气相和溶液中金属离子与腺嘌呤配位选择性的理论研究

在B3LYP/6-31G(d,p)水平,全优化Mg2+、Ca2+、Mn2+、Co2+、Zn2+、Cu2+、Ni2+、Cd2+ (用有效实势(ECP) 方法处理)与腺嘌呤(A) N(1)、N(7)位点配位的两类配合物气相结构,通过相互作用能和自由能分析分别得出两位点对所研究金属离子的选择性顺序;后采用Onsager模型,优化其在水溶液(=78.39)中的结构,讨论溶剂效应对上述顺序的影响;通过相对自由能分析分别得出气相和溶液中,同种金属对两位点的选择性规律。溶液中金属离子与N(7)位配位的相对优选顺序为:Co2+ > Mg2+ > Cd2+ > Ca2+ > Zn2+ > Mn2+ > Ni2+ > Cu2+。     

金属离子(Na~+、K~+、Ca~(2+)、Mg~(2+)、Zn~(2+))与鸟嘌呤异构体配合物的稳定性

在B3LYP/6-311++G**水平上用极化连续介质模型(PCM)系统研究了金属离子(M+/2+=Na+,K+,Ca2+,Mg2+,Zn2+)和十三种鸟嘌呤异构体形成的配合物GnxM+/2+(n为鸟嘌呤异构体的编号,x表示M+/2+与鸟嘌呤异构体的结合位点)在气(g)液(a)两相中的稳定性顺序.着重探讨了液相中配合物的稳定性差异,并且从溶质-溶剂效应、结合能、形变能及异构体的相对能量等几个方面分析了造成稳定顺序发生变化的原因.报道了溶液中这五种金属离子与鸟嘌呤异构体结合形成的六种基态配合物:aG1N2,N3Na+,aG1N2,N3K+,aG1O6,N7Ca2+,aG1N2,N3Mg2+(aG1O6,N7Mg2+),aG2N3,N9Zn2+.可以看出,除了在Zn2+配合物中鸟嘌呤异构体为G2外,构成其余四种金属离子配合物的鸟嘌呤异构体都是G1,但结合位点不同.同时对气相中各类配合物稳定性也进行了系统的排序,并报道了几种较稳定的配合物,如:gG3N1,O6K+,gG5N1,O6K+,gG3N1,O6Ca2+/Mg2+,gG4O6,N7Ca2+/Mg2+.     

Cu2+对腺嘧啶-胸腺嘧啶碱基对阴离子质子转移的影响

采用B3LYP/DZP++方法研究了腺嘌呤-胸腺嘧啶(A-T)碱基对阴离子(AT)-的单质子转移机理以及金属离子Cu2+对(AT)-碱基对质子转移的影响.(AT)-碱基对的单质子转移路径是由胸腺嘧啶N25位上的质子H26沿分子间的氢键N25-H26…N10转移到腺嘌呤的N10位.金属Cu2+可通过络合作用分别吸附在(AT)-碱基对O24、O28、N4、N13上,从而影响(AT)-碱基对中质子转移过程.Cu2+络合作用在胸腺嘧啶(T)的O24、O28上时,发生了从胸腺嘧啶到腺嘌呤方向上的单质子转移反应;而作用在腺嘌呤(A)的N4、N13上时,得到了双质子转移的稳定产物.     

5-氟胞嘧啶气相及水助质子转移异构化的理论研究

采用密度泛函B3LYP/6-311G**方法,对6种5-氟胞嘧啶异构体孤立分子的稳定性及质子转移引起的酮式-烯醇式、氨基式-亚胺式互变异构反应机理进行了计算研究,获得了零点能、吉布斯自由能及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.计算结果表明,气相中烯醇-氨基式FC4是最稳定的异构体.分子内质子转移设计了FC1→FC2和FC1→FC6两条通道,分别标记为P(1)和P(2),各通道速控步骤的活化能和速率常数分别为155.9 kJ·mol-1,4.70×10-15 s-1和173.1 kJ·mol-1,1.41×10-18 s-1.水助催化时,相应通道P(3) 和P(4) 速控步骤的活化能和速率常数分别为51.0 kJ·mol-1,1.41×103 s-1和88.2 kJ·mol-1,4.53×10-3 s-1.可见,水分子的加入极大地降低了质子转移的活化能垒.另外发现,水分子参与形成协同的双质子转移机理比水助单质子转移机理更利于降低活化能垒.     

