The integrated DL_POLY/DL_FIELD/DL_ANALYSER software platform for molecular dynamics simulations for exploration of the synthonic interactions in saturated benzoic acid/hexane solutions

References

• EPSRC Grand Challenge Network in Directed Assembly. [accessed 2014 Dec 3]; Available from: http://beyondthemolecule.org.uk/d6/.
   Google Scholar
• Desiraju GR. Designer crystals: intermolecular interactions, network structures and supramolecular synthons. Acta Crystallogr, Sect A: Found Crystallogr. 1996;52:C2–C2. doi: 10.1107/S0108767396098947
   Google Scholar
• Thalladi VR, Goud BS, Hoy VJ, et al. Supramolecular synthons in crystal engineering. Structure simplification, synthon robustness and supramolecular retrosynthesis. Chem Commun. 1996;3:401–402. doi: 10.1039/cc9960000401
   Google Scholar
• Etter MC. Encoding and decoding hydrogen-bond patterns of organic-compounds. Acc Chem Res. 1990;23(4):120–126. doi: 10.1021/ar00172a005
   Web of Science ®Google Scholar
• Etter MC, Macdonald JC, Bernstein J. Graph-set analysis of hydrogen-bond patterns in organic-crystals. Acta Crystallogr, Sect B: Struct Sci. 1990;46:256–262. doi: 10.1107/S0108768189012929
   PubMed Web of Science ®Google Scholar
• Roberts KJ, Hammond RB, Ramachandran V, et al. Synthonic engineering: from molecular and crystallographic structure to the rational design of pharmaceutical solid dosage forms. In: Abramov Y, editor. Computational approaches in pharmaceutical solid state chemistry. Hoboken (NJ): Wiley; 2016. p. 175–207.
   Google Scholar
• Pickering J, Hammond RB, Ramachandran V, et al. Synthonic Engineering modelling tools for product and process design. In: Roberts KJ, Docherty R, Tamura R, editors. Engineering crystallography: From molecule to crystal to functional form. Dordrecht: Springer Netherlands; 2017. p. 155–176.
   Google Scholar
• Rosbottom I, Roberts KJ, Docherty R. The solid state, surface and morphological properties of p-aminobenzoic acid in terms of the strength and directionality of its intermolecular synthons. CrystEngComm. 2015;17(30):5768–5788. doi: 10.1039/C5CE00302D
   Web of Science ®Google Scholar
• Moldovan AA, Rosbottom I, Ramachandran V, et al. Crystallographic structure, intermolecular packing energetics, crystal morphology and surface chemistry of salmeterol xinafoate (form I). J Pharm Sci. 2017;106(3):882–891. doi: 10.1016/j.xphs.2016.11.016
   PubMed Web of Science ®Google Scholar
• Nguyen TTH, Rosbottom I, Marziano I, et al. Crystal morphology and interfacial stability of RS-Ibuprofen in relation to its molecular and synthonic structure. Cryst Growth Des. 2017;17(6):3088–3099. doi: 10.1021/acs.cgd.6b01878
   Web of Science ®Google Scholar
• Rosbottom I, Ma CY, Turner TD, et al. Influence of solvent composition on the crystal morphology and structure of p-aminobenzoic acid crystallized from mixed ethanol and nitromethane solutions. Cryst Growth Des. 2017;17(8):4151–4161. doi: 10.1021/acs.cgd.7b00425
   Web of Science ®Google Scholar
• Rosbottom I, Roberts KJ. Crystal growth and morphology of molecular crystals. In: Roberts KJ, Docherty R, Tamura R, editors. Engineering crystallography: from molecule to crystal to functional form. Dordrecht: Springer Netherlands; 2017. p. 109–131.
