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Kashirskii DA, Sashina ES, Artamonova TV, Myznikov LV. Analysis of Hydrogen Bonding Network in the Systems Containing Chloride-Based Ionic Liquids with Cellulose/Cellobiose by Fourier-Transform Infrared Spectroscopy. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s107036321805016x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Bestaoui-Berrekhchi-Berrahma N, Springborg M, Berrekhchi-Berrahma C, Sekkal-Rahal M. DFT and MP2 conformational study of 3,6-anhydro-α-d-galactose in gas phase and in aqueous solvent. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.01.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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Yan S, Yao L. DFT application in conformational determination of cellobiose. Carbohydr Res 2015; 404:117-23. [DOI: 10.1016/j.carres.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/08/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
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4
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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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Liu H, Man R, Wang Z, Liao J, Li X, Ma S, Yi P. Study on the cooperativity of hydrogen bonds between H2Y and HX (X = F, Cl, Br; Y = O, S, Se). JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2014. [DOI: 10.1142/s0219633614500370] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The structure characteristics, interaction energies, cooperative energies of the complexes between chalcogen hydrides ( H 2 Y ) and halogen hydrides (HX) have been studied theoretically at the MP2 level with aug-cc-pVTZ basis set in this paper. The conclusions show that there are strong interactions between H 2 Y and HX. The stability of the complex is decided by the electronegativity of the negatively charged atom. The cooperativity is observed in the two or three hydrogen bonds of each trimer structures in title system. The values of the cooperative energies and the cooperative contributions all illustrate that the cooperativity is of great importance in these complexes. The "atoms in molecules" (AIM) analyses show that the complexes in title system are mainly electrostatic interactions (closed-shell interactions) in character. For H ⋯ O bonds in H 2 O ⋯ HF ⋯ H 2 O , H 2 O ⋯ HBr ⋯ H 2 O and HF ⋯ H 2 O ⋯ HF , the 1 < |Vc|/Gc < 2 and -Gc < Hc < 0 indicate the interactions in these compounds are between closed-shell interaction and opened-shell interaction.
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Affiliation(s)
- Hexiu Liu
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Ruilin Man
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Zhaoxu Wang
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Jianping Liao
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Xiaofang Li
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Songjiang Ma
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
| | - Pinggui Yi
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, P. R. China
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Schnupf U, Momany FA. COSMO-DFTr study of cellulose fragments: Structural features, relative energy, and hydration energies. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.08.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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7
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Bestaoui-Berrekhchi-Berrahma N, Derreumaux P, Sekkal-Rahal M, Springborg M, Sayede A, Yousfi N, Kadoun AED. Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water. J Mol Model 2012; 19:893-904. [PMID: 23086461 DOI: 10.1007/s00894-012-1621-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Accepted: 10/01/2012] [Indexed: 10/27/2022]
Abstract
We examined the conformational preferences of the 2-O-sulfated-3,6-α-D-anhydrogalactose (compound I) and two 1,3 linked disaccharides constituting-κ or ι-carrageenans using density functional and ab initio methods in gas phase and aqueous solution. Systematic modifications of two torsion angles leading to 324 and 144 starting geometries for the compound I and each disaccharide were used to generate adiabatic maps using B3LYP/6-31G(d). The lower energy conformers were then fully optimized using B3LYP, B3PW91 and MP2 with several basis sets. Overall, we discuss the impact of full relaxation on the energy and structure of the dominant conformations, present the performance comparison with previous molecular mechanics calculations if available, and determine whether our results are impacted, when polarization and diffuse functions are added to the 6-31G(d) basis set, or when the MP2 level of theory is used.
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Momany FA, Schnupf U. DFTr Studies of Five- and Six-Residue Cyclic-β(1→4) Cellulosic Molecules. Biopolymers 2012; 97:568-76. [DOI: 10.1002/bip.22039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 01/12/2012] [Accepted: 01/19/2012] [Indexed: 11/09/2022]
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Bazooyar F, Momany FA, Bolton K. Validating empirical force fields for molecular-level simulation of cellulose dissolution. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.01.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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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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Momany FA, Schnupf U. DFTMD studies of β-cellobiose: conformational preference using implicit solvent. Carbohydr Res 2011; 346:619-30. [PMID: 21333280 DOI: 10.1016/j.carres.2011.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Revised: 01/04/2011] [Accepted: 01/06/2011] [Indexed: 10/18/2022]
Abstract
Previous DFT in vacuo studies on the conformational preferences for cellobiose showed that upon optimization the φ(H)-anti conformations were of lower energy than the syn forms. Upon optimization using an implicit solvation method, COSMO, the syn or observed form was still not predicted to be of lower energy than the φ(H)-anti form, even though optimization after addition of several explicit water molecules did show a relative energy difference favoring the syn form. In order to examine the predictive ability of COSMO on this carbohydrate, constant energy dynamics, DFTMD, simulations were carried out on low energy syn and φ(H)-anti conformations with and without COSMO included during the dynamics. The resulting analysis confirmed that when COSMO is included in the dynamics, the syn conformations become energetically favored over the φ(H)-anti forms suggesting that both solvent and entropy play roles in dictating the solution conformation of cellobiose. Analysis of the dynamic runs includes distributions of selected dihedral angles versus time, conformational transitions, and populations of some quasi-planar, boat, skew forms during the simulations.
