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Zhao J, Yu P, Dong T, Wu Y, Yang F, Wang J. Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy. Commun Chem 2024; 7:82. [PMID: 38605209 PMCID: PMC11009226 DOI: 10.1038/s42004-024-01170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanzhou Wu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Yang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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2
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Complex investigation of H-bond in Water-N-methylacetamide system: Volumetric properties, DFT, IR, MD analysis. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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3
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Laity PR, Holland C. Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020551. [PMID: 35056868 PMCID: PMC8781151 DOI: 10.3390/molecules27020551] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 02/05/2023]
Abstract
The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.
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Biswas S, Mallik BS. Probing the vibrational dynamics of amide bands of N-methylformamide, N, N-dimethylacetamide, and N-methylacetamide in water. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.113001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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5
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Di Gioacchino M, Bruni F, Ricci MA. N-Methylacetamide Aqueous Solutions: A Neutron Diffraction Study. J Phys Chem B 2019; 123:1808-1814. [PMID: 30739453 DOI: 10.1021/acs.jpcb.9b00246] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydration of N-methylacetamide (NMA) in solution has been determined by neutron diffraction with isotopic Hydrogen/Deuterium substitution (NDIS), augmented by Monte Carlo simulation. This study is representative of the hydration of the peptide bonds characteristic of proteins and might shed light on aggregation phenomena in intrinsically disordered proteins. It is found that NMA forms hydrogen bonds with water at both O and H peptide sites, although of different lengths and strengths. The comparison with the case of tripeptide glutathione evidences differences in both hydration and propensity for aggregation.
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Affiliation(s)
- Michael Di Gioacchino
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Fabio Bruni
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
| | - Maria Antonietta Ricci
- Dipartimento di Scienze , Universitá degli Studi Roma Tre , via della Vasca Navale 84 , 00146 Roma , Italy
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6
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Kang NS, Kang YK. Assessment of CCSD(T), MP2, and DFT methods for the calculations of structures and interaction energies of the peptide backbone with water molecules. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.08.063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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7
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Petelski AN, Peruchena NM, Pamies SC, Sosa GL. Insights into the self-assembly steps of cyanuric acid toward rosette motifs: a DFT study. J Mol Model 2017; 23:263. [PMID: 28808800 DOI: 10.1007/s00894-017-3428-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 07/19/2017] [Indexed: 11/28/2022]
Abstract
The nature of non-covalent interactions in self-assembling systems is a topic that has aroused great attention in literature. In this field, the 1,3,5-triazinane-2,4,6-trione or cyanuric acid (CA) is one of the most widely used molecules to formulate self-assembled materials or monolayers. In the present work, a variety of molecular aggregates of CA are examined using three different DFT functionals (B3LYP, B3LYP-D3, and ω-B97XD) in the framework of the quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis. Herein, a step by step aggregation path is proposed and the origin of cooperative effects is also examined. It is shown that a greater cooperativity is not always associated with a greater binding energy, and the greatest cooperative effect occurs with highly directional hydrogen bonds. The intramolecular charge transfers play a key role in this effect. Graphical abstract The noncovalent interactions in cyanuric acid supramolecules were analyzed. The calculations provide insights into the self-assembly steps from dimers to rosette-like motif. The complexes with collinear hydrogen bonds show positive cooperativity, while in the arrangement with double hydrogen bonds the cooperative effect is essentially zero.
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Affiliation(s)
- Andre N Petelski
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina.,Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina
| | - Nélida M Peruchena
- Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina. .,Laboratorio de Estructura Molecular y Propiedades (LEMYP), Área de Química Física, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avenida Libertad 5460 (3400), Corrientes, Argentina.
| | - Silvana C Pamies
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina
| | - Gladis L Sosa
- Grupo de Investigación en Química Teórica y Experimental (QuiTEx), Departamento de Ingeniería Química, Facultad Regional Resistencia, Universidad Tecnológica Nacional, French 414 (H3500CHJ), Resistencia, Chaco, Argentina. .,Instituto de Química Básica y Aplicada del Nordeste Argentino (IQUIBA-NEA), UNNE-CONICET, Avenida Libertad 5460 (3400), Corrientes, Argentina.
