Skip to main content
SpringerLink
Log in

Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment

  • Regular Article
  • Published:
Theoretical Chemistry Accounts Aims and scope Submit manuscript

Abstract

Dimethyl phosphate (DMP) anion has been used extensively as a model compound to simulate the properties of phosphate group. A 35-point DMP anion potential model is constructed based on the atom-bond electronegativity equalization fluctuating charge molecular force field (ABEEM/MM), and it is employed to study the properties of gas-phase DMP anion and DMP-(H2O) n (n = 1–3) clusters. The ABEEM/MM model reproduces well the properties obtained by available experiments and QM calculations, including charge distributions, geometries, and conformational energies of gas-phase DMP-water complexes. Furthermore, molecular dynamics simulation on the DMP anion in aqueous solution based on the ABEEM/MM shows that a remarkable first hydration shell around the nonesterified oxygen atom of DMP anion is formed with a coordination number of 5.2. It is also found that two hydrogen atoms of one water molecule form two hydrogen bonds with two nonesterified oxygen atoms of DMP anion simultaneously. This work could be used as a starting point for us to establish the ABEEM/MM nucleic acid force field.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  1. Guan Y, Wurrey CJ, Thomas GJ Jr (1994) Biophys J 66:225–235. doi:10.1016/S0006-3495(94)80767-2

