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求助1-dimensional hindered rotor approximation 相关问题！
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最近，我在做多氮化合物的叠氮基关环的机理研究，由于叠氮基单键旋转，反应物存在正反异构，因此，我们分别做反应物ap-DAT 和sp-DAT的关环动力学，得到反应能垒和速率常数。现在，收到审稿人的意见，极力要求采用他提出的1-dimensional hindered rotor approximation 和Multidimensional methods 来重新计算我们研究的多氮化合物体系。我的问题有两点： 1.1-dimensional hindered rotor approximation 和Multidimensional methods 到底是什么理论，用来做什么？ 2.审稿人提到的计算程序：software such as MSTor, Variflex, and PAPER，要怎样获得？ 还请各位高手帮忙解决这一棘手的问题，不胜感激！！！ 审稿人的意见如下： Dear Authors, Below I expand briefly on the points I made in my reviews. I include some references on the subject that in my personal opinion are good and hopefully helpful. There is a wide literature available on the issue of torsional motion in molecules, so I encourage you to supplement my list by articles that seem most instructive to you. My main complaint is that, the paper treats and describes different conformers as separate chemical species. Whether that is a valid assumption is not shown in the paper. Judging from your results, it does not seem to be the case. There are many approaches to include different conformers (multiple structures) in the partition function or density of states calculation and to capture the transition between harmonic oscillator and free rotor as a function of T. By “multistructural”, I mean approximations that take into account the fact that a molecule samples region of phase space that can include more than one conformational minimum (all methods mentioned below would fall into this category). By “1D” method I mean separable 1-dimensional hindered rotor approximation. Approximations for treating the high-amplitude rovibrational motions in molecules and their references include: MS-LH1,2,3 Multistructural locally harmonic approximation that expresses the partition function as a sum over the contributions from all the known conformers as calculated using the harmonic oscillator formula. 1-dimensional hindered rotor approximation4,5,6,7,8 This approximation assumes that the vibrations/rotations along different bonds are well described by separate 1-dimensional potentials. These potentials are obtained from electronic structure calculations as partial optimizations along each of the torsional coordinates. This also assumes that normal mode frequencies can be assigned to torsional motions (this is easier to fulfill for small molecules, but may be also true for the molecules studied in this paper). Here is a nice paper on the accuracy of such approaches: 9 Multidimensional methods interpolate the conformational potential energy surface from the known points on the conformational energy surface. These approaches include: • MS-T(U) (for uncoupled)1 and MS-T(C) (“coupled”)10 methods that use the user-provided information on conformational minima, • two-dimensional coupled treatment of Fernandes-Ramos11 • multidimentional treatment based on the potential energy surface provided on a multidimensional grid12 Many examples of use of these methods in the rate constant calculations are available in the literature.13,2,14 With one exception, the above approximations are implemented in Sample Text I hope this helps. With kind regards, Bibliography: 1 J. Zheng, T. Yu, E. Papajak, I.M. Alecu, S.L. Mielke, and D.G. Truhlar, Phys. Chem. Chem. Phys. 13, 10885 (2011). 2 X. Xu, E. Papajak, J. Zheng, and D.G. Truhlar, Phys. Chem. Chem. Phys. 14, 4204 (2012). 3 R. Meana-Pañeda and A. Fernández-Ramos, J. Am. Chem. Soc. 134, 346 (2012). 4 P.Y. Ayala and B.H. Schlegel, Journal of Chemical Physics 108, 2314 (1998). 5 B.A. Ellingson, V.A. Lynch, S.L. Mielke, and D.G. Truhlar, J. Chem. Phys. 125, 084305 (2006). 6 Y.-Y. Chuang and D.G. Truhlar, J. Chem. Phys. 112, 1221 (2008). 7 K.S. Pitzer, J. Chem. Phys. 10, 428 (1942). 8 K.S. Pitzer, J. Chem. Phys. 14, 239 (1946). 9 C.Y. Lin, E.I. Izgorodina, and M.L. Coote, J. Phys. Chem. A 112, 1956 (2008). 10 J. Zheng and D.G. Truhlar, Journal of Chemical Physics 9, 2875 (2013). 11 A. Fernández-Ramos, J. Chem. Phys. 138, 134112 (2013). 12 Y. Georgievskii, J.A. Miller, M.P. Burke, and S.J. Klippenstein, J. Phys. Chem. A 117, 12146 (2013). 13 T. Yu, J. Zheng, and D.G. Truhlar, Chem. Sci. 2, 2199 (2011). 14 J. Zheng, R. Meana-Pañeda, and D.G. Truhlar, J. Am. Chem. Soc. 140320120118003 (2014). 15 J. Zheng, S.L. Mielke, K.L. Clarkson, and D.G. Truhlar, Computer Physics Communications 183, 1803 (2012). 16 J. Zheng, R. Meana-Pañeda, and D.G. Truhlar, Computer Physics Communications 184, 2032 (2013). 17 S.J. Klippenstein, A.F. Wagner, S. Robertson, R.C. Dunbar, D.M. Wardlaw, VARIFLEX, Version 1.0, A Chemical Kinetics Computer Program, Argonne National Laboratory, 1999 |
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2楼2015-03-13 08:21:27