Theoretical mechanistic study on the ion-molecule reaction of SiCN+/SiNC+ with H2O

The gas-phase ion-molecule reactions play very important roles in interstellar and in plasma chemistry. Motivated by recent astrophysical detection of the SiCN/SiNC radicals and laboratory characterization of some SiCN-containing species, we carried out a detailed potential energy survey on the SiCN+/SiNC(+) + H2O reaction at the Becke's three-parameter Lee-Yang-Parr-B3LYP/6-311G(d,p) and coupled cluster with single, double, and triple excitations-CCSD(T)/6-311 + G(2df,p) (single-point) levels as an attempt towards understanding the SiCN+/SiNC+ reaction mechanisms. In contrast to the carbene-featured analogous CCN+/CNC(+) + H2X (X=O,S) reactions, the title reaction SiCN+/SiNC(+) + H2O are not associated with any competitive silylene-insertion characters. Moreover, the -CN <--> -NC interconversion has a low barrier and plays an important role in determining the final product distributions. This is also in marked difference from the CCN+/CNC+ reaction. It is shown that the isomeric sila-cations SiCN+ and SiNC+ can both react with H2O to barrierlessly generate the major product P1 HOSi(+) + HCN and the minor one P3 HOSi(+) + HNC, whereas other low-lying products such as P2 SiNCO(+) + H2, and P(0) H2NSi(+) + CO are kinetically unfeasible. The high efficiency of the SiCN+/SiNC+ reaction towards H2O and the potential importance of SiCN+/SiNC+ ion chemistry in interstellar and SiCN-based microelectric and photoelectric processes strongly appeals for future laboratory investigations on the SiCN+/SiNC+ chemical reactivity.     

Interstellar problems and matrix solutions.

The application of the matrix isolation technique, which is but one of the experimental techniques pioneered in George Pimentel's laboratories, to interstellar problems is described. Following a brief discussion of the interstellar medium (ISM) three areas are reviewed in which matrix experiments are particularly well-suited to contribute the information which is sorely needed to further our understanding of the ISM. The first involves the measurement of the spectroscopic properties of reactive species. The second is the determination of reaction rates and the elucidation of reaction pathways involving atoms, radicals and ions which are likely to interact on grain surfaces and in grain mantles. The third entails the determination of the spectroscopic, photochemical and photophysical properties of interstellar and cometary ice analogs. Significant, but limited, progress has been made in these three areas and a tremendous amount of work is required to fully address the variety of unique chemical and spectroscopic questions posed by the astronomical observations.     

Extra-Terrestrial Gas-Phase Stereoinversion in Amino Acid Leucine: Thermal and Photochemical Channels

Enantiomeric-excess of the left-handed enantiomer of proteinogenic amino acids has been reported in the meteoritic samples of carbonaceous chondrites. Such chiral-bias is recently being believed due to the removal of right-handed enantiomer through its selective destruction by circularly polarized ultraviolet (UV) radiations in interstellar space. The present work through quantum mechanical computations explores various thermal and photochemical channels for stereoinversion in proteinogenic amino acid Leucine, under the gas-phase conditions akin to different temperature zones of interstellar medium (ISM). A thermochemical and kinetic analysis for the feasibility of the proposed channels is also carried out in different regions of ISM. The initiation of stereoinversion along all the ground-state thermal channels is found to be restricted by a very high energy barrier which, however, is proposed to be substantially reduced if the initial step proceeds via an excited-state. This work reveals that the stereoinversion in Leucine is quite feasible in ISM, provided it is initiated photochemically by UV radiations, which are abundant in ISM.     

