Structure and cooperativity of the hydrogen bonds in sodium dihydrogen triacetate

Geometry and energetics of low energy conformers of sodium dihydrogen triacetate (SDHTA) and its anion are studied using density functional theory (DFT) at the Becke, Lee‐Yang‐Parr hybrid functional (BLYP) and Becke, three‐parameter, Lee‐Yang‐Parr hybrid functional (B3LYP) levels. For both cases, two structures of comparable energy are found, which have different symmetry with respect to the two hydrogen bonds (HBs). DFT‐based Born–Oppenheimer molecular dynamics simulations are performed for SDHTA, which show that both structures are visited at room temperature conditions. The trajectory analysis further reveals that the two HBs behave anticooperative, that is, on average elongation of one HB is accompanied by a compression of the other one. This is in accord with nuclear magnetic resonance (NMR) experimental studies for a similar counter ion–dihydrogen triacetate complex. © 2012 Wiley Periodicals, Inc.     

Functional and Basis Set Dependence for Time-Dependent Density Functional Theory Trajectory Surface Hopping Molecular Dynamics: Cis-Azobenzene Photoisomerization

Within three functionals (TD-B3LYP, TD-BHandHLYP, and TD-CAM-B3LYP) in combination with four basis sets (3-21g, 6-31g, 6-31g(d), and cc-pvdz), global switching (GS) trajectory surface hopping molecular dynamics has been performed for cis-to-trans azobenzene photoisomerization up to the S₁(nπ*) excitation. Although all the combinations show artificial double-cone structure of conical intersection between ground and first excited states, simulated quantum yields and lifetimes are in good agreement with one another; 0.6 (±5%) and 40.5 fs (±10%) by TD-B3LYP, 0.5 (±10%) and 35.5 fs (±4%) by TD-BHandHLYP, and 0.44 (±9%) and 35.2 fs (±10%) by TD-CAM-B3LYP. By analyzing distributions of excited-state population decays, hopping spots, and typical trajectories with performance of 12 functional/basis set combinations, it has been concluded that functional dependence for given basis set is slightly more sensitive than basis set dependence for given functional. The present GS on-the-fly time-dependent density functional theory (TDDFT) trajectory surface hopping simulation can provide practical benchmark guidelines for conical intersection driven excited-state molecular dynamics simulation involving in large complex system within ordinary TDDFT framework. © 2019 Wiley Periodicals, Inc.     

Determination of glass transition temperature of polyimides from atomistic molecular dynamics simulations and machine-learning algorithms

Glass transition temperature (T_g) plays an important role in controlling the mechanical and thermal properties of a polymer. Polyimides as an important category of engineering plastics have wide applications because of their superior heat resistance and mechanical strength. The capability of predicting T_g for a polyimide a priori is therefore highly desirable in order to expedite the design and discovery of new polyimide polymers with targeted properties and applications. Here we explore three different approaches to either compute T_g for a polyimide via all-atom molecular dynamics simulations or predict T_g via a mathematical model generated by using machine-learning algorithms to analyze existing data collected from the literature. Our simulations reveal that T_g can be determined from examining the diffusion coefficient of simple gas molecules in a polyimide as a function of temperature and the results are comparable to those derived from data on polymer density versus temperature and actually closer to the available experimental data. Furthermore, the predictive model of T_g derived with machine-learning algorithms can be used to estimate T_g successfully within an uncertainty of about 20 degrees, even for polyimides yet to be synthesized experimentally.     

Theoretical studies of the reactions of CF3CHCLOCHF2/CF3CHFOCHF2 with OH radical and Cl atom and their product radicals with OH

