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1.
Nat Mater ; 22(11): 1361-1369, 2023 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-37709929

RESUMEN

Evidence shows that charge carriers in organic semiconductors self-localize because of dynamic disorder. Nevertheless, some organic semiconductors feature reduced mobility at increasing temperature, a hallmark for delocalized band transport. Here we present the temperature-dependent mobility in two record-mobility organic semiconductors: dinaphtho[2,3-b:2',3'-f]thieno[3,2-b]-thiophene (DNTT) and its alkylated derivative, C8-DNTT-C8. By combining terahertz photoconductivity measurements with atomistic non-adiabatic molecular dynamics simulations, we show that while both crystals display a power-law decrease of the mobility (µ) with temperature (T) following µ ∝ T -n, the exponent n differs substantially. Modelling reveals that the differences between the two chemically similar semiconductors can be traced to the delocalization of the different states that are thermally accessible by charge carriers, which in turn depends on their specific electronic band structure. The emerging picture is that of holes surfing on a dynamic manifold of vibrationally dressed extended states with a temperature-dependent mobility that provides a sensitive fingerprint for the underlying density of states.

2.
Proc Natl Acad Sci U S A ; 118(39)2021 09 28.
Artículo en Inglés | MEDLINE | ID: mdl-34556577

RESUMEN

Proteins achieve efficient energy storage and conversion through electron transfer along a series of redox cofactors. Multiheme cytochromes are notable examples. These proteins transfer electrons over distance scales of several nanometers to >10 µm and in so doing they couple cellular metabolism with extracellular redox partners including electrodes. Here, we report pump-probe spectroscopy that provides a direct measure of the intrinsic rates of heme-heme electron transfer in this fascinating class of proteins. Our study took advantage of a spectrally unique His/Met-ligated heme introduced at a defined site within the decaheme extracellular MtrC protein of Shewanella oneidensis We observed rates of heme-to-heme electron transfer on the order of 109 s-1 (3.7 to 4.3 Å edge-to-edge distance), in good agreement with predictions based on density functional and molecular dynamics calculations. These rates are among the highest reported for ground-state electron transfer in biology. Yet, some fall 2 to 3 orders of magnitude below the Moser-Dutton ruler because electron transfer at these short distances is through space and therefore associated with a higher tunneling barrier than the through-protein tunneling scenario that is usual at longer distances. Moreover, we show that the His/Met-ligated heme creates an electron sink that stabilizes the charge separated state on the 100-µs time scale. This feature could be exploited in future designs of multiheme cytochromes as components of versatile photosynthetic biohybrid assemblies.


Asunto(s)
Grupo Citocromo c/metabolismo , Citocromos/metabolismo , Electrones , Hemo/metabolismo , Histidina/metabolismo , Metionina/metabolismo , Shewanella/metabolismo , Grupo Citocromo c/química , Citocromos/química , Transporte de Electrón , Hemo/química , Histidina/química , Metionina/química , Simulación de Dinámica Molecular , Nanocables , Oxidación-Reducción
3.
Acc Chem Res ; 55(6): 819-830, 2022 03 15.
Artículo en Inglés | MEDLINE | ID: mdl-35196456

