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Author: Grafiati
Published: 6 September 2023

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1

Laasonen, K. "Ab Initio Molecular Dynamics." Materials Science Forum 155-156 (May 1994): 149–64. http://dx.doi.org/10.4028/www.scientific.net/msf.155-156.149.

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2

Williams, D. E. "Ab initio molecular packing analysis." Acta Crystallographica Section A Foundations of Crystallography 52, no. 2 (March 1, 1996): 326–28. http://dx.doi.org/10.1107/s0108767395016679.

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3

Murrell, J. N. "Ab initio molecular orbital theory." Journal of Organometallic Chemistry 309, no. 3 (August 1986): C72—C73. http://dx.doi.org/10.1016/s0022-328x(00)99651-7.

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4

Olcari, Luigi. "Ab initio molecular orbital theory." Inorganica Chimica Acta 119, no. 2 (September 1986): 234. http://dx.doi.org/10.1016/s0020-1693(00)84345-5.

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5

W, J. O.-T. "Ab initio molecular orbital theory." Journal of Molecular Structure: THEOCHEM 151 (May 1987): 392. http://dx.doi.org/10.1016/0166-1280(87)85077-7.

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6

Krack, Matthias, and Michele Parrinello. "All-electron ab-initio molecular dynamics." Physical Chemistry Chemical Physics 2, no. 10 (2000): 2105–12. http://dx.doi.org/10.1039/b001167n.

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7

Tsuchida, Eiji. "Ab initio mass tensor molecular dynamics." Journal of Chemical Physics 134, no. 4 (January 28, 2011): 044112. http://dx.doi.org/10.1063/1.3543898.

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8

Tapavicza, Enrico, Gregory D. Bellchambers, Jordan C. Vincent, and Filipp Furche. "Ab initio non-adiabatic molecular dynamics." Physical Chemistry Chemical Physics 15, no. 42 (2013): 18336. http://dx.doi.org/10.1039/c3cp51514a.

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9

Curchod, Basile F. E., and Todd J. Martínez. "Ab Initio Nonadiabatic Quantum Molecular Dynamics." Chemical Reviews 118, no. 7 (February 21, 2018): 3305–36. http://dx.doi.org/10.1021/acs.chemrev.7b00423.

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10

Bowen-Jenkins, Philippa E., David L. Cooper, and W. Graham Richards. "Ab initio computation of molecular similarity." Journal of Physical Chemistry 89, no. 11 (May 1985): 2195–97. http://dx.doi.org/10.1021/j100257a012.

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11

Northey, Thomas, Nikola Zotev, and Adam Kirrander. "Ab Initio Calculation of Molecular Diffraction." Journal of Chemical Theory and Computation 10, no. 11 (October 10, 2014): 4911–20. http://dx.doi.org/10.1021/ct500096r.

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12

Soldán, Pavel, and Wolfgang P. Kraemer. "Molecular ion LiHe+: ab initio study." Chemical Physics 393, no. 1 (January 2012): 135–39. http://dx.doi.org/10.1016/j.chemphys.2011.11.040.

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13

Cooper, D. L. "Ab initio determination of molecular properties." Endeavour 12, no. 2 (January 1988): 92. http://dx.doi.org/10.1016/0160-9327(88)90096-8.

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14

Bifone, Angelo, H. J. M. de Groot, and Francesco Buda. "Ab initio molecular dynamics of rhodopsin." Pure and Applied Chemistry 69, no. 10 (January 1, 1997): 2105–10. http://dx.doi.org/10.1351/pac199769102105.

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15

Niklasson, Anders M. N., C. J. Tymczak, and Matt Challacombe. "Time-reversible ab initio molecular dynamics." Journal of Chemical Physics 126, no. 14 (April 14, 2007): 144103. http://dx.doi.org/10.1063/1.2715556.

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16

JUN, S., S. PENDURTI, I. H. LEE, S. Y. KIM, H. S. PARK, and Y. H. KIM. "ACTION-DERIVED AB INITIO MOLECULAR DYNAMICS." International Journal of Applied Mechanics 01, no. 03 (September 2009): 469–82. http://dx.doi.org/10.1142/s1758825109000277.

