An efficient method for accurate evaluation of the site–site direct correlation functions of molecular fluids

The direct correlation function (DCF) plays an important role in liquid integral-equation theories and non-mean-field applications of the classical density functional theory (DFT). While for a simple fluid the DCF can easily be calculated from the radial distribution function via the Fourier transform and/or, for special cases, can be derived from analytical solutions of the Ornstein–Zernike equation, computation of the site–site DCFs of a molecular fluid is more challenging because of numerical issues associated with solving the matrix integral equations. This paper describes a new theoretical method for accurate evaluation of the site–site DCFs of molecular fluids by combination of molecular simulation and analytical asymptotic analysis. The computational procedure entails four steps: (1) molecular simulation is used to calculate the site–site total correlation functions (TCFs) in real space; (2) the reference-interaction-site model (RISM) is used to calculate the site–site DCFs in Fourier space at large wavenumbers; (3) asymptotic expressions are derived for the TCFs and DCFs in the limit of small wavenumbers; and (4) site–site DCFs over the entire range are obtained by interpolation of the asymptotic results. The numerical procedure has been illustrated by application to bulk SPC/E water. Accurate evaluation of the site–site DCFs for water lays a foundation for future applications of the DFT to aqueous systems with atomic details.     

Theoretical study of the [Si,C, P,O] potential energy surface

The structures, energetics, spectroscopies and stability of the doublet [Si, C, P, O] radical are explored at the density functional theory and ab initio levels. Eighteen isomers connected by 22 interconversion transition states are located at the DFT/B3LYP/6-311G(d) level. The structures of the kinetically stable isomers and the relevant transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311 + G(2df) single-point energy calculations. At the QCISD/6-311G(d) level, the lowest-lying isomer is the cyclic O-cCSiP 8 (0.0 kcal/mol) with considerable kinetic stability of 22.0 kcal/mol. In addition, two bent isomers OSiCP 1 (7.3 kcal/mol) and SiCPO 3 (34.7 kcal/mol) also possess considerable kinetic stability (more than 10.0 kcal/mol). As a result, three isomers 1, 3 and 8 are predicted to be possible candidates for future experimental and astrophysical detection. The bonding nature of the three isomers is analysed. The calculated results are compared with those of the analogous radical [Si, C, N, O]. Implications in the laboratory and interstellar space are also discussed. The predicted structures and spectroscopic properties are expected to be informative for the identification of [Si, C, P, O] in the laboratory and space.     

Theoretical study on structures and stability of SiC3S isomers

Various levels of calculations are carried out to explore the potential energy surfaces (PES) of singlet and triplet SiC₃S, a molecule of potential interest in interstellar chemistry. At the DFT/B3LYP/6-311G(d) level, a total of 57 minimum isomers and 92 interconversion transition states are located. The structures of the most relevant isomers and transition states are further optimized at the QCISD/6-311G(d) level followed by CCSD(T)/6-311?+?G(2df) single-point energy calculations. At the QCISD level, the lowest-lying isomer is the chain-like SiCCCS ³ 1 (0.0?kcal/mol) with a great kinetic stability of 54.1?kcal/mol. In addition, ring isomers CC-cCSSi ¹ 9 (19.8?kcal/mol), S-cCCCSi ¹ 12 (30.4?kcal/mol), S-cCCSiC ¹ 18 (9.4?kcal/mol), S-cSiCCC ¹ 21 (34.4?kcal/mol) and cage-like isomer cage-SiSCCC ¹ 23 (51.8?kcal/mol) also possess considerable kinetic stability (more than 10.0?kcal/mol). As a result, these six isomers are predicted to be possible candidates for future experimental and astrophysical detection. The bond natures and possible formation pathways in interstellar space of the SiCCCS are discussed. The predicted structure and spectroscopic properties for it are expected to be informative for the identification of SiC₃S and even larger SiC _n S species either in laboratory or in space.     

Solvent effects and potential of mean force study of the S_N2 reaction of CH_3F+CN~- in water

We used a combined quantum mechanics and molecular mechanics(QM/MM) method to investigate the solvent effects and potential of mean force of the CH_3F+CN~- reaction in water. Comparing to gas phase, the water solution substantially affects the structures of the stationary points along the reaction path. We quantitatively obtained the solvent effects' contributions to the reaction: 1.7 kcal/mol to the activation barrier and -26.0 kcal/mol to the reaction free energy.The potential mean of force calculated with the density functional theory/MM theory has a barrier height at 19.7 kcal/mol,consistent with the experimental result at 23.0 kcal/mol; the calculated reaction free energy at -43.5 kcal/mol is also consistent with the one estimated based on the gas-phase data at -39.7 kcal/mol.     

