1
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Hudek M, Kubiak-Ossowska K, Johnston K, Ferro VA, Mulheran PA. Chitin and Chitosan Binding to the α-Chitin Crystal: A Molecular Dynamics Study. ACS OMEGA 2023; 8:3470-3477. [PMID: 36713729 PMCID: PMC9878639 DOI: 10.1021/acsomega.2c07495] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 12/16/2022] [Indexed: 06/18/2023]
Abstract
Understanding the binding of chitosan oligomers to the surface of a chitin nanocrystal is important for improving the enzymatic deacetylation of chitin and for the design of chitin/chitosan composite films. Here, we study the binding of several chito-oligomers to the (100) surface of an α-chitin crystal using molecular dynamics (MD), steered MD, and umbrella sampling. The convergence of the free energy was carefully considered and yielded a binding energies of -12.5 and -2 kcal mol-1 for 6-monomer-long chitin and uncharged chitosan oligomers, respectively. We also found that the results for the umbrella sampling were consistent with the force profile from the steered MD and with classical MD simulations of the adsorption process. Our results give insight into the molecular-scale interactions, which can be helpful for the design of new chitin composite films. Furthermore, the free energy curves we present can be used to validate coarse-grained models for chitin and chitosan, which are necessary to study the self-assembly of chitin crystals due to the long time scale of the process.
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Affiliation(s)
- Magdalena Hudek
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
| | - Karina Kubiak-Ossowska
- ARCHIE-WeSt,
Department of Physics, University of Strathclyde, 107 Rottenrow East, GlasgowG4 0NG, Scotland
| | - Karen Johnston
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
| | - Valerie A. Ferro
- Strathclyde
Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, GlasgowG4 0RE, Scotland
| | - Paul A. Mulheran
- Department
of Chemical and Process Engineering, University
of Strathclyde, 75 Montrose Street, GlasgowG1 1XJ, Scotland
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2
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Baishya T, Sharma P, Gomila RM, Frontera A, Barceló-Oliver M, Verma AK, Bhattacharyya MK. Fumarato and Phthalato Bridged Dinuclear Metal-Organic Cu(II) and Mn(II) Compounds involving Infinite Fumarate-water Assemblies and Unusual Structure-guiding H-bonded Synthons: Antiproliferative Evaluation and Theoretical Studies. NEW J CHEM 2022. [DOI: 10.1039/d2nj01860h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two new dinuclear coordination compounds viz. [Cu2(µ-fum)(phen)2(H2O)6](fum)•6H2O (1) and [Mn2(µ-phth)2(phen)4]•2H2O (2) (phen = 1,10-phenanthroline, fum = fumarate and phth = phthalate) have been synthesized and characterized by elemental analysis, single...
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3
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Theoretical insight into the hybridization effect of donor and acceptor atoms on the cooperativity of C-H···N hydrogen bonds. J Mol Model 2021; 27:119. [PMID: 33818695 DOI: 10.1007/s00894-021-04724-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
In the present work, the influence of hybridization on cooperativity between C-H···N hydrogen bonds is theoretically investigated. Here, C2H6, C2H4, and C2H2 are considered as hydrogen bonding donor while NH3, N2H4, N2H2, and N2 act as the hydrogen bonding acceptor. The calculations are performed at MP2/aug-cc-pVTZ level. It is observed that the stability of systems is amplified as C(sp) > C(sp2) > C(sp3) and also N(sp3) > N(sp2) > N(sp). The role of interaction and deformation energies on the stability of the systems is examined. The results indicate the contribution of interaction energy is dominant in all complexes. The strength of C-H···N hydrogen bond is estimated using interaction energy. In agreement with cooperative energies, the C-H···N hydrogen bond is respectively weakened/strengthened in the triads containing C(sp) and C(sp2)/C(sp3) where two hydrogen bonds coexist. On the other hand, the C-H···N hydrogen bond is strengthened in the ternary systems including N(sp3) and N(sp2) while an opposite behavior is obtained in the triad having N(sp).
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4
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Nath H, Dutta D, Sharma P, Frontera A, Verma AK, Barceló-Oliver M, Devi M, Bhattacharyya MK. Adipato bridged novel hexanuclear Cu(ii) and polymeric Co(ii) coordination compounds involving cooperative supramolecular assemblies and encapsulated guest water clusters in a square grid host: antiproliferative evaluation and theoretical studies. Dalton Trans 2020; 49:9863-9881. [DOI: 10.1039/d0dt01007c] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel adipato bridged Cu(ii) and Co(ii) complexes synthesized by considering cytotoxicity, apoptosis, ROS generation, molecular docking and pharmacophore features.
