Density Functional Tight-Binding Studies of Carbon Nanotube Structures

A density functional tight-binding self-consistent charge approach has been used to study the structures and elastic properties of nine model carbon nanotubes of different helicities and diameters between 5.5 and 10.8 A. The systems contain from 112 to 268 atoms and were optimized under periodic boundary conditions in the axial direction. Both the carbon networks and the overall tube dimensions were optimized. Most of the C—C bond lengths are slightly lengthened relative to graphene (two-dimensional graphite); the others remain essentially the same or are shorter. There is overall a longitudinal compression of the tube. The strain energy per atom, relative to graphene, varies inversely with the square of the tube radius. The Young's moduli decrease with increasing radius but do not depend upon chirality. The Poisson ratios are nearly constant. The consequences of removing an electron from each system were also investigated. In most instances, the tube dimensions were little affected; in only a few cases is there a change in length or radius (positive or negative) as large as 0.10%. The Young's moduli remain the same as for the neutral systems, but the Poisson ratios tend to increase for metals and semimetals and to decrease for semiconductors.     

Density Functional Theory Study of MoO3 Molecule Encapsulated inside Single-walled Carbon Nanotubes~

The binding energies, geometric structures and electronic properties of molybdenum trioxide (MoO3) molecule encapsulated inside (8,0), (9,0), (10,0) and (14,0) single-walled carbon nanotubes (SWNTs) have been investigated using density functional theory (DFT) method. Due to curvature effect, the calculated binding energy values are different, the variation of which indicated that the stability of MoO3 /SWNT systems increases with increasing the radius of SWNTs. At the same time, owing to the presence of MoO3 molecule, the band gap of MoO3 /SWNTs systems decreases. The analysis of density of states (DOS) reveals hybridization between C-2p and Mo-4d and between C-2p and O-2p orbitals near the Fermi level, which results in electron transfer from SWNTs to MoO3 molecule. The present computations suggest that electronic properties of SWNTs can be modified by doping MoO3 molecule.     

三硝基均苯三酚及其碱金属盐晶体的周期性密度泛函理论研究

对三硝基均苯三酚(TNPG)及其碱金属盐晶体进行DFT-B3LYP周期性计算研究, 求得其能带和电子结构, 探讨了结构-性能关系. 研究结果表明, 晶胞结构参数的计算值与实验值吻合较好. TNPG的导电性介于半导体和绝缘体之间, 而其碱金属盐均为半导体. 金属离子的引入使TNPG阴离子和金属阳离子通过配位键形成三维无限网状结构, 这种网状结构与晶体的半导体性质相关联. TNPG及其碱金属盐的前线轨道主要是由C—NO₂的原子轨道组成, 配位水和金属离子对前线轨道的组成没有贡献. TNPG碱金属盐的带隙均比TNPG的小, 根据“最易跃迁原理”可推测碱金属盐均比TNPG敏感, 这与实验事实相符. 同时, 金属离子的引入增大了酚羟基上的氧原子的活性, 这也可能是导致碱金属盐比TNPG敏感的原因之一.     

Halogen Bonding in Haspin-Halogenated Tubercidin Complexes: Molecular Dynamics and Quantum Chemical Calculations

Haspin, an atypical serine/threonine protein kinase, is a potential target for cancer therapy. 5-iodotubercidin (5-iTU), an adenosine derivative, has been identified as a potent Haspin inhibitor in vitro. In this paper, quantum chemical calculations and molecular dynamics (MD) simulations were employed to identify and quantitatively confirm the presence of halogen bonding (XB), specifically halogen∙∙∙π (aromatic) interaction between halogenated tubercidin ligands with Haspin. Consistent with previous theoretical finding, the site specificity of the XB binding over the ortho-carbon is identified in all cases. A systematic increase of the interaction energy down Group 17, based on both quantum chemical and MD results, supports the important role of halogen bonding in this series of inhibitors. The observed trend is consistent with the experimental observation of the trend of activity within the halogenated tubercidin ligands (F < Cl < Br < I). Furthermore, non-covalent interaction (NCI) plots show that cooperative non-covalent interactions, namely, hydrogen and halogen bonds, contribute to the binding of tubercidin ligands toward Haspin. The understanding of the role of halogen bonding interaction in the ligand–protein complexes may shed light on rational design of potent ligands in the future.     