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Action-derived molecular dynamics (ADMD) is a numerical method to search for minimum-energy dynamic pathways on the potential-energy surface of an atomic system. The method is based on Hamilton's least-action principle and has been developed for problems of activated processes, rare events, and long-time simulations. In this paper, ADMD is further extended to incorporate ab initio total-energy calculations, which enables the detailed electronic analysis of transition states as well as the exploration of energy landscapes. Three numerical examples are solved to demonstrate the capability of this action-derived ab initio molecular dynamics (MD). The proposed approach is expected to circumvent the severe time-scale limitation of conventional ab intio MD simulations.
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17

Bifone, Angelo, Huub J. M. de Groot, and Francesco Buda. "Ab initio molecular dynamics of retinals." Chemical Physics Letters 248, no. 3-4 (January 1996): 165–72. http://dx.doi.org/10.1016/0009-2614(95)01312-1.

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18

Marx, Dominik, and Michele Parrinello. "Ab initio path-integral molecular dynamics." Zeitschrift f�r Physik B Condensed Matter 95, no. 2 (June 1994): 143–44. http://dx.doi.org/10.1007/bf01312185.

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19

Madhavan, P. V., and J. L. Written. "Molecular symmetry in Ab initio calculations." Journal of Computational Physics 70, no. 1 (May 1987): 253–61. http://dx.doi.org/10.1016/0021-9991(87)90013-1.

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20

Kutzelnigg, Werner. "Ab initio calculation of molecular properties." Journal of Molecular Structure: THEOCHEM 202 (December 1989): 11–61. http://dx.doi.org/10.1016/0166-1280(89)87003-4.

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21

Madden, PA. "Ab-initio molecular dynamics studies of molecular systems." Journal de Chimie Physique 88 (1991): 2519. http://dx.doi.org/10.1051/jcp/1991882519.

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22

Liu, Jinfeng, and Xiao He. "Fragment-based quantum mechanical approach to biomolecules, molecular clusters, molecular crystals and liquids." Physical Chemistry Chemical Physics 22, no. 22 (2020): 12341–67. http://dx.doi.org/10.1039/d0cp01095b.

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To study large molecular systems beyond the system size that the current state-of-the-art ab initio electronic structure methods could handle, fragment-based quantum mechanical (QM) approaches have been developed over the past years, and proved to be efficient in dealing with large molecular systems at various ab initio levels.
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23

Car, Roberto, P. Blöchl, and E. Smargiassi. "Ab Initio Molecular Dynamics of Semiconductor Defects." Materials Science Forum 83-87 (January 1992): 433–46. http://dx.doi.org/10.4028/www.scientific.net/msf.83-87.433.

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24

Fedorov, Dmitry A., Matthew J. Otten, Stephen K. Gray, and Yuri Alexeev. "Ab initio molecular dynamics on quantum computers." Journal of Chemical Physics 154, no. 16 (April 28, 2021): 164103. http://dx.doi.org/10.1063/5.0046930.

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25

Bartha, F., and C. Kozmutza. "Molecular symmetry in ab initio calculations. II." Acta Physica Hungarica 58, no. 3-4 (December 1985): 227–32. http://dx.doi.org/10.1007/bf03155717.

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26

Bartha, F., E. Kapuy, and C. Kozmutza. "Molecular symmetry in ab initio calculations. I." Acta Physica Hungarica 58, no. 3-4 (December 1985): 219–25. http://dx.doi.org/10.1007/bf03155716.

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27

Bartha, F., E. Kapuy, and C. Kozmutza. "Molecular symmetry in AB initio calculations. V." Acta Physica Hungarica 59, no. 3-4 (June 1986): 347–53. http://dx.doi.org/10.1007/bf03053782.

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28

Bartha, F., E. Kapuy, C. Kozmutza, and Zs Ozoróczy. "Molecular symmetry in AB initio calculations. IV." Acta Physica Hungarica 59, no. 3-4 (June 1986): 339–46. http://dx.doi.org/10.1007/bf03053781.

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29

Bartha, F., E. Kapuy, and C. Kozmutza. "Molecular symmetry in ab initio calculations. III." Acta Physica Hungarica 59, no. 3-4 (June 1986): 333–38. http://dx.doi.org/10.1007/bf03053780.

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30

Kotochigova, S., and I. Tupitsyn. "Accurate ab initio calculation of molecular constants." Journal of Research of the National Institute of Standards and Technology 103, no. 2 (March 1998): 201. http://dx.doi.org/10.6028/jres.103.013.

