Ting-Hua Tang

Structure and fragmentation of b2 ions in peptide mass spectra

In a number of cases the b2 ion observed in peptide mass spectra fragments directly to the a1 ion. The present study examines the scope of this reaction and provides evidence as to the structure(s) of the b2 ions undergoing fragmentation to the a1 ion. The b2 ion H-Ala-Gly+ fragments, in part, to the a1 ion, whereas the isomeric b2 ion H-Gly-Ala+ does not fragment to the a1 ion. Ab initio calculations of ion energies show that this different behavior can be rationalized in terms of protonated oxazolone structures for the b2 ions provided one assumes a reverse activation energy of ∼1 eV for the reaction b2 → a2; such a reverse activation energy is consistent with experimental kinetic energy release measurements. Experimentally, the H-Aib-Ala+ b2 ion, which must have a protonated oxazolone structure, fragments extensively to the a1 ion. We conclude that the proposal by Eckart et al. (J. Am. Soc. Mass Spectrom. 1998, 9, 1002) that the b2 ions which undergo fragmentation to a1 ions have an immonium ion structure is not necessary to rationalize the results, but that the fragmentation does occur from a protonated oxazolone structure. It is shown that the b2 → a1 reaction occurs extensively when the C-terminus residue in the b2 ion is Gly and with less facility when the C-terminus residue is Ala. When the C-terminus residue is Val or larger, the b2 → a1 reaction cannot compete with the b2 → a2 fragmentation reaction. Some preliminary results on the fragmentation of a2 ions are reported.

A quantum chemical study on selected π-type hydrogen-bonded systems

Abstract π-Type hydrogen-bonded systems consisting of acetylene, ethylene, cyclopropane or benzene as proton acceptors and hydrogen fluoride as proton donor have been studied. The calculated π-type hydrogen-bond stabilization energies for C 2 H 2 ·HF, C 2 H 4 ·HF, C 3 H 6 ·HF and C 6 H 6 ·HF are 4.54, 4.71, 4.64 and 4.81 kcal mol −1 , respectively, from MP2/6-31G ∗∗ /6-31G ∗ calculations. The detailed bond connecting descriptions, which are taken from the molecular graphs, have been made on the basis of topological analysis of the electronic density distribution. The stabilization of C 2 H 4 ·HF and C 3 H 6 ·HF π-type hydrogen-bonded systems at the 3-21G level are discussed.

Electron distribution in cationic fragments generated mass spectrometrically from peptides

Ab initio Hartree‐Fock (HF/6-31G, HF/6-31G* and HF/6-31G**) methods have been used to study the mechanism of the formation of cationic fragments from peptides. The results show that the simplest B 3 ion of nominal structure HCONHCH2CONHCH2CO 1 , can be fragmented into the A3 ion in the first step by the loss of CO, but not directly into the B2 ion. In addition, the A3 ion can be further fragmented into the B2 ion. The calculated activation barrier of the first reaction (from B3 to A3 )i s 26.2 kcal/mol at the HF/6-31G** level of theory. The second reaction (from B3 to B2) has much higher energy barrier (77.15 kcal/mol at HF/6-31G** level of theory). The third reaction (from A3 to B2) and the fourth reaction (from B2 to A2) have barriers of 28.82 and 25.59 kcal/mol, respectively. In addition to the energetics of the fragmentation, the electronic structure and bonding of the main stationary points have been analyzed by Bader’s theory of atoms in molecules (AIM). q 1999 Elsevier Science B.V. All rights reserved.

A charge density topological approach on the equilibrium gas-phase basicity of selected nitrogen-containing organic molecules

Abstract Within the charge density topological approach, the −▿ϱ values of nonbonded charge concentration of methylamines and some other nitrogen bases have been calculated. There are very good linear relationships between −▿ϱ values of nonbonded charge concentration and the gas basicities of these two groups of molecules.

A theoretical study of substituted norcaradiene with some strong electron withdrawing groups at position 7

Abstract The valence isomeric equilibria between cycloheptatriene and norcaradiene and, as well, their substituted derivatives at position 7 containing strong electron withdrawing groups (7-cyano, 7,7-dicyano and 7,7-difluoro substituted) were investigated computationally using ab initio methods and charge density topological analysis at the 6-31G ∗ , 6-31G ∗* and MP2/6-31G ∗* levels of theory. The calculated relevant cross sections of the potential energy surface shows that the 7,7-dicyanonorcaradiene, in which the CN group acts as a σ- and π-acceptor, behaves as a stable neutral homoaromatic compound. As a comparison, the destabilized 7,7-difluoronorcaradiene, in which fluorine substituents act as a σ-acceptor and a π-donor, was studied also.

