1
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Slipchenko LV. Detangling Solvatochromic Effects by the Effective Fragment Potential Method. J Phys Chem A 2024; 128:656-669. [PMID: 38193780 DOI: 10.1021/acs.jpca.3c06194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Understanding molecular interactions in complex systems opens avenues for the efficient design of new materials with target properties. Energy decomposition methods provide a means to obtain a detailed picture of intermolecular interactions. This work introduces a molecular modeling approach for decomposing the solvatochromic shifts of the electronic excited states into the contributions of the individual molecular fragments of the environment surrounding the chromophore. The developed approach is implemented for the QM/EFP (quantum mechanics/effective fragment potential) model that provides a rigorous first-principles-based description of the electronic states of the chromophores in complex polarizable environments. On the example of two model systems, water pentamer and hydrated uracil, we show how the decomposition of the solvatochromic shifts into the contributions of individual solvent water molecules provides a detailed picture of the intermolecular interactions in the ground and excited states of these systems. The analysis also demonstrates the nonadditivity of solute-solvent interactions and the significant contribution of solute polarization to the total values of solvatochromic shifts.
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Affiliation(s)
- Lyudmila V Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47906, United States
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2
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Photosynthetic reaction center variants made via genetic code expansion show Tyr at M210 tunes the initial electron transfer mechanism. Proc Natl Acad Sci U S A 2021; 118:2116439118. [PMID: 34907018 DOI: 10.1073/pnas.2116439118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2021] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides were engineered to vary the electronic properties of a key tyrosine (M210) close to an essential electron transfer component via its replacement with site-specific, genetically encoded noncanonical amino acid tyrosine analogs. High fidelity of noncanonical amino acid incorporation was verified with mass spectrometry and X-ray crystallography and demonstrated that RC variants exhibit no significant structural alterations relative to wild type (WT). Ultrafast transient absorption spectroscopy indicates the excited primary electron donor, P*, decays via a ∼4-ps and a ∼20-ps population to produce the charge-separated state P+HA - in all variants. Global analysis indicates that in the ∼4-ps population, P+HA - forms through a two-step process, P*→ P+BA -→ P+HA -, while in the ∼20-ps population, it forms via a one-step P* → P+HA - superexchange mechanism. The percentage of the P* population that decays via the superexchange route varies from ∼25 to ∼45% among variants, while in WT, this percentage is ∼15%. Increases in the P* population that decays via superexchange correlate with increases in the free energy of the P+BA - intermediate caused by a given M210 tyrosine analog. This was experimentally estimated through resonance Stark spectroscopy, redox titrations, and near-infrared absorption measurements. As the most energetically perturbative variant, 3-nitrotyrosine at M210 creates an ∼110-meV increase in the free energy of P+BA - along with a dramatic diminution of the 1,030-nm transient absorption band indicative of P+BA - formation. Collectively, this work indicates the tyrosine at M210 tunes the mechanism of primary electron transfer in the RC.
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3
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Studying hydrogen bonding and dynamics of the acetylate groups of the Special Pair of Rhodobacter sphaeroides WT. Sci Rep 2019; 9:10528. [PMID: 31324886 PMCID: PMC6642110 DOI: 10.1038/s41598-019-46903-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 11/17/2022] Open
Abstract
Although the cofactors in the bacterial reaction centre of Rhodobacter sphaeroides wild type (WT) are arranged almost symmetrically in two branches, the light-induced electron transfer occurs selectively in one branch. As origin of this functional symmetry break, a hydrogen bond between the acetyl group of PL in the primary donor and His-L168 has been discussed. In this study, we investigate the existence and rigidity of this hydrogen bond with solid-state photo-CIDNP MAS NMR methods offering information on the local electronic structure due to highly sensitive and selective NMR experiments. On the time scale of the experiment, the hydrogen bond between PL and His-L168 appears to be stable and not to be affected by illumination confirming a structural asymmetry within the Special Pair.
