Multireference ab initio quantum mechanics/molecular mechanics study on intermediates in the catalytic cycle of cytochrome P450(cam)

We have investigated the elusive reactive species of cytochrome P450(cam) (Compound I), the hydroxo complex formed during camphor hydroxylation, and the ferric hydroperoxo complex (Compound 0) by combined quantum mechanical/molecular mechanical (QM/MM) calculations, employing both density functional theory (DFT) and correlated ab initio methods. The first two intermediates appear multiconfigurational in character, especially in the doublet state and less so in the quartet state. DFT(B3LYP)/MM calculations reproduce the relative energies from correlated ab initio QM/MM treatments quite well, except for the splitting of the lowest A(1u)-A(2u) radical states. The inclusion of dynamic correlation is crucial for the proper ab initio treatment of these intermediates.     

Semiempirical PM5 molecular orbital study on chlorophylls and bacteriochlorophylls: comparison of semiempirical, ab initio, and density functional results

The semiempirical PM5 method has been used to calculate fully optimized structures of magnesium-bacteriochlorin, magnesium-chlorin, magnesium-porphin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), and d, and bacteriochlorophylls a, b, c, d, e, f, g, and h with all homologous structures. Hartree-Fock/6-31G* ab initio and density functional B3LYP/6-31G* methods were used to optimize structures of methyl chlorophyllide a, chlorophyll c(1), and methyl bacteriochlorophyllides a and c for comparison. Spectroscopic transition energies of the chromophores and their 1:1 or 1:2 solvent complexes were calculated with the Zindo/S CIS method. The self-consistent reaction field model was used to estimate solvent shifts. The PM5 calculations predict planar structure of the porphyrin ring and central position of the four coordinated magnesium atoms in all pigments studied, in accord with the experimental, ab initio, and density functional results, a significant improvement as compared to the older semiempirical PM3 approach. Only small differences in PM5 and B3LYP/6-31G* or Hartree-Fock/6-31G* minimum energy geometries of the reference molecules were observed. Calculations show that in 1:1 solvent complexes, where the magnesium atom is five coordinated, the magnesium atom is shifted out of the plane of the porphyrin ring towards the solvent molecule, while the hexa coordinated 1:2 complexes are again planar. The PM5 method gives atomic charges that are comparable with those obtained from the Hartree-Fock/6-31G* and B3LYP/6-31G* calculations. The single point ZINDO/S CIS calculations with PM5 minimum energy structure gave excellent correlations between calculated and experimental transition energies of the chlorophylls and bacteriochlorophylls studied. Such correlations may be used for prediction of transition energies of the chromophores in protein binding sites. Calculations also predict existence of dark electronic states below the main Soret absorption band in all chromophores studied. The results suggest that the semiempirical PM5 method is a fairly reliable and computationally efficient method in predicting molecular parameters of porphyrin-like molecules.     

Theoretical determinations of ionization potentials of dopamine

Adiabatic and vertical ionization potentials (IPs) of nine conformers of dopamine in the gas phase are determined using density functional theory (DFT) B3LYP, B3P86, B3PW91 methods and high level ab initio HF method with 6-311++G** basis set, respectively. And the nine stable cationic states have been found in the ionization process of dopamine. Vertical ionization potentials of nine conformers of dopamine are calculated using the older outer-valence Green’s function (OVGF) calculations at 6-311++G** basis set. Vibrational frequencies and infrared spectrum intensities of G1b and G1b⁺ at B3LYP/6-311++G** level are discussed.     

Theory Study on Structures and Vibrational Frequencies of Pyruvic acid

Anumberoftheoreticalstudiesexistforpyruvicacid.IthasbeenstudiedatthesemiempiricalINDOandAMIlevell'2.AttheahinitiolevelstudiesofpyruvicacidrangefromthecalculationofenergiesattheSTO-3Glevel'tocalculationsofenergiesusingtheHF/3-2iG',HF/4-21G',HF/6-3iG*andMP2/4-21Gmethods.ExceptforthestudyofMurtoetal.,allthestudieshavefocussedontheenergiesandgeometriesofpyruvicacid.Moreoveralltheexistingtheoreticalstudieshavefocusedtheirattentionontheorientationofthecarboxylhydrogenextensively.Theorienta…     

