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Journal articles on the topic 'Oppenheimer Molecular'

Author: Grafiati

Published: 6 September 2023

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1

Jasper, Ahren W., Shikha Nangia, Chaoyuan Zhu, and Donald G. Truhlar. "Non-Born−Oppenheimer Molecular Dynamics." Accounts of Chemical Research 39, no. 2 (February 2006): 101–8. http://dx.doi.org/10.1021/ar040206v.

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2

Cassidy, David C. "Oppenheimer's first paper: Molecular band spectra and a professional style." Historical Studies in the Physical and Biological Sciences 37, no. 2 (March 1, 2007): 247–70. http://dx.doi.org/10.1525/hsps.2007.37.2.247.

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Beginning early in the 20th century spectroscopists attributed the infrared band spectra emitted by diatomic molecules to quantum vibration and rotation modes of the molecules. Because of these relatively simple motions, band spectra offered a convenient .rst phenomenon to which to apply formulations of the new quan-tum mechanics in 1926. In his .rst paper, completed in Cambridge in May 1926, Oppenheimer presented a derivation of the frequencies and relative intensities of the observed spectral lines on the basis of Paul Dirac's new quantum commutator algebra. At the same time Lucy Mensing published a similar derivation utiliz-ing matrix mechanics, as did Edwin Fues utilizing wave mechanics. Analyses of Oppenheimer's paper and of its historical and scienti.c contexts offer insights into the new quantum mechanics and its utilization and reception during this brief period of competing formalisms, and into the characteristic features of Oppenheimer's later style of research and publication.

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3

Sordoni, Vania. "Molecular scattering and Born-Oppenheimer approximation." Journal of the London Mathematical Society 81, no. 1 (December 21, 2009): 202–24. http://dx.doi.org/10.1112/jlms/jdp067.

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4

Mátyus, Edit. "Pre-Born–Oppenheimer molecular structure theory." Molecular Physics 117, no. 5 (October 14, 2018): 590–609. http://dx.doi.org/10.1080/00268976.2018.1530461.

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5

Niklasson, Anders M. N., and Christian F. A. Negre. "Shadow energy functionals and potentials in Born–Oppenheimer molecular dynamics." Journal of Chemical Physics 158, no. 15 (April 21, 2023): 154105. http://dx.doi.org/10.1063/5.0146431.

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In Born–Oppenheimer molecular dynamics (BOMD) simulations based on the density functional theory (DFT), the potential energy and the interatomic forces are calculated from an electronic ground state density that is determined by an iterative self-consistent field optimization procedure, which, in practice, never is fully converged. The calculated energies and forces are, therefore, only approximate, which may lead to an unphysical energy drift and instabilities. Here, we discuss an alternative shadow BOMD approach that is based on backward error analysis. Instead of calculating approximate solutions for an underlying exact regular Born–Oppenheimer potential, we do the opposite. Instead, we calculate the exact electron density, energies, and forces, but for an underlying approximate shadow Born–Oppenheimer potential energy surface. In this way, the calculated forces are conservative with respect to the approximate shadow potential and generate accurate molecular trajectories with long-term energy stabilities. We show how such shadow Born–Oppenheimer potentials can be constructed at different levels of accuracy as a function of the integration time step, δt, from the constrained minimization of a sequence of systematically improvable, but approximate, shadow energy density functionals. For each energy functional, there is a corresponding ground state Born–Oppenheimer potential. These pairs of shadow energy functionals and potentials are higher-level generalizations of the original “zeroth-level” shadow energy functionals and potentials used in extended Lagrangian BOMD [Niklasson, Eur. Phys. J. B 94, 164 (2021)]. The proposed shadow energy functionals and potentials are useful only within this extended dynamical framework, where also the electronic degrees of freedom are propagated as dynamical field variables together with the atomic positions and velocities. The theory is quite general and can be applied to MD simulations using approximate DFT, Hartree–Fock, or semi-empirical methods, as well as to coarse-grained flexible charge models.

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6

Bubin, Sergiy, Michele Pavanello, Wei-Cheng Tung, Keeper L. Sharkey, and Ludwik Adamowicz. "Born–Oppenheimer and Non-Born–Oppenheimer, Atomic and Molecular Calculations with Explicitly Correlated Gaussians." Chemical Reviews 113, no. 1 (October 2012): 36–79. http://dx.doi.org/10.1021/cr200419d.

