Search

Context: Milk has nutrient-rich but thermal sensitive matrix that undergoes varying degrees of Maillard reaction (MR) at heating conditions. The MR mainly occurs between lysine residues (Lys) and lactose composed of glucose (Glc) and galactose (Gal), which are abundantly sourced from dairy products. In the present study, the MRs of Glc and Gal with Lys at the initial and intermediate stages have been investigated theoretically using density functional theory (DFT) to simulate the gaseous and aqueous phases. Reaction mechanisms have been proposed, and relative energy changes of different steps were calculated according to the total mass balance. The calculations reveal that both Nα- and Nε-amine groups of Lys can react with the carbonyl functional group of Glc and Gal with the similar potential energy profiles, and Gal is more reactive than Glc. However, the barrier in Nε-channel is lower than in Nα-channel, indicating a faster reaction rate through the former channel compared with the latter. The 5-hydroxymethyl-2-furfural (HMF) and derivative are formed under 3-deoxysone route in the intermediate stage. The calculation results are helpful for proposing a reasonable MR mechanism and suggesting possible control methods of the MRs. Methods: In this study, different levels of DFT calculations have been conducted to investigate the mechanisms and favorability of generating MR products in Glc-Lys and Gal-Lys models at initial and intermediate stages in the gaseous and aqueous conditions. In order to elucidate the molecular models from the perspectives of chemistry and geometry, DFT calculations were performed by the mean of B3LYP functional at basis sets of 6–311 + + G (d, p) and 6–311 + + G (2df, 2p) with optional solvation settings. To examine the solvation effect, the study further constructed models with solvent H2O and calculated in wB97XD functional with 6–31 + G (d) basis set. All computations were carried out Gaussian 09 suite of quantum chemistry software. [ABSTRACT FROM AUTHOR]

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their own dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. A specially developed method of visual differential analysis of structural features of (bio)macromolecular structures is applied for these studies. The results obtained of a number of physical properties (interacting energies, dipole moments, polarization values) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on FF, such as COO- and NH3 + , since they determine many properties of the structures under study. The data obtained are useful for further analysis of the possible adhesion and capture of medical molecular components by active layers of FF-based PNT, which can be designed for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis. [ABSTRACT FROM AUTHOR]

Lignin and phenolic compounds have been shown as the main recalcitrance for biomass decomposition, as they inhibit a number of lignocellulose-degrading enzymes. Understanding the inhibition mechanisms and energetic competitions with the native substrate is essential for the development of lignin resistive enzymes. In this study, atomistic detail of the size-dependent effects and binding modes of monomeric coniferyl alcohol, dimeric oligolignol, and tetrameric oligolignol made from coniferyl alcohols on the GH11 xylanase from Bacillus firmus strain K-1 was investigated by using molecular docking and atomistic molecular dynamics (MD) simulations. From the MD simulation results on the docked conformation of oligolignol binding within the "Cleft" and the "N-terminal," changes were observed both for protein conformations and positional binding of ligands, as binding with "Thumb" regions was found for all oligolignin models. Moreover, the uniquely stable "N-terminal" binding of the coniferyl alcohol monomer had no effect on the highly fluctuated Thumb region, showing no sign of inhibitory effect, and was in good agreement with recent studies. However, the inhibitory effect of oligolignols was size dependent, as the estimated binding energy of the tetrameric oligolignol became stronger than that of the xylohexaose substrate, and the important binding residues were identified for future protein engineering attempts to enhance the lignin resistivity of GH11. [ABSTRACT FROM AUTHOR]

Sunscreen-based photoprotection is an important strategy to prevent photoaging and skin cancer. Among the effective and modern sunscreens, triazine compounds are known as an important class based on their physical-chemical properties, such as photostability and UV broad-spectrum absorption (UVA and UVB). Molecular modeling and quantum mechanical calculations approaches can be helpful to orientate the design of sunscreens. Herein, a case study is presented to demonstrate the importance of the molecular modeling as a design tool for promising sunscreen candidates based on the synthesis research previously described of bemotrizinol, a broad-spectrum photostable organic UV filter present in many sunscreens products. Time-dependent density functional theory (TD-DFT) calculations performed in gas phase on the isolated organic UV filters proved to reproduce the experimental UV absorption, guiding the choice of the most efficient candidate as sunscreen. The present work highlights the importance of molecular modeling as an effective tool to support synthesis research, increasing the possibility of obtaining promising compounds with reduced costs and effluent production. [ABSTRACT FROM AUTHOR]

Context: Physical molecular models have played a fundamental role in the understanding of chemical reactions on heterogeneous catalysts and on metal nanoparticles. To date, these physical models have been based on separate models of the metal nanoparticle (NP) or surface and of the substrate and the molecular structure of reactant and product adsorbates and their intermediates. In this paper, we try to provide a new miniature physical molecular model, the sphere-in-contact model of heterogeneous catalysts and metal nanoparticles that can build inexpensive, small and efficient molecular models that can be transported or shipped easily and that depict the chemical reaction as a whole, showing reactants, intermediates, products, the metal nanoparticle bound to the substrate which can give information about a reaction mechanism. These models reveal that there are certain rules with respect to the kind of sites you observe at the metal NP interface with the support by small movement of the nanoparticle. Methods: We have used in this study physical molecular models using the sphere-in-contact model. This is the first time such physical models are built for heterogeneous catalytic reactions and metal nanoparticles, and they are constructed out of spheres that fuse together when exposed to water. [ABSTRACT FROM AUTHOR]

Polyvinyl alcohol (PVA) is a material with a variety of applications in separation, biotechnology, and biomedicine. Using combined Monte Carlo and molecular dynamics techniques, we present an extensive comparative study of second- and third-generation force fields Universal, COMPASS, COMPASS II, PCFF, and the newly developed INTERFACE, as applied to this system. In particular, we show that an INTERFACE force field provides a possibility of composing a reliable atomistic model to reproduce density change of PVA matrix in a narrow temperature range (298-348 K) and calculate a thermal expansion coefficient with reasonable accuracy. Thus, the INTERFACE force field may be used to predict mechanical properties of the PVA system, being a scaffold for hydrogels, with much greater accuracy than latter approaches. [ABSTRACT FROM AUTHOR]

Protein modeling and molecular dynamics hold a unique toolset to aide in the characterization of clinical variants that may result in disease. Not only do these techniques offer the ability to study under characterized proteins, but they do this with the speed that is needed for time-sensitive clinical cases. In this paper we retrospectively study a clinical variant in the XIAP protein, C203Y, while addressing additional variants seen in patients with similar gastrointestinal phenotypes as the C203Y mutation. In agreement with the clinical tests performed on the C203Y patient, protein modeling and molecular dynamics suggest that direct interactions with RIPK2 and Caspase3 are altered by the C203Y mutation and subsequent loss of Zn coordination in the second BIR domain of XIAP. Interestingly, the variant does not appear to alter interactions with SMAC, resulting in further damage to the caspase and NOD2 pathways. To expand the computational strategy designed when studying XIAP, we have applied the molecular modeling tools to a list of 140 variants seen in CFTR associated with cystic fibrosis, and a list of undiagnosed variants in 17 different genes. This paper shows the exciting applications of molecular modeling in the classification and characterization of genetic variants identified in next generation sequencing. [ABSTRACT FROM AUTHOR]

