Association of Cu2+ with uracil and its thio derivatives: a theoretical study.

The structures and relative stabilities of the complexes between Cu2+ and uracil, 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil were investigated by B3LYP/6-311+G(2df,2p)//B3LYP/6-31G* DFT calculations. In those systems in which both types of basic centers, that is, a carbonyl and a thiocarbonyl group, are present, association of Cu2+ with the oxygen atom is systematically favored, in contrast to what was found for the corresponding Cu+ complexes. This can be understood by considering that association of Cu2+ is immediately followed by oxidation of the base, which accumulates the negative charge at the oxygen atoms. Similarly, for 2,4-dithiouracil the most basic site for Cu+ attachment is the sulfur atom at the 4-position, while for association of Cu2+ it is sulfur at the 2-position. In contrast, differences between uracil-Cu+ and uracil-Cu2+ complexes are very small, and in both cases the oxygen atom at the 4-position is the most basic. Cu2+ binding energies are about 4 and 1.2 times larger than Cu+ binding energies and proton affinities, respectively. Uracil- and thiouracil-Cu2+ complexes are thermodynamically unstable but kinetically stable with respect to their dissociation into uracil*+ + Cu+ or thiouracil*+ + Cu+. The Cu2+ binding energies vary with the difference between the second ionization potential of the metal and the first ionization potential of the base. regardless of the reference acid (H+, Cu+, Cu2+) the basicity trend is 2,4-dithiouracil > 4-thiouracil > 2-thiouracil > uracil.     

Protonation of 5‐methylhydantoin and its thio derivatives in the gas phase: A theoretical study

The gas phase proton affinities of 5‐methylhydantoin and its thio derivatives were theoretically studied through the use of high‐level density functional theory calculations. The structure of all possible tautomers and their conformers were optimized at the B3LYP/6‐311+(d,p) level of theory. Final energies were obtained at the B3LYP/6‐311+(2df,2p) level. The imidazolidone derivatives 5‐methyl‐2,4‐dioxo imidazolidine, 5‐methyl‐2‐oxo‐4‐thio imidazolidine, 5‐methyl‐2‐thio‐4‐oxo imidazolidine, and 5‐methyl‐2,4‐dithio imidazolidine possess moderately strong proton affinities. Protonation at sulfur would be larger than protonation at oxygen. The most stable protonated forms of 2O4O and 2S4O have the proton attached to the heteroatom in position 2, whereas protonation of 2O4S and 2S4S preferentially takes place at position 4. The barriers for proton migration between the different tautomers are rather large. The energy decomposition analysis analysis of the O? H⁺ and S? H⁺ interactions suggests that the bonding interactions come mainly from the covalent bond formation. The contribution of the Coulomb attraction is rather small. © 2012 Wiley Periodicals, Inc.     

Interaction of low-energy electrons with linear diphenylethynyl derivatives in the gas phase

The gas phase electron impact spectroscopy has been used to study the relative efficiency of excitation into singlet states and energies of singlet-triplet transitions for two electroactive organic materials, anthracene and biphenyl-containing diphenylethynyl derivatives. The probability of the lowest singlet-triplet transition in anthracene-containing molecule was found to be much higher than that in anthracene which is connected with triple bonds. No noticeable contribution of the triple bonds into singlet spectra of the studied molecules was observed. There are a number of intense transitions in the range higher than 10 eV. The optical spectrum calculated using the density functional theory is in good agreement with experimental electron energy loss and optical absorption spectra.     

Structures and energetics of electrosprayed uracil(n)Ca2+ clusters (n = 14-4) in the gas phase

