Ab initio molecular dynamics simulations of excited hydrogen halides and methyl halides

Using excited-state ab initio molecular dynamics simulations employing the complete-active-space self-consistent-field approach, we study the mechanism of photodissociation in terms of time evolution of structure, kinetic energy, charges and potential energy for the first excited state of hydrogen halides and methyl halides. Although the hydrogen halides and methyl halides are similar in the photodissociation mechanism, their dynamics are slightly different. The presence of the methyl group causes delay in photodissociation as compared to hydrogen halides.

Dissociation Constants of Weak Acids from ab Initio Molecular Dynamics Using Metadynamics: Influence of the Inductive Effect and Hydrogen Bonding on pK(a) Values

The theoretical estimation of the dissociation constant, or pK(a), of weak acids continues to be a challenging field. Here, we show that ab initio CarParrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free-energy profile of the dissociation reaction provide reasonable estimates of the pK(a) value. Water molecules, sufficient to complete the three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid, and the difference in their values provides the estimate for pK(a). We show for a series of organic acids that CPMD simulations in conjunction with metadynamics can provide reasonable estimates of pK(a) values. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cis- and trans-butenedioic acid, and the isomers of hydroxybenzoic acid. These systems were chosen to highlight that the procedure could correctly account for the influence of the inductive effect as well as hydrogen bonding on pK(a) values of weak organic acids. In both situations, the CPMD metadynamics procedure faithfully reproduces the experimentally observed trend and the magnitudes of the pK(a) values.

Estimating successive pK(a) values of polyprotic acids from ab initio molecular dynamics using metadynamics: the dissociation of phthalic acid and its isomers

Estimation of the dissociation constant, or pK(a), of weak acids continues to be a central goal in theoretical chemistry. Here we show that ab initio Car-Parrinello molecular dynamics simulations in conjunction with metadynamics calculations of the free energy profile of the dissociation reaction can provide reasonable estimates of the successive pK(a) values of polyprotic acids. We use the distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic group as the collective variable to explore the free energy profile of the dissociation process. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule, were included explicitly in the computation procedure. Two distinct minima corresponding to the dissociated and un-dissociated states of the acid are observed and the difference in their free energy values provides the estimate for pK(a), the acid dissociation constant. We show that the method predicts the pK(a) value of benzoic acid in good agreement with experiment and then show using phthalic acid (benzene dicarboxylic acid) as a test system that both the first and second pK(a) values as well, as the subtle difference in their values for different isomers can be predicted in reasonable agreement with experimental data.

Ab Initio Molecular Dynamics Simulations of Amino Acids in Aqueous Solutions: Estimating pK(a) Values from Metadynamics Sampling

Changes in the protonation and deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. Here, we report calculations of the free-energy profile for the protonation deprotonation reaction of the 20 canonical alpha amino acids in aqueous solutions using ab initio Car-Parrinello molecular dynamics simulations coupled with metad-ynamics sampling. We show here that the calculated change in free energy of the dissociation reaction provides estimates of the multiple pK(a) values of the amino acids that are in good agreement with experiment. We use the bond-length-dependent number of the protons coordinated to the hydroxyl oxygen of the carboxylic and the amine groups as the collective variables to explore the free-energy profiles of the Bronsted acid-base chemistry of amino acids in aqueous solutions. We ensure that the amino acid undergoing dissociation is solvated by at least three hydrations shells with all water molecules included in the simulations. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pK(a) values with a mean relative error, with respect to experimental results, of 0.2 pK(a) units.

Ab initio molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.

Ab initio Molecular Dynamics Simulations of the Structural Response of Solids to Ultrashort Laser and XUV Pulses

The theoretical model and underlying physics described in this thesis are about the interaction of femtosecond-laser and XUV pulses with solids. The key to understand the basics of such interaction is to study the structural response of the materials after laser interaction. Depending on the laser characteristics, laser-solid interaction can result in a wide range of structural responses such as solid-solid phase transitions, vacuum phonon squeezing, ultrafast melting, generation of coherent phonons, etc. During my research work, I have modeled the systems irradiated by low-, medium- and high-laser intensities, and studied different types of structural dynamics of solids at various laser fluences.

