Structural determination of large molecules through the reassembly of optimized fragments

Journal of Molecular Graphics and Modelling

Volumn 27, Issue 3, 2008, Pages 364-375

  Lee, Jung Goo ^a   Lee, Yoon Sup ^b   Roland, Christopher ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

^b Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

Ab initio; Divide and conquer; FORM; Geometry optimization

Indexed keywords

ALUMINA; CARBON NANOTUBES; DENSITY FUNCTIONAL THEORY; HYDROCARBONS; MOLECULES; OPTIMIZATION; ORGANIC COMPOUNDS; ORGANIC POLYMERS; PARAFFINS; PROBABILITY DENSITY FUNCTION; SINGLE-WALLED CARBON NANOTUBES (SWCN); STRUCTURAL DESIGN;

AB INITIO; DIVIDE AND CONQUER; FORM; GEOMETRY OPTIMIZATION;

STRUCTURAL OPTIMIZATION;

ALANINE DERIVATIVE; ALUMINUM DERIVATIVE; DECANE; HYDROCARBON; HYDROGEN; NANOTUBE; VANCOMYCIN;

ACCURACY; ANALYTIC METHOD; ARTICLE; CHEMICAL STRUCTURE; DENSITY FUNCTIONAL THEORY; FRAGMENTATION REACTION; HYDROGEN BOND; MATHEMATICAL COMPUTING; PREDICTION; PRIORITY JOURNAL; QUANTUM MECHANICS; STRUCTURE ANALYSIS;

ALANINE; ALGORITHMS; ALKANES; MODELS, MOLECULAR; ORGANIC CHEMICALS; PARTICLE SIZE;

EID: 53549134934     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2008.06.004     Document Type: Article

References (59)

