1
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Adsorption and Decomposition of Glycerol on Pristine and Oxygen Modified Au(111) Surfaces. Top Catal 2019. [DOI: 10.1007/s11244-019-01199-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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2
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Ashouri M, Maghari A, Karimi-Jafari MH. Hydrogen bonding motifs in a hydroxy-bisphosphonate moiety: revisiting the problem of hydrogen bond identification. Phys Chem Chem Phys 2015; 17:13290-300. [DOI: 10.1039/c5cp00693g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Relative energy of conformers are highly correlated with their sum of local density of potential energy at H-bond critical points.
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Affiliation(s)
- Mitra Ashouri
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - Ali Maghari
- Department of Physical Chemistry
- School of Chemistry
- College of Science
- University of Tehran
- Tehran
| | - M. H. Karimi-Jafari
- Department of Bioinformatics
- Institute of Biochemistry and Biophysics
- University of Tehran
- Tehran
- Iran
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3
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4
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Bell F, Ruan QN, Golan A, Horn PR, Ahmed M, Leone SR, Head-Gordon M. Dissociative Photoionization of Glycerol and its Dimer Occurs Predominantly via a Ternary Hydrogen-Bridged Ion–Molecule Complex. J Am Chem Soc 2013; 135:14229-39. [DOI: 10.1021/ja405511v] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Franziska Bell
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Qiao N. Ruan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Amir Golan
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Paul R. Horn
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Musahid Ahmed
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Stephen R. Leone
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
| | - Martin Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California
94720, United States
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Goursot A, Mineva T, Vásquez-Pérez JM, Calaminici P, Köster AM, Salahub DR. Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study. Phys Chem Chem Phys 2013. [PMID: 23202583 DOI: 10.1039/c2cp43514d] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper highlights the relevance of including the high-energy conformational states sampled by Born-Oppenheimer molecular dynamics (BOMD) in the calculation of time-averaged NMR chemical shifts. Our case study is the very flexible glycerol molecule that undergoes interconversion between conformers in a nonrandom way. Along the sequence of structures from one backbone conformer to another, transition states have been identified. The three (13)C NMR chemical shifts of the molecule were estimated by averaging their calculated values over a large set of BOMD snapshots. The simulation time needed to obtain a good agreement with the two signals present in the experimental spectrum is shown to be dependent on the atomic orbital basis set used for the dynamics, with a necessary longer trajectory for the most extended basis sets. The large structural deformations with respect to the optimized conformer geometries that occur along the dynamics are related to a kinetically driven conformer distribution. Calculated conformer type populations are in good agreement with experimental gas phase microwave results.
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Affiliation(s)
- A Goursot
- ICGM, UMR 5253 CNRS, Ecole de chimie de Montpellier, 8 rue de l'Ecole Normale, 34296 Montpellier, Cédex 5, France.
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Hosseinnejad T, Ahmadi SJ, Karimi-Jafari MH. Computational study on the structure and properties of ternary complexes of Ln3+ (Ln = La, Ce, Nd AND Sm) with 5,7-dichloroquinoline-8-ol and 4-vinyl pyridine. J STRUCT CHEM+ 2013. [DOI: 10.1134/s0022476613020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Arabieh M, Karimi-Jafari MH, Ghannadi-Maragheh M. Low-energy conformers of pamidronate and their intramolecular hydrogen bonds: a DFT and QTAIM study. J Mol Model 2012; 19:427-38. [DOI: 10.1007/s00894-012-1564-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 08/06/2012] [Indexed: 10/27/2022]
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8
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Jeong KH, Byun BJ, Kang YK. Conformational Preferences of Glycerol in the Gas Phase and in Water. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.3.917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Egorov AV, Lyubartsev AP, Laaksonen A. Molecular dynamics simulation study of glycerol-water liquid mixtures. J Phys Chem B 2011; 115:14572-81. [PMID: 22004353 DOI: 10.1021/jp208758r] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
To study the effects of water on conformational dynamics of polyalcohols, Molecular Dynamics simulations of glycerol-water liquid mixtures have been carried out at different concentrations: 42.9 and 60.0 wt % of glycerol, respectively. On the basis of the analysis of backbone conformer distributions, it is found that the surrounding water molecules have a large impact on the populations of the glycerol conformers. While the local structure of water in the liquid mixture is surprisingly close to that in pure liquid water, the behavior of glycerols can be divided into three different categories where roughly 25% of them occur in a structure similar to that in pure liquid of glycerol, ca. 25% of them exist as monomers, solvated by water, and the remaining 50% of glycerols in the mixture form H-bonded strings as remains of the glycerol H-bond network. The typical glycerol H-bond network still exists even at the lower concentration of 40 wt % of glycerol. The microheterogeneity of water-glycerol mixtures is analyzed using time-averaged distributions of the sizes of the water aggregates. At 40 wt % of glycerol, the cluster sizes from 3 to 10 water molecules are observed. The increase of glycerol content causes a depletion of clusters leading to smaller 3-5 molecule clusters domination. Translational diffusion coefficients have been calculated to study the dynamical behavior of both glycerol and water molecules. Rotational-reorientational motion is studied both in overall and in selected substructures on the basis of time correlation functions. Characteristic time scales for different motional modes are deduced on the basis of the calculated correlation times. The general conclusion is that the presence of water increases the overall mobility of glycerol, while glycerol slows the mobility of water.