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Affiliation(s)
- F A Momany
- Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604, USA.
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Yousfi N, Sekkal-Rahal M, Sayede A, Springborg M. Relaxed energetic maps of kappa-carrabiose: a DFT study. J Comput Chem 2010; 31:1312-20. [PMID: 20127880 DOI: 10.1002/jcc.21497] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The B3LYP density function was used with the 6-31G(d) basis set to perform relaxed energetic contour maps of the charged form of kappa-carrabiose in the gas phase and for the neutral form first in the gas phase and then by simulating the presence of water as solvent using the Onsager model. Only one starting conformation has been considered to perform all the calculations. Rigid energetic maps have been then constructed either by addition of diffuse or polarization functions to the basis set obtaining in that way 6-31+G(d)//6-31G(d), 6-31+G(d,p)//6-31G(d), and 6-311++G(d,p)//6-31G(d) energetic maps that have been carefully examined. The obtained structures corresponding to the lower energy conformers have been then fully optimized using different basis sets with the B3LYP method, a reversion in term of energy has been observed for the two first minima in the case of the charged disaccharide in the gas phase, this was attributed to the large grid of 30 degrees that could lead to the exclusion of an intermediate value corresponding to the real minimum of energy. We thus suggest that after establishing potential energy maps it is essential to proceed to full optimizations of the lower energy conformers. Calculations using the more accurate correlated method MP2 with the 6-31G(d) basis set have also been performed for conformers of the two disaccharides in the gas phase.
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Affiliation(s)
- N Yousfi
- Faculté des Sciences, Laboratoire L2MSM, Université Djillali Liabes de Sidi Bel Abbes, B.P. 89, Sidi Bel Abbes 22000, Algeria
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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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16
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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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Shen T, Langan P, French AD, Johnson GP, Gnanakaran S. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence. J Am Chem Soc 2009; 131:14786-94. [DOI: 10.1021/ja9034158] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongye Shen
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Paul Langan
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Alfred D. French
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Glenn P. Johnson
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - S. Gnanakaran
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
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Bosma WB, Schnupf U, Willett J, Momany FA. Density functional study of the infrared spectrum of glucose and glucose monohydrates in the OH stretch region. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2009.03.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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The (α-1,6) glycosidic bond of isomaltose: a tricky system for theoretical conformational studies. Carbohydr Res 2009; 344:1235-47. [DOI: 10.1016/j.carres.2009.04.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 04/19/2009] [Accepted: 04/21/2009] [Indexed: 11/23/2022]
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20
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Schnupf U, Willett J, Momany FA. DFT conformation and energies of amylose fragments at atomic resolution. Part 2: ‘band-flip’ and ‘kink’ forms of α-maltotetraose. Carbohydr Res 2009; 344:374-83. [DOI: 10.1016/j.carres.2008.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/06/2008] [Accepted: 11/19/2008] [Indexed: 10/21/2022]
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21
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DFT conformation and energies of amylose fragments at atomic resolution. Part 1: Syn forms of alpha-maltotetraose. Carbohydr Res 2008; 344:362-73. [PMID: 19111747 DOI: 10.1016/j.carres.2008.11.017] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2008] [Revised: 11/14/2008] [Accepted: 11/19/2008] [Indexed: 11/21/2022]
Abstract
DFT optimization studies of 90 syn alpha-maltotetraose (DP-4) amylose fragments have been carried out at the B3LYP/6-311++G** level of theory. The DP-4 fragments studied include V-helix, tightly bent conformations, a boat, and a (1)C(4) conformer. The standard hydroxymethyl rotamers (gg, gt, tg) were examined at different locations in the residue sequence, and their influence on the bridge conformations phi/psi values and conformer energy is described. Hydroxyl groups were considered to be homodromic, that is, they are either in the all clockwise, 'c', or all counterclockwise, 'r'. Energy differences between conformations are examined in order to assess the stability of the different conformations and to identify the sources of energy that dictate amylose polymer formation. A small nearly cyclic compact structure is of low energy as one would expect when these flexible molecules are studied in vacuo. Many conformations in which the only differences are a single hydroxymethyl variation in the residue sequence show similar energies and bridge conformations, with trends being a result of the hydroxymethyl as well as hydroxyl orientation. In general the 'c' structures are of lower energy than the 'r' structures, although this is only true for the in vacuo state. The solvent dependence on conformational preference of several low-energy DP-4 structures was investigated via the continuum solvation method COSMO. These results suggest that the 'r' structures may be favored for fully solvated molecules.
