1932
0
  1. Home
  2. A-Z Publications
  3. Annual Review of Physical Chemistry
  4. Volume 69, 2018
  5. Article

Annual Review of Physical Chemistry

Volume 69, 2018

Addressing the Challenge of Molecular Change: An Interim Report

Abstract

Invited by the editorial committee of the to “contribute my autobiography,” I present it here, as I understand the term. It is about my parents, my mentors, my coworkers, and my friends in learning and the scientific problems that we tried to address. Courtesy of the editorial assistance of Annual Reviews, some of the science is in the figure captions and sidebars. I am by no means done: I am currently trying to fuse the quantitative rigor of physical chemistry with systems biology while also dealing with a post–Born-Oppenheimer regime in electronic dynamics and am attempting to instruct molecules to perform advanced logic.

Keyword(s): autobiography, chemistry under extreme conditions, dynamical stereochemistry, molecular logic machines, molecular reaction dynamics, nonadiabatic electronic dynamics, quantum mechanics of molecular rate processes, surprisal analysis, systems biology
Loading

Article metrics loading...

/content/journals/10.1146/annurev-physchem-102717-010036
2018-04-20
2024-04-26
Loading full text...

Full text loading...

/deliver/fulltext/physchem/69/1/annurev-physchem-102717-010036.html?itemId=/content/journals/10.1146/annurev-physchem-102717-010036&mimeType=html&fmt=ahah