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8
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Ireta J. Polyalanine α-helix microsolvation: assessing the energy of the peptide desolvation penalty with density functional theory. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1981-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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9
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Sun CL, Ding F, Ding YL, Li Y. The effect of water molecules upon the hydrogen-bonding cooperativity of three-stranded antiparallel β-sheet models. RSC Adv 2014. [DOI: 10.1039/c3ra45892j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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10
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Angelina EL, Andujar SA, Tosso RD, Enriz RD, Peruchena NM. Non-covalent interactions in receptor-ligand complexes. A study based on the electron charge density. J PHYS ORG CHEM 2013. [DOI: 10.1002/poc.3250] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Emilio L. Angelina
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Sebastián A. Andujar
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Rodrigo D. Tosso
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Ricardo D. Enriz
- Departamento de Química, Facultad de Química, Bioquímica y Farmacia; Universidad Nacional de San Luis; Chacabuco 917, San Luis (5700) San Luis Argentina
- Instituto Multidiciplinario de Investigaciones Biológicas (IMIBIO-SL, CONICET); Chacabuco y Pedrenera (5700) San Luis Argentina
| | - Nélida M. Peruchena
- Lab. Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Av. Libertad 5470 Corrientes 3400 Argentina
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11
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Beck JP, Gaigeot MP, Lisy JM. Anharmonic vibrations of N-H in Cl(-)(N-methylacetamide)1(H2O)(0-2)Ar2 cluster ions. Combined IRPD experiments and BOMD simulations. Phys Chem Chem Phys 2013; 15:16736-45. [PMID: 23986352 DOI: 10.1039/c3cp52418c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Infrared Predissociation (IRPD) spectra of Cl(-)(NMA)1(H2O)0-2Ar2 combined with Born-Oppenheimer Molecular Dynamics (BOMD) IR spectra have been acquired, providing the structure and dynamics of these systems. We show that the chloride ion is bound to the hydrogen of the amide N-H group, forming a strong ionic hydrogen bond, weakening the N-H stretch, and shifting it to lower frequency. The presence of water molecules enhances the ionic hydrogen bond by binding to the amide carbonyl oxygen of NMA and shifts the N-H stretch further to lower frequency. The BOMD IR spectra can recapture all, but about 100 cm(-1), of the 600 to 700 cm(-1) shifts due to the strong N-H stretch anharmonicities observed in experiments. This residual error was found to be due to the lack of zero point energy in the classical treatment of motion in the BOMD method.
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Affiliation(s)
- Jordan P Beck
- Concordia University Wisconsin, 12800 N. Lakeshore Drive, Mequon, Wisconsin 53097, USA
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12
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Varfolomeev MA, Klimovitskii AE, Abaidullina DI, Madzhidov TI, Solomonov BN. "Additive" cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 91:75-82. [PMID: 22366617 DOI: 10.1016/j.saa.2012.01.061] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 05/31/2023]
Abstract
Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.
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Affiliation(s)
- Mikhail A Varfolomeev
- Department of Physical Chemistry, Chemical Institute, Kazan (Volga region) Federal University, Kremlevskaya 18, 420008 Kazan, Russia.
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13
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Marianski M, Dannenberg JJ. Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory. J Phys Chem B 2012; 116:1437-45. [PMID: 22201227 DOI: 10.1021/jp209177u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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14
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Kobko N, Marianski M, Asensio A, Wieczorek R, Dannenberg JJ. A Density Functional Theory Evaluation of Hydrophobic Solvation: Ne, Ar and Kr in a 50-Water Cluster. Implications for the Hydrophobic Effect. COMPUT THEOR CHEM 2011; 990:214-221. [PMID: 22666658 DOI: 10.1016/j.comptc.2011.11.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
The physical explanation for the hydrophobic effect has been the subject of disagreement. Physical organic chemists tend to use a explanation related to pressure, while many biochemists prefer an explanation that involves decreased entropy of the aqueous solvent. We present DFT calculations at the B3LYP/6-31G(d,p) and X3LYP/6-31G(d,p) levels on the solvation of three noble gases (Ne, Ar, and Kr) in clusters of 50 waters. Vibrational analyses show no substantial decreases in the vibrational entropies of the waters in any of the three clusters. The observed positive free energies of transfer from the gas phase or from nonpolar solvents to water appear to be due to the work needed to make a suitable hole in the aqueous solvent. We distinguish between hydrophobic solvations (explicitly studied here) and the hydrophobic effect that occurs when a solute (or transition state) can decrease its volume through conformational change (which is not possible for the noble gases).