The original version of this article unfortunately contained mistakes. Table 1 was missing and the presentation of Table 2 was incorrect. In Table 2, the second [λexp (nm)] and last [MADa] columns, many values are wrongly in the same cell/line. For example, in column 2, line 2, the first number (342) should be above the other (318). [ABSTRACT FROM AUTHOR]

Understanding to the pressure-driven desorption of methane in shale formations is crucial for the establishment of predictive models used in shale gas development. Based on the grand canonical Monte-Carlo simulations of methane adsorption in illite slits of 1–5-nm wide, the pressure-driven desorption processes of methane in the nanoslits are studied with non-equilibrium molecular dynamics simulations. External forces are applied to the methane molecules to mimic a pressure drop that releases the adsorbed molecules and pushes them flowing directionally. Effect of pressure drop and slit aperture on the interchange between adsorbed and free phases of methane is investigated by a statistic analysis on the velocity and density distributions of methane molecules in the nanoslits under various conditions. A minimum pressure drop that initiates the methane desorption in the illite slit exists and varies with slit aperture. Our simulations reveal the microscopic mechanism of pressure-driven methane desorption, which would be useful for subsequent studies on the prediction of mineable yields for shale formations. [ABSTRACT FROM AUTHOR]

We report a protocol for the evaluation of theoretical half-wave potential (E1/2) using a set of 22 mixed chelate copper (II) complexes containing 1,10-phenanthroline and 2,2′-bipyridine derivatives as primary ligands, and acetylacetonate or glycinate as secondary ligands (formally from the Casiopeínas® family) for which accurate experimental values were determined in a 2/5 mixture of ethanol/water. We have calibrated the BP86, PBE, PBE0, B3LYP, M06-2X, and ω-B97XD functionals, using the Los Alamos LANL2DZ and Stuttgart-Köln SDDAll effective core potentials for the Cu and Fe atoms and the 6-311+G* basis set for the C, H, O, and N atoms. To address the solvent effects, we have saturated the first solvation shell with up to 9 water molecules for the explicit model and compared it with the Continuum Like-Polarizable Continuum Model (CPCM) implicit solvent scheme. We found that the PBE/LANL2DZ-6-311+G* protocol (with the CPCM implicit solvent scheme with an effective dielectric constant ε = 64.9121 for the 2/5 mixture of ethanol/water) yields the overall best performance. The theoretical values are compared with experimental data, three of which are reported here for the first time. We find good correlations between the theoretical and experimental E1/2 values for the 2,2′-bipyridine derivatives (R2 = 0.987, MAE = 86 mV) and 1,10-phenanthroline derivatives (R2 = 0.802, MAE = 58.4 mV). The correlation trends have been explained in terms of the copper atom's ability to be reduced in the presence of the ligands. The Gibbs free energy differences at 298 K obtained for the redox reactions show that the more flexible secondary ligands (acetylacetonate) lead to larger entropic contributions which, as expected, increase the average MAE values as compared with the more rigid ligands (glycine). The present protocol yields lower MAEs as compared with previous approaches for similar mixed and flexible Cu(II) complexes. [ABSTRACT FROM AUTHOR]

Detailed electrostatic potential (ESP) analyses were performed to compare the directionality of halogen bonds with those of hydrogen bonds and lithium bonds. To do this, the interactions of HOOOH with the molecules XF (X = Cl, Br, H, Li) were investigated. For each molecule, the percentage of the van der Waals (vdW) molecular surface that intersected with the ESP surface was used to roughly quantify the directionality of the halogen/hydrogen/lithium bond associated with the molecule. The size of the region of intersection was found to increase in the following order: ClF < BrF < HF < LiF. The maximum ESP in the region of intersection, V, was observed to become more positive according to the sequence ClF < BrF < HF < LiF. For ClF and BrF, the positive electrostatic potential was concentrated in a very small region of the vdW molecular surface. On the other hand, for HF and LiF, the positive electrostatic potential was more diffusely scattered across the vdW surface than for ClF and BrF. Also, the optimized geometries of the dipolymers HOOOH··· XF (X = Cl, Br, H, Li) indicated that halogen bonds are more directional than hydrogen bonds and lithium bonds, consistent with the results of ESP analyses. [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Rising mortality due to cancer has led to the development and identification of newer targets and molecules to cure the disease. Telomerase is one of the attractive targets for design of many chemotherapeutic drugs. This research highlights the designing of novel telomerase inhibitors using ligand-based (3D-QSAR) and structure-based (molecular docking and molecular dynamics simulation) approaches. For the development of the 3D-QSAR model, 37 synthetic molecules reported earlier as telomerase inhibitors were selected from diversified literature. Three different alignment methods were explored; among them, distill alignment was found to be the best method with good statistical results and was used for the generation of QSAR model. Statistically significant CoMSIA model with a correlation coefficient (r2ncv) value of 0.974, leave one out (q2) value of 0.662 and predicted correlation coefficient (r2pred) value of 0.560 was used for the analysis of QSAR. For the MDS study, A-chain of telomerase was stabilised for 50 ns with respect to 1-atm pressure, with an average temperature of 299.98 k and with potential energy of 1,145,336 kJ/m converged in 997 steps. Furthermore, the behaviour study of variants towards the target revealed that active variable gave better affinity without affecting amino acid sequences and dimensions of protein which was accomplished through RMSD, RMSF and Rg analysis. Results of molecular docking study supported the outcomes of QSAR contour maps as ligand showed similar interactions with surrounded amino acids which were identified in contour map analysis. The results of the comprehensive study might be proved valuable for the development of potent telomerase inhibitors. [ABSTRACT FROM AUTHOR]

Quercetin is the most abundant flavonoid with potent antioxidant activities. In the current research, the antioxidant properties of quercetin and quercetin-DNA complex were investigated theoretically and experimentally. Free radical scavenging experiments with thiobarbituric acid–reactive substances (TBARS) and 1,1-diphenyl-2-trinitrophenylhydrazine (DPPH) indicate that quercetin can protect DNA from free radical damage, and the antioxidant activity of the quercetin-DNA complex is stronger than quercetin. Deoxyriboseadenine-quercetin-dimethylphosphinic acid (DA-Q-P) model was extracted from molecular docking. The contributions of hydroxyl groups in quercetin and DA-Q-P model molecules to the antioxidant activity were investigated by computation of bond dissociation enthalpy (BDE) parameter and Fukui function, at B3LYP/6-311++G(2d,2p) level of theory. The results outlined that the hydroxyl groups from the B ring (3′-OH and 4′-OH) have a lower BDE compared with the ones from the A and C rings (3-OH, 5-OH, and 7-OH) and hence define antioxidant activity. The computational result based on Fukui function shows that the B ring is an electrophilic region. The interaction of antioxidant with DNA discovered at the molecular level could provide the structural basis of the antioxidant property of active ingredients in the flavonoids. It is of great significance to study the interaction mechanism between the small drug molecules with DNA at the molecular level. [ABSTRACT FROM AUTHOR]

