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Journal articles on the topic 'Ab initio molecular dynamics. DFT'

Author: Grafiati

Published: 21 December 2024

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1

Muriel, Wilver A., Juan F. Botero-Cadavid, Carlos Cárdenas, and William Rodríguez-Córdoba. "A theoretical study of the photodynamics of salicylidene-2-anthrylamine in acetonitrile solution." Physical Chemistry Chemical Physics 20, no. 46 (2018): 29399–411. http://dx.doi.org/10.1039/c8cp06145a.

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The ultrafast photoinduced processes of salicylidene-2-anthrylamine (2-AntSA) in acetonitrile solution have been investigated using DFT/TD-DFT static electronic structure calculations and excited state ab initio molecular dynamics simulations.

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2

Marinho, Enesio, and Pedro Alves da Silva Autreto. "Me-graphane: tailoring the structural and electronic properties of Me-graphene via hydrogenation." Physical Chemistry Chemical Physics 23, no. 15 (2021): 9483–91. http://dx.doi.org/10.1039/d0cp06684b.

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3

Vojvodin, Cameron S., Sean T. Holmes, Lara K. Watanabe, Jeremy M. Rawson, and Robert W. Schurko. "Multi-component crystals containing urea: mechanochemical synthesis and characterization by ³⁵Cl solid-state NMR spectroscopy and DFT calculations." CrystEngComm 24, no. 14 (2022): 2626–41. http://dx.doi.org/10.1039/d1ce01610e.

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This work discusses the mechanochemical synthesis and characterization of five urea multicomponent crystals by XRD, solid-state NMR, DFT and ab initio molecular dynamics calculations to provide insights into their molecular-level structures.

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4

Pezzotti, Simone, Daria Ruth Galimberti, and Marie-Pierre Gaigeot. "Deconvolution of BIL-SFG and DL-SFG spectroscopic signals reveals order/disorder of water at the elusive aqueous silica interface." Physical Chemistry Chemical Physics 21, no. 40 (2019): 22188–202. http://dx.doi.org/10.1039/c9cp02766a.

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Through the prism of the rather controversial and elusive silica/water interface, ab initio DFT-based molecular dynamics simulations of the structure and non-linear SFG spectroscopy of the interface are analysed.

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5

Laconsay, Croix J., Ka Yi Tsui, and Dean J. Tantillo. "Tipping the balance: theoretical interrogation of divergent extended heterolytic fragmentations." Chemical Science 11, no. 8 (2020): 2231–42. http://dx.doi.org/10.1039/c9sc05161a.

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We interrogate a type of heterolytic fragmentation called a ‘divergent fragmentation’ using density functional theory (DFT), natural bond orbital (NBO) analysis, ab initio molecular dynamics (AIMD), and external electric field (EEF) calculations.

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6

Chen, Chun-Teh, Francisco J. Martin-Martinez, Gang Seob Jung, and Markus J. Buehler. "Polydopamine and eumelanin molecular structures investigated with ab initio calculations." Chemical Science 8, no. 2 (2017): 1631–41. http://dx.doi.org/10.1039/c6sc04692d.

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A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

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7

Lou, Ping. "Hybrid structures of a BN nanoribbon/single-walled carbon nanotube: ab initio study." RSC Advances 5, no. 68 (2015): 55458–67. http://dx.doi.org/10.1039/c5ra08331a.

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Hybrid structures of a zigzag edge BN nanoribbon/single-walled carbon nanotube, have been studied via standard spin-polarized density functional theory (DFT) calculations as well as ab initio molecular dynamics (MD) simulations.

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8

Sheng, Tian, Jin-Yu Ye, Wen-Feng Lin, and Shi-Gang Sun. "An insight into methanol oxidation mechanisms on RuO2(100) under an aqueous environment by DFT calculations." Physical Chemistry Chemical Physics 19, no. 11 (2017): 7476–80. http://dx.doi.org/10.1039/c6cp08522a.

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In this work, we have studied methanol oxidation mechanisms on RuO₂(100) by using density functional theory (DFT) calculations and ab initio molecular dynamics (MD) simulations with some explicit interfacial water molecules.

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9

Hu, Jiye, Kyongjin Pang, and Bizhang Dong. "Mechanism and identify photolysis products of fluopyram under TiO2: Experiments, DFT and ab initio Molecular dynamics study." SDRP Journal of Earth Sciences & Environmental Studies 4, no. 4 (2019): 681–90. http://dx.doi.org/10.25177/jeses.4.3.ra.504.

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10

Saiz, Fernan, and Nick Quirke. "The excess electron in polymer nanocomposites." Physical Chemistry Chemical Physics 20, no. 43 (2018): 27528–38. http://dx.doi.org/10.1039/c8cp04741c.

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We have used ab initio molecular dynamics and density-functional theory (DFT) calculations at the B3LYP/6-31G** level of theory to evaluate the energy and localisation of excess electrons at a number of representative interfaces of polymer nanocomposites.

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11

Krynski, M., W. Wrobel, J. R. Dygas, M. Malys, F. Krok, and I. Abrahams. "An ab initio study of oxide ion dynamics in type-II Bi3NbO7." Journal of Materials Chemistry A 3, no. 43 (2015): 21882–90. http://dx.doi.org/10.1039/c5ta03989d.

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12

Kim, Chang-Eun, Jonathan M. Skelton, Aron Walsh, and Aloysius Soon. "Solid-state chemistry of glassy antimony oxides." Journal of Materials Chemistry C 3, no. 43 (2015): 11349–56. http://dx.doi.org/10.1039/c5tc02191j.

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Using hybrid density-functional theory (DFT) and ab initio molecular dynamics, we calculate and characterize glassy amorphous antimony oxides in elevated oxygen environments, and provide information on how their atomic and electronic structures change as a function of their oxygen environment.

