Ab initio structure of the active site of phosphotriesterase

This research exploits two recent developments to obtain a fundamental understanding of the metalloenzyme active site using the bimetallic enzyme phosphotriesterase as an example of this class. First is the theoretical prediction that the structure and spectroscopy of a native metalloenzyme active site is qualitatively determined by the supermolecule complex of the metal(s) and the first shell of ligands with proper charge states including waters directly bonded to ionic ligands. The second is the development of an effective potential for representing the molecular environment interacting with an all-electron active site in the quantum Hamiltonian. The GAMESS suite of electronic structure codes has implemented this new methodology, effective fragment potentials (EFP), to make theoretical calculations on structure, spectroscopy, and reactivity tractable for systems involving hundreds of atoms. Since there are transition metal cations at the active site of these enzymes, the all-electron part of the complex is calculated with relativistic compact effective potentials (CEP) and their concomitant basis sets. A realistic representation of the active site with its protein environment can be obtained using a combination of the CEP and EFP. This presentation will determine the inherent electronic and structural characteristics of phosphotriesterase using ab initio quantum mechanical methods. A single X-ray structure for the Zn-Zn enzyme is leveraged to obtain the structure of the Cd-Cd enzyme and to examine the consequences of protonating the active site.     

An insight into the environmental effects of the pocket of the active site of the enzyme. Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase

We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.     

Ab initio study of lithiathion of the Si4(-) cluster

The potential energy surfaces of the Li(n)Si(4)(-) (n = 0-5) clusters were explored using the Kick Coalescence method. We found that, for those systems with n ≤ 2, the butterfly and parallelogram Si(4)(2-) kernels prevail as building blocks; however, when n ≥ 3, the Si(4)(4-) tetrahedral kernel, which is commonly found in heavier alkali monosilicides, MSi (M = Na, K, Rb, Cs), arises as the prevailing building block. In addition, by a natural population analysis (NPA) we found that the maximum charge transfer -4 from Li atoms to Si atoms is attained when n = 3. The addition of more Li atoms to the Si(4)(4-) system does not increase the charge transfer, but keeps it almost constant at the maximum value. We also calculated theoretical vertical electron detachment energies (VDEs) for low-lying isomers of the Li(n)Si(4)(-) (n = 0-4) clusters in order to facilitate their experimental identification.     

Ab initio study of AmCl(+): f-f spectroscopy and chemical binding

A valence full configuration interaction study with a polarized double-zeta quality basis set has been carried out for the lowest 49 electronic states of AmCl(+). The calculations use a pseudopotential treatment for the core electrons and incorporate a one-electron spin-orbit interaction operator. Electrons in the valence s, p, d, and f subshells were included in the active space. The resulting electronic potential energy curves are largely repulsive. The chemical bonding is ionic in character with negligible participation of 5f electrons. The molecular f-f spectroscopy of AmCl(+) arises essentially from an in situ Am(2+) core with states slightly redshifted by the presence of chloride ion. Am(+)+Cl asymptotes which give rise to the few attractive potential energy curves can be predicted by analysis of the f-f spectroscopy of isolated Am(+) and Am(2+). The attractive curves have substantial binding energies, on the order of 75-80 kcal/mol, and are noticeably lower than recent indirect measurements on the isovalent EuCl(+). An independent empirical correlation supports the predicted reduction in AmCl(+) binding energy. The energies of the repulsive curves are strongly dependent on the selection of the underlying atomic orbitals while the energies of the attractive curves do not display this sensitivity. The calculations were carried out using our recently developed parallel spin-orbit configuration interaction software.     

Ab initio study of the cyclooctatetraenyl radical

Ab initio calculations have been carried out on the 1,3,5,7- and 1,2,4,7-tetraene configurations of the cyclooctatetraenyl radical at UHF, ROHF, MCSCF, ROCISD, QCISD, and CCSD(T) levels of theory with 6-311G(d,p) and cc-pVDZ basis sets. Although spin contamination is present, the ROCISD calculations support the energies obtained from less intensive, UHF-based coupled cluster calculations over the energies obtained from MCSCF analysis of the pi-electron orbitals. The 1,3,5,7-form is a local minimum at the coupled cluster levels, higher in energy than the resonance-stabilized 1,2,4,7-form by 10-13 kJ/mol, but bounded by a barrier of less than 0.5 kJ/mol. The isomerization surface connecting these two structures is described and results reported from integration of the vibrational Schr?dinger equation on that surface. Excited vibrational states at energies just above the isomerization barrier are dominated by the character of the 1,3,5,7-tetraenyl radical, which suggests that chemistry involving this intermediate at typical combustion temperatures may branch at this juncture.     

