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Theoretical computations (molecular dynamics and combined quantum chemical and molecular mechanical geometry optimizations) have been performed on horse liver alcohol dehydrogenase. The results provide evidence that Glu‐68, a highly conserved residue located 0.47 nm from the catalytic zinc ion, may intermittently coordinate to the zinc ion. Structures with Glu‐68 coordinated to the zinc ion are al
The coordination chemistry of the structural zinc ion in horse liver alcohol dehydrogenase has been examined by quantum chemical geometry optimisations. It is shown that all four cysteine ligands are deprotonated in the enzyme, not only two of them as has been suggested. The Zn-S bond lengths are very sensitive to the theoretical treatment; in vacuum they are predicted to be 15 pm longer than in t
The coordination number of the catalytic zinc ion in alcohol dehydrogenase has been studied by integrated ab initio quantum-chemical and molecular mechanics geometry optimisations involving the whole enzyme. A four-coordinate active-site zinc ion is 100-200 kJ/mol more stable than a five-coordinate one, depending on the ligands. The only stable binding site for a fifth ligand at the zinc ion is op
Calculations of the electric field gradient (EFG) at the cadmium nucleus have been carried out on Cd2+ in the field of two point charges, CdF2, CdCl2, and CdF2Cl2 2- at the RHF, MPn (n = 2, 3, 4), and CCSD(T) levels of theory, in order to evaluate the effects of electron correlation, relativity, and basis set truncation. The EFG has furthermore been calculated in two large molecules (approximately
The electronic spectrum of the blue copper protein plastocyanin has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method). The six lowest electronic transitions have been calculated and assigned with an error of less than 2000 cm-1. The singly occupied orbital in the ground state is Cu 3d-S(Cys) 3pπ antibonding with some N(His) 2pσ character. The brigh
The significance of the so-called trigger reaction in the reaction mechanism of the calicheamicin γI 1 anti-cancer drug has been studied with ab initio quantum chemical methods. The structures of four fragments of calicheamicin γI 1, consisting of either 39 or 41 atoms, have been fully optimized using the Becke-Perdew86 density functional method and the 6-31G* basis sets. The four structures const
The structure of eleven complexes of cadmium-substituted alcohol dehydrogenase with or without coenzyme and with different non-protein cadmium ligands has been estimated by combined quantum chemical and molecular mechanical geometry optimisations. The geometry of the optimised complexes is similar to the crystal structure of cadmium-substituted alcohol dehydrogenase, indicating that the method beh
Four methods for deriving partial atomic charges from the quantum chemical electrostatic potential (CHELP, CHELPG, Merz-Kollman, and RESP) have been compared and critically evaluated. It is shown the charges strongly depend on how and where the potential points are selected. Two alternative methods are suggested to avoid the arbitrariness in the point-selection schemes and van der Waals exclusion
The electronic spectrum of the azurin Met121Gln mutant, a model of the blue copper protein stellacyanin, has been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method), including the effect of the protein and solvent by point charges. The six lowest electronic transitions have been calculated and assigned with an error of less than 2400 cm-1. The ground-sta
The role of the cysteine thiolate ligand for the unusual copper coordination geometry in the blue copper proteins has been studied by comparing the electronic structure, geometry, and energetics of a number of small Cu(II) complexes. The geometries have been optimised with the density functional B3LYP method, and energies have been calculated by multi- configurational second-order perturbation the
The inner-sphere reorganization energy for several copper complexes related to the active site in blue-copper protein has been calculated with the density functional B3LYP method. The best model of the blue-copper proteins, Cu(Im)2(SCH3)(S(CH'3)2)(0/+), has a self-exchange inner-sphere reorganization energy of 62 kJ/mol, which is at least 120 kJ/mol lower than for Cu(H2O)(+/2+)/4 This lowering of
The electronic spectra of three rhombic type 1 blue copper proteins, nitrite reductase, pseudoazurin, and cucumber basic protein, have been studied by ab initio multiconfigurational second-order perturbation theory (the CASPT2 method). The six lowest excitations have been calculated and assigned with an error of less than 1800 cm-1. The singly occupied orbital in the ground-state forms a strongly
The molecular and electronic structures of Co(II)-substituted azurin have been investigated using several realistic models of the metal coordination sphere. The geometry of the models was optimized using the hybrid density functional B3LYP method and compared to the structures obtained for similar Cu(II) models. It is found that Co(II) prefers a distorted tetrahedral structure with four strong bon
Semiempirical calculations, based on the so-called angular overlap model, have been compared with ab initio methods (MP2) for the calculation of nuclear quadrupole interactions (NQI's) in cadmium complexes with biologically relevant ligands (H2O, OH-, cysteinate, carboxylate, and imidazole). The assumptions on which the semiempirical model is based have been tested and the comparison indicates tha
The relative energies of different coordination modes (bidentate, monodentate, syn, and anti) of a carboxylate group bound to a zinc ion have been studied by the density functional method B3LYP with large basis sets on realistic models of the active site of several zinc proteins. In positively charged four-coordinate complexes, the mono- and bidentate coordination modes have almost the same energy
Free energy perturbations have been performed on two blue copper proteins, plastocyanin and nitrite reductase. By changing the copper coordination geometry, force constants, and charges, we have estimated the maximum energy with which the proteins may distort the copper coordination sphere. By comparing this energy with the quantum chemical energy cost for the same perturbation on the isolated cop
The reduction potentials of blue copper sites vary between 180 and about 1000 mV. It has been suggested that the reason for this variation is that the proteins constrain the distance between the copper ion and its axial ligands to different values. We have tested this suggestion by performing density functional B3LYP calculations on realistic models of the blue copper proteins, including solvent e
Quantum chemical geometry optimisations have been performed on realistic models of the active site of myoglobin using density functional methods. The energy of the hydrogen bond between the distal histidine residue and CO or O2 has been estimated to be 8 kJ/mol and 32 kJ/mol, respectively. This 24 k J/mol energy difference accounts for most of the discrimination between CO and O2 by myoglobin (abo
Theoretical investigations of the structure and function of the blue copper proteins are described. We have studied the optimum vacuum geometry of oxidised and reduced copper sites, the relative stability of trigonal and tetragonal Cu(II) structures, the relation between the structure and electronic spectra, the reorganisation energy, and reduction potentials. Our calculations give no support to t
Theoretical investigations of the structure and function of the blue copper proteins and the dimeric CuA site are described. We have studied the optimum vacuum geometry of oxidised and reduced copper sites, the relative stability of trigonal and tetragonal Cu(II) structures, the relation between the structure and electronic spectra, the reorganisation energy, and reduction potentials. We also comp
