Trapped, cooled, solved: Cold‐ion spectroscopy was used to solve the three‐dimensional gas‐phase structure of the natural decapeptide gramicidin S. Experiments provide a detailed set of spectroscopic and structural constraints that unambiguously identify the most stable calculated structure of the isolated peptide. These results provide new information for modeling the biological activity of this antibiotic.

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We extended a previously developed force matching approach to systems with covalent QM/MM boundaries and describe its user-friendly implementation in the publicly available software package CPMD. We applied this approach to the challenging case of the retinal protonated Schiff base in dark state bovine rhodopsin. We were able to develop a highly accurate force field that is able to capture subtle structural changes within the chromophore that have a pronounced influence on the optical properties. The optical absorption spectrum calculated from configurations extracted from a MD trajectory using the new force field is in excellent agreement with QM/MM and experimental references.

We benchmark the performance of various computational approaches, ranging from the classical nonpolarizable force fields AMBER FF96 and FF99SB, the polarizable force fields AMBER FF02polEP and AMOEBAbio09 to the semiempirical DFT method SCC‐DFTB. The test set consists of nine conformations of gas‐phase protonated gramicidin S, a cyclic decapeptide. We discuss their structural features in relation to the intrinsic lowest energy structure, which has been solved recently by a combination of cold ion spectroscopy and high level theoretical methods (Nagornova et al., Angew Chem Int Ed 2011, 50, 5383). As a reference, we use the energetics at the M05‐2X level of theory. The latter has been validated as a suitable reference method in predicting the correct ground state structure of gas‐phase protonated bare and microsolvated tryptophan as well as gas‐phase protonated gramicidin S by comparison to experiment. We discuss the performance of the different more approximate methods in relation to their potential use as efficient and reliable tools to explore conformational space for the generation of candidate structures before refinement at the DFT level. © 2012 Wiley Periodicals, Inc.

In this work we assess the performance of different dispersion-corrected density functional theory (DFT) approaches (M06, M06-2X, DFT-D3, and DCACP) in reproducing high-level wave function based benchmark calculations on the weakly bound halogen dimers X2···X2 and X2···Ar (for X = F, Cl, Br, and I), as well as the prototype halogen bonded complexes H3CX···OCH2 (X = Cl, Br, I). In spite of the generally good performance of all tested methods for weakly bound systems, their performance for halogen-containing compounds varies largely. We find maximum errors in the energies with respect to the CCSD(T) reference values of 0.13 kcal/mol for DCACP, 0.22 kcal/mol for M06-2X, 0.47 kcal/mol for BLYP-D3, and 0.77 kcal/mol for M06. The root-mean-square deviations are 0.13 kcal/mol for DCACP and M06-2X, 0.44 kcal/mol for M06, and 0.51 kcal/mol for BLYP-D3.