• 제목/요약/키워드: Intermolecular Potential

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Influence of vacancy defects on vibration analysis of graphene sheets applying isogeometric method: Molecular and continuum approaches

  • Tahouneh, Vahid;Naei, Mohammad Hasan;Mashhadi, Mahmoud Mosavi
    • Steel and Composite Structures
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    • 제34권2호
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    • pp.261-277
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    • 2020
  • The main objective of this research paper is to consider vibration analysis of vacancy defected graphene sheet as a nonisotropic structure via molecular dynamic and continuum approaches. The influence of structural defects on the vibration of graphene sheets is considered by applying the mechanical properties of defected graphene sheets. Molecular dynamic simulations have been performed to estimate the mechanical properties of graphene as a nonisotropic structure with single- and double- vacancy defects using open source well-known software i.e., large-scale atomic/molecular massively parallel simulator (LAMMPS). The interactions between the carbon atoms are modelled using Adaptive Intermolecular Reactive Empirical Bond Order (AIREBO) potential. An isogeometric analysis (IGA) based upon non-uniform rational B-spline (NURBS) is employed for approximation of single-layered graphene sheets deflection field and the governing equations are derived using nonlocal elasticity theory. The dependence of small-scale effects, chirality and different defect types on vibrational characteristic of graphene sheets is investigated in this comprehensive research work. In addition, numerical results are validated and compared with those achieved using other analysis, where an excellent agreement is found. The interesting results indicate that increasing the number of missing atoms can lead to decrease the natural frequencies of graphene sheets. It is seen that the degree of the detrimental effects differ with defect type. The Young's and shear modulus of the graphene with SV defects are much smaller than graphene with DV defects. It is also observed that Single Vacancy (SV) clusters cause more reduction in the natural frequencies of SLGS than Double Vacancy (DV) clusters. The effectiveness and the accuracy of the present IGA approach have been demonstrated and it is shown that the IGA is efficient, robust and accurate in terms of nanoplate problems.

MNDO Studies on Intramolecular Proton Transfer Equilibria of Acetamide and Methyl Carbamate$^1$

  • Lee, Ik-Choon;Kim, Chang-Kon;Seo, Heon-Su
    • Bulletin of the Korean Chemical Society
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    • 제7권5호
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    • pp.395-399
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    • 1986
  • Intramolecular proton transfer equilibria of acetamide and methyl carbamate have been studied theoretically by MNDO MO method. For both substrates, carbonyl-O protonated tautomer was found to be the most stable form, the next most stable one being N-protonated form. Gas phase proton transfers take place by the 1,3-proton rearrangement process and in all cases have prohibitively high activation barriers. When however one solvate water molecule participates in the process, the barriers are lowered substantially and the process proceeds in an intermolecular manner through the intermediacy of the water molecule via a triple-well type potential energy surface; three wells correspond to reactant(RC), intermediate(IC) and product complex(PC) of proton donor-acceptor pairs whereas two transition states(TS) have proton-bridge structure. General scheme of the process can be represented for a substrate with two basic centers(heteroatoms) of A and B as, $$ABH\limits^+\;+\;H_2O\;{\to}\;ABH\limits^+{\cdots}{\limits_{RC}}OH_2\;{\to}\;AB{\cdots}H\limits_{TS}^+{\cdots}{\limits_{1}}OH_2\;{\to}\;AB{\cdots}{\limits_{IC}}H\limits^+OH_2\;{\to}\;BA{\cdots}H\limits_{TS}^+{\cdots}{\limits_{2}}OH_2\;{\to}\;BA H\limits^+{\cdots}{\limits_{PC}}OH_2\;{\to}\;BAH\limits^+\;+\;H_2O$$ Involvement of a second solvate water had negligible effect on the relative stabilities of the tautomers but lowered barrier heights by 5∼6 Kcal/mol. It was calculated that the abundance of the methoxy-O protonated tautomer of the methyl carbamate will be negligible, since the tautomer is unfavorable thermodynamically as well as kinetically. Fully optimized stationary points are reported.

