Substituted 3-phenylpropenoates and related analogs: electron ionization mass spectral fragmentation and density functional theory calculations

Analysis of ethyl 3-(2-chlorophenyl)propenoate by electron ionization mass spectrometry showed the distinct loss of an ortho chlorine. To characterize the structural requisites for the observed mass fragmentation, a series of 30 halogen-substituted 3-phenylpropenoate-related structures were examined. All ester-containing alkene derivatives exhibited loss of the distinctive chlorine from the 2-position of the phenyl ring. Analogous derivatives with the halogen (chlorine or bromine) in the para position did not evidence selective halogen loss. Results demonstrated that substituted 3-phenylpropenoates and their analogs fragment via the formation of a previously reported benzopyrylium intermediate. To understand the correlation between the intramolecular radical substitution and the abundance and selectivity of the chlorine (or other halogen) displacement, density functional theory calculations were performed to determine the charge on the principal cation involved in the chlorine loss (in the ortho, meta, and para positions), the charge for the neutral radical (noncation), the excess alpha-electron density on the relevant atom and the energy to form the cation from the neutral atom (ionization energy). Results showed that the selectivity and extent of halogen displacement correlated highly to the electrophilicity of the radical cation as well as the neutral radical. These data further support the proposed fragmentation mechanism involving intramolecular radical elimination.     

Relationship between Hammett's parameters and in silico density functional with tandem mass ESI‐CID fragmentation: Dihydropyridines as prototypes

Over the years, with the instrumental analysis evolution, the relationships between the carried‐out results with the data of theoretical analysis in silico and the Hammett's parameters have been reported. They have been very useful for chemical characterization of small organic molecules. Thus, this work aims at showing the feasibility and limitations for Hammett's and density functional theory applications in electrospray ionization–collision‐induced dissociation (ESI‐CID) fragmentation provision. For this, 13 dihydropyrimidinones para, meta, and orto monosubstituted were studied using ESI and CID in positive mode. As a result, it was observed that the main fragmentation includes the isocyanate and ethanol loses at low energy. Nevertheless, at higher energies, radical ions formed by McLafferty rearrangement were observed. The Hammett plots were correlated fragmentation profiles, showing good linearity for the [M + H]⁺, which does not occur to radical ions and carbocation's. These tendencies had demonstrated that the stability of protonate and activation energy of secondary ions changes with the pKa. The density functional theory studies indicated that, both nitrogen atoms in the dihydropyrimidinone's prototypes are capable of being protonated. However, the activation energy of fragmentation products is not changed. Therefore, this work has shown information, which can be useful to understand tandem mass spectrometry in ESI‐CID conditions for small organic molecules series. This is the first step for normalization of fragmentation pathway.     

质子转移反应质谱的建立与性能研究

报道了自行研制的质子转移反应质谱的基本结构和性能。利用水蒸气辉光放电产生了反应离子H3O ,以合成空气为反应气体,测量了H3O 与合成空气中的水反应产生的团簇离子H3O (H2O)n的质谱。实验发现,当漂移管电场与分子密度比值为144Td时,增加的离子能量可以阻止团簇离子H3O (H2O)n的形成,质谱观察到的离子主要是H3O ,其纯度可达99%以上,这时H3O 与有机物分子如甲苯的质子转移反应的产物离子也呈单一形式,团簇离子得到很好地抑制。根据离子强度和离子反应时间等参数,获得了PTR-MS目前的检出限为10-8(V/V)。利用PTR-MS对标准浓度甲苯及其稀释气体进行检测,表明PTR-MS在线定量检测准确性良好,线性动态范围跨越3个数量级,能够应用于大气中痕量挥发性有机物的实时在线测量。     

Quantum chemical mass spectrometry: ab initio prediction of electron ionization mass spectra and identification of new fragmentation pathways

The electron ionization mass spectra of four organic compounds are predicted based on the results of quantum chemical calculations at the DFT/B3LYP/6‐311 + G* level of theory. This prediction is performed ‘ab initio’, i.e. without any prior knowledge of the thermodynamics or kinetics of the reactions under consideration. Using a set of rules determining which routes will be followed, the fragmentation of the molecules' bonds and the complete resulting fragmentation pathways are studied. The most likely fragmentation pathways are identified based on calculated reaction energies ΔE when bond cleavage is considered and on activation energies ΔE^? when rearrangements are taken into account; the final intensities of the peaks in the spectrum are estimated from these values. The main features observed in the experimental mass spectra are correctly predicted, as well as a number of minor peaks. In addition, the results of the calculations allow us to propose fragmentation pathways new to empirical mass spectrometry, which have been experimentally verified using tandem mass spectrometry measurements. Copyright © 2016 John Wiley & Sons, Ltd.     

