Charge-Transfer Matrix Elements by FMO-LCMO Approach: Hole Transfer in DNA with Parameter Tuned Range-Separated DFT

A scheme for computing charge-transfer matrix elements with the linear combination of fragment molecular orbitals and the 'nonempirically tuned range-separated' density functional is presented. It takes account of the self-consistent orbital relaxation induced by environmental Coulomb field and the exchange interaction in fragment pairs at low computational scaling along the system size. The accuracy was confirmed numerically on benchmark systems of imidazole and furane homo-dimer cations. Applications to hole transfers in DNA nucleobase pairs and in a $\pi$-stack adenine octomer highlight the effects of orbital relaxation.Comment: 10 pages, 8 figure

Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling TDA and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (HL) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe[2+] and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe[2+] ion, its replacement by Zn[2+], or its removal are found to affect the T[DA] value by factors within 2.2. The calculated T[DA] values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments

FMO3-LCMO study of electron transfer coupling matrix element and pathway: Application to hole transfer between two tryptophans through cis- and trans-polyproline-linker systems

Long-distance electron transfer (ET) plays an essential role in biological energy conversion. [1–5] Representative is those in photosynthetic reaction centers in which photon energy is converted to electrochemical energy via series of ETs through redox centers embedded in transmembrane protein. A simple but fundamental question open to microscopic investigation is how the protein environment is involved in the ET; the protein structure could be involved passively by simply holding the redox centers at appropriate spatial configuration or actively by providing intermediate virtual states for superexchange ET mechanism

Fragment Molecular Orbital Study on Electron Tunneling Mechanisms in Bacterial Photosynthetic Reaction Center

The tunneling mechanisms of electron transfers (ETs) in photosynthetic reaction center of Blastochloris viridis are studied by the ab initio fragment molecular orbital (FMO) method combined with the generalized Mulliken-Hush (GMH) and the bridge Green function (GF) calculations of the electronic coupling <i>T</i>_DA and the tunneling current method for the ET pathway analysis at the fragment-based resolution. For the ET from batctriopheophytin (H_L) to menaquinone (MQ), a major tunneling current through Trp M250 and a minor back flow via Ala M215, Ala M216, and His M217 are quantified. For the ET from MQ to ubiquinone, the major tunneling pathway via the nonheme Fe²⁺ and His L190 is identified as well as minor pathway via His M217 and small back flows involving His L230, Glu M232, and His M264. At the given molecular structure from X-ray experiment, the spin state of the Fe²⁺ ion, its replacement by Zn²⁺, or its removal are found to affect the <i>T</i>_DA value by factors within 2.2. The calculated <i>T</i>_DA values, together with experimentally estimated values of the driving force and the reorganization energy, give the ET rates in reasonable agreement with experiments

Computational study on the roles of amino acid residues in the active site formation mechanism of blue-light photoreceptors

To examine the functional roles of the active site methionine (M-site) and glutamic acid (E-site) residues of blue-light photoreceptors, we performed in silico mutation at the M-site in a systematic manner and focused on the hydrogen bonding between the E-site and the substrate: the cyclobutane–pyrimidine dimer (CPD). Fragment molecular orbital calculations with electron correlations demonstrated that substitution of the M-site methionine with either alanine or glutamine always destabilizes the interaction energy between the E-site and the CPD by more than 12.0 kcal/mol, indicating that the methionine and glutamic acid residues cooperatively facilitate the enzymatic reaction in the active site