The mechanisms and dynamics studies of the OH radical and Cl atom with CF(3)CHClOCHF(2) and CF(3)CHFOCHF(2) have been carried out theoretically. The geometries and frequencies of all the stationary points are optimized at the B3LYP/6-311G(d,p) level, and the energy profiles are further refined by interpolated single-point energies (ISPE) method at the G3(MP2) level of theory. For each reaction, two H-abstraction channels are found and four products (CF(3)CHFOCF(2), CF(3)CFOCHF(2), and CF(3)CHClOCF(2), CF(3)CClOCHF(2)) are produced during the above processes. The rate constants for the CF(3)CHClOCHF(2)/CF(3)CHFOCHF(2) + OH/Cl reactions are calculated by canonical variational transition-state theory (CVT) within 200-2000 K, and the small-curvature tunneling is included. The total rate constants calculated from the sum of the individual rate constants and the branching ratios are in good agreement with the experimental data. The Arrhenius expressions for the reactions are obtained. Our calculation shows that the substitution of Cl by F decreases the reactivity of CF(3)CHClOCHF(2) toward OH and Cl. In addition, the mechanisms of subsequent reactions of product radicals and OH radical are further investigated at the G3(MP2)//B3LYP/6-311G(d,p) level, and the main products are predicted in the this article.     

一类五核平面开口型过渡金属原子簇电子吸收光谱和二阶非线性光学性质的TDDFT研究

运用TDDFT B3LYP/LanL2DZ方法, 研究了一类具有非中心对称的五核平面开口构型过渡金属原子簇化合物[MoS₄Cu₄(py)₆X₂] (X＝Br, I)的电子吸收光谱和静态二阶非线性极化率, 估算了晶体的宏观二阶非线性光学系数. 电子吸收光谱的计算结果与实验测量结果比较符合; 碘系簇合物的静态二阶非线性极化率大于溴系. 详细讨论了该类金属簇合物电子吸收光谱的归属及其相关联的电子跃迁方式; 在微观水平上阐述了其二阶非线性光学性质的起源. 研究结果表明外围无机卤素配体4p/5p轨道到簇芯[MoS₄]杂化轨道的电子转移对静态二阶非线性极化率的贡献大于有机配体的贡献; 而过渡金属簇芯内的电子转移也有较大的贡献. 这对于理解过渡金属原子簇化合物内的电子转移对光学激发的作用以及用来设计新的无机-有机杂化二阶非线性光学材料有较大的帮助.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

Molecular Dynamics Simulation of the Self-assembled Monolayers of 1-Adamantanethiolate and Its Derivatives on Au（111） Surfaces

The self-assembled monolayers （SAMs） of 1-adamantanethiolate and its derivatives on Au（111） surface were investigated. Density functional theory （DFT） calculation indicates that the most stable configuration for absorption is at the face centered cubic （fcc）-bridge site. Canonical ensemble molecular dynamics （MD） simulations were carried out to study the structures and energies of the SAMs. The ordered structures of the SAMs were analyzed by means of radial distribution function and the relative stability of the SAMs was compared. It was concluded by the comparison of various contributions to the SAM formation energy that the formation of the SAMs was determined by the intermolecular nonbonding interaction and the chemical bonding interaction of sulfur and gold.     

分子动力学与第一原理研究二氧化铈(CeO2)n (n=1～5)纳米粒子的结构性质

二氧化铈纳米粒子(CeO2)n(n=1～5)材料为固态氧化燃料电池中的催化剂,因此了解其不同尺寸结构的性质是非常重要的.在本论文中使用分子动力学(molecular dynamics)模拟结合火焰算法(FIRE algorithm)计算得到二氧化铈的最小能量结构.再应用密度泛函理论方法(density functional theory)对这些结构进一步计算,得到更精确的最低能量结构.     

5-氟尿嘧啶和5-氯尿嘧啶及其互变异构体的理论计算研究

采用HF/3-21G方法, 对6种气相和水相中可能存在的5-氟尿嘧啶(和5-氯尿嘧啶)互变异构体进行了构象分析.采用B3LYP/6-311＋G**方法对处于优势构象时的各互变异构体进行了几何全优化, 并计算出它们的总能量、焓、熵、吉布斯自由能. Onsager反应场溶剂模型用于水相的计算. 计算结果表明, 5-氟尿嘧啶和5-氯尿嘧啶在气相中和水相中主要以双酮形式存在. 5-氟尿嘧啶和5-氯尿嘧啶的熵效应小, 对互变异构平衡没有显著的影响, 而焓变对互变异构产生了主要的影响. 讨论了水溶剂化作用对异构体的能量、电荷分布和偶极矩的影响. 溶剂化自由能与异构体的气相偶极矩存在相关性. 另外, 详细地将5-氟尿嘧啶和5-氯尿嘧啶与尿嘧啶进行了对比, 获得三者最稳定异构体间电子结构异同的有用信息.     