1. Goedecker S. Linear scaling electronic structure methods. Rev. Mod. Phys. 71 (1999) 1085-1123
2. Wu S.Y., and Jayanthi C.S. Order-N methodologies and their applications. Phys. Rep. 358 (2002) 1-74
3. Yang W. Direct calculation of electron density in density-functional theory. Phys. Rev. Lett. 66 (1991) 1438-1441
4. Yang W. Direct calculation of electron density in density-functional theory: implementation for benzene and a tetrapeptide. Phys. Rev. A 44 (1991) 7823-7826
5. Lee J.-G., and Friesner R.A. Atomic charges for large molecules derived from electrostatic potentials: fragment density matrix approach. J. Phys. Chem. 97 (1993) 3515-3519
6. Walker P.D., and Mezey P.G. Molecular electron density lego approach to molecule building. J. Am. Chem. Soc. 115 (1993) 12423-12430
7. Gadre S.R., Shirsat R.N., and Limaye A.C. Molecular tailoring approach for simulation of electrostatic properties. J. Phys. Chem. 98 (1994) 9165-9169
8. Babu K., and Gadre S.R. Ab initio quality one-electron properties of large molecules: development and testing of molecular tailoring approach. J. Comput. Chem. 24 (2003) 484-495
9. Dixon S.L., and Merz Jr. K.M. Semiempirical molecular orbital calculations with linear system size scaling. J. Chem. Phys. 104 (1996) 6643-6649
10. Dixon S.L., and Merz Jr. K.M. Fast accurate semiempirical molecular orbital calculations for macromolecules. J. Chem. Phys. 107 (1997) 879-893
11. van der Vaart A., Gogonea V., Dixon S.L., and Merz Jr. K.M. Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. J. Comput. Chem. 21 (2000) 1494-1504
12. van der Vaart A., Suarez D., and Merz Jr. K.M. Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems. J. Chem. Phys. 113 (2000) 10512-10523
13. Lee T.-S., York D.M., and Yang W. Linear-scaling semiempirical quantum calculations for macromolecules. J. Chem. Phys. 105 (1996) 2744-2750
14. Akama T., Kobayashi M., and Nakai H. Implementation of divide-and-conquer method including Hartree-Fock exchange interaction. J. Comput. Chem. 28 (2007) 2003-2012
15. Kitaura K., Sawai T., Asada T., Nakano T., and Uebayasi M. Pair interaction molecular orbital method: an approximate computational method for molecular interactions. Chem. Phys. Lett. 312 (1999) 319-324
16. Fukuzawa K., Kitaura K., Uebayasi M., Nakata K., Kaminuma T., and Nakano T. Ab initio quantum mechanical study of the binding energies of human estrogen receptor a with its ligands: an application of fragment molecular orbital method. J. Comput. Chem. 26 (2004) 1-10 (and references therein)
17. Santamaria R., Mondragon-Sanchez J.A., and Cunningham M.A. Building wave functions for large molecules from their fragments. Phys. Rev. A 64 (2001) 1-8 042501
18. Zhang D.W., and Zhang J.Z.H. Molecular fractionation with conjugate caps for full quantum mechanical calculation of protein-molecule interaction energy. J. Chem. Phys. 119 (2003) 3599-3605
19. Bettens R.P.A., and Lee A.M. A new algorithm for molecular fragmentation in quantum chemical calculations. J. Phys. Chem. A 110 (2006) 8777-8785
20. Lee J.-G., Jeong H.Y., and Lee H. An efficient method to compute partial atomic charges of large molecules using reassociation of fragments. Bull. Korean Chem. Soc. 24 (2003) 369-376
21. Wang B., Brothers E.N., van der Vaart A., and Merz Jr. K.M. Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach. J. Chem. Phys. 120 (2004) 11392-11400
22. York D.M., Lee T.-S., and Yang W. Parameterization and efficient implementation of a solvent model for linear-scaling semiempirical quantum mechanical calculations of biological macromolecules. Chem. Phys. Lett. 263 (1996) 297-304
23. Liu H., Elstner M., Kaxiras E., Frauenheim T., Hermans J., and Yang W. Quantum mechanics simulation of protein dynamics on long timescale. Proteins 44 (2001) 484-489
24. Khandogin J., Musier-Forsyth K., and York D.M. Insights into the regioselectivity and RNA-binding of nity of HIV-1 nucleocapsid protein from linear-scaling quantum methods. J. Mol. Biol. 330 (2003) 993-1004
25. Khandogin J., and York D.M. Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods. Proteins 56 (2004) 724-737
26. Westerhoff L.M., and Merz Jr. K.M. Quantum mechanical description of the interactions between DNA and water. J. Mol. Graphics Modell. 24 (2006) 440-455
27. Zhao Q., and Yang W. Analytical energy gradients and geometry optimization in the divide-and-conquer method for large molecules. J. Chem. Phys. 102 (1995) 9598-9603
28. Yang W., and Lee T.-S. A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules. J. Chem. Phys. 103 (1995) 5674-5678
