Machine learning molecular dynamics for the simulation of infrared spectra

Abstract

Artificial neural networks are combined with molecular dynamics to simulate molecular infrared spectra including anharmonicities and temperature effects.

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References 73

1. 1.

   Bishop C. M., Pattern Recognition and Machine Learning, Springer, New York, 1st edn, 2006.

   Not in our library

2. 2.

   Goodfellow I., Bengio Y. and Courville A., Deep Learning, MIT Press, 2016.

   Not in our library

3. 3.
   Quantum-chemical insights from deep tensor neural networks · 2017

   No notice
4. 4.

   Wei J. N., Duvenaud D., Aspuru Guzik A. ACS Cent. Sci. 2016;2:725-732.

   Not in our library10.1021/acscentsci.6b00219

5. 5.

   Faber F. A., Hutchison L., Huang B., Gilmer J., Schoenholz S. S., Dahl G. E., Vinyals O., Kearnes S., Riley P. F. and von Lilienfeld O. A., arXiv:1702.05532, 2017.

   Not in our library10.1021/acs.jctc.7b00577

6. 6.

   Gómez Bombarelli R., Aguilera Iparraguirre J., Hirzel T. D., Duvenaud D., Maclaurin D., Blood Forsythe M. A., Chae H. S., Einzinger M., Ha D.-G., Wu T., Markopoulos G., Jeon S., Kang H., Miyazaki H., Numata M., Kim S., Huang W., Hong S. I., Baldo M., Adams R. P., Aspuru Guzik A. Nat. Mater. 2016;15:1120-1127.

   Not in our library10.1038/nmat4717

7. 7.

   Hase F., Valleau S., Pyzer-Knapp E., Aspuru Guzik A. Chem. Sci. 2016;7:5139-5147.

   Not in our library10.1039/c5sc04786b

8. 8.

   Behler J. Phys. Chem. Chem. Phys. 2011;13:17930-17955.

   Not in our library10.1039/c1cp21668f

9. 9.

   Handley C. M., Popelier P. L. A. J. Phys. Chem. A. 2010;114:3371-3383.

   Not in our library10.1021/jp9105585

10. 10.

    Behler J. J. Phys.: Condens. Matter. 2014;26:183001.

    Not in our library10.1088/0953-8984/26/18/183001

11. 11.

    Behler J. J. Chem. Phys. 2016;145:170901.

    Not in our library10.1063/1.4966192

12. 12.

    Smith J. S., Isayev O., Roitberg A. E. Chem. Sci. 2017;8:3192-3203.

    Not in our library10.1039/c6sc05720a

13. 13.

    Botu V., Batra R., Chapman J., Ramprasad R. J. Phys. Chem. C. 2017;121:511-522.

    Not in our library

14. 14.

    Bartók A. P., Csányi G. Int. J. Quantum Chem. 2015;115:1051-1057.

    Not in our library

15. 15.

    Li Z., Kermode J. R., De Vita A. Phys. Rev. Lett. 2015;114:096405.

    Not in our library10.1103/physrevlett.114.096405

16. 16.

    Yao K., Herr J. E., Brown S. N., Parkhill J. J. Phys. Chem. Lett. 2017;8:2689-2694.

    Not in our library10.1021/acs.jpclett.7b01072

17. 17.

    Marx D. and Hutter J., Ab Initio Molecular Dynamics: Basic Theory and Advanced Methods, Cambridge University Press, Cambridge, reprint edn, 2012.

    Not in our library

18. 18.

    Newton I., Philosophiae naturalis principia mathematica, J. Societatis Regiae ac Typis J. Streater, 1687.

    Not in our library

19. 19.

    Barbatti M. WIREs Comput. Mol. Sci. 2011;1:620-633.

    Not in our library

20. 20.

    Gaigeot M.-P. Phys. Chem. Chem. Phys. 2010;12:3336-3359.

    Not in our library10.1039/b924048a

21. 21.

    Thomas M., Brehm M., Fligg R., Vöhringer P., Kirchner B. Phys. Chem. Chem. Phys. 2013;15:6608-6622.

    Not in our library10.1039/c3cp44302g

22. 22.

    Mai S., Marquetand P., González L. Int. J. Quantum Chem. 2015;115:1215-1231.

    Not in our library

23. 23.

