金属串配合物[MM′M″(dpa)4(Cl)2](M=Co,Ni;M′,M″=Co,Rh)电子输运的理论研究

采用密度泛函理论DFT/BP86方法研究金属串配合物[MM'M″(dpa)₄(Cl)₂] [MM'M″=CoCoCo(1), CoCoRh(2), CoRhRh(3), NiCoRh(4)] 的结构和电子输运性质. 结果表明, 配合物1, 2和4的最稳定自旋态均存在1个(MM'M″)⁶⁺的离域$\sigma_{3}^{3}$键($\sigma^{2}\sigma_{nb}^{1}\sigma^{*0}$); 但配合物3具有1个(MM'M″)⁶⁺的离域$\sigma_{3}^{4}$键($\sigma^{2}\sigma_{nb}^{2}\sigma^{*0}$)和2个$\pi_{3}^{5}$键($\pi^{4}\pi_{nb}^{4}\pi^{*2}$), 故Rh—Rh键和Co—Rh键较强; Rh的引入使M—M键增强, Ni的引入则使M—M键减弱, 键强次序为Rh—Rh>Co—Rh>Co—Co>Ni—Co. 配合物14的传输通道均含有π和σ型轨道. 正偏压下, 配合物2和3的电流大于配合物1和4的. 负偏压下, 配合物4中出现负微分电阻效应. 配合物3中形成传输通道的σ_nbα/β和π^*α/β轨道能级分裂明显, (MM'M″)⁶⁺对β自旋的π^*轨道的贡献(88%)比α自旋(74%)的大, 使β自旋的电子更易传输, 具有较好的自旋过滤效应(70%80%).     

Cε3-Cε4蛋白寡核苷酸适配子结合位点的预测与筛选

采用NPDock程序对Cε3-Cε4蛋白与其核酸适配子A1的结合位点进行了预测与筛选, 筛选出A1与Cε3-Cε4蛋白结合的关键位点. 同时, 根据蛋白与DNA片段复合物结合界面中氨基酸残基和碱基统计分析发现, 结合界面氨基酸富集碱基G能力最强, 富集碱基T和C能力次之. 本文建立了以NPDock程序虚拟对接为基础的高效适配子优化方法, 为相关研究提供了实验参考.     

2,4-二羟基苯乙酮缩异烟酰腙的实验和DFT理论研究:合成、晶体结构和性质及量化计算

合成了一种酰腙类Schiff碱2,4-二羟基苯乙酮缩异烟酰腙(C₁₄H₁₃N₃O₃,H₂L),经元素分析、红外光谱、紫外光谱、荧光光谱和热重分析等技术手段进行了表征。 用X射线单晶衍射测定了它的晶体结构,该晶体属单斜晶系,C2/c空间群,晶胞参数a=2.0102(2) nm,b=0.75891(8) nm,c=1.9530(2) nm,α= 90°,β=111.481(12)°,γ=90°,V=2.7725(5) nm³,Z=4,D_c=1.4292 g/cm³,R₁=0.0422,wR₂=0.1113,F(000)=1256。 同时进行了量子化学计算研究。 使用Gaussian09量子化学程序包, 在密度泛函理论(DFT)的B3LYP/6-31G(d)水平,对化合物的分子结构进行全参数优化计算,获得了热力学参数和几何结构参数,对分子的总能量及前线分子轨道、Mulliken电荷分布进行了分析讨论;同时,用TD-DEF方法计算了化合物的电子吸收光谱和荧光发射光谱。     

水溶液中氨基酸侧链对G∶C碱基对间氢键影响的理论研究

利用量子化学方法研究了气相和水溶液下,氨基酸侧链与鸟嘌呤和胞嘧啶间的氢键作用.应用B3LYP/6-31+G(d,p)方法优化复合物几何结构,使用MP2/aug-cc-p VDZ方法进行复合物能量、自然键轨道(NBO)电荷和二阶稳定化能的计算.结果表明,水溶液可使氨基酸侧链与碱基或碱基对之间氢键键能显著减小;带电复合物气相和水溶液氢键键能之差范围为50.63~146.48 k J/mol,中性为0.17~24.94 k J/mol;电荷的转移量与氢键键能成正比,电荷转移量越多,复合物越稳定;二阶稳定化能与氢键键长成反比,与电荷转移量成正比,且气相与水溶液氢键二阶稳定化能之比约为两相的电荷转移量之比.水溶液对该类体系中氢键作用具有明显影响.     