Natural hIFNγ is a glycoprotein with two N-glycosylation sites in each monomer chain, which are independently and differentially glycosylated. Although glycosylation is not necessary for the activity of the cytokine, it was proposed that it protects the cytokine from proteolytic degradation and thus extends its circulatory half-life. Here, we report the development of model structures of glycosylated full-length native hIFNγ homodimers. Our aim is to shed light on the mechanism through which glycosylation preserves the integrity of the cytokine molecule. To this end, we employ molecular dynamics simulations to study the interaction of the carbohydrate chains with the receptor-binding sites in the cytokine and with its flexible highly positively charged C-termini. The glycans interact primarily with the globular part of the protein, but also occasionally form contacts with the solvent-exposed and sensitive to proteases C-terminal tails. We show that the glycans restrict the C-termini wagging motion into the solvent, limit their flexibility and keep them closer to the α-helical globule of hIFNγ, thus possibly protecting them from proteolytic processing. [ABSTRACT FROM AUTHOR]

Molecular modeling of ferroelectric composites containing polyvinylidene fluoride (PVDF) and either graphene (G) or graphene oxide (GO) were performed using the semi-empirical quantum approximation PM3 in HyperChem. The piezo properties of the composites were analyzed and compared with experimental data obtained for P(VDF-TrFE)-GO films. Qualitative agreement was obtained between the results of the modeling and the experimental results in terms of the properties of the measured effective piezoelectric coefficient d and its decrease in the presence of G/GO in comparison with the average computed piezoelectric coefficient < d >. When models incorporating one or several G layers with 54 carbon atoms were investigated, the average piezoelectric coefficient < d > was found to decrease to −9.8 pm/V for the one-sided model PVDF/G and to −18.98 pm/V for the sandwich model G/PVDF/G as compared with the calculated piezoelectric coefficient for pure PVDF (< d > = −42.2 pm/V computed in present work, and = −38.5 pm/V, obtained from J Mol Model 35 (2013) 19:3591-3602). When models incorporating one or several GO layers with 98 carbon atoms were considered, the piezoelectric coefficient was found to decrease to −14.6 pm/V for the one-sided PVDF/GO model and to −29.8 pm/V for the sandwich GO/PVDF/GO model as compared with the same calculated piezoelectric coefficient for pure PVDF. [ABSTRACT FROM AUTHOR]

The potential energy surfaces in gas phase and in aqueous solution for the nitration of benzene, chlorobenzene, and phenol have been elucidated with density functional theory at the M06-2X/6-311G(d,p) level combined with the polarizable continuum solvent model (PCM). Three reaction intermediates have been identified along both surfaces: the unoriented π-complex (I), the oriented reaction complex (II), and the σ-complex (III). In order to obtain quantitatively reliable results for positional selectivity and for modeling the expulsion of the proton, it is crucial to take solvent effects into consideration. The results are in agreement with Olah's conclusion from over 40 years ago that the transition state leading to (II) is the rate-determining step in activated cases, while it is the one leading to (III) for deactivated cases. The simplified reactivity approach of using the free energy for the formation of (III) as a model of the rate-determining transition state has previously been shown to be very successful for halogenations, but problematic for nitrations. These observations are rationalized with the geometric and energetic resemblance, and lack of resemblance respectively, between (III) and the corresponding rate determining transition state. At this level of theory, neither the σ-complex (III) nor the reaction complex (II) can be used to accurately model the rate-determining transition state for nitrations. [ABSTRACT FROM AUTHOR]

Correlated ab initio methods [CASPT2 and R-CCSD(T)] in conjunction with the ANO-RCC basis sets in large contraction were used to calculate potential energy curves (PECs) of the ground and excited electronic states of CsH (doublets and quartets) with the inclusion of the scalar relativistic effects and spin-orbit interaction. The ground XΣ state is a rather fragile van der Waals molecular ion. The binding energy of this XΣ state provided by both computational methods is estimated to be 0.02-0.04 eV, and is compared with the reported experimental binding energy (0.51-0.77 eV). This large binding energy can be attributed to the AΣ state, and can thus explain the apparent disagreement between theory and experiment. The spectroscopic constants of all bound states were calculated from the PECs and compared with previous published data for XΣ and AΣ states. [ABSTRACT FROM AUTHOR]

In this work, the dual-descriptor is studied in matrix form $f^{(2)}(\mathbf {r},\mathbf {r^{\prime }})$ and both coordinates condensed to atoms, resulting in atomic and diatomic (or where applicable, bond) condensed single values. This double partitioning method of the dual-descriptor matrix is proposed within the Hirshfeld-I atoms-in-molecule framework although it is easily extended to other atoms-in-molecules methods. Diagonalizing the resulting atomic and bond dual-descriptor matrices gives eigenvalues and eigenvectors describing the reactivity of atoms and bonds. The dual-descriptor function is the diagonal element of the underlying matrix. The extra information contained in the atom and bond resolution is highlighted and the effect of choosing either the fragment of molecular response or response of molecular fragment approach is quantified. [ABSTRACT FROM AUTHOR]

The quantitative structure-property relationship (QSPR) methodology was applied to describe and seek the relationship between the structures and energetic properties (and sensitivity) for some common energy compounds. An extended series of structural and energetic descriptors was obtained with density functional theory (DFT) B3LYP and semi-empirical PM3 approaches. Results indicate that QSPR model constructed using quantum descriptors can be applied to verify the confidence of calculation results compared with experimental data. It can be extended to predict the properties of similar compounds. [ABSTRACT FROM AUTHOR]

Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some of the cardiovascular disorders related to cathepsin S. A highly selective inhibitor of human as well as animal cathepsin S, RO5444101, was recently reported to attenuate the progression of atherosclerotic lesions. Here, we attempted to gain insight into the molecular mechanism of action of RO5444101 on cathepsin S by performing molecular docking and molecular dynamics (MD) simulation studies. The results of our studies correlate well with relevant reported experimental data and potentially explain the selectivity of this inhibitor for cathepsin S rather than cathepsin L1/L, cathepsin L2/V, and cathepsin K, which share conserved catalytic sites and have sequence similarities of 49%, 50%, and 55%, respectively, with respect to cathepsin S. In contrast to those closely related cathepsins, 20 ns MD simulation data reveal that the overall interaction of cathepsin S with RO5444101 is more stable and involves more protein-molecule interactions than the interactions of the inhibitor with the other cathepsins. This study therefore considerably improves our understanding of the molecular mechanism responsible for cathepsin S inhibition and facilitates the identification of potential novel selective inhibitors of cathepsin S. [ABSTRACT FROM AUTHOR]

Leishmaniasis is a tropical neglected disease that imposes major health concerns in many endemic countries worldwide and requires urgent attention to the identification of new drug targets as well as drug candidates. In the current study, we propose homoserine kinase (HSK) inhibition as a strategy to induce pathogen mortality via generating threonine deficiency. We introduce a homology-based molecular model of leishmanial HSK that appears to possess all conserved structural as well as functional features in the GHMP kinase family. Furthermore, 200 ns molecular dynamics data of the enzyme in open and closed state attempts to provide the mechanistic details involved in the substrate as well as phosphate binding to this enzyme. We discuss the structural and functional significance of movements involved in various loops (motif 1, 2, 3) and lips (upper and lower) in the transition of leishmanial HSK from closed to open state. Virtual screening data of more than 40,000 compounds from the present investigation tries to identify a few potential HSK inhibitors that possess important features to act as efficient HSK inhibitors. These compounds can be considered an effective starting point for the identification of novel drug-like scaffolds. We hope the structural wealth that is offered in this report will be utilized in designing competent experimental and therapeutic interventions for leishmaniasis management. [ABSTRACT FROM AUTHOR]