Molecular simulation investigations on the coating of Al-alloy surface by nano-SiO2-epoxy composite

To improve corrosion protections, a better understanding of the coating behavior and therefore the interaction properties between the inhibitor and the surface is a vital factor. Density functional theory (DFT) simulations were used to explore the adsorption properties of the pure epoxy and nano-SiO₂-epoxy composites on the Al₂Cu surface. The interaction energies and transferred charges of adsorbed composites on the Al₂Cu surface and their optimized structures with various interacting orientations are investigated. It is found that nano-SiO₂-epoxy adsorb more strongly on Al₂Cu substrate in comparison with the epoxy matrix with interaction energies of ˗228.084 kcal/mol and ˗35.341 kcal/mol, respectively. The validity of our computational methods was evaluated by experiments as well as high-level quantum chemistry method. The atom-in-molecules analysis with DFT indicates that the interaction nature is typical for electrostatics. The stability of the adsorption behavior of composites on the surface was also explored by DFT-based molecular dynamics simulation.     

Density and bond-orientational relaxations in supercooled water

ABSTRACT

Recent computational studies have reported evidence of a metastable liquid–liquid phase transition (LLPT) in molecular models of water under deeply supercooled conditions. A competing hypothesis suggests, however, that non-equilibrium artefacts associated with coarsening of the stable crystal phase have been mistaken for an LLPT in these models. Such artefacts are posited to arise due to a separation of time scales in which density fluctuations in the supercooled liquid relax orders of magnitude faster than those associated with bond-orientational order. Here, we use molecular simulation to investigate the relaxation of density and bond-orientational fluctuations in three molecular models of water (ST2, TIP5P and TIP4P/2005) in the vicinity of their reported LLPT. For each model, we find that density is the slowly relaxing variable under such conditions. We also observe similar behaviour in the coarse-grained mW model of water. Our findings, therefore, challenge the key physical assumption underlying the competing hypothesis.     

Equation of state for the Lennard-Jones truncated and shifted fluid with a cut-off radius of 2.5 σ based on perturbation theory and its applications to interfacial thermodynamics

ABSTRACT

An equation of state is presented for describing thermodynamic properties of the Lennard-Jones truncated and shifted (LJTS) potential with a cut-off radius of 2.5 σ. It is developed using perturbation theory with a hard-sphere reference term and labelled with the acronym PeTS (perturbed truncated and shifted). The PeTS equation of state describes the properties of the bulk liquid and vapour and the corresponding equilibrium of the LJTS fluid well. Furthermore, it is developed so that it can be used safely in the entire metastable and unstable region, which is an advantage compared to existing LJTS equations of state. This makes the PeTS equation of state an interesting candidate for studies of interfacial properties. The PeTS equation of state is applied here in two theories of interfaces, namely density gradient theory (DGT) and density functional theory (DFT). The influence parameter of DGT as well as the interaction averaging diameter of DFT are fitted to data of the surface tension of the LJTS fluid obtained from molecular simulation. The results from both theories agree very well with those from the molecular simulations.     

Adsorption of mercaptopurine drug on the BN nanotube,nanosheet and nanocluster: a density functional theory study

ABSTRACT

We have investigated the interaction of mercaptopurine (MP) drug with BN nanotube, nanosheet and nanocluster using density functional theory calculations in the gas phase, and aqueous solution. We predicted that the MP drug tends to be physically adsorbed on the surface of BN nanosheet with an adsorption energy (E_ad) about ?3.2?kcal/mol. The electronic properties of BN nanosheet are not affected by the MP drug, and this sheet is not a sensor. But the electronic properties of BN nanotube and nanocluster are significantly sensitive to this drug in both gas phase, and aqueous solution. The BN nanocluster suffers from a long recovery time (8.8?×?10⁸?s) because of a strong interaction (E_ad?=??28.6?kcal/mol), and this cluster is not a proper sensor for MP detection. But the BN nanotube benefits from a short recovery time about 49.5?s at room temperature, and may be a promising candidate for application in the MP sensors. The water solvent decreases the strength of interaction between the BN nanotube, and MP drug, but it does not affect the electronic sensitivity of the nanotube sensibly.     