Predictions of nitrogen isotropic hyperfine coupling constants in the nitroxide radicals with the aid of DF/HF calculations

Nitrogen isotropic hyperfine coupling constants in different nitroxide radicals calculated via ab initio hybrid density functional/Hartree-Fock methods (UB3LYP and UB1LYP) with 6-31G(d) basis set of Gaussian 98 were found to be in a good agreement with the experimental EPR results. UB3LYP/6-31G(d) and UBLYP/6-31G(d) calculated atomic spin populations and spin density maps in the gas phase correspond to the general features of the experimentally obtained data by polarized neutron diffraction studies in the solid state. The results were analyzed in terms of unpaired electron delocalization and the influence of the surrounding on the radical centers.     

Quantum chemical simulation of excited states of chlorophylls, bacteriochlorophylls and their complexes

The present review describes the use of quantum chemical methods in estimation of structures and electronic transition energies of photosynthetic pigments in vacuum, in solution and imbedded in proteins. Monomeric Mg-porphyrins, chlorophylls and bacteriochlorophylls and their solvent 1:1 and 1:2 complexes were studied. Calculations were performed for Mg-porphyrin, Mg-chlorin, Mg-bacteriochlorin, mesochlorophyll a, chlorophylls a, b, c(1), c(2), c(3), d and bacteriochlorophylls a, b, c, d, e, f, g, h, plus several homologues. Geometries were optimised with PM3, PM3/CISD, PM5, ab initio HF (6-31G*/6-311G**) and density functional B3LYP (6-31G*/6-311G**) methods. Spectroscopic transition energies were calculated with ZINDO/S CIS, PM3 CIS, PM3 CISD, ab initio CIS, time-dependent HF and time-dependent B3LYP methods. Estimates for experimental transition energies were obtained from linear correlations of the calculated transition energies of 1:1 solvent complexes against experimentally recorded solution energies (scaling). According to the calculations in five-coordinated solvent complexes the magnesium atom lies out of the porphyrin plane, while in six-coordinated complexes the porphyrin is nearly planar. Charge densities on magnesium and nitrogen atoms were strongly dependent on the computational method deployed. Several dark states of low oscillator strength below the main Soret band were predicted for solvent complexes and chlorophylls and bacteriochlorophylls in protein environment. Such states, though not yet identified experimentally, might serve as intermediate states for excitation energy transfer in photosynthetic complexes. Q(y), Q(x) and Soret transition energies were found to depend on the orientation of the acetyl group and external pressure. A method to estimate site energies and dimeric interaction energies and to simulate absorption and CD spectra of photosynthetic complexes is described. Simulations for the light harvesting complexes Rhodospirillum molischianum, chlorosomes of Chlorobium tepidum and Chloroflexus aurantiacus, and LHC-II of Spinacia oleracea are presented as examples.     

Density functional theory study on the structure and vibrational frequencies of glycylglycine

Eleven possible conformers of glycylglycine have been studied by using the BLYP, B3LYP methods of density functional theory and the HF method at the basis set of 6-311++G**. BLYP (using Becke's and Lee-Yang-Parr's correlation functionals), ab initio Hartree-Fock (HF) and hybrid DFT/HF B3LYP calculations have been carried out to study the structure and vibrational spectra of glycylglycine. Glycylglycine crystal structure has been determined by X-ray diffraction analysis. The title compound has been crystallizes in the orthorhombic space group C1, with Z=4. And the unit cell parameters are: a=8.1184(12)A, b=9.5542(14)A, c=7.8192(11)A and V=577.95(15)A(3). Molecular conformation calculations have got 11 possible conformers. In these possible conformers, the most stable one has been selected. The BLYP/6-311++G** and scaled HF/6-311++G** frequencies correspond well with available experimental assignments of the normal vibrational modes. Comparison of the observed fundamental vibrational frequencies of glycylglycine and calculated results by density functional B3LYP and Hartree-Fock (HF) methods indicates that B3LYP is superior to the scaled Hartree-Fock (HF) for molecular vibrational issues.     

