Charge-Transfer versus Charge-Separated Triplet Excited States of [ReI(dmp)(CO)3(His124)(Trp122)]+ in Water and in Modified Pseudomonas aeruginosa Azurin Protein

A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.     

Tertiary contact formation in alpha-synuclein probed by electron transfer

To explore tertiary contact formation in alpha-synuclein, a natively unfolded protein implicated in Parkinson's disease, we have measured the rates of reaction between a powerful electron donor, the tryptophan (W) triplet excited state, and an acceptor, 3-nitro-tyrosine (Y(NO2)) in six different variants, probing loop sizes between 15 and 132 residues. Electron transfer rates decrease with loop size with the fastest contact time of 140 ns for the N-terminal pair and the slowest of 1.2 mus for the N- to C-terminal pair. Diffusion coefficients ranging from approximately 2 x 10-6 to approximately 10-5 cm2 s-1 were extracted from simultaneous fits of the W to Y(NO2) electron (triplet excited state) and energy transfer (singlet excited state) kinetics.     

Measurement of submicrosecond intramolecular contact formation in peptides at the single-molecule level

We describe a single-molecule-sensitive method to determine the rate of contact formation and dissociation between tryptophan and an oxazine derivative (MR121) on the basis of measurements of the photon distance distribution. Two short peptides (15 and 20 amino acids) derived from the transactivation domain of the human oncoprotein p53 were investigated. With the fluorophore attached at the N-terminal end of the flexible peptides, fluorescence of the dye is efficiently quenched upon contact formation with a tryptophan residue. The mechanism responsible for the efficient fluorescence quenching observed in the complexes is assumed to be a photoinduced electron-transfer reaction occurring predominantly at van der Waals contact. Fluorescence fluctuations caused by intramolecular contact formation and dissociation were recorded using confocal fluorescence microscopy with two avalanche photodiodes and the time-correlated single-photon-counting technique, enabling a temporal resolution of 1.2 ns. Peptides containing a tryptophan residue at positions 9 and 8, respectively, show contact formation with rate constants of 1/120 and 1/152 ns(-1), respectively. Whereas the rate constants of contact formation most likely directly report on biopolymer chain mobility, the dissociation rate constants of 1/267 and 1/742 ns(-1), respectively, are significantly smaller and reflect strong hydrophobic interactions between the dye and tryptophan. Fluorescence experiments on point-mutated peptides where tryptophan is exchanged by phenylalanine show no fluorescence quenching.     

Folding processes of the B domain of protein A to the native state observed in all-atom ab initio folding simulations

Reaching the native states of small proteins, a necessary step towards a comprehensive understanding of the folding mechanisms, has remained a tremendous challenge to ab initio protein folding simulations despite the extensive effort. In this work, the folding process of the B domain of protein A (BdpA) has been simulated by both conventional and replica exchange molecular dynamics using AMBER FF03 all-atom force field. Started from an extended chain, a total of 40 conventional (each to 1.0 micros) and two sets of replica exchange (each to 200.0 ns per replica) molecular dynamics simulations were performed with different generalized-Born solvation models and temperature control schemes. The improvements in both the force field and solvent model allowed successful simulations of the folding process to the native state as demonstrated by the 0.80 A C(alpha) root mean square deviation (RMSD) of the best folded structure. The most populated conformation was the native folded structure with a high population. This was a significant improvement over the 2.8 A C(alpha) RMSD of the best nativelike structures from previous ab initio folding studies on BdpA. To the best of our knowledge, our results demonstrate, for the first time, that ab initio simulations can reach the native state of BdpA. Consistent with experimental observations, including Phi-value analyses, formation of helix II/III hairpin was a crucial step that provides a template upon which helix I could form and the folding process could complete. Early formation of helix III was observed which is consistent with the experimental results of higher residual helical content of isolated helix III among the three helices. The calculated temperature-dependent profile and the melting temperature were in close agreement with the experimental results. The simulations further revealed that phenylalanine 31 may play critical to achieve the correct packing of the three helices which is consistent with the experimental observation. In addition to the mechanistic studies, an ab initio structure prediction was also conducted based on both the physical energy and a statistical potential. Based on the lowest physical energy, the predicted structure was 2.0 A C(alpha) RMSD away from the experimentally determined structure.     

