Quantum Chemistry Aspects of the Solvent Effects on 3,4-Dimethyl-2,5-dihydrothiophen-1,1-dioxide Pyrolysis Reaction

On the potentials of sialic acid derivatives as inhibitors for the mumps virus: A molecular dynamics and quantum chemistry investigation

Mumps virus is an infectious pathogen causing major health problems for humans such as encephalitis, orchitis, and parotitis. Therefore, designing an inhibitor for this virus is of great medical and public health importance. With this goal in mind, we investigate the affinity of different sialic acid-based compounds (ligands) against the hemagglutinin-neuraminidase (HN) protein of the mumps virus, using a combination of molecular dynamics (MD) simulations and quantum chemistry calculations. Our MD simulation results indicate that the ligands form stable complexes with the HN protein through a combination of electrostatic, van der Waals (vdW), and hydrogen bond (H-bond) interactions, which the electrostatic interactions play a more important role in the complexation process. Based on the obtained results from the structural analysis Arg381, Arg291, and Arg49 play a key role in the binding site interactions with the different ligands, in comparison with other residues. There are some candidates such as Neu5Acα2-6Galβ1-4GlcNAcβ, Neu5Acα2-3Galβ1-3GlcNacβ1-3Galβ1-4Glc, and Neu5Acα2-6Galβ1-4GlcNAcβ1-3Galβ1-4Glc that form more stable complexes with the HN than the α2-3-Sialyllactose confirmed by the calculated Gibbs binding energies (-39.65, -46.93, and -36.49 kcal.mol^-1, respectively). To investigate the relationship between the molecular properties of the selected compounds and their affinity to the HN receptor, density functional theory dispersion corrected (DFT-D3) calculations were employed. According to our DFT-D3 results, neutral sialic acid-based compounds have lower reactivity to the mumps virus than the negativity charge structures. Moreover, by increasing the electronic chemical potential (μ) the vdW and H-bond interactions between drugs and the HN protein increase. In other words, by elevating the electron tendency of the selected ligands their affinity to the mumps virus increases. Our quantum chemistry calculations reveal that in addition to the structural features the molecular properties of the drugs can play important roles in their affinity and reactivity against the virus. The results of this study can provide useful details to design new compounds or improve their properties against the mumps virus.

Revealing electronic features governing hydrolysis of cephalosporins in the active site of the L1 metallo-β-lactamase

The QM/MM simulations followed by electron density feature analysis are carried out to deepen the understanding of the reaction mechanism of cephalosporin hydrolysis in the active site of the L1 metallo-β-lactamase. The differences in reactivity of ten similar cephalosporin compounds are explained by using an extended set of bonding descriptors. The limiting step of the reaction is characterized by the proton transfer to the nitrogen atom of the cephalosporin thiazine ring accompanied with formation of the C₄ Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> C₃ double bond in its N–C₄–C₃ fragment. The temporary N⋯H–O_w hydrogen bond, which is formed in the transition state of the limiting step of the reaction was recognized as a key atomic interaction governing the reactivity of various cephalosporins. Non-local real-space bonding descriptors show that different extent of localization of electron lone pair at N atom in the transition state affect the reactivity of compounds: smaller electron localization is typical for the less reactive species. In particular, the Fermi hole analysis shows how exchange electron correlation in the N⋯H–O_w fragment control electron lone pair localization. Delocalization tensor, linear response kernel and source function indicate that features of electron delocalization in the N–C₄–C₃ fragment of cephalosporins in the transition state complexes determine the differences in C₄–C₃ bond for substrates with high and low rate constants. The C₄–C₃ bond of the N–C₄–C₃ fragment at the transition state is similar to that of the preceding intermediate for the less reactive species and resembles the features of the enzyme–product complex for more reactive compounds. The power and limitations of the descriptors applied for solving the problem are discussed and the generality of approach is stressed.

Combination of QM/MM and modern bonding descriptors explains different reactivity of cephalosporins in the active site of the L1 metallo-β-lactamase.

Sensing Ability of Hybrid Cyclic Nanopeptides Based on Thiourea Cryptands for Different Ions, A Joint DFT-D3/MD Study

Theoretical studies, including quantum chemistry (QM) calculations and 25 ns molecular dynamic (MD) simulations, were performed on two types of hybrid cyclic nanopeptides (HCNPs) that are constructed of tren-capped cryptand (HCNP1) and 1,3,5-triethylbenzene-capped cryptand (HCNP2) for selective complex formation with OAC^-, NO₃^-, HSO₄^-, F^-, Br^-, and Cl^- ions in the gas phase and DMSO. Obtained data by M05-2X, M05-2X-D3, B3LYP, and B3LYP-D3 functionals indicated that HCNPs form a stable complex with F^- in comparison to other ions. DFT-D3 results and quantum theory of atoms in molecules (QTAIM) analysis indicated that dispersion and electrostatic interactions are the most important driving forces in HCNP-ion complex formation, respectively. Moreover, HOMO-LUMO analysis reveals that the reactivity of HCNP2, due to a lower band gap, is more than HCNP1. High sensing ability of the studied HCNPs for different ions was confirmed by Fermi level shifting of HNCPs to higher values during the complex formation. Finally, MD simulation results in DMSO are in good agreement with QM calculations and indicate that F^- forms the most stable complexes with HCNPs because of stronger electrostatic interactions.