Theoretical Simulations of Thermochromic and Aggregation-Induced Emission Behaviors of a Series of Red-Light Anthracene-o-carborane Derivatives

Quantum mechanical and molecular dynamics simulations have been carried out on a series of anthracene-o-carborane derivatives (ANT-H, ANT-Ph, ANT-Me and ANT-TMS) with rare red-light emission in the solid state. The simulation of the heating process of the crystals and further comparison of the molecular structures and excited-state properties before and after heating help us to disclose the thermochromic behavior, that is, the red-shift emission is caused by elongation of the C1−C2 bond in the carborane moiety after heating. Thus, we believe that the molecular structure in the crystal is severely affected by heating. Transformation of the molecular conformation appears in the ANT-H crystal with increasing temperature. More specifically, the anthracene moiety moves from nearly parallel to the C1−C2 bond to nearly perpendicular, causing the short-wavelength emission to disappear after heating. As for the aggregation-induced emission phenomenon, the structures and photophysical properties were investigated comparatively in both the isolated and crystal states; the results suggested that the energy dissipation in crystal surroundings was greatly reduced through hindering structure relaxation from the excited to the ground state. We expect that discussion of the thermochromic behavior will provide a new analysis perspective for the molecular design of o-carborane derivatives.     

On the Electrochemical Deposition and Dissolution of Divalent Metal Ions

The deposition of Cu²⁺ and Zn²⁺ from aqueous solution has been investigated by a combination of classical molecular dynamics, density functional theory, and a theory developed by the authors. For both cases, the reaction proceeds through two one‐electron steps. The monovalent ions can get close to the electrode surface without losing hydration energy, while the divalent ions, which have a stronger solvation sheath, cannot. The 4s orbital of Cu interacts strongly with the sp band and more weakly with the d band of the copper surface, while the Zn 4s orbital couples only to the sp band of Zn. At the equilibrium potential for the overall reaction, the energy of the intermediate Cu⁺ ion is only a little higher than that of the divalent ion, so that the first electron transfer can occur in an outer‐sphere mode. In contrast, the energy of the Zn⁺ ion lies too high for a simple outer‐sphere reaction to be favorable; in accord with experimental data this suggests that this step is affected by anions.     

Investigation of the Adsorption and Self Assembly of Isocyanide Derivatives on Au（111） Surface

The adsorption and self-assembly of isocyanide derivatives on Au（111） surface were investigated by density functional theory （DFF） and molecular dynamics simulation. The calculation for phenyl isocyanide by DFT was based on cluster and slab models. The self-assembled monolayers of 2-isocyanoazulene and 1,3-diethoxycarbony 1- 2-isocyanoazulene on Au（111） were simulated using Au-C force field parameters developed by us. It was found that the top site was the most preferred position, and the isocyanoazulene and its derivatives could form the ordered face to edge self-assembled monolayer on gold surface indeed, and the molecules stood on the gold surface vertically.     

Modeling of heavy-atom-ligand NMR spin-spin coupling in solution: molecular dynamics study and natural bond orbital analysis of Hg-C coupling constants

Ab initio molecular dynamics (MD) and relativistic density functional NMR methods were applied to calculate the one‐bond Hg? C NMR indirect nuclear spin–spin coupling constants (J) of [Hg(CN)₂] and [CH₃HgCl] in solution. The MD averages were obtained as J(¹⁹⁹Hg? ¹³C)=3200 and 1575 Hz, respectively. The experimental Hg? C spin–spin coupling constants of [Hg(CN)₂] in methanol and [CH₃HgCl] in DMSO are 3143 and 1674 Hz, respectively. To deal with solvent effects in the calculations, finite “droplet” models of the two systems were set up. Solvent effects in both systems lead to a strong increase of the Hg? C coupling constant. From a relativistic natural localized molecular orbital (NLMO) analysis, it was found that the degree of delocalization of the Hg 5d_σ nonbonding orbital and of the Hg? C bonding orbital between the two coupled atoms, the nature of the trans Hg? C/Cl bonding orbital, and the s character of these orbitals, exhibit trends upon solvation of the complexes that, when combined, lead to the strong increase of J(Hg? C).     

