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Ding G, Yang B, Chen K, Wang H, Chen J, Mei Q. Enhanced Self-Assembly and Spontaneous Separation for Ultrathin, Air‒Floating Graphene Macrofilms and their Application in Ultrasensitive In-Site Growth Sensors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2408550. [PMID: 39161077 DOI: 10.1002/adma.202408550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 07/28/2024] [Indexed: 08/21/2024]
Abstract
Self-assembled graphene films at air-liquid interface have great potential for multiple applications. However, the large size and ultrathin thickness for graphene-based films are hardly achieved simultaneously because of poor assembly ability of graphene oxide (GO) and cautious film transfer process (FTP). Herein, the ethanol-based binary solution with supramolecular clusters and weak polarity is introduced to enhance the assembly performance of GO. In this regime, GO film is formed within 52 s, and its formation temperature can be as low as -20 °C. More importantly, the attractive force between the formed GO film and this binary solution is 62% lower than that between GO film and traditional aqueous solution. On this basis, for the first time a spontaneous separation of the self-assembled GO film from solution is reported, and the air‒floating graphene films (AGFs) with nanoscale thickness and centimeter-scale diameter are prepared without FTP. By means of this separation behavior, the in situ growth AGFs sensors are fabricated, and they express fast response and ultrahigh sensitivity to imperceptible change in temperature and disturbances that are hardly recognized by common sensors. Therefore, a new accessible strategy is demonstrated to prepare ultrathin graphene macrofilms, which can be the excellent candidates for multifunctional, ultrasensitive sensors.
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Affiliation(s)
- Guomin Ding
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Bowen Yang
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Kun Chen
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Hong Wang
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Junlei Chen
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
| | - Qilin Mei
- School of Materials Science and Engineering, Wuhan University of Technology, Wuhan, 430070, P. R. China
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2
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The Hydrophobic Effect Studied by Using Interacting Colloidal Suspensions. Int J Mol Sci 2023; 24:ijms24032003. [PMID: 36768326 PMCID: PMC9916416 DOI: 10.3390/ijms24032003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/14/2023] [Accepted: 01/17/2023] [Indexed: 01/21/2023] Open
Abstract
Interactions between nanoparticles (NPs) determine their self-organization and dynamic processes. In these systems, a quantitative description of the interparticle forces is complicated by the presence of the hydrophobic effect (HE), treatable only qualitatively, and due to the competition between the hydrophobic and hydrophilic forces. Recently, instead, a sort of crossover of HE from hydrophilic to hydrophobic has been experimentally observed on a local scale, by increasing the temperature, in pure confined water and studying the occurrence of this crossover in different water-methanol solutions. Starting from these results, we then considered the idea of studying this process in different nanoparticle solutions. By using photon correlation spectroscopy (PCS) experiments on dendrimer with OH terminal groups (dissolved in water and methanol, respectively), we show the existence of this hydrophobic-hydrophilic crossover with a well defined temperature and nanoparticle volume fraction dependence. In this frame, we have used the mode coupling theory extended model to evaluate the measured time-dependent density correlation functions (ISFs). In this context we will, therefore, show how the measured spectra are strongly dependent on the specificity of the interactions between the particles in solution. The observed transition demonstrates that just the HE, depending sensitively on the system thermodynamics, determines the hydrophobic and hydrophilic interaction properties of the studied nanostructures surface.