RESUMEN

Organic semiconductors (OSs) are an exciting class of materials that have enabled disruptive technologies in this century including large-area electronics, flexible displays, and inexpensive solar cells. All of these technologies rely on the motion of electrical charges within the material and the diffusivity of these charges critically determines their performance. In this respect, it is remarkable that the nature of the charge transport in these materials has puzzled the community for so many years, even for apparently simple systems such as molecular single crystals: some experiments would better fit an interpretation in terms of a localized particle picture, akin to molecular or biological electron transfer, while others are in better agreement with a wave-like interpretation, more akin to band transport in metals.Exciting recent progress in the theory and simulation of charge carrier transport in OSs has now led to a unified understanding of these disparate findings, and this Account will review one of these tools developed in our laboratory in some detail: direct charge carrier propagation by quantum-classical nonadiabatic molecular dynamics. One finds that even in defect-free crystals the charge carrier can either localize on a single molecule or substantially delocalize over a large number of molecules depending on the relative strength of electronic couplings between the molecules, reorganization, or charge trapping energy of the molecule and thermal fluctuations of electronic couplings and site energies, also known as electron-phonon couplings.Our simulations predict that in molecular OSs exhibiting some of the highest measured charge mobilities to date, the charge carrier forms "flickering" polarons, objects that are delocalized over 10-20 molecules on average and that constantly change their shape and extension under the influence of thermal disorder. The flickering polarons propagate through the OS by short (≈10 fs long) bursts of the wave function that lead to an expansion of the polaron to about twice its size, resulting in spatial displacement, carrier diffusion, charge mobility, and electrical conductivity. Arguably best termed "transient delocalization", this mechanistic scenario is very similar to the one assumed in transient localization theory and supports its assertions. We also review recent applications of our methodology to charge transport in disordered and nanocrystalline samples, which allows us to understand the influence of defects and grain boundaries on the charge propagation.Unfortunately, the energetically favorable packing structures of typical OSs, whether molecular or polymeric, places fundamental constraints on charge mobilities/electronic conductivity compared to inorganic semiconductors, which limits their range of applications. In this Account, we review the design rules that could pave the way for new very high-mobility OS materials and we argue that 2D covalent organic frameworks are one of the most promising candidates to satisfy them.We conclude that our nonadiabatic dynamics method is a powerful approach for predicting charge carrier transport in crystalline and disordered materials. We close with a brief outlook on extensions of the method to exciton transport, dissociation, and recombination. This will bring us a step closer to an understanding of the birth, survival, and annihiliation of charges at interfaces of optoelectronic devices.


Asunto(s)
Simulación de Dinámica Molecular , Semiconductores , Difusión , Electrónica , Electrones
4.
J Chem Phys ; 159(23)2023 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-38117021

RESUMEN

Coupled trajectory mixed quantum-classical (CTMQC) dynamics is a rigorous approach to trajectory-based non-adiabatic dynamics, which has recently seen an improvement to energy conservation via the introduction of the CTMQC-E algorithm. Despite this, the method's two key quantities distinguishing it from Ehrenfest dynamics, the modified Born-Oppenheimer momentum and the quantum momentum, require regularization procedures in certain circumstances. Such procedures in the latter can cause instabilities, leading to undesirable effects, such as energy drift and spurious population transfer, which is expected to become increasingly prevalent when the system gets larger as such events would happen more frequently. We propose a further modification to CTMQC-E, which includes a redefinition of the quantum momentum, CTMQC-EDI (double intercept), such that it has no formal divergences. We then show for Tully models I-III and the double arch model that the algorithm has greatly improved total energy conservation and negligible spurious population transfer at all times, in particular in regions of strong non-adiabatic coupling. CTMQC-EDI, therefore, shows promise as a numerically robust non-adiabatic dynamics technique that accounts for decoherence from first principles and that is scalable to large molecular systems and materials.

5.
J Am Chem Soc ; 144(10): 4623-4632, 2022 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-35239359

RESUMEN

Transition metal oxide materials have attracted much attention for photoelectrochemical water splitting, but problems remain, e.g. the sluggish transport of excess charge carriers in these materials, which is not well understood. Here we use periodic, spin-constrained and gap-optimized hybrid density functional theory to uncover the nature and transport mechanism of holes and excess electrons in a widely used water splitting material, bulk-hematite (α-Fe2O3). We find that upon ionization the hole relaxes from a delocalized band state to a polaron localized on a single iron atom with localization induced by tetragonal distortion of the six surrounding iron-oxygen bonds. This distortion is responsible for sluggish hopping transport in the Fe-bilayer, characterized by an activation energy of 70 meV and a hole mobility of 0.031 cm2/(V s). By contrast, the excess electron induces a smaller distortion of the iron-oxygen bonds resulting in delocalization over two neighboring Fe units. We find that 2-site delocalization is advantageous for charge transport due to the larger spatial displacements per transfer step. As a result, the electron mobility is predicted to be a factor of 3 higher than the hole mobility, 0.098 cm2/(V s), in qualitative agreement with experimental observations. This work provides new fundamental insight into charge carrier transport in hematite with implications for its photocatalytic activity.

