Theoretical Studies on Mechanisms of Cycloaddition Reaction between Dichlorovinylidene and Formaldehyde: Concerted and Stepwise?

The mechanism of cycloaddition reaction between singlet dichlorovinylidene (R1) and formaldehyde (R2) has been investigated with MP2 and B3LYP /6-31G* methods, including geometry optimization, vibrational analysis, and energy for the involved stationary points on the potential energy surface. Energies from both methods are also further corrected by CCSD(T)/6-31G* single-point calculations. Although the relative energies do differ especially for the loose conformations such as transition states and intermediates, generally the geometries predicted by MP2 and B3LYP are in good agreement. CCSD(T) relative energies for the stationary points predicted by MP2 and B3LYP agree quite well, and they are more comparative to those from B3LYP than those from MP2. The results also show that both three-centered and [2+2] cycloadditions can happen in concerted pathways. The former leads to a stable three-membered ring product (P1), while the two intermediates (INT1c and INT1d) from the latter are not so stable and will rearrange into either P1 or a more stable four-membered ring product (P2). The orbital interactions are also discussed for the leading intermediates and products

Interaction of I50V Mutant and I50L/A71V Double Mutant HIV-Protease with Inhibitor TMC114 (Darunavir): Molecular Dynamics Simulation and Binding Free Energy Studies

In the present work, the binding of inhibitor TMC114 (darunavir) to wild-type (WT), single (I50V) as well as double (I50L/A71V) mutant HIV-proteases (HIV-pr) was investigated with all-atom molecular dynamics (MD) simulations as well as molecular mechanic-Poisson–Boltzmann surface area (MM-PBSA) calculation. For both the apo and complexed HIV-pr, many intriguing effects due to double mutant, I50L/A71V, are observed. For example, the flap–flap distance and the distance from the active site to the flap residues in the apo I50L/A71V-HIV-pr are smaller than those of WT- and I50V–HIV-pr, probably making the active site smaller in volume and closer movement of flaps. For the complexed HIV-pr with TMC114, the double mutant I50L/A71V shows a less curling of the flap tips and less flexibility than WT and the single mutant I50V. As for the other previous studies, the present results also show that the single mutant I50V decreases the binding affinity of I50V–HIV-pr to TMC, resulting in a drug resistance; whereas the double mutant I50L/A71V increases the binding affinity, and as a result of the stronger binding, the I50L/A71V may be well adapted by the TMC114. The energy decomposition analysis suggests that the increase of the binding for the double mutant I50L/A71V–HIV-pr can be mainly attributed to the increase in electrostatic energy by −5.52 kacl/mol and van der Waals by −0.42 kcal/mol, which are canceled out in part by the increase of polar solvation energy of 1.99 kcal/mol. The I50L/A71V mutant directly increases the binding affinity by approximately −0.88 (Ile50 to Leu50) and −0.90 (Ile50′ to Leu50′) kcal/mol, accounting 45% for the total gain of the binding affinity. Besides the direct effects from the residues Leu50 and Leu50′, the residue Gly49′ increases the binding affinity of I50L/A71V–HIV-pr to the inhibitor by −0.74 kcal/mol, to which the electrostatic interaction of Leu50's backbone contributes by −1.23 kcal/mol. Another two residues Ile84 and Ile47′ also increase the binding affinity by −0.22 and −0.29 kcal/mol, respectively, which can be mainly attributed to van der Waals terms (Δ<i>T</i>_vdw = −0.21 and −0.39 kcal/mol)

Effects of Alloyed Metal on the Catalysis Activity of Pt for Ethanol Partial Oxidation: Adsorption and Dehydrogenation on Pt₃M (M = Pt, Ru, Sn, Re, Rh, and Pd)