Clusters of uracil (U) about a calcium dication, U(n)Ca(2+) (n = 14-4), have been studied in the gas phase by both experimental and theoretical methods. Temperature dependent blackbody infrared radiative dissociation (BIRD) experiments were performed on U(n)Ca(2+) clusters with n = 14-5 and the observed Arrhenius parameters are reported here. Master equation modeling of the BIRD kinetics data was carried out to determine threshold dissociation energies. Initial geometry calculations were performed using the B3LYP density functional and 3-21G(d) basis set. A sample of ten conformations per cluster was obtained through a simulated annealing study. These structures were optimized using B3LYP/6-31G(d) level of theory. Fragment-based hybrid many body interaction (HMBI) MP2/6-311++G(2df,2p)/Amoeba calculations were performed on representative conformations to determine theoretical binding energies. Results were examined in relation to cluster size (n). A significant increase in the energy required to remove uracil from U(6)Ca(2+) when compared to larger clusters supports previous reports that the calcium ion is coordinated by six uracil molecules in the formation of an inner shell. For clusters larger than n = 6, an odd-even alternation in threshold dissociation energies was observed, suggesting that the outer shell uracil molecules bind as dimers to the inner core. Proposed binding schemes are presented. Multiple structures of U(5)Ca(2+) are suggested as being present in the gas phase where the fifth uracil may be either part of the first or second solvation shell.     

Interactions of uracil and its derivatives with polyfunctional acids

Russian Chemical Bulletin - The previously obtained experimental and quantum chemical data on the composition, structure, stability, and thermodynamic properties of complexes of uracil and a series...     

Assisted intramolecular proton transfer in (uracil)2Ca2+ complexes

The structure and relative stability of the complexes between uracil dimers and Ca²⁺, as well as the proton transfer (PT) processes within these dimers, have been investigated by the density functional theory methods. Although in uracil dimers PT occurs as an almost synchronous double PT processes that connect the diketo dimer with a keto-enol dimer, the process within the most stable (uracil)₂Ca²⁺ complexes is much more complicated, and the product of the reaction looks like the result of an intramolecular PT from one of the NH groups of one monomer to one of the carbonyl groups of the same monomer. An analysis of the force profile along the reaction coordinate shows that the intimate mechanism implies three elementary steps, two intermolecular PTs, and an in-plane displacement of one monomer with respect to the other. The result of this so-called assisted intramolecular proton transfer is the formation of a dimer in which only one monomer is a keto-enol derivative, the other monomer being apparently unchanged, although it suffers significant structural rearrangements along the reaction coordinate. Quite importantly, this dimer is significantly stabilized upon Ca²⁺ association; therefore, while the most stable uracil dimers correspond systematically to associations involving only the diketo forms, in (uracil)₂Ca²⁺ complexes the most stable structures correspond to those in which one of the monomers is a keto-enol uracil isomer.     

Collision-induced dissociation of uracil and its derivatives

The collision-induced dissociation of protonated uracil has been studied by tandem mass spectrometry using models extensively labeled with stable isotopes, and derivatives of the kinds found in nucleic acids. Following collisional activation at 30 eV translational energy, protonated uracil dissociates through two principal pathways which do not occur in electron ionization mass spectra: (1) elimination of NH3 almost entirely from N-3, followed by loss of CO from C-4, 0⁴; (2) loss of H2O, equally from 0² and 0⁴. Elimination of HNCO, also the principal dissociation process from odd-electron molecular ions, proceeds primarily by loss of N-3, C-Z, O² and 10% from N-l, C-Z, 0². Several secondary dissociation products are formed with quantitative site specificity of skeletal atoms: C,HO+ (4-C0, C-5, C-6); H2CN+ (N-l, C-6); C2H2+ (N-l, C-5, C-6). First-step dissociation reactions are interpreted in terms of pyrimidine ring opening at likely sites of protonation after collisional activation of MH+. Collision-induced dissociation mass spectra of uracils with structural themes common to nucleic acids (methylation, replacement of 0 by S, C-5 substitution) follow analogous reaction paths which permit assignment of sites of substitution, and exhibit ion abundance changes attributed to differences in substituent basicity and electron density.     

