Hydration structure and dynamics of phosphoric acid and its anions-Ultrafast 2D-IR spectroscopy and ab initio molecular dynamics simulations.

The hydration shells of phosphate ions and phosphate groups of nucleotides and phospholipid membranes display markedly different structures and hydrogen-bond strengths. Understanding phosphate hydration requires insight into the spatial arrangements of water molecules around phosphates and in thermally activated structure fluctuations on ultrafast time scales. Femtosecond two-dimensional infrared spectroscopy of phosphate vibrations, particularly asymmetric stretching vibrations between 1000 and 1200 cm-1, and ab initio molecular dynamics (AIMD) simulations are combined to map and characterize dynamic local hydration structures and phosphate-water interactions.

Ultrafast terahertz Stark spectroscopy reveals the excited-state dipole moments of retinal in bacteriorhodopsin.

The photoinduced all-trans to 13-cis isomerization of the retinal Schiff base represents the ultrafast first step in the reaction cycle of bacteriorhodopsin (BR). Extensive experimental and theoretical work has addressed excited-state dynamics and isomerization via a conical intersection with the ground state. In conflicting molecular pictures, the excited state potential energy surface has been modeled as a pure S[Formula: see text] state that intersects with the ground state, or in a 3-state picture involving the S[Formula: see text] and S[Formula: see text] states.

Transient Terahertz Stark Effect: A Dynamic Probe of Electric Interactions in Polar Liquids.

Electric forces acting on molecules in liquids at ambient temperature fluctuate at terahertz (THz) frequencies with a direct impact on their electronic and optical properties. We introduce the transient THz Stark effect to modify the electronic absorption spectra of dye molecules and, thus, elucidate and determine the underlying molecular interactions and dynamics. Picosecond electric fields of megavolts/cm induce a nonequilibrium response of the prototypical Betaine-30 in polar solution that is probed via transient absorption changes.

Coherent polaron dynamics of electrons solvated in polar liquids.

An electron solvated in a polar liquid is an elementary quantum system with properties governed by electric interactions with a fluctuating molecular environment. In the prevailing single particle picture, the quantum ground and excited states are determined by a self-consistent potential, as defined by the particular local configuration of the solvation shell. This description neglects collective many-body excitations, which arise from the coupling of electronic degrees of freedom and nuclear motions of the environment.

Short-Range Cooperative Slow-down of Water Solvation Dynamics Around SO -Mg Ion Pairs.

The presence of ions affects the structure and dynamics of water on a multitude of length and time scales. In this context, pairs of Mg and SO ions in water constitute a prototypical system for which conflicting pictures of hydration geometries and dynamics have been reported. Key issues are the molecular pair and solvation shell geometries, the spatial range of electric interactions, and their impact on solvation dynamics.

Field-Induced Electron Generation in Water: Solvation Dynamics and Many-Body Interactions.

The solvated electron represents an elementary quantum system in a liquid environment. Electrons solvated in water have raised strong interest because of their prototypical properties, their role in radiation chemistry, and their relevance for charge separation and transport. Nonequilibrium dynamics of photogenerated electrons in water occur on ultrafast time scales and include charge transfer, localization, and energy dissipation processes.

The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface.

The structure and dynamics of polyanionic biomolecules, like RNA, are decisively determined by their electric interactions with the water molecules and the counterions in the environment. The solvation dynamics of the biomolecules involves a subtle balance of non-covalent and many-body interactions with structural fluctuations due to thermal motion occurring in a femto- to subnanosecond time range. This complex fluctuating many particle scenario is crucial in defining the properties of biological interfaces with far reaching significance for the folding of RNA structures and for facilitating RNA-protein interactions.

Contact pairs of RNA with magnesium ions-electrostatics beyond the Poisson-Boltzmann equation.

The electrostatic interaction of RNA with its aqueous environment is most relevant for defining macromolecular structure and biological function. The attractive interaction of phosphate groups in the RNA backbone with ions in the water environment leads to the accumulation of positively charged ions in the first few hydration layers around RNA. Electrostatics of this ion atmosphere and the resulting ion concentration profiles have been described by solutions of the nonlinear Poisson-Boltzmann equation and atomistic molecular dynamics (MD) simulations.

Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of .

While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of (). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH cofactor that facilitates reduction of the photoproduct.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H O Complex in Solution.

The front cover artwork is provided by the groups of Prof. Ehud Pines (BGU, Israel) and Dr. Benjamin Fingerhut (MBI, Berlin).

Phosphate Vibrations Probe Electric Fields in Hydrated Biomolecules: Spectroscopy, Dynamics, and Interactions.

Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO) stretching vibration ν(PO), allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes.

Terahertz Polaron Oscillations of Electrons Solvated in Liquid Water.

The terahertz (THz) response of solvated electrons in liquid water is studied in nonlinear ultrafast pump-probe experiments. Free electrons with concentrations from c_{e}=4 to 140×10^{-6} moles/liter are generated by high-field THz or near-infrared multiphoton excitation. The time-resolved change of the dielectric function as mapped by broadband THz pulses exhibits pronounced oscillations persisting up to 30 ps.

Infrared and NMR Spectroscopic Fingerprints of the Asymmetric H O Complex in Solution.

Infrared (IR) absorption in the 1000-3700 cm range and H NMR spectroscopy reveal the existence of an asymmetric protonated water trimer, H O in acetonitrile. The core H O motif persists in larger protonated water clusters in acetonitrile up to at least 8 water molecules. Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations reveal irreversible proton transport promoted by propagating the asymmetric H O structure in solution.

Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations.

Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the molecular level. Here, we demonstrate that contact ion pairs of magnesium (Mg) and phosphate groups embedded in local water shells stabilize the tertiary equilibrium structure of transfer RNA (tRNA).

On the role of non-diagonal system-environment interactions in bridge-mediated electron transfer.

Bridge-mediated electron transfer (ET) between a donor and an acceptor is prototypical for the description of numerous most important ET scenarios. While multi-step ET and the interplay of sequential and direct superexchange transfer pathways in the donor-bridge-acceptor (D-B-A) model are increasingly understood, the influence of off-diagonal system-bath interactions on the transfer dynamics is less explored. Off-diagonal interactions account for the dependence of the ET coupling elements on nuclear coordinates (non-Condon effects) and are typically neglected.

Regulatory Impact of the C-Terminal Tail on Charge Transfer Pathways in Cryptochrome.

Interconnected transcriptional and translational feedback loops are at the core of the molecular mechanism of the circadian clock. Such feedback loops are synchronized to external light entrainment by the blue light photoreceptor cryptochrome (CRY) that undergoes conformational changes upon light absorption by an unknown photoexcitation mechanism. Light-induced charge transfer (CT) reactions in CRY (dCRY) are investigated by state-of-the-art simulations that reveal a complex, multi-redox site nature of CT dynamics on the microscopic level.

Field-Induced Tunneling Ionization and Terahertz-Driven Electron Dynamics in Liquid Water.

Liquid water at ambient temperature displays ultrafast molecular motions and concomitant fluctuations of very strong electric fields originating from the dipolar HO molecules. We show that such random intermolecular fields induce the tunnel ionization of water molecules, which becomes irreversible if an external terahertz (THz) pulse imposes an additional directed electric field on the liquid. Time-resolved nonlinear THz spectroscopy maps charge separation, transport, and localization of the released electrons on a few-picosecond time scale.

Change of Hydration Patterns upon RNA Melting Probed by Excitations of Phosphate Backbone Vibrations.

The water hydration shell has a decisive impact on the structural and functional properties of RNA. Changes of the RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process that is barely characterized. To discern hydration geometries around the backbone phosphate groups of an RNA double helix at the molecular level, we combine two-dimensional infrared spectroscopy of phosphate vibrations with theoretical simulations.

Contact Ion Pairs of Phosphate Groups in Water: Two-Dimensional Infrared Spectroscopy of Dimethyl Phosphate and ab Initio Simulations.

The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated ions, and the molecular coupling mechanisms are far from being understood. In a combined experimental and theoretical approach, we address the properties of contact ion pairs of the prototypical system dimethyl phosphate with Na, Ca, and Mg ions in water.

Coupled excitation energy and charge transfer dynamics in reaction centre inspired model systems.

Functional operation conditions of reaction centre core complexes require the tight coupling of exciton states to concomitant charge separation. Rigorous theoretical treatment of such integrated excitation energy transfer (EET) and charge transfer (CT) dynamics is particularly challenging due to (i) appreciable system sizes, (ii) inter-site and system-bath couplings of similar magnitude that render the Born-Markov approximation invalid, (iii) substantial reorganization energies of CT states, and (iv) the presence of complex structured spectral densities due to vibrational modes of the surroundings. We present numerical simulations on bacterial reaction centre (bRC) inspired model systems that utilize the recently developed MACGIC-iQUAPI method [Richter et al.

Hydrated Excess Protons in Acetonitrile/Water Mixtures: Solvation Species and Ultrafast Proton Motions.

The solvation structure of protons in aqueous media is highly relevant to electric properties and to proton transport in liquids and membranes. At ambient temperature, polar liquids display structural fluctuations on femto- to picosecond time scales with a direct impact on proton solvation. We use two-dimensional infrared (2D-IR) spectroscopy to follow proton dynamics in acetonitrile/water mixtures with the Zundel cation HO prepared in neat acetonitrile as a benchmark.

Phosphate-Magnesium Ion Interactions in Water Probed by Ultrafast Two-Dimensional Infrared Spectroscopy.

Electric interactions between ions and ionic molecular groups in aqueous solution play a fundamental role in chemistry and biology. While Mg ions are known to strongly affect the structure and folding dynamics of biomolecules, the relevance of different solvation geometries and the underlying interactions are mainly unresolved. We study dynamics and couplings between the hydrated Mg and the dimethylphosphate anion, an established model system for the DNA and RNA backbone.

Decay Pathways of Thymine Revisited.

The decay of electronically excited states of thymine (Thy) and thymidine 5'-monophosphate (TMP) was studied by time-resolved UV/vis and IR spectroscopy. In addition to the well-established ultrafast internal conversion to the ground state, a so far unidentified UV-induced species is observed. In DO, this species decays with a time constant of 300 ps for thymine and of 1 ns for TMP.

Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study.

The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks.

Simulating Coherent Multidimensional Spectroscopy of Nonadiabatic Molecular Processes: From the Infrared to the X-ray Regime.

Crossings of electronic potential energy surfaces in nuclear configuration space, known as conical intersections, determine the rates and outcomes of a large class of photochemical molecular processes. Much theoretical progress has been made in computing strongly coupled electronic and nuclear motions at different levels, but how to incorporate them in different spectroscopic signals and the approximations involved are less established. This will be the focus of the present review.