   Google Scholar
• Ramachandran V, Murnane D, Hammond RB, et al. Formulation pre-screening of inhalation powders using computational atom–atom systematic search method. Mol Pharm. 2014;12(1):18–33. doi: 10.1021/mp500335w
   PubMedGoogle Scholar
• Kashchiev D, Vekilov PG, Kolomeisky AB. Kinetics of two-step nucleation of crystals. J Chem Phys. 2005;122(24):244706. doi: 10.1063/1.1943389
   PubMed Web of Science ®Google Scholar
• Vekilov PG. Two-step mechanism for the nucleation of crystals from solution. J Cryst Growth. 2005;275(1–2):65–76. doi: 10.1016/j.jcrysgro.2004.10.068
   Web of Science ®Google Scholar
• Hamad S, Moon C, Catlow CRA, et al. Kinetic insights into the role of the solvent in the polymorphism of 5-fluorouracil from molecular dynamics simulations. J Phys Chem B. 2006;110(7):3323–3329. doi: 10.1021/jp055982e
   PubMed Web of Science ®Google Scholar
• Erdemir D, Lee AY, Myerson AS. Nucleation of crystals from solution: Classical and two-step models. Acc Chem Res. 2009;42(5):621–629. doi: 10.1021/ar800217x
   PubMed Web of Science ®Google Scholar
• Vekilov PG. Nucleation. Cryst Growth Des. 2010;10(12):5007–5019. doi: 10.1021/cg1011633
   PubMed Web of Science ®Google Scholar
• Vekilov PG. The two-step mechanism of nucleation of crystals in solution. Nanoscale. 2010;2(11):2346–2357. doi: 10.1039/c0nr00628a
   PubMed Web of Science ®Google Scholar
• Jawor-Baczynska A, Moore BD, Lee HS, et al. Population and size distribution of solute-rich mesospecies within mesostructured aqueous amino acid solutions. Faraday Discuss. 2014;167:425–440. doi: 10.1039/c3fd00066d
   Web of Science ®Google Scholar
• Jawor-Baczynska A, Sefcik J, Moore BD. 250 nm glycine-rich nanodroplets are formed on dissolution of glycine crystals but are too small to provide productive nucleation sites. Cryst Growth Des. 2013;13(2):470–478. doi: 10.1021/cg300150u
   Web of Science ®Google Scholar
• Di Tommaso D, Watson KL. Density functional theory study of the oligomerization of carboxylic acids. J Phys Chem A. 2014;118(46):11098–11113. doi: 10.1021/jp509100u
   PubMed Web of Science ®Google Scholar
• Gaines E, Maisuria K, Di Tommaso D. The role of solvent in the self-assembly of m-aminobenzoic acid: a density functional theory and molecular dynamics study. CrystEngComm. 2016;18(16):2937–2948. doi: 10.1039/C6CE00130K
   Web of Science ®Google Scholar
• DL_Software is the collective term for a range of scientific software developed at the Daresbury Laboratory, spanning across multi-length and -time scales. Available from: https://www.scd.stfc.ac.uk/Pages/Materials-Modelling-Software.aspx.
   Google Scholar
• Todorov IT, Smith W, Trachenko K, et al. DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism. J Mater Chem. 2006;16(20):1911–1918. doi: 10.1039/b517931a
   Web of Science ®Google Scholar
• Yong CW. Descriptions and implementations of DL_F notation: a natural chemical expression system of atom types for molecular simulations. J Chem Inf Model. 2016;56(8):1405–1409. doi: 10.1021/acs.jcim.6b00323
   PubMed Web of Science ®Google Scholar
• Yong C, Todorov I. DL_ANALYSER notation for atomic interactions (DANAI): a natural annotation system for molecular interactions, using ethanoic acid liquid as a test case. Molecules. 2018;23(1):36. doi: 10.3390/molecules23010036
   Web of Science ®Google Scholar
• Brooks BR, Bruccoleri RE, Olafson BD, et al. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem. 1983;4(2):187–217. doi: 10.1002/jcc.540040211
   Web of Science ®Google Scholar
• Cornell WD, Cieplak P, Bayly CI, et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1995;117(19):5179–5197. doi: 10.1021/ja00124a002
   Web of Science ®Google Scholar
• Damm W, Frontera A, Tirado–Rives J, et al. OPLS all-atom force field for carbohydrates. J Comput Chem. 1997;18(16):1955–1970. doi: 10.1002/(SICI)1096-987X(199712)18:16<1955::AID-JCC1>3.0.CO;2-L
   Web of Science ®Google Scholar
• Mayo SL, Olafson BD, Goddard WA. Dreiding - a generic force-field for molecular simulations. J Phys Chem. 1990;94(26):8897–8909. doi: 10.1021/j100389a010
   Web of Science ®Google Scholar
• Sun H, Mumby SJ, Maple JR, et al. An ab Initio CFF93 all-atom force field for polycarbonates. J Am Chem Soc. 1994;116(7):2978–2987. doi: 10.1021/ja00086a030
   Web of Science ®Google Scholar