    Article  CAS  Google Scholar 

  2. Guan Y, Choy GS-C, Glaser R, Thomas GJ Jr (1995) J Phys Chem 99:12054–12062. doi:10.1021/j100031a039

    Article  CAS  Google Scholar 

  3. Jayaram B, Mezei M, Beveridge DL (1987) J Comput Chem 8:917–942. doi:10.1002/jcc.540080702

    Article  CAS  Google Scholar 

  4. Jayaram B, Mezei M, Beveridge DL (1988) J Am Chem Soc 110:1691–1694. doi:10.1021/ja00214a005

    Article  CAS  Google Scholar 

  5. Jayaram B, Ravishanker G, Beveridge DL (1988) J Phys Chem 92:1032–1034. doi:10.1021/j100316a009

    Article  CAS  Google Scholar 

  6. Liang CX, Ewig CS, Stouch TR, Hagler AT (1993) J Am Chem Soc 115:1537–1545. doi:10.1021/ja00057a046

    Article  CAS  Google Scholar 

  7. Landin J, Pascher I, Cremer D (1995) J Phys Chem 99:4471–4485. doi:10.1021/j100013a017

    Article  CAS  Google Scholar 

  8. Kamitakahara A, Hsu CL, Pranata J (1995) J Mol Struct Theochem 334:29–35. doi:10.1016/0166-1280(94)03966-O

    Article  CAS  Google Scholar 

  9. Florián J, Baumruk V, Štrajbl M, Bednárová L, Štĕpánek J (1996) J Phys Chem 100:1559–1568. doi:10.1021/jp9520299

    Article  Google Scholar 

  10. Florián J, Štrajbl M, Warshel A (1998) J Am Chem Soc 120:7959–7966. doi:10.1021/ja9710823

    Article  Google Scholar 

  11. Pichierri F, Sarai A (1999) J Mol Struct Theochem 460:103–116. doi:10.1016/S0166-1280(98)00309-1

    Article  CAS  Google Scholar 

  12. Murashov VV, Leszczynski J (1999) J Phys Chem B 103:8391–8397. doi:10.1021/jp9915735

    Article  CAS  Google Scholar 

  13. Murashov VV, Leszczynski J (2000) J Mol Struct Theochem 529:1–14. doi:10.1016/S0166-1280(00)00524-8

    Article  CAS  Google Scholar 

  14. Banavali NK, Mackerell AD Jr (2001) J Am Chem Soc 123:6747–6755. doi:10.1021/ja010295w

    Article  CAS  Google Scholar 

  15. Kuo IF, Tobias DJ (2001) J Phys Chem B 105:5827–5832. doi:10.1021/jp003900a

    Article  CAS  Google Scholar 

  16. Schwegler E, Galli G, Gygi F (2001) Chem Phys Lett 342:434–440. doi:10.1016/S0009-2614(01)00604-2

    Article  CAS  Google Scholar 

  17. Petrov AS, Pack GR, Lamm G (2004) J Phys Chem B 108:6072–6081. doi:10.1021/jp037517s

    Article  CAS  Google Scholar 

  18. Petrov AS, Funseth-Smotzer J, Pack GR (2005) Int J Quantum Chem 102:645–655. doi:10.1002/qua.20442

    Article  CAS  Google Scholar 

  19. Potoff JJ, Issa Z, Manke CW Jr, Jena BP (2008) Cell Biol Int 32:361–366. doi:10.1016/j.cellbi.2008.03.002

    Article  CAS  Google Scholar 

  20. Karplus M (2002) Acc Chem Res 35:321–323. doi:10.1021/ar020082r

    Article  CAS  Google Scholar 

  21. Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TEIII (2000) Acc Chem Res 33:889–897. doi:10.1021/ar000033j

    Article  CAS  Google Scholar 

  22. Giudice E, Lavery R (2002) Acc Chem Res 35:350–357. doi:10.1021/ar010023y

    Article  CAS  Google Scholar 

  23. Simonson T, Archontis G, Karplus M (2002) Acc Chem Res 35:430–437. doi:10.1021/ar010030m

    Article  CAS  Google Scholar 

  24. Saiz L, Klein ML (2002) Acc Chem Res 35:482–489. doi:10.1021/ar010167c

    Article  CAS  Google Scholar 

  25. Mackerell AD Jr, Wiórkiewicz-Kuczera J, Karplus M (1995) J Am Chem Soc 117:11946–11975. doi:10.1021/ja00153a017

    Article  CAS  Google Scholar 

  26. Foloppe N, Mackerell AD Jr (2000) J Comput Chem 21:86–104. doi:10.1002/(SICI)1096-987X(20000130)21:2<86::AID-JCC2>3.0.CO;2-G

    Article  CAS  Google Scholar 

  27. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM Jr, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179–5197. doi:10.1021/ja00124a002

    Article  CAS  Google Scholar 

  28. Soares TA, Hünenberger PH, Kastenholz MA, Kräutler V, Lenz T, Lins RD, Oostenbrink C, van Gunsteren WF (2005) J Comput Chem 26:725–737. doi:10.1002/jcc.20193

    Article  CAS  Google Scholar 

  29. Shaik MS, Devereux M, Popelier PLA (2008) Mol Phys 106:1495–1510. doi:10.1080/00268970802060708

    Article  CAS  Google Scholar 

  30. van der Spole D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJC (2005) J Comput Chem 26:1701–1718. doi:10.1002/jcc.20291

    Article  Google Scholar 

  31. Aduri R, Psciuk BT, Saro P, Taniga H, Schlegel HB, Santalucia J (2007) J Chem Theory Comput 3:1464–1475. doi:10.1021/ct600329w

    Article  CAS  Google Scholar 

  32. Jorgensen WL (2007) J Chem Theory Comput 3:1877. doi:10.1021/ct700252g

    Article  CAS  Google Scholar 

  33. Bret C, Field MJ, Hemmingsen L (2000) Mol Phys 98:751–763. doi:10.1080/002689700162108

    Article  CAS  Google Scholar 

  34. Xie W, Pu J, MacKerell AD Jr, Gao J (2007) J Chem Theory Comput 3:1878–1889. doi:10.1021/ct700146x

    Article  CAS  Google Scholar 

  35. Xie W, Gao J (2007) J Chem Theory Comput 3:1890–1900. doi:10.1021/ct700167b

    Article  CAS  Google Scholar 

  36. Soteras I, Curutchet C, Bidon-Chanal A, Dehez F, Ángyán JG, Orozco M, Chipot C, Luque FJ (2007) J Chem Theory Comput 3:1901–1913. doi:10.1021/ct7001122

    Article  CAS  Google Scholar 

  37. Dehez F, Ángyán JG, Gutiérrez IS, Luque FJ, Schulten K, Chipot C (2007) J Chem Theory Comput 3:1914–1926. doi:10.1021/ct700156a

    Article  CAS  Google Scholar 

  38. Nakagawa S, Mark P, Ågren H (2007) J Chem Theory Comput 3:1947–1959. doi:10.1021/ct700132w

    Article  CAS  Google Scholar 

  39. Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG (2007) J Chem Theory Comput 3:2011–2033. doi:10.1021/ct7001418

    Article  CAS  Google Scholar 

  40. Olson RM, Marenich AV, Cramer CJ, Truhlar DG (2007) J Chem Theory Comput 3:2046–2054. doi:10.1021/ct7001607

    Article  CAS  Google Scholar 

  41. Marenich AV, Olson RM, Chamberlin AC, Cramer CJ, Truhlar DG (2007) J Chem Theory Comput 3:2055–2067. doi:10.1021/ct7001539

    Article  CAS  Google Scholar 

  42. Schnieders MJ, Ponder JW (2007) J Chem Theory Comput 3:2083–2097. doi:10.1021/ct7001336

    Article  CAS  Google Scholar 

  43. Geerke DP, van Gunsteren WF (2007) J Chem Theory Comput 2:2128–2137. doi:10.1021/ct700164k

    Article  Google Scholar 

  44. Mennucci B, Cappelli C, Cammi R, Tomasi J (2007) Theor Chem Acc 117:1029–1039. doi:10.1007/s00214-006-0221-2

    Article  CAS  Google Scholar 

  45. Holt A, Karlström G (2008) J Comput Chem 29:1084–1091. doi:10.1002/jcc.20867

    Article  CAS  Google Scholar 

  46. Holt A, Karlström G (2008) J Comput Chem 29:1905–1911. doi:10.1002/jcc.20952

    Article  CAS  Google Scholar 

  47. Holt A, Karlström G (2008) J Comput Chem 29:2033–2038. doi:10.1002/jcc.20976

    Article  CAS  Google Scholar 

  48. Lussetti E, Pastore G, Smargiassi E (2008) Mol Phys 106:9–21. doi:10.1080/00268970701786361

    Article  CAS  Google Scholar 

  49. Defusco A, Schofield DP, Jordan KD (2007) Mol Phys 105:2681–2696. doi:10.1080/00268970701620669

    Article  CAS  Google Scholar 

  50. Plattner N, Bandi T, Doll JD, Freeman DL, Meuwly M (2008) Mol Phys 106:1675–1684. doi:10.1080/00268970802314394

    Article  CAS  Google Scholar 

  51. Sakharov DV, Lim C (2009) J Comput Chem 30:191–202. doi:10.1002/jcc.21048

    Article  CAS  Google Scholar 

  52. Yang ZZ, Zhang Q (2006) J Comput Chem 27:1–10. doi:10.1002/jcc.20317

    Article  Google Scholar 

  53. Yang ZZ, Wang CS (1997) J Phys Chem A 101:6315–6321. doi:10.1021/jp9711048

    Article  CAS  Google Scholar 

  54. Wang CS, Yang ZZ (1999) J Chem Phys 110:6189–6197. doi:10.1063/1.478524

    Article  CAS  Google Scholar 

  55. Yang ZZ, Cui BQ (2007) J Chem Theory Comput 3:1561–1568. doi:10.1021/ct600379n

    Article  CAS  Google Scholar 

  56. Yang ZZ, Wang CS (2003) J Theor Comput Chem 2:273–299. doi:10.1142/S0219633603000434

    Article  CAS  Google Scholar 

  57. Yang ZZ, Wu Y, Zhao DX (2004) J Chem Phys 120:2541–2557. doi:10.1063/1.1640345

    Article  CAS  Google Scholar 

  58. Wu Y, Yang ZZ (2004) J Phys Chem A 108:7563–7576. doi:10.1021/jp0493881

    Article  CAS  Google Scholar 

  59. Yang ZZ, Li X (2005) J Phys Chem A 109:3517–3520. doi:10.1021/jp051106p

    Article  CAS  Google Scholar 

  60. Li X, Yang ZZ (2005) J Chem Phys 122:084514. doi:10.1063/1.1853372

    Article  Google Scholar 

