1
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Liang D, Liu J, Heinz H, Mason SE, Hamers RJ, Cui Q. Binding of polar and hydrophobic molecules at the LiCoO 2 (001)-water interface: force field development and molecular dynamics simulations. NANOSCALE 2022; 14:7003-7014. [PMID: 35470836 DOI: 10.1039/d2nr00672c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A classical model in the framework of the INTERFACE force field has been developed for treating the LiCoO2 (LCO) (001)/water interface. In comparison to ab initio molecular dynamics (MD) simulations based on density functional theory, MD simulations using the classical model lead to generally reliable descriptions of interfacial properties, such as the density distribution of water molecules. Water molecules in close contact with the LCO surface form a strongly adsorbed layer, which leads to a free energy barrier for the adsorption of polar or charged molecules to the LCO surface. Moreover, due to the strong hydrogen bonding interactions with the LCO surface, the first water layer forms an interface that exhibits hydrophobic characters, leading to favorable adsorption of non-polar molecules to the interface. Therefore, despite its highly polar nature, the LCO (001) surface binds not only polar/charged but also non-polar solutes. As an application, the model is used to analyze the adsorption of reduced nicotinamide adenine dinucleotide (NADH) and its molecular components to the LCO (001) surface in water. The results suggest that recently observed redox activity of NADH at the LCO/water interface was due to the co-operativity between the ribose component, which drives binding to the LCO surface, and the nicotinamide moiety, which undergoes oxidation.
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Affiliation(s)
- Dongyue Liang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Juan Liu
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80303-0596, USA
- Department of Materials Science and Engineering, Dalian Maritime University, Dalian, Liaoning 116026, China
| | - Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80303-0596, USA
| | - Sara E Mason
- Department of Chemistry, University of Iowa, E331 Chemistry Building, Iowa City, Iowa 52242, USA
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue Boston, MA 02215, USA.
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2
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Inagaki T, Nagaoka M. Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian-based constant potential molecular dynamics simulation study. J Comput Chem 2019; 40:2131-2145. [PMID: 31155755 DOI: 10.1002/jcc.25865] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 01/02/2023]
Abstract
Computational models including electrode polarization can be essential to study electrode/electrolyte interfacial phenomena more realistically. We present here a constant-potential classical molecular dynamics simulation method based on the extended Lagrangian formulation where the fluctuating electrode atomic charges are treated as independent dynamical variables. The method is applied to a graphite/ionic liquid system for the validation and the interfacial kinetics study. While the correct adiabatic dynamics is achieved with a sufficiently small fictitious mass of charge, static properties have been shown to be almost insensitive to the fictitious mass. As for the kinetics study, electrical double layer (EDL) relaxation and ion desorption from the electrode surface are considered. We found that the polarization slows EDL relaxation greatly whereas it has little impact on the ion desorption kinetics. The findings suggest that the polarization is essential to estimate the kinetics in nonequilibrium processes, not in equilibrium. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Taichi Inagaki
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Institute for Molecular Science, Myodaiji, Okazaki, Aichi, 444-8585, Japan
| | - Masataka Nagaoka
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Nishikyo-ku, Kyoto, 615-8510, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Honmachi, Kawaguchi, 332-0012, Japan
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3
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Biriukov D, Kroutil O, Kabeláč M, Ridley MK, Machesky ML, Předota M. Oxalic Acid Adsorption on Rutile: Molecular Dynamics and ab Initio Calculations. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:7617-7630. [PMID: 31117719 DOI: 10.1021/acs.langmuir.8b03984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Detailed analysis of the adsorption of oxalic acid ions, that is, oxalate and hydrogenoxalate, on the rutile (110) surface was carried out using molecular dynamics augmented by free energy calculations and supported by ab initio calculations. The predicted adsorption on perfect nonhydroxylated and hydroxylated surfaces with surface charge density from neutral to +0.208 C/m2 corresponding to pH values of about 6 and 3.7, respectively, agrees with experimental adsorption data and charge-distribution multisite ion complexation model predictions obtained using the most favorable surface complexes identified in our simulations. We found that outer-sphere complexes are the most favorable, owing to strong hydrogen binding of oxalic acid ions with surface hydroxyls and physisorbed water. The monodentate complex, the most stable among inner-sphere complexes, was about 15 kJ/mol higher in energy, but separated by a large energy barrier. Other inner-sphere complexes, including some previously suggested in the literature as likely adsorption structures such as bidentate and chelate complexes, were found to be unstable both by classical and by ab initio modeling. Both the surfaces and (hydrogen)oxalate ions were modeled using charges scaled to 75% of the nominal values in accord with the electronic continuum theory and our earlier parameterization of (hydrogen)oxalate ions, which showed that nominal charges exaggerate ion-water interactions.
