QM/MM Simulations of Vibrational Spectra in Bacteriorhodopsin and Channelrhodopsin-2 Supporting Information

نویسندگان

  • Kai Welke
  • Hiroshi C. Watanabe
  • Tino Wolter
  • Michael Gaus
  • Marcus Elstner
چکیده

Here, we document the performance of different DFT and DFTB methods with respect to the C−O stretch vibration, both in terms of absolute frequencies and effects of hydrogen bonds on the frequencies. We demonstrate, that PBE/def2-TZVP is a suitable reference for the C−O stretch frequency in carboxylic acids. In the following text, the abbreviations ME (mean error), MAE (mean absolute error), MSE (mean squared error) and GGA (generalized gradient approximation) are used.

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

QM/MM simulations of vibrational spectra of bacteriorhodopsin and channelrhodopsin-2.

Channelrhodopsin-2 is a light-gated ion channel, which has been studied intensively over the last decade. Vibrational spectroscopic experiments started to shed light on the structural changes, that occur during the photocycle, especially in the hydrogen-bonded network surrounding the protonated D156 and C128 - the DC gate. However, the interpretation of these experiments was only based on homol...

متن کامل

Retinal isomerization and water-pore formation in channelrhodopsin-2

Channelrhodopsin-2 (ChR2) is a light-sensitive ion channel widely used in optogenetics. Photoactivation triggers a trans-to-cis isomerization of a covalently bound retinal. Ensuing conformational changes open a cation-selective channel. We explore the structural dynamics in the early photocycle leading to channel opening by classical (MM) and quantum mechanical (QM) molecular simulations. With ...

متن کامل

Supporting Information for: Computational Insights on Crystal Structures of the Oxygen- Evolving Complex of Photosystem II with either Ca or Ca Substituted by Sr

SUPPORTING INFORMATION S1. Method details for QM/MM S2. Spin densities for Ca and Sr QM/MM models in the S1, S0, S-1, and S-2 states S3. Interatomic distances for OEC atoms in QM/MM models S4. Structural changes due to Ca/Sr substitution in QM/MM models of the S1, S0, S-1, and S-2 states S5. EXAFS simulations S6. RMSDs of QM/MM models against XRD coordinates S7. QM/MM optimized coordinates QM/M...

متن کامل

Theoretical Studies of the Vibrational Spectra and Molecular Structures of Dosulepin and Doxepin

Dosulepin and doxepin are tricyclic antidepressants. The molecular geometries, harmonic vibrational frequencies, quantum chemical parameters and thermodynamic properties of dosulepin and doxepin were calculated by Generalized Gradient Approximation methods developed by Perdew and Wang (GGA-PW91) and Becke-Lee-Yang-Parr (GGA-BLYP) in the gas phase and solution media. The local reactivity of thes...

متن کامل

New Book Proposal Excited-State Hydrogen Bonding and Hydrogen Tranfser

This chapter reviews recent results on the vibrational dynamics of hydrogen-bonded nucleic acid base pairs putting special emphasis on the signatures of hydrogen bonding in linear and nonlinear infrared spectroscopy. Hybrid QM/MM trajectory simulations are discussed as a means for obtaining information on geometric correlations and hydrogen bond fluctuations in the condensed phase. A detailed a...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2012