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13

Lee, Byung Do, Jin-Woong Lee, Joonseo Park, Min Young Cho, Woon Bae Park, and Kee-Sun Sohn. "Argyrodite configuration determination for DFT and AIMD calculations using an integrated optimization strategy." RSC Advances 12, no. 48 (2022): 31156–66. http://dx.doi.org/10.1039/d2ra05889h.

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When constructing a partially occupied model structure for use in density functional theory (DFT) and ab initio molecular dynamics (AIMD) calculations, the selection of appropriate configurations has been a vexing issue. We suggest a reasonable strategy to sort out this issue.

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14

Batista, Patrick R., Lucas C. Ducati, and Jochen Autschbach. "Solvent effect on the 195Pt NMR properties in pyridonate-bridged PtIII dinuclear complex derivatives investigated by ab initio molecular dynamics and localized orbital analysis." Physical Chemistry Chemical Physics 23, no. 22 (2021): 12864–80. http://dx.doi.org/10.1039/d0cp05849a.

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Ab initio molecular dynamics and relativistic DFT calculations were combined to provide a much more realistic computational model that reproduces the large magnitudes of the Pt^III–Pt^III NMR coupling constants and ¹⁹⁵Pt^III chemical shifts.

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15

Tereshchuk, Polina, Maurício J. Piotrowski, and Juarez L. F. Da Silva. "Atomic structure of the La/Pt(111) and Ce/Pt(111) surfaces revealed by DFT+U calculations." RSC Advances 5, no. 1 (2015): 521–28. http://dx.doi.org/10.1039/c4ra10322j.

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16

Gao, Fei, Eric J. Bylaska, and William J. Weber. "Defect Properties in GaN: Ab Initio and Empirical Potential Calculations." Materials Science Forum 475-479 (January 2005): 3087–90. http://dx.doi.org/10.4028/www.scientific.net/msf.475-479.3087.

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The defect properties and atomic configurations in GaN have been comparatively investigated using density functional theory (DFT) and molecular dynamics method with two representative potentials. The DFT calculations show that the relaxation of vacancies is generally small, but the relaxation around antisite defects is large. The N interstitials, starting from any possible configurations, eventually relax into a N+-N< 0 2 11 > split interstitial. In the case of Ga interstitials, the most stable configuration is a Ga octahedral interstitial, but the Ga+-Ga< 0 2 11 > split interstitial can bridge the gap between non-bounded Ga atoms. The formation energies of vacancies and antisite defects obtained using the Stillinger-Weber potential (SW) are in reasonable agreement with those obtained by DFT calculations, whereas the Tersoff-Brenner (TB) potential better describes the behavior of N interstitials.

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17

Schwenk, C. F., and B. M. Rode. "Ab initio QM/MM MD simulations of the hydrated Ca2+ ion." Pure and Applied Chemistry 76, no. 1 (January 1, 2004): 37–47. http://dx.doi.org/10.1351/pac200476010037.

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The comparison of two different combined quantum mechanical (QM)/molecular mechanical (MM) simulations treating the quantum mechanical region at Hartree-Fock (HF) and B3-LYP density functional theory (DFT) level allowed us to determine structural and dynamical properties of the hydrated calcium ion. The structure is discussed in terms of radial distribution functions, coordination number distributions, and various angular distributions and the dynamical properties, as librations and vibrations, reorientational times and mean residence times were evaluated by means of velocity autocorrelation functions. The QM/MM molecular dynamics (MD) simulation results prove an eightfold-coordinated complex to be the dominant species, yielding average coordination numbers of 7.9 in the HF and 8.0 in the DFT case. Structural and dynamical results show higher rigidity of the hydrate complex using DFT. The high instability of calcium ion's hydration shell allows the observation of water-exchange processes between first and second hydration shell and shows that the mean lifetimes of water molecules in this first shell (<100 ps) have been strongly overestimated by conclusions from experimental data.

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18

Lou, Ping. "Room-temperature metal-free ferromagnetism, stability, and spin transport properties in topologically fluorinated silicon carbide nanotubes." RSC Advances 6, no. 46 (2016): 39595–604. http://dx.doi.org/10.1039/c6ra00839a.

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A new topologically fluorinated armchair single-walled silicon carbide nanotube has been predicted via first principles density functional theory (DFT) and nonequilibrium Green's function method, as well as ab initio molecular dynamic (MD) simulations.

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19

Dixit, Mudit, Dan Thomas Major, and Sourav Pal. "Hydrogen adsorption in ZIF-7: A DFT and ab-initio molecular dynamics study." Chemical Physics Letters 651 (May 2016): 178–82. http://dx.doi.org/10.1016/j.cplett.2016.03.030.

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20

Karibayev, Mirat, Bauyrzhan Myrzakhmetov, Yanwei Wang, and Almagul Mentbayeva. "Enhanced Chemical Stability of Tetramethylammonium Head Groups via Deep Eutectic Solvent: A Computational Study." Molecules 29, no. 20 (October 14, 2024): 4869. http://dx.doi.org/10.3390/molecules29204869.

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The chemical stability of tetramethylammonium (TMA) head groups, both with and without the presence of a choline chloride and ethylene glycol-based deep eutectic solvent (DES), was studied using Density Functional Theory (DFT) calculations and ab initio Molecular Dynamics (MD) simulations. DFT calculations of transition state energetics (ΔEreaction, ΔGreaction, ΔEactivation, and ΔGactivation) for key degradation mechanisms, ylide formation (YF) and nucleophilic substitution (SN2), suggested that the presence of DES enhances the stability of the TMA head groups compared to systems without DES. Ab initio MD simulations across hydration levels (HLs) 1 to 5 indicated that without DES, YF dominates at lower HLs, while SN2 does not occur. In contrast, both mechanisms are suppressed in the presence of DES. Temperature also plays a role: without DES, YF dominates at 298 K, while SN2 becomes prominent at 320 K and 350 K. With DES, both degradation mechanisms are inhibited. These findings suggest DES could improve the chemical stability of TMA head groups in anion exchange membranes.

