QM/MM methods in studies of coinage metals: copper, silver, and gold interacting with biological and organic molecules

References

• Kardos J, Héja L, Simon Á, et al. Correction to: copper signalling: causes and consequences. Cell Commun Signaling. 2018;16:1–22.
   PubMed Web of Science ®Google Scholar
• Abbaspour N, Hurrell R, Kelishadi R. Review on iron and its importance for human health. J Res Med Sci. 2014;19:164–174.
   PubMed Web of Science ®Google Scholar
• Yang M, Chen X, Su Y, et al. the fluorescent palette of DNA-Templated silver nanoclusters for biological applications. Front Chem. 2020;8:1–8.
   PubMed Web of Science ®Google Scholar
• Petty JT, Fan C, Story SP, et al. Optically enhanced, near-ir, silver cluster emission altered by single base changes in the dna template. J Phys Chem A. 2011;115:7996–8003.
   Web of Science ®Google Scholar
• Schultz D, Gardner K, Oemrawsingh SSR, et al. Evidence for rod-shaped dna-stabilized silver nanocluster emitters. Adv Mater. 2013;25:2797–2803.
   PubMed Web of Science ®Google Scholar
• Brust M, Walker M, Bethell D, et al. Synthesis of thiol-derivatised gold nanoparticles in a two-phase liquid–liquid system. J Chem Soc Chem Commun. 1994:801–802.
   Google Scholar
• Walter M, Akola J, Lopez-Acevedo O, et al., A unified view of ligand-protected gold clusters as superatom complexes, Proceedings of the National Academy of Sciences 105 (2008), pp. 9157–9162.
   Google Scholar
• Häkkinen H. The gold–sulfur interface at the nanoscale. Nat Chem. 2012;4:443–455.
   PubMed Web of Science ®Google Scholar
• Genji Srinivasulu Y, Yao Q, Goswami N, et al. Interfacial engineering of gold nanoclusters for biomedical applications. Mater Horiz. 2020;7:2596–2618. Available at.
   Web of Science ®Google Scholar
• Knight WD, Clemenger K, de Heer WA, et al. Electronic shell structure and abundances of sodium clusters. Phys Rev Lett. 1984;52:2141–2143.
   Web of Science ®Google Scholar
• Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys Rev. 1964;136:B864–B871.
   Web of Science ®Google Scholar
• Soler JM, Artacho E, Gale JD, et al. The SIESTA method forab initioorder-nmaterials simulation. J Phys. 2002;14:2745–2779. Available at.
   Google Scholar
• Brooks BR, Brooks III CL, Mackerell AD Jr., et al. Charmm: the biomolecular simulation program. J Comput Chem. 2009;30:1545–1614.
   PubMed Web of Science ®Google Scholar
• Enkovaara J, Rostgaard C, Mortensen JJ, et al. Electronic structure calculations with GPAW: a real-space implementation of the projector augmented-wave method. J Phys Condens Matter. 2010;22:253202.
   PubMed Web of Science ®Google Scholar
• Hutter J, Iannuzzi M. Cpmd: car-parrinello molecular dynamics. Zeitschrift Für Kristallographie - Crystalline Materials. 2005;220:549–551. Available at.
   Google Scholar
• Hutter J, Iannuzzi M, Schiffmann F, et al. cp2k: atomistic simulations of condensed matter systems. WIREs Comput Mol Sci. 2014;4:15–25.
   Web of Science ®Google Scholar
• Case DA, Darden TA, Cheatham III, et al. Amber 10:1–304. 2008. www.ambermd.org
   Google Scholar
• Cui Q, Pal T, Xie L. Biomolecular qm/mm simulations: what are some of the “burning issues”? J Phys Chem A. 2021;125:689–702.
   Web of Science ®Google Scholar
• Blumberger J. Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment. Phys Chem Chem Phys. 2008;10:5651–5667.
   PubMed Web of Science ®Google Scholar
• Futera Z, Platts JA, Burda JV. Binding of piano-stool Ru(II) complexes to DNA; QM/MM study. J Comput Chem. 2012;33:2092–2101.