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31

Paquet, Eric, and Herna L. Viktor. "Computational Methods for Ab Initio Molecular Dynamics." Advances in Chemistry 2018 (April 29, 2018): 1–14. http://dx.doi.org/10.1155/2018/9839641.

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Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.
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32

Durandurdu, Murat. "Amorphous zirconia: ab initio molecular dynamics simulations." Philosophical Magazine 97, no. 16 (February 23, 2017): 1334–45. http://dx.doi.org/10.1080/14786435.2017.1296201.

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33

Dobado, J. A., José Molina Molina, and Dolores Portal Olea. "Ab initio molecular study of hydrogen peroxide." Journal of Molecular Structure: THEOCHEM 433, no. 1-3 (July 1998): 181–92. http://dx.doi.org/10.1016/s0166-1280(98)00024-4.

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34

Yamamoto, Jun-ichi. "Ab initio molecular dynamics simulation on reaction." Journal of Molecular Structure: THEOCHEM 957, no. 1-3 (October 2010): 55–60. http://dx.doi.org/10.1016/j.theochem.2010.07.008.

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35

Martínez, Todd J. "Ab Initio Reactive Computer Aided Molecular Design." Accounts of Chemical Research 50, no. 3 (March 21, 2017): 652–56. http://dx.doi.org/10.1021/acs.accounts.7b00010.

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36

Gdanitz, Robert J. "Ab initio prediction of molecular crystal structures." Current Opinion in Solid State and Materials Science 3, no. 4 (August 1998): 414–18. http://dx.doi.org/10.1016/s1359-0286(98)80054-5.

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37

Gibson, Douglas A., and Emily A. Carter. "Ab initio molecular dynamics of pseudorotating Li5." Chemical Physics Letters 271, no. 4-6 (June 1997): 266–72. http://dx.doi.org/10.1016/s0009-2614(97)00484-3.

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38

Novak, Igor. "Ab Initio vs Molecular Mechanics Thermochemistry: Homocubanes." Journal of Chemical Information and Computer Sciences 44, no. 3 (May 2004): 903–6. http://dx.doi.org/10.1021/ci0300285.

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39

Crawford, T. Daniel. "Ab initio calculation of molecular chiroptical properties." Theoretical Chemistry Accounts 115, no. 4 (December 6, 2005): 227–45. http://dx.doi.org/10.1007/s00214-005-0001-4.

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40

Surh, Michael P., K. J. Runge, T. W. Barbee, E. L. Pollock, and C. Mailhiot. "Ab initio calculations for solid molecular hydrogen." Physical Review B 55, no. 17 (May 1, 1997): 11330–41. http://dx.doi.org/10.1103/physrevb.55.11330.

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41

Iglesias, E., T. L. Sordo, and J. A. Sordo. "Molecular associations from ab initio pair potentials." Journal of Molecular Structure: THEOCHEM 309, no. 2 (June 1994): 81–91. http://dx.doi.org/10.1016/0166-1280(94)80065-0.

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42

Iglesias, E., T. L. Sordo, and J. A. Sordo. "Molecular associations from ab initio pair potentials." Journal of Molecular Structure: THEOCHEM 309, no. 2 (June 1994): 93–103. http://dx.doi.org/10.1016/0166-1280(94)80066-9.

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43

Kresse, G. "Ab initio molecular dynamics for liquid metals." Journal of Non-Crystalline Solids 192-193 (December 1995): 222–29. http://dx.doi.org/10.1016/0022-3093(95)00355-x.

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44

Iglesias, E., T. L. Sordo, and J. A. Sordo. "Molecular associations from ab initio pair potentials." Computer Physics Communications 67, no. 2 (December 1991): 268–84. http://dx.doi.org/10.1016/0010-4655(91)90022-d.

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45

Mercier, Patrick H. J., and Yvon Le Page. "Kaolin polytypes revisited ab initio." Acta Crystallographica Section B Structural Science 64, no. 2 (March 14, 2008): 131–43. http://dx.doi.org/10.1107/s0108768108001924.

