Conformational analysis of arginine in gas phase—A strategy for scanning the potential energy surface effectively

Abstract

Abstract:The determination of all possible low-lying energy conformers of flexible molecules is of fundamental interest for various applications. It necessitates a reliable conformational search that is able to detect all important minimum structures and calculates the energies on an adequate level of theory. This work presents a strategy to identify low-energy conformers using arginine as an example by means of a force-field based conformational search in combination with high-level geometry optimizations (RI-MP2/TZVPP1). The methods used for various stages in the conformational search strategy are shown and various pitfalls are discussed. We can show that electronic energies calculated on a DFT level of theory with standard exchange-correlation functionals strongly underestimate the intramolecular stabilization resulting from stacked orientations of the guanidine and carbonyl moiety of arginine due to the deficiency of DFT to describe dispersion effects. In this case by usage of electron correlation methods, low energy conformers comprising stacked arrangements that are counterintuitive become favorable.

Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine

“…3 Therefore, whether zwitterions can be predominantly preferred in the gas phase has been extensively discussed. [13][14][15][16][17][18][19] These charged structures do not have effective conformational distributions due to the relatively high Gibbs free energies. [10][11][12] The zwitterions, as local minima on the potential energy surface (PES), only theoretically exist for arginine and histidine.…”

Interactions of Zn(II) with single and multiple amino acids. Insights from density functional and ab initio calculations

“…S15). Figure shows good linear relationships are applicable to other M; in addition, the linear characteristics may not be altered by mutations . Noting the sidechains of AA can interact with M and may cause deviations, which will be studied in the future.…”

“…Fourth, some binding isomers of Zn 2+ interactions with three and four glycines were calculated. Fifth, the binding affinities of M with glycine numbers ( n ) were correlated, and other AA were also considered . Sixth, DFT to treat metal‐containing protein systems was assessed by comparing with MP2 results.…”

Hybrid optimization with improved tabu search

“…The only information which is obtainable in these unknown systems is the input-output behaviour. As examples in engineering applications; one can point at fluid power circuits [10], electronic circuit designs [2], balancing of hydraulic turbines [43], computational chemistry [40], developing optical fibers [51], signal setting problems [6], non-destructive control [5], optimization of electromagnetic devices [21] and others. The diversity of applications has led to a great deal of interest to develop global continuous optimization methods (GCOM) which are capaDue to the lack of information about the behaviour of an unknown system, no specific assumptions are being made.…”