Comparison of the stability of thymine tautomers and the interaction of its tautomers with Na+, K+, Mg2+ and Ca2+ in gas and solvent phases

The present study compared the interactions among Na ⁺, K ⁺, Mg²⁺ and Ca²⁺, thymine and its tautomers in the gas and solvent phase, an interaction dependent upon the electronic construction of the tautomers. Three types of cation interaction with thymine and its tautomers were observed. In the first one, the metal cations interacted with a lone pair of nitrogen or oxygen of the tautomers. In the second type, there was an interaction among the cations, nitrogen and oxygen at the same time; the last one was that of cations with the electron density of thymine π-system, where the cations were perpendicular to the ring of thymine. The interaction of metals cation with tautomers was studied in the gas and solvent phases; a comparison was then made between interactions in two phases. The interaction energy for all complexes indicated the stability of complexes, an energy which was higher in Ca²⁺ and Mg²⁺ compared with Na⁺ and K⁺. Concerning K⁺ and Na⁺, the stability of all complexes of tautomers was greater than that of thymine complexes; however, the stability of certain Ca²⁺ and Mg²⁺ complexes was lower than the complexes of thymine.     

Electron affinities of the radicals derived from thymine tautomers

The structures, energies, and electron affinities of the tautomers of dehydrogenated thymine radicals (T-H) have been studied theoretically. Geometry optimizations were carried out utilizing the density functional theory (DFT) methods with double-ζ quality basis sets plus polarization and diffuse functions (DZP++). These methods have been carefully calibrated for the prediction of electron affinities. Significant structural differences were found among thymine 24 dehydrogenated radicals and their corresponding anions from thymine tautomers. The electron affinities for these radicals are in the range of 0.96 and 3.88 eV, contrasting with the much smaller electron affinities associated with the closed-shell thymine tautomers. Among these investigated radicals those with removal of a hydrogen atom from the nitrogen atoms present the larger electron affinities (EAs).     

A theoretical prediction on the ground‐state complexes bound by metal ions to thymine base isomers

Stability orderings of 150 stable complexes formed by metal ions (Na⁺, K⁺, Ca²⁺, Mg²⁺, and Zn²⁺) and 13 stable thymine tautomers in both solvent and gas phases are obtained, and the optimal binding site for a metal ion in a specific thymine tautomer is identified. Results indicate that the complex with the canonical thymine tautomer (T1) is more stable than those with the rare ones, and the monodentate complex M–T1o4(o2) are their ground‐state form in the solvent phase. The ground‐state thymine complexes bound by Ca²⁺, Mg²⁺, or Zn²⁺ become bidentate M–T3o4lo2,n3, which is derived from a rare thymine tautomer T3o4l, whereas those bound by Na⁺ and K⁺ are still monodentate complexes M–T1o4(o2), however, in the gas phase. The differences in stability are discussed in detail from the binding strength of metal ions, relative energy of the corresponding thymine tautomers, and solution effect. Copyright © 2011 John Wiley & Sons, Ltd.     

Interaction studies of cysteine with Li+, Na+, K+, Be2+, Mg2+, and Ca2+ metal cation complexes

The coordination geometries, electronic features, metal ion affinities, entropies, and the energetics of Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺, and Ca²⁺ metal cations with different possible conformations of cysteine complexes were studied. The complexes were optimized using density functional theory (B3LYP) and second order Moller–Plesset Perturbation (MP2) theory methods using 6‐311 + +G** basis set. The interactions of the metal cations at different nucleophilic sites of cysteine conformations were considered after a careful selection among several binding sites. All the metal cations coordinate with cysteine in a tridentate manner and also the most preferred position for the interaction. It is found that, the overall structural parameters of cysteine are not altered by metal ion substitution, but, the metal ion‐binding site has undergone a noticeable change. All the complexes were characterized by an electrostatic interaction between ligand and metal ions that appears slightly more pronounced for lithium and beryllium metal complexes. The metal ion affinity (MIA) and basis set superposition error (BSSE) corrected interaction energy were also computed for all the complexes. The effect of metal cations on the infrared (IR) stretching vibrational modes of amino N? H bond, side chain thiol group S? H bond, hydroxyl O? H bond, and Carbonyl C?O bond in cysteine molecules have also been studied. The nature of the metal ion‐ligand bond and the coordination properties were examined using natural bond order (NBO) at bond critical point (electron density and their Laplacian of electron density) through Atoms in Molecules (AIM) analyses. Copyright © 2010 John Wiley & Sons, Ltd.     