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4
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Saggu M, Fried SD, Boxer SG. Local and Global Electric Field Asymmetry in Photosynthetic Reaction Centers. J Phys Chem B 2019; 123:1527-1536. [PMID: 30668130 DOI: 10.1021/acs.jpcb.8b11458] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The origin of unidirectional electron transfer in photosynthetic reaction centers (RCs) has been widely discussed. Despite the high level of structural similarity between the two branches of pigments that participate in the initial electron transfer steps of photosynthesis, electron transfer only occurs along one branch. One possible explanation for this functional asymmetry is the differences in the electrostatic environment between the active and the inactive branches arising from the charges and dipoles of the organized protein structure. We present an analysis of electric fields in the RC of the purple bacterium Rhodobacter sphaeroides using the intrinsic carbonyl groups of the pigments as vibrational reporters whose vibrational frequency shifts can be converted into electric fields based on the vibrational Stark effect and also provide Stark effect data for plant pigments that can be used in future studies. The carbonyl stretches of the isolated pigments show pronounced Stark effects. We use these data, solvatochromism, molecular dynamics simulations, and data in the literature from IR and Raman spectra to evaluate differences in fields at symmetry-related positions, in particular at the 9-keto and 2-acetyl positions of the pigments involved in primary charge separation.
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Affiliation(s)
- Miguel Saggu
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Stephen D Fried
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
| | - Steven G Boxer
- Department of Chemistry , Stanford University , Stanford , California 94305-5080 , United States
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5
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Tiwari V, Jonas DM. Electronic energy transfer through non-adiabatic vibrational-electronic resonance. II. 1D spectra for a dimer. J Chem Phys 2018; 148:084308. [DOI: 10.1063/1.5003193] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vivek Tiwari
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
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6
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Tiwari V, Peters WK, Jonas DM. Electronic energy transfer through non-adiabatic vibrational-electronic resonance. I. Theory for a dimer. J Chem Phys 2017; 147:154308. [DOI: 10.1063/1.5005835] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vivek Tiwari
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - William K. Peters
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
| | - David M. Jonas
- Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, Colorado 80309, USA
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7
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Abstract
David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.
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8
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Lehrich SW, Hildebrandt A, Korb M, Lang H. Electronic modification of redox active ferrocenyl termini and their influence on the electrontransfer properties of 2,5-diferrocenyl- N -phenyl-1 H -pyrroles. J Organomet Chem 2015. [DOI: 10.1016/j.jorganchem.2014.12.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Saggu M, Carter B, Zhou X, Faries K, Cegelski L, Holten D, Boxer SG, Kirmaier C. Putative hydrogen bond to tyrosine M208 in photosynthetic reaction centers from Rhodobacter capsulatus significantly slows primary charge separation. J Phys Chem B 2014; 118:6721-32. [PMID: 24902471 PMCID: PMC4064694 DOI: 10.1021/jp503422c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
![]()
Slow, ∼50
ps, P* → P+HA– electron
transfer is observed in Rhodobacter
capsulatus reaction centers (RCs) bearing the native
Tyr residue at M208 and the single amino acid change of isoleucine
at M204 to glutamic acid. The P* decay kinetics are unusually homogeneous
(single exponential) at room temperature. Comparative solid-state
NMR of [4′-13C]Tyr labeled wild-type and M204E RCs
show that the chemical shift of Tyr M208 is significantly altered
in the M204E mutant and in a manner consistent with formation of a
hydrogen bond to the Tyr M208 hydroxyl group. Models based on RC crystal
structure coordinates indicate that if such a hydrogen bond is formed
between the Glu at M204 and the M208 Tyr hydroxyl group, the −OH
would be oriented in a fashion expected (based on the calculations
by Alden et al., J. Phys. Chem.1996, 100, 16761–16770) to destabilize P+BA– in free energy. Alteration
of the environment of Tyr M208 and BA by Glu M204 via this
putative hydrogen bond has a powerful influence on primary charge
separation.
