Molecular dynamics at water interfaces: from astrophysical to biochemical applications

This PhD thesis investgates the chemical and physical interactions between water and systems of different sizes. The first section illustrates the chemical context of the projects and methodological basis used. The second part studies the dynamics and reactivity of small systems of astrochemical interest on top of water ice, at each step the complexity of the model is increased. Initially the ice surface is characterized, then different aspects of the reaction are examined. The final part explores the interactions between water molecules and two different proteins, to understand water’s role as solvent and how it influences protein macromolecule dynamics. The appendix includes a discussion on the interatomic interaction of water and the contribution apported in CHARMM software package are presented

Genesis of Polyatomic Molecules in Dark Clouds: CO2_2 Formation on Cold Amorphous Solid Water

Understanding the formation of molecules under conditions relevant to interstellar chemistry is fundamental to characterize the chemical evolution of the universe. Using reactive molecular dynamics simulations with model-based or high-quality potential energy surfaces provides a means to specifically and quantitatively probe individual reaction channels at a molecular level. The formation of CO$_2$ from collision of CO($^1 \Sigma$) and O($^1$D) is characterized on amorphous solid water (ASW) under conditions typical in cold molecular clouds. Recombination takes place on the sub-nanosecond time scale and internal energy redistribution leads to stabilization of the product with CO$_2$ remaining adsorbed on the ASW on extended time scales. Using a high-level, reproducing kernel-based potential energy surface for CO$_2$, formation into and stabilization of CO$_2$ and COO is observed.Comment: 33 pages, 13 figure

Polarizable Multipolar Molecular Dynamics Using Distributed Point Charges

Distributed point charge models (DCM) and their minimal variants (MDCM) have been integrated with tools widely used for condensed-phase simulations, including a virial-based barostat and a slow-growth algorithm for thermodynamic integration. Minimal DCM is further developed with a systematic approach to reduce fitting errors in the electrostatic interaction energy and a new fragment-based approach offers considerable speedup of the MDCM fitting process for larger molecules with increased numbers of off-centered charged sites. Finally, polarizable (M)DCM is also introduced in the present work. The developments are used in condensed-phase simulations of popular force fields with commonly applied simulation conditions. (M)DCM equivalents for a range of widely used water force fields and for fluorobenzene (PhF) are developed and applied along with the original models to evaluate the impact of reformulating the electrostatic term. Comparisons of the molecular electrostatic potential (MEP), electrostatic interaction energies, and bulk properties from molecular dynamics simulations for a range of models from simple TIP$n$P ($n = 3-5$) to the polarizable, multipolar iAMOEBA models for water and an existing quadrupolar model for PhF confirm that DCMs retain the accuracy of the original models, providing a homogeneous, efficient, and generic point charge alternative to a multipolar electrostatic model for force field development and multilevel simulations.Comment: 84 pages, 12 figures, journal articl

O-2 formation in cold environments

The diffusional dynamics of atomic oxygen in and on amorphous solid water (ASW) to form molecular oxygen is characterized. Reactive molecular dynamics simulations to study bond breaking and bond formation show that vibrational relaxation of the highly excited diatomic occurs on the 10 ns to 100 ns time scale. The relaxation process is highly nonexponential and can be characterized by a stretched exponential decay reminiscent of the dynamics of glasses. The stretched exponents range from = 0.15 for relaxation on the surface to = 0.21 for the dynamics in bulk. It is also found that coupling of the O-2 relaxation to the internal water modes occurs which speeds up the vibrational relaxation by a factor of 4. Extrapolation of the stretched exponential decay to 1 s yields a final vibrational quantum number v = 2 for O-2(X-3 sigma-g), consistent with experimental results from photolysis of SO2 on ASW at 193 nm which find v 3. Desorption energies of water from the surface range from 1.5 to 2.0 kcal mol(-1) compared with 1.8 kcal mol(-1) found from experiment, depending on whether the water molecules are flexible or not

Data structures for photoadsorption within the ExoMol project

The ExoMol data base currently provides comprehensive line lists for modelling the spectroscopic properties of molecules in hot atmospheres. Extending the spectral range of the data provided to ultraviolet (UV) wavelengths brings into play three processes not currently accounted for in the ExoMol data structure, namely photodissociation, which is an important chemical process in its own right, the opacity contribution due to continuum absorption, and predissociation which can lead to significant and observable line-broadening effects. Data structures are proposed which will allow these processes to be correctly captured and the (strong) temperature-dependent effects predicted for UV molecular photoabsorption in general and photodissociation in particular to be represented

Development of the Italian Version of the National Institutes of Health Stroke Scale It-NIHSS

Background and Purpose-The National Institutes of Health Stroke Scale (NIHSS) is a basic component of the assessment of patients with acute stroke. To foster and standardize the use of the NIHSS among Italian health professionals, we translated the scale, dubbed into Italian the training and test videotapes devised by the National Institutes of Health researchers, and conducted a series of certification courses using the translated videos. Methods-Translation, text adaptation, video dubbing, and editing of the Italian NIHSS videotapes relied on a team of bilingual stroke neurologists. Three waves of training courses were organized for mixed classes of medical and nonmedical health professionals. The certification test was based on the usual set of 5 videotaped patients. Scoring rules were those provided by the National Institutes of Neurological Disorders and Stroke. Reliability of the Italian NIHSS was assessed using kappa statistics and compared with that of the original NIHSS. Results-During 3 years, 850 nurses, 460 nonneurologist physicians, and 246 neurologists were trained. Pass rates were respectively 44%, 75%, and 87%, respectively. Overall, 80% of scale items showed moderate to excellent reliability. Independent significant predictors of test failure at multivariate logistic regression were nurse profession (OR, 5.41; 95% CI, 4.07 to 7.20), older age (OR, 1.03; 95% CI, 1.02 to 1.05), and first edition of the course (OR, 3.13; 95% CI, 2.43 to 4.05). The agreement across all items between NIHSS and the Italian NIHSS was 80% (kappa = 0.70 +/- 0.18, z < 0.001). Conclusions-The Italian translation, supervised by experienced vascular neurologists, did not influence the clinimetric characteristics of the NIHSS. Our findings support the implementation of NIHSS video training in languages other than English. (Stroke. 2009; 40: 2557-2559.

