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1.
2-Aminoimidazolone and 5-formyluracil are major one-electron photooxidation products of guanine and thymine in oligodeoxynucleotides (ODNs). Herein we report the HPLC isolation and tandem mass spectrometric characterization of ODNs carrying those types of base modifications. Collision-activated dissociation (CAD) of the deprotonated ODN ions leads to cleavages of the 3' C-O bond adjacent to the modification site, which provides enough information for locating the sites of modification. The cleavage 3' to 5-formyl-2'-deoxyuridine is in contrast to the observation that there is no cleavage 3' to an unmodified thymidine under similar conditions. In addition we observed that at high charge states, the loss of 5-formyluracil as an anion and the resulting strand cleavage is predominant over cleavages at other sites.  相似文献   

2.
The charge state distribution and CID fragmentation of two series of deprotonated oligodeoxynucleotide (ODN) 9-mers (5'-GGTTXTTGG-3' and 5'-CCAAYAACC-3', X/Y = G, C, A, or T) have been studied in detail in an ion trap in an effort to understand the intrinsic properties of DNA in vacuo. The distribution of charge states (-2 to -6) is similar for both the X- and Y-series, with the most abundant being the -4 charge state. The T-rich X-series prefers higher charge states (-6 and -5) than does the Y-series. Calculations show that phosphate groups located nearest a thymine are more acidic than those near an adenine, cytosine, or guanine, thus explaining why the X-series prefers higher charge states. We use the term "charge level" to define the ratio of the charge state to the total number of phosphate groups present in the ODN. We find, consistent with previous studies, that the initial step of fragmentation is loss of nucleobase either as an anion or as a neutral. We observe the former for ODNs with charge levels greater than 50% and the latter for ODNs with charge levels below 50%. The overall anionic base loss follows the trend A(-) > G(-) approximately T(-) > C(-); electrostatic potential calculations indicate that this trend follows delocalization of electron density for each anion, with A(-) being the most stabilized through delocalization. For neutral base loss, thymine (TH) is rarely cleaved, while the preferences for AH, GH, and CH loss vary. Proton affinity (PA) calculations show that a nearby negatively charged phosphate enhances the PA of proximally located nucleobases; this PA enhancement probably plays a role in promoting neutral base loss. The trends differ by charge level. At a charge level of 37.5% (-3 charge state), AH loss is preferred over CH and GH loss, regardless of sequence. However, at a charge level of 25% (-2 charge state), the terminal bases are preferentially lost over the internal bases, regardless of identity. By reconstructing the ODN sequences from structurally informative (a-BH) and w ions, we are able to identify the charge locations for the -3 and -2 charge states. For the -3 charge state, one charge resides on each "most terminal" phosphate, with the third being in the middle. For the -2 charge state, each charge resides on the penultimate phosphate groups. We compare our data to earlier experiments in an effort to generalize trends.  相似文献   

3.
The formation and collisionally activated dissociation (CAD) behavior of a series of complexes containing cyclic or linear diketone ligands and alkali, alkaline earth, or transition metal ions are investigated. Electrospray ionization (ESI) is utilized for introduction of the metal ion complexes into a quadrupole ion trap mass spectrometer. The proximity of the carbonyl groups is crucial for formation and detection of ion complexes by ESI. For example, no metal ion complexes are observed for 1,4-cyclohexanedione, but they are readily detected for the isomers, 1,2-and 1,3-cyclohexanedione. Although the diketones form stable doubly charged complexes, the formation of singly charged alkaline earth complexes of the type (nL + M2+ ? H+)+ where L = 1,3-cyclohexanedione or 2,4-pentanedione is the first evidence of charge reduction. CAD investigations provide further evidence of charge reduction processes occurring in the gas-phase complexes. The CAD studies indicate that an intramolecular proton transfer between two diketone ligands attached to a doubly charged metal ion, followed by elimination of the resulting protonated ligand, produces the charge reduced complex. For transition metal complexation, the preference for formation of doubly charged versus singly charged complexes correlates with the keto-enol distribution of the diketones in solution.  相似文献   

