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Computational Molecular Engineering for Nanodevices and Nanosystems

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Practical Aspects of Computational Chemistry I

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Abstract

Molecular electrostatic potentials (MEPs), electronics (moletronics), and vibrational electronics (vibronics) are novel scenarios to process information at the molecular level. These, along with the traditional current-voltage scenario can be used to design and develop molecular devices and systems for even more extended applications than traditional electronics. Successful control and communication features between scenarios would yield “smart” devices able to take decisions and act under difficult conditions. The design of molecular devices is a primordial step in the development of devices at the nanometer scale, enabling the next generation of sensors of chemical and biological agents molecularly sensitive, selective, and intelligent.

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References

  1. Allen MP, Tildesley DJ (1990) Computer simulation of liquids. Clarendon, Oxford

    Google Scholar 

  2. Seminario JM, Derosa PA, Bozard BH, Chagarlamudi K (2005) Vibrational study of a molecular device using molecular dynamics simulations. J Nanosci Nanotechnol 5:1–11

    Google Scholar 

  3. Seminario JM, Yan L, Ma Y (2005) Scenarios for molecular-level signal processing. Proc IEEE 93:1753–1764

    CAS  Google Scholar 

  4. Yan L, Ma Y, Seminario JM (2006) Terahertz signal transmission in molecular systems. Int J High Speed Electron Syst 16:669–675

    CAS  Google Scholar 

  5. Politzer P, Truhlar DG (1981) Chemical applications of atomic and molecular electrostatic potentials. Plenum Press, New York

    Google Scholar 

  6. Tour JM, Kosaki M, Seminario JM (1998) Molecular scale electronics: a synthetic/ computational approach to digital computing. J Am Chem Soc 120:8486–8493

    CAS  Google Scholar 

  7. Tour JM, Kozaki M, Seminario JM (2001) Use of molecular electrostatic potential for molecular scale computation. U.S. Patent 6259277

    Google Scholar 

  8. Politzer P, Seminario JM (1989) Computational analysis of the structures, bond properties, and electrostatic potentials of some nitrotetrahedranes and nitroazatetrahedranes. J Phys Chem 93:4742–4745

    CAS  Google Scholar 

  9. Scrocco E, Tomasi J (1973) The electrostatic molecular potential as a tool for the interpretation of molecular properties. Top Curr Chem 42:95–170

    CAS  Google Scholar 

  10. Jeffrey GA (1991) The application of charge-density research to chemistry and drug design. Plenum Press, New York

    Google Scholar 

  11. Murray JS, Sen K (eds) (1996) Molecular electrostatic potentials. Concepts and applications. Theoretical and computational chemistry. Elsevier, Amsterdam, p 665

    Google Scholar 

  12. Yan L, Seminario JM (2006) Moletronics modeling towards molecular potentials. Int J Quantum Chem 106:1964–1969

    CAS  Google Scholar 

  13. Naray-Szabo G, Ferenczy GG (1995) Molecular electrostatics. Chem Rev 95:829–847

    CAS  Google Scholar 

  14. Politzer P, Murray J (1991) Molecular electrostatic potentials and chemical reactivity. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry, vol 2. VCH Publishers, New York, pp 273–312

    Google Scholar 

  15. Seminario JM, Yan L, Ma Y (2005) Encoding and transport of information in molecular and biomolecular systems. Proc IEEE Nanotechnol Conf 5:65–68

    Google Scholar 

  16. Seminario JM, Yan L (2005) Molecular logical devices in cascade configuration with information encoded as electrostic potentials. J Am Chem Soc vol. Submitted

    Google Scholar 

  17. Hehre WJ, Radom L, Schleyer PvR, Pople JA (1986) Ab initio molecular orbital theory. Wiley, New York

    Google Scholar 

  18. Seminario JM, Yan L (2005) Ab initio analysis of electron currents in thioalkanes. Int J Quantum Chem 102:711–723

    CAS  Google Scholar 

  19. MJT Frisch GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam NJ, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2009) Gaussian-09, Revision A.01. Gaussian, Inc, Wallingford