6.
Phys Chem Chem Phys ; 24(25): 15365-15375, 2022 Jun 29.
Artículo en Inglés | MEDLINE | ID: mdl-35703465

RESUMEN

Metal oxide/water interfaces play an important role in biology, catalysis, energy storage and photocatalytic water splitting. The atomistic structure at these interfaces is often difficult to characterize by experimental techniques, whilst results from ab initio molecular dynamics simulations tend to be uncertain due to the limited length and time scales accessible. In this work, we train a committee neural network potential to simulate the hematite/water interface at the hybrid DFT level of theory to reach the nanosecond timescale and systems containing more than 3000 atoms. The NNP enables us to converge dynamical properties, not possible with brute-force ab initio molecular dynamics. Our simulations uncover a rich solvation dynamics at the hematite/water interface spanning three different time scales: picosecond H-bond dynamics between surface hydroxyls and the first water layer, in-plane/out-of-plane tilt motion of surface hydroxyls on the 10 ps time scale, and diffusion of water molecules from the oxide surface characterized by a mean residence lifetime of about 60 ps. Calculation of vibrational spectra confirm that H-bonds between surface hydroxyls and first layer water molecules are stronger than H-bonds in bulk water. Our study showcases how state of the art machine learning approaches can routinely be utilized to explore the structural dynamics at transition metal oxide interfaces with complex electronic structure. It foreshadows that c-NNPs are a promising tool to tackle the sampling problem in ab initio electrochemistry with explicit solvent molecules.


Asunto(s)
Simulación de Dinámica Molecular , Agua , Difusión , Compuestos Férricos , Redes Neurales de la Computación , Agua/química
7.
Proc Natl Acad Sci U S A ; 116(9): 3425-3430, 2019 02 26.
Artículo en Inglés | MEDLINE | ID: mdl-30755526

RESUMEN

The bacterium Shewanella oneidensis has evolved a sophisticated electron transfer (ET) machinery to export electrons from the cytosol to extracellular space during extracellular respiration. At the heart of this process are decaheme proteins of the Mtr pathway, MtrC and MtrF, located at the external face of the outer bacterial membrane. Crystal structures have revealed that these proteins bind 10 c-type hemes arranged in the peculiar shape of a staggered cross that trifurcates the electron flow, presumably to reduce extracellular substrates while directing electrons to neighboring multiheme cytochromes at either side along the membrane. Especially intriguing is the design of the heme junctions trifurcating the electron flow: they are made of coplanar and T-shaped heme pair motifs with relatively large and seemingly unfavorable tunneling distances. Here, we use electronic structure calculations and molecular simulations to show that the side chains of the heme rings, in particular the cysteine linkages inserting in the space between coplanar and T-shaped heme pairs, strongly enhance electronic coupling in these two motifs. This results in an [Formula: see text]-fold speedup of ET steps at heme junctions that would otherwise be rate limiting. The predicted maximum electron flux through the solvated proteins is remarkably similar for all possible flow directions, suggesting that MtrC and MtrF shuttle electrons with similar efficiency and reversibly in directions parallel and orthogonal to the outer membrane. No major differences in the ET properties of MtrC and MtrF are found, implying that the different expression levels of the two proteins during extracellular respiration are not related to redox function.


Asunto(s)
Grupo Citocromo c/genética , Transporte de Electrón/genética , Modelos Moleculares , Shewanella/genética , Secuencia de Aminoácidos/genética , Proteínas de la Membrana Bacteriana Externa/química , Proteínas de la Membrana Bacteriana Externa/genética , Grupo Citocromo c/química , Citocromos/química , Citocromos/genética , Electrones , Hemo/química , Hemo/genética , Oxidación-Reducción , Shewanella/química , Shewanella/patogenicidad
8.
Biophys J ; 120(17): 3807-3819, 2021 09 07.
Artículo en Inglés | MEDLINE | ID: mdl-34265263