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3
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Ghanghas R, Vasudevan S. Geometries of hydrogen bonds in water-ethanol mixtures from ab initio molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:23570-23577. [PMID: 36129380 DOI: 10.1039/d2cp01238c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We outline a simple procedure to determine the geometry of hydrogen bonds between different molecular species in binary mixtures from ab initio molecular dynamics (AIMD) trajectories. Here we determine the geometry of the hydrogen bonds arising from intermolecular OH⋯O interactions between different H-bonded pairs, water-water, ethanol-ethanol and water-ethanol in water-alcohol mixtures at different compositions by plotting the intermolecular non-bonded OH⋯O and O⋯O distances, and the ∠HO⋯O (θ) angles for each of the possible pairs in the ensemble. Two regions separate out in each of the scatter-plots; the one with short OH⋯O and O⋯O intermolecular distances and almost linear ∠HO⋯O angles may be identified as the region where the intermolecular OH⋯O geometry would be favorable for hydrogen bonding. Using the different geometric criteria for each of the three possible H-bonded pairs we estimate the average number of water and ethanol molecules that are hydrogen bonded to a water molecule, and to an ethanol molecule, respectively, at different mole fractions of the mixture. We validate the results from values of the chemical shift of the two OH resonances (water and ethanol) in the proton NMR spectra of the mixtures at different concentrations as these values are known to be sensitive to the local chemical environment of the resonating nuclei.
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Affiliation(s)
- Ritu Ghanghas
- Department of Inorganic and Physical Chemistry, IISc, Bangalore, India.
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4
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Nagasaka M, Bouvier M, Yuzawa H, Kosugi N. Hydrophobic Cluster Formation in Aqueous Ethanol Solutions Probed by Soft X-ray Absorption Spectroscopy. J Phys Chem B 2022; 126:4948-4955. [PMID: 35748647 DOI: 10.1021/acs.jpcb.2c02990] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydrophobic cluster structures in aqueous ethanol solutions at different concentrations have been investigated by soft X-ray absorption spectroscopy (XAS). In the O K-edge XAS, we have found that hydrogen bond structures among water molecules are enhanced in the middle-concentration region by the hydrophobic interaction of the ethyl groups in ethanol. In the C K-edge XAS, the lower energy features arise from a transition from the terminal methyl C 1s electron to an unoccupied orbital of 3s Rydberg character, which is sensitive to the nearest-neighbor intermolecular interactions. From the comparison of C K-edge XAS with the inner-shell calculations, we have found that ethanol clusters are easily formed in the middle-concentration region due to the hydrophobic interaction of the ethyl group in ethanol, resulting in the enhancement of the hydrogen bond structures among water molecules. This behavior is different from aqueous methanol solutions, where the methanol-water mixed clusters are more predominant in the middle-concentration region due to the relatively weak hydrophobic interactions of the methyl group in methanol.
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Affiliation(s)
- Masanari Nagasaka
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Mathilde Bouvier
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Hayato Yuzawa
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan
| | - Nobuhiro Kosugi
- Institute for Molecular Science, Myodaiji, Okazaki 444-8585, Japan.,SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
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5
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6
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Serva A, Havenith M, Pezzotti S. The role of hydrophobic hydration in the free energy of chemical reactions at the gold/water interface: Size and position effects. J Chem Phys 2021; 155:204706. [PMID: 34852496 DOI: 10.1063/5.0069498] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Metal/water interfaces catalyze a large variety of chemical reactions, which often involve small hydrophobic molecules. In the present theoretical study, we show that hydrophobic hydration at the Au(100)/water interface actively contributes to the reaction free energy by up to several hundreds of meV. This occurs either in adsorption/desorption reaction steps, where the vertical distance from the surface changes in going from reactants to products, or in addition and elimination reaction steps, where two small reactants merge into a larger product and vice versa. We find that size and position effects cannot be captured by treating them as independent variables. Instead, their simultaneous evaluation allows us to map the important contributions, and we provide examples of their combinations for which interfacial reactions can be either favored or disfavored. By taking a N2 and a CO2 reduction pathway as test cases, we show that explicitly considering hydrophobic effects is important for the selectivity and rate of these relevant interfacial processes.
