Accurate interaction energies at density functional theory level by means of an efficient dispersion correction

QCMS2 as a new method for providing insight into peptide fragmentation: The influence of the side-chain and inter-side-chain interactions

The identification of peptides and proteins from tandem mass spectra is a difficult task and multiple tools have been developed to aid this identification. We present a new method called quantum chemical mass spectrometry for materials science (QCMS² ), which is based on quantum chemical calculations of bond orders, reaction, and transition-state energies at the DFT/B3LYP/6-311+G* level of theory. The method was used to describe the fragmentation pathways of five X-His-Ser tripeptides with X = Asn, Asp, Glu, Ser, and Trp, thereby focusing on the influence of the side chain and inter-side-chain interactions on the fragmentation. The main features in the mass spectra of the five tripeptides were correctly reproduced, and a number of fragments were assigned to fragmentations involving the side chain and the influence of inter-side-chain interactions. Product ion spectra were recorded to evaluate the capabilities and limitations of QCMS² and a number of conventional tools.

Quantum chemical mass spectrometry: Ab initio study of b2 -ion formation mechanisms for the singly protonated Gln-His-Ser tripeptide

RATIONALE

Both amide bond protonation triggering peptide fragmentations and the controversial b₂ -ion structures have been subjects of intense research. The involvement of histidine (H), with its imidazole side chain that induces specific dissociation patterns involving inter-side-chain (ISC) interactions, in b₂ -ion formation was investigated, focusing on the QHS model tripeptide.

METHODS

To identify the effect of histidine on fragmentations issued from ISC interactions, QHS was selected for a comprehensive analysis of the pathways leading to the three possible b₂ -ion structures, using quantum chemical calculations performed at the DFT/B3LYP/6-311+G* level of theory. Electrospray ionization ion trap mass spectrometry allowed the recording of MS² and MS³ tandem mass spectra, whereas the Quantum Chemical Mass Spectrometry for Materials Science (QCMS² ) method was used to predict fragmentation patterns.

RESULTS

Whereas it is very difficult to differentiate among protonated oxazolone, diketopiperazine, or lactam b₂ -ions using MS² and MS³ mass spectra, the calculations indicated that the QH b₂ -ion (detected at m/z 266) is probably a mixture of the lactam and oxazolone structures formed after amide nitrogen protonation, making the formation of diketopiperazine less likely as it requires an additional step for its formation.

CONCLUSIONS

In contrast to glycine-histidine-containing b₂ -ions, known to be issued from the backbone-imidazole cyclization, we found that interactions between the side chains were not obvious to perceive, neither from a thermodynamics nor from a fragmentation perspective, emphasizing the importance of the whole sequence on the dissociation behavior usually demonstrated from simple glycine-containing tripeptides.

Quantum Chemical Mass Spectrometry: Verification and Extension of the Mobile Proton Model for Histidine

The quantum chemical mass spectrometry for materials science (QCMS²) method is used to verify the proposed mechanism for proton transfer - the Mobile Proton Model (MPM) - by histidine for ten XHS tripeptides, based on quantum chemical calculations at the DFT/B3LYP/6-311+G* level of theory. The fragmentations of the different intermediate structures in the MPM mechanism are studied within the QCMS² framework, and the energetics of the proposed mechanism itself and those of the fragmentations of the intermediate structures are compared, leading to the computational confirmation of the MPM. In addition, the calculations suggest that the mechanism should be extended from considering only the formation of five-membered ring intermediates to include larger-ring intermediates. Graphical Abstract ᅟ.

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.

Perspective: Advances and challenges in treating van der Waals dispersion forces in density functional theory

Electron dispersion forces play a crucial role in determining the structure and properties of biomolecules, molecular crystals, and many other systems. However, an accurate description of dispersion is highly challenging, with the most widely used electronic structure technique, density functional theory (DFT), failing to describe them with standard approximations. Therefore, applications of DFT to systems where dispersion is important have traditionally been of questionable accuracy. However, the last decade has seen a surge of enthusiasm in the DFT community to tackle this problem and in so-doing to extend the applicability of DFT-based methods. Here we discuss, classify, and evaluate some of the promising schemes to emerge in recent years. A brief perspective on the outstanding issues that remain to be resolved and some directions for future research are also provided.