Basicity of trifluoromethylsulfonylformamidines. DFT and FTIR study and NBO analysis

The effect of the electron–acceptor substituent CF₃SO₂ at the imine nitrogen atom on the basicity and the electron distribution in N,N‐alkylformamidines ( 1 , 2 , 3 , 4 , 5 ) was studied experimentally by the FTIR spectroscopy and theoretically at the DFT (B3LYP/6‐311+G(d,p)) level of theory, including the natural bond orbital (NBO) analysis. The calculated proton affinities of the imine nitrogen atom and the sulfonyl oxygen (PA_N′ and PA_O) depend on the atomic charges, the C?N′ and N′―S bond polarity and on the energy of interaction of the amine nitrogen and the oxygen lone pairs with antibonding π* and σ*‐orbitals. The basicity of the imine nitrogen atom is increased with the increase of the electron‐donating power of the substituent at the amine nitrogen atom due to stronger interaction n_N → π*_C?N′, but is decreased for the electron‐withdrawing groups MeSO₂ and CF₃SO₂ at the imine nitrogen atom in spite of the increase of this conjugation. Protonation of ( 1 , 2 , 3 , 4 , 5 ) in CH₂Cl₂ solution in the presence of CF₃SO₃H occurs at the imine nitrogen atom, while the formation of hydrogen bonds with 4‐fluorophenol takes place at the sulfonyl oxygen atom, whose basicity is lower than that of N,N′‐dimethylmethanesulfonamide but higher than of N,N′‐dimethyltrifluoromethanesulfonamide. Copyright © 2015 John Wiley & Sons, Ltd.     

基于对氨基苯甲酸和邻菲罗啉构筑的铕(Ⅲ)配合物的荧光传感

利用水热法合成了一种新的配合物,[Eu(PABA)₃(phen)(H₂O)]·2H₂O(1)(PABA= 对氨基苯甲酸根,phen=1,10-邻菲罗啉)。该配合物为单核分子,中心离子Eu3+的配位数9,环境为{EuO₇N₂},形成了一种扭曲的单帽四方反棱柱多面体。该配合物通过氢键进一步构筑成为三维超分子结构。配合物1在紫外灯下显现为亮红色,其荧光光谱在595和618 nm处出现了2条尖锐的发射峰,分别对应于Eu3+的5D₀→7F₁和5D₀→7F₂跃迁。研究了水溶液中不同阴离子、阳离子以及溶剂对配合物1荧光的影响,实验结果表明不同阴离子、阳离子和溶剂对该配合物的荧光强度有不同程度的影响,在各自实验条件下,F-,Pb2+和硝基苯对该配合物有显著的荧光猝灭效应。基于荧光猝灭机理,该配合物可作为F-,Pb2+和硝基苯的荧光探针。     

Proton transfer reactions of hydrazine‐boranes

Hydrazine‐borane and hydrazine‐diborane contain, respectively, 15.4 and 16.9 wt% of hydrogen and are potential materials for hydrogen storage. In this work we present the gas‐phase complexation energies, acidities, and basicities of hydrazine‐borane and hydrazine‐bisborane calculated at MP2/6‐311 + G(d,p) level. We also report the release of dihydrogen from both protonated complexes (ΔG_{hydrazine‐borane} = ?20.9 kcal/mol and ΔG_{hydrazine‐bisborane} = ?27.2 kcal/mol) which is much more exergonic than from analogues amine‐boranes. The addition of the first BH₃ to the hydrazine releases 17.1 kcal/mol, and the second addition releases 15.8 kcal/mol. The attachment of BH₃ also increases the N―H acidity of hydrazine by 46.3 kcal/mol. It was found that the B―H deprotonation leads to intramolecular rearrangement. The basicity values for hydrazine‐borane and ‐bisborane are 180 and 172.8 kcal/mol, respectively. For both complexes the protonation centres are located at the boron moiety. The protonated structure of hydrazine‐bisborane is cyclic and can be described as H₂ captured between a negatively charged B―H hydrogen and positive boron (B―H??H2??B). Atoms in molecules analysis are used to investigate bond paths in concerning structures. Copyright © 2015 John Wiley & Sons, Ltd.     