4.
To address fundamental questions in bioinorganic chemistry, such as metal ion selectivity, accurate computational protocols for both the gas-phase association of metal-ligand complexes and solvation/desolvation energies of the species involved are needed. In this work, we attempt to critically evaluate the performance of the ab initio and DFT electronic structure methods available and recent solvation models in calculations of the energetics associated with metal ion complexation. On the example of five model complexes ([M(II)(CH(3)S)(H(2)O)](+), [M(II)(H(2)O)(2)(H(2)S)(NH(3))](2+), [M(II)(CH(3)S)(NH(3))(H(2)O)(CH(3)COO)], [M(II)(H(2)O)(3)(SH)(CH(3)COO)(Im)], [M(II)(H(2)S)(H(2)O)(CH(3)COO)(PhOH)(Im)](+) in typical coordination geometries) and four metal ions (Fe(2+), Cu(2+), Zn(2+), and Cd(2+); representing open- and closed-shell and the first- and second-row transition metal elements), we provide reference values for the gas-phase complexation energies, as presumably obtained using the CCSD(T)/aug-cc-pVTZ method, and compare them with cheaper methods, such as DFT and RI-MP2, that can be used for large-scale calculations. We also discuss two possible definitions of interaction energies underlying the theoretically predicted metal-ion selectivity and the effect of geometry optimization on these values. Finally, popular solvation models, such as COSMO-RS and SMD, are used to demonstrate whether quantum chemical calculations can provide the overall free enthalpy (ΔG) changes in the range of the expected experimental values for the model complexes or match the experimental stability constants in the case of three complexes for which the experimental data exist. The data presented highlight several intricacies in the theoretical predictions of the experimental stability constants: the covalent character of some metal-ligand bonds (e.g., Cu(II)-thiolate) causing larger errors in the gas-phase complexation energies, inaccuracies in the treatment of solvation of the charged species, and difficulties in the definition of the reference state for Jahn-Teller unstable systems (e.g., [Cu(H(2)O)(6)](2+)). Although the agreement between the experimental (as derived from the stability constants) and calculated values is often within 5 kcal·mol(-1), in more complicated cases, it may exceed 15 kcal·mol(-1). Therefore, extreme caution must be exercised in assessing the subtle issues of metal ion selectivity quantitatively.  相似文献   

5.
Alkylation and oxidation constitute major routes of DNA damage induced by endogenous and exogenous genotoxic agents. Understanding the biological consequences of DNA lesions often necessitates the availability of oligodeoxyribonucleotide (ODN) substrates harboring these lesions, and sensitive and robust methods for validating the identities of these ODNs. Tandem mass spectrometry is well suited for meeting these latter analytical needs. In the present study, we evaluated how the incorporation of an ethyl group to different positions (i.e., O 2, N3, and O 4) of thymine and the oxidation of its 5-methyl carbon impact collisionally activated dissociation (CAD) pathways of electrospray-produced deprotonated ions of ODNs harboring these thymine modifications. Unlike an unmodified thymine, which often manifests poor cleavage of the C3′–O3′ bond, the incorporation of an alkyl group to the O 2 position and, to a much lesser extent, the O 4 position, but not the N3 position of thymine, led to facile cleavage of the C3′–O3′ bond on the 3′ side of the modified thymine. Similar efficient chain cleavage was observed when thymine was oxidized to 5-formyluracil or 5-carboxyluracil, but not 5-hydroxymethyluracil. Additionally, with the support of computational modeling, we revealed that proton affinity and acidity of the modified nucleobases govern the fragmentation of ODNs containing the alkylated and oxidized thymidine derivatives, respectively. These results provided important insights into the effects of thymine modifications on ODN fragmentation.
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6.
In this article, we describe the unique fragmentations of oligodeoxynucleotides (ODNs) whose phosphate groups are completely depleted of protons and replaced with metal ions. The production of the ubiquitous [a(n) - base] ions still occurs, but no longer by transfer of an acidic phosphate proton to an adjoining 3' base. Nor is the extent of the reaction determined by the proton affinity of that base. Rather, the reaction now occurs via a cleavage 3' to both pyrimidines and purines; cleavage 3' to pyrimidine is more favorable than that 3' to purine. We also demonstrate that an ODN is more stable in the gas phase when its phosphate groups are bound to metal ions than when its phosphate groups are attached to hydrogens. This study also provides further evidence for the ODN fragmentation mechanism that involves H transfer to a nucleobase. To establish the structural utility of this new fragmentation, we applied it to distinguishing small ODNs containing a photomodified cis,syn-cyclobutane pyrimidine dimer from the parent ODNs, a system that cannot be distinguished by collisional activation of precursor species that do not contain metal ions.  相似文献   

