Extended basis CNDO calculations of linear and nonlinear electric susceptibilities of some molecular dianions and carbonions using coupled Hartree–Fock perturbation theory

The results of calculating the average polarizabilities, first and second hyperpolarizabilities and molar Kerr constants of C₅H, C₆H, 2-C₁₀H, 2-C₁₄H, C₈H and C₈H are reported. The main elements of our computational scheme are McWeeny's coupled Hartree–Fock perturbation theory and an extended basis CNDO wave function. It is shown that the studied anions have nonlinearities within the same order of magnitude as their respective uncharged parent molecules. The Kerr constants of these anions are analyzed and the contribution of the various terms is appraised.     

Gas‐phase formation of protonated benzene during collision‐induced dissociation of certain protonated mono‐substituted aromatic molecules produced in electrospray ionization

Protonated benzene, C₆H, has been studied extensively to understand the structure and energy of a protonated organic molecule in the gas phase. The formation of C₆H is either through direct protonation of benzene, i.e., chemical ionization, or through fragmentation of certain radical cations produced from electron ionization or photon ionization. We report a novel observation of C₆H as a product ion formed in the collision‐induced dissociation (CID) of protonated benzamide and related molecules produced via electrospray ionization (ESI). The formation of C₆H from these even‐electron precursor ions during the CID process, which has not been previously reported, is proposed to occur from the protonated molecules via a proton migration in a five‐membered ring intermediate followed by the cleavage of the mono‐substituent C? C bond and concurrent formation of an ion‐molecule complex. This unique mechanism has been scrutinized by examining some deuterated molecules and a series of structurally related model compounds. This finding provides a convenient mean to generate C₆H, a reactive intermediate of considerable interest, for further physical or chemical investigation. Further studies indicate that the occurrence of C₆H in liquid chromatography/electrospray ionization tandem mass spectrometry (LC/ESI‐MS/MS) appears to be a rather common phenomenon for many compounds that contain ‘benzoyl‐type’ moieties. Hence, the observation of the C₆H ion in LC/ESI‐MS/MS can be used as an informative fragmentation pathway which should facilitate the identification of a great number of compounds containing the ‘benzoyl‐type’ and similar structural features. These compounds are frequently present in food and pharmaceutical products as leachable impurities that require strict control and rapid elucidation of their identities. Copyright © 2010 John Wiley & Sons, Ltd.     

Study of chemical bonding in H2 and HF molecules: Wave function and density functional theory (DFT) parameters approach

Balint Kurti's Fourier grid Hamiltonian method is employed to obtain the molecular wave function and equilibrium bond length for H₂ and HF molecules. The density functional theory parameter, namely, the chemical hardness (η) value, was determined for some diatomic hydride molecules using this wave function and the results are found to be in good agreement with the values obtained from the ab initio HF–SCF method. A new formula for chemical hardness (η=1/2Dr, where D is the proportionality constant and r is the internuclear distance) is introduced in binding energy and change of hardness equations to determine the chemical hardness and chemical potential values for different bond lengths. The binding energy and change of hardness values are calculated for H₂, H, H, HF, HF⁺, and HF⁻ molecules and the bond stability is discussed. Finally, the concept of an atom in a molecule is examined in the context of DFT parameters and comparison is made between an atom in a molecule and the isolated atom. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 76: 662–669, 2000     

Theoretical study of one‐electron bonds in a series of high‐spin lithium–beryllium–hydrogen clusters: “Valence shell single‐electron repulsion” rule and electron localization function analysis

A series of high‐spin clusters containing Li, H, and Be in which the valence shell molecular orbitals (MOs) are occupied by a single electron has been characterized using ab initio and density functional theory (DFT) calculations. A first type (⁵Li₂, ⁿ⁺¹LiH_n+ (n = 2–5), ⁸Li₂H) possesses only one electron pair in the lowest MO, with bond energies of ～3 kcal/mol. In a second type, all the MOs are singly occupied, which results in highly excited species that nevertheless constitute a marked minimum on their potential energy surface (PES). Thus, it is possible to design a larger panel of structures (⁸LiBe, ⁷Li₂, ⁸Li, ⁴LiH⁺, ⁶BeH, ⁿ⁺³LiH (n = 3, 4), ⁿ⁺²LiH (n = 4–6), ⁸Li₂H, ⁹Li₂H, ²²Li₃Be₃ and ²²Li₆H), single‐electron equivalent to doublet “classical” molecules ranging from CO to C₆H₆. The geometrical structure is studied in relation to the valence shell single‐electron repulsion (VSEPR) theory and the electron localization function (ELF) is analyzed, revealing a striking similarity with the corresponding structure having paired electrons. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Ab initio study of the reaction of CHO+ with H2O and NH3