Vitrinite in coal, the mainly generating methane maceral, plays an important role in hydrocarbon generation of coal. This study aims at obtaining products formation mechanism of vitrinite pyrolysis, and hence determining the chemical bond, molecular liquefaction activity, and reactions mechanism of methane and C during pyrolysis. The ReaxFF molecular dynamics (MD) simulation was carried out at temperature of 1500 K in order to investigate the mechanism of vitrinite pyrolysis. Initially, a minimum energy conformational structure model was constrained by a combination of elemental and carbon-13 nuclear magnetic resonance (C NMR) literature data. The model analysis shows the chemical and physical parameters of vitrinite pyrolysis are broadly consistent with the experimental data. Based on the molecular model, ReaxFF MD simulations further provide information of unimolecule such as bond length, and chemical shift, and hence the total population and energy of main products. Molecules bond and pyrolysis fragments, based on active bond analyzed, revealed pyrolysis products of single vitrinite molecule with aliphatic C-C bond, especially ring and chain aliphatic as liquefaction activity. The molecular cell whose density is 0.9 g/cm with lowest energy accords with the experimental density 1.33 g/cm. The content of main products after pyrolysis, classifying as CH, HO, and H, was changed along with the increasing temperature. The gas molecule, fragments and generation pathways of CO, H, CH, and CH were also elucidated. These results show agreement with experimental observations, implying that MD simulation can provide reasonable explanation for the reaction processes involved in coal vitrinite pyrolysis. Thus the mechanism of coal hydrocarbon generation was revealed at the molecular level. [ABSTRACT FROM AUTHOR]

The structure and properties of diphenylalanine (FF) peptide nanotubes (PNT) based on phenylalanine were investigated by various molecular modeling methods. The main approach employed semi-empirical quantum-chemical methods (PM3 and AM1). Ab initio, density functional theory methods and molecular mechanical approaches were also used. Both model structures and structures extracted from experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by natural self-assembly revealed important differences depending on chirality: d and l. In both the cases, the effect of chirality on the results of self-assembly of FF PNT was established: PNT based on the d-FF has large condensation energy E0 in the transverse direction, and form thicker and shorter PNT bundles than those based on l-FF. A topological difference was established: model PNT were optimized into structures consisting of rings, while naturally self-assembled PNT consisted of helical turns. The latter nanotubes differed from the original l-FF and d-FF and formed helix structures of different chirality signs in accordance with the alternation rule of chirality due to macromolecule hierarchy. A topological transition between ring and helix turn PNT structures is discussed: self-assembled natural helix structures are favorable and their energy is lower by a value of the order of one to several eV. [ABSTRACT FROM AUTHOR]

We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force field (GAFF). For the latter, comparison to quantum chemical calculations shows significant errors in terms of complex structure and formation energy. This is corrected by the newly created force field that is commensurate with GAFF but uses tailor-made ion-ligand van der Waals parameters. On this basis, we elucidate the association of additives with oil-hematite interfaces from molecular dynamics simulations. [ABSTRACT FROM AUTHOR]

Antimicrobial peptides (AMPs) are best known for their bactericidal properties; however, due to their unique and flexible structures, they have also been proposed as potential selective sorbents for specific molecules. In the present study, we aimed to design and produce a new peptide-based microextraction fiber for preconcentrating morphine in urine samples. The binding of morphine to the peptide was first evaluated by computational simulation using the Molecular Operating Environment (MOE) 2015.10 software. A similar study was then performed using DS BIOVIA Materials Studio 2017 v17.1.0.48, which confirmed the results of the simulation carried out with MOE. Afterwards, those results were also confirmed by experimental research. In the experimental evaluation, carbon nanotubes (CNTs) were initially carboxylated with H2SO4/HNO3 (3:1) and then functionalized with the peptide. FTIR analysis, Raman measurements, and SEM imaging were used to confirm that CNT functionalization was successful as well as to check the nanostructure of the fiber. To evaluate the functionality of the fiber, it was inserted into a microtube containing a urine sample that included morphine and then sonicated for 5 min at 40 °C. Afterwards, the fiber was washed with methanol 20% (H2O/methanol) and the resulting sample was analyzed by HPLC. This procedure was repeated for different concentrations of morphine in the urine sample. The computational and experimental results showed that a morphine concentration as low as 0.25 ppb in urine could be adsorbed and detected using the peptide fiber. Therefore, given its semi-selective binding affinity for morphine, this peptide-based fiber can be considered a new approach to the detection of small amounts of morphine in biological samples. [ABSTRACT FROM AUTHOR]

Calculations were done by applying the B3LYP/6-31++G(d) method on the zwitterionic l-diglycine and l-dialanine to study the solvent effects on their structures and vibrational features. Three models of solvation (implicit, explicit, and explicit in implicit) were used and the subsequent resulting values compared. Even though both dipeptides surrounded by 12 water molecules seem sufficient to stabilize their zwitterionic characters, notably to avoid the proton transfer between the backbone (N H $_{3}^{+}$, COO ) groups, the hybrid model of solvation (explicit in implicit noted 12W/Continuum) appears to be in better agreement with available IR and Raman experiments than explicit and implicit models. The harmonic vibrational modes derived from geometry optimization of l-diglycine and l-dialanine in 12W/Continuum, agree with the available IR and Raman experimental values within 1 % for l-diglycine and 2 % for l-dialanine, and they appear more accurate than those found using the explicit model (12W). [Figure not available: see fulltext.] [ABSTRACT FROM AUTHOR]

Context: Ultrathin overlays are preventive maintenance measures; the tensile and shear stresses generated inside a structural layer under vehicle load are greater than those of conventional thickness asphalt pavement. Therefore, asphalt binders must use high-viscosity and elasticity unique cementing materials to ensure stability. To investigate the modification mechanism of styrene–butadiene–styrene (SBS)/ethylene-butyl acrylate-glycidyl methacrylate copolymer (PTW) high-viscosity modified asphalt binder suitable for ultrathin overlays, the compatibility and molecular behavior of SBS/PTW high-viscosity modified asphalt binder were analyzed by the molecular dynamics (MD) method. These research results provide a reference for preparing ultrathin overlay high-performance composite modified asphalt binder. Methods: SBS molecular models, PTW molecular models, asphalt binder molecular models, SBS/asphalt binder blend systems, and SBS/PTW/asphalt binder blend systems were sequentially constructed using Materials Studio (MS) software. The compatibility of SBS, PTW, and SBS/PTW with asphalt binder and the diffusion coefficients of SBS, PTW, and SBS/PTW in the asphalt binder were investigated separately using the MD method. The mechanical properties and molecular behavior of SBS, PTW, and SBS/PTW blended with asphalt binder were studied. The research results indicate that the compatibility of PTW with asphalt binder is better than that of SBS with asphalt binder. PTW can effectively decrease the solubility parameter of asphalt binder and improve the compatibility between SBS and asphalt binder. PTW effectively improves the diffusion coefficient and interaction energy of SBS in asphalt binder by up to 29% and 83%. In addition, SBS/PTW had a significant positive effect on the mechanical properties of the asphalt binders, increasing the elastic modulus (E), bulk modulus (K), and shear modulus (G) of the asphalt binder by 4.6%, 9.5%, and 3.5%, respectively, compared to SBS. The results indicate that the SBS/PTW modified asphalt binder composite can significantly improve the high-temperature shear resistance of asphalt binder. Meanwhile, SBS and PTW improve the self-aggregation behavior between asphalt binder component molecules. The distance between the center of mass of asphalt binder and resin system molecules is increased. PTW enhances the extensibility of the branched chains of asphalt binder component molecules and improves the interaction between asphalt binder components and the chains. This further enhances the density and stability of the asphalt binder molecular structure system, improving the physical properties of the asphalt binder. [ABSTRACT FROM AUTHOR]