多氯代菲分子结构和热力学性质的密度泛函理论研究

采用密度泛函理论方法在B3LYP/6-311G(d, p)水平上对527个多氯代菲分子的几何结构进行了全优化并计算得到它们的热力学性质(等容热容( )、熵(S$)、标准生成焓(ΔfH$)和标准生成Gibbs自由能(ΔfG$)), 研究了这些性质与取代的氯原子数目和位置的关系, 根据各异构体的相对标准生成Gibbs自由能(Δr,fG$)的大小, 得到它们的热力学稳定性顺序. 计算结果表明: 绝大多数多氯代菲分子具有非平面的几何构型, 在多氯代菲分子中存在三种类型的分子内弱相互作用(H…H、C—H…Cl和Cl…Cl相互作用), 随着分子中取代的氯原子数目的增加, 多氯代菲最稳定异构体的ΔfH$和ΔfG$开始时逐渐减小, 然后又快速增加. 具有相同数目氯原子的多氯代菲异构体的ΔfH$和ΔfG$与氯原子的取代位置有很大的关系. 多氯代菲异构体的相对热力学稳定性主要由分子内的离域π键和Cl…Cl核排斥作用的强弱决定.     

DFT (density functional theory) studies on cycloisomerization of 15–membered triazatriacetylenic macrocycle

The mechanism as well the stereochemistry of cascade cycloisomerization of 15–membered triazatriacetylenic macrocycle was investigated theoretically by using M062X/6–31+G(d,p) and M062X/LANL2DZ calculations. The results showed that the mechanism and outcome of the reaction depended on the absence and presence of a transition metal catalyst. So that, in thermal-induced condition, the reaction had to experience several suprafacial concerted reactions including Ene-reaction (DG^#=35.38 kcal/mol), Diels–Alder cycloaddition (DG^# = 17.16 kcal/mol), and sigmatropic H-shift rearrangement (DG^# = 56.21 kcal/mol) to produce diastereoselective fused cis–tetracyclic aromatic bearing a pyrrole moiety by following kinetic considerations. Also, the [2+2+2] cycloaddition mechanism was neglected in thermal–induced conditions because of high activation free Gibbs energy (DG^# = 63.90 kcal/mol). In the presence of palladium catalyst, Pd(0) formed an adduct by coordinating to C = C bonds and decreased the DG^# of the process to 29.58 kcal/mol, and consequently provided a facilitated media for the reaction to follow the [2+2+2] to produce more stable fused tetracyclic benzenoid aromatic by passing through the lower energy barrier.     

Studies of Structural and Thermodynamic Properties for Polychlorinated Thianthrenes by Density Functional Theory

The structural and thermodynamic （PCTAs） in the ideal gas state at 298.15 K and 1.013 properties of 75 polychlorinated thianthrenes ×10^5 Pa have been calculated at the B3LYP/6- 31G＊ level using Gaussian 98 program. Based on the output data of Gaussian, the isodesmic reactions were designed to calculate standard enthalpy of formation （△fH^θ） and standard free energy of formation （△fH^θ） of PCTAs congeners. The relations of these thermodynamic parameters with the number and position of C1 atom substitution （Npcs） were discussed, and it was found that there exists high correlation between thermodynamic parameters （total energy （TE）, zero-point vibrational energy （ZPE）, thermal correction to energy （Eth）, heat capacity at constant volume （Cv^θ）, entropy （S^θ）, enthalpy （H^θ）, free energy （G^θ）, standard enthalpies of formation （△fH^θ） and standard Gibbs energies of formation （△fG^θ）） and Npcs. On the basis of the relative magnitude of their △fG^θ, the order of relative stability of PCTA congeners was theoretically proposed. In addition, the correlations between structural parameters and Npcs were also discussed. The good correlations were found between molecular average polarizability （α）, energy of the highest occupied molecular orbital （EHOMO）, molecular volume （Vm） and Npcs, and all R^2 values are larger than 0.95. Moreover, it was supposed that the isomer groups with higher toxicity should be Tri-CTA and TCTA.     

