Density functional study of guanine and uracil quartets and of guanine quartet/metal ion complexes

The structures and interaction energies of guanine and uracil quartets have been determined by B3LYP hybrid density‐functional calculations. The total interaction energy ΔE^T of the C_4h‐symmetric guanine quartet consisting of Hoogsteen‐type base pairs with two hydrogen bonds between two neighbor bases is −66.07 kcal/mol at the highest level. The uracil quartet with C6 H6O4 interactions between the individual bases has only a small interaction energy of −20.92 kcal mol⁻¹, and the interaction energy of −24.63 kcal/mol for the alternative structure with N3 H3O4 hydrogen bonds is only slightly more negative. Cooperative effects contribute between 10 and 25% to all interaction energies. Complexes of metal ions with G‐quartets can be classified into different structure types. The one with Ca²⁺ in the central cavity adopts a C_4h‐symmetric structure with coplanar bases, whereas the energies of the planar and nonplanar Na⁺ complexes are almost identical. The small ions Li⁺, Be²⁺, Cu⁺, and Zn²⁺ prefer a nonplanar S₄‐symmetric structure. The lack of coplanarity prevents probably a stacking of these base quartets. The central cavity is too small for K⁺ ions and, therefore, this ion favors in contrast to all other investigated ions a C₄‐symmetric complex, which is 4.73 kcal/mol more stable than the C_4h‐symmetric one. The distance 1.665 Å between K⁺ and the root‐mean‐square plane of the guanine bases is approximately half of the distance between two stacked G‐quartets. The total interaction energy of alkaline earth ion complexes exceeds those with alkali ions. Within both groups of ions the interaction energy decreases with an increasing row position in the periodic table. The B3LYP and BLYP methods lead to similar structures and energies. Both methods are suitable for hydrogen‐bonded biological systems. Compared with the before‐mentioned methods, the HCTH functional leads to longer hydrogen bonds and different relative energies for two U‐quartets. Finally, we calculated also structures and relative energies with the MMFF94 forcefield. Contrary to all DFT methods, MMFF94 predicts bifurcated C HO contacts in the uracil quartet. In the G‐quartet, the MMFF94 hydrogen bond distances N2 H22N7 are shorter than the DFT distances, whereas the N1 H1O6 distances are longer. © 2000 John Wiley & Sons, Inc. J Comput Chem 22: 109–124, 2001     

Ab Initio energetics of Si?O bond cleavage

A multilevel approach that combines high‐level ab initio quantum chemical methods applied to a molecular model of a single, strain‐free Si O Si bridge has been used to derive accurate energetics for Si O bond cleavage. The calculated Si O bond dissociation energy and the activation energy for water‐assisted Si O bond cleavage of 624 and 163 kJ mol⁻¹, respectively, are in excellent agreement with values derived recently from experimental data. In addition, the activation energy for H₂O‐assisted Si O bond cleavage is found virtually independent of the amount of water molecules in the vicinity of the reaction site. The estimated reaction energy for this process including zero‐point vibrational contribution is in the range of −5 to 19 kJ mol⁻¹. © 2017 Wiley Periodicals, Inc.     

On the ion‐pair dissociation mechanisms in the small NaCl·(H2O)6 cluster: A perspective from reaction path search calculations

We performed reaction path search calculations for the NaCl·(H₂O)₆ cluster using the global reaction route mapping (GRRM) code to understand the atomic‐level mechanisms of the NaCl → Na⁺ + Cl⁻ ionic dissociation induced by water solvents. Low‐lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the Na Cl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7–3.7 Å and that the Na Cl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc.     

Gas-phase reactions of doubly charged alkaline earth and transition metal complexes of acetonitrile, pyridine, and methanol generated by electrospray ionization

Formation and low energy collision-induced dissociation (CID) of doubly charged metal(II) complexes ([metal(II)+L _n ]²⁺, metal(II)=Co(II), Mn(II), Ca(II), Sr(II) and L = acetonitrile, pyridine, and methanol) were investigated. Complexes of [metal(II)+L _n ]²⁺ where n≤7 were obtained using electrospray ionization. Experimental parameters controlling the dissociation pathways for [Co(II)+(CH₃CN)₂]²⁺ were studied and a strong dependence of these processes on the collision energy was found. However, the dissociation pathways appear to be independent of the cone potential, indicating low internal energy of the precursor ions. In order to probe how these processes are related to intrinsic parameters of the ligand such as ionization potential and metal ion coordination, low energy CID spectra of [metal(II)+L _n ]²⁺ for ligands such as acetonitrile, pyridine, and methanol were compared. For L = pyridine, all metals including the alkaline earth metals Ca and Sr were reduced to the bare [metal(I)]⁺ species. Hydride transfer was detected upon low energy CID of [metal(II)+L _n ]²⁺ for metal(II)=Co(II) and Mn(II) and L = methanol, and corroborated by signals for [metal(II)+H^?]⁺ and [metal(II)+H^?+CH₃OH]⁺, as well as by the complementary ion [CH₃O]⁺.     