血红素近轴侧基氢键的ABEEM/MM分子动力学模拟

应用ABEEM/MM浮动电荷力场对鲸鱼肌红蛋白及突变体进行了分子动力学模拟. 结果表明, 血红素近轴侧基不存在稳定的双氢键, 该氢键对轴配体咪唑的取向不起决定性作用, 而咪唑的取向与键联的组氨酸有密切联系. 同时表明, 血红素轴配体的柔性与其邻近的氨基酸和咪唑体积有关.     

ABEEMσπ和OPLS-AA力场对蛋白质GA88/GB88的分子动力学模拟

将原子与键电负性均衡方法融入分子力学方法,即利用ABEEMσπ浮动电荷力场与ABEEM-7P水模型相结合的方法及OPLS-AA固定电荷力场方法,对GA88和GB88蛋白进行了水溶液(温度295 K)和真空中的分子动力学模拟.比较两种方法得到的两个蛋白质的结构与实验结构的均方根偏差,分析了两种方法得到的两个蛋白质的回旋半径、氢键分布、径向分布及电荷分布情况.结果表明,ABEEMσπ和OPLS-AA力场均能正确模拟蛋白质结构,得到的各项偏差值接近,但从各偏差的波动大小可见,ABEEMσπ力场的模拟更稳定;回旋半径模拟很好地体现了蛋白质的"电致紧缩"现象;氢键分布、径向分布及电荷分布表明,与OPLS-AA固定电荷力场相比,ABEEMσπ浮动电荷力场能更好地体现蛋白质和周围水分子的极化效应.     

外围取代基团对卟啉铂(Ⅱ)配合物发光性能的影响

设计合成了具有不同外围取代基的卟啉铂(Ⅱ)配合物PtTEMP, PtTBMP, PtOMPP和PtDMPP, 并对其结构和光电性能进行了表征. 晶体结构分析结果表明, 这些卟啉铂(Ⅱ)配合物具有较理想的平面配位构型, β-位叔丁基的引入有效抑制了分子间的π-π相互作用. 外围取代基几乎不影响配合物的吸收和发光性质, 最大发射峰位于646~656 nm之间, 为配体中心的 ³π^*-π磷光发射. 空间位阻效应更强的叔丁基取代配合物(PtTBMP)的溶液态荧光量子效率和外量子效率最高, 分别为0.58和6.3%. 3个甲氧基取代的PtDMPP的发光效率优于2个甲氧基取代的PtOMPP, 二者的溶液态荧光量子效率分别为0.36和0.29, 外量子效率分别为2.4%和1.7%.     

ABEEM/MM浮动电荷力场应用于血红素结构的研究

运用拟合的参数, 应用ABEEM/MM浮动电荷力场对血红素分子结构进行了模拟. 结果表明, 该力场与CHARMM力场相比, 能更好地模拟晶体结构. 计算的ruffing构象能与B3LYP/6-31G*计算结果的线性相关系数在0.98以上, 同时表明血红素分子中twist-angle对ruffing构象具有明显影响. ABEEM/MM力场计算的细胞色素c552中血红素分子的电荷分布与CHARMM固定电荷力场的比较, 更准确地反映了血红素分子的电荷分布以及极化现象.     