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Affiliation(s)
| | - Ondřej Kroutil
- Faculty of Chemistry, Materials Research Centre , Brno University of Technology , Purkyňova 118 , 612 00 Brno , Czech Republic
| | | | - Moira K Ridley
- Department of Geosciences , Texas Tech University , Lubbock , Texas 79409-1053 , United States
| | - Michael L Machesky
- Illinois State Water Survey, University of Illinois , 1506 Coral Cove Drive , Champaign , Illinois 61821 , United States
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4
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Prakash A, Sprenger K, Pfaendtner J. Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation. Biochem Biophys Res Commun 2018; 498:274-281. [DOI: 10.1016/j.bbrc.2017.07.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 07/09/2017] [Accepted: 07/11/2017] [Indexed: 12/20/2022]
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5
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Wei Q, Zhao W, Yang Y, Cui B, Xu Z, Yang X. Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality. Chemphyschem 2018; 19:690-702. [DOI: 10.1002/cphc.201701241] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/18/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Qichao Wei
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Weilong Zhao
- Department of Polymer Science; University of Akron; Akron OH 44325-3909 USA
| | - Yang Yang
- Department of Chemistry; Haverford College; Haverford PA 19041 USA
| | - Beiliang Cui
- Network Information Center; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Zhijun Xu
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
| | - Xiaoning Yang
- College of Chemical Engineering; State Key Laboratory of Materials-Oriented Chemical Engineering; Nanjing Tech University; Nanjing 210009 P.R. China
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6
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Schwaminger S, Blank‐Shim SA, Borkowska‐Panek M, Anand P, Fraga‐García P, Fink K, Wenzel W, Berensmeier S. Experimental characterization and simulation of amino acid and peptide interactions with inorganic materials. Eng Life Sci 2018; 18:84-100. [PMID: 32624891 PMCID: PMC6999452 DOI: 10.1002/elsc.201700019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 06/02/2017] [Accepted: 07/03/2017] [Indexed: 02/06/2023] Open
Abstract
Inspired by nature, many applications and new materials benefit from the interplay of inorganic materials and biomolecules. A fundamental understanding of complex organic-inorganic interactions would improve the controlled production of nanomaterials and biosensors to the development of biocompatible implants for the human body. Although widely exploited in applications, the interaction of amino acids and peptides with most inorganic surfaces is not fully understood. To date, precisely characterizing complex surfaces of inorganic materials and analyzing surface-biomolecule interactions remain challenging both experimentally and computationally. This article reviews several approaches to characterizing biomolecule-surface interactions and illustrates the advantages and disadvantages of the methods presented. First, we explain how the adsorption mechanism of amino acids/peptides to inorganic surfaces can be determined and how thermodynamic and kinetic process constants can be obtained. Second, we demonstrate how this data can be used to develop models for peptide-surface interactions. The understanding and simulation of such interactions constitute a basis for developing molecules with high affinity binding domains in proteins for bioprocess engineering and future biomedical technologies.
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Affiliation(s)
| | | | | | - Priya Anand
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Paula Fraga‐García
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
| | - Karin Fink
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Wolfgang Wenzel
- Institute of NanotechnologyKarlsruhe Institute of TechnologyKarlsruheGermany
| | - Sonja Berensmeier
- Bioseparation Engineering GroupTechnical University of MunichMünchenGermany
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7
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Abstract
Desolvation barriers are present for solute-solvent exchange events, such as ligand binding to an enzyme active site, during protein folding, and at battery electrodes. For solution-grown crystals, desolvation at kink sites can be the rate-limiting step for growth. However, desolvation and the associated kinetic barriers are poorly understood. In this work, we use rare-event simulation techniques to investigate attachment/detachment events at kink sites of a NaCl crystal in water. We elucidate the desolvation mechanism and present an optimized reaction coordinate, which involves one solute collective variable and one solvent collective variable. The attachment/detachment pathways for Na+ and Cl- are qualitatively similar, with quantitative differences that we attribute to different ion sizes and solvent coordination. The attachment barriers primarily result from kink site desolvation, while detachment barriers largely result from breaking ion-crystal bonds. We compute ion detachment rates from kink sites and compare with results from an independent study. We anticipate that the reaction coordinate and desolvation mechanism identified in this work may be applicable to other alkali halides.
