scholarly journals Quantifying Fluctuations of Average Environments for Embedding Calculations

2021 ◽  
Author(s):  
Cristina Gonzalez ◽  
Christopher A. Rumble ◽  
Daniel Borgis ◽  
Tomasz A. Wesolowski
Keyword(s):  
Spectroscopic Properties ◽  
Dynamics Simulation ◽  
Good Representation ◽  
Solvatochromic Shift ◽  
Electronic Density ◽  
Embedding Theory ◽  
Quantum Confinement Effects ◽  
Solvent Environment ◽  
Average Description ◽  
Density Measure

In the context of employing embedding methods to study spectroscopic properties, the viability and effectiveness of replacing an ensemble of calculations by a single calculation using an average description of the system of study are evaluated. This work aims to provide a baseline of the expected fluctuations in the average description of the system obtained in the two cases: from calculations of an ensemble of geometries, and from an average environment constructed with the same ensemble. To this end, the classical molecular dynamics simulation of a very simple system was used: a rigid molecule of acetone in a solution of rigid water. We perform a careful numerical analysis of the fluctuations of the electrostatic potential felt by the solute, as well as the fluctuations in the effect on its electronic density, measure through the dipole moment and the atomic charges derived from the corresponding potential. At the same time, we inspect the accuracy of the methods used to construct average environments. Finally, the proposed approach to generate the embedding potential from an average environment density is applied to estimate the solvatochromic shift of the first excitation of acetone. In order to account for quantum-confinement effects that may be important in certain cases, the fluctuations on the shift due to the interaction with the solvent are evaluated using Frozen-Density Embedding Theory. Our results demonstrate that, for normally-behaved environments, the constructed average environment is a reasonably good representation of a discrete solvent environment.

scholarly journals Solvent Effects on Catechol Crystal Habits and Aspect Ratios: A Combination of Experiments and Molecular Dynamics Simulation Study

Crystals ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 316 ◽  
Author(s):  
Dan Zhu ◽  
Shihao Zhang ◽  
Pingping Cui ◽  
Chang Wang ◽  
Jiayu Dai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Solvent Effects ◽  
Dynamics Simulation ◽  
Crystal Habit ◽  
Aspect Ratios ◽  
Solvent Environment ◽  
Solvent Adsorption ◽  
Attachment Energy

This work could help to better understand the solvent effects on crystal habits and aspect ratio changes at the molecular level, which provide some guidance for solvent selection in industrial crystallization processes. With the catechol crystal habits acquired using both experimental and simulation methods in isopropanol, methyl acetate and ethyl acetate, solvent effects on crystal morphology were explored based on the modified attachment energy model. Firstly, morphologically dominant crystal faces were obtained with the predicted crystal habit in vacuum. Then, modified attachment energies were calculated by the molecular dynamics simulation to modify the crystal shapes in a real solvent environment, and the simulation results were in agreement with the experimental ones. Meanwhile, the surface properties such as roughness and the diffusion coefficient were introduced to analyze the solvent adsorption behaviors and the radial distribution function curves were generated to distinguish diverse types of interactions like hydrogen bonds and van der Waals forces. Results show that the catechol crystal habits were affected by the combination of the attachment energy, surface structures and molecular interaction types. Moreover, the changing aspect ratios of catechol crystals are closely related to the existence of hydrogen bonds which contribute to growth inhibition on specific faces.

scholarly journals Classical molecular dynamics simulation of electronically non-adiabatic processes

2016 ◽  
Vol 195 ◽  
pp. 9-30 ◽  
Author(s):  
William H. Miller ◽  
Stephen J. Cotton
Keyword(s):  
Molecular Dynamics ◽  
Potential Energy Surfaces ◽  
Degrees Of Freedom ◽  
Classical Mechanics ◽  
Electronic States ◽  
Dynamics Simulation ◽  
Arbitrary Form ◽  
Electronic Density ◽  
Classical Molecular Dynamics ◽  
Adiabatic Processes