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Affiliation(s)
- Miguel Saggu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
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10
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11
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Abstract
Molecular dynamics simulations of biomolecules have matured into powerful tools of structural biology. In addition to the commonly used empirical force field potentials, quantum mechanical descriptions are gaining popularity for structure optimization and dynamic simulations of peptides and proteins. In this chapter, we introduce methodological developments such as the QM/MM framework and linear-scaling QM that make efficient calculations on large biomolecules possible. We identify the most common scenarios in which quantum descriptions of peptides and proteins are employed, such as structural refinement, force field development, treatment of unusual residues, and predicting spectroscopic and exited state properties. The benefits and shortcomings of QM potentials, in comparison to classical force fields, are discussed, with special emphasis on the sampling problems of protein conformational space. Finally, recent examples of QM/MM calculations in light-sensitive membrane proteins illustrate typical applications of the reviewed methods.
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Affiliation(s)
- Thomas Steinbrecher
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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12
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Yamasaki H, Nakamura H. Electron density based interaction energy estimation of the special pair in the photosynthetic reaction center. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.03.087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Reimers JR, Hush NS, Crossley MJ. Inter-porphyrin coupling: how strong should it be for molecular electronics applications? J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424602000919] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Porphyrins and phthalocyanines have now been assembled in a multitude of different architectures, each of which may be identified with a different scenario of the coupling acting between the porphyrins. The synthetic flexibility of these compounds makes possible the design of particular molecules for specific applications in molecular electronics, both in naturally occurring and synthetic devices. Here, we form an overview of these features and focus on the coupling strength, considering what values are appropriate for different molecular electronics applications. In particular, we focus on model compounds that have been prepared as mimics of naturally occurring photosynthetic functional units, oligoporphyrins molecular wires, and stacked systems in which small changes in geometry can affect significant changes in the inter-porphyrin coupling and hence produce dramatic changes in device properties.
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Affiliation(s)
| | - Noel S. Hush
- School of Chemistry, The University of Sydney, NSW 2006, Australia
- School of Molecular and Microbial Biosciences, The University of Sydney, NSW 2006, Australia
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14
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Heckmann A, Lambert C. Organic Mixed-Valence Compounds: A Playground for Electrons and Holes. Angew Chem Int Ed Engl 2011; 51:326-92. [DOI: 10.1002/anie.201100944] [Citation(s) in RCA: 414] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Indexed: 11/05/2022]
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15
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Heckmann A, Lambert C. Organische gemischtvalente Verbindungen: ein Spielplatz für Elektronen und Löcher. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100944] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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16
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Liu YF, Yang DP, Shi DH, Sun JF. A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: Strengthening and weakening. J Comput Chem 2011; 32:3475-84. [DOI: 10.1002/jcc.21932] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Revised: 07/04/2011] [Accepted: 08/01/2011] [Indexed: 12/27/2022]
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17
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Wawrzyniak PK, Beerepoot MTP, de Groot HJM, Buda F. Acetyl group orientation modulates the electronic ground-state asymmetry of the special pair in purple bacterial reaction centers. Phys Chem Chem Phys 2011; 13:10270-9. [DOI: 10.1039/c1cp20213h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Electronic structure of the primary electron donor of Blastochloris viridis heterodimer mutants: High-field EPR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1617-26. [DOI: 10.1016/j.bbabio.2010.06.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Revised: 05/18/2010] [Accepted: 06/04/2010] [Indexed: 11/22/2022]
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19
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Daviso E, Prakash S, Alia A, Gast P, Neugebauer J, Jeschke G, Matysik J. The electronic structure of the primary electron donor of reaction centers of purple bacteria at atomic resolution as observed by photo-CIDNP 13C NMR. Proc Natl Acad Sci U S A 2009; 106:22281-6. [PMID: 20018724 PMCID: PMC2799707 DOI: 10.1073/pnas.0908608106] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2009] [Indexed: 11/18/2022] Open
Abstract
Composed of the two bacteriochlorophyll cofactors, P(L) and P(M), the special pair functions as the primary electron donor in bacterial reaction centers of purple bacteria of Rhodobacter sphaeroides. Under light absorption, an electron is transferred to a bacteriopheophytin and a radical pair is produced. The occurrence of the radical pair is linked to the production of enhanced nuclear polarization called photochemically induced dynamic nuclear polarization (photo-CIDNP). This effect can be used to study the electronic structure of the special pair at atomic resolution by detection of the strongly enhanced nuclear polarization with laser-flash photo-CIDNP magic-angle spinning NMR on the carotenoid-less mutant R26. In the electronic ground state, P(L) is strongly disturbed, carrying a slightly negative charge. In the radical cation state, the ratio of total electron spin densities between P(L) and P(M) is 2:1, although it is 2.5:1 for the pyrrole carbons, 2.2:1 for all porphyrinic carbons, and 4:1 for the pyrrole nitrogen. It is shown that the symmetry break between the electronic structures in the electronic ground state and in the radical cation state is an intrinsic property of the special pair supermolecule, which is particularly attributable to a modification of the structure of P(L). The significant difference in electron density distribution between the ground and radical cation states is explained by an electric polarization effect of the nearby histidine.