四种新型仲胺配合物的合成、表征及与ct-DNA相互作用的光谱研究

合成了新型仲胺类配体L(N,N’-二(4-甲基苄基)乙二胺)及其四种过渡金属的硝酸盐配合物,[ML2(H2O)2]2+.2NO3-(M=CuⅡ,CoⅡ,NiⅡ,ZnⅡ),利用元素分析、红外、1H NMR等对其结构进行了表征,其中用X-ray单晶衍射解析了Cu-L单晶结构,为波谱分析推测的分子结构进行了验证。通过紫外、荧光光谱研究了该四种金属配合物与小牛胸腺DNA的相互作用,结果表明配合物与DNA的作用方式均为静电结合,Cu-L,Co-L,Ni-L,Zn-L与DNA的结合常数分别为:1.67×103,2.5×103,1.35×103和9.85×102。     

Non-intrusive, on-line, simultaneous multi-species impurity monitoring in hydrogen using LIBS

Laser-induced breakdown spectroscopy (LIBS) has been evaluated for on-line, simultaneous multi-species impurity monitoring in hydrogen. A miniature spectrometer with spectral coverage of 620–800 nm and a gated detection system with spectral coverage of 40 nm were both used to record LIBS spectra from the spark produced in sample gas by a frequency-doubled Nd YAG laser. The effect of pressure on detecting the impurity (e.g., nitrogen, argon, and oxygen) in hydrogen was studied. LIBS spectra with different impurity levels of nitrogen, argon, and oxygen were recorded, and the intensity of the spectral lines of Ar, O, N, and H observed were used to form calibration plots for impurity measurement. The limits of detection (LODs) for oxygen, argon, and nitrogen in hydrogen were estimated from the calibration obtained with both the gated and ungated detection. The hydrogen impurity measurements based on the ungated miniature system show reliable and reproductive results. But the LODs with this system are about four times higher than the LODs obtained with a gated detection system in this work.     

Raman spectroscopy of alkali halide hydration: hydrogen bond relaxation and polarization

The solute–solvent interaction of salts has a striking impact on various biological and industrial processes but its mechanism remains yet mysterious despite intensive studies since 1888 when Franz Hofmeister established the salt series. A combination of confocal Raman spectroscopy and contact angle measurements has enabled us to resolve the hydrogen bond relaxation (O:H―O, HB) and the associated charge polarization dynamics at different molecular site because of alkali halides hydration. Results show consistently that salt hydration softens the O:H phonon but stiffens H―O phonon cooperatively. The extent of HB relaxation and polarization is proportional to the electronegativity difference and ionic radius, following the order of Hofmeister series: X (R/η) = I (2.2/2.5) > Br (1.96/2.8) > Cl (1.81/3.0) > F (1.33/4.0) ≈ 0 for anions, and Y(R/η) = Na (0.98/0.9) > K (1.33/0.8) > Rb (1.49/0.8) > Cs (1.65/0.8) for cations. Observations suggest that ions create each an electric field that aligns, stretches, and polarizes water molecules, which relaxes the O:H―O bond cooperatively, depresses the molecular dynamics, and enhances the hydration shell viscosity and the skin stress. Exercises also demonstrate that Raman spectroscopy performs as a powerful tool for probing the molecular‐site‐resolved HB network relaxation dynamics in terms of phonon stiffness, molecular fluctuation dynamics, and phonon abundance transition under external stimulus. Copyright © 2016 John Wiley & Sons, Ltd.     