   PubMed Web of Science ®Google Scholar
• Kritayakornupong C. Ab initio QM/MM molecular dynamics simulations of Ru3+ in aqueous solution. Chem Phys Lett. 2007;441:226–231.
   Web of Science ®Google Scholar
• Moret ME, Tapavicza E, Guidoni L, et al. Quantum mechanical/molecular mechanical (QM/MM) Car-Parrinello simulations in excited states. Chimia (Aarau). 2005;59:493–498.
   Web of Science ®Google Scholar
• Moret ME, Tavernelli I, Rothlisberger U. Combined QM/MM and classical molecular dynamics study of [Ru(bpy) 3] 2+ in water. J Phys Chem B. 2009;113:7737–7744.
   PubMed Web of Science ®Google Scholar
• Aresta M, Dibenedetto A, Amodio E, et al. Synthesis, characterization, and reactivity of cationic hydride [HPd(diphosphine) 2] + CF 3 SO 3 -, the missing member of the family [HM(dppe) 2] + X - (M = Ni, Pd, Pt). DFT QM/MM structural predictions for the [HPd(dppe) 2] + moiety. Inorg Chem. 2002;41:6550–6552.
   PubMed Web of Science ®Google Scholar
• Saleh M, Hofer TS. Palladium(II) in liquid ammonia: an investigation of structural and dynamical properties by applying quantum mechanical charge field molecular dynamics (QMCF-MD). 46 (2017).
   Google Scholar
• Zvereva EE, Katsyuba SA, Dyson PJ, et al. Leaching from palladium nanoparticles in an ionic liquid leads to the formation of ionic monometallic species. J Phys Chem Lett. 2017;8:3452–3456.
   PubMed Web of Science ®Google Scholar
• Zvereva EE, Katsyuba SA, Dyson PJ, et al. Solvation of palladium clusters in an ionic liquid: a QM/MM molecular dynamics study. J Phys Chem C. 2016;120:4596–4604.
   Web of Science ®Google Scholar
• Nakagaki M, Aono S, Kato M, et al. Delocalization of excited state and emission spectrum of platinum (II) bipyridine complex in crystal: periodic QM/MM study delocalization of excited state and emission spectrum of platinum. J Phys Chem C. 2020;124:10453–10461.
   Web of Science ®Google Scholar
• Dohn AO, Jónsson EO, Levi G, et al. Grid-Based Projector Augmented Wave (GPAW) implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) electrostatic embedding and application to a solvated diplatinum complex. J Chem Theory Comput. 2017;13:6010–6022.
   PubMed Web of Science ®Google Scholar
• Levi G, Pápai M, Henriksen NE, et al. Solution structure and ultrafast vibrational relaxation of the PtPOP complex revealed by ΔsCF-QM/MM Direct Dynamics Simulations. J Phys Chem C. 2018;122:7100–7119.
   Web of Science ®Google Scholar
• Saleheen M, Zare M, Faheem M, et al. Computational investigation of aqueous phase effects on the dehydrogenation and dehydroxylation of polyols over Pt(111). J Phys Chem C. 2019;123:19052–19065.
   Web of Science ®Google Scholar
• Warshel A, Levitt M. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol. 1976;103:227–249.
   PubMed Web of Science ®Google Scholar
• Lin H, Truhlar DG. QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc. 2007;117:185–199.
   Web of Science ®Google Scholar
• Duster AW, Wang CH, Garza CM, et al. Adaptive quantum/molecular mechanics: what have we learned, where are we, and where do we go from here? Wiley Interdiscip Rev Comput Mol Sci. 2017;7:e1310.
   Web of Science ®Google Scholar
• Lambros E, Lipparini F, Cisneros GA, et al. A many-body, fully polarizable approach to qm/mm simulations. J Chem Theory Comput. 2020;16:7462–7472.
   PubMed Web of Science ®Google Scholar
• Pan X, Rosta E, Shao Y. Representation of the qm subsystem for long-range electrostatic interaction in non-periodic ab initio qm/mm calculations. Molecules. 2018;23:2500.
