19 research outputs found
Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches
We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore鈥損rotein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore
The Dynamic Origin of Color Tuning in Proteins Revealed by a Carotenoid Pigment
Understanding
the microscopic origin of the color tuning in pigment鈥損rotein
complexes is a challenging yet fundamental issue in photoactive biological
systems. Here, we propose a possible interpretation by using a state-of-the-art
multiscale strategy based on the integration of quantum chemistry
and polarizable atomistic embeddings into a dynamic description. By
means of such a strategy we are able to resolve the long-standing
dispute over the coloration mechanism in the crustacyanin protein.
It is shown that the combination of the dynamical flexibility of the
carotenoid pigments (astaxanthin) with the responsive protein environment
is essential to obtain quantitative predictions of the spectral tuning.
The strong linear correlation between the excitation energies and
the bond length alternation in the long-chain carotenoids modulated
by the dynamical protein environment is a novel finding explaining
the high color tunability in crustacyanin
Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches
We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore鈥損rotein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore
Bathochromic Shift in Green Fluorescent Protein: A Puzzle for QM/MM Approaches
We present an extensive investigation of the vertical excitations of the anionic and neutral forms of wild-type green fluorescent protein using time-dependent density functional theory (TDDFT), multiconfigurational perturbation theory (CASPT2), and quantum Monte Carlo (QMC) methods within a quantum mechanics/molecular mechanics (QM/MM) scheme. The protein models are constructed via room-temperature QM/MM molecular dynamics simulations based on DFT and are representative of an average configuration of the chromophore鈥損rotein complex. We thoroughly verify the reliability of our structures through simulations with an extended QM region, different nonpolarizable force fields, as well as partial reoptimization with the CASPT2 approach. When computing the excitations, we find that wave function as well as density functional theory methods with long-range corrected functionals agree in the gas phase with the extrapolation of solution experiments but fail in reproducing the bathochromic shift in the protein, which should be particularly significant in the neutral case. In particular, while all methods correctly predict a shift in the absorption between the anionic and neutral forms of the protein, the location of the theoretical absorption maxima is significantly blue-shifted and too close to the gas-phase values. These results point to either an intrinsic limitation of nonpolarizable force-field embedding in the computation of the excitations or to the need to explore alternative protonation states of amino acids in the close vicinity of the chomophore
In-Silico Design of a Donor鈥揂ntenna鈥揂cceptor Supramolecular Complex for Photoinduced Charge Separation
We
investigate via density functional theory a series of donor鈥揳ntenna鈥揳cceptor
molecular rectifiers designed as modules for artificial photosynthesis
devices. We consider triad modules containing phenothiazine (PTZ)
as the electron donor and different derivatives of naphthalene diimide
(NDI) as the antenna and secondary electron acceptor. The choice of
the molecular components in the triad is guided by the redox and optical
properties of each subunit. Using time-dependent DFT in combination
with the long-range corrected xc-functional CAM-B3LYP we investigate
how photoinduced charge transfer states are affected by systematic
modifications of the triad molecular structure. In particular, we
show how by controlling the length of the molecular bridges connecting
the different charge separator subunits it is possible to control
the driving force for the relaxation of the excitonic state into the
full charge-separated state. On the basis of these findings we propose
a supramolecular triad consisting of inexpensive and readily available
molecular components that can find its implementation in artificial
devices for solar energy transduction
Elucidation of the Electrocatalytic Nitrite Reduction Mechanism by Bio-Inspired Copper Complexes
Mononuclear copper
complexes relevant to the active site of copper
nitrite reductases (CuNiRs) are known to be catalytically active for
the reduction of nitrite. Yet, their catalytic mechanism has thus
far not been resolved. Here, we provide a complete description of
the electrocatalytic nitrite reduction mechanism of a bio-inspired
CuNiR catalyst Cu(tmpa) (tmpa = tris(2-pyridylmethyl)amine) in aqueous
solution. Through a combination of electrochemical studies, reaction
kinetics, and density functional theory (DFT) computations, we show
that the protonation steps take place in a stepwise manner and are
decoupled from electron transfer. The rate-determining step is a general
acid-catalyzed protonation of a copper-ligated nitrous acid (HNO2) species. In view of the growing urge to convert nitrogen-containing
compounds, this work provides principal reaction parameters for efficient
electrochemical nitrite reduction. This contributes to the investigation
and development of nitrite reduction catalysts, which is crucial to
restore the biogeochemical nitrogen cycle
Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum
Chlorosome antennae
form an interesting class of materials for
studying the role of structural motifs and dynamics in nonadiabatic
energy transfer. They perform robust and highly quantum-efficient
transfer of excitonic energy while allowing for compositional variation
and completely lacking the usual regulatory proteins. Here, we first
cast the geometrical analysis for ideal tubular scaffolding models
into a formal framework, to relate effective helical properties of
the assembly structures to established characterization data for various
types of chlorosomes. This analysis shows that helicity is uniquely
defined for chlorosomes composed of bacteriochlorophyll (BChl) <i>d</i> and that three chiral angles are consistent with the nuclear
magnetic resonance (NMR) and electron microscope data for BChl <i>c</i>, including two novel ones that are at variance with current
interpretations of optical data based on perfect cylindrical symmetry.
