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French AD. Combining Computational Chemistry and Crystallography for a Better Understanding of the Structure of Cellulose. Adv Carbohydr Chem Biochem 2021; 80:15-93. [PMID: 34872656 DOI: 10.1016/bs.accb.2021.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The approaches in this article seek to enhance understanding of cellulose at the molecular level, independent of the source and the particular crystalline form of cellulose. Four main areas of structure research are reviewed. Initially, the molecular shape is inferred from the crystal structures of many small molecules that have β-(1→4) linkages. Then, conformational analyses with potential energy calculations of cellobiose are covered, followed by the use of Atoms-In-Molecules theory to learn about interactions in experimental and theoretical structures. The last section covers models of cellulose nanoparticles. Controversies addressed include the stability of twofold screw-axis conformations, the influence of different computational methods, the predictability of crystalline conformations by studies of isolated molecules, and the twisting of model cellulose crystals.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana, USA
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Conley K, Godbout L, Whitehead M(T, van de Ven TG. Origin of the twist of cellulosic materials. Carbohydr Polym 2016; 135:285-99. [DOI: 10.1016/j.carbpol.2015.08.029] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 08/03/2015] [Accepted: 08/10/2015] [Indexed: 10/23/2022]
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Abstract
The article reviews the significant contributions to, and the present status of, applications of computational methods for the characterization and prediction of protein-carbohydrate interactions. After a presentation of the specific features of carbohydrate modeling, along with a brief description of the experimental data and general features of carbohydrate-protein interactions, the survey provides a thorough coverage of the available computational methods and tools. At the quantum-mechanical level, the use of both molecular orbitals and density-functional theory is critically assessed. These are followed by a presentation and critical evaluation of the applications of semiempirical and empirical methods: QM/MM, molecular dynamics, free-energy calculations, metadynamics, molecular robotics, and others. The usefulness of molecular docking in structural glycobiology is evaluated by considering recent docking- validation studies on a range of protein targets. The range of applications of these theoretical methods provides insights into the structural, energetic, and mechanistic facets that occur in the course of the recognition processes. Selected examples are provided to exemplify the usefulness and the present limitations of these computational methods in their ability to assist in elucidation of the structural basis underlying the diverse function and biological roles of carbohydrates in their dialogue with proteins. These test cases cover the field of both carbohydrate biosynthesis and glycosyltransferases, as well as glycoside hydrolases. The phenomenon of (macro)molecular recognition is illustrated for the interactions of carbohydrates with such proteins as lectins, monoclonal antibodies, GAG-binding proteins, porins, and viruses.
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Affiliation(s)
- Serge Pérez
- Department of Molecular Pharmacochemistry, CNRS, University Grenoble-Alpes, Grenoble, France.
| | - Igor Tvaroška
- Department of Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic; Department of Chemistry, Faculty of Natural Sciences, Constantine The Philosopher University, Nitra, Slovak Republic.
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Bazooyar F, Bohlén M, Bolton K. Computational studies of water and carbon dioxide interactions with cellobiose. J Mol Model 2015; 21:16. [DOI: 10.1007/s00894-014-2553-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Accepted: 11/30/2014] [Indexed: 11/29/2022]
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Computerized Models of Carbohydrates. POLYSACCHARIDES 2015. [DOI: 10.1007/978-3-319-16298-0_33] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Jiang Z, Fang Y, Xiang J, Ma Y, Lu A, Kang H, Huang Y, Guo H, Liu R, Zhang L. Intermolecular Interactions and 3D Structure in Cellulose–NaOH–Urea Aqueous System. J Phys Chem B 2014; 118:10250-7. [DOI: 10.1021/jp501408e] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Zhiwei Jiang
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Yan Fang
- Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Junfeng Xiang
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yanping Ma
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ang Lu
- Department
of Chemistry, Wuhan University, Wuhan 430072, China
| | - Hongliang Kang
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Yong Huang
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hongxia Guo
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Ruigang Liu
- State
Key Laboratory of Polymer Physics and Chemistry, Beijing National
Laboratory of Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Lina Zhang
- Department
of Chemistry, Wuhan University, Wuhan 430072, China
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French AD, Johnson GP, Cramer CJ, Csonka GI. Conformational analysis of cellobiose by electronic structure theories. Carbohydr Res 2012; 350:68-76. [PMID: 22265378 DOI: 10.1016/j.carres.2011.12.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA.