Both classical and quantum mechanics (as well as hybrids thereof, i.e., semiclassical approaches) find widespread use in simulating dynamical processes in molecular systems. For large chemical systems, however, which involve potential energy surfaces (PES) of general/arbitrary form, it is usually the case that only classical molecular dynamics (MD) approaches are feasible, and their use is thus ubiquitous nowadays, at least for chemical processes involving dynamics on a single PES (i.e., within a single Born–Oppenheimer electronic state). This paper reviews recent developments in an approach which extends standard classical MD methods to the treatment of electronically non-adiabatic processes, i.e., those that involve transitions between different electronic states. The approach treats nuclear and electronic degrees of freedom (DOF) equivalently (i.e., by classical mechanics, thereby retaining the simplicity of standard MD), and provides “quantization” of the electronic states through a symmetrical quasi-classical (SQC) windowing model. The approach is seen to be capable of treating extreme regimes of strong and weak coupling between the electronic states, as well as accurately describing coherence effects in the electronic DOF (including the de-coherence of such effects caused by coupling to the nuclear DOF). A survey of recent applications is presented to illustrate the performance of the approach. Also described is a newly developed variation on the original SQC model (found universally superior to the original) and a general extension of the SQC model to obtain the full electronic density matrix (at no additional cost/complexity).

Effect of the Solvent Environment on the Spectroscopic Properties and Dynamics of the Lowest Excited States of Carotenoids

2000 ◽  
Vol 104 (18) ◽  
pp. 4569-4577 ◽  
Author(s):  
Harry A. Frank ◽  
James A. Bautista ◽  
Jesusa Josue ◽  
Zeus Pendon ◽  
Roger G. Hiller ◽  
...  
Keyword(s):  
Excited States ◽  
Spectroscopic Properties ◽  
Solvent Environment

Thermoelectric Modeling of Si-Si1−xGex Ordered Nanowire Composites

2005 ◽  
Vol 886 ◽  
Author(s):  
Ming Y. Tang ◽  
Mildred S. Dresselhaus ◽  
Ronggui Yang ◽  
Gang Chen
Keyword(s):  
Thermoelectric Materials ◽  
Model Systems ◽  
Thermoelectric Performance ◽  
Core Shell ◽  
Host Matrix ◽  
Electronic Density ◽  
Quantum Confinement Effects ◽  
Interface Scattering ◽  
Low Dimensional ◽  
Shell Nanowires

ABSTRACTThermoelectrics have always been attractive for power generation and cooling because of power reliability and environmentally friendly issues. However, this concept remains non-competitive due to the limitation in the efficiency of available thermoelectric materials and device designs [1]. In the 1990s, Hicks and Dresselhaus predicted the possibility of a dramatic enhancement in thermoelectric performance based on the special behavior of low dimensional materials [2, 3]. This enhancement is in part due to the increase in quantum confinement effects, the increase in electronic density of states at specified energies, and the increase in the phonon interface scattering for low dimensional structures.Nanowires and core-shell nanowires can be considered to be model systems to illustrate representative behavior in low dimensional thermoelectric materials. It is expected that a system made out of nanowires or core-shell nanowires would have a higher thermoelectric performance than its bulk counterpart due to an increase in the number of interfaces. The interfaces that are introduced must be such that phonons are scattered more strongly than are electrons. Theoretical studies have been carried out to better understand the transport properties of Si-Si1−xGex ordered nanowire composites. The composite is modeled as having Si wires embedded in a Si1−xGex host matrix. Thus, core-shell Si/Si1−xGex nanowires can be considered as a building block of the composite. The effect of the wire diameter and the shell alloy composition on ZT is presented.

scholarly journals Field-dependent specific heat of the canonical underdoped cuprate superconductor $$\hbox {YBa}_2\hbox {Cu}_4\hbox {O}_8$$

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jeffery L. Tallon ◽  
John W. Loram
Keyword(s):  
Specific Heat ◽  
Hole Concentration ◽  
Characteristic Temperature ◽  
Mean Field ◽  
Impurity Scattering ◽  
Spectroscopic Properties ◽  
Cuprate Superconductor ◽  
Electronic Density ◽  
Field Dependent ◽  
The Impact