    Google Scholar 

  20. McWeeny R, Diercksen G (1968) Self-consistent perturbation theory. II. Extension to open shells. J Chem Phys 49:4852–4856

    CAS  Google Scholar 

  21. Petersson GA, Al-Laham MA (1991) A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms. J Chem Phys 94:6081–6090

    CAS  Google Scholar 

  22. Petersson GA, Bennett A, Tensfeldt TG, Al-Laham MA, Shirley WA, Mantzaris J (1988) A complete basis set model chemistry. I. The total energies of closed-shell atoms and hydrides of the first-row elements. J Chem Phys 89:2193–2218

    CAS  Google Scholar 

  23. Wang P, Moorefield CN, Lic S, Hwang S-H, Shreiner CD, Newkome GR (2006) TerpyridineCuII-mediated reversible nanocomposites of single-wall carbon nanotubes: towards metallo-nanoscale architectures. Chem Commun 10:1091–1093

    Google Scholar 

  24. Hay PJ, Wadt WR (1985) Ab initio effective core potentials for molecular calculations. Potentials for K to Au including the outermost core orbitals. J Chem Phys 82:299–310

    CAS  Google Scholar 

  25. Wadt WR, Hay PJ (1985) Ab initio effective core potentials for molecular calculations. Potentials for main group elements Na to Bi. J Chem Phys 82:284–298

    CAS  Google Scholar 

  26. Kohn W, Sham LJ (1965) Self-consistent equations including exchange and correlation effects. Phys Rev A 140:1133–1138

    Google Scholar 

  27. Perdew JP, Chevary JA, Vosko SH, Jackson KA, Pederson MR, Singh DJ, Fiolhais C (1992) Atoms, molecules, solids, and surfaces: applications of the generalized gradient approximation for exchange and correlation. Phys Rev B 46:6671–6687

    CAS  Google Scholar 

  28. Perdew JP, Wang Y (1992) Accurate and simple analytic representation of the electron-gas correlation energy. Phys Rev B 45:13244–13249

    CAS  Google Scholar 

  29. Seminario JM, Maffei MG, Agapito LA, Salazar PF (2006) Energy correctors for accurate prediction of molecular energies. J Phys Chem A 110:1060–1064

    CAS  PubMed  Google Scholar 

  30. Seminario JM (1993) Energetics using DFT: comparisons to precise ab initio and experiment. Chem Phys Lett 206:547–554

    CAS  Google Scholar 

  31. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the method of constraint satisfaction with parametrization for thermochemistry, thermochemical kinetics, and noncovalent interactions. J Chem Theor Comput 2:364–382

    Google Scholar 

  32. Seminario JM, Ma Y, Tarigopula V (2006) The NanoCell: a chemically assembled molecular electronic circuit. IEEE Sensors 6:1614–1626

    CAS  Google Scholar 

  33. Hong S, Jauregui LA, Rangel NL, Cao H, Day BS, Norton ML, Sinitskii AS, Seminario JM (2008) Impedance measurements on a DNA junction. J Chem Phys 128:201103

    Google Scholar 

  34. Bellido EP, Bobadilla AD, Rangel NL, Zhong H, Norton ML, Sinitskii A, Seminario JM (2009) Current-voltage-temperature characteristics of DNA origami. Nanotechnology 20:175102

    PubMed  Google Scholar 

  35. Bobadilla AD, Bellido EP, Rangel NL, Zhong H, Norton ML, Sinitskii A, Seminario JM (2009) DNA origami impedance measurement at room temperature. J Chem Phys 130:171101

    PubMed  Google Scholar 

  36. Cristancho D, Seminario JM (2010) Polypeptides in alpha-helix conformation perform as diodes. J Chem Phys 132:065102

    PubMed  Google Scholar 

  37. Rangel NL, Sotelo JC, Seminario JM (2009) Mechanism of carbon nanotubes unzipping into graphene ribbons. J Chem Phys 131:031105

    PubMed  Google Scholar 

  38. Rangel NL, Seminario JM (2010) Vibronics and plasmonics based graphene sensors. J Chem Phys 132:125102

    PubMed  Google Scholar 

  39. Rangel NL, Seminario JM (2010) Single molecule detection using graphene electrodes. J Physics B 43:155101

    Google Scholar 

  40. Rangel NL, Seminario JM (2008) Graphene terahertz generators for molecular circuits and sensors. J Phys Chem A 112:13699–13705

    CAS  PubMed  Google Scholar 

  41. Rangel NL, Seminario JM (2008) Nanomicrointerface to read molecular potentials into current-voltage based electronics. J Chem Phys 128:114711

    PubMed  Google Scholar 

  42. Rangel NL, Williams KS, Seminario JM (2009) Light-activated molecular conductivity in the photoreactions of vitamin D3. J Phys Chem A 113:6740–6744

    CAS  PubMed  Google Scholar 

  43. Wang K, Rangel NL, Kundu S, Sotelo JC, Tovar RM, Seminario JM, Liang H (2009) Switchable molecular conductivity. J Am Chem Soc 131:10447–10451

    CAS  PubMed  Google Scholar 

  44. Hashimoto A, Suenaga K, Gloter A, Urita K, Iijima S (2004) Direct evidence for atomic defects in graphene layers. Nature 430:870–873

    CAS  PubMed  Google Scholar 

  45. Wakabayashi K, Fujita M, Ajiki H, Sigrist M (1999) Electronic and magnetic properties of nanographite ribbons. Phys Rev B 59:8271

    CAS  Google Scholar 

  46. Barone V, Hod O, Scuseria GE (2006) Electronic structure and stability of semiconducting graphene nanoribbon. Nano Lett 6:2748–2754

    CAS  PubMed  Google Scholar 

  47. Han MY, Özyilmaz B, Zhang Y, Kim P (2007) Energy band-gap engineering of graphene nanoribbons. Phys Rev Lett 98:206805

    PubMed  Google Scholar 

  48. Binning G, Rohrer H (1982) Scanning tunneling microscopy. Helv Phys Acta 55:726–735

    Google Scholar 

  49. Blum AS, Kushmerick JG, Long DP, Patterson CH, Yang JC, Henderson JC, Yao Y, Tour JM, Shashidhar R, Ratna BR (2005) Molecularly inherent voltage-controlled conductance switching. Nature 4:167–172

    CAS  Google Scholar 

  50. Ariga K, Hill JP, Endo H (2007) Developments in molecular recognition and sensing at interfaces. Int J Mol Sci 8:864–883

    CAS  PubMed Central  Google Scholar 

  51. Von Neumann J (1966) Theory of self-reproduction automata. In: Burks A (ed) La vie artificielle. University of Illinois Press, Paris

    Google Scholar 

  52. Wolfram S (1984) Cellular automata as models of complexity. Nature 311:419–424

    Google Scholar 

  53. Wolfram S (1984) Universality and complexity in cellular automata. Phys D 10:1–35

    Google Scholar 

  54. Scrocco E, Tomasi J (1978) Electronic molecular structure, reactivity and intermolecular forces: a heuristic interpretation by means of electrostatic molecular potentials. Adv Quantum Chem 11:115

    CAS  Google Scholar 

  55. Valia Dimitrova SI, Galabov B (2002) Electrostatic potential at atomic sites as a reactivity descriptor for hydrogen bonding. Complexes of monosubstituted acetylenes and ammonia. J Phys Chem A 106:11801–11805

    Google Scholar 

  56. Geerlings PL, Langenaeker W, De Proft F, Baeten A (1996) Molecular electrostatic potentials vs. DFT [density-functional theory] descriptors of reactivity. General Review, pp 587–617

    Google Scholar 

  57. Robbins AM, Jin P, Brinck T, Murray JS, Politzer P (2006) Electrostatic potential as a measure of gas phase carbocation stability. Int J Quantum Chem 106:2904–2909

    CAS  Google Scholar 

  58. Dhumal NR, Patil UN, Gejji SP (2004) Molecular electrostatic potentials and electron densities in nitroazacubanes. J Chem Phys 120:749–755

    CAS  PubMed  Google Scholar 

  59. Murray JS, Lane P, Politzer P (1998) Effects of strongly electron-attracting components on molecular surface electrostatic potentials; application to predicting impact sensitivities of energetic molecules. Mol Phys 93:187–194

    CAS  Google Scholar 

  60. Cheng X-l, Wang K-m, Zhang H, Yang X-d (2002) Relationships between impact sensitivities and the electrostatic potentials for five nitroaniline explosives. Inst Atomic Mol Phys 19: 94–100

    CAS  Google Scholar 

  61. Politzer P, Murray JS (1996) Relationships between dissociation energies and electrostatic potentials of C–NO2 bonds: applications to impact sensitivities. J Mol Struct 376:419–424

    CAS  Google Scholar 

  62. Seminario JM, Yan L, Ma Y (2005) Nano-detectors using molecular circuits operating at THz frequencies. In: Jensen JO, Theriault JM (eds) Chemical and biological standoff detection III, vol 5995. SPIE, Bellingham, pp 230–244

    Google Scholar 

  63. Hao Hu ZL, Weitao Y (2007) Fitting molecular electrostatic potentials from quantum mechanical calculations. J Chem Theor Comput 3:1004–1013

    Google Scholar 

  64. Hall CMSGG (1984) Fitting electron densities of molecules. Int J Quantum Chem 25:881–890

    CAS  Google Scholar 

  65. Pinjari RV, Joshi KA, Gejji SP (2006) Molecular electrostatic potentials and hydrogen bonding in alpha-, beta-, and ç-cyclodextrins. J Phys Chem A 110:13073–13080

    CAS  PubMed  Google Scholar 

  66. Seminario JM, Yan L (2007) Cascade configuration of logical gates processing information encoded in molecular potentials. Int J Quantum Chem 107:754–761

    CAS  Google Scholar 

  67. Seminario JM, Cordova LE, Derosa PA (2003) An Ab initio approach to the calculation of current-voltage characteristics of programmable molecular devices. Proc IEEE 91:1958–1975

    CAS  Google Scholar 

  68. Seminario JM, Zacarias AG, Tour JM (1998) Theoretical interpretation of conductivity measurements of thiotolane sandwich. A molecular scale electronic controller. Am Chem Soc 120:3970–3974

    CAS  Google Scholar 

  69. Seminario JM (2007) Quantum current-voltage relation for a single electron. J Phys B 40:F275–F276

    CAS  Google Scholar 

  70. Seminario JM, Zacarias AG, Tour JM (1999) Molecular current-voltage characteristics. J Phys Chem A 103:7883–7887

    CAS  Google Scholar 

  71. Xu G-b, Xu Q-x (2007) Development of advanced Hf based high-k gate dielectrics. Dianzi Qijian Inst Microelectron 30:1194–1199

    CAS  Google Scholar 

  72. Lee C, Choi DS, Park HR, Kim CS, Wang KL (2001) Side contact single electron devices for integrated circuit. J Korean Phys Soc 39:S442–S446

    CAS  Google Scholar 

  73. Wada Y (1997) Atom electronics: a proposal of atom/molecule switching devices. Surf Sci 30:265–278

    Google Scholar 

  74. Yang C, Zhong Z, Lieber CM (2005) Encoding electronic properties by synthesis of axial modulation-doped silicon nanowires. Science 310:1304–1307

    CAS  PubMed  Google Scholar 

  75. Yuan Taur DAB, W Chen, Frank DJ, Ismail KE, Shih-Hsien Lo, Sai-Halasz GA, Viswanathan RG, Wann HC, Wind SJ, Wong H (1997) CMOS scaling into the nanometer regime. Proc IEEE 85:486–504

    Google Scholar 

  76. Moore GE (1965) Cramming more components onto integrated circuits. Electronics 38: 114–117

    Google Scholar 

  77. Seminario JM, Derosa PA (2001) Molecular gain in a thiotolane system. J Am Chem Soc 123:12418–12419

    CAS  PubMed  Google Scholar 

  78. Seminario JM, Yan L, Ma Y (2006) Encoding and transport of information in molecular and biomolecular systems. Trans IEEE Nanotechnol 5:436–440

