On-the-fly adiabatically switched semiclassical initial value representation molecular dynamics for vibrational spectroscopy of biomolecules

被引:18
作者
Botti, Giacomo [1 ]
Ceotto, Michele [1 ]
Conte, Riccardo [1 ]
机构
[1] Univ Milan, Dipartimento Chim, Via Golgi 19, I-20133 Milan, Italy
基金
欧洲研究理事会;
关键词
HERMAN-KLUK PROPAGATOR; MATRIX-ISOLATION; AMINO-ACIDS; GLYCINE; PROLINE; CONFORMERS; ENERGIES; SPECTRA; SYSTEMS;
D O I
10.1063/5.0075220
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
Semiclassical (SC) vibrational spectroscopy is a technique capable of reproducing quantum effects (such as zero-point energies, quantum resonances, and anharmonic overtones) from classical dynamics runs even in the case of very large dimensional systems. In a previous study [Conte et al. J. Chem. Phys. 151, 214107 (2019)], a preliminary sampling based on adiabatic switching has been shown to be able to improve the precision and accuracy of semiclassical results for challenging model potentials and small molecular systems. In this paper, we investigate the possibility to extend the technique to larger (bio)molecular systems whose dynamics must be integrated by means of ab initio "on-the-fly " calculations. After some preliminary tests on small molecules, we obtain the vibrational frequencies of glycine improving on pre-existing SC calculations. Finally, the new approach is applied to 17-atom proline, an amino acid characterized by a strong intramolecular hydrogen bond.
引用
收藏
页数:11
相关论文
共 83 条
[1]   Representing molecular ground and excited vibrational eigenstates with nuclear densities obtained from semiclassical initial value representation molecular dynamics [J].
Aieta, Chiara ;
Bertaina, Gianluca ;
Micciarelli, Marco ;
Ceotto, Michele .
JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (21)
[2]   Anharmonic quantum nuclear densities from full dimensional vibrational eigenfunctions with application to protonated glycine [J].
Aieta, Chiara ;
Micciarelli, Marco ;
Bertaina, Gianluca ;
Ceotto, Michele .
NATURE COMMUNICATIONS, 2020, 11 (01)
[3]   Machine learning unifies the modeling of materials and molecules [J].
Bartok, Albert P. ;
De, Sandip ;
Poelking, Carl ;
Bernstein, Noam ;
Kermode, James R. ;
Csanyi, Gabor ;
Ceriotti, Michele .
SCIENCE ADVANCES, 2017, 3 (12)
[4]   Tunneling Lifetime of the ttc/VIp Conformer of Glycine in Low-Temperature Matrices [J].
Bazso, Gabor ;
Magyarfalvi, Gabor ;
Tarczay, Gyoergy .
JOURNAL OF PHYSICAL CHEMISTRY A, 2012, 116 (43) :10539-10547
[5]   On-the-fly ab initio semiclassical evaluation of third-order response functions for two-dimensional electronic spectroscopy [J].
Begusic, Tomislav ;
Vanicek, Jiri .
JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (18)
[6]   Reduced rovibrational coupling Cartesian dynamics for semiclassical calculations: Application to the spectrum of the Zundel cation [J].
Bertaina, G. ;
Di Liberto, G. ;
Ceotto, M. .
JOURNAL OF CHEMICAL PHYSICS, 2019, 151 (11)
[7]   Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone φ, ψ and Side-Chain χ1 and χ2 Dihedral Angles [J].
Best, Robert B. ;
Zhu, Xiao ;
Shim, Jihyun ;
Lopes, Pedro E. M. ;
Mittal, Jeetain ;
Feig, Michael ;
MacKerell, Alexander D., Jr. .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (09) :3257-3273
[8]   Wigner Distribution by Adiabatic Switching in Normal Mode or Cartesian Coordinates and Molecular Applications [J].
Bose, Amartya ;
Makri, Nancy .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2018, 14 (11) :5446-5458
[9]   Herman-Kluk propagator is free from zero-point energy leakage [J].
Buchholz, Max ;
Fallacara, Erika ;
Gottwald, Fabian ;
Ceotto, Michele ;
Grossmann, Frank ;
Ivanov, Sergei D. .
CHEMICAL PHYSICS, 2018, 515 :231-235
[10]   Simplified approach to the mixed time-averaging semiclassical initial value representation for the calculation of dense vibrational spectra [J].
Buchholz, Max ;
Grossmann, Frank ;
Ceotto, Michele .
JOURNAL OF CHEMICAL PHYSICS, 2018, 148 (11)