    Marquetand P., Nogueira J., Mai S., Plasser F., González L. Molecules. 2016;22:49.

    Not in our library

24. 24.

    Simons J. Mol. Phys. 2009;107:2435-2458.

    Not in our library

25. 25.

    de Vries M. S., Hobza P. Annu. Rev. Phys. Chem. 2007;58:585-612.

    Not in our library10.1146/annurev.physchem.57.032905.104722

26. 26.

    Roy T. K., Gerber R. B. Phys. Chem. Chem. Phys. 2013;15:9468-9492.

    Not in our library10.1039/c3cp50739d

27. 27.

    Meyer H.-D. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012;2:351-374.

    Not in our library

28. 28.

    Thomas P. S., Carrington Jr T. J. Phys. Chem. A. 2015;119:13074-13091.

    Not in our library10.1021/acs.jpca.5b10015

29. 29.

    Andrade X., Sanders J. N., Aspuru Guzik A. Proc. Natl. Acad. Sci. U. S. A. 2012;109:13928-13933.

    Not in our library10.1073/pnas.1209890109

30. 30.

    Mandelshtam V. A., Taylor H. S. J. Chem. Phys. 1997;107:6756-6769.

    Not in our library

31. 31.

    Behler J., Parrinello M. Phys. Rev. Lett. 2007;98:146401.

    Not in our library10.1103/physrevlett.98.146401

32. 32.

    Gastegger M., Marquetand P. J. Chem. Theory Comput. 2015;11:2187-2198.

    Not in our library10.1021/acs.jctc.5b00211

33. 33.

    Gastegger M., Kauffmann C., Behler J., Marquetand P. J. Chem. Phys. 2016;144:194110.

    Not in our library10.1063/1.4950815

34. 34.

    Grimme S. J. Chem. Phys. 2006;124:034108.

    Not in our library10.1063/1.2148954

35. 35.

    Behler J. Int. J. Quantum Chem. 2015;115:1032-1050.

    Not in our library

36. 36.

    Behler J. J. Chem. Phys. 2011;134:074106.

    Not in our library10.1063/1.3553717

37. 37.

    Blank T. B., Brown S. D. J. Chemom. 1994;8:391-407.

    Not in our library

38. 38.

    Li J., Jiang B., Guo H. J. Chem. Phys. 2013;139:204103.

    Not in our library10.1063/1.4832697

39. 39.

    Botu V., Ramprasad R. Int. J. Quantum Chem. 2015;115:1074-1083.

    Not in our library

40. 40.

    Manzhos S., Yamashita K., Carrington Jr T. Comput. Phys. Commun. 2009;180:2002-2012.

    Not in our library

41. 41.

    Yao K., Herr J. E., Parkhill J. J. Chem. Phys. 2017;146:014106.

    Not in our library10.1063/1.4973380

42. 42.

    Malshe M., Narulkar R., Raff L. M., Hagan M., Bukkapatnam S., Agrawal P. M., Komanduri R. J. Chem. Phys. 2009;130:184102.

    Not in our library10.1063/1.3124802

43. 43.

    Darley M. G., Handley C. M., Popelier P. L. A. J. Chem. Theory Comput. 2008;4:1435-1448.

    Not in our library10.1021/ct800166r

44. 44.

    Handley C. M., Popelier P. L. A. J. Chem. Theory Comput. 2009;5:1474-1489.

    Not in our library10.1021/ct800468h

45. 45.

    Artrith N., Morawietz T., Behler J. Phys. Rev. B. 2011;83:153101.

    Not in our library

46. 46.

    Faraji S., Ghasemi S. A., Rostami S., Rasoulkhani R., Schaefer B., Goedecker S., Amsler M. Phys. Rev. B. 2017;95:104105.

    Not in our library

47. 47.

    Morawietz T., Sharma V., Behler J. J. Chem. Phys. 2012;136:064103.

    Not in our library10.1063/1.3682557

48. 48.

    Breneman C. M., Wiberg K. B. J. Comput. Chem. 1990;11:361-373.

    Not in our library

49. 49.

    Bachrach S. M., in Population Analysis and Electron Densities from Quantum Mechanics, John Wiley & Sons, Inc., 2007, pp. 171–228.

    Not in our library

50. 50.