The adsorption and dehydrogenation reactions of ethanol over bimetallic clusters Pt3M (M = Pt, Ru, Sn, Re, Rh, and Pd) have been extensively investigated with density functional theory. Both the α-hydrogen and hydroxyl adsorptions on Pt, as well as on the alloyed transition metal M sites of PtM, were considered as initial reaction steps. The adsorptions of ethanol on Pt and M sites of some PtM clusters through the α-hydrogen were well established. Although the α-hydrogen adsorption on the Pt site is weaker than the hydroxyl adsorption, the potential energy profiles show that the dehydrogenation by the α-hydrogen path has much lower energy barrier than that by the hydroxyl path. Generally, for the α-hydrogen path, the adsorption is a rate-determining-step because of the rather low dehydrogenation barrier for the α-hydrogen adsorption complex (thermodynamic control), whereas the hydroxyl path is determined by its dehydrogenation step (kinetic control). The effects of alloyed metal on the catalytic activity of Pt for ethanol partial oxidation, including adsorption energy, energy barrier, electronic structure, and eventually rate constant, are discussed. Among all of the alloyed metals investigated, only Sn was found to enhance the rate constant of the dehydrogenation by the α-hydrogen path on the Pt site of Pt3Sn as compared with that on Pt alone, which explains why PtSn is the most active catalyst for the oxidation of ethanol

Interaction between Glycine/Glycine Radicals and Intrinsic/Boron-Doped (8,0) Single-Walled Carbon Nanotubes: A Density Functional Theory Study

The adsorptions of a glycine molecule as well as dehydrogenated radicals on the side walls of both intrinsic and boron-doped (B-doped) single-walled (8,0) carbon nanotubes (SWCNTs) were investigated by a density functional theory. A glycine molecule tends to physically adsorb on intrinsic SWCNTs yet chemically adsorb on B-doped SWCNTs as a result of a somewhat chemical bond between the electron-rich nitrogen atom of the glycine molecule and the electron-scarce boron atom of the doped SWCNT. Opposite to the previous report (J. Phys. Chem. B 2006, 110, 6048−6050), it is found in the present study that both the N-centered and C-centered glycine radicals can form quite stable complexes with intrinsic as well as B-doped (8,0) SWCNTs. When the B-doped SWCNT interacts with glycine radicals, although there is a competition between B and the neighbor C in the nanotube axis direction, glycine radicals preferentially bind to the C site. The encapsulations of a glycine molecule into SWCNTs with various diameters are also discussed. We find that the encapsulation process is endothermic for (8,0) and (9,0) SWCNTs, while it is exothermic for (10,0) SWCNTs, indicating that the critical diameter of the zigzag SWCNT for the encapsulation is 7.83 Å, the diameter of (10,0)

On the Binding Strength Sequence for Nucleic Acid Bases and C₆₀ with Density Functional and Dispersion-Corrected Density Functional Theories: Whether C₆₀ Could Protect Nucleic Acid Bases from Radiation-Induced Damage

The major objective of this paper is to address a controversial binding sequence between nucleic acid bases (NABs) and C60 by investigating adsorptions of NABs and their cations on C60 fullerene with a variety of density functional theories including two novel hybrid meta-GGA functionals, M05-2x and M06-2x, as well as a dispersion-corrected density functional, PBE-D. The M05-2x/6-311++G** provides the same binding sequence as previously reported, guanine (G) > cytosine (C) > adenine (A) > thymine (T); however, M06-2x switches the binding strengths of A and C, and PBE-D eventually results in the following sequence, G > A > T > C, which is the same as the widely accepted hierarchy for the stacking of NABs on other carbon nanomaterials such as single-walled carbon nanotube and graphite. The results indicate that the questionable relative binding strength is due to insufficient electron correlation treatment with the M05-2x or even the M06-2x method. The binding energy of G@C60 obtained with the M06-2x/6-311++G(d,p) and the PBE-D/cc-pVDZ is −7.10 and −8.07 kcal/mol, respectively, and the latter is only slightly weaker than that predicted by the MP2/6-31G(d,p) (−8.10 kca/mol). Thus, the PDE-D performs better than the M06-2x for the observed NAB@C60 π-stacked complexes. To discuss whether C60 could prevent NABs from radiation-induced damage, ionization potentials of NABs and C60 and frontier molecular orbitals of the complexes NABs@C60 and (NABs@C60)+ are also extensively investigated. These results revealed that when an electron escapes from the complexes, a hole was preferentially created in C60 for T and C complexes, while for G and A the hole delocalizes over the entire complex, rather than a localization on the C60 moiety. The interesting finding might open a new strategy for protecting DNA from radiation-induced damage and offer a new idea for designing C60-based antiradiation drugs

