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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 (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 (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 pub

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3

Sordoni, Vania. "Molecular scattering and Born-Oppenheimer approximation." Journal of the London Mathematical Society 81, no. 1 (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 (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 (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 sol

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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 (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 (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 (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 (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 (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 (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 (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 (2013): 110–37. http://dx.doi.org/10.3390/e16010110.

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15

Niklasson, Anders M. N., Peter Steneteg, Anders Odell, et al. "Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation." Journal of Chemical Physics 130, no. 21 (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 (2017): 5479–85. http://dx.doi.org/10.1021/acs.jctc.7b00937.

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18

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

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19

Fromsejer, Rasmus, Kurt V. Mikkelsen та Lars Hemmingsen. "Dynamics of nuclear recoil: QM-BOMD simulations of model systems following β-decay". Physical Chemistry Chemical Physics 23, № 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 (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 (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 (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 (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 (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 (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 MX<sub>2</sub> surface (MoSe<sub>2</sub> or WS<sub>2</sub>) 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<sup>+</sup>-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 та William Tiznado. "Searching for double σ- and π-aromaticity in borazine derivatives". RSC Advances 10, № 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, et al. "Ecuaciones de Bloch Ópticas en Sistemas Complejos con Acoplamiento Intramolecular." Revista Politécnica 46, no. 2 (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

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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 (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 (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 (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 (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 (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 (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 (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 (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 (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 (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, CH<sub>2</sub>OO, and hydrogen sulfide (H<sub>2</sub>S) 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<sup>+</sup>) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics and Li<sup>+</sup>(EC)<sub>n</sub>(DMC)<sub>m</sub> 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 (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<sub>B</sub>(r)) to represent the environment, the ensemble averaged density (〈ρ<sub>B</sub>〉(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 (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-NH<sub>2</sub> peptide in the far-infrared spectral domain, i.e. for radiation below 800 cm<sup>−1</sup>.

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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 (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 (2014): 154105. http://dx.doi.org/10.1063/1.4897632.

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