How to make chemical-bonding analysis of VASP results: lobster users guide 1.0.0 (original) (raw)

Molecular Modeling and Electronic Structure Calculations

2017

This laboratory is designed to use the program GAMESS (General Atomic Molecular Electronic Structure System, developed in Gordon research group at Iowa State) through a website called nanoHUB (www.nanoHUB.org) to determine the geometric and electronic properties of numerous small molecules. GAMESS uses ab initio and semi-empirical calculations to determine these properties. Ab initio (“from first principles”) calculations solve the Schrödinger equation using the exact computational expression for the energy of the electrons. The particular ab initio method that we will use for this lab is called HartreeFock (HF). HF uses an approximate wavefunction to solve Schrödinger, so the resulting molecular properties are approximate, but for many applications the accuracy is adequate for interpreting experiments. Semi-empirical calculations use an approximate energy expression for the electrons, but solve for the exact wavefunction associated with this expression. Usually the energy expressio...

2_deLange_et_al-2018-J_Comp_Chem.pdf

Atomic interaction lines (AILs) and the QTAIM's molecular graphs provide a predominantly two-center viewpoint of interatomic interactions. While such a bicentric interpretation is sufficient for most covalent bonds, it fails to adequately describe both formal multicenter bonds as well as many non-covalent interactions with some multicenter character. We present an extension to our Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) electron density (ED) decomposition scheme, with which we can measure how any atom-pair's delocalized density concentrates, depletes or reduces the electron density in the vicinity of a bond critical point. We apply our method on five classical bonds/interactions, ranging from formal either two-or three-center bonds, a non-covalent interaction (an intramolecular hydrogen bond) to organometallic bonds with partial multicenter character. By use of 3D representation of specific atom-pairs contributions to the delocalized density we (i) fully recover previous notion of multicenter bonding in diborane and predominant bicentric character of a single covalent CAC bond, (ii) reveal a multicenter character of an intramolecular H-bond and (iii) illustrate, relative to a Schrock carbene, a larger degree of multicenter MAC interaction in a Fischer carbene (due to a presence of a heteroatom), whilst revealing the holistic nature of AILs from multicenter ED decomposition.

MOLCAS: a program package for computational chemistry

Computational Materials Science, 2003

The program system MOLCAS is a package for calculations of electronic and structural properties of molecular systems in gas, liquid, or solid phase. It contains a number of modern quantum chemical methods for studies of the electronic structure in ground and excited electronic states. A macromolecular environment can be modeled by a combination of quantum chemistry and molecular mechanics. It is further possible to describe a crystalline material using model potentials. Solvent effects can be treated using continuum models or by combining quantum chemical calculations with molecular dynamics or Monte-Carlo simulations.

4_delange_et_al_2017_Struct_Chem.pdf

We have discovered, using developed by us recently FALDI and FAMSEC computational techniques, fundamentally distinct mechanisms of intramolecular red-and blue-shifted H-bond formation that occurred in different conformers of the same molecule (amino-acid β-alanine) involving the same heteroatoms (O-H⋅⋅⋅N and N-H⋅⋅⋅O). Quantitative topological, geometric and energetic data of both H-bonds obtained with well-known QTAIM and IQA methodologies agree with what is known regarding H-bonding in general. However, the FALDI charge and decomposition scheme for calculating in real space 3D conformational deformation densities provided clear evidence that the process of electron density redistribution taking place on the formation of the stronger red-shifted H-bond is fundamentally distinct from the weaker blue-shifted H-bond. Contributions made by atoms of the X-H⋅⋅⋅Y-Z fragment (IUPAC notation) as well as distinct atoms on the H-bond formation were fully explored. The FAMSEC energy decomposition approach showed that the atoms involved in formation of the red-shifted H-bond interact in a fundamentally different fashion, both locally and with the remainder of the molecule, as compared with those of the blue-shifted H-bond. Excellent correlations of trends obtained with QTAIM, IQA, FAMSEC and FALDI techniques were obtained. Commentary regarding IUPAC recommended definition of an H-bond and validity of observed AILs (or bond paths) of the two H-bond kinds is also discussed.