산화환원효소에 의한 휴믹산의 산화중합반응 (Oxidative Coupling Reaction of Purified Aldrich Humic Acid by Horseradish Peroxidase)

  • 지상현;김도군;김정현;고석오
    • 대한환경공학회지
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    • 제32권11호
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    • pp.1054-1062
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    • 2010
  • 휴믹물질의 산화중합반응은 천연 효소나 금속산화물 촉매에 의해 유도될 수 있다. 본 연구에서는 천연 효소인 horseradish peroxidase (HRP)에 의한 휴믹산의 특성 변화와 이러한 변화된 특성이 정밀여과 공정에 미치는 영향을 평가하였다. 정제된 Aldrich 휴믹산(PAHA)이 HRP 및 과산화수소 존재 하에 산화중합되어 보다 크고 복잡한 분자를 형성하였으며, 크기배제크로마토그래피(SEC, size exclusion chromatography, SEC)에서도 평균분자량의 증가가 관찰되었다. 또한, HRP 및 $H_2O_2$ 주입량이 증가함에 따라 PAHA의 분자량은 더욱 증가하였다. 휴믹물질의 화학적 안정성은 산화중합반응에 기인한 휴믹 분자 상호간의 공유결합이 촉진됨에 따라 향상되었으며, 형광 분광 및 적외선 분광 분석 결과, 산화중합반응에 의한 PAHA 분자 작용기의 변화도 확인되었다. 수처리 공정에 미치는 영향을 평가하기 위해, 정밀여과를 적용한 결과, 산화중합반응 산물은 높은 분자량으로 인해 그 제거효율이 크게 향상되었다. 이는 산화중합된 자연유기물이 정밀여과에 의해 제거될 수 있음을 증명하는 것이다.