An MP4(full,SDTQ)/6-311++G(d,p)//MP2(full)/6-311++G(d,p) ab initio study was performed of the reactions of formyl and isoformyl cations with H₂O and NH₃, which play an important role in flame and interstellar chemistries. Two different confluent channels were located leading to CO+H₃O⁺/NH. The first one corresponds to the approach of the neutral molecule to the carbon atom of the cations. The second one leads to the direct proton transfer from the cations to the neutrals. At 900 K the separate products CO+H₃O⁺/NH are the most stable species along the Gibbs energy profiles for the processes. For the reaction with H₂O the reaction channel leading to HC(OH) (protonated formic acid) is disfavored with respect to the two CO+H₃O⁺ channels in agreement with the experimental evidence that H₃O⁺ is the major ion observed in hydrocarbon flames. According to our calculations, NH+H₂O are considerably more stable in Gibbs energy than NH₃+H₃O⁺;NH will predominate in the reaction zone when ammonia is added to CH₄+Ar diffusion flame, as experimentally observed. At 100 K the most stable structures are the intermediate complexes CO…HOH/HNH. Particularly the CO…HOH complex has a lifetime large enough to be detected and, therefore, could play a certain role in interstellar chemistry. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1432–1443, 1999     

Structure and dissociation energy of weakly bound H (n = 5−8) complexes

The geometrical parameters, vibrational frequencies, and dissociation energies for H (n = 5–8) clusters have been investigated using high level ab initio quantum mechanical techniques with large basis sets. The highest level of theory employed in this study is TZ2P CCSD(T). The C₁ structure of H is predicted to be a global minimum, while the C_s structure of H is calculated to be a transition state. Harmonic vibrational frequencies are also determined at the DZP and TZ2P CCSD levels of theory. The dissociation energies, D_e, for H (n = 5–8) have been predicted using energy differences at each optimized geometry, and zero‐point vibrational energies (ZPVEs) are considered to compare with experimental values. The dissociation energies (D_o) have been predicted to be 1.69, 1.65, 1.65, and 1.46 kcal · mol for H, H, H (C₁ symmetry) and H, respectively, at the TZ2P CCSD(T) level of theory. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Fundamental Aspects of Ionic Dissociations: The Fragmentation Pathways of Excited Bicyclobutane Cations

A most recently developed method to quantify the fragmentation pathways of excited radical cations is presented. Using bicyclobutane cation as an illustrative example, the RRKM analysis of the breakdown diagram determined by He-Iα photoelectron-photoion coincidence spectroscopy is outlined. The results imply complete isomerization to 1,3-butadiene cation preceding the dissociative processes. The rate-energy functions of four competitive primary fragmentation reactions, leading to C₃H, C₄H, C₄H and C₂H are established. There is compelling evidence that the production of C₂H fragment ions does not compete effectively with these four reactions. The extent of kinetic and competitive shift effects is determined. The derived enthalpies of formation are in excellent accord with the available high quality reference data. The relative importance of different fragmentation pathways which ultimately lead to fragment ions of identical mass to charge ratio is assessed.     

Li+?F− in aqueous solution

The energy hypersurface for the system Li(H₂O)–F(H₂O) is investigated using the polarization model. A possible mechanism for the production of HF in this solution droplet is observed.     

The spin-density-functional formalism for quantum mechanical calculations: Test on diatomic molecules with an efficient numerical method

We have applied the spin-density-functional (SDF ) formalism with the local-spin-density (LSD ) approximation to a number of small molecules with the primary aim of testing the approximation for molecular applications. A new numerical method to solve the one-electron wave equation is developed, utilizing the special features of the SDF formalism. We have calculated energy curves, dissociation energies, and equilibrium distances for some diatomic molecules [H (²Σ, ²Σ), H₂(¹Σ, ³Σ), He (¹Σ), and He₂(¹Σ)] and the vibrational frequencies of H₂. The deviations from the experimental results are typically 1/2 eV for the energies and ≤ 0.1 Å for the distances. We discuss the LSD approximation using the concept of an exchange-correlation hole and make predictions about the applicability to other molecules. The LSD approximation is compared with the Hartree-Fock and multiple-scattering-Xα methods and some difficulties in the latter methods are pointed out. It is argued that the SDF formalism within the LSD approximation has physical advantages compared to the Hartree-Fock and Xα methods and that it should provide a simple and useful method for a broad range of applications.     

