Polar nanoregions in water: A study of the dielectric properties of TIP4P/2005, TIP4P/2005f and TTM3F

Elton, Daniel C.; Fernández-Serra, M.-V.

doi:10.1063/1.4869110

Cited by 44 publications

(44 citation statements)

References 102 publications

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“…Despite the fact that the employed number of lipids is quite common in membrane simulations, balancing between accuracy and efficiency of simulated properties 62 , we have embedded the major LHCII (spinach) with all pigments (Chls, Cars) in a larger membrane patch that includes between 480–490 united-atom UA-POPC lipids 63, 64 , along with around 22200 TIP4P waters (Fig. 3a,b) 65 . This raised the number of simulated atoms roughly 3-fold, to 120000.…”

Section: Resultsmentioning

confidence: 99%

A pathway for protective quenching in antenna proteins of Photosystem II

Papadatos

Charalambous

Daskalakis

2017

Sci Rep

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Photosynthesis is common in nature, converting sunlight energy into proton motive force and reducing power. The increased spectral range absorption of light exerted by pigments (i.e. chlorophylls, Chls) within Light Harvesting Complexes (LHCs) proves an important advantage under low light conditions. However, in the exposure to excess light, oxidative damages and ultimately cell death can occur. A down-regulatory mechanism, thus, has been evolved (non-photochemical quenching, NPQ). The mechanistic details of its major component (qE) are missing at the atomic scale. The research herein, initiates on solid evidence from the current NPQ state of the art, and reveals a detailed atomistic view by large scale Molecular Dynamics, Metadynamics and ab initio Simulations. The results demonstrate a complete picture of an elaborate common molecular design. All probed antenna proteins (major LHCII from spinach-pea, CP29 from spinach) show striking plasticity in helix-D, under NPQ conditions. This induces changes in Qy bands in excitation and absorption spectra of the near-by pigment pair (Chl613-614) that could emerge as a new quenching site. Zeaxanthin enhances this plasticity (and possibly the quenching) even at milder NPQ conditions.

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Section: Resultsmentioning

confidence: 99%

A pathway for protective quenching in antenna proteins of Photosystem II

Papadatos

Charalambous

Daskalakis

2017

Sci Rep

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“…4,5 The decay of F(r) at distances >1 nm (see the inset in Figure 1) indicates that a cell of (∼4 nm) 3 is required to recover a bulk region where the dipole moments of water molecules are uncorrelated (see also Figure S2 of the SI of Ref. 4).…”

Section: Resultsmentioning

confidence: 99%

“…Understanding dipolar correlations in liquid water [1][2][3][4][5] is of interest to several fields of water science, encompassing aqueous solvation, [6][7][8][9][10] spectroscopy of water at surfaces and interfaces, 11,12 and the phase diagram of water, including the possible coexistence of two liquids. [13][14][15][16] Recently, we showed how dipolar fluctuations are modified by the presence of surfaces in liquid water up to strikingly large distances, i.e., tens of nanometers, giving rise to strong anisotropies in the components of the dielectric relaxation.…”

Section: Introductionmentioning

confidence: 99%

Dipolar correlations in liquid water

Zhang

Galli

2014

The Journal of Chemical Physics

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We present an analysis of the dipolar correlations in water as a function of temperature and density and in the presence of simple ionic solutes, carried out using molecular dynamics simulations and empirical potentials. We show that the dipole-dipole correlation function of the liquid exhibits sizable oscillations over nanodomains of about 1.5 nm radius, with several isosbestic points as a function of temperature; the size of the nanodomains is nearly independent on temperature and density, between 240 and 400 K and 0.9 and 1.3 g/cm(3), but it is substantially affected by the presence of solvated ions. In the same range of thermodynamic conditions, the decay time (τ) of the system dipole moment varies by a factor of about 30 and 1.5, as a function of temperature and density, respectively. At 300 K, we observed a maximum in τ as a function of density, and a corresponding shallow maximum in the tetrahedral order parameter, in a range where the diffusion coefficient, the pressure and the dielectric constant increase monotonically.

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“…23,53 This idea is inconsistent with classical molecular dynamics simulations, which can satisfactorily reproduce the dielectric response of water, even though they do not contain charged defects. 54,55 Furthermore, Popov et al note that the dielectric relaxation does not depend on pH, as it would in Artemov & Volkov's model. 7 Popov et al propose Debye relaxation is due entirely to Bjerrumlike defects, which carry an effective charge.…”

Section: Propagation Of Defectsmentioning

confidence: 91%

The origin of the Debye relaxation in liquid water and fitting the high frequency excess response

Elton

2017

Phys. Chem. Chem. Phys.

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We critically review the literature on the Debye absorption peak of liquid water and the excess response found on the high frequency side of the Debye peak. We find a lack of agreement on the microscopic phenomena underlying both of these features. To better understand the molecular origin of Debye peak we ran large scale molecular dynamics simulations and performed several different distance-dependent decompositions of the low frequency dielectric spectra, finding that it involves processes that take place on scales of 1.5-2.0 nm. We also calculated the k-dependence of the Debye relaxation, finding it to be highly dispersive. These findings are inconsistent with models that relate Debye relaxation to local processes such as the rotation/translation of molecules after H-bond breaking. We introduce the spectrumfitter Python package for fitting dielectric spectra and analyze different ways of fitting the high frequency excess, such as including one or two additional Debye peaks. We propose using the generalized Lydanne-Sachs-Teller (gLST) equation as a way of testing the physicality of model dielectric functions. Our attempts at fitting the experimental spectrum using the gLST relation as a constraint indicate that the traditional way of fitting the excess response with secondary and tertiary Debye relaxations is problematic. All of our work is consistent with the recent theory of Popov et al. (2016) that Debye relaxation is due to the migration of Bjerrum-like defects in the hydrogen bond network. Under this theory, the mechanism of Debye relaxation in liquid water is similar to the mechanism in ice, but the heterogeneity and power-law dynamics of the H-bond network in water results in excess response on the high frequency side of the peak.

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Polar nanoregions in water: A study of the dielectric properties of TIP4P/2005, TIP4P/2005f and TTM3F

Cited by 44 publications

References 102 publications

A pathway for protective quenching in antenna proteins of Photosystem II

A pathway for protective quenching in antenna proteins of Photosystem II

Dipolar correlations in liquid water

The origin of the Debye relaxation in liquid water and fitting the high frequency excess response

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