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21

Mazurek, Anna Helena, Łukasz Szeleszczuk, and Dariusz Maciej Pisklak. "A Review on Combination of Ab Initio Molecular Dynamics and NMR Parameters Calculations." International Journal of Molecular Sciences 22, no. 9 (April 22, 2021): 4378. http://dx.doi.org/10.3390/ijms22094378.

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This review focuses on a combination of ab initio molecular dynamics (aiMD) and NMR parameters calculations using quantum mechanical methods. The advantages of such an approach in comparison to the commonly applied computations for the structures optimized at 0 K are presented. This article was designed as a convenient overview of the applied parameters such as the aiMD type, DFT functional, time step, or total simulation time, as well as examples of previously studied systems. From the analysis of the published works describing the applications of such combinations, it was concluded that including fast, small-amplitude motions through aiMD has a noticeable effect on the accuracy of NMR parameters calculations.

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22

Mariñoso Guiu, Joan, Antoni Macià, and Stefan T. Bromley. "How to accurately model IR spectra of nanosized silicate grains." Proceedings of the International Astronomical Union 15, S350 (April 2019): 431–33. http://dx.doi.org/10.1017/s174392132000006x.

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AbstractWe assess the accuracy of various computational methods for obtaining infrared (IR) spectra of nanosized silicate dust grains directly from their atomistic structure and atomic motions. First, IR spectra for a selection of small nanosilicate clusters with a range of sizes and chemical compositions are obtained within the harmonic oscillator approximation employing density functional theory (DFT) based quantum chemical calculations. To check if anharmonic effects play a significant role in the IR spectra of these nanoclusters, we further obtain their IR spectra from finite temperature DFT-based ab initio molecular dynamics (AIMD). Finally, we also study the effect of temperature on the broadening of the obtained IR spectra peaks in larger nanosilicate grains with a range of crystallinities. In this case, less computationally costly classical molecular dynamics simulations are necessary due to the large number of atoms involved. Generally, we find that although DFT-based methods are more accurate, surprisingly good IR spectra can also be obtained from classical molecular dynamics calculations.

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23

Wong, Stephanie Y. Y., Pierre-Nicholas Roy, and Alex Brown. "Ab initio electronic structure and direct dynamics simulations of CH3OCl." Canadian Journal of Chemistry 87, no. 7 (July 2009): 1022–29. http://dx.doi.org/10.1139/v09-073.

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The ground (X1A′) and two lowest lying excited singlet states (11A″ and 21A′) of methyl hypochlorite have been examined using ab initio electronic structure techniques to validate computationally efficient methods, upon which direct dynamics can be based, versus high-level ones, for which direct dynamics would be intractable. Ground-state equilibrium geometries and vibrational frequencies determined using density functional theory (DFT) with the 6-31G(d) basis set are tested against coupled-cluster theory (CCSD(T)) results from the literature. Vertical excitation energies and transition dipole moments calculated at the complete active space self-consistent field CASSCF/6-31+G(d) level of theory are benchmarked against multireference configuration interaction (MRCI) results with the aug-cc-pVXZ (X = D, T, Q) family of basis sets. The excited-state gradients that will govern the classical dynamics are compared for CASSCF/6-31+G(d) versus MRCI/aug-cc-pVXZ (X = D, T). To carry out the ab initio molecular dynamics (AIMD), existing electronic structure codes have been interfaced with the molecular modelling toolkit (MMTK), an open-source program library for molecular simulation applications. We use two examples to demonstrate the use of direct dynamics in MMTK: a canonical ground-state trajectory to sample positions and momenta, and an excited-state microcanonical trajectory based on CASSCF. The work presented here forms the basis for future study of the photodissociation of CH3OCl. As well, the implementation of AIMD within MMTK provides a useful tool for examining a variety of other research problems.

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24

LUKEŠ, VLADIMÍR, ROLAND ŠOLC, MARIO BARBATTI, HANS LISCHKA, and HARALD-FRIEDRICH KAUFFMANN. "TORSIONAL POTENTIALS AND FULL-DIMENSIONAL SIMULATION OF ELECTRONIC ABSORPTION SPECTRA OF para-PHENYLENEVINYLENE OLIGOMERS USING SEMIEMPIRICAL HAMILTONIANS." Journal of Theoretical and Computational Chemistry 09, no. 01 (February 2010): 249–63. http://dx.doi.org/10.1142/s0219633610005645.

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A systematic study of torsional potential curves in electronic ground state based on second-order Møller–Plesset energy (MP2), density functional theory (DFT), and Austin mode 1 (AM1) methods is presented for para-phenylenevinylene oligomers constructed from two to four aromatic rings. The semiempirical AM1 approach gives the correct location of potential energy minima in comparison with the reference MP2 calculations and literature data. However, the semiempirical AM1 energy barriers at perpendicular orientation are ca. 30% smaller than the MP2 ones. The DFT calculations indicate optimal planar structures and the barriers are three times higher than MP2 values. Excited-state potential energy curves evaluated from vertical excitations at the time-dependent density functional theory (TD-DFT) and ab initio CI levels exhibit much steeper increase of values in the vicinity of perpendicular orientation than in the semiempirical Zerner's intermediate neglect of differential overlap (ZINDO) and ab initio RI-CC2 cases. The effects of vibrational motion of phenylene rings on the torsional broadening of absorption spectra were estimated from semi-classical molecular dynamics simulations and harmonic oscillator sampling. The simulated spectra agree well with the experiment and allow estimating the conformer distribution of the molecules.