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7

Odell, Anders, Anna Delin, Börje Johansson, Marc J. Cawkwell, and Anders M. N. Niklasson. "Geometric integration in Born-Oppenheimer molecular dynamics." Journal of Chemical Physics 135, no. 22 (December 14, 2011): 224105. http://dx.doi.org/10.1063/1.3660689.

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8

Patchkovskii, Serguei. "Electronic currents and Born-Oppenheimer molecular dynamics." Journal of Chemical Physics 137, no. 8 (August 28, 2012): 084109. http://dx.doi.org/10.1063/1.4747540.

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9

Martínez, Enrique, Marc J. Cawkwell, Arthur F. Voter, and Anders M. N. Niklasson. "Thermostating extended Lagrangian Born-Oppenheimer molecular dynamics." Journal of Chemical Physics 142, no. 15 (April 21, 2015): 154120. http://dx.doi.org/10.1063/1.4917546.

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10

Niklasson, Anders M. N., and Marc J. Cawkwell. "Generalized extended Lagrangian Born-Oppenheimer molecular dynamics." Journal of Chemical Physics 141, no. 16 (October 28, 2014): 164123. http://dx.doi.org/10.1063/1.4898803.

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11

Mojica-Sánchez, Juan Pablo, Tania Isabel Zarate-López, José Manuel Flores-Álvarez, Juan Reyes-Gómez, Kayim Pineda-Urbina, and Zeferino Gómez-Sandoval. "Magnesium oxide clusters as promising candidates for hydrogen storage." Physical Chemistry Chemical Physics 21, no. 41 (2019): 23102–10. http://dx.doi.org/10.1039/c9cp05075b.

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12

Cawkwell, M. J., and Anders M. N. Niklasson. "Energy conserving, linear scaling Born-Oppenheimer molecular dynamics." Journal of Chemical Physics 137, no. 13 (October 7, 2012): 134105. http://dx.doi.org/10.1063/1.4755991.

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13

Cafiero, Mauricio, and Ludwik Adamowicz. "Molecular structure in non-Born–Oppenheimer quantum mechanics." Chemical Physics Letters 387, no. 1-3 (March 2004): 136–41. http://dx.doi.org/10.1016/j.cplett.2004.02.006.

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14

Lin, Lin, Jianfeng Lu, and Sihong Shao. "Analysis of Time Reversible Born-Oppenheimer Molecular Dynamics." Entropy 16, no. 1 (December 27, 2013): 110–37. http://dx.doi.org/10.3390/e16010110.

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15

Niklasson, Anders M. N., Peter Steneteg, Anders Odell, Nicolas Bock, Matt Challacombe, C. J. Tymczak, Erik Holmström, Guishan Zheng, and Valery Weber. "Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation." Journal of Chemical Physics 130, no. 21 (June 7, 2009): 214109. http://dx.doi.org/10.1063/1.3148075.

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16

Nottoli, Michele, Benedetta Mennucci, and Filippo Lipparini. "Excited state Born–Oppenheimer molecular dynamics through coupling between time dependent DFT and AMOEBA." Physical Chemistry Chemical Physics 22, no. 35 (2020): 19532–41. http://dx.doi.org/10.1039/d0cp03688a.

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We present the implementation of excited state Born–Oppenheimer molecular dynamics (BOMD) using a polarizable QM/MM approach based on time-dependent density functional theory (TDDFT) formulation and the AMOEBA force field.

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17

Peters, Laurens D. M., Jörg Kussmann, and Christian Ochsenfeld. "Efficient and Accurate Born–Oppenheimer Molecular Dynamics for Large Molecular Systems." Journal of Chemical Theory and Computation 13, no. 11 (October 25, 2017): 5479–85. http://dx.doi.org/10.1021/acs.jctc.7b00937.

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18

Malyi, Oleksandr I., Vadym V. Kulish, and Clas Persson. "In search of new reconstructions of (001) α-quartz surface: a first principles study." RSC Adv. 4, no. 98 (2014): 55599–603. http://dx.doi.org/10.1039/c4ra10726h.

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19

Fromsejer, Rasmus, Kurt V. Mikkelsen, and Lars Hemmingsen. "Dynamics of nuclear recoil: QM-BOMD simulations of model systems following β-decay." Physical Chemistry Chemical Physics 23, no. 45 (2021): 25689–98. http://dx.doi.org/10.1039/d1cp02112e.