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8
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Ohwaki T, Ozaki T, Okuno Y, Ikeshoji T, Imai H, Otani M. Li deposition and desolvation with electron transfer at a silicon/propylene-carbonate interface: transition-state and free-energy profiles by large-scale first-principles molecular dynamics. Phys Chem Chem Phys 2018. [DOI: 10.1039/c7cp08569a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the result of a large-scale first-principles molecular dynamics simulation under different electric biases performed to understand the charge transfer process coupling with lithium deposition and desolvation processes.
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Affiliation(s)
- Tsukuru Ohwaki
- Device Functional Analysis Department
- NISSAN ARC
- Ltd
- Yokosuka
- Japan
| | - Taisuke Ozaki
- Institute for Solid State Physics
- The University of Tokyo
- Kashiwa
- Japan
| | - Yukihiro Okuno
- Research and Development Headquarters
- FUJIFILM Corporation
- Minamiashigara
- Japan
| | - Tamio Ikeshoji
- Device Functional Analysis Department
- NISSAN ARC
- Ltd
- Yokosuka
- Japan
| | - Hideto Imai
- Device Functional Analysis Department
- NISSAN ARC
- Ltd
- Yokosuka
- Japan
| | - Minoru Otani
- Research Center for Computational Design of Advanced Functional Materials
- National Institute of Advanced Industrial Science and Technology (AIST)
- Tsukuba 305-8568
- Japan
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9
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YazdanYar A, Aschauer U, Bowen P. Interaction of biologically relevant ions and organic molecules with titanium oxide (rutile) surfaces: A review on molecular dynamics studies. Colloids Surf B Biointerfaces 2017; 161:563-577. [PMID: 29149762 DOI: 10.1016/j.colsurfb.2017.11.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/22/2017] [Accepted: 11/01/2017] [Indexed: 01/06/2023]
Abstract
The surface of a biomaterial can play a major role in its biological fate since the surface is the primary pathway for its interaction with the body. As the natural response of the body to a foreign material is to encapsulate it with a fibrous material, the interactions between the body and the biomaterial are mediated by this fibrous layer. Initial interactions occur between the biomaterial surface, water, ionic species and organic molecules, which then mediate further interactions with body tissues. Surface engineering can influence these interactions and hence, improve the biocompatibility of the biomaterial. Therefore, both experimental and computational studies have been interested in phenomena happening at the solid-solution interface as their mechanisms and driving forces can point to new directions for biomaterial design and evaluation. In this review, we summarize the computational work on the interaction of titanium oxide surfaces (mainly rutile) with solvated ions and organic molecules by means of molecular dynamics, with a certain relevance to bioactivity testing protocols. The primary goal of this review is to present the current state of the art and draw attention to points where further investigations are required.
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Affiliation(s)
- Azade YazdanYar
- Department of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
| | - Ulrich Aschauer
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Paul Bowen
- Department of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
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10
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Abstract
Nanomaterials provide tremendous opportunities to advance human welfare in many areas including energy storage, catalysis, photovoltaic energy conversion, environmental remediation, and agriculture. As nanomaterials become incorporated into commercial processes and consumer products in increasing amounts, it will be essential to develop an understanding of how these materials interact with the environment. The broad spectrum and complexity of nanomaterials drive a need for molecular-level design rules. Ultimately a grand challenge is to use the power of chemistry to ensure that nanoenabled technologies can come to fruition in an environmentally benign manner.
