Molecular Dynamics Simulations and Instantaneous Normal-Mode Analysis of the Vibrational Relaxation of the C-H Stretching Modes of N-methylacetamide-d in Liquid Deuterated Water

被引:15
作者
Bastida, Adolfo [1 ]
Soler, Miguel A. [1 ]
Zuniga, Jose [1 ]
Requena, Alberto [1 ]
Kalstein, Adrian [2 ]
Fernandez-Alberti, Sebastian [2 ]
机构
[1] Univ Murcia, Dept Quim Fis, E-30100 Murcia, Spain
[2] Univ Nacl Quilmes, Bernal, Argentina
关键词
IR-RAMAN SPECTROSCOPY; ENERGY-TRANSFER; AMIDE-I; POLYATOMIC LIQUIDS; TEMPERATURE-DEPENDENCE; INFRARED-SPECTROSCOPY; STRUCTURAL DYNAMICS; FREQUENCY-SHIFTS; AB-INITIO; QUANTUM;
D O I
10.1021/jp106998h
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
Nonequilibrium molecular dynamics (MD) simulations and instantaneous normal mode (INMs) analyses are used to study the vibrational relaxation of the C-H stretching modes (v(s)(CH3)) of deuterated N-triethylacetamide (NMAD) in aqueous (D2O) solution. The INMs are identified unequivocally in terms of the equilibrium normal modes (ENMs), or groups of them, using a restricted version of the recently proposed Min-Cost assignment method. After excitation of the parent v(s)(CH3) modes with one vibrational quantum, the vibrational energy is shown to dissipate through both intramolecular vibrational redistribution (IVR) and intermolecular vibrational energy transfer (VET). The decay of the vibrational energy of the v(s)(CH3) modes is well fitted to a triple exponential function, with each characterizing a well-defined stage of the entire relaxation process. The first, and major, relaxation stage corresponds to a coherent ultrashort (tau(re1) = 0.07 ps) energy transfer from the parent v(s)(CH3) modes to the methyl bending modes delta(CH3), so that the initially excited state rapidly evolves into a mixed stretch bend state. In the second stage, characterized by a time of 0.92 ps, the vibrational energy flows through IVR to a number of mid-range-energy vibrations of the solute. In the third stage, the vibrational energy accumulated in the excited modes dissipates into the bath through an indirect VET process mediated by lower-energy modes, on a time scale of 10.6 ps. All the specific relaxation channels participating in the whole relaxation process are properly identified. The results from the simulations are finally compared with the recent experimental measurements of the v(s)(CH3) vibrational energy relaxation in NMAD/D2O(1) reported by Dlott et al. (J. Phys. Chem. A 2009, 113, 75.) using ultrafast infrared-Raman spectroscopy.
引用
收藏
页码:11450 / 11461
页数:12
相关论文
共 102 条
[1]   ESTABLISHMENT OF A MOLECULAR-VIBRATION DECAY ROUTE IN A LIQUID [J].
ALFANO, RR ;
SHAPIRO, SL .
PHYSICAL REVIEW LETTERS, 1972, 29 (25) :1655-&
[2]   Picosecond thermometer in the amide I band of myoglobin -: art. no. 128101 [J].
Austin, RH ;
Xie, AH ;
van der Meer, L ;
Redlich, B ;
Lindgård, PA ;
Frauenfelder, H ;
Fu, D .
PHYSICAL REVIEW LETTERS, 2005, 94 (12)
[3]   Energy transport in peptide helices: A comparison between high- and low-energy excitations [J].
Backus, Ellen H. G. ;
Nguyen, Phuong H. ;
Botan, Virgiliu ;
Pfister, Rolf ;
Moretto, Alessandro ;
Crisma, Marco ;
Toniolo, Claudio ;
Stock, Gerhard ;
Hamm, Peter .
JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 112 (30) :9091-9099
[4]   Instantaneous normal modes, resonances, and decay channels in the vibrational relaxation of the amide I mode of N-methylacetamide-D in liquid deuterated water [J].
Bastida, Adolfo ;
Angel Soler, Miguel ;
Zuniga, Jose ;
Requena, Alberto ;
Kalstein, Adrian ;
Fernandez-Alberti, Sebastian .
JOURNAL OF CHEMICAL PHYSICS, 2010, 132 (22)
[5]   MOLECULAR-DYNAMICS WITH COUPLING TO AN EXTERNAL BATH [J].
BERENDSEN, HJC ;
POSTMA, JPM ;
VANGUNSTEREN, WF ;
DINOLA, A ;
HAAK, JR .
JOURNAL OF CHEMICAL PHYSICS, 1984, 81 (08) :3684-3690
[6]   Energy transport in peptide helices [J].
Botan, Virgiliu ;
Backus, Ellen H. G. ;
Pfister, Rolf ;
Moretto, Alessandro ;
Crisma, Marco ;
Toniolo, Claudio ;
Nguyen, Phuong H. ;
Stock, Gerhard ;
Hamm, Peter .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (31) :12749-12754
[7]   HARMONIC DYNAMICS OF PROTEINS - NORMAL-MODES AND FLUCTUATIONS IN BOVINE PANCREATIC TRYPSIN-INHIBITOR [J].
BROOKS, B ;
KARPLUS, M .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES, 1983, 80 (21) :6571-6575
[8]  
Brooks C.L., 1988, ADV CHEM PHYS, V71, P1
[9]   Vibrational frequency shifts and relaxation rates for a selected vibrational mode in cytochrome c [J].
Bu, LT ;
Straub, JE .
BIOPHYSICAL JOURNAL, 2003, 85 (03) :1429-1439
[10]   THE SHORT-TIME DYNAMICS OF MOLECULAR LIQUIDS - INSTANTANEOUS-NORMAL-MODE THEORY [J].
BUCHNER, M ;
LADANYI, BM ;
STRATT, RM .
JOURNAL OF CHEMICAL PHYSICS, 1992, 97 (11) :8522-8535