三羟甲基氨基甲烷水杨醛类席夫碱质子转移异构化的理论研究

采用密度泛函(DFT)中的B3LYP方法,在6-311+G(d,p)基组水平上对三羟甲基氨基甲烷水杨醛席夫碱气相、水溶剂及甲醇溶剂中的分子内质子转移和衍生席夫碱的互变异构反应机理进行了计算研究,获得了反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数.液相计算采用Onsager模型.结果表明,不论在气相、水溶剂还是甲醇溶剂中,三羟甲基氨基甲烷水杨醛席夫碱(L3=H,L5=H)烯醇亚胺式异构体R1和醌型的酮烯胺异构体P1可以共存,但以苯环型的烯醇亚胺式R1为主要形式.当由苯环型的烯醇亚胺R1向醌型的酮烯胺P1分子内质子转移时活化能较低,室温常压下反应容易进行.水和甲醇溶剂对异构化反应影响较小.当—NO2,—OMe取代生成衍生席夫碱时(L3=H,L5=NO2;L3=OMe,L5=H),结果表明,苯环型的烯醇亚胺式和醌型的酮烯胺式异构体都能共存,质子转移异构化反应的活化能垒也较低.     

p-羟基苯丙酮酸互变异构反应机理溶剂效应的理论研究

采用密度泛函B3LYP方法,在6-31+G**基组水平上对p-羟基苯丙酮酸质子转移引起的烯醇式-酮式互变异构反应机理进行了计算研究,获得了互变异构过程的反应焓、活化能、活化吉布斯自由能和质子转移反应的速率常数等参数。Onsager反应场溶剂模型用于水相和甲醇相的计算,计算结果表明,p-羟基苯丙酮酸无论在气相还是水相、甲醇相中,其酮式异构体都是最稳定的存在形式,烯醇式异构体也会以一定量共存。气相中孤立分子内质子转移几何构型改变较显著,异构化反应需要较大的活化能,不利于发生质子转移,Onsager模型计算方法对质子转移反应的影响较小。     

金属离子与腺嘌呤异构体复合物的稳定性

在B3LYP/6-311++G**//6-31+G*基组水平上结合PCM模型系统的优化了气相和液相环境中14种腺嘌呤异构体与四种金属离子(Na+,K+,Mg2+,Ca2+)形成的132个稳定复合物。通过能量对比,得到了所有复合物异构体在气液两相中的稳定性顺序及不同金属离子与同一异构体形成的复合物的能量排序,首次给出了液相中这些不同金属离子复合物的最稳定结构。结果发现溶剂效应导致了液相中的复合物稳定性顺序与气相中的相比发生了很大变化;同一异构体与不同金属离子形成的复合物其稳定性在排序中也变化很大。对于这些变化,本文分别从金属离子与腺嘌呤的复合物在气相中的结合能(EBE)及在液相中的溶质溶剂相互作用能(Epol)能等方面进行了系统的阐述     

8-氨基喹啉取代苯甲酰胺衍生物对汞离子和铜离子的识别

设计合成了可识别金属离子的荧光传感分子8-氨基喹啉取代苯甲酰胺衍生物,通过核磁共振谱和质谱表征其结构;利用其光谱性质研究了该系列物质对过渡金属离子Cu2+,Hg2+,Pb2+,Zn2+,Ni2+和Cd2+的识别性质,初步探讨了其识别机理。实验表明:在乙腈中,8-氨基喹啉苯甲酰胺的吸收光谱在509nm处对Cu2+有响应,溶液由无色变成红色;而其荧光光谱对Hg2+和Cu2+有良好的选择性,荧光增强倍率分别高达368和192,与金属离子形成结合比为1:1配合物。     

均三嗪衍生物应用于Fe3+和Cu2+的选择性识别研究

合成了2,4-二甲基-6-(4’-N,N-二甲氨基苯乙烯基)-1,3,5-均三嗪(1)和2-苯乙烯基-4,6-二甲基-1,3,5-均三嗪(2)两种化合物,并对其进行了1H NMR,MS,元素分析等表征.采用吸收光谱法研究了金属离子与化合物间的相互作用,结果显示:化合物1对Fe3+和Cu2+表现出高选择性光谱响应,其最大吸收波长由393 nm分别红移至525 nm和513 nm,溶液颜色由黄色变为粉红色.化合物1与Fe3+结合形成1∶1型配合物,其结合常数为1.8×104L mol-1;与Cu2+结合形成2∶1型配合物,其结合常数为2.6×1010L mol-1.化合物2仅对Fe3+呈现显著的光谱变化,其最大吸收波长由304nm红移至357 nm,而Cu2+的加入未引起光谱明显变化,2与Fe3+亦形成1∶1型配合物,结合常数为1.0×105L mol-1.结果表明Fe3+可能与化合物1和2中三嗪N配位,而Cu2+与化合物1中甲氨基中的N配位.同时考察了其它金属离子如Li+,K+,Mg2+,Ca2+,Co3+,Ni2+,Ag+,Cd2+,Hg2+和Zn2+等离子对化合物1和2吸收光谱的影响,结果显示两者光谱均无明显变化,据此提出了高选择性Fe3+,Cu2+的识别体系.     