Solvent effects on the n-->pi* electronic transition in formaldehyde: a combined coupled cluster/molecular dynamics study

We present a study of the blueshift of the n-->pi* electronic transition in formaldehyde in aqueous solution using a combined coupled cluster/molecular mechanics model including mutual polarization effects in the Hamiltonian. In addition, we report ground and excited state dipole moments. Configurations are generated from molecular dynamics simulations with two different force fields, one with and one without an explicit polarization contribution. A statistical analysis using 1200 configurations is presented. Effects of explicit polarization contributions are found to be significant. It is found that the main difference in the effects on the excitation energies arises from the fact that the two force fields result in different liquid structures, and thus a different set of configurations is generated for the coupled cluster/molecular mechanics calculations.     

Dipole-induced self-assembly of helical beta-peptides

In this work, the interactions between beta-peptides are investigated for helix-forming peptides using molecular simulation. The role of electrostatic interactions in the self-assembly of these peptides is studied by calculating the dipole moment of various 14-helical beta-peptides using molecular dynamics simulations. The stability of a beta-peptide that is known to form a liquid crystalline phase is determined by calculating the potential of mean force using the expanded ensemble density of states method. This peptide is found to form a mechanically stable 14-helix in an implicit solvent model. The interaction between two of these peptides is examined by calculating the potential of mean force between the two peptides in implicit solvent. The peptides are shown to favorably associate in an end-to-end manner, driven largely by dipolar interactions. In order to understand the possible structures that form when many peptides interact in solution, a coarse-grained model is developed. Brownian dynamics simulations of the coarse-grained model at intermediate concentrations (1-50 mM) are performed, and the aggregation behavior is understood by calculating the diffusivity and the radial distribution function. An analysis of the resultant structures reveals that the coarse-grained model of the peptide leads to the formation of spherical clusters.     

Force-field development and molecular dynamics simulations of ferrocene-peptide conjugates as a scaffold for hydrogenase mimics

The increasing importance of hydrogenase enzymes in the new energy research field has led us to examine the structure and dynamics of potential hydrogenase mimics, based on a ferrocene-peptide scaffold, using molecular dynamics (MD) simulations. To enable this MD study, a molecular mechanics force field for ferrocene-bearing peptides was developed and implemented in the CHARMM simulation package, thus extending the usefulness of the package into peptide-bioorganometallic chemistry. Using the automated frequency-matching method (AFMM), optimized intramolecular force-field parameters were generated through quantum chemical reference normal modes. The partial charges for ferrocene were derived by fitting point charges to quantum-chemically computed electrostatic potentials. The force field was tested against experimental X-ray crystal structures of dipeptide derivatives of ferrocene-1,1'-dicarboxylic acid. The calculations reproduce accurately the molecular geometries, including the characteristic C2-symmetrical intramolecular hydrogen-bonding pattern, that were stable over 0.1 micros MD simulations. The crystal packing properties of ferrocene-1-(D)alanine-(D)proline-1'-(D)alanine-(D)proline were also accurately reproduced. The lattice parameters of this crystal were conserved during a 0.1 micros MD simulation and match the experimental values almost exactly. Simulations of the peptides in dichloromethane are also in good agreement with experimental NMR and circular dichroism (CD) data in solution. The developed force field was used to perform MD simulations on novel, as yet unsynthesized peptide fragments that surround the active site of [Ni-Fe] hydrogenase. The results of this simulation lead us to propose an improved design for synthetic peptide-based hydrogenase models. The presented MD simulation results of metallocenes thereby provide a convincing validation of our proposal to use ferrocene-peptides as minimal enzyme mimics.     

Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

Primary photoinduced processes in bimetallic dyads with extended aromatic bridges. tetraazatetrapyridopentacene complexes of ruthenium(II) and osmium(II)

The photophysics of the binuclear complexes [(phen)2M(tatpp)M(phen)2]4+, where M = Ru or Os, phen = 1,10-phenanthroline, and tatpp = 9,11,20,22-tetraazatetrapyrido[3,2-a:2'3'-c:3',2'-l:2',3']pentacene, has been studied in acetonitrile and dichloromethane by femtosecond and nanosecond time-resolved techniques. The results demonstrate that complexes of different metals have different types of lowest excited state: a tatpp ligand-centered (LC) triplet in the case of Ru(II); a metal-to-ligand charge-transfer (MLCT) triplet state in the case of Os(II). The excited-state kinetics is strongly solvent-dependent. In the Ru(II) system, the formation and decay of the LC state take place, respectively, in 25 ps and ca. 5 ns in CH3CN and in 0.5 ps and 1.3 micros in CH2Cl2. These solvent effects can be rationalized on the basis of a thermally activated decay of the LC state through the upper MLCT state. In the Os(II) system, the formation and decay of the MLCT state take place, respectively, in 3.8 and 60 ps in CH3CN and in 0.5 and 4 ps in CH2Cl2. These effects are consistent with the solvent sensitivity of the MLCT energy, in terms of driving force and energy-gap law arguments. The relevance of these results for the use of ladder-type aromatic bridges as potential molecular wires is discussed.     

Force field‐dependent solution properties of glycine oligomers

Molecular simulations can be used to study disordered polypeptide systems and to generate hypotheses on the underlying structural and thermodynamic mechanisms that govern their function. As the number of disordered protein systems investigated with simulations increase, it is important to understand how particular force fields affect the structural properties of disordered polypeptides in solution. To this end, we performed a comparative structural analysis of Gly₃ and Gly₁₀ in aqueous solution from all atom, microsecond molecular dynamics (MD) simulations using the CHARMM 27 (C27), CHARMM 36 (C36), and Amber ff12SB force fields. For each force field, Gly₃ and Gly₁₀ were simulated for at least 300 ns and 1 μs, respectively. Simulating oligoglycines of two different lengths allows us to evaluate how force field effects depend on polypeptide length. Using a variety of structural metrics (e.g., end‐to‐end distance, radius of gyration, dihedral angle distributions), we characterize the distribution of oligoglycine conformers for each force field and show that each sample conformation space differently, yielding considerably different structural tendencies of the same oligoglycine model in solution. Notably, we find that C36 samples more extended oligoglycine structures than both C27 and ff12SB. © 2015 Wiley Periodicals, Inc.     

Photoinduced CC‐coupling Reactions of Rigid Diastereomeric Benzophenone‐Methionine Dyads

The reactions of ketone/methionine systems are widely used as efficient and selective sources of biorelevant radical species. In this study, we address intramolecular variants of this couple with respect to its photosynthetic utility and as a mechanistic model of underlying elementary reaction steps of biological importance, especially with respect to the study of photoinitiated electron transport in complex peptides. The outcomes of this study are two‐fold: (1) steady‐state irradiation of sterically constrained benzophenone/methionine dyads afforded stable photocyclization products with high yield and product selectivity. (2) Mechanistic insights into the triplet‐triggered product formation were obtained from an analysis of the flash photolysis results and the molecular structure of the stable product formed upon irradiation. Time‐resolved experiments identified (net) hydrogen‐atom transfer from the methionine as the mechanism of the triplet quenching and the resulting biradicals as the major precursor of the isolated stable product. Both the analyses of triplet quenching and stable‐product formation in the diastereomeric pairs point to effects of chiral center configuration, i.e., significant stereoselectivity is observed for all elementary steps. The underlying stereochemical restraints were quantitatively addressed by means of molecular dynamics simulations.     

乙醇醛的分子动态结构

以量子化学计算作为起点, 为最简单的糖类分子——乙醇醛开发了两套分子力学力场参数: 基于肽类的力场和基于醛类的力场. 分子动力学模拟结果表明, 所开发的类醛力场参数能够较好地描述乙醇醛分子在水中的结构以及水分子在其周围的分布. 通过瞬时简正模式分析, 得到了3N-6个模式的瞬时振动频率和振动跃迁偶极矩等振动光谱参数的统计分布及其相关性. 结合量子化学计算和分子动力学模拟对生物分子体系的多元振动光谱参数进行预测和评估, 为从化学键水平出发模拟宽带飞秒二维红外相关光谱提供了一个新方法.     