A theoretical density functional study of association of Zn2+ with oxazolidine and its thio derivatives in the gas phase

We have performed density functional theory (DFT) calculations in order to study the gas‐phase interaction of oxo‐ and thio‐oxazolidine derivatives with Zn²⁺. The calculations were performed at B3LYP/6‐311+(2df,2p) level of theory. It has been found, in all cases, that the direct association of Zn²⁺ with the carbonyl and thiocarbonyl groups takes place at the heteroatom attached to position 2 irrespective of its nature. This preference has been attributed to the resonance effects caused by the nearest heteroatoms (oxygen and nitrogen). The most stable complexes correspond to structures with Zn²⁺ bridging between the heteroatom at position 2 or 4 of the 4‐ or 2‐enol (or the 4‐ or 2‐enethiol) tautomer and the dehydrogenated ring nitrogen atom, N3. Zn²⁺ association has a clear catalytic effect on the tautomerization processes which connect the oxo–thione forms with the enol–enethiol tautomers. Hence, although the enol–enethiol tautomers of oxazolidine and its thio derivatives should not be observed in the gas phase, the corresponding Zn²⁺ complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Zn²⁺ binding energies. Copyright © 2010 John Wiley & Sons, Ltd.     

Calorimetric and computational study of 2H-1, 4-benzoxazin-3(4H)-one and of related species

The standard molar enthalpy of formation in the gas phase of 2H-1,4-benzoxazin-3(4H)-one was derived from the standard energy of combustion determined by static bomb combustion calorimetry in oxygen atmosphere and from the standard sublimation enthalpy determined by Calvet microcalorimetry. In addition, we report the results of a systematic theoretical study of the keto and enol tautomers in benzoxazinones and diones using density functional theory. The keto tautomers are computed to be more stable than the enols. Tautomerization energies are reported.     

M-RNA碱基复合物(M=Ca~+和Mg~+)特征振动的密度泛函理论分析

采用密度函数理论的B3LYP交换关联能泛函在6-311+G(2df,2p)基组水平上,优化计算了Ca+,Mg+与RNA碱基嘧啶各同分异构体形成稳定复合物的结构,发现其中C1M,T1M和U1M(M=Ca+和Mg+)为最稳定复合物,并对这些复合物红外振动进行了计算.计算结果显示碱基嘧啶单体主要存在的两个红外特征振动,是由环振动和环外氧原子及与其成键的环上碳原子之间产生伸缩振动引起的.当形成复合物时,由于离子的参与,使单体碱基分子的振动情况发生了改变,主要表现在离子倾向于与环外负电子原子N和O原子成键,使与离子直接作用环外原子参与的特征振动频率减小,谱线红移;不与离子直接作用环外原子引起的特征振动频率增大,谱线蓝移.     

SIMS,EID and flash-filament investigation of O2, H2, (O2 + H2) and H2O interaction with vanadium

Comparative investigations of secondary ion emission, electron induced ion emission and flash filament signals from polycrystalline vanadium surfaces exposed to well-defined O₂, H₂, H₂O and (O₂ + H₂) doses (<500 L) have been carried out. The vanadium target could be heated and bombarded by either electrons (300 eV) or ions (3 keV) under ultra high vacuum conditions (<10^?10 Torr). The investigations were carried out with a computer controlled ultra high vacuum mass spectrometer. The experimental results establish exact reproducible spectra of well defined surface layers. They give detailed insight into the reactions between H₂, O₂ H₂O and vanadium, and some interactions between these species. They further indicate the importance of bulk and surface diffusion as well as the influence of the probing ion and electron bombardment. A clear distinction between bulk oxygen, surface oxides, and adsorbed oxygen for the vanadium-oxygen interaction at room temperature could be established. For the interaction of hydrogen with clean and oxygen covered vanadium surfaces the formation of adsorbed hydrogen, bulk solution of hydrogen, and the formation of OH groups and H₂O could be demonstrated. A detection limit below 10^?5 of one single monolayer for metal bonded hydrogen could be established.     

