碱基与氮甲基乙酰胺相互作用的从头算和ABEEMσπ研究

选取氮甲基乙酰胺(N-Methylacetamide,NMA)和DNA碱基为研究对象,应用ABEEMσπ/MM方法研究了NMA与碱基之间形成的二聚体的几何构型、电荷分布及结合能等性质,并进行了相应的从头算(abinitio)MP2水平研究,在B3LYP/6-311 ++G(d,p)水平下对结构进行了优化.将2种方法的研究结果进行比较发现,所获得的构型、电荷及结合能之间具有很好的一致性,NMA与DNA碱基相互作用的强度大小依次为:鸟嘌呤＞胸腺嘧啶＞胞嘧啶＞腺嘌呤,且证明了ABEEMσπ/MM模型的参数具有很好的可转移性.     

6-烷基鸟嘌呤与DNA碱基间氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对鸟嘌呤及顺(cis-)、反式(anti-)-6-烷基鸟嘌呤(O⁶-AlkylG)与DNA碱基(胸腺嘧啶T、胞嘧啶C、腺嘌呤A、鸟嘌呤G)的氢键二聚体结构进行了优化. 在MP2/cc-pVXZ(X＝D,T)// B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)分析了碱基间的弱相互作用. 计算结果显示, 鸟嘌呤6-O烷基化改变了碱基间的氢键作用模式, 使碱基对发生了明显的螺旋桨式扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小. O⁶-AlkylG对DNA碱基间的氢键作用是去稳定化的, 去稳定化影响的顺序为GC＞GG＞GA≈GT. 计算结果与文献给出的实验结论基本一致.     

应用ABEEM/MM力场探究Na~+与氮-甲基乙酰胺及水的相互作用

应用量子化学方法 MP2/6-311++G(d,p)//B3LYP/6-31+G(d,p)和原子-键电负性均衡浮动电荷分子力场(ABEEM/MM),对[Na(H_2O)n]+(n=3～8),[Na(NMA)n]+(n=3～8)和[Na(NMA)n(H_2O)m]+(n+m=4,6)(NMA=氮-甲基乙酰胺)体系的结构、结合能和电荷分布进行研究.在计算结果的基础上,构建上述体系的ABEEM/MM可极化势能函数,优选并确定相关参数.结果表明,ABEEM/MM的计算结果与量子化学的计算结果相符:Na+与配体间距离的平均绝对偏差(AAD)小于0. 007 nm,相对均方根偏差(RRMSD)小于3. 5%,夹角的AAD小于2. 4°,RRMSD小于2. 0%,结合能的AAD小于8. 9 k J/mol,RRMSD小于12. 4%;ABEEM/MM电荷分布与量子力学(QM)电荷分布的线性相关系数在0. 97以上.     

DNA甲基化-非甲基化碱基间堆积作用的理论研究

运用二级Mфller-Plesset(MP2)理论方法和cc-pVDZ基组优化了6-甲基鸟嘌呤(O6-MethylG),4-甲基胸腺嘧啶(O4-MethylT)以及5-甲基胞嘧啶(C5-MethylC)与DNA碱基鸟嘌呤(G),腺嘌呤(A),胞嘧啶(C),胸腺嘧啶(T)之间的堆积构型.在MP2/aug-cc-pVXZ//MP2/cc-pVDZ(X=D,T)水平上,采用完全基组外推方法校正了堆积碱基对间的相互作用能,并用完全均衡校正法(CP)校正了基组重叠误差(BSSE).MP2计算结果表明,DNA碱基甲基化使得嘧啶-嘧啶、嘧啶-嘌呤堆积碱基间的平行旋转角发生明显改变,并使堆积碱基间的相互作用能增大.在MP2/cc-pVDZ计算级别上得到了各堆积碱基对的全电子波函数,并用分子中的原子理论(AIM)分析了堆积碱基对间的弱相互作用.AIM分析结果显示,甲基化增强了堆积碱基间的π-π作用,且甲基氢与相邻碱基间形成H2CH…X(X=O,N,CH3,NH2)等类型的氢键.甲基化损伤使碱基间重叠程度增大、π-π作用增强以及堆积碱基间形成多个氢键,是堆积作用能增加的主要原因.     