Sesquiterpenoids Bioconversion Analysis by Wood Rot Fungi

  • Lee, Su-Yeon;Ryu, Sun-Hwa;Choi, In-Gyu;Kim, Myungkil
    • 한국균학회소식:학술대회논문집
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    • 한국균학회 2016년도 춘계학술대회 및 임시총회
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    • pp.19-20
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    • 2016
  • Sesquiterpenoids are defined as $C_{15}$ compounds derived from farnesyl pyrophosphate (FPP), and their complex structures are found in the tissue of many diverse plants (Degenhardt et al. 2009). FPP's long chain length and additional double bond enables its conversion to a huge range of mono-, di-, and tri-cyclic structures. A number of cyclic sesquiterpenes with alcohol, aldehyde, and ketone derivatives have key biological and medicinal properties (Fraga 1999). Fungi, such as the wood-rotting Polyporus brumalis, are excellent sources of pharmaceutically interesting natural products such as sesquiterpenoids. In this study, we investigated the biosynthesis of P. brumalis sesquiterpenoids on modified medium. Fungal suspensions of 11 white rot species were inoculated in modified medium containing $C_6H_{12}O_6$, $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ for 20 days. Cultivation was stopped by solvent extraction via separation of the mycelium. The metabolites were identified as follows: propionic acid (1), mevalonic acid lactone (2), ${\beta}$-eudesmane (3), and ${\beta}$-eudesmol (4), respectively (Figure 1). The main peaks of ${\beta}$-eudesmane and ${\beta}$-eudesmol, which were indicative of sesquiterpene structures, were consistently detected for 5, 7, 12, and 15 days These results demonstrated the existence of terpene metabolism in the mycelium of P. brumalis. Polyporus spp. are known to generate flavor components such as methyl 2,4-dihydroxy-3,6-dimethyl benzoate; 2-hydroxy-4-methoxy-6-methyl benzoic acid; 3-hydroxy-5-methyl phenol; and 3-methoxy-2,5-dimethyl phenol in submerged cultures (Hoffmann and Esser 1978). Drimanes of sesquiterpenes were reported as metabolites from P. arcularius and shown to exhibit antimicrobial activity against Gram-positive bacteria such as Staphylococcus aureus (Fleck et al. 1996). The main metabolites of P. brumalis, ${\beta}$-Eudesmol and ${\beta}$-eudesmane, were categorized as eudesmane-type sesquiterpene structures. The eudesmane skeleton could be biosynthesized from FPP-derived IPP, and approximately 1,000 structures have been identified in plants as essential oils. The biosynthesis of eudesmol from P. brumalis may thus be an important tool for the production of useful natural compounds as presumed from its identified potent bioactivity in plants. Essential oils comprising eudesmane-type sesquiterpenoids have been previously and extensively researched (Wu et al. 2006). ${\beta}$-Eudesmol is a well-known and important eudesmane alcohol with an anticholinergic effect in the vascular endothelium (Tsuneki et al. 2005). Additionally, recent studies demonstrated that ${\beta}$-eudesmol acts as a channel blocker for nicotinic acetylcholine receptors at the neuromuscular junction, and it can inhibit angiogenesis in vitro and in vivo by blocking the mitogen-activated protein kinase (MAPK) signaling pathway (Seo et al. 2011). Variation of nutrients was conducted to determine an optimum condition for the biosynthesis of sesquiterpenes by P. brumalis. Genes encoding terpene synthases, which are crucial to the terpene synthesis pathway, generally respond to environmental factors such as pH, temperature, and available nutrients (Hoffmeister and Keller 2007, Yu and Keller 2005). Calvo et al. described the effect of major nutrients, carbon and nitrogen, on the synthesis of secondary metabolites (Calvo et al. 2002). P. brumalis did not prefer to synthesize sesquiterpenes under all growth conditions. Results of differences in metabolites observed in P. brumalis grown in PDB and modified medium highlighted the potential effect inorganic sources such as $C_4H_{12}N_2O_6$, $KH_2PO_4$, $MgSO_4$, and $CaCl_2$ on sesquiterpene synthesis. ${\beta}$-eudesmol was apparent during cultivation except for when P. brumalis was grown on $MgSO_4$-free medium. These results demonstrated that $MgSO_4$ can specifically control the biosynthesis of ${\beta}$-eudesmol. Magnesium has been reported as a cofactor that binds to sesquiterpene synthase (Agger et al. 2008). Specifically, the $Mg^{2+}$ ions bind to two conserved metal-binding motifs. These metal ions complex to the substrate pyrophosphate, thereby promoting the ionization of the leaving groups of FPP and resulting in the generation of a highly reactive allylic cation. Effect of magnesium source on the sesquiterpene biosynthesis was also identified via analysis of the concentration of total carbohydrates. Our current study offered further insight that fungal sesquiterpene biosynthesis can be controlled by nutrients. To profile the metabolites of P. brumalis, the cultures were extracted based on the growth curve. Despite metabolites produced during mycelia growth, there was difficulty in detecting significant changes in metabolite production, especially those at low concentrations. These compounds may be of interest in understanding their synthetic mechanisms in P. brumalis. The synthesis of terpene compounds began during the growth phase at day 9. Sesquiterpene synthesis occurred after growth was complete. At day 9, drimenol, farnesol, and mevalonic lactone (or mevalonic acid lactone) were identified. Mevalonic acid lactone is the precursor of the mevalonic pathway, and particularly, it is a precursor for a number of biologically important lipids, including cholesterol hormones (Buckley et al. 2002). Farnesol is the precursor of sesquiterpenoids. Drimenol compounds, bi-cyclic-sesquiterpene alcohols, can be synthesized from trans-trans farnesol via cyclization and rearrangement (Polovinka et al. 1994). They have also been identified in the basidiomycota Lentinus lepideus as secondary metabolites. After 12 days in the growth phase, ${\beta}$-elemene caryophyllene, ${\delta}$-cadiene, and eudesmane were detected with ${\beta}$-eudesmol. The data showed the synthesis of sesquiterpene hydrocarbons with bi-cyclic structures. These compounds can be synthesized from FPP by cyclization. Cyclic terpenoids are synthesized through the formation of a carbon skeleton from linear precursors by terpene cyclase, which is followed by chemical modification by oxidation, reduction, methylation, etc. Sesquiterpene cyclase is a key branch-point enzyme that catalyzes the complex intermolecular cyclization of the linear prenyl diphosphate into cyclic hydrocarbons (Toyomasu et al. 2007). After 20 days in stationary phase, the oxygenated structures eudesmol, elemol, and caryophyllene oxide were detected. Thus, after growth, sesquiterpenes were identified. Per these results, we showed that terpene metabolism in wood-rotting fungi occurs in the stationary phase. We also showed that such metabolism can be controlled by magnesium supplementation in the growth medium. In conclusion, we identified P. brumalis as a wood-rotting fungus that can produce sesquiterpenes. To mechanistically understand eudesmane-type sesquiterpene biosynthesis in P. brumalis, further research into the genes regulating the dynamics of such biosynthesis is warranted.

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