DNA photolyases are flavoproteins that are responsible for the repair photocycle of UV damaged DNA. The key cofactor in DNA photolyase is flavin molecules. It is believed that with the help of electron-transfer redox cycle of anionic hydroquinone (FADH-), which is the fully reduced form of flavin molecule, the photolyase breaks down the mutagenic photoproduct cyclobutane pyrimidine dimers (CPDs) by absorbing energy from UV-light to repair damaged DNA.
The design of a proper molecular model with a good balance between the size of the model system and the computational capacity is essential for theoretical modeling of biological systems. We have shown in this letter that two models of FADH-: one is the often used model system M-NHD and the other is model M-IHD which the intramolecular hydrogen bond between the isoalloxazine ring and the ribityl moiety is included. Our work shown that the often used model system, a lumiflavin (7,8-dimethy-10-methyl-isoalloxazine), can not correctly describe geometrical and electronic structures of FADH- in DNA photolyase. The intramolecular hydrogen bond has great impact on the electronic structure and the optical absorption/emisson of FADH- molecule in solution and protein. The calculated equilibrium geometry and spectra for M-IHD in the protein and in the solution are in very reasonable agreement with the experimental ones. The intramolecular hydrogen bond is found to play a significant role in controlling photochemical properties of FADH- in DNA photolyase. Our calculations have indicated that such an intramolecular hydrogen bond should always be included in theoretical models for studying DNA photolyase.
Ai. et al. J. Phys. Chem. Lett., Article ASAP DOI: 10.1021/jz900434z
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The Mechanism of Iridium(III) Catalyzed CO2 Hydrogenation
We have studied the mechanism of the iridium(III) catalyzed hydrogenation of CO2 in aqueous base. The reaction was reported by Nozaki and co-workers in 2009 and showed an extraordinary turnover number (TON) and turnover frequency (TOF). Hydrogenation of carbon
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Importance of the Intramolecular Hydrogen Bond on Photochemistry of Anionic Hydroquinone (FADH.) in DNA Photolyase
DNA photolyases are flavoproteins that are responsible for the repair photocycle of UV damaged DNA. The key cofactor in DNA photolyase is fla
vin molecules. It is believed that with the help of electron-transfer redox cycle of anionic hydroquinone (FADH-), which is the fully
reduced form of flavin molecule...
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Product Protection, a Key to Developing High Performance Methane Selective Oxidation Catalysts
Selective oxidation of methane(CH4) to methanol (CH3OH) was achieved by Periana in 1998, by using a platinum(II)
complex as the catalyst in fuming sulfuric acid (H2SO4) at 220°C. The transformation of methane to methanol is
complicated by the fact that the homolytic bond strength of the C-H bond is higher in methane than in methanol...
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Ab Initio Study of Coherent Anti-Stokes Raman Scattering (CARS) of the 1,3,5-Trinitro-1,3,5-Triazacyclohexane (RDX) Explosion Molecule.
Advances in coherent anti-Stokes Raman scattering (CARS) over the recent years have turned this technique into a unique and powerful tool used worldwide to probe structure and function of molecular or composite materials in biology.
In the biomedical area, CARS detection makes it is possible...
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Time-dependent closed and open-shell density functional theory from the perspective of partitioning techniques and projections
The application of density functional theory has grown immensely the last two decades. Our department has taken strong interest in the development of time-dependent density functional thoery...
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Theoretical studies of angle-resolved ion yield spectra of core-to-valence transitions of acetylene Gas phase experiments cannot get information on symmetries of particular photo-excited states. Our theoretical multi-mode approach includes ab initio calculations of the potential energy surfaces of the ground and inner-shell excited states, and their transition dipole moments. The theory explains quantitatively the experimental data for the acetylene molecule.
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Simulation of Inelastic Electronic Tunneling Spectra of Adsorbates from First-Principles
Vibration spectrum is a fingerprint property of molecules, clusters, or more complex structures such as single molecule adsorbed on metal surfaces. We implement an approach for first principles simulations for inelastic electron tunneling spectra...
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Reaction mechanism of the dinuclear zinc enzyme N-Acyl-L-homoserine Lactone Hydrolase is investigated by DFT. This enzyme is responsible for quorum sensing, the way bacteria communicate with one another through extracellular signaling molecules to monitor their own population density.
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Controlling Errors in Self–Consistent
Field Calculations
A mathematical framework to directly relate
computational approximations in Hartree–Fock/Kohn–Sham
calculations to the accuracy in the electron density is proposed.
This framework has the potential to eliminate the need for ad
hoc parameters in large Hartree–Fock/Kohn–Sham
calculations.
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Properties of a Biophotovoltaic Nanodevice
Properties of an on-chip photovoltaic nanodevice are demonstrated where the
dyes comprise green florescent proteins. A correlation between UV-vis spectrum of the GFP and the zero external potential bias (ZEPB) of the device is reported. The temperature dependence suggests the ZEPB photocurrent to reflect a liquid crystal type ordering where the current declines monotonically with
increasing temperature...
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Hartree-Fock calculations with linearly scaling memory usage
We present in this paper an implementation of a set of algorithms for performing Hartree-Fock calculations with resource requirements in terms of both time and memory directly proportional to the system size. In particular, a way of computing the Hartree-Fock exchange...
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Temperature-Dependent Statistical Behavior of Single Molecular Conductance in Aqueous Solution
We have combined molecular dynamics simulations with first principles calculations to study electron transport in a single molecule...
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Lossless negative dielectric constant from quantum dot exciton polaritons. Prospects for a lossless negative dielectric constant material for optical devices were studied in this project using a mixture of two types of quantum dots. The simulations indicated that with sufficient gain...» read more »
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