Transferable atoms: an intra-atomic perspective through the study of homogeneous oligopeptides

Abstract

Quantifying an atom's transferability, in a force field context, demands a quantitative understanding of how an atom 'experiences' the surrounding environment both intra-atomically and interatomically. Here we investigate the intra-atomic (E intra A) viewpoint through the study of the atoms C α , H α , N, O, and S in a series of 'mono'-, tri-and penta-peptides. The remaining inter-atomic viewpoint consists of an electrostatic (via multipole moments), exchange and correlation components respectively, of which the electrostatic component has been previously reported. Together these four energy components, as calculated from the Interacting Quantum Atoms (IQA) partitioning approach, express the foundation of the Quantum Chemical Topological Force Field (QCTFF). In order to have transferability within a force field, smaller sample systems must be calculated and developed as representative of larger target systems. The C α , H α , N, O and S atoms in a tri-peptide are energetically comparable to those in their pentapeptide configurations, within 2.1 kJ/mol in absolute value (1 exception). Across all five elements, this energy difference is on average ∼0.3 kJ/mol. On average, the tri-peptide sample systems represent a ∼8.2Å atomic horizon around the central atoms of interest. Thus, both the previous knowledge of the ∼10.3Å horizon sphere and ∼0.4 kJ/mol error required by the electrostatic multipole moments, determine how two of the four key QCTFF energy components are affected by an atom's molecular environment. Dedication: It is a pleasure to contribute to a special issue in honour of Andreas Savin, a most generous host with whom I have enjoyed several discussions. As a deep and valiant thinker, a true scientist such as Andreas will surely continue to work in this capacity beyond his official retirement.

Unfavorable regions in the ramachandran plot: Is it really steric hindrance? The interacting quantum atoms perspective

“…The minimal energy discrepancies across Gly, Val, and Ile corroborate fragment transferability, which force field developers need in their atom typing. The results presented also support some of our other work on IQA and transferability.…”

“…The IQA approach has been used to study many different chemical systems such as the interactions of Zn(II) complexes, organoselenium molecules, halogen‐trinitromethanes, halogen bonding, and hydrogen bonding . IQA has also been used to shed light on chemical phenomena such as steric repulsion, hyperconjugation, reactions, and transferability . The broad applicability of IQA, and its well‐defined and robust quantitative nature make it ideal for the current investigation.…”

“…The investigation will allow us to identify the key atoms, both single and group thereof, that are responsible for both high‐ and low‐energy regions in the respective Ramachandran plots, along with any global trends that consistently appear across the three systems investigated. The existence of global trends at the atomic level will indicate transferability within the systems, a key cornerstone of many force fields and a topic we have previously reported on for oligopeptide chain …”

Infrared intensity analysis of hydroxyl stretching modes in carboxylic acid dimers by means of the charge–charge flux–dipole flux model

“…The intraatomic energy contribution of an atom Ω is composed by the kinetic energy of its electrons, T (Ω), the attraction energy between the electron density and the nucleus of this atom, V en (Ω), and the electron–electron interaction energy inside Ω, V ee (Ω) . Similarly, the interatomic energy for a pair of atoms, Ω and Ω ′ , can be decomposed into attraction energy between the nucleus of the first atom and the electron density distribution ascribed to the second one, V ne (Ω, Ω ′ ), and vice‐versa, V en (Ω, Ω ′ ), repulsion energy between their nuclei, V nn (Ω, Ω ′ ), and the electron–electron interaction between electron density distributions of this pair.…”

Accurate prediction of the energetics of weakly bound complexes using the machine learning method kriging

“…Conversely, the interatomic energy, V AA 0 inter , is more negative to the closer two molecules are because the interatomic, and therefore intermolecular, bonding is stronger. The relationship between IQA's intra-atomic and interatomic energies has been a topic of discussion in previous publications by our group [28,57,58]. Fig.…”