The mechanism of double proton transfer in dimers of uracil and 2-thiouracil--the reaction force perspective

The intermolecular double proton transfer in dimers of uracil and 2-thiouracil is studied through density functional theory calculations. The reaction force framework provides the basis for characterizing the mechanism that in all cases has been associated to a dynamic balance between polarization and charge transfer effects. It has been found that the barriers for proton transfer depend upon the nature of the acceptor atoms and its position within the seminal monomer. Actually, the change in the nature of the hydrogen bonds connecting the two monomers along the reaction coordinate may favor or disfavor the double-proton transfer.     

Diels-Alder reaction mechanisms of substituted chiral anthracene: A theoretical study based on the reaction force and reaction electronic flux

Quantum chemical calculations were used to study the mechanism of Diels-Alder reactions involving chiral anthracenes as dienes and a series of dienophiles. The reaction force analysis was employed to obtain a detailed scrutiny of the reaction mechanisms, it has been found that thermodynamics and kinetics of the reactions are quite consistent: the lower the activation energy, the lower the reaction energy, thus following the Bell-Evans-Polanyi principle. It has been found that activation energies are mostly due to structural rearrangements that in most cases represented more than 70% of the activation energy. Electronic activity mostly due to changes in σ and π bonding were revealed by the reaction electronic flux (REF), this property helps identify whether changes on σ or π bonding drive the reaction. Additionally, new global indexes describing the behavior of the electronic activity were introduced and then used to classify the reactions in terms of the spontaneity of their electronic activity. Local natural bond order electronic population analysis was used to check consistency with global REF through the characterization of specific changes in the electronic density that might be responsible for the activity already detected by the REF. Results show that reactions involving acetoxy lactones are driven by spontaneous electronic activity coming from bond forming/strengthening processes; in the case of maleic anhydrides and maleimides it appears that both spontaneous and non-spontaneous electronic activity are quite active in driving the reactions.     

尿嘧啶水助质子转移反应机理的研究

用密度泛函理论,在B3LYP/6-311++G**计算水平下分别对尿嘧啶所有的气相、液相、过渡态和质子转移异构体的结构进行全优化,获得它们在气相和水相中的几何结构和电子结构,PGM反应场溶剂模型用于水相计算.结果显示:在气相和水相中,水参与反应降低了互变异构质子迁移的反应活化能,对互变异构质子迁移的反应起到催化作用,但...     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Interaction between RNA segment (adenine‐uracil) and model of protein unit (formamide): A density‐functional theory study

Various possible structures of adenine‐uracil‐formamide hydrogen‐bond complexes were optimized at 6‐311++G(d,p) level, and the binding energies of these complexes were also calculated at DFT B3LYP/6‐311++G(d,p) level. Eight stable cyclic structures being involved in the interaction are found on the potential energy surface. By analyzing the structure, NPA charge and interaction energy of complexes, we obtain the most stable geometry structure. The results show that the interactions between formamide and adenine‐uracil (A‐U) base pair affect the stabilities of the base pairs. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

靛蓝及其取代物的密度泛函理论研究

运用量子化学中密度泛函理论(DFT)方法,在B3LYP／6-31G^ 水平上对靛蓝及其芳环4,4′-,5,5′-,6,6′-,7,7′-取代衍生物进行理论计算．探讨了F,Cl,Br,NO2,CH3O,CH3在不同位置的取代对分子的几何构型、电子结构和电子光谱的影响,获得与实验结果相一致的结论．还用含时密度泛函理论(TD-DFT)方法在相同水平计算其电子光谱．结果表明靛蓝及其芳环取代衍生物的最低激发单重态(S1)均源自HOMO-LUMO(π-π^*)跃迁．     

Understanding the acid-base properties of adenosine: the intrinsic basicities of N1, N3 and N7