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Affiliation(s)
- Robert J. Hamers
- Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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11
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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12
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Cui Q, Hernandez R, Mason SE, Frauenheim T, Pedersen JA, Geiger F. Sustainable Nanotechnology: Opportunities and Challenges for Theoretical/Computational Studies. J Phys Chem B 2016; 120:7297-306. [PMID: 27388532 DOI: 10.1021/acs.jpcb.6b03976] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
For assistance in the design of the next generation of nanomaterials that are functional and have minimal health and safety concerns, it is imperative to establish causality, rather than correlations, in how properties of nanomaterials determine biological and environmental outcomes. Due to the vast design space available and the complexity of nano/bio interfaces, theoretical and computational studies are expected to play a major role in this context. In this minireview, we highlight opportunities and pressing challenges for theoretical and computational chemistry approaches to explore the relevant physicochemical processes that span broad length and time scales. We focus discussions on a bottom-up framework that relies on the determination of correct intermolecular forces, accurate molecular dynamics, and coarse-graining procedures to systematically bridge the scales, although top-down approaches are also effective at providing insights for many problems such as the effects of nanoparticles on biological membranes.
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Affiliation(s)
- Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Sara E Mason
- Department of Chemistry, University of Iowa , E331 Chemistry Building, Iowa City, Iowa 52242-1294, United States
| | - Thomas Frauenheim
- Bremen Center for Computational Materials Science, Univ of Bremen , D-28359 Bremen, Germany
| | - Joel A Pedersen
- Departments of Soil Science, Civil & Environmental Engineering, and Chemistry, University of Wisconsin-Madison , 1525 Observatory Drive, Madison, Wisconsin 53706, United States
| | - Franz Geiger
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60201, United States
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13
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Zhao W, Xu Z, Cui Q, Sahai N. Predicting the Structure-Activity Relationship of Hydroxyapatite-Binding Peptides by Enhanced-Sampling Molecular Simulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:7009-7022. [PMID: 27329793 DOI: 10.1021/acs.langmuir.6b01582] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Understanding the molecular structural and energetic basis of the interactions between peptides and inorganic surfaces is critical to their applications in tissue engineering and biomimetic material synthesis. Despite recent experimental progresses in the identification and functionalization of hydroxyapatite (HAP)-binding peptides, the molecular mechanisms of their interactions with HAP surfaces are yet to be explored. In particular, the traditional method of molecular dynamics (MD) simulation suffers from insufficient sampling at the peptide-inorganic interface that renders the molecular-level observation dubious. Here we demonstrate that an integrated approach combining bioinformatics, MD, and metadynamics provides a powerful tool for investigating the structure-activity relationship of HAP-binding peptides. Four low charge density peptides, previously identified by phage display, have been considered. As revealed by bioinformatics and MD, the binding conformation of the peptides is controlled by both the sequence and the amino acid composition. It was found that formation of hydrogen bonds between lysine residue and phosphate ions on the surface dictates the binding of positively charged peptide to HAP. The binding affinities of the peptides to the surface are estimated by free energy calculation using parallel-tempering metadynamics, and the results compare favorably to measurements reported in previous experimental studies. The calculation suggests that the charge density of the peptide primarily controls the binding affinity to the surface, while the backbone secondary structure that may restrain side chain orientation toward the surface plays a minor role. We also report that the application of enhanced-sampling metadynamics effects a major advantage over the steered MD method by significantly improving the reliability of binding free energy calculation. In general, our novel integration of diverse sampling techniques should contribute to the rational design of surface-recognition peptides in biomedical applications.
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Affiliation(s)
| | | | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , Madison, Wisconsin 53706-1322, United States
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14
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Lu X, Fang D, Ito S, Okamoto Y, Ovchinnikov V, Cui Q. QM/MM free energy simulations: recent progress and challenges. MOLECULAR SIMULATION 2016; 42:1056-1078. [PMID: 27563170 DOI: 10.1080/08927022.2015.1132317] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Shingo Ito
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Victor Ovchinnikov
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St., Boston, MA 02138
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
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15
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Heinz H, Ramezani-Dakhel H. Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities. Chem Soc Rev 2016; 45:412-48. [PMID: 26750724 DOI: 10.1039/c5cs00890e] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico.
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Affiliation(s)
- Hendrik Heinz
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO 80309, USA.