7.
Formation of inner- and outer-sphere complexes of environmentally important divalent ions on the goethite surface was examined by applying the charge distribution CD model for inner- and outer-sphere complexation. The model assumes spatial charge distribution between the surface (0-plane) and the next electrostatic plane (1-plane) for innersphere complexation and between the 1-plane and the head end of the diffuse double layer (2-plane) for the outersphere complexation. The latter approach has been used because the distance of closest approach to a charged surface may differ for different ions. The surface structural approach implies the use of a Three-Plane model for the compact part (Stern layer) of solid-solution interface, which is divided into two layers. The thickness of each layer depends on the capacitance and the local dielectric constant. The new approach has been applied to describe the adsorption of magnesium, calcium, strontium, and sulfate ions. It is shown that the concept can successfully describe the development of surface charge in the presence of Ca(+2), Mg(+2), Sr(+2), and SO4(-2) as a function of loading, pH, and salt level, and also the shift in the isoelectric point (IEP) of goethite. The CD modeling revealed that, for the conditions studied, magnesium is mainly adsorbed as a bidentate innersphere complex, calcium can be a combination of bidentate innersphere and a monodentate inner- or outer-sphere complexes, and strontium is probably adsorbed as an outersphere complex. Sulfate is present as a mixture of inner- and outer-sphere monodentate complexes. Outersphere complexation is less pH dependent than innersphere complexation. The CD model predicts that the outersphere complexation of divalent cations and anions is relatively favorable at respectively low and high pH. Increase of ion loading favors the formation of innersphere complexes.  相似文献   

8.
Recently, one of the most common conditions that manifests as joint and muscle inflammation is rheumatoid arthritis. One of the treatments for this arthritis includes non‐steroidal anti‐inflammatory drugs (NSAIDs) of the oxicam family, and the widest used drug in this family is tenoxicam (Tenox). In this study, the complexation properties of the drug Tenox with Ca(II), Sr(II) and Ba(II) ions in a (dichloromethane + water) binary solvent system are reported. The formed metal complexes were characterized structurally, thermally, and biologically. Tenox was found to act as a chelate monoanionic ligand towards all metal ions with complexation stoichiometry of 1:2 (Metal: Tenox) for Ca(II) and Sr(II) ions, and 1:1 for Ba(II) ions. The Tenox ligand behaves as a bidentate ligand when coordinated with Sr(II) or Ba(II) ions and as a tridentate ligand when coordinated with Ca(II) ions. The Sr(II) and Ba(II) complex of the Tenox ligand exhibited marked inhibitory effect on the cell growth of the C. albicans species.  相似文献   