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Affiliation(s)
- Eugenio Daviso
- Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands
| | - Shipra Prakash
- Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands
| | - A. Alia
- Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands
| | - Peter Gast
- Leiden Institute of Physics, 2300 RA Leiden, The Netherlands; and
| | | | - Gunnar Jeschke
- Laboratorium für Physikalische Chemie, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Jörg Matysik
- Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands
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20
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Mechanism of Charge Separation in Purple Bacterial Reaction Centers. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_19] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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21
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Silverman LN, Kanchanawong P, Treynor TP, Boxer SG. Stark spectroscopy of mixed-valence systems. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2008; 366:33-45. [PMID: 17827128 DOI: 10.1098/rsta.2007.2137] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Many mixed-valence systems involve two or more states with different electric dipole moments whose magnitudes depend upon the charge transfer distance and the degree of delocalization; these systems can be interconverted by excitation of an intervalence charge transfer transition. Stark spectroscopy involves the interaction between the change in dipole moment of a transition and an electric field, so the Stark spectra of mixed-valence systems are expected to provide quantitative information on the degree of delocalization. In limiting cases, a classical Stark analysis can be used, but in intermediate cases the analysis is much more complex because the field affects not only the band position but also the intrinsic bandshape. Such non-classical Stark effects lead to widely different bandshapes. Several examples of both classes are discussed. Because electric fields are applied to immobilized samples, complications arise from inhomogeneous broadening, along with other effects that limit our ability to extract unique parameters in some cases. In the case of the radical cation of the special pair in photosynthetic reaction centres, where the mixed-valence system is in a very complex but structurally well-defined environment, a detailed analysis can be performed.
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Affiliation(s)
- Lisa N Silverman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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22
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Yin S, Dahlbom MG, Canfield PJ, Hush NS, Kobayashi R, Reimers JR. Assignment of the Qy absorption spectrum of photosystem-I from Thermosynechococcus elongatus based on CAM-B3LYP calculations at the PW91-optimized protein structure. J Phys Chem B 2007; 111:9923-30. [PMID: 17672486 DOI: 10.1021/jp070030p] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Qy absorption spectrum of Photosystem-I from Thermosynecochoccus elongatus (formerly Synecochoccus elongatus) is calculated using the CAM-B3LYP density functional and INDO schemes based on a quantum-mechanically refined structure for the entire photosystem obtained using the PW91 density functional. These methods present a priori predictions of the absorption and linear dichroism spectra and include protein electrostatic effects, short range inductive effects, long-range and short-range exciton couplings, and superexchange effects involving aromatic residues and carotenes. CAM-B3LYP is used as it is the only known density functional that correctly describes the Q bands of chlorophylls, all other methods contaminating them with erroneous charge-transfer excitations. A critical feature is found to be the use of fully optimized heavy-atom coordinates, with those obtained from just X-ray crystallography providing a poor description of the electronic properties of the chromophores. The result is a realistic first-principles prediction of the observed absorption band that identifies the nature of the red-shifted chlorophylls as well as the energies of the reaction-center chlorophylls and the exciton couplings acting between them. The "special pair" appears more like a dimer of dimers than a self-contained functional unit, with the exciton couplings between its members and the accessory chlorophylls exceeding the internal coupling.