DYRK1B protein kinase is an emerging anticancer target due to its overexpression in a variety of cancers and its role in cancer chemoresistance through maintaining cancer cells in the G0 (quiescent) state. Consequently, there is a growing interest in the development of potent and selective DYRK1B inhibitors for anticancer therapy. One of the major off-targets is another protein kinase, GSK3β, which phosphorylates an important regulator of cell cycle progression on the same residue as DYRK1B and is involved in multiple signaling pathways. In the current work, we performed a detailed comparative structural analysis of DYRK1B and GSK3β ATP-binding sites and identified key regions responsible for selectivity. As the crystal structure of DYRK1B has never been reported, we built and optimized a homology model by comparative modeling and metadynamics simulations. Calculation of interaction energies between docked ligands in the ATP-binding sites of both kinases allowed us to pinpoint key residues responsible for potency and selectivity. Specifically, the role of the gatekeeper residues in DYRK1B and GSK3β is discussed in detail, and two other residues are identified as key to selectivity of DYRK1B inhibition versus GSK3β. The analysis presented in this work was used to support the design of potent and selective azaindole-quinoline-based DYRK1B inhibitors and can facilitate development of more selective inhibitors for DYRK kinases. [ABSTRACT FROM AUTHOR]

Context: The use of Molecular Dynamics (MD) simulations to examine the mechanical characteristics of polymer composites reinforced with calcium carbonate (CaCO3) and graphene (GR) is represented in this work. The effects of CaCO3 and GR nanoadditives in polylactic acid (PLA) matrix in different concentrations were evaluated using the results of MD simulations. Experimental analyses have been conducted to validate the results of MD based on the mechanical properties of fabricated nanocomposites, including modulus of elasticity, shear modulus, and Poisson's ratio. The modeling, computation, and analysis of several simulations on the improved mechanical characteristics of PLA/CaCO3 and PLA/GR nanocomposites are introduced and discussed. The results revealed that the addition of GR nanoparticles were more effective in enhancing the mechanical properties of PLA components as compared with that of CaCO3 nanoparticles, as the modulus of elasticity, shear modulus and Poisson's ratio increased by approximately 21%, 17%, and 16% for addition of 3 wt% GR nanoparticles in the PLA matrix, respectively. Methods: The mechanical behavior of PLA/CaCO3 and PLA/GR nanocomposites have been simulated based on the molecular dynamic technique using material studio (MS) that enabled the analyses of synergy between the polymer molecules and the nanoparticles. Molecular models for a system of nanocomposites were built by embedding the nano-clusters into an amorphous PLA matrix. Nanoparticles have been modeled as spherical nanoclusters of graphite and calcite unit cells. Molecular models of the pure PLA matrix were also developed for comparison. The relaxed systems of MD simulations have been carried out to calculate the mechanical properties of nanocomposites containing 1, 3 and 5 wt% nanofiller contents. To validate the results of the simulations, the PLA/CaCO3 and PLA/GR nanocomposite granules, containing different weight ratios of the nanofillers in the matrix, have been synthesized by melt-blending technique. These granules have been used to produce tensile test samples by injection molding technique, with different fractions of nanoparticles in the matrix, to study the effects of such nanoadditives on the mechanical properties of the PLA nanocomposites. [ABSTRACT FROM AUTHOR]

A sphere-in-contact model is presented that is used to build physical models of carbon materials such as graphite, graphene, carbon nanotubes and fullerene. Unlike other molecular models, these models have correct scale and proportions because the carbon atoms are represented by their atomic radius, in contrast to the more commonly used space-fill models, where carbon atoms are represented by their van der Waals radii. Based on a survey taken among 65 undergraduate chemistry students and 28 PhD/postdoctoral students with a background in molecular modeling, we found misconceptions arising from incorrect visualization of the size and location of the electron density located in carbon materials. Based on analysis of the survey and on a conceptual basis we show that the sphere-in-contact model provides an improved molecular representation of the electron density of carbon materials compared to other molecular models commonly used in science textbooks (i.e., wire-frame, ball-and-stick, space-fill). We therefore suggest that its use in chemistry textbooks along with the ball-and-stick model would significantly enhance the visualization of molecular structures according to their electron density. [ABSTRACT FROM AUTHOR]

While canonical molecular orbitals have been used in computational chemistry for almost a century, the use of localized molecular orbitals is relatively new, and generating them has been difficult until recently. This has impeded their routine use in modeling chemical systems and reactions so that, even though localized molecular orbitals can now be generated easily, their usefulness in interpreting chemical phenomena has not been properly appreciated. Localized molecular orbitals can provide useful insights into chemical phenomena such as two-electron bonds, π delocalization, and lone pairs. A potentially important application would be interpreting the phenomena that occur in chemical reactions, in particular those reactions which can be described using the Lewis curly-arrow electron pushing convention. This paper considers how canonical and localized molecular orbitals are generated, their usefulness and limitations, and some issues that could be considered controversial regarding their nature, and it presents examples of the usefulness of LMOs in describing six chemical systems and one reaction. [ABSTRACT FROM AUTHOR]

Context: Graphene has been used as reinforcement of polymeric nanocomposites to increase mechanical and electrical properties. Recently, graphene suspensions have been used for the development of nanofluids in automotive applications, where improvements in convection heat transfer coefficients and pressure drops have been reported. However, dispersions of graphene sheets in a polymeric matrix as well as in a solvent medium are difficult to achieve; that is because Van der Waals, π - π and Coulombic interactions cause agglomerations. Surface chemical modifications have been considered as viable options to improve the graphene integration. In this work, we studied the colloidal stability of aqueous solutions of graphene sheets functionalized with (i) carboxylic groups, (ii) 3-amino-propyl tri-ethoxy silane (amphiphilic behavior), (iii) graphene oxide, and (iv) pristine graphene. Results show that the lower sedimentation velocity corresponds to the graphene functionalized with carboxylic groups, which presents the higher colloidal stability. However, the amphiphilic group enhances the interaction energy between graphene and the solvent; we believe that there is a threshold percentage of functionalization that improves the colloidal stability of graphene. Method: Transport properties of graphene solutions were estimated by using Non-Equilibrium Molecular Dynamics simulations to generate Poiseuille flow in an NVT ensemble. Simulations were developed in the LAMMPS code. The COMPASS Force Field was used for the graphene systems and the TIP3P for the water molecules. Bonds and angles of hydrogen atoms were kept rigid by using the shake algorithm. The molecular models were built through MedeA and visualized with the Ovito software. [ABSTRACT FROM AUTHOR]