   PubMed Web of Science ®Google Scholar
• Watanabe HC, Kubař T, Elstner M. Size-consistent multipartitioning qm/mm: a stable and efficient adaptive qm/mm method. J Chem Theory Comput. 2014;10:4242–4252.
   PubMed Web of Science ®Google Scholar
• Bernstein N, Várnai C, Solt I, et al. Qm/mm simulation of liquid water with an adaptive quantum region. Phys Chem Chem Phys. 2012;14:646–656.
   PubMed Web of Science ®Google Scholar
• Brunk E, Rothlisberger U. Mixed quantum mechanical/molecular mechanical molecular dynamics simulations of biological systems in ground and electronically excited states. Chem Rev. 2015;115:6217–6263. Available at.
   PubMed Web of Science ®Google Scholar
• Watanabe HC, Cui Q. Quantitative analysis of QM/MM boundary artifacts and correction in adaptive QM/MM simulations. J Chem Theory Comput. 2019;15:3917–3928.
   PubMed Web of Science ®Google Scholar
• Karelina M, Kulik HJ. Systematic quantum mechanical region determination in QM/MM simulation. J Chem Theory Comput. 2017;13:563–576.
   PubMed Web of Science ®Google Scholar
• Laio A, VandeVondele J, Rothlisberger U. A hamiltonian electrostatic coupling scheme for hybrid car–parrinello molecular dynamics simulations. J Chem Phys. 2002;116:6941–6947.
   Web of Science ®Google Scholar
• Rackers JA, Ponder JW. Classical pauli repulsion: an anisotropic, atomic multipole model. J Chem Phys. 2019;150:084104.
   PubMed Web of Science ®Google Scholar
• Marefat Khah A, Reinholdt P, Olsen JMH, et al. Avoiding electron spill-out in qm/mm calculations on excited states with simple pseudopotentials. J Chem Theory Comput. 2020;16:1373–1381.
   PubMed Web of Science ®Google Scholar
• Friesner RA, Guallar V. Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (qm/mm) methods for studying enzymatic catalysis. Annu Rev Phys Chem. 2005;56:389.
   PubMed Web of Science ®Google Scholar
• Senn HM, Thiel W. Qm/mm methods for biomolecular systems. Angewandte Chemie. 2009;48:1198–1229.
   Web of Science ®Google Scholar
• Swart M. Addremove: a new link model for use in qm/mm studies. Int J Quantum Chem. 2003;91:177–183.
   Web of Science ®Google Scholar
• Singh UC, Kollman PA. A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: applications to the ch3cl+ cl- exchange reaction and gas phase protonation of polyethers. J Comput Chem. 1986;7:718–730.
   Web of Science ®Google Scholar
• Wu XP, Gagliardi L, Truhlar DG. Parametrization of combined quantum mechanical and molecular mechanical methods: bond-tuned link atoms. Molecules. 2018;23:1309.
   PubMed Web of Science ®Google Scholar
• Murphy RB, Philipp DM, Friesner RA. A mixed quantum mechanics/molecular mechanics (qm/mm) method for large-scale modeling of chemistry in protein environments. J Comput Chem. 2000;21:1442–1457.
   Web of Science ®Google Scholar
• Loco D, Lagardère L, Cisneros GA, et al. Towards large scale hybrid qm/mm dynamics of complex systems with advanced point dipole polarizable embeddings. Chem Sci. 2019;10:7200–7211.
   PubMed Web of Science ®Google Scholar
• Nochebuena J, Naseem-Khan S, Cisneros GA. Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials. Wiley Interdiscip Rev Comput Mol Sci. 2021;11:e1515.
   PubMed Web of Science ®Google Scholar
• Dohn AO. Multiscale electrostatic embedding simulations for modeling structure and dynamics of molecules in solution: a tutorial review. Int J Quantum Chem. 2020;120:1–22.
   Web of Science ®Google Scholar
• Roßbach S, Ochsenfeld C. Influence of coupling and embedding schemes on qm size convergence in qm/mm approaches for the example of a proton transfer in dna. J Chem Theory Comput. 2017;13:1102–1107.
   PubMed Web of Science ®Google Scholar
• Khnayzer RS, McCusker CE, Olaiya BS, et al. Robust cuprous phenanthroline sensitizer for solar hydrogen photocatalysis. J Am Chem Soc. 2013;135:14068–14070.