O6-鸟嘌呤和O4-胸腺嘧啶甲基化与DNA碱基异常氢键作用的理论研究

用密度泛函B3LYP方法在6-311＋G**基组水平上对顺(cis-)、反式(anti-)O⁶-甲基鸟嘌呤(O⁶-MeG)和O⁴-甲基胸腺嘧啶(O⁴-MeT)与DNA碱基(腺嘌呤A、鸟嘌呤G)的非Watson-Crick氢键二聚体进行了优化. 在MP2/cc-pVXZ (X＝D,T)//B3LYP/6-311＋G**水平上, 采用完全基组外推方法校正了氢键二聚体的相互作用能, 并用完全均衡校正法(CP)校正了基组重叠误差(BSSE). 此外, 在B3LYP/6-311＋G**水平上计算了各氢键碱基对的全电子波函数, 并用分子中的原子理论(AIM)和电子密度拓扑方法分析了碱基间的弱相互作用. 计算结果显示, 甲基化使碱基对间的氢键作用模式发生了明显的扭转和不同程度的位移, 碱基间的电子密度分布和氢键作用能明显减小, 甲基化对O⁶-MeG和O⁴-MeT与DNA碱基间的氢键作用是去稳定化的, 这种影响主要来自于大体积的甲基的空间效应和给电子效应, 且对顺式的影响明显大于反式. 计算结果与文献给出的实验结论基本一致.     

双铂核药物与DNA作用的理论研究

利用分子力学和量子化学方法研究了双铂核药物［{trans-PtCl(NH₃)₂}₂(μ-NH₂(CH₂)_nNH₂)］²⁺与寡聚DNA片段d(ATATG*TACATAT)·d(ATGTG*TACATAT)复合物的几何构型和电子结构. 计算结果表明,Pt配合物与DNA中碱基G的N7原子形成了较强的配位键,并与O6原子之间存在较强的静电作用,使药物与DNA产生稳定作用,药物中的烃链的伸缩性使得DNA在键合药物后其构型并未发生大的变化. 同时,铂配合物中配体NH₃上的H与其邻近的鸟嘌呤的O6,DNA中磷酸根上的O以及与其邻近的碱基T上的O或N等电负性较大的原子间形成的氢键及弱氢键也是影响Pt配合物与DNA键合及其几何结构变化的重要因素. 这些化学键和氢键是药物分子能够对DNA进行识别的重要基础. 因此,可以认为药物结合后所引起DNA的变形较小可能是药物与顺铂产生不同的抗癌机理的主要原因.     

精氨酸侧链和核酸碱基间离子氢键作用强度分析

采用MP2/6-31+G(d,p)方法优化得到了22个由精氨酸侧链与碱基尿嘧啶、 胸腺嘧啶、 胞嘧啶、 鸟嘌呤及腺嘌呤形成的氢键复合物的气相稳定结构, 使用包含BSSE校正的MP2/aug-cc-pVTZ方法计算得到了复合物的气相结合能, 通过MP2/6-31+G(d,p)方法和PCM模型优化得到了复合物的水相稳定结构, 采用MP2/aug-cc-pVTZ方法和PCM模型计算得到了复合物的水相结合能. 研究发现, 精氨酸侧链与碱基间的离子氢键作用强度与单体间电荷转移量、 氢键临界点电子密度及二阶作用稳定化能密切相关. 与中性氢键相比, 离子氢键作用具有更显著的共价作用成分. 研究还发现, 精氨酸侧链和碱基间形成的氢键复合物的稳定性次序可以通过氢键受体碱基分子上氧原子和氮原子的质子化反应焓变进行预测, 质子化反应焓变越负, 形成的氢键复合物越稳定.     

DNA碱基(对)及其Zn2+复合物对CO2,N2,H2小分子的吸附

用M062X/6-31+G^*方法探讨了腺嘌呤(A)、 胸腺嘧啶(T)、 鸟嘌呤(G)、 胞嘧啶(C)及其碱基对(AT, GC)以及Zn²⁺复合物(AAA-Zn²⁺, AAT-Zn²⁺和GGC-Zn²⁺)对混合小分子H₂, N₂, CO₂的吸附情况, 系统研究了其相互作用模式及吸附强度, 预测了常见混合气体分子与碱基(对)及复合物的吸附位置. 研究表明, CO₂倾向于以氢键的形式结合到碱基(对)的氨基氢或亚氨基氢上, 而N₂和H₂分子则倾向于结合到这些碱基(对)的平面π电子上, 以堆垛的形式存在. 根据吸附强度大小, 预测了由这些碱基为骨架合成的金属有机骨架(MOF)吸附材料对小分子的选择性吸附顺序为H₂22. 研究表明, 以AT对结合金属Zn²⁺为节点的纯天然碱基对构成的MOF要比实验合成的AA碱基对与Zn²⁺结合的MOF具备更好的吸附和分离性能.     