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25

Hanh, Tran Thi Thu. "Adsorption capacity of a hydrogen atom on the 2D silicon carbide surface." Communications in Physics 33, no. 3 (September 5, 2023): 321. http://dx.doi.org/10.15625/0868-3166/18091.

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Hydrogen adsorption on two-dimensional (2D) silicon carbide (SiC) was studied using molecular dynamics and ab initio calculations. By investigating a converged density functional theory (DFT) calculation, the stable adsorption sites of a hydrogen atom on the 2D SiC were found at the top sites (TSi and TC, of which the most stable adsorption site is TSi). The adsorption of a hydrogen atom on 2D silicon carbide led to local structural changes in silicon carbide.

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26

Molla, M. R., A. Z. Ziauddin Ahmed, and G. M. Bhuiyan. "Static and Dynamic Properties of Elemental Liquid Pd: An Orbital Free Molecular Dynamic Study." Journal of Nepal Physical Society 6, no. 1 (August 6, 2020): 59–67. http://dx.doi.org/10.3126/jnphyssoc.v6i1.30522.

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We have studied the static and dynamic properties of liquid metal, namely Pd at thermodynamic state T=1853K within the scope of the orbital free ab-initio molecular dynamics (OF-AIMD) simulation technique. In this simulation process, electronic energy is calculated by using the Hohenberg-Kohn version of DFT. Here the electron-ion interaction energy functional is approximated by a local pseudopotential prescribed by Bhuiyan et al. The local density approximation is used to describe the exchange-correlation energy functional. The static structure factor, S(q), pair distribution function, g(r), coordination number, Nc, and isothermal compressibility, κT, are studied which are familiar as static properties. The single particle and collective dynamics namely diffusion coefficient, dynamic structure factor, velocity of sound, shear viscosity etc. are also studied. The results of calculation agree well with experimental as well as other theoretical values.

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27

Ludt, Christian, Dirk C. Meyer, and Matthias Zschornak. "Ferroelectric Phase Transition in Barium Titanate Revisited with Ab Initio Molecular Dynamics." Materials 17, no. 5 (February 23, 2024): 1023. http://dx.doi.org/10.3390/ma17051023.

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The ferroelectric phase transition of the perovskite barium titanate as well as its technical importance regarding the switching of respective polar properties is well known and has been thoroughly studied, both experimentally and on theoretical grounds. While details about the phase diagram as well as transition temperatures are experimentally well known, the theoretical approaches still face difficulties in contributing a detailed description of these phase transitions. Within this work, a new methodological approach is introduced to revisit the ferroelectric phase transition with first-principles methods. With the chosen ab initio molecular dynamics (AIMD) method in combination with the applied NpT ensemble, we are able to join the accuracy of density functional theory (DFT) with ambient conditions, realized using a thermostat and barostat in an MD simulation. The derived phase diagram confirms recent corrections in the theoretical models and reproduces the phase boundary pressure dependence of TC. In conclusion of the statistical atomistic dynamics, the nature of the transition can be described in a more detailed way. In addition, this work paves the way towards locally patterned piezoelectrica by means of acoustic standing waves as well as piezoelectrically induced acoustic resonators.

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28

He, Yurong, Peng Zhao, Wenping Guo, Yong Yang, Chun-Fang Huo, Yong-Wang Li, and Xiao-Dong Wen. "Hägg carbide surfaces induced Pt morphological changes: a theoretical insight." Catalysis Science & Technology 6, no. 17 (2016): 6726–38. http://dx.doi.org/10.1039/c6cy00764c.

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Comprehensive spin-polarized density functional theory (DFT) combined with ab initio molecular dynamic (AIMD) simulations have been performed to explore the structures, energies, and diffusion behavior of platinum on Fe₅C₂ surfaces with importance in Fischer–Tropsch (F–T) catalysis.

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29

Abramyan, Ara, Zhiwei Liu, and Vojislava Pophristic. "An ab-initio study of pyrrole and imidazole arylamides." Journal of the Serbian Chemical Society 78, no. 11 (2013): 1789–95. http://dx.doi.org/10.2298/jsc130929104a.

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Arylamide foldamers have been shown to have a number of biological and medicinal applications. For example, a class of pyrrole-imidazole polyamide foldamers is capable of binding specific DNA sequences and preventing development of various gene disorders, most importantly cancer. Molecular dynamics (MD) simulations can provide crucial details in understanding the atomic level events related to foldamer/DNA binding. An important first step in the accurate simulation of these foldamer/DNA systems is the reparametrization of force field parameters for torsion around the aryl-amide bonds. Here we highlight our Density Functional Theory (DFT) potential energy profiles and derived force field parameters for four aryl-amide bond types for the pyrrole and imidazole building blocks extensively used in foldamer design for the DNA-binding polyamides. These results contribute to developing of computational tools for an appropriate molecular modeling of pyrrole-imidazole polyamide/DNA binding, and provide an insight into the chemical factors that influence the flexibility of the pyrrole-imidazole polyamides, and their binding to DNA.

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30

Shiranirad, Mozhdeh, and Niall J. English. "Development of Machine Learning Atomistic Potential for Molecular Simulation of Hematite–Water Interfaces." Crystals 14, no. 11 (October 28, 2024): 930. http://dx.doi.org/10.3390/cryst14110930.