σ, π aromaticity and anti-aromaticity as retrieved by the linear response kernel

The chemical importance of the linear response kernel from conceptual Density Functional Theory (DFT) is investigated for some σ and π aromatic and anti-aromatic systems. The effect of the ring size is studied by looking at some well known aromatic and anti-aromatic molecules of different sizes, showing that the linear response is capable of correctly classifying and quantifying the aromaticity for five- to eight-membered aromatic and anti-aromatic molecules. The splitting of the linear response in σ and π contributions is introduced and its significance is illustrated using some σ-aromatic molecules. The linear response also correctly predicts the aromatic transition states of the Diels-Alder reaction and the acetylene trimerisation and shows the expected behavior along the reaction coordinate, proving that the method is accurate not only at the minimum of the potential energy surface, but also in non-equilibrium states. Finally, the reason for the close correlation between the linear response and the Para Delocalisation Index (PDI), found in previous and the present study, is proven mathematically. These results show the linear response to be a reliable DFT-index to probe the σ and π aromaticity or anti-aromaticity of a broad range of molecules.

On the potential application of DFT methods in predicting the interaction-induced electric properties of molecular complexes. Molecular H-bonded chains as a case of study

A detailed analysis of the selected DFT functionals for the calculations of interaction-induced dipole moment, polarizability and first-order hyperpolarizability has been carried out. The hydrogen-bonded model chains consisting of HF, H(2)CO and H(3)N molecules have been chosen as a case study. The calculations of the components of the static electric properties using the diffuse Dunning's basis set (aug-cc-pVDZ) have been performed employing different types of density functionals (B3LYP, LC-BLYP, PBE0, M06-2X and CAM-B3LYP). Obtained results have been compared with those gained at the CCSD(T) level of theory. The counterpoise correction scheme, namely site-site function counterpoise, has been applied in order to eliminate basis set superposition error. The performed tests allow to conclude that the DFT functionals can provide a useful tool for prediction of the interaction-induced electric properties, however a caution has to be urged to their decomposition to the two- and many-body terms.

Should negative electron affinities be used for evaluating the chemical hardness?

Despite recent advances in computing negative electron affinities using density-functional theory, it is an open issue as to whether it is appropriate to use negative electron affinities, instead of zero electron affinity, to compute the chemical hardness of atoms and molecules with metastable anions. We seek to answer this question using the accepted empirical rules linking the chemical hardness to the atomic size and the polarizability; we also propose a new correlation with the C6 London dispersion coefficient. For chemical reactivity in the gas phase, it seems to make no difference whether negative, or zero, electron affinities are used for systems with metastable anions. For reactions in solution the evidence that is presently available is insufficient to establish a preference. In addressing this issue, we noted that electron affinity data from which atomic chemical hardness values are computed are out of date; an update to Pearson's classic 1988 table [Inorg. Chem., 1988, 27, 734-740] is thus provided.

Density functional method including weak interactions: Dispersion coefficients based on the local response approximation

A new method to calculate the atom-atom dispersion coefficients in a molecule is proposed for the use in density functional theory with dispersion (DFT-D) correction. The method is based on the local response approximation due to Dobson and Dinte [Phys. Rev. Lett. 76, 1780 (1996)], with modified dielectric model recently proposed by Vydrov and van Voorhis [J. Chem. Phys. 130, 104105 (2009)]. The local response model is used to calculate the distributed multipole polarizabilities of atoms in a molecule, from which the dispersion coefficients are obtained by an explicit frequency integral of the Casimir-Polder type. Thus obtained atomic polarizabilities are also used in the damping function for the short-range singularity. Unlike empirical DFT-D methods, the local response dispersion (LRD) method is able to calculate the dispersion energy from the ground-state electron density only. It is applicable to any geometry, free from physical constants such as van der Waals radii or atomic polarizabilities, and computationally very efficient. The LRD method combined with the long-range corrected DFT functional (LC-BOP) is applied to calculations of S22 weakly bound complex set [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. Binding energies obtained by the LC-BOP+LRD agree remarkably well with ab initio references.