The interplay of chemical structure, physical properties, and structural design as a tool to modulate the properties of melanins within mesopores

The design of modern devices that can fulfil the requirements for sustainability and renewable energy applications calls for both new materials and a better understanding of the mixing of existing materials. Among those, surely organic–inorganic hybrids are gaining increasing attention due to the wide possibility to tailor their properties by accurate structural design and materials choice. In this work, we’ll describe the tight interplay between porous Si and two melanic polymers permeating the pores. Melanins are a class of biopolymers, known to cause pigmentation in many living species, that shows very interesting potential applications in a wide variety of fields. Given the complexity of the polymerization process beyond the formation and structure, the full understanding of the melanins’ properties remains a challenging task. In this study, the use of a melanin/porous Si hybrid as a tool to characterize the polymer’s properties within mesopores gives new insights into the conduction mechanisms of melanins. We demonstrate the dramatic effect induced on these mechanisms in a confined environment by the presence of a thick interface. In previous studies, we already showed that the interactions at the interface between porous Si and eumelanin play a key role in determining the final properties of composite materials. Here, thanks to a careful monitoring of the photoconductivity properties of porous Si filled with melanins obtained by ammonia-induced solid-state polymerization (AISSP) of 5,6-dihydroxyindole (DHI) or 1,8-dihydroxynaphthalene (DHN), we investigate the effect of wet, dry, and vacuum cycles of storage from the freshly prepared samples to months-old samples. A computational study on the mobility of water molecules within a melanin polymer is also presented to complete the understanding of the experimental data. Our results demonstrate that: (a) the hydration-dependent behavior of melanins is recovered in large pores (≈ 60 nm diameter) while is almost absent in thinner pores (≈ 20 nm diameter); (b) DHN-melanin materials can generate higher photocurrents and proved to be stable for several weeks and more sensitive to the wet/dry variations

Anomalous evolution of broadband optical absorption reveals dynamic solid state reorganization during eumelanin build-up in thin films

The origin of eumelanin optical properties remains a formidable conundrum preventing a detailed understanding of the complex photo-protective role of these widespread natural pigments and the rational design of innovative bioinspired materials for optoelectronic applications. Here we report the unusual kinetic and thickness-dependent evolution of the optical properties of black eumelanin polymers generated by spontaneous aerial polymerization of 5,6-dihydroxyindole (DHI) thin films (0.1-1 μm), consistent with peculiar solid state reorganization mechanisms governing broadband absorption. The complete reversal of eumelanin UV-visible transmittance spectrum curvature on passing from 0.2 to 0.5 μm thick films, the marked increase in visible extinction coefficients with increasing film thickness and the higher UV extinction coefficients in slowly vs. rapidly generated polymers concur to support distinct dynamic regimes of solid-state molecular reorganization at the nanoscale level and to do affect the development of broadband visible absorption. Solid state control of molecular reorganization disclosed herein may delineate new rational strategies for tuning optical properties in eumelanin thin films for optoelectronic applications

Water Dynamics Around Proteins: T- and R-States of Hemoglobin and Melittin

The water dynamics, as characterized by the local hydrophobicity (LH), is investigated for tetrameric hemoglobin and dimeric melittin. For the T0 to R0 transition in Hb it is found that LH provides additional molecular-level insight into the Perutz mechanism, i.e., the breaking and formation of salt bridges at the alpha1 / beta2 and alpha2 / beta1 interface is accompanied by changes in LH. For Hb in cubic water boxes with 90 Aengstroem and 120 Aengstroem edge length it is observed that following a decrease in LH as a consequence of reduced water density or change of water orientation at the protein/water interface the alpha / beta interfaces are destabilized; this is a hallmark of the Perutz stereochemical model for the T to R transition in Hb. The present work thus provides a dynamical view of the classical structural model relevant to the molecular foundations of Hb function. For dimeric melittin, earlier results by Cheng and Rossky (Nature, 1998, 392, 696-699) are confirmed and interpreted on the basis of LH from simulations in which the protein structure is frozen. For the flexible melittin dimer the changes in the local hydration can be as much as 30 % than for the rigid dimer, reflecting the fact that protein and water dynamics are coupled

ExoMol line lists – L: high-resolution line lists of H3+, H2D+, D2H+, and D3+

New MiZo line lists are presented for the D2H+ and D$_3^+$ isotopologues of H$_3^+$. These line lists plus the existing H$_3^+$ MiZATeP and the Sochi H2D+ line lists are updated using empirical energy levels generated using the MARVEL procedure for H$_3^+$, H2D+ and D2H+, and effective Hamiltonian energies for D$_3^+$ for which there is significantly less laboratory data available. These updates allow accurate frequencies for far infrared lines for these species to be predicted. Assignments of the energy levels of H$_3^+$ and D$_3^+$ are extended using a combination of high accuracy variational calculations and analysis of transition intensities. All line lists are made available via www.exomol.com