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16
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Zhang L, Yethiraj A, Cui Q. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models. J Chem Theory Comput 2015; 10:2845-59. [PMID: 26586509 DOI: 10.1021/ct500218p] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The binding of peptides and proteins to the surface of complex lipid membranes is important in many biological processes such as cell signaling and membrane remodeling. Computational studies can aid experiments by identifying physical interactions and structural motifs that determine the binding affinity and specificity. However, previous studies focused on either qualitative behaviors of protein/membrane interactions or the binding affinity of small peptides. Motivated by this observation, we set out to develop computational protocols for bimolecular binding to charged membranes that are applicable to both peptides and large proteins. In this work, we explore a method based on an implicit membrane/solvent model (generalized Born with a simple switching in combination with the Gouy-Chapman-Stern model for a charged interface), which we expect to lead to useful results when the binding does not implicate significant membrane deformation and local demixing of lipids. We show that the binding free energy can be efficiently computed following a thermodynamic cycle similar to protein-ligand binding calculations, especially when a Bennett acceptance ratio based protocol is used to consider both the membrane bound and solution conformational ensembles. Test calculations on a series of peptides show that our computational approach leads to binding affinities in encouraging agreement with experimental data, including for the challenging example of the bringing of flexible MARCKS-ED peptides to membranes. The calculations highlight that for a membrane with a significant fraction of anionic lipids, it is essential to include the effect of ion adsorption using the Stern model, which significantly modifies the effective surface charge. This implicit membrane model based computational protocol helps lay the groundwork for more systematic analysis of protein/peptide binding to membranes of complex shape and composition.
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Affiliation(s)
- Leili Zhang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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17
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Murphy CJ, Vartanian A. Biological Responses to Engineered Nanomaterials: Needs for the Next Decade. ACS CENTRAL SCIENCE 2015; 1:117-23. [PMID: 27162961 PMCID: PMC4827556 DOI: 10.1021/acscentsci.5b00182] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Indexed: 05/20/2023]
Abstract
The interaction of nanomaterials with biomolecules, cells, and organisms is an enormously vital area of current research, with applications in nanoenabled diagnostics, imaging agents, therapeutics, and contaminant removal technologies. Yet the potential for adverse biological and environmental impacts of nanomaterial exposure is considerable and needs to be addressed to ensure sustainable development of nanomaterials. In this Outlook four research needs for the next decade are outlined: (i) measurement of the chemical nature of nanomaterials in dynamic, complex aqueous environments; (ii) real-time measurements of nanomaterial-biological interactions with chemical specificity; (iii) delineation of molecular modes of action for nanomaterial effects on living systems as functions of nanomaterial properties; and (iv) an integrated systems approach that includes computation and simulation across orders of magnitude in time and space.
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Affiliation(s)
- Catherine J. Murphy
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Ariane
M. Vartanian
- Department of Chemistry, University of Illinois at Urbana−Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United States
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18
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Goyal P, Yang S, Cui Q. Microscopic basis for kinetic gating in Cytochrome c oxidase: insights from QM/MM analysis. Chem Sci 2015; 6:826-841. [PMID: 25678950 PMCID: PMC4321873 DOI: 10.1039/c4sc01674b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps.
Understanding the mechanism of vectorial proton pumping in biomolecules requires establishing the microscopic basis for the regulation of both thermodynamic and kinetic features of the relevant proton transfer steps. For the proton pump cytochrome c oxidase, while the regulation of thermodynamic driving force for key proton transfers has been discussed in great detail, the microscopic basis for the control of proton transfer kinetics has been poorly understood. Here we carry out extensive QM/MM free energy simulations to probe the kinetics of relevant proton transfer steps and analyze the effects of local structure and hydration level. We show that protonation of the proton loading site (PLS, taken to be a propionate of heme a3) requires a concerted process in which a key glutamic acid (Glu286H) delivers the proton to the PLS while being reprotonated by an excess proton coming from the D-channel. The concerted nature of the mechanism is a crucial feature that enables the loading of the PLS before the cavity containing Glu286 is better hydrated to lower its pKa to experimentally measured range; the charged rather than dipolar nature of the process also ensures a tight coupling with heme a reduction, as emphasized by Siegbahn and Blomberg. In addition, we find that rotational flexibility of the PLS allows its protonation before that of the binuclear center (the site where oxygen gets reduced to water). Together with our recent study (P. Goyal, et al., Proc. Natl. Acad. Sci. U. S. A., 2013, 110, 18886–18891) that focused on the modulation of Glu286 pKa, the current work suggests a mechanism that builds in a natural sequence for the protonation of the PLS prior to that of the binuclear center. This provides microscopic support to the kinetic constraints revealed by kinetic network analysis as essential elements that ensure an efficient vectorial proton transport in cytochrome c oxidase.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Shuo Yang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
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19
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Mori T, Hamers RJ, Pedersen JA, Cui Q. Correction to An Explicit Consideration of Desolvation is Critical to Binding Free Energy Calculations of Charged Molecules at Ionic Surfaces. J Chem Theory Comput 2014; 10:5738. [DOI: 10.1021/ct500942q] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Sultan AM, Hughes ZE, Walsh TR. Binding affinities of amino acid analogues at the charged aqueous titania interface: implications for titania-binding peptides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:13321-13329. [PMID: 25317483 DOI: 10.1021/la503312d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.
