Đánh giá hiệu suất của các mô hình hòa tan liên tục khác nhau trong việc tính toán năng lượng hydrat hóa của phân tử, polyme và bề mặt: so sánh giữa các mô hình SMD, VASPsol và FDPB

Tomasi J (2004) Thirty years of continuum solvation chemistry: a review, and prospects for the near future. Theoretical chemistry accounts. Springer, New York, pp 184–203 Tomasi J, Mennucci B (2002) Self-consistent reaction field methods. Encyclopedia of computational chemistry. Hoboken, Wiley Herbert JM (2021) Dielectric continuum methods for quantum chemistry. Wiley Interdisc Rev Comput Mol Sci 11:e1519 Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3093 Fattebert JL, Gygi F (2003) First-principles molecular dynamics simulations in a continuum solvent. Int J Quantum Chem 93:139–147. https://doi.org/10.1002/qua.10548 Fattebert JL, Gygi F (2002) Density functional theory for efficient ab initio molecular dynamics simulations in solution. J Comput Chem 23:662–666. https://doi.org/10.1002/jcc.10069 Klapper I, Hagstrom R, Fine R et al (1986) Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification. Proteins Struct Funct Bioinform 1:47–59. https://doi.org/10.1002/prot.340010109 Gilson MK, Sharp KA, Honig BH (1988) Calculating the electrostatic potential of molecules in solution: method and error assessment. J Comput Chem 9:327–335. https://doi.org/10.1002/jcc.540090407 Gilson MK, Honig B (1988) Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins Struct Funct Bioinform 4:7–18. https://doi.org/10.1002/prot.340040104 Rocchia W, Sridharan S, Nicholls A et al (2002) Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects. J Comput Chem 23:128–137. https://doi.org/10.1002/jcc.1161 Labat F, Civalleri B, Dovesi R (2018) Implicit solvation using a generalized finite-difference approach in CRYSTAL: implementation and results for molecules, polymers, and surfaces. J Chem Theory Comput 14:5969–5983. https://doi.org/10.1021/acs.jctc.8b00762 Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378–6396. https://doi.org/10.1021/jp810292n Mathew K, Sundararaman R, Letchworth-Weaver K et al (2014) Implicit solvation model for density-functional study of nanocrystal surfaces and reaction pathways. J Chem Phys 140:84106. https://doi.org/10.1063/1.4865107 Mathew K, Kolluru VSC, Mula S et al (2019) Implicit self-consistent electrolyte model in plane-wave density-functional theory. J Chem Phys 151:234101. https://doi.org/10.1063/1.5132354 Tomasi J, Mennucci B, Cancès E (1999) The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level. J Mole Struct THEOCHEM 464:211–226 Tomasi J, Cancès E, Pomelli CS et al (2007) Modern theories of continuum models. Continuum solvation models in chemical physics: from theory to applications. Wiley, Hoboken, pp 1–123 Lee B, Richards FM (1971) The interpretation of protein structures: estimation of static accessibility. J Mole Biol 55:379. https://doi.org/10.1016/0022-2836(71)90324-X Pascual-Ahuir JL, Silla E (1990) GEPOL: an improved description of molecular surfaces. I. Building the spherical surface set. J Comput Chem 11:1047–1060. https://doi.org/10.1002/jcc.540110907 Pomelli CS, Tomasi J, Cammi R (2001) A symmetry adapted tessellation of the GEPOL surface: applications to molecular properties in solution. J Comput Chem 22:1262–1272. https://doi.org/10.1002/jcc.1083 Frediani L, Cammi R, Pomelli CS et al (2004) New developments in the symmetry-adapted algorithm of the polarizable continuum model. J Comput Chem 25:375–385. https://doi.org/10.1002/jcc.10381 Scalmani G, Rega N, Cossi M, Barone V (2002) Finite elements molecular surfaces in continuum solvent models for large chemical systems. J Comput Methods Sci Eng 2:469–474. https://doi.org/10.3233/JCM-2002-23-423 Cramer CJ, Truhlar DG (2008) A universal approach to solvation modeling. Acc Chem Res 41:760–768 Bondi A (1964) Van der waals volumes and radii. J Phys Chem 68:441–451. https://doi.org/10.1021/j100785a001 Mantina M, Chamberlin AC, Valero R et al (2009) Consistent van der Waals radü for the whole main group. J Phys Chem A 113:5806–5812. https://doi.org/10.1021/jp8111556 Cossi M (2004) Continuum solvation model for infinite periodic systems. Chem Phys Lett 