In this research, we present a preliminary computational study of four Dermaseptin-related peptides from the skin exudate of the gliding tree frog Agalychnis spurrelli. Experimentally, the amino acid sequence of these peptides was elucidated through molecular cloning and tandem mass spectrometry and synthetic peptides were assayed against E. coli, S. aureus, and C. albicans to determine their antimicrobial properties. With the sequences on hand, a computational study of the structures was carried out, obtaining their physicochemical properties, secondary structure, and their similarity to other known peptides. A molecular docking study of these peptides was also performed against cell membrane and several enzymes are known to be vital for the organisms. Results showed that Dermaseptin-related peptides are α-helical cationic peptides with an isoelectric point above 9.70 and a positive charge of physiological pH. Introducing theses peptides in a database, it was determined that their identity compared with known peptides range from 36 to 82% meaning these four Dermaseptins are novel peptides. This preliminary study of molecular docking suggests the mechanism of action of this peptide is not given by the inhibition of essential enzymatic pathways, but by cell lysis. [ABSTRACT FROM AUTHOR]

Menthol is an often used skin penetration enhancer because of its high efficiency and relative safety, but the mechanism how it works has not been fully understood up to date. In this study, quercetin was used as a model molecule to investigate the permeability enhancement of menthol through skin lipids. The skin is modeled as a ceramide (CER2) bilayer. Potential of mean force (PMF) calculations on quercetin in both CER2 and menthol-involved CER2 bilayers have been performed. The results show that the free energy minimum of quercetin in the presence of menthol molecules shifts toward the headgroup region of the bilayer, and the central energy barrier decreases, facilitating the penetration of quercetin. The presence of menthol molecules enhances the permeability of quercetin. This study may shed light on the mechanism of penetration enhancer, providing useful information in the design of more efficient transdermal drug delivery system. [ABSTRACT FROM AUTHOR]

Chalcones have been reported to present biological activities that are potentialized when a sulfonamide group is attached. A comprehensive structural study was performed for arylsulfonamide chalcone N-(2-(3–4-methoxyphenyl-propanoyl)-phenyl)-benzene-sulfonamide in order to describe its supramolecular arrangement and its physicochemical properties. The molecular packing arrangement was described by X-ray diffraction and Hirshfeld surfaces (HS). Theoretical calculations were performed using density functional theory (DFT), molecular electrostatic potential (MEP) mapping, ab initio Car-Parrinelo molecular dynamics (CPMD) and the quantum theory of atoms in molecules (QTAIM). The solid-state arrangement is stabilized by C– H⋯O and C–H⋯π interactions observed on HS and MEP map. The topological analysis was evaluated by QTAIM. [ABSTRACT FROM AUTHOR]

Macrocyclic compounds are of growing interest as a new class of therapeutics, especially as inhibitors binding to protein–protein interfaces. As molecular modeling is a well-established complimentary tool in modern drug design, the number of attempts to develop reliable docking strategies and algorithms to accurately predict the binding mode of macrocycles is rising continuously. Standard molecular docking approaches need to be adapted to this application, as a comprehensive yet efficient sampling of all ring conformations of the macrocycle is necessary. To overcome this issue, we designed a molecular dynamics-based docking protocol for macrocycles, in which the challenging sampling step is addressed by conventional molecular dynamics (750 ns) simulations performed at moderately high temperature (370 K). Consecutive flexible docking with the DynaDock approach based on multiple, pre-sampled ring conformations yields highly accurate poses with ligand RMSD values lower than 1.8 Å. We further investigated the value of molecular dynamics-based complex stability estimations for pose selection and discuss its applicability in combination with standard binding free energy estimations for assessing the quality of poses in future blind docking studies. [ABSTRACT FROM AUTHOR]

Atomistic simulations have progressively attracted attention in the study of physical-chemical properties of innovative nanomaterials. GROMACS and LAMMPS are currently the most widespread open-source software for molecular dynamics simulations thanks to their good flexibility, numerous functionalities and responsive community support. Nevertheless, the very different formats adopted for input and output files are limiting the possibility to transfer GROMACS simulations to LAMMPS. In this article, we present GRO2LAM, a modular and open-source Python 2.7 code for rapidly translating input files and parameters from GROMACS to LAMMPS format. The robustness of the tool has been assessed by comparing the simulation results obtained by GROMACS and LAMMPS, after the format conversion by GRO2LAM. Specifically, three nanoscale configurations of interest in both engineering and biomedical fields are studied, namely a carbon nanotube, an iron oxide nanoparticle, and a protein immersed in water. In perspective, GRO2LAM may be the first step to achieve a full interoperability between molecular dynamics software. This would allow to easily exploit their complementary potentialities and post-processing functionalities. Moreover, GRO2LAM could facilitate the cross-check of simulation results, guaranteeing the reproducibility of molecular dynamics models and testing their robustness. [ABSTRACT FROM AUTHOR]

The treatment of bacterial infections is currently threatened by the emergence of pathogenic bacteria producing β-lactamase, which catalyzes the hydrolysis of β-lactams. Although the hydrolysis of the substrate nitrocefin by a metallo-β-lactamase, namely β-lactamase N1 from USA300 (a typical methicillin-resistant Staphylococcus aureus), has previously been reported in the literature, its mechanism remains elusive. Here, we show that molecular modeling and quantum-mechanical/molecular mechanics (QM/MM) calculations describing the complex of β-lactamase N1 with nitrocefin (the substrate of β-lactamase N1) can predict the catalytic mechanism of nitrocefin hydrolysis by β-lactamase N1. Molecular dynamics simulation shows that the catalytic reaction begins with hydrogen bond formation between Gln171 and a water molecule, which is thereby captured for nitrocefin hydrolysis by β-lactamase N1. In addition, the carboxyl group coordinates Zn2 in a chelating fashion. The binding energy decompositions suggest that Phe169 anchors nitrocefin by π-stacking interactions between the benzene rings. Specifically, Phe169 and Zn2 position the nitrocefin in specific orientations. The active site of β-lactamase N1 contains two residues (Gln171 and Phe169) that we expected to be crucial for guiding the nitrocefin hydrolysis reaction. Compelling evidence is provided that the mutants F169A and Q171A show lower enzymatic activity than the wild-type protein. On the basis of the QM/MM calculations, we propose that nitrocefin hydrolysis is initiated by the interaction between the oxygen atom of water and the C18 atom of nitrocefin, leading to the opening of the four-membered ring of nitrocefin and the formation of a substrate intermediate. In the next step, a hydrogen atom transfers from the nitrogen atom to the C11 atom of nitrocefin, resulting in the stable product. [ABSTRACT FROM AUTHOR]

The Eringen's nonlocal elasticity theory is employed to examine the free vibration of a rotating cantilever single-layer graphene sheet (SLGS) under low and high temperature conditions. The governing equations of motion and the related boundary conditions are obtained through Hamilton's principle based on the first-order shear deformation theory (FSDT) of nanoplates. The generalized differential quadrature method (GDQM) is utilized to solve the nondimensional equations of motion. The molecular dynamics (MD) simulation is conducted, and fundamental frequencies of the rotating cantilever square SLGS are computed using the fast Fourier transform (FFT). The comparison of MD and GDQM results leads to finding the appropriate value of the nonlocal parameter for the first time. As an interesting result, this value of the nonlocal parameter is independent of the angular velocity. Results indicate that increases in various parameters, such as the angular velocity, hub radius, nonlocal parameter, and temperature changes in low temperature conditions, leads the first and the second frequencies to increase. In addition, it can be seen that the influence of the hub radius or nonlocal parameters on frequencies cannot be ignored in high angular velocities. Moreover, it is not possible to neglect the angular velocity or nonlocal parameter in high hub radius. The results show that the influence of parameters such as setting angle or nonlocal parameter on the first and the second frequencies increases when some parameters increase, such as the angular velocity, hub radius or temperature change. [ABSTRACT FROM AUTHOR]

