Adaptive-Partitioning Redistributed Charge and Dipole Schemes for QM/MM Dynamics Simulations: On-the-fly Relocation of Boundaries that Pass through Covalent Bonds

2011 ◽  
Vol 7 (11) ◽  
pp. 3625-3634 ◽  
Author(s):  
Soroosh Pezeshki ◽  
Hai Lin
Keyword(s):  
Covalent Bonds ◽  
Adaptive Partitioning ◽  
Pass Through ◽  
Dynamics Simulations

scholarly journals On the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics Simulations

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
R. Ansari ◽  
A. Momen ◽  
S. Rouhi ◽  
S. Ajori
Keyword(s):  
Molecular Dynamics ◽  
Boundary Conditions ◽  
Molecular Dynamics Simulations ◽  
Natural Frequency ◽  
Structural Method ◽  
Covalent Bonds ◽  
Carbon Nanocones ◽  
Single Walled Carbon ◽  
Vibrational Behavior ◽  
Dynamics Simulations

The vibrational behavior of single-walled carbon nanocones is studied using molecular structural method and molecular dynamics simulations. In molecular structural approach, point mass and beam elements are employed to model the carbon atoms and the connecting covalent bonds, respectively. Single-walled carbon nanocones with different apex angles are considered. Besides, the vibrational behavior of nanocones under various types of boundary conditions is studied. Predicted natural frequencies are compared with the existing results in the literature and also with the ones obtained by molecular dynamics simulations. It is found that decreasing apex angle and the length of carbon nanocone results in an increase in the natural frequency. Comparing the vibrational behavior of single-walled carbon nanocones under different boundary conditions shows that the effect of end condition on the natural frequency is more prominent for nanocones with smaller apex angles.

The crystal structure of tedhadleyite, Hg2+Hg101+O4l2(Cl,Br)2, from the Clear Creek Claim, San Benito County, California

2009 ◽  
Vol 73 (2) ◽  
pp. 227-234 ◽  
Author(s):  
M. A. Cooper ◽  
F. C. Hawthorne
Keyword(s):  
Crystal Structure ◽  
Direct Methods ◽  
The Other ◽  
Covalent Bonds ◽  
Pass Through

AbstractThe crystal structure of tedhadleyite, ideally Hg2+Hg101+O4l2(Cl,Br)2,triclinic, AĪ, a 7.0147(5), b 11.8508(7), c 12.5985(8) Å, α 115.583(5), β 82.575(2), γ 100.619(2)º, V 927.0(2) Å3, Z = 2,was solved by direct methods and refined to an R1 index of 4.5% for 2677 unique reflections. There are six symmetrically distinct Hg sites in tedhadleyite: Hg(1) is occupied by Hg2+ and Hg(2–6) are occupied by Hg+ that forms three [Hg–Hg]2+ dimers with Hg–Hg separations between 2.527 and 2.556 Å. These [Hg–Hg]2+ dimers have strong covalent bonds to O atoms,forming pseudo-linear O–Hg–Hg–O arrangements,and weak bonds to halogen and O atoms at high angles to the dimer axis. The [O–Hg–Hg-O] groups share anions to form four-membered square rings of composition [Hg8O4] that link along [100] via [O–Hg–Hg-O] groups and along [001] via [O–Hg–O] groups, forming rectangular rings of composition [Hg14O8]. The rings form a corrugated layer that interweaves with a symmetrically related layer whereby the [O–Hg(6)–Hg(6)–O] linking groups of one layer pass through the centres of the square [Hg8O4] rings of the other layer to form [Hg11O4] complex slabs parallel to (010) that link through Hg-I and Hg-Br,Cl bonds.

scholarly journals Extending Scaled-Interaction Adaptive-Partitioning QM/MM to Covalently Bonded Systems

