Fragmentations of Hydroxymethyl Radical Cation: An Ab Initio Study

The probable fragmentation channels of hydroxymethyl radical cation were studied through the H‐and H₂‐abstraction and C‐O bond breaking reactions including their related isomerization reactions. The energy barriers for hydroxymethyl cation undergoing isomerization reactions are generally higher than those undergoing the concerted 1,2‐elimination reactions to generate CHO⁺ and H₂. The fragmentation reaction to form CHO⁺ and H₂ through the 1,2‐elimination pathways is the major fragmentation channel for hydroxymethyl cation, consistent with the experimental observation. H abstraction from the hydroxyl group of CH₂OH⁺ is more difficult than that from the methylene group. The feasible path to lose H is to generate CHOH₂⁺ through hydrogen transfer reaction as the first step and then to undergo H‐elimination to generate trans‐CHOH⁺. Among all the reactions found in this study, the OH‐elimination to generate CH₂⁺ has the highest energy barrier. Our calculation results indicate that the major signals contributed from the related species of hydroxymethyl cation found in the mass spectrum should be m/e 29, m/e 30.     

Differentiation of Diastereoisomers of Protected 1,2-Diaminoalkylphosphonic Acids by EI Mass Spectrometry and Density Functional Theory

Electron ionization mass spectrometry and density functional theory (DFT) calculations have been used to study the fragmentation of diastereoisomers of protected 1,2-diaminoalkylphosphonic acids. The loss of a diethoxyphosphoryl group and the elimination of diethyl phosphonate were found to be competitive fragmentation processes, which can be used to differentiate both stereoisomers. Selective deuterated analogs and product- and precursor-ion mass spectra allowed the elucidation of the fragmentation mechanisms. The structures of the transition states and product ions were optimized using the density functional theory (DFT), and free energy calculations confirmed the observed differences in the formation and relative intensities of specific fragment ions.

Studying the Chemistry of Cationized Triacylglycerols Using Electrospray Ionization Mass Spectrometry and Density Functional Theory Computations

Analysis of triacylglycerols (TAGs), found as complex mixtures in living organisms, is typically accomplished using liquid chromatography, often coupled to mass spectrometry. TAGs, weak bases not protonated using electrospray ionization, are usually ionized by adduct formation with a cation, including those present in the solvent (e.g., Na⁺). There are relatively few reports on the binding of TAGs with cations or on the mechanisms by which cationized TAGs fragment. This work examines binding efficiencies, determined by mass spectrometry and computations, for the complexation of TAGs to a range of cations (Na⁺, Li⁺, K⁺, Ag⁺, NH₄ ⁺). While most cations bind to oxygen, Ag⁺ binding to unsaturation in the acid side chains is significant. The importance of dimer formation, [2TAG + M]⁺ was demonstrated using several different types of mass spectrometers. From breakdown curves, it became apparent that two or three acid side chains must be attached to glycerol for strong cationization. Possible mechanisms for fragmentation of lithiated TAGs were modeled by computations on tripropionylglycerol. Viable pathways were found for losses of neutral acids and lithium salts of acids from different positions on the glycerol moiety. Novel lactone structures were proposed for the loss of a neutral acid from one position of the glycerol moiety. These were studied further using triple-stage mass spectrometry (MS³). These lactones can account for all the major product ions in the MS³ spectra in both this work and the literature, which should allow for new insights into the challenging analytical methods needed for naturally occurring TAGs.

密度泛函理论处理激发态与多重态结构研究进展

用密度泛函理论处理分子激发态和电子多重态结构是密度泛函理论发展的重要方面, 研究工作一直很活跃。本文对近年来在这一领域取得的重要进展作简要的综述。     

羟基自由基和鸟嘌呤-胞嘧啶碱基对反应的密度泛函理论研究

为了解决年龄衰老、基因突变和癌症等问题, 理解DNA的氧化损伤机理非常重要. 本文利用密度泛函方法和极化连续介质模型在液相条件下研究了羟基自由基夺取鸟嘌呤-胞嘧啶(GC)碱基对上5 个氢原子的反应机理. 研究结果表明, 所有的脱氢反应路径都是放热过程, 热力学上五个脱氢反应路径形成自由基的稳定性顺序是(H2b-GC)^·>(GC-H4b)^·>(GC-H6)^·>(GC-H5)^·~(H8-GC)^·, 其中H2b反应路径的能量变化最大, 说明该反应平衡时的转化率最高. 动力学上, 相对于反应复合物的局部反应能垒大小顺序是H2b     