We use this information as a starting point for investigating dynamic
and static heterogeneity at the molecular level by unconstrained molecular
dynamics. We first identify a rotational degree of freedom, along
the Mg鈥揙H coordination bond, that alternates along the syn鈥揳nti
stacks and underlies the (flexible) curvature on a larger scale. Because
rotation directly relates to the formation or breaking of interstack
hydrogen bonds of the O鈥揌路路路O顥籆 structural
motif along the syn鈥揳nti stacks, we analyzed the relative fractions
of hydrogen-bonded and the nonbonded regions, forming stripe domains
in otherwise spectroscopically homogeneous curved slabs. The ratios
7:3 for BChl <i>c</i> and 9:1 for BChl <i>d</i> for the two distinct structural components agree well with the signal
intensities determined by NMR. In addition, rotation with curvature-independent
formation of stripe domains offers a viable explanation for the localization
and dispersion of exciton states over two fractions, as observed in
single chlorosome fluorescence decay studies
Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum
Chlorosome antennae
form an interesting class of materials for
studying the role of structural motifs and dynamics in nonadiabatic
energy transfer. They perform robust and highly quantum-efficient
transfer of excitonic energy while allowing for compositional variation
and completely lacking the usual regulatory proteins. Here, we first
cast the geometrical analysis for ideal tubular scaffolding models
into a formal framework, to relate effective helical properties of
the assembly structures to established characterization data for various
types of chlorosomes. This analysis shows that helicity is uniquely
defined for chlorosomes composed of bacteriochlorophyll (BChl) <i>d</i> and that three chiral angles are consistent with the nuclear
magnetic resonance (NMR) and electron microscope data for BChl <i>c</i>, including two novel ones that are at variance with current
interpretations of optical data based on perfect cylindrical symmetry.
We use this information as a starting point for investigating dynamic
and static heterogeneity at the molecular level by unconstrained molecular
dynamics. We first identify a rotational degree of freedom, along
the Mg鈥揙H coordination bond, that alternates along the syn鈥揳nti
stacks and underlies the (flexible) curvature on a larger scale. Because
rotation directly relates to the formation or breaking of interstack
hydrogen bonds of the O鈥揌路路路O顥籆 structural
motif along the syn鈥揳nti stacks, we analyzed the relative fractions
of hydrogen-bonded and the nonbonded regions, forming stripe domains
in otherwise spectroscopically homogeneous curved slabs. The ratios
7:3 for BChl <i>c</i> and 9:1 for BChl <i>d</i> for the two distinct structural components agree well with the signal
intensities determined by NMR. In addition, rotation with curvature-independent
formation of stripe domains offers a viable explanation for the localization
and dispersion of exciton states over two fractions, as observed in
single chlorosome fluorescence decay studies
Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum
Chlorosome antennae
form an interesting class of materials for
studying the role of structural motifs and dynamics in nonadiabatic
energy transfer. They perform robust and highly quantum-efficient
transfer of excitonic energy while allowing for compositional variation
and completely lacking the usual regulatory proteins. Here, we first
cast the geometrical analysis for ideal tubular scaffolding models
into a formal framework, to relate effective helical properties of
the assembly structures to established characterization data for various
types of chlorosomes. This analysis shows that helicity is uniquely
defined for chlorosomes composed of bacteriochlorophyll (BChl) <i>d</i> and that three chiral angles are consistent with the nuclear
magnetic resonance (NMR) and electron microscope data for BChl <i>c</i>, including two novel ones that are at variance with current
interpretations of optical data based on perfect cylindrical symmetry.
We use this information as a starting point for investigating dynamic
and static heterogeneity at the molecular level by unconstrained molecular
dynamics. We first identify a rotational degree of freedom, along
the Mg鈥揙H coordination bond, that alternates along the syn鈥揳nti
stacks and underlies the (flexible) curvature on a larger scale. Because
rotation directly relates to the formation or breaking of interstack
hydrogen bonds of the O鈥揌路路路O顥籆 structural
motif along the syn鈥揳nti stacks, we analyzed the relative fractions
of hydrogen-bonded and the nonbonded regions, forming stripe domains
in otherwise spectroscopically homogeneous curved slabs. The ratios
7:3 for BChl <i>c</i> and 9:1 for BChl <i>d</i> for the two distinct structural components agree well with the signal
intensities determined by NMR. In addition, rotation with curvature-independent
formation of stripe domains offers a viable explanation for the localization
and dispersion of exciton states over two fractions, as observed in
single chlorosome fluorescence decay studies
Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of Chlorobaculum tepidum
Chlorosome antennae
form an interesting class of materials for
studying the role of structural motifs and dynamics in nonadiabatic
energy transfer. They perform robust and highly quantum-efficient
transfer of excitonic energy while allowing for compositional variation
and completely lacking the usual regulatory proteins. Here, we first
cast the geometrical analysis for ideal tubular scaffolding models
into a formal framework, to relate effective helical properties of
the assembly structures to established characterization data for various
types of chlorosomes. This analysis shows that helicity is uniquely
defined for chlorosomes composed of bacteriochlorophyll (BChl) <i>d</i> and that three chiral angles are consistent with the nuclear
magnetic resonance (NMR) and electron microscope data for BChl <i>c</i>, including two novel ones that are at variance with current
interpretations of optical data based on perfect cylindrical symmetry.
We use this information as a starting point for investigating dynamic
and static heterogeneity at the molecular level by unconstrained molecular
dynamics. We first identify a rotational degree of freedom, along
the Mg鈥揙H coordination bond, that alternates along the syn鈥揳nti
stacks and underlies the (flexible) curvature on a larger scale. Because
rotation directly relates to the formation or breaking of interstack
hydrogen bonds of the O鈥揌路路路O顥籆 structural
motif along the syn鈥揳nti stacks, we analyzed the relative fractions
of hydrogen-bonded and the nonbonded regions, forming stripe domains
in otherwise spectroscopically homogeneous curved slabs. The ratios
7:3 for BChl <i>c</i> and 9:1 for BChl <i>d</i> for the two distinct structural components agree well with the signal
intensities determined by NMR. In addition, rotation with curvature-independent
formation of stripe domains offers a viable explanation for the localization
and dispersion of exciton states over two fractions, as observed in
single chlorosome fluorescence decay studies