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Affiliation(s)
- Andrei V Egorov
- Faculty of Physics, St. Petersburg University, St. Petersburg, Russia
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Auneau F, Michel C, Delbecq F, Pinel C, Sautet P. Unravelling the mechanism of glycerol hydrogenolysis over rhodium catalyst through combined experimental-theoretical investigations. Chemistry 2011; 17:14288-99. [PMID: 22069214 DOI: 10.1002/chem.201101318] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 08/18/2011] [Indexed: 11/09/2022]
Abstract
We report herein a detailed and accurate study of the mechanism of rhodium-catalysed conversion of glycerol into 1,2-propanediol and lactic acid. The first step of the reaction is particularly debated, as it can be either dehydration or dehydrogenation. It is expected that these elementary reactions can be influenced by pH variations and by the nature of the gas phase. These parameters were consequently investigated experimentally. On the other hand, there was a lack of knowledge about the behaviour of glycerol at the surface of the metallic catalyst. A theoretical approach on a model Rh(111) surface was thus implemented in the framework of density functional theory (DFT) to describe the above-mentioned elementary reactions and to calculate the corresponding transition states. The combination of experiment and theory shows that the dehydrogenation into glyceraldehyde is the first step for the glycerol transformation on the Rh/C catalyst in basic media under He or H(2) atmosphere.
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Affiliation(s)
- Florian Auneau
- Université de Lyon, Institut de Recherches sur la Catalyse et l'Environnement de Lyon, IRCELYON, Université Lyon I, CNRS, UMR5256, 2, Avenue Albert Einstein, 69626 Villeurbanne Cedex, France
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11
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Michel C, Auneau F, Delbecq F, Sautet P. C–H versus O–H Bond Dissociation for Alcohols on a Rh(111) Surface: A Strong Assistance from Hydrogen Bonded Neighbors. ACS Catal 2011. [DOI: 10.1021/cs200370g] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Carine Michel
- Université de Lyon, CNRS, Institut de Chimie de Lyon, Ecole Normale Supérieure de Lyon, 15 Parvis Descartes, BP7000, F-69342 Lyon Cedex 07, France
| | - Florian Auneau
- Université de Lyon, CNRS, Institut de Chimie de Lyon, Ecole Normale Supérieure de Lyon, 15 Parvis Descartes, BP7000, F-69342 Lyon Cedex 07, France
- Université de Lyon, CNRS, Institut de Recherches sur la Catalyse et l’Environnement de Lyon IRCELYON, Université Lyon I, UMR5256, 2, avenue Albert Einstein, F-69626 Villeurbanne Cedex, France
| | - Françoise Delbecq
- Université de Lyon, CNRS, Institut de Chimie de Lyon, Ecole Normale Supérieure de Lyon, 15 Parvis Descartes, BP7000, F-69342 Lyon Cedex 07, France
| | - Philippe Sautet
- Université de Lyon, CNRS, Institut de Chimie de Lyon, Ecole Normale Supérieure de Lyon, 15 Parvis Descartes, BP7000, F-69342 Lyon Cedex 07, France
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12
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Kongpatpanich K, Nanok T, Boekfa B, Probst M, Limtrakul J. Structures and reaction mechanisms of glycerol dehydration over H-ZSM-5 zeolite: a density functional theory study. Phys Chem Chem Phys 2011; 13:6462-70. [PMID: 21369602 DOI: 10.1039/c0cp01720e] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The initial stage of glycerol conversion over H-ZSM-5 zeolite has been investigated using density functional theory (DFT) calculations on an embedded cluster model consisting of 128 tetrahedrally coordinated atoms. It is found that glycerol dehydration to acrolein and acetol proceeds favourably via a stepwise mechanism. The formation of an alkoxide species upon the first dehydration requires the highest activation energy (42.5 kcal mol(-1)) and can be considered as the rate determining step of the reaction. The intrinsic activation energies for the first dehydration are virtually the same for both acrolein and acetol formation, respectively, suggesting the competitive removal of the primary and secondary OH groups. A high selectivity to acrolein at moderate temperatures can be attributed to the selective activation of the stronger adsorption mode of glycerol through the secondary OH group and the kinetically favoured subsequent consecutive steps. In addition, the less reactive nature of acrolein relative to acetol precludes it from being converted to other products upon conversion to glycerol. In accordance with typical endothermic reactions, the forward rate constant for glycerol dehydration significantly increases with increasing reaction temperature.
