Hugo F. M. C. Martiniano

Insights on Hydrogen-Bond Lifetimes in Liquid and Supercooled Water

We study the temperature dependence of the lifetime of geometric and geometric/energetic water hydrogen-bonds (H-bonds), down to supercooled water, through molecular dynamics. The probability and lifetime of H-bonds that break either by translational or librational motions and those of energetic broken H-bonds, along with the effects of transient broken H-bonds and transient H-bonds, are considered. We show that the fraction of transiently broken energetic H-bonds increases at low temperatures and that this energetic breakdown is caused by oxygen-oxygen electrostatic repulsions upon too small amplitude librations to disrupt geometric H-bonds. Hence, differences between geometric and energetic continuous H-bond lifetimes are associated with large H-bond energy fluctuations, in opposition to moderate geometric fluctuations, within common energetic and geometric H-bond definition thresholds. Exclusion of transient broken H-bonds and transient H-bonds leads to H-bond definition-independent mean lifetimes and activation energies, ~11 kJ/mol, consistent with the reactive flux method and experimental scattering results. Further, we show that power law decay of specific temporal H-bond lifetime probability distributions is associated with librational and translational motions that occur on the time scale (~0.1 ps) of H-bond breaking /re-forming dynamics. While our analysis is diffusion-free, the effect of diffusion on H-bond probability distributions where H-bonds are allowed to break and re-form, switching acceptors in between, is shown to result in neither exponential nor power law decay, similar to the reactive flux correlation function.

Ab initio calculation of the electronic absorption spectrum of liquid water

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O-H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

ELECTRONIC PROPERTIES OF HYDROGEN BOND NETWORKS: IMPLICATIONS FOR SOLVENT EFFECTS IN POLAR LIQUIDS

The electronic properties of polar liquids where the structures are characterized by hydrogen bond networks are reviewed. Emphasis is placed on theoretical predictions of liquid state electronic properties such as the electric dipole moment, electron binding energies, and electronic density of states. A discussion on the relationship between the structure of the hydrogen bond (HB) network and the electronic properties of water is presented. Born–Oppenheimer molecular dynamics results for proton transfer (PT) in ionized phenol–water clusters illustrate the link between charge fluctuations of the HB network and the PT dynamics

A biobjective feature selection algorithm for large omics datasets

This work used the EGI, European Grid Infrastructure, with the support of the IBERGRID, Iberian Grid Infrastructure, and INCD (Portugal); NCG‐INGRID‐PT; FCT, Grant/Award Number: UID/Multi/04046/2013

A Feature Selection Algorithm Based on Heuristic Decomposition

Feature selection is one of the most important concepts in data mining when dimensionality reduction is needed. The performance measures of feature selection encompass predictive accuracy and result comprehensibility. Consistency based feature selection is a significant category of feature selection research that substantially improves the comprehensibility of the result using the parsimony principle. In this work, the feature selection algorithm LAID, Logical Analysis of Inconsistent Data, is applied to large volumes of data. In order to deal with hundreds of thousands of attributes, a problem de-composition strategy associated with a set covering problem formulation is used. The algorithm is applied to artificial datasets with genome-like characteristics of patients with rare diseases.

Fast and slow dynamics and the local structure of liquid and supercooled water next to a hydrophobic amino acid.

We study, through molecular dynamics simulations, the structure and orientational dynamics of water next to a blocked hydrophobic amino acid, valine (Val), above and below the freezing point of water. The structure and the orientational dynamics of waters with four water neighbors (4WN) and less than four water neighbors (L4WN) in the Vals coordination sphere are deconvoluted. We find that in spite of the excluded volume effects waters with L4WN have faster librational dynamics than bulk water, reminiscent of water at the liquid-vapor interface, and faster orientational dynamics than waters with 4WN, at every temperature. Furthermore, our results show that the pronounced decrease of the orientational retardation factor below ∼255 K observed experimentally is mostly caused by the acceleration of the orientational dynamics of waters with L4WN, while waters with 4WN exhibit only moderate acceleration. The differences between the hydrogen-bond acceptor switching mechanism in the shell and the bulk are also analyzed, and no evidence of especially slow OH groups neither in the 4WN nor in the L4WN populations is found. Finally, we show that waters with 4WN have higher tetrahedrality than bulk water at every temperature although this difference decreases at both high and low temperatures.