基于羟苯基苯并咪唑的Zn2+比率荧光探针

通过羰基将两分子2-(4-氨基-2-羟苯基)苯并咪唑(4-AHBI)连接,合成了结构高度对称的新化合物N,N′-二-[3-羟基-4-(2-苯并咪唑)苯基]脲(C27H20N6O3,1),测试了不同溶剂条件下1的紫外吸收和荧光发射光谱,研究了1对Zn2+的选择性识别作用。结果表明,随着溶剂极性的增大,1的紫外吸收峰发生蓝移,激发态分子内质子转移(ESIPT)荧光发射峰明显增强。与4-AHBI相比,1在乙腈溶液中的紫外吸收强度增强约3.5倍,最大吸收峰红移8 nm,荧光发射增强8倍多。1在乙腈溶液中的Zn2+荧光响应行为表明1与Zn2+的结合将导致1在445 nm处的荧光强度不断降低,而在395 nm处出现的新峰的荧光强度不断增强,具有比率荧光探针的特点,而且检测范围较宽,可达1×10-6-1×10-2 mol.L-1。     

Theoretical study of three predominant tautomers of 2-oxo-6-methylpurine and their two transition state structures

The three predominantly stable tautomers of 2-oxo-6-methylpurine were studied in gas phase and aqueous solution by means of quantum mechanical calculations. Two transition state structures connecting these three tautomeric forms on the free energy surface were determined. The activation free energy for the intramolecular proton transfer in gas phase was calculated to be considerably smaller than the bond energy of either N-H or O-H: 59.01 and 30.37 kcal/mol for N9→N3 and N1→O2, respectively, obtained at the QCISD(T)/6-31G+(d)//MP2(full)/6-31G(d) level of theory.     

DFT Study on the Os+-catalytic Reduction Reaction of N2O with He in the Gas Phase

The Os+-catalytic reduction of N<,2>O by H<,2> in gas phase has been theoretically investigated with B3LYP method.The reaction mechanisms on the sextet and quartet surfaces were found to be similar.The calculated sextet potential energy profiles show that the two reactions involved in the catalytic cycle, Os<'+>+ N<,2>O→OsO<'+>+N<,2> and OsO<'+>+H2→Os<'+>+H<,2>O, have barriers of 28.3 and 123.3 kJ/mol, respectively.In contrast, the reactions on the quartet surfaces are energetically much more favorable.These results rationalize the experimentally observed low catalytic reactivity of sextet (ground-state) Os<'+>.Further, the crossing between the sextet and quartet Surfaces are also suggested and qualitatively discussed.     

Conformations, energies, and intramolecular hydrogen bonds in dicarboxylic acids: implications for the design of synthetic dicarboxylic acid receptors

The various conformers of the dicarboxylic acids HO2C--(CH2)n--CO2H, n = 1-4, were obtained using density functional methods (DFT), both in the gas phase and in the aqueous phase using a polarized continuum model (PCM). Several new conformers were identified, particularly for the two larger molecules glutaric (n = 3) and adipic acid (n =4). The PCM results show that the stability of most conformers were affected, many becoming unstable in the aqueous phase; and the energy ordering of conformers is also different. The results suggest that conformational preferences could be important in determining the design and stability of appropriate synthetic receptors for glutaric and adipic acid. Geometry changes between gas and aqueous phases were most marked in those conformers containing an intramolecular hydrogen bond. Additional calculations have probed the strength of intramolecular hydrogen bonds in these dicarboxylic acids. In the cases of glutaric and adipic acid, the strength of the intramolecular hydrogen bond were estimated to be around 28-29 kJ/mol, without any vibrational energy correction. The intramolecular hydrogen bond energies in malonic and succinic acid were also estimated from the calculated H-bond distances using an empirical relationship. Intramolecular H-bond redshifts of 170-250 cm(-1) have been estimated from the results of the harmonic frequency analyses.     