Ab initio modelling of peptide biosynthesis

Abstract Ab initio calculations (HF/3–21G) have been used to study the mechanism of peptide biosynthesis (R1COOR2 + R3NH2 → R1CONHR3 + R2OH). Two or four water molecules are included to represent the primary solvent shell. The studies show that the reaction proceeds via a gauche or trans transition state if it starts from the reactants gauche or trans complex. The energy barrier of the reaction with two water molecules is calculated to be 27.96 (gauche) or 26.85 kcal mol−1 (trans), while that of the reaction with four water molecules is only 14.82 (gauche) or 13.21 kcal mol−1 (trans).

Is there an O–H⋯C hydrogen bond in the cation of cis o-cresol?

Ab initio and DFT geometry optimization, followed by the application of Bader’s theory atoms in molecules (AIM) have been applied to probe the proposed O‐H· · ·C3‐ hydrogen bond in cis o-cresol. No evidence was found to support the presence of such novel type hydrogen bond. It is concluded that the observed ir frequency shift (25 cm 21 ) should be explained by some

An ab initio study on ribo and deoxy-ribo models for nucleosides and nucleotides

Abstract An exploratory set of ab initio molecular orbital computations were carried out on various conformations of ribose and deoxy-ribose model compounds to establish the nature of possible interactions between the 5′-hydroxyl and the oxygen of the ribose ring. Moreover, the investigation was extended to the hydrogen bonding between the two adjacent hydroxyls 2′- and 3′- to explore their effect on the stabilization of the whole system. The consistent presence of a rather unusual weak hydrogen bond between the proton of C2′–H and the O5′ of the hydroxy methyl group for the g−g− conformation of the–CH2–OH functional group has been studied by using Baders atoms in molecules (AIM) method.

A theoretical study of markovnikov and anti-markovnikov protonation of olefines by HeH+

Abstract A theoretical study of the first step in the reaction mechanism of the electrophilic addition reaction of protonation was done on the following two systems: CH 2 =CH 2 +HeHP + →CH 3 CH + 2 +He (1) CH 3 -CH=CH 2 +HeH + →(CH 3 ) 2 CH + or CH 3 -CH 2 -CH 2 + +He (2) In this study, He is considered as the proton carrier. The energy-gradient method was used to optimize the molecular geometries for critical points along the reaction coordinate using the 3-2 IG basis set for the self-consistent-field (SCF) calculations. Single-point energies were determined with the 6-31G ∗∗ basis set for all relevant geometries optimized at the 3-21G basis set level. The related potential curves of the reactions studied were investigated. The results obtained reveal that reaction (1) is a multistep reaction, where first the He-H bond is broken, forming an open cationic intermediate C 2 H 5 + ·He. Further along the reaction coordinate, the product was found to be a “bridged structure” of C 2 H 5 + . It was also found that reaction (2) proceeds according to Markovnikovs rule, i.e. the H + of HeH + adds onto the double bond of the carbon atom having the greatest number of hydrogen atoms. This leads to the formation of the more stable secondary carbocation. The key intermediate in this reaction is an open isopropyi cation. Along the reaction coordinate, another product complex which has a semi-closed bridged structure is also formed. Using the topological theory of electronic density distribution suggested by Bader, the molecular graphs and the properties of the bond critical points of the reactants, transition states, intermediates and products were studied.

Flip-flops in fluorinated o-cresol

Abstract Ab initio geometry optimizations are used to investigate the side chain fluorinated cis o -cresols, HOC 6 H 4 CH 3− n F n ( n =1, 2, and 3). The three ground states are found to contain hydrogen bonded hexagon, which may flip flop between two equivalent positions relative to the phenyl ring. In the cases n =2 and n =3 the activation energy for the flip-flop is about the same and less than 1 kJ/mol, whereas it is an order of magnitude higher for n =1. The difference in activation energies is associated with the dynamics of the flip-flop and the stoichiometry of the cresol.