RESUMEN

Hemoglobin-mediated transport of dioxygen (O2) critically depends on the stability of the reduced (Fe2+) form of the heme cofactors. Some protein mutations stabilize the oxidized (Fe3+) state (methemoglobin, Hb M), causing methemoglobinemia, and can be lethal above 30%. The majority of the analyses of factors influencing Hb oxidation are retrospective and give insights only for inner-sphere mutations of heme (His58, His87). Herein, we report the first all-atom molecular dynamics simulations on both redox states and calculations of the Marcus electron transfer (ET) parameters for the α chain Hb oxidation and reduction rates for Hb M. The Hb wild-type (WT) and most of the studied α chain variants maintain globin structure except the Hb M Iwate (H87Y). The mutants forming Hb M tend to have lower redox potentials and thus stabilize the oxidized (Fe3+) state (in particular, the Hb Miyagi variant with K61E mutation). Solvent reorganization (λsolv 73-96%) makes major contributions to reorganization free energy, whereas protein reorganization (λprot) accounts for 27-30% except for the Miyagi and J-Buda variants (λprot ∼4%). Analysis of heme-solvent H-bonding interactions among variants provide insights into the role of Lys61 residue in stabilizing the Fe2+ state. Semiclassical Marcus ET theory-based calculations predict experimental kET for the Cyt b5-Hb complex and provide insights into relative reduction rates for Hb M in Hb variants. Thus, our methodology provides a rationale for the effect of mutations on the structure, stability, and Hb oxidation reduction rates and has potential for identification of mutations that result in methemoglobinemia.


Asunto(s)
Electrones , Metahemoglobina , Hemo , Hemoglobinas/genética , Hemoglobinas/metabolismo , Metahemoglobina/metabolismo , Oxidación-Reducción , Estudios Retrospectivos
9.
J Chem Phys ; 155(24): 244110, 2021 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-34972358

RESUMEN

The development of highly efficient methods for the calculation of electronic coupling matrix elements between the electron donor and acceptor is an important goal in theoretical organic semiconductor research. In Paper I [F. Gajdos, S. Valner, F. Hoffmann, J. Spencer, M. Breuer, A. Kubas, M. Dupuis, and J. Blumberger, J. Chem. Theory Comput. 10, 4653 (2014)], we introduced the analytic overlap method (AOM) for this purpose, which is an ultrafast electronic coupling estimator parameterized to and orders of magnitude faster than density functional theory (DFT) calculations at a reasonably small loss in accuracy. In this work, we reparameterize and extend the AOM to molecules containing nitrogen, oxygen, fluorine, and sulfur heteroatoms using 921 dimer configurations from the recently introduced HAB79 dataset. We find again a very good linear correlation between the frontier orbital overlap, calculated ultrafast in an optimized minimum Slater basis, and DFT reference electronic couplings. The new parameterization scheme is shown to be transferable to sulfur-containing polyaromatic hydrocarbons in experimentally resolved dimeric configurations. Our extension of the AOM enables high-throughput screening of very large databases of chemically diverse organic crystal structures and the application of computationally intense non-adiabatic molecular dynamics methods to charge transport in state-of-the-art organic semiconductors, e.g., non-fullerene acceptors.

10.
J Chem Phys ; 155(23): 234115, 2021 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-34937363

RESUMEN

A new molecular dataset called HAB79 is introduced to provide ab initio reference values for electronic couplings (transfer integrals) and to benchmark density functional theory (DFT) and density functional tight-binding (DFTB) calculations. The HAB79 dataset is composed of 79 planar heterocyclic polyaromatic hydrocarbon molecules frequently encountered in organic (opto)electronics, arranged to 921 structurally diverse dimer configurations. We show that CASSCF/NEVPT2 with a minimal active space provides a robust reference method that can be applied to the relatively large molecules of the dataset. Electronic couplings are largest for cofacial dimers, in particular, sulfur-containing polyaromatic hydrocarbons, with values in excess of 0.5 eV, followed by parallel displaced cofacial dimers. V-shaped dimer motifs, often encountered in the herringbone layers of organic crystals, exhibit medium-sized couplings, whereas T-shaped dimers have the lowest couplings. DFT values obtained from the projector operator-based diabatization (POD) method are initially benchmarked against the smaller databases HAB11 (HAB7-) and found to systematically improve when climbing Jacob's ladder, giving mean relative unsigned errors (MRUEs) of 27.7% (26.3%) for the generalized gradient approximation (GGA) functional BLYP, 20.7% (15.8%) for hybrid functional B3LYP, and 5.2% (7.5%) for the long-range corrected hybrid functional omega-B97X. Cost-effective POD in combination with a GGA functional and very efficient DFTB calculations on the dimers of the HAB79 database give a good linear correlation with the CASSCF/NEVPT2 reference data, which, after scaling with a multiplicative constant, gives reasonably small MRUEs of 17.9% and 40.1%, respectively, bearing in mind that couplings in HAB79 vary over 4 orders of magnitude. The ab initio reference data reported here are expected to be useful for benchmarking other DFT or semi-empirical approaches for electronic coupling calculations.