三维超分子配合物[Zn（C_（12）H_8N_3）_2·H_2O]的水热合成、晶体结构及光致发光1

通过水热法合成了一种三维超分子配合物Zn（C12H8N3）2.H2O,经元素分析、紫外和红外光谱对其进行表征。用X射线单晶衍射测定了其晶体结构,该配合物晶体属单斜晶系,P21/c空间群,晶胞参数为：a=1.25239（10）nm,b=1.30233（11）nm,c=1.33167（11）nm,β=102.6950（10）°,Z=4,[Zn（C12H8N3）2.H2O],Mr=471.81,V=2.1189（3）nm^3,Dc=1.479g·cm^-3,μ=1.189mm^-1,F（000）=968,R1=0.0300,WR2=0.1017,GOF=1.005。该化合物由1个Zn（Ⅱ）离子、2个2-（2-吡啶基）苯并咪唑阴离子和1分子配位水组成。其中2-（2-吡啶基）苯并咪唑的1位氮原子、吡啶环上氮原子及水分子中氧原子与锌（Ⅱ）离子配位,形成五配位的畸变三角双锥结构,单胞分子之间通过氢键O（w）-H…N和π-π堆积作用相互构成三维网状超分子体系。固态荧光测试显示,该配合物具有强的蓝色荧光发射（λmax=456nm）。     

Interaction of cations with 2′‐deoxythymidine nucleoside and analysis of the nature and strength of cation bonds

Binding of Mg²⁺, Ca²⁺, Zn²⁺, and Cu⁺ metal ions with 2′‐deoxythymidine (dT) nucleoside was studied using a density functional theory method and a 6‐311++G(d,p) basis set. This work demonstrated that the interaction of dT with these cations is tri‐coordinated η (O2, O4′, O5′). Among the four types of cations, Zn²⁺ cation exhibited the most tendency to interact with the dT. Cations via their interaction with dT can affect the N‐glycosidic bond length, the values of pseudorotation of the sugar ring, the orientation of the base unit with respect to the sugar ring, and the acidity of the O5′H, O3′H, and N3H groups in the dT nucleoside. Natural bond orbital analysis was performed to calculate the charge transfer and natural population analysis of the complexes. Quantum theory of atoms in molecules was also applied to determine the nature of interactions. It was shown that in dT–Mg²⁺ and dT–Ca²⁺ complexes, the bonds are electrostatic (closed‐shell) interactions, although they are partially covalent and partially electrostatic interactions in dT–Zn²⁺ and dT–Cu⁺ complexes. Copyright © 2011 John Wiley & Sons, Ltd.     

Nitrosonium complexes of 2,11‐dithia‐5,6,8,9‐tetramethyl[32](1,4)cyclophane: a combined experimental and theoretical study

¹H and ¹³C NMR studies and quantum chemical calculations show the interaction between 2,11‐dithia‐5,6,8,9‐tetramethyl[3₂](1,4)cyclophane and nitrosonium cation to result in the formation of π‐ and n‐complexes. According to DFT/B3LYP/6‐31G(2d,p) calculations, formation of nitrosonium complexes is a strongly exothermic process both in gas phase and in SO₂. Affinity of single‐charged complexes to NO⁺ is usually larger than that of double‐charged and triple‐charged complexes, affinity of all the charged complexes to nitrosonium cation in SO₂ being larger than that in gas phase. The π‐complex with nitrosonium cation coordinated to the methylated aromatic ring is the most stable with structural characteristics being close to those obtained by X‐ray diffraction for nitrosonium π‐complexes of hexamethylbenzene and other arenes. The N―O bond lengths in all the complexes are quite close to each other and larger than that in NO⁺ cation. The S―N bond length increases upon transition from single‐charged to double‐charged and polycharged complexes. Copyright © 2014 John Wiley & Sons, Ltd.     