    Wiberg K. B., Rablen P. R. J. Comput. Chem. 1993;14:1504-1518.

    Not in our library

51. 51.

    Mackerell A. D. J. Comput. Chem. 2004;25:1584-1604.

    Not in our library10.1002/jcc.20082

52. 52.

    Baker C. M. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2015;5:241-254.

    Not in our library10.1002/wcms.1167

53. 53.

    Neese F. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2012;2:73-78.

    Not in our library

54. 54.

    Becke A. D. Phys. Rev. A. 1988;38:3098-3100.

    Not in our library10.1103/physreva.38.3098

55. 55.

    Dirac P. A. M. Proc. R. Soc. London, Ser. A. 1929;123:714-733.

    Not in our library

56. 56.

    Perdew J. P. Phys. Rev. B. 1986;33:8822-8824.

    Not in our library10.1103/physrevb.33.8822

57. 57.

    Vosko S. H., Wilk L., Nusair M. Can. J. Phys. 1980;58:1200-1211.

    Not in our library

58. 58.

    Slater J. C. Phys. Rev. 1951;81:385-390.

    Not in our library

59. 59.

    Weigend F., Ahlrichs R. Phys. Chem. Chem. Phys. 2005;7:3297-3305.

    Not in our library10.1039/b508541a

60. 60.

    Lee C., Yang W., Parr R. G. Phys. Rev. B. 1988;37:785-789.

    Not in our library10.1103/physrevb.37.785

61. 61.

    Eichkorn K., Treutler O., Öhm H., Häser M., Ahlrichs R. Chem. Phys. Lett. 1995;240:283-290.

    Not in our library

62. 62.

    Vahtras O., Almlöf J., Feyereisen M. W. Chem. Phys. Lett. 1993;213:514-518.

    Not in our library

63. 63.

    Behler J., RUNNER – A program for constructing high-dimensional neural network potentials, Universität Göttingen, 2017.

    Not in our library

64. 64.

    Python Reference Manual, ed. G. van Rossum and F. L. Drake, PythonLabs, Virginia, USA, 2001, http://www.python.org, access date 06.04.2017.

    Not in our library

65. 65.

    van der Walt S., Colbert S. C., Varoquaux G. Comput. Sci. Eng. 2011;13:22-30.

    Not in our library

66. 66.

    Bergstra J., Breuleux O., Bastien F., Lamblin P., Pascanu R., Desjardins G., Turian J., Warde Farley D. and Bengio Y., Proceedings of the Python for Scientific Computing Conference, SciPy, 2010.

    Not in our library

67. 67.

    Chmiela S., Tkatchenko A., Sauceda H. E., Poltavsky I., Schütt K. T., Müller K.-R. Sci. Adv. 2017;3:e1603015.

    Not in our library10.1126/sciadv.1603015

68. 68.

    Chu P., Guenther F., Rhoderick G. and Lafferty W., in NIST Chemistry WebBook NIST Standard Reference Database Number 69, ed. P. Linstrom and W. Mallard, National Institute of Standards and Technology, Gaithersburg MD, p. 20899, retrieved April 24, 2017,.

    Not in our library10.18434/t4d303

69. 69.

    Grimme S., Antony J., Ehrlich S., Krieg H. J. Chem. Phys. 2010;132:154104.

    Not in our library10.1063/1.3382344

70. 70.

    Grimme S., Ehrlich S., Goerigk L. J. Comput. Chem. 2011;32:1456-1465.

    Not in our library10.1002/jcc.21759

71. 71.

    Fischer S. A., Ueltschi T. W., El-Khoury P. Z., Mifflin A. L., Hess W. P., Wang H.-F., Cramer C. J., Govind N. J. Phys. Chem. B. 2016;120:1429-1436.

    Not in our library10.1021/acs.jpcb.5b03323

72. 72.

    Cimas A., Vaden T. D., de Boer T. S. J. A., Snoek L. C., Gaigeot M.-P. J. Chem. Theory Comput. 2009;5:1068-1078.

    Not in our library10.1021/ct900057s

73. 73.

    Vaden T. D., de Boer T. S. J. A., Simons J. P., Snoek L. C., Suhai S., Paizs B. J. Phys. Chem. A. 2008;112:4608-4616.

    Not in our library10.1021/jp800069n

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