Gas-phase reactions of protonated tryptophan

The gas phase reactions of protonated tryptophan have been examined in a quadrupole ion trap using a combination of collision induced dissociation, hydrogen-deuterium exchange, regiospecific deuterium labeling and molecular orbital calculations (at the B3LYP/6-31G* level of theory). The loss of ammonia from protonated tryptophan is observed as the primary fragmentation pathway, with concomitant formation of a [M + H - NH(3)](+) ion by nucleophilic attack from the C3 position of the indole side chain. Hydrogen-deuterium exchange and regiospecific deuterium labeling reveals that scrambling of protons in the C2 and C4 positions of the indole ring, via intramolecular proton transfer from the thermodynamically preferred site of protonation at the amino nitrogen, precedes ammonia loss. Molecular orbital calculations have been employed to demonstrate that the activation barriers to intramolecular proton transfer are lower than that for NH(3) loss.     

Electronic structure and reactivity of guanylthiourea: A quantum chemical study

Electronic structure analysis of guanylthiourea (GTU) and its isomers has been carried out using quantum chemical methods. Two major tautomeric classes (thione and thiol) have been identified on the potential energy (PE) surface. In both the cases conjugation of pi‐electrons and intramolecular H‐bonds have been found to play a stabilizing role. Various isomers of GTU on its PE surface have been analyzed in two different groups (thione and thiol). The interconversion from the most stable thione conformer ( GTU‐1 ) to the most stable thiol conformer ( GTU‐t1 ) was found to take place via bimolecular process which involves protonation at sulfur atom of GTU‐1 followed by subsequent C? N bond rotation and deprotonation. The detailed analysis of the protonation has been carried out in gas phase and aqueous phase (using CPMC model). Sulfur atom (S1) was found to be the preferred protonation site (over N4) in GTU‐1 in gas phase whereas N4 was found to be the preferred site of protonation in aqueous medium. The mechanism of S‐alkylation reaction in GTU has also been studied. The formation of alkylated analogs of thiol isomers (alkylated guanylthiourea) is believed to take place via bimolecular process which involves alkyl cation attack at S atom followed by C? N bond rotation and deprotonation. The reactive intermediate RS(NH₂)C? N? C(NH₂)₂⁺ belongs to the newly identified ^⊕N(←L)₂ class of species and provides the necessary dynamism for easy conversion of thione to thiol. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Metal-ion-coordinating properties of the dinucleotide 2'-deoxyguanylyl(5'-->3')-2'-deoxy-5'-guanylate (d(pGpG)3-): isomeric equilibria including macrochelated complexes relevant for nucleic acids

The interaction between divalent metal ions and nucleic acids is well known, yet knowledge about the strength of binding of labile metal ions at the various sites is very scarce. We have therefore studied the stabilities of complexes formed between the nucleic acid model d(pGpG) and the essential metal ions Mg2+ and Zn2+ as well as with the generally toxic ions Cd2+ and Pb2+ by potentiometric pH titrations; all four ions are of relevance in ribozyme chemistry. A comparison of the present results with earlier data obtained for M(pUpU)- complexes allows the conclusion that phosphate-bound Mg2+ and Cd2+ form macrochelates by interaction with N7, whereas the also phosphate-coordinated Pb2+ forms a 10-membered chelate with the neighboring phosphate diester bridge. Zn2+ forms both types of chelates with formation degrees of about 91% and 2.4% for Zn[d(pGpG)]cl/N7 and Zn[d(pGpG)]-cl/PO, respectively; the open form with Zn2+ bound only to the terminal phosphate group, Zn[d(pGpG)]-op, amounts to about 6.8 %. The various intramolecular equilibria have also been quantified for the other metal ions. Zn2+, Cu2+, and Cd2+ also form macrochelates in the monoprotonated M[H;d(pGpG)] species (the proton being at the terminal phosphate group), that is, the metal ion at N7 interacts to some extent with the P(O)2(OH)- group. Thus, this study demonstrates that the coordinating properties of the various metal ions toward a pGpG unit in a nucleic acid differ: Mg2+, Zn2+, and Cd2+ have a significant tendency to bridge the distance between N7 and the phosphate group of a (d)GMP unit, although to various extents, whereas Pb2+ (and possibly Ca2+) prefer a pure phosphate coordination.     

Study of intramolecular interactions in aspirin

A detailed quantum chemical study of the solvent effects in the intramolecular hydrogen bonding, conformational stability, and reactivity of aspirin has been performed using density functional theory (DFT) at the B3LYP/6‐31G(d) theory level. Seven conformational isomers, three of them presenting intramolecular hydrogen bonds, have been located. Thermochemical functions have been computed, and relative energies and free enthalpies have been determined in gas and aqueous phases. Several molecular properties have been calculated to predict the ability of aspirin to acylate cyclooxygenase (COX) enzymes. A six‐membered‐ring hydrogen‐bonded conformer was found to be the most reactive species. The solvation in aqueous phase increases the reactivity and strengthens intramolecular hydrogen bonding.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.