Probing the Reactivity and Radical Nature of Oxidized Transition Metal-Thiolate Complexes by Mass Spectrometry

Transition metal thiolate complexes such as [PPN]⁺[RuL₃]^- (PPN?=?bis(triphenylphosphoranylidene) ammonium and L?=?diphenylphosphinobenzenethiolate) are known to undergo addition reactions with unsaturated hydrocarbons via the formation of new C-S bonds in solution upon oxidation. The reaction mechanism is proposed to involve metal-stabilized thiyl radical intermediates, a new type of distonic ions such as [RuL₃]⁺ ion in the case of [PPN]⁺[RuL₃]^-. This study presents the reactivity and structure investigation of [RuL₃]⁺ by mass spectrometry (MS) in conjunction with ion/molecule reactions. The addition reactions of [RuL₃]⁺ with alkenes or methyl ketones in the gas phase are indeed observed, in agreement with the proposed mechanism. Such reactivity is also maintained by several fragment ions of [RuL₃]⁺, indicating the preserved thiyl diradical core structure is responsible for the addition reaction. The thiyl radical nature of [RuL₃]⁺ was further verified by the ion/molecule reaction of [RuL₃]⁺ with dimethyl disulfide, in which the characteristic CH₃S? transfer occurs, both at atmospheric pressure and also at low pressure (~mTorr). These results provide, for the first time, clear mass spectrometric evidence of the radical nature of [RuL₃]⁺ (i.e., the distonic ion structure of [RuL₃]⁺), arising from the oxidation of non-innocent thiolate ligands of the complex [PPN]⁺[RuL₃]^-. Similar thiolate complexes, including ReL₃ and NiL₂, were also examined. Although reactions of oxidized ReL₃ or NiL₂ with CH₃SSCH₃ take place at atmospheric pressure, the corresponding reaction did not occur in vacuum. Consistent with these data, the addition of ethylene was not observed either, indicating lower reactivities of [ReL₃]⁺ and [NiL₂]⁺ in comparison to [RuL₃]⁺.      

密度泛函理论辅助研究大黄素型蒽醌化合物电喷雾质谱的裂解过程

从红树植物尖瓣海莲(Bruguiera sexangula var.rhynchopetala)来源的一株青霉菌属真菌Penicillium sp.次级代谢产物中,分离鉴定出三个大黄素型蒽醌化合物,分别为:大黄素1,3,8-三-羟基-6-甲基蒽醌(1,3,8-trihydroxy-6-methyl anthraquinone,JGWY-C)、1,3,5,8-四羟基-6甲基蒽醌(1,3,5,8-tetrahydroxy-6-methyl-anthraquinone,JGWY-D)和1,3,8-三羟基6-羟甲基蒽醌(1,3,8-trihydroxy-6 hydroxymethyl-anthraquinone,JGWY-B).采用电喷雾离子阱质谱技术(ESI-IT-MSn)对三个化合物的裂解过程及碎片离子结构进行研究,并运用密度泛函理论计算方法,优化各碎片离子的稳定几何构型和裂解过程的能量变化,进一步验证裂解途径分析的可靠性.实验结果表明:大黄素型蒽醌化合物中酚羟基具有一定的酸性,更容易在负离子模式下形成氧负离子,A环和B环酚羟基在多级裂解过程中易脱去CO和CO2小分子.这一裂解过程可以作为药物快速检测和药代动力学研究中质谱的特征碎片离子峰.此外,化合物JGWY-B碰撞诱导裂解α位-CH2OH脱去H2形成醛基,这一过程也得到理论计算的支持.该研究为大黄素型蒽醌化合物的结构鉴定和检测提供了有用的质谱依据.     