Ab initio studies of negative ion-molecule(s) clusters present in the atmosphere. II. OH−(H2O)n for n = 0, 2, 3, 4

Ab initio calculations are performed with 6–31G basis set to study the geometry and binding of the H₃O, H₅O, H₇O, and H₉O complexes. The H₃O complex is also investigated with the 6–31 G* basis set and MP 2 (Moller–Plesset perturbation theory of second order).     

The Gas-Phase Ion/Molecule Reactions of C3H5X (X = C1, Br,I)

The ion/molecule reactions of the molecular ion, the C₃H ion, and the C₃H ion obtained from 3-chloropropene. 1-bromopropene, 2-bromopropene, 3-bromopropene, bromocyclopropane. and 3-iodopropene have been studied with their neutral precursor in a Fourier-transform mass spectrometer (FT/ICR). The molecular ions react to yield primarily C₆H except for the ion derived from 1-bromopropene that is unreactive. The kinetics of the 3-bromopropene molecular ion reveals that 18% of these ions must possess a different structure which is unreactive. The fact that C₃H ions obtained from 2-bromopropene are the only ones to undergo proton transfer is taken as evidence that only this parent compound gives rise to 2-propenyl cations by low-energy electron impact. The C₃H ions generated in these systems are shown to be roughly an equal mixture of propargylium ions that react to yield C₆H and unreactive cyclopropenium ions.     

The structures,thermochemistry, and electron affinities of hydrogenated silicon clusters Si6Hn/Si6H (n = 3–14)

The hydrogenated silicon clusters structures, electron affinities, and dissociation energies of the Si₆H_n/Si₆H (n = 3?14) species have been systematically investigated by means of three density functional theory (DFT) methods. The basis set used in this work is of double‐ζ plus polarization quality with additional diffuse s‐ and p‐type functions, denoted DZP++. The geometries are fully optimized with each DFT method independently. Three different types of energy separations presented in this work are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). The first Si? H dissociation energies D_e (Si₆H_n→ Si₆H_n?1+H) for the neutral Si₆H_n and D_e (Si₆H→Si₆H+H) for the anionic Si₆H species have also been reported. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Reaction mechanism of platinum dimer cation with ammonia based on the relativistic density functional study

The gas‐phase reactions between Pt and NH₃ have been investigated using the relativistic density functional approach (ZORA‐PW91/TZ2P). The quartet and doublet potential energy surfaces of Pt + NH₃ have been explored. The minimum energy reaction path proceeds through the following steps: Pt(⁴Σ_u) + NH₃ → q‐1 → d‐2 → d‐3 → d‐4 → d‐Pt₂NH⁺ + H₂. In the whole reaction pathway, the step of d‐2 → d‐3 is the rate‐determining step with a energy barrier of 36.1 kcal/mol, and exoergicity of the whole reaction is 12.0 kcal/mol. When Pt₂NH⁺ reacts with NH₃ again, there are two rival reaction paths in the doublet state. One is degradation of NH and another is loss of H₂. In the case of degradation of NH, the activation energy is only 3.4 kcal/mol, and the overall reaction is exothermic by 8.9 kcal/mol. Thus, this reaction is favored both thermodynamically and kinetically. However, in the case of loss of H₂, the rate‐determining step's energy barrier is 64.3 kcal/mol and the overall reaction is endothermic by 8.5 kcal/mol, so it is difficult to take place. Predicted relative energies and barriers along the suggested reaction paths are in reasonable agreement with experimental observations. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Redshifts and blueshifts of OH vibrations

Ab initio calculations of potential energy, dipole moment, equilibrium OH distance, force constants, and anharmonic frequencies, and correlations between these quantities, are presented for a water molecule and an OH^? ion in a uniform electric field of varying field strength. It is explained why a bound H₂O molecule in nature always experiences a frequency downshift with respect to the free molecule, and a bound OH^? ion either a downshift or an upshift. The frequency-field variation is well accounted for by the expression Δν_OH ∝ ?E_∥·(dμ/dr_OH + 1/2 · ?μ/?r_OH). A frequency maximum occurs at the field strength where ?μ/?r_OH ～ 0. Two cases can be discerned: (1) the frequency maximum falls at a positive field strength when dμ/dr_OH is negative (this is the situation for OH^?), and (2) the maximum frequency falls at a negative field when dμ/dr_OH is positive (this occurs for water). In general, for an OH bond in a bonding situation where the intermolecular interactions are dominated by electrostatic forces, the nonlinearity of the frequency shift with respect to an applied field is governed by how close to the frequency maximum one is, i.e., by both dμ/dr_OH and ?μ/?r_OH. Correlation curves between the external linear force constant, k^ext, and r_OH,e are closely linear over the whole field range studied here, whereas the frequency vs. r_OH,e and force constants vs. r_OH,e correlation curves form two approximately linear, parallel branches, corresponding to “before” and “after” the maximum in the frequency vs. field curves. Each branch of the v vs. r_OH,e curves has a slope of ～ ?16,000 cm^?1/Å. © 1993 John Wiley & Sons, Inc.     