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French AD. Combining computational chemistry and crystallography for a better understanding of the structure of cellulose. Adv Carbohydr Chem Biochem 2012; 67:19-93. [PMID: 22794182 DOI: 10.1016/b978-0-12-396527-1.00002-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Raman and infrared spectra of cellobiose in the solid state: What can be learned from single-molecule calculations? Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.082] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pincu M, Cocinero EJ, Mayorkas N, Brauer B, Davis BG, Gerber RB, Simons JP. Isotopic Hydration of Cellobiose: Vibrational Spectroscopy and Dynamical Simulations. J Phys Chem A 2011; 115:9498-509. [DOI: 10.1021/jp112109p] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Madeleine Pincu
- Department of Chemistry, University of California, Irvine, California 92697, United States
| | - Emilio J. Cocinero
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, (UPV − EHU), Apartado 644, E-48940, Bilbao, Spain
| | - Nitzan Mayorkas
- Department of Physics, Ben Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Brina Brauer
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - Benjamin G. Davis
- Department of Chemistry, University of Oxford, Chemical Research Laboratory, Mansfield Road, Oxford OX1 3TA, U.K
| | - R. Benny Gerber
- Department of Chemistry, University of California, Irvine, California 92697, United States
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University, Jerusalem 91904, Israel
| | - John P. Simons
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, U.K
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Schnupf U, Willett JL, Momany FA. 27 ps DFT molecular dynamics simulation of α-maltose: A reduced basis set study. J Comput Chem 2010; 31:2087-97. [DOI: 10.1002/jcc.21495] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Cocinero EJ, Gamblin DP, Davis BG, Simons JP. The building blocks of cellulose: the intrinsic conformational structures of cellobiose, its epimer, lactose, and their singly hydrated complexes. J Am Chem Soc 2009; 131:11117-23. [PMID: 19722675 DOI: 10.1021/ja903322w] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical beta1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4' epimer. Left to their own devices they both adopt a cis (anti-phi/syn-psi) glycosidic configuration, supported in the epimer by strong, cooperative inter-ring hydrogen bonding. In the cellulose disaccharide, however, where the OH-4'(Glc) group is equatorial, the cooperativity is reduced and the corresponding inter-ring hydrogen bonding is relatively weak. The cis conformational preference is still retained in their singly hydrated complexes. In the cellulose disaccharide insertion of the water molecule at the favored binding site between OH-4' and the neighboring hydroxyl group OH-6' promotes a structural reorganization to create a configuration that parallels that of its unhydrated epimer and greatly strengthens the inter-ring hydrogen bonding. In the C-4' epimer, the axial orientation of OH-4' blocks this binding site and the bound water molecule simply adds on at the end of the (OH-O)(n) chain, which has a negligible effect on the (already strong) inter-ring bonding. The implications of these results are discussed with respect to the structure and insolubility of native cellulose polymers.
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Affiliation(s)
- Emilio J Cocinero
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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Stortz CA, Johnson GP, French AD, Csonka GI. Comparison of different force fields for the study of disaccharides. Carbohydr Res 2009; 344:2217-28. [PMID: 19758584 DOI: 10.1016/j.carres.2009.08.019] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Revised: 08/13/2009] [Accepted: 08/18/2009] [Indexed: 11/30/2022]
Abstract
Eighteen empirical force fields and the semi-empirical quantum method PM3CARB-1 were compared for studying beta-cellobiose, alpha-maltose, and alpha-galabiose [alpha-D-Galp-(1-->4)-alpha-D-Galp]. For each disaccharide, the energies of 54 conformers with differing hydroxymethyl, hydroxyl, and glycosidic linkage orientations were minimized by the different methods, some at two dielectric constants. By comparing these results and the available crystal structure data and/or higher level density functional theory results, it was concluded that the newer parameterizations for force fields (GROMOS, GLYCAM06, OPLS-2005 and CSFF) give results that are reasonably similar to each other, whereas the older parameterizations for Amber, CHARMM or OPLS were more divergent. However, MM3, an older force field, gave energy and geometry values comparable to those of the newer parameterizations, but with less sensitivity to dielectric constant values. These systems worked better than MM2 variants, which were still acceptable. PM3CARB-1 also gave adequate results in terms of linkage and exocyclic torsion angles. GROMOS, GLYCAM06, and MM3 appear to be the best choices, closely followed by MM4, CSFF, and OPLS-2005. With GLYCAM06 and to a lesser extent, CSFF, and OPLS-2005, a number of the conformers that were stable with MM3 changed to other forms.
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Affiliation(s)
- Carlos A Stortz
- Departamento de Química Orgánica-CIHIDECAR, FCEyN-Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires, Argentina.
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Stortz CA, French AD. Disaccharide conformational maps: adiabaticity in analogues with variable ring shapes. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020701663339] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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