Molecular dynamics simulations of the orientation properties of cytochrome <Emphasis Type="Italic">c</Emphasis> on the surface of single-walled carbon nanotubes

Electron transfer between cytochrome c (Cytc) and electrodes can be influenced greatly by the orientation of protein on the surface of the electrodes. In the present study, different initial orientations of Cytc on the surface of five types of single-walled carbon nanotubes (SWNTs), with different diameters and chirality, were constructed. Properties of the orientations of proteins on the surface of these tubes were first investigated through molecular dynamics simulations. It was shown that variations in SWNT diameter do not significantly affect the orientation; however, the chirality of the SWNTs is crucial to the orientation of the heme embedded in Cytc, and the orientation of the protein can consequently be influenced by the heme orientation. A new electron pathway between Cytc and SWNT, which hopefully benefits electron transfer efficiency, has also been proposed. This study promises to provide theoretical guidance for the rational design of bio-sensors or bio-fuel cells by using Cytc-decorated carbon nanotube electrodes.     

Examination of the quality of various force fields and solvation models for the equilibrium simulations of GA88 and GB88

Elucidating the relationship between sequence and conformation is essential for the understanding of functions of proteins. While sharing 88 % sequence identity and differing by only seven residues, GA88 and GB88 have completely different structures and serve as ideal systems for investigating the relationship between sequence and function. Benefiting from the continuous advancement of the computational ability of modern computers, molecular dynamics (MD) simulation is now playing an increasingly important role in the study of proteins. However, the reliability of MD simulations is limited by the accuracy of the force fields and solvent model approximations. In this work, several AMBER force fields (AMBER03, AMBER99SB, AMBER12SB, AMBER14SB, AMBER96) and solvent models (TIP3P, IGB5, IGB7, IGB8) have been employed in the simulations of GA88 and GB88. The statistical results from 19 simulations show that GA88 and GB88 both adopt more compact structures than the native structures. GB88 is more stable than GA88 regardless of the force fields and solvent models utilized. Most of the simulations overestimated the salt bridge interaction. The combination of AMBER14SB force field and IGB8 solvent model shows the best overall performance in the simulations of both GA88 and GB88. AMBER03 and AMBER12SB also yield reasonable results but only in the TIP3P explicit solvent model.     

Altered torquoselectivity of fluorine in the iron-tricarbonyl-mediated thermal ring opening of 3-fluorocyclobutene: a density-functional exploration

There are eight possible pathways for the iron-tricarbonyl-assisted thermal electrocyclic ring opening of fluorocyclobutene due to variations in the orientation of the binding of Fe(CO)₃ relative to the fluorine substituent (R₁ or R₂), stereoselectivity (conrotatory or disrotatory, i.e., C or D), and the torquoselectivity of fluorine (inward-facing or outward-facing, i.e., in or out). A density functional study revealed that the energetically favored pathway is R₁ Din. Not only is the D mode favored energetically, but the in configuration was observed to be the lowest-lying mode of R₁, despite the general tendency of fluorine substituents to prefer an out configuration. Data on the activation hardness and aromaticity indices such as BAC and HOMA lead to the same conclusion. However, the R₂ mode surprisingly shows no particular preference for either the Cout or the Dout pathway (i.e., the R₂ mode shows less stereoselectivity than R₁). This behavior occurs due to the influences of both the fluorine substituent and metal coordination. Also, the geminal bond orbitals σ(C–F) and σ*(C–F) appear to participate in ring opening, given the excellent correlation of ?BE with the activation barrier of the transition state.     

TD-M06-2X insights into the absorption and emission spectra of dichlorvos and its molecularly imprinted recognition by methacrylic acid

The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in methanol, water, and chloroform in the molecularly imprinted recognition were investigated systematically. The M06-2X results revealed that: 1) the hydroxyl groups in polar solvents such as methanol and water may markedly influence the weak interactions, and then alter the adsorption and emission spectra; 2) the electronic excitation in absorption spectra of dichlorvos is dominated by the configuration HOMO?→?LUMO, but in the most stable dichlorvos-MAA it becomes the ππ* excitation of HOMO?→?LUMO?+?1; 3) Mulliken charges reveal that dichlorvos almost dissociates to Cl^- and a cation in its S₁ excitation state; 4) the phosphorescence spectra of dichlorvos-MAA are relatively weak.

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Graphical Abstract The absorption and emission spectra of dichlorvos and the dichlorvos-MAA complex in the molecularly imprinted recognition of dichlorvos were investigated systematically in methanol, water, and chloroform as solvents.