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Affiliation(s)
- Hiren Nath
- Department of Chemistry
- Cotton University
- Guwahati-781001
- India
| | - Debajit Dutta
- Department of Chemistry
- Cotton University
- Guwahati-781001
- India
| | - Pranay Sharma
- Department of Chemistry
- Cotton University
- Guwahati-781001
- India
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Akalesh K. Verma
- Department of Zoology
- Cell & Biochemical Technology laboratory
- Cotton University
- Guwahati-781001
- India
| | | | - Mary Devi
- Department of Zoology
- Cell & Biochemical Technology laboratory
- Cotton University
- Guwahati-781001
- India
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5
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Chen Y, Zhang H, Guo F, Zhou W, Deng C, Zhang J, Liao J. The O1/H3-preferred 1:1 H-bonding and the electron-cloud migration induced by H-bonding or non-specific interactions: A systematic study on the interactions between dimethyl phthalate and 1-, 2- or 3-alkanol (C2-C6). J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Sun X, Qian X. Atomistic Molecular Dynamics Simulations of the Lower Critical Solution Temperature Transition of Poly( N-vinylcaprolactam) in Aqueous Solutions. J Phys Chem B 2019; 123:4986-4995. [PMID: 31124684 DOI: 10.1021/acs.jpcb.9b01711] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Poly( N-vinylcaprolactam) (PVCL) is a thermo-responsive polymer, which exhibits a lower critical solution temperature (LCST) in an aqueous solution. The LCST of this hydrophilic-to-hydrophobic transition is found to be strongly dependent on the salt-type and salt-concentration as well as on the molecular weight and concentration of the polymer. Here, atomistic molecular dynamics simulations have been successfully conducted for the first time to investigate the LCST transition of a 100 degree of polymerization PVCL chain in water, 1 M NaCl, 3.5 M NaCl, and 0.5 M CaCl2 solutions. Our results show that steric hindrance resulting from the bulky 7-member ring on the PVCL chain plays a critical role in the conformational transition. Moreover, the degrees of hydration and dehydration below or above the transition temperature are highly dependent on the specific solution condition and temperature. Water molecules are found to be trapped inside the collapsed polymer chains leading to the varying degrees of hydration and dehydration of the polymer chain in different solutions. Calculated water diffusion coefficients for both trapped and free water molecules agree very well with experimental measurements.
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Affiliation(s)
- Xiaoquan Sun
- Department of Biomedical Engineering , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Xianghong Qian
- Department of Biomedical Engineering , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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7
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Ling S, Chen W, Fan Y, Zheng K, Jin K, Yu H, Buehler MJ, Kaplan DL. Biopolymer nanofibrils: structure, modeling, preparation, and applications. Prog Polym Sci 2018; 85:1-56. [PMID: 31915410 PMCID: PMC6948189 DOI: 10.1016/j.progpolymsci.2018.06.004] [Citation(s) in RCA: 168] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biopolymer nanofibrils exhibit exceptional mechanical properties with a unique combination of strength and toughness, while also presenting biological functions that interact with the surrounding environment. These features of biopolymer nanofibrils profit from their hierarchical structures that spun angstrom to hundreds of nanometer scales. To maintain these unique structural features and to directly utilize these natural supramolecular assemblies, a variety of new methods have been developed to produce biopolymer nanofibrils. In particular, cellulose nanofibrils (CNFs), chitin nanofibrils (ChNFs), silk nanofibrils (SNFs) and collagen nanofibrils (CoNFs), as the four most abundant biopolymer nanofibrils on earth, have been the focus of research in recent years due to their renewable features, wide availability, low-cost, biocompatibility, and biodegradability. A series of top-down and bottom-up strategies have been accessed to exfoliate and regenerate these nanofibrils for versatile advanced applications. In this review, we first summarize the structures of biopolymer nanofibrils in nature and outline their related computational models with the aim of disclosing fundamental structure-property relationships in biological materials. Then, we discuss the underlying methods used for the preparation of CNFs, ChNFs, SNF and CoNFs, and discuss emerging applications for these biopolymer nanofibrils.
