Self-consistent Cluster-embedding Method Research Articles

Equivalent potential of water for the electronic structure of glycine

First-principles, all-electron, ab initio calculations have been performed to construct an equivalent potential of water for the electronic structure of glycine (Gly) in solution. The calculation involved three steps. The first step was to search for the minimum-energy geometric structure of the Gly + nH₂O system. The second step was to calculate the electronic structure of Gly with the potential of water molecules via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step was to calculate the electronic structure of Gly with the potential of dipoles after replacing the water molecules with dipoles. The results show that the occupied molecular orbitals of Gly are raised by about 0.0524 Ry on average due to the effect of water. The effect of water can be simulated well using the dipole potential. The equivalent potential obtained can be applied directly to electronic structure calculations of proteins in solution using the SCCE method.

Equivalent potential of water for electronic structure of asparagine

AbstractThe equivalent potential of water for the electronic structure of asparagine(Asn) is constructed by using the first‐principles, all‐electron, ab initio calculation. The process is composed of three steps. The first step is to determine the geometric structure of Asn+nH2O system with a minimum energy. The second step is to calculate the electronic structure of Asn with the potential of water molecules by using the self‐consistent cluster‐embedding (SCCE) method, based on the result obtained in the first step. The last step is to calculate the electronic structure of Asn with the potential of dipole after replacing water molecules with dipoles. The results show that the major effect of water molecules on Asn' electronic structure be raising the occupied electronic states by 0.034 Ry on average and narrowing energy gap by 0.91%. The effect of water on the electronic structure of Asn can be well simulated by using dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010

The equivalent dipole potential of water for the electronic structure of threonine

The equivalent potential of water for the electronic structure of threonine (Thr) in solution is constructed by the first-principles, all-electrons, ab initio calculations. The main process of calculation consists of three steps. First, the geometric structure of the cluster containing Thr and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Thr with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Thr with the potential of dipoles is calculated. The results show that the major effect of water on the electronic structure of Thr is to raise the occupied molecular orbitals near the Fermi level by about 0.01 Ry on average, and its energy gap is almost not changed. The effect of water on the electronic structure of Thr can be simulated by dipoles potential.

Simulation of water potential for the electronic structure of serine

First-principles, all-electron, ab initio calculations have been performed to construct an equivalent water potential for the electronic structure of serine (Ser) in solution. The calculation is composed of three steps. The first step is to search for the configuration of the Ser + nH2O system with a minimum energy. The second step is to calculate the electronic structure of Ser with the water molecule potential via the self-consistent cluster-embedding method (SCCE), based on the result obtained in the first step. The last step is to calculate the electronic structure of Ser with the dipole potential after replacing the water molecules with dipoles. The results show that the occupied states of Ser are raised by about 0.017 Ry on average due to the effect of water. The water effect can be successfully simulated by using the dipole potential. The obtained equivalent potential can be applied directly to the electronic structure calculation of protein in solution by using the SCCE method.

The equivalent potential of water molecules for electronic structure of alanine

Using ab initio calculations based on density functional theory, an equivalent potential of water molecules for the electronic structure of Ala in solution has been obtained. The calculation process consists of three steps: first, the geometric structure of Ala + nH2O system is determined by searching for the lowest energy of the system using free cluster calculation method. Second, based on the geometric structure obtained, the electronic structure of Ala with the potential of water molecules is calculated using a self-consistent cluster-embedding method. Finally, after replacing water molecules with dipoles, the electronic structure of Ala with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Ala with the potential of dipoles is close to that of water molecules. The calculated results show that the main effect of water molecules is to raise the state for methyl CH3 by about 0.14 Ry, raising all other eigenvalues by about 0.059 Ry, and widening the energy gap by about 25%. In contrast, the replacement of water molecules by dipoles is comparatively efficient, showing that the effect of water molecules on the electronic structure of Ala can be simulated by a dipole potential, which would be a shortcut calculation.