  61. Li X, Yang ZZ (2005) J Phys Chem A 109:4102–4111. doi:10.1021/jp0458093

    Article  CAS  Google Scholar 

  62. Li X, Gong LD, Yang ZZ (2008) Sci China Ser B 51:1221–1230. doi:10.1007/s11426-008-0129-x

    Article  CAS  Google Scholar 

  63. Yang ZZ, Qian P (2006) J Chem Phys 125:064311. doi:10.1063/1.2210940

    Article  Google Scholar 

  64. Zhang Q, Yang ZZ (2005) Chem Phys Lett 403:242–247. doi:10.1016/j.cplett.2005.01.011

    Article  CAS  Google Scholar 

  65. Guan QM, Yang ZZ (2007) J Theor Comput Chem 6:731–746. doi:10.1142/S0219633607003520

    Article  CAS  Google Scholar 

  66. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JAJ, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03. Gaussian, Inc., Wallingford

    Google Scholar 

  67. Becke AD (1993) J Chem Phys 98:5648–5652. doi:10.1063/1.464913

    Article  CAS  Google Scholar 

  68. Lee C, Yang W, Parr RG (1998) Phys Rev B 37:785–789. doi:10.1103/PhysRevB.37.785

    Article  Google Scholar 

  69. Møller C, Plesset MS (1934) Phys Rev 46:618–622. doi:10.1103/PhysRev.46.618

    Article  Google Scholar 

  70. Boys SF, Bernardi F (1970) Mol Phys 19:553–566. doi:10.1080/00268977000101561

    Article  CAS  Google Scholar 

  71. Weiner SJ, Kollman PA, Case DA, Singh C, Ghio C, Alagona G, Profeta S Jr, Weiner P (1984) J Am Chem Soc 106:765–784. doi:10.1021/ja00315a051

    Article  CAS  Google Scholar 

  72. Wolf B, Hanlon S (1975) Biochemistry 14:1661–1670. doi:10.1021/bi00679a018

    Article  CAS  Google Scholar 

  73. Alber F, Folkers G, Carloni P (1999) J Phys Chem B 103:6121–6126. doi:10.1021/jp9901038

    Article  CAS  Google Scholar 

  74. Alagona G, Ghio C, Kollman PA (1985) J Am Chem Soc 107:2229–2239. doi:10.1021/ja00294a004

    Article  CAS  Google Scholar 

Download references

Acknowledgments

We are very grateful to the editor and reviewers’ nice suggestions on the manuscript. We also greatly thank Professor Jay William Ponder for providing the Tinker programs. This work was supported by the grant from the National Natural Science Foundation of China (No. 20633050, 20703022 and 20873055), and the Department of Education of Liaoning Province (No. 2007T091, 20060494, and LNET RC0503). Supporting Information Available: The ABEEM/MM fluctuating charge model and parameters for DMP anion are included in the Appendix.

Author information

Authors and Affiliations

  1. School of Chemistry and Chemical Engineering, Liaoning Normal University, 116029, Dalian, People’s Republic of China

    Fang-Fang Wang, Dong-Xia Zhao & Li-Dong Gong

Authors
  1. Fang-Fang Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Dong-Xia Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Li-Dong Gong
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Li-Dong Gong.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOC 50 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Wang, FF., Zhao, DX. & Gong, LD. Ab initio and ABEEM/MM fluctuating charge model studies of dimethyl phosphate anion in a microhydrated environment. Theor Chem Acc 124, 139–150 (2009). https://doi.org/10.1007/s00214-009-0592-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00214-009-0592-2

Keywords

Search

Navigation