Improved embedded molecular cluster model

We demonstrate that boundary effects (i.e., displacements of the cluster boundary atoms from their lattice sites and the difference between effective charges of the perfect crystal atoms and those of the cluster atoms in the case of a cluster with no point defect in it) in an embedded molecular cluster (EMC) model can be radically reduced. A new embedding scheme is proposed. It includes search for the structural elements (SE) of which perfect crystal is composed, use of corresponding to these SE expression for the total energy, and application of the degree of localization of equations consistent with the wave functions of the cluster. To get equations for the cluster wave functions, the problem of varied subsystem in the field of the frozen remaining part of the whole electron system” is investigated in the framework of a one-electron approximation. The consideration is general for every task of this type. Homogeneous equations resulting directly from variation of the total energy expression are obtained and transformed to the eigenvalue problem equations. Orthogonality constraints are not imposed during variation. A particular case of the equations describing mutually orthogonal one-electron wave functions of the cluster staying nonorthogonal to those of the remaining crystal is found. A proposed embedding scheme is realized in the CLUSTER code based on the calculation scheme of the semiempirical INDO method. Boundary effects both in the standard (cluster in the field of the infinite lattice of nonpoint spherical charges) and new embedding scheme are investigated, calculating the clusters of LiF, MgO, NaCl, KCl, and AgCl crystals. Significant reduction of the boundary effects in the new embedding scheme is achieved. Reasons for the boundary effects are discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Transport behavior of oxygen and nitrogen through organasilicon-containing polystyrenes by molecular simulation

Molecular dynamics (MD) simulations have been used to study the transport properties of oxygen and nitrogen in the para-substituted polystyrenes which possess one to four Si atoms in each substituent. The Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to construct the polymers. Diffusion coefficients were obtained from molecular dynamics (NVT ensemble) with up to 3 ns simulation times. After molecular dynamic simulation, the trajectories of the small molecules in the polymer matrix were obtained. Then diffusion coefficients have been calculated from the Einstein relationship revealing a considerable agreement between the simulated and the experimental data. And solubility coefficients have been calculated by the Grand Canonical Monte Carlo (GCMC) method. The solubility of oxygen increased with increasing Si content in the polymer membrane. The para-substituted polystyrenes with a branched substituent at the alpha-position showed higher permeability than those of the nonbranched ones. The higher the glass transition temperature (T(g)) of the membrane, the larger the diffusion coefficients of oxygen and nitrogen obtained.     

Implementation of a protein reduced point charge model toward molecular dynamics applications

A reduced point charge model was developed in a previous work from the study of extrema in smoothed charge density distribution functions generated from the Amber99 molecular electrostatic potential. In the present work, such a point charge distribution is coupled with the Amber99 force field and implemented in the program TINKER to allow molecular dynamics (MD) simulations of proteins. First applications to two polypeptides that involve α-helix and β-sheet motifs are analyzed and compared to all-atom MD simulations. Two types of coarse-grained (CG)-based trajectories are generated using, on one hand, harmonic bond stretching terms and, on the other hand, distance restraints. Results show that the use of the unrestrained CG conditions are sufficient to preserve most of the secondary structure characteristics but restraints lead to a better agreement between CG and all-atom simulation results such as rmsd, dipole moment, and time-dependent mean square deviation functions.     

Account for electron contributions in embedded atom model for iron and nickel in molecular dynamics simulation

Potentials of embedded atom model (EAM) are calculated in analytical form for liquid iron and nickel. A series of models of these metals is created up to the temperature of 4000–4200 K. It is shown that these potentials enable us to obtain good agreement between the density of models and real metals; upon heating, however, the energy of the models is reduced relative to the real energies. It is established that the divergence of energies at ～4000 K is 32 kJ/mol for iron and 33 kJ/mol for nickel. It is shown that most of this divergence is determined by the contribution from the heat energy of electrons; after subtracting this contribution, a divergence of energies of 8.1 kJ/mol for iron and 14.3 kJ/mol for nickel remains. It is concluded that this divergence could be due partly to the insufficient adequacy of EAM potential in describing broad temperature ranges.     

