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THE INTERACTION OF PROTONATED OCTOPAMINE AND NOREPINEPHRINE WITH Β1-ADRENERGIC RECEPTOR: MOLECULAR DOCKING AND DYNAMICAL SIMULATION 质子化章鱼胺和去甲肾上腺素与Β1-adrenergic受体的相互作用:分子对接和动力学模拟
IF 0.4 Q3 Engineering Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.02
Žiko B. Milanović, D. Dimić, J. M. Markovic, Marijana Stanojević-Pirković, Edina H. Avdović, Z. Marković
In the current study, the interaction mechanisms between protonated neurotransmitters: octopamine (4-(2-amino-1-hydroxyethyl)phenol) and norepinephrine (4-[(1R)-2-amino-1-hydroxyethyl]benzene-1,2-diol) with the β-1 adrenergic receptor (β1AR) were examined by molecular docking, molecular dynamics (MD) simulations and MM/PBSA free energy calculations. The investigated receptor belongs to the G-protein coupled receptor group. The investigation was carried out at physiological pH=7.4. It was estimated that both compounds exist in the protonated form in the water at physiological pH. It was found that both protonated neurotransmitters established similar interactions with amino acid residues of the receptor, such as salt bridges, conventional hydrogen bonds, π-σ, and T-shaped π-π interactions, as shown by molecular docking simulations. As the initial structures for MD simulation with a total time of 10ns the most stable docking structures were used. The presented results are expected to provide some useful information for the design of specific β1AR agonists.
本研究通过分子对接、分子动力学(MD)模拟和MM/PBSA自由能计算,研究了质子化神经递质章鱼胺(4-(2-氨基-1-羟乙基)苯酚)和去甲肾上腺素(4-[(1R)-2-氨基-1-羟乙基]苯-1,2-二醇)与β-1肾上腺素能受体(β1AR)的相互作用机制。所研究的受体属于g蛋白偶联受体群。研究在生理pH=7.4的条件下进行。通过分子对接模拟发现,两种质子化的神经递质均与受体的氨基酸残基建立了类似的相互作用,如盐桥、常规氢键、π-σ和t形π-π相互作用。总时间为10ns的MD仿真初始结构采用最稳定的对接结构。本研究结果有望为设计特异性β1AR激动剂提供一些有用的信息。
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引用次数: 0
AN EXPERIMENTAL AND THEORETICAL STUDY OF THE REACTIVITY OF SELECTED CATECHOLAMINES AND THEIR PRECURSORS TOWARDS ASCORBYL RADICAL 选定的儿茶酚胺及其前体对抗坏血酸自由基反应性的实验和理论研究
IF 0.4 Q3 Engineering Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.01
D. Dimić, Đura Nakarada, M. Mojović, J. M. Markovic
Ascorbyl radical is often used as a biomarker of oxidative stress in human organism. It is a product of the antioxidant activity of ascorbic acid and it is not expected to react further with biologically important molecules. For the first time, the reactivity of catecholamines and their precursors was investigated theoretically and experimentally towards ascorbyl radical and the main structural parameters governing activity were analyzed. It was shown that catechol moiety plays an important role, which classifies norepinephrine and 3,4-dihydroxyphenylacetic acid as the most reactive when compared to homovanillic acid, vanillylmandelic acid, and octopamine. DFT methods have been employed to determine the most probable mechanism of the reaction. Based on the change in reaction enthalpy it was concluded that Hydrogen Atom Transfer (HAT) is a preferred mechanism both in water and pentyl ethanoate. The stabilization interactions in ascorbic acid, its anion and radical are carefully analyzed in order to understand the preferability of the mentioned mechanism. The stability of the ascorbyl radical is explained in detail. The results prove that ascorbyl radical is not just a product of antioxidant activity, but also a potentially harmful species in an organism.