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Affiliation(s)
- Shiwei Yin
- School of Chemistry, The University of Sydney, NSW 2006, Australia
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23
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Kanchanawong P, Dahlbom MG, Treynor TP, Reimers JR, Hush NS, Boxer SG. Charge Delocalization in the Special-Pair Radical Cation of Mutant Reaction Centers of Rhodobacter sphaeroides from Stark Spectra and Nonadiabatic Spectral Simulations. J Phys Chem B 2006; 110:18688-702. [PMID: 16970500 DOI: 10.1021/jp0623894] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stark and absorption spectra for the hole-transfer band of the bacteriochlorophyll special pair in the wild-type and L131LH, M160LH, and L131LH/M160LH mutants of the bacterial reaction center of Rhodobacter sphaeroides are presented, along with extensive analyses based on nonadiabatic spectral simulations. Dramatic changes in the Stark spectra are induced by the mutations, changes that are readily interpreted in terms of the redox-energy asymmetry and degree of charge localization in the special-pair radical cation. The effect of mutagenesis on key properties such as the electronic coupling within the special pair and the reorganization energy associated with intervalence hole transfer are determined for the first time. Results for the L131LH and M160LH/L131LH mutants indicate that these species can be considered as influencing the special pair primarily through modulation of the redox asymmetry, as is usually conceptualized, but M160LH is shown to develop a wide range of effects that can be interpreted in terms of significant mutation-induced structural changes in and around the special pair. The nonadiabatic spectra simulations are performed using both a simple two-state 1-mode and an extensive four-state 70-mode model, which includes the descriptions of additional electronic states and explicitly treats the major vibrational modes involved. Excellent agreement between the two simulation approaches is obtained. The simple model is shown to reproduce key features of the Stark effect of the main intervalence transition, while the extensive model quantitatively reproduces most features of the observed spectra for both the electronic and the phase-phonon regions, thus giving a more comprehensive description of the effect of the mutations on the properties of the special-pair radical cation. These results for a series of closely related mixed-valence complexes show that the Stark spectra provide a sensitive indicator for the properties of the mixed-valence complexes and should serve as an instructive example on the application of nonadiabatic simulations to the study of mixed-valence complexes in general as well as other chemical systems akin to the photosynthetic special pair.
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Affiliation(s)
- Pakorn Kanchanawong
- Biophysics Program and Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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24
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A theoretical study of electronic excited states of photosynthetic reaction center in Rhodopseudomonas viridis. ACTA ACUST UNITED AC 2006. [DOI: 10.1007/s11426-004-0065-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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25
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A priori evaluation of the solvent contribution to the reorganization energy accompanying intramolecular electron transfer: Predicting the nature of the Creutz–Taube ion. Chem Phys 2005. [DOI: 10.1016/j.chemphys.2005.06.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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26
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Villar R, Gil MJ, García JI, Martínez-Merino V. Are AM1 ligand-protein binding enthalpies good enough for use in the rational design of new drugs? J Comput Chem 2005; 26:1347-58. [PMID: 16021597 DOI: 10.1002/jcc.20276] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have examined the performance of semiempirical quantum mechanical methods in solving the problem of accurately predicting protein-ligand binding energies and geometries. Firstly, AM1 and PM3 geometries and binding enthalpies between small molecules that simulate typical ligand-protein interactions were compared with high level quantum mechanical techniques that include electronic correlation (e.g., MP2 or B3LYP). Species studied include alkanes, aromatic systems, molecules including groups with hypervalent sulfur or with donor or acceptor hydrogen bonding capability, as well as ammonium or carboxylate ions. B3LYP/6-311+G(2d,p) binding energies correlated very well with the BSSE corrected MP2/6-31G(d) values. AM1 binding enthalpies also showed good correlation with MP2 values, and their systematic deviation is acceptable when enthalpies are used for the comparison of interaction energies between ligands and a target. PM3 otherwise gave erratic energy differences in comparison to the B3LYP or MP2 approaches. As one would expect, the geometries of the binding complexes showed the known limitations of the semiempirical and DFT methods. AM1 calculations were subsequently applied to a test set consisting of "real" protein active site-ligand complexes. Preliminary results indicate that AM1 could be a valuable tool for the design of new drugs using proteins as templates. This approach also has a reasonable computational cost. The ligand-protein X-ray structures were reasonably reproduced by AM1 calculations and the corresponding AM1 binding enthalpies are in agreement with the results from the "small molecules" test set.