在星际媒介中合成H2NCH2CN分子的理论研究

在早期地球原始化学生命起源过程中, 氨基酸是重要的必需的生物化合物, 生成肽和蛋白. 为了探究一个可能的新的氨基酸起源, 采用密度泛函理论(B3LYP)在6-311++G(d, p) 基组水平上研究了在星际媒介条件下在气相中和在模拟的冰颗粒表面上的化学反应: CH2NH分子和两个异构体分子HNC/HCN通过Strecker合成生成H2NCH2CN(氨基乙氰, 一个重要的苷氨基酸前置分子). 在研究体系中, CH2NH、HCN、HNC 和H2O分子存在于星际密集分子云中, 且早于地球广泛存在. 研究证明, 这些分子之间在星际媒介条件下和在冰颗粒表面上通过Strecker合成路线很容易生成H2NCH2CN. 所以, H2NCH2CN分子在宇宙的星际密集分子云中是广泛存在的. 还讨论了H2NCH2CN分子在新的氨基酸起源中所起的作用, 以及在通过“原始汤”生命起源理论解析早期地球生命起源中可能所起的作用.     

Theoretical prediction of new dipole-bound singlet states for anions of interstellar interest

Anions that exhibit dipole-bound singlet states have been proposed as a potential class of molecules that may be identified in the interstellar medium. Using high-level coupled cluster theory, we have computed the dipole moments, electron binding energies, and excited states of 14 neutral radicals and their corresponding closed-shell anions. We have calibrated our methods against experimental data for CH(2)CN(-) and CH(2)CHO(-) and demonstrated that coupled cluster theory can closely reproduce experimental dipole moments, electron binding energies, and excitation energies. Using these same methods, we predict the existence of dipole-bound excited states for six of the 14 previously unknown anions, including CH(2)SiN(-), SiH(2)CN(-), CH(2)SiHO(-), SiN(-), CCOH(-), and HCCO(-). In addition, we predict the existence of a valence-bound excited state of CH(2)SiN(-) with an excitation wavelength near 589 nm.     

星际媒介H2NCH2CN与H2O反应中的H2O分子偶合质子转移机理和氢隧道效应

H2NCH2CN+H2O→H2NCH2C(OH)NH是一个重要的反应, 涉及到星际媒介中甘氨酸的形成, 与早期地球上的氨基酸起源有关. 如果没有考虑氢隧道效应, 在MP2/6-311+G(d,p)级别上计算反应能垒是254.7 kJ·mol-1, 在星际媒介中该气相反应很难进行. 在星际媒介冰颗粒表面上, 水分子催化反应增强了该化学反应的活性. H2NCH2CN与(H2O)3反应中的两个水分子作为催化剂降低活化能77.5 kJ·mol-1和活化自由能70.9 kJ·mol-1, 并且通过氢键桥协同传递质子. 量子氢隧道对于该反应进行至关紧要,采用小弯曲隧道(SCT)近似和正则变分过渡态理论(CVT)方法研究. 温度50 K时, 速率常数kSCT/CVT为1.86×10-23 cm3·molecule-1·s-1, 表明在星际媒介中通过质子隧道机理该反应容易进行. 研究结果与地球上的氨基酸起源于地球本身物质的观点相一致.     

Synthesis of MII[N(SiMe3)2][Me3SiNC(tBu)NSiMe3] (M = Sn,Ge) from amidinate precursors: active catalysts for phenyl isocyanate cyclization

Mixed amidinato amido complexes [Me3SiNC(tBu)NSiMe3]M[N(SiMe3)2] (M = Sn 2, Ge 3) were prepared by the reaction of [Me3SiNC(tBu)NSiMe3]Li (1a) with SnCl2 and GeCl2(dioxane) in ether. The N(SiMe3)2 ligand in these compounds is derived from the rearrangement of the [Me3SiNC(tBu)NSiMe3]- anion with extrusion of tBuCN. The susceptibility of [Me3SiNC(tBu)NSiMe3]- to rearrangement appears to be dependent on reaction solvent and on the coordinated metal center. Single-crystal X-ray diffraction studies of 2 and 3 are presented. Replacement of Me for tBu in the ligand allowed [Me3SiNC(Me)NSiMe3]2SnII (4) to be isolated, and an X-ray structure of this compound is reported. The isolation of 4 indicates that steric factors also play a role in the stability of [Me3SiNC(tBu)NSiMe3]-. Compounds 2 and 3 are outstanding catalysts for the cyclotrimerization of phenyl isocyanates to perhydro-1,3,5-triazine-2,4,6-triones (isocyanurates) at room temperature. In contrast, complex 4 catalytically reacts with phenyl isocyanate to produce isocyanate dimer and trimer in a 52:35 ratio.     