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Schnupf U, Willett JL, Bosma WB, Momany FA. DFT conformational studies of α-maltotriose. J Comput Chem 2008; 29:1103-12. [DOI: 10.1002/jcc.20872] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Schnupf U, Willett JL, Bosma WB, Momany FA. DFT studies of the disaccharide, α-maltose: relaxed isopotential maps. Carbohydr Res 2007; 342:2270-85. [PMID: 17669381 DOI: 10.1016/j.carres.2007.06.026] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 06/12/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
The disaccharide, alpha-maltose, forms the molecular basis for the analysis of the structure of starch, and determining the conformational energy landscape as the molecule oscillates around the glycosidic bonds is of importance. Thus, it is of interest to determine, using density functionals and a medium size basis set, a relaxed isopotential contour map plotted as a function of the phi(H) and psi(H) dihedral angles. The technical aspects include the method of choosing the starting conformations, the choice of scanning step size, the method of constraining the specific dihedral angles, and the fitting of data to obtain well defined contour maps. Maps were calculated at the B3LYP/6-31+G( *) level of theory in 5 degrees intervals around the (phi(H),psi(H))=(0 degrees ,0 degrees ) position, out to approximately +/-30 degrees or greater, for gg-gg'-c, gg-gg'-r, gt-gt'-c, gt-gt'-r, tg-tg'-c, and tg-tg'-r conformers, as well as one-split gg(c)-gg'(r) conformer. The results show that the preferred conformation of alpha-maltose in vacuo depends strongly upon the hydroxyl group orientations ('c'/'r'), but the energy landscape moving away from the minimum-energy position is generally shallow and transitions between conformational positions can occur without the addition of significant energy. Mapped deviations of selected parameters such as the dipole moment; the C1-O1-C4', H1-C1-O1, and H4'-C4'-O1 bond angles; and deviations in hydroxymethyl rotamers, O5-C5-C6-O6, O5'-C5'-C6'-O6', C5-C6-O6-H, and C5'-C6'-O6'-H', are presented. These allow visualization of the structural and energetic changes that occur upon rotation about the glycosidic bonds. Interactions across the bridge are visualized by deviations in H(O2)...O3', H(O3')...O2, and H1...H4' distances and the H(O2)-O2-C2-C1 and H'(O3')-O3'-C3'-C4' hydroxyl dihedral angles.
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Affiliation(s)
- Udo Schnupf
- Plant Polymer Research, National Center for Agricultural Utilization Research, ARS, USDA, 1905 N. University St., Peoria, IL 61604, United States
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Navarrete-López AM, Garza J, Vargas R. Relationship between the Critical Points Found by the Electron Localization Function and Atoms in Molecules Approaches in Adducts with Hydrogen Bonds. J Phys Chem A 2007; 111:11147-52. [DOI: 10.1021/jp074592k] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Alejandra M. Navarrete-López
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, México D. F., México
| | - Jorge Garza
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, México D. F., México
| | - Rubicelia Vargas
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, Col. Vicentina, Iztapalapa, C. P. 09340, México D. F., México
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Momany FA, Schnupf U, Willett JL, Bosma WB. DFT study of α-maltose: influence of hydroxyl orientations on the glycosidic bond. Struct Chem 2007. [DOI: 10.1007/s11224-007-9191-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Schnupf U, Willett JL, Bosma WB, Momany FA. DFT study of α- and β-d-allopyranose at the B3LYP/6-311++G∗∗ level of theory. Carbohydr Res 2007; 342:196-216. [PMID: 17204259 DOI: 10.1016/j.carres.2006.12.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2006] [Revised: 11/16/2006] [Accepted: 12/05/2006] [Indexed: 11/21/2022]
Abstract
One hundred and two conformations of alpha- and beta-D-allopyranose, the C-3 substituted epimer of glucopyranose, were geometry optimized using the density functional, B3LYP, and the basis set, 6-311++G **. Full geometry optimization was performed on different ring geometries and on the hydroxymethyl rotamers (gg/gt/tg). Analytically derived Hessians were used to calculate zero point energy, enthalpy, and entropy. The lowest energy and free energy conformation found is the alpha-tg(g-)-4C1-c conformation, which is only slightly higher in electronic (approximately 0.2 kcal/mol) and free energy than the lowest energy alpha-D-glucopyranose. The in vacuo calculations showed a small (approximately 0.3 kcal/mol) energetic preference for the alpha- over the beta-anomer for allopyranose in the 4C1 conformation, whereas in the 1C4 conformation a considerable (approximately 1.6 kcal/mol) energetic preference for the beta- over the alpha-anomer for allopyranose was encountered. The results are compared to previous aldohexose calculations in vacuo. Boat and skew forms were found that remained stable upon gradient optimization although many starting boat conformations moved to other skew forms upon optimization. As found for glucose, mannose, and galactose the orientation and interaction of the hydroxyl groups make the most significant contributions to the conformation/energy relationship in vacuo. A comparison of different basis sets and density functionals is made in the Discussion section, confirming the appropriateness of the level of theory used here.
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Affiliation(s)
- Udo Schnupf
- Plant Polymer Research, USDA, ARS, National Center for Agricultural Utilization Research, 1815 N. University St., Peoria, IL 61604, USA.
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Stepwise hydration of cellobiose by DFT methods: 1. Conformational and structural changes brought about by the addition of one to four water molecules. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.07.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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