The Journal of Physical Chemistry Letters

As models for probing the interactions between TiO2 surfaces and the dye molecules employed in dye-sensitized solar cells, carboxylic acids are an important class of molecules. In this work, we present a scanning tunneling microscopy (STM) and low-energy electron diffraction (LEED) study of three small carboxylic acids (formic, acetic, and benzoic) that were reacted with the TiO2(110) surface via a dipping procedure. The three molecules display quite different adsorption behavior, illustrating the different interadsorbate interactions that can occur. After exposure to a 10 mM solution, formic acid forms a rather disordered formate overlayer with two distinct binding geometries. Acetic acid forms a well-ordered (2 × 1) acetate overlayer similar to that observed following deposition from vapor. Benzoic acid forms a (2 × 2) overlayer, which is stabilized by intermolecular interactions between the phenyl groups.

When working with hyperpolarized species, it is often difficult to maintain a stable level of magnetization over consecutive experiments, which renders their detection at the trace level cumbersome, even when combined with chemical exchange saturation transfer (CEST). We report herein the use of ultra-fast Z-spectroscopy as a powerful means to detect low concentrations of (129)Xe NMR-based sensors and to measure the in-out xenon exchange. Modifications of the original sequence enable a multiplexed detection of several sensors, as well as the extraction of the exchange buildup rate constant in a single-shot fashion.

Oxygen-17 detected DNP NMR of a water/glycerol glass enabled an 80-fold enhancement of signal intensities at 82 K, using the biradical TOTAPOL. The >6,000-fold savings in acquisition time enables (17)O-(1)H distance measurements and heteronuclear correlation experiments. These experiments are the initial demonstration of the feasibility of DNP NMR on quadrupolar (17)O.

The tautomerism of aromatic heterocycles is of great interest because it directly affects their chemical properties and biological function. The tautomerism of 2-pyridone, 6-chloro-2-pyridone, and 4-pyrimidinone have been examined in D(2)O using FTIR, two-dimensional IR (2D IR) spectroscopy and density functional theory (DFT) calculations. Using the 2D IR cross-peak patterns, the lactim tautomer of 6-chloro-2-pyridone was separated from the lactam tautomer, and its population was observed to increase with temperature. The equilibrium constant of [lac-tam]/[lactim] was determined to be 2.1 at room temperature for 6-chloro-2-pyridone. Similarly, the N1H and N3H lactam tautomers of 4-pyrimidinone were identified with 2D IR. To assign the vibrational modes of different tautomers, DFT calculations of these chemical species were performed with explicit water molecules, and the hydration effects on the vibrational frequencies and intensities were established.

We report that the waiting time delay in 2D IR pulse sequences can be used to suppress signals from structurally disordered regions of amyloid fibrils. At a waiting time delay of 1.0 ps, the random coil vibrational modes of amylin fibrils are no longer detectable, leaving only the sharp excitonic vibrational features of the fibril β-sheets. Isotope labeling with (13)C(18)O reveals that structurally disordered residues decay faster than residues protected from solvent. Since structural disorder is usually accompanied by hydration, we conclude that the shorter lifetimes of random-coil residues is due to solvent exposure. These results indicate that 2D IR pulse sequences can utilize the waiting time to better resolve solvent-protected regions of peptides and that local mode lifetimes should be included in simulations of 2D IR spectra.

Long-lived oscillations in 2D spectra of chlorophylls are at the heart of an ongoing debate. Their physical origin is either a multipigment effect, such as excitonic coherence, or localized vibrations. We show how relative phase differences of diagonal- and cross-peak oscillations can distinguish between electronic and vibrational (vibronic) effects. While direct discrimination between the two scenarios is obscured when peaks overlap, their sensitivity to temperature provides a stronger argument. We show that vibrational (vibronic) oscillations change relative phase with temperature, while electronic oscillations are only weakly dependent. This highlights that studies of relative phase difference as a function of temperature provide a clear and easily accessible method to distinguish between vibrational and electronic coherences.