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A novel approach for constructing a machine-learned potential energy surface (MLP) from unlabeled training data is presented. Utilizing neural networks augmented with a pool-based active learning sampling method, a potential energy surface (PES) is developed for the accurate modeling of interfaces of hematite iron oxide and water, fitting the much more expensive density functional theory (DFT). Molecular dynamics simulations were performed using this DFT-based PES to characterize the structural and energetic properties of the system. By utilizing the developed machine learning potential (MLP), it was possible to simulate much larger systems for extended periods of time, which will be important for leveraging machine learning potentials as accurate and pragmatic simulation-led molecular design and prototyping tools whilst preserving the ab initio accuracy.

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31

Wang, Weihua, Wenling Feng, Wenliang Wang, and Ping Li. "Theoretical Investigations on the Reactivity of Methylidyne Radical toward 2,3,7,8-Tetrachlorodibenzo-p-Dioxin: A DFT and Molecular Dynamics Study." Molecules 23, no. 10 (October 18, 2018): 2685. http://dx.doi.org/10.3390/molecules23102685.

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To explore the potential reactivity of the methylidyne radical (CH) toward 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), the reaction mechanism between them has been systematically investigated employing the density functional theory (DFT) and ab initio molecular dynamics simulations. The relevant thermodynamic and kinetic parameters in the possible reaction pathways have been discussed as well as the IR spectra and hyperfine coupling constants (hfcc’s) of the major products. Different from the reaction of the CH radical with 2,3,7,8-tetrachlorodibenzofuran, CH radical can attack all the C-C bonds of TCDD to form an initial intermediate barrierlessly via the cycloaddition mechanism. After then, the introduced C-H bond can be further inserted into the C-C bond of TCDD, resulting in the formation of a seven-membered ring structure. The whole reactions are favorable thermodynamically and kinetically. Moreover, the major products have been verified by ab initio molecular dynamics simulations. The distinct IR spectra and hyperfine coupling constants of the major products can provide some help for their experimental detection and identification. In addition, the reactivity of the CH radical toward the F- and Br-substituted TCDDs has also been investigated. Hopefully, the present findings can provide new insights into the reactivity of the CH radical in the transformation of TCDD-like dioxins.

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32

Laporte, Sara, Fabio Finocchi, Lorenzo Paulatto, Marc Blanchard, Etienne Balan, François Guyot, and Antonino Marco Saitta. "Strong electric fields at a prototypical oxide/water interface probed by ab initio molecular dynamics: MgO(001)." Physical Chemistry Chemical Physics 17, no. 31 (2015): 20382–90. http://dx.doi.org/10.1039/c5cp02097b.

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33

Haddad, Elie, Simon Sprocq, Leonard Schue, Vladimir Pimonov, Mickael Dolle, Richard Martel, and Alain Rochefort. "Electronic and Vibrational Properties of Episulfide-Graphene Materials." ECS Meeting Abstracts MA2023-01, no. 13 (August 28, 2023): 1320. http://dx.doi.org/10.1149/ma2023-01131320mtgabs.

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Our group has investigated the stability of sulfur adatoms on graphene obtained by a direct reaction of highly oriented pyrolytic graphite (HOPG) with elemental sulfur. With the help of density functional theory (DFT) calculations, we have developed different models of the structure and evaluated the electronic and vibrational properties of synthesized graphene-sulfur (GS) materials. Our structural models are based on sulfur atoms covalently attached to graphene. The DFT electronic structure calculations support the formation of a strong and stable sulfur bonding to graphene and give a chemical composition in good agreement with the experimental proportion of sulfur to carbon. In addition, ab-initio molecular dynamics simulations allow us to confirm the stability on S-G bonds. The vibrational modes calculated with DFT support the vibrational signatures of the GS materials observed using Raman spectroscopy.

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34

Krishnan, Yogeshwaran, Aaron Byrne, and Niall English. "Vibrational Study of Iodide-Based Room-Temperature Ionic-Liquid Effects on Candidate N719-Chromophore/Titania Interfaces for Dye-Sensitised Solar-Cell Applications from Ab-Initio Based Molecular-Dynamics Simulation." Energies 11, no. 10 (September 26, 2018): 2570. http://dx.doi.org/10.3390/en11102570.

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The accurate ab-initio modelling of prototypical and well-representative photo-active interfaces for candidate dye-sensitised solar cells is a challenging problem. To this end, using ab-initio molecular-dynamics (AIMD) simulation based on Density Functional Theory (DFT), the effects of explicit solvation by iodide-based, I−[bmim]+ room-temperature ionic liquids (RTILs) have been assessed on modelling a N719-chromophore sensitising dye adsorbed onto an anatase-titania (101) surface. In particular, the vibrational spectra for this model photo-active interface were calculated by means of Fourier transformed mass-weighted velocity autocorrelation functions. These were compared with experiment and against each other to gain an understanding of how using iodine-based RTILs as the electrolytic hole acceptor alters the dynamical properties of the widely-used N719 dye. The effect of Perdew-Burke-Ernzerhof (PBE) and Becke-Lee-Yang-Parr (BLYP) functionals on the vibrational spectra were assessed. PBE generally performed best in producing spectra which matched the typically expected experimental frequency modes.

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35

Chentouf, Sara, Jean Marc Raulot, Hafid Aourag, and Thierry Grosdidier. "Density Functional Theory and Ab Initio Molecular Dynamics Study of the Effect of Ti and Zr Transition Metals in D0₃ Fe₃Al." Materials Science Forum 706-709 (January 2012): 1095–99. http://dx.doi.org/10.4028/www.scientific.net/msf.706-709.1095.

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The formation energies of the T.M impurities Ti and Zr were calculated using DFT calculations at absolute zero and ab initio MD simulations at 300 K. We found that, with increasing temperature, Zr impurities become more stable and prefer to segregate at the interface of ∑5 (310)[001] grain boundary. In the case of Ti, the results show that it remains a stable defect when temperature increases.