   PubMed Web of Science ®Google Scholar
• Iwamura M, Takeuchi S, Tahara T. Real-time observation of the photoinduced structural change of bis (2, 9-dimethyl-1, 10-phenanthroline) copper (i) by femtosecond fluorescence spectroscopy: a realistic potential curve of the jahn- teller distortion. J Am Chem Soc. 2007;129:5248–5256.
   PubMed Web of Science ®Google Scholar
• Garakyaraghi S, Danilov EO, McCusker CE, et al. Transient absorption dynamics of sterically congested Cu(I) MLCT excited states. J Phys Chem A. 2015;119:3181–3193.
   PubMed Web of Science ®Google Scholar
• Shaw GB, Grant CD, Shirota H, et al. Ultrafast structural rearrangements in the MLCT excited state for copper(I) bis- phenanthrolines in solution. J Am Chem Soc. 2007;129:2147–2160.
   PubMed Web of Science ®Google Scholar
• Lutsenko S. Human copper homeostasis: a network of interconnected pathways. Curr Opin Chem Biol. 2010;14:211–217.
   PubMed Web of Science ®Google Scholar
• Magistrato A, Pavlin M, Qasem Z, et al. Copper trafficking in eukaryotic systems: current knowledge from experimental and computational efforts. Curr Opin Struct Biol. 2019;58:26–33. Available at.
   PubMed Web of Science ®Google Scholar
• Huard DJE, Demissie A, Kim D, et al. Atomic structure of a fluorescent Ag 8 cluster templated by a multistranded DNA scaffold. J Am Chem Soc. 2019;141:11465–11470.
   PubMed Web of Science ®Google Scholar
• Jadzinsky PD, Calero G, Ackerson CJ, et al. Structure of a thiol monolayer-protected gold nanoparticle at 1.1 Å resolution. Science. 2007;318:430–433.
   PubMed Web of Science ®Google Scholar
• Dupradeau FY, Pigache A, Zaffran T, et al. The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building. Phys Chem Chem Phys. 2010;12:7821–7839.
   PubMed Web of Science ®Google Scholar
• Zhang Y, Traber P, Zedler L, et al. Cu(i) vs. Ru(ii) photosensitizers: elucidation of electron transfer processes within a series of structurally related complexes containing an extended π-system. Phys Chem Chem Phys. 2018;20:24843–24857.
   PubMed Web of Science ®Google Scholar
• Lindon JC, Tranter GE, Koppenaal D. Encyclopedia of spectroscopy and spectrometry. Cambridge: Academic Press; 2016.
   Google Scholar
• Penfold TJ, Karlsson S, Capano G, et al. Solvent-induced luminescence quenching: static and time-resolved X-ray absorption spectroscopy of a copper(I) phenanthroline complex. J Phys Chem A. 2013;117:4591–4601.
   PubMed Web of Science ®Google Scholar
• Levi G, Biasin E, Dohn AO, et al. On the interplay of solvent and conformational effects in simulated excited-state dynamics of a copper phenanthroline photosensitizer. Phys Chem Chem Phys. 2020;22:748–757.
   PubMed Web of Science ®Google Scholar
• Perkal O, Qasem Z, Turgeman M, et al. Cu(I) controls conformational states in human Atox1 metallochaperone: an EPR and multiscale simulation study. J Phys Chem B. 2020;124:4399–4411.
   PubMed Web of Science ®Google Scholar
• Rodriguez-Granillo A, Crespo A, Estrin DA, et al. Copper-transfer mechanism from the human chaperone Atox1 to a metal-binding domain of wilson disease protein. J Phys Chem B. 2010;114:3698–3706.
   PubMed Web of Science ®Google Scholar
• Vidossich P, Magistrato A. QM/MM molecular dynamics studies of metal binding proteins. Biomolecules. 2014;4:616–645.
   PubMedGoogle Scholar
• Espinosa Leal LA, Karpenko A, Swasey S. The role of hydrogen bonds in the stabilization of silver-mediated cytosine tetramers. J Phys Chem Lett. 2015;6:4061–4066.