抗坏血酸自由基常被用作人体氧化应激的生物标志物。它是抗坏血酸抗氧化活性的产物,预计它不会与生物学上重要的分子进一步反应。首次从理论上和实验上研究了儿茶酚胺及其前体对抗坏血酸自由基的反应性,并分析了影响活性的主要结构参数。结果表明,儿茶酚部分起着重要的作用,其中去甲肾上腺素和3,4-二羟基苯乙酸与同型香草酸、香草酸和章鱼胺相比,反应性最强。DFT方法已被用来确定最可能的反应机理。根据反应焓的变化,得出了在水和乙醇戊酯中,氢原子转移(HAT)都是首选的反应机理。对抗坏血酸及其阴离子和自由基的稳定相互作用进行了详细分析,以了解上述机制的优选性。对抗坏血酸自由基的稳定性作了详细的解释。结果证明,抗坏血酸自由基不仅是抗氧化活性的产物,而且在生物体中也是一种潜在的有害物质。
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引用次数: 2
DO EQUOL’S C-RING HYDROGENS CONTRIBUTE TO FREE RADICAL SCAVENGING? 马酚的c环氢有助于清除自由基吗?
IF 0.4 Q3 Engineering Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.05
Ana D. Amic, D. Milenković, J. M. Markovic, Z. Marković
Free radical scavenging potency of physiologically active equol molecule, derived by gut microbiota from soy isoflavone daidzein, was investigated by using M06-2X/6-311++G(d,p) level of theory, accompanied with the TST and Eckart tunneling corrections for the estimation of rate constants. Phenolic hydrogens of equol are recognized as much more abstractable than C-ring hydrogens. This finding is opposite to the one very recently suggested, but in accordance with well-known facts related to the flavonoid chemistry and phenolic O−H vs C−H reactivity.
利用M06-2X/6-311++G(d,p)水平的理论,结合TST和Eckart隧道修正法估算速率常数,研究了肠道微生物群从大豆异黄酮大豆黄酮中提取的生理活性雌马酚分子的自由基清除能力。雌酚的酚氢被认为比C环氢更容易被提取。这一发现与最近提出的相反,但与类黄酮化学和酚类O−H与C−H反应性相关的众所周知的事实一致。
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引用次数: 3
RESOLVENT ENERGY AND ESTRADA INDEX OF BENZENOID HYDROCARBONS 苯类烃的分解能和estada指数
IF 0.4 Q3 Engineering Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.04
Izudin Redžepović, Boris Furtula
The relationship between the resolvent and Estrada indices for the alkanes has been recently demonstrated. That relationship involved the first Zagreb index besides these two eigenvalue-based molecular descriptors. In this paper, the quality of the correlation is tested in the case of isomeric benzenoid hydrocarbons, where the first Zagreb index is constant. Extraordinary linear correlations are identified for all studied groups of isomeric benzenoid hydrocarbons. Additionally, the relationship of these indices with the boiling points of a set of benzenoid hydrocarbons is presented.
烷烃的溶剂指数和Estrada指数之间的关系最近得到了证明。除了这两个基于特征值的分子描述符外,这种关系还包括第一个萨格勒布指数。在本文中,在第一萨格勒布指数恒定的情况下,对异构苯烃的相关性质量进行了测试。在所有被研究的异构苯碳氢化合物基团中都发现了异常的线性相关性。此外,还给出了这些指标与一类苯烃沸点的关系。
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引用次数: 1
ANTIOXIDATIVE AND INHIBITION POTENCY OF CYNODONTIN 犬牙草素的抗氧化和抑制作用
IF 0.4 Q3 Engineering Pub Date : 2020-06-01 DOI: 10.24874/JSSCM.2020.01.06
J. Đorović, M. Antonijević, Z. Marković
The antioxidant activity of cynodontin was studied in the absence and the presence of free radical species. This in silico study was performed in water and benzene, with the aim to simulate polar and non-polar environment. To determine the most probable mechanism of antioxidant action, density functional theory (DFT) was employed. The change in reaction enthalpy of cynodontin with three different free radicals (hydroxyl, hydroperoxyl, and methyl peroxyl radical) were examined and presented. SET-PT (Single Electron Transfer – Proton Transfer) mechanism is not an operative mechanism of antioxidant action. The obtained results imply that the possible mechanism of antioxidant action in water is SPLET (Sequential Proton Loss Electron Transfer), while in benzene HAT (Hydrogen atom transfer) and SPLET are competitive mechanisms. The molecular docking study was performed in order to estimate the inhibition potency of the investigated compound toward human leukocyte elastase (HLE). The obtained results indicate that numerous interactions determine the inhibition activity towards the investigated protein.
