液体和非晶态NiAl3合金结构的从头算分子动力学模拟

应用从头算分子动力学方法模拟了液体以及淬冷形成的NiAl₃合金体系,得到了它们的对相关函数、结构因子、键对分析信息.结果分析表明,在淬冷条件下得到的体系呈现非晶态性质,且非晶态结构类似于液态NiAl₃合金的结构,可以用液体结构近似描述非晶态性质.还进行了电子结构分析,得到液体NiAl₃合金的电子态密度和电荷分布.在液体镍铝合金中,镍为电子受体,部分电子由铝向镍转移,支持了Candy等人的XPS实验结果.镍铝间强烈作用,形成带有弱共价键性质的金属键.镍在合金中相当分散,这能部分解释由淬冷形成的NiAl₃合金制得的骨架镍催化剂活性增强的原因.     

Polarizable Atomistic Calculation of Site Energy Disorder in Amorphous Alq3

A polarizable molecular dynamics simulation and calculation scheme for site energy disorder is presented in amorphous tris(8‐hydroxyquinolinato)aluminum (Alq₃) by means of the charge response kernel (CRK) method. The CRK fit to the electrostatic potential and the tight‐binding approximation are introduced, which enables modeling of the polarizable electrostatic interaction for a large molecule systematically from an ab initio calculation. The site energy disorder for electron and hole transfers is calculated in amorphous Alq₃ and the effect of the polarization on the site energy disorder is discussed.     

液体和非晶态Ni64B36合金结构的从头算分子动力学模拟

运用从头算分子动力学模拟了液体以及猝冷后形成的非晶态Ni₆₄B₃₆合金体系, 得到了它们的对相关函数、结构因子、键对分析方面的结构信息, 与实验结果相当一致; 结果表明, 猝冷得到的合金性质与液体合金性质相似, 为非晶态结构. B原子多数以B—B双原子成键形式分散于Ni原子构成的骨架中. 电子态密度分析表明, Ni 3d电子最活泼, 因此在合金中Ni为活性位. 轨道电荷分析从电子结构角度揭示了在NiB 催化剂中B作为修饰剂的机理.     

Polynitrogen clusters containing five-membered rings

Possible structures of N₁₅ cluster were examined by ab initio (MP2) and density functional theory (DFT) methods with the 6-31G* basis set. Their stabilities were compared together with other polynitrogen clusters N_n (n = 8, 10–14) reported in the literature. The order of stability was made respectively according to even or odd numbers of the total nitrogen atoms in clusters. It is found that both for even-numbered clusters N_2n (n = 4–7) and odd-numbered clusters N_{2n + 1} (n = 5–7) the thermodynamically most stable isomers are all based on pentazole units; for each one of N_n (n = 8, 10–15) clusters, the more conjugated the five-membered ring the more stable is the isomer; and, the more side-chains the N₅ ring links the less stable is the isomer. Another finding is that the larger the cluster the less stable is the cluster for every series of clusters of (a) containing two five-membered rings with an even number of total nitrogen atoms [N₁₀ (D_2d), N₁₂ (C_2h), N₁₄ (C_2h)], (c) containing one five-membered ring and a side-chain with an even number of total nitrogen atoms [N₈ (C_S), N₁₀ (C_S), N₁₂ (C_S), N₁₄ (C_S)], (d) containing one five-membered ring and a side-chain with an odd number of total nitrogen atoms [N₁₁ (C_S), N₁₃ (C_S), N₁₅ (C_S)], (e) chain clusters with an even number of total nitrogen atoms [N₈ (C_2h), N₁₀ (C_2h), N₁₂ (C_2h), N₁₄ (C_2h)], and (f) chain clusters with an odd number of total nitrogen atoms [N₁₁ (C_2v), N₁₃ (C_2v), N₁₅ (C_2v)]. For another series of clusters with two five-membered ring units [N₁₁ (C₂), N₁₃ (C_2v), and N₁₅ (C_2v)] (series b) the N₁₃ (C_2v) shows the best stability. It is also found that the even-numbered nitrogen clusters are more stable than the odd-numbered ones in comparison of series (a) with (b), (c) with (d), and (e) with (f). © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Azolylpentazoles as high-energy materials: a computational study