Force-field parameters for the simulation of tetrahedral intermediates of serine hydrolases

CHARMM force-field parameters are reported for the tetrahedral intermediate of serine hydrolases. The fitting follows the standard protocol proposed for CHARMM22. The reference data include ab initio (RHF/6-31G*) interaction energies of complexes between water and the model compound 1,1-dimethoxyethoxide, torsional profiles of related model compounds from correlated ab initio (MP2/6-311+G*//B3LYP/6-31+G*) calculations, as well as molecular geometries and vibrational frequencies from density functional theory (B3LYP/6-31+G*). The optimized parameters reproduce the target data well. Their utility is demonstrated by a QM/MM study of the tetrahedral intermediate in Bacillus subtilis lipase A, and by classical molecular modeling of enantioselectivity in Pseudomonas aeruginosa lipase and its mutants.     

On the vibrational spectra and structural parameters of methyl, silyl, and germyl azide from theoretical predictions and experimental data

The infrared and Raman spectra of methyl, silyl, and germyl azide (XN3 where X=CH3, SiH3 and GeH3) have been predicted from ab initio calculations with full electron correlation by second order perturbation theory (MP2) and hybrid density function theory (DFT) by the B3LYP method with a variety of basis sets. These predicted data are compared to previously reported experimental data and complete vibrational assignments are provided for all three molecules. It is shown that several of the assignments recently proposed [J. Mol. Struct. (Theochem.) 434 (1998) 1] for methyl azide are not correct. Structural parameters for CH3N3 and GeH3N3 have been obtained by combining the previously reported microwave rotational constants with the ab initio MP2/6-311+G(d,p) predicted values. These "adjusted r0" parameters have very small uncertainties of +/-0.003 A for the XH distances and a maximum of +/-0.005 A for the heavy atom distances and +/-0.5 degrees for the angles. The predicted distance for the terminal NN bond which is nearly a triple bond is much better predicted by the B3LYP calculations, whereas the fundamental frequencies are better predicted by the scaled ab initio calculations. The results are discussed and compared to those obtained for some similar molecules.     

Comparative studies on the structures,infrared spectrum,and thermodynamic properties of phthalocyanine using ab initio Hartree–Fock and density functional theory methods

The molecular structure, vibrational spectrum, standard thermodynamic functions, and enthalpy of formation of free base phthalocyanine (Pc) have been studied using the density functional theory B3LYP procedure, as well as the ab initio Hartree–Fock method. Various basis sets 3‐21G, 6‐31G*, and LANL2DZ have been employed. The results obtained at various levels are discussed and compared with each other and with the available experimental data. It is shown that calculations performed at the Hartree–Fock level cannot produce a reliable geometry and related properties such as the dipole moment of Pc and similar porphyrin‐based systems. Electron correlation must be included in the calculations. The basis set has comparatively less effect on the calculated results. The results derived at the B3LYP level using the smaller 3‐21G and LANL2DZ basis sets are very close to those produced using the medium 6‐31G* basis set. The geometry of Pc obtained at the B3LYP level has D_2h symmetry and the diameter of the central macrocycle is about 4 Å. The enthalpy of formation of Pc in the gas phase has been predicted to be 1518.50 kJ/mol at the B3LYP/6‐311G(2d,2p)//B3LYP/6‐31G* level via an isodesmic reaction. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Theoretical study of light-metal tetrahydroborates

Ab initio calculations of the structural, energetic, vibrational, and magnetic characteristics of the lowest-lying structures for isolated molecules and ions of light-metal tetrahydroborates (Li, Na, Be, Mg, and Al) have been performed by the perturbation theory (MP2), quadratic configuration interaction (QCISD(T)), coupled cluster (CCSD(T)), and density functional theory (B3LYP) methods using the 6-31G*, 6-31G**, 6-311+G**, and 6-311++G** basis sets. The trends in the behavior of the structural parameters, the energies of different decomposition pathways, barriers to internal rotation of BH₄ groups, normal mode frequencies, magnetic shielding constants, and spin density distribution (in radicals) have been analyzed in various related series of these compounds. The results obtained by ab initio methods and at the DFT level are compared. The economical approximation B3LYP/6-311++G**//B3LYP/6-311+G** adequately reproduces the results obtained at the higher level of theory CCSD(T)/6-311++G*s*//MP2/6-31G* even though it requires considerably shorter CPU times and smaller amounts of memory.     