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from ?22.9 to ?33.9 kcal/mol for formaldehyde, and from ?44.3 to ?66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde → HCO + H, HCO → H + CO, and CO → C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST‐based rates are consistent with HREELS observation. © 2013 Wiley Periodicals, Inc.     

The Early Steps of Molecule-to-Material Conversion in Chemical Vapor Deposition (CVD): A Case Study

Transition metal complexes with β-diketonate and diamine ligands are valuable precursors for chemical vapor deposition (CVD) of metal oxide nanomaterials, but the metal-ligand bond dissociation mechanism on the growth surface is not yet clarified in detail. We address this question by density functional theory (DFT) and ab initio molecular dynamics (AIMD) in combination with the Blue Moon (BM) statistical sampling approach. AIMD simulations of the Zn β-diketonate-diamine complex Zn(hfa)₂TMEDA (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate; TMEDA = N,N,N′,N′-tetramethylethylenediamine), an amenable precursor for the CVD of ZnO nanosystems, show that rolling diffusion of this precursor at 500 K on a hydroxylated silica slab leads to an octahedral-to-square pyramidal rearrangement of its molecular geometry. The free energy profile of the octahedral-to-square pyramidal conversion indicates that the process barrier (5.8 kcal/mol) is of the order of magnitude of the thermal energy at the operating temperature. The formation of hydrogen bonds with surface hydroxyl groups plays a key role in aiding the dissociation of a Zn-O bond. In the square-pyramidal complex, the Zn center has a free coordination position, which might promote the interaction with incoming reagents on the deposition surface. These results provide a valuable atomistic insight on the molecule-to-material conversion process which, in perspective, might help to tailor by design the first nucleation stages of the target ZnO-based nanostructures.     

Exploring the Mechanism of Ionic Liquids to Improve the Extraction Efficiency of Essential Oils Based on Density Functional Theory and Molecular Dynamics Simulation

Highlights

• According to the design of the experiment (DoE), multivariate analysis models were used to optimize the critical process parameters combined with multi-objective optimization.
• Based on the optimized operating conditions, the MILT-HD method not only enhances the extraction efficiency from Amomi fructus but also reduces energy demands and CO₂ emissions.
• Based on the density functional theoretical (DFT) and molecular dynamics (MD) simulations, the mechanisms for ionic liquids (ILs) to improve the extraction efficiency of essential oil was comprehensively revealed.

AbstractIn this paper, Amomi fructus (Latin) was used to explore the mechanism of ionic liquids (ILs) in improving the extraction efficiency of essential oils. Microwave assisted ionic liquid treatment followed by a hydro-distillation (MILT-HD) process for isolating Amomi fructus essential oil was optimized by multi-objective optimization. Under optimum operating conditions, the IL-assisted extraction method not only enhances extraction efficiency but also reduces energy demands and CO₂ emissions. Since the hydrogen bond structure network of cellulose in the cell wall is an important reason for hindering diffusion of essential oils, the mechanism of ILs was explored by density functional theoretical (DFT) and molecular dynamics (MD) simulations. According to DFT calculations, ILs can facilitate the cleavage of cellulose chains and have strong non-covalent interactions with cellulose. Based on the MD simulations, the degree of destruction of the cellulose hydrogen bond structure was explored. According to the DFT and MD simulations, the ILs can significantly destroy cellulose structure, thereby promoting essential oil release from the plant. These results were confirmed by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). This work is conducive to better understand the MILT-HD process for isolating essential oil and comprehensively understand the mechanism of ILs in the extraction process.     

