A general,most basic rule for ion dissociation: Protonated molecules

Contrary to the common but potentially misleading belief that when a protonated molecule is excited, it is its most stable protomer that will mandatorily dissociate, we demonstrate herein that, when rationalizing or predicting the chemistry of such ions, we should always search for the most labile protomer. This “most labile protomer” rule, based on the mobile proton model, states therefore that when a protonated molecule is heated, during ionization or by collisions for instance, the loosely bonded proton (H⁺) can acquire enough energy to detach itself from the most basic site of the molecule and then freely “walk through” the molecular framework to eventually find, if available, another protonation site, forming other less stable but more labile protomers, that is, protomers that may display lower dissociation thresholds. To demonstrate the validity of the “most labile protomer” rule as well as the misleading nature of the “most stable protomer” rule, we have selected several illustrative molecules and have collected their ESI(+)-MS/MS. To compare energies of precursors and products, we have also performed PM7 calculations and elaborated potential energy surface diagrams for their possible protomers and dissociation thresholds. We have also applied the “most labile protomer” rule to reinterpret—exclusively via classical charge-induced dissociation cleavages—several dissociation processes proposed for protonated molecules. In an accompanying letter, we have also applied a similar “most labile electromer” rule to ionized molecules.     

Ultrafast vectorial and scalar dynamics of ionic clusters: azobenzene solvated by oxygen

The ultrafast dynamics of clusters of trans-azobenzene anion (A-) solvated by oxygen molecules was investigated using femtosecond time-resolved photoelectron spectroscopy. The time scale for stripping off all oxygen molecules from A- was determined by monitoring in real time the transient of the A- rise, following an 800 nm excitation of A- (O2)n, where n = 1-4. A careful analysis of the time-dependent photoelectron spectra strongly suggests that for n > 1 a quasi-O4 core is formed and that the dissociation occurs by a bond cleavage between A- and conglomerated (O2)n rather than a stepwise evaporation of O2. With time and energy resolutions, we were able to capture the photoelectron signatures of transient species which instantaneously rise (<100 fs) then decay. The transient species are assigned as charge-transfer complexes: A.O2- for A- O2 and A.O4-(O2)n-2 for A-(O2)n, where n = 2-4. Subsequent to an ultrafast electron recombination, A- rises with two distinct time scales: a subpicosecond component reflecting a direct bond rupture of the A- -(O2)n nuclear coordinate and a slower component (1.6-36 ps, increasing with n) attributed to an indirect channel exhibiting a quasistatistical behavior. The photodetachment transients exhibit a change in the transition dipole direction as a function of time delay. Rotational dephasing occurs on a time scale of 2-3 ps, with a change in the sign of the transient anisotropy between A- O2 and the larger clusters. This behavior is a key indicator of an evolving cluster structure and is successfully modeled by calculations based on the structures and inertial motion of the parent clusters.     

Lithium diisopropylamide solvated by hexamethylphosphoramide: substrate-dependent mechanisms for dehydrobrominations

Lithium diisopropylamide-mediated dehydrobrominations of exo-2-bromonorbornane, 1-bromocyclooctene, and cis-4-bromo-tert-butylcyclohexane were studied in THF solutions and THF solutions with added hexamethylphosphoramide (HMPA). Rate studies reveal a diverse array of mechanisms based on mono-, di-, and trisolvated monomers as well as triple ions. The results are contrasted with analogous eliminations in THF in the absence of HMPA.     

Infrared spectroscopy of small sodium-doped water clusters: interaction with the solvated electron

The measured vibrational OH-stretch spectra of size-selected Na(H2O)n clusters for n=8, 10, 16, and 20 are compared with first-principle calculations, which account for the interaction of the sodium cation, the electron, and the water molecules with the hydrogen-bonded network. The calculated harmonic frequencies are corrected by comparing similar results obtained for pure water clusters with experiment. The experimental spectra are dominated by intensity peaks between 3350 and 3550 cm(-1), which result from the interaction of the H atoms with the delocalized electron cloud. The calculations, which are all based upon the average spectra of the four lowest-energy isomers, indicate that most of the peaks at the lower end of this range (3217 cm(-1) for n=8) originate from the interaction of one H atom with the electron distribution in a configuration with a single hydrogen-bonding acceptor. Those at the upper end (3563 cm(-1) for n=8) come from similar interactions with two acceptors. The doublets, which arise from the interaction of both H atoms with the electron, appear in the red-shifted part of the spectrum. They are with 3369/3443 cm(-1) quite pronounced for n=8 but slowly vanish for the larger clusters where they mix with the other spectral interactions of the hydrogen-bonded network, namely, the fingerprints of the free, the double, and the single donor OH positions known from pure water cluster spectroscopy. For all investigated sizes, the electron is sitting at the surface of the clusters.     