HNCO与CX（X=F，Cl，Br）自由基反应机理的密度泛函理论研究

用量子化学密度泛函理论的B3LYP方法,在6-31+G~*水平上按BERNY能量梯度解 析全参数优化了HNCO与CX（X=F,Cl,Br）反应势能面上各驻点的几何构型,通过 振动频率分析确认了中间体和过渡态,内禀反应坐标（IRC）对反应物、中间体、 过渡态和产物的相关性予以证实,对各驻点进行了零点能校正（ZPE）在此基础上 计算了反应能垒。研究结果表明,与HNCO和其它小分子自由基反应不同,HNCO与 CX自由基反应首先发生分子间H原子迁移,随后N与CX的C（1）原子相互靠近成键并 生成较稳定的中间体,再发生N-C（2）键的断裂,完成N向C（1）上的迁移并进一 步解离为产物。反应按反应物→TS1→IM→TS2→产物通道进行。反应为放热反应。     

Doxorubicin Encapsulation in Carbon Nanotubes Having Haeckelite or Stone–Wales Defects as Drug Carriers: A Molecular Dynamics Approach

Doxorubicin (DOX), a recognized anticancer drug, forms stable associations with carbon nanotubes (CNTs). CNTs when properly functionalized have the ability to anchor directly in cancerous tumors where the release of the drug occurs thanks to the tumor slightly acidic pH. Herein, we study the armchair and zigzag CNTs with Stone–Wales (SW) defects to rank their ability to encapsulate DOX by determining the DOX-CNT binding free energies using the MM/PBSA and MM/GBSA methods implemented in AMBER16. We investigate also the chiral CNTs with haeckelite defects. Each haeckelite defect consists of a pair of square and octagonal rings. The armchair and zigzag CNT with SW defects and chiral nanotubes with haeckelite defects predict DOX-CNT interactions that depend on the length of the nanotube, the number of present defects and nitrogen doping. Chiral nanotubes having two haeckelite defects reveal a clear dependence on the nitrogen content with DOX-CNT interaction forces decreasing in the order 0N > 4N > 8N. These results contribute to a further understanding of drug-nanotube interactions and to the design of new drug delivery systems based on CNTs.     

Surface Modification Strategy for Enhanced NO2 Capture in Metal–Organic Frameworks

The interaction strength of nitrogen dioxide (NO₂) with a set of 43 functionalized benzene molecules was investigated by performing density functional theory (DFT) calculations. The functional groups under study were strategically selected as potential modifications of the organic linker of existing metal–organic frameworks (MOFs) in order to enhance their uptake of NO₂ molecules. Among the functional groups considered, the highest interaction energy with NO₂ (5.4 kcal/mol) was found for phenyl hydrogen sulfate (-OSO₃H) at the RI-DSD-BLYP/def2-TZVPP level of theory—an interaction almost three times larger than the corresponding binding energy for non-functionalized benzene (2.0 kcal/mol). The groups with the strongest NO₂ interactions (-OSO₃H, -PO₃H₂, -OPO₃H₂) were selected for functionalizing the linker of IRMOF-8 and investigating the trend in their NO₂ uptake capacities with grand canonical Monte Carlo (GCMC) simulations at ambient temperature for a wide pressure range. The predicted isotherms show a profound enhancement of the NO₂ uptake with the introduction of the strongly-binding functional groups in the framework, rendering them promising modification candidates for improving the NO₂ uptake performance not only in MOFs but also in various other porous materials.     