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Affiliation(s)
- Kanokwan Kongpatpanich
- Laboratory for Computational and Applied Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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13
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Goursot A, Mineva T, Bissig C, Gruenberg J, Salahub DR. Structure, dynamics, and energetics of lysobisphosphatidic acid (LBPA) isomers. J Phys Chem B 2010; 114:15712-20. [PMID: 21053942 DOI: 10.1021/jp108361d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lysobisphosphatidic acid (LBPA), or bis(monoacylglycerol)phosphate, is a very interesting lipid, that is mainly found in late endosomes. It has several intriguing characteristics, which differ from those of other animal glycerophospholipids, that may be related to its specific functions, particularly in the metabolism of cholesterol. Its phosphodiester group is bonded at the sn-1 (sn-1') positions of the glycerols rather than at sn-3 (sn-3'); the position of the two fatty acid chains is still under debate but, increasingly, arguments favor the sn-2, sn-2' position in the native molecule, whereas isolation procedures or acidic conditions lead to the thermodynamically more stable sn-3, sn-3' structure. Because of these peculiar features, it can be expected that LBPA shape and interactions with membrane lipids and proteins are related to its structure at the molecular level. We applied quantum mechanical methods to study the structures and stabilities of the 2,2' and 3,3' LBPA isomers, using a step-by-step procedure from glycerol to precursors (in vitro syntheses) and to the final isoforms. The structures of the two positional LBPA isomers are substantially different, showing that the binding positions of the fatty acid chains on the glycerol backbone determine the shape of the LBPA molecule and thus, possibly, its functions. The 3,3' LBPA structures obtained are more stable with respect to the 2,2' form, as expected from experiment. If one argues that the in vivo synthesis starts from the present glycerol conformers and considering the most stable bis(glycero)phosphate structures, the 2,2' isoform should be the most probable isomer.
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Affiliation(s)
- A Goursot
- UMR 5253 CNRS/ENSCM/UM2/UM1 Ecole de Chimie de Montpellier, 8 rue de l'Ecole Normale, 34296, Montpellier, Cedex 5, France
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Kaminský J, Kapitán J, Baumruk V, Bednárová L, Bouř P. Interpretation of Raman and Raman Optical Activity Spectra of a Flexible Sugar Derivative, the Gluconic Acid Anion. J Phys Chem A 2009; 113:3594-601. [DOI: 10.1021/jp809210n] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jakub Kaminský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Josef Kapitán
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Vladimír Baumruk
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, 166 10 Prague, Czech Republic, Faculty of Mathematics and Physics, Charles University, Institute of Physics, Ke Karlovu 5, 12116 Prague 2, Czech Republic, and Department of Chemistry of Natural Compounds, Institute of Chemical Technology, 166 28 Prague, Czech Republic
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A semi-empirical and ab initio combined approach for the full conformational searches of gaseous lysine and lysine–H2O complex. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.02.016] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Yongye AB, Foley BL, Woods RJ. On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J Phys Chem A 2008; 112:2634-9. [PMID: 18311953 PMCID: PMC4201037 DOI: 10.1021/jp710544s] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The rotational isomeric states (RIS) of glycerol at infinite dilution have been characterized in the aqueous phase via a 1 micros conventional molecular dynamics (MD) simulation, a 40 ns enhanced sampling replica exchange molecular dynamics (REMD) simulation, and a reevaluation of the experimental NMR data. The MD and REMD simulations employed the GLYCAM06/AMBER force field with explicit treatment of solvation. The shorter time scale of the REMD sampling method gave rise to RIS and theoretical scalar 3J(HH) coupling constants that were comparable to those from the much longer traditional MD simulation. The 3J(HH) coupling constants computed from the MD methods were in excellent agreement with those observed experimentally. Despite the agreement between the computed and the experimental J-values, there were variations between the rotamer populations computed directly from the MD data and those derived from the experimental NMR data. The experimentally derived populations were determined utilizing limiting J-values from an analysis of NMR data from substituted ethane molecules and may not be completely appropriate for application in more complex molecules, such as glycerol. Here, new limiting J-values have been derived via a combined MD and quantum mechanical approach and were used to decompose the experimental 3J(HH) coupling constants into population distributions for the glycerol RIS.