     

Melt-phase behavior of collapsed PMMA/PVC chains revealed by multiscale simulations

Single- and double-chain models of three stereoregular polymers, iso- and syndiotactic poly(methyl methacrylate) and isotactic poly(vinyl chloride), were extensively simulated using systematic coarse-grained (CG) potentials. It was found that, in vacuum, all of these long chains collapse in a two-stage process from their fully extended configurations into coils, and the two chains in each double-chain model ultimately become intertwined. Strong intermolecular interactions were found to occur between two chains of the same polymer (“like pairs”), which helps to explain the high densities of single-component melts. However, the intermolecular interactions between two chains of different polymers (“unlike pairs”) were stronger than those in like pairs. The enthalpy of mixing for unlike pairs—obtained from their intermolecular interaction energies—was negative, indicating that the two binary blends considered here are homogeneous systems. Moreover, a more negative enthalpy of mixing is suggested to correlate with better miscibility. These results agree well with corresponding experimental and simulated results, once again validating the accuracy of CG potentials when they are used to explore structural and energetic properties. The local structure captured by the isolated long chains dictates the ability to elucidate melt-phase behavior. A scheme involving the preparation of bulk models with initially collapsed chains was proposed; such CG models could be widely used to rapidly screen pairs of polymers for specific applications.

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Graphical Abstract Melt phase behaviors dictated by isolated chains

     

Pharmacophore development and screening for discovery of potential inhibitors of ADAMTS-4 for osteoarthritis therapy

In the development of osteoarthritis, aggrecan degrades prior to cartilage destruction. Aggrecanase-1 (ADAMTS-4) is considered to be the major enzyme responsible for cleaving the Glu373–Ala374 bond in the interglobular domain of aggrecan in humans. Therefore, inhibitors of ADAMTS-4 have therapeutic potential in the treatment of osteoarthritis. In the present work, we developed a chemical feature based pharmacophore model of ADAMTS-4 inhibitors using the HipHop module within the Catalyst program package in order to elucidate the structure–activity relationship and to carry out in-silico screening. The Maybridge database was screened using Hypo1 as a 3D query, and the best-fit hits that followed Lipinski’s rule of five were subsequently screened to select the compounds. The hit compounds were then docked into the active site of ADAMTS-4, and interactions were visualized to determine the potential lead molecules. After subjecting all of the hits to various screening and filtering processes, 13 compounds were finally evaluated for their in vitro inhibitory activities. This study resulted in the identification of two lead compounds with potent inhibitory effects on ADAMTS-4 activity, with IC₅₀ values of 0.042 μM and 0.028 μM, respectively. These results provide insight into the pharmacophoric requirements for the development of more potent ADAMTS-4 inhibitors.

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Graphical Abstract The aggrecan-degrading metalloprotease ADAMTS-4 has been identified as a novel therapeutic target for osteoarthritis. In this work, we used HipHop-based pharmacophore modeling and virtual screening of the Maybridge database to identify novel ADAMTS-4 inhibitors. These novel lead compounds act as potent and specific inhibitors for the ADAMTS-4 enzyme and could have therapeutic potential in the treatment of OA

     

Exploring the cocrystallization potential of urea and benzamide

The cocrystallization landscape of benzamide and urea interacting with aliphatic and aromatic carboxylic acids was studied both experimentally and theoretically. Ten new cocrystals of benzamide were synthesized using an oriented samples approach via a fast dropped evaporation technique. Information about types of known bi-component cocrystals augmented with knowledge of simple binary eutectic mixtures was used for the analysis of virtual screening efficiency among 514 potential pairs involving aromatic carboxylic acids interacting with urea or benzamide. Quantification of intermolecular interaction was achieved by estimating the excess thermodynamic functions of binary liquid mixtures under supercooled conditions within a COSMO-RS framework. The smoothed histograms suggest that slightly more potential pairs of benzamide are characterized in the attractive region compared to urea. Finally, it is emphasized that prediction of cocrystals of urea is fairly direct, while it remains ambiguous for benzamide paired with carboxylic acids. The two known simple eutectics of urea are found within the first two quartiles defined by excess thermodynamic functions, and all known cocrystals are outside of this range belonging to the third or fourth quartile. On the contrary, such a simple separation of positive and negative cases of benzamide miscibility in the solid state is not observed. The difference in properties between urea and benzamide R2,2(8) heterosynthons is also documented by alterations of substituent effects. Intermolecular interactions of urea with para substituted benzoic acid analogues are stronger compared to those of benzamide. Also, the amount of charge transfer from amide to aromatic carboxylic acid and vice versa is more pronounced for urea. However, in both cases, the greater the electron withdrawing character of the substituent, the higher the binding energy, and the stronger the supermolecule polarization via the charge transfer mechanism.