The structures of highly energetic substituted pentazole compounds and their decomposition to give dinitrogen and the corresponding azide were investigated by ab initio quantum chemical methods. The substituents include azolyl groups (five-membered aromatic rings with different numbers of nitrogen atoms), CH(3), CN, and F. The decomposition pathway was followed for several substituted azolyl- and phenylpentazoles and compared to the known experimental and theoretical results. The NMR parameters of most of the as-yet unknown pentazole compounds were predicted. The activation energy for the decomposition increases, while the decomposition energy of the substituted pentazole decreases with greater electron-donating character of the substituent of the pentazole. Thus, anionic pentazoles are more stable than neutral pentazoles. Methylpentazole is predicted to be among the most stable pentazoles, even though it does not contain an aromatic system.     

Reversible proton transfer dynamics in bacteriorhodopsin

In a previous study of ab initio dynamics, the proton transfer in bacteriorhodopsin from protonated asp96 in the cytoplasmic region toward the deprotonated Schiff base was investigated. A quantum mechanics/molecular mechanics model was constructed from the X-ray structure of bacteriorhodopsin E204Q mutant. In this model, asp96, asp85, and thr89 as well as most of the retinal chromophore and the Schiff base link of lys216 were treated quantum mechanically while the rest of the atoms were treated molecular mechanically. A channel was found in the X-ray structure allowing a water chain to form between the asp96 and Schiff base. In the present study, a chain of four waters from asp96 to the Schiff base N coupled with one branching water supports proton transfer as a concerted event in about 3.5 ps. With both a neutral asp85 and a branched water, the dynamics is now found to be more complicated than observed in the initial study for the transition from the photocycle late M state to the N state. Proton transfer is also observed from the Schiff base back to asp96 demonstrating that there is no effective barrier to proton transfer larger than kT in a strong H-bonded network. The binding of the branched water to the four water chains can dynamically hinder the proton transfer.     

Influence of Ag substitution on the local structure and glass-forming ability of Al86Ni(8-x)Y6Agx (X = 0,1,2) liquids

The local structure of Al₈₆Ni_(8-x)Y₆Ag_x (X = 0,1,2) molten and glassy alloy was investigated by ab initio molecular dynamics simulation. It transpired that the Al₈₆Ni_(8-x)Y₆Ag_x alloy can be considered as a combination of Ni- and Y-centred Al clusters with Ag as ‘glue atoms’. First and second Ag–Ag coordination was scarcely found in Al₈₆Ni₇Y₆Ag₁, but a medium-range order between 7.5 and 9 Å was observed. The enhanced glass-forming ability and thermal stability of the alloy compared with Al₈₆Ni₈Y₆ can be attributed to the medium-range order of the Ag–Ag correlation. A second Ag–Ag coordination occurs in Al₈₆Ni₆Y₆Ag₂ and results in a decrease in glass-forming ability. The inter-atomic distances between all constituting elements increase during cooling. This increase is ascribed to a change in distribution of clusters around Al atoms towards clusters with higher coordination number around Al.     

几种钙钛矿型晶体极化性能的从头算分子动力学研究

对具有钙钛矿结构的钛酸钡(BT)、钛酸铅(PT)、锆酸铅(PZ)、三种钛/锆比例的锆钛酸铅(PZT)和镁铌酸铅(PMN)的部分构型建立了复晶胞模型, 并运用从头算分子动力学方法CPMD对其极化性能进行了模拟. 计算结果表明自发极化强度与B格点原子类型和其偏离所处氧笼中心距离有关; d₃₃/χ_e最大值: 25%/75% (Ti/Zr)的PZT的出现在(111)方向, 其它晶体均出现在(001)方向; PZ, PZT, PMN的d₃₃/χ_e值较高; g₃₃×χ_e最大值出现在(001)或(110)方向; PT和PZT的 g₃₃×χ_e值较大.     