• Dauber-Osguthorpe P, Roberts VA, Osguthorpe DJ, et al. Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system. Proteins Struct Funct Bioinf. 1988;4(1):31–47. doi: 10.1002/prot.340040106
   PubMed Web of Science ®Google Scholar
• Schmid N, Eichenberger AP, Choutko A, et al. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur Biophys J. 2011;40(7):843–856. doi: 10.1007/s00249-011-0700-9
   PubMed Web of Science ®Google Scholar
• Davey RJ, Dent G, Mughal RK, et al. Concerning the relationship between structural and growth synthons in crystal nucleation: solution and crystal chemistry of carboxylic acids as revealed through IR spectroscopy. Cryst Growth Des. 2006;6(8):1788–1796. doi: 10.1021/cg060058a
   Web of Science ®Google Scholar
• Burton RC, Ferrari ES, Davey RJ, et al. The relationship between solution structure and crystal nucleation: a neutron scattering study of supersaturated methanolic solutions of benzoic acid. J Phys Chem B. 2010;114(26):8807–8816. doi: 10.1021/jp103099j
   PubMed Web of Science ®Google Scholar
• Banks JL, Beard HS, Cao Y, et al. Integrated modeling program, applied chemical theory (IMPACT). J Comput Chem. 2005;26(16):1752–1780. doi: 10.1002/jcc.20292
   PubMed Web of Science ®Google Scholar
• Infantes L, Chisholm J, Motherwell S. Extended motifs from water and chemical functional groups in organic molecular crystals. CrystEngComm. 2003;5(85):480–486. doi: 10.1039/b312846f
   Google Scholar
• Vanommeslaeghe K, Hatcher E, Acharya C, et al. CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem. 2010;31(4):671–690.
   PubMed Web of Science ®Google Scholar
• Wang J, Wolf RM, Caldwell JW, et al. Development and testing of a general amber force field. J Comput Chem. 2004;25(9):1157–1174. doi: 10.1002/jcc.20035
   PubMed Web of Science ®Google Scholar
• Holmback X, Rasmuson AC. Size and morphology of benzoic acid crystals produced by drowning-out crystallisation. J Cryst Growth. 1999;198-199:780–788. doi: 10.1016/S0022-0248(98)01027-6
   Web of Science ®Google Scholar
• Sullivan RA, Davey RJ, Sadiq G, et al. Revealing the roles of desolvation and molecular self-assembly in crystal nucleation from solution: benzoic and p-Aminobenzoic acids. Cryst Growth Des. 2014;14(5):2689–2696. doi: 10.1021/cg500441g
   Web of Science ®Google Scholar
• McArdle P, Hu Y, Lyons A, et al. Predicting and understanding crystal morphology: the morphology of benzoic acid and the polymorphs of sulfathiazole. CrystEngComm. 2010;12(10):3119–3125. doi: 10.1039/c001071e
   Web of Science ®Google Scholar
• Liang ZZ, Chen JF, Ma Y, et al. Qualitative rationalization of the crystal growth morphology of benzoic acid controlled using solvents. Crystengcomm. 2014;16(27):5997–6002. doi: 10.1039/c4ce00776j
   Web of Science ®Google Scholar
• Clydesdale G, Docherty R, Roberts KJ. HABIT - a program for predicting the morphology of molecular crystals. Comput Phys Commun. 1991;64(2):311–328. doi: 10.1016/0010-4655(91)90040-R
   Web of Science ®Google Scholar
• Docherty R, Clydesdale G, Roberts KJ, et al. Application of Bravais-Friedel-Donnay-Harker, attachment energy and ising-models to predicting and understanding the morphology of molecular-crystals. J Phys D Appl Phys. 1991;24(2):89–99. doi: 10.1088/0022-3727/24/2/001
   Web of Science ®Google Scholar
• Momany FA, Carruthers LM, McGuire RF, et al. Intermolecular potentials from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbons, carboxylic acids, amines, and amides. J Phys Chem. 1974;78(16):1595–1620. doi: 10.1021/j100609a005
   Web of Science ®Google Scholar
• Gasteiger J, Marsili M. New model for calculating atomic charges in molecules. Tetrahedron Lett. 1978;19:3181–3184. doi: 10.1016/S0040-4039(01)94977-9
   Google Scholar
• Gasteiger J, Marsili M. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron. 1980;36(22):3219–3228. doi: 10.1016/0040-4020(80)80168-2
   Web of Science ®Google Scholar
• Berendsen HJC, Postma JPM, Gunsteren WFv, et al. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81(8):3684–3690. doi: 10.1063/1.448118
   Web of Science ®Google Scholar
• Piana S, Gale JD. Understanding the barriers to crystal growth: dynamical simulation of the dissolution and growth of urea from aqueous solution. J Am Chem Soc. 2005;127(6):1975–1982. doi: 10.1021/ja043395l
   PubMed Web of Science ®Google Scholar
• Biovia DS. Biovia materials studio 2016.0. San Diego: Dassault Systèmes; 2016.