Literature Cited

  1. Chen X, Bradforth SE. 1.  2008. The ultrafast dynamics of photodetachment. Annu. Rev. Phys. Chem. 59:203–31 [Google Scholar]
  2. Messina F, Bräm O, Cannizzo A, Chergui M. 2.  2013. Real-time observation of the charge transfer to solvent dynamics. Nat. Commun. 4:2119 [Google Scholar]
  3. Tang Y, Suzuki Y-i, Shen H, Sekiguchi K, Kurahashi N. 3.  et al. 2010. Time-resolved photoelectron spectroscopy of bulk liquids at ultra-low kinetic energy. Chem. Phys. Lett. 494:111–16 [Google Scholar]
  4. Levine RD. 4.  1967. Nonreactive molecular encounters. J. Chem. Phys. 46:331–45 [Google Scholar]
  5. Levine RD. 5.  1969. Quantum Mechanics of Molecular Rate Processes Oxford, UK: Oxford Univ. Press
  6. Berry RS. 6.  1957. The interaction of vibrational and electronic motion in alkali halide molecules. J. Chem. Phys. 27:1288–95 [Google Scholar]
  7. Faist MB, Levine RD. 7.  1976. Collisional ionization and elastic scattering in alkali–halogen atom collisions. J. Chem. Phys. 64:2953–70 [Google Scholar]
  8. Remacle F, Nest M, Levine RD. 8.  2007. Laser steered ultrafast quantum dynamics of electrons in LiH. Phys. Rev. Lett. 99:183902 [Google Scholar]
  9. Secrest D, Johnson RB. 9.  1966. Exact quantum-mechanical calculation of a collinear collision of a particle with a harmonic oscillator. J. Chem. Phys. 45:4556–70 [Google Scholar]
  10. Bernstein RB, Dalgarno A, Massey H, Percival IC. 10.  1963. Thermal scattering of atoms by homonuclear diatomic molecules. Proc. R. Soc. Lond. 274:427 [Google Scholar]
  11. Levine RD, Johnson BR, Muckerman JT, Bernstein RB. 11.  1968. Computational investigation of internal excitation in nonreactive molecular collisions: resonances in rotational excitation. J. Chem. Phys. 49:56–64 [Google Scholar]
  12. Levine RD. 12.  1968. Adiabatic approximation for nonreactive subexcitation molecular collisions. J. Chem. Phys. 49:51–55 [Google Scholar]
  13. Nakamura H. 13.  2012. Nonadiabatic Transition: Concepts, Basic Theories and Applications London: World Sci, 2nd ed.. [Google Scholar]
  14. Wu SF, Johnson BR, Levine RD. 14.  1973. Quantum-mechanical computational studies of chemical reactions: III. Collinear A+BC reaction with some model potential-energy surfaces. Mol. Phys. 25:839–56 [Google Scholar]
  15. Ren Z. 15.  2014. State-to-State Dynamical Research in the F+H2 Reaction System Berlin: Springer
  16. Levine RD, Bernstein RB. 16.  1974. Molecular Reaction Dynamics New York: Oxford Univ. Press
  17. Bhagavan MR, Hoare MR. 17.  1971. Book review. Trans. Faraday Soc. 67:3392–93 [Google Scholar]
  18. Brumer P, Shapiro M. 18.  2012. Quantum Control of Molecular Processes Weinheim, Ger.: Wiley–VCH, 2nd ed..
  19. Light JC. 19.  1964. Phase-space theory of chemical kinetics. J. Chem. Phys. 40:3221 [Google Scholar]
  20. Bernstein RB, Levine RD. 20.  1972. Entropy and chemical change. I. Characterization of product (and reactant) energy distributions in reactive molecular collisions: information and entropy deficiency. J. Chem. Phys. 57:434–49 [Google Scholar]
  21. Kinsey JL. 21.  1971. Microscopic reversibility for rates of chemical reactions carried out with partial resolution of the product and reactant states. J. Chem. Phys. 54:1206–17 [Google Scholar]
  22. Ben‐Shaul A, Levine RD, Bernstein RB. 22.  1972. Entropy and chemical change. II. Analysis of product energy distributions: temperature and entropy deficiency. J. Chem. Phys. 57:5427–47 [Google Scholar]
  23. Kompa KL. 23.  1973. Chemical lasers. Chemical Lasers1–92 Berlin: Springer [Google Scholar]
  24. Valentini JJ, Gerrity DP. 24.  1986. State-to-state dynamics of the hydrogen exchange reaction. Int. J. Chem. Kinet. 18:937–48 [Google Scholar]
  25. Levine RD, Bernstein RB. 25.  1974. Energy disposal and energy consumption in elementary chemical reactions. Information theoretic approach. Acc. Chem. Res. 7:393–400 [Google Scholar]
  26. Kaplan H, Levine RD, Manz J. 26.  1976. The defendence of the reaction rate constant on reagent excitation: the implications of detailed balance. Chem. Phys. 12:447–61 [Google Scholar]
  27. Steinfeld JI, Francisco JS, Hase WL. 27.  1999. Chemical Kinetics and Dynamics Saddle River Valley, NJ: Prentice Hall, 2nd ed..
