The bondons: the quantum particles of the chemical bond

By employing the combined Bohmian quantum formalism with the U(1) and SU(2) gauge transformations of the non-relativistic wave-function and the relativistic spinor, within the Schrödinger and Dirac quantum pictures of electron motions, the existence of the chemical field is revealed along the associate bondon particle B̶ characterized by its mass (m_B̶), velocity (v_B̶), charge (e_B̶), and life-time (t_B̶). This is quantized either in ground or excited states of the chemical bond in terms of reduced Planck constant ħ, the bond energy E_bond and length X_bond, respectively. The mass-velocity-charge-time quaternion properties of bondons’ particles were used in discussing various paradigmatic types of chemical bond towards assessing their covalent, multiple bonding, metallic and ionic features. The bondonic picture was completed by discussing the relativistic charge and life-time (the actual zitterbewegung) problem, i.e., showing that the bondon equals the benchmark electronic charge through moving with almost light velocity. It carries negligible, although non-zero, mass in special bonding conditions and towards observable femtosecond life-time as the bonding length increases in the nanosystems and bonding energy decreases according with the bonding length-energy relationship Ebond[kcal/mol]×Xbond[A0]=182019, providing this way the predictive framework in which the B̶ particle may be observed. Finally, its role in establishing the virtual states in Raman scattering was also established.     

Co(Ⅱ)掺杂锐钛矿二氧化钛的理论研究

采用基于密度泛函理论(DFT)框架下的第一性原理平面波赝势(PWPP)方法,模拟计算Co(Ⅱ)掺杂锐钛矿TiO2,讨论了Co(Ⅱ)掺杂对锐钛矿的晶体结构、能隙、态密度等的影响。结果表明Co(Ⅱ)掺杂锐钛矿TiO2晶体后,Co(Ⅱ)的3d轨道进入禁带并与氧的2p轨道作用,使禁带宽度(Eg)变小,TiO2的吸收带红移,从而有助于TiO2的光催化活性。     

Keggin型多阴离子[XW12O40]n-(X=Si,Ge,P,As)电子性质的密度泛函理论研究

采用密度泛函理论方法研究了Keggin型多阴离子[XW12O40]n-(X=Si,Ge,P,As)的电子性质,在几何优化基础上,分析杂原子对体系的几何结构,电子性质,氧化还原性质的影响。结果表明:杂原子对多阴离子的键长有影响,变化规律与杂原子半径递变一致;杂原子的电子性质影响多阴离子的氧化性,多阴离子的氧化能力随杂原子的电负性增大而提高;杂原子的核电荷数越大,该多阴离子的氧化性越强;多阴离子的酸强度与杂原子的电负性次序一致。     

Cu、N共掺杂锐钛矿型二氧化钛的理论研究

采用基于密度泛函理论(DFT)框架下的第一性原理平面波赝势(PWPP)方法,模拟计算了Cu、N共掺杂锐钛矿TiO2,讨论了Cu掺杂、N掺杂、Cu、N共掺杂对锐钛矿TiO2的晶体结构、能隙、态密度等的影响.结果表明Cu、N共掺杂锐钛矿TiO2晶体后,导带主要由N-2p和Ti-3d轨道上的电子构成,价带主要由O-2p和Cu...     

Thermodynamic Insight into the Effects of Water Displacement and Rearrangement upon Ligand Modifications using Molecular Dynamics Simulations

Computational methods, namely molecular dynamics (MD) simulations in combination with inhomogeneous fluid solvation theory (IFST) were used to retrospectively investigate various cases of ligand structure modifications that led to the displacement of binding site water molecules. Our findings are that water displacement per se is energetically unfavorable in the discussed examples, and that it is merely the fine balance between change in protein–ligand interaction energy, ligand solvation free energies, and binding site solvation free energies that determine if water displacement is favorable or not. We furthermore evaluated if we can reproduce experimental binding affinities by a computational approach combining changes in solvation free energies with changes in protein–ligand interaction energies and entropies. In two of the seven cases, this estimation led to large errors, implying that accurate predictions of relative binding free energies based on solvent thermodynamics is challenging. Nevertheless, MD simulations can provide insight regarding which water molecules can be targeted for displacement.     

Ni-Co-B非晶态合金电子性质的理论研究

根据 Ni- Co- B非晶态合金结构的短程有序、Ni、Co、B之间是较强的化学作用以及化学键理论 ,利用一系列原子簇模型 Ni4-n Con B2 ( n=0～ 4)对 Ni- Co- B非晶态合金用 DFT方法进行较高水平的量子化学计量 ,结果表明 ,模型体系 Ni4-n Con B2 中 ,B原子供给 Ni原子、Co原子电子 ,这与非晶态合金的实验结果一致 ,同时计算结果也表明了在三元非晶态合金 Ni- Co- B中 ,很可能存在与二元 Ni- B非晶态合金类似的 B- B近距离直接接触 ;Co原子得电子能力强于 Ni原子 ,钴的引入对镍的电子结构有调变作用     

The electronic structure effect in heterogeneous catalysis

Using a combination of density functional theory calculations and X-ray emission and absorption spectroscopy for nitrogen on Cu and Ni surfaces, a detailed picture is given of the chemisorption bond. It is suggested that the adsorption bond strength and hence the activity of transition metal surfaces as catalysts for chemical reactions can be related to certain characteristics of the surface electronic structure.     