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Affiliation(s)
- Alessandra Serva
- Sorbonne Université, CNRS, Physico-Chimie des Electrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France
| | - Martina Havenith
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
| | - Simone Pezzotti
- Department of Physical Chemistry II, Ruhr University Bochum, 44780 Bochum, Germany
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7
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8
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Unraveling molecular interactions in binary liquid mixtures with time-resolved thermal-lens-spectroscopy. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116322] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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9
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Peters EM, Svärd M, Forsberg K. Phase equilibria of ammonium scandium fluoride phases in aqueous alcohol mixtures for metal recovery by anti-solvent crystallization. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.117449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Abstract
Molecular dynamics (MD) simulations have been widely applied to computer-aided drug design (CADD). While MD has been used in a variety of applications such as free energy perturbation and long-time simulations, the accuracy of the results from those methods depends strongly on the force field used. Force fields for small molecules are crucial, as they not only serve as building blocks for developing force fields for larger biomolecules but also act as model compounds that will be transferred to ligands used in CADD. Currently, a wide range of small molecule force fields based on additive or nonpolarizable models have been developed. While these nonpolarizable force fields can produce reasonable estimations of physical properties and have shown success in a variety of systems, there is still room for improvements due to inherent limitations in these models including the lack of an electronic polarization response. For this reason, incorporating polarization effects into the energy function underlying a force field is believed to be an important step forward, giving rise to the development of polarizable force fields. Recent simulations of biological systems have indicated that polarizable force fields are able to provide a better physical representation of intermolecular interactions and, in many cases, better agreement with experimental properties than nonpolarizable, additive force fields. Therefore, this chapter focuses on the development of small molecule force fields with emphasis on polarizable models. It begins with a brief introduction on the importance of small molecule force fields and their evolution from additive to polarizable force fields. Emphasis is placed on the additive CHARMM General Force Field and the polarizable force field based on the classical Drude oscillator. The theory for the Drude polarizable force field and results for small molecules are presented showing their improvements over the additive model. The potential importance of polarization for their application in a wide range of biological systems including CADD is then discussed.
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Affiliation(s)
- Fang-Yu Lin
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland, Baltimore, MD, USA.
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11
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Lam RK, Smith JW, Saykally RJ. Communication: Hydrogen bonding interactions in water-alcohol mixtures from X-ray absorption spectroscopy. J Chem Phys 2016; 144:191103. [DOI: 10.1063/1.4951010] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Royce K. Lam
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jacob W. Smith
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720, USA and Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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12
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Lemkul J, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chem Rev 2016; 116:4983-5013. [PMID: 26815602 PMCID: PMC4865892 DOI: 10.1021/acs.chemrev.5b00505] [Citation(s) in RCA: 427] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Indexed: 11/28/2022]
Abstract
Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena.
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Affiliation(s)
- Justin
A. Lemkul
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Jing Huang
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
| | - Benoît Roux
- Department
of Biochemistry and Molecular Biology, University
of Chicago, Chicago, Illinois 60637, United
States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Baltimore, Maryland 21201, United States
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13
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Ghoraishi MS, Hawk JE, Phani A, Khan MF, Thundat T. Clustering mechanism of ethanol-water mixtures investigated with photothermal microfluidic cantilever deflection spectroscopy. Sci Rep 2016; 6:23966. [PMID: 27046089 PMCID: PMC4820714 DOI: 10.1038/srep23966] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/15/2016] [Indexed: 11/09/2022] Open
Abstract
The infrared-active (IR) vibrational mode of ethanol (EtOH) associated with the asymmetrical stretching of the C-C-O bond in pico-liter volumes of EtOH-water binary mixtures is calorimetrically measured using photothermal microfluidic cantilever deflection spectroscopy (PMCDS). IR absorption by the confined liquid results in wavelength dependent cantilever deflections, thus providing a complementary response to IR absorption revealing a complex dipole moment dependence on mixture concentration. Solvent-induced blue shifts of the C-C-O asymmetric vibrational stretch for both anti and gauche conformers of EtOH were precisely monitored for EtOH concentrations ranging from 20-100% w/w. Variations in IR absorption peak maxima show an inverse dependence on induced EtOH dipole moment (μ) and is attributed to the complex clustering mechanism of EtOH-water mixtures.