Guanidinium (Gdm(+)) is a widely used denaturant, but it is still largely unknown how it operates at the molecular level. In particular, the effect of guanidinium on the different types of secondary structure motifs of proteins is at present not clear. Here, we use two-dimensional infrared spectroscopy (2D-IR) to investigate changes in the secondary structure of two proteins with mainly α-helical or β-sheet content upon addition of Gdm-(13)C(15)N3·Cl. We find that upon denaturation, the β-sheet protein shows a complete loss of β-sheet structure, whereas the α-helical protein maintains most of its secondary structure. These results suggest that Gdm(+) disrupts β-sheets much more efficiently than α-helices, possibly because in the former, hydrophobic interactions are more important and the number of dangling hydrogen bonds is larger.

Probing underlying free energy landscape, pathways, and mechanism is the key for understanding protein folding in theory and experiment. Recently time-resolved two-dimensional infrared (2DIR) with femtosecond laser pulses, has emerged as a promising tool for investigating the protein folding dynamics on faster timescales than possible by NMR. We have employed molecular dynamics simulations to compute 2DIR spectra of the folding process of a peptide, Beta3s. Simulated non-chiral and chiral 2DIR signals illustrate the variation of the spectra as the peptide conformation evolves along the free energy landscape. Chiral spectra show stronger changes than the non-chiral signals because cross peaks caused by the formation of the β-sheet are clearly resolved. Chirality-induced 2DIR may be used to detect the folding of β-sheet proteins with high spectral and temporal resolution.

This paper presents the first observation of coincidental emission of photons, electrons and secondary ions from individual C(60) keV impacts. An increase in photon, electron and secondary ion yields is observed as a function of C(60) projectile energy. The effect of target structure/composition on photon and electron emissions at the nanometer level is shown for a CsI target. The time-resolved photon emission may be characterized by a fast component emission in the UV-Vis range with a short decay time, while the electron and secondary ion emission follow a Poisson distribution.

Two-dimensional (2D) optical spectroscopy techniques based on ultrashort laser pulses have been recently extended to the optical domain in the ultraviolet (UV) spectral region. UV-active aromatic side chains can thus be used as local highly specific markers for tracking dynamics and structural rearrangements of proteins. Here we demonstrate that 2D electronic spectra of a model proteic system, a tetrapeptide with two aromatic side chains, contain enough structural information to distinguish between two different configurations with distant and vicinal side chains. For accurate simulations of the 2DUV spectra in solution, we combine a quantum mechanics/molecular mechanics approach based on wave function methods, accounting for interchromophores coupling and environmental effects, with nonlinear response theory. The proposed methodology reveals effects, such as charge transfer between vicinal aromatic residues that remain concealed in conventional exciton Hamiltonian approaches. Possible experimental setups are discussed, including multicolor experiments and signal manipulation techniques for limiting undesired background contributions and enhancing 2DUV signatures of specific electronic couplings.

We present a new approach to combine λ dynamics with meta-dynamics (named λ-meta dynamics) to compute free energy surface with respect to λ. Particularly, the λ-meta dynamics method extends meta-dynamics to a single virtual variable λ, i.e., the coupling parameter between solute and solvent, to compute absolute solvation free energy as an exemplary application. We demonstrate that λ-meta dynamics simulations can recover the accurate potential of mean force surface with respect to λ compared to the benchmark results from traditional λ-dynamics with umbrella sampling. The solvation free energy results for five small organic molecules from λ-meta dynamics simulations using the same filling scheme show that the statistical errors are within ±0.5 kcal/mol. The new λ-meta dynamics method is general and other variables such as order parameters to describe conformational changes can be easily combined with λ-meta dynamics. This should allow for efficient samplings on high-dimension free energy landscapes.

Surface-plasmon-initiated interference effects of polyelectrolyte-coated gold nanorods on the two-photon absorption of an organic chromophore were investigated. With polyelectrolyte bearing gold nanorods of 2,4,6 and 8 layers, the role of the plasmonic fields as function of distance on such effects was examined. An unusual distance dependence was found: enhancements in the two-photon cross-section were at a minimum at an intermediate distance, then rose again at a further distance. The observed values of enhancement were compared to theoretical predictions using finite element analysis and showed good agreementdue to constructive and destructive interference effects.