2020 ◽  
Author(s):  
Zenghui Yang
Keyword(s):  
Charge Density ◽  
Computational Cost ◽  
Original Form ◽  
Time Step ◽  
Covalent Bonds ◽  
Simple Modification ◽  
Adaptive Partitioning ◽  
Covalently Bonded ◽  
Continuous Potential ◽  
Simple Molecules

Quantum mechanics/molecular mechanics (QM/MM) is the method of choice for atomistic simulations of large systems that can be partitioned into active and environmental regions. Adaptive-partitioning (AP) methods extend the applicability of QM/MM, allowing active zones to change during the simulation. AP methods achieve continuous potential energy surface (PES) by introducing buffer regions in which atoms have both QM and MM characters. Most of the existing AP-QM/MM methods require multiple QM calculations per time step, which can be expensive for systems with many atoms in buffer regions. Although one can lower the computational cost by grouping atoms into fragments, this may not be possible for all systems, especially for applications in covalent solids. The SISPA method [J. Chem. Theory Comput. 2017, 13, 2342] differs from other AP-QM/MM methods by only requiring one QM calculation per time step, but it has the flaw that the QM charge density and wavefunction near the buffer/MM boundary tend to those of isolated atoms/fragments. Besides, regular QM/MM methods for treating covalent bonds cut by the QM/MM boundary are incompatible with SISPA. Due to these flaws, SISPA in its original form cannot treat covalently bonded systems properly. In this work, I show that a simple modification to the SISPA method improves the treatment of covalently bonded systems. I also study the effect of correcting the charge density in SISPA by developing a density-corrected pre-scaled algorithm. I demonstrate the methods with simple molecules and bulk solids.

Detecting DNA Using a Single Graphene Pore by Molecular Dynamics Simulations

2012 ◽  
Vol 503 ◽  
pp. 423-426 ◽  
Author(s):  
Wei Si ◽  
Jing Jie Sha ◽  
Lei Liu ◽  
Jia Peng Li ◽  
Xiao Long Wei ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Dna Sequencing ◽  
Molecular Dynamics Simulations ◽  
Electrical Field ◽  
Graphene Membrane ◽  
Pass Through ◽  
Dynamics Simulations

DNA charged negatively could be transported through a solid nanopore by the force of an electrical field. Recently, the nice properties of graphene attract a lot of researchers. In this paper, A single graphene membrane was punched to form a nanopore and a ds-DNA was driven to pass through the pore by all-atom molecular dynamics simulations. The single graphene membrane was demonstrated useful in DNA sequencing. It suggested that the velocity of DNA translocating through a single graphene pore could be controlled by adjusting the appropriate voltage and the diameter of the nanopore.

scholarly journals Quinone binding in respiratory complex I: Going through the eye of a needle. The squeeze-in mechanism of passing the narrow entrance of the quinone site

2021 ◽  
Author(s):  
Nithin Dhananjayan ◽  
Panyue Wang ◽  
Igor Leontyev ◽  
Alexei A. Stuchebrukhov
Keyword(s):  
Conformational Changes ◽  
Complex I ◽  
Respiratory Complex ◽  
Quinone Binding ◽  
Bacterial Enzyme ◽  
Respiratory Complex I ◽  
Electron Reduction ◽  
Pass Through ◽  
Dynamics Simulations ◽  
Ubiquinone Binding

AbstractAt the joint between the membrane and hydrophilic arms of the enzyme, the structure of the respiratory complex I reveals a tunnel-like Q-chamber for ubiquinone binding and reduction. The narrow entrance of the quinone chamber located in ND1 subunit forms a bottleneck (eye of a needle) which in all resolved structures was shown to be too small for a bulky quinone to pass through, and it was suggested that a conformational change is required to open the channel. The closed bottleneck appears to be a well-established feature of all structures reported so-far, both for the so-called open and closed states of the enzyme, with no indication of a stable open state of the bottleneck. We propose a squeeze-in mechanism of the bottleneck passage, where dynamic thermal conformational fluctuations allow quinone to get in and out. Here, using molecular dynamics simulations of the bacterial enzyme, we have identified collective conformational changes that open the quinone chamber bottleneck. The model predicts a significant reduction—due to a need for a rare opening of the bottleneck—of the effective bi-molecular rate constant, in line with the available kinetic data. We discuss possible reasons for such a tight control of the quinone passage into the binding chamber and mechanistic consequences for the quinone two-electron reduction. Graphic abstract

scholarly journals Graphyne-3: A Highly Efficient Candidate for Separation of Small Gas Molecules From Gaseous Mixtures