Context: Thermal aging significantly deteriorates the mechanical properties and service performance of epoxy resins used for the high-voltage bushing. Current studies on the thermal aging behavior of epoxy resins mainly focus on experimental observations. However, an in-depth understanding of the mechanism of thermal aging of epoxy resins requires the monitoring of structural evolution of epoxy resins during thermal aging at the molecular level. To thoroughly analyze the intrinsic factors affecting structural evolution and the effect of thermal aging on the mechanical properties of epoxy resin for high-voltage bushing, epoxy resin models with different crosslinking degrees were established and thermal aging treatments at various temperatures and time periods were carried out by molecular dynamics simulation. It was found that the tensile strength of the epoxy resin was enhanced with the increase of the crosslinking degree, which was related to the elevation of the proportion of C-N and O–H bonds in its structure. With the increase of thermal aging temperature, the tensile strength of the epoxy resin decreased, which was related to the formation of weak bonds. At the early stage of thermal aging and after a period of high-temperature thermal aging, the strength of epoxy resin significantly decreases. The thermal aging of the epoxy resin is accelerated under external loading. In addition, the crosslinking degree and curing agent also affect the thermal aging resistance of epoxy resins. The results of this study can provide guidance for predicting and improving the thermal aging resistance of epoxy resins. Methods: Materials Studio was used to construct molecular models and complete crosslinking reactions. DGEBA and 44DDS (or 33DDS) were mixed at a ratio of 2:1, followed by crosslinking reaction. During this process, the Nose method was used to control temperature, the Berendsen method was used to control pressure, and the polymer consistent force field (PCFF) was used to control the motion and force of atoms. Isobaric-isothermal ensemble (NPT ensemble) was used to heat up epoxy resin models to various thermal aging temperatures of 400 K, 500 K, 600 K and 700 K. The models were maintained at these temperatures for different thermal aging times of 100 ps, 200 ps, 300 ps, 400 ps, 500 ps, 600 ps, 700 ps and 800 ps. Afterwards, the models were cooled down to 300 K and subjected to uniaxial tensile testing at this temperature with a strain rate of 1 × 109 s−1. The structural configurations and stress-strain data during the tensile process were recorded. The flow stress of the material was derived by counting the average stress in the 20–50% strain interval. [ABSTRACT FROM AUTHOR]

Being monocyclic planar, benzene retains 6π Hückel aromatic backbone. However, for larger analogues, the repulsion between vicinal C-H bonds makes them nonplanar, as for [10]-annulene. Thus, on this basis, a planar 10-π-aromatic C10H10 is unreachable. A detailed structural comparison among the C3H3+, C4H42+, C5H5−, C6H6, C7H7+, C8H82+, C9H9−, and C10H10 systems supports that the repulsion between vicinal C-H bonds is the primary reason for the loss of planarity, despite the favorable aromatic electron count. In this respect, here we have discussed ten-membered monocyclic planar 10-π-aromatic, (CH)5(XH)5 {X = Si, Ge, Sn} systems, modeled by using DFT. From NBO analysis and the overall magnetic behavior it is shown that (CH)5(GeH)5, (CH)5(SnH)5 molecules are promising planar 10-π-aromatic system. Thus, such species represent plausible Hückel aromatic rings retaining a ten-membered backbone as discussed here, which may lead to the characterization of novel species expanding the chemistry of larger aromatic rings. We believe that the present study may open new avenues in the formation of 10-π-aromatic species.Molecular modeling in quest of a planar 10-membered 10-π-electron aromatic system [ABSTRACT FROM AUTHOR]

To identify ionic liquids (ILs) that could be used as solvents in isobutylene (IB) polymerization, the interactions between IB and eight different ILs based on the 1-butyl-3-methylimidazolium cation ([Bmim]+) were investigated using density functional theory (DFT). The anions in the ILs were chloride, hexafluorophosphate, tetrafluoroborate, bis[(trifluoromethyl)sulfonyl]imide, tetrachloroaluminate ([AlCl4]−), tetrachloroferrate, acetate, and trifluoroacetate. The interaction geometries were explained by changes in the total energy, intermolecular distances, Hirshfeld charges, and the electrostatic potential surface. The IL solvents were screened by comparing their interaction intensities with IB to the interaction intensities of reference ILs ([AlCl4]−-based ILs) with IB. The microscopic mechanism for IB dissolution was rationalized by invoking a previously reported microscopic mechanism for the dissolution of gases in ILs. Computation results revealed that hydrogen (H) bonding between C2-H on the imidazolium ring and the anions plays a key role in ion pair (IP) formation. The addition of IB leads to slight changes in the dominant interactions of the IP. IB molecules occupied cavities created by small angular rearrangements of the anions, just as CO2 does when it is dissolved in an IL. The limited total free space in the ILs and the much larger size of IB than CO2 were found to be responsible for the poor solubility of IB compared with that of CO2 in the ILs. [ABSTRACT FROM AUTHOR]

Context: Dopamine β -monooxygenase (D β M) is an essential enzyme in the organism that regioselectively converts dopamine into R-norepinephrine, the key step of the reaction, studied in this paper, is a hydrogen atom transfer (HAT) from dopamine to a superoxo complex on D β M, forming a hydroperoxo intermediate and dopamine radical. It was found that the formation of a hydrogen bond between dopamine and the D β M catalyst strengthens the substrate-enzyme interaction and facilitates the HAT which takes place selectively to give the desired enantiomeric form of the product. Six reactions leading to the hydroperoxo intermediate were analyzed in detail using theoretical and computational tools in order to identify the most probable reaction mechanism. The reaction force analysis has been used to demonstrate that the nature of the activation energy is mostly structural and largely due to the initial approach of species in order to get closer to each other to facilitate the hydrogen abstraction. On the other hand, the reaction electronic flux revealed that electronic activity driving the reactions is triggered by polarization effects and, in the most probable reaction among the six studied, it takes place in a concerted and non-spontaneous way. Chemical events driving the reaction have been identified and the energy absorbed or delivered by each one was quantified in detail., Methods: The dopamine and a computational model of the copper superoxo complex on D β M were optimized at B3LYP-D3(BJ)/6-311 G(d,p) level theory in the Gaussian 16 software package. Optimization and IRC calculations were performed in the gas phase and through the PCM solvation model to mimic the protein medium. Non-covalent interactions were plotted using the NCI-plot software., Competing Interests: Declarations. Conflict of interest: We declare that one of the co-authors (Dr. Alejandro Toro-Labbé) is an Editor of the journal for this Collection QUITEL 2023. We sent the cover letter to another Editor (Dr. Margot Paulino) to assume responsibility for overseeing peer review. This manuscript is part of a doctoral thesis prepared for completion of a graduate degree (Dr. Forero-Girón) at Pontificia Universidad Católica de Chile [99]., (© 2025. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Context: Polyimide (PI) and aramid, as functional polymer materials, have significant application prospects in special fields such as fire prevention and arc resistance. Blends of materials can not only improve the physical and chemical properties of a single material, but also save costs, so in order to improve the performance of polyimide, it is of great practical importance to study the properties of PI and aramid blends. Molecular dynamics simulation results showed that the two materials are compatible. The solubility parameters of PI tend to stabilize when the polymerization degree exceeded 10; aramid-1313 and aramid-1414 tend to stabilize at polymerization degrees of 10 and 15 or more, respectively. On this basis, the binding energy, diffusion coefficient, and mechanical properties of PI/aramid-1313 and PI/aramid-1414 blends with different mass ratios were analyzed. It was found that with the continuous increase of aramid content, the binding energy of the blends continue to improve, limiting the gas molecules diffusion ability. The mechanical properties of the materials also continue to improve. The simulation results provided in this paper can provide theoretical guidance for experiments on PI blends and shorten the research time and cost. Methods: To investigate the properties of PI and aramid blends, the PI/aramid composite system models were constructed using the Amorphous Cell module in Materials Studio software. Subsequently, molecular dynamics simulations of the PI/aramid composite system were performed using the Forcite module, while the interactions between atoms and molecules were described using the COMPASS II force field. [ABSTRACT FROM AUTHOR]