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Affiliation(s)
- Shengjie Ling
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
| | - Wenshuai Chen
- Key Laboratory of Bio-based Material Science & Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Yimin Fan
- College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Ke Zheng
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Kai Jin
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Haipeng Yu
- Key Laboratory of Bio-based Material Science & Technology, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Markus J. Buehler
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - David L. Kaplan
- Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA
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8
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9
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Vu A, Wickramasinghe SR, Qian X. Polymeric Solid Acid Catalysts for Lignocellulosic Biomass Fractionation. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b05286] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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10
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de Oliveira PMC, Silva JAB, Longo RL. Benchmark, DFT assessments, cooperativity, and energy decomposition analysis of the hydrogen bonds in HCN/HNC oligomeric complexes. J Mol Model 2017; 23:56. [PMID: 28161784 DOI: 10.1007/s00894-017-3235-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/13/2017] [Indexed: 02/05/2023]
Abstract
Hydrogen cyanide (HCN) and its tautomer hydrogen isocyanide (HNC) are relevant for extraterrestrial chemistry and possible relation to the origin of biomolecules. Several processes and reactions involving these molecules depend on their intermolecular interactions that can lead to aggregates and liquids especially due to the hydrogen bonds. It is thus important to comprehend, to describe, and to quantify their hydrogen bonds, mainly their nature and the cooperativity effects. A systematic study of all linear complexes up to pentamers of HCN and HNC is presented. CCSD(T)/CBS energy calculations, with and without basis set superposition error (BSSE) corrections for energies and geometries, provided a suitable set of benchmarks. Approximated methods based on the density functional theory (DFT) such as BP86, PBE, TPSS, B3LYP, CAM-B3LYP with and without dispersion corrections and long-range corrections, were assessed to describe the interaction energies and cooperativity effects. These assessments are relevant to select DFT functionals for liquid simulations. Energy decomposition analysis was performed at the PBE/STO-TZ2P level and provided insights into the nature of the hydrogen bonds, which are dominated by the electrostatic component. In addition, several linear relationships between the various energy components and the interaction energy were obtained. The cooperativity energy was also found to be practically linear with respect to the interaction energy, which may be relevant for designing and/or correcting empirical force fields. Graphical Abstract Hydrogen bonds in HCN/HNC oligomeric complexesᅟ.
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Affiliation(s)
| | - Juliana A B Silva
- Centro Acadêmico do Agreste, Universidade Federal de Pernambuco, 55002-970, Caruaru, PE, Brazil
| | - Ricardo L Longo
- Departamento de Química Fundamental, Universidade Federal de Pernambuco, 50740-540, Recife, PE, Brazil.
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11
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Masoodi HR, Bagheri S, Ranjbar M. Theoretical study of cooperativity between hydrogen bond‒hydrogen bond, halogen bond‒halogen bond and hydrogen bond‒halogen bond in ternary FX…diazine…XF (X = H and Cl) complexes. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1236992] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Hamid Reza Masoodi
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Sotoodeh Bagheri
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
| | - Mahdiyeh Ranjbar
- Department of Chemistry, Faculty of Science, Vali-e-Asr University of Rafsanjan, Rafsanjan, Iran
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12
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Yurdakul Ş, Badoğlu S, Özkurt L. An experimental and theoretical investigation of free Oxazole in conjunction with the DFT analysis of Oxazole⋯(H₂O)n complexes. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 162:48-60. [PMID: 26978786 DOI: 10.1016/j.saa.2016.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/26/2016] [Accepted: 02/14/2016] [Indexed: 06/05/2023]
Abstract
The mid-IR spectrum of Oxazole (Oxa) is recorded. This spectrum is interpreted with the help of B3LYP/6-311++G(d,p) calculations and potential energy distribution (PED) analysis. The experimental spectrum is concordant with the theoretical data. Geometrical parameters and the atomic charges are also theoretically obtained and presented. Solvent effects on the geometrical parameters, vibrational frequencies, and electronic properties of Oxa are analyzed theoretically in chloroform, ethanol, and water. Besides, hydrogen bonded Oxa⋯(H2O)n (n=1, 2,…, 10) complexes are investigated within the PCM solvation model. It is found that the interaction energies in Oxa⋯(H2O)n complexes are influenced by the number of water molecules, and by the arrangement of water molecules.