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Tiwari, Nidhi, Seenivasan Hariharan, and Ashwani K. Tiwari. "Effect of temperature on CO oxidation over Pt(111) in two-dimensional confinement." Journal of Chemical Physics 157, no. 14 (October 14, 2022): 144701. http://dx.doi.org/10.1063/5.0116783.

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Confined catalysis between a two-dimensional (2D) cover and metal surfaces has provided a unique environment with enhanced activity compared to uncovered metal surfaces. Within this 2D confinement, weakened adsorption and lowered activation energies were observed using surface science experiments and density functional theory (DFT) calculations. Computationally, the role of electronic and mechanical factors responsible for the improved activity was deduced only from static DFT calculations. This demands a detailed investigation on the dynamics of reactions under 2D confinement, including temperature effects. In this work, we study CO oxidation on a 2D graphene covered Pt(111) surface at 90 and 593 K using DFT-based ab initio molecular dynamics simulations starting from the transition state configuration. We show that CO oxidation in the presence of a graphene cover is substantially enhanced (2.3 times) at 90 K. Our findings suggest that 2D confined spaces can be used to enhance the activity of chemical reactions, especially at low temperatures.

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Mpourmpakis, Giannis, Emmanuel Tylianakis, and George Froudakis. "Hydrogen Storage in Carbon Nanotubes: A Multi-Scale Theoretical Study." Journal of Nanoscience and Nanotechnology 6, no. 1 (January 1, 2006): 87–90. http://dx.doi.org/10.1166/jnn.2006.17909.

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A Combination of quantum and classical calculations has been performed to investigate the hydrogen storage in single-walled carbon nanotubes (SWNTs). The ab-initio calculations at the Density Functional level of Theory (DFT) show the nature of hydrogen interaction in selected sites of a (5,5) tube walls. On top of this, Molecular Dynamics simulations model large scale nanotube systems and reproduce the storage capacity under variant temperature conditions. Our results indicate that the interaction of hydrogen with SWNTs is very weak and slightly increase of temperature, causes hydrogen diffusion from the tube walls.

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Alnemrat, Sufian, Joseph P. Hooper, Lidong Guo, and Zongbi Bao. "Structural and bonding properties of small hydrocarbons inside Ca(squarate)-metal organic framework: ab-initio study." Journal of Physics Communications 6, no. 4 (April 1, 2022): 045001. http://dx.doi.org/10.1088/2399-6528/ac53f9.

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Abstract Ab−initio Molecular Dynamic (MD) and static Density Functional Theory (DFT) are used to study the structural and bonding properties of small hydrocarbon adsorbates inside Ca(squarate)−Metal Organic Framework (MOF). Car−Parrinello Molecular Dynamics (CPMD) simulations of a single−adsorbate−MOF structure are used to obtain the adsorbate most preferred site of adsorption. This site is used for further structural and bonding analyses using static DFT. Unlike many other MOFs; we found that the Ca(squarate)−MOF physisorbs and weakly binds small adsorbate molecules such as C2H2, C2H4, C2H6, and C3H8 with no observed charge transfer and minimal hybridization with the MOF orbitals. No covalent bonding is seen near the preferred site of adsorption. The calculated binding energies decreases as the H content in the adsorbate molecule increases and found to be −18.71 kJ/mol, −18.14 kJ/mol, −15.75 kJ/mol, and—4.47 kJ/mol for C2H2, C2H4, C2H6, and C3H8 molecules respectively. Density of State (DOS) and a Crystal Orbital Overlap Population (COOP) analyses show that the interactions between C and H atoms in the molecule and C and O atoms in the MOF have antibonding characteristics near the Fermi level. These antibonding states tend to destabilize the overall electronic structure of the combined adsorbate/MOF system and hence decrease the binding energies of these adsorbates inside the MOF.

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39

Becker, Andreas, Nadine Nettelmann, Ulrike Kramm, Winfried Lorenzen, Martin French, and Ronald Redmer. "Modeling giant planets and brown dwarfs." Proceedings of the International Astronomical Union 6, S276 (October 2010): 473–74. http://dx.doi.org/10.1017/s1743921311020850.

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AbstractWe present new results in modeling the interiors of Giant Planets (GP) and Brown Dwarfs (BD). In general models of the interior rely on equation of state data for planetary materials which have considerable uncertainties in the high-pressure domain. Our calculations are based on ab initio equation of state (EOS) data for hydrogen, helium, hydrogen-helium mixtures and water as the representative of all heavier elements or ices using finite-temperature density functional theory molecular dynamics (FT-DFT-MD) simulations. We compare results for the BD Gliese 229B calculated with Saumon-Chabrier-Van Horn EOS (SCVH95) and our EOS data.

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40

Hu, Hang, and Alejandro D. Rey. "Multi-step modeling of liquid crystals using ab initio molecular packing and hybrid quantum mechanics/molecular mechanics simulations." Journal of Theoretical and Computational Chemistry 16, no. 02 (March 2017): 1750012. http://dx.doi.org/10.1142/s0219633617500122.