C2H与HO2双自由基反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论(DFT)对C₂H与HO₂双自由基的单重态反应进行了研究.在UB3LYP/6-311G水平上优化了反应通道上各驻点(反应物、中间体、过渡态和产物)的几何构型.在CCSD(T)/6-311G^{**水平上计算了各物种的单点能,并对总能量进行了零点能校正.研究结果表明,反应物中自由基C₂H的边端C进攻自由基HO₂的边端O是主要的进攻方式.首先形成了中间体1(HCCOOH),由此经过不同的反应通道可以得到主要产物P1,次要产物P2,P3和P5.生成P1的反应热为-814.40kJ/mol.自由基C₂H的中间C进攻自由基HO₂的边端O是次要的进攻方式,可以得到产物P4和P6.根据势能面分析,所有反应均是放热反应.}     

阳离子－π体系相互作用的理论研究 2: 铵离子－二苯复 合物体系的密度泛函 研究

运用密度泛函B3LYP/6-31G^*方法对离子-二苯复合物体系的可能构型进行了结构优化,得到了复合物的能量低构型为:铵离子位于两个苯环平面之间分别以两个氢原子和苯环作用,频率计算结果表明该构型为稳定结.复全物的键长、原子净电荷、分子轨道系数、前沿轨道能量、Mullicken键级等都表明,铵氢原子和与之接近的苯环碳原子之间通过s-π相互作用而实现铵与两个苯环的结合,结合时电子从苯环向铵转移复合物.它们之间的结合方式和铵离子－苯复合物及典型键的结合方式相似,计算得到的热力学参数证明了这一点.复合物的红外特征振动频率位于230cm^-^1附近,振动方式为铵平行于苯平面来回振动。     

HNO与O自由基反应的密度泛函理论研究

用密度泛函理论(DFT)和从头算方法，对HNO与O自由基反应进行了研究。在(U)B3LYP/6-311G^**和(U)B3LYP/aug-cc-pVTZ水平下优化了反应通道上各驻点(反应物、中间体、过渡态及产物)的几何构型。在(U)QCISD/aug-cc-pVTZ水平下计算了各物种的单点能，并对总能量进行了零点能校正。研究结果表明，HNO与O自由基反应过程中存在O → N、O → O和O → H进攻的竞争机制，且存在着多条反应通道。采用过渡态理论计算了600～2 000 K温度范围内3条慢反应通道的速率常数。求得lnk和1/T之间的线性关系。3种通道的阿累尼乌斯指前因子分别为1.469 × 10¹⁰、1.22 × 10¹⁰(1.06 × 10¹⁰)和2.26 × 10¹³。     

Structure of AcMet-Gly and Its Interaction with Palladium(II) Tetraaqua Complex Studied by Electrospray Mass Spectrometry and Density Functional Theory

Introduction Palladium(II) complexes, as a promising artificial metallopeptidase, have been extensively studied for se-lective cleavage of methionine and histidine-containing dipeptides,1-11 oligopeptides12-16 and proteins.16-20 Dipeptides AcMet-aa and AcHis-aa, in which the amino-terminus is protected by acetylation and aa is an amino acid residue, are usually cleaved at the Met-aa and His-aa bond with a modest but significant turn-over.6,7,9 In oligopeptides which contain Met or His or b…     

Interactions of Anionic and Neutral Serine with Pure and Metal-doped Graphene Studied by Density Functional Theory

We present a theoretical study of interactions of anionic and neutral serine (Ser) on pure or metal-doped graphene surfaces using density functional theory calculations. Interactions of both types of Ser with the pure graphene surface show weak non-covalent interactions due to the formation of -COOH…π, -COO^-…π, and -OH…π interactions. On metaldoped graphene, covalent interactions to the surface dominate, due to the formation of strong metal-O and O-metal-O interactions. Furthermore, the doped Fe, Cr, Mn, Al, or Ti enhances the ability of graphene to attract both types of Ser by a combination of the adsorption energy, the density of states, the Mulliken atomic charges, and differences of electron density. At the same time, the interaction strengths of anionic Ser on various graphene surfaces are stronger than those of neutral Ser. These results provide useful insights for the rational design and development of graphene-based sensors for the two forms of Ser by introducing appropriate doped atoms. Ti and Fe are suggested to be the best choices among all doped atoms for the anionic Ser and neutral Ser, respectively.     

Bonding in Halide and Interhalide Complexes with Ammonia: Studies by Microwave Spectroscopy and Density Functional Theory

Electron density redistribution and quadrupole coupling constants (QCC) in XY···NH₃ complexes were analyzed. Data on bond lengths and QCC calculated by the BHandHLYP/aug-cc-pVTZ were used to compare the results obtained with experimental data of rotational spectroscopy. Analysis of QCC values and of the results of approximation of the natural bonding orbitals reveals prevailing electrostatic nature of intermolecular interaction.     