多氯咔唑系列化合物的热力学性质的密度泛函理论研究

采用Gaussian 03程序中的密度泛函(DFT)方法, 在B3LYP/6-31G*水平上对135个多氯咔唑系列化合物(PCCZs)进行了全优化计算, 得到了298.15 K, 1.013×105 Pa标准状态下各分子的热力学性质. 设计等键反应, 计算了PCCZs系列化合物的标准生成热(ΔfHÖ)和标准生成自由能(ΔfGÖ), 研究了这些参数与氯原子的取代位置及取代数目(NPCS)之间的关系, 结果表明: 熵(SÖ), ΔfHÖ, ΔfGÖ与NPCS之间有很强的相关性. 并根据ΔfGÖ的相对大小, 从理论上求得异构体的相对稳定性的顺序. 此外, 以Gaussian 03程序的输出文件为基础, 采用统计热力学程序计算了PCCZs化合物在200至1800 K的摩尔恒压热容(Cp,m), 并用最小二乘法求得Cp,m与温度之间的相关方程, 发现Cp,m与T, T－1和T－2之间有着很好的相关性.     

Efficient Use of Carbon Fibers as Heating Elements for Curing of Epoxy Matrix Composites

The aim of this study is to achieve a fully cured thermoset matrix that is heated by a direct electric current passing through the reinforcement fibers i.e., the Joule heating effect. Two types of fibers were used as heating elements for curing the epoxy resins. Kanthal resistance fibers were used as reference heating elements and subsequently, they were replaced by a Torayca Carbon Tow of the same radius. The specimens were cured by the heat produced by a direct electric current passing through the fibers and achieving temperatures of 50 °C and 70 °C. Specimens cured in a conventional oven were also manufactured, to compare the resistance heating method to the conventional one. Next, all specimens were mechanically characterized in a quasi-static three-point bending mode of loading and experimental results were compared to derive useful conclusions concerning the applicability of the technique to polymer/composite materials mass production. Finally, a preliminary economical study concerning power consumption needed for the application of both the traditional oven curing and the carbon fibers heating elements use for the manufacturing of the same amounts of materials is presented, showing a maximum financial benefit that can be achieved, on the order of 68%.     

An Ab Initio Molecular Orbital Theory and Density Functional Theory (DFT) Study of Conformers and Rotamers of 4-Substituted (Methyl, Hydroxymethyl, Methanoyl, Ethanoyl, Cyano, Fluoro, Chloro, Bromo, Acetoxy) Tetrahydro-2H-thiopyran-1,1-dioxides

The structures and energies of axial and equatorial conformers and rotamers of 4-substituted tetrahydro-2H-thiopyran-1,1-dioxides (tetrahydrothiopyran-1,1-dioxides, thiacyclohexane-1,1-dioxides, thiane-1,1-dioxides, and 1,1-dioxothianes; CH₃, CH₂OH, CHO, COCH₃, CN, F, Cl, Br, and OCOCH₃) were calculated using the hybrid density functionals B3LYP, B3P86, and B3PW91, as well as MP2 and the 6-31G(d), 6-31G(2d), 6-31G(3d), 6-31G(d,p), and 6-31+G(d) basis sets. MP2/6-31+G(d)/ /HF/6-31+G(d) [–G° = 1.73 kcal/mol], B3P86/6-31G(d) [–G° = 1.75 kcal/mol], and B3PW91/6-31G(d) [–G° = 1.85 kcal/mol] gave conformational free energy (G°) values at 180 K for 4-methyltetrahydro-2H-thiopyran-1,1-dioxide which were similar to the reported experimental values for methylcyclohexane (–G° = 1.80 kcal/mol), 4-methyltetrahydro-2H-thiopyran (–G° = 1.80 kcal/mol), and other 4-methyl-substituted heterocycles. All levels of theory showed that the conformational preferences of the 4-methanoyl (4-formyl), 4-ethanoyl (4-acetyl), and 4-cyano substituents were small. The HF calculations gave conformational free energy (G°) values for 4-chlorotetrahydro-2H-thiopyran-1,1dioxide which were closer to the experimental value than the MP2 and density functional methods. The best agreement with available experimental data for 4-bromotetrahydro-2H-thiopyran-1,1-dioxide was obtained from the HF/6-31G(2d), HF/6-31G(3d), and B3LYP/6-31G(2d) calculations, and, for 4-acetoxytetrahydro-2H-thiopyran-1,1-dioxide, from the HF/6–31G(3d) calculations. The conformational free energies (G°) and relative energies (E) of the conformers and rotamers have been compared with the correspondingly substituted cyclohexanes and tetrahydro-2H-thiopyrans and are discussed in terms of dipole–dipole (electrostatic) interactions and repulsive nonbonded interactions (steric) in the most stable axial and equatorial conformers. The axial S=O bond lengths are shorter than the equatorial S=O bond lengths and the C2–C3 bond lengths in the substituents with carbon-bonded to the ring are shorter than the C3–C4 and C4–C-5 bond lengths. In contrast, the C2–C3 bond lengths in the 4-halogen and 4-acetoxy substituents are longer than the C3–C4 and C4–C-5 bond lengths.     