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20

Martinez, André, and Vania Sordoni. "On the Born-Oppenheimer approximation of diatomic molecular resonances." Journal of Mathematical Physics 56, no. 10 (October 2015): 102102. http://dx.doi.org/10.1063/1.4933323.

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21

Jasper, Ahren W., and Donald G. Truhlar. "Non-Born-Oppenheimer molecular dynamics of Na⋯FH photodissociation." Journal of Chemical Physics 127, no. 19 (November 21, 2007): 194306. http://dx.doi.org/10.1063/1.2798763.

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22

Odell, Anders, Anna Delin, Börje Johansson, Nicolas Bock, Matt Challacombe, and Anders M. N. Niklasson. "Higher-order symplectic integration in Born–Oppenheimer molecular dynamics." Journal of Chemical Physics 131, no. 24 (December 28, 2009): 244106. http://dx.doi.org/10.1063/1.3268338.

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23

Niklasson, Anders M. N. "Density-Matrix Based Extended Lagrangian Born–Oppenheimer Molecular Dynamics." Journal of Chemical Theory and Computation 16, no. 6 (May 4, 2020): 3628–40. http://dx.doi.org/10.1021/acs.jctc.0c00264.

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24

Garashchuk, Sophya, John C. Light, and Vitaly A. Rassolov. "The diagonal Born–Oppenheimer correction to molecular dynamical properties." Chemical Physics Letters 333, no. 6 (January 2001): 459–64. http://dx.doi.org/10.1016/s0009-2614(00)01297-5.

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25

Worth, Graham A., and Lorenz S. Cederbaum. "BEYOND BORN-OPPENHEIMER: Molecular Dynamics Through a Conical Intersection." Annual Review of Physical Chemistry 55, no. 1 (June 2004): 127–58. http://dx.doi.org/10.1146/annurev.physchem.55.091602.094335.

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26

Ho, Thi H., Viet Q. Bui, Thang Bach Phan, Yoshiyuki Kawazoe, and Hung M. Le. "Atomistic observation of the collision and migration of Li on MoSe2 and WS2 surfaces through ab initio molecular dynamics." Phys. Chem. Chem. Phys. 19, no. 40 (2017): 27332–42. http://dx.doi.org/10.1039/c7cp05847k.

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We present in this study a theoretical investigation of the collision of Li with the MX₂ surface (MoSe₂ or WS₂) by employing the Born–Oppenheimer molecular dynamics (MD) approach.

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27

Jalife, Said, Sukanta Mondal, Jose Luis Cabellos, Gerardo Martinez-Guajardo, Maria A. Fernandez-Herrera, and Gabriel Merino. "The cubyl cation rearrangements." Chemical Communications 52, no. 16 (2016): 3403–5. http://dx.doi.org/10.1039/c5cc10568d.

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Born–Oppenheimer molecular dynamics simulations and high-level ab initio computations predict that the cage-opening rearrangement of the cubyl cation to the 7H⁺-pentalenyl cation is feasible in the gas phase.

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28

Moqadam, Mahmoud, Enrico Riccardi, Thuat T. Trinh, Anders Lervik, and Titus S. van Erp. "Rare event simulations reveal subtle key steps in aqueous silicate condensation." Physical Chemistry Chemical Physics 19, no. 20 (2017): 13361–71. http://dx.doi.org/10.1039/c7cp01268c.

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A replica exchange transition interface sampling (RETIS) study combined with Born–Oppenheimer molecular dynamics (BOMD) is used to investigate the dynamics, thermodynamics and the mechanism of the early stages of the silicate condensation process.

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29

Pino-Rios, Ricardo, Alejandro Vásquez-Espinal, Osvaldo Yañez, and William Tiznado. "Searching for double σ- and π-aromaticity in borazine derivatives." RSC Advances 10, no. 50 (2020): 29705–11. http://dx.doi.org/10.1039/d0ra05939k.

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Evolutionary algorithms, Born–Oppenheimer molecular dynamics and the magnetic criteria of aromaticity have been used to evaluate the stability and σ–π aromaticity of borazine derivatives in order to expand the family of double aromatics systems.

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30

Paz, José Luis, Eleana Ruiz-Hinojosa, Ysaias Alvarado, Luis Lascano, Lenys Fernández, Patricio Espinoza-Montero, and César Costa-Vera. "Ecuaciones de Bloch Ópticas en Sistemas Complejos con Acoplamiento Intramolecular." Revista Politécnica 46, no. 2 (November 1, 2020): 29–38. http://dx.doi.org/10.33333/rp.vol46n2.03.