9.
The 2,6-bis(5,6-dialkyl-1,2,4-triazin-3-yl)pyridines (DATPs) belong to a new family of extracting agents recently developed in the framework of nuclear fuel reprocessing. These molecules exhibit exceptional properties to separate actinides(III) from lanthanides(III) in nitric acid solutions. A previous work showed that electrospray ionization mass spectrometry (ESI-MS) is a reliable technique to provide solution data such as stoichiometries and conditional stability constants of various DATP complexes with europium and evidenced the unusual capability of DiPTP [bis(di-iso-propyltriazinyl)pyridine] ligand to form 1:3 complexes in nitric acid solution. This latter result is further investigated by considering DiPTP complexation features with the complete lanthanide family. As a starting point of the experimental procedure used for stability constant evaluation, the intensity distribution of ions detected by ESI-MS is studied for solutions containing Ln(NO(3))(3) in water/methanol (1:1 v/v) with the pH value set at 2.8 and 4.6 by HNO(3) additions. At pH 2.8, the nitrate anions are found to prevent lanthanides from processes occurring within the ion source: redox phenomena or gas-phase reactions with methanol which give species such as [Ln(MeO)(2)](+). Thus, the total intensity of MS signals from [Ln(NO(3))(2)(H(2)O)(p)(MeOH)(n)](+) ions is found proportional to the metal ion concentration. At pH 4.6, with lower nitrate concentration, the nature of the species identified on mass spectra depends on the electronic properties of the lanthanide elements. It is shown that Ln(III) complexation with DiPTP leads to the exclusive formation of 1:3 complexes with the whole lanthanide series which may be due not only to the hydrophobic exterior of the ligand but also to the unusual electronic density distribution in DATP ligands as compared with other aza-aromatic ligands. The conditional stability constants of the 1:3 lanthanide(III) complexes with DiPTP have been determined at pH 2.8 and are found to increase almost regularly from La (log beta(3)(app) = 11.7 +/- 0.1) to Lu (log beta(3)(app) = 16.7 +/- 0.8). Moreover, the kinetic stability of the gas-phase 1:3 complexes obtained by electrospray has been investigated by energy-resolved collision-induced dissociation and provides useful information on the bonding and structure.  相似文献   

10.
We report gas-phase electronic photodissociation spectra of the undercoordinated bromoiridate complexes IrBr(4)(-) and IrBr(5)(-) at photon energies from 1 to 5.6 eV. Both ions have open-shell ground states with low-symmetry structures. The fragmentation is characterized by thresholds for the loss of one Br atom for IrBr(4)(-) and one or two Br atoms for IrBr(5)(-). The experimental spectra consist of ligand-to-metal charge transfer transitions and reveal a large density of electronic states that can be recovered by time-dependent density functional theory.  相似文献   

11.
We report the effect of metal-ion adduction on the fragmentation of oligodeoxynucleotides (ODNs) bearing DNA photoproducts. When protons on backbone phosphates of ODNs are completely replaced with metal ions, cleavages occur readily within the photoproduct moiety, whereas those cleavages do not occur in photomodified ODNs in which the phosphates are associated with protons. For example, thymine/adenine (TA*) photoproducts revert to their undamaged precursors upon collisional activation, the pyrimidine(6-4)pyrimidone product and its Dewar valence isomer show a characteristic neutral loss of C4H3NO3, and dimeric adenine photoproducts show a distinctive loss of NH2CN from the adenine six-membered ring. The product-ion mass spectra of photodamaged ODNs that are adducted to metal ions are complementary in terms of structure information to those spectra of ODNs in which the phosphates are associated with protons. The results also demonstrate that the energy required for strand cleavages is higher for ODNs adducted with metal ions than that for ODNs bound with protons. Furthermore, the loss of a pyrimidine is more favorable than the loss of a purine in the fragmentation of ODNs associated with metal ions.  相似文献   

12.
[reaction: see text] We describe an efficient template-directed photoligation of oligodeoxynucleotides (ODNs) using alpha-5-cyanovinyldeoxyuridine (alpha(C)U). An efficient photoligation was produced by photoirradiation of an ODN containing alpha(C)U at the 3' end with an ODN containing thymine at the 5' end in the presence of a template ODN. This photoligation method is a new and efficient way to synthesize branched ODNs.  相似文献   

13.
The effects of metal cationization on collisionally activated dissociation (CAD) of phospholipids were investigated by electrospray ionization with quadrupole ion trap tandem mass spectrometry. The metal ions include Li(+), Na(+), K(+), Sr(2+), Ba(2+), and the first transition series. CAD of the transition metal ion-bound lipid complexes gave significant yields of product ions that identify the positions of the two fatty acyl substituents on the glycerophospholipid backbone. The cobalt(II) ion, which has a single naturally occurring isotope, was expected to be a better cationization reagent as it produces simpler mass spectra than other transition metal ions. CAD of the cobalt(II) ion complexes of glycerophosphoethanolamines, glycerophosphoglycerols and glycerophosphoserines yielded product ions that revealed information regarding both the lipid classes and the regiospecific positions of the two fatty acyl substituents.  相似文献   