Dispersion corrected double high-hybrid and gradient-corrected density functional theory study of light cation–dihydrogen (M+–H2, where M = Li, Na, B and Al) van der Waals complexes

Structure, frequencies, H–H stretching frequency shifts, interaction energy, depth of the potential well and dissociation energy of the light cation–dihydrogen (M⁺–H₂, where M = Li, Na, B, and Al) van der Waals complexes have been studied in detail using dispersion corrected double-hybrid and gradient-corrected density functional methods in conjunction with correlation consistent valence triple-ζ basis set. Equilibrium bond distance and dissociation energy agree very well with the experimental and theoretical values wherever available. The dissociation energies of Li⁺–H₂, B⁺–H₂, Na⁺–H₂, and Al⁺–H₂ van der Waals complexes calculated from the potential energy curves at mPW2PLYP-D/cc-pVTZ level are 4.83, 3.68, 2.42, and 1.25 kcal/mol, respectively, at a distances of 1.95, 2.25, 2.40, and 2.95 Å. Among all these complexes, Al⁺–H₂ complex is comparatively less stable, as their dissociation energy as well as depth of the potential well are smaller compared to others complexes. The symmetry-adapted perturbation theory (SAPT) has been applied to quantify the nature of interactions. The SAPT results show that the contribution of dispersion and induction are significant, although electrostatic dominates.     

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe₂L₃⁴⁺ ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu^I or Ag^I. The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS³ of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu^I and Ag^I complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe₂^IL₂²⁺ and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.     

Theoretical predictions of the nitrogen heterocyclic compounds with metal and noble gas (metal = Cu,Ag, Au)

Here, we report a new type of Ng-containing compounds formed between the Ng-M group and nitrogen heterocyclic compounds, (CH₂)_nHNCuNg⁺ (n = 2, 3), (CH)₄NMNg, and (CH)₅NCuNg⁺ (M = Cu, Ag, Au; Ng = Ar, Kr, Xe). Quantum chemistry computations were carried out to optimize their geometric structures and calculate the dissociation energies, dissociation enthalpy, and dissociation free energy change. The stability of these Ng-bonding complexes was inspected by investigating the three dissociation processes of the these compounds into (a) Ng, M, and nitrogen heterocycle C_nN; (b) C_nN + MNg⁺; and (c) C_nNM + Ng, which are all endothermic and nonspontaneous, these dissociation processes are also turned out to be endergonic in nature at standard state. The natural bond orbital, atoms in molecules, and energy decomposition analysis based on the molecular wavefunction show that the M-Ng and M-N bonds have some covalent and electrostatic characters.     

Identification of decomposition reactions for HMDSO organosilicon using quantum chemical calculations

Hexamethyldisiloxane [HMDSO, (CH₃)₃-SiOSi-(CH₃)₃] is an important precursor for SiO₂ formation during flame-based silica material synthesis. As a result, HMDSO reactions in flame have been widely investigated experimentally, and many results have indicated that HMDSO decomposition reactions occur very early in this process. In this paper, quantum chemical calculations are performed to identify the initial decomposition of HMDSO and its subsequent reactions using the density functional theory at the level of B3LYP/6-311+G (d, p). Four reaction pathways—(a) Si O bond dissociation of HMDSO, (b) Si C bond dissociation of HMDSO, (c) dissociation and recombination of Si O and Si C bonds, and (d) elimination of a methane molecule from HMDSO—have been examined and identified. From the results, it is found that the barrier of 84.38 kcal/mol and Si O bond dissociation energy of 21.55 kcal/mol are required for the initial decomposition reaction of HMDSO in the first pathway, but the highest free energy barrier (100.69 kcal/mol) is found in the third reaction pathway. By comparing the free energy barriers and reaction rate constants, it is concluded that the most possible initial decomposition reaction of HMDSO is to eliminate the CH₃ radical by Si C bond dissociation.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Theoretical prediction of the contact distance dependence of the electron transfer reactivity of the ClO/ClO− coupling system