铂配合物与DNA碱基对间相互作用的理论研究

用量子化学方法研究一系列Pt(II)配合物作用于嘌呤碱基N7位点后对Watson-Crick碱基对AT、GC的影响. 计算结果显示铂配体与碱基对AT、GC的作用以静电作用为主，同时极化作用也是影响GC碱基对的重要因素. 静电作用极大地增强了铂化嘌呤碱基与嘧啶碱基间的相互作用，而嘌呤碱基与嘧啶碱基间作用与未铂化碱基对作用相近. Pd(II) 和 Ni(II)的相关研究得到类似的结果. 碱基对间氢键作用“二阶微扰能”分析结果与氢键强弱变化一致.     

液液萃取-气相色谱-质谱联用技术测定废水中N-甲基甲酰苯胺、N-甲基苯胺和甲酰苯胺

建立了液液萃取-气相色谱-质谱(GC-MS)联用测定废水中N-甲基甲酰苯胺(NMF)、N-甲基苯胺(NMA)和甲酰苯胺(FA)的分析方法。考察了萃取溶剂、盐加入量和pH等影响萃取效果的参数。结果表明,当以二氯甲烷为萃取剂,将pH调至11.85,15%NaCl溶液加入量为1%(体积比)条件下,NMF、NMA和FA的萃取效果最佳。以N,N-二乙基苯胺(DEA)为内标,在GC-MS选择离子模式下测定NMF、NMA和FA,该方法对三种目标物的平均回收率为97.5%~101.0%,相对标准偏差为4.3%~6.3%(n=6),检测限(S/N=3)为0.0018~0.0023μg/L,测得某废水样品中NMF、NMA和FA的含量依次为0.94±0.08、0.14±0.02和0.12±0.02g/L。     

Theoretical studies of uracil–(H2O)n (n = 1–7) clusters by ab initio and ABEEMσπ/MM fluctuating charge model

Uracil–(H₂O)_n (n = 1–7) clusters were systemically investigated by ab initio methods and the newly constructed ABEEMσπ/MM fluctuating charge model. Water molecules have been gradually placed in an average plane containing uracil. The geometries of 38 uracil–water complexes were obtained using B3LYP/6-311++G** level optimizations, and the energies were determined at the MP2/6-311++G** level with BSSE corrections. The ABEEMσπ/MM potential model gives reasonable properties of these clusters when comparing with the present ab initio data. For interaction energies, the root mean square deviation is 0.96 kcal/mol, and the linear coefficient reaches 0.997. Furthermore, the ABEEMσπ charges changed when H₂O interacted with the uracil molecule, especially at the sites where the hydrogen bond form. These results show that the ABEEMσπ/MM model is fine giving the overall characteristic hydration properties of uracil–water systems in good agreement with the high-level ab initio calculations.     

Mg<Superscript>2+</Superscript>/Ca<Superscript>2+</Superscript> binding to DNA bases: a quantum chemical method and ABEEMσπ/MM fluctuating charge model study

The interactions of Mg²⁺ and Ca²⁺ binding to adenine, cytosine, guanine, and thymine at various binding sites were studied by a high-level quantum chemical method and ABEEMσπ/MM fluctuating charge model. The geometries and binding energies of M²⁺-bases complexes were determined at CCSD(T)/6-311 ++G(2d,2p)//MP2/6-311 ++G(2d,2p) level of theory, with the basis set superposition error corrections for the binding energy calculations. In comparison with the ab initio results, an accurate classical metal cation–base interaction potential was constructed and parameterized in terms of ABEEMσπ/MM model. It is revealed that Mg²⁺/Ca²⁺ prefers to bind with bases at the bidentate position (between two nitrogen atoms or oxygen and nitrogen atoms in purine and pyrimidine), where the binding energy is the largest. Moreover, the distance between M²⁺ and the base increases from Mg²⁺ to Ca²⁺, while the binding energy of Mg²⁺–base is greater than that of Ca²⁺-base. The ABEEMσπ/MM potential gives reasonable geometries and binding energies compared with the present quantum chemical calculations, and the overall percentage RMSDs are 1.4 and 1.6% for geometries and binding energies, respectively. Furthermore, the transferability of the parameters of the new potential is validated by investigation of Mg²⁺/Ca²⁺ binding to tautomer of bases, and results from our potential also show quite good consistency with those of MP2/6-311 ++G(2d,2p)//B3LYP/6-311 ++G(d,p) method, with the overall percentage RMSDs of 2.2 and 4.7% for geometries and binding energies, respectively. This work will serve as a basis for further investigations of the mechanisms of cation effects on the structure and property of nucleic acids.     