Grid‐based density functional calculations of many‐electron systems

Exploratory variational pseudopotential density functional calculations are performed for the electronic properties of many‐electron systems in the 3D cartesian coordinate grid (CCG). The atom‐centered localized gaussian basis set, electronic density, and the two‐body potentials are set up in the 3D cubic box. The classical Hartree potential is calculated accurately and efficiently through a Fourier convolution technique. As a first step, simple local density functionals of homogeneous electron gas are used for the exchange‐correlation potential, while Hay‐Wadt‐type effective core potentials are employed to eliminate the core electrons. No auxiliary basis set is invoked. Preliminary illustrative calculations on total energies, individual energy components, eigenvalues, potential energy curves, ionization energies, and atomization energies of a set of 12 molecules show excellent agreement with the corresponding reference values of atom‐centered grid as well as the grid‐free calculation. Results for three atoms are also given. Combination of CCG and the convolution procedure used for classical Coulomb potential can provide reasonably accurate and reliable results for many‐electron systems. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

Kinetic energy density for orbital‐free density functional calculations by axiomatic approach

An axiomatic approach is herein used to determine the physically acceptable forms for general D‐dimensional kinetic energy density functionals (KEDF). The resulted expansion captures most of the known forms of one‐point KEDFs. By statistically training the KEDF forms on a model problem of noninteracting kinetic energy in 1D (six terms only), the mean relative accuracy for 1000 randomly generated potentials is found to be better than the standard KEDF by several orders of magnitudes. The accuracy improves with the number of occupied states and was found to be better than for a system with four occupied states. Furthermore, we show that free fitting of the coefficients associated with known KEDFs approaches the exactly analytic values. The presented approach can open a new route to search for physically acceptable kinetic energy density functionals and provide an essential step toward more accurate large‐scale orbital free density functional theory calculations.     

Novel method of self‐interaction corrections in density functional calculations

It is demonstrated that the commonly applied self‐interaction correction (SIC) used in density functional theory does not remove all self‐interaction. We present as an alternative a novel method that, by construction, is totally free from self‐interaction. The method has the correct asymptotic 1/r dependence. We apply the new theory to localized f electrons in praseodymium and compare with the old version of SIC, the local density approximation (LDA) and with an atomic Hartree–Fock calculation. The results show a lowering of the f level, a contraction of the f electron cloud and a lowering of the total energy by 13 eV per 4 f electron compared to LDA. The equilibrium volume of the new SIC method is close to the ones given by LDA and the older SIC method and is in good agreement with experiment. The experimental cohesive energy is in better agreement using the new SIC method, both compared to LDA and another SIC method. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 247–252, 2001     

Protonated primary amines induced thymine quintets studied by electrospray ionization mass spectrometry and density functional theory calculations

As the novel magic number clusters of nucleobases, the thymine quintets induced by ammonium ion (NH₄⁺), and particularly by its derivatives such as protonated alkyl amines and protonated aryl amines, have been studied by electrospray ionization mass spectrometry (ESI‐MS) and density functional theory (DFT) calculations. The DFT‐optimized geometry of NH₄⁺ induced thymine quintet ([T₅ + NH₄]⁺) reveals some new features including three additional hydrogen bonds between NH₄⁺ and its surrounding thymine molecules when compared with that of the alkali metal ions induced thymine quintets. In addition, the fourth hydrogen atom of NH₄⁺ is sticking out the assembly, and, thus, it might be replaced by an organic group R to form the protonated primary amine induced thymine quintet ([T₅ + R ? NH₃]⁺), a hypothesis that has been confirmed by both DFT calculations and ESI‐MS experiments. Furthermore, the relative abilities of the different protonated primary amines for inducing the thymine quintets are investigated by ESI‐MS competition experiments, and the results have shown a clear trend of stronger ability as the alkyl chain gets longer or as the aryl ring gets larger for the alkyl amines or the aryl amines. Two basic influence factors are consequently identified: one is the ability of the alkyl amine to accept proton, another is the π–π stacking interaction between the aryl ring and the π‐surface of the thymine molecule(s), whose explanations are strongly supported by multiple types of thermochemical data, various control experiments and DFT calculations. Copyright © 2014 John Wiley & Sons, Ltd.     

Comment on “density and physical current density functional theory” by Xiao‐Yin Pan and Viraht Sahni

A recent paper by Xiao‐Yin Pan and Viraht Sahni [Int. J. Quant. Chem. 110, 2833 (2010)] claims that current density functional theory should be based on the physical current density rather than the paramagnetic current density, as in the standard Vignale‐Rasolt formulation. In this comment we show that the claims in the paper by Pan and Sahni are erroneous. © 2012 Wiley Periodicals, Inc.     

