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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
K2[Pt(NO3)4]·1/2H2O was prepared from ca 0.4 M solutions of platinum(II) perchlorate in perchloric acid by addition of KHCO3 and KNO3. Its crystal structure was determined from X-ray intensity data collected with a CAD-4 diffractometer. Monochromatic MoKα-radiation was used. The space group is I4/m with Z = 4; a = 7.5277(4) and c = 20.470(3) Å. The refinement converged to R = 0.036. The structure K2[Pt(NO3)4]·Full-size image (<1 K)H2O was prepared from ca 0.4 M solutions of platinum(II) perchlorate in perchloric acid by addition of KHCO3 and KNO3. Its crystal structure was determined from X-ray intensity data collected with a CAD-4 diffractometer. Monochromatic MoKα-radiation was used. The space group is I4/m with Z = 4; a = 7.5277(4) and c = 20.470(3) Å. The refinement converged to R = 0.
The purpose of this study was to investigate the adsorption mechanism in reversed-phase chromatography (RPC) of proteins and to develop a model for the effect of dual mobile phase modulators—a salt and an organic solvent—on this process. Two different adsorption mechanisms were considered: (1) pure association of a protein molecule and one or more ligands and (2) displacement of the organic modula
Laminar burning velocities of hydrocarbon blends of relevance to natural gas combustion, with addition of 0, 10, 35 and 50% hydrogen, were measured using the heat flux method. Hydrocarbon blends were methane (80%)/ethane (20%), methane (80%)/propane (20%) and methane (80%)/ethane (10%)/propane (10%), and in addition experiments were performed using pure methane as a fuel. For the first time it was