Context: Graphene oxide(GO) has been widely used in asphalt modification due to its excellent properties. To reveal the interaction effect between GO and asphalt materials, the microscopic behavior and molecular structure changes of asphalt and GO/asphalt were investigated by molecular dynamics (MD) simulations. Mean square displacement (MSD) results showed that GO significantly inhibited the diffusion of molecules of asphalt components. Radial distribution function (RDF) results that GO destroys the original sol-type structure of asphalt. Simultaneously, GO adsorbed resins at low-temperature, adsorbed asphaltenes at high-temperature, and dispersed as a dispersed phase in the light components. The concentration of the dispersed phase in the asphalt colloidal structure was increased and the mutual attraction was enhanced. This improves the deformation resistance at high temperature, but weakens the ductility at low temperatures. Methods: To investigate the mechanism of action of GO-modified asphalt, the asphalt model and the GO/asphalt composite system model were constructed using the Amorphous Cell module in Materials Studio 2020 software. Subsequently, molecular dynamics simulations of the GO/asphalt composite system were performed using the Forcite module, while the interactions between atoms and molecules were described using the COMPASS II force field. [ABSTRACT FROM AUTHOR]

Context: This research assesses the influence of polypropylene (PP) fibers, both homopolymer and hydroxylated (PPOH), on the tensile properties of calcium silicate hydrate (C-S-H) composites through molecular dynamics (MD) simulations. Our models explore C-S-H matrices integrated with PP and PPOH fibers at varying polymerization degrees. The results demonstrate that both PP and PPOH fibers significantly influence the tensile strength and Young's modulus of the composites. Notably, PPOH fibers contribute to more substantial mechanical enhancements than PP, attributed to the increased polarity and enhanced intermolecular interactions from the hydroxyl groups. The study reveals a nonlinear relationship between polymer additive content and mechanical performance, with optimal properties at a polymerization degree of 20. Additionally, stress-strain analysis indicates that PPOH composites exhibit superior ductility and fracture energy, particularly at polymerization degrees of 20, showing enhanced ultimate strain and fracture energy by up to 9.6% and 13.9%, respectively, compared to PP counterparts. These results highlight the crucial role of tailored polymer additive composition and chemical modifications in maximizing the mechanical efficacy of C-S-H-based materials, enhancing their durability and structural performance., Methods: All MD simulations were conducted using LAMMPS. The models employed a combination of Clayff and Cvff force fields. During the entire tensile simulation, the system was configured under the NPT ensemble at 300 K., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.)

Context: Levobunolol is a β-blocker drug prescribed for the control and prevention of cardiovascular events, such as individuals with cardiac arrhythmia or a history of myocardial infarction. Creating a levobunolol-specific molecularly imprinted polymer (MIP) allows for enhanced selectivity, efficient sample preparation, controlled drug delivery, and improved sensing and detection capabilities. In this sense, the aim of this study was to obtain through DFT calculations the synthesis protocol of a MIP for levobunolol testing different functional monomers (FMs), solvents, and cross-linker agents (CLAs). The analysis of structural and energetic data led to the identification of the optimal MIP synthesis parameters, which involves the use of (trifluoromethyl)-arylic acid (TFMAA) as the functional monomer, toluene and chloroform as the solvents, and pentaerythritol triacrylate (PETRA) as the cross-linking agent. This rational design offers valuable insights for experimentalists seeking to efficiently synthesize a MIP for this important β-blocker drug. Methods: DFT calculations were conducted using the B97D functional along with the Pople's split valence 6-31G(d,p) basis set, which includes polarization functions on all atoms (B97D/6-31G(d,p)). [ABSTRACT FROM AUTHOR]

Context To investigate the impact of moisture on gas adsorption in gas-fat coal, Shanxi gas-fat coal was chosen as the research subject. The Adsorption module within molecular simulation software was utilized to construct gas-fat coal models with moisture contents of 0%, 1.14%, 2.26%, and 3.72%. The results revealed that the isothermal adsorption curves of gas-fat coal under different moisture contents all followed the Langmuir adsorption curve (Type Ι), wherein the Langmuir volume of gas-fat coal was most sensitive to changes in moisture content within the range of 0 to 1.14%. A linear equation was found to better characterize the influence of moisture on gas content in Shanxi gas-fat coal, represented by the formula η = 1/(1 + 1.98078w), where, η represents the moisture impact coefficient; w is the moisture content; 1.98078 is the coefficient of moisture influence of Shanxi gasifier coal. Coupled with changes in the surface free energy of gas-fat coal, the pressure exerted a positive effect on the adsorption of gas on the coal surface, enhancing the adsorption space of methane within gas-fat coal. Methods Using Materials Studio software, the adsorption capacity and adsorption heat of methane were computed at various temperatures (323 K, 333 K, 343 K) and pressures (0.5–8 MPa). Furthermore, a comparative analysis was conducted to assess the applicability of classical linear equations, linear equations, power function equations, and exponential function equations in quantitatively characterizing the influence of moisture. [ABSTRACT FROM AUTHOR]

Context: The functionalization of graphene is the best way to improve its interfacial compatibility and dispersibility in polymer matrix to obtain high-performance composites. In this study, three nanocomposite models with different salt layer thicknesses were established and simulated by molecular dynamics method to understand the effect of oxygen-containing functional groups on the impermeability of epoxy coatings. Molecular dynamics (MD) simulation results show that the nanocomposites have better impermeability than pure epoxy resin. The thickness of salt solution affects the permeation rate of salt solution and the interfacial properties of nanocomposites. The salt solution molecules trapped in the coating are mainly concentrated at the interface between graphene and epoxy resin, which is the main reason for the decrease in interface properties of epoxy coating. Methods: In this paper, Material Studio 8.0 was used to construct nanocomposite models with different salt layer thicknesses (GO/SW7Å, GO/SW10Å, and GO/SW13Å), and MD simulations were performed using a large-scale atomic and molecular parallel simulator (LAMMPS). [ABSTRACT FROM AUTHOR]