Temperature Profiles and Heat Fluxes Observed in Molecular Dynamics Simulations of Force-Driven Liquid Flows

Physical Chemistry Chemical Physics
This paper concentrates on the unconventional temperature profiles and heat fluxes observed in non-equilibrium molecular dynamics (MD) simulations of force-driven liquid flows in nano-channels. Using MD simulations of liquid argon flows in gold nano-channels, we investigate manifestation of the first law of thermodynamics for the MD system, and compare it with that of the continuum fluid mechanics. While the energy equation for the continuum system results in heat conduction determined by viscous heating, the first law of thermodynamics in the MD system includes an additional slip-heating term. Interaction strength between argon and gold molecules are varied in order to investigate the effects of slip-velocity on the slip-heating term and the resulting temperature profiles. Heat fluxes and temperature profiles from “continuum”, “continuum augmented with slip-heating”, and “heat conduction due to power input by the driving force” are modeled and compared with the MD...  Read more

Atomistic non-adiabatic dynamics of the LH2 complex with a GPU-accelerated ab initio exciton model

Physical Chemistry Chemical Physics
We recently outlined an efficient multi-tiered parallel ab initio excitonic framework that utilizes time dependent density functional theory (TDDFT) to calculate ground and excited state energies and gradients of large supramolecular complexes in atomistic detail – enabling us to undertake non-adiabatic simulations which explicitly account for the coupled anharmonic vibrational motion of all the constituent atoms in a supramolecular system. Here we apply that framework to the 27 coupled bacterio-cholorophyll-a chromophores which make up the LH2 complex, using it to compute an on-the-fly nonadiabatic surface-hopping (SH) trajectory of electronically excited LH2. Part one of this article is focussed on calibrating our ab initio exciton Hamiltonian using two key parameters: a shift δ, which corrects for the error in TDDFT vertical excitation energies; and an effective dielectric constant ε, which describes the average screening of the transition-dipole coupling between chromophores....  Read more

Sodium – Carboxylate Contact Ion Pair Formation Induces Stabilization of Palmitic Acid Monolayers at High pH

Physical Chemistry Chemical Physics
Sea spray aerosols (SSA) are known to have an organic coating that is mainly composed of fatty acids. In this study, the effect of pH and salt on the stability and organization of a palmitic acid (PA) monolayer is investigated by surface vibrational spectroscopy and molecular dynamics simulations. Results indicate that alkyl chain packing becomes more disordered as the carboxylic headgroup becomes deprotonated. This is associated with packing mismatch of charged and neutral species as charged headgroups penetrate deeper into the solution phase. At pH 10.7, when the monolayer is ~99% deprotonated,, palmitate (PA–) molecules desorb and solubilize into the bulk solution where there is spectroscopic evidence for aggregate formation. Yet, addition of 100 mM NaCl to the bulk solution is found to drive PA– molecules to the aqueous surface. Free energy calculations show that PA– molecules become stabilized within the interface with increasing NaCl concentration. Formation of contact...  Read more

Buckling behaviour of composites with double wall nanotubes from carbon and phosphorous

Physical Chemistry Chemical Physics
Due to weak interaction among phosphorus atoms in black phosphorene, the nanotube obtained by curling single-layer black phosphorus is not as stable as a carbon nanotube (CNT) at finite temperature. In the present work, we recommend a new 1D composite material with a double-wall nanotube (DWNT) from a black phosphorus nanotube (BPNT) and a CNT. The dynamic response of the composite DWNTs is simulated using molecular dynamics approach. Effects of factors including temperature, slenderness and configurations of DWNTs on dynamic behavior of the composite are discussed. Comparing with a single-wall BPNT, the composite DWNTs under uniaxial compression shows some unique properties. When the BPNT is embedded in a CNT which will not only isolate BPNT from the ambient condition, but also improve the capability of axial deformation of BPNT, the system will not collapse rapidly even if the BPNT has been buckled.Read more

Kinetics of the Crystalline Nuclei Growth in Glassy Systems

Physical Chemistry Chemical Physics
In this work, we study the crystalline nuclei growth in glassy systems focusing primarily on the early stages of the process, at which the size of a growing nucleus is still comparable with the critical size. On the basis of molecular dynamics simulation results for two crystallizing glassy systems, we evaluate the growth laws of the crystalline nuclei and the parameters of the growth kinetics at the temperatures corresponding to deep supercoolings; herein, the statistical treatment of the simulation results is done within the mean-first-passage-time method. It is found for the considered systems at different temperatures that the crystal growth laws rescaled onto the waiting times of the critically-sized nucleus follow the unified dependence, that can simplify significantly theoretical description of the post-nucleation growth of crystalline nuclei. The evaluated size-dependent growth rates are characterized by transition to the steady-state growth regime, which depends on the...  Read more