Non-iterative phase behavior model with application to surfactant flooding and limited compositional simulation

Hand's method is typically used to empirically calculate the equilibrium compositions for ternary systems between two liquid phases. Oil field application of Hand's method is generally limited to surfactant phase behavior with oil and brine, primarily because the excess oil and brine phases are nearly immiscible. Hand's method is not accurate to represent liquid–vapor equilibrium, especially as oil and gas become miscible. It also requires iterations, which means there is no guarantee of convergence.     

Response properties of embedded molecules through the polarizable embedding model

The polarizable embedding (PE) model is a fragment-based quantum-classical approach aimed at accurate inclusion of environment effects in quantum-mechanical response property calculations. The aim of this tutorial review is to give insight into the practical use of the PE model. Starting from a set of molecular structures and until you arrive at the final property, there are many crucial details to consider in order to obtain trustworthy results in an efficient manner. To lower the threshold for new users wanting to explore the use of the PE model, we describe and discuss important aspects related to its practical use. This includes directions on how to generate input files and how to run a calculation.     

Towards the biaxial nematic phase through molecular design

In this article, the search for the elusive biaxial nematic phase (NB) in liquid crystals is considered. The structure of the phase is described along with theoretical and computational work which suggests how it might be realised. An overview of the work of the Exeter group in this area is then given showing the different approaches adopted and illustrating how one of these has led to a new type of amphiphilicity based on shape.     

Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.     

Iterative fluctuation charge model: a new variable charge molecular dynamics method

In molecular simulations, calculation of environmentally dependent atomic charges is still a demanding task. Empirical and semiempirical methods have been proposed and applied to a wide range of problems with different success. In this paper, a new scheme based on the concept of electronegativity equalization is presented and its advantages over several other methods are discussed. This method is an extension of the fluctuation charge model [S. W. Rick, S. J. Stuart, and B. J. Berne, J. Chem. Phys. 101, 6141 (1994)]. By allowing multiple electronic iterations at each nuclear step, the condition of electronegativity equalization can be satisfied to a selected precision. Molecular dynamics simulations using this new method, as well as several other methods, are performed on alpha quartz. Analysis of the simulated results shows that it is advantageous to use the iterative fluctuation charge model in several different situations.     

Effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide

The effect of partial charge parametrization on the fluid phase behavior of hydrogen sulfide is investigated with grand canonical histogram reweighting Monte Carlo simulations. Four potential models, based on a Lennard-Jones + point charge functional form, are developed. It is shown that Lennard-Jones parameters can be tuned such that partial charges for the sulfur atom in the range -0.40 < q(s) < -0.252 will lead to an accurate reproduction of experimental vapor-liquid equilibria. Each of the parameter sets developed in this work are used to predict the pressure composition behavior H2S-n-pentane at 377.6 K. While the mixture calculation provides a means of reducing the number of candidate parameter sets, multiple parameter sets were found to yield an excellent reproduction of both the pure component and mixture phase behavior.     

Identifying the mechanisms of polymer friction through molecular dynamics simulation

Mechanisms governing the tribological behavior of polymer-on-polymer sliding were investigated by molecular dynamics simulations. Three main mechanisms governing frictional behavior were identified. Interfacial "brushing" of molecular chain ends over one another was observed as the key contribution to frictional forces. With an increase of the sliding speed, fluctuations in frictional forces reduced in both magnitude and periodicity, leading to dynamic frictional behavior. While "brushing" remained prevalent, two additional irreversible mechanisms, "combing" and "chain scission", of molecular chains were observed when the interfaces were significantly diffused.     

Long-range light-modulated charge transport across the molecular heterostructure doped protein biopolymers