Structure and photoabsorption properties of cationic alkali dimers solvated in neon clusters

We present a theoretical investigation of the structure and optical absorption of M(2)(+) alkali dimers (M=Li,Na,K) solvated in Ne(n) clusters for n=1 to a few tens Ne atoms. For all these alkali, the lowest-energy isomers are obtained by aggregation of the first Ne atoms at the extremity of the alkali molecule. This particular geometry, common to other M(2)(+)-rare gas clusters, is intimately related to the shape of the electronic density of the X (2)Σ(g)(+) ground state of the bare M(2)(+) molecules. The structure of the first solvation shell presents equilateral Ne(3) and capped pentagonal Ne(6) motifs, which are characteristic of pure rare gas clusters. The size and geometry of the complete solvation shell depend on the alkali and were obtained at n=22 with a D(4h) symmetry for Li and at n=27 with a D(5h) symmetry for Na. For K, our study suggests that the closure of the first solvation shell occurs well beyond n=36. We show that the atomic arrangement of these clusters has a profound influence on their optical absorption spectrum. In particular, the XΣ transition from the X (2)Σ(g)(+) ground state to the first excited (2)Σ(u)(+) state is strongly blueshifted in the Frank-Condon area.     

2,4-Dihydroxy and O2 Protonated Tautomers of dThd and Thd Coexist in the Gas Phase: Methylation Alters Protonation Preferences versus dUrd and Urd

The gas-phase structures of protonated thymidine, [dThd + H]⁺, and its modified form, protonated 5-methyluridine, [Thd + H]⁺, are examined by infrared multiple photon dissociation (IRMPD) action spectroscopy combined with electronic structure calculations. IRMPD action spectra are measured over the ranges extending from ~600 to 1900 cm^–1 and ~2800 to 3800 cm^–1 using the FELIX free electron laser and an optical parametric oscillator/amplifier (OPO/OPA) laser system, respectively. Comparisons between the B3LYP/6-311+G(d,p) linear IR spectra calculated for the stable low-energy conformers and the measured IRMPD spectra are used to determine the most favorable tautomeric conformations of [dThd + H]⁺ and [Thd + H]⁺ and to identify those populated in the experiments. Both B3LYP and MP2 levels of theory predict a minor 2,4-dihydroxy tautomer as the ground-state conformer of [dThd + H]⁺ and [Thd + H]⁺ indicating that the 2'-hydroxyl substituent of Thd does not exert a significant impact on the structural features. [dThd + H]⁺ and [Thd + H]⁺ share parallel IRMPD spectral profiles and yields in both the FELIX and OPO regions. Comparisons between the measured IRMPD and calculated IR spectra suggest that minor 2,4-dihydroxy tautomers and O2 protonated conformers of [dThd + H]⁺ and [Thd + H]⁺ are populated in the experiments. Comparison of this work to our previous IRMPD spectroscopy study of protonated 2'-deoxyuridine and uridine suggests that the 5-methyl substituent alters the preferences of O2 versus O4 protonation.

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Aggregation-induced chemical reactions: acid dissociation in growing water clusters

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.     

Rotational dynamics of CO solvated in small He clusters: a quantum Monte Carlo study

The rotational dynamics of CO single molecules solvated in small He clusters (CO @ HeN) has been studied using reptation quantum Monte Carlo simulations for cluster sizes up to N = 30. Our results are in good agreement with the rotovibrational features of the infrared spectrum recently determined for this system and provide a deep insight into the relation between the structure of the cluster and its dynamics. Simulations for large N also provide a prediction of the effective moment of inertia of CO in the He nanodroplet regime, which has not been measured so far.     

Protonated nitro group: structure, energy and conjugation

Structure of protonated nitro compounds was investigated by calculations at the levels MP2(FC)/6-311++G(2d,2p)//MP2(FC)/6-311++G(2d,2p)(nitromethane and reference compounds) or B3LYP/6-311+G(d,p)//B3LYP/6-311+G(d,p)(nitrobenzene and its 18 meta- and para-substituted derivatives). The group NO2H+ reveals many similarities with the isoelectronic group CO2H as the preferred conformation, conformational equilibrium, and stabilization by interaction (resonance) within the group quantified by means of isodesmic reactions. However, there is a difference in the interaction with donor groups (for instance in 4-nitroaniline) that is much stronger with NO2H+ than with CO2H. This interaction may be called resonance and may be described by standard resonance formulas, but these formulas predict only partially the geometry and cannot explain the great interaction energy.     