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Affiliation(s)
- Nadya Kobko
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, 695 Park Avenue, New York NY 10065
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15
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Chen YF, Dannenberg JJ. The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials. J Comput Chem 2011; 32:2890-5. [PMID: 21717481 DOI: 10.1002/jcc.21870] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 05/01/2011] [Accepted: 05/23/2011] [Indexed: 01/27/2023]
Abstract
We report density functional theory calculations at the B3LYP/D95(d,p) level on several different cyclic H-bonding dimers, where the monomers of each are connected by a pair of N-H···O=C H-bonding interactions, and the H-bonding donors and acceptors on each monomer are separated by polarizable spacers. Depending on the structures, the individual H-bonds vary in strength (enthalpy) by over a factor of four, from 2.41 to 10.99 kcal/mol. We attribute most of the variation in interaction energies to differences in the extent of polarization due to each of the H-bonds, which can either combine constructively or destructively. The dipole-dipole interactions between the pair of H-bonds also contribute somewhat to the relative stabilities. The relevance of these results to the design of self-assembling materials is discussed.
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Affiliation(s)
- Yung-Fou Chen
- Department of Chemistry, Hunter College and the Graduate School, City University of New York, 695 Park Avenue, New York, New York 10065, USA
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16
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Angelina EL, Peruchena NM. Strength and Nature of Hydrogen Bonding Interactions in Mono- and Di-Hydrated Formamide Complexes. J Phys Chem A 2011; 115:4701-10. [DOI: 10.1021/jp1105168] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Emilio L. Angelina
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física, Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Avda. Libertad 5460, (3400) Corrientes, Argentina
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17
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Varfolomeev MA, Abaidullina DI, Gainutdinova AZ, Solomonov BN. FTIR study of H-bonds cooperativity in complexes of 1,2-dihydroxybenzene with proton acceptors in aprotic solvents: influence of the intramolecular hydrogen bond. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2010; 77:965-972. [PMID: 20863750 DOI: 10.1016/j.saa.2010.08.032] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/26/2010] [Accepted: 08/19/2010] [Indexed: 05/29/2023]
Abstract
FTIR spectroscopic study of hydrogen bonding of 1,2-dihydroxybenzene (catechol) with proton acceptors has been carried out. The influence of intramolecular and intermolecular hydrogen bonds on the strengths of each other in complexes of 1,2-dihydroxybenzene with various proton acceptors has been analyzed. It was shown that intramolecular hydrogen bond is strengthened when 1,2-dihydroxybenzene interacts with bases (ethers, amines, nitriles, etc.) in inert solvents. The contribution of the cooperativity of intramolecular hydrogen bonds in the frequency of stretching vibrations of O-H groups linearly depends on the proton acceptor ability of the bases. The solvent effect on hydrogen bond cooperativity in 1,2-dihydroxybenzene-base complexes has been studied. The approach to determine the influence of cooperative effects on the formation of intermolecular complexes with 1,2-dihydroxybenzene is proposed. It was shown that the strength of intramolecular hydrogen bonds in the complexes of 1,2-dihydroxybenzene with bases due to cooperativity of interactions increases by 30-70%, and the strength of intermolecular hydrogen bond by 7-22%.
