Density-functional theory molecular

Forda, M.J., Hoft, R.C. and Gale, J.D. (2006) Adsorption and dimerisation of thiol molecules on Au(lll) using a Z-matrix approach in density functional theory. Molecular Simulation, 32, 1219-1225. 

Amara, P. V., Volbeda, A., Fontecilla-Camps, J. C. and Field, M. J. A. (1999) Hybrid density functional theory/molecular mechanics study of nickel-iron hydrogenase Investigation of the active site redox states./. Am. Chem. Soc., 121, 4468-77. 

A review of the Journal of Physical Chemistry A, volume 110, issues 6 and 7, reveals that computational chemistry plays a major or supporting role in the majority of papers. Computational tools include use of large Gaussian basis sets and density functional theory, molecular mechanics, and molecular dynamics. There were quantum chemistry studies of complex reaction schemes to create detailed reaction potential energy surfaces/maps, molecular mechanics and molecular dynamics studies of larger chemical systems, and conformational analysis studies. Spectroscopic methods included photoelectron spectroscopy, microwave spectroscopy circular dichroism, IR, UV-vis, EPR, ENDOR, and ENDOR induced EPR. The kinetics papers focused on elucidation of complex mechanisms and potential energy reaction coordinate surfaces. 

LINEAR RESPONSE THEORY IN CONNECTION TO DENSITY FUNCTIONAL THEORY/MOLECULAR DYNAMICS AND COUPLED CLUSTER/MOLECULAR DYNAMICS METHODS... 

RESPONSE FUNCTIONS FOR THE DENSITY FUNCTIONAL THEORY/MOLECULAR MECHANICS METHOD... 

This section considers how to derive the response functions for the density functional theory molecular mechanics method and the derivation of these response functions is similar to the procedure of obtaining density functional theory response functions for molecules in vacuum [58]. For the method and the derivation, we utilize the adiabatic approximation and thereby we assume that vxc[p](r, t) = vxc[p](r). 

K. Aidas, K.V. Mikkelsen, J. Kongsted, Modelling spectroscopic properties of large molecular systems, the combined density functional theory/molecular mechanics approach, J. Chem. Meth. Sci. Eng. 7 (2007) 135. 

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-... 

Several different kinds of quantum-chemical descriptors have been defined, and these can be broadly divided into energy-based descriptors, local quantum-chemical properties, descriptors based on the Density Functional Theory, molecular orbital energies, superdelocalizability indices, frontier orbital electron densities, and polarizabilities [Cartier and Rivail, 1987 Bergmann and Hinze, 1996 Karelson et al, 1996]. 

S. R A. Sauer, On the accuracy of density functional theory to predict shifts in nuclear magnetic resonance shielding constants due to hydrogen bonding, J. Chem. Theory Comput. 4 (2008) 267 A. Mogelhoj, K. Aidas, K. V. Mikkelsen, S. P. A. Sauer, J. Kongsted, Prediction of Spin-Spin Coupling Constants in Solution based on Combined Density Functional Theory/Molecular Mechanics, J. Chem. Phys. 130 (2009) 134508. 

X. P. Long, J. B. Nicholas, M. F. Guest and R. L. Ornstein A combined density functional theory/molecular mechanics formalism and its application to small water clusters, J. Mol. Struct. 412, 121-133 (1997). 

K. Aidas, K. V. Mikkelsen and J. Kongsted, Modelling Spectroscopic Properties of Large Molecular Systems. The Combined Density Functional Theory/Molecular Mechanics Approach , J. Comput. Methods Sci. Eng., 2007, 7, 135. 

Benes, O., Zeller, R, Salanne, M., and Konings, R.J.M. (2009) Density functional theory, molecular dynamics, and differential scanning calorimetry study of the RbF-CsF phase diagram. J. Chem. Phys, 130, 134716. 

Mogelhoj, A., Aidas, K., Mikkelsen, K. V., Sauer, S. P. A., Kongsted, J. (2009). Prediction of spin-spin coupling constants in solution based on combined density functional theory/molecular mechanics. Journal of Chemical Physics, 130, 134508. 

Levine, B. G., Ko, C., Quenneville, J., 8c Martinez, T. J. (2006). Conical intersections and double excitations in time-dependent density functional theory. Molecular Physics, 104(5-7), 1039-1051. 

Stephens PJ, Cheeseman JR, Frisch MJ, Ashvar CS and Devlin FJ (1996) Ab initio calculation of atomic axial tensors and vibrational rotational strengths using density functional theory. Molecular Physics 89 579-594. 

DFT/MM Density functional theory/molecular mechanical. Term used to define generically the class of density functional theory QM/MM methods. N/A... 

I. I. Zakharov, Z. R. Ismagilov, S. Ph. Ruzankin, V. F. Anufrienko, S. A. Yashnik and O. I. Zakharova. Density functional theory molecular cluster study of copper interaction with nitric oxide dimer in Cu-ZSM-5 catalysts. J. Phys. Chem. C 111, 2007, 3080-3089. 

---