We investigated rearrangements of the hydrogen-bond network in water by measuring fluctuations in the OH-stretching frequency of HOD in liquid D2O with femtosecond infrared spectroscopy. Using simulations of an atomistic model of water, we relate these frequency fluctuations to intermolecular dynamics. The model reveals that OH frequency shifts arise from changes in the molecular electric field that acts on the proton. At short times, vibrational dephasing reflects an underdamped oscillation of the hydrogen bond with a period of 170 femtoseconds. At longer times, vibrational correlations decay on a 1.2-picosecond time scale because of collective structural reorganizations.

Although it is widely accepted that the local structure of liquid water has tetrahedral arrangements of molecules ordered by hydrogen bonds, the mechanism by which water molecules switch hydrogen-bonded partners remains unclear. In this mechanism, the role of nonhydrogen-bonded configurations (NHBs) between adjacent molecules is of particular importance. A molecule may switch hydrogen-bonding partners either (i) through thermally activated breaking of a hydrogen bond that creates a dangling hydrogen bond before finding a new partner or (ii) by infrequent but rapid switching events in which the NHB is a transition state. Here, we report a combination of femtosecond 2D IR spectroscopy and molecular dynamics simulations to investigate the stability of NHB species in an isotopically dilute mixture of HOD in D 2O. Measured 2D IR spectra reveal that hydrogen-bonded configurations and NHBs undergo qualitatively different relaxation dynamics, with NHBs returning to hydrogen-bonded frequencies on the time scale of water's fastest intermolecular motions. Simulations of an atomistic model for the OH vibrational spectroscopy of water yield qualitatively similar 2D IR spectra to those measured experimentally. Analysis of NHBs in simulations by quenching demonstrates that the vast majority of NHBs are in fact part of a hydrogen-bonded well of attraction and that virtually all molecules return to a hydrogen-bonding partner within 200 fs. The results from experiment and simulation demonstrate that NHBs are intrinsically unstable and that dangling hydrogen bonds are an insignificant species in liquid water.femtosecond 2D IR spectroscopy ͉ molecular dynamics ͉ liquids O n average, molecules in liquid water are tetrahedrally coordinated but appear to engage in 10% fewer hydrogen bonds than in ice. Support for this estimate comes broadly, from latent heats of melting and vaporization, from x-ray and neutron scattering, and in very detailed form from molecular dynamics (MD) simulations (1-3). The role of nonhydrogen-bonded configurations (NHBs) in water's rapidly changing structure remains uncertain, lying at the heart of differences between mixture and continuum models of water (1, 3-8). Implicitly or explicitly, the interpretation of many experiments and MD simulations conceives of NHBs as broken or dangling hydrogen bonds, stable species that interconvert with a hydrogen-bonded configuration (HB) at a rate determined by the free energy barrier separating them. But it is also possible that NHBs are intrinsically unstable species that appear transiently during natural fluctuations about a hydrogen bond or when molecules trade hydrogen-bonding partners. These two scenarios not only provide qualitatively different interpretations of water's structure and how it evolves, but also imply different pictures for how water mediates chemical and biological processes. We have distinguished between these scenarios by using a combination of femtosecond 2D IR spectroscopy and MD simulations, finding that NHBs are inherently unstable, reforming ...

We present an investigation into hydrogen bonding dynamics and kinetics in water using femtosecond infrared spectroscopy of the OH stretching vibration of HOD in D(2)O. Infrared vibrational echo peak shift and polarization-selective pump-probe experiments were performed with mid-IR pulses short enough to capture all relevant dynamical processes. The experiments are self-consistently analyzed with a nonlinear response function expressed in terms of three dynamical parameters for the OH stretching vibration: the frequency correlation function, the lifetime, and the second Legendre polynomial dipole reorientation correlation function. It also accounts for vibrational-relaxation-induced excitation of intermolecular motion that appears as heating. The long time, picosecond behavior is consistent with previous work, but new dynamics are revealed on the sub-200 fs time scale. The frequency correlation function is characterized by a 50 fs decay and 180 fs beat associated with underdamped intermolecular vibrations of hydrogen bonding partners prior to 1.4 ps exponential relaxation. The reorientational correlation function observes a 50 fs librational decay prior to 3 ps diffusive reorientation. Both of these correlation functions compare favorably with the predictions from classical molecular dynamics simulations. The time-dependent behavior can be separated into short and long time scales by the 340 fs correlation time for OH frequency shifts. The fast time scales arise from dynamics that are mainly local: fluctuations in hydrogen bond distances and angles within relatively fixed intermolecular configurations. On time scales longer than the correlation time, dephasing and reorientations reflect collective reorganization of the liquid structure. Since the OH transition frequency and dipole are only weakly sensitive to these collective coordinates, this is a kinetic regime which gives an effective rate for exchange of intermolecular structures.

The parABS system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. ParB binds to parS sites on plasmids and chromosomes and associates with broad regions of adjacent DNA, a phenomenon known as spreading. Although essential for ParB function, the mechanism of spreading remains poorly understood. Using single-molecule approaches, we discovered that Bacillus subtilis ParB (Spo0J) is able to trap DNA loops. Point mutants in Spo0J that disrupt DNA bridging are defective in spreading and recruitment of structural maintenance of chromosomes (SMC) condensin complexes in vivo. DNA bridging helps to explain how a limited number of Spo0J molecules per parS site (~20) can spread over many kilobases and suggests a mechanism by which ParB proteins could facilitate the loading of SMC complexes. We show that DNA bridging is a property of diverse ParB homologs, suggesting broad evolutionary conservation.

The analysis of line shapes in two-dimensional optical and infrared spectroscopies is a powerful approach to characterizing the dynamics of molecules in the condensed phase. Changes in line shape from diagonally elongated to symmetric as a function of waiting time arise from evolution of the transition frequency. We describe a number of quantitative measures of frequency fluctuations and spectral diffusion through the analysis of two-dimensional (2D) line shapes. These metrics are identical to the system's frequency correlation function and independent of population relaxation in the limit of a short time approximation for the 2D response. We also test the broader applicability of these expressions for analyzing three-level vibrational systems and experiments with finite pulses.