Proton dissociation and transfer in hydrated phosphoric acid clusters

The dynamics and mechanisms of proton dissociation and transfer in hydrated phosphoric acid (H₃PO₄) clusters under excess proton conditions were studied based on the concept of presolvation using the H₃PO₄–H₃O⁺–nH₂O complexes (n = 1–3) as the model systems and ab initio calculations and Born–Oppenheimer molecular dynamics (BOMD) simulations at the RIMP2/TZVP level as model calculations. The static results showed that the smallest, most stable intermediate complex for proton dissociation (n = 1) is formed in a low local‐dielectric constant environment (e.g., ε = 1), whereas proton transfer from the first to the second hydration shell is driven by fluctuations in the number of water molecules in a high local‐dielectric constant environment (e.g., ε = 78) through the Zundel complex in a linear H‐bond chain (n = 3). The two‐dimensional potential energy surfaces (2D‐PES) of the intermediate complex (n = 1) suggested three characteristic vibrational and ¹H NMR frequencies associated with a proton moving on the oscillatory shuttling and structural diffusion paths, which can be used to monitor the dynamics of proton dissociation in the H‐bond clusters. The BOMD simulations over the temperature range of 298–430 K validated the proposed proton dissociation and transfer mechanisms by showing that good agreement between the theoretical and experimental data can be achieved with the proposed rate‐determining processes. The theoretical results suggest the roles played by the polar solvent and iterate that insights into the dynamics and mechanisms of proton transfer in the protonated H‐bond clusters can be obtained from intermediate complexes provided that an appropriate presolvation model is selected and that all of the important rate‐determining processes are included in the model calculations. © 2015 Wiley Periodicals, Inc.     

Zwitterion-dianion complexes and anion-anion clusters with negative dissociation energies

Clusters of oxalate and malonate dianions with glycine in its zwitterionic form were found by ab initio and density functional theory calculations. Proton transfer is impeded by an electrostatic barrier, but the resulting anion-anion pairs form complexes despite having negative dissociation energies. A variety of X-/Y- species with exothermic dissociation energies ranging from 10 to 141 kcal mol-1, but large enough barriers to be experimentally produced, are reported. These dianions may represent an unrecognized control element in nature and provide a unique opportunity to probe electrostatic effects and a wealth of novel clusters.     

Characterization of solvated electrons in hydrogen cyanide clusters: (HCN)n- (n=3, 4)

Theoretical studies of the solvated electrons (HCN)n- (n=3, 4) reveal a variety of electron trapping possibilities in the (HCN)n (n=3, 4) clusters. Two isomers for (HCN)3- and four isomers for (HCN)4- are obtained at the MP2aug-cc-pVDZ+dBF (diffusive bond functions) level of theory. In view of vertical electron detachment energies (VDEs) at the CCSD(T) level, the excess electron always "prefers" locating in the center of the system, i.e., the isomer with higher coordination number shows larger VDE value. However, the most stable isomers of the solvated electron state (HCN)3- and (HCN)4- are found to be the linear Cinfinitynu and Dinfinityh structures, respectively, but not the fullyl symmetric structures which have the largest VDE values.     

Ultraviolet photolysis of adenine: dissociation via the 1pi sigma* state

High resolution total kinetic energy release (TKER) spectra of the H atom fragments resulting from photodissociation of jet-cooled adenine molecules at 17 wavelengths in the range 280>lambda(phot)>214 nm are reported. TKER spectra obtained at lambda(phot)>233 nm display broad, isotropic profiles that peak at low TKER ( approximately 1800 cm(-1)) and are largely insensitive to the choice of excitation wavelength. The bulk of these products is attributed to unintended multiphoton dissociation processes. TKER spectra recorded at lambda(phot)相似文献   

核酸碱基互变异构体的结构、稳定性及其物理化学性质

核酸碱基是DNA及RNA分子的重要组成部分, 在基因遗传信息的传递方面起着主导作用. 核酸碱基存在多种互变异构体, 它们在DNA及RNA分子中主要以最稳定的异构体形式存在, 但是在气相或凝聚相中也有少量的其他异构体形式存在. 核酸碱基的稀有互变异构体往往能够引起碱基对的错配对, 这可能会导致DNA及RNA分子形成不规则的结构, 并进一步导致DNA或RNA双螺旋的自发突变. 因此, 对核酸碱基的互变异构体进行系统的研究, 有助于人们深入认识DNA和RNA分子的结构和性质. 国际上有很多研究小组已经通过实验和理论对核酸碱基互变异构体的结构、相对能量及其性质进行了研究. 本文对文献中有关核酸碱基互变异构体的实验和理论研究进行了综述. 在对前人研究进行归纳总结的基础上, 我们利用密度泛函计算对核酸碱基的互变异构体进行了排序, 得到的最优异构体结构参数和相对能量与实验值相比较为一致. 此外, 因为核酸碱基的物理化学性质可以为生物、化学、材料等方面的研究提供重要的基础性信息, 因此我们还对它们的电子亲和能、电离能、质子亲和能等研究进行了总结.     

