Literature DB >> 26593664

An Efficient N(3)-Scaling Propagation Scheme for Simulating Two-Dimensional Infrared and Visible Spectra.

Chungwen Liang1, Thomas L C Jansen1.   

Abstract

In this paper, we develop and test a new approximate propagation scheme for calculating two-dimensional infrared and visible spectra. The new scheme scales one order more efficiently with the system size than the existing schemes. A Trotter type of approximation is used for the matrix exponent that describes the time evolution of the quantum system. This is needed for calculating the third-order response functions governing the two-dimensional infrared and visible spectra. The method is tested on a model dimer system, the amide I spectrum of the Gramicidin A antimicrobial peptide, the spectrum of the OH stretching vibration of bulk water, and a homogeneous J-aggregate. Errors due to the approximation are hardly observable in the calculated spectra. Scaling simulations with different system sizes are used to demonstrate that the new scheme is indeed scaling with the system size to the third power, one order faster than the existing methods.

Entities:  

Year:  2012        PMID: 26593664     DOI: 10.1021/ct300045c

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  15 in total

Review 1.  Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Authors:  Carlos R Baiz; Bartosz Błasiak; Jens Bredenbeck; Minhaeng Cho; Jun-Ho Choi; Steven A Corcelli; Arend G Dijkstra; Chi-Jui Feng; Sean Garrett-Roe; Nien-Hui Ge; Magnus W D Hanson-Heine; Jonathan D Hirst; Thomas L C Jansen; Kijeong Kwac; Kevin J Kubarych; Casey H Londergan; Hiroaki Maekawa; Mike Reppert; Shinji Saito; Santanu Roy; James L Skinner; Gerhard Stock; John E Straub; Megan C Thielges; Keisuke Tominaga; Andrei Tokmakoff; Hajime Torii; Lu Wang; Lauren J Webb; Martin T Zanni
Journal:  Chem Rev       Date:  2020-06-29       Impact factor: 60.622

2.  Distinguishing gramicidin D conformers through two-dimensional infrared spectroscopy of vibrational excitons.

Authors:  Paul Stevenson; Andrei Tokmakoff
Journal:  J Chem Phys       Date:  2015-06-07       Impact factor: 3.488

3.  IR Spectroscopy Can Reveal the Mechanism of K+ Transport in Ion Channels.

Authors:  Steven E Strong; Nicholas J Hestand; Alexei A Kananenka; Martin T Zanni; J L Skinner
Journal:  Biophys J       Date:  2019-11-20       Impact factor: 4.033

4.  Refinement of Peptide Conformational Ensembles by 2D IR Spectroscopy: Application to Ala‒Ala‒Ala.

Authors:  Chi-Jui Feng; Balamurugan Dhayalan; Andrei Tokmakoff
Journal:  Biophys J       Date:  2018-06-19       Impact factor: 4.033

5.  Probing the Effects of Gating on the Ion Occupancy of the K+ Channel Selectivity Filter Using Two-Dimensional Infrared Spectroscopy.

Authors:  Huong T Kratochvil; Michał Maj; Kimberly Matulef; Alvin W Annen; Jared Ostmeyer; Eduardo Perozo; Benoît Roux; Francis I Valiyaveetil; Martin T Zanni
Journal:  J Am Chem Soc       Date:  2017-05-12       Impact factor: 15.419

6.  Site-Specific Peptide Probes Detect Buried Water in a Lipid Membrane.

Authors:  Jennifer C Flanagan; Carlos R Baiz
Journal:  Biophys J       Date:  2019-03-19       Impact factor: 4.033

7.  Insulin Dissociates by Diverse Mechanisms of Coupled Unfolding and Unbinding.

Authors:  Adam Antoszewski; Chi-Jui Feng; Bodhi P Vani; Erik H Thiede; Lu Hong; Jonathan Weare; Andrei Tokmakoff; Aaron R Dinner
Journal:  J Phys Chem B       Date:  2020-06-25       Impact factor: 2.991

8.  Computational IR Spectroscopy of Insulin Dimer Structure and Conformational Heterogeneity.

Authors:  Chi-Jui Feng; Anton Sinitskiy; Vijay Pande; Andrei Tokmakoff
Journal:  J Phys Chem B       Date:  2021-04-30       Impact factor: 2.991

9.  Simple Quantum Dynamics with Thermalization.

Authors:  Thomas L C Jansen
Journal:  J Phys Chem A       Date:  2017-12-20       Impact factor: 2.781

10.  Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles.

Authors:  Pim W J M Frederix; Julien Idé; Yigit Altay; Gaël Schaeffer; Mathieu Surin; David Beljonne; Anna S Bondarenko; Thomas L C Jansen; Sijbren Otto; Siewert J Marrink
Journal:  ACS Nano       Date:  2017-07-21       Impact factor: 15.881

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