研究了在不存在和存在自由基物质的情况下,食蟹齿素的抗氧化活性。这项计算机研究是在水和苯中进行的,目的是模拟极地和非极地环境。为了确定抗氧化作用的最可能机制,采用了密度泛函理论(DFT)。考察并介绍了氢氧化锡与三种不同自由基(羟基、氢过氧基和甲基过氧基)反应焓的变化。SET-PT(单电子转移-质子转移)机制不是抗氧化作用的有效机制。结果表明,在水中抗氧化作用的可能机制是SPLET(顺序质子损失电子转移),而在苯中HAT(氢原子转移)和SPLET是竞争机制。进行分子对接研究是为了估计所研究的化合物对人类白细胞弹性蛋白酶(HLE)的抑制效力。所获得的结果表明,许多相互作用决定了对所研究的蛋白质的抑制活性。
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引用次数: 4
VISCOSITY VARIATION EFFECT ON THE MAGNETIC FLUID LUBRICATION OF A SHORT BEARING 粘度变化对短轴承磁流体润滑的影响
IF 0.4 Q3 Engineering Pub Date : 2019-12-01 DOI: 10.24874/jsscm.2019.13.02.05
J. Patel, G. Deheri
The performance of a magnetic fluid based short bearing is examined with the effect of viscosity variation. The pressure temperature relation of Tipei (1962) concerning viscosity variation is adopted here. The Neuringer-Rosensweig’s model has been considered for the magnetic fluid flow. The related modified Reynolds type equation is solved for the calculation of pressure distribution leading to the computation of load bearing capacity. The graphical representations indicate that the positive effect of viscosity variation gets aided considerably by the ferrofluid lubrication.
在粘度变化的影响下,研究了磁流体短轴承的性能。本文采用Tipei(1962)关于粘度变化的压力-温度关系式。Neuringer-Rosensweig模型已被考虑用于磁流体的流动。求解相应的修正雷诺型方程,计算压力分布,进而计算承载能力。图解表明,铁磁流体润滑极大地辅助了黏度变化的积极作用。
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引用次数: 5
A Proposed Method for Determining Propulsion Coefficient Based on Testing Motor Freighters on Danube Waterway Network 一种基于多瑙河航道网机动货运试验确定推进系数的方法
IF 0.4 Q3 Engineering Pub Date : 2019-09-30 DOI: 10.24874/jsscm.2019.13.01.09
R. Rajković, D. Mitic, A. Lebl, S. Rajković
The paper presents a proposal of mathematical models for the determination of propulsion coefficient, ηpp, intended for the analysis of motor freighters applied on the river watercourses. As the main paper contribution three different model types are developed, depending on the variable which contributes to ηpp value. These variables are: 1. the freighter sailing velocity, (v); 2. the installed capacity of the main drive motor of outboard unit, (Ninst); 3. the combination of these two variables, (Ninst,v). The models are verified on the examples of several motor freighters which are applied at Danube river. The special attention is paid to the determination of the optimum approximation function in each case. In all three cases it is a quadratic function. The correlation coefficient for the comparison in all analyzed examples is higher than 0.87, being even higher than 0.99 for the first model.