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Affiliation(s)
- Anas M Sultan
- Institute for Frontier Materials, Deakin University , Geelong, VIC 3216, Australia
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21
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Goyal P, Qian HJ, Irle S, Lu X, Roston D, Mori T, Elstner M, Cui Q. Molecular simulation of water and hydration effects in different environments: challenges and developments for DFTB based models. J Phys Chem B 2014; 118:11007-27. [PMID: 25166899 PMCID: PMC4174991 DOI: 10.1021/jp503372v] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
We discuss the description of water and hydration effects that employs an approximate density functional theory, DFTB3, in either a full QM or QM/MM framework. The goal is to explore, with the current formulation of DFTB3, the performance of this method for treating water in different chemical environments, the magnitude and nature of changes required to improve its performance, and factors that dictate its applicability to reactions in the condensed phase in a QM/MM framework. A relatively minor change (on the scale of kBT) in the O-H repulsive potential is observed to substantially improve the structural properties of bulk water under ambient conditions; modest improvements are also seen in dynamic properties of bulk water. This simple change also improves the description of protonated water clusters, a solvated proton, and to a more limited degree, a solvated hydroxide. By comparing results from DFTB3 models that differ in the description of water, we confirm that proton transfer energetics are adequately described by the standard DFTB3/3OB model for meaningful mechanistic analyses. For QM/MM applications, a robust parametrization of QM-MM interactions requires an explicit consideration of condensed phase properties, for which an efficient sampling technique was developed recently and is reviewed here. The discussions help make clear the value and limitations of DFTB3 based simulations, as well as the developments needed to further improve the accuracy and transferability of the methodology.
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Affiliation(s)
- Puja Goyal
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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22
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Mudunkotuwa IA, Grassian VH. Histidine adsorption on TiO2 nanoparticles: an integrated spectroscopic, thermodynamic, and molecular-based approach toward understanding nano-bio interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:8751-8760. [PMID: 24978817 DOI: 10.1021/la500722n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nanoparticles in biological media form dynamic entities as a result of competitive adsorption of proteins on nanoparticle surfaces called protein coronas. The protein affinity toward nanoparticle surfaces potentially depends on the constituent amino acid side chains which are on the protein exterior and thus exposed to the solution and available for interaction. Therefore, studying the adsorption of individual amino acids on nanoparticle surfaces can provide valuable insights into the overall evolution of nanoparticles in solution and the protein corona that forms. In the current study, the surface adsorption of l-histidine on TiO2 nanoparticles with a diameter of 5 nm at pH 7.4 (physiological pH) is studied from both macroscopic and molecular perspectives. Quantitative adsorption measurements of l-histidine on 5 nm TiO2 particles yield maximum adsorption coverage of 6.2 ± 0.3 × 10(13) molecules cm(-2) at 293 K and pH 7.4. These quantitative adsorption measurements also yield values for the equilibrium constant and free energy of adsorption of K = 4.3 ± 0.5 × 10(2) L mol(-1) and ΔG = -14.8 ± 0.3 kJ mol(-1), respectively. Detailed analysis of the adsorption between histidine and 5 nm TiO2 nanoparticle surfaces with attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy indicates both the imidazole side chain and the amine group interacting with the nanoparticle surface and the adsorption to be reversible. The adsorption results in no change in surface charge and therefore does not change nanoparticle-nanoparticle interactions and thus aggregation behavior of these 5 nm TiO2 nanoparticles in aqueous solution.
