Density function theory

密度泛函理论
  • 文章类型: Journal Article
    在批量生产中通常采用Sn掺杂来制备Ti3AlC2,因为它可以降低合成温度,同时提高相纯度。然而,过量的Sn掺杂通常会降低Ti3AlC2的抗氧化性。因此,适当的Sn掺杂浓度是一个至关重要的问题。在这项工作中,采用理论计算和实验相结合的方法,系统地研究了Sn掺杂浓度对Ti3AlC2氧化行为的影响。密度泛函理论计算表明,有和没有Sn掺杂的Ti3AlC2的(001)表面的氧吸附机制是相似的,和Ti-O键总是优先形成。分子动力学模拟进一步表明Al原子在氧化过程中具有更快的扩散速率。因此,在高温下可以迅速形成连续的Al2O3层。然而,当Sn掺杂浓度超过10mol%时,Al2O3层的连续性被破坏,从而损害Ti3AlC2的抗氧化性。此外,氧化实验验证了上述结果。还提出了不同Sn掺杂浓度的Ti3AlC2的氧化机理。
    Sn doping is usually adopted to prepare Ti3AlC2 in mass production because it can reduce the synthesis temperature while increasing the phase purity. However, excessive Sn doping usually deteriorates the oxidation resistance of Ti3AlC2. Therefore, an appropriate Sn doping concentration is a vital issue. In this work, the effect of Sn doping concentration on the oxidation behavior of Ti3AlC2 was systematically investigated by combining theoretical calculations and experimental methods. Density function theory calculations suggest that the oxygen adsorption mechanisms for the (001) surface of Ti3AlC2 with and without Sn doping are similar, and Ti-O bonds are always preferentially formed. The molecular dynamics simulation further indicates that Al atoms have a faster diffusion rate during the oxidation process. Therefore, a continuous Al2O3 layer can form rapidly at high temperature. Nevertheless, when the Sn doping concentration exceeds 10 mol%, the continuity of the Al2O3 layer is destroyed, thereby impairing the oxidation resistance of Ti3AlC2. Furthermore, oxidation experiments verify the above results. The oxidation mechanisms of Ti3AlC2 with different Sn doping concentrations are also proposed.
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  • 文章类型: Journal Article
    研究表面活性剂对Wiser烟煤可浮性的影响对提高煤的洁净度和利用价值具有重要意义。利用密度泛函理论和分子动力学模拟方法,本研究构建了Wiser烟煤模型,并研究了不同表面活性剂的影响,包括阴离子表面活性剂十二烷基苯磺酸钠,阳离子表面活性剂十六烷基三甲基溴化铵(CTAB),和非离子表面活性剂脂肪醇乙氧基化醚。重点研究了这些分子的电荷分布特性以及二元表面活性剂对烟煤疏水性的改性作用。结果表明,最大的静电势集中在氧/氮/含硫官能团附近,如磺酸基团,季铵阳离子,环氧乙烷,羟基,羧基,和硫键。这些官能团表现出接受/递送电子以形成氢键的倾向。在测试的表面活性剂中,CTAB揭示了前沿轨道能量的微小差异,测量3.187eV,从而证明了与其它两种表面活性剂相比优异的捕获能力。确定系统内的吸附反应是自发的,超过60%的相互作用力归因于静电力。此外,与水分子的斥力大小遵循以下趋势:磺酸盐基团(2.20)<环氧乙烷(2.43)<季铵阳离子(2.57),表明CTAB具有更优异的防水性。研究结果表明,CTAE二元表面活性剂被证明对改善烟煤的疏水性最有效。这项研究提供了减少浪费的宝贵见解,污染,和资源浪费。
    Investigating surfactant effects on the floatability of Wiser bituminous coal holds significant importance in improving coal cleanliness and utilization value. Using density functional theory and molecular dynamics simulation methods, this study constructed models of Wiser bituminous coal and examined the impact of different surfactants, including the anionic surfactant sodium dodecyl benzene sulfonate, the cationic surfactant hexadecyl trimethyl ammonium bromide (CTAB), and the non-ionic surfactant fatty alcohol ethoxylated ether. The focus was on investigating the charge distribution characteristics of these molecules and the modifying effect of binary surfactants on the hydrophobicity of bituminous coal. Results revealed that the maximum electrostatic potential was concentrated near oxygen/nitrogen/sulfur-containing functional