Vibrational and electronic absorption spectroscopy of dibenzo[b,def]chrysene and its ions

The vibrational and electronic absorption spectra of dibenzo[b,def]chrysene (DBC) and its ions in argon matrixes have been recorded. Assignment of the observed infrared (IR) bands has been made by comparison with the density functional theory (DFT) computations of harmonic vibrational frequencies (with 6-31G(d,p) or 6-311+G(d,p) basis sets). Extensive time-dependent (TD) DFT calculations of vertical excitation energies have aided in the assignment of the experimental electronic absorption transitions. In general, the theoretical predictions are in good agreement with the observed ultraviolet and visible bands. By correlating IR and UV-visible band intensities (after UV photolysis), it has been shown that both DBC cations and anions are formed. The IR band intensity distributions of the DBC ions differ markedly from neutral DBC. A synthetic spectrum composed of neutral, cationic, and anionic DBC contributions compares reasonably well with the interstellar features of the "unidentified infrared" (UIR) bands from the reflection nebula NGC 7023. Finally, it is shown that the electronic absorption bands of the DBC ions lie in close proximity to several of the diffuse interstellar visible absorption bands (DIBs).     

Ion-molecule reaction mechanism of SiCN+/SiNC+ + HX (X = H, CH3, F, OH, NH2)

In contrast to the abundant data on the neutral-neutral reactions, little is known about the ion-molecule reactions involving silicon ions. A detailed mechanistic study at the B3LYP/6-311G(d,p) and CCSD(T)/6-311+G(2df,p) (single-point) computational levels was reported for the reactions of SiCN+/SiNC+ with a series of -bonded molecules HX (X = H, CH3, F, NH2). Together with the recently studied SiCN+/SiNC+ + H2O reactions, all of these reactions have nucleophilic substitution as their major pathway. Insertion is a much slower reaction. By contrast, the known atomic Si+ and C2N+ ion-molecule reactions go by insertion. Generally, the initial gas-phase condensation between SiCN+/SiNC+ and HX (except the nonionic H2) effectively forms the adduct HX...SiCN+/HX...SiNC+. The stability of the adduct increases with the electron-donating ability of X. Even at low temperatures, reactions with the electron donors NH3, H2O, and HF proceed rapidly to generate the fragments SiX+ + HCN (dominant) and SiX+ + HNC (minor). This suggests that such reactions may be useful in the synthesis of novel Si-X bonded species. However, the reactions of SiCN+ with completely saturated CH4 and H2 produce fragments only at high temperatures, and SiNC+ may even be unreactive. The calculated results may be helpful for understanding the chemistry of SiCN-based microelectric and photoelectric processes in addition to astrophysical processes in which the [Si,C,N]+ ion is involved. The results can also provide useful mechanistic information for the analogous ion-molecule reactions of the monovalent silicon-bearing ions.     

Multiply-charged ions and interstellar chemistry

Gaseous molecules and ions, and even dust grains, can accumulate charge in the interstellar medium (ISM) by harvesting the energy of UV photons, cosmic rays, helium ions and metastable atoms. This Perspective views the various modes of gas-phase formation of multiply-charged cations and the possible impact of their reactions on the chemical and ionization structure of the ISM, in the light of what is still very limited knowledge. Emphasis is given to gas-phase reactions of multiply-charged cations with atoms, molecules and electrons that lead to charge reduction, charge separation and chemical bond formation and these are examined for multiply-charged atoms, small molecules, hydrocarbons, polycyclic aromatic hydrocarbons and fullerenes, primarily as dications but also as a function of charge state. The increased electrostatic interaction due to multiple charge is seen to promote bonding to individual charge sites on large molecules (e.g. fullerenes) and allow ensuing "surface" chemistry under the influence of Coulomb repulsion. The unique ability of multiply charged cations to undergo charge separation reactions, either unimolecular or bimolecular, can feature in the production in the ISM of internally cold, but translationally hot, cations of lower charge state or hot atoms that may provide the driving force for subsequent chemical reactions in what is otherwise an ultracold environment. Available chemical kinetic models that account for the role of multiply-charged ions in the ISM are few and of limited scope and the observation of these ions in the ISM has remained elusive.     