11.
Phys Chem Chem Phys ; 22(19): 10699-10709, 2020 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-32091520

RESUMEN

Iron oxides such as hematite (α-Fe2O3) play an important role in diverse fields ranging from biogeochemistry to photocatalysis. Here we perform calculations of both the electron and electron hole polaron structures and associated reorganisation energies for a series of bulk iron oxides: hematite (α-Fe2O3), lepidocrocite (γ-FeOOH), goethite (α-FeOOH) and white rust (Fe(OH)2). Through the use of gap-optimized hybrid functionals and large supercells under periodic boundary conditions, we remove some of the complications and uncertainties present in earlier cluster model calculations. It is found that while the electron hole polaron in these materials generally localises onto a single iron site, the electron polaron localises across two iron sites of the same spin layer as a consequence of the lower reorganisation energy for electrons compared to holes. An exception to these trends is the hole of goethite, which according to our calculations does not form a localised polaron.

12.
J Chem Phys ; 153(4): 044702, 2020 Jul 28.
Artículo en Inglés | MEDLINE | ID: mdl-32752720

RESUMEN

The electronic and charge transport properties of porphyrin and tetra-indole porphyrinoid single layer covalent organic frameworks (COFs) are investigated by means of density functional theory calculations. Ultrathin diacetylene-linked COFs based on oxidized tetra-indole cores are narrow gap 2D semiconductors, featuring a pronounced anisotropic electronic band structure due to the combination of dispersive and flat band characteristics, while registering high room temperature charge carrier mobilities. The capability of bandgap and charge carrier localization tuning via the careful selection of fourfold porphyrin and porphyrinoid cores and twofold articulated linkers is demonstrated, with the majority of systems exhibiting electronic gap values between 1.75 eV and 2.3 eV. Tetra-indoles are also capable of forming stable monolayers via non-articulated core fusing, resulting in 2D morphologies with extended π-conjugation and semi-metallic behavior.

13.
J Am Chem Soc ; 141(38): 15190-15200, 2019 09 25.
Artículo en Inglés | MEDLINE | ID: mdl-31454482

RESUMEN

Multiheme cytochromes attract much attention for their electron transport properties. These proteins conduct electrons across bacterial cell walls and along extracellular filaments and when purified can serve as bionanoelectronic junctions. Thus, it is important and necessary to identify and understand the factors governing electron transfer in this family of proteins. To this end we have used ultrafast transient absorbance spectroscopy, to define heme-heme electron transfer dynamics in the representative multiheme cytochrome STC from Shewanella oneidensis in aqueous solution. STC was photosensitized by site-selective labeling with a Ru(II)(bipyridine)3 dye and the dynamics of light-driven electron transfer described by a kinetic model corroborated by molecular dynamics simulation and density functional theory calculations. With the dye attached adjacent to STC Heme IV, a rate constant of 87 × 106 s-1 was resolved for Heme IV → Heme III electron transfer. With the dye attached adjacent to STC Heme I, at the opposite terminus of the tetraheme chain, a rate constant of 125 × 106 s-1 was defined for Heme I → Heme II electron transfer. These rates are an order of magnitude faster than previously computed values for unlabeled STC. The Heme III/IV and I/II pairs exemplify the T-shaped heme packing arrangement, prevalent in multiheme cytochromes, whereby the adjacent porphyrin rings lie at 90° with edge-edge (Fe-Fe) distances of ∼6 (11) Å. The results are significant in demonstrating the opportunities for pump-probe spectroscopies to resolve interheme electron transfer in Ru-labeled multiheme cytochromes.