The proton affinity and the structure of protonated species of methylsilane

An ab initio LCAO-MO-SCF calculation was made on the proton affinity (PA ) of methylsilane (CH₃SiH₃) by using STO -3G, MIDI -1, and MIDI -1* basis sets. Three types of protonated methylsilane are taken into account, and their geometrical parameters are optimized. The calculated PA of CH₃SiH₃ is 160.5 kcal/mol, which exceeds that of SiH₄ by 11.5 kcal/mol. The protonated species (I) which refers to Si—C bond protonation is shown to be most favorable, and to be a weak σ-complex between CH₄ and SiH. Other two species are also σ-complexes between H₂ molecule and SiH₃CH or CH₃SiH, and similar to CH, SiH, GeH, and C₂H.     

The mass spectra of organic compounds. 7th Communication. 4,4-Dimethyl-1-pentene

Loss of CH, CH₄, C₂H₄, C₃H, C₃H₆ and C₃H₇ from the molecular ions of a number of ¹³C-labeled analogs of 4,4-dimethyl-1-pentene was studied both in normal (source) 70-eV electron impact (EI) spectra dn in metastable spectra. For loss of CH in the source, 96% of the methyl comes frm positions of 5, 5′ and 5″, while the remainder comes from position 1. In the metastable spectra, loss of C-1 (16%) and C-3 (9%) is increasing in importance. The loss of ethylene is a particular case: either C-1 or C-3 are lost with any other C-atom from positions 2,5,5′, and 5″ (8 × 10%) in the metastable spectra, the probability for simultaneous loss of C-1 and C-3 being 6%. If C-1 seems to these two positions become completely equivalent in the metastable time range. The T-values (kinetic energy release) for the different positions show small, but statisticaly different values and a small isotope effect. Loss of C₃H₅ (allylic cleavage) is 100% C-1, C-2 and C-3, i.e., no evidence for skeletal rearrangement is seen. This is also true for loss of C₃C₆ (McLafferty rearrangement) within the source, but in metastable decay the other positions gain in importance. The neutral fragment C₃H appears to be the the result of consecutive loss of CH and C₃H₄, rather than a one-step loss of propyl radical or the inverse reactions sequence. No metastable reaction can be seen for this reaction. Decomposition of labeled C₆H and C₅H secondary ions occurs in an essentially random fashion.     

Aromaticity of ionic structures: Investigation and application of NICS value and 4n + 2 rule

At DFT/B3LYP/6‐31G** theoretical level, C₆H and C (n = 0, ?2, and +2), C₆H and C (n = 0, ±2, ±4, and ±6), C₆H (n = 0–6), as well as C₆H₆‐A and C₆‐A (A = Be, B, N, O, Mg, Al, Si, S, and Fe) structures were investigated. Comparing NICS values of C₆H and C (n = 0, ?2, and +2), we discovered that C₆H, C₆H were antiaromatic, and C₆H₆, C₆, C, C had aromaticity with negative NICS values. According to research of C₆H and C (n = 0, ±2, ±4, ±6), C₆H (n = 0–6), we sustained that their σ and π orbit were different and the locations of electrons were difficult to confirm in ionic structures. Thus, neither 4n + 2 rule nor NICS values can precisely estimate the aromaticity of ionic structures. Besides, through WBI (NBO) research of C₆H₆‐A and C₆‐A (A = Be, B, N, O, Mg, Al, Si, S, and Fe) structures, we found that C₆H₆ was easy to accept electrons, contrarily, C₆ was prone to bestowing electrons. Moreover, C₆H₆ took the symmetrical carbon atoms form feeble interaction or bond, and C₆ used all carbon atoms to impact with other atom. C₆H₆ generated two contrapuntal single bonds with oxygen, sulfur, and nitrogen atoms, whereas C₆ molecule formed double bond with oxygen and nitrogen atoms, two conjoint single bonds with sulfur atom. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Negative ion fragmentations of deprotonated peptides containing post‐translational modifications. An unusual cyclisation/rearrangement involving phosphotyrosine; a joint experimental and theoretical study