微乳胶粒的形成与表面活性剂的作用——粗粒化力场分子动力学模拟研究

从微观机理上研究表面活性剂对微乳胶粒形成的影响有利于推动微乳状液在各个领域的应用研究．本文采用分子动力学模拟方法研究了微乳胶粒的形成过程及表面活性剂对微乳胶粒形成的影响．正十二烷（C12H26）和十二烷基硫酸钠（SDS）作为油分子和表面活性剂分子的模型,Martini粗粒化（coarse．grained,CG）力场描述分子间和分子内的相互作用,对含有不同浓度的正十二烷和表面活性剂的12个模型分别进行了100ns的分子动力学模拟．模拟结果显示,不含表面活性剂的体系迅速发生水油相分离,且分离过程伴随着势能的明显下降;含有表面活性剂的体系中,在相同时间内通过模拟得到了稳定的、表面活性剂分子包裹油分子的胶粒．对不同温度下模拟得到的数据分析发现,胶粒形成初期的动力学特征可以近似地表达为二级反应,聚集活化能为14．6kJ／mol．     

A fluorescence-based method for direct measurement of submicrosecond intramolecular contact formation in biopolymers: an exploratory study with polypeptides.

A fluorescent amino acid derivative (Fmoc-DBO) has been synthesized, which contains 2,3-diazabicyclo[2.2.2]oct-2-ene (DBO) as a small, hydrophilic fluorophore with an extremely long fluorescence lifetime (325 ns in H2O and 505 ns in D2O under air). Polypeptides containing both the DBO residue and an efficient fluorescence quencher allow the measurement of rate constants for intramolecular end-to-end contact formation. Bimolecular quenching experiments indicated that Trp, Cys, Met, and Tyr are efficient quenchers of DBO (k(q) = 20, 5.1, 4.5, and 3.6 x 10(8) M(-1) x s(-1) in D2O), while the other amino acids are inefficient. The quenching by Trp, which was selected as an intrinsic quencher, is presumed to involve exciplex-induced deactivation. Flexible, structureless polypeptides, Trp-(Gly-Ser)n-DBO-NH2, were prepared by standard solid-phase synthesis, and the rates of contact formation were measured through the intramolecular fluorescence quenching of DBO by Trp with time-correlated single-photon counting, laser flash photolysis, and steady-state fluorometry. Rate constants of 4.1, 6.8, 4.9, 3.1, 2.0, and 1.1 x 10(7) s(-1) for n = 0, 1, 2, 4, 6, and 10 were obtained. Noteworthy was the relatively slow quenching for the shortest peptide (n = 0). The kinetic data are in agreement with recent transient absorption studies of triplet probes for related peptides, but the rate constants are significantly larger. In contrast to the flexible structureless Gly-Ser polypeptides, the polyproline Trp-Pro4-DBO-NH2 showed insignificant fluorescence quenching, suggesting that a high polypeptide flexibility and the possibility of probe-quencher contact is essential to induce quenching. Advantages of the new fluorescence-based method for measuring contact formation rates in biopolymers include high accuracy, fast time range (100 ps-1 micros), and the possibility to perform measurements in water under air.     

The Thermodynamics of Folding of a β Hairpin Peptide Probed Through Replica Exchange Molecular Dynamics Simulations

Peptides that possess a well defined native state are ideal model systems to study the folding of proteins. They possess many of the complexities of larger proteins, yet their small size renders their study computationally tractable. Recent advances in sampling techniques, including replica exchange molecular dynamics, now permit a full characterization of the thermodynamics of folding of small peptides. These simulations not only yield insight into the folding of larger proteins, but equally importantly, they allow, through comparison with experiment, an objective test of the accuracy of force fields, water models and of different numerical schemes for dealing with electrostatic interactions. In this account, we present a molecular dynamics simulation of a small β-hairpin peptide using the replica exchange algorithm and illustrate how this enhanced sampling scheme enables a thorough characterization of the native and unfolded states, and sheds new light into its folding mechanism.     