Accurate ab initio potential for the Na+...I* complex

High-level ab initio calculations employing the multireference configuration interaction and coupled clusters methods with a correlation-consistent sequence of basis sets have been used to obtain accurate potential energy curves for the complex of the sodium cation with the iodine atom. Potential curves for the first two electronic Lambda-S states have very different characters: the potential for the 2pi state has a well depth of approximately 10 kcal/mol, while the 2sigma state is essentially unbound. This difference is rationalized in terms of the anisotropic interaction of the quadrupole moment of the iodine atom with the sodium cation, which is stabilizing in the case of the 2pi state and destabilizing in the case of the 2sigma state. The effects of spin-orbit coupling have been accounted for with both ab initio and semiempirical approaches, which have been found to give practically the same results. Inclusion of spin-orbit interactions does not affect the X(omega = 32) ground state, which retains its 2pi character, but it results in two omega = 12 spin-orbit states, with mixed 2sigma and 2pi characters and binding energies roughly half of that of the ground spin-orbit state. Complete basis set (CBS) extrapolations of potential curves, binding energies, and equilibrium geometries were also performed, and used to calculate a number of rovibronic parameters for the Na+...I* complex and to parameterize model potentials. The final CBS-extrapolated and zero-point vibrational energy-corrected binding energy is 10.2 kcal/mol. Applications of the present results for simulations of NaI photodissociation femtosecond spectroscopy are discussed.     

Interaction of angelicin with DNA‐bases (III) DFT and ab initio second‐order Moeller–Plesset study

Angelicin geometry was optimized at MP2/6‐31+G(d,p) level and compared with X‐ray experimental data. The highest π‐electron density was found to be localized on C1? C2 and on C13? C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD‐DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc‐pVDZ, MP2/6‐31G(d,p) and MP2/cc‐pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

O+HCl→OH+Cl反应的立体动力学的准经典轨线研究

运用准经典轨线方法, 基于Peterson从头计算势能面对O+HCl→OH+Cl反应的立体动力学性质进行了研究. 讨论了在31.77和51.04 kJ/mol两种碰撞能情况下极化依赖的微分反应截面(2π/σ)(dσ₀₀/dω_t), (2π/σ)(dσ₂₀/dω_t), (2π/σ)(dσ₂₂₊/dω_t)和(2π/σ)(dσ_21-/dω_t)以及描述k-j′两矢量相关和k-k′-j′三矢量相关的分布函数P(θ_r)和P(φ_r). 计算得到的P(θ_r)分布表明, 产物分子的转动角动量j′具有强烈的取向分布, 并且产物转动角动量的取向效应对散射能的变化比较敏感. 而P(φ_r)的分布表明, 产物分子虽然具有沿着y轴的取向效应, 但是没有明显的定向效应.     

Computational study of the halogen atom-benzene complexes

The structures of halogen atom-benzene complexes were investigated by modern DFT and ab initio computational methods. The spectroscopic properties of the complexes are also predicted and are in good agreement with experiment where such data have been reported. The fluorine atom-benzene complex is predicted to be a sigma complex due to the strength of a C-F bond. The chlorine atom-benzene complex is predicted to have an eta(1) pi complex structure, which is only slightly more favorable (1.1 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than a sigma complex but is significantly more stable (4.4 kcal/mol with the BH&HLYP/6-311++G method including the ZPE correction) than the eta(6) pi complex. The bromine and iodine benzene complexes are also predicted to prefer an eta(1) pi complex structure.     

A theoretical and NMR lanthanide‐induced shift (LIS) investigation of the conformations of lactams.