Glucose derivatives substitution and cyclic peptide diameter effects on the stability of the self-assembled cyclic peptide nanotubes; a joint QM/MD study

Dynamical behavior and the stability of eighteen nanostructures composed of cyclic peptide (CP) with the general structure of the cyclo(CO(CH₂)_{n=4, 6, 10}COCyst), in the gas phase, water and chloroform were investigated during 50ns molecular dynamic (MD) simulations. CP dimers and cyclic peptide nanotubes (CPNTs) are more stable in chloroform than water and this stability is reversely correlated with the ring size of the CP units. Also the effect of glucose derivatives substitution, d-glucose (S1) and N-methyl-d-glucamine (S2), on the stability and other physicochemical properties of the CP dimers and CPNTs were evaluated. These substitutions increase the inner-subunits hydrogen bonds (H-bond) which in turn increase the stability of these structures. Moreover, the S2 substitution in comparison to the S1 makes dimers and CPNTs more stable. Gibbs free energy analysis based on the MM-PBSA and MM-GBSA calculations confirmed that substitutions affect the stability of the studied nanostructures, considerably and an increase in the length of the CPNT units reduces their stability. Quantum chemistry calculations on the dimer structures using the density functional theory (DFT) and DFT-D3 methods were performed. Based on the DFT-D3 calculations, it was revealed that the dispersion interactions play a key role in the dimerization process. The ring size increment, elevates the dispersion interaction energy which is accordance with the MD results. H-bond formation between the CO and NH groups of the CP units inside the dimers have been analyzed by using the quantum theory of atoms in molecules and natural bond orbital description. Finally, through these analyses, the electrostatic interaction between the mentioned groups have been evaluated.

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

A DFT study of solvent effects on the kinetics and mechanism of the [3,3] hetero-Cope rearrangement of 1-butene thiobenzoate

Quantum chemistry calculations have been applied to investigate the kinetics and mechanism of the hetero-Cope [3,3]-sigmatropic rearrangement of 1-butene thiobenzoate in the gas phase and different solvents. Of the two proposed mechanisms, concerted and biradical paths, a concerted mechanism with an activation Gibbs free energy of 27 kcal mol–1 was preferred. Based on natural bond orbital analysis, the electronic charge distribution at the transition state was affected by the solvent, through the perturbation in the electronic energy levels. The interaction energy of LpS25 → π*C1–C2 was larger in the solvent which means S25–C1 bond formation is more advanced in solution. C1 atomic charge reduction (0.26 e) and atomic charge increase for the S25 atom (0.23 e) indicated charge transfer from C1 to S25 during transition state formation.

Stereoelectronic Effects: A Powerful Concept in Explaining Kinetic and Thermodynamic Aspects of Retro Cheletropic Reactions

Kinetic and thermodynamic aspects of the retro cheletropic reaction of sulfur dioxide extrusion have been investigated. The interaction of the X–S bond (X=NH, S, O and CH2) and oxygen lone pairs of SO2 showed remarkable stereoelectronic effects and its correlation with the difference between computed and empirical bond length (Δl) have been analysed. The facility of the reaction in the case of four derivatives (X=NH, S, O and CH2) has been investigated from the viewpoint of product delocalisation energy. In addition, substitution effects have been studied on the relative Gibbs free energy of reaction for the oxygen derivative (X=O). Moreover, a correlation has been found between the Gibbs free energy of reaction in the presence of the substituent and Δl as a criterion for the value of the interaction between the X–S bond and oxygen lone pairs of the SO2 group. Finally, a new method based on electron density has been used for evaluation of the synchronicity values of the reaction. According to the corresponding diagrams, the calculated synchronicity values of the Wiberg bond indices and electron density are in good agreement.

A combined molecular dynamic and quantum mechanic study of the solvent and guest molecule effect on the stability and length of heterocyclic peptide nanotubes

Guest molecules and solvents affect the stability and length of the heterocyclic peptide nanotube through the electrostatic interactions.

Theoretical investigation of the chemoselectivity and synchronously pyrazole ring formation mechanism from ethoxymethylenemalononitrile and hydrazine hydrate in the gas and solvent phases: DFT, meta-GGA studies and NBO analysis

Chemoselectivity of the nucleophilic attack of nitrogen atom has been changed in the presence of the solvent due to Rds changes.