A mathematical and computational review of Hartree-Fock SCF methods in Quantum Chemistry

We present here a review of the fundamental topics of Hartree-Fock theory in Quantum Chemistry. From the molecular Hamiltonian, using and discussing the Born-Oppenheimer approximation, we arrive to the Hartree and Hartree-Fock equations for the electronic problem. Special emphasis is placed in the most relevant mathematical aspects of the theoretical derivation of the final equations, as well as in the results regarding the existence and uniqueness of their solutions. All Hartree-Fock versions with different spin restrictions are systematically extracted from the general case, thus providing a unifying framework. Then, the discretization of the one-electron orbitals space is reviewed and the Roothaan-Hall formalism introduced. This leads to a exposition of the basic underlying concepts related to the construction and selection of Gaussian basis sets, focusing in algorithmic efficiency issues. Finally, we close the review with a section in which the most relevant modern developments (specially those related to the design of linear-scaling methods) are commented and linked to the issues discussed. The whole work is intentionally introductory and rather self-contained, so that it may be useful for non experts that aim to use quantum chemical methods in interdisciplinary applications. Moreover, much material that is found scattered in the literature has been put together here to facilitate comprehension and to serve as a handy reference.Comment: 64 pages, 3 figures, tMPH2e.cls style file, doublesp, mathbbol and subeqn package

Random-phase approximation and its applications in computational chemistry and materials science

The random-phase approximation (RPA) as an approach for computing the electronic correlation energy is reviewed. After a brief account of its basic concept and historical development, the paper is devoted to the theoretical formulations of RPA, and its applications to realistic systems. With several illustrating applications, we discuss the implications of RPA for computational chemistry and materials science. The computational cost of RPA is also addressed which is critical for its widespread use in future applications. In addition, current correction schemes going beyond RPA and directions of further development will be discussed.Comment: 25 pages, 11 figures, published online in J. Mater. Sci. (2012

A quantum chemistry study of curvature effects on boron nitride nanotubes/nanosheets for gas adsorption

Quantum chemistry calculations were performed to investigate the effect of the surface curvature of a Boron Nitride (BN) nanotube/nanosheet on gas adsorption. Curved boron nitride layers with different curvatures interacting with a number of different gases including noble gases, oxygen, and water on both their convex and concave sides of the surface were studied using density functional theory (DFT) with a high level dispersion corrected functional. Potential energy surfaces of the gas molecules interacting with the selected BN surfaces were investigated. In addition, the charge distribution and electrostatic potential contour of the selected BN surfaces are discussed. The results reveal how the curvature of the BN surfaces affects gas adsorption. In particular, small curvatures lead to a slight difference in the physisorption energy, while large curvatures present distinct potential energy surfaces, especially for the short-range repulsion

Oxidative protein labeling in mass-spectrometry-based proteomics

Oxidation of proteins and peptides is a common phenomenon, and can be employed as a labeling technique for mass-spectrometry-based proteomics. Nonspecific oxidative labeling methods can modify almost any amino acid residue in a protein or only surface-exposed regions. Specific agents may label reactive functional groups in amino acids, primarily cysteine, methionine, tyrosine, and tryptophan. Nonspecific radical intermediates (reactive oxygen, nitrogen, or halogen species) can be produced by chemical, photochemical, electrochemical, or enzymatic methods. More targeted oxidation can be achieved by chemical reagents but also by direct electrochemical oxidation, which opens the way to instrumental labeling methods. Oxidative labeling of amino acids in the context of liquid chromatography(LC)–mass spectrometry (MS) based proteomics allows for differential LC separation, improved MS ionization, and label-specific fragmentation and detection. Oxidation of proteins can create new reactive groups which are useful for secondary, more conventional derivatization reactions with, e.g., fluorescent labels. This review summarizes reactions of oxidizing agents with peptides and proteins, the corresponding methodologies and instrumentation, and the major, innovative applications of oxidative protein labeling described in selected literature from the last decade

Energy Analysis on Small to Medium Sized H-Bonded Complexes

peer reviewedDimers (water-methanol, guanine-cytosine) as well as trimers (methanol-water-imidazole, formamide-methylformate-formamide), are studied as H-bonded complexes of increasing complexity. All the investigated conformations have been fully optimized. In particular, it is the first time that all the intra- and intermolecular parameters of the guanine-cytosine complex are left variable. In minimal basis sets, the planar conformation has been found to be a first-order critical point. The minimal basis set MINI-1 has been adapted to provide nearly planar amides. The stability of the complexes is accounted for by four energy components of the same order: the first-order term (electrostatic + exchange), the polarization, the charge transfer and the correlation terms. In the case of the studied trimers, the energy components, apart from the electrostatic one, have been found to be nearly additive