Molecular mechanics (MM) with MMFF94 and MMX force fields and ab initio (RHF/6‐31G*,RHF/6‐311G**, and B3LYP/6‐311G**) calculations are used with lanthanide‐induced shift (LIS) to investigate the conformations of N‐methyl‐2‐pyrrolidone 1 , N‐methyl‐2‐piperidone 2 , ε‐caprolactam 3, γ‐valerolactam (1,5‐dimethyl‐2‐pyrrolidone) 4, 2 ‐ azetidinone 5 , 4‐methyl azetidinone 6 , 4‐phenyl azetidinone 7 , and N‐methyl‐4‐phenyl azetidinone 8 . The Yb(fod)₃ paramagnetic induced shifts of all the ¹H and ¹³C nuclei are measured and the corresponding diamagnetic complexation shifts obtained by the addition of Lu(fod)₃. The complexation model (two‐, three‐, or four‐site) used depends on the relative rates of the processes involved. The amide inversion is the same order as that of the 5‐ and 6‐membered lactam rings and much faster than the lanthanide complexation and the inversion of the 7‐membered ring. Both MM and ab initio calculations give an envelope conformation for 1 with C‐4 out of the ring plane in agreement with the LIS analysis. For the piperidone ring of 2 , the half‐chair is calculated as the most stable form. The LIS analysis confirms this but cannot exclude a small amount (<2%) of the boat conformation. For 3 , the LIS analysis gives a minimum for 90:10% chair to boat conformation, and 4 exists in two envelope conformations with the C₅‐Me ps‐eq and ps‐ax in an eq/ax ratio of 94:6%. In 2‐azetidinone 5 , the ab initio calculations gave both ring and nitrogen planar, but the MMFF94 calculations give a butterfly ring and pyramidal nitrogen. The LIS analysis for 5 gave good agreement (Rcryst 0.46%) for the MMFF94 geometry with endo NH but the planar ab initio geometries worse agreement (Rcryst = 1.1%). For 4‐methyl‐2‐azetidinone 6 , the MMFF94 geometry gave good agreement (Rcryst 0.96%) with two butterfly conformations with axial and equatorial methyl groups in 1:1 ratio. All the planar geometries gave worse agreement (Rcryst >1.5%). In 4‐phenyl azetidinone 7 , the MMFF94 geometry with 60% of the axial conformer gave Rcryst 1.2% but the other geometries Rcryst >1.5%. In contrast the N‐methyl‐4‐phenyl‐2‐azetidinone 8 gave good agreement for all the geometries. The butterfly conformation gave Rcryst 1.1% for 80% of the axial conformer and the planar geometries Rcryst 0.98%. The LIS results confirm the ab initio and MM optimised geometries, but the conformer energies at times differ from the calculated values. They also differ considerably from the corresponding values for the lactones studied previously, and possible reasons for this are discussed.     

Theoretical study of vitamin properties from combined QM-MM methods: Comparison of chemical shifts and energy

The combination of quantum mechanics (QM) and molecular mechanics (MM) methods has become an alternative tool for many applications for which pure QM and MM are not suitable. The QM-MM method has been used for different types of problems, for example, structural biology, surface phenomena, and the liquid phase. In this paper, we have implemented these methods for vitamins, an important kind of biological molecule, and then compared results. The calculations were done by the full ab initio method (HF/3–21 g and HF/6–31 g) and QM-MM (ONIOM) method with HF(3–21 g)/AM1/UFF; then, we found that the geometry obtained by the QM-MM method is very accurate and this rapid method can be used in place of time consuming ab initio methods for large molecules. A comparison of energy values in the QM-MM and QM methods is given. We compare chemical shifts and conclude that the QM-MM method is a perturbed full QM method. The text was submitted by the authors in English.     

A study of N-methylacetamide in water clusters: based on atom-bond electronegativity equalization method fused into molecular mechanics

N-methylacetamide (NMA) is a very interesting compound and often serves as a model of the peptide bond. The interaction between NMA and water provides a convenient prototype for the solvation of the peptides in aqueous solutions. Here we present NMA-water potential model based on atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) that is to take ABEEM charges of all atoms, bonds, and lone-pair electrons of NMA and water molecules into the electrostatic interaction term in molecular mechanics. The model has the following characters: (1)it allows the charges in system to fluctuate responding to the ambient environment; (2) for two major types of intermolecular hydrogen bonds, which are the hydrogen bond forming between the lone-pair electron on amide oxygen and the water hydrogen, and the one forming between the lone-pair electron on water oxygen and the amide hydrogen, we take special treatments in describing the electrostatic interaction by the use of the parameters k(lpO=, H) and k(lpO(-), HN(-)), respectively. The newly constructed potential model based on ABEEM/MM is first applied to amide-water clusters and reproduces gas-phase state properties of NMA(H(2)O)(n) (n=1-3) including optimal structures, dipole moments, ABEEM charge distributions, energy difference of the isolated trans- and cis-NMA, interaction energies, hydrogen bonding cooperative effects, and so on, whose results show the good agreement with those measured by available experiments and calculated by ab initio methods. In order to further test the reasonableness of this model and the correctness and transferability of the parameters, many static properties of the larger NMA-water complexes NMA(H(2)O)(n) (n=4-6) are also studied including optimal structures and interaction energies. The results also show fair consistency with those of our quantum chemistry calculations.