Hybrid quantum mechanical/molecular

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/... 

Maseras F (1999) Hybrid Quantum Mechanics/Molecular Mechanics Methods in Transition Metal Chemistry. 4 165-191 Maseras F, see Drudis-Sole G (2005) 12 79-107 Mangeney P,see Rolands (2005) 15 191-229 Mayoral JA, see FraUe JM (2005) 15 149-190 Medaer BP, see Mehrmann SJ (2004) 6 153-180... 

Abstract The development and applications of hybrid quantum mechanical/molecular mechanics... 

A second approach is based on the methodology first explored in the seminal work by Warshel and Levitt as early as 1976 [21], and is the use of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations whereby a subsection of the system is treated by QM methods, the remainder (environment) is treated by standard molecular mechanics (MM) methods, and a coupling potential is used to connect the two regions [22], This methodology will then be exemplified with work developed in this group in recent years [23-26],... 

The second approach described here for inclusion of environment effects is the use of hybrid quantum mechanics/molecular mechanics methods (QM/MM). In a QM/MM calculation [21,22], the system is partitioned in two regions A QM region, typically consisting of a relatively small number of atoms relevant for the specific process being studied, and a MM region with all the remaining atoms. 

Hartree-Fock, DFT or CCSD levels. Because they can reproduce such quantities, APMM procedures should account for an accurate description of the interactions including polarization cooperative effects and charge transfer. They should also enable the reproduction of local electrostatic properties such as dipole moments an also facilitate hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) embeddings. 

Field MJ (1997) Hybrid quantum mechanical molecular mechanical fluemating charge models for condensed phase simulations. Mol Phys 91(5) 835-845... 

Molecular mechanics calculations have become a well established tool in the area of coordination chemistry, including the coordination chemistry of nickel375-379 where they are often applied for the analysis or the prediction of structures,380 the computation of isomer or conformer ratios and metal ion selectivities,381,382 and for simulating spectroscopic properties in combination with AOM calculations or by hybrid quantum mechanics/molecular mechanics (QMMM) methods.383,384 Details of the various approaches, e.g., the incorporation of d-electron stabilization energy... 

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... 

The description of pure quantum mechanics (QM) methods presented in Section 3 has shown how in most cases they provide an accurate description of the electronic subtleties involved at the transition metal center of a catalytic process, but that they are unable to introduce the whole bulk of the catalyst substituents, which can be critical for selectivity issues. The description of pure molecular mechanics (MM) methods presented in subsection 4.1 has shown how these methods can easily introduce the steric bulk of the substituents, and accurately describe their steric interactions, but that they struggle badly when trying to describe properly the transition metal center and its immediate environment. The logical solution to this complementary limitations is to divide the chemical system in two regions, and to use a different description for each of them, QM for the metal and its environment, MM for the rest of the system. This is precisely the basic idea of hybrid quantum mechanics / molecular mechanics (QM/MM) methods. 

Maseras F (1999) Hybrid Quantum Mechanics/Molecular Mechanics Methods in Transition Metal Chemistry. 4 165-191... 

Hybrid quantum mechanics/molecular dynamics (method) Self-consistent field (method)... 

A concerted rather than a stepwise reaction involving a tetrahedral intermediate is supported for die papain-catalysed hydrolysis of amides. The TS for die hydrolysis has been determined by using a hybrid quantum mechanical/molecular mechanical potential, QM(AM1)/MM.216... 

P. Sherwood. Hybrid quantum mechanics/molecular mechanics approaches, In J. Grotendorst, Modern Methods and Algorithms of Quantum Chemistry, Proceedings (2 ed.), NIC Series, 3, John von Neumann Institute for Computing, Jtilich, 285, 2000. 

The theoretical study of heme groups has become more common in recent years because of the appearance of new methodologies and the increase in computer power. In particular, the application of the IMOMM (Integrated Molecular Orbital Molecular Mechanics), a hybrid Quantum Mechanics/Molecular Mechanics (QM/ MM) scheme, has allowed the accurate study of transition metal systems [140-142]. 

Nunez S, Antoniou D, Schramm VL, Schwartz SD (2004) Promoting vibrations in human purine nucleoside phosphorylase. A molecular dynamics and hybrid quantum mechanical/molecular mechanical study. J. Am. Chem. Soc. 126 15720-15729... 

Another frequently used approach to reduce the computational effort is the hybrid quantum mechanical/molecular mechanical (QM/MM) framework which will be discussed in more detail below. 

---