  28. Procaccia I, Levine RD. 28.  1976. Potential work: a statistical‐mechanical approach for systems in disequilibrium. J. Chem. Phys. 65:3357–64 [Google Scholar]
  29. Alhassid Y, Levine RD, Karp JS, Steadman SG. 29.  1979. Information-theoretic analysis of energy disposal in heavy-ion transfer reactions. Phys. Rev. C 20:1789–813 [Google Scholar]
  30. Alhassid Y, Levine RD. 30.  1977. Entropy and chemical change. III. The maximal entropy (subject to constraints) procedure as a dynamical theory. J. Chem. Phys. 67:4321–39 [Google Scholar]
  31. Alhassid Y, Levine RD. 31.  1978. Connection between the maximal entropy and the scattering theoretic analyses of collision processes. Phys. Rev. A 18:89–116 [Google Scholar]
  32. Clary DC, Nesbet RK. 32.  1978. Quantum dynamical examination of surprisal theory for the three-dimensional hydrogen exchange reaction. Chem. Phys. Lett. 59:437–42 [Google Scholar]
  33. Wyatt RE. 33.  1975. Information-theoretic analysis of quantum mechanical reaction cross sections. Chem. Phys. Lett. 34:167–69 [Google Scholar]
  34. Levine RD, Wulfman CE. 34.  1979. Energy transfer to a Morse oscillator. Chem. Phys. Lett. 60:372–76 [Google Scholar]
  35. Iachello F, Levine RD. 35.  2005. Algebraic Theory of Molecules New York: Oxford Univ. Press
  36. Benjamin I, Levine RD. 36.  1987. Comment on the high stretch overtones of water. J. Mol. Spectrosc. 126:486–87 [Google Scholar]
  37. Kais S, Serra P. 37.  2003. Finite-Size Scaling for Atomic and Molecular Systems Advances in Chemical Physics, Vol. 125, ed. I Prigogine, SA Rice Hoboken, NJ: Wiley
  38. Kais S, Herschbach DR, Levine RD. 38.  1989. Dimensional scaling as a symmetry operation. J. Chem. Phys. 91:7791–96 [Google Scholar]
  39. Tishby NZ, Levine RD. 39.  1984. Time evolution via a self-consistent maximal-entropy propagation—the reversible case. Phys. Rev. A 30:1477–90 [Google Scholar]
  40. Zandee L, Bernstein RB. 40.  1979. Laser ionization mass spectrometry: extensive fragmentation via resonance‐enhanced multiphoton ionization of a molecular benzene beam. J. Chem. Phys. 70:2574–75 [Google Scholar]
  41. Silberstein J, Levine RD. 41.  1981. Statistical fragmentation patterns in multiphoton ionization: a comparison with experiment. J. Chem. Phys. 75:5735–43 [Google Scholar]
  42. Lichtin DA, Bernstein RB, Newton KR. 42.  1981. Experimental appraisal of the maximal‐entropy theory of multiphoton ionization‐fragmentation: the alternative ionization pathway test. J. Chem. Phys. 75:5728–34 [Google Scholar]
  43. Ohmichi N, Silberstein J, Levine RD. 43.  1981. Electronically excited products in multiphoton dissociation: a computational study. Chem. Phys. Lett. 84:228–32 [Google Scholar]
  44. Raz T, Even U, Levine RD. 44.  1995. Fragment size distribution in cluster impact: shattering versus evaporation by a statistical approach. J. Chem. Phys. 103:5394–409 [Google Scholar]
  45. Raz T, Levine RD. 45.  1995. On the burning of air. Chem. Phys. Lett. 246:405–12 [Google Scholar]
  46. Raz T, Levine RD. 46.  1994. 4-center reactions induced by cluster-impact. J. Am. Chem. Soc. 116:11167–68 [Google Scholar]
  47. Campbell E, Levine RD. 47.  2000. Delayed ionization and fragmentation en route to thermionic emission: statistics and dynamics. Annu. Rev. Phys. Chem. 51:65–98 [Google Scholar]
  48. Campbell EEB, Raz T, Levine RD. 48.  1996. Internal energy dependence of the fragmentation patterns of C60 and C60+. Chem. Phys. Lett. 253:261–67 [Google Scholar]
  49. Gross A, Levine RD. 49.  2006. Mechanical simulation of the pressure and the relaxation to thermal equilibrium of a hot and dense rare gas cluster. J. Phys. Chem. B 110:24070–76 [Google Scholar]
  50. Gross A, Levine RD. 50.  2007. The entropy of a single large finite system undergoing both heat and work transfer. Mol. Phys. 105:419–27 [Google Scholar]
  51. Gross A, Levine RD. 51.  2003. Spectroscopic characterization of collision-induced electronic deformation energy using sum rules. J. Chem. Phys. 119:4283–93 [Google Scholar]
  52. Kornweitz H, Gross A, Birnbaum G, Levine RD. 52.  2005. Probing electronic rearrangement during chemical reactions. Phys. Scr. 73:C1 [Google Scholar]