On the basis of the structures and properties of the ClO/ClO^? system obtained at the density functional theory (DFT) (UB3LYP) level, employing the 6‐311+G(3df) standard basis set, the electron transfer reactivity of this system is investigated. The results indicate that there are five possible stable coupling complexes that correspond to the generous minima on the global potential energy surfaces (PES). The most stable coupling complex is planar EC4, in which there is a O? O linkage with two trans‐Cl atoms. Their stabilization energies are calculated to be 20.57 (EC1: C₁), 20.54 (EC2: C₂, ²B), 20.69 (EC3: C₁), 20.70 (EC4: C_s, ²A′), and 20.69 (EC.5: C_2h, ²B_u) kcal/mol at the B3LYP/6‐311+G(3df) level; with the correction of the basis set superposition error (BSSE), the stability order of these encounter complexes is EC4 > EC.5 > EC3 > EC1 > EC2. Based on the five encounter complexes, five coupling modes are designed for the study of the electron transfer reactivity of this system. The dissociation energy curves at the activated states and the corresponding activation energies of these five coupling modes are obtained and are compared at the B3LYP/6‐311+G(3df) and MP2/6‐311+G* levels. The inapplicability of DFT methods has also been discussed in this article in predicting the energy curves, especially with a long contact distance, in which DFT methods give the abnormal behavior for the dissociations of the complexes caused by the “inverse symmetry breaking” problem. On the basis of the golden rule of the time‐dependent perturbation theory, the electron transfer reactivity and the contact distance dependence of the various electron transfer kinetics parameters (e.g., activation energy, coupling matrix element) have been analyzed at the UMP2(full)/6‐311+G* level. The electron transfer can take place over a range of contact distances, but the most effective coupling distance corresponds to only a small range. The coupling orientation analyses also indicate that the most favorable coupling mode to the electron transfer does not always correspond to the most stable encounter complex mechanism. Some highly energetic coupling modes are more favorable for the electron transfer. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio MO calculations on the stable conformations and their binding energies of the ion-molecule complexes: Ion = H+, Li+, Na+, K+ Be2+, and molecule = CO and N2

The most stable conformation of ion-molecule complexes involving a CO molecule were surveyed by the use of Hartree-Fock (HF) MO and third-order Moller-Plesset perturbation (MP3) methods with a 6–31G* basis set ion = H⁺, Li⁺, Na⁺, K⁺, Bc²⁺, Mg²⁺, and Ca²⁺. The MP3 level of theory reveals the ion-CO conformation in which the ion bonds to a carbon atom of CO to be the most stable; these MP3 results are contrary to the HF ones. Binding energies of ion-molecule complexes involving CO and N₂ were computed; MP3 energies are in good agreement with the experimental ones. The computed binding energies of cation-N₂ are about one-third of cation-NH₃ due to the absence of dipole moment and the smaller polarizability of N₂. The decrease in binding energy in cation-CO and -N₂ complexes, with increasing cation size, is mainly caused by the decrease of the electrostatic and polarization stabilizations.     

New insight into the substituent effects on the hydrolytic deamination of saturated and unsaturated cytosine

Ab initio calculations were carried out to understand the effect of electron donating groups (EDG) and electron withdrawing groups (EWG) at the C5 position of cytosine (Cyt) and saturated cytosine (H₂Cyt) of the deamination reaction. Geometries of the reactants, transition states, intermediates, and products were fully optimized at the B3LYP/6-31G(d,p) level in the gas phase as this level of theory has been found to agree very well with G3 theories. Activation energies, enthalpies, and Gibbs energies of activation along with the thermodynamic properties (ΔE, ΔH, and ΔG) of each reaction were calculated. A plot of the Gibbs energies of activation (ΔG^‡) for C5 substituted Cyt and H₂Cyt against the Hammett σ-constants reveal a good linear relationship. In general, both EDG and EWG substituents at the C5 position in Cyt results in higher ΔG^‡ and lower σ values compared to those of H₂Cyt deamination reactions. C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) increase ΔG^‡ values for Cyt, while the same substituents decrease ΔG^‡ values for H₂Cyt which is likely due to steric effects. However, the Hammett σ-constants were found to decrease at the C5 position of cytosine (Cyt) and saturated cytosine (H2Cyt) on the deamination reaction. Both ΔG^‡ and σ values decrease for the substituents Cl and Br in the Cyt reaction, while ΔG^‡ values increase and σ decrease in the H₂Cyt reaction. This may be due to high polarizability of bromine which results in a greater stabilization of the transition state in the case of bromine compared to chlorine. Regardless of the substituent at C5, the positive charge on C4 is greater in the TS compared to the reactant complex for both the Cyt and H₂Cyt. Moreover, as the charges on C4 in the TS increase compared to reactant, ΔG^‡ also increase for the C5 alkyl substituents ( H,  CH₃,  CH₂CH₃,  CH₂CH₂CH₃) in Cyt, while ΔG^‡ decrease in H₂Cyt. In addition, analysis of the frontier MO energies for the transition state structures shows that there is a correlation between the energy of the HOMO–LUMO gap and activation energies.     

HNgBeF3 (Ng = Ar‐Rn): Superhalogen‐supported noble gas insertion compounds

Ab initio and density functional theory‐based calculations are performed to study the structure, stability, and nature of bonding of superhalogen‐supported noble gas (Ng) compounds of the type HNgY where (Ng = Ar‐Rn; Y = BeF₃). Here, BeF₃ acts as the superhalogen. Calculations show that the HNgBeF₃ spontaneously dissociates into product following the dissociation channels: HNgBeF₃ → HBeF₃ + Ng and HNgBeF₃ → Ng + HF + BeF₂. The transition states are optimized and the energy barriers are computed to show the metastable behavior of HNgBeF₃. HNgBeF₃ molecules are kinetically stable with respect to the first dissociation process having energy barriers of 1.0, 5.0, 10.6, and 13.9 kcal/mol for Ar, Kr, Xe, and Rn analogues, respectively, at CCSD(T)/Aug‐cc‐pVTZ level. These calculations suggest that the HXeBeF₃ and HRnBeF₃ can be shown to be stable up to ∼100 K temperature with a half‐life of ∼10² seconds. The nature of H Ng and two different types of Ng F bonds in HNgBeF₃ molecules is explored through the natural bond orbital and electron density analyses. The large Wiberg bond index (WBI) values for the H Ng bond indicate the formation of almost a single bond in between H‐atoms and Ng‐atoms, whereas small WBI values for the two Ng F bonds indicate a noncovalent interaction in between them. The electron density analysis further supports the covalency of the H Ng bond and noncovalent interaction in the two Ng F bonds in HNgBeF₃.     

Mono- and Mixed Metal Complexes of Eu3+, Gd3+, and Tb3+ with a Diketone,Bearing Pyrazole Moiety and CHF2-Group: Structure,Color Tuning,and Kinetics of Energy Transfer between Lanthanide Ions

Three novel lanthanide complexes with the ligand 4,4-difluoro-1-(1,5-dimethyl-1H-pyrazol-4-yl)butane-1,3-dione (HL), namely [LnL₃(H₂O)₂], Ln = Eu, Gd and Tb, were synthesized, and, according to single-crystal X-ray diffraction, are isostructural. The photoluminescent properties of these compounds, as well as of three series of mixed metal complexes [Eu_xTb_1-xL₃(H₂O)₂] (Eu_xTb_1-xL₃), [EuxGd_1-xL₃(H₂O)₂] (Eu_xGd_1-xL₃), and [Gd_xTb_1-xL₃(H₂O)₂] (Gd_xTb_1-xL₃), were studied. The Eu_xTb_1-xL₃ complexes exhibit the simultaneous emission of both Eu³⁺ and Tb³⁺ ions, and the luminescence color rapidly changes from green to red upon introducing even a small fraction of Eu³⁺. A detailed analysis of the luminescence decay made it possible to determine the observed radiative lifetimes of Tb³⁺ and Eu³⁺ and estimate the rate of excitation energy transfer between these ions. For this task, a simple approximation function was proposed. The values of the energy transfer rates determined independently from the luminescence decays of terbium(III) and europium(III) ions show a good correlation.     

Collisional dissociation of CH2Br+2 in selected internal energy states

The collisionally induced dissociation of CH₂Br⁺₂ to yield CH₂Br⁺ + Br has been investigated by photoelectronphotoion coincedence spectroscopy in which nominally zero kinetic electrons were detected. The reactant CH₂Br⁺₂ ions were produced by photoionzation with intenal energies of 0.0, 0.20 and 0.60 eV. For all three internal energies, the kinetic energy threshold for dissociation is just equal to the energy defect.     

Structures,Unimolecular Fragmentations,and Reactivities of the Self‐Assembled Multimetallic/Peptide Complexes [Mnn(GlyGly‐H)2n−1]+ and [Mnn+1(GlyGly‐H)2n]2+

Complexes of Mn²⁺ with deprotonated GlyGly are investigated by sustained off‐resonance irradiation collision‐induced dissociation (SORI‐CID), infrared multiple‐photon dissociation spectroscopy, ion–molecule reactions, and computational methods. Singly [Mn_n(GlyGly‐H)_2n?1]⁺ and doubly [Mn_n+1(GlyGly‐H)_2n]²⁺ charged clusters are formed from aqueous solutions of MnCl₂ and GlyGly by electrospray ionization. The most intense ion produced was the singly charged [M₂(GlyGly‐H)₃]⁺ cluster. Singly charged clusters show extensive fragmentations of small neutral molecules such as water and carbon dioxide as well as dissociation pathways related to the loss of NH₂CHCO and GlyGly. For the doubly charged clusters, however, loss of GlyGly is observed as the main dissociation pathway. Structure elucidation of [Mn₃(GlyGly‐H)₄]²⁺ clusters has also been done by IRMPD spectroscopy as well as DFT calculations. It is shown that the lowest energy structure of the [Mn₃(GlyGly‐H)₄]²⁺ cluster is deprotonated at all carboxylic acid groups and metal ions are coordinated with carbonyl oxygen atoms, and that all amine nitrogen atoms are hydrogen bonded to the amide hydrogen. A comparison of the calculated high‐spin (sextet) and low‐spin (quartet) state structures of [Mn₃(GlyGly‐H)₄]²⁺ is provided. IRMPD spectroscopic results are in agreement with the lowest energy high‐spin structure computed. Also, the gas‐phase reactivity of these complexes towards neutral CO and water was investigated. The parent complexes did not add any water or CO, presumably due to saturation at the metal cation. However, once some of the ligand was removed via CO₂ laser IRMPD, water was seen to add to the complex. These results are consistent with high‐spin Mn²⁺ complexes.     

Electron-Capture and -Transfer Dissociation of Peptides Tagged with Tunable Fixed-Charge Groups: Structures and Dissociation Energetics

Pyridiniummethylcarbonyl moieties that were previously designed on the basis of electronic structure analysis are now utilized as fixed-charge tags with tunable electronic properties to be used for N-terminal peptide derivatization and sequencing by electron-transfer dissociation. Dipeptides AK and KA were derivatized at the peptide N-terminus with 4-dimethylaminopyridinium-N-acetyl (DMAP-ac) and pyridinium-N-acetyl (pyrid-ac) tags of increasing intrinsic recombination energies. Upon the capture of a free electron or electron transfer from fluoranthene anions, (DMAP-ac-AK+H)²⁺, (DMAP-ac-KA+H)²⁺, (pyrid-ac-AK+H)²⁺ and (pyrid-ac-KA+H)²⁺ ions, as well as underivatized (AK+2H)²⁺, completely dissociated. The fixed-charge tags steered the dissociation upon electron transfer to form abundant backbone N–C_α bond cleavages, whereas the underivatized peptide mainly underwent H-atom and side-chain losses. Precursor ion structures for the tagged peptides were analyzed by an exhaustive conformational search combined with B3LYP/6-31+G(d,p) geometry optimization and single-point energy calculations in order to select the global energy minima. Structures, relative energies, transition states, ion–molecule complexes, and dissociation products were identified for several charge-reduced species from the tagged peptides. The electronic properties of the charge tags and their interactions with the peptide moieties are discussed. Electrospray ionization and electron-transfer dissociation of larger peptides are illustrated with a DMAP-tagged pentapeptide.     

Doubly-charged ethane ions: Solution to the dilemma of stability predicted by theory and instability observed in experiment

Potential energy curves have been computed for [C₂H₆]²⁺ ions and the results used to interpret the conspicuous absence of these ions in 2E mass spectra and in charge-stripping experiments. The energies and structures of geometry-optimized ground-state singlet and excited-state triplet [C₂H₆]²⁺ ions have been determined along with energies for different decomposition barriers and dissociation asymptotes. Although singlet and triplet [C₂H₆]²⁺ ions can exist as stable entities, they possess low energy barriers to decomposition. Vertical Franck-Condon transitions, involving electron impact ionization of ethane as well as charge-stripping collisions of [C₂H₆]⁺ ions, produce [C₂H₆]²⁺ ions which promptly dissociate since they are formed with energies in excess of various decomposition barriers. Appearance energies computed for doubly-charged ethane fragment ions are in accordance with experimental values.