An ab-initio study of some homolytic substitution reactions of acyl radicals at silicon, germanium and tint

Ab initio calculations using the 6-311G**, cc-pVDZ, and (valence) double-zeta pseudopotential (DZP) basis sets, with (MP2, QCISD, CCSD(T)) and without (UHF) the inclusion of electron correlation, and density functional (BHandHLYP, B3LYP) calculations predict that homolytic substitution reactions of acetyl radicals at the silicon atoms in disilane can proceed via both backside and frontside attack mechanisms. At the highest level of theory (CCSD(T)/cc-pVDZ//MP2/cc-pVDZ), energy barriers (deltaE double dagger) of 77.2 and 81.9 kJ mol(-1) are calculated for the backside and frontside reactions respectively. Similar results are obtained for reactions involving germanium and tin with energy barriers (deltaE double dagger) of 53.7-84.2, and 55.0-89.7 kJ mol(-1) for the backside and frontside mechanisms, respectively. These data suggest that both homolytic substitution mechanisms are feasible for homolytic substitution reactions of acetyl radicals at silicon, germanium, and tin. BHandHLYP calculations provide geometries and energy barriers for backside and frontside transition states in good agreement with those obtained by traditional ab initio techniques.     

Spectroscopic and quantum chemical study of the novel compound cyclopropylmethylselenol

An investigation into the properties of the novel compound cyclopropylmethylselenol has been undertaken by use of Stark-modulation microwave spectroscopy and high-level quantum chemical calculations. Ground-state spectra belonging to six isotopomers of a single conformer of the molecule were recorded and assigned. This conformer, predicted to be the lowest in energy by a series of quantum chemical calculations, possesses a synclinal arrangement of the H-C-C-Se atoms. In addition to the assignment of these ground-state spectra, transitions attributable to vibrationally excited states of the 78Se- and 80Se-containing isotopomers were identified. A tentative assignment of these excited-state spectra to specific vibrational modes has been made with the assistance of a density functional theory calculation at the B3LYP/6-311++G(3df,2pd) level of theory. Close agreement was found between experimental ground-state rotational constants and ab initio equilibrium values calculated at the MP2/aug-cc-pVTZ level of theory. Good agreement was also noted between certain r(s) principal axis coordinates of atoms in the molecule and the corresponding ab initio r(e) values. Limited evidence in favor of the formation of a weak intramolecular hydrogen bond between the H atom of the selenol group and electron density associated with the cyclopropyl ring is discussed.     

Conformational behavior of some hydroxamic acids

The conformational preferences of a few hydroxamic acids are investigated by the density functional B3LYP/6-311++G**//B3LYP16-31G* and semiempirical AM1 and PM3 methods in this work. It is found that both semiempirical methods give satisfactory results in comparison with sophisticated DFT and ab initio calculations, except for the activation barriers, which are overestimated. Of the two semiempirical methods, while the PM3 method gives better results for relative stabilities, AM1 geometries are in slightly better agreement with the experiments. The keto forms are found to be most stable and the reaction pathways for the interconversion between the keto and enol forms have been deduced. The effect of solvation on the reaction has also been investigated, as has the effect of methyl substitution at the carbon and nitrogen atoms. All the investigated acids exhibit N-acid behavior.     

Classical force field parameters for the heme prosthetic group of cytochrome c

Accurate force fields are essential for describing biological systems in a molecular dynamics simulation. To analyze the docking of the small redox protein cytochrome c (cyt c) requires simulation parameters for the heme in both the reduced and oxidized states. This work presents parameters for the partial charges and geometries for the heme in both redox states with ligands appropriate to cyt c. The parameters are based on both protein X-ray structures and ab initio density functional theory (DFT) geometry optimizations at the B3LYP/6-31G* level. The simulations with the new parameter set reproduce the geometries of the X-ray structures and the interaction energies between water and heme prosthetic group obtained from B3LYP/6-31G* calculations. The parameter set developed here will provide new insights into docking processes of heme containing redox proteins.