Intramolecular dynamics in small radicals with anisotropic magnetic interactions

The ESR lineshape of one electron spin coupled by anisotropic hyperfine interaction to two nuclei is calculated when two different configurations of the molecule interchange by a simple reaction scheme. The spectrum calculation includes the anisotropic electron Zeeman interaction and the nonsecular terms of the electron spin. The lineshape, which simulates both a nonsaturated CW or a pulse experiment, is calculated numerically by using a density matrix theory within the Liouville formalism. The theory is tested against the X-band spectra of-CH₂ in ZnAc single crystal for three different orientations of the magnetic field. The present theoretical lineshape reproduces all the experimental “forbidden” transitions and predicts that they are important for certain crystal orientations. The calculated reorientation barrier of the methylene in the present work is 7.17 kcal/mol which is closer to an estimated minimum value of 9 kcal/mol, than the previous value of 5–6 kcal/mol obtained by an analysis with the modified Bloch equations.     

A theoretical study of CHx chemisorption on the Ni(100) and Ni(111) surfaces

Cluster model calculations have been performed for CH_x, x = 0−3, chemisorbed on Ni(100) and Ni(111). The predicted chemisorption energies, at the present level of theory, based on bond-prepared clusters for Ni(100) are for carbon 150 kcal/mol, for CH 136 kcal/mol, for CH₂ 91 kcal/mol and for CH₃ 46 kcal/mol. The corresponding energies for Ni(111) are for CH 120 kcal/mol, for CH₂ 88 cal/mol and for CH₃ 49 kcal/mol. These chemisorption energies lead to similar stabilities for all CH_x fragments on both Ni(100) and Ni(111). Large basis sets and multi-reference correlation treatments are found to be very important in particular for the multiply bonded species. The vibrational C-H stretching frequencies predicted for CH_x on Ni(111) are for CH 3054 cm⁻¹ (2980 cm⁻¹), for CH₂ 3204 cm⁻¹ and for CH₃ 2709 cm⁻¹ (2680 cm⁻¹), where the available experimental values are given in parent The predicted ionization spectra of adsorbed CH_x are also in general agreement with experimental findings.     

Isoniazid drug adsorption on the pristine and Al-doped zinc oxide nanosheets: a molecular modeling

Experimental works have exposed that Al-doping in the structure of ZnO nanostructures intensely increases their electronic sensitivity toward various chemicals. Herein, density functional theory calculations were employed to inspect the Al-doping effect on the sensitivity of a ZnO nanosheet (ZnOS) to the isoniazid (IS) drug. The pristine ZnOS physically adsorbs an IS molecule with adsorption energy (E _ad) of ?6.8?kcal/mol, and the sensing response value of 2.3 at 298?K. Replacing a Zn atom by an Al atom strengthens the interaction, increasing the E _ad to ?20.8?kcal/mol. Also, the Al-doping significantly increases the sensing response value to 150.3 by rising the electrical conductivity of the sheet. A short recovery time of 11.3 s is predicted for the Al-ZnOS-based sensor. The water solvent somewhat strengthens the interaction of IS drug with the Al-ZnOS, increasing the sensing response from 150.3 to 175.8. We concluded that the Al-doping makes the ZnOS a promising sensor for IS drug detection.     

电场和温度对聚合物空间电荷陷阱性能的影响

模拟分子的结构和行为有助于更深刻地分析空间电荷陷阱性能变化的微观机理.利用Materials studio软件建立聚乙烯模型,通过分子链段运动产生的能量和自由体积变化对微观结构和电荷陷阱进行分析.结果表明:温度由298 K逐渐升高至363 K的过程中,聚合物分子热运动加剧导致的滑移扩散现象,使自由体积和陷阱能级在363 K处分别出现1542.07 ~3和0.66 eV的最大值和最小值.然而在Z轴方向施加0.0007 Hartree/Bohr(1 Hartree/Bohr=5.2×10~(11)V/m)电场作用时,由于电致伸缩产生Maxwell应力,使分子链段出现局部有序排列,增大范德瓦耳斯能至-360.18 kcal/mol(1 kcal/mol=4.18 kJ/mol),而自由体积降低了279.77 ~3,导致陷阱能级减小0.45 eV.当363 K和0.0007 Hartree/Bohr联合作用时,聚乙烯的陷阱能级相比同温无电场作用降低0.17 eV.分子模拟结果与实测结果相符.利用分子热运动和电致伸缩效应,初步探讨了材料自由体积和范德瓦耳斯相互作用能变化的微观机理,证实分子链段运动改变了微观结构,从而影响电荷陷阱特性.并且与温度相比,电场作用会使材料产生更低能级的空间电荷陷阱.     