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A density functional theory (DFT) based multi-step simulation method is used to characterize the detailed molecular structure and inter/intra- molecular interactions of two benchmark liquid crystals (LC) 5CB, 8CB and a novel tri-biphenyl ring bent core LC material. The method uses hybrid DFT at the B3LYP/6-31G* level to obtain molecular structure and Raman data. These results are fed to a crystal packing simulation to find possible crystal structures. A pico-second quantum mechanics/molecular mechanics (QM/MM) simulation model is built for the selected structures with lower overall energy as well as optimal density. The stabilized crystal structures are then extended into a super cell, heated and simulated using a mixed force field and nano-second molecular dynamics (MD). The described simulation process sequence provides predictions of molecular Raman spectrum, LC density, isotropic depolarization ratio, ratio of differential polarizability, order parameters, molecular structures, and rotating Raman spectrum of the different mesophases. The Raman spectra, order parameters and depolarization ratios all agree well with existing experimental and previous simulation results. The study of the novel tri-biphenyl ring bent core LC system shows that the ratio of differential polarizability depends on intra-molecular interactions. The findings presented in this manuscript contribute to the on-going efforts to establish links between LC molecular structures and their properties, including optical behavior.

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Kang, Qingxin, Guofeng Wang, Qing Liu, Xiaochong Sui, Yongkang Liu, Yuqing Chen, Shuyi Luo, and Zhenlun Li. "Investigation for oxidation mechanism of CrN: A combination of DFT and ab initio molecular dynamics study." Journal of Alloys and Compounds 885 (December 2021): 160940. http://dx.doi.org/10.1016/j.jallcom.2021.160940.

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42

Rodríguez-Santiago, Luis, Jorge Alí-Torres, Pietro Vidossich, and Mariona Sodupe. "Coordination properties of a metal chelator clioquinol to Zn2+ studied by static DFT and ab initio molecular dynamics." Physical Chemistry Chemical Physics 17, no. 20 (2015): 13582–89. http://dx.doi.org/10.1039/c5cp01615k.

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Xie, Ke Qiang, Jian Wen Tang, Xiu Min Chen, Wen Hui Ma, Bin Yang, and Zi Li Liu. "Structure Simulation Calculation of Impurities B with Fe, Al or Ca in Metallurgical Grade Silicon." Materials Science Forum 750 (March 2013): 216–19. http://dx.doi.org/10.4028/www.scientific.net/msf.750.216.

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Ab initio molecular dynamics (MD) calculations had been performed in this work to simulate the interactions of B with Fe, Al or Ca in metallurgical-grade silicon (MG-Si). The temperature of the MD simulations is 0K, the simulation time is 1ps. All the calculations were performed by using the CASTEP module of Materials Studio 4.3 software package. The geometry optimizations of impurities B with Fe, Al and Ca in MG-Si were performed with density functional theory (DFT) calculation. The Density of States of the optimized structures was calculated and the results have the potential application in guiding the boron removal from MG-Si by acid leaching.

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44

Łuczyńska, Katarzyna, Kacper Drużbicki, Tomasz Runka, Norbert Pałka, and Jan Węsicki. "Vibrational Response of Felodipine in the THz Domain: Optical and Neutron Spectroscopy Versus Plane-Wave DFT Modeling." Journal of Infrared, Millimeter, and Terahertz Waves 41, no. 11 (December 15, 2019): 1301–36. http://dx.doi.org/10.1007/s10762-019-00634-9.

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Abstract We present a joint experimental and computational terahertz (THz) spectroscopy study of the most stable polymorph (form I) of an antihypertensive pharmaceutical solid, felodipine (FLD). The vibrational response has been analyzed at room temperature by combining optical (THz-TDS, FT-IR, THz-Raman) and neutron (INS) terahertz spectroscopy. With the challenging example of a large and flexible molecular solid, we illustrate the complementarity of the experimental techniques. We show how the results can be understood by employing ab initio modeling and discuss current progress in the field. To this end, we employ plane wave formulation of density functional theory (plane wave DFT) along with harmonic lattice dynamics calculations (HLD) and ab initio molecular dynamics (AIMD) simulations. Based on a comprehensive theoretical analysis, we discover an inconsistency in the commonly accepted structural model, which can be linked to a distinct librational dynamics of the side ester chains. As a result, only a moderate agreement with the experimental spectra can be achieved. We, therefore, propose an alternative structural model, effectively accounting for the influence of the large-amplitude librations and allowing for a comprehensive analysis of the vibrational resonances up to 4.5 THz. In that way, we illustrate the applicability of the computationally supported THz spectroscopy to detect subtle structural issues in molecular solids. While the provided structural model can be treated as a guess, the problem calls for further revision by means of high-resolution crystallography. The problem also draws a need of extending the THz experiments toward low-temperature conditions and single-crystal samples. On the other hand, the studied system emerges as a challenge for the DFT modeling, being extremely sensitive to the level of the theory used and the resulting description of the intermolecular forces. FLD form I can be, hence, considered as a testbed for the use of more sophisticated theoretical approaches, particularly relying on an advanced treatment of the van der Walls forces and going beyond zero-temperature conditions and harmonic approximation.

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Baba, Takeshi, Keitaro Sodeyama, Yoshiumi Kawamura, and Yoshitaka Tateyama. "Li-ion transport at the interface between a graphite anode and Li2CO3 solid electrolyte interphase: ab initio molecular dynamics study." Physical Chemistry Chemical Physics 22, no. 19 (2020): 10764–74. http://dx.doi.org/10.1039/c9cp06608j.

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DFT calculation based free energy profile for Li-ion transport across graphite anode/Li₂CO₃ SEI interface, indicating how to understand the profile change between discharging and charging in battery.

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46

Abdel-Mottaleb, M. S. A. "On the Nature of Interplay among Major Flexibility Channels in Molecular Rotors." Journal of Chemistry 2019 (January 2, 2019): 1–14. http://dx.doi.org/10.1155/2019/8359527.