Protic Ammonium Carboxylate Ionic Liquids: Insight into Structure, Dynamics and Thermophysical Properties by Alkyl Group Functionalization

Physical Chemistry Chemical Physics
This study is aimed at characterising the structure, dynamics and thermophysical properties of five alkylammonium carboxylate ionic liquids (ILs) from classical molecular dynamics simulations. The structural features of these ILs were characterised by calculating the site–site radial distribution functions, g(r), spatial distribution functions and structure factors. The structural properties demonstrate that ILs show greater interaction between cations and anions when alkyl chain length increases on the cation or anion. In all ILs, spatial distribution functions show that the anion is close to the acidic hydrogen atoms of the ammonium cation. We determined the role of alkyl group functionalization of both the charged entities, cations and anions, on the dynamical behavior and the transport coefficients of this family of ionic liquids. The dynamics of ILs are described by studying the mean square displacement (MSD) of the centres of mass of the ions, diffusion coefficients, ionic...  Read more

Production of doubly-charged highly reactive species from the long-chain amino acid GABA initiated by Ar9+ ionization

Physical Chemistry Chemical Physics
We present a combined experimental and theoretical study of the fragmentation of multiply- charged γ-aminobutyric acid molecules (GABAz+, z = 2,3) in the gas phase. The combination of ab initio molecular dynamics simulations with multiple-coincidence mass spectrometry techniques allows us to observe and identify doubly-charged fragments in coincidence with another charged moiety. The present results indicate that double and triple electron capture lead to the formation of doubly-charged reactive nitrogen and oxygen species (RNS and ROS) with different probability due to the different charge localisation and fragmentation behaviour of GABA2+ and GABA3+. The MD simulations unravel the fast (femtosecond) formation of large doubly charged species, observed in the experimental microsecond timescale. The excess of positive charge is stabilised by the presence of cyclic X −member (X = 3 − 5) ring structures....  Read more

Structural and Dynamical instability of DNA by high occurrence of d5SICS and dNaM unnatural nucleotides

Physical Chemistry Chemical Physics
In vivo inclusion of unnatural base pairs (UBPs) into functional DNA was recently reported for compounds 2,6-dimethyl-2H-isoquiniline-1-thione (d5SICS, X) and 2-methoxy-3-methylnaphthalene (dNaM, Y) in a modified E. coli strand, for which high fidelity replication was observed. Yet, little is known about possible genetic consequences they have in largely substituted DNA. Using a converged microsecond long molecular dynamics (MD) simulation of the sequences 5’-GCGCAAXTTGCGC-3’ and 5’-GCGCXAXTXGCGC-3’, where X represents the UBP, we show that in the system with only a single XY UBP pair present, the global RMS deviation from canonical B-DNA in our control simulations is ~3 Å and a fully converged ensemble is achieved within 2 µs. With three UBPs, deviation increases to ~5 Å and convergence is not achieved within 10 µs of sampling time. With five UBPs no convergence is observed and the double helix collapses into a globular structure. A fully optimized structure of the trimer...  Read more

Delineating the role of ripples on thermal expansion of 2D honeycomb materials: graphene, 2D h-BN and monolayer (ML)-MoS2

Physical Chemistry Chemical Physics
We delineated the role of thermally excited ripples on thermal expansion properties of 2D honeycomb materials (free-standing graphene, 2D h-BN, and ML-MoS2), by explicitly carrying out three-dimensional (3D) and two-dimensional (2D) molecular dynamics simulations. In 3D simulations, the in-plane lattice parameter (a-lattice) of graphene and 2D h-BN shows thermal contraction over a wide range of temperatures and exhibits a strong system size dependence. The 2D simulations of the very same system show a reverse trend, where the a-lattice is expanding in the whole computed temperature range. Contrary to graphene and 2D h-BN, the a-lattice of ML-MoS2 shows thermal expansion in both 2D and 3D simulations and their system size dependence is marginal. By analyzing the phonon dispersion at 300 K, we found that the discrepancy between 2D and 3D simulations of graphene and 2D h-BN is due to the absence of out-of-plane bending mode (ZA) in 2D simulations, which is responsible for thermal...  Read more