Asunto(s)
Complejos de Coordinación/metabolismo , Citocromos/metabolismo , Luz , Complejos de Coordinación/química , Citocromos/química , Transporte de Electrón , Simulación de Dinámica Molecular
14.
Faraday Discuss ; 221(0): 501-525, 2019 Dec 16.
Artículo en Inglés | MEDLINE | ID: mdl-31538635

RESUMEN

Investigation of many electronic processes in molecules and materials, such as charge and exciton transport, requires a computational framework that incorporates both non-adiabatic electronic effects and nuclear quantum effects, in particular at low temperatures. We have recently developed an efficient semi-empirical fewest switches surface hopping method, denoted fragment orbital-based surface hopping (FOB-SH), that was tailored towards highly efficient simulation of charge transport in molecular materials, yet with nuclei treated classically. In this work, we extend FOB-SH and include nuclear quantum effects by combining it with ring-polymer molecular dynamics (RPMD) in three different flavours: (i) RPSH with bead approximation (RPSH-BA) as suggested in Shushkov et al., J. Chem. Phys., 2012, 137, 22A549, (ii) a modification of (i) denoted RPSH with weighted bead approximation (RPSH-wBA) and (iii) the isomorphic Hamiltonian method of Tao et al., J. Chem. Phys., 2018, 148, 10237 (SH-RP-iso). We present here applications to hole transfer in a molecular dimer model and analyze detailed balance and internal consistency of all three methods and investigate the temperature and driving force dependence of the hole transfer rate. We find that RPSH-BA strongly underestimates and RPSH-wBA overestimates the exact excited state population, while SH-RP-iso gives satisfactory results. We also find that the latter predicts a flattening of the rate vs. driving force dependence in the Marcus inverted regime at low temperature, as often observed experimentally. Overall, our results suggest that FOB-SH combined with SH-RP-iso is a promising method for including zero point motion and tunneling in charge transport simulations in molecular materials and biological systems.

15.
Chem Rev ; 117(15): 10319-10357, 2017 Aug 09.
Artículo en Inglés | MEDLINE | ID: mdl-28644623

RESUMEN

The booming field of molecular electronics has fostered a surge of computational research on electronic properties of organic molecular solids. In particular, with respect to a microscopic understanding of transport and loss mechanisms, theoretical studies assume an ever-increasing role. Owing to the tremendous diversity of organic molecular materials, a great number of computational methods have been put forward to suit every possible charge transport regime, material, and need for accuracy. With this review article we aim at providing a compendium of the available methods, their theoretical foundations, and their ranges of validity. We illustrate these through applications found in the literature. The focus is on methods available for organic molecular crystals, but mention is made wherever techniques are suitable for use in other related materials such as disordered or polymeric systems.

16.
Phys Chem Chem Phys ; 21(48): 26368-26386, 2019 Dec 11.
Artículo en Inglés | MEDLINE | ID: mdl-31793569

RESUMEN

Charge transport in high mobility organic semiconductors is in an intermediate regime between small polaron hopping and band transport limits. We have recently shown that surface hopping non-adiabatic molecular dynamics is a powerful method for prediction of charge transport mechanisms in organic materials and for near-quantitative prediction of charge mobilities at room temperature where the effects of nuclear zero-point motion and tunneling are still relatively small [S. Giannini et al., Nat. Commun., 2019, 10, 3843]. Here we assess and critically discuss the extensions to Tully's original method that have led to this success: (i) correction for missing electronic decoherence, (ii) detection of trivial crossings and (iii) removal of decoherence correction-induced spurious charge transfer. If any one of these corrections is not included, the charge mobility diverges with system size, each for different physical reasons. Yet if they are included, convergence with system size, detailed balance and good internal consistency are achieved.