Efficient modeling of liquid phase photoemission spectra and reorganization energies: Difficult case of multiply charged anions

An efficient approach for quantitative modeling of liquid phase photoelectron spectra, reorganization energies, and redox potentials with DFT‐based molecular dynamics simulations is presented. The method is based on a large scale cluster‐continuum approach combined with the so‐called reflection principle (RP). Finite size clusters of solute molecules with solvating water molecules are at first generated using either classical molecular dynamics or molecular dynamics with a quantum thermostat which accounts for nuclear quantum effects. In the next step, the electron binding energies are calculated. Finite‐size corrections for (i) positions of electron binding energies and (ii) width of the spectrum are evaluated via a dielectric continuum approach. The performance of such a reflection principle with additional broadening approach (RP‐AB) for oxidation of multiply charged iron anions, [Fe(CN)₆]⁴⁻ and [Fe(CN)₆]³⁻ is demonstrated. The role of nuclear quantum effects is discussed as well as the relation between spectroscopic data and electrochemical quantities. Results are compared with recent liquid photoemission experiments, explaining the obstacles for applying liquid phase photoemission spectroscopy as a direct method for obtaining absolute redox potentials and suggesting a way to overcome them. © 2017 Wiley Periodicals, Inc.     

Ab initio molecular dynamics study of the keto-enol tautomerism of acetone in solution.

We have studied the keto-enol interconversion of acetone to understand the mechanism of tautomerism relevant to numerous organic and biochemical processes. Applying the ab initio metadynamics method, we simulated the keto-enol isomerism both in the gas phase and in the presence of water. For the gas-phase intramolecular mechanism we show that no other hydrogen-transfer reactions can compete with the simple keto-enol tautomerism. We obtain an intermolecular mechanism and remarkable participation of water when acetone is solvated by neutral water. The simulations reveal that C deprotonation is the kinetic bottleneck of the keto-enol transformation, in agreement with experimental observations. The most interesting finding is the formation of short H-bonded chains of water molecules that provide the route for proton transfer from the carbon to the oxygen atom of acetone. The mechanistic picture that emerged from the present study involves proton migration and emphasizes the importance of active solvent participation in tautomeric interconversion.     

Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular-orbital method

To analyze large-scale cluster systems theoretically, we recently developed an "integrated multicenter molecular-orbital" (IMiC-MO) method. This method calculates the force of an entire system by dividing the system into small regions. We used the method to analyze the effect of cluster size and the process of hydrogen bond network (HBN) growth to form H(+)(H(2)O)(n) (n = 9, 17, and 33) clusters. Our simulations reveal that H(3)O(+) and water molecules in the first solvation shell function take an important role to grow the HBN. In addition, the number of hydrogen donors in each water molecule is strongly related to the shape of the HBN.     

Experimental and Theoretical Study of the Ultrafast Dynamics of a Ni2Dy2-Compound in DMF After UV/Vis Photoexcitation

We present a combined experimental and theoretical study of the ultrafast transient absorption spectroscopy results of a {Ni₂Dy₂}-compound in DMF, which can be considered as a prototypic molecule for single molecule magnets. We apply state-of-the-art ab initio quantum chemistry to quantitatively describe the optical properties of an inorganic complex system comprising ten atoms to form the chromophoric unit, which is further stabilized by surrounding ligands. Two different basis sets are used for the calculations to specifically identify two dominant peaks in the ground state. Furthermore, we theoretically propagate the compound's correlated many-body wavefunction under the influence of a laser pulse as well as relaxation processes and compare against the time-resolved absorption spectra. The experimental data can be described with a time constant of several hundreds of femtoseconds attributed to vibrational relaxation and trapping into states localized within the band gap. A second time constant is ascribed to the excited state while trap states show lifetimes on a longer timescale. The theoretical propagation is performed with the density-matrix formalism and the Lindblad superoperator, which couples the system to a thermal bath, allowing us to extract relaxation times from first principles.     

Coexistence of Three Ferroic Orders in the Multiferroic Compound [(CH3)4N][Mn(N3)3] with Perovskite‐Like Structure

The perovskite azido compound [(CH₃)₄N][Mn(N₃)₃], which undergoes a first‐order phase change at T_t=310 K with an associated magnetic bistability, was revisited in the search for additional ferroic orders. The driving force for such structural transition is multifold and involves a peculiar cooperative rotation of the [MnN₆] octahedral as well as order/disorder and off‐center shifts of the [(CH₃)₄N]⁺ cations and bridging azide ligands, which also bend and change their coordination mode. According to DFT calculations the latter two give rise to the appearance of electric dipoles in the low‐temperature (LT) polymorph, the polarization of which nevertheless cancels out due to their antiparallel alignment in the crystal. The conversion of this antiferroelectric phase to the paraelectric phase could be responsible for the experimental dielectric anomaly detected at 310 K. Additionally, the structural change involves a ferroelastic phase transition, whereby the LT polymorph exhibits an unusual and anisotropic thermal behavior. Hence, [(CH₃)₄N][Mn(N₃)₃] is a singular material in which three ferroic orders coexist even above room temperature.     

