Home About us Contact
|
Home About us Contact | ||
|
|
||
Large Basis Sets (large + basis_set)
Selected AbstractsQuantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Polina Georgieva Abstract Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] A path from Ih to C1 symmetry for C20 cage moleculeJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2005Zhigang Wang Abstract The symmetry of the C20 cage is studied based on the intrinsical relationship among point groups (Bradley, C. J.; Cracknell, A. P. The Mathematical Theory of Symmetry in Solids; Claredon Press: Oxford, 1972). The structure of the C20 cage with Ih symmetry is constructed, as are eight other structures with subgroup symmetry. A path from Ih symmetry to C1 symmetry is obtained for the closed-shell electronic state, and the structure with D2h symmetry is the most stable on this path. Using the D2h structure the correlation energy correction is studied on the condition of restricted excitation space at the CCSD(T) level. We obtain curves on the relation between the orbital numbers and the total energy at the CCSD(T), CCSD, and MP2 level, respectively. The results of these curves obtained from MP2 and CCSD(T) methods have the same tendency, while the results of CCSD gradually diverge with an increase in orbital numbers. When the orbitals used in the calculation reach 460, the total energy is ,759.644 hartree at MP2 level and is ,759.721 hartree by the CCSD(T) method. From the calculation results, we find that a large basis set can improve the reliability of the MP2 method, and to restrict excitation space is necessary when using the CCSD(T) method. © 2005 Wiley Periodicals, Inc. J Comput Chem 12: 1279,1283, 2005 [source] Reaction Mechanism of Porphyrin Metallation Studied by Theoretical MethodsCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2005Yong Shen Dr. Abstract We have studied the reaction mechanism for the insertion of Mg2+ and Fe2+ into a porphyrin ring with density functional calculations with large basis set and including solvation, zero-point and thermal effects. We have followed the reaction from the outer-sphere complex, in which the metal is coordinated with six water molecules and the porphyrin is doubly protonated, until the metal ion is inserted into the deprotonated porphyrin ring with only one water ligand remaining. This reaction involves the stepwise displacement of five water molecules and the removal of two protons from the porphyrin ring. In addition, a step seems to be necessary in which a porphyrin pyrrolenine nitrogen atom changes its interaction from a hydrogen bond to a metal-bound solvent molecule to a direct coordination to the metal ion. If the protons are taken up by a neutral imidazole molecule, the deprotonation reactions are exothermic with minimal barriers. However, with a water molecule as an acceptor, they are endothermic. The ligand exchange reactions were approximately thermoneutral (±20 kJ,mol,1, with one exception) with barriers of up to 72 kJ,mol,1 for Mg and 51 kJ,mol,1 for Fe. For Mg, the highest barrier was found for the formation of the first bond to the porphyrin ring. For Fe, a higher barrier was found for the formation of the second bond to the porphyrin ring, but this barrier is probably lower in solution. No evidence was found for an initial pre-equilibrium between a planar and a distorted porphyrin ring. Instead, the porphyrin becomes more and more distorted as the number of metal,porphyrin bonds increase (by up to 191 kJ,mol,1). This strain is released when the porphyrin becomes deprotonated and the metal moves into the ring plane. Implications of these findings for the chelatase enzymes are discussed. [source] Theoretical versus experimental geometries in S-bridged manganese carbonyl complexesJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2003Juan F. Van der Maelen Uría The experimental geometry obtained from single-crystal X-ray diffraction for a number of binuclear S-bridged manganese complexes is compared with the results of theoretical calculations made at the ab initio level by using Hartree,Fock and density functional theory methods with medium-size and large basis sets. The optimized geometries obtained were somewhat relaxed when compared with the experimental ones, with very similar bond and torsion angles but longer bond lengths. The mean square deviation for bond lengths (angles) was found to be between 0.046,Ĺ (1.1°) and 0.004,Ĺ (0.7°) depending on the theoretical model used. [source] An ab initio potential energy surface and vibrational energy levels of ZnH2JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2010Zheng Guo Huang Abstract A three-dimensional potential energy surface of the electronic ground state of ZnH2 () molecule is constructed from more than 7500 ab initio points calculated at the internally contracted multireference configuration interaction with the Davidson correction (icMRCI+Q) level employing large basis sets. The calculated relative energies of various dissociation reactions are in good agreement with the previous theoretical/experimental values. Low-lying vibrational energy levels of ZnH2, ZnD2, and HZnD are calculated on the three-dimensional potential energy surface using the Lanczos algorithm, and found to be in good agreement with the available experimental band origins and the previous theoretical values. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Translation of STO charge distributionsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2005J. Fernández Rico Abstract Barnett and Coulson's ,-function method (M. P. Barnett and C. A. Coulson, Philos. Trans. R. Soc., Lond. A 1951, 243, 221) is one of the main sources of algorithms for the solution of multicenter integrals with Slater-type orbitals. This method is extended here from single functions to two-center charge distributions, which are expanded at a third center in terms of spherical harmonics times analytical radial factors. For s,s distributions, the radial factors are given by a series of factors corresponding to the translation of s -type orbitals. For distributions with higher quantum numbers, they are obtained from those of the s,s distributions by recurrence. After analyzing the convergence of the series, a computational algorithm is proposed and its practical efficiency is tested in three-center (AB|CC) repulsion integrals. In cases of large basis sets, the procedure yields about 12 correct significant figures with a computational cost of a few microseconds per integral. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 846,855, 2005 [source] Ab initio prediction of optical rotation: Comparison of density functional theory and Hartree-Fock methods for three 2,7,8-trioxabicyclo[3.2.1]octanesCHIRALITY, Issue 4 2002P.J. Stephens Abstract We report ab initio calculations of the frequency-dependent electric dipole-magnetic dipole polarizabilities, ,(,), at the sodium D line frequency and, thence, of the specific rotations, [,]D, of 2,7,8-trioxabicyclo[3.2.1]octane, 1, and its 1-methyl derivative, 2, using the Density Functional Theory (DFT) and Hartree-Fock/Self-Consistent Field (HF/SCF) methodologies. Gauge-invariant (including) atomic orbitals (GIAOs) are used to ensure origin-independent [,]D values. Using large basis sets which include diffuse functions DFT [,]D values are in good agreement with experimental values (175.8° and 139.2° for (1S,5R)- 1 and - 2, respectively); errors are in the range 25,35°. HF/SCF [,]D values, in contrast, are much less accurate; errors are in the range 75,95°. The use of small basis sets which do not include diffuse functions substantially lowers the accuracy of predicted [,]D values, as does the use of the static limit approximation: ,(,) , ,(o). The use of magnetic-field-independent atomic orbitals, FIAOs, instead of GIAOs, leads to origin-dependent, and therefore nonphysical, [,]D values. We also report DFT calculations of [,]D for the 1-phenyl derivative of 1, 3. DFT calculations find two stable conformations, differing in the orientation of the phenyl group, of very similar energy, and separated by low barriers. Values of [,]D predicted using two different algorithms for averaging over phenyl group orientations are in good agreement with experiment. In principle, the absolute configuration (AC) of a chiral molecule can be assigned by comparison of the optical rotation predicted ab initio to the experimental value. Our results demonstrate the critical importance of the choice of ab initio methodology in obtaining reliable optical rotations and, hence, ACs, and show that, at the present time, DFT constitutes the method of choice. Chirality 14:288,296, 2002. © 2002 Wiley-Liss, Inc. [source] | ||||||||||