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18
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Nagaraju M, Narahari Sastry G. Effect of alkyl substitution on H-bond strength of substituted amide-alcohol complexes. J Mol Model 2010; 17:1801-16. [DOI: 10.1007/s00894-010-0886-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Accepted: 10/20/2010] [Indexed: 11/28/2022]
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19
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Baldwin RL. Desolvation Penalty for Burying Hydrogen-Bonded Peptide Groups in Protein Folding. J Phys Chem B 2010; 114:16223-7. [DOI: 10.1021/jp107111f] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Robert L. Baldwin
- Biochemistry Department, Beckman Center, Stanford University Medical Center, Stanford, California 94305-5307, United States
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Deshmukh MM, Gadre SR. Estimation of N-H...O=C intramolecular hydrogen bond energy in polypeptides. J Phys Chem A 2009; 113:7927-32. [PMID: 19496581 DOI: 10.1021/jp9031207] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The previously proposed molecular tailoring approached (MTA) [Deshmukh, M. M.; Gadre, S. R.; Bartolotti, L. J. J. Phys. Chem. A 2006, 110, 12519] for the estimation of intramolecular O-H...O hydrogen bond energy is extended to that for the N-H...O=C bond within polypeptides. The methodology is initially tested on a tetrapeptide containing two types of N-H...O=C hydrogen bonds and is found to distinguish between them. The estimated values are in good agreement with the trends predicted by the geometrical parameters. Furthermore, this methodology is applied to partially as well as fully substituted, capped polyglycines that contain five glycine residues (acetyl-(gly)(5)-NH(2)) to check the effect of substituents on the energetics of hydrogen bonds. The estimated N-H...O=C bond energy values lie in the range of 4-6 kcal/mol. These estimated values are not only in concurrence with the geometric parameters but also able to reflect the subtle effects of substituents for the substituted polypeptides studied in the present work.
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Affiliation(s)
- Milind M Deshmukh
- Homi Bhabha Centre for Science Education, Tata Institute of Fundamental Research, V. N. Purav Marg, Mankhurd, Mumbai-400 088, India.
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Mantz YA, Branduardi D, Bussi G, Parrinello M. Ensemble of Transition State Structures for the Cis−Trans Isomerization of N-Methylacetamide. J Phys Chem B 2009; 113:12521-9. [DOI: 10.1021/jp8106556] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yves A. Mantz
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Davide Branduardi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Giovanni Bussi
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Michele Parrinello
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zurich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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Tang Z, Zhou X, Chen X, Lin H. Optimized structures and vibration frequencies of the ether–water complex: a DFT and FTIR study. Struct Chem 2009. [DOI: 10.1007/s11224-009-9488-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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23
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Estimation on the intramolecular 10-membered ring NH···OC hydrogen-bonding energies in glycine and alanine peptides. J Comput Chem 2009; 30:1251-60. [DOI: 10.1002/jcc.21141] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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24
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Tsai MIH, Xu Y, Dannenberg JJ. Ramachandran revisited. DFT energy surfaces of diastereomeric trialanine peptides in the gas phase and aqueous solution. J Phys Chem B 2009; 113:309-18. [PMID: 19072621 DOI: 10.1021/jp8063646] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report DFT calculations at the B3LYP/D95(d,p) level on the gas phase, aqueous solvation and solvated energies as functions of the central psi and phi dihedral angles (in steps of 5 degrees each) of acetyl-(L)Ala-(L)Ala-(L)Ala-NH(2) (3AL) and its diastereomer, acetyl-(L)Ala-(D)Ala-(L)Ala-NH(2) (3AD). In addition to structures without internal H-bonds (C(5) interactions are neglected), many (95) structures containing internal H-bonds were completely optimized. The only minima for non-H-bonding structures in the gas phase correspond to extended beta-strands for both diastereomers. Some (but not all) structures with internal H-bonds are more stable than those without them. The energy landscapes for the solvated species show multiple minima for the non-H-bonding species and a single minimum for the H-bonding species (3(10)-helix), suggesting that the equilibrium conformational mixture in water be composed of the extended beta-strand, polyproline II, 3(10)-helix, and alpha-helix-like (with no H-bonds) conformations which are all within about 1 kcal/mol of each other. Most H-bonding structures are destabilized relative to the non-H-bonding structures in aqueous solution, but some with large dipole moments are not. The large dipole moment of the alpha-helix-like conformation leads to its increased stability in water (vs the gas phase). Significant qualitative and quantitative differences are reported for the energy landscapes of the two diastereomers when one is compared with the mirror image of the other landscape (particularly in the beta-turn region), suggesting that the differences in the energies of the unfolded peptides need to be considered when considering the stabilities of folded peptides and proteins with single amino acid mutations.