Molecular dynamics simulation and density functional theory insight into the cocrystal explosive of hexaazaisowurtzitane/nitroguanidine

Theoretical methods involving molecular dynamics (MD) simulation and density functional theory were performed to investigate the different molecular ratios, mechanical Properties, structure, trigger bond, and intermolecular interaction of hexaazaisowurtzitane (CL‐20)/nitroguanidine (NQ) cocrystal explosive. Results of MD simulation show that CL‐20 and NQ packed in ratios of 1:1 present the larger binding energy and better mechanical properties than any other molecular ratios, which indicates 1:1 cocrystal can form the stable crystal structure. Shorter length and larger dissociation energy of trigger bond in composite structure than in isolated CL‐20 component suggests that the cocrystal may exhibit less sensitive than CL‐20. Analyses of atoms in molecules, reduced density gradient, and natural bond orbital confirm that intermolecular interactions are mainly derived from a series of weak hydrogen bond and strong vdW forces, involving of NH···O, CH···O, CH···N, O···N, and O···O. Additionally, composite structures of 2 and 3 bringing us more attractive performance will act as a key role in constructing of CL‐20/NQ cocrystal explosive. © 2015 Wiley Periodicals, Inc.     

Conformational preference and mechanism of decarboxylation of levodopa. A quantum dynamics/quantum mechanics study

The present study addresses the conformational preferences and the mechanism of decarboxylation of levodopa (LD). LD is used to increase dopamine concentrations in the treatment of Parkinson's disease. LD crosses the protective blood–brain barrier, where it is converted into dopamine by the process of decarboxylation. Molecular dynamics simulation has been carried out at the DFT/6‐31++G level of theory to identify the global minimum structure of LD. Conformational preferences of the amino acid side chain of LD has been investigated at the B3LYP/6‐311++G** level of theory. Fourier transform analysis has been performed to identify the origin of the rotational barriers. Electrostatic dipole moment and bond interactions underlie the observed potential energy barriers for rotation of the amino acid side chain of LD. The vital biological process of decarboxylation of LD has been examined in the gas phase and in aqueous solution. Without the presence of water, there is only one possible route for the decarboxylation of LD. In this concerted mechanism, a proton transfer and breakage of the C₁₀—C₁₈ bond, take place simultaneously (ΔE^# = 73.2 kcal/mol). In solution, however, two possible decarboxylation routes are available for LD. The first involve the formation of a zwitterionic intermediate (ΔE^# = 72.4 kcal/mol). The zwitterionic form of LD have been localized using explicitly bound water molecules to model short‐range solvent effects and self‐consistent reaction field polarized continuum model to estimate long‐range solvent interactions. The second route involve the formation of a cyclic structure in which a water molecule acts as a bridge linking the anticarboxylic hydrogen and α‐position carbon atom (ΔE^# = 59.8 kcal/mol). Natural bond orbital (NBO) analysis reveals that the conformational and overall stability of the amino acid side chain is facilitated by the antiperiplanar interactions between the phenyl moiety C—H and C—C bonds and C—X bonds of the amino acid side chain. However, much of the major donor–acceptor interactions is of the lone pair type and is localized within the amino acid side chain itself. Results of the present work reveal that NBO data reflect nicely and identify clearly reaction coordinates at the transition species. © 2013 Wiley Periodicals, Inc.     

Three 1‐phenylindolin‐2‐one derivatives displaying different molecular dipole moments and different crystallographic symmetries

Three 1‐phenylindolin‐2‐one derivatives, namely 1‐phenylindolin‐2‐one, C₁₄H₁₁NO, (I), 5‐bromo‐1‐phenylindolin‐2‐one, C₁₄H₁₀BrNO, (II), and 5‐iodo‐1‐phenylindolin‐2‐one, C₁₄H₁₀INO, (III), have been synthesized and their structures determined. Compounds (I) and (II) crystallized in the centrosymmetric space groups Pbca and P2₁/c, respectively, while compound (III) crystallized in the polar space group Aea2. Density functional theory (DFT) calculations show that the molecular dipole moment gradually decreases in the order (I) > (II) > (III). The relatively smaller dipole moment of (III) and the larger non‐electrostatic intermolecular interactions may be the main reasons for the noncentrosymmetric and polar structure of (III).