2021 ◽  
Author(s):  
Khatereh Azizi ◽  
S. Mehdi Vaez Allaei ◽  
Arman Fathizadeh ◽  
Ali Sadeghi ◽  
Muhammad Sahimi
Keyword(s):  
Density Functional ◽  
Gas Permeation ◽  
Ternary Mixtures ◽  
Density Profiles ◽  
Functional Theory ◽  
Gaseous Mixtures ◽  
Mechanical And Electrical Properties ◽  
Gas Molecules ◽  
Pass Through ◽  
Dynamics Simulations

Abstract Two-dimensional nanosheets, such as the general family of graphenes have attracted considerable attention over the past decade, due to their excellent thermal, mechanical, and electrical properties. We report on the result of a study of separation of gaseous mixtures by a model graphyne-3 membrane, using extensive molecular dynamics simulations and density functional theory. Four binary and one ternary mixtures of H2, CO2, CH4 and C2H6 were studied. Theresults indicate the excellence of graphyne-3 for separation of small gas molecules from the mixtures. In particular, the H2 permeance through the membrane is on the order of 107 gas permeation unit, by far much larger than those in other membranes, and in particular in graphene. To gain deeper insights into the phenomenon, we also computed the density profiles and the residence times of the gases near the graphyne-3 surface, as well as their interaction energies with the membrane. The results indicate clearly the tendency of H2 to pass through the membrane at high rates, leaving behind C2H6 and larger molecules on the surface. In addition, the possibility of chemisorption is clearly ruled out. These results, together with the very good mechanical properties of graphyne-3, confirm that it is an excellent candidate for separating small gas molecules from gaseous mixtures, hence opening the way for its industrial use.

Hydrocarbon Reactions in Carbon Nanotubes: Pyrolysis

2000 ◽  
Vol 651 ◽  
Author(s):  
Steven J. Stuart ◽  
Brad M. Dickson ◽  
Donald W. Noid ◽  
Bobby G. Sumpter
Keyword(s):  
Covalent Bonds ◽  
Activation Barriers ◽  
First Order ◽  
Bond Order Potential ◽  
Arrhenius Temperature Dependence ◽  
Dynamics Simulations ◽  
Hydrocarbon Reactions ◽  
Recombination Reactions ◽  
Arrhenius Temperature ◽  
Confined System

AbstractMolecular dynamics simulations have been used to study the pyrolysis of eicosane (C2042 both in the gas phase and when confined to the interior of a (7,7) carbon nanotube. A reactive bond-order potential was used to model the thermal decomposition of covalent bonds. The unimolecular dissociation is first-order in both cases. The decomposition kinetics demonstrate Arrhenius temperature dependence, with similar activation barriers in both geometries. The decomposition rate is slower by approximately 30% in the confined system. This rate decrease is observed to be a result of recombination reactions due to collisions with the nanotube wall.

scholarly journals Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

Nanomaterials ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2143
Author(s):  
Daniel R. Marzolf ◽  
Aidan M. McKenzie ◽  
Matthew C. O’Malley ◽  
Nina S. Ponomarenko ◽  
Coleman M. Swaim ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Charge Transfer ◽  
Model Systems ◽  
Covalent Attachment ◽  
Chemical Labeling ◽  
Covalent Bonds ◽  
Time Resolved ◽  
Redox Active ◽  
Dynamics Simulations ◽  
Ultrafast Charge Transfer

Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4–8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.

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