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Affiliation(s)
- Imali A Mudunkotuwa
- Department of Chemistry, University of Iowa , Iowa City, Iowa 52242, United States
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23
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Gaus M, Lu X, Elstner M, Cui Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications. J Chem Theory Comput 2014; 10:1518-1537. [PMID: 24803865 PMCID: PMC3985940 DOI: 10.1021/ct401002w] [Citation(s) in RCA: 220] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Indexed: 01/06/2023]
Abstract
We report the parametrization of the approximate density functional tight binding method, DFTB3, for sulfur and phosphorus. The parametrization is done in a framework consistent with our previous 3OB set established for O, N, C, and H, thus the resulting parameters can be used to describe a broad set of organic and biologically relevant molecules. The 3d orbitals are included in the parametrization, and the electronic parameters are chosen to minimize errors in the atomization energies. The parameters are tested using a fairly diverse set of molecules of biological relevance, focusing on the geometries, reaction energies, proton affinities, and hydrogen bonding interactions of these molecules; vibrational frequencies are also examined, although less systematically. The results of DFTB3/3OB are compared to those from DFT (B3LYP and PBE), ab initio (MP2, G3B3), and several popular semiempirical methods (PM6 and PDDG), as well as predictions of DFTB3 with the older parametrization (the MIO set). In general, DFTB3/3OB is a major improvement over the previous parametrization (DFTB3/MIO), and for the majority cases tested here, it also outperforms PM6 and PDDG, especially for structural properties, vibrational frequencies, hydrogen bonding interactions, and proton affinities. For reaction energies, DFTB3/3OB exhibits major improvement over DFTB3/MIO, due mainly to significant reduction of errors in atomization energies; compared to PM6 and PDDG, DFTB3/3OB also generally performs better, although the magnitude of improvement is more modest. Compared to high-level calculations, DFTB3/3OB is most successful at predicting geometries; larger errors are found in the energies, although the results can be greatly improved by computing single point energies at a high level with DFTB3 geometries. There are several remaining issues with the DFTB3/3OB approach, most notably its difficulty in describing phosphate hydrolysis reactions involving a change in the coordination number of the phosphorus, for which a specific parametrization (3OB/OPhyd) is developed as a temporary solution; this suggests that the current DFTB3 methodology has limited transferability for complex phosphorus chemistry at the level of accuracy required for detailed mechanistic investigations. Therefore, fundamental improvements in the DFTB3 methodology are needed for a reliable method that describes phosphorus chemistry without ad hoc parameters. Nevertheless, DFTB3/3OB is expected to be a competitive QM method in QM/MM calculations for studying phosphorus/sulfur chemistry in condensed phase systems, especially as a low-level method that drives the sampling in a dual-level QM/MM framework.
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Affiliation(s)
- Michael Gaus
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Xiya Lu
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology, Kaiserstr.
12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
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24
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Mori T, Hamers RJ, Pedersen JA, Cui Q. Integrated Hamiltonian sampling: a simple and versatile method for free energy simulations and conformational sampling. J Phys Chem B 2014; 118:8210-20. [PMID: 24641518 DOI: 10.1021/jp501339t] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Motivated by specific applications and the recent work of Gao and co-workers on integrated tempering sampling (ITS), we have developed a novel sampling approach referred to as integrated Hamiltonian sampling (IHS). IHS is straightforward to implement and complementary to existing methods for free energy simulation and enhanced configurational sampling. The method carries out sampling using an effective Hamiltonian constructed by integrating the Boltzmann distributions of a series of Hamiltonians. By judiciously selecting the weights of the different Hamiltonians, one achieves rapid transitions among the energy landscapes that underlie different Hamiltonians and therefore an efficient sampling of important regions of the conformational space. Along this line, IHS shares similar motivations as the enveloping distribution sampling (EDS) approach of van Gunsteren and co-workers, although the ways that distributions of different Hamiltonians are integrated are rather different in IHS and EDS. Specifically, we report efficient ways for determining the weights using a combination of histogram flattening and weighted histogram analysis approaches, which make it straightforward to include many end-state and intermediate Hamiltonians in IHS so as to enhance its flexibility. Using several relatively simple condensed phase examples, we illustrate the implementation and application of IHS as well as potential developments for the near future. The relation of IHS to several related sampling methods such as Hamiltonian replica exchange molecular dynamics and λ-dynamics is also briefly discussed.
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Affiliation(s)
- Toshifumi Mori
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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