groups like sulfonic acid groups, quaternary ammonium cations, ethylene oxide, hydroxyl groups, carboxyl groups, and sulfur bonds. These functional groups exhibited a propensity for accepting/delivering electrons to form hydrogen bonds. Among the surfactants tested, CTAB revealed the slightest difference in frontier orbital energy, measuring 3.187 eV, thereby demonstrating a superior trapping ability compared with the other two surfactants. Adsorption reactions within the system were determined to be spontaneous, with over 60% of the interaction force attributed to electrostatic forces. Moreover, the repulsive force magnitude with water molecules followed the trend: sulfonate group (2.20 Å) < ethylene oxide (2.43 Å) < quaternary ammonium cation (2.57 Å), indicating more excellent water repellency of CTAB. Findings showed that CTAE binary surfactants proved most effective in modifying the hydrophobicity of bituminous coal. This study offers valuable insights into reducing waste, pollution, and resource wastage.
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  • 文章类型: Journal Article
    Na超离子导体(NASICON),具有出色的结构稳定性和高工作电压,是一种有吸引力的材料,可以克服钠离子电池的低比能量和较大体积变形的限制。在这项研究中,发现理想的NASICON阴极材料,开发了基于密度泛函理论(DFT)计算和机器学习(ML)的筛选平台。利用以前的124545个电极数据库生成了一个训练数据库,构建了一组3126个潜在的NASICON结构[NaxMyM\'1-y(PO4)3],在金属位点具有27种掺杂剂,在聚阴离子中心位点具有6种掺杂剂。开发的ML代理模型识别出796种满足以下标准的材料:形成能<0.0eV/atom,船体上方的能量≤0.025eV/原子,体积变化≤4%,理论容量≥50mAh/g。然后使用机器学习原子间势(MLIP)选择掺杂NASICON结构的热力学稳定构型,能够快速考虑各种掺杂位点的配置。对796个筛选材料进行DFT计算,以获得能量密度,平均电压,和音量变化。最后,确定50个平均电压≥3.5V的候选者。建议的平台通过缩小对具有所需性能的材料的关注来加速对最佳NASICON材料的探索,节省大量资源。
    The Na super ionic conductor (NASICON), which has outstanding structural stability and a high operating voltage, is an appealing material for overcoming the limits of low specific energy and larger volume distortion of sodium-ion batteries. In this study, to discover ideal NASICON cathode materials, a screening platform based on density functional theory (DFT) calculations and machine learning (ML) is developed. A training database was generated utilizing the previous 124 545 electrode databases, and a test set of 3126 potential NASICON structures [NaxMyM\'1-y(PO4)3] with 27 dopants at the metal site and 6 dopants at the polyanion central site was constructed. The developed ML surrogate model identifies 796 materials that satisfy the following criteria: formation energy of <0.0 eV/atom, energy above hull of ≤0.025 eV/atom, volume change of ≤4%, and theoretical capacity of ≥50 mAh/g. The thermodynamically stable configurations of doped NASICON structures were then selected using machine learning interatomic potential (MLIP), enabling rapid consideration of various dopant site configurations. DFT calculations are followed on 796 screened materials to obtain energy density, average voltage, and volume change. Finally, 50 candidates with an average voltage of ≥3.5 V are identified. The suggested platform accelerates the exploration for optimal NASICON materials by narrowing the focus on materials with desired properties, saving considerable resources.