29. Lewis J.P., Liu S., Lee T.-S., and Yang W. A linear-scaling quantum mechanical investigation of cytidine deaminase. J. Comput. Phys. 151 (1999) 242-263
30. Deev V., and Collins M.A. Approximate ab initio energies by systematic molecular fragmentation. J. Chem. Phys. 122 (2005) 1-12 154102
31. Li S., Li W., and Fang T.J. Am. Chem. Soc. 127 (2005) 7215-7226
32. Billeter S.R., Turner A.J., and Thiel W. Linear scaling geometry optimisation and transition state search hybrid delocalised internal coordinates. Phys. Chem. Chem. Phys. 2 (2000) 2177-2186
33. Németh K., Coulaud O., Monard G., and Ángyán J.G. An efficient method for the coordinate transformation problem of massively three-dimensional networks. J. Chem. Phys. 114 (2001) 9747-9753
34. Németh K., and Challacombe M. The quasi-independent curvilinear coordinate approximation for geometry optimization. J. Chem. Phys. 121 (2004) 2877-2885
35. Paizs B., Fogarasi G., and Pulay P. An efficient direct method for geometry optimization of large molecules in internal coordinates. J. Chem. Phys. 109 (1998) 6571-6576
36. Paizs B., Baker J., Sihai S., and Pulay P. Geometry optimization of large biomolecules in redundant internal coordinates. J. Chem. Phys. 113 (2000) 6566-6572
37. Pulay P. Convergence acceleration of iterative sequences. The case of scf iteration. Chem. Phys. Lett. 73 (1980) 393-398
38. Pulay P. Improved SCF convergence acceleration. J. Comput. Chem. 3 (1982) 556-560
39. Csaszar P., and Pulay P. Geometry optimization by direct inversion in the iterative subspace. J. Mol. Struct. 114 (1984) 31-34
40. Farkas O., and Schlegel H.B. Methods for optimizing large molecules. Part III. An improved algorithm for geometry optimization using direct inversion in the iterative subspace (GDIIS). Phys. Chem. Chem. Phys. 4 (2002) 11-15
41. Farkas O., and Schlegel H.B. Geometry optimization methods for modeling large molecules. Theor. Chem. 666-667 (2003) 31-39
42. Zhao Q., and Nicholas J.B. Transition-state optimization using the divide-and-conquer method: reaction of trans-2-butene with HF. J. Chem. Phys. 104 (1996) 767-770
43. Lennartz C., Schäfer A., Terstegen F., and Thiel W. Enzymatic reactions of triosephosphate isomerase: a theoretical calibration study. J. Phys. Chem. B 106 (2002) 1758-1767
44. Also, it may be difficult to obtain accurate molecular structures with soft (shallow) potential surfaces by FORM.
45. Frisch M.J., et al. Gaussian 03 Revision C. 02 (2004), Gaussian Inc., Wallingford, C.T
46. Zhou Z., Steigerwald M., Hybertsen M., Brus L., and Friesner R.A. Electronic structure of tubular aromatic molecules derived from the metallic (5,5) armchair single wall carbon nanotube. J. Am. Chem. Soc. 126 (2004) 3597-3607
47. Zhou Z., Sfeir M.Y., Zhang L., Hyberstsen M.S., Steigerwald M., and Brus L. Graphite, tubular pahs, and the diffuse interstellar bands. Astrophys. J. 638 (2005) L105-L108
48. Lee J.-G., Sagui C., and Roland C. First principles investigation of vancomycin and teicoplanin binding to bacterial cell wall termini. J. Am. Chem. Soc. 126 (2004) 8384-8385
49. Lee J.-G., Sagui C., and Roland C. Quantum simulations of the structure and binding of glycopeptide antibiotic aglycons to cell wall analogues. J. Phys. Chem. B 109 (2005) 20588-20596
50. Cerius2 4.8, User's Manual, Accelrys Inc., San Diego, CA, USA, 2003.
51. Schlegel H.B. Optimization of equilibrium geometries and transition structures. J. Comput. Chem. 3 (1982) 214-218
52. Schlegel H.B. In: Yarkony D.R. (Ed). Modern Electronic Structure Theory (1999), World Scientific, Singapore
53. Pulay P., and Fogarasi G. Geometry optimization in redundant internal coordinates. J. Chem. Phys. 96 (1992) 2856-2860
54. Fletcher R. Practical Methods of Geometry Optimization. second edition (1981), Wiley Interscience, Chichester
55. Fragmentation details for other molecules are shown in supplementary material.
56. The geometry of C520H20 by the conventional B3LYP calculations started from that by FORM-4. Therefore, the cpu information is unavailable.
57. CCDC 157312, Cambridge Crystallographic Data Centre.
58. Preliminary calculation results of the ESP charges, the diagonal force constants of bond stretching and the vibrational frequencies for hexa-alanine by FORM/HF/6-31G* showed good agreement with those obtained by the conventional method (the numbers are listed in the supplementary material).
59. However, application of FORM to certain implicit solvation models may not work well.