  53. Levine RD. 53.  1972. Molecular collisions and reactive scattering. MTP Int. Rev. Sci., Vol. 1: Theoretical Chemistry W Byers-Brown, ch. 7 London: Butterworths [Google Scholar]
  54. Ben‐Nun M, Levine RD, Fleming GR. 54.  1996. Solvent‐induced nonadiabatic transitions in iodine: an ultrafast pump–probe computational study. J. Chem. Phys. 105:3035–56 [Google Scholar]
  55. Ben-Nun M, Levine RD. 55.  1995. Short-time dynamics on several electronic states: formalism and computational study of I2 in rare gas solvents. Chem. Phys. 201:163–87 [Google Scholar]
  56. Martinez TJ, Ben-Nun M, Levine RD. 56.  1996. Multi-electronic-state molecular dynamics: a wave function approach with applications. J. Phys. Chem. 100:7884–95 [Google Scholar]
  57. Martinez TJ, Levine RD. 57.  1996. First‐principles molecular dynamics on multiple electronic states: a case study of NaI. J. Chem. Phys. 105:6334–41 [Google Scholar]
  58. Ben-Nun M, Martinez TJ. 58.  2002. Ab initio quantum molecular dynamics. Advances in Chemical Physics 121 I Prigogine, SA Rice 439–512 Hoboken, NJ: Wiley [Google Scholar]
  59. Schechter I, Levine RD. 59.  1986. Dynamical stereochemistry of the hydrogen exchange reaction: A computational study. Int. J. Chem. Kinet. 18:1023–45 [Google Scholar]
  60. Remacle F, Levine RD, Ratner MA. 60.  1998. Charge directed reactivity. Chem. Phys. Lett. 285:25–33 [Google Scholar]
  61. Remacle F, Levine RD, Schlag EW, Weinkauf R. 61.  1999. Electronic control of site selective reactivity: a model combining charge migration and dissociation. J. Phys. Chem. A 103:10149–58 [Google Scholar]
  62. Weinkauf R, Schanen P, Yang D, Soukara S, Schlag EW. 62.  1995. Elementary processes in peptides: electron mobility and dissociation in peptide cations in the gas phase. J. Phys. Chem. 99:11255–65 [Google Scholar]
  63. Beverly KC, Sample JL, Sampaio JF, Remacle F, Heath JR, Levine RD. 63.  2002. Quantum dot artificial solids: understanding the static and dynamic role of size and packing disorder. PNAS 99:6456–59 [Google Scholar]
  64. Remacle F, Levine RD. 64.  1998. On the inverse Born–Oppenheimer separation for high Rydberg states of molecules. Int. J. Quantum Chem. 67:85–100 [Google Scholar]
  65. Rabani E, Levine RD, Even U. 65.  1995. A quantitative model for the dynamics of high Rydberg states of molecules: the iterated map and its kinetic limit. Ber. Bunsenges. Phys. Chem. 99:310–22 [Google Scholar]
  66. Rabani E, Levine RD, Mühlpfordt A, Even U. 66.  1995. Dynamics and kinetics of molecular high Rydberg states in the presence of an electrical field: an experimental and classical computational study. J. Chem. Phys. 102:1619–38 [Google Scholar]
  67. Remacle F, Levine RD. 67.  2006. An electronic time scale in chemistry. PNAS 103:6793–98 [Google Scholar]
  68. Nikodem A, Levine RD, Remacle F. 68.  2017. Spatial and temporal control of populations, branching ratios, and electronic coherences in LiH by a single one-cycle infrared pulse. Phys. Rev. A 95:053404 [Google Scholar]
  69. Nalewajski RF, Parr RG. 69.  2000. Information theory, atoms in molecules, and molecular similarity. PNAS 97:8879–82 [Google Scholar]
  70. Morales J, Martínez TJ. 70.  2001. Classical fluctuating charge theories: the maximum entropy valence bond formalism and relationships to previous models. J. Phys. Chem. A 105:2842–50 [Google Scholar]
  71. Mandal SH, Sanyal G, Mukherjee D. 71.  1998. A thermal cluster-cumulant theory. Microscopic Quantum Many-Body Theories and Their Applications J Navarro, A Polls 1–93 Berlin: Springer [Google Scholar]
  72. Graziani F, Desjarlais MP, Redmer R, Trickey SB. 72. , eds. 2014. Frontiers and Challenges in Warm Dense Matter Cham, Switz.: Springer
  73. Faist MB, Levine RD. 73.  1977. On the product electronic state distribution in reactions of alkali dimers with halogen atoms. Chem. Phys. Lett. 47:5–10 [Google Scholar]
  74. Nest M, Remacle F, Levine RD. 74.  2008. Pump and probe ultrafast electron dynamics in LiH: a computational study. N. J. Phys. 10:025019 [Google Scholar]
  75. Mignolet B, Levine RD, Remacle F. 75.  2012. Localized electron dynamics in attosecond-pulse-excited molecular systems: probing the time-dependent electron density by sudden photoionization. Phys. Rev. A 86:053429 [Google Scholar]