Adenosine (Ado) can accept three protons, at N1, N3, and N7, to give H(3) (Ado)(3+) , and thus has three macro acidity constants. Unfortunately, these constants do not reflect the real basicity of the N sites due to internal repulsions, for example, between (N1)H(+) and (N7)H(+). However, these macroconstants are still needed for the evaluations and the first two are taken from our own earlier work, that is, pK(H)(H(3))((Ado)) = -4.02 and pK(H)(H(2))((Ado)) = -1.53; the third one was re-measured as pK(H)(H)((Ado)) = 3.64 ± 0.02 (25 °C; I=0.5 M, NaNO(3)), because it is the main basis for evaluating the intrinsic basicities of N7 and N3. Previously, contradicting results had been published for the micro acidity constant of the (N7)H(+) site; this constant has now been determined in an unequivocal manner, and that of the (N3)H(+) site was obtained for the first time. The micro acidity constants, which describe the release of a proton from an (N)H(+) site under conditions for which the other nitrogen atoms are free and do not carry a proton, decrease in the order pk(N7-N1)(N7(Ado)N1·H)) = 3.63 ± 0.02 > pk(N7-N1)(H·N7(Ado)N1) = 2.15 ± 0.15 > pk(N3-N1,N7)(H·N3(Ado)N1,N7) =1.5 ± 0.3, reflecting the decreasing basicity of the various nitrogen atoms, that is, N1>N7>N3. Application of the above-mentioned microconstants allows one to calculate the percentages (formation degrees) of the tautomers formed for monoprotonated adenosine, H(Ado)(+) , in aqueous solution; the results are 96.1, 3.2, and 0.7% for N7(Ado)N1·H(+), (+)H·N7(Ado)N1, and (+)H·N3(Ado)N1,N7, respectively. These results are in excellent agreement with theoretical DFT calculations. Evidently, H(Ado)(+) exists to the largest part as N7(Ado)N1·H(+) having the proton located at N1; the two other tautomers are minority species, but they still form. These results are not only meaningful for adenosine itself, but are also of relevance for nucleic acids and adenine nucleotides, as they help to understand their metal ion-binding properties; these aspects are briefly discussed.     

CH3SS与OH自由基反应机理的理论研究

应用密度泛函理论(DFT)对CH3SS与OH自由基单重态反应机理进行了研究.在B3PW91/6-311+G(d,p)水平上优化了反应通道上各驻点(反应物、中间体、过渡态和产物)的几何构型,用内禀反应坐标(IRC)计算和频率分析方法对过渡态进行了验证.在QCISD(T)/6-311++G(d,p)水平上计算了各物种的单点能,并对总能量进行了零点能校正.研究结果表明,CH3SS与OH反应为多通道反应,有5条可能的反应通道.反应物首先通过不同的S—O键相互作用形成具有竞争反应机理的中间体IM1和IM2.再经过氢迁移、脱氢和裂解等机理得到主要产物P1(CH2SS+H2O),次要产物P2(CH2S+HSOH),P3(CH3SH+1SO)和P4(CH2SSO+H2),其中最低反应通道的势垒为174.6kJ.mol-1.     

Evolution of Structural, Electronic and Optical Properties of Monoclinic ZrO2 under High Pressure： A First Principles Study

The structural, electronic and optical properties of the monoclinic ZrO2 were studied by ab initio calculations based on the density functional theory and pseudopotential method. The calculated lattice parameters and band gap are in agreement with the experimental and other theoretical values. The evolution of lattice parameters and electronic properties were illustrated under high pressure. Meanwhile, the optical properties, such as adsorption coefficients, imaginary part of dielectric function, and energy loss function, were investigated under both ambient and high pressures.     

Effects of Electron Donating Ability of Substituents and Molecular Conjugation on the Electronic Structures of Organic Radicals

The geometries and electronic structures of a series of electron donor-acceptor radical molecules have been studied theoretically. The computational results show that the introduction of substituents with strong electron donating ability into tri-(2,4,6-trichlorophenyl) methyl(TTM) radicals enables the radical molecules to form the non-Aufbau electronic structure. The difficulty of forming the non-Aufbau electronic structure decreases with the enhancement of the electron donating ability of the substituent, but the expansion of the molecular conjugated system is not conducive to the formation. The hybridization of different fragments in molecular orbitals results in the disproportionation of orbital energy level and forms a staggered energy level structure. The electronic structure of radical molecules can be adjusted by substituents and molecular skeleton profoundly, which is a very effective means for molecular design.     

The Adsorption Behavior of Gas Molecules on Co/N Co–Doped Graphene

Herein, we have used density functional theory (DFT) to investigate the adsorption behavior of gas molecules on Co/N₃ co–doped graphene (Co/N₃–gra). We have investigated the geometric stability, electric properties, and magnetic properties comprehensively upon the interaction between Co/N₃–gra and gas molecules. The binding energy of Co is −5.13 eV, which is big enough for application in gas adsorption. For the adsorption of C₂H₄, CO, NO₂, and SO₂ on Co/N–gra, the molecules may act as donors or acceptors of electrons, which can lead to charge transfer (range from 0.38 to 0.7 e) and eventually change the conductivity of Co/N–gra. The CO adsorbed Co/N₃–gra complex exhibits a semiconductor property and the NO₂/SO₂ adsorption can regulate the magnetic properties of Co/N₃–gra. Moreover, the Co/N₃–gra system can be applied as a gas sensor of CO and SO₂ with high stability. Thus, we assume that our results can pave the way for the further study of gas sensor and spintronic devices.     