    Google Scholar 

  79. Calizo I, Balandin AA, Bao W, Miao F, Lau CN (2007) Temperature dependence of the Raman spectra of graphene and graphene multilayers. Nano Lett 7:2645–2649

    CAS  PubMed  Google Scholar 

  80. Song H, Kim Y, Jang YH, Jeong H, Reed MA, Lee T (2009) Observation of molecular orbital gating. Nature 462:1039–1043

    CAS  PubMed  Google Scholar 

  81. Knobel RG, Cleland AN (2003) Nanometre-scale displacement sensing using a single electron transistor. Nature 424:291–293

    CAS  PubMed  Google Scholar 

  82. Sazonova V, Yaish Y, Ustunel H, Roundy D, Arias TA, McEuen PL (2004) A tunable carbon nanotube electromechanical oscillator. Nature 431:284–287

    CAS  PubMed  Google Scholar 

  83. Witkamp B, Poot M, van der Zant HSJ (2006) Bending-mode vibration of a suspended nanotube resonator. Nano Lett 6:2904–2908

    CAS  PubMed  Google Scholar 

  84. Portnoi ME, Kibis OV, Rosenau da Costa M (2007) Terahertz applications of carbon nanotubes. Superlattices Microstruct 43:399–407

    Google Scholar 

  85. Rutherglen C, Jain D, Burke P (2009) Nanotube electronics for radiofrequency applications. Nat Nanotechnol 4:811–819

    CAS  PubMed  Google Scholar 

  86. Han W, Nezich D, Jing K, Palacios T (2009) Graphene frequency multipliers. Electron Device Lett IEEE 30:547–549

    Google Scholar 

  87. Wang Z, Zhang Z, Xu H, Ding L, Wang S, Peng L-M (2010) A high-performance top-gate graphene field-effect transistor based frequency doubler. Appl Phys Lett 96:173104–173104-3

    Google Scholar 

  88. Han W, Hsu A, Wu J, Jing K, Palacios T (2010) Graphene-based ambipolar RF mixers. Electron Device Lett IEEE 31:906–908

    Google Scholar 

  89. Rangel N, Gimenez A, Sinitskii A, Seminario JM (2011) Graphene signal mixer for sensing applications. J Phys Chem 115(24):12128–12134

    CAS  Google Scholar 

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Acknowledgements

We acknowledge financial support from the U. S. Defense Threat Reduction Agency DTRA through the U. S. Army Research Office, Project No. W91NF-06-1-0231; from the ARO/DURINT project # W91NF-07-1-0199, and the ARO/MURI project # W911NF-11-1-0024. We also thanks Jeremy Katusak for a thorough check of the final manuscript.

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Authors and Affiliations

  1. Department of Chemical Engineering, Texas A&M University, College Station, TX, USA

    Norma L. Rangel, Paola A. Leon-Plata & Jorge M. Seminario

  2. Materials Science and Engineering, Texas A&M University, College Station, TX, USA

    Norma L. Rangel & Jorge M. Seminario

  3. Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, USA

    Jorge M. Seminario

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  1. Norma L. Rangel
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  2. Paola A. Leon-Plata
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  3. Jorge M. Seminario
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Correspondence to Jorge M. Seminario .

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Editors and Affiliations

  1. Department of Chemistry, Jackson State University, 17910, P.O. Box 17910, 1400 Lynch St., Jackson, 39217, Mississippi, USA

    Jerzy Leszczynski

  2. Dept. Chemistry, Jackson State University, J. R. Lynch St. 1325, Jackson, 39217, Mississippi, USA

    Manoj K. K. Shukla

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Rangel, N.L., Leon-Plata, P.A., Seminario, J.M. (2011). Computational Molecular Engineering for Nanodevices and Nanosystems. In: Leszczynski, J., Shukla, M.K. (eds) Practical Aspects of Computational Chemistry I. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0919-5_12

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