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Affiliation(s)
- M. S. Ghoraishi
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Canada
| | - J. E. Hawk
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Canada
| | - Arindam Phani
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Canada
| | - M. F. Khan
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Canada
| | - T. Thundat
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Canada
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14
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Sappidi P, Natarajan U. Polyelectrolyte conformational transition in aqueous solvent mixture influenced by hydrophobic interactions and hydrogen bonding effects: PAA-water-ethanol. J Mol Graph Model 2015; 64:60-74. [PMID: 26803232 DOI: 10.1016/j.jmgm.2015.12.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 11/18/2015] [Accepted: 12/18/2015] [Indexed: 10/22/2022]
Abstract
Molecular dynamics simulations of poly(acrylic acid) PAA chain in water-ethanol mixture were performed for un-ionized and ionized cases at different degree-of-ionization 0%, 80% and 100% of PAA chain by Na(+) counter-ions and co-solvent (ethanol) concentration in the range 0-90vol% ethanol. Aspects of structure and dynamics were investigated via atom pair correlation functions, number and relaxation of hydrogen bonds, nearest-neighbor coordination numbers, and dihedral angle distribution function for back-bone and side-groups of the chain. With increase in ethanol concentration, chain swelling is observed for un-ionized chain (f=0) and on the contrary chain shrinkage is observed for partially and fully ionized cases (i.e., f=0.8 and 1). For un-ionized PAA, with increase in ethanol fraction ϕeth the number of PAA-ethanol hydrogen bonds increases while PAA-water decreases. Increase in ϕeth leads to PAA chain expansion for un-ionized case and chain shrinkage for ionized case, in agreement with experimental observations on this system. For ionized-PAA case, chain shrinkage is found to be influenced by intermolecular hydrogen bonding with water as well as ethanol. The localization of ethanol molecules near the un-ionized PAA backbone at higher levels of ethanol is facilitated by a displacement of water molecules indicating presence of specific ethanol hydration shell, as confirmed by results of the RDF curves and coordination number calculations. This behavior, controlled by hydrogen bonding provides a significant contribution to such a conformational transition behavior of the polyelectrolyte chain. The interactions between counter-ions and charges on the PAA chain also influence chain collapse. The underlying origins of polyelectrolyte chain collapse in water-alcohol mixtures are brought out for the first time via explicit MD simulations by this study.
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Affiliation(s)
- Praveenkumar Sappidi
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai 600036, India
| | - Upendra Natarajan
- Macromolecular Modeling and Simulation Lab, Department of Chemical Engineering, Indian Institute of Technology (IIT) Madras, Chennai 600036, India.
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15
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Gereben O, Pusztai L. Investigation of the structure of ethanol-water mixtures by molecular dynamics simulation I: analyses concerning the hydrogen-bonded pairs. J Phys Chem B 2015; 119:3070-84. [PMID: 25635651 DOI: 10.1021/jp510490y] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Series of molecular dynamics simulations for ethanol-water mixtures with 20-80 mol % ethanol content, pure ethanol, and water were performed. In each mixture, for ethanol the OPLS force field was used, combined with three different water force fields, the SPC/E, the TIP4P-2005, and the SWM4-DP. Water potential models were distinguished on the basis of deviations between calculated and measured total scattering X-ray structure factors aided by ethanol-water pair binding energy comparison. No single water force field could provide the best agreement with experimental data at all concentrations: at the ethanol content of 80% the SWM-DP, for 60 mol % the SWM4-DP and the TIP4P-2005, whereas for the 40 and 20 mol % mixtures TIP4P-2005 water force field provided the closest match. Coordination numbers and hydrogen bonds/molecule values were calculated, revealing that the oxygen-oxygen first coordination numbers strongly overestimate the average number of hydrogen bonds/molecule. The center-of-molecule distributions indicate that the ethanol-ethanol first coordination sphere expands with increasing water concentration while the size of the first water-water coordination sphere does not change. Various two and three-dimensional distributions were calculated that reveal the differences between simulations with different water force fields. Detailed conformational analyses of the hydrogen-bonded pairs were performed; drawings of the characteristic molecular arrangements are provided.
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Affