Isomeric structures of protonated carbon dioxide

Equilibrium structures of protonated carbon dioxide are explored by ab initio molecular orbital theory. The hydroxycarbonyl cation (I) is found to be most stable; the associated proton affinity is calculated to be 130 kcal/mol, in reasonable agreement with experimental data. The dioxiryl cation (IV), about 90 kcal/mol less stable than I, is found to be a second minimum on the potential energy surface. The reaction path connecting isomers I and IV appears to involve barriers of significant magnitude; consequently, it is possible that both HCO⁺₂ and CO₂H⁺ may be detectible experimentally or serve as reaction intermediates.     

A theoretical study of protonated N2O

Ab initio MO calculations predict the preferred site of protonation of N₂O to be at the oxygen atom, and yield a structure of N₂OH⁺ and protonation energies in excellent accord with experiment.     

A theoretical study of dihydrogen bonds in small protonated rings: Aziridine and azetidine cations

B3LYP/6-311++G(d,p) calculations were used to predict some molecular properties of the C₂H₆N⁺?BeH₂, C₂H₆N⁺?MgH₂, C₃H₈N⁺?BeH₂ and C₃H₈N⁺?MgH₂ dihydrogen-bonded complexes. In these systems, it was demonstrated that the C₂H₆N⁺ and C₃H₈N⁺ protonated rings are potential candidates to bind with protonic hydrogens derived from alkaline earth metal compounds, BeH₂ and MgH₂. In terms of structural parameters and quantification of the dihydrogen bond energies, we should mention that the C₂H₆N⁺ three-membered ring provides the formation of stronger bound systems, which are 4.0 kJ mol^?1 more stables than C₃H₈N⁺ four-membered ones. As complement, the analysis of the infrared spectrum indicated that red-shifts and blue-shifts are occurring in the N–H bonds of both C₂H₆N⁺ and C₃H₈N⁺ cationic rings. However, these two vibrational shifts were also verified on BeH₂ and MgH₂, what lead us to affirm that cationic compounds derived from small nitrogen rings and earth alkaline molecules are able to form unusual dihydrogen-bonded complexes by means of distinct spectroscopic phenomena, the red-shits and blue-shifts.     

Preliminary theoretical study of perfluorodimethyl ether and its protonated form

3-21G RHF calculations on (CF₃)₂O and (CF₃)₂OH⁺ molecules are carried out to assess the changes induced in the molecular properties of ether links in poly (perfluoro ethers) interacting with acid sites at contact surfaces. Geometry of the species, vibrational frequencies, proton affinity, and energetics of the (CF₃)₂OH⁺ fragmentation provide a preliminary basis to understand problems raised by lubricant degradation. © 1993 John Wiley & Sons, Inc.     

Isomeric effects on the self‐assembly of a plausible prebiotic nucleoside analogue: A theoretical study

The self‐assembly properties of N(9)‐(2,3‐dihydroxypropyl adenine) (DHPA), a plausible prebiotic nucleoside analogue of adenosine, were investigated using density functional theory. Two different isomers were considered, and it is found that while both isomers can form a variety of structures, including chains, one of them is also able to form cages and helixes. When these results were put in the context of substrate supported molecular self‐assembly, it is concluded that gas‐phase self‐assembly studies that consider isomer identity and composition not only can aid interpreting the experimental results, but also reveal structures that might be overlooked otherwise. In particular, this study suggest that a double‐helical structure made of DHPA molecules which could have implications in prebiotic chemistry and nanotechnology, is stable even at room temperature. For example electrical properties (energy gap of 4.52eV) and a giant permanent electrical dipole moment (49.22 Debye) were found in our larger double‐helical structure (3.7 nm) formed by 14 DHPA molecules. The former properties could be convenient for construction of organic dielectric‐based devices.     

Molecular structures and infrared spectra of SiZrH4: A theoretical study

Molecular structures of the SiZrH₄ complex were investigated at BPW91, BPW91/IEF-PCM, B3LYP, and MP2 levels of theory with substantial basis sets. Relative stability of the stable conformers is fairly dependent on the methods, solvent effects, and zero-point energy corrections. All the four levels of calculations indicated that the singlet HSi(μ-H)ZrH₂, trans-Si(μ-H)₂ZrH₂, cis-Si(μ-H)₂ZrH₂, and the triplet Si(μ-H)₃ZrH are stable and comparable in energy. The energy of these four isomers is well below that of the Zr(³F₂) + SiH₄ system. The trans-dibridged, rather than the tribridged, isomer was always predicted to be the most stable one by all the four levels of calculations. For the two dibridged isomers, the two SiH₂ stretching modes are highly coupled with the two ZrH₂ stretching modes. And such coupling cannot be removed by the full deuteration.     

A theoretical and spectroscopic study of conformational structures of piroxicam

Piroxicam (PRX) has been widely studied in an attempt to elucidate the causes and mechanisms of its side effects, mainly the photo-toxicity. In this paper fluorescence spectra in non-protic solvents and different polarities were carried out along with theoretical calculations. Preliminary potential surfaces of the keto and enol forms were obtained at AM1 level of theory providing the most stable conformers, which had their structure re-optimized through the B3LYP/CEP-31G(d,p) method. From the optimized structures, the electronic spectra were calculated using the TD-DFT method in vacuum and including the solvent effect through the PCM method and a single water molecule near PRX. A new potential surface was constructed to the enol tautomer at DFT level and the most stable conformers were submitted to the QST2 calculations. The experimental data showed that in apolar media, the solution fluorescence is raised. Based on conformational analysis for the two tautomers, keto and enol, the results indicated that the PRX-enol is the main tautomer related to the drug fluorescence, which is reinforced by the spectra results, as well as the interconvertion barrier obtained from the QST2 calculations. The results suggest that the PRX one of the enol conformers presents great possibility of involvement in the photo-toxicity mechanisms.     

Excited-state properties and environmental effects for protonated schiff bases: a theoretical study.

Complete active space self-consistent field (CASSCF), multireference configuration interaction (MRCI), density functional theory (DFT), time dependent DFT (TDDFT) and the singles and doubles coupled-cluster (CC2) methodologies have been used to study the ground state and excited states of protonated and neutral Schiff bases (PSB and SB) as models for the retinal chromophore. Systems with two to four conjugated double bonds are investigated. Geometry relaxation effects are studied in the excited pipi* state using the aforementioned methods. Taking the MRCI results as reference we find that CASSCF results are quite reliable even though overshooting of geometry changes is observed. TDDFT does not reproduce bond alternation well in the pipi* state. CC2 takes an intermediate position. Environmental effects due to solvent or protein surroundings have been studied in the excited states of the PSBs and SBs using a water molecule and solvated formate as model cases. Particular emphasis is given to the proton transfer process from the PSB to its solvent partner in the excited state. It is found that its feasibility is significantly enhanced in the excited state as compared to the ground state, which means that a proton transfer could be initiated already at an early step in the photodynamics of PSBs.     

Gas-phase chemistry of ionized and protonated GeF4: a joint experimental and theoretical study

The gas-phase ion chemistry of GeF(4) and of its mixtures with water, ammonia and hydrocarbons was investigated by ion trap mass spectrometry (ITMS) and ab initio calculations. Under ITMS conditions, the only fragment detected from ionized GeF(4) is GeF(3)(+). This cation is a strong Lewis acid, able to react with H(2)O, NH(3) and the unsaturated C(2)H(2), C(2)H(4) and C(6)H(6) by addition-HF elimination reactions to form F(2)Ge(XH)(+), FGe(XH)(2)(+), Ge(XH)(3)(+) (X = OH or NH(2)), F(2)GeC(2)H(+), F(2)GeC(2)H(3)(+) and F(2)GeC(6)H(5)(+). The structure, stability and thermochemistry of these products and the mechanistic aspects of the exemplary reactions of GeF(3)(+) with H(2)O, NH(3) and C(6)H(6) were investigated by MP2 and coupled cluster calculations. The experimental proton affinity (PA) and gas basicity (GB) of GeF(4) were estimated as 121.5 ± 6.0 and 117.1 ± 6.0 kcal mol(-1), respectively, and GeF(4)H(+) was theoretically characterized as an ion-dipole complex between GeF(3)(+) and HF. Consistently, it reacts with simple inorganic and organic molecules to form GeF(3)(+)-L complexes (L = H(2)O, NH(3), C(2)H(2), C(2)H(4), C(6)H(6), CO(2), SO(2) and GeF(4)). The theoretical investigation of the stability of these ions with respect to GeF(3)(+) and L disclosed nearly linear correlations between their dissociation enthalpies and free energies and the PA and GB of L. Comparing the behavior of GeF(3)(+) with the previously investigated CF(3)(+) and SiF(3)(+) revealed a periodically reversed order of reactivity CF(3)(+) < GeF(3)(+) < SiF(3)(+). This parallels the order of the Lewis acidities of the three cations.     

Ring opening reaction of protonated polyfluorinated benzenes in the gas phase. A theoretical MNDO study

The MNDO calculations of protonated polyfluorobenzenes [Ph-F_n]H⁺ indicate the possibility of a relatively free migration of the hydrogen proton with energy barriers of 125–145 kJ mol^?1. At a higher degree of substitution (n) the protonation of the ipso carbon atom occupied by fluorine becomes energetically feasible, along with analogous migrations of fluorine, which, however, are energetically the most advantageous (ΔE_a ～ 230 kJ mol^?1). In addition to bridged fluoronium ions, relatively stable cyclic intermediates were also found, which make possible a rearrangement to the difluoromethylenecyclopentadienyl cation and thus the elimination of CF₂ observed in collision-induced dissociation mass spectra.     

The gas-phase hydrogen-bonded complex between ozone and hydroperoxyl radical. A theoretical study

We report a theoretical study on the gas-phase hydrogen-bonded complexes formed between ozone and hydroperoxyl radical, which are of interest in atmospheric chemistry. We have employed CASSCF, CASPT2, QCISD, and CCSD(T) theoretical approaches employing 6-311+G(2df,2p) and aug-cc-pVTZ basis sets, and we have found three complexes whose stabilities are computed to be 2.02, 1.19, and 1.34 kcal/mol, respectively, at 0 K. In addition, we have also found three transition states connecting these complexes that lie below the energy of the separate reactants. To help for possible experimental identification of these hydrogen-bonded complexes, we report also the computed harmonic vibrational frequencies along with the frequency shifts of the complexes, relative to the monomers, and the computed rotational constants.     

Density functional potential energy hypersurface of protonated ozone: A comparison between different gradient-corrected nonlocal functionals

The more stable isomers obtained by protonation of both cyclic and open-chain forms of ozone (O₃) were studied by the linear combination of Gaussian-type orbitals-density functional (LCGTO-DF) method. Features of the first-order saddle points connecting them were also investigated. Nonlocal corrections to the exchange-correlation energy were added using different kinds of functionals. The calculated proton affinity (PA) values at 298 K compare favorably with the recent experimental determination. © 1997 John Wiley & Sons, Inc.     

A theoretical study on the electronic structures of TiO2: Effect of Hartree-Fock exchange

The effects of the Fock exchange on the geometries and electronic structures of TiO2 have been investigated by introducing a portion of Hartree-Fock (HF) exchange into the traditional density functional. Our results indicate that the functional with 13% HF exchange can correctly predict the band gap and the electronic structures of rutile TiO2, and such an approach is also suitable to describe the structural and electronic properties of anatase and brookite phases. For the TiO2 (110) surfaces, although the surface relaxations are insensitive to the variation of HF exchange, there are larger effects on the positions of the occupied surface-induced states. When 13% HF exchange is employed, the predicted band gap of the perfect surface and position of defect state of the reduced surface are consistent with the experimental values. Moreover, the electronic structures of TiO2 (110) surface are carefully reexamined by using this hybrid density functional method.     

Molecular structures of alumina nanoballs and nanotubes: a theoretical study

Molecular structures of alumina nanoballs and nanotubes have been determined. Tetrahedral, octahedral, and icosahedral alumina nanostructures were derived from Platonic solids and Archimedean polyhedra and were optimized by quantum chemical methods. I(h)-symmetric balls, resembling their isovalence electronic analogues, fullerenes, are preferred. The nanoballs consist of adjacent Al(5)O(5) and Al(6)O(6) rings, similar to C(5)- and C(6)-rings of fullerenes. The structural characteristics of alumina nanoballs are dominated by pi-electron donation from oxygen to aluminum. Alumina nanotubes can be derived from icosahedral nanoballs. The tubes alternate between D(5d)- and D(5h)-symmetries and are capped by halves of the icosahedral balls.     

The fragmentation pathways of protonated glycine: A computational study

Numerous studies have demonstrated that protonated aliphatic amino acids, [H2NCHRCO2H + H]+, fragment in the gas phase to form iminium ions, H2N=CHR+. Unfortunately none of these studies have probed the structure of the neutral(s) lost as well as the mechanism of fragmentation. Three main mechanisms have been previously proposed: (1) loss of the combined elements of H2O and CO; (2) loss of dihydroxycarbene (HO)2C: and (3) loss of formic acid, HC(=O)OH. Herein, ab initio and density functional theory calculations have been used to calculate the key reactants, transition states, and products of these and several other competing reaction channels in the fragmentation of protonated glycine. The loss of the combined elements of H2O and CO is thermodynamically and kinetically favored over the alternative formic acid or (HO)2C fragmentation processes.     

A theoretical study of electronic structures and intermolecular magnetic interactions for spiro-biphenalenyls

In order to inquire into the mechanism of the change in the magnetism of spiro-biphenalnyls, intermolecular magnetic interaction has been investigated in terms of the effective exchange integral of the Heisenberg model for dimeric pairs of diethyl-substituted spiro-biphenalenyl. Variation of the magnetic interaction with respect to temperature has been evaluated for X-ray crystallographic structures at several temperature points by Kohn–Sham hybrid-DFT. The intermolecular magnetic interactions have been calculated for the π-dimers to be antiferromagnetic at each temperature, which has decreased by approximately 30% in the magnitude from 100 to 173 K. In addition, the interactions have been almost none at 100 and 173 K except for one pair and the remaining pair had ferromagnetic interaction. Therefore, it has been found that the change in their magnetism is understood by the formation of a ferromagnetic dimer-pair at 173 K. Moreover, the natural orbital analysis for the electronic structure of diethyl-substituted spiro-biphenelenyl has shown our solutions are essentially identified to Haddon’s proposal in terms of the valence bond picture.     

Si2CN分子结构的理论研究

在B3LYP／6－311G（d）水平上对Si2CN的各种可能异构体进行了研究，得到了其几何构型，结果表明：Si2CN有11个稳定的异构体，能量最低的是直线型异构体SiCNSi1,其次是四元环构型具有SiC桥键，电子态为^2A″的cSiSiCN6，第三稳定的是具有CSiSi三元环和环外NC键的N－cCSiSi10^2A1，第四稳定的是四元环具有SiN桥键^2A″电子态异构体cSiSiCN7。     

Si_2P_2分子结构和光谱的理论研究

用密度泛函方法 [B3LYP/6- 31 1G(d) ]研究了Si2 P2 分子的各种可能异构体的结构、能量和红外光谱 .结果表明 :Si2 P2 分子有 5个稳定的异构体 ,能量最低的异构体为具有P—P桥键的蝴蝶形结构 ,其次为具有Si—Si桥键的菱形结构 ,而具有Si—Si中心键的直线结构能量最高 .并进一步将Si2 P2 和C2 N2分子在结构和能量上的差异进行了比较和分析 .     

Border reactivity of polycyclic aromatic hydrocarbons and soot platelets toward ozone. A theoretical study

PAH-based models, with an even or odd number of unsaturated carbon atoms and π electrons (even and odd PAHs for short), are selected to investigate, by molecular and periodic methods, their electron distribution and border reactivity toward ozone, and also to represent local features and edge reactivity of even or odd soot platelets. These results will contrast those previously collected for the internal positions of similar even (J. Phys. Chem. A 2005, 109, 10929.) or odd systems (J. Phys. Chem. A 2008, 112, 973.). Topologically different peripheral positions, representative of armchair and zigzag borders, exhibit different reactivity right from the beginning. Ozone attacks start off either to give primary ozonides by concerted addition or, nonconcertedly, to first produce trioxyl intermediates. Then, a variety of pathways are described, whose viability depends on both model and position. They can open the way to the possible formation of epoxide, aldehyde, and phenol groups (all entailing O(2) production) or ether (+CO(2)), lactone (+H(2)CO), and ketone functionalities. To sum up, functionalization, regardless of how achieved, can give a number of groups, most of which actually observed in PAH ozonization experimental studies. This picture can be matched up to the results on internal sites of our preceding papers, for which epoxidation was the only outcome. Most interestingly, formation of a ketone group may turn an even system into an odd one (and conversely) while involving production of HOO(?).