The characteristic fragmentations of a pTyr group in the negative ion electrospray mass spectrum of the [M–H]^? anion of a peptide or protein involve the formation of PO (m/z 79) and the corresponding [(M‐H)^?–HPO₃]^? species. In some tetrapeptides where pTyr is the third residue, these characteristic anion fragmentations are accompanied by ions corresponding to H₂PO and [(M‐H)^?–H₃PO₄]^? (these are fragmentations normally indicating the presence of pSer or pThr). These product ions are formed by rearrangement processes which involve initial nucleophilic attack of a C‐terminal ‐CO [or ‐C(?NH)O^?] group at the phosphorus of the Tyr side chain [an S_N2(P) reaction]. The rearrangement reactions have been studied by ab initio calculations at the HF/6‐31+G(d)//AM1 level of theory. The study suggests the possibility of two processes following the initial S_N2(P) reaction. In the rearrangement (involving a C‐terminal carboxylate anion) with the lower energy reaction profile, the formation of the H₂PO and [(M‐H)^?–H₃PO₄]^? anions is endothermic by 180 and 318 kJ mol^?1, respectively, with a maximum barrier (to a transition state) of 229 kJ mol^?1. The energy required to form H₂PO by this rearrangement process is (i) more than that necessary to effect the characteristic formation of PO from pTyr, but (ii) comparable with that required to effect the characteristic α, β and γ backbone cleavages of peptide negative ions. Copyright © 2009 John Wiley & Sons, Ltd.     

Nonlinear dynamics in the oxidations of substituted thioureas I: The reaction of 4‐methyl‐3‐thiosemicarbazide with acidic iodate [1]

The substituted thiourea, 4‐methyl‐3‐thiosemicarbazide, was oxidized by iodate in acidic medium. In high acid concentrations and in stoichiometric excess of iodate, the reaction displays an induction period followed by the formation of aqueous iodine. In stoichiometric excess of methylthiosemicarbazide and high acid concentration, the reaction shows a transient formation of aqueous iodine. The stoichiometry of the reaction is: 4IO + 3CH₃NHC(S)NHNH₂ + 3H₂O → 4I⁻ + 3SO + 3CH₃NHC(O)NHNH₂ + 6H⁺ (A). Iodine formation is due to the Dushman reaction that produces iodine from iodide formed from the reduction of iodate: IO + 5I⁻ + 6H⁺ → 3I₂(aq) + 3H₂O (B). Transient iodine formation is due to the efficient acid catalysis of the Dushman reaction. The iodine produced in process B is consumed by the methylthiosemicarbazide substrate. The direct reaction of iodine and methylthiosemicarbazide was also studied. It has a stoichiometry of 4I₂(aq) + CH₃NHC(S)NHNH₂ + 5H₂O → 8I⁻ + SO + CH₃NHC(O)NHNH₂ + 10H⁺ (C). The reaction exhibits autoinhibition by iodide and acid. Inhibition by I⁻ is due to the formation of the triiodide species, I, and inhibition by acid is due to the protonation of the sulfur center that deactivates it to further electrophilic attack. In excess iodate conditions, the stoichiometry of the reaction is 8IO + 5CH₃NHC(S)NHNH₂ + H₂O → 4I₂ + 5SO + 5CH₃NHC(O)NHNH₂ + 2H⁺ (D) that is a linear combination of processes A and B. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 193–203, 2000     

Decomposition of 1,1,2,2-tetrafluorocyclopropane. Arrhenius parameters and their influence on the chemical activation results

The kinetics of the gas-phase thermal decomposition of 1,1,2,2-tetrafluorocyclopropane (TFC) to 1,1-difluoroethylene and CF₂ was studied in the temperature range of 507.0-577.0 K and with a total pressure of 200 to 300 torr of a 1:100 mixture of reactant and C₂H₄. Also at 557.0 K experiments were made at different total pressures, in the range 2–20 torr with neat TFC and between 20–300 torr with the C₂H₄/TFC mixture, confirming that the reaction is in the high pressure limit. The reaction is first-order and the rate constants fit the following Arrhenius relationship: From this value of the activation energy, the data for the decomposition of chemically activated TFC were revised. The new results yield a minimum energy of the activated molecule of 98 ± 4 kcal/mol and ΔH(TFC) = ?155.4 ± 7 kcal/mol, while an analysis of the kinetic data yields ΔH(TFC) = ?159 ± 9 kcal/mol.