  76. Ajay J, Šmydke J, Remacle F, Levine RD. 76.  2016. Probing in space and time the nuclear motion driven by nonequilibrium electronic dynamics in ultrafast pumped N2. J. Phys. Chem. A 120:3335–42 [Google Scholar]
  77. van den Wildenberg S, Mignolet B, Levine RD, Remacle F. 77.  2017. Pumping and probing vibrational modulated coupled electronic coherence in HCN using short UV fs laser pulses: a 2D quantum nuclear dynamical study. Phys. Chem. Chem. Phys. 19:19837–46 [Google Scholar]
  78. Remacle F, Levine RD. 78.  2001. Towards a molecular logic machine. J. Chem. Phys. 114:10239–46 [Google Scholar]
  79. Remacle F, Speiser S, Levine RD. 79.  2001. Intermolecular and intramolecular logic gates. J. Phys. Chem. B 105:5589–91 [Google Scholar]
  80. Remacle F, Heath JR, Levine RD. 80.  2005. Electrical addressing of confined quantum systems for quasiclassical computation and finite state logic machines. PNAS 102:5653–58 [Google Scholar]
  81. Mol JA, Verduijn J, Levine RD, Remacle F, Rogge S. 81.  2011. Integrated logic circuits using single-atom transistors. PNAS 108:13969–72 [Google Scholar]
  82. Orbach R, Remacle F, Levine RD, Willner I. 82.  2012. Logic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates. PNAS 109:21228–33 [Google Scholar]
  83. Lilienthal S, Klein M, Orbach R, Willner I, Remacle F, Levine RD. 83.  2017. Continuous variables logic via coupled automata using a DNAzyme cascade with feedback. Chem. Sci. 8:2161–68 [Google Scholar]
  84. Fresch B, Hiluf D, Collini E, Levine RD, Remacle F. 84.  2013. Molecular decision trees realized by ultrafast electronic spectroscopy. PNAS 110:17183–88 [Google Scholar]
  85. Fresch B, Cipolloni M, Yan T-M, Collini E, Levine RD, Remacle F. 85.  2015. Parallel and multivalued logic by the two-dimensional photon-echo response of a rhodamine–DNA complex. J. Phys. Chem. Lett. 6:1714–18 [Google Scholar]
  86. Remacle F, Kravchenko-Balasha N, Levitzki A, Levine RD. 86.  2010. Information-theoretic analysis of phenotype changes in early stages of carcinogenesis. PNAS 107:10324–29 [Google Scholar]
  87. Kravchenko-Balasha N, Levitzki A, Goldstein A, Rotter V, Gross A. 87.  et al. 2012. On a fundamental structure of gene networks in living cells. PNAS 109:4702–7 [Google Scholar]
  88. Zadran S, Remacle F, Levine RD. 88.  2013. miRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients. PNAS 110:19160–65 [Google Scholar]
  89. Shin Young S, Remacle F, Fan R, Hwang K, Wei W. 89.  et al. 2011. Protein signaling networks from single cell fluctuations and information theory profiling. Biophys. J. 100:2378–86 [Google Scholar]
  90. Remacle F, Levine RD. 90.  2015. Statistical thermodynamics of transcription profiles in normal development and tumorigeneses in cohorts of patients. Eur. Biophys. J. 44:709–26 [Google Scholar]
  91. Alter O. 91.  2007. Genomic signal processing: from matrix algebra to genetic networks. Microarray Data Analysis: Methods and Applications MJ Korenberg 17–60 Totowa, NJ: Humana Press [Google Scholar]
  92. Golub GH, van Loan CF. 92.  1996. Matrix Computations Baltimore, MD: Johns Hopkins Univ. Press
  93. Zadran S, Arumugam R, Herschman H, Phelps ME, Levine RD. 93.  2014. Surprisal analysis characterizes the free energy time course of cancer cells undergoing epithelial-to-mesenchymal transition. PNAS 111:13235–40 [Google Scholar]
  94. Kravchenko-Balasha N, Shin YS, Sutherland A, Levine RD, Heath JR. 94.  2016. Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement. PNAS 113:5520–25 [Google Scholar]
  95. Levine RD. 95.  2008. Autobiographical sketch. Mol. Phys. 106:193–201 [Google Scholar]
/content/journals/10.1146/annurev-physchem-102717-010036
Loading
Addressing the Challenge of Molecular Change: An Interim Report
Annual Review of Physical Chemistry 69, 1 (2018); https://doi.org/10.1146/annurev-physchem-102717-010036
/content/journals/10.1146/annurev-physchem-102717-010036
/content/journals/10.1146/annurev-physchem-102717-010036
Loading

Data & Media loading...

  • Article Type: Review Article

Most Cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error