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Affiliation(s)
- Midas I-Hsien Tsai
- Department of Chemistry, City University of New York, New York 10065, USA
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25
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Scheiner S, Kar T. Spectroscopic and Structural Signature of the CH−O Hydrogen Bond. J Phys Chem A 2008; 112:11854-60. [DOI: 10.1021/jp806984g] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
| | - Tapas Kar
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300
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26
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Shirota H, Ushiyama H. Hydrogen-Bonding Dynamics in Aqueous Solutions of Amides and Acids: Monomer, Dimer, Trimer, and Polymer. J Phys Chem B 2008; 112:13542-51. [DOI: 10.1021/jp803627u] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hideaki Shirota
- Division of Nanoscience, Graduate School of Advanced Integration Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan, and Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hiroshi Ushiyama
- Division of Nanoscience, Graduate School of Advanced Integration Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan, and Department of Chemical System Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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27
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Solomonov BN, Varfolomeev MA, Abaidullina DI. Solvent effect on H-bond cooperativity factors in ternary complexes of methanol, octan-1-ol, 2,2,2-trifluoroethanol with some bases. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2008; 69:985-90. [PMID: 17627874 DOI: 10.1016/j.saa.2007.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2007] [Revised: 05/18/2007] [Accepted: 06/04/2007] [Indexed: 05/16/2023]
Abstract
Cooperative hydrogen bonds in ternary complexes (ROH)(2)...B (ROH-alcohols; B-bases) formed in pure bases (B) and solutions in n-hexane, carbon tetrachloride, benzene and 1,2-dichloroethane were studied by FTIR spectroscopy. Based on the observations, the authors were able to propose an original method of evaluating solvent effects on cooperativity factors in the complexes. Frequencies of cooperative hydrogen bonds OH...B (nu(b)) were determined for ternary complexes of pyridine with aliphatic alcohols (methanol, octan-1-ol) and for 2,2,2-trifluoroethanol with three different bases (acetonitrile, diethyl ether, tetrahydrofuran). The solvent shifts of nu(b) were found to correlate with an empirical thermochemical parameter of the solvent, S(VW). The cooperativity factors were determined for the complexes (ROH)(2)...B in all studied media. It has been found that the cooperativity factors are almost independent of the solvent. In addition, a method was proposed of estimating the frequencies and cooperativity factors for ternary complexes (ROH)(2)...B in the gas phase. It has been found that in gas phase the cooperativity factors are practically the same as in condensed media.
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Affiliation(s)
- Boris N Solomonov
- Chemical Institute, Kazan State University, Kremlevskaya 18, Kazan 420008, Russia.
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28
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Panuszko A, Gojło E, Zielkiewicz J, Śmiechowski M, Krakowiak J, Stangret J. Hydration of Simple Amides. FTIR Spectra of HDO and Theoretical Studies. J Phys Chem B 2008; 112:2483-93. [PMID: 18247601 DOI: 10.1021/jp7099509] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Aneta Panuszko
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Emilia Gojło
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Jan Zielkiewicz
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Maciej Śmiechowski
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Joanna Krakowiak
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
| | - Janusz Stangret
- Department of Physical Chemistry, Chemical Faculty, Gdańsk University of Technology, Narutowicza 11/12, 80-952 Gdańsk, Poland
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29
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Wieczorek R, Dannenberg JJ. Amide I Vibrational Frequencies of α-Helical Peptides Based upon ONIOM and Density Functional Theory (DFT) Studies. J Phys Chem B 2008; 112:1320-8. [DOI: 10.1021/jp077527j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert Wieczorek
- Department of Chemistry, City University of New YorkHunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, and Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, Wroclaw, Poland
| | - J. J. Dannenberg
- Department of Chemistry, City University of New YorkHunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, and Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, Wroclaw, Poland
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30