Ab initio molecular dynamics approach to tunneling splitting in polyatomic molecules

An ab initio molecular dynamics approach is combined with the semiclassical tunneling method of Makri and Miller, which is applied to estimations of tunneling splitting in the umbrella inversion of ammonia and the intramolecular hydrogen transfer in malonaldehyde. In the application to malonaldehyde, effects of multidimensionality are examined by assigning quantum zero-point energies only to significant vibrational modes and changing the amount of energy given to other degrees of freedom. The calculated tunneling splitting values are in good agreement with the corresponding experimental values for both molecules.     

Binding of Cationic and Neutral Phenanthridine Intercalators to a DNA Oligomer Is Controlled by Dispersion Energy: Quantum Chemical Calculations and Molecular Mechanics Simulations

Correlated ab initio as well as semiempirical quantum chemical calculations and molecular dynamics simulations were used to study the intercalation of cationic ethidium, cationic 5‐ethyl‐6‐phenylphenanthridinium and uncharged 3,8‐diamino‐6‐phenylphenanthridine to DNA. The stabilization energy of the cationic intercalators is considerably larger than that of the uncharged one. The dominant energy contribution with all intercalators is represented by dispersion energy. In the case of the cationic intercalators, the electrostatic and charge‐transfer terms are also important. The ΔG of ethidium intercalation to DNA was estimated at ?4.5 kcal mol^?1 and this value agrees well with the experimental result. Of six contributions to the final free energy, the interaction energy value is crucial. The intercalation process is governed by the non‐covalent stacking (including charge‐transfer) interaction while the hydrogen bonding between the ethidium amino groups and the DNA backbone is less important. This is confirmed by the evaluation of the interaction energy as well as by the calculation of the free energy change. The intercalation affects the macroscopic properties of DNA in terms of its flexibility. This explains the easier entry of another intercalator molecule in the vicinity of an existing intercalation site.     

Complex Reaction Environments and Competing Reaction Mechanisms in Zeolite Catalysis: Insights from Advanced Molecular Dynamics

The methanol‐to‐olefin process is a showcase example of complex zeolite‐catalyzed chemistry. At real operating conditions, many factors affect the reactivity, such as framework flexibility, adsorption of various guest molecules, and competitive reaction pathways. In this study, the strength of first principle molecular dynamics techniques to capture this complexity is shown by means of two case studies. Firstly, the adsorption behavior of methanol and water in H‐SAPO‐34 at 350 °C is investigated. Hereby an important degree of framework flexibility and proton mobility was observed. Secondly, the methylation of benzene by methanol through a competitive direct and stepwise pathway in the AFI topology was studied. Both case studies clearly show that a first‐principle molecular dynamics approach enables unprecedented insights into zeolite‐catalyzed reactions at the nanometer scale to be obtained.     

Reference-Quality Free Energy Barriers in Catalysis from Machine Learning Thermodynamic Perturbation Theory

For the first time, we report calculations of the free energies of activation of cracking and isomerization reactions of alkenes that combine several different electronic structure methods with molecular dynamics simulations. We demonstrate that the use of a high level of theory (here Random Phase Approximation—RPA) is necessary to bridge the gap between experimental and computed values. These transformations, catalyzed by zeolites and proceeding via cationic intermediates and transition states, are building blocks of many chemical transformations for valorization of long chain paraffins originating, e.g., from plastic waste, vegetable oils, Fischer–Tropsch waxes or crude oils. Compared with the free energy barriers computed at the PBE+D2 production level of theory via constrained ab initio molecular dynamics, the barriers computed at the RPA level by the application of Machine Learning thermodynamic Perturbation Theory (MLPT) show a significant decrease for isomerization reaction and an increase of a similar magnitude for cracking, yielding an unprecedented agreement with the results obtained by experiments and kinetic modeling.