UV photodesorption of interstellar CO ice analogues: from subsurface excitation to surface desorption

Carbon monoxide is after H(2) the most abundant molecule identified in the interstellar medium (ISM), and is used as a major tracer for the gas phase physical conditions. Accreted at the surface of water-rich icy grains, CO is considered to be the starting point of a complex organic--presumably prebiotic--chemistry. Non-thermal desorption processes, and especially photodesorption by UV photons, are seen as the main cause that drives the gas-to-ice CO balance in the colder parts of the ISM. The process is known to be efficient and wavelength-dependent, but, the underlying mechanism and the physical-chemical parameters governing the photodesorption are still largely unknown. Using monochromatized photons from a synchrotron beamline, we reveal that the molecular mechanism responsible for CO photoejection is an indirect, (sub)surface-located process. The local environment of the molecules plays a key role in the photodesorption efficiency, and is quenched by at least an order of magnitude for CO interacting with a water ice surface.     

Gas-Phase Synthesis of Triphenylene (C18H12)

For the last decades, the hydrogen-abstraction−acetylene-addition (HACA) mechanism has been widely invoked to rationalize the high-temperature synthesis of PAHs as detected in carbonaceous meteorites (CM) and proposed to exist in the interstellar medium (ISM). By unravelling the chemistry of the 9-phenanthrenyl radical ([C₁₄H₉]^.) with vinylacetylene (C₄H₄), we present the first compelling evidence of a barrier-less pathway leading to a prototype tetracyclic PAH – triphenylene (C₁₈H₁₂) – via an unconventional hydrogen abstraction–vinylacetylene addition (HAVA) mechanism operational at temperatures as low as 10 K. The barrier-less, exoergic nature of the reaction reveals HAVA as a versatile reaction mechanism that may drive molecular mass growth processes to PAHs and even two-dimensional, graphene-type nanostructures in cold environments in deep space thus leading to a better understanding of the carbon chemistry in our universe through the untangling of elementary reactions on the most fundamental level.     

Theoretical studies of azapentalenes. Part 4: Theoretical study of the properties of 3a,6a-diazapentalene

A theoretical study of the properties of the isolated 3a,6a-diazapentalene by means of DFT, B3LYP/6-311++G(d,p) and ab initio methods, MP2/6-311++G(d,p), has been carried out. In addition, the complexes formed with hydrogen bond donor, acceptors, cations, and anions have been studied and analyzed. Ring opening into 1,5-diazocine as well as basicity and acidity properties of 3a,6a-diazapentalene have been explored. Their ability to form HB complexes and the complexes formed with anions and cations have been studied.     