乙炔基自由基C2H与氧气反应的密度泛函理论研究

应用量子化学从头算和密度泛函理论(DFT)对C₂H自由基和O₂的反应进行了研究.在B3LYP/6-311G^**水平上优化了反应通道上各驻点(反应物、中间体、过渡态和产物)的几何构型,并计算出它们的振动频率和零点振动能(ZPVE).各物种的总能量由CCSD(T)/6-311G^**//B3LYP/6-311G^**给出,并对能量进行了零点能校正.计算结果表明,反应物中自由基C₂H中的边端C进攻O₂形成了中间体1 (HCCOO),中间体1是一个加合产物.由中间体1经过不同的反应通道可以生成不同的产物P₁ (HCO+CO), P₂ (HCCO+O), P₃(CO₂+CH), P₄ (C₂O+OH)和P₅ (2CO+H).反应通道之间存在着竞争机制.其中P₁, P₂是主要产物,其次还有一定比例的P5生成,而产物P₃, P₄的生成几率较低.各条反应通道化学反应热的计算与实验吻合较好.     

N'-苯亚甲基-苯并酰肼气相高温分解反应机理的密度泛函研究

利用密度泛函理论研究了N'-苯亚甲基-苯并酰肼气相高温分解生成苯腈和苯甲酰胺的反应机理.首先用B3LYP/6-31G(d,p)方法优化反应中反应物、过渡态、中间体及产物的几何构型,然后通过振动分析确认了过渡态的结构,并通过内禀反应坐标方法(IRC)确认能量最低的反应途径.报道了3条可能的反应通道,包括1条直接协同高温分解反应和2条先成环后协同高温分解反应途径,其中直接协同高温分解反应由于能垒低.因此发生的几率较大.     

Hydricity of 3d Transition Metal Complexes from Density Functional Theory: A Benchmarking Study

A range of modern density functional theory (DFT) functionals have been benchmarked against experimentally determined metal hydride bond strengths for three first-row TM hydride complexes. Geometries were found to be produced sufficiently accurately with RI-BP86-D3(PCM)/def2-SVP and further single-point calculations with PBE0-D3(PCM)/def2-TZVP were found to reproduce the experimental hydricity accurately, with a mean absolute deviation of 1.4 kcal/mol for the complexes studied.     

含平面配位碳的过渡金属烃配合物MnHnC密度泛函理论研究

用密度泛函理论研究了含平面配位碳中心的过渡金属配合物MnHnC(n=4, M=Ni, Pd, Pt; n=5, M=Cu, Ag, Au)的结构和稳定性, 发现平面四配位碳满足八隅律规则, 而平面五配位碳与过渡金属配体形成部分离子键. 同时讨论了形成含两个或多个平面四配位碳中心的链状配合物M2n+2H2n+2Cn的可能性.     

The Structure of Gas Phase Tin Oxide Ions Generated by Laser Ablation: A Combined Fourier Transform Mass Spectrometry and Density Functional Theory Study

The radical ion series (SnO)⁺ _2-6, (SnO)^– _2-6, (SnO)_0-5Sn⁺ and (SnO)_1-6O^– have been generated by the high power laser ablation of SnO and SnO₂ targets positioned inside an ICR cell. In all ablation spectra obtained, and for any particular size Sn _x core, the tin-rich clusters (SnO) _x Sn⁺ were more abundant than the corresponding oxygen-equivalent clusters (SnO)⁺ _x , while the oxygen-rich clusters (SnO) _x O^– were always more abundant than the oxygen-equivalent clusters (SnO)^– _x . High yields of the ions (SnO)_1,3Sn⁺, (SnO)_3,6O^– and (SnO)^– ₆ suggest high stabilities for these species. Low energy CID studies revealed that loss of neutral (SnO) _x units is the preferred, and for most ions investigated the exclusive, dissociation pathway. Global minima for the smaller cations and anions are proposed on the basis of local density functional theory (DFT) calculations. Calculated dissociation energies for the neutral and charged clusters were found to compare well with effusion cell and FTICR results. DFT also predicts that, for any cluster with the same size Sn _x core, IE(SnO) _x x Sn and EA(SnO) _x O>EA(SnO) _x . A correlation between ion abundances and DFT heats of formation is evident, and the ground state geometries provide insight into the evolution of structural versus size trends. Without assistance from the calculations, erroneous conclusions regarding the structures of the experimentally-sampled clusters might have been drawn from the low energy CID results.