嗜热蛋白酶PH1704别构中心量子化学计算与突变体动力学

通过量子化学计算, 确定嗜热菌Pyrococcus horikoshii OT3的PH1704蛋白酶别构位点的关键残基为Arg113, Tyr120和Asn129. 其中, Arg113及Asn129与别构抑制剂结合, 参与别构调控. Tyr120残基位于亚基交界面附近, 并与亲核残基Cys100之间以氢键相连, 可通过影响亚基聚合来影响酶的亲核催化. DJ-1超家族的4种构建蛋白的结构显示, 120位点位于亚基交界面处, 影响亚基的聚合, 进而影响蛋白酶的活力, 并间接参与别构调控. 分子生物学实验显示, 突变体R113T/Y120P/N129D的k_cat/k_m(L·μmol^-1·min^-1)值是野生型k_cat/k_m值的6倍, h系数由野生型的0.86转变为1.3, 负协同效应消失. 113和129位点处阴离子别构剂脱离, 从而破坏113, 120和129位点间的封闭环结构, 使AC交界面α7螺旋(124~129, 524~529)间聚合度增强; 120位点残基由Tyr转变为Pro, 与Cys100间氢键断裂, 亲核进攻的阻力减小, 从而使酶活力提高, 别构负调控消失.     

黑果枸杞叶多糖LRLP3的结构、抗氧化活性及免疫活性

黑果枸杞叶经水提醇沉, 离子交换柱层析和凝胶柱层析分离纯化, 得到平均分子量为79400的均一多糖组分LRLP3. 对该多糖的理化性质、 结构、 抗氧化活性及免疫活性的研究结果表明, LRLP3为多分支结构, 主链为(1→3)βGalp, 大部分半乳糖6位存在分支; 支链由(1→6)βGalp, (1→4)βGalp, (1→3)βAraf, (1→3)αArap, (1→5)βAraf和(1→2,4)αRhap组成, 非还原末端由αAraf, βGalp和βGlcp组成. LRLP3具有较强的还原能力, 可显著清除1,1-二苯基-2-三硝基苯肼(DPPH)自由基、 羟自由基和超氧阴离子自由基, 有效抑制Cu²⁺/H₂O₂诱导的蛋白氧化损伤和H₂O₂诱导的细胞氧化损伤. LRLP3在体外对未经诱导和经刀豆蛋白(ConA)或脂多糖(LPS)诱导的小鼠脾细胞增殖均有促进作用.     

孤对键弱化效应研究

在H_2O_2、N_2H_4、F_2分子中,O—O、N—N、F—F键的键长分别是0.148、0.148、0.144nm,虽比C_2H_6分子中的C—C键(0.154nm)短,但其σ键键能分别是146、160、155kJ/mol,却比C—C键能(365 kJ/mol)小约2.5倍,通常称这类原子的单键键能的反常现象为“孤对键弱化效应”。传统观点认为,半径很小的N、O、F等在化合时必须相当接近才能键合,孤对电子的排斥作用阻止了其相互接近,削弱了键能,降低了键的稳定性。显然,将这种削弱效应考虑为原子间效应是不合理的。本文用键参数图解法对“孤对键弱化效应”提出了合理的解释。     

Evaluation of the individual hydrogen bonding energies in N-methylacetamide chains

The individual hydrogen bonding energies in N-methylacetamide chains were evaluated at the MP2/6-31+G** level including BSSE correction and at the B3LYP/6-311++G(3df,2pd) level including BSSE and van der Waals correction. The calculation results indicate that compared with MP2 results, B3LYP calculations without van der Waals correction underestimate the individual hydrogen bonding energies about 5.4 kJ mol^?1 for both the terminal and central hydrogen bonds, whereas B3LYP calculations with van der Waals correction produce almost the same individual hydrogen bonding energies as MP2 does for those terminal hydrogen bonds, but still underestimate the individual hydrogen bonding energies about 2.5 kJ mol^?1 for the hydrogen bonds near the center. Our calculation results show that the individual hydrogen bonding energy becomes more negative (more attractive) as the chain becomes longer and that the hydrogen bonds close to the interior of the chain are stronger than those near the ends. The weakest individual hydrogen bonding energy is about ?29.0 kJ mol^?1 found in the dimer, whereas with the growth of the N-methylacetamide chain the individual hydrogen bonding energy was estimated to be as large as ?62.5 kJ mol^?1 found in the N-methylacetamide decamer, showing that there is a significant hydrogen bond cooperative effect in N-methylacetamide chains. The natural bond orbital analysis indicates that a stronger hydrogen bond corresponds to a larger positive charge for the H atom and a larger negative charge for the O atom in the N-H?O=C bond, corresponds to a stronger second-order stabilization energy between the oxygen lone pair and the N-H antibonding orbital, and corresponds to more charge transfer between the hydrogen bonded donor and acceptor molecules.     