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Affiliation(s)
- Şenay Yurdakul
- Department of Physics, Faculty of Science, Gazi University, Teknikokullar, 06500, Ankara, Turkey.
| | - Serdar Badoğlu
- Department of Physics, Faculty of Science, Gazi University, Teknikokullar, 06500, Ankara, Turkey
| | - Lütfiye Özkurt
- Department of Physics, Faculty of Science, Gazi University, Teknikokullar, 06500, Ankara, Turkey
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13
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Deringer VL, Englert U, Dronskowski R. Nature, Strength, and Cooperativity of the Hydrogen-Bonding Network in α-Chitin. Biomacromolecules 2016; 17:996-1003. [DOI: 10.1021/acs.biomac.5b01653] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Volker L. Deringer
- Institute of Inorganic Chemistry and ‡Jülich−Aachen
Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Ulli Englert
- Institute of Inorganic Chemistry and ‡Jülich−Aachen
Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
| | - Richard Dronskowski
- Institute of Inorganic Chemistry and ‡Jülich−Aachen
Research
Alliance (JARA-HPC), RWTH Aachen University, Landoltweg 1, 52056 Aachen, Germany
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14
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Lee CM, Kubicki JD, Fan B, Zhong L, Jarvis MC, Kim SH. Hydrogen-Bonding Network and OH Stretch Vibration of Cellulose: Comparison of Computational Modeling with Polarized IR and SFG Spectra. J Phys Chem B 2015; 119:15138-49. [PMID: 26615832 DOI: 10.1021/acs.jpcb.5b08015] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Hydrogen bonds play critical roles in noncovalent directional interactions determining the crystal structure of cellulose. Although diffraction studies accurately determined the coordinates of carbon and oxygen atoms in crystalline cellulose, the structural information on hydrogen atoms involved in hydrogen-bonding is still elusive. This could be complemented by vibrational spectroscopy; but the assignment of the OH stretch peaks has been controversial. In this study, we performed calculations using density functional theory with dispersion corrections (DFT-D2) for the cellulose Iβ crystal lattices with the experimentally determined carbon and oxygen coordinates. DFT-D2 calculations revealed that the OH stretch vibrations of cellulose are highly coupled and delocalized through intra- and interchain hydrogen bonds involving all OH groups in the crystal. Additionally, molecular dynamics (MD) simulations of a single cellulose microfibril showed that the conformations of OH groups exposed at the microfibril surface are not well-defined. Comparison of the computation results with the experimentally determined IR dichroism of uniaxially aligned cellulose microfibrils and the peak positions of various cellulose crystals allowed unambiguous identification of OH stretch modes observed in the vibrational spectra of cellulose.
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Affiliation(s)
- Christopher M Lee
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University , University Park, Pennsylvania United States.,Center for Lignocellulose Structure and Formation, The Pennsylvania State University , University Park, Pennsylvania United States
| | - James D Kubicki
- Department of Geological Sciences, University of Texas at El Paso , El Paso, Texas 79968, United States.,Center for Lignocellulose Structure and Formation, The Pennsylvania State University , University Park, Pennsylvania United States
| | - Bingxin Fan
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University , University Park, Pennsylvania United States.,Center for Lignocellulose Structure and Formation, The Pennsylvania State University , University Park, Pennsylvania United States
| | - Linghao Zhong
- Department of Chemistry, The Pennsylvania State University , Mont Alto, Pennsylvania 17237, United States.,Center for Lignocellulose Structure and Formation, The Pennsylvania State University , University Park, Pennsylvania United States
| | - Michael C Jarvis
- School of Chemistry, University of Glasgow , Glasgow G12 8QQ, Scotland, U.K
| | - Seong H Kim
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University , University Park, Pennsylvania United States.,Center for Lignocellulose Structure and Formation, The Pennsylvania State University , University Park, Pennsylvania United States
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15
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Du H, Qian X. The hydration properties of carboxybetaine zwitterion brushes. J Comput Chem 2015; 37:877-85. [DOI: 10.1002/jcc.24234] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 09/30/2015] [Accepted: 10/04/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Hongbo Du
- Department of Biomedical Engineering; University of Arkansas; Fayetteville Arkansas 72701
| | - Xianghong Qian
- Department of Biomedical Engineering; University of Arkansas; Fayetteville Arkansas 72701
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16
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Qian X, Liu D. Free energy landscape for glucose condensation and dehydration reactions in dimethyl sulfoxide and the effects of solvent. Carbohydr Res 2014; 388:50-60. [DOI: 10.1016/j.carres.2014.02.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/30/2014] [Accepted: 02/07/2014] [Indexed: 10/25/2022]
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17
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Qian X. Free Energy Surface for Brønsted Acid-Catalyzed Glucose Ring-Opening in Aqueous Solution. J Phys Chem B 2013; 117:11460-5. [DOI: 10.1021/jp402739q] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xianghong Qian
- Department of Chemical Engineering, University of Arkansas, Fayetteville, Arkansas 72701, United States
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18
