Limitations of ab initio molecular dynamics simulations of simple reactions: F + H2 as a prototype

Silva, Antônio J. R. da; Cheng, Hsiu‐Yao; Gibson, Douglas A; Sorge, Kathy L.; Liu, Zhihua; Carter, Emily A.

doi:10.1016/s1386-1425(97)89474-7

Cited by 9 publications

(5 citation statements)

References 40 publications

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“…Several methods exist for calculating forces on the atoms from quantum mechanics and propagating the nuclei classically. Generally, one either carries out an extended Lagrangian (fictitious wave function) dynamics as first proposed by Car and Parrinello 32 or one optimizes the wave function at each time step, staying on the Born−Oppenheimer surface. , Both Parrinello and Gibson et al . provide an in-depth discussion of the merits of both approaches.…”

Section: Calculational Detailsmentioning

confidence: 99%

“…Despite these limitations, one can use this technique to gain considerable qualitative insight via a representative set of trajectories. AIMD of simple molecular reactions have employed, for example, variants of Hartree−Fock theory [e.g., in the reactions of: F + C 2 H 4 , thymine dimer with its cation, CH 2 O - with H 3 CCl, and H 2 O + H 3 CCl], density functional theory (e.g., HO + NO 2 and a double proton transfer in (HCOOH) 2 ) and complete-active-space self-consistent-field (CASSCF) theory [e.g., F + H 2 → FH + H] for evaluation of the forces on the atoms.…”

Section: Introductionmentioning

confidence: 99%

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Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

et al. 2001

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We present complete active space self-consistent field (CASSCF) ab initio molecular dynamics (AIMD) simulations of the preparation of the metastable species vinylidene, and its subsequent, highly exothermic isomerization to acetylene, via electron removal from vinylidene anion (D(2)C=C(-) --> D(2)C=C: --> DC triple bond CD). After equilibrating vinylidene anion-d(2) at either 600 +/- 300 K (slightly below the isomerization barrier) or 1440 K +/- 720 K (just above the isomerization barrier), we remove an electron to form a vibrationally excited singlet vinylidene-d(2) and follow its dynamical evolution for 1.0 ps. Remarkably, we find that none of the vinylidenes equilibrated at 600 K and only 20% of the vinylidenes equilibrated at 1440 K isomerized, suggesting average lifetimes >1 ps for vibrationally excited vinylidene-d(2). Since the anion and neutral vinylidene are structurally similar, and yet extremely different geometrically from the isomerization transition state (TS), neutral vinylidene is not formed near the TS so that it must live until it has sufficient instantaneous kinetic energy in the correct vibrational mode(s). The origin of the delay is explained via both orbital rearrangement and intramolecular vibrational energy redistribution (IVR) effects. Unique signatures of the isomerization dynamics are revealed in the anharmonic vibrational frequencies extracted from the AIMD, which should be observable by ultrafast vibrational spectroscopy and in fact are consistent with currently available experimental spectra. Most interestingly, of those trajectories that did isomerize, every one of them violated conventional transition-state theory by recrossing back to vinylidene multiple times, against conventional notions that expect highly exothermic reactions to be irreversible. The dynamical motion responsible for the multiple barrier recrossings involves strong mode-coupling between the vinylidene CD(2) rock and a local acetylene DCC bend mode that has been recently observed experimentally. The multiple barrier recrossings can be used, via a generalized definition of lifetime, to reconcile extremely disparate experimental estimates of vinylidene's lifetime (differing by at least 6 orders of magnitude). Last, a caveat: These results are constrained by the approximations inherent in the simulation (classical nuclear motion, neglect of rotation-vibration coupling, and restriction to C(s) symmetry); refinement of these predictions may be necessary when more exact simulations someday become feasible.

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Section: Calculational Detailsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

et al. 2001

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“…AIMD has been traditionally limited to simulating relatively small systems (∼1000 atoms) and short times (∼100 ps). − , Traditional methods often fail to achieve accurate simulations for multiscale problems, such as various time and space scales involved. Studying chemical reactions, such as adsorption, surface reactions, diffusion, and catalysis, requires simulations that can provide an understanding of underlying processes, which are inherently multiscale.…”

Section: Application Of Mlffmentioning

confidence: 99%

“…By doing so, researchers can increase the simulation size without compromising simulation accuracy. Moreover, the MLFF overcomes the limitations of AIMD simulations regarding space-time dimensions. − …”

Section: Fundamentals Of Mlffmentioning

confidence: 99%

Applications and Advances in Machine Learning Force Fields

Wu,

Yang,

Zhao

et al. 2023

J. Chem. Inf. Model.

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Force fields (FFs) form the basis of molecular simulations and have significant implications in diverse fields such as materials science, chemistry, physics, and biology. A suitable FF is required to accurately describe system properties. However, an off-the-shelf FF may not be suitable for certain specialized systems, and researchers often need to tailor the FF that fits specific requirements. Before applying machine learning (ML) techniques to construct FFs, the mainstream FFs were primarily based on first-principles force fields (FPFF) and empirical FFs. However, the drawbacks of FPFF and empirical FFs are high cost and low accuracy, respectively, so there is a growing interest in using ML as an effective and precise tool for reconciling this trade-off in developing FFs. In this review, we introduce the fundamental principles of ML and FFs in the context of machine learning force fields (MLFF). We also discuss the advantages and applications of MLFF compared to traditional FFs, as well as the MLFF toolkits widely employed in numerous applications.

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“…DPD incorporates short-range, soft repulsion potentials while simulating the dynamics of the system, which lends itself to higher time steps than MD [ 40 ]. AIMD may utilize DFT methods or other correlated wavefunction methods such as Møller–Plesset theory or coupled cluster methods to provide a more realistic analysis of the system to more closely resemble experimental conditions [ 41 , 42 , 43 , 44 , 45 ]. This can provide even more precise results but can vastly increase the computational cost and significantly limit the practical timescale, up to only a few picoseconds, for a given level of detail [ 33 , 46 ].…”

Section: Introductionmentioning

confidence: 99%

Review of Recent Computational Research on the Adsorption of PFASs with a Variety of Substrates

Minervino,

Belfield

2024

IJMS

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The widespread use and impervious nature of per- and polyfluorinated alkyl substances (PFASs) is leading to potentially harmful exposure in numerous environments. One avenue to explore remediation of PFAS-contaminated environments involves investigating how well PFASs adsorb onto various substrates. In the current review, we focus on summarizing recent computational research, largely involving density functional theory (DFT) and molecular dynamics (MD), into the adsorption and interaction of PFASs with a variety of substrates with an aim to provide insight and inspire further research that may lead to solutions to this critical problem that impacts the environment and human health.

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Limitations of ab initio molecular dynamics simulations of simple reactions: F + H2 as a prototype

Cited by 9 publications

References 40 publications

Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

Applications and Advances in Machine Learning Force Fields

Review of Recent Computational Research on the Adsorption of PFASs with a Variety of Substrates

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Limitations of ab initio molecular dynamics simulations of simple reactions: F + H2 as a prototype

Cited by 9 publications

References 40 publications

Long Live Vinylidene! A New View of the H2CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

Long Live Vinylidene! A New View of the H2CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

Applications and Advances in Machine Learning Force Fields

Review of Recent Computational Research on the Adsorption of PFASs with a Variety of Substrates

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Product

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Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics

Long Live Vinylidene! A New View of the H₂CC: → HC⋮CH Rearrangement from ab Initio Molecular Dynamics