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Kříž P, Beránek J, Spiwok V. Free Energy Differences from Molecular Simulations: Exact Confidence Intervals from Transition Counts. J Chem Theory Comput 2023; 19:2102-2108. [PMID: 36926862 PMCID: PMC10100533 DOI: 10.1021/acs.jctc.2c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Here, we demonstrate a method to estimate the uncertainty (confidence intervals and standard errors) of free energy differences calculated by molecular simulations. The widths of confidence intervals and standard errors can be calculated solely from temperature and the number of transitions between states. Uncertainty (95% confidence interval) lower than ±1 kcal/mol can be achieved by a simulation with four forward and four reverse transitions. For a two-state Markovian system, the confidence interval is exact, regardless the number of transitions.
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Affiliation(s)
- Pavel Kříž
- Faculty of Mathematics and Physics, Charles University, 186 75 Prague, Czech Republic
| | - Jan Beránek
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
| | - Vojtěch Spiwok
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, 166 28 Prague, Czech Republic
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Nishida Y, Aono R, Dohi H, Ding W, Uzawa H. 1H-NMR Karplus Analysis of Molecular Conformations of Glycerol under Different Solvent Conditions: A Consistent Rotational Isomerism in the Backbone Governed by Glycerol/Water Interactions. Int J Mol Sci 2023; 24:ijms24032766. [PMID: 36769086 PMCID: PMC9916874 DOI: 10.3390/ijms24032766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Glycerol is a symmetrical, small biomolecule with high flexibility in molecular conformations. Using a 1H-NMR spectroscopic Karplus analysis in our way, we analyzed a rotational isomerism in the glycero backbone which generates three kinds of staggered conformers, namely gt (gauche-trans), gg (gauche-gauche), and tg (trans-gauche), at each of sn-1,2 and sn-2,3 positions. The Karplus analysis has disclosed that the three rotamers are consistently equilibrated in water keeping the relation of 'gt:gg:tg = 50:30:20 (%)' at a wide range of concentrations (5 mM~540 mM). The observed relation means that glycerol in water favors those symmetric conformers placing 1,2,3-triol groups in a gauche/gauche geometry. We have found also that the rotational isomerism is remarkably changed when the solvent is replaced with DMSO-d6 or dimethylformamide (DMF-d7). In these solvents, glycerol gives a relation of 'gt:gg:tg = 40:30:30 (%)', which means that a remarkable shift occurs in the equilibrium between gt and tg conformers. By this shift, glycerol turns to also take non-symmetric conformers orienting one of the two vicinal diols in an antiperiplanar geometry.
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Affiliation(s)
- Yoshihiro Nishida
- Molecular Chirality Research Center, Department of Applied Biological Chemistry, Institute of Environmental Horticulture, Chiba University, Matsudo 271-8510, Japan
- Correspondence:
| | - Reina Aono
- Molecular Chirality Research Center, Department of Applied Biological Chemistry, Institute of Environmental Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Hirofumi Dohi
- Molecular Chirality Research Center, Department of Applied Biological Chemistry, Institute of Environmental Horticulture, Chiba University, Matsudo 271-8510, Japan
| | - Wuxiao Ding
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hirotaka Uzawa
- Nanomaterials Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba 305-8565, Japan
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Nagy PI. Competing intramolecular vs. intermolecular hydrogen bonds in solution. Int J Mol Sci 2014; 15:19562-633. [PMID: 25353178 PMCID: PMC4264129 DOI: 10.3390/ijms151119562] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/17/2014] [Accepted: 10/13/2014] [Indexed: 11/17/2022] Open
Abstract
A hydrogen bond for a local-minimum-energy structure can be identified according to the definition of the International Union of Pure and Applied Chemistry (IUPAC recommendation 2011) or by finding a special bond critical point on the density map of the structure in the framework of the atoms-in-molecules theory. Nonetheless, a given structural conformation may be simply favored by electrostatic interactions. The present review surveys the in-solution competition of the conformations with intramolecular vs. intermolecular hydrogen bonds for different types of small organic molecules. In their most stable gas-phase structure, an intramolecular hydrogen bond is possible. In a protic solution, the intramolecular hydrogen bond may disrupt in favor of two solute-solvent intermolecular hydrogen bonds. The balance of the increased internal energy and the stabilizing effect of the solute-solvent interactions regulates the new conformer composition in the liquid phase. The review additionally considers the solvent effects on the stability of simple dimeric systems as revealed from molecular dynamics simulations or on the basis of the calculated potential of mean force curves. Finally, studies of the solvent effects on the type of the intermolecular hydrogen bond (neutral or ionic) in acid-base complexes have been surveyed.
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Affiliation(s)
- Peter I Nagy
- Center for Drug Design and Development, the University of Toledo, Toledo, OH 43606-3390, USA.
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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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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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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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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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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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Yunda NG, Lagodzinskaya GV, Kazakov AI, Korolev AM, Rubtsov YI, Manelis GB, Eremenko LT. Nitration equilibrium in the glycerol-aqueous-nitric-acid system 3. PMR parameters, conformational structure, and main properties of glycerol and its nitrates. Russ Chem Bull 1991. [DOI: 10.1007/bf00965425] [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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Van Alsenoy C, Klimkowski V, Ewbank J, Schäfer L. Ab initio studies of structural features not easily amenable to experiment. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0166-1280(85)80055-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Van Den Enden L, Van Alsenoy C, Scarsdale J, Schäfer L. Ab initio studies of structural features not easily amenable to experiment. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0166-1280(83)80197-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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