Extended timescale 2D IR probes of proteins: p-cyanoselenophenylalanine

Physical Chemistry Chemical Physics
The importance of dynamics to the function of proteins is well appreciated, but the difficulty in their measurement impedes investigation into their precise role(s). 2D IR spectroscopy is a developing approach for the study of dynamics and has motivated efforts to develop spectrally resolved IR probe groups that enable its application for measuring the dynamics at specific sites in a protein. A challenge with this approach is that the timescales accessible are limited by the vibrational lifetimes of the probes. Toward development of better probes for 2D IR spectroscopy of protein dynamics, we report the characterization of p-cyano-seleno-phenylalanine (CNSePhe), a derivative of the well established IR probe p-cyano-phenylalanine (CNPhe), by FT IR, pump-probe, and 2D IR spectroscopy. The incorporation of the heavy Se atom decouples the CN vibration from the rest in the molecule. Although this leads to a reduction of the transition dipole strength, and thus a reduction in signal...  Read more

Surface Induced Crystallization of Polymeric Nano-particles: Effect of Surface Roughness

Faraday Discussions
.Molecular dynamics simulations are conducted to study crystallization of a polymeric system as a drop in isolated state and on a surface. It is shown that crystallization kinetics for the polymeric system as a particle on a smooth surface is much faster than in isolated form. We show however as the surface becomes rough the crystallization rate of the polymeric particle decreases. The effect of roughness was compared for two cases of a polymer drop partially (Wenzel state) and fully wetting the cavities (fully confined) on a rough surface. In both cases it was observed that crystallization was slower than that on a smooth surface, and crystal growth rate was decreased by increasing the characteristic roughness ratio. The crystallization on rough surfaces was still faster than that of the isolated polymer drop.Read more

Thermal Conductivity of glassy GeTe4 by First-Principles Molecular Dynamics

Physical Chemistry Chemical Physics
A transient thermal regime is achieved in glassy GeTe4 by first-principles molecular dynamics following the recently proposed ``approach-to-equilibrium" methodology.1 The temporal and spatial evolution of the temperature do comply with the time-dependent solution of the heat equation. We demonstrate that the time scales required to create the hot and the cold parts of the system and observe the resulting approach to equilibrium are accessible to first-principles molecular dynamics. Such a strategy provides the thermal conductivity from the characteristic decay time. We rationalize in detail the impact on the thermal conductivity of the initial temperature difference, the equilibration duration, and the main simulation features.Read more

Photophysics of a Copper Phenanthroline Elucidated by Trajectory and Wavepacket-based Quantum Dynamics: A Synergetic Approach.

Physical Chemistry Chemical Physics
On-the-fly excited state molecular dynamics is an attractive method for studying non-equilibrium processes in excited states and is beginning to emerge as a mature approach much like its ground state counterparts. In contrast to quantum wavepacket dynamics methods, it negates the need for modelling potential energy surfaces, which usually confine nuclear motion within a reduced number of vibrational modes. In addition, on-the-fly molecular dynamics techniques are easily combined with the atomistic description of the solvents (through the QM/MM approach) allowing to explicitly address the effect of the environment. Herein, we study the nonadiabatic relaxation of photoexcited [Cu(dmp)2]+ (dmp = 2,9-dimethyl-1,10-phenanthroline) using QM/MM Trajectory Surface Hopping (TSH). We show that the decay of the initially excited singlet state into the lowest singlet (S1) state occurs within 100 fs, in agreement with previous experiments, and is slightly influenced by the nature of the solvent....  Read more

Insights into the Molecular Interaction between Two Polyoxygenated Cinnamoylcoumarin Derivatives and Human Serum Albumin

Physical Chemistry Chemical Physics
Ligand binding studies on human serum albumin (HSA) are crucial in pharmacological properties determination of drug candidates. Here, two representatives of coumarin–chalcone hybrids were selected and their binding mechanism was identified via thermodynamics techniques, curve resolution analysis and computational methods at molecular levels. The binding parameters were derived using spectroscopic approaches and the results point to only one pocket located near Trp214 residue in subdomain IIA of HSA. The protein tertiary structure was altered during the ligand binding and formed an intermediate structure to create stronger ligand binding interactions. The best binding mode of ligand was initially estimated by docking on an ensemble of HSA crystallographic structures and by molecular dynamics (MD) simulations. Per residue interaction energies were calculated over the MD trajectories as well. Reasonable agreement was found between experimental and theoretical results about the nature...  Read more

The origin of the measured chemical shift of 129Xe in UiO-66 and UiO-67 revealed by DFT investigations

Physical Chemistry Chemical Physics
The NMR chemical shift of the xenon isotope 129Xe inside the metal-organic frameworks (MOFs) UiO-66 and UiO-67 (UiO - University of Oslo) has been investigated both with density functional theory (DFT) and in situ high-pressure 129Xe NMR measurements. The experiments reveal a decrease of the total chemical shift comparing the larger isoreticular MOF (UiO-67) with the smaller one (UiO-66), even though one may expect an increase due to the higher amount of adsorbed Xe atoms. We are able to calculate contributions to the chemical shift individually. This allows us to evaluate the shift inside the different pores independently. To compare the theoretical results with the experimental ones, we performed molecular dynamics simulations of Xe in the MOFs. For this purpose, the pores were completely filled with Xe to gain insight into the distribution of Xe at high pressures. The resulting trend of the total shift agrees well between...  Read more