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Affiliation(s)
- Austin B. Yongye
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
| | - B. Lachele Foley
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602
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17
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Chen M, Lin Z. Ab initiostudies of aspartic acid conformers in gas phase and in solution. J Chem Phys 2007; 127:154314. [DOI: 10.1063/1.2777161] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Jamróz ME, Jarosz M, Witowska-Jarosz J, Bednarek E, Tecza W, Jamróz MH, Dobrowolski JC, Kijeński J. Mono-, di-, and tri-tert-butyl ethers of glycerol. A molecular spectroscopic study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2007; 67:980-8. [PMID: 17085068 DOI: 10.1016/j.saa.2006.09.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Revised: 09/17/2006] [Accepted: 09/18/2006] [Indexed: 05/12/2023]
Abstract
MS, NMR, IR and Raman molecular spectroscopy techniques were applied to characterize 3-tert-butoxy-propane-1,2-diol, 1,3-di-tert-butoxy-propan-2-ol, and 1,2,3-tri-tert-butoxy-propane. These ethers are the main products of glycerol etherification reaction and are excellent oxygen additives for diesel fuel. Computational DFT/ B3LYP/6-31G** studies were performed to support and rationalize both vibrational spectroscopy analysis and the isomer ratio.
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Affiliation(s)
- Małgorzata E Jamróz
- Industrial Chemistry Research Institute, 8 Rydygiera Street, 01-793 Warsaw, Poland.
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Schettino V, Chelli R, Marsili S, Barducci A, Faralli C, Pagliai M, Procacci P, Cardini G. Problems in molecular dynamics of condensed phases. Theor Chem Acc 2007. [DOI: 10.1007/s00214-006-0223-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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21
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Lopes Jesus AJ, Tomé LIN, Eusébio MES, Redinha JS. Determination of the Enthalpy of Solute−Solvent Interaction from the Enthalpy of Solution: Aqueous Solutions of Erythritol and l-Threitol. J Phys Chem B 2006; 110:9280-5. [PMID: 16671745 DOI: 10.1021/jp0561221] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work the enthalpy of the solute-solvent interaction of erythritol and L-threitol in aqueous solution was determined from the values obtained for the enthalpy of solvation. The values for this property were calculated from those determined for the enthalpies of solution and sublimation. To determine the values of the enthalpy of solute-solvent interaction, the solvation process is considered as taking place in three steps: opening a cavity in the solvent to hold the solute molecule, changing the solute conformation when it passes from the gas phase into solution, and interaction between the solute and the solvent molecules. The cavity enthalpy was calculated by the scaled particle theory and the conformational enthalpy change was estimated from the value of this function in the gas phase and in solution. Both terms were determined by DFT calculations. The solvent effect on the solute conformation in solution was estimated using the CPCM solvation model. The importance of the cavity and conformational terms in the interpretation of the enthalpy of solvation is noted. While the cavity term has been used by some authors, the conformational term is considered for the first time. The structural features in aqueous solution of erythritol and L-threitol are discussed.
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Affiliation(s)
- A J Lopes Jesus
- Department of Chemistry, University of Coimbra, 3004-535, Coimbra, Portugal
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Yu W, Lin Z, Huang Z. Coexistence of Dihydrogen, Blue- and Red-Shifting Hydrogen Bonds in an Ultrasmall System: Valine. Chemphyschem 2006; 7:828-30. [PMID: 16526077 DOI: 10.1002/cphc.200500721] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Wenbo Yu
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei 230026, P. R. China
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23
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Exploration of the full conformational landscapes of gaseous aromatic amino acid phenylalanine: An ab initio study. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2005.10.043] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zhang M, Huang Z, Lin Z. Systematic ab initio studies of the conformers and conformational distribution of gas-phase tyrosine. J Chem Phys 2005; 122:134313. [PMID: 15847471 DOI: 10.1063/1.1869471] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A full structural assignment of the conformers of gaseous tyrosine is presented. A total of 1296 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and optimized at the B3LYP6-311G* level of theory and then subjected to further optimization at the B3LYP6-311++G** level. A total of 76 conformers are found and their dipole moments, rotational constants, and harmonic frequencies are determined. Accurate relative energies are given at the MP26-311G(2df,p)B3LYP6-311++G** level of theory. Characteristic H-bonding types are classified and listed for all the conformers. The four most stable conformers display an intramolecular H bond, COOH...NH(2), and an additional H-bonding interaction between the amino group and pi electron of the aromatic ring. The results further confirm that the global minimum conformations of the aromatic amino acids have the same H-bonding type. Combined with statistical mechanics principles, conformational distributions at various temperatures are computed and the temperatures with which the theoretical results match that of experiments are indicated.