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  • 文章类型: Journal Article
    富锂层氧化物阴极由于其高能量密度而成为有前途的储能材料。然而,循环过程中的氧损失限制了它们的实际应用。在这里,我们揭示了Li含量对拓扑抑制富锂正极材料中氧损失的重要作用,以及氧离子与过渡金属(TM)组分的迁移网络之间的关系。利用第一性原理计算结合渗流理论和蒙特卡罗模拟,我们发现,当TM层中的TM浓度超过5/6时,TM离子可以有效地包裹氧化的氧物种,从而阻碍了氧离子渗透网络的形成。这项研究证明了在富锂阴极中合理的成分设计对于有效抑制不可逆氧释放和增强阴极循环性能的重要性。本文受版权保护。保留所有权利。
    Lithium-rich layer oxide cathodes are promising energy storage materials due to their high energy densities. However, the oxygen loss during cycling limits their practical applications. Here, the essential role of Li content on the topological inhibition of oxygen loss in lithium-rich cathode materials and the relationship between the migration network of oxygen ions and the transition metal (TM) component are revealed. Utilizing first-principles calculations in combination with percolation theory and Monte Carlo simulations, it is found that TM ions can effectively encage the oxidized oxygen species when the TM concentration in TM layer exceeds 5/6, which hinders the formation of a percolating oxygen migration network. This study demonstrates the significance of rational compositional design in lithium-rich cathodes for effectively suppressing irreversible oxygen release and enhancing cathode cycling performance.
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  • 文章类型: Journal Article
    二维范德华(2DvdW)材料广泛应用于自旋轨道转矩(SOT)器件中。最近的研究已经证明了2DvdWZrSe3的低晶体对称性和大自旋霍尔电导率,表明其在低功耗SOT器件中的潜在应用。这里,我们研究了SOTs的界面贡献和ZrSe3/Py(Ni80Fe20)和ZrSe3/Cu/Py异质结构中电流诱导的磁化转换。样品的SOT效率通过自旋扭矩铁磁共振(ST-FMR)检测,并观察到面外阻尼状扭矩(τB)。当在界面处插入1nmCu时,τB与场状扭矩(τA)之间的比率从0.175降低到0.138,然后当Cu嵌入的厚度为2nm时下降到0.001,表明Cu嵌入抑制了SOT的τB成分。此外,SOT效率从3.05提高到5.21,这可能归因于Cu嵌入有利于改善Py和ZrSe3之间的界面。理论计算表明,Cu间隔层可以将ZrSe3的导电性从半导体变为导体,从而降低肖特基势垒并增加自旋电流的传输效率。此外,磁光克尔效应(MOKE)显微镜用于验证这些结构中电流驱动的磁化切换。与ZrSe3/Py双层相比,当插入1nmCu时,ZrSe3/Cu/Py的临界电流密度降低,在ZrSe3/Cu/Py结构中证明了更高的SOT效率和更低的功耗。
    Two-dimensional van der Waals (2D vdW) materials are widely used in spin-orbit torque (SOT) devices. Recent studies have demonstrated the low crystal symmetry and large spin Hall conductivity of 2D vdW ZrSe3, indicating its potential applications in low-power SOT devices. Here, we study the interfacial contribution of SOTs and current-induced magnetization switching in the ZrSe3/Py (Ni80Fe20) and ZrSe3/Cu/Py heterostructures. SOT efficiencies of samples are detected by the spin-torque ferromagnetic resonance (ST-FMR), and out-of-plane damping-like torque (τB) is observed. The ratio between τB and the field-like torque (τA) decreases from 0.175 to 0.138 when inserting 1 nm Cu at the interface and then drops to 0.001 when the thickness of Cu intercalation is 2 nm, indicating that Cu intercalation inhibits the τB component of SOT. Moreover, the SOT efficiency is increased from 3.05 to 5.21, which may be attributed to the Cu intercalation being beneficial to improve the interface between Py and ZrSe3. Theoretical calculation has shown that the Cu spacer can change the conductivity of ZrSe3 from semiconductor to conductor, thereby decreasing the Schottky barrier and increasing the transmission efficiency of the spin current. Furthermore, magneto-optical Kerr effect (MOKE) microscopy is employed to verify the current-driven magnetization switching in these structures. In comparison to the ZrSe3/Py bilayer, the critical current density of ZrSe3/Cu/Py is reduced when inserting 1 nm Cu, demonstrating the higher SOT efficiency and lower power consumption in ZrSe3/Cu/Py structures.
