Direct Observation of Ligand Rebinding Pathways in Hemoglobin Using Femtosecond Mid-IR Spectroscopy

The dynamics of NO rebinding in hemoglobin (Hb) was directly observed using femtosecond mid-IR spectroscopy after photodeligation of NO from HbNO in D₂O at 283 K. Time-resolved spectra of bound NO appeared to have a single feature peaked at 1616 cm^–1 but were much better described by two Gaussians with equal intensities but different rebinding kinetics, where the feature at 1617 cm^–1 rebinds faster than the one at 1614 cm^–1. It is possible that the two bands each correspond to one of two subunit constituents of the tetrameric Hb. Transient absorption spectra of photodeligated NO revealed three evolving bands near 1858 cm^–1 and their red-shifted replicas. The red-shifted replicas arise from photodeligated NO in the vibrationally excited <i>v</i> = 1 state. More than 10% of the NO was dissociated into the vibrationally excited <i>v</i> = 1 state when photolyzed by a 580 nm pulse. The three absorption bands for the deligated NO could be attributed to three NO sites in or near the heme pocket. The kinetics of the three transient bands for the deligated NO, as well as the recovery of the bound NO population, was most consistent with a kinetics scheme that incorporates time-dependent rebinding from one site that rapidly equilibrates with the other two sites. The time dependence results from a time-dependent rebinding barrier due to conformational relaxation of protein after deligation. By assigning each absorption band to a site in the heme pocket of Hb, a pathway for rebinding of NO to Hb was proposed

Predicting RNA Structures via a Simple van der Waals Correction to an All-Atom Force Field

We proposed a simple van der Waals backbone correction (O2′ and OP) to the AMBER ff12 force field in conjunction with the OPC water via an unequal Lorentz–Berthelot combination rule. As tested on four different tetranuceotides such as r­(GACC), r­(CCCC), r­(AAAA), and r­(CAAU), this new force field correctly captured each native fold as the largest population. For a RNA tetraloop (UUCG) tested, the stability of its native fold is substantially improved

Ultrafast and Efficient Transport of Hot Plasmonic Electrons by Graphene for Pt Free, Highly Efficient Visible-Light Responsive Photocatalyst

We report that reduced graphene-coated gold nanoparticles (r-GO-AuNPs) are excellent visible-light-responsive photocatalysts for the photoconversion of CO₂ into formic acid (HCOOH). The wavelength-dependent quantum and chemical yields of HCOOH shows a significant contribution of plasmon-induced hot electrons for CO₂ photoconversion. Furthermore, the presence and reduced state of the graphene layers are critical parameters for the efficient CO₂ photoconversion because of the electron mobility of graphene. With an excellent selectivity toward HCOOH (>90%), the quantum yield of HCOOH using r-GO-AuNPs is 1.52%, superior to that of Pt-coated AuNPs (quantum yield: 1.14%). This indicates that r-GO is a viable alternative to platinum metal. The excellent colloidal stability and photocatalytic stability of r-GO-AuNPs enables CO₂ photoconversion under more desirable reaction conditions. These results highlight the role of reduced graphene layers as highly efficient electron acceptors and transporters to facilitate the use of hot electrons for plasmonic photocatalysts. The femtosecond transient spectroscopic analysis also shows 8.7 times higher transport efficiency of hot plasmonic electrons in r-GO-AuNPs compared with AuNPs

Density Functional Theory Study on the Cross-Linking of Mussel Adhesive Proteins

The water-resistant adhesion of mussel adhesive proteins (MAPs) to a wet surface requires a cross-linking step, where the catecholic ligands of MAPs coordinate to various transition-metal ions. Fe­(III), among the range of metal ions, induces particularly strong cross-linking. The molecular details underlying this cross-linking mediated by transition-metal ions are largely unknown. Of particular interest is the metal–ligand binding energy, which is the molecular origin of the mechanical properties of cross-linked MAPs. Using density functional theory, this study examined the structures and binding energies of various trivalent metal ions (Ti–Ga) forming coordination complexes with a polymeric ligand similar to a MAP. These binding energies were 1 order of magnitude larger than the physisorption energy of a catechol molecule on a metallic surface. On the other hand, the coordination strength of Fe­(III) with the ligand was not particularly strong compared to the other metal ions studied. Therefore, the strong cross-linking in the presence of Fe­(III) is ascribed to its additional ability as an oxidant to induce covalent cross-linking of the catecholic groups of MAPs

Probing Ground-to-CT State Electronic Coupling for the System with No Apparent Charge Transfer Absorption Intensity by Ultrafast Visible-Pump/Mid-IR-Probe Spectroscopy

New π-stacked [Ru(tpy)₂]²⁺ (<b>T_T</b>)-benzoquinone (Q) donor–acceptor (D–A) systems, [Ru(6-(2-cyclohexa-2′,5′-diene-1,4-dione)-2,2′:6′,2″-terpyridine)(2,2′:6′,2″-terpyridine)][PF₆]₂ (<b>TQ_T</b>), and [Ru(6-(2-cyclohexa-2′,5′-diene-1,4-dione)-2,2′:6′,2″-terpyridine)(4′-phenyl-2,2′:6′,2″-terpyridine)][PF₆]₂ (<b>TQ_TPh</b>) have been synthesized and characterized. Orthogonal alignment of Q to the tpy ligand imposes this unit juxtaposed cofacially on the central pyridyl ring in another tpy with a typical van der Waals distance. The low-energy electronic absorptions of these complexes are mainly metal-to-ligand charge transfer (MLCT) in nature, similar to that observed in <b>T_T</b> benchmark system, and do not exhibit distinguishable metal-to-Q charge transfer (MQCT) absorption in spite of the proximal location of the electron acceptor unit (Q) to the electron donor unit (<b>T_T</b>). TD-DFT calculation supports the experimental results that the collective oscillator strength of MQCT bands remains ∼0.002. Due to the negligible intensity of MQCT bands, evaluation of <i>H</i>_DA between the ground and the lowest energy MQCT states are not available through conventional Mulliken–Hush analysis. For such systems, <i>H</i>_DA values were successfully evaluated from the relative difference (ξ) of the carbonyl stretching frequency between the neutral Q and its one-electron radical anion, which was determined by an ultrafast visible-pump/mid-IR-probe (TrIR) spectroscopic method. TrIR results showed that the partial charge localized on the Q moiety in the MQCT state was ca. −0.97<i>e</i>, and the corresponding <i>H</i>_DA was ∼1600 cm^–1. This value was in good agreement with that estimated by the Mulliken population analysis of the ground-state geometry