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The well known 36 distinguishable transformations between adjacent kaolin layers are split into 20 energetically distinguishable transformations (EDT) and 16 enantiomorphic transformations, hereafter denoted EDT*. For infinitesimal energy contribution of interactions between non-adjacent layers, the lowest-energy models must result from either (a) repeated application of an EDT or (b) alternate application of an EDT and its EDT*. All modeling, quantum input preparation and interpretation was performed with Materials Toolkit, and quantum optimizations with VASP. Kaolinite and dickite are the lowest-energy models at zero temperature and pressure, whereas nacrite and HP-dickite are the lowest-enthalpy models under moderate pressures based on a rough enthalpy/pressure graph built from numbers given in the supplementary tables. Minor temperature dependence of this calculated 0 K graph would explain the bulk of the current observations regarding synthesis, diagenesis and transformation of kaolin minerals. Other stackings that we list have energies so competitive that they might crystallize at ambient pressure. A homometric pair of energetically distinguishable ideal models, one of them for nacrite, is exposed. The printed experimental structure of nacrite correctly corresponds to the stable member of the pair. In our opinion, all recent literature measurements of the free energy of bulk kaolinite are too negative by ∼ 15 kJ mol−1 for some unknown reason.
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46

Jain, Swati, and Arpita Yadav. "An Ab Initio Study of At2Antagonists." Chemical Biology & Drug Design 71, no. 3 (March 2008): 271–77. http://dx.doi.org/10.1111/j.1747-0285.2008.00634.x.

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47

Senekowitsch, J., S. V. ONeil, Hans-J. Werner, and P. J. Knowles. "Ab initio characterization of NF2+." Journal of Physics B: Atomic, Molecular and Optical Physics 24, no. 7 (April 14, 1991): 1529–38. http://dx.doi.org/10.1088/0953-4075/24/7/008.

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48

Jørgensen, Uffe Gråe. "Molecular Data for Stellar Opacities." Highlights of Astronomy 10 (1995): 576–78. http://dx.doi.org/10.1017/s1539299600012107.

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In total, 40 neutral diatomic molecules, 2 molecular ions, and 7 polyatomic molecules are known from observed photospheric stellar spectra. Line data for opacity computations (i.e., lists of line frequencies, intensities, and excitation energies) exist for 17 of these molecules, although the data are complete only for a handful of them. A detailed description of stellar photospheric molecules can be found in Tsuji (1986), and the existing opacity data have been reviewed by Jorgensen (1995).Listed line frequencies in the data bases are either the measured values, or based on computed molecular constants obtained from fits to measured values. Attempts to compute ab initio line frequencies have so far resulted in lower accuracy than what is obtained by use of molecular constants. Published line strengths include measured values as well as ab initio values. For strong bands the ab initio intensities are as accurate as the laboratory values, whereas measured values for weak bands are generally more accurate than the ab initio values. The primary advantage of ab initio computations is therefore that the complete set of all transitions can be obtained. Exploratory studies have shown that completeness of the line data is crucial for the obtained stellar photospheric structure.As an alternative to the ab initio computations of the line intensities, fits to experimental data have been attempted. The most promising method seems to be to fit the dipole function by use of a Padé approximant. Combined with a potential fitted to experimental energy levels, such a dipole function can in principle be used to predict the complete list of band intensities and line intensities for all bands with energies up to the molecular dissociation energy. The part of the dipole function which corresponds to the largest stretching (or bending) of the molecule is the most uncertain in such fits as well as in ab initio computations. This part is responsible for most of the many weak transitions, and large uncertainties are therefore to be excepted in the computed intensities of the weak spectral bands. As these are of major importance for the stellar photospheric structure (due to their huge number and their pseudo continuous appearance in the spectrum), a particularly large effort is desirable in comparing computed intensities with laboratory data for a representative sample of weak bands. Unfortunately, only few measurements of weak bands exist.
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49

Zhanserkeev, Asylbek A., Justin J. Talbot, and Ryan P. Steele. "Adiabatic Molecular Orbital Tracking in Ab Initio Molecular Dynamics." Journal of Chemical Theory and Computation 17, no. 8 (July 29, 2021): 4675–85. http://dx.doi.org/10.1021/acs.jctc.1c00553.

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50

Mandix, Kim, Arne Colding, Knud Elming, Leif Sunesen, and Irene Shim. "Ab initio investigation of phloroglucinol." International Journal of Quantum Chemistry 46, no. 1 (1993): 159–70. http://dx.doi.org/10.1002/qua.560460116.

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