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Urban JJ, Tillman BG, Cronin WA. Fluoroolefins as peptide mimetics: a computational study of structure, charge distribution, hydration, and hydrogen bonding. J Phys Chem A 2007; 110:11120-9. [PMID: 16986846 DOI: 10.1021/jp062881n] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The design of peptide mimetic compounds is greatly facilitated by the identification of functionalities that can act as peptide replacements. The fluoroalkene moiety has recently been employed for that purpose. The purpose of this work is to characterize prototypical fluoroalkenes (fluoroethylene and 2-fluoro-2-butene) with respect to key properties of peptides (amides) including structure, charge distribution, hydration, and hydrogen bonding. The results are compared to those obtained for model peptides (formamide, N-methylacetamide). Calculations have been carried out at the MP2 and B3LYP levels of theory with the 6-311++G(2d,p) and 6-311++G(2d,2p) basis sets. The results suggest that the fluoroalkene is similar in steric requirements to a peptide bond but that there is less charge separation. Calculations of the hydration free energies with the PCM bulk continuum solvent model indicate that the fluoroalkene has much smaller hydration free energies than an amide but that the difference in solvation free energy for cis and trans isomers is comparable. In studies of complexes with water molecules, the fluoroalkene is found to engage in interactions that are analogous to backbone hydrogen-bonding interactions that govern many properties of natural peptides and proteins but with smaller interaction energies. In addition, key structural differences are noted when the fluoroalkene is playing the role of hydrogen-bond acceptor which may have implications in binding, aggregation, and conformational preferences in fluoroalkene peptidomimetics. The issue of cooperativity in hydrogen-bonding interactions in complexes with multiple waters has also been investigated. The fluoroalkene is found to exhibit cooperative effects that mirror those of the peptide but are smaller in magnitude. Thus, pairwise addivitity of interactions appears to more adequately describe the fluoroalkenes than the peptides they are intended to mimic.
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Affiliation(s)
- Joseph J Urban
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis, Maryland 21402, USA.
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31
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Miller DJ, Lisy JM. Modeling competitive interactions in proteins: vibrational spectroscopy of M+(n-methylacetamide)1(H2O)n=0-3, M=Na and K, in the 3 microm region. J Phys Chem A 2007; 111:12409-16. [PMID: 17696509 DOI: 10.1021/jp073521i] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To properly understand the preferred structures and biological properties of proteins, it is important to understand how they are influenced by their immediate environment. Competitive intrapeptide, peptide...water, ion...water, and ion...peptide interactions, such as hydrogen bonding, play a key role in determining the structures, properties, and functionality of proteins. The primary types of hydrogen bonding involving proteins are intramolecular amide...amide (N-H...O=C) and intermolecular amide...water (O-H...O=C and H-O...H-N). n-Methylacetamide (NMA) is a convenient model for investigating these competitive interactions. An analysis of the IR photodissociation (IRPD) spectra of M+(n-methylacetamide)1(H2O)n=0-3 (M=Na and K) in the O-H and N-H spectral regions is presented. Ab initio calculations (MP2/cc-pVDZ) are used as a guide in identifying both the type and location of hydrogen bonds present. In larger clusters, where several structural isomers may be present in the molecular beam, ab initio calculations are also used to suggest assignments for the observed spectral features. The results presented offer insight to the nature of ion...NMA interactions in an aqueous environment and reveal how different ion...ligand pairwise interactions direct the extent of water...water and water...NMA hydrogen bonding observed.
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Affiliation(s)
- Dorothy J Miller
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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32
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Kötting C, Kallenbach A, Suveyzdis Y, Eichholz C, Gerwert K. Surface change of Ras enabling effector binding monitored in real time at atomic resolution. Chembiochem 2007; 8:781-7. [PMID: 17385754 DOI: 10.1002/cbic.200600552] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ras, the prototype of the Ras superfamily, acts as a molecular switch for cell growth. External growth signals induce a GDP-to-GTP exchange. This modifies the Ras surface (Ras(on)GTP) and enables effector binding, which then activates signal-transduction pathways. GTP hydrolysis, catalysed by Ras and GAP, returns the signal to "off" (Ras(off)GDP). Oncogenic mutations in Ras prevent this hydrolysis, and thereby cause uncontrolled cell growth. In the Ras(off)-to-Ras(on) transition, the Ras surface is changed by a movement of the switch I loop that controls effector binding. We monitored this surface change at atomic resolution in real time by time-resolved FTIR (trFTIR) spectroscopy. In the transition from Ras(off) to Ras(on) a GTP-bound intermediate is now identified, in which effector binding is still prevented (Ras(off)GTP). The loop movement from Ras(off)GTP to Ras(on)GTP was directly monitored by the C=O vibration of Thr35. The structural change creates a binding site with a rate constant of 5 s(-1) at 260 K. A small molecule that shifted the equilibrium from the Ras(on)GTP state towards the Ras(off)GTP state would prevent effector binding, even if hydrolysis were blocked by oncogenic mutations. We present a spectroscopic fingerprint of both states that can be used as an assay in drug screening for such small molecules.