384:179–184. https://doi.org/10.1016/j.cplett.2003.11.108 Klamt A, Schüürmann G (1993) COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2:799–805. https://doi.org/10.1039/P29930000799 Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001. https://doi.org/10.1021/jp9716997 Cossi M, Rega N, Scalmani G, Barone V (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669–681. https://doi.org/10.1002/jcc.10189 Luty BA, Davis ME, McCammon JA (1992) Electrostatic energy calculations by a Finite-difference method: Rapid calculation of charge–solvent interaction energies. J Comput Chem 13:768–771. https://doi.org/10.1002/jcc.540130610 Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978–1988. https://doi.org/10.1021/j100058a043 Tannor DJ, Marten B, Murphy R et al (1994) Accurate first principles calculation of molecular charge distributions and solvation energies from Ab Initio quantum mechanics and continuum dielectric theory. J Am Chem Soc 116:11875–11882. https://doi.org/10.1021/ja00105a030 Wang J, Cai Q, Li ZL et al (2009) Achieving energy conservation in Poisson-Boltzmann molecular dynamics: accuracy and precision with finite-difference algorithms. Chem Phys Lett 468:112–118. https://doi.org/10.1016/j.cplett.2008.12.049 Li L, Li C, Sarkar S et al (2012) DelPhi: a comprehensive suite for DelPhi software and associated resources. BMC Biophys 5:9. https://doi.org/10.1186/2046-1682-5-9 Madura JD, Briggs JM, Wade RC et al (1995) Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comput Phys Commun 91:57–95. https://doi.org/10.1016/0010-4655(95)00043-F Bashford D (1997) An object-oriented programming suite for electrostatic effects in biological molecules: An experience report on the MEAD project. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, pp 233–240 Wang M, Wong CF (2006) Calculation of solvation free energy from quantum mechanical charge density and continuum dielectric theory. J Phys Chem A 110:4873–4879. https://doi.org/10.1021/jp0565195 Cramer CJ (2013) Essentials of computational chemistry: theories and models, 2nd edn. Wiley, Hoboken Hirshfeld FL (1977) Bonded-atom fragments for describing molecular charge densities. Theoret Chim Acta 44:129–138. https://doi.org/10.1007/BF00549096 Marenich AV, Jerome SV, Cramer CJ, Truhlar DG (2012) Charge model 5: an extension of hirshfeld population analysis for the accurate description of molecular interactions in gaseous and condensed phases. J Chem Theo Comput 8:527–541. https://doi.org/10.1021/ct200866d Vilseck JZ, Tirado-Rives J, Jorgensen WL (2014) Evaluation of CM5 charges for condensed-phase modeling. J Chem Theory Comput 10:2802–2812. https://doi.org/10.1021/ct500016d Vassetti D, Labat F (2021) Evaluation of the performances of different atomic charge and nonelectrostatic models in the finite-difference Poisson–Boltzmann approach. Int J Quantum Chem 121:e26560. https://doi.org/10.1002/qua.26560 Connolly ML (1983) Analytical molecular surface calculation. J Appl Crystallogr 16:548–558. https://doi.org/10.1107/s0021889883010985 Connolly ML (1983) Solvent-accessible surfaces of proteins and nucleic acids. Science 221:709–713 Fisicaro G, Genovese L, Andreussi O et al (2016) A generalized Poisson and Poisson-Boltzmann solver for electrostatic environments. J Chem Phys 144:014103. https://doi.org/10.1063/1.4939125 Fisicaro G, Genovese L, Andreussi O et al (2017) Soft-Sphere continuum solvation in electronic-structure calculations. J Chem Theory Comput 13:3829–3845. https://doi.org/10.1021/acs.jctc.7b00375 Yin WJ, Krack M, Li X et al (2017) Periodic continuum solvation model integrated with first-principles calculations for solid surfaces. Prog Nat Sci Mater Int 27:283–288. https://doi.org/10.1016/j.pnsc.2017.03.003 Sinstein M, Scheurer C, Matera S et al (2017) Efficient implicit solvation method for full potential DFT. J Chem Theory Comput 13:5582–5603. https://doi.org/10.1021/acs.jctc.7b00297 Dziedzic J, Helal HH, Skylaris CK et al (2011) Minimal parameter implicit solvent model for ab initio electronic-structure calculations. EPL 95:43001. https://doi.org/10.1209/0295-5075/95/43001 Dziedzic J, Fox SJ, Fox T et al (2013) Large-scale DFT calculations in implicit solvent—A case study