Monte Carlo methods in Materials Studio

REFERENCES

• Materials Studio. Accelrys Software Inc., San Diego. Note that some of these codes were also offered as part of the Cerius 2 application that preceded Materials Studio; 2013. Available from http://accelrys.com/products/materials-studio/.
   Google Scholar
• HammersleyJM, HandscombDC. Monte Carlo methods, Methuen's monographs on applied probability and statistics. London: Methuen & Co Ltd; 1964.
   Google Scholar
• MetropolisN, RosenbluthAW, RosenbluthMN, TellerAH, TellerE. Equation of state calculations by fast computing machines. J Chem Phys. 1953;21:1087–1092.
   Web of Science ®Google Scholar
• KirkpatrickS, GelattCD, VecchiMP. Optimization by simulated annealing. Science. 1983;220:671–680.
   PubMed Web of Science ®Google Scholar
• LiuJHY, BrameldKA, BrantDA, GoddardWAIII. Conformational analysis of aqueous pullulan oligomers: an effective computational approach, Polymer. 2002;43:509–516.
   Google Scholar
• PetersKE. Petroleum tricyclic terpanes: predicted physicochemical behavior from molecular mechanics calculations. Org Geochem. 2000;31:497–507.
   Web of Science ®Google Scholar
• SurinM, HennebicqE, EgoC, MarsitzkyD, GrimsdaleAC, MllenK, BrdasJL, LazzaroniR, LeclreP. Correlation between the microscopic morphology and the solid-state photoluminescence properties in fluorene-based polymers and copolymers. Chem Mater. 2004;16:994–1001.
   Web of Science ®Google Scholar
• BlancoM. Molecular silverware. I. General solutions to excluded volume constrained problems. J Comput Chem. 1991;12:237–247.
   Web of Science ®Google Scholar
• AkkermansRLC. Mesoscale model parameters from molecular cluster calculations. J Chem Phys. 2008;128:244904.
   PubMed Web of Science ®Google Scholar
• WuD, PaddisonSJ, ElliottJA. Effect of molecular weight on hydrated morphologies of the short-side-chain perfluorosulfonic acid membrane. Macromolecules. 2009;42:3358–3367.
   Web of Science ®Google Scholar
• LinCM, LiCS, ShengYJ, WuDT, TsaoHK. Size-dependent properties of small unilamellar vesicles formed by model lipids. Langmuir. 2012;28:689–700.
   PubMed Web of Science ®Google Scholar
• PajulaK, TaskinenM, LehtoVP, KetolainenJ, KorhonenO. Predicting the formation and stability of amorphous small molecule binary mixtures from computationally determined Flory–Huggins interaction parameter and phase diagram. Mol Pharmaceut. 2010;7:795–804.
   PubMed Web of Science ®Google Scholar
• RenH, ZhangQ, ChenX, ZhaoW, ZhangJ, ZhangH, ZengR, XuS. A molecular simulation study of a series of cyclohexanone formaldehyde resins: properties and applications in plastic printing. Polymer. 2007;48:887–893.
   Web of Science ®Google Scholar
• WoodCD, TanB, TrewinA, NiuH, BradshawD, RosseinskyMJ, KhimyakYZ, CampbellNL, KirkR, StöckelE, CooperAI. Hydrogen storage in microporous hypercrosslinked organic polymer networks. Chem Mater. 2007;19:2034–2048.
   Web of Science ®Google Scholar
• WoodCD, TanB, TrewinA, SuF, RosseinskyMJ, BradshawD, SunY, ZhouL, CooperAI. Microporous organic polymers for methane storage. Adv Mater. 2008;20:1916–1921.
   Web of Science ®Google Scholar
• LiA, LuRF, WangY, WangX, HanKL, DengWQ. Lithium-doped conjugated microporous polymers for reversible hydrogen storage. Angew Chem Int Ed. 2010;49:3330–3333.
   PubMed Web of Science ®Google Scholar
• YangJZ, LiuQL, WangT. Analyzing adsorption and diffusion behaviors of ethanol/water through silicalite membranes by molecular simulation. J Membr Sci. 2007;291:1–9.
   Web of Science ®Google Scholar
• HuiyongC, HongxiaX, XianyingC, YuQ. Experimental and molecular simulation studies of a ZSM-5–MCM-41 micro-mesoporous molecular sieve. Micropor Mesopor Mater. 2009;118:396–402.
   Web of Science ®Google Scholar
• GreathouseJA, OckwigNW, CriscentiLJ, GuilingerTR, PohlP, AllendorfMD. Computational screening of metal–organic frameworks for large-molecule chemical sensing. Phys Chem Chem Phys. 2010;12:12621–12629.
   PubMed Web of Science ®Google Scholar
• KhaledK. Electrochemical behavior of nickel in nitric acid and its corrosion inhibition using some thiosemicarbazone derivatives. Electrochim Acta. 2010;55:5375–5383.