Ab initio study of bonding trends among cyanamidophosphates (

Ab initio calculations on the experimentally known anions [POn(NCN)4-n]3- are used to show that intramolecular forces are sufficient to determine their existence and structure. Structures are predicted for the analogous cyanamidosulphates and perchlorates. If one of the oxygens of the XO4q group is replaced by nitrogen or fluorine, further new anions are obtained. An example is NSO3(3)-. Remarkably, the NArO3- anion is predicted to have strong inner bonding and is, together with ArO4, a candidate for an argon species.     

Ab initio study of (13)C(alpha) chemical shift anisotropy tensors in peptides

This study reports magnitudes and the orientation of the (13)C(alpha) chemical shift anisotropy (CSA) tensors of peptides obtained using quantum chemical calculations. The dependency of the CSA tensor parameters on the energy optimization of hydrogen atom positions and hydrogen bonding effects and the use of zwitterionic peptides in the calculations are examined. Our results indicate that the energy optimization of the hydrogen atom positions in crystal structures is necessary to obtain accurate CSA tensors. The inclusion of intermolecular effects such as hydrogen bonding in the calculations provided better agreement between the calculated and experimental values; however, the use of zwitterionic peptides in calculations, with or without the inclusion of hydrogen bonding, did not improve the results. In addition, our calculated values are in good agreement with tensor values obtained from solid-state NMR experiments on glycine-containing tripeptides. In the case of peptides containing an aromatic residue, calculations on an isolated peptide yielded more accurate isotropic shift values than the calculations on extended structures of the peptide. The calculations also suggested that the presence of an aromatic ring in the extended crystal peptide structure influences the magnitude of the delta(22) which the present level of ab initio calculations are unable to reproduce.     

Ab initio calculation of core-electron binding energies in small molecules

Vertical ionization potentials for core orbitals of HF, H₂O, CO, HCN, and H₂CO are calculated with an ab initio transition operator method, followed by Rayleigh-Schrödinger perturbation theory. The results are improved by using a transition atomic basis set. Relativistic corrections are estimated. The average absolute deviation of our final results from experiment is 0.4 eV for the eight cases studied.     

Ab initio study of epitaxial growth on stepped Si(100) surface

Diffusion of a Si adatom over the reconstructed Si(100) surface with a single-height step on it is studied using the pseudopotential total energy method. The S_B rebonded step is shown to act as a good sink for adatoms descending onto the lower ledge. This is due to the presence of deep traps on the lower terrace and to the negative Ehrlich-Schwoebel barrier (the activation barrier for descent from the edge is 0.23 eV lower than for the motion on a flat surface). The diffusion characteristics of the adatom on both terraces are virtually unaffected by the presence of the step. However, the dimer buckling sequence on a lower terrace is strongly dependent on the position of the adatom along the diffusion path. © 1997 John Wiley & Sons, Inc.     

Ab initio study of molecular oxygen adsorption on Pu (111) surface

Using the generalized gradient approximation to density functional theory (DFT), molecular and dissociative oxygen adsorptions on a Pu (111) surface has been studied in detail. Dissociative adsorption with a layer‐by‐layer alternate spin arrangement of the plutonium layer is found to be energetically more favorable, and adsorption of oxygen does not change this feature. Hor1 (O₂ is parallel to the surface and lattice vectors) approach on the center2 (center of the unit cell, where there is a Pu atom directly below on the third layer) site, both without and with spin polarization, was found to be the preferred chemisorbed site among all cases studied with chemisorption energies of 8.365 and 7.897 eV, respectively. The second‐highest chemisorption energy occurs at the Ver (O₂ is vertical to the surface) approach of the bridge site with chemisorption energies of 8.294 eV (non‐spin‐polarized) and 7.859 eV (spin‐polarized), respectively. We find that 5f electrons are more localized in the spin‐polarized case than the non‐spin‐polarized counterparts. Localization of the 5f electrons is higher in the oxygen‐adsorbed plutonium layers compared with the bare layers. The ionic part of O? Pu bonding plays a significant role in the chemisorption process, along with Pu 5f? O 2p hybridization. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio study of K adsorption on a Ag(100) surface

Ab initio Hartree–Fock calculations are reported for the chemisorption of K on Ag using three different types of clusters to model the system. Geometry optimization is done in 4 degrees of freedom. It is found that since there is an absence of complete charge transfer between the adsorbate and substrate, the interaction can be interpreted as being predominately covalent in nature.     

Ab initio quantum Monte Carlo study of the binding of a positron to alkali-metal hydrides

Quantum Monte Carlo methods are used to investigate the binding of a positron to the alkali-metal hydrides, XH (X = Na and K). We obtain positron affinities for the NaH and KH molecules of 1.422(10) eV and 2.051(39) eV, respectively. These are considerably larger than the previous results of 1.035 eV and 1.273 eV obtained from multireference single- and double-excitation configuration interaction calculations. Together with our previous results for [LiH;e(+)] [Y. Kita et al., J. Chem. Phys. 131, 134310 (2009)], our study confirms the strong correlation between the positron affinity and dipole moment of alkali-metal hydrides.     

