Polydopamine and eumelanin molecular structures investigated with ab initio calculations

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin.

[1]  Yen Wei,et al.  Polydopamine coated shape memory polymer: enabling light triggered shape recovery, light controlled shape reprogramming and surface functionalization† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6sc00584e , 2016, Chemical science.

[2]  Young Jo Kim,et al.  Evidence of Porphyrin‐Like Structures in Natural Melanin Pigments Using Electrochemical Fingerprinting , 2016, Advanced materials.

[3]  Hongzhi Wang,et al.  Origami-inspired active graphene-based paper for programmable instant self-folding walking devices , 2015, Science Advances.

[4]  Feng Zhou,et al.  Brushing up from “anywhere” under sunlight: a universal surface-initiated polymerization from polydopamine-coated surfaces† †Electronic supplementary information (ESI) available: Materials, experimental details and supporting data are reported. See DOI: 10.1039/c4sc03851g Click here for additional d , 2015, Chemical science.

[5]  Marleen Kamperman,et al.  Jack of all trades: versatile catechol crosslinking mechanisms. , 2014, Chemical Society reviews.

[6]  M. Buehler,et al.  Polydopamine and eumelanin: from structure-property relationships to a unified tailoring strategy. , 2014, Accounts of chemical research.

[7]  T. Lu,et al.  Strong underwater adhesives made by self-assembling multi-protein nanofibres. , 2014, Nature nanotechnology.

[8]  R. Tang,et al.  Antigenically shielded universal red blood cells by polydopamine-based cell surface engineering , 2014 .

[9]  K. Wakamatsu,et al.  Degree of polymerization of 5,6‐dihydroxyindole‐derived eumelanin from chemical degradation study , 2014, Pigment cell & melanoma research.

[10]  Danke Xu,et al.  Bioinspired polydopamine nanospheres: a superquencher for fluorescence sensing of biomolecules , 2014 .

[11]  M. Buehler,et al.  Molecular mechanics of elastic and bendable caffeine co-crystals. , 2014, Physical chemistry chemical physics : PCCP.

[12]  M. Buehler,et al.  Excitonic effects from geometric order and disorder explain broadband optical absorption in eumelanin , 2014, Nature Communications.

[13]  Lehui Lu,et al.  Polydopamine and its derivative materials: synthesis and promising applications in energy, environmental, and biomedical fields. , 2014, Chemical reviews.

[14]  M. Buehler,et al.  Tuning heterogeneous poly(dopamine) structures and mechanics: in silico covalent cross-linking and thin film nanoindentation. , 2014, Soft matter.

[15]  K. Wakamatsu,et al.  Melanins and melanogenesis: methods, standards, protocols , 2013, Pigment cell & melanoma research.

[16]  Radosław Mrówczyński,et al.  Structure of polydopamine: a never-ending story? , 2013, Langmuir : the ACS journal of surfaces and colloids.

[17]  Markus J Buehler,et al.  Impact tolerance in mussel thread networks by heterogeneous material distribution , 2013, Nature Communications.

[18]  M. Alfè,et al.  Building‐Block Diversity in Polydopamine Underpins a Multifunctional Eumelanin‐Type Platform Tunable Through a Quinone Control Point , 2013 .

[19]  M. Buehler,et al.  Self-Assembly of Tetramers of 5,6-Dihydroxyindole Explains the Primary Physical Properties of Eumelanin: Experiment, Simulation, and Design ARTICLE , 2022 .

[20]  Yimin Sun,et al.  Mussel-inspired synthesis of polydopamine-functionalized graphene hydrogel as reusable adsorbents for water purification. , 2013, ACS applied materials & interfaces.

[21]  In Taek Song,et al.  Non‐Covalent Self‐Assembly and Covalent Polymerization Co‐Contribute to Polydopamine Formation , 2012 .

[22]  S. Grimme,et al.  Why the standard B3LYP/6-31G* model chemistry should not be used in DFT calculations of molecular thermochemistry: understanding and correcting the problem. , 2012, The Journal of organic chemistry.

[23]  M. Buehler,et al.  Molecular mechanics of dihydroxyphenylalanine at a silica interface , 2012 .

[24]  S. Grimme,et al.  A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems. , 2012, The Journal of chemical physics.