on the T4 lysozyme L99A/M102Q protein. Int J Quantum Chem 113:771–785. https://doi.org/10.1002/qua.24075 Scherlis DA, Fattebert JL, Gygi F et al (2006) A unified electrostatic and cavitation model for first-principles molecular dynamics in solution. J Chem Phys 124:74103. https://doi.org/10.1063/1.2168456 Scherlis DA, Fattebert JL, Marzari N (2006) Stacking of oligo- and polythiophene cations in solution: surface tension and dielectric saturation. J Chem Phys 124:194902. https://doi.org/10.1063/1.2198811 Sánchez VM, Sued M, Scherlis DA (2009) First-principles molecular dynamics simulations at solid-liquid interfaces with a continuum solvent. J Chem Phys 131:74103. https://doi.org/10.1063/1.3254385 Wang HF, Liu ZP (2009) Formic acid oxidation at Pt/H2O interface from periodic DFT calculations integrated with a continuum solvation model. J Phys Chem C 113:17502–17508. https://doi.org/10.1021/jp9059888 Fishman M, Zhuang HL, Mathew K et al (2013) Accuracy of exchange-correlation functionals and effect of solvation on the surface energy of copper. Phys Rev B Condens Matter Mater Phys 87:245402. https://doi.org/10.1103/PhysRevB.87.245402 Perdew JP, Burke K, Ernzerhof M (1996) Generalized gradient approximation made simple. Phys Rev Lett 77:3865–3868. https://doi.org/10.1103/PhysRevLett.77.3865 Perdew JP, Burke K, Ernzerhof M (1997) Erratum: generalized gradient approximation made simple (Physical Review Letters (1996) 77 (3865)). Phys Rev Lett 78:1396 Marenich AV, Cramer CJ, Truhlar DG (2013) Generalized born solvation model SM12. J Chem Theo Comput 9:609–620. https://doi.org/10.1021/ct300900e Frisch MJ, Trucks GW, Schlegel HB, et al (2013) Gaussian 09, Gaussian, Inc., Wallingford CT Mennucci B, Cancès E, Tomasi J (1997) Evaluation of solvent effects in isotropic and anisotropic dielectrics and in ionic solutions with a unified integral equation method: theoretical bases, computational implementation, and numerical applications. J Phys Chem B 101:10506–10517. https://doi.org/10.1021/jp971959k Scalmani G, Frisch MJ (2010) Continuous surface charge polarizable continuum models of solvation. I. General formalism. J Chem Phys 132:114110. https://doi.org/10.1063/1.3359469 Kresse G, Furthmüller J (1996) Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set. Phys Rev B Condens Matter Mater Phys 54:11169–11186. https://doi.org/10.1103/PhysRevB.54.11169 Kresse G, Furthmüller J (1996) Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set. Comput Mater Sci 6:15–50. https://doi.org/10.1016/0927-0256(96)00008-0 Dovesi R, Orlando R, Erba A et al (2014) C <scp>RYSTAL14</scp>: a program for the ab initio investigation of crystalline solids. Int J Quantum Chem 114:1287–1317. https://doi.org/10.1002/qua.24658 Dovesi R, Erba A, Orlando R et al (2018) Quantum-mechanical condensed matter simulations with CRYSTAL. Wiley Interdiscip Rev Comput Mole Sci 8:e1360. https://doi.org/10.1002/wcms.1360 Hayryan S, Hu CK, Skřivánek J et al (2005) A new analytical method for computing solvent-accessible surface area of macromolecules and its gradients. J Comput Chem 26:334–343. https://doi.org/10.1002/jcc.20125 Vassetti D, Civalleri B, Labat F (2020) Analytical calculation of the solvent-accessible surface area and its nuclear gradients by stereographic projection: a general approach for molecules, polymers, nanotubes, helices, and surfaces. J Comput Chem 41:1464–1479. https://doi.org/10.1002/jcc.26191 Duarte Ramos Matos G, Kyu DY, Loeffler HH et al (2017) Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the freesolv database. J Chem Eng Data 62:1559–1569 Mobley DL, Shirts M, Lim N, et al (2018) MobleyLab/FreeSolv: Version 0.52. https://doi.org/10.5281/zenodo.1161245 Löfgren J, Rahm JM, Brorsson J, Erhart P (2020) Computational assessment of the efficacy of halides as shape-directing agents in nanoparticle growth. Phys Rev Mater 4:096001. https://doi.org/10.1103/PhysRevMaterials.4.096001 VASPsol convergence when involving I (Iodine) · Issue #34 · henniggroup/VASPsol · GitHub. https://github.com/henniggroup/VASPsol/issues/34. Accessed 19 Apr 2021 Monkhorst HJ, Pack JD (1976) Special points for Brillouin-zone integrations. Phys Rev B 13:5188–5192. https://doi.org/10.1103/PhysRevB.13.5188 