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  • 文章类型: Journal Article
    简介:癌症是世界上第二大死亡原因,尽管有几种癌症治疗药物。因此,癌症研究界强调计算技术,以加快发现新的抗癌药物。方法:在目前的研究中,对Zinc15化合物库(271种甲氨蝶呤(MTX)和光氨蝶呤(PTX)的衍生物)进行了基于QSAR的虚拟筛选,以预测其对二氢叶酸还原酶(DHFR)的抑制活性,潜在的抗癌药物靶标。基于深度学习的ADMET参数用于使用多元线性回归(MPL)方法生成2DQSAR模型,其中保留交叉验证(LOO-CV)Q2和相关系数R2值高达0.77和0.81,分别。结果:从QSAR模型和虚拟筛选分析,最高命中数(09,27,41,68,74,85,99,180)的pIC50范围为5.85~7.20,最小结合评分为-11.6~-11.0kcal/mol,我们接受了进一步调查.使用消息传递神经网络(MPNN)模型的ADMET属性显示了基于亲脂性特征LogP(0.19-2.69)和生物利用度(76.30%至78.46%)的选定命中作为口服药物的潜力。临床毒性评分为31.24%~35.30%,用化合物180观察到的毒性评分最低(8.30%)。进行DFT计算以确定稳定性,所选化合物的物理化学参数和化学反应性。通过100ns分子动力学模拟分析进一步验证了对接结果。结论:与标准参考药物MTX和PTX相比,发现有希望的先导化合物得到认可,这些药物具有最佳的抗癌活性,并且可以在实验验证后产生新疗法。此外,建议通过体外和体内方法揭示已识别的命中的抑制潜力。
    Introduction: Cancer is the second most prevalent cause of mortality in the world, despite the availability of several medications for cancer treatment. Therefore, the cancer research community emphasized on computational techniques to speed up the discovery of novel anticancer drugs. Methods: In the current study, QSAR-based virtual screening was performed on the Zinc15 compound library (271 derivatives of methotrexate (MTX) and phototrexate (PTX)) to predict their inhibitory activity against dihydrofolate reductase (DHFR), a potential anticancer drug target. The deep learning-based ADMET parameters were employed to generate a 2D QSAR model using the multiple linear regression (MPL) methods with Leave-one-out cross-validated (LOO-CV) Q2 and correlation coefficient R2 values as high as 0.77 and 0.81, respectively. Results: From the QSAR model and virtual screening analysis, the top hits (09, 27, 41, 68, 74, 85, 99, 180) exhibited pIC50 ranging from 5.85 to 7.20 with a minimum binding score of -11.6 to -11.0 kcal/mol and were subjected to further investigation. The ADMET attributes using the message-passing neural network (MPNN) model demonstrated the potential of selected hits as an oral medication based on lipophilic profile Log P (0.19-2.69) and bioavailability (76.30% to 78.46%). The clinical toxicity score was 31.24% to 35.30%, with the least toxicity score (8.30%) observed with compound 180. The DFT calculations were carried out to determine the stability, physicochemical parameters and chemical reactivity of selected compounds. The docking results were further validated by 100 ns molecular dynamic simulation analysis. Conclusion: The promising lead compounds found endorsed compared to standard reference drugs MTX and PTX that are best for anticancer activity and can lead to novel therapies after experimental validations. Furthermore, it is suggested to unveil the inhibitory potential of identified hits via in-vitro and in-vivo approaches.