L-edge spectroscopy of 3d transition metals provides important electronic structure information and has been used in many fields. However, the use of this method for studying dilute aqueous systems, such as metalloenzymes, has not been prevalent because of severe radiation damage and the lack of suitable detection systems. Here we present spectra from a dilute Mn aqueous solution using a high-transmission zone-plate spectrometer at the Linac Coherent Light Source (LCLS). The spectrometer has been optimized for discriminating the Mn L-edge signal from the overwhelming O K-edge background that arises from water and protein itself, and the ultrashort LCLS X-ray pulses can outrun X-ray induced damage. We show that the deviations of the partial-fluorescence yield-detected spectra from the true absorption can be well modeled using the state-dependence of the fluorescence yield, and discuss implications for the application of our concept to biological samples.

An extended accelerated molecular dynamics (AMD) methodology called adaptive AMD is presented. Adaptive AMD (Ad-AMD) is an efficient and robust conformational space sampling algorithm that is particularly-well suited to proteins with highly structured potential energy surfaces exhibiting complex, large-scale collective conformational transitions. Ad-AMD simulations of substrate-free P450cam reveal that this system exists in equilibrium between a fully and partially open conformational state. The mechanism for substrate binding depends on the size of the ligand. Larger ligands enter the P450cam binding pocket, and the resulting substrate-bound system is trapped in an open conformation via a population shift mechanism. Small ligands, which fully enter the binding pocket, cause an induced-fit mechanism, resulting in the formation of an energetically stable closed conformational state. These results are corroborated by recent experimental studies and potentially provide detailed insight into the functional dynamics and conformational behavior of the entire cytochrome-P450 superfamily.

Vibrational reporters have shown significant promise as sensitive probes of local environments in proteins and nucleic acids. The utility of two potential vibrational probes, the cyanate and azide groups in phenyl cyanate and 3-azidopyridine, respectively, has been hindered by accidental Fermi resonance. Anharmonic coupling, between the fundamental -OCN or -N(3) asymmetric stretch vibration with a near resonant combination band, results in an extremely broad and complex absorption profile for each of these probes. A total of eight phenyl cyanate and six 3-azidopyridine isotopomers were synthesized and studied. Isotopic editing effectively modulated the accidental Fermi resonance - the absorption profiles of several isotopomers were greatly simplified while others remained complex. The origins of the observed profiles are discussed. Addition of a single neutron to the middle atom of the oscillator converted the absorption profile to essentially a single band resulting from either the cyanate or azide asymmetric stretch vibration.

The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMD(MSλD)) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMD(MSλD) framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMD(MSλD) simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMD(MSλD) simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids.

Acinetobacter baumannii is an important human pathogen that can form biofilms and persist under harsh environmental conditions. Biofilm formation and virulence are modulated by blue light, which is thought to be regulated by a BLUF protein, BlsA. To understand the molecular mechanism of light sensing, we have used steady-state and ultrafast vibrational spectroscopy to compare the photoactivation mechanism of BlsA to the BLUF photosensor AppA from Rhodobacter sphaeroides. Although similar photocycles are observed, vibrational data together with homology modeling identify significant differences in the β5 strand in BlsA caused by photoactivation, which are proposed to be directly linked to downstream signaling.

We develop a microscopic theory for ion transport across a transmembrane channel with an internal binding site. The ion flux is determined by the rate constants for binding to the internal site from the two sides of the membrane and the corresponding unbinding rate constants. The binding rate constants are formulated in terms of diffusion-influenced reactions. The theory allows a reconciliation of experimental data on the conductance of the influenza A M2 proton channel with the structure and dynamics of the protein.

We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation.

Thioxolone acts as a prodrug in the presence of carbonic anhydrase II (CA II), whereby the molecule is cleaved by thioester hydrolysis to the carbonic anhydrase inhibitor, 4-mercaptobenzene-1,3-diol (TH0). Thioxolone was soaked into the proton transfer mutant H64A of CA II in an effort to capture a reaction intermediate via X-ray crystallography. Structure determination of the 1.2 Å resolution data revealed the TH0 had been modified to a 4,4'-disulfanediyldibenzene-1,3-diol, a product of crystallization conditions, and a zinc ligated 2,4-dihydroxybenzenesulfenic acid, most likely induced by radiation damage. Neither ligand was likely a result of an enzymatic mechanism.