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Proponemos modificaciones de las ecuaciones de Bloch ópticas convencionales para un sistema molecular, cuando consideramos los efectos de acoplamiento intramolecular. Modelamos la molécula aislada como curvas de energía de Born-Oppenheimer que consisten en dos estados electrónicos cruzados descritos como potenciales armónicos, con los mínimos desplazados en coordenadas nucleares y energía. Consideramos dos estados vibracionales y una perturbación, que puede surgir de una correlación residual electrón-electrón y/o términos de acoplamiento spin-órbita en el Hamiltoniano del sistema, causando la separación de las dos curvas según la regla del cruce evitado. Las ecuaciones extendidas de Bloch ópticas permiten establecer la dinámica de un sistema molecular de estados adiabáticos sujeto a la interacción de un reservorio térmico e interactuando con campos electromagnéticos. En las ecuaciones se observa que haciendo nulo el factor de acoplamiento intramolecular, se recuperan las ecuaciones de Bloch ópticas convencionales para un sistema molecular con potenciales armónicos cuyos mínimos se encuentran exactamente en la misma coordenada nuclear sujeto a la aproximación Born-Oppenheimer.

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31

Polack, Étienne, Geneviève Dusson, Benjamin Stamm, and Filippo Lipparini. "Grassmann Extrapolation of Density Matrices for Born–Oppenheimer Molecular Dynamics." Journal of Chemical Theory and Computation 17, no. 11 (October 8, 2021): 6965–73. http://dx.doi.org/10.1021/acs.jctc.1c00751.

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32

Tachibana, Akitomo, and Toshihiro Iwai. "Complete molecular Hamiltonian based on the Born-Oppenheimer adiabatic approximation." Physical Review A 33, no. 4 (April 1, 1986): 2262–69. http://dx.doi.org/10.1103/physreva.33.2262.

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33

Hogreve, H. "Monotonicity of Born-Oppenheimer electronic energies for excited molecular states." Journal of Physics A: Mathematical and General 26, no. 1 (January 7, 1993): 159–70. http://dx.doi.org/10.1088/0305-4470/26/1/017.

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34

Wang, Lee-Ping, and Chenchen Song. "Car–Parrinello Monitor for More Robust Born–Oppenheimer Molecular Dynamics." Journal of Chemical Theory and Computation 15, no. 8 (July 18, 2019): 4454–67. http://dx.doi.org/10.1021/acs.jctc.9b00439.

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35

Vértesi, T., Á. Vibók, G. J. Halász, and M. Baer. "The Berry phase revisited: application to Born–Oppenheimer molecular systems." Journal of Physics B: Atomic, Molecular and Optical Physics 37, no. 23 (November 23, 2004): 4603–20. http://dx.doi.org/10.1088/0953-4075/37/23/003.

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36

Sun, Tao, and Renata M. Wentzcovitch. "Direct determination of electric current in Born–Oppenheimer molecular dynamics." Chemical Physics Letters 554 (December 2012): 15–19. http://dx.doi.org/10.1016/j.cplett.2012.10.052.

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37

Sutcliffe, B. T., and R. Guy Woolley. "Comment on ‘Molecular structure in non-Born–Oppenheimer quantum mechanics’." Chemical Physics Letters 408, no. 4-6 (June 2005): 445–47. http://dx.doi.org/10.1016/j.cplett.2005.04.022.

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38

Retegan, Marius, Marilia Martins-Costa, and Manuel F. Ruiz-López. "Free energy calculations using dual-level Born–Oppenheimer molecular dynamics." Journal of Chemical Physics 133, no. 6 (August 14, 2010): 064103. http://dx.doi.org/10.1063/1.3466767.

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39

Bubin, Sergiy, and Ludwik Adamowicz. "Non-Born–Oppenheimer study of positronic molecular systems: e+LiH." Journal of Chemical Physics 120, no. 13 (April 2004): 6051–55. http://dx.doi.org/10.1063/1.1651056.

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40

Estácio, Sílvia Gomes, and B. J. Costa Cabral. "Born–Oppenheimer molecular dynamics of phenol in a water cluster." Chemical Physics Letters 456, no. 4-6 (May 2008): 170–75. http://dx.doi.org/10.1016/j.cplett.2008.03.035.

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41

Lefebvre, R., and M. Garcia Sucre. "Born-oppenheimer approach to the vibronic structure of molecular dimers." International Journal of Quantum Chemistry 1, S1 (June 18, 2009): 339–50. http://dx.doi.org/10.1002/qua.560010640.