Effects of Electronic Structure of Adjacent Carbon on the Strength of C─F⋯H─F Organofluorine Hydrogen Bonds

We investigate the effects of the electronic structure of carbon atom on the organofluorine hydrogen bonds, C─F⋯H─F. Our results show that we can modulate the strength of organofluorine hydrogen bonds by adjusting the volume of fluorine atom in C─F via changing the electronic structure of adjacent carbon atoms. Different with the conventional hydrogen bonds, we found that instead of carbon rehybridization and hyperconjugative effects, the magnitude of fluorine atomic volume plays important roles in determining the strength of the C─F⋯H─F organofluorine hydrogen bonds. The lone pair electrons at both the proximal and the vicinal carbon dramatically reinforce the strength of C─F⋯H─F organofluorine hydrogen bond with its interaction energy in the range of about 15–25 kcal/mol, that is, the carbanion-mediated organofluorine hydrogen bond could be very strong. Due to the high electronegativity of fluorine atom, it easily attracts the excess electron from the proximal and vicinal carbon, which results in the increase of its volume and negative charge. The enhanced volume of fluorine atom gives rise to the large polarization energy, and its enhanced negative charge favors the large electrostatic interaction, both of which substantially contribute to making the organofluorine hydrogen bonds strong. © 2019 Wiley Periodicals, Inc.     

Theoretical analysis of fluoroglycine conformers

Seven different optimized conformers of α‐fluoroglycine (H₂NCHFCOOH) were obtained from ab initio calculations. Some of these conformers are exceptionally stable compared to similar conformers of glycine. Conformers in which the lone pair of electrons on the nitrogen atom are antiperiplanar to the C F bond are more stable than conformers that do not have such an arrangement. The stability difference between conformers with such an arrangement and conformers that have the lone pair of electrons synperiplanar to the C F bond is about 27 kJ/mol (calculated at the MP2/6‐31+G* level). Conformers that have the lone pair of electrons antiperiplanar to the C F bond possess a longer C F bond, a shorter C N bond, and sp²‐like amino bond angles. For some conformers an unusual hydrogen bond involving the acidic carboxylic acid hydrogen and the electronegative fluorine atom is observed. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 426–431, 2000     

环多肽晶体的浮动电荷极化力场模拟

利用原子键电负性均衡结合分子力场方法(ABEEM/MM)对五种环多肽晶体进行了研究. 与传统力场相比, 该方法中的静电势包含了分子内和分子间的静电极化作用, 以及分子内电荷转移影响, 同时加入了化学键等非原子中心电荷位点, 合理地体现了分子中的电荷分布. 相对其他极化力场模型, 具有计算量较小的特点. 该模型下计算得到的环多肽分子单元相对实验测得的结构的原子位置、氢键长度和二面角的均方根偏差分别为0.009 nm、0.013 nm和5.16°, 能够很好地重复实验结果. 总体上, 其结果优于或相当于其他力场模型, 适用于对实际蛋白质体系的模拟和研究.     