Theoretical study on structures and stability of Si2CP isomers

The structures, energetics, spectroscopies, and isomerization of various doublet Si2CP species are explored theoretically. In contrast to the previously studied SiC2N and SiC2P radicals that have linear SiCCN and SiCCP ground states, the title Si2CP radical has a four-membered-ring form cSiSiPC 1 (0.0 kcal/mol) with Si-C cross-bonding as the ground-state isomer at the CCSD(T)/6-311G(2df)//B3LYP/6-311G(d)+ZPVE level, similar to the Si2CN radical. The second low-lying isomer 2 at 11.6 kcal/mol has a SiCSiP four-membered ring with C-P cross-bonding, yet it is kinetically quite unstable toward conversion to 1 with a barrier of 3.5 kcal/mol. In addition, three cyclic species with divalent carbene character, i.e., cSiSiCP 7, 7' with C-P cross-bonding and cSiCSiP 8 with Si-Si cross-bonding, are found to possess considerable kinetic stability, although they are energetically high lying at 44.4, 46.5, and 41.4 kcal/mol, respectively. Moreover, a linear isomer SiCSiP 5 at 44.3 kcal/mol also has considerable kinetic stability and predominantly features the interesting cumulenic /Si=C=Si=P/* form with a slight contribution from the silicon-phosphorus triply bonded form /Si=C*-Si[triple bond]P/. The silicon-carbon triply bonded form *Si[triple bond]C-Si[triple bond]P/ has negligible contribution. All five isomers are expected to be observable in low-temperature environments. Their bonding nature and possible formation strategies are discussed. For relevant species, the QCISD/6-311G(d) and CCSD(T)/6-311+G(2df) (single-point) calculations are performed to provide more reliable results. The calculated results are compared to those of the analogous C3N, C3P, SiC2N, and Si2CN radicals with 17 valence electrons. Implications in interstellar space and P-doped SiC vaporization processes are also discussed.     

The chemistry and complexes of small cyano anions

The chemistry of the anions dicyanamide and tricyanomethanide (dca and tcm, respectively) has produced a plethora of discoveries over the past few decades, particularly in relation to transition-metal coordination polymers with magnetic coupling. Over recent years there have been an increasing number of reports of heterofunctionalised cyano-containing anions, typically derivatives of dicyanomethanide. Our own group has been particularly concerned with the amide- and nitroso-functionalised anions carbamoyldicyanomethanide (cdm) and dicyanonitrosomethanide (dcnm), respectively. This feature article examines the fascinating diversity of materials and complexes that can be obtained using small cyano anions, ranging from coordination polymers to heterometallic clusters and hydrogen bonding networks. In particular, we focus on results from our own laboratories in the past few years. The magnetic properties of these materials are briefly discussed.     

Determination of inorganic anions in human saliva by zwitterionic micellar capillary electrophoresis

Capillary electrophoresis (CE) using sulfobetaine-type zwitterionic micelles as the background electrolyte (BGE) has been used to determine inorganic anions in human saliva. The zwitterionic micelles resulted in unique migration behavior for the separation of inorganic anions. They also prevented adsorption of proteins on the inner wall of the capillary. These properties of the zwitterionic micelles enabled the direct determination of inorganic anions in human saliva. Three species of inorganic anions, NO2-, NO3-, and SCN-, were found in real samples and the analysis was achieved within 3 min. Direct UV-absorption was used as the detection method and the detection limits for these anions were 2.0, 1.0, and 5.0 micromol L(-1), respectively (0.09, 0.06, and 0.30 microg mL(-1)).     

Luminescent rhenium(I) complexes with acetylamino- and trifluoroacetylamino-containing phenanthroline ligands: anion-sensing study

A series of rhenium complexes with acetylamino- and trifluoroacetylamino-containing 1,10-phenanthroline ligands have been synthesized, characterized and their photophysical and electrochemical properties studied. These complexes were found to show significant UV-vis and emission changes on addition of CN(-), F(-) and AcO(-) anions. Their reactivity towards CN(-), F(-) and AcO(-) anions, was also investigated by UV-vis, emission and (1)H NMR spectroscopy. The reaction product between the trifluoroacetylamino-containing 1,10-phenanthroline ligand and the CN(-) anion has also been structurally characterized by X-ray crystallography.     