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42

Kumar, Manoj, Jie Zhong, Joseph S. Francisco, and Xiao C. Zeng. "Criegee intermediate-hydrogen sulfide chemistry at the air/water interface." Chemical Science 8, no. 8 (2017): 5385–91. http://dx.doi.org/10.1039/c7sc01797a.

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We carry out Born–Oppenheimer molecular dynamic simulations to show that the reaction between the smallest Criegee intermediate, CH₂OO, and hydrogen sulfide (H₂S) at the air/water interface can be observed within few picoseconds.

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43

Borodin, Oleg, Marco Olguin, P. Ganesh, Paul R. C. Kent, Joshua L. Allen, and Wesley A. Henderson. "Competitive lithium solvation of linear and cyclic carbonates from quantum chemistry." Physical Chemistry Chemical Physics 18, no. 1 (2016): 164–75. http://dx.doi.org/10.1039/c5cp05121e.

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The composition of the lithium cation (Li⁺) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics and Li⁺(EC)_n(DMC)_m cluster calculations.

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44

DOLTSINIS, NIKOS L., and DOMINIK MARX. "FIRST PRINCIPLES MOLECULAR DYNAMICS INVOLVING EXCITED STATES AND NONADIABATIC TRANSITIONS." Journal of Theoretical and Computational Chemistry 01, no. 02 (October 2002): 319–49. http://dx.doi.org/10.1142/s0219633602000257.

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Extensions of traditional molecular dynamics to excited electronic states and non-Born–Oppenheimer dynamics are reviewed focusing on applicability to chemical reactions of large molecules, possibly in condensed phases. The latter imposes restrictions on both the level of accuracy of the underlying electronic structure theory and the treatment of nonadiabaticity. This review, therefore, exclusively deals with ab initio "on the fly" molecular dynamics methods. For the same reason, mainly mixed quantum-classical approaches to nonadiabatic dynamics are considered.

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45

Laktionov, Andrey, Emilie Chemineau-Chalaye, and Tomasz A. Wesolowski. "Frozen-density embedding theory with average solvent charge densities from explicit atomistic simulations." Physical Chemistry Chemical Physics 18, no. 31 (2016): 21069–78. http://dx.doi.org/10.1039/c6cp00497k.

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Besides molecular electron densities obtained within the Born–Oppenheimer approximation (ρ_B(r)) to represent the environment, the ensemble averaged density (〈ρ_B〉(r)) is also admissible in frozen-density embedding theory (FDET) [Wesolowski, Phys. Rev. A, 2008, 77, 11444].

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46

Miller, Johanna L. "A solid-state failure of the Born–Oppenheimer approximation." Physics Today 76, no. 2 (February 1, 2023): 16–17. http://dx.doi.org/10.1063/pt.3.5172.

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47

Mahé, Jérôme, Sander Jaeqx, Anouk M. Rijs, and Marie-Pierre Gaigeot. "Can far-IR action spectroscopy combined with BOMD simulations be conformation selective?" Physical Chemistry Chemical Physics 17, no. 39 (2015): 25905–14. http://dx.doi.org/10.1039/c5cp01518a.

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The combination of conformation selective far-IR/UV double resonance spectroscopy with Born–Oppenheimer molecular dynamics (BOMD) simulations is presented here for the structural characterization of the Ac-Phe-Pro-NH₂ peptide in the far-infrared spectral domain, i.e. for radiation below 800 cm⁻¹.

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48

Herbert, John M., and Martin Head-Gordon. "Accelerated, energy-conserving Born–Oppenheimer molecular dynamics via Fock matrix extrapolation." Physical Chemistry Chemical Physics 7, no. 18 (2005): 3269. http://dx.doi.org/10.1039/b509494a.

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49

Fonseca, A. C., and M. T. Pena. "Faddeev-Born-Oppenheimer equations for molecular three-body systems: Application toH2+." Physical Review A 36, no. 10 (November 1, 1987): 4585–603. http://dx.doi.org/10.1103/physreva.36.4585.

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50

Simmen, Benjamin, Edit Mátyus, and Markus Reiher. "Electric transition dipole moment in pre-Born–Oppenheimer molecular structure theory." Journal of Chemical Physics 141, no. 15 (October 21, 2014): 154105. http://dx.doi.org/10.1063/1.4897632.

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