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Affiliation(s)
- R Villar
- Dep. Química Aplicada, Universidad Pública de Navarra, Campus Arrosadía, E-31006 Pamplona, Spain
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27
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Reimers JR, Hush NS. A Unified Description of the Electrochemical, Charge Distribution, and Spectroscopic Properties of the Special-Pair Radical Cation in Bacterial Photosynthesis. J Am Chem Soc 2004; 126:4132-44. [PMID: 15053603 DOI: 10.1021/ja036883m] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We apply our four-state 70-vibration vibronic-coupling model for the properties of the photosynthetic special-pair radical cation to: (1) interpret the observed correlations between the midpoint potential and the distribution of spin density between the two bacteriochlorophylls for 30 mutants of Rhodobacter sphaeroides, (2) interpret the observed average intervalence hole-transfer absorption energies as a function of spin density for six mutants, and (3) simulate the recently obtained intervalence electroabsorption Stark spectrum of the wild-type reaction center. While three new parameters describing the location of the sites of mutation with respect to the special pair are required to describe the midpoint-potential data, a priori predictions are made for the transition energies and the Stark spectrum. In general, excellent predictions are made of the observed quantities, with deviations being typically of the order of twice the experimental uncertainties. A unified description of many chemical and spectroscopic properties of the bacterial reaction center is thus provided. Central to the analysis is the assumption that the perturbations made to the reaction center, either via mutations of protein residues or by application of an external electric field, act only to independently modify the oxidation potentials of the two halves of the special pair and hence the redox asymmetry E0. While this appears to be a good approximation, clear evidence is presented that effects of mutation can be more extensive than what is allowed for. A thorough set of analytical equations describing the observed properties is obtained using the Born-Oppenheimer adiabatic approximation. These equations are generally appropriate for intervalence charge-transfer problems and include, for the first time, full treatment of both symmetric and antisymmetric vibrational motions. The limits of validity of the adiabatic approach to the full nonadiabatic problem are obtained.
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Jordanides XJ, Scholes GD, Shapley WA, Reimers JR, Fleming GR. Electronic Couplings and Energy Transfer Dynamics in the Oxidized Primary Electron Donor of the Bacterial Reaction Center. J Phys Chem B 2004. [DOI: 10.1021/jp036516x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xanthipe J. Jordanides
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Gregory D. Scholes
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Warwick A. Shapley
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Jeffrey R. Reimers
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, The University of Sydney, NSW 2006, Australia
| | - Graham R. Fleming
- Department of Chemistry, University of California, Berkeley, and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and School of Chemistry, The University of Sydney, NSW 2006, Australia
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Kriegl JM, Nienhaus GU. Structural, dynamic, and energetic aspects of long-range electron transfer in photosynthetic reaction centers. Proc Natl Acad Sci U S A 2004; 101:123-8. [PMID: 14691247 PMCID: PMC314149 DOI: 10.1073/pnas.2434740100] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2003] [Indexed: 11/18/2022] Open
Abstract
Intramolecular electron transfer within proteins plays an essential role in biological energy transduction. Electron donor and acceptor cofactors are bound in the protein matrix at specific locations, and protein-cofactor interactions as well as protein conformational changes can markedly influence the electron transfer rates. To assess these effects, we have investigated charge recombination from the primary quinone acceptor to the special pair bacteriochlorophyll dimer in wild-type reaction centers of Rhodobacter sphaeroides and four mutants with widely modified free energy gaps. After light-induced charge separation, the recombination kinetics were measured in the light- and dark-adapted forms of the protein from 10 to 300 K. The data were analyzed by using the spin-boson model, which allowed us to self-consistently determine the electronic coupling energy, the distribution of energy gaps, the spectral density of phonons, and the reorganization energy. The analysis revealed slow changes of the energy gap after charge separation. Interesting correlations of the control parameters governing electron transfer were found and related to structural and dynamic properties of the protein.