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Esrafili MD, Behzadi H. Investigation into the nature of interactions in aspirin–water clusters including SAPT, AIM and NBO theories. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.758848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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19
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Lee CM, Mohamed NMA, Watts HD, Kubicki JD, Kim SH. Sum-frequency-generation vibration spectroscopy and density functional theory calculations with dispersion corrections (DFT-D2) for cellulose Iα and Iβ. J Phys Chem B 2013; 117:6681-92. [PMID: 23738844 DOI: 10.1021/jp402998s] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sum-frequency-generation (SFG) vibration spectroscopy selectively detects noncentrosymmetric vibrational modes in crystalline cellulose inside intact lignocellulose. However, SFG peak assignment in biomass samples is challenging due to the complexity of the SFG processes and the lack of reference SFG spectra from the two crystal forms synthesized in nature, cellulose Iα and Iβ. This paper compares SFG spectra of laterally aligned cellulose Iα and Iβ crystals with vibration frequencies calculated from density functional theory with dispersion corrections (DFT-D2). Two possible hydrogen-bond networks A and B ( Nishiyama et al. Biomacromolecules 2008 , 9 , 3133 ) were investigated for both polymorphs. From DFT-D2 calculations the energetically favorable structures for cellulose Iα and Iβ had CH2OH groups in tg conformations and network A hydrogen bonding. The calculated frequencies of C-H stretch modes agreed reasonably well with the peak positions observed with SFG and were localized vibrations; thus, peak assignments to specific alkyl groups were proposed. DFT-D2 calculations underestimated the distances between hydrogen-bonded oxygen atoms compared to the experimentally determined values; therefore, the OH stretching calculated frequencies were ~100 cm(-1) lower than observed. The SFG peak assignments through comparison with DFT-D2 calculations will guide the SFG analysis of the crystalline cellulose structure in plant cell walls and lignocellulose biomass.
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Affiliation(s)
- Christopher M Lee
- Department of Chemical Engineering and Materials Research Institute, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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20
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Kabanda MM, Ebenso EE. Structures, Stabilization Energies, and Binding Energies of Quinoxaline···(H2O)n, Quinoxaline Dimer, and Quinoxaline···Cu Complexes: A Theoretical Study. J Phys Chem A 2013; 117:1583-95. [PMID: 23343309 DOI: 10.1021/jp309356b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mwadham M. Kabanda
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
| | - Eno E. Ebenso
- Department of Chemistry, North-West University (Mafikeng Campus), Private Bag x2046, Mmabatho 2735,
South Africa
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21
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Mammino L, Kabanda MM. The role of additional O–H…O intramolecular hydrogen bonds for acylphloroglucinols' conformational preferencesin vacuoand in solution. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.700483] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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22
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Qian X, Lei J, Wickramasinghe SR. Novel polymeric solid acid catalysts for cellulose hydrolysis. RSC Adv 2013. [DOI: 10.1039/c3ra43987a] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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23
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DFT study of 17O, 1H and 13C NMR chemical shifts in two forms of native cellulose, I and I. Carbohydr Res 2012; 347:99-106. [DOI: 10.1016/j.carres.2011.10.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2011] [Revised: 10/19/2011] [Accepted: 10/26/2011] [Indexed: 11/19/2022]
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24
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Parthasarathi R, Bellesia G, Chundawat SPS, Dale BE, Langan P, Gnanakaran S. Insights into Hydrogen Bonding and Stacking Interactions in Cellulose. J Phys Chem A 2011; 115:14191-202. [DOI: 10.1021/jp203620x] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - S. P. S. Chundawat
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - B. E. Dale
- Great Lakes Bioenergy Research Center, East Lansing, Michigan 48824, United States
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - P. Langan
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6475, United States
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25
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The effects of acetate anion on cellulose dissolution and reaction in imidazolium ionic liquids. Carbohydr Res 2011; 346:1985-90. [DOI: 10.1016/j.carres.2011.05.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 05/15/2011] [Accepted: 05/19/2011] [Indexed: 11/24/2022]
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Moon RJ, Martini A, Nairn J, Simonsen J, Youngblood J. Cellulose nanomaterials review: structure, properties and nanocomposites. Chem Soc Rev 2011; 40:3941-94. [PMID: 21566801 DOI: 10.1039/c0cs00108b] [Citation(s) in RCA: 2530] [Impact Index Per Article: 194.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This critical review provides a processing-structure-property perspective on recent advances in cellulose nanoparticles and composites produced from them. It summarizes cellulose nanoparticles in terms of particle morphology, crystal structure, and properties. Also described are the self-assembly and rheological properties of cellulose nanoparticle suspensions. The methodology of composite processing and resulting properties are fully covered, with an emphasis on neat and high fraction cellulose composites. Additionally, advances in predictive modeling from molecular dynamic simulations of crystalline cellulose to the continuum modeling of composites made with such particles are reviewed (392 references).
