Potential energy hybrid

A Fortran90 library for the simulation of molecular systems using molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM)/ MM) potential energy functions. http //www.ibs.fr/ext/labos/LDM/projet6/... 

Eigure 3 represents an illustrative biological application an Asp Asn mutation, carried out either in solution or in complex with a protein [25,26]. The calculation uses a hybrid amino acid with both an Asp and an Asn side chain. Eor convenience, we divide the system into subsystems or blocks [27] Block 1 contains the ligand backbone as well as the solvent and protein (if present) block 2 is the Asp moiety of the hybrid ligand side chain block 3 is the Asn moiety. We effect the mutation by making the Asn side chain gradually appear and the Asp side chain simultaneously disappear. We choose initially the hybrid potential energy function to have the form... 

Smooth COSMO solvation model. We have recently extended our smooth COSMO solvation model with analytical gradients [71] to work with semiempirical QM and QM/MM methods within the CHARMM and MNDO programs [72, 73], The method is a considerably more stable implementation of the conventional COSMO method for geometry optimizations, transition state searches and potential energy surfaces [72], The method was applied to study dissociative phosphoryl transfer reactions [40], and native and thio-substituted transphosphorylation reactions [73] and compared with density-functional and hybrid QM/MM calculation results. The smooth COSMO method can be formulated as a linear-scaling Green s function approach [72] and was applied to ascertain the contribution of phosphate-phosphate repulsions in linear and bent-form DNA models based on the crystallographic structure of a full turn of DNA in a nucleosome core particle [74],... 

As an example, consider a solution mixture of two molecules, 1 and 2. The system is described by the hybrid potential energy function ... 

The QM/MM methodology [1-7] has seen increasing application [8-16] and has been recently reviewed [17-19], The classical solvent molecules may also be assigned classical polarizability tensors, although this enhancement appears to have been used to date only for simulations in which the solute is also represented classically [20-30], The treatment of the electronic problem, whether quantal, classical, or hybrid, eventually leads to a potential energy surface governing the nuclear coordinates. 

The structure of CNTs can be understood as sheets of graphene (i.e. monolayers of sp2 hybridized carbon, see Chapter 2) rolled-up into concentric cylinders. This results in the saturation of part of the dangling bonds of graphene and thus in a decrease of potential energy, which counterbalances strain energy induced by curvature and thus stabilizes the CNTs. Further stabilization can be achieved by saturating the dangling bonds at the tips of the tubes so that in most cases CNTs are terminated by fullerene caps. Consequently, the smallest stable fullerene, i.e. C60, which is - 0.7 nm in diameter, thus determines the diameter of the smallest CNT. The fullerene caps can be opened by chemical and heat treatment, as described in Section 1.5. 

Figure 13.4 Torsional potential energy surfaces about the two C-O bonds linking the anomeric centers of sucrose at the MM3 level (a), 2-tetrahydrofuranyl-2-tetrahydropyranyl ether at the MM3 level (b), the same ether at the HF/6-31G(d) level (c), and the sum of the difference between the last two with the first (d). Thus, the last surface may be viewed either as the effect of the sucrose hydroxyl groups on the energy surface, evaluated at the MM3 level, added to the framework surface calculated at the ab initio level, or as an MM3 surface that has been partially conected quantum mechanically. Solid triangles represent anomeric torsions in sucrose units found in various X-ray crystal structures. Note that the hybrid surface is the only one that clusters the large majority of these triangles within low-energy contours...

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