Determination of H2S,COS, CS2 and SO2 by an aluminium nitride nanocluster: DFT studies

ABSTRACT

Density functional theory calculations were used to investigate the potential application of an AlN nanocluster in the detection of H₂S, COS, CS₂ and SO₂ gases. In overall, the order of strength of interaction of these gases with the nanocluster is as follows: SO₂ (E_ad?=??17.6?kcal/mol)?>?H₂S (E_ad?=??14.0?kcal/mol)?>?COS (E_ad?=??8.4?kcal/mol)?>?CS₂ (E_ad?=??4.5?kcal/mol). This indicates that by increasing the electric dipole moment, the adsorption energy becomes more negative. We found that the Al₁₂N₁₂ nanocluster may be a promising work function-type sensor for SO₂ gas among the studied gases. Also, it is an electronic sensor for both SO₂ and CS₂ gases but selectively acts between them because of their different effects on the electrical conductivity. It is neither work function-type nor electronic sensor for H₂S and COS gases. The AlN nanocluster benefits from a short recovery time about 7.7?s and 18.0?ms for desorption of SO₂ and CS₂ gases from its surface at room temperature, respectively. It is also concluded that this cluster can work at a humid environment.     

The interaction of a gold atom with carbon nanohorn and carbon nanotube tips and their complexes with a CO molecule: A first principle calculation

The interactions of a gold atom with: (a) a single-wall carbon nanohorn (SWNH) conic tip; (b) with a single-wall carbon nanotube (SWNT) tip; and (c) their complexes with a CO molecule were studied using first-principle calculations based on density functional theory. The analysis of the pyramidalization angle (θ_p) as well as the π-orbital misalignment angles indicate that there should be many reactive carbon sites on the tips of SWNH and SWNT. It was found that SWNH provides reactive sites that can more selectively interact with the target atom. We identified five sites on both the SWNT tip and the nanohorn where attachment of a gold atom leads to a stable complex. This metal is found to be bi-coordinated with the tip of SWNH, while it is mono-coordinated with the SWNT tip. The largest interaction energies are –10.75 kcal/mol and –16.17 kcal/mol, respectively. The CO probe molecule binds to Au on the Au/SWNH or Au/SWNT tips with interaction energies of –22.34 and –18.29 kcal/mol, respectively. The main contributions of the interaction with both carbon nanostructures stems from σ-donation and π-backbonding. The results suggest that SWNHs could be one of the promising candidates for the development of high-specifity nanosensors.     

Effects of subsurface Na,H and C on the bonding of carbon to nickel surfaces

This paper reports the results of a theoretical study of Na, H and C subsurface atomic species in nickel and demonstrates how these interstitial atoms influence the reactivity of the Ni(111) surface and the structure of carbon species adsorbed on the surface. The benzene molecule, C₆H₆, in planar and nonplanar geometries, is used to probe bonding at the surface. Adsorption energies are calculated by ab initio configuration interaction techniques modelling the surface as an embedded cluster. Adsorption energies of planar C₆H₆ at the most stable, three-fold, adsorption site are 18 kcal/mol for the Ni(111) surface, and 10, 19 and 44 kcal/mol in the presence of the Na, H and C interstitials, respectively. The energies required for the planar to puckered distortion are 99 kcal/mol on Ni(111), 69 kcal/mol with the Na interstitial, 83 kcal/mol with H, and 134 kcal/mol with C compared to 198 kcal/mol for distortion of C₆H₆ in the gas phase. The possible relevance of these results to the nucleation of diamond on nickel are discussed. The results indicate that subsurface Na stabilizes tetrahedrally bonded carbon subunits of the diamond structure while subsurface C may make it easier for the overlayer to revert to a planar graphite structure.     