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Affiliation(s)
- Carsten Kötting
- Lehrstuhl für Biophysik, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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33
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Baldwin RL. Energetics of protein folding. J Mol Biol 2007; 371:283-301. [PMID: 17582437 DOI: 10.1016/j.jmb.2007.05.078] [Citation(s) in RCA: 211] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 05/23/2007] [Accepted: 05/25/2007] [Indexed: 10/23/2022]
Abstract
The energetics of protein folding determine the 3D structure of a folded protein. Knowledge of the energetics is needed to predict the 3D structure from the amino acid sequence or to modify the structure by protein engineering. Recent developments are discussed: major factors are reviewed and auxiliary factors are discussed briefly. Major factors include the hydrophobic factor (burial of non-polar surface area) and van der Waals interactions together with peptide hydrogen bonds and peptide solvation. The long-standing model for the hydrophobic factor (free energy change proportional to buried non-polar surface area) is contrasted with the packing-desolvation model and the approximate nature of the proportionality between free energy and apolar surface area is discussed. Recent energetic studies of forming peptide hydrogen bonds (gas phase) are reviewed together with studies of peptide solvation in solution. Closer agreement is achieved between the 1995 values for protein unfolding enthalpies in vacuum given by Lazaridis-Archontis-Karplus and Makhatadze-Privalov when the solvation enthalpy of the peptide group is taken from electrostatic calculations. Auxiliary factors in folding energetics include salt bridges and side-chain hydrogen bonds, disulfide bridges, and propensities to form alpha-helices and beta-structure. Backbone conformational entropy is a major energetic factor which is discussed only briefly for lack of knowledge.
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Affiliation(s)
- Robert L Baldwin
- Department of Biochemistry, Beckman Center, Stanford University Medical Center, Stanford, CA 94305, USA.
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34
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Salvador P, Asensio A, Dannenberg JJ. The Effect of Aqueous Solvation upon α-Helix Formation for Polyalanines. J Phys Chem B 2007; 111:7462-6. [PMID: 17552560 DOI: 10.1021/jp071899a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The incremental free energies of aqueous solution for acetyl(ala)NNH2 in its extended unfolded and alpha-helical conformations are compared using the SM5.2 solvation method of Cramer and Truhlar. A combination of density functional theory (DFT) at the B3LYP/D95(d,p) and AM1 has been employed using the ONIOM method. The incremental solvation energies of alpha-helical structures are very similar for both ONIOM and AM1 optimized structures as these structures do not significantly change upon solution. However, the conformations of the unfolded peptides change from extended beta-strand to polyproline II conformations upon aqueous solution. The incremental solvation free energy per residue of the polyproline II structure is about 2 kcal/mol/residue greater than that for the alpha-helix, representing an upper limit for the difference between the solvation energies. However, most of this difference disappears when the energy required to distort the optimized gas-phase extended beta-strand structure to the optimized polyproline II solution structure is included in the analysis, leaving an estimated difference in incremental solvation free energy of 0.3-0.5 kcal/mol favoring the unfolded structure. The solution structure sacrifices the stability derived from the intramolecular C5 H-bonds for more favorable interactions with the aqueous solvent.
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Affiliation(s)
- Pedro Salvador
- Department of Chemistry, City University of New York, Hunter College and the Graduate School, New York, New York 10021, USA
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