The equivalent potential of water for electronic structure of aspartic acid

The equivalent potential of water for the electronic structure of aspartic acid (Asp(-)) in solution is constructed by the first-principles, all-electrons, ab initio calculations. Aspartic acid is a hydrophilic amino acid which is negatively charged in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Asp(-) and water molecules is calculated by the free cluster calculation. Then, based on the obtained geometric structure, the electronic structure of Asp(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Asp(-) with the potential of dipoles is calculated. The results show that the major effect of water on Asp(-)'s electronic structure is lowering the occupied molecular orbitals by about 0.02 Ry on average, and narrowing energy gap by 10.8%. The effect of water on the electronic structure of Asp(-) can be simulated by dipoles potential.

Equivalent potential of water molecules for electronic structure of glutamic acid

The fundamental importance of the electronic structure of molecules is widely recognized. To get reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. Here, the first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of glutamic acid, which is a hydrophilic amino acid and is negatively charged (Glu(-)) in neutral water solution. The main process of calculation consists of three steps. Firstly, the geometric structure of the cluster containing Glu(-) and water molecules is calculated by free cluster calculation. Then, based on the geometric structure, the electronic structure of Glu(-) with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Glu(-) with the potential of dipoles is calculated. Our calculations show that the major effect of water molecules on Glu(-)'s electronic structure is lowering the occupied electronic states by about 0.017 Ry, and broadening energy gap by 12%. The effect of water molecules on the electronic structure of Glu(-) can be well simulated by dipoles potential.

The equivalent potential of water molecules for electronic structure of cysteine

In order to get more reliable electronic structure of protein in aqueous solution, it is necessary to construct a simple, easy-use equivalent potential of water molecules for protein's electronic structure calculation. The first-principles, all-electron, ab initio calculations have been performed to construct the equivalent potential of water molecules for the electronic structure of Cys. The process consists of three steps. First, the electronic structure of the cluster containing Cys and water molecules is calculated. Then, based on the structure, the electronic structure of Cys with the potential of water molecules is calculated using the self-consistent cluster-embedding method. Finally, the electronic structure of Cys with the potential of dipoles is calculated. The dipoles are adjusted so the electronic structure of Cys with the potential of dipoles is close to that of water molecules. The calculations show that the major effect of water molecules on Cys' electronic structure is lowering the occupied electronic states by about 0.032 Ry, and broadening energy gap by 16%. The effect of water molecules on the electronic structure of Cys can be simulated by dipoles potential.

Electronic structure of CoO

The electronic structure of CoO is studied by a self-consistent cluster-embedding method. The localized and band properties are found in both ground state and excited states. An explanation for the insulating nature of CoO is proposed which is consistent with the one for NiO proposed previously. The simulations of both the spin-ordered states and the spin-disordered states (with local antiferromagnetic order) give a good description of the magnetic properties of CoO. It is found theoretically that CoO remains as an insulator when it goes from the paramagnetic phase to antiferromagnetic phase.

Self-consistent cluster-embedding calculation method and the calculated electronic structure of NiO.

The self-consistent cluster-embedding method is discussed theoretically. A definition of the total energy for an embedded cluster has been introduced. The method has two advantages. (i) It can describe both localized and band properties, including their excitations. (ii) It can give a good description of the magnetic properties for both spin-ordered and spin-disordered states. The electronic structure of NiO is studied using a high-quality basis set to calculate the electronic structure of a small embedded cluster and an antiferromagnetic insulating ground state is obtained. The picture has both localized and band properties. A small energy gap separates the unoccupied and occupied nickel 3d orbitals which are well localized. Each 3d orbital is attached to a particular nickel ion. Below the 3d levels are two diffuse oxygen 2p bands, and above the 3d levels are oxygen 3s, nickel 4s, and oxygen 3p bands. Experimental data concerning photoemission and optical absorption can be interpreted naturally. The spin magnetic moment of the nickel ion is calculated correctly. The simulation of the spin-disordered state shows that NiO remains as an insulator in the paramagnetic state. The N\'eel temperature of NiO is calculated directly to give a reasonable result. The Hubbard U parameter for nickel 3d electrons is estimated. The calculation shows that the excited nickel 3d electrons are also well localized and the overlaps are less than 4.5%. We propose the following: The overlap of the excited 3d electrons is too small to form a metallic band, but the overlap is sufficient for the ``hole'' to migrate through the crystal. In this sense, NiO is a charge-transfer insulator with a gap of about 4 eV (mostly from oxygen to nickel). The calculated small energy gap (about 0.5 eV) provides the activation energy of NiO which is supported by the experimental results.