[25]  B. Freeman,et al.  Elucidating the structure of poly(dopamine). , 2012, Langmuir : the ACS journal of surfaces and colloids.

[26]  M. Buehler,et al.  Deposition Mechanism and Properties of Thin Polydopamine Films for High Added Value Applications in Surface Science at the Nanoscale , 2011, BioNanoScience.

[27]  Almar Postma,et al.  Polydopamine--a nature-inspired polymer coating for biomedical science. , 2011, Nanoscale.

[28]  Stefan Grimme,et al.  Effect of the damping function in dispersion corrected density functional theory , 2011, J. Comput. Chem..

[29]  Sung Min Kang,et al.  Simultaneous Reduction and Surface Functionalization of Graphene Oxide by Mussel‐Inspired Chemistry , 2011 .

[30]  Joon-Seok Lee,et al.  Spatial control of cell adhesion and patterning through mussel-inspired surface modification by polydopamine. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[31]  Paul Meredith,et al.  The supramolecular structure of melanin , 2009 .

[32]  C. Cramer,et al.  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. , 2009, The journal of physical chemistry. B.

[33]  Efthimios Kaxiras,et al.  Theoretical models of eumelanin protomolecules and their optical properties. , 2008, Biophysical journal.

[34]  Haeshin Lee,et al.  Mussel-Inspired Surface Chemistry for Multifunctional Coatings , 2007, Science.

[35]  A. Napolitano,et al.  The first 5,6-dihydroxyindole tetramer by oxidation of 5,5',6,6'-tetrahydroxy- 2,4'-biindolyl and an unexpected issue of positional reactivity en route to eumelanin-related polymers. , 2007, Organic letters.

[36]  Efthimios Kaxiras,et al.  Structural model of eumelanin. , 2006, Physical review letters.

[37]  F. Weigend,et al.  Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: Design and assessment of accuracy. , 2005, Physical chemistry chemical physics : PCCP.

[38]  B. Powell,et al.  Chemical and structural disorder in eumelanins: a possible explanation for broadband absorbance. , 2005, Biophysical journal.

[39]  S. González,et al.  Electrochemical self-assembly of melanin films on gold. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[40]  P. Geerlings,et al.  Conceptual density functional theory. , 2003, Chemical reviews.

[41]  C. A. Ramsden,et al.  Tyrosinase autoactivation and the chemistry of ortho-quinone amines. , 2003, Accounts of chemical research.

[42]  J. Simon,et al.  A Hierarchical Self-Assembly of Eumelanin , 2000 .

[43]  A. Napolitano,et al.  Oxidative polymerisation of 5,6-dihydroxyindole-2-carboxylic acid to melanin: A new insight , 1996 .

[44]  J Cheng,et al.  X-ray characterization of melanins--I. , 1994, Pigment cell research.

[45]  G. Zajac,et al.  Tunneling microscopy verification of an x‐ray scattering‐derived molecular model of tyrosine‐based melanin , 1994 .

[46]  G. Zajac,et al.  The fundamental unit of synthetic melanin: a verification by tunneling microscopy of X-ray scattering results. , 1994, Biochimica et biophysica acta.

[47]  Steve Plimpton,et al.  Fast parallel algorithms for short-range molecular dynamics , 1993 .

[48]  A. Becke.  Density-functional thermochemistry. III. The role of exact exchange , 1993 .

[49]  A. Becke.  A New Mixing of Hartree-Fock and Local Density-Functional Theories , 1993 .

[50]  A. Becke,et al.  Density-functional exchange-energy approximation with correct asymptotic behavior. , 1988, Physical review. A, General physics.

[51]  Parr,et al.  Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. , 1988, Physical review. B, Condensed matter.

[52]  B. Kalyanaraman,et al.  Semiquinone anion radicals of catechol(amine)s, catechol estrogens, and their metal ion complexes. , 1985, Environmental health perspectives.

[53]  Markus J. Buehler,et al.  Molecular mechanics of mussel adhesion proteins , 2014 .

[54]  Frank Neese,et al.  The ORCA program system , 2012 .

[55]  Alan R. Katritzky,et al.  Advances in Heterocyclic Chemistry , 1960 .

[56]  Juyoung Yoon,et al.  Chem Soc Rev , 2020 .