.01 program, on the complexes of CO adsorbed on (Fe, Ni, Zn)-doped graphene nanosheets. The order of the changes of charge density for the Langmuir adsorption of CO on Fe-doped, Ni-doped, and Zn-doped graphene nanosheets has been investigated. This shows the greatest change of charge density for the Ni-doped graphene nanosheet. However, based on NMR spectroscopy, sharp peaks around the Ni-doped area on the surface of the graphene nanosheet have been observed. In addition, the Ni-doped graphene nanosheet has a large effect on the bond orbitals of C-Ni in the adsorption of CO, having the maximum occupancy. The values of $\Delta G_{ads}^o$, calculated through IR, showed that $\Delta G_{ads,\mathrm{CO}\to \mathrm{Fe}-\mathrm{doped} \mathrm{GR}}^o$ has the highest value, because of a charge density transfer from the oxygen atom in carbon monoxide to the Fe-doped graphene nanosheet. The frontier molecular orbitals, HOMO and LUMO, and the band energy gap accompanying some chemical reactivity parameters, have revealed the attributes of the molecular electrical transport of (Fe, Ni, Zn)-doped graphene nanosheets for the adsorption of CO. As a result, since a CO molecule interacts simultaneously with a Fe, Ni, or Zn atom and the C-C nanosheet, at first it might be separated, as in this state a CO atom constructs a physical bond with the Fe, Ni, or Zn atom, and then the other could be adsorbed chemically on the C-C nanosheet surface. Finally, our results have shown that a considerable amount of charge transfer occurs between CO molecules and TM-doped graphene nanosheets after adsorption, which suggests that TM-doped graphene is more sensitive and selective to the adsorption of CO than a pristine graphene surface. Full article

The modeling of the activity of anesthetics is a real challenge because of their unique electronic and structural characteristics. Microscopic approaches relevant to the typical features of these systems have been developed based on the advancements in the theory of intermolecular interactions. By stressing the quantum chemical point of view, here, we review the advances in the field highlighting differences and similarities among the chemicals within this group. The binding of the anesthetics to their partners has been analyzed by Symmetry-Adapted Perturbation Theory to provide insight into the nature of the interaction and the modeling of the adducts/complexes allows us to rationalize their anesthetic properties. A new approach in the frame of microtubule concept and the importance of lipid rafts and channels in membranes is also discussed. Full article

Statins are important drugs in the regulation of cholesterol levels in the human body that have as a primary target the enzyme β-hydroxy-β-methylglutaryl-CoA reductase (HMGR). This enzyme plays a crucial role in the mevalonate pathway, catalyzing the four-electron reduction of HMG-CoA to mevalonate. A second reduction step of this reaction mechanism has been the subject of much speculation in the literature, with different conflicting theories persisting to the present day. In this study, the different mechanistic hypotheses were evaluated with atomic-level detail through a combination of molecular dynamics simulations (MD) and quantum mechanics/molecular mechanics (QM/MM) calculations. The obtained Gibbs free activation and Gibbs free reaction energy (15 kcal mol⁻¹ and −40 kcal mol⁻¹) show that this hydride step takes place with the involvement of a cationic His405 and Lys639, and a neutral Glu98, while Asp715 remains in an anionic state. The results provide an atomic-level portrait of this step, clearly demonstrating the nature and protonation state of the amino acid residues involved, the energetics associated, and the structure and charge of the key participating atoms in the several intermediate states, finally elucidating this missing step. Full article

A combination of selective 1D Total Correlation Spectroscopy (TOCSY) and ¹H-¹³C Heteronuclear Multiple Bond Correlation (HMBC) NMR techniques has been employed for the identification of methyl linolenate primary oxidation products without the need for laborious isolation of the individual compounds. Complex hydroperoxides and diastereomeric endo-hydroperoxides were identified and quantified. Strongly deshielded C–O–O–H ¹H-NMR resonances of diastereomeric endo-hydroperoxides in the region of 8.8 to 9.6 ppm were shown to be due to intramolecular hydrogen bonding interactions of the hydroperoxide proton with an oxygen atom of the five-member endo-peroxide ring. These strongly deshielded resonances were utilized as a new method to derive, for the first time, three-dimensional structures with an assignment of pairs of diastereomers in solution with the combined use of ¹H-NMR chemical shifts, Density Functional Theory (DFT), and Our N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM) calculations. Full article

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M₁/M₂), an associated bridge hydroxide (W¹(OH⁻)), an M₁-bound water/hydroxide (W²), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W¹(OH⁻) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W¹(OH⁻) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His³⁰⁴/Asp²⁷⁴ tandem, with W² assigned as a water molecule: W²(H₂O). Arg²⁷⁵, proximal to M₁, stabilizes the substrate and TS by binding both the ester oxygen (O^γ) and a phosphoryl oxygen (O¹) in a bidentate fashion; in the product state, Tyr⁴⁵¹ aids in decoupling Arg²⁷⁵ from O¹ of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH^‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg²⁷⁵ is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg²⁷⁵ plays during the hydroxide attack was not correctly accounted for. Full article

In this work, I have analyzed the structure of binary mixtures of 1-butyl-3-methylimidazolium chloride ionic liquid, [C₄C₁im]Cl, and water, using computational NMR spectroscopy. The structure of the complex fluid phase, where the ionic and hydrophobic nature of ionic liquids is further complicated by the addition of water, is first generated by classical Molecular Dynamics (MD) and then validated by calculating the NMR properties with DFT at the ONIOM(B3LYP/cc-pVTZ//B3LYP/3-21G) on clusters extracted during the MD trajectories. Three ionic liquid/water mixtures have been considered with the [C₄C₁im]Cl mole fraction of 1.00, 0.50, and 0.01, that is the pure ionic liquid [C₄C₁im]Cl, the equimolar [C₄C₁im]Cl/water mixture, and a diluted solution of [C₄C₁im]Cl in water. A good agreement is obtained with published experimental data that, at the same time, validates the structural features obtained from the MD and the force field used, and provides an example of the power of NMR spectroscopy applied to complex fluid phases. Full article