Density functional theory mechanical hybrids

This book starts with seven chapters devoted to methods for the computation of molecular structure molecular mechanics, semiempirical methods, wave function-based quantum chemistry, density-functional theory methods, hybrid methods, an assessment of the accuracy and applicability of these methods, and finally 3D structure generation and conformational analysis. 

Orlova et al. (2003) theoretically studied the mechanism of the firefly bioluminescence reaction on the basis of the hybrid density functional theory. According to their conclusion, changes in the color of light emission by rotating the two rings on the 2-2 axis is unlikely, whereas the participation of the enol-forms of oxyluciferin in bioluminescence is plausible but not essential to explain the multicolor emission. They predicted that the color of the bioluminescence depends on the polarization of the oxyluciferin molecule (at its OH and O-termini) in the microenvironment of the luciferase active site the... 

Amara, P., Volbeda, A., Fontecilla-Camps, J. C., Field, M. J., 1999, A Hybrid Density Functional Theory/Mo-lecular Mechanics Study of Nickel-Iron Hydrogenase Investigation of the Active Site Redox States , J. Am. Chem. Soc., 121, 4468. 

The quantum-mechanical energy curve was calculated at the B3LYP/6-311++G level of hybrid density-functional theory, as described in Appendix A. However, due to B3LYP convergence failures beyond Ji 3A, the quantities shown in Figs. 2.4—2.8 were calculated at HF/6-311++G" level. 

Figure 5. Normal modes for vibration of tetrahedral [Cr04] (chromate). There are four distinct vibrational frequencies, including one doubly-degenerate vibration (E symmetry) and two triply-degenerate vibrations (F2 symmetry), for a total of nine vibrational modes. Arrows show the characteristic motions of each atom during vibration, and the length of each arrow is proportional to the magnitude of atomic motion. Only F2 modes involve motion of the central chromium atom, and as a result their vibrational frequencies are affected by Cr-isotope substitution. The normal modes shown here were calculated with an ab initio quantum mechanical model, using hybrid Hartree-Fock/Density Functional Theory (B3LYP) and the 6-31G(d) basis set—other ab initio and empirical force-field models give very similar results.

Hypercube, Inc. at http //www.hyper.com offers molecular modeling packages under the HyperChem name. HyperChem s newest version, Hyper-Chem Release 7.5, is a full 32-bit application, developed for the Windows 95, 98, NT, ME, 2000, and XP operating systems. Density Functional Theory (DFT) has been added as a basic computational engine to complement Molecular Mechanics, Semiempirical Quantum Mechanics and ab initio Quantum Mechanics. The DFT engine includes four combination or hybrid functions, such as the popular B3-LYP or Becke-97 methods. The Bio+ force field in HyperChem represents a version of the Chemistry at HARvard using Molecular Mechanics (CHARMM) force field. Release 7.5 of HyperChem updates... 

Pu JZ, JL Gao, DG Truhlar (2005) Generalized hybrid-orbital method for combining density functional theory with molecular mechanicals. ChemPhysChem 6 (9) 1853—1865... 

Amara P, Volbeda A, Fontecilla-Camps JC, Field MJ (1999) A hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase investigation of the active site redox states J. Am. Chem. Soc. 121 4468—1477... 

In a third theoretical model the [FeNi]-hydrogenase from D. gigas is modeled using a hybrid density functional theory-molecular mechanics (DFT/MM) method [92]. In this model approximately 30 atoms of the active site (including the four cysteine residues) are modeled with DFT while molecular mechanics is used for the rest of the atoms within a A radius (about 300 atoms). The next shell includes about 10 000 protein and solvent atoms within 27 A of the active site whose posi-... 

A novel approach is reported for the accurate evaluation of pore size distributions for mesoporous and microporous silicas from nitrogen adsorption data. The model used is a hybrid combination of statistical mechanical calculations and experimental observations for macroporous silicas and for MCM-41 ordered mesoporous silicas, which are regarded as the best model mesoporous solids currently available. Thus, an accurate reference isotherm has been developed from extensive experimental observations and surface heterogeneity analysis by density functional theory the critical pore filling pressures have been determined as a function of the pore size from adsorption isotherms on MCM-41 materials well characterized by independent X-ray techniques and finally, the important variation of the pore fluid density with pressure and pore size has been accounted for by density functional theory calculations. The pore size distribution for an unknown sample is extracted from its experimental nitrogen isotherm by inversion of the integral equation of adsorption using the hybrid models as the kernel matrix. The approach reported in the current study opens new opportunities in characterization of mesoporous and microporous-mesoporous materials. 

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