   Google Scholar
• Clark SJ, Segall MD, Pickard CJ, et al. First principles methods using CASTEP. Z Kristallogr. 2005;220:567–570.
   Web of Science ®Google Scholar
• Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys Rev. 1964;136:B864–B871. doi: 10.1103/PhysRev.136.B864
   Web of Science ®Google Scholar
• Kohn W, Sham LJ. Self-consistent equations including exchange and correlation effects. Phys Rev. 1965;140:A1133–A1138. doi: 10.1103/PhysRev.140.A1133
   Web of Science ®Google Scholar
• Payne MC, Teter MP, Allan DC, et al. Iterative minimization for ab initio total-energy calculations: molecular dynamics and conjugate gradients. Rev Mod Phys. 1992;64:1045–1097. doi: 10.1103/RevModPhys.64.1045
   Web of Science ®Google Scholar
• Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Phys Rev Lett. 1996;77:3865–3868. doi: 10.1103/PhysRevLett.77.3865
   PubMed Web of Science ®Google Scholar
• McNellis ER, Meyer J, Reuter K. Azobenzene at coinage metal surfaces: role of dispersive van der Waals interactions. Phys Rev B. 2009;80:205414. doi: 10.1103/PhysRevB.80.205414
   Web of Science ®Google Scholar
• Tkatchenko A, Scheffler M. Accurate molecular Van Der Waals interactions from ground-state electron density and free-atom reference data. Phys Rev Lett. 2009;102:0730051–4. doi: 10.1103/PhysRevLett.102.073005
   Web of Science ®Google Scholar
• Monkhorst HJ, Pack JD. Special points for Brillouin-zone integrations*. Phys Rev B. 1976;13:5188–5192. doi: 10.1103/PhysRevB.13.5188
   Web of Science ®Google Scholar
• Pfrommer BG, Côté M, Louie S, et al. Relaxation of crystals with the Quasi-Newton method. J Comput Phys. 1997;131:233–240. doi: 10.1006/jcph.1996.5612
   Web of Science ®Google Scholar
• Refson K, Clark SJ, Tulip PR. Variational density functional perturbation theory for dielectrics and lattice dynamics. Phys Rev B. 2006;73:155114. doi: 10.1103/PhysRevB.73.155114
   Web of Science ®Google Scholar
• Ribeiro da Silva MAV, Monte MJS, Santos LMNBF. The design, construction, and testing of a new Knudsen effusion apparatus. J Chem Thermodyn. 2006;38(6):778–787. doi: 10.1016/j.jct.2005.08.013
   Web of Science ®Google Scholar
• Di Tommaso D. The molecular self-association of carboxylic acids in solution: testing the validity of the link hypothesis using a quantum mechanical continuum solvation approach. CrystEngComm. 2013;15(33):6564–6577. doi: 10.1039/c3ce40539g
   Web of Science ®Google Scholar
• Cruz-Cabeza AJ, Davey RJ, Sachithananthan SS, et al. Aromatic stacking - a key step in nucleation. Chem Commun. 2017;53(56):7905–7908. doi: 10.1039/C7CC02423A
   PubMed Web of Science ®Google Scholar
• Greathouse JA, Geatches DL, Pike DQ, et al. Methylene blue adsorption on the basal surfaces of kaolinite: structure and thermodynamics from quantum and classical molecular simulation. Clays Clay Miner. 2015;63(3):185–198. doi: 10.1346/CCMN.2015.0630303
   Web of Science ®Google Scholar