本文提出了一个确定推进系数ηpp的数学模型,用于分析在河道上使用的机动货轮。作为论文的主要贡献,根据影响ηpp值的变量,开发了三种不同的模型类型。这些变量是:1。货轮航行速度,(v);2.舷外机主驱动电机的装机容量,(Ninst);3.这两个变量的组合,(Ninst,v)。通过在多瑙河应用的几艘汽车货轮的实例验证了模型的正确性。特别注意在每种情况下最佳逼近函数的确定。在这三种情况下,它都是一个二次函数。在所有分析的例子中,比较的相关系数都高于0.87,甚至高于第一个模型的0.99。
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引用次数: 0
1D and 3D Modeling of Modern Automotive Exhaust Manifold 现代汽车排气歧管的1D和3D建模
IF 0.4 Q3 Engineering Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.05
Barhm Mohamad, A. Zelentsov
This paper presents the simulation of the multi-cylinder 4-stroke cycle spark-ignition engine using a commercial simulation tool, AVL BOOST and Fire. Various models were examined to select the appropriate models that would best serve to analyze the main components of the exhaust systems: the plenum chamber, the muffler and the exhaust manifold branch junction. For the plenum chamber and the muffler, the whole duct model was tested. In order to analyze the exhaust manifold branch junction, a complicated model which reflects the actual shape and involves pressure drops, velocity magnitude and sound pressure was compared to a simplified one. However, the results from 1D and 3D model calculations compared with Honda K20B Engine experimental data also show that both models are applicable with satisfying accuracy for exhaust manifold branch junction. The simplified 1D model is recommended in regard to convenience in modeling and efficiency in calculation.
本文使用商用模拟工具AVL BOOST和Fire对多缸四冲程循环火花点火式发动机进行了仿真。对各种模型进行了检查,以选择最适合分析排气系统主要部件的适当模型:增压室、消声器和排气歧管分支接头。针对增压室和消声器,对整个风管模型进行了试验研究。为了分析排气歧管分支连接,将一个反映实际形状并包含压降、速度大小和声压的复杂模型与一个简化模型进行了比较。然而,1D和3D模型计算结果与本田K20B发动机实验数据的比较也表明,这两个模型都适用于排气歧管分支连接,具有令人满意的精度。考虑到建模的方便性和计算的效率,建议使用简化的1D模型。
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引用次数: 6
Aerodynamic performances improvement of NACA 4415 profile by passive flow control using vortex generators 采用涡流发生器的被动流动控制改善NACA 4415型面的气动性能
IF 0.4 Q3 Engineering Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.02
Hocine Hares, G. Mebarki, M. Brioua, M. Naoun
Improvement of the airfoil NACA 4415 aerodynamic performances by flow control using a passive technique was achieved in this study. Gothic-shaped vortex generators were added at the profile upper surface. Vortex Generators (VG) were used to avoid boundary layer separation at the profile trailing edge, thus reducing the drag force and improving aerodynamic performances. A numerical simulation with fluent code was performed. A parametric study was carried out to determine optimal disposition and dimensions of the VG. Six VG parameters were tested; thickness (E), height (H), length (L), aspect ratio (r), incidence angle (α) and the VG position relative to the chord of the profile (XVG). The results show an increase in the lift coefficient for the profile with vortex generators in the range of high attack angles. Optimal dimensions and positions of the VG were obtained.
本研究采用被动技术通过流量控制改善了NACA4415翼型的气动性能。剖面上表面增加了哥特式涡流发生器。涡流发生器(VG)用于避免剖面后缘的边界层分离,从而降低阻力并改善气动性能。用fluent代码进行了数值模拟。通过参数研究确定VG的最佳配置和尺寸。测试了六个VG参数;厚度(E)、高度(H)、长度(L)、纵横比(r)、入射角(α)和VG相对于轮廓弦的位置(XVG)。结果表明,在高攻角范围内,带有涡流发生器的剖面的升力系数有所增加。获得了VG的最佳尺寸和位置。
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引用次数: 4
Computational Analysis of Hip Implant Surfaces 髋关节植入物表面的计算分析
IF 0.4 Q3 Engineering Pub Date : 2019-09-01 DOI: 10.24874/jsscm.2019.13.01.07
Aleksandra Vulovic, N. Filipovic
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引用次数: 11
期刊
Journal of the Serbian Society for Computational Mechanics
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