Metastable BrO2+ and NBr2+ molecules in the gas phase

The doubly positively charged gas-phase molecules BrO(2+) and NBr(2+) have been produced by prolonged high-current energetic oxygen (17 keV (16)O(-)) ion surface bombardment (ion beam sputtering) of rubidium bromide (RbBr) and of ammonium bromide (NH(4)Br) powdered ionic salt samples, respectively, pressed into indium foil. These novel species were observed at half-integer m∕z values in positive ion mass spectra for ion flight times of roughly ～12 μs through a magnetic-sector secondary ion mass spectrometer. Here we present these experimental results and combine them with a detailed theoretical investigation using high level ab initio calculations of the ground states of BrO(2+) and NBr(2+), and a manifold of excited electronic states. NBr(2+) and BrO(2+), in their ground states, are long-lived metastable gas-phase molecules with well depths of 2.73 × 10(4) cm(-1) (3.38 eV) and 1.62 × 10(4) cm(-1) (2.01 eV); their fragmentation channels into two monocations lie 2.31 × 10(3) cm(-1) (0.29 eV) and 2.14 × 10(4) cm(-1) (2.65 eV) below the ground state minimum. The calculated lifetimes for NBr(2+) (v(") < 35) and BrO(2+) (v(") < 18) are large enough to be considered stable against tunneling. For NBr(2+), we predicted R(e) = 3.051 a(0) and ω(e) = 984 cm(-1); for BrO(2+), we obtained 3.033 a(0) and 916 cm(-1), respectively. The adiabatic double ionization energies of BrO and NBr to form metastable BrO(2+) and NBr(2+) are calculated to be 30.73 and 29.08 eV, respectively. The effect of spin-orbit interactions on the low-lying (Λ + S) states is also discussed.     

Ca2+、La3+及Eu3+对NaDC胶团的作用

在水溶液中将脱氧胆酸钠（ＮａＤＣ）分别与ＣａＣＬ２、ＥｕＣｌ３及ＬａＣｌ３反应,改变反应物浓度和配比,合成了系列脱氧胆酸络全物。利用红外光谱（ＦＴＩＲ）、元素分析、ＩＣＰ分析及Ｘ身材线粉末衍射谱,对它们的组成和结构进行了研究。结果表明：水溶液中ＣａＣｌ２与ＮａＤＣ的反应不是简单离子间的反应,改变其反应物浓度和配比,生成组成和结构不同的络合物;而ＬｎＣｌ３与ＮａＤＣ反应时,反应物浓度和配比的改变不影     

Theoretical and experimental studies of cationized uracil complexes in the gas phase

Cationized uracil clusters were generated in the gas phase by electrospray ionization (ESI). Mass spectrometry experiments showed that with particular experimental conditions, decameric uracil clusters are magic number clusters. MS/MS experiments demonstrated that the structure of these decameric uracil clusters depends substantially on the size and the charge of the cation. On the basis of the ab initio and density functional theory (DFT) quantum chemistry calculations, structures for these decameric clusters were proposed. These structures are in agreement with the experimental mass spectra of modified nucleobases. Theoretical calculations showed that complexes experimentally observed using ESI-MS techniques, are not naturally the most stable in the gas phase.     

The acidity of uracil and uracil analogs in the gas phase: four surprisingly acidic sites and biological implications

The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have deltaH(acid) values of 331-333 kcal mol(-1); the acidity of the N3 sites fall between 347-352 kcal mol(-1). The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol(-1), and 369 kcal mol(-1) in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol(-1). Calculations conducted at B3LYP/6-31+G* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed.     

Mechanistic aspects of the reaction of Th+ and Th2+ with water in the gas phase

Density functional theory calculations were performed to study the gas-phase reaction of Th(+) and Th(2+) with water. An in-depth analysis of the reaction pathways leading to different reaction products is presented. The obtained results are compared to experimental data and to the previously studied reactions of U cations with water.     

Interaction of neutral and zwitterionic glycine with Zn2+ in gas phase: ab initio and SIBFA molecular mechanics calculations