Unique agreement of experimental and computational infrared spectroscopy: a case study of lithium bromide solvation in an important electrochemical solvent

Physical Chemistry Chemical Physics
Infrared (IR) spectroscopy is a widely used and invaluable tool in the studies of solvation phenomena in electrolyte solutions. Using state-of-the-art chemometric analysis of a spectral series measured in a concentration-dependent manner, the spectrum of the solute-affected solvent can be extracted, providing a detailed view of the structural and energetic states of the solvent molecules influenced by the solute. Concurrently, ab initio molecular dynamics (AIMD) simulations provide the solvation shell picture at an atomistic detail level and allow for a consistent decomposition of the theoretical IR spectrum in terms of distance-dependent contributions of the solvent molecules. Here, we show for the first time how the chemometric techniques designed with the analysis of experimental data in mind can be harnessed to extract corresponding information from the computed IR spectra for mutual benefit, but without any mutual input. The wide applicability of this two-track approach...  Read more

Inclusion of lipopeptides into the DMPC lipid bilayer prevents Aβ peptide insertion

Physical Chemistry Chemical Physics
Using all-atom explicit water model and replica exchange with solute tempering molecular dynamics we have studied the binding of Abeta10-40 peptide to the mixed cationic bilayer composed of DMPC lipids and C14-KAAK lipopeptides (LP). Using as a control our previous replica exchange simulations probing binding of the same peptide to the zwitterionic DMPC bilayer we assessed the impact of lipopeptides on Abeta binding mechanism. We found that binding to the mixed DMPC+LP bilayer does not enhance Abeta helix propensity as much as binding to the pure DMPC bilayer. Tertiary interactions also differ in the peptide bound to the DMPC+LP bilayer due to reduced helix content, salt bridge disruption, and formation of new long-range hydrophobic interactions. More importantly, we showed that mixing lipopeptides into the DMPC bilayer prevents Abeta10-40 insertion forcing the peptide to reside on the bilayer surface and considerably destabilizes Abeta-bilayer interactions leading to formation of a...  Read more

Swelling-induced structural changes and microparticle uptake of gelatin gels probed by NMR and CLSM

Soft Matter
Gelatin gels are increasingly involved in many industrial applications due to several advantages including cost efficiency and biocompatibility. Generally, their production requires the use of aqueous solvents, which cause a significant swelling, due to the ability of solvent molecules to penetrate through the gel microstructure and increase its volume. Since swelling mechanisms and their effect on gel structure are not fully understood, further investigations are required. In this work, we combine macroscopic measurements of the swelling ratio (SR) with Nuclear Magnetic Resonance (NMR) and Confocal Laser Scanning Microscopy (CLSM) to investigate changes in gelatin structure as a function of both polymer concentration and swelling time. SR values increase as a function of time until a maximum is reached and then show a slight drop for all the gelatin concentrations after 24 h swelling time, probably due to a network relaxation process. NMR allows to determine mass transport and...  Read more

X-Ray Crystallographic and Computational Study on Uranyl-Salophen Complexes Bearing Nitro Groups

Dalton Transactions
In the solid state, salophen-UO2 complexes bearing one, two or three NO2 groups, lack of the pronounced ligand curvature which represents a structural hallmark for this class of compounds. A detailed structural study based on single crystal X-ray crystallography and computational methods, comprising Molecular Dynamics, gas phase Hartree Fock and DFT calculations, probes the coordination properties of the uranyl cation.Read more

Distribution of Dopant Ions Around Poly(3,4-ethylenedioxythiophene) Chains: A Theoretical Study

Physical Chemistry Chemical Physics
The effect of counterions and multiple polymer chains on the properties and structure of poly(3,4-ethylenedioxythiophene) (PEDOT) doped with have been examined using density functional theory (DFT) calculations with periodic boundary conditions (PBC). Calculations on a one-dimensional periodic model with four explicit polymer repeat units and two molecules indicate that the latters are separated as much as possible, the salt structure and band gap obtained from such distribution being in excellent agreement with those determined experimentally. On the other hand, DFT calculations on periodic models that include two chains indicate that neighboring PEDOT chains are shifted along the molecular axis by a half of the repeat unit length, dopant ions intercalated between the polymer molecules acting as cement. In order to support these structural features, classical Molecular Dynamics (MD) simulations have been performed on a multiphasic system consisting of 69 explicit PEDOT chains...  Read more