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Volumn 9, Issue 18, 2003, Pages 4396-4404

Car-Parrinello molecular dynamics study of the rearrangement of the valeramide radical cation

Author keywords

Amides; Intramolecular hydrogen transfer; Mass spectrometry; Molecular dynamics; Radical cations; Temperature effects

Indexed keywords

ACTIVATION ENERGY; CARBON; COMPUTER SIMULATION; DISSOCIATION; FREE RADICALS; HYDROGEN; IONIZATION; MASS SPECTROMETRY; MOLECULAR DYNAMICS; POSITIVE IONS; THERMAL EFFECTS;

EID: 0141561869     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/chem.200305127     Document Type: Article
Times cited : (7)

References (44)
  • 9
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    • A. H. Zewail, Angew. Chem. 2000, 112, 2689; Angew. Chem. Int. Ed. 2000, 39, 2587.
    • (2000) Angew. Chem. , vol.112 , pp. 2689
    • Zewail, A.H.1
  • 10
    • 0034604660 scopus 로고    scopus 로고
    • A. H. Zewail, Angew. Chem. 2000, 112, 2689; Angew. Chem. Int. Ed. 2000, 39, 2587.
    • (2000) Angew. Chem. Int. Ed. , vol.39 , pp. 2587
  • 22
    • 0000323669 scopus 로고    scopus 로고
    • Ab initio molecular dynamics: Theory and implementation
    • (Ed.: J. Grotendorst), NIC Series 1, Forschungszentrum Jülich, Jülich (Germany)
    • D. Marx, J. Hutter, Ab Initio Molecular Dynamics: Theory and Implementation, In Modern Methods and Algorithms of Quantum Chemistry (Ed.: J. Grotendorst), NIC Series 1, Forschungszentrum Jülich, Jülich (Germany), 2000.
    • (2000) Modern Methods and Algorithms of Quantum Chemistry
    • Marx, D.1    Hutter, J.2
  • 34
    • 0141728274 scopus 로고    scopus 로고
    • note
    • The temperature was obtained as an average during the CPMD run. Instead of using a thermostat, another common method of adjusting the system to a desired temperature is to use, as the initial temperature for the CPMD simulation, a temperature which is approximately two times higher than the desired one. As time progresses, the system adjusts to the desired temperature and fluctuates around an average value, which in the present case equals 519 K.
  • 37
    • 0141616348 scopus 로고    scopus 로고
    • note
    • The system was adjusted to the particular constraint value within 1000 steps of the simulation. Therefore, the first ≈1000 steps were not taken into account for an estimation of the average force (average Lagrangian) acting on the system as a result of the constraint introduced in the system. After 1000 steps of the simulation, the average value of the Lagrangian fluctuates around a mean value that is taken for the estimation of the free energy through the integration scheme (for technical details, see refs. [20, 21]).
  • 38
    • 0141728271 scopus 로고    scopus 로고
    • note
    • 1).
  • 39
    • 0141839556 scopus 로고    scopus 로고
    • note
    • Average temperatures of 521 K and 523 K as obtained during the CPMD trajectories.
  • 40
    • 0141504862 scopus 로고    scopus 로고
    • note
    • More specifically, this corresponds to a part of the translational energy that is associated with only one degree of freedom, namely the reaction coordinate. In case there are no other factors that might energetically facilitate a reaction (e.g. an entropy increase during a process or an exothermic reaction), only the thermal motion of the system in the direction of a reaction coordinate makes the reaction feasible.
  • 41
    • 0141839562 scopus 로고    scopus 로고
    • note
    • For details of the labeling code, see ref. [5]. A superscript in the labeling scheme points to one specific conformer although, in the case of the CPMD studies, because of the dynamical picture, we refrain from addressing a particular conformer. Therefore, labeled structures without a superscript represent a conformational subspace.
  • 42
    • 0141616346 scopus 로고    scopus 로고
    • note
    • A change in only one O-H distance is depicted in the inset in Figure 5. The distance between the other hydrogen atom attached to C4 and oxygen was also monitored resulting in a picture comparable to the that depicted in the inset of Figure 5.
  • 43
    • 0141839555 scopus 로고    scopus 로고
    • note
    • The short CPMD simulations for a particular value of the constrained parameter lasted for at least 0.9 ps. The system was adjusted to the particular constraint value within ≈3000 steps of the simulation. Therefore, the first 3000 steps were not taken into account for an estimation of the average force acting on the system as a result of the constraint introduced into the system.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.