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  • 文章类型: Journal Article
    同质对映选择性催化是当今制造对映纯物质的基石,但其技术实施受到众所周知的障碍,如缺乏表现出长期稳定性的可持久催化剂。具有催化活性的金属间化合物钯-镓(PdGa),在其表面保留先天的本体手性,代表了通过多相催化研究不对称化学反应的有前途的系统,与工业过程具有前瞻性相关性。这里,这项工作通过扫描隧道显微镜(STM)和光谱学(STS)研究了10,10'-二溴-9,9'-双蒽(DBBA)在PdGa:A(1'1'1'1'$\\bar{1}\\bar{1}\\bar{1}$)Pd3终止表面上的吸附。观察到分子的高度对映选择性吸附在室温以下演变成接近100%的对映体过量。这种异常高的对映体过量归因于S至R手性构象异构体的温度活化转化。R构象体的尖端诱导的键裂解显示了DBBA脱溴的非常高的区域选择性。实验结果由密度泛函理论原子模拟解释。这项工作将手性转移的知识扩展到非平面分子的对映选择性吸附上,并显示了PdGa表面的整体效应,从而产生了强大的区域选择性脱溴作用。
    Homogenous enantioselective catalysis is nowadays the cornerstone in the manufacturing of enantiopure substances, but its technological implementation suffers from well-known impediments like the lack of endurable catalysts exhibiting long-term stability. The catalytically active intermetallic compound Palladium-Gallium (PdGa), conserving innate bulk chirality on its surfaces, represent a promising system to study asymmetric chemical reactions by heterogeneous catalysis, with prospective relevance for industrial processes. Here, this work investigates the adsorption of 10,10\'-dibromo-9,9\'-bianthracene (DBBA) on the PdGa:A( 1 ¯ 1 ¯ 1 ¯ $\\bar{1}\\bar{1}\\bar{1}$ ) Pd3-terminated surface by means of scanning tunneling microscopy (STM) and spectroscopy (STS). A highly enantioselective adsorption of the molecule evolving into a near 100% enantiomeric excess below room temperature is observed. This exceptionally high enantiomeric excess is attributed to temperature activated conversion of the S to the R chiral conformer. Tip-induced bond cleavage of the R conformer shows a very high regioselectivity of the DBBA debromination. The experimental results are interpreted by density functional theory atomistic simulations. This work extends the knowledge of chirality transfer onto the enantioselective adsorption of non-planar molecules and manifests the ensemble effect of PdGa surfaces resulting in robust regioselective debromination.
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  • 文章类型: Journal Article
    磁铁矿是一种还原性含铁(II)矿物,其还原性被认为对地下水和厌氧地下环境中污染物的降解很重要。然而,由于自然和人为干扰,地下环境的氧化还原条件经常从厌氧变为需氧,通过含Fe(II)的矿物与O2之间的相互作用产生活性氧(ROS)。尽管如此,在有氧条件下磁铁矿诱导的ROS产生的机制知之甚少,这可能在As(III)氧化中起关键作用。在这里,我们发现磁铁矿在有氧条件下可以激活O2并诱导As(III)的氧化转化。As(III)氧化归因于磁铁矿八面体氧合中通过结构Fe(II)产生的ROS。电子顺磁共振和猝灭测试证实,O2•-,H2O2和·OH由磁铁矿产生。此外,密度泛函理论计算与实验相结合表明,O2•-最初是通过单电子从结构Fe(II)转移到吸附的O2而形成的;然后通过一系列自由基反应将O2•-转化为•OH和H2O2。其中,O2·-和H2O2是负责As(III)氧化的主要ROS,约占砷(III)氧化的52%和19%。值得注意的是,由于(III)氧化主要发生在磁铁矿表面,和As进一步固定在磁铁矿结构内。这项研究为磁铁矿在确定氧化还原波动的地下环境中As的命运和转化中的作用提供了坚实的证据。
    Magnetite is a reductive Fe(II)-bearing mineral, and its reduction property is considered important for degradation of contaminants in groundwater and anaerobic subsurface environments. However, the redox condition of subsurface environments frequently changes from anaerobic to aerobic owing to natural and anthropogenic disturbances, generating reactive oxygen species (ROS) from the interaction between Fe(II)-bearing minerals and O2. Despite this, the mechanism of ROS generation induced by magnetite under aerobic conditions is poorly understood, which may play a crucial role in As(III) oxidation. Herein, we found that magnetite could activate O2 and induce the oxidative transformation of As(III) under aerobic conditions. As(III) oxidation was attributed to the ROS generated via structural Fe(II) within the magnetite octahedra oxygenation. The electron paramagnetic resonance and quenching tests confirmed that O2•-, H2O2, and •OH were produced by magnetite. Moreover, density function theory calculations combined with experiments demonstrated that O2•- was initially formed via single electron transfer from the structural Fe(II) to the adsorbed O2; O2•- was then converted to •OH and H2O2 via a series of free radical reactions. Among them, O2•-and H2O2 were the primary ROS responsible for As(III) oxidation, accounting for approximately 52 % and 19 % of As(III) oxidation. Notably, As(III) oxidation mainly occurred on the magnetite surface, and As was immobilized further within the magnetite structure. This study provides solid evidence regarding the role of magnetite in determining the fate and transformation of As in redox-fluctuating subsurface environments.