Applying many-body expansion aiming to make ab in initio molecular dynamics more efficient

In this present work we present a methodology that aims to apply the many-body expansion to decrease the computational cost of ab initio molecular dynamics, keeping acceptable accuracy on the results. We implemented this methodology in a program which we called ManBo. In the many-body expansion approach, we partitioned the total energy E of the system in contributions of one body, two bodies, three bodies, etc., until the contribution of the Nth body [1-3]: E = E1 + E2 + E3 + …EN. The E1 term is the sum of the internal energy of the molecules; the term E2 is the energy due to interaction between all pairs of molecules; E3 is the energy due to interaction between all trios of molecules; and so on. In Manbo we chose to truncate the expansion in the contribution of two or three bodies, both for the calculation of the energy and for the calculation of the atomic forces. In order to partially include the many-body interactions neglected when we truncate the expansion, we can include an electrostatic embedding in the electronic structure calculations, instead of considering the monomers, pairs and trios as isolated molecules in space. In simulations we made we chose to simulate water molecules, and use the Gaussian 09 as external program to calculate the atomic forces and energy of the system, as well as reference program for analyzing the accuracy of the results obtained with the ManBo. The results show that the use of the many-body expansion seems to be an interesting approach for reducing the still prohibitive computational cost of ab initio molecular dynamics. The errors introduced on atomic forces in applying such methodology are very small. The inclusion of an embedding electrostatic seems to be a good solution for improving the results with only a small increase in simulation time. As we increase the level of calculation, the simulation time of ManBo tends to largely decrease in relation to a conventional BOMD simulation of Gaussian, due to better scalability of the methodology presented. References [1] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 3, 46 (2007). [2] E. E. Dahlke and D. G. Truhlar; J. Chem. Theory Comput., 4, 1 (2008). [3] R. Rivelino, P. Chaudhuri and S. Canuto; J. Chem. Phys., 118, 10593 (2003).

Insights into the nature of the coupling interactions between uracil corrosion inhibitors and copper : a DFT and molecular dynamics study

In this study, the nature of the coupling interactions between copper and uracil as well as its several derivatives has been systematically investigated employing the atoms in molecules (AIM) theory and energy decomposition analyses. The whole interaction process has been investigated through the analyses of the radial distribution functions of the Cu⋯X (X = S and O) contact on the basis of the ab initio molecular dynamics. No direct relationship between the adsorption strengths and inhibition efficiencies of the inhibitors has been observed. Additionally, the possibility of the methyl-substituted dithiouracil species to act as copper corrosion inhibitors has been tested.

Rational molecular dynamics scheme for predicting optimum concentration loading of nano-additive in phase change materials

The present study deals with the diffusion and phase transition behaviour of paraffin reinforced with carbon nano-additives namely graphene oxide (GO) and surface functionalized single walled carbon nanotubes (SWCNT). Bulk disordered systems of paraffin hydrocarbons impregnated with carbon nano-additives have been generated in realistic equilibrium conformations for potential application as latent heat storage systems. Ab initio molecular dynamics(MD) in conjugation with COMPASS forcefield has been implemented using periodic boundary conditions. The proposed scheme allows determination of optimum nano-additive loading for improving thermo-physical properties through analysis of mass, thermal and transport properties; and assists in determination of composite behaviour and related performance from microscopic point of view. It was observed that nanocomposites containing 7.8% surface functionalised SWCNT and 55% GO loading corresponds to best latent heat storage system. The propounded methodology could serve as a by-pass route for economically taxing and iterative experimental procedures required to attain the optimum composition for best performance. The results also hint at the large unexplored potential of ab-initio classical MD techniques for predicting performance of new nanocomposites for potential phase change material applications. (C) 2015 Author(s).

Elementary steps in aqueous proton transfer reactions : a first principles molecular dynamics study

