The classical molecular dynamics (MD) simulation method, which makes use of empirical potential functions, is widely used in many fields of chemistry, ranging from inorganic materials to biological systems. It is laborious and impractical, however, to construct empirical potential functions to describe bond breaking and bond formation for systems with many atoms. Instead of requiring such empirical potential functions to investigate chemical reactions, the method of direct dynamics can be applied, in which the energy and forces of the system are computed directly from a quantum mechanical treatment. Ab initio MO-MD method, which is the molecular dynamics method based on ab initio MO calculations, has been extended to be able to take account of many solvent molecules based on the hybrid QM/MM-vib approach. We apply this method to organic reactions in solution to get an insight into the reaction mechanisms.
Nonlinear optical materials are considered to be important for advanced optical technology in the future.At present, many researches and developments are carried out to create new inorganic and organic materials.With progress in researches on organic nonlinear optical materials, many attempts using computational chemistry such as molecular orbital method have been done to understand the mechanism of nonlinear optical phenomena at molecular level and to design new materials. Here the present status of the molecular design of organic nonlinear optical materials by computational chemistry is reviewed.
Several modeled theoretical works have been carried out for the open states caused by local deformations in DNA. These models are based on the Dynamic Plane Base Rotator (DPBR) approach, but simplify the potentials of the base-stacking as well as the interbase H bondings. In the present work, we exactly introduce the realistic potentials of the above interactions by ab initio calculations, and investigate the generation and propagation of the open states in DNA double helices. The actual potentials reveal that the open states do not propagate as a sine-Gordon type solitary wave but rather play a stationary wave. This is because the actual potential strongly differs from the conventional cosine potential which produces the sine-Gordon solitons. An inclusion of the sugar phosphate backbone strengthens the stacking potential and causes a possibility of another type of the DNA open states.
Basis set effect in evaluation of base pair formation energy of non-Watson-Crick type mismatched base pair between guanine (G) and uracil (U) was studied from 6-31G* to 6-311++G** basis set on the Hartree-Fock and the second-order Møller-Plesset level of theory. The calculated values of the tautomerism energies and mismatched base pair formation energies significantly fluctuated depending on the basis set used. However, we can tentatively conclude that, the mismatched base pair between the enol tautomer of guanine (G') and U is likely to be more stable than the mismatched base pair between G and the enol tautomer of uracil (U').
Quantum chemical calculations have been performed to clarify the function of the active catalytic subunit (C-subunit) of cAMP-dependent protein kinase (cAPK) that plays an important role in the regulation of blood glucose. It was found that the phosphorylation of Ser residue by cAPK proceeds via two elementary reactions; (i) an intermediate is formed from the enzyme-substrate complex (ES-complex), and (ii) the phosphorylated Ser is released from the active site. In the intermediate between the two elementary reactions, the Ser of the substrate is attached to the γ-phosphoric acid of the ATP, and the γ-phosphorus atom has a five-coordinated structure. The former elementary reaction is the rate-determining step, and the activation energy required for this phosphorylation reaction has been estimated to be 29.04kcal/mol. Hence, this phosphorylation reaction is expected to proceed at a body temperature of about 310K.
A simple charge density distribution representation program is developed using Mesa . We used the contour map evaluation algorithm developed by Yabe . Detailed description of the algorithm and the implementation method on Mesa are discussed. As an example of this method, we show a charge density distribution map calculated by the first principle Molecular Dynamics program CAMP-Atami (JCPE : P089) for Si diamond structure with 8 atom system. The example program code will be distributed through JCPE.
A reaction database system on Internet is described. The main feature lies in the representation of reaction schemes, where the mapping between atoms of a reactant and a product is preserved as the information of a reaction, enabling the classification of atoms from the viewpoint of chemical reaction. As a result, the reaction sites on a reactant and a product are extracted hierarchically based on the classification of atoms. It allows the retrieval from the point of chemical reaction as well as simple substructure searching. The system is implemented using Java as a client-server system on Internet, and is opened to the public aiming at both retrieval and update via Internet.
The program was made for generating the VRML file from the simulation results by MXDORTO in order to display the molecular structure independent on the platform. Generated VRML file is displayable by using Web browser and the plug-in software even in not only on Windows but also on Macintosh and on the Unix machine. The viewpoint of displayed molecular structure can be freely changed by using the function of the Web browser and the plug-in software.
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