Role of conformational isomerism in solvent-mediated charge transfer in chiral (S) 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM): condensed-phase to jet-cooled spectroscopic studies

Intramolecular charge-transfer reaction in chiral (S) 1,2,3,4-tetrahydro-3-isoquinoline methanol (THIQM) has been investigated in the condensed phase and in jet-cooled conditions by means of laser-induced fluorescence, dispersed emission, resonance-enhanced two-photon ionization, and IR-UV double resonance experiments, as well as quantum chemical calculations. In the condensed phase, THIQM only shows local emission in nonpolar and protic solvents and dual emission in aprotic polar solvents, where the solvent-polarity dependent Stokes shifted emission is ascribed to a state involving charge transfer from the nitrogen lone pair to the benzene π-cloud. Ab initio calculations reveal two low-energy conformers, which are observed in jet-cooled conditions. In the most stable conformer, THIQM(I), the CH(2)OH substituent acts as a hydrogen bond donor to the nitrogen lone pair in the equatorial position, while the second most stable conformer, THIQM(II), corresponds to the opposite NH···O hydrogen bond, with the nitrogen lone pair in the axial position. The two low-energy jet-cooled conformers of THIQM evidenced from the laser-induced fluorescence and dispersed emission spectra only show structured local emission. Complexes with usual solvents reproduce the condensed phase properties. The jet-cooled complex with aprotic polar solvent acetonitrile shows both local emission and charge transfer emission as observed in solution. The jet-cooled hydrate mainly shows local emission due to the unavailability of the nitrogen lone pair through intermolecular hydrogen bonding.     

Quantum mechanical analysis of 1,2-ethanediol conformational energetics and hydrogen bonding

A proper understanding of the conformational energetics of 1,2-ethanediol (ethylene glycol) is important to the construction of molecular mechanics force fields for the treatment of carbohydrates since these biologically important molecules have a prevalence of vicinal hydroxyl groups. In the present study, quantum mechanical analysis of the 10 unique minimum-energy conformations of ethylene glycol is performed by using 10 model chemistries ranging from HF/6-311++G(d,p) up to a hybrid method that approximates CCSD(T)/cc-pVQZ. In addition, natural bond orbital (NBO) analysis of these conformations with deletion of pairings of CO bond/antibonding and lone pair/antibonding orbitals is used to investigate contributions from the "gauche" effect to ethylene glycol conformational energetics. MP2 with the "correlation consistent" basis sets and DFT/6-311++G(d,p) do the best job of matching the approximate CCSD(T)/cc-pVQZ energies while MP2/6-31G(d) and Hartree-Fock both fare poorly. NBO analysis shows the conformational energies to be independent of the deletion of matrix elements associated with (i) CO bonding and antibonding orbital interactions and (ii) lone pair and antibonding orbital interactions, whereas the energetic ordering correlates with geometric parameters consistent with internal hydrogen bonds. Thus, the present results suggest that standard molecular mechanics potential energy functional forms, which lack explicit terms to account for stereoelectronic effects, are appropriate for carbohydrates.     

The Double‐Faced Nature of Hydrogen Bonding in Hydroxy‐Functionalized Ionic Liquids Shown by Neutron Diffraction and Molecular Dynamics Simulations

We characterize the double‐faced nature of hydrogen bonding in hydroxy‐functionalized ionic liquids by means of neutron diffraction with isotopic substitution (NDIS), molecular dynamics (MD) simulations, and quantum chemical calculations. NDIS data are fit using the empirical potential structure refinement technique (EPSR) to elucidate the nearest neighbor H???O and O???O pair distribution functions for hydrogen bonds between ions of opposite charge and the same charge. Despite the presence of repulsive Coulomb forces, the cation–cation interaction is stronger than the cation–anion interaction. We compare the hydrogen‐bond geometries of both “doubly charged hydrogen bonds” with those reported for molecular liquids, such as water and alcohols. In combination, the NDIS measurements and MD simulations reveal the subtle balance between the two types of hydrogen bonds: The small transition enthalpy suggests that the elusive like‐charge attraction is almost competitive with conventional ion‐pair formation.