Molecular mechanics principle

In the course of these studies, it was realized that the rotation of, for example, a backbone C—C bond in n-alkane produces periodical variation in the C—C bond length as well as in the C—C—X (X = H, C) valence angles . These observations are the most striking evidence for the molecular mechanics principle, wherein the dynamics of molecules is assumed to respond to a mechanical modeP . 

Quantum mechanical calculations generally have only one carbon atom type, compared with the many types of carbon atoms associated with a molecular mechanics force field like AMBER. Therefore, the number of quantum mechanics parameters needed for all possible molecules is much smaller. In principle, very accurate quantum mechanical calculations need no parameters at all, except fundamental constants such as the speed of light, etc. 

Ab initio methods, unlike either molecular mechanics or semi-empirical methods, use no experimental parameters in their computations. Instead, their computations are based solely on the laws of quantum mechanics—the first principles referred to in the name ah initio—and on the values of a small number of physical constants ... 

After the discovery of quantum mechanics in 1925 it became evident that the quantum mechanical equations constitute a reliable basis for the theory of molecular structure. It also soon became evident that these equations, such as the Schrodinger wave equation, cannot be solved rigorously for any but the simplest molecules. The development of the theory of molecular structure and the nature of the chemical bond during the past twenty-five years has been in considerable part empirical — based upon the facts of chemistry — but with the interpretation of these facts greatly influenced by quantum mechanical principles and concepts. 

The above statements are valid for monomolecular layers only. In the case of polymer films with layer thickness into the p-range, as are usually produced by electropolymerization, account must also be taken of the fact that the charge transport is dependent on both the electron exchange reactions between neighbouring oxidized and reduced sites and the flux of counterions in keeping with the principle of electroneutrality Although the molecular mechanisms of these processes... 

Yoshihara Y. and Mori K. (1997). Basic principles and molecular mechanisms of olfactory axon pathfinding. Cell Tissue Res 290, 457-463. 

An alternative approach is to replace an accurate but expensive first-principle-based technique by a reliable model potential. Such potentials, broadly referred to as molecular mechanics (MM), generally cannot account for bond-breaking, but can, in principle, account for the range of intermolecular interactions. However, using a fitted pair-wise potential may result in losing quantitative accuracy, predictability, and the underlying physics. 

Chelli R, Procacci P (2002) A transferable polarizable electrostatic force field for molecular mechanics based on the chemical potential equalization principle. J Chem Phys 117(20) 9175—9189... 

Figure 13.2 Combination of three atomic p orbitals to form three n molecular orbitals in the allyl radical. The bonding n molecular orbital is formed by the combination of the three p orbitals with lobes of the same sign overlapping above and below the plane of the atoms. The nonbonding n molecular orbital has a node at C2. The antibonding n molecular orbital has two nodes between Cl and C2, and between C2 and C3. The shapes of molecular orbitals for the allyl radical calculated using quantum mechanical principles are shown alongside the schematic orbitals.

Figure 13.3 The n molecular orbitals of the allyl cation. The allyl cation, like the allyl radical, is a conjugated unsaturated system. The shapes of molecular orbitals for the allyl cation calculated using quantum mechanical principles are shown alongside the schematic orbitals. 

Molecular mechanics force fields rest on four fundamental principles. The first principle is derived from the Bom-Oppenheimer approximation. Electrons have much lower mass than nuclei and move at much greater velocity. The velocity is sufficiently different that the nuclei can be considered stationary on a relative scale. In effect, the electronic and nuclear motions are uncoupled, and they can be treated separately. Unlike quantum mechanics, which is involved in determining the probability of electron distribution, molecular mechanics focuses instead on the location of the nuclei. Based on both theory and experiment, a set of equations are used to account for the electronic-nuclear attraction, nuclear-nuclear repulsion, and covalent bonding. Electrons are not directly taken into account, but they are considered indirectly or implicitly through the use of potential energy equations. This approach creates a mathematical model of molecular structures which is intuitively clear and readily available for fast computations. The set of equations and constants is defined as the force... 

The solutions A = af — 47r2t l2 yield the normal vibration frequencies of the molecule. In principle, force constants can therefore be derived from observed vibrational spectra. However, most force constants used in molecular mechanics are not too well established experimentally. 

In this chapter we will focus on one particular, recently developed DFT-based approach, namely on first-principles (Car-Parri-nello) molecular dynamics (CP-MD) [9] and its latest advancements into a mixed quantum mechanical/molecular mechanical (QM/MM) scheme [10-12] in combination with the calculation of various response properties [13-18] within DFT perturbation theory (DFTPT) and time-dependent DFT theory (TDDFT) [19]. 

In an attempt to aid interpretation of the IR spectrum of MbCO we decided to model the full protein by use of a hybrid quantum mechanics/molecular mechanics approach (QM/MM), to evaluate changes in the CO stretching frequency for different protein conformations. The QM/MM method used [44] combines a first-principles description of the active center with a force-field treatment (using the CHARMM force field) of the rest of the protein. The QM-MM boundary is modeled by use of link atoms (four in the heme vinyl and propionate substituents and one on the His64 residue). Our QM region will include the CO ligand, the porphyrin, and the axial imidazole (Fig. 3.13). The vinyl and propionate porphyrin substituents were not included, because we had previously found they did not affect the properties of the Fe-ligand bonds (Section 3.3.1). It was, on the other hand, crucial to include the imidazole of the proximal His (directly bonded to the... 

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