   Web of Science ®Google Scholar
• KhaledK. Experimental, density function theory calculations and molecular dynamics simulations to investigate the adsorption of some thiourea derivatives on iron surface in nitric acid solutions. Appl Surface Sci. 2010;256:6753–6763.
   Web of Science ®Google Scholar
• MusaAY, JalghamRT, MohamadAB. Molecular dynamic and quantum chemical calculations for phthalazine derivatives as corrosion inhibitors of mild steel in 1 M HCl. Corros Sci. 2012;56:176–183.
   Web of Science ®Google Scholar
• LiangMK, DeschaumeO, PatwardhanSV, PerryCC. Direct evidence of ZnO morphology modification via the selective adsorption of ZnO-binding peptides. J Mater Chem. 2011;21:80–89.
   Web of Science ®Google Scholar
• TheodorouDN, SuterUW. Detailed molecular structure of a vinyl polymer glass. Macromolecules. 1985;18:1467–1478.
   Web of Science ®Google Scholar
• LiuH, LiY, KrauseWE, RojasOJ, PasquinelliMA. The soft-confined method for creating molecular models of amorphous polymer surfaces. J Phys Chem B. 2012;116:1570–1578.
   PubMed Web of Science ®Google Scholar
• PengF, PanF, SunH, LuL, JiangZ. Novel nanocomposite pervaporation membranes composed of poly(vinyl alcohol) and chitosan-wrapped carbon nanotube. J Membr Sci. 2007;300:13–19.
   Web of Science ®Google Scholar
• LinY, ChenX. Investigation of moisture diffusion in epoxy system: experiments and molecular dynamics simulations. Chem Phys Lett. 2005;412:322–326.
   Web of Science ®Google Scholar
• PanF, PengF, JiangZ. Diffusion behavior of benzene/cyclohexane molecules in poly(vinyl alcohol)–graphite hybrid membranes by molecular dynamics simulation. Chem Eng Sci. 2007;62:703–710.
   Web of Science ®Google Scholar
• HölckO, DermitzakiE, WunderleB, BauerJ, MichelB. Basic thermo-mechanical property estimation of a 3D-crosslinked epoxy/SiO2 interface using molecular modelling. Microelectron Reliab. 2011;51:1027–1034.
   Web of Science ®Google Scholar
• DinnebierRE, DingL, MaK, NeumannMA, TanpipatN, LeusenFJJ, StephensPW, WagnerM. Crystal structure of a rigid ferrocene-based macrocycle from high-resolution X-ray powder diffraction. Organometallics. 2001;20:5642–5647.
   Web of Science ®Google Scholar
• NeumannMA, PressW, NöldekeC, AsmussenB, PragerM, IbbersonRM. The crystal structure of methane phase III. J Chem Phys. 2003;119:1586–1589.
   Web of Science ®Google Scholar
• CormaA, D'iaz-CabanasMJ, JiangJ, AfeworkiM, DorsetDL, SoledSL, StrohmaierKG. Extra-large pore zeolite (ITQ-40) with the lowest framework density containing double four- and double three-rings. Proc Natl Acad Sci. 2010;107:13997–14002.
   PubMed Web of Science ®Google Scholar
• LuneauD, BortaA, ChumakovY, JacquotJF, JeanneauE, LescopC, ReyP. Molecular magnets based on two-dimensional Mn(II)-nitronyl nitroxide frameworks in layered structures. Inorg Chim Acta. 2008;361:3669–3676.
   Web of Science ®Google Scholar
• DovaE, PescharR, SakataM, KatoK, SchenkH. High-spin- and low-spin-state structures of [Fe(chloroethyltetrazole)6](ClO4)2 from synchrotron powder diffraction data. Chemistry – Eur J. 2006;12:5043–5052.
   PubMed Web of Science ®Google Scholar
• NeumannMA, PerrinMA. energy ranking of molecular crystals using density functional theory calculations and an empirical van der Waals correction. J Phys Chem B. 2005;109:15531–15541.
   PubMed Web of Science ®Google Scholar
• DayGM, ChisholmJ, ShanN, MotherwellWDS, JonesW. An Assessment of lattice energy minimization for the prediction of molecular organic crystal structures. Cryst Growth Des. 2004;4:1327–1340.
   Web of Science ®Google Scholar
• CrossWI, BlagdenN, DaveyRJ, PritchardRG, NeumannMA, RobertsRJ, RoweRC. A whole output strategy for polymorph screening: combining crystal structure prediction, graph set analysis, and targeted crystallization experiments in the case of diflunisal. Cryst Growth Des. 2003;3:151–158.
   Web of Science ®Google Scholar
• LeusenFJJ. Crystal structure prediction of diastereomeric salts: a step toward rationalization of racemate resolution. Cryst Growth Des. 2003;3:189–192.
   Web of Science ®Google Scholar
• SarmaJARP, DesirajuGR. The supramolecular synthon approach to crystal structure prediction. Cryst Growth Des. 2002;2:93–100.
   Web of Science ®Google Scholar