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Affiliation(s)
- Robert J Moon
- The Forest Products Laboratory, US Forest Service, Madison, WI, USA.
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Cellulose Chemistry Meets Click Chemistry: Syntheses and Properties of Cellulose-Based Glycoclusters with High Structural Homogeneity. Polymers (Basel) 2011. [DOI: 10.3390/polym3010489] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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28
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Simulation studies of the insolubility of cellulose. Carbohydr Res 2010; 345:2060-6. [DOI: 10.1016/j.carres.2010.06.017] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2010] [Revised: 06/05/2010] [Accepted: 06/25/2010] [Indexed: 11/18/2022]
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30
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Dong H, Nimlos MR, Himmel ME, Johnson DK, Qian X. The effects of water on beta-D-xylose condensation reactions. J Phys Chem A 2009; 113:8577-85. [PMID: 19572686 DOI: 10.1021/jp9025442] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Car-Parrinello-based ab initio molecular dynamics simulations (CPMD) combined with metadynamics (MTD) simulations were used to determine the reaction energetics for the beta-D-xylose condensation reaction to form beta-1,4-linked xylobiose in a dilute acid solution. Protonation of the hydroxyl group on the xylose molecule and the subsequent breaking of the C-O bond were found to be the rate-limiting step during the xylose condensation reaction. Water and water structure was found to play a critical role in these reactions due to the proton's high affinity for water molecules. The reaction free energy and reaction barrier were determined using CPMD-MTD. We found that solvent reorganization due to proton partial desolvation must be taken into account in order to obtain the correct reaction activation energy. Our calculated reaction free energy and reaction activation energy compare well with available experimental results.
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Affiliation(s)
- Haitao Dong
- Department of Mechanical Engineering, Colorado State University, Fort Collins, Colorado 80523, USA
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The noncellulosomal family 48 cellobiohydrolase from Clostridium phytofermentans ISDg: heterologous expression, characterization, and processivity. Appl Microbiol Biotechnol 2009; 86:525-33. [PMID: 19830421 DOI: 10.1007/s00253-009-2231-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 08/29/2009] [Accepted: 08/31/2009] [Indexed: 10/20/2022]
Abstract
Family 48 glycoside hydrolases (cellobiohydrolases) are among the most important cellulase components for crystalline cellulose hydrolysis mediated by cellulolytic bacteria. Open reading frame (Cphy_3368) of Clostridium phytofermentans ISDg encodes a putative family 48 glycoside hydrolase (CpCel48) with a family 3 cellulose-binding module. CpCel48 was successfully expressed as two soluble intracellular forms with or without a C-terminal His-tag in Escherichia coli and as a secretory active form in Bacillus subtilis. It was found that calcium ion enhanced activity and thermostability of the enzyme. CpCel48 had high activities of 15.1 U micromol(-1) on Avicel and 35.9 U micromol(-1) on regenerated amorphous cellulose (RAC) with cellobiose as a main product and cellotriose and cellotetraose as by-products. By contrast, it had very weak activities on soluble cellulose derivatives (e.g., carboxymethyl cellulose (CMC)) and did not significantly decrease the viscosity of the CMC solution. Cellotetraose was the smallest oligosaccharide substrate for CpCel48. Since processivity is a key characteristic for cellobiohydrolases, the new initial false/right attack model was developed for estimation of processivity by considering the enzyme's substrate specificity, the crystalline structure of homologous Cel48 enzymes, and the configuration of cellulose chains. The processivities of CpCel48 on Avicel and RAC were estimated to be approximately 3.5 and 6.0, respectively. Heterologous expression of secretory active cellobiohydrolase in B. subtilis is an important step for developing recombinant cellulolytic B. subtilis strains for low-cost production of advanced biofuels from cellulosic materials in a single step.
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