PdCl2催化芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应的机理研究

:采用密度泛函理论(DFT)中的M06方法, 以二甲基甲酰胺(DMF)溶剂, 研究了无催化剂、PdCl2为催化剂催化芳基硼酸与溴代芳烃的交叉偶联反应的反应机理. 使用6-311+G*基组 (Pd采用赝势基组LanL2DZ) 对芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应过程中所有反应物、中间体、过渡态和产物的几何构型进行了优化, 同时进行了频率计算, 各过渡态都有唯一虚频, 确认了中间体和过渡态的合理性; 通过自然键轨道(NBO)理论和AIM理论分析了分子轨道间的相互作用. 结果发现: 在没有催化剂的条件下, Suzuki-Miyaura偶联反应形成的反应速控步骤活化能为49.70 kcal/mol, 在PdCl2催化作用下, 反应速控步骤活化能为31.08 kcal/mol, 比较研究结果, PdCl2能有效催化该反应的进行, 我们的研究结果与实验结果相吻合.     

PdCl_2催化芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应的机理研究

采用密度泛函理论(DFT)中的M06方法,以二甲基甲酰胺(DMF)溶剂,研究了无催化剂、PdCl_2为催化剂催化芳基硼酸与溴代芳烃的交叉偶联反应的反应机理.使用6-311+G*基组(Pd采用赝势基组Lan L2DZ)对芳基硼酸与溴代芳烃Suzuki-Miyaura偶联反应过程中所有反应物、中间体、过渡态和产物的几何构型进行了优化,同时进行了频率计算,各过渡态都有唯一虚频,确认了中间体和过渡态的合理性;通过自然键轨道(NBO)理论和分子内原子理论(AIM)理论分析了分子轨道间的相互作用.结果发现:在没有催化剂的条件下,Suzuki-Miyaura偶联反应形成的反应速控步骤活化能为49.70 kcal/mol,在PdCl_2催化作用下,反应速控步骤活化能为31.08 kcal/mol,比较研究结果,PdCl_2能有效催化该反应的进行,我们的研究结果与实验结果相吻合.     

On the heat of formation of nitromethane

Two experimental values (?19.3 ± 0.3 and ?17.8 ± 0.1 kcal/mol) for the gas phase heat of formation (δ_fH) (298k) of nitromethane have been reported. Although these values differ by only 1.5 kcal/mol, substantially greater differences in theoretical and experimental results occur when these differing values are used to calculate thermodynamic properties. This is especially evident when these two values for the δ_fH of nitromethane are used to calculate thermodynamic properties of polynitro compounds. For example, when density functional theory (DFT) is coupled with the use of isodesmic reactions, the Δ_fH of octanitrocubane is calculated to be 160.6 or 172.6 kcal/mol, depending on which value is used. It should also be appreciated that several computational theories depend upon having access to reliable experimental data for testing and development. We have examined this discrepancy using several computational models and several levels of theory. Our results coupled with a comprehensive review of the literature support the lower (?19.3 ± 0.3 kcal/mol) experimental value. This is problematic because the higher value (?17.8 ± 0.1 kcal/mol) has been used in the development and/or testing of several semiempirical quantum mechanical models as well as ab initio Gaussian theory (G2 and G3). Copyright © 2008 John Wiley & Sons, Ltd.     

针对电子极化子迁移的哈伯德U修正受限密度泛函理论方法：TiO2实例研究

极化子的形成和迁移对过渡金属氧化物的物理和化学性质有重要影响. 含哈伯德$U$修正的密度泛函理论和受限密度泛函理论方法经常被应用于小极化子迁移性质的理论研究. 本文在投影缀加波框架中实现了哈伯德$U$修正的受限密度泛函理论(cDFT+U),并将其应用于体相TiO₂中的极化子迁移性质的计算. 确认了哈伯德U的取值对极化子性质的理论预测有重要影响. 采用基于cDFT计算所获得的哈伯德U值,可对TiO₂金红石和锐钛矿相中的极化子性质获得与实验符合很好的描述. 本文表明,使用与理论上一致的方式计算获得的哈伯德U值,cDFT+U有望成为一种有效的不需经验输入而计算过渡金属氧化物极化子性质的第一性原理方法.