Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 4. Transition Metals with π-Bonds

Firman, Timothy K.; Landis, Clark R.

doi:10.1021/ja002586v

Cited by 58 publications

(68 citation statements)

References 76 publications

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“…Models based on classical mechanical constructs such as molecular mechanical (MM) force fields that are based on empirical potentials describing small-amplitude vibrations, torsions, van der Waals interactions, and electrostatic interactions have been widely used in molecular dynamics (MD) simulations of large and complex organic and biological systems as well as inorganic and solid-state systems [26][27][28][29][30][31]. However, the MM force fields are unable to describe the changes in the electronic structure of a system undergoing a chemical reaction.…”

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confidence: 99%

QM/MM: what have we learned, where are we, and where do we go from here?

2006

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This paper briefly reviews the current status of the most popular methods for combined quantum mechanical/molecular mechanical (QM/MM) calculations, including their advantages and disadvantages. There is a special emphasis on very general link-atom methods and various ways to treat the charge near the boundary. Mechanical and electric embedding are contrasted. We consider methods applicable to gas-phase organic chemistry, liquid-phase organic and organometallic chemistry, biochemistry, and solid-state chemistry. Then we review some recent tests of QM/MM methods and summarize what we learn about QM/MM from these studies. We also discuss some available software. Finally, we present a few comments about future directions of research in this exciting area, where we focus on more intimate blends of QM with MM.

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confidence: 99%

QM/MM: what have we learned, where are we, and where do we go from here?

2006

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“…The energy difference between the elongated tetrahedral structure shown in Figure 3 and rigorous tetrahedral coordination is less than 2 kcal mol Ϫ1 (using the current parameters), which is sufficiently small not to be resolvable by X-ray diffraction. The qualitative ligand field energy level diagram shown in Figure 4 shows that the electronic driving force is a second order effect because, to first order, the splitting of the t 2 orbitals is barycentered and hence, for a d 8 configuration, the stabilization energy accompanying the distortion is zero. The ground state for the T d parent [CuCl 4 ] 2Ϫ species is 2 T 2 , and we expect to see the opposite sense of distortion compared to d 8 and one that is now first order (see Fig.…”

Section: Illustrative Uses Of Dommimoementioning

confidence: 99%

“…The qualitative ligand field energy level diagram shown in Figure 4 shows that the electronic driving force is a second order effect because, to first order, the splitting of the t 2 orbitals is barycentered and hence, for a d 8 configuration, the stabilization energy accompanying the distortion is zero. The ground state for the T d parent [CuCl 4 ] 2Ϫ species is 2 T 2 , and we expect to see the opposite sense of distortion compared to d 8 and one that is now first order (see Fig. 4 from high-to low-spin, the LFSE easily dominates and a square planar structure results (Fig.…”

Section: Illustrative Uses Of Dommimoementioning

confidence: 99%

“…6,[13][14][15][16][17] The d electrons can exert profound structural and energetic effects. For example, d 9 and high-spin d 4 species display large Jahn-Teller distortions, low-spin d 6 complexes are usually sixcoordinate and kinetically inert, and d 8 complexes are generally octahedral when high-spin and square-planar when low-spin. This range of features of coordination complexes can be traced back to the ligand field stabilization energy (LFSE) and so we have added an explicit calculation of the LFSE to conventional MM.…”

Section: Introductionmentioning

confidence: 99%

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DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment

Deeth

Fey²,

Williams-Hubbard

2004

J Comput Chem

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The ligand field molecular mechanics (LFMM) model, which incorporates the ligand field stabilization energy (LFSE) directly into the potential energy expression of molecular mechanics (MM), has been implemented in the "chemically aware" molecular operating environment (MOE) software package. The new program, christened DommiMOE, is derived from our original in-house code that has been linked to MOE via its applications programming interface and a number of other routines written in MOE's native scientific vector language (SVL). DommiMOE automates the assignment of atom types and their associated parameters and popular force fields available in MOE such as MMFF94, AMBER, and CHARMM can be easily extended to provide a transition metal simulation capability. Some of the unique features of the LFMM are illustrated using MMFF94 and some simple [MCl)]2- and [Ni(NH3)n]2+ species. These studies also demonstrate how density functional theory calculations, especially on experimentally inaccessible systems, provide important data for designing improved LFMM parameters. DommiMOE treats Jahn-Teller distortions automatically, and can compute the relative energies of different spin states for Ni(II) complexes using a single set of LFMM parameters.

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“…The directional force field YETI incorporates more flexibility in selection of appropriate valence [22,23]. Further force field enhancements include addition of polarizable bonds [24,25], directionality based on orbital hybridization [26], and ligand field stabilization energy [27,28]. Unfortunately, the more sophisticated force fields are not readily available for the use in MMP-ligand modeling.…”

Section: Introductionmentioning

confidence: 99%

Simulation‐Based Predictions of Binding Affinities of Matrix Metalloproteinase Inhibitors

Khandelwal¹,

Lukáčová²,

Kroll³

et al. 2004

QSAR Comb. Sci.

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Inhibitory potencies of 28 hydroxamate derivatives to matrix metalloproteinase 9 (MMP‐9) have been modeled using the Linear Response method that describes free energy of binding as a linear combination of ensemble averages of van der Waals, electrostatic, and cavity‐related terms. Individual terms are differences in the respective quantities between the bound and free ligands, which were determined using two methods: a hybrid Monte Carlo method within the frame of Surface‐generalized Born Continuum Solvation Model and Molecular Dynamics simulation. The MD simulations of ligands in the hydrated MMP‐9 active site, as well as of free ligands in water were carried out for 200 ps. The time‐averaged structures of the ligands bound with the protein and of the free ligands were collected at 5, 10, 25, 50, 100, and 200 ps. The best correlations between experimental and calculated binding energies, obtained using the training set containing 21 structurally diverse compounds, explained about 90% of experimental variance. The predicted binding affinities for the test set of 7 inhibitors were in good agreement with the experimental data (RMSE=0.944). Similar RMSE values were observed with 200 random selections of the 7‐member test set. The loss of polar and nonpolar solvent accessible surface areas upon binding was identified as the main phenomenon contributing to affinity, accompanied by the enhancement of van der Waals interactions upon binding.

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Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 4. Transition Metals with π-Bonds

Cited by 58 publications

References 76 publications

QM/MM: what have we learned, where are we, and where do we go from here?

QM/MM: what have we learned, where are we, and where do we go from here?

DommiMOE: An implementation of ligand field molecular mechanics in the molecular operating environment

Simulation‐Based Predictions of Binding Affinities of Matrix Metalloproteinase Inhibitors

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