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Affiliation(s)
- Jan M Kriegl
- Department of Biophysics, University of Ulm, D-89069 Ulm, Germany
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Braun P, Végh AP, von Jan M, Strohmann B, Hunter CN, Robert B, Scheer H. Identification of intramembrane hydrogen bonding between 131 keto group of bacteriochlorophyll and serine residue α27 in the LH2 light-harvesting complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2003; 1607:19-26. [PMID: 14556909 DOI: 10.1016/j.bbabio.2003.08.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intramembrane hydrogen bonding and its effect on the structural integrity of purple bacterial light-harvesting complex 2, LH2, have been assessed in the native membrane environment. A novel hydrogen bond has been identified by Raman resonance spectroscopy between a serine residue of the membrane-spanning region of LH2 alpha-subunit, and the C-13(1) keto carbonyl of bacteriochlorophyll (BChl) B850 bound to the beta-subunit. Replacement of the serine by alanine disrupts this strong hydrogen bond, but this neither alters the strongly red-shifted absorption nor the structural arrangement of the BChls, as judged from circular dichroism. It also decreases only slightly the thermal stability of the mutated LH2 in the native membrane environment. The possibility is discussed that weak H-bonding between the C-13(1) keto carbonyl and a methyl hydrogen of the alanine replacing serine(-4) or the imidazole group of the nearby histidine maintains structural integrity in this very stable bacterial light-harvesting complex. A more widespread occurrence of H-bonding to C-13(1) not only in BChl, but also in chlorophyll proteins, is indicated by a theoretical analysis of chlorophyll/polypeptide contacts at <3.5 A in the high-resolution structure of Photosystem I. Nearly half of the 96 chlorophylls have aa residues suitable as hydrogen bond donors to their keto groups.
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Affiliation(s)
- P Braun
- Department Biologie 1, Section Botanik, Universität München, Menzinger Str. 67, D-80638 Munich, Germany.
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Reimers JR, Hush NS. Modeling the bacterial photosynthetic reaction center. VII. Full simulation of the intervalence hole–transfer absorption spectrum of the special-pair radical cation. J Chem Phys 2003. [DOI: 10.1063/1.1589742] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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32
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Reimers JR, Shapley WA, Rendell AP, Hush NS. Modelling the bacterial photosynthetic reaction center. VI. Use of density-functional theory to determine the nature of the vibronic coupling between the four lowest-energy electronic states of the special-pair radical cation. J Chem Phys 2003. [DOI: 10.1063/1.1569910] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Brewer SH, Franzen S. A quantitative theory and computational approach for the vibrational Stark effect. J Chem Phys 2003. [DOI: 10.1063/1.1578471] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Abstract
The combination of quantum mechanics and molecular mechanics (QM/MM) methods is one of the most promising approaches to study the structure, function and properties of proteins. The number of QM/MM applications on metalloproteins is steadily increasing, especially studies with density functional methods on redox-active metal centres. Recent developments include new parameterised methods to treat covalent bonds between the quantum and classical systems, methods to obtain free energy from QM/MM results, and the combination of quantum chemistry and protein crystallography.
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Affiliation(s)
- Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, PO Box 124 S-221 00, Lund, Sweden.
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Ceccarelli M, Marchi M. Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center: Structure and Interactions. J Phys Chem B 2003. [DOI: 10.1021/jp0270001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matteo Ceccarelli
- CECAM, Centre Européen de Calcul Atomique et Moleculaire, Ecole Normale Superieure de Lyon, 46 Allée d'Italie, 69364 Lyon, France
| | - Massimo Marchi
- Commissariat à l'Energie Atomique, DSV-DBJC-SBFM, Centre d'Études, Saclay, 91191 Gif-sur-Yvette Cedex, France
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