Synthesis,Kinetic and Conformational Studies of 2-Substituted-5-(β-d-glucopyranosyl)-pyrimidin-4-ones as Potential Inhibitors of Glycogen Phosphorylase

Dysregulation of glycogen phosphorylase, an enzyme involved in glucose homeostasis, may lead to a number of pathological states such as type 2 diabetes and cancer, making it an important molecular target for the development of new forms of pharmaceutical intervention. Based on our previous work on the design and synthesis of 4-arylamino-1-(β-d-glucopyranosyl)pyrimidin-2-ones, which inhibit the activity of glycogen phosphorylase by binding at its catalytic site, we report herein a general synthesis of 2-substituted-5-(β-d-glucopyranosyl)pyrimidin-4-ones, a related class of metabolically stable, C-glucosyl-based, analogues. The synthetic development consists of a metallated heterocycle, produced from 5-bromo-2-methylthiouracil, in addition to protected d-gluconolactone, followed by organosilane reduction. The methylthio handle allowed derivatization through hydrolysis, ammonolysis and arylamine substitution, and the new compounds were found to be potent (μM) inhibitors of rabbit muscle glycogen phosphorylase. The results were interpreted with the help of density functional theory calculations and conformational analysis and were compared with previous findings.     

Density Functional Theory Study on (Cl2GaN3)n(n=1–4) Clusters

The molecular geometries, vibrational properties, and thermodynamic properties of the clusters (Cl₂GaN₃)_n(n=1–4) have been predicted at the B3LYP/6‐311+G* level. The optimized clusters (Cl₂GaN₃)_n (n=2–4) all possess cyclic structures containing Ga N_α Ga linkages. The relationships between geometrical parameters and oligomerization degree n are discussed. The gas‐phase structures of the trimers prefer to exist in boat‐twisting conformation. As for the tetramer, the S₄ symmetry structure is the most stable. The infrared spectra are obtained and assigned by vibrational analysis. Thermodynamic properties derived from the infrared spectra on the basis of statistical thermodynamic principles are linearly correlated with the oligomerization degree n as well as the temperature. Meanwhile, thermodynamic analysis of the gas‐phase reaction suggests that the oligomerization is exothermic and favorable under high temperature.     

Reactivity and Selectivity of Captodative Olefins as Dienes in Hetero‐Diels–Alder Reactions

The reactivity and selectivity of the the captodative olefins 1‐acylvinyl benzoates 1a – 1f and 3a as heterodienes in hetero‐Diels–Alder reactions in the presence of electron‐rich dienophiles is described. Heterodienes 1 undergo regioselective cycloaddition with the alkyl vinyl etherdienophiles 6a , b and 9 to give the corresponding dihydro‐2H‐pyrans 7, 8 , and 10 under thermal conditions. The reactivity of these cycloadditions depends, to a large extent, on the electronic demand of the substituent in the aroyloxy group of the heterodiene. Frontier‐molecular‐orbital (FMO; ab initio) and density‐functional‐theory (DFT) calculations of the ground and transition states account for the reactivity and regioselectivity observed in these processes.