Ab initio study of the photochemistry of aminopyrimidine

Complete active space self‐consistent field (CASSCF), multi‐reference configuration interaction calculations (MR‐CISD), and equation of motion coupled‐cluster with singles and doubles (EOM‐CCSD) calculations are presented in order to elucidate the photodeactivation pathways of 6‐aminopyrimidine after vertical excitation to the S₁ ¹nπ* state. Vertical excitation energies are reported up to the S₇ state. Two S₁ excited state minima, both of ¹nπ* character, and three strongly puckered ¹ππ* minima on the crossing seam (MXS) between the S₀ and the S₁ potential energy surface were found. Nonadiabatic reaction paths are discussed by linearly interpolating between the two minima and all MXS, which explain and extend observations made in recent surface‐hopping dynamics CASSCF investigations [Barbatti and Lischka, J Phys Chem A 2007, 111, 2852]. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

乙酰胆碱水解反应的从头算研究

本文对乙酰胆碱水解反应历程进行了从头算分子轨道研究。首先, 我们在RHF/6-31G级别上研究了乙酰胆碱的水解反应的势能面, 找到了反应过程中的两个过渡态和连接这两个过渡态的中间体。然后进行了RHF/6-31G**级别上的单点能量计算。优化结果表明在两个过渡态中都包含有四元环状结构, 而且, 两个过渡态的四元环中存在着不同的分子内氢键。计算结果还表明,乙酰胆碱最终分解成胆碱和乙酸盐部分时, 酯键的断裂发生在羰基碳和酯基氧之间。最后, 进一步考虑溶剂化效应, 我们还运用量子Onsager模型, 在RHF/6-31G**级别上对整个水解反应的反应物、产物、中间体和过渡态分别进行了从头算自洽反应场能量计算, 求出了包含溶剂化效应在内的反应的能垒及总反应热。     

Ab initio study of the transition-metal carbene cations

The geometries and bonding characteristics of the first-row transition-metal carbene cations MCH_2~ were investigated by ab initio molecular orbital theory (HF/LANL2DZ). All of MCH_2~ are coplanar. In the closed shell structures the C bonds to M with double bonds; while in the open shell structures the partial double bonds are formed, because one of the σ and π orbitals is singly occupied. It is mainly the π-type overlap between the 2p_x orbital of C and 4p_x, 3d_(xz), orbitals of M~ that forms the π orbitals. The dissociation energies of C—M bond appear in periodic trend from Sc to Cu. Most of the calculated bond dissociation energies are close to the experimental ones.     

Ab initio CI study of the nitric oxide dimer (N2O2)

Configuration interaction (CI) studies of the ground and electronically excited states are reported for nitric oxide dimer (N₂O₂) in itscis equilibrium geometry. The lowest triplet state (³ B ₂) is found to lie only 0.43 eV above the ground state (¹ A ₁). The¹ A ₁ ¹ B ₁ transition is shown to be responsible for the rising absorption in the near infrared region observed experimentally. The transition of¹ A ₁¹ A ₂ calculated in the visible spectrum range of 701 nm (1.77 eV) is symmetry forbidden.     

Ab initio study of the KrH+ photodissociation

The multireference spin-orbit configuration interaction method is employed to calculate potential energy curves for the ground and low-lying excited states of the KrH(+) cation. For the first time, the spin-orbit interaction is taken into account and electric dipole moments are computed for transitions to the states responsible for the first absorption continuum (A band) of KrH(+). On this basis, the partial and total absorption spectra in this energy range are obtained. It is shown that the A-band absorption is dominated by the parallel A (1)Sigma(+)<--X (1)Sigma(+) transition. In the low-energy part of the band (<83x10(3) cm(-1)) the absorption is mainly caused by the spin-forbidden b (3)Pi(0(+) )<--X (1)Sigma(+) excitation, while perpendicular transitions to the B (1)Pi and b (3)Pi(1) states are significantly weaker. The branching ratio Gamma for the photodissociation products is calculated and it is shown to increase smoothly from 0 in the red tail of the band to 1 at E>or=90x10(3) cm(-1). The latter value corresponds to the exclusive formation of the spin-excited Kr(+)((2)P(12)) ions, which may be used to obtain laser generation on the Kr(+)((2)P(12)-(2)P(32)) transition.     

Ab initio ONIOM-molecular dynamics (MD) study on the deamination reaction by cytidine deaminase

We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.