14.
Nine aminoglycoside antibiotics were analyzed in two quadrupole ion trap mass spectrometers using electrospray ionization. Structural information was obtained via collision-activated dissociation (CAD) and infrared multi-photon dissociation (IRMPD) of the protonated species. Several of the compounds, having multiple basic sites, preferred the doubly protonated form while some existed in the singly charged state or were distributed between single and doubly protonated species, allowing comparison of the fragmentation patterns of the two charge states. In general, IRMPD is as efficient as CAD, produces more low-mass fragment ions, and is more universally applied owing to its low dependence on trapping, pressure and tuning conditions. Alkali metal complexation using Li(+) and Na(+) was probed as a means of producing different fragmentation patterns, but in most cases the resulting fragmentation patterns were simplified versions of those obtained for the protonated analogs.  相似文献   

15.
Ionizing radiation triggers the activation of caged oligodeoxynucleotides (ODNs) with a 2-oxoalkyl leaving group to give the corresponding normal uncaged strands. We designed and synthesized ODNs caged by a 2-oxopropyl group at a given thymine N(3) position (d(oxo)T) to evaluate their one-electron reduction characteristics. Upon hypoxic X-radiolysis in aqueous solution, the caged ODNs released the 2-oxopropyl group to produce the corresponding uncaged ODNs. Digestion by a restriction enzyme Swa I revealed that caged ODN pre-irradiated in hypoxia could form an ordinary duplex with its complementary strand.  相似文献   

16.
The first examples of azide complexes of calcium, strontium or barium with crown ethers have been prepared and fully characterised, notably [Ba([18]crown-6)(N3)2(MeOH)], [Sr([15]crown-5)(N3)2(H2O)], [Ca([15]crown-5)(N3)2(H2O)] and [Sr([15]crown-5)(N3(NO3)]. Crystal structures reveal the presence of a variety of coordination modes for the azide groups including kappa 1-, mu-1,3- and linkages via H-bonded water molecules, in addition to azide ions. The [Ba([18]crown-6)(N3)2(MeOH)].1/3 MeOH contains dinuclear cations with three mu-1,3-NNN bridges, the first example of this type in main group chemistry. The structures obtained have been compared with molecular structures computed by density functional theory (DFT). This has allowed the effects of the crystal lattice to be investigated. A study of the M--N terminal metal-azide bond length and charge densities on the metal (M) and terminal nitrogen centre (N terminal) in these complexes has allowed the nature of the metal-azide bond to be investigated in each case. As in our earlier work on alkali metal azide-crown ether complexes, the bonding in the alkaline-earth complexes is believed to be predominantly ionic or ion-dipole in character, with the differences in geometries reflecting the balance between maximising the coordination number of the metal centre, and minimising ligand-ligand repulsions.  相似文献   

17.
A series of chalcones were characterized by electrospray ionization tandem mass spectrometry (MS(n)). Several ionization modes were evaluated, including protonation, deprotonation and metal complexation, with metal complexation being the most efficient. Collision-activated dissociation (CAD) was used to characterize the structures, and losses commonly observed include H(2), H(2)O, CO and CO(2), in addition to methyl radicals for the methoxy-containing chalcones. CAD of the metal complexes, especially [Co(II) (chalcone-H) 2,2'-bipyridine](+), allowed the most effective differentiation of the isomeric chalcones with several diagnostic fragment ions appearing upon activation of the metal complexes. MS(n) experiments were performed to support identification of some fragment ions and to verify the proposed fragmentation pathways. In several cases, MS(n) indicated that specific neutral losses occurred by stepwise pathways, such as the neutral loss of 44 u as CH3* and HCO*, or CH(4) and CO, in addition to CO(2).  相似文献   