气体再燃低NOx燃烧中NO与NHi的反应机理研究

采用量子化学密度泛函理论(DFT)对NO与NH_i自由基的反应机理进行了研究,并结合经典过渡态理论对各反应速率常数进行了计算。结果表明,NO与NH₂自由基的反应体系可通过六个反应通道形成N₂+H₂O、N₂O+H₂和N₂H+OH。从能量变化和反应速率两方面考虑,产物N₂+H₂O最容易生成,其最佳反应通道为NO+NH₂→→N₂+H₂O;NO与NH自由基的反应体系可通过七个反应通道形成N₂+OH、N₂O+H和N₂H+O;其中,N₂+OH最容易生成,最佳反应通道为NO+NH→→N₂+OH。比较发现, NH比NH₂自由基更易与NO发生反应生成N₂。因此,在实际运行中改变操作条件,实现NH₂等向NH方向转化,有利于NO_x的还原。     

Theoretical studies of the geometries of H2GeNaF and its insertion reaction with R?H (RF,OH, NH2, CH3)

The geometries and insertion reactions of germylene H₂GeNaF with R? H (R?F, OH, NH₂, CH₃) have been investigated at the B3LYP/6‐311+G level of theory. The potential barriers of the four reactions are ～52, 120, 184, and 257 kJ/mol, including the ZPVE corrections, respectively. Here, all the mechanisms of the four reactions are identical to each other; i.e., an intermediate has been located during the insertion reaction. The intermediate could dissociate into substituted germylane and NaF with the barrier corresponding to the dissociation energy. Correspondingly, the reaction energies for the four reactions are ?43, ?4, 21, and 51 kJ/mol, respectively. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Effects of hydroxyl group on H2 dissociation on graphene: A density functional theory study

Graphene-based materials are promising for hydrogen production and storage. In this work, using density functional theory calculations, we explored how a hydroxyl group influences H₂ dissociation on graphene. Presence of the hydroxyl group makes the binding of H atom with graphene stronger, as the binding energy of H atom with the hydroxyl-modified graphene is higher than that with the pristine graphene. The para-site is the most favorable site for H₂ dissociation on both the pristine and hydroxyl-modified graphene. The energy barrier of H₂ dissociation at para-site on the pristine graphene is 3.10 eV whereas that on the hydroxyl-modified graphene is 2.46 eV, indicating a more facile H₂ dissociation on the hydroxyl-modified graphene.     

Ground and excited state double hydrogen transfer in symmetric and asymmetric potentials: comparison of 2,7,12,17-tetra-n-propylporphycene with 9-acetoxy-2,7,12,17-tetra-n-propylporphycene

Analysis of time-resolved anisotropy of transient absorption enabled determination of room temperature ground and excited state rate constants for intramolecular double hydrogen transfer in two similar porphycenes, one of them with symmetric and the other, with asymmetric character of a double minimum potential for hydrogen motion. The perturbation preserves a quasi-symmetric minimum in S(0), but the rate decreases approximately two times. In S(1), the perturbed potential becomes strongly asymmetric, and the downhill hydrogen transfer occurs with a rate higher than that observed for a symmetrical compound.     

DFT和热力学研究氢键协同效应及对关联1H NMR的影响

用DFT方法在B3LYP／6—311 G(d,p)水平下研究了甲醇线性和环状分子簇．对于不同大小的分子簇之间定义了协同因子,计算得到的协同因子可以验证氢键的强协同效应,环状分子簇之间的协同效应远远大于线性分子簇,做为理论验证和比较,热力学模型分别采用含氢键缔合的格子流体状态方程(LFHB),以及含氢键协同效应的LFHB,关联醇一惰性体系的^1H核磁共振化学位移．考虑协同效应的关联结果优于原始的LFHB,比较量子化学计算的和热力学模型中采用的协同因子,认为甲醇和乙醇在溶液中更可能大部分以线性缔合形式存在。     

Niobium Doping in BiVO4: Interplay Between Effective Mass,Stability, and Pressure

We have applied density functional theory to study the electronic structure changes caused by Nb incorporation in BiVO₄ and the application of external pressure. The overall solubility of Nb in BiVO₄ is usually high, and the presence of oxygen vacancies affect the dopability of Nb in BiVO₄. Through the analyses of the chemical-potential landscape, we have determined the single-phase stability zone of BiVO₄ with the Nb doping. The most favorable Nb doping is simultaneous substitutions at both V- and Bi-sites. Even though Nb substitution at only V-site is next favorable, the band gap change is not very significant which agrees with an earlier experiment. However, it does change the electron effective mass by 20 % owing to the presence of Nb 4d bands in the conduction bands, which explains better catalytic activity by Nb-doped BiVO₄. In addition, application of external pressure the single-phase stability zone in the chemical-potential landscape. We have also focused on the local structural distortions near the Nb doping site, especially on the BiO₈ octahedra. We have shown here that pressure-induced symmetrization of BiO₈ dodecahedron lowers the electron's effective mass further and therefore can help to improve the photoconduction property of BiVO₄.