17.
J Am Chem Soc ; 139(7): 2581-2584, 2017 02 22.
Artículo en Inglés | MEDLINE | ID: mdl-28173705

RESUMEN

The interaction of water with metal oxide surfaces plays a crucial role in the catalytic and geochemical behavior of metal oxides. In a vast majority of studies, the interfacial structure is assumed to arise from a relatively static lowest energy configuration of atoms, even at room temperature. Using hematite (α-Fe2O3) as a model oxide, we show through a direct comparison of in situ synchrotron X-ray scattering with density functional theory-based molecular dynamics simulations that the structure of the (11̅02) termination is dynamically stabilized by picosecond water exchange. Simulations show frequent exchanges between terminal aquo groups and adsorbed water in locations and with partial residence times consistent with experimentally determined atomic sites and fractional occupancies. Frequent water exchange occurs even for an ultrathin adsorbed water film persisting on the surface under a dry atmosphere. The resulting time-averaged interfacial structure consists of a ridged lateral arrangement of adsorbed water molecules hydrogen bonded to terminal aquo groups. Surface pKa prediction based on bond valence analysis suggests that water exchange will influence the proton-transfer reactions underlying the acid/base reactivity at the interface. Our findings provide important new insights for understanding complex interfacial chemical processes at metal oxide-water interfaces.

19.
J Am Chem Soc ; 139(48): 17237-17240, 2017 12 06.
Artículo en Inglés | MEDLINE | ID: mdl-29119787

RESUMEN

Multi-heme proteins have attracted much attention recently due to their prominent role in mediating extracellular electron transport (ET), but one of their key fundamental properties, the rate constants for ET between the constituent heme groups, have so far evaded experimental determination. Here we report the set of heme-heme theoretical ET rate constants that define electron flow in the tetra-heme protein STC by combining a novel projector-operator diabatization approach for electronic coupling calculation with molecular dynamics simulation of ET free energies. On the basis of our calculations, we find that the protein limited electron flux through STC in the thermodynamic downhill direction (heme 1→4) is ∼3 × 106 s-1. We find that cysteine linkages inserting in the space between the two terminal heme pairs 1-2 and 3-4 significantly enhance the overall electron flow, by a factor of about 37, due to weak mixing of the sulfur 3p orbital with the Fe-heme d orbitals. While the packing density model, and to a higher degree, the pathway model of biological ET partly capture the predicted rate enhancements, our study highlights the importance of the atomistic and chemical nature of the tunneling medium at short biological tunneling distances. Cysteine linkages are likely to enhance electron flow also in the larger deca-heme proteins MtrC and MtrF, where heme-heme motifs with sub-optimal edge-to-edge distances are used to shuttle electrons in multiple directions.


Asunto(s)
Cisteína/metabolismo , Transporte de Electrón , Electrones , Hemoproteínas/química , Hemoproteínas/metabolismo , Modelos Moleculares , Termodinámica
20.
J Chem Phys ; 147(21): 214113, 2017 Dec 07.
Artículo en Inglés | MEDLINE | ID: mdl-29221382

RESUMEN

We have recently introduced an efficient semi-empirical non-adiabatic molecular dynamics method for the simulation of charge transfer/transport in molecules and molecular materials, denoted fragment orbital-based surface hopping (FOB-SH) [J. Spencer et al., J. Chem. Phys. 145, 064102 (2016)]. In this method, the charge carrier wavefunction is expanded in a set of charge localized, diabatic electronic states and propagated in the time-dependent potential due to classical nuclear motion. Here we derive and implement an exact expression for the non-adiabatic coupling vectors between the adiabatic electronic states in terms of nuclear gradients of the diabatic electronic states. With the non-adiabatic coupling vectors (NACVs) available, we investigate how different flavours of fewest switches surface hopping affect detailed balance, internal consistency, and total energy conservation for electron hole transfer in a molecular dimer with two electronic states. We find that FOB-SH satisfies detailed balance across a wide range of diabatic electronic coupling strengths provided that the velocities are adjusted along the direction of the NACV to satisfy total energy conservation upon a surface hop. This criterion produces the right fraction of energy-forbidden (frustrated) hops, which is essential for correct population of excited states, especially when diabatic couplings are on the order of the thermal energy or larger, as in organic semiconductors and DNA. Furthermore, we find that FOB-SH is internally consistent, that is, the electronic surface population matches the average quantum amplitudes, but only in the limit of small diabatic couplings. For large diabatic couplings, inconsistencies are observed as the decrease in excited state population due to frustrated hops is not matched by a corresponding decrease in quantum amplitudes. The derivation provided here for the NACV should be generally applicable to any electronic structure approach where the electronic Hamiltonian is constructed in a diabatic electronic state basis.

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