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As a part of our interest in the excited-state dynamics of flexible materials, we have undertaken a theoretical investigation to the photo-induced reactions of 2-[4-(dimethylamino)benzylidene]malononitrile (BMN) by a combination of the density functional theory, its extended time-dependent (TD-DFT) single reference, and ab initio molecular dynamic (MD) simulations. The results showed that double-bond twisting and the neighbor single-bond twisting togetherness in the excited singlet state is the most important nonradiative deactivation channel to the ground state. Double- and single-bond twisting insert clear intersections among the potential energy surfaces of the singlet states (especially S1/S0) leading to fluorescence quenching. Furthermore, effects of molecular dynamic simulations on molecular properties in the femtosecond to picosecond time domain are studied to validate the results. In agreement with the experimental results, the findings conclude the existence of a flexible geometry-dependent single emission band. Such a study may give information on how the molecule could be externally modified/fixed to yield a desired effect, i.e., more fluorescence or more nonradiative decay.

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47

Karakas, A., Y. Ceylan, M. Karakaya, M. Taser, B. B. Terlemez, N. Eren, Y. El Kouari, M. Lougdali, A. K. Arof, and B. Sahraoui. "One-photon Absorption Characterizations, Dipole Polarizabilities and Second Hyperpolarizabilities of Chlorophyll a and Crocin." Open Chemistry 16, no. 1 (December 21, 2018): 1242–47. http://dx.doi.org/10.1515/chem-2018-0134.

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AbstractThe dispersion-free dipole polarizability (α) computations for chlorophyll a (1) and crocin (2) have been achieved by density functional theory (DFT) at B3LYP/ 6-31G(d) level. The measured one-photon absorption (OPA) wavelengths are quite consistence with the theoretically obtained values. Ab-initio quantum chemical calculations (time-dependent Hartree-Fock (TDHF)) have been implemented to reveal the static second hyperpolarizabilities (γ) and dynamic dipole polarizabilities of the title molecules. The examined compounds display γ with non-zero values, introducing their third-order nonlinear optical (NLO) phenomena. The first and second frontier molecular orbitals of the investigated molecules have been also derived from DFT.

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48

Tachikawa, Hiroto, and Hiroshi Kawabata. "Interaction between Thymine Dimer and Flavin−Adenine Dinucleotide: A DFT and Direct Ab Initio Molecular Dynamics Study." Journal of Physical Chemistry B 112, no. 24 (June 2008): 7315–19. http://dx.doi.org/10.1021/jp801564t.

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49

Berisha, Avni, Rajesh Hadhlar, and Omar Dagdag. "Ab initio exploration of modified carbon nanotubes as potential corrosion inhibitors." Macedonian Journal of Chemistry and Chemical Engineering 43, no. 1 (May 19, 2024): 115–26. http://dx.doi.org/10.20450/mjcce.2024.2806.

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In order to develop novel unexplored potential corrosion inhibitors, covalently modified single-walled carbon nanotubes (SWCNT) via benzoic (–PhCOOH) and aniline (–PhNH2) groups are being investigated as corrosion inhibitors for the first time. Utilizing a comprehensive approach, this study employed density functional theory (DFT), Monte Carlo (MC), and molecular dynamics simulations (MD) to assess the adsorption behavior of modified nanotubes as corrosion inhibitors on the Cu(111) surface within a simulated aqueous HCl corrosion medium. The results provided molecular information on the adsorption capability, geometry adsorption centers, and adsorption energies (Eads) of carbon nanotubes on the surface of Cu(111). The adsorption energy values unveiled robust interactions between SWCNT–PhCOOH and SWCNT–PhNH2 inhibitors and the Cu(111) surface, suggesting a highly effective corrosion protection mechanism. The calculated Eads values exhibited notable ranges, spanning from –260.82 to –308.18 kcal/mol for SWCNT–PhCOOH and –220.92 to –261.01 kcal/mol for SWCNT–PhNH2 with the maximum probability values, representing the most favorable adsorption scenarios, determined to be –292.96 and –229.39 kcal/mol, respectively. A key insight from Monte Carlo simulations underscored the inherent spontaneity of the adsorption process, corroborated by the consistently negative Eads values. These findings collectively underscore the substantial affinity of the inhibitors to the copper surface, contributing to a deeper comprehension of their corrosion inhibition capabilities.

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ZAKIRUR-REHMAN and SARDAR SIKANDAR HAYAT. "THERMAL DIFFUSION DYNAMIC BEHAVIOR OF TWO-DIMENSIONAL Ag-SMALL CLUSTERS ON Ag(1 1 1) SURFACE." Surface Review and Letters 22, no. 05 (August 27, 2015): 1550067. http://dx.doi.org/10.1142/s0218625x15500675.

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In this paper, the thermal diffusion behavior of small two-dimensional Ag -islands on Ag (1 1 1) surface has been explored using molecular dynamics (MD) simulations. The approach is based on semi-empirical potentials. The key microscopic processes responsible for the diffusion of Ag 1−5 adislands on Ag (1 1 1) surface are identified. The hopping and zigzag concerted motion along with rotation are observed for Ag one-atom to three-atom islands while single-atom and multi-atom processes are revealed for Ag four-atom and five-atom islands, during the diffusion on Ag (1 1 1) surface. The same increasing/decreasing trend in the diffusion coefficient and effective energy barrier is observed in both the self learning kinetic Monte Carlo (SLKMC) and MD calculations, for the temperature range of 300–700 K. An increase in the value of effective energy barrier is noticed with corresponding increase in the number of atoms in Ag -adislands. A reasonable linear fit is observed for the diffusion coefficient for studied temperatures (300, 500 and 700 K). For the observed diffusion mechanisms, our findings are in good agreement with ab initio density-functional theory (DFT) calculations for Al / Al (1 1 1) while the energy barrier values are in same range as the experimental values for Cu / Ag (1 1 1) and the theoretical values using ab initio DFT supplemented with embedded-atom method for Ag / Ag (1 1 1).

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