Thermally induced mixing of water dominated interstellar ices

Despite considerable attention in the literature being given to the desorption behaviour of smaller volatiles, the thermal properties of complex organics, such as ethanol (C(2)H(5)OH), which are predicted to be formed within interstellar ices, have yet to be characterized. With this in mind, reflection absorption infrared spectroscopy (RAIRS) and temperature programmed desorption (TPD) have been used to probe the adsorption and desorption of C(2)H(5)OH deposited on top of water (H(2)O) films of various thicknesses grown on highly oriented pyrolytic graphite (HOPG) at 98 K. Unlike many other molecules detected within interstellar ices, C(2)H(5)OH has a comparable sublimation temperature to H(2)O and therefore gives rise to a complicated desorption profile. RAIRS and TPD show that C(2)H(5)OH is incorporated into the underlying ASW film during heating, due to a morphology change in both the C(2)H(5)OH and H(2)O ices. Desorption peaks assigned to C(2)H(5)OH co-desorption with amorphous, crystalline (CI) and hexagonal H(2)O-ice phases, in addition to C(2)H(5)OH multilayer desorption are observed in the TPD. When C(2)H(5)OH is deposited beneath ASW films, or is co-deposited as a mixture with H(2)O, complete co-desorption is observed, providing further evidence of thermally induced mixing between the ices. C(2)H(5)OH is also shown to modify the desorption of H(2)O at the ASW-CI phase transition. This behaviour has not been previously reported for more commonly studied volatiles found within astrophysical ices. These results are consistent with astronomical observations, which suggest that gas-phase C(2)H(5)OH is localized in hotter regions of the ISM, such as hot cores.     

Understanding the Peculiarities of Azide and Thiocyanate Binding in Proteins: Use of the Small Molecule Structural Data

Abstract

The complexation and supramolecular recognition of two polyfunctional anions, thiocyanate and azide, have been analysed using the X-ray structural data retrieved from the Brookhaven Protein Database (for macromolecules) and the Cambridge Structural Database (for small molecule structures). The following structural aspects have been considered: - hydrogen-bond acceptor function of the anions; - analysis of the coordination features of anions with the metals; - influence of metal complexation on the H-donor accepting properties of the anions. Lastly, a comparison of the modes of binding of the two anionic substrates was carried out. Their extraordinary activity as hydrogen-bond acceptors allows these anions to serve as a strong bridge between different molecular fragments. The coordination of thiocyanate or azide anion by the metal atoms in coordination compounds gives rise to a redistribution of anionic charge in both entities which in turn, controls the hydrogen-bonding acceptor properties of the terminal atom of the anion. The results presented in this paper provide structural information of the role of anion binding in proteins and to our knowledge, afford the first study of the binding behaviour of thiocyanate and azide in systematic manner.     

Electron photodetachment from aqueous anions. 3. Dynamics of Geminate pairs derived from photoexcitation of mono- vs polyatomic anions

Photostimulated electron detachment from aqueous inorganic anions is the simplest example of solvent-mediated electron transfer reaction. As such, this photoreaction became the subject of many ultrafast studies. Most of these studied focused on the behavior of halide anions, in particular, iodide, that is readily accessible in the UV. In this study, we contrast the behavior of these halide anions with that of small polyatomic anions, such as pseudohalide anions (e.g., HS(-)) and common polyvalent anions (e.g., SO(3)(2-)). Geminate recombination dynamics of hydrated electrons generated by 200 nm photoexcitation of aqueous anions (I(-), Br(-), OH(-), HS(-), CNS(-), CO(3)(2-), SO(3)(2-), and Fe(CN)(6)(4-)) have been studied. Prompt quantum yields for the formation of solvated, thermalized electrons and quantum yields for free electrons were determined. Pump-probe kinetics for 200 nm photoexcitation were compared with kinetics obtained at lower photoexcitation energy (225 or 242 nm) for the same anions, where possible. Free diffusion and mean force potential models of geminate recombination dynamics were used to analyze these kinetics. These analyses suggest that for polyatomic anions (including all polyvalent anions studied) the initial electron distribution has a broad component, even at relatively low photoexcitation energy. There seems to be no well-defined threshold energy below which the broadening of this electron distribution does not occur, as is the case for halide anions. The constancy of (near-unity) prompt quantum yields vs the excitation energy as the latter is scanned across the lowest charge-transfer-to-solvent band of the anion is observed for halide anions but not for other anions: the prompt quantum yields are considerably less than unity and depend strongly on the excitation energy. Our study suggests that halide anions are in the class of their own; electron photodetachment from polyatomic, especially polyvalent, anions exhibits qualitatively different behavior.