Durand P, Barthelat JC (1975) A theoretical method to determine atomic pseudopotentials for electronic structure calculations of molecules and solids. Theoret Chim Acta 38:283–302. https://doi.org/10.1007/BF00963468 Ouazzani T, Lichanot A, Plsani C, Roetti C (1993) Relaxation and electronic structure of surfaces in lithium sulphide: a Hartree-Fock ab initio approach. J Phys Chem Solids 54:1603–1611. https://doi.org/10.1016/0022-3697(93)90356-V Nizam M, Bouteiller Y, Silvi B et al (1988) A theoretical investigation of the electronic structure and some thermodynamic properties of β-pbf2. J Phys C Solid State Phys 21:5351–5359. https://doi.org/10.1088/0022-3719/21/31/006 Voityuk AA, Vyboishchikov SF (2020) Fast and accurate calculation of hydration energies of molecules and ions. Phys Chem Chem Phys 22:14591–14598. https://doi.org/10.1039/d0cp02667k Marenich AV, Kelly CP, Thompson JD, et al Minnesota Solvation Database Version 2012, University of Minnesota, Minneapolis Steinmann SN, Sautet P, Michel C (2016) Solvation free energies for periodic surfaces: comparison of implicit and explicit solvation models. Phys Chem Chem Phys 18:31850–31861. https://doi.org/10.1039/c6cp04094b Moon DG, Rehan S, Yeon DH et al (2019) A review on binary metal sulfide heterojunction solar cells. Sol Energy Mater Sol Cells 200:109963. https://doi.org/10.1016/j.solmat.2019.109963 Im SH, Kim HJ, Kim SW et al (2011) All solid state multiply layered PbS colloidal quantum-dot-sensitized photovoltaic cells. Energy Environ Sci 4:4181–4186. https://doi.org/10.1039/c1ee01774h Nozik AJ, Beard MC, Luther JM et al (2010) Semiconductor quantum dots and quantum dot arrays and applications of multiple exciton generation to third-generation photovoltaic solar cells. Chem Rev 110:6873–6890. https://doi.org/10.1021/cr900289f Kundu TK, Mukherjee M, Chakravorty D, Cross LE (1998) Dielectric behavior of nanocomposites of lead sulphide and ferroelectric glass ceramics. J Appl Phys 83:4380–4384. https://doi.org/10.1063/1.367196 Bandyopadhyay S, Chatterjee B, Nag P, Bandyopadhyay A (2015) Nanocrystalline PbS as ammonia gas sensor: synthesis and characterization. Clean Soil Air Water 43:1121–1127. https://doi.org/10.1002/clen.201400437 Keim MF, Markl G (2015) Weathering of galena: Mineralogical processes, hydrogeochemical fluid path modeling, and estimation of the growth rate of pyromorphite. Am Miner 100:1584–1594. https://doi.org/10.2138/am-2015-5183 Deringer VL, Dronskowski R (2016) Stabilities and reconstructions of clean PbS and PbSe Surfaces: DFT results and the role of dispersion forces. J Phys Chem C 120:8813–8820. https://doi.org/10.1021/acs.jpcc.6b02173 Wright K, Hillier IH, Vaughan DJ, Vincent MA (1999) Cluster models of the dissociation of water on the surface of galena (PbS). Chem Phys Lett 299:527–531. https://doi.org/10.1016/S0009-2614(98)01312-8 Chen J, Long X, Chen Y (2014) Comparison of multilayer water adsorption on the hydrophobic galena (PbS) and hydrophilic pyrite (FeS2) surfaces: a DFT study. J Phys Chem C 118:11657–11665. https://doi.org/10.1021/jp5000478 Zemann J (1965) Crystal structures, 2nd edition, Vol. 2 by R. W. G. Wyckoff. Acta Crystallographica 19:490–490 Deringer VL, Dronskowski R (2013) Stabilities and reconstructions of PbTe crystal surfaces from density-functional theory. J Phys Chem C 117:24455–24461. https://doi.org/10.1021/jp408699a Zhang L, Song Q, Zhang SB (2010) Exceptionally strong hydrogen bonds affect the surface energy of colloidal nanocrystals: methylamine and water adsorption on PbS. Phys Rev Lett 104:116101. https://doi.org/10.1103/PhysRevLett.104.116101 Zherebetskyy D, Scheele M, Zhang Y et al (2014) Hydroxylation of the surface of PbS nanocrystals passivated with oleic acid. Science 344:1380–1384. https://doi.org/10.1126/science.1252727 Kim CE, Tak YJ, Butler KT et al (2015) Lattice-mismatched heteroepitaxy of IV-VI thin films on PbTe(001): an ab initio study. Phys Rev B Condens Matter Mater Phys 91:085307. https://doi.org/10.1103/PhysRevB.91.085307 Wandelt K (Editor) (2012) Surface and Interface Science, Volumes 1 and 2: Volume 1 - Concepts and Methods; Volume 2 - Properties of Elemental Surfaces, Wiley