La nature des acides dans un environnement aqueux est primordiale dans de nombreux aspects de la chimie et de la biologie. La caractéristique principale d'un acide est sa capacité à transférer un proton vers une molécule d'eau ou vers n'importe quelle base, mais ce procédé n'est pas aussi simple qu'il y paraît. Il peut au contraire être extrêmement complexe et dépendre de manière cruciale de la solvatation des différents intermédiaires de réaction impliqués. Cette thèse décrit les études computationnelles basées sur des simulations de dynamique moléculaire ab initio qui ont pour but d'obtenir une description à l'échelle moléculaire des divers procédés de transferts de proton entre acide et bases dans un milieu aqueux. Pour cela, nous avons étudié une serie de système, dont l'acide hydrofluorique aqueux, l'acide trifluoroacétique aqueux, et un système modèle constitué d'un phénol et d'une entité carboxylate reliés entre eux par une molécule d'eau en solution aqueuse. Deux états intermédiaires ont été identifiés pour le transfert d'un proton depuis un acide. Ces intermédiaires apparaissent stabilisés par un motif local de solvatation via des ponts H. Leurs signatures spectroscopiques ont été caractérisées au moyen de la spectroscopie infrarouge, en utilisant le formalisme de la dynamique moléculaire ab initio, qui inclut l'effet quantique nucléaire de manière explicite. Cette étude a aussi identifié trois chemins de réaction élémentaire, qui sont responsable pour le transfert d'un proton d'un acide à une base, ainsi que leurs échelles de temps caractéristiques. Les conclusions tirées de ces études sont discutées dans les détails, au niveau moléculaire, avec une emphase sur les comparaisons entre les résultats théoriques et les mesures expérimentales obtenues dans a littérature ou via des collaborateurs.

Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.

Quantum molecular dynamics and ab initio studies of the crystal structure of hydrogen and deuterium

Hydrogen isotopes play a critical role both in inertial and magnetic confinemen Nuclear Fusion. Since the preferent fuel needed for this technology is a mixture of deuterium and tritium. The study of these isotopes particularly at very low temperatures carries a technological interest in other applications. The present line promotes a deep study on the structural configuration that hydrogen and deuterium adopt at cryogenic temperatures and at high pressures. Typical conditions occurring in present Inertial Fusion target designs. Our approach is aims to determine the crystal structure characteristics, phase transitions and other parameters strongly correlated to variations of temperature and pressure.

Molecular dynamics and simulations study on the vibrational and electronic solvatochromism of benzophenone

Solvent plays a key role in diverse physico-chemical and biological processes. Therefore, understanding solute-solvent interactions at the molecular level of detail is of utmost importance. A comprehensive solvatochromic analysis of benzophenone (Bzp) was carried out in various solvents using Raman and electronic spectroscopy, in conjunction with Density Functional Theory (DFT) calculations of supramolecular solute-solvent clusters generated using classical Molecular Dynamics Simulations (c-MDSs). The >C=O stretching frequency undergoes a bathochromic shift with solvent polarity. Interestingly, in protic solvents this peak appears as a doublet: c-MDS and ad hoc explicit solvent ab initio calculations suggest that the lower and higher frequency peaks are associated with the hydrogen bonded and dangling carbonyl group of Bzp, respectively. Additionally, the dangling carbonyl in methanol (MeOH) solvent is 4 cm(-1) blue-shifted relative to acetonitrile solvent, despite their similar dipolarity/polarizability. This suggests that the cybotactic region of the dangling carbonyl group in MeOH is very different from its bulk solvent structure. Therefore, we propose that this blue-shift of the dangling carbonyl originates in the hydrophobic solvation shell around it resulting from extended hydrogen bonding network of the protic solvents. Furthermore, the 1(1)n pi* (band I) and 1(1)pi pi* (band II) electronic transitions show a hypsochromic and bathochromic shift, respectively. In particular, these shifts in protic solvents are due to differences in their excited state-hydrogen bonding mechanisms. Additionally, a linear relationship is obtained for band I and the >C=O stretching frequency (cm(-1)), which suggests that the different excitation wavelengths in band I correspond to different solvation states. Therefore, we hypothesize that the variation in excitation wavelengths in band I could arise from different solvation states leading to varying solvation dynamics. This will have implications for ultrafast processes associated with electron-transfer, charge transfer, and also the photophysical aspects of excited states. (C) 2016 AIP Publishing LLC.

Molecular dynamics simulation of hydrogen enhancing dislocation emission

The interactive pair potential between Al and H is obtained based on the ab initio calculation and the Chen-Mobius 3D lattice inversion formula. By utilizing the pair potentials calculated, the effects of hydrogen on the dislocation emission from crack tip have been studied. The simulated result shows that hydrogen can reduce the cohesive strength for Al single crystal, and then the critical stress intensity factor for partial dislocation emission decreases from 0.11 MPa root m (C-H = 0) to 0.075 MPa root m (C-H=0.72%) and 0.06 MPa root m (C-H = 1.44%). This indicates thar hydrogen can enhance the dislocation emission. The simulation also shows that atoms of hydrogen can gather and turn into small bubbles, resulting in enhancement of the equilibrium vacancy concentration.