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  • 文章类型: Journal Article
    亚油酸氧化的影响在日常食物消费中不容忽视。这项研究使用气相色谱-质谱(GC-MS)鉴定了180°C下甲基亚油酸的非挥发性氧化产物和挥发性氧化产物,并使用密度泛函理论研究了氧化机理。对非挥发性氧化产物的分析表明存在三种主要的氧化产物。三种主要的氧化产物被确定为氢过氧化物,过氧化物连接的二聚体,和杂环化合物的比例为2.70:1:3.69(mmol/mmol/mmol)。发现次级氧化产物的挥发性成分包括醛类(40.77%),烷烃(19.89%),醇(9.02%),呋喃(6.11%),环氧化物(0.46%),酸(2.50%)。DFT计算证明二次氧化产物主要来自过氧化物(77%)。最后,我们期待我们的研究对脂质自动氧化和人类健康做出积极贡献。
    The impact of the oxidation of linoleic acid cannot be overlooked in daily food consumption. This study used gas chromatography-mass spectrometry (GC-MS) to identify both nonvolatile oxidation products and volatile oxidation products of methyl linoleic acid at 180 °C and density function theory to investigate oxidation mechanisms. An analysis of nonvolatile oxidation products revealed the presence of three primary oxidation products. The three primary oxidation products were identified as hydroperoxides, peroxide-linked dimers, and heterocyclic compounds in a ratio of 2.70:1:3.69 (mmol/mmol/mmol). The volatile components of secondary oxidation products were found including aldehydes (40.77%), alkanes (19.89%), alcohols (9.02%), furans (6.11%), epoxides (0.46%), and acids (2.50%). DFT calculation proved that the secondary oxidation products mainly came from peroxides (77%). Finally, we look forward to our research contributing positively to lipid autoxidation and human health.
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  • 文章类型: Journal Article
    Remdesivir(RDV)是对抗SARS-CoV-2病毒大流行的有效药物。RDV作用机制中的关键步骤之一是将其掺入正在生长的RNA链中。RDV,一种腺苷类似物,与尿苷在互补链中形成Watson-Crick(WC)型氢键,这种相互作用的强度将控制RDV的功效。虽然有大量关于天然碱基对中WCH键的结构和能量信息,尚未在原子水平上研究RDV与尿苷的相互作用。在这篇文章中,我们的目标是弥合这个差距,为了理解RDV及其氢键相互作用,通过在M06-2X/cc-pVDZ水平下采用密度泛函理论(DFT)。相互作用的能量,QTAIM分析,对RDV执行NBO和SAPT2,腺苷,以及它们与尿苷的复合物,以深入了解氢键的性质。计算表明RDV具有相似的几何形状,精力充沛,分子轨道,和芳香作为腺苷,表明RDV是一种有效的腺苷类似物。重要的几何参数,例如腺苷拉伸振动模式中的键距离和红移,RDV和尿苷识别两个WC型H键。使用QTAIM参数和计算的氢键能计算这两个H键的相对强度。最后,SAPT2研究在最小值和非平衡碱基对距离下进行,以了解主要的分子间物理力。这项研究,基于对各种计算的全面分析,表明腺苷和RDV具有相似的结构,精力充沛,和氢键行为。
    Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.
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