Anharmonic

Pesiherbe G H and Hase W L 1996 Statistical anharmonic unimolecular rate constants for the... 

Troe J 1995 Simplified models for anharmonic numbers and densities of vibrational states. I. Application to NO2 and Chem. Phys. 190 381-92... 

Song K and Hase W L 1999 Fitting classical microcanonical unimolecular rate constants to a modified RRK expression anharmonic and variational effects J. Chem. Phys. 110 6198-207... 

Wolf R J and Hase W L 1980 Quasiperiodic trajectories for a multidimensional anharmonic classical Hamiltonian excited above the unimolecular threshold J. Chem. Phys. 73 3779-90... 

Treanor C E, Rich J W and Rehm R G 1968 Vibrational relaxation of anharmonic oscillators with exchange-dominated collisions J. Chem. Phys. 48 1798-807... 

Hollenstein H, Marquardt R, Quack M and Suhm M A 1994 Dipole moment function and equilibrium structure of methane In an analytical, anharmonic nine-dimenslonal potential surface related to experimental rotational constants and transition moments by quantum Monte Carlo calculations J. Chem. Phys. 101 3588-602... 

Marquardt R and Quack M 1989 Infrared-multlphoton excitation and wave packet motion of the harmonic and anharmonic oscillators exact solutions and quasiresonant approximation J. Chem. Phys. 90 6320-7... 

After transforming to Cartesian coordinates, the position and velocities must be corrected for anharmonicities in the potential surface so that the desired energy is obtained. This procedure can be used, for example, to include the effects of zero-point energy into a classical calculation. 

Eqs. (D.5)-(D.7). However, when perturbations occur due to anharmonicity, the wave functions in Eqs. (D.11)-(D.13) will provide the conect zeroth-order ones. The quantum numbers and v h are therefore not physically significant, while V2 arid or V2 and I2 = m, are. It should also be pointed out that the degeneracy in the vibrational levels will be split due to anharmonicity [28]. 

The influence of solvent can be incorporated in an implicit fashion to yield so-called langevin modes. Although NMA has been applied to allosteric proteins previously, the predictive power of normal mode analysis is intrinsically limited to the regime of fast structural fluctuations. Slow conformational transitions are dominantly found in the regime of anharmonic protein motion. 

Hayward et al. 1994] Hayward, S., Kitao, A., Go, N. Harmonic and anharmonic aspects in the dynamics of BPTI A normal mode analysis and principal component analysis. Prot. Sci. 3 (1994) 936-943 [Head-Gordon and Brooks 1991] Head-Gordon, T., Brooks, C.L. Virtual rigid body dynamics. Biopol. 31 (1991) 77-100... 

Steven Hayward, Akio Kitao, and Nobuhiro Go. Harmonic and anharmonic aspects in the dynamics of BPTI A normal mode analysis and principal component analysis. Physica Scripta, 3 936-943, 1994. 

The LIN method ( Langevin/Implicit/Normal-Modes ) combines frequent solutions of the linearized equations of motions with anharmonic corrections implemented by implicit integration at a large timestep. Namely, we express the collective position vector of the system as X t) = Xh t) + Z t). (In LN, Z t) is zero). The first part of LIN solves the linearized Langevin equation for the harmonic reference component of the motion, Xh t)- The second part computes the residual component, Z(t), with a large timestep. 

R. M. Levy, O. de la Luz Rojas, and R. A. Friesner. Quasi-harmonic method for calculating vibrational spectra from classical simulations on multidimensional anharmonic potential surfaces. J. Phys. Chem., 88 4233-4238, 1984. 

Among the main theoretical methods of investigation of the dynamic properties of macromolecules are molecular dynamics (MD) simulations and harmonic analysis. MD simulation is a technique in which the classical equation of motion for all atoms of a molecule is integrated over a finite period of time. Harmonic analysis is a direct way of analyzing vibrational motions. Harmonicity of the potential function is a basic assumption in the normal mode approximation used in harmonic analysis. This is known to be inadequate in the case of biological macromolecules, such as proteins, because anharmonic effects, which MD has shown to be important in protein motion, are neglected [1, 2, 3]. 

Harmonic analysis (normal modes) at given temperature and curvature gives complete time behavior of the system in the harmonic limit [1, 2, 3]. Although the harmonic model may be incomplete because of the contribution of anharmonic terms to the potential energy, it is nevertheless of considerable importance because it serves as a first approximation for which the theory is highly developed. This model is also useful in SISM which uses harmonic analysis. 

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