   PubMed Web of Science ®Google Scholar
• Runge E, Gross EKU. Density-functional theory for time-dependent systems. Phys Rev Lett. 1984;52:997–1000.
   Web of Science ®Google Scholar
• Yanai T, Tew DP, Handy NC. A new hybrid exchange–correlation functional using the coulomb-attenuating method (cam-b3lyp). Chem Phys Lett. 2004;393:51–57.
   Web of Science ®Google Scholar
• Perdew JP, Burke K, Ernzerhof M. Generalized gradient approximation made simple. Phys Rev Lett. 1996;77:3865–3868.
   PubMed Web of Science ®Google Scholar
• Makkonen E, Rinke P, Lopez-Acevedo O, et al. Optical properties of silver-mediated DNA from molecular dynamics and time dependent density functional theory. Int J Mol Sci. 2018;19:2346
   PubMed Web of Science ®Google Scholar
• Chen X, Makkonen E, Golze D, et al. Silver-stabilized guanine duplex: structural and optical properties. J Phys Chem Lett. 2018;9:4789–4794.
   PubMed Web of Science ®Google Scholar
• Ramazanov RR, Sych TS, Reveguk ZV, et al. Ag-DNA emitter: Metal nanorod or supramolecular complex? J Phys Chem Lett. 2016;7:3560–3566.
   PubMed Web of Science ®Google Scholar
• Chen X, Boero M, Lopez-Acevedo O. Atomic structure and origin of chirality of DNA-stabilized silver clusters. Phys Rev Mater. 2020;4:065601.
   Web of Science ®Google Scholar
• Tang W, Sanville E, Henkelman G. A grid-based bader analysis algorithm without lattice bias. J Phys. 2009;21:084204. Available at.
   Google Scholar
• Lopez-Acevedo O, Clayborne PA, Häkkinen H. Electronic structure of gold, aluminum, and gallium superatom complexes. Phys Rev B. 2011;84:035434.
   Google Scholar
• Kliuev PN, Sokolov PA, Ramazanov RR. QM/MM-MD dissociation of Ag+ and H+ mediated cytosine pairs: monomers and dimers. J Organomet Chem. 2020;919:121333. Available at.
   Web of Science ®Google Scholar
• Akola J, Walter M, Whetten RL, et al. On the structure of thiolate-protected Au 25. J Am Chem Soc. 2008;130:3756–3757.
   PubMed Web of Science ®Google Scholar
• Rojas-Cervellera V, Rovira C, Akola J. How do water solvent and glutathione ligands affect the structure and electronic properties of Au 25 (SR) 18 – ? J Phys Chem Lett. 2015;6:3859–3865. Available at.
   PubMed Web of Science ®Google Scholar
• Perdew JP, Ernzerhof M, Burke K. Rationale for mixing exact exchange with density functional approximations. J Chem Phys. 1996;105:9982–9985. Available at.
   Web of Science ®Google Scholar
• Chevrier DM, Raich L, Rovira C, et al. Molecular-scale ligand effects in small gold–thiolate nanoclusters. J Am Chem Soc. 2018;140:15430–15436.
   PubMed Web of Science ®Google Scholar
• Perić M, Sanader Maršić Ž, Russier-Antoine I, et al. Ligand shell size effects on one- and two-photon excitation fluorescence of zwitterion functionalized gold nanoclusters. Phys Chem Chem Phys. 2019;21:23916–23921.
   PubMed Web of Science ®Google Scholar
• Banerjee S, Montgomery JA, Gascón JA. A QM/MM approach for the study of monolayer-protected gold clusters. J Mater Sci. 2012;47:7686–7692.
   Web of Science ®Google Scholar
• Pereiro M, Baldomir D, Arias JE. A first-principles study of the influence of helium atoms on the optical response of small silver clusters. J Chem Phys. 2011;134:084307. Available at.
   PubMed Web of Science ®Google Scholar
• Schira R, Rabilloud F. Effects of rare-gas matrices on the optical response of silver nanoclusters. J Phys Chem C. 2018;122:27656–27661.
   Web of Science ®Google Scholar