H3O+, NO+和O+·2离子同九种烷氧基醇化合物反应的研究

在用选择离子流动管质谱(SIFT-MS)分析常用指甲油清洗垫发现大量4-丁酸内脂(γ-butyrolactone, GBL)和2-丁氧基乙醇(2-butoxy-1-ethanol)等挥发性气体后, 运用选择离子流动管(SIFT)对H3O , NO 和O ·2离子同九种烷氧基醇化合物(R1-O-R2OH)之间的反应进行了研究. 获得了这些反应在潮湿空气条件下进行的情况, 并运用产物离子水合物的种类和分布来确认产物离子的结构和反应机理. 还研究了在不同载气压力下进行的反应. 结果表明, 这些化合物同H3O 和NO 的反应都是先生成初生态离子-分子络合物, (H3O .M)*和(NO .M)*, 然后经不同反应渠道生成各种离子产物. 这些初生态络合物同反应体系中存在的气体分子(如氦气, 氮气和氧气分子)的碰撞对最终离子产物的形成和分布也有影响. 这些化合物同O2 ·反应会生成各种离解碎片离子, 但不能确定这些离子是否经由初生态络合物(O2 ·.M)*生成. 该项研究提供了用SIFT-MS在空气和潮湿气体中分析这些化合物所需的反应速率常数和离子产物等动力学数据, 并将进一步应用到药物成瘾及滥用和呼吸道疾病的诊断和分析等领域.     

The pKa theoretical estimation of C―H,N―H,O―H and S―H acids in dimethylsulfoxide solution

A scheme for the pK_a estimation of organic acids in dimethylsulfoxide (DMSO) solution based on quantum chemical calculations is proposed. The procedure of pK_a calculation requires several steps. The first is the calculation of the gas phase acidity of the compound. The G3MP2B3, G4MP2 as well as CBS‐QB3 composite methods made it possible to estimate values of gas phase acidities of an extensive set of structures with a high confidence level (standard deviations equal to 1.15, 1.13 and 1.29 kcal mol^?1, respectively; the test set included 91 compounds). The second step is the computation of the solvation correction with the integral equation formalism version of polarizable continuum model (IEF‐PCM)–B3LYP/6‐311+G(d,p) approximation. Within the bounds of our approach, the medium properties were covered only by the PCM model, i.e. the proposed procedure neglects specific interactions between DMSO and the solute. It was determined that the approach to pK_a estimation mentioned above is the most balanced in terms of accuracy, resource intensity and computation time cost. In the third step, the error of the pK_a calculation was decreased by correlation allowances. Correlation allowances were determined for each acid class (62 С―Н, 55 N―Н, 24 O―Н and 5 S―Н acids) in the range of 50 units in terms of logarithmic scale using the test set including 146 compounds. Seven O―H acids showing the ability to form cyclic dimers were separated into a discrete group. The proposed methodology was applied to the estimation of pK_a for trans‐ and cis‐dimethyl‐4,5‐dihydro‐3H‐pyrazol‐3,5‐dicarboxylates as well as for 5‐fluorouracil subject to competitive dissociation, the latter by N1―H or N3―H bonds. Copyright © 2014 John Wiley & Sons, Ltd.     

稀土茜素黄R配合物的合成、表征及荧光性质

合成了 4种茜素黄R稀土配合物 ,通过对元素分析、红外光谱、紫外光谱和核磁共振氢谱的分析 ,确定它们的组成为 :Na[REL2 ]·2H2 O(RE =Sm ,Eu ,Tb ,Y ,NaHL =茜素黄R)。红外光谱表明 :配体以羧羰基的氧与稀土离子以单齿配位 ;配体的酚羟基离解 ,脱去质子后羟基氧与稀土离子配位 ;即酚氧和羧羰基的氧与稀土离子形成一个六元螯合环。配体的吸收峰 398nm在形成配合物后移于 35 1～ 35 5nm ,发生了较大位移 ,这说明稀土离子与配体成键 ;配合物IR在 4 15～ 4 35cm-1之间出现的新吸收峰归属为RE—O键的伸缩振动 ,佐证了配合物的形成 ;硝基中的氧和偶氮的氮原子未参与配位 ;IR还说明有两个水分子配位于稀土离子。紫外灯下可以看到Eu(Ⅲ )的配合物很强的红色荧光 ;荧光光谱测定 :Na[EuL2 ]·2H2 O有两个荧光发射峰分属于Eu的 5D0 → 7F1和5D0 → 7F2 跃迁。