Benchmarking implicit solvent folding simulations of the amyloid beta(10-35) fragment

A pathogenetic feature of Alzhemier disease is the aggregation of monomeric beta-amyloid proteins (Abeta) to form oligomers. Usually these oligomers of long peptides aggregate on time scales of microseconds or longer, making computational studies using atomistic molecular dynamics models prohibitively expensive and making it essential to develop computational models that are cheaper and at the same time faithful to physical features of the process. We benchmark the ability of our implicit solvent model to describe equilibrium and dynamic properties of monomeric Abeta(10-35) using all-atom Langevin dynamics (LD) simulations, since Alphabeta(10-35) is the only fragment whose monomeric properties have been measured. The accuracy of the implicit solvent model is tested by comparing its predictions with experiment and with those from a new explicit water MD simulation, (performed using CHARMM and the TIP3P water model) which is approximately 200 times slower than the implicit water simulations. The dependence on force field is investigated by running multiple trajectories for Alphabeta(10-35) using the CHARMM, OPLS-aal, and GS-AMBER94 force fields, whereas the convergence to equilibrium is tested for each force field by beginning separate trajectories from the native NMR structure, a completely stretched structure, and from unfolded initial structures. The NMR order parameter, S2, is computed for each trajectory and is compared with experimental data to assess the best choice for treating aggregates of Alphabeta. The computed order parameters vary significantly with force field. Explicit and implicit solvent simulations using the CHARMM force fields display excellent agreement with each other and once again support the accuracy of the implicit solvent model. Alphabeta(10-35) exhibits great flexibility, consistent with experiment data for the monomer in solution, while maintaining a general strand-loop-strand motif with a solvent-exposed hydrophobic patch that is believed to be important for aggregation. Finally, equilibration of the peptide structure requires an implicit solvent LD simulation as long as 30 ns.     

Triplet photophysics of gold(III) porphyrins

Gold porphyrins are often used as electron-accepting chromophores in donor-acceptor complexes for the study of photoinduced electron transfer, and they can also be involved in triplet-triplet energy-transfer interactions with other chromophores. Since the lowest excited singlet state is very short-lived (240 fs), the triplet state is usually the starting point for the transfer reactions, and it is therefore crucial to understand its photophysics. The triplet state of various gold porphyrins has been reported to have a lifetime of around 1.5 ns at room temperature and to have a biexponential decay both in emission and in transient absorption with decay times of around 10 and 100 micros at 80 K. In this paper, the triplet photophysics of two gold porphyrins (Au(III) 5,15-bis(3,5-di-tert-butylphenyl)-2,8,12,18-tetraethyl-3,7,13,17-tetramethylporphyrin and Au(III) 5,10,15,20-tetra(3,5-di-tert-butylphenyl)porphyrin) are studied by steady-state and time-resolved absorption and emission spectroscopy over a wide temperature range (4-300 K). The study reveals the existence of a dark state with an approximate lifetime of 50 ns, which was not previously observed. This state acts as an intermediate between the short-lived singlet and the triplet state manifold. In addition, we present DFT calculations, in which the core electrons of the central metal were replaced by a pseudopotential to account for the relativistic effects, which suggest that the lowest excited singlet state is an optically forbidden ligand-to-metal charge-transfer (LMCT) state. This LMCT state is an obvious candidate for the experimentally observed dark state, and it is shown to dictate the photophysical properties of gold porphyrins by acting as a gate for triplet state formation versus direct return to the ground state.     

Exploring the parameter space of the coarse‐grained UNRES force field by random search: Selecting a transferable medium‐resolution force field

We explored the energy‐parameter space of our coarse‐grained UNRES force field for large‐scale ab initio simulations of protein folding, to obtain good initial approximations for hierarchical optimization of the force field with new virtual‐bond‐angle bending and side‐chain‐rotamer potentials which we recently introduced to replace the statistical potentials. 100 sets of energy‐term weights were generated randomly, and good sets were selected by carrying out replica‐exchange molecular dynamics simulations of two peptides with a minimal α‐helical and a minimal β‐hairpin fold, respectively: the tryptophan cage (PDB code: 1L2Y) and tryptophan zipper (PDB code: 1LE1). Eight sets of parameters produced native‐like structures of these two peptides. These eight sets were tested on two larger proteins: the engrailed homeodomain (PDB code: 1ENH) and FBP WW domain (PDB code: 1E0L); two sets were found to produce native‐like conformations of these proteins. These two sets were tested further on a larger set of nine proteins with α or α + β structure and found to locate native‐like structures of most of them. These results demonstrate that, in addition to finding reasonable initial starting points for optimization, an extensive search of parameter space is a powerful method to produce a transferable force field. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009