The interaction of Zn²⁺ with glycine (Gly) in the gas phase is studied by a combination of ab initio and molecular mechanics techniques. The structures and energetics of the various isomers of the Gly–Zn²⁺ complex are first established via high‐level ab initio calculations. Two low‐energy isomers are characterized: one in which the metal ion interacts with the carboxylate end of zwitterionic glycine, and another in which it chelates the amino nitrogen and the carbonyl oygen of neutral glycine. These calculations lead to the first accurate value of the gas‐phase affinity of glycine for Zn²⁺. Ab initio calculations were also used to evaluate the performance of various implementations of the SIBFA force field. To assess the extent of transferability of the distributed multipoles and polarizabilities used in the SIBFA computations, two approaches are followed. In the first, approach (a), these quantities are extracted from the ab initio Hartree–Fock wave functions of glycine or its zwitterion in its entirety, and for each individual Zn²⁺‐binding conformation. In the second, approach (b), they are assembled from the appropriate constitutive fragments, namely methylamine and formic acid for neutral glycine, and protonated methylamine and formate for the zwitterion; they undergo the appropriate vector or matrix rotation to be assembled in the conformation studied. The values of the Zn²⁺–glycine interaction energies are compared to those resulting from ab initio SCF and MP2 computations using both the all‐electron 6‐311+G(2d,2p) basis set and an effective core potential together with the valence CEP 4‐31G(2d) basis set. Approach (a) values closely reproduce the ab initio ones, both in terms of the total interaction energies and of the individual components. Approach (b) can provide a similar match to ab initio interaction energies as does approach (a), provided that the two constitutive Gly building blocks are considered as separate entities having mutual interactions that are computed simultaneously with those occurring with Zn²⁺. Thus, the supermolecule is treated as a three‐body rather than a two‐body system. These results indicate that the current implementation of the SIBFA force field should be adequate to undertake accurate studies on zinc metallopeptides. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 963–973, 2000     

Interaction of trichlorogermane with acetylene and its derivatives

Conclusions In the presence of ether, trichlorogermane reacts with acetylene, forming Cl₃GeCH = CHGeCl₃, while without ether, Cl₃GeCH₂GeCl₃ is exclusively formed.Let us express our gratitude to L. A. Leites, V. A. Petukhov, A. N. Egorochkin, and G. N. Kartsev for taking the IR. Raman, UV, and NMR spectra and the dipole moments.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8 pp. 1515–1518, August, 1964     

On the stability and lifetime of GaO2+ in the gas phase

The electronic structure, stability, and lifetime of GaO²⁺ have been investigated using high-level ab initio calculations. The potential energy curves have been calculated at the CCSD(T)/aug-cc-pV5Z and at the MS-CASPT2/ANO-RCC levels of theory. Lifetimes were evaluated using the Exterior Complex Scaling (ECS) method and B-spline basis functions. Our calculations show that GaO²⁺ is a metastable species in the gas phase, since the diatomic dication, in its ground state, lies 97.1?kcal/mol above the Ga⁺ (¹S)?+?O⁺ (⁴S) dissociation limit. However, the energy barrier that has to be overcome to reach this limit is 3?kcal/mol high so that five vibrational resonances can be accommodated between the bottom of the well and the top of the barrier. The evaluated lifetimes vary from hundreds of femtoseconds to approximately 1?s, so at least two of them have long enough lifetimes (1?s and 91???s) to be detected using mass spectrometry techniques, in agreement with the experimental evidence. In the experiment (Fiser et al. in Eur J Mass Spectrom 15:315?C324, 2009), GaO²⁺ was observed for an ion flight time of about ~12???s through a magnetic-sector mass spectrometer and unambiguously identified by its isotopic abundance. Our results also show that isotopic effects on the resonances?? energies and on their lifetimes, when ⁷⁰Ga is replaced by ⁶⁹Ga or ⁷¹Ga, are very small (~0.1 and ~1%, respectively), reflecting the large mass of the system.     

Theoretical study on the reactions of Nb and Nb+ with CO2 in gas phase

Density functional theory calculations have been performed to explore the potential energy surfaces of C? O bond activation in CO₂ molecule by gas‐phase Nb atom and Nb⁺ cation for better understanding the reaction mechanism of second‐row metal with CO₂. The minimum‐energy reaction path is found to involve the spin inversion in the different reaction steps. This potential energy curve‐crossing dramatically affects the reaction energetic. The present results show that the mechanism is insertion‐elimination mechanism along the C? O bond activation reaction. All theoretical results not only support the existing conclusions inferred from early experiment but also complement the pathway and mechanism for this reaction. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011