Antiproliferative effect of secofriedelanophyllemblicine, a triterpenoid present in the roots of <i>Phyllanthus emblica</i> L

Phyllanthus emblica L. is a widely distributed tropical medicinal plant with good therapeutic properties. In the present study, the chemical constituents isolation of the roots of P. emblica were carried out and six known compounds (1-6) were purified and their structures were determined by means of spectroscopic analysis. The known triterpenoid, secofriedelanophyllemblicine (1), was selected to check for its cytotoxic effect on a series of human tumor cells and normal cells. Secofriedelanophyllemblicine exhibited cell growth inhibition specifically on MCF-7 breast cancer cells when compared to other tested cell lines. Further flow cytometric analysis showed that secofriedelanophyllemblicine could inhibit cell proliferation and induced G2 phase arrest in the cell-cycle progression of MCF-7 cells. The gathered results suggest that secofriedelanophyllemblicine is a cell-cycle regulator in MCF-7 human breast cancer cells and might be used as a candidate chemopreventive agent for breast cancer prevention and intervention.</p

Life-Cycle Assessment of a Regulatory Compliant U.S. Municipal Solid Waste Landfill

Landfills receive over half of all U.S. municipal solid waste (MSW) and are the third largest source of anthropogenic methane emissions. Life-cycle assessment (LCA) of landfills is complicated by the long duration of waste disposal, gas generation and control, and the time over which the engineered infrastructure must perform. The objective of this study is to develop an LCA model for a representative U.S. MSW landfill that is responsive to landfill size, regulatory thresholds for landfill gas (LFG) collection and control, practices for LFG management (i.e., passive venting, flare, combustion for energy recovery), and four alternative schedules for LFG collection well installation. Material production required for construction and operation contributes 68–75% to toxicity impacts, while LFG emissions contribute 50–99% to global warming, ozone depletion, and smog impacts. The current non-methane organic compound regulatory threshold (34 Mg yr–1) reduces methane emissions by <7% relative to the former threshold (50 Mg yr–1). Requiring landfills to continue collecting LFG until the flow rate is 3 min–1 reduces emissions by 20–52%, depending on the waste decay rate. In general, for landfills already required to collect gas, collecting gas longer is more important than collecting gas earlier to reduce methane emissions

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In the field of Internet of Things (IoT), terminal security has always been an extremely important independent research topic. In the terminal security research, in addition to the security enhancement of terminal entities, the security status evaluation of terminal security has also become an independent subset of the security research in the IoT field. However, it should also be noted that the security attributes of IoT terminals can include many aspects, so judging the security of IoT terminals based on the overall security form is not enough for the security of terminal entities. This paper introduces the concept of volatility from the overall situation assessment to the meta attributes that constitute the overall security situation, and preliminarily realizes the construction of a concise model based on historical data to judge the meta attributes that may affect the overall security in the future. At the same time, a concise verification system is built based on the application scenario of the power IoT terminals currently under research to preliminarily realize trend prediction, further expand the trust evaluation of IoT terminals, and clarify the direction of further research.</div

Symbol definition table used in this paper.

In the field of Internet of Things (IoT), terminal security has always been an extremely important independent research topic. In the terminal security research, in addition to the security enhancement of terminal entities, the security status evaluation of terminal security has also become an independent subset of the security research in the IoT field. However, it should also be noted that the security attributes of IoT terminals can include many aspects, so judging the security of IoT terminals based on the overall security form is not enough for the security of terminal entities. This paper introduces the concept of volatility from the overall situation assessment to the meta attributes that constitute the overall security situation, and preliminarily realizes the construction of a concise model based on historical data to judge the meta attributes that may affect the overall security in the future. At the same time, a concise verification system is built based on the application scenario of the power IoT terminals currently under research to preliminarily realize trend prediction, further expand the trust evaluation of IoT terminals, and clarify the direction of further research.</div