Protonated N-confused porphyrin dimer: formation, structure, and guest binding

The protonation of 3,3'-bis(meso-tetratolyl-2-aza-21-carbaporphyrin) with various acids was studied. The stepwise formation of mono-, di-, and tetracationic species was shown on the basis of UV-vis-near-IR and low-temperature (1)H NMR. Upon going from di- to tetraprotonated form, the bis(porphyrinoid) skeleton changes its conformation from cisoid to bent-transoid, which was found by single-crystal X-ray analyses, 2D NMR, and density functional theory (DFT) calculations. The formation of cation-anion complexes was established in both the solid state and solution. The substitution of anions was studied by spectrophotometric and (1)H NMR titrations. A pronounced decrease of the HOMO-LUMO gap in the tetraprotonated species was shown by cyclovoltametry and time-dependent DFT calculations.     

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.     

Photoinduced dissociation of water and transport of hydrogen between silver clusters

Theoretical electronic structure calculations are reported for the dissociation of water adsorbed on a 31-atom silver cluster, Ag31, and subsequent transfer of a H to a second Ag31 cluster leaving OH on the first cluster. Both ground and excited electronic state processes are considered for two choices of Ag cluster separation, 6.35 and 7.94 A, on the basis of preliminary calculations for a range of separation distances. The excited electronic state of interest is formed by photoemission of an electron from one Ag cluster and transient attachment of the photoemitted electron to the adsorbed water molecule. A very large energy barrier is found for the ground-state process (3.53 eV at a cluster separation of 6.35 A), while the barrier in the excited state is small (0.38 eV at a cluster separation of 6.35 A). In the excited state, partial occupancy of an OH antibonding orbital facilitates OH stretch and concomitant movement of the negatively charged OH toward the electron-hole in the metal cluster. The excited-state pathway for dissociation of water and transfer of H begins with the formation of an excited electronic state at 3.59-3.82 eV. Stretch of the OH bond occurs with little change in energy (0.38-0.54 eV up to a stretch of 1.96 A). In this region of OH stretch the molecule must return to the ground-state potential energy surface to fully dissociate and to transfer H to the other Ag cluster. Geometry optimizations are carried out using a simplex algorithm and a semigrid method. These methods allow the total energy to be calculated directly using configuration interaction theory.     

Fragmentation dynamics of size-selected pyrrole clusters prepared by electron impact ionization: forming a solvated dimer ion core

Structure and dynamics of size-selected charged pyrrole clusters have been studied by means of molecular beam scattering experiments and ab initio calculations. Small neutral Pyn clusters were produced in Py/He mixture expansions, and the scattering experiment with a secondary beam of He-atoms was exploited to select the neutral clusters of different sizes. The complete size-selected fragmentation patterns for the neutral dimer to the tetramer after an electron impact ionization at 70 eV were obtained from the measurements of the angular and velocity distributions at different fragment masses. All the investigated cluster sizes decay mainly to the monomer ions Py+1 (from 60 to 80% of the corresponding neutral size) and to the dimer ion Py+2 (20-30%). The trimer ions Py+3 are generated to less than 10% from the neutral trimer and tetramer. To explain the observed results, we have calculated the structures and energetics of pyrrole clusters up to the trimer for the neutral and the ionic state using DFT and PMP2 methods. The ab initio calculations show that ionized pyrrole clusters are formed with a dimeric core that is solvated by neutral pyrrole molecules. In addition, the ground and ionic state of Py-Ar complexes were calculated at CCSD(T) level with extended basis in relevance to the mixed clusters produced in supersonic expansions of Py seeded in Ar. The calculated dissociation energies of the Py-Ar and (Py-Ar)+ complexes indicate that Ar atoms are able to rapidly evaporate after ionization. The combined analysis of the fragmentation probabilities, and calculations allowed us to estimate the distribution of energy deposited in the clusters after the electron impact, which peaks above 1 eV and has a tail up to 5 eV.