When the Born-Oppenheimer approximation is valid, electrons adiabatically follow the nuclear motion in molecules. For strong nonadiabatic coupling between electronic states, one encounters a diabatic motion where the electrons remain local and do not adapt to molecular geometry changes. We show that the mentioned limiting cases are reflected differently in the asymmetry of time-resolved photoelectron momentum distributions. Whereas for adiabatic dynamics, the asymmetry directly maps the time-dependent average nuclear momentum, in the diabatic case, the asymmetry is determined by a nonclassical interference effect arising from the mixing of wave function components in different electronic states, which is present at times nonadiabatic transitions take place.

Bundles of single-walled nanotubes are promising candidates for storage of hydrogen, methane, and other hydrogen-rich molecules, but experiments are hindered by nonuniformity of the tubes. We overcome the problem by investigating methane adsorption on aggregates of fullerenes containing up to six C(60); the systems feature adsorption sites similar to those of nanotube bundles. Four different types of adsorption sites are distinguished, namely, registered sites above the carbon hexagons and pentagons, groove sites between adjacent fullerenes, dimple sites between three adjacent fullerenes, and exterior sites. The nature and adsorption energies of the sites in C(60) aggregates are determined by density functional theory and molecular dynamics (MD) simulations. Excellent agreement between experiment and theory is obtained for the adsorption capacity in these sites.

Adsorption of dissolved molecules onto solid surfaces can be extremely sensitive to the atomic-scale properties of the solute and surface, causing difficulties for the design of fluidic systems in industrial, medical and technological applications. In this communication, we show that the Langmuir isotherm for adsorption of a small molecule to a realistic, heterogeneous surface can be predicted from atomic structures of the molecule and surface through molecular dynamics (MD) simulations. We highlight the method by studying the adsorption of dimethyl-methylphosphonate (DMMP) to amorphous silica substrates and show that subtle differences in the atomic-scale surface properties can have drastic effects on the Langmuir isotherm. The sensitivity of the method presented is sufficient to permit the optimization of fluidic devices and to determine fundamental design rules for controlling adsorption at the nanoscale.

Graphene, carbon nanotubes, and fullerenes are of great interest due to their unique properties and diverse applications in biology, molecular electronics, and materials science. Therefore, there is demand for methods that can accurately model the interface between carbon surfaces and their environment. In this letter we compare results for complexes of water, potassium ion, and chloride ion with graphene, carbon nanotube, and fullerene surfaces using a standard non-polarizable force field (OPLS-AA), a polarizable force field (OPLS-AAP), DFT, and ab initio theory. For interactions with water, OPLS-AA with the TIP3P or TIP4P water models describes the interactions with benzene (C(6)H(6)) and coronene (C(24)H(12)) well; however, for acenes larger than circumcoronene (C(54)H(18)) and especially for C(60), the interaction energies are somewhat too weak and polarization is needed. For ions interacting with carbon surfaces, inclusion of polarization is essential, and OPLS-AAP is found to perform well in comparison to the highest-level quantum mechanical methods. Overall, OPLS-AAP provides an accurate and computationally efficient force field for modeling condensed-phase systems featuring carbon surfaces.

Nature often colocalizes successive steps in a metabolic pathway. Such organization is predicted to increase the effective concentration of pathway intermediates near their recipient active sites and to enhance catalytic efficiency. Here, the pathway of a two-step reaction is modeled using a simple spherical approximation for the enzymes and substrate particles. Brownian dynamics are used to simulate the trajectory of a substrate particle as it diffuses between the active site zones of two different enzyme spheres. The results approximate distances for the most effective reaction pathways, indicating that the most effective reaction pathway is one in which the active sites are closely aligned. However, when the active sites are too close, the ability of the substrate to react with the first enzyme was hindered, suggesting that even the most efficient orientations can be improved for a system that is allowed to rotate or change orientation to optimize the likelihood of reaction at both sites.