344 related articles for article (PubMed ID: 18231687)
1. Two-dimensional free-energy surface on the exchange reaction of alkyl chloride/chloride using the QM/MM-MC method.
Ohisa M; Yamataka H; Dupuis M; Aida M
Phys Chem Chem Phys; 2008 Feb; 10(6):844-9. PubMed ID: 18231687
[TBL] [Abstract][Full Text] [Related]
2. Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.
Xiang Y; Warshel A
J Phys Chem B; 2008 Jan; 112(3):1007-15. PubMed ID: 18166038
[TBL] [Abstract][Full Text] [Related]
3. A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions.
Hori K; Yamaguchi T; Uezu K; Sumimoto M
J Comput Chem; 2011 Apr; 32(5):778-86. PubMed ID: 21341291
[TBL] [Abstract][Full Text] [Related]
4. Geometry optimization based on linear response free energy with quantum mechanical/molecular mechanical method: applications to Menshutkin-type and Claisen rearrangement reactions in aqueous solution.
Higashi M; Hayashi S; Kato S
J Chem Phys; 2007 Apr; 126(14):144503. PubMed ID: 17444719
[TBL] [Abstract][Full Text] [Related]
5. Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.
Hu H; Lu Z; Parks JM; Burger SK; Yang W
J Chem Phys; 2008 Jan; 128(3):034105. PubMed ID: 18205486
[TBL] [Abstract][Full Text] [Related]
6. Mechanism of the hydration of carbon dioxide: direct participation of H2O versus microsolvation.
Nguyen MT; Matus MH; Jackson VE; Vu TN; Rustad JR; Dixon DA
J Phys Chem A; 2008 Oct; 112(41):10386-98. PubMed ID: 18816037
[TBL] [Abstract][Full Text] [Related]
7. Cope elimination: elucidation of solvent effects from QM/MM simulations.
Acevedo O; Jorgensen WL
J Am Chem Soc; 2006 May; 128(18):6141-6. PubMed ID: 16669683
[TBL] [Abstract][Full Text] [Related]
8. Variational and perturbative formulations of quantum mechanical/molecular mechanical free energy with mean-field embedding and its analytical gradients.
Yamamoto T
J Chem Phys; 2008 Dec; 129(24):244104. PubMed ID: 19123492
[TBL] [Abstract][Full Text] [Related]
9. Are mixed explicit/implicit solvation models reliable for studying phosphate hydrolysis? A comparative study of continuum, explicit and mixed solvation models.
Kamerlin SC; Haranczyk M; Warshel A
Chemphyschem; 2009 May; 10(7):1125-34. PubMed ID: 19301306
[TBL] [Abstract][Full Text] [Related]
10. Computation of the free energy change associated with one-electron reduction of coenzyme immersed in water: a novel approach within the framework of the quantum mechanical/molecular mechanical method combined with the theory of energy representation.
Takahashi H; Ohno H; Kishi R; Nakano M; Matubayasi N
J Chem Phys; 2008 Nov; 129(20):205103. PubMed ID: 19045881
[TBL] [Abstract][Full Text] [Related]
11. Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.
Rosta E; Klähn M; Warshel A
J Phys Chem B; 2006 Feb; 110(6):2934-41. PubMed ID: 16471904
[TBL] [Abstract][Full Text] [Related]
12. Synthesis and micellar properties of surface-active ionic liquids: 1-alkyl-3-methylimidazolium chlorides.
El Seoud OA; Pires PA; Abdel-Moghny T; Bastos EL
J Colloid Interface Sci; 2007 Sep; 313(1):296-304. PubMed ID: 17509607
[TBL] [Abstract][Full Text] [Related]
13. Transition-state characterization of the ammonia ionization process in aqueous solution via the free-energy gradient method.
Nagaoka M; Nagae Y; Koyano Y; Oishi Y
J Phys Chem A; 2006 Apr; 110(13):4555-63. PubMed ID: 16571063
[TBL] [Abstract][Full Text] [Related]
14. Investigation of the dominant hydration structures among the ionic species in aqueous solution: novel quantum mechanics/molecular mechanics simulations combined with the theory of energy representation.
Takahashi H; Ohno H; Yamauchi T; Kishi R; Furukawa S; Nakano M; Matubayasi N
J Chem Phys; 2008 Feb; 128(6):064507. PubMed ID: 18282056
[TBL] [Abstract][Full Text] [Related]
15. Computational methods for the study of enzymic reaction mechanisms III: a perturbation plus QM/MM approach for calculating relative free energies of protonation.
Cummins PL; Gready JE
J Comput Chem; 2005 Apr; 26(6):561-8. PubMed ID: 15726569
[TBL] [Abstract][Full Text] [Related]
16. Multicanonical ab inito QM/MM molecular dynamics simulation of a peptide in an aqueous environment.
Jono R; Watanabe Y; Shimizu K; Terada T
J Comput Chem; 2010 Apr; 31(6):1168-75. PubMed ID: 19847783
[TBL] [Abstract][Full Text] [Related]
17. Calculation of solvation free energy from quantum mechanical charge density and continuum dielectric theory.
Wang M; Wong CF
J Phys Chem A; 2006 Apr; 110(14):4873-9. PubMed ID: 16599457
[TBL] [Abstract][Full Text] [Related]
18. Hybrid quantum/classical path integral approach for simulation of hydrogen transfer reactions in enzymes.
Wang Q; Hammes-Schiffer S
J Chem Phys; 2006 Nov; 125(18):184102. PubMed ID: 17115733
[TBL] [Abstract][Full Text] [Related]
19. Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations.
Acevedo O; Jorgensen WL
J Am Chem Soc; 2005 Jun; 127(24):8829-34. PubMed ID: 15954791
[TBL] [Abstract][Full Text] [Related]
20. Evaluating boundary dependent errors in QM/MM simulations.
Solt I; Kulhánek P; Simon I; Winfield S; Payne MC; Csányi G; Fuxreiter M
J Phys Chem B; 2009 Apr; 113(17):5728-35. PubMed ID: 19341253
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]