AbstractThe cuprate superconductor $$\hbox {YBa}_2\hbox {Cu}_4\hbox {O}_8$$ YBa 2 Cu 4 O 8 , in comparison with most other cuprates, has a stable stoichiometry, is largely free of defects and may be regarded as the canonical underdoped cuprate, displaying marked pseudogap behaviour and an associated distinct weakening of superconducting properties. This cuprate ‘pseudogap’ manifests as a partial gap in the electronic density of states at the Fermi level and is observed in most spectroscopic properties. After several decades of intensive study it is widely believed that the pseudogap closes, mean-field like, near a characteristic temperature, $$T^*$$ T ∗ , which rises with decreasing hole concentration, p. Here, we report extensive field-dependent electronic specific heat studies on $$\hbox {YBa}_2\hbox {Cu}_4\hbox {O}_8$$ YBa 2 Cu 4 O 8 up to an unprecedented 400 K and show unequivocally that the pseudogap never closes, remaining open to at least 400 K where $$T^*$$ T ∗ is typically presumed to be about 150 K. We show from the NMR Knight shift and the electronic entropy that the Wilson ratio is numerically consistent with a weakly-interacting Fermion system for the near-nodal states. And, from the field-dependent specific heat, we characterise the impact of fluctuations and impurity scattering on the thermodynamic properties.

scholarly journals Computational Modeling of the Interaction of Silver Nanoparticles with the Lipid Layer of the Skin

2018 ◽  
Vol 2018 ◽  
pp. 1-9 ◽  
Author(s):  
Andrea Fabara ◽  
Sebastián Cuesta ◽  
Fernanda Pilaquinga ◽  
Lorena Meneses
Keyword(s):  
Molecular Dynamics ◽  
Silver Nanoparticles ◽  
Molecular Dynamics Simulation ◽  
Density Functional ◽  
Silver Cluster ◽  
Biological Molecules ◽  
Dynamics Simulation ◽  
Silver Clusters ◽  
Lipid Layer ◽  
Electronic Density

Silver nanoparticles are recognized for numerous physical, biological, and pharmaceutical applications. Their main uses in the medical field comprise diagnostic and therapeutic applications. In this project, the interaction between silver nanoparticles and the lipid layer of the skin was studied in order to know how nanoparticles behave when they are in contact with the skin. Energies of the silver nanoparticles were calculated through the optimization of silver clusters using density functional theory implemented in the Gaussian program 09W. Biological molecules such as glucose, stearic acid, palmitic acid, and quercetin present in coated nanoparticles and in the skin were also optimized. The silver clusters containing 6 atoms were proven to be the most stable complexes. Moreover, a study of molecular orbital describing HOMO interactions of the clusters was performed showing that the electronic density was around the silver cluster. Molecular dynamics simulation was performed using Abalone program. Silver nanoparticles seemed to have very good clearance properties in our molecular dynamics simulation because over a certain period of time, the silver cluster got far away from the biological molecules.

Hybrid Electronic-density-functional/molecular-dynamics Simulation on Parallel Computers: Oxidation of Si Surface

2000 ◽  
Vol 653 ◽  
Author(s):  
Shuji Ogata ◽  
Fuyuki Shimojo ◽  
Aiichiro Nakano ◽  
Priya Vashishta ◽  
Rajiv K. Kalia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Density Functional ◽  
Interatomic Potential ◽  
Classical System ◽  
Real Space ◽  
Dynamics Simulation ◽  
Quantum Mechanical ◽  
Electronic Density ◽  
Classical Systems

AbstractA hybrid quantum mechanical/molecular dynamics simulation scheme is developed by embedding a quantum mechanical system described by the real-space density-functional theory in a classical system of atoms interacting via an empirical interatomic potential. A novel scaled position method for handshake atoms coupling the quantum and the classical systems is introduced. Hybrid simulation run for oxidation of Si (100) surface is performed to demonstrate seamless coupling of the quantum and the classical systems.

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