Tyrosine-glycine revisited: Resolving the discrepancy between theory and experiment

Holroyd, Leo F.; Mourik, Tanja van

doi:10.1016/j.cplett.2014.12.055

Cited by 6 publications

(5 citation statements)

References 22 publications

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“…As the global free energy minima of WG and WGG at 300 K match the experimental results 9 , it is suggested that the high population structures at about 300 K might have approximately been kept during the supersonic cooling process 20 . Similar result is also found recently on the IR spectra of YG conformers (Y = tyrosine) 21 . However, the number of conformations predicted by the free energy consideration is substantially more than that observed experimentally.…”

Section: Introductionsupporting

confidence: 91%

Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane

Yang

Liu

Lin

2017

Sci Rep

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Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.

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Section: Introductionsupporting

confidence: 91%

Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane

Yang

Liu

Lin

2017

Sci Rep

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“…Interestingly, the need of performing thermal corrections was emphasized in a recent study of the Tyr-Gly dipeptide. 229 While the most stable conformer was a folded and H-bonded one at 0 K, thermal corrections at 400 K made non-H-bonded conformers more stable. This finding was in accordance with spectroscopic results, which did not find any H-bonded conformers.…”

Section: Applicationsmentioning

confidence: 95%

“…Also, it was shown that the ranking of conformers differed on the free energy surface from the ranking on the PES, pointing out the importance of free energy analysis (via, for example, thermal corrections from statistical thermodynamics). Interestingly, the need of performing thermal corrections was emphasized in a recent study of the Tyr-Gly dipeptide . While the most stable conformer was a folded and H-bonded one at 0 K, thermal corrections at 400 K made non-H-bonded conformers more stable.…”

Section: Applicationsmentioning

confidence: 99%

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

Kubař²,

et al. 2016

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Semiempirical (SE) methods can be derived from either Hartree–Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.

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“…Modern quantum-mechanical (QM) computations provide a much more accurate description of potential energy surfaces compared to the available RNA FFs . Unfortunately, the applicability of accurate QM methods is limited to single-point calculations and geometry optimizations of moderately sized biomolecules up to a few hundred atoms. ,− QM single-point energies suffer from the lack of conformational sampling for highly flexible molecules, which hinders the calculation of free energies and enthalpies. Furthermore, widely applied continuum solvation models lack specific solvent–solute interactions that are known to influence the solute geometry to various degrees. , Nevertheless, QM computations of complete nucleic acid building blocks were proven to be a viable tool for supporting the interpretation of MD simulations and identifying potential pitfalls of the FF description. − …”

Section: Introductionmentioning

confidence: 99%

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

et al. 2016

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Classical force field (FF) molecular dynamics (MD) simulations of RNA tetranucleotides have substantial problems in reproducing conformer populations indicated by NMR experiments. To provide more information about the possible sources of errors, we performed quantum mechanical (QM, TPSS-D3/def2-TZVP) and molecular mechanics (MM, AMBER parm99bsc0+χ) calculations of different r(CCCC), r(GACC), and r(UUUU) conformers obtained from explicit solvent MD simulations. Solvent effects in the static QM and MM calculations were mimicked using implicit solvent models (COSMO and Poisson-Boltzmann, respectively). The comparison of QM and MM geometries and energies revealed that the two methodologies provide qualitatively consistent results in most of the cases. Even though we found some differences, these were insufficient to indicate any systematic corrections of the RNA FF terms that could improve the performance of classical MD in simulating tetranucleotides. On the basis of these findings, we inferred that the overpopulation of intercalated conformers in the MD simulations of RNA tetramers, which were not observed experimentally, might be predominantly caused by imbalanced water-solvent and water-water interactions. Apart from the large-scale QM calculations performed to assess the performance of the AMBER FF, a representative spectrum of faster QM methods was tested.

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Tyrosine-glycine revisited: Resolving the discrepancy between theory and experiment

Abstract: Energies of 20 conformers of the Tyr-Gly dipeptide were computed using DSD-PBEP86-D3BJ/aug-cc-VTZ, with geometries from M06-2X/6-31+G* and

Cited by 6 publications

References 22 publications

Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane

Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane

Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications

Comparative Assessment of Different RNA Tetranucleotides from the DFT-D3 and Force Field Perspective

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