硫靛染料发色体结构与性质的泛函理论研究

在密度泛函理论(DFT)的B3LYP/6-31 G*水平上对硫靛染料发色体的几何结构进行优化计算,在获得基态稳定结构的基础上,应用含时密度泛函理论(TD—DFT)方法在相同水平计算电子吸收光谱。探讨了给电子基团对电子吸收光谱的影响。结果表明:给电子基团给电子能力的增强使光谱产生一定的红移。通过对前线轨道组成进行自然布居分析,揭示了硫靛染料的发光均源自分子中HOMO-LUMO(π→π*)电子跃迁。     

Zn3V2O8的电子结构与光学性质的理论研究

采用平面波超软赝势密度泛函理论的方法研究了Zn3V2O8的能带结构、电子态密度和光学特性.能带结果显示Zn3V2O8呈间接带隙的绝缘体型能带,其禁带宽度为2.9 eV.详细的电子态密度结果显示其费米面上的态密度达到20 e/eV,费米能级附近的能级由Zn3p、V3p和O2p电子形成,Zn3d和O2s之间有强的杂化作用.介电性能结果显示在4.4 ～5.7 eV附近有强的吸收峰,在20.6 eV附近有一个次强吸收峰;吸收光谱显示在6.8 eV处有强吸收,在20.7 eV处有一个较弱的吸收峰.     

CdGeAs2晶体的结构、弹性和电子性能的模拟计算和分析

利用基于密度泛函理论的平面波赝势法对CdGeAs2晶体的结构,弹性和电子性能进行了研究.CdCeAs2晶体具有6个独立的弹性常数,利用计算的弹性性能可以判断晶体具有机械稳定性、延性和弹性各向异性等力学特点.通过总的和部分态密度分析了不同能带的贡献成分.计算的结构参数及弹性常数与实验值基本吻合.CdGeAs2晶体具有直接...     

Nitroarenes as Antitubercular Agents: Stereoelectronic Modulation to Mitigate Mutagenicity

Nitroarenes are less preferred in drug discovery due to their potential to be mutagenic. However, several nitroarenes were shown to be promising antitubercular agents with specific modes of action, namely, nitroimidazoles and benzothiazinones. The nitro group in these compounds is activated through different mechanisms, both enzymatic and non‐enzymatic, in mycobacteria prior to binding to the target of interest. From a whole‐cell screening program, we identified a novel lead nitrobenzothiazole (BT) series that acts by inhibition of decaprenylphosphoryl‐β‐d ‐ribose 2′‐epimerase (DprE1) of Mycobacterium tuberculosis (Mtb). The lead was found to be mutagenic to start with. Our efforts to mitigate mutagenicity resulted in the identification of 6‐methyl‐7‐nitro‐5‐(trifluoromethyl)‐1,3‐benzothiazoles (cBTs), a novel class of antitubercular agents that are non‐mutagenic and exhibit an improved safety profile. The methyl group ortho to the nitro group decreases the electron affinity of the series, and is hence responsible for the non‐mutagenic nature of these compounds. Additionally, the co‐crystal structure of cBT in complex with Mtb DprE1 established the mode of binding. This investigation led to a new non‐mutagenic antitubercular agent and demonstrates that the mutagenic nature of nitroarenes can be solved by modulation of stereoelectronic properties.     

Understanding the Electronic Structures and Absorption Properties of Porphyrin Sensitizers YD2 and YD2-o-C8 for Dye-Sensitized Solar Cells

The electronic structures and excitation properties of dye sensitizers determine the photon-to-current conversion efficiency of dye sensitized solar cells (DSSCs). In order to understand the different performance of porphyrin dye sensitizers YD2 and YD2-o-C8 in DSSC, their geometries and electronic structures have been studied using density functional theory (DFT), and the electronic absorption properties have been investigated via time-dependent DFT (TDDFT) with polarizable continuum model for solvent effects. The geometrical parameters indicate that YD2 and YD2-o-C8 have similar conjugate length and charge transfer (CT) distance. According to the experimental spectra, the HSE06 functional in TDDFT is the most suitable functional for describing the Q and B absorption bands of porphyrins. The transition configurations and molecular orbital analysis suggest that the diarylamino groups are major chromophores for effective CT excitations (ECTE), and therefore act as electron donor in photon-induced electron injection in DSSCs. The analysis of excited states properties and the free energy changes for electron injection support that the better performance of YD2-o-C8 in DSSCs result from the more excited states with ECTE character and the larger absolute value of free energy change for electron injection.     

三联吡啶铂(Ⅱ)配合物光谱性质的密度泛函研究

采用密度泛函理论方法(DFT),对三联吡啶铂(Ⅱ)配合物的结构与电子光谱进行了系统研究.筛选的PBE/LanL2DZ(6-311+G(d))—BMK/LanL2DZ(6-31+G(d))方法,计算结果能较好地与实验值吻合:对光谱峰波长的计算,吸收光谱和发射光谱平均误差分别为14 nm和17 nm.通过对前线分子轨道的分析,归属了各光谱峰的跃迁类型.计算结果表明,不同推拉电子效应的取代基对配合物光谱峰的位置和跃迁类型具有较大影响,为已有的实验结论提供了有力的理论阐述.