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Affiliation(s)
- Meiling Zhang
- Structure Research Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
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Huang Z, Lin Z. Detailed Ab Initio Studies of the Conformers and Conformational Distributions of Gaseous Tryptophan. J Phys Chem A 2005; 109:2656-9. [PMID: 16833572 DOI: 10.1021/jp0461201] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic and extensive conformational search has been performed to characterize the gas-phase tryptophan structures. A total of 648 unique trial structures were generated by allowing for all combinations of internal single-bond rotamers and were optimized at the DFT/B3LYP/6-311G* level of theory. A total of 45 local minima conformers were found. Further optimization of the 45 conformers with B3LYP and MP2/6-311++G** did not produce meaningful structural change, and accurate geometries, dipole moments, rotational constants, harmonic frequencies, and relative energies were then determined. Combined with statistical mechanics principles, the conformational distributions of gas-phase tryptophan at different temperatures are shown. The results clearly support the conclusion drawn by Compagnon et al. that only one dominant isomer existed in the molecular beam at 85 K and add further evidence that the supersonic jet expansion or embedding helium droplets did not produce an equilibrium distribution.
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Affiliation(s)
- Zhijian Huang
- Structure Research Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
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27
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Jesus AJL, Tomé LIN, Rosado MTS, Leitão MLP, Redinha JS. Conformational study of erythritol and threitol in the gas state by density functional theory calculations. Carbohydr Res 2005; 340:283-91. [PMID: 15639248 DOI: 10.1016/j.carres.2004.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2004] [Revised: 11/26/2004] [Accepted: 11/27/2004] [Indexed: 10/26/2022]
Abstract
Density functional theory calculations using the B3LYP functional and the 6-311++G(d,p) basis set were carried out on the isolated molecules of erythritol and L-threitol. For the meso isomer, a relatively large number of conformers have to be considered to describe the gas state structure. The lowest energy conformer is characterized by the establishment of a strong intramolecular H-bond between the two terminal hydroxyl groups, giving rise to a seven-membered ring and two additional weaker H-bonds between vicinal OH groups. In the case of L-threitol, two conformers are predominant in the gas state, and both are stabilized by the formation of a cyclic system of four intramolecular hydrogen bonds involving all OH groups. The conformational stability in both diastereomers is discussed in terms of the electronic energy and of the Gibbs energy. The weighted mean enthalpy of both diastereomers in the gas state at 298.15 K was obtained from the thermodynamic data and Boltzmann populations of the low-energy conformers.
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Callam CS, Singer SJ, Lowary TL, Hadad CM. Computational analysis of the potential energy surfaces of glycerol in the gas and aqueous phases: effects of level of theory, basis set, and solvation on strongly intramolecularly hydrogen-bonded systems. J Am Chem Soc 2001; 123:11743-54. [PMID: 11716731 DOI: 10.1021/ja011785r] [Citation(s) in RCA: 91] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 126 possible conformations of 1,2,3-propanetriol (glycerol) have been studied by ab initio molecular orbital and density functional theory calculations in the gas and aqueous phases at multiple levels of theory and basis sets. The partial potential energy surface for glycerol as well as an analysis of the conformational properties and hydrogen-bonding trends in both phases have been obtained. In the gas phase at the G2(MP2) and CBS-QB3 levels of theory, the important, low-energy conformers are structures 100 and 95. In the aqueous phase at the SM5.42/HF/6-31G* level of theory, the lowest energy conformers are structures 95 and 46. Boltzmann distributions have been determined from these high-level calculations, and good agreement is observed when these distributions are compared to the available experimental data. These calculations indicate that the enthalpic and entropic contributions to the Gibbs free energy are important for an accurate determination of the conformational and energetic preferences of glycerol. Different levels of theory and basis sets were used in order to understand the effects of nonbonded interactions (i.e., intramolecular hydrogen bonding). The efficiency of basis set and level of theory in dealing with the issue of intramolecular hydrogen bonding and reproducing the correct energetic and geometrical trends is discussed, especially with relevance to practical computational methods for larger polyhydroxylated compounds, such as oligosaccharides.
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Affiliation(s)
- C S Callam
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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