Biological electron transfer (ET) across proteins is ubiquitous, such as the notable photosynthesis example, where light-induced charge separation takes place within the reaction center, followed by sequential ET via intramolecular cofactors within the protein. Far from biology, carbon dots (C-Dots) with their unique optoelectronic properties can be considered as game-changers for next-generation advanced technologies. Here, we use C-Dots for making heterostructure (HS) configurations by conjugating them to a natural ET mediator, the hemin molecule, thus making an electron donor–acceptor system. We show by transient absorption and emission spectroscopy that the rapid intramolecular charge separation happens following light excitation, which can be ascribed to an ultrafast electron and hole transfer (HT) from the C-Dot donor to the hemin acceptor. Upon integrating the HS into a protein matrix, we show that this HT within the HS configuration is 3.3 times faster compared to the same process in solution, indicating the active role of the protein in supporting the rapid light-induced long-range intermolecular charge separation. We further use impedance, electrochemical, and transient photocurrent measurements to show that the light-induced transient charge separation results in an enhanced ET and HT efficiency across the protein biopolymer. The charge conduction across our protein biopolymers, reaching nearly 0.01 S cm⁻¹, along with the simplicity and low-cost of their formation promotes their use in a variety of optoelectronic devices, such as artificial photosynthesis, photo-responsive protonic–electronic transistors, and photodetectors.

This work reports on a chimeric protein matrix with C-Dot–hemin heterostructures as cofactors. We show how the protein environment facilitates an ultrafast charge separation, resulting in long-range electron conduction across the protein matrix.     

Theory and simulation of charge transfer through DNA – nanotube contacts

We address the problem of charge transfer between a single-stranded adenine oligomer and semiconducting boron nitride nanotubes from a theoretical and numerical perspective. The model structures have been motivated by computer simulations; sample geometries are used as the input of an electronic structure theory that is based upon an extended Su-Schrieffer-Heeger Hamiltonian. By analyzing the emerging potential energy surfaces, we obtain hole transfer rates via Marcus’ theory of charge transfer. In the presence of nanotubes, these rates exceed those of isolated DNA single strands by a factor of up to 10⁴. This enhancement can be rationalized and quantified as a combination of a template effect and the participation of the tube within a superexchange mechanism.     

Computer simulation study of water using a fluctuating charge model

Hydrogen bonding in small water clusters is studied through computer simulation methods using a sophisticated, empirical model of interaction developed by Ricket al (S W Rick, S J Stuart and B J Berne 1994J. Chem. Phys. 101 6141) and others. The model allows for the charges on the interacting sites to fluctuate as a function of time, depending on their local environment. The charge flow is driven by the difference in the electronegativity of the atoms within the water molecule, thus effectively mimicking the effects of polarization of the charge density. The potential model is thus transferable across all phases of water. Using this model, we have obtained the minimum energy structures of water clusters up to a size often. The cluster structures agree well with experimental data. In addition, we are able to distinctly identify the hydrogens that form hydrogen bonds based on their charges alone, a feature that is not possible in simulations using fixed charge models. We have also studied the structure of liquid water at ambient conditions using this fluctuating charge model.     

Photoinduced charge shift and charge recombination through an alkynyl spacer for an expanded acridinium-based dyad

The photophysical and electrochemical properties of a dyad comprising an expanded acridinium light-harvester, coupled via a triple bond to a trialkyloxybenzene donor, are described. Laser excitation of the dyad in 1,2-dichloroethane (DCE) results in rapid charge shift (5 ps) followed by slower charge recombination (81 ps) to completely restore the ground state. Discrimination between forward and return electron transfer (k(ret)/k(for) ~ 16) is rather poor. There is no indication of triplet formation on the expanded acridinium-based group following charge recombination.     

Investigation of physical state and phase behavior of polyester-imides

Changes in properties of linear aromatic heterocyclic polymers of the polyimide class after introduction of ester linkages into their dianhydride component and of the oxygen and sulfur atoms into their diamine component have been studied. Thermomechanical, dilatometric, thermographic characteristics and x-ray diffraction patterns of poly(ester amic acids) and polyester-imides have been investigated. On heating, poly(ester amic acids) and amorphous polyesterimides exhibited a peculiar effect of self-orientation of macromolecules. The x-ray diffraction patterns of unoriented films indicate that they exhibit axial-planar texture with the c axis of macromolecules in the film plane. The formation of the texture is preceded by mutual arrangement of macromolecules, i.e., by a precrystallization process beginning in the amorphous state. Because of this, on heating at temperatures ranging from 200 to 380°C, polyester-imides yield highly crystalline products. Crystallographic parameters of the polymer lattices on x-ray diffraction patterns and dichroism of absorption bands in polarized infrared spectra, the most probable conformations of macromolecules of some polyesterimides are proposed.