18.
Ba deposition on a theta-Al(2)O(3)/NiAl(100) substrate and its oxidation with gas-phase O(2) at various surface temperatures are investigated using X-ray photoelectron spectroscopy (XPS), Auger electron spectroscopy (AES), and temperature programmed desorption (TPD) techniques. Oxidation of metallic Ba by gas-phase O(2) at 800 K results in the growth of 2D and 3D BaO surface domains. Saturation of a metallic Ba layer deposited on theta-Al(2)O(3)/NiAl(100) with O(2)(g) at 300 K reveals the formation of BaO(2)-like surface states. These metastable peroxide (O(2)(2-)) states are converted to regular oxide (O(2-)) states at higher temperatures (800 K). In terms of thermal stability, BaO surface layers (theta(Ba) < 5 ML) that are formed by O(2)(g) assisted oxidation on the theta-Al(2)O(3)/NiAl(100) substrate are significantly more stable (with a desorption/decomposition temperature of c.a. 1050 K) than the thick (2 < theta(Ba) < 10 ML) metallic/partially oxidized Ba layers prepared in the absence of gas-phase O(2), whose multilayer desorption features appear as low as 700 K.  相似文献   

19.
Cobalt(ll), nickel(II) and copper(II) acetates react with thymine compound (H2L) to form complexes having the general formula [MH2L(OAC)2(H2O)2]nH2O. However, the interaction of iron(III) chloride with thymine in acetic acid-water medium yields a new complex of the type [FeH2L(OAC)2H2O]OAC.H2O. All the thymine complexes have been characterized by elemental analyses, spectral and magnetic studies where thymine acts as a neutral ligand and the acetate ion behaves as a strong nucleophile during complexation. 6-aryl and thiazolylazo thymine compounds and their metal complexes were synthesized and characterized where the ligands act as a bidentate dibasic. The azo group is not involved in the structure. Thermal decomposition studies of the azo complexes were explained to give more information on the structure of the investigated materials. The effect of some transition metal cations such as Co11, Ni11 and CuII on the electrical behaviour of 6-(2-thiazolylazo)thymine compound is studied. The data obtained obeyed the relation sigma = sigma degrees exp ( - E/2kT) over the temperature range 30-150 degrees C. The observed conductivities of the different complexes follow the order Co < Ni < Cu. It is clear that this trend is depending on the decreasing of the ionic radii and the increasing stability of metal complexes. The calculated mobility of charge carriers is ranged from 10(-5) to 10(-9)cm2/V s suggesting that the conduction of the studied complexes takes place by hopping mechanism.  相似文献   

20.
Tunell I  Lim C 《Inorganic chemistry》2006,45(12):4811-4819
Many of the group IA and IIA metal ions, such as Na+, K+, Mg2+, and Ca2+, play crucial roles in biological functions. Previous theoretical studies generally focus on the number of water molecules bound to a particular (as opposed to all) alkali or alkaline earth cations and could not establish a single preferred CN for the heavier alkali and alkaline earth ion-water complexes. Crystal structures of hydrated Na+, K+, and Rb+ also cannot establish the preferred number of inner-shell water molecules bound to these cations. Consequently, it is unclear if the gas-phase CNs of group IA metal hydrates increase with increasing ion size, as observed for the group IIA series from the Cambridge Structural Database, and if the same factors govern the gas-phase CNs of both group IA and IIA ion-water complexes. Thus, in this work, we determine the number of water molecules directly bound to the series of alkali (Li+, Na+, K+, and Rb+) and alkaline earth (Be2+, Mg2+, Ca2+, Sr2+, and Ba2+) metal ions in the gas phase by computing the free energy for forming an isolated metal-aqua complex as a function of the number of water molecules at 298 K. The preferred gas-phase CNs of group IA hydrates appear insensitive to the ion size; they are all 4, except for Rb+, where a CN of 6 seems as likely. In contrast, the preferred gas-phase CNs of the group IIA dications increase with increasing ion size; they are 4 for Be2+, 6 for Mg2+ and Ca2+, and 7 for Sr2+ and Ba2+. An entropic penalty disfavors a gas-phase CN greater than 4 for group IA hydrates, but it does not dictate the gas-phase CNs of group IIA hydrates. Instead, interactions between the metal ion and first-shell water molecules and between first-shell and second-shell water molecules govern the preferred gas-phase CNs of the group IIA metal hydrates.  相似文献   

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