Excited‐State Proton Transfer and Intramolecular Charge Transfer in 1,3‐Diketone Molecules

The photophysical signature of the tautomeric species of the asymmetric (N,N‐dimethylanilino)‐1,3‐diketone molecule are investigated using approaches rooted in density functional theory (DFT) and time‐dependent DFT (TD‐DFT). In particular, since this molecule, in the excited state, can undergo proton transfer reactions coupled to intramolecular charge transfer events, the different radiative and nonradiative channels are investigated by making use of different density‐based indexes. The use of these tools, together with the analysis of both singlet and triplet potential energy surfaces, provide new insights into excited‐state reactivity allowing one to rationalize the experimental findings including different behavior of the molecule as a function of solvent polarity.     

Proton affinities of molecules containing nitrogen and oxygen: Comparing density functional results to experiment

Summary Proton affinities were calculated using density functional theory for 11 small molecules whose primary protonation site is on nitrogen, and eight small molecules that protonate on oxygen. Calculations were performed using both the local spin density approximation and nonlocal gradient corrections to the exchange correlation functional. The results were not sensitive to whether the nonlocal gradient correction was implemented on the final local spin density optimized geometry or whether the correction was included in the self-consistent calculation of the energy at each optimization step. Although negligible basis set dependence was found using the analytic Gaussian basis sets, numerical basis sets required augmentation by a double set of polarization functions to achieve reasonable agreement with experiment. All calculations systematically underestimated oxygen proton affinities.     

Improvement of initial guess via grid‐cutting for efficient grid‐based density functional calculations

We introduced an efficient initial guess method, namely the grid‐cutting, which is specialized for grid‐based density functional theory (DFT) calculations. It produces initial density and orbitals through pre‐DFT calculations in an inner simulation box made by cutting out the outer region of a full‐size one. To assess its performance, we carried out DFT calculations for small molecules included in the G2‐1 set and two large molecules with various combinations of mixing and diagonalization conditions, relative size of the inner box, and grid spacing. For all cases, the grid‐cutting method was more efficient than conventional ones such as extended Hückel, superposition of atomic densities, and linear combination of atomic orbitals. For instance, it was about 20% faster in computational time and about 45% smaller in the number of self‐consistent‐field cycles than the superposition of atomic densities because it provided high‐quality initial density and orbitals closer to the corresponding fully converged values. In addition, it showed good performance for non‐Coulombic model systems such as harmonic oscillator.     

A solvation‐free‐energy functional: A reference‐modified density functional formulation

The three‐dimensional reference interaction site model (3D‐RISM) theory, which is one of the most applicable integral equation theories for molecular liquids, overestimates the absolute values of solvation‐free‐energy (SFE) for large solute molecules in water. To improve the free‐energy density functional for the SFE of solute molecules, we propose a reference‐modified density functional theory (RMDFT) that is a general theoretical approach to construct the free‐energy density functional systematically. In the RMDFT formulation, hard‐sphere (HS) fluids are introduced as the reference system instead of an ideal polyatomic molecular gas, which has been regarded as the appropriate reference system of the interaction‐site‐model density functional theory for polyatomic molecular fluids. We show that using RMDFT with a reference HS system can significantly improve the absolute values of the SFE for a set of neutral amino acid side‐chain analogues as well as for 504 small organic molecules. © 2015 Wiley Periodicals, Inc.     

Positive chemical ionization triple‐quadrupole mass spectrometry and ab initio computational studies of the multi‐pathway fragmentation of phthalates

We report the first positive chemical ionization (PCI) fragmentation mechanisms of phthalates using triple‐quadrupole mass spectrometry and ab initio computational studies using density functional theories (DFT). Methane PCI spectra showed abundant [M + H]⁺, together with [M + C₂H₅]⁺ and [M + C₃H₅]⁺. Fragmentation of [M + H]⁺, [M + C₂H₅]⁺ and [M + C₃H₅]⁺ involved characteristic ions at m/z 149, 177 and 189, assigned as protonated phthalic anhydride and an adduct of phthalic anhydride with C₂H₅⁺ and C₃H₅⁺, respectively. Fragmentation of these ions provided more structural information from the PCI spectra. A multi‐pathway fragmentation was proposed for these ions leading to the protonated phthalic anhydride. DFT methods were used to calculate relative free energies and to determine structures of intermediate ions for these pathways. The first step of the fragmentation of [M + C₂H₅]⁺ and [M + C₃H₅]⁺ is the elimination of [R? H] from an ester group. The second ester group undergoes either a McLafferty rearrangement route or a neutral loss elimination of ROH. DFT calculations (B3LYP, B3PW91 and BPW91) using 6‐311G(d,p) basis sets showed that McLafferty rearrangement of dibutyl, di(‐n‐octyl) and di(2‐ethyl‐n‐hexyl) phthalates is an energetically more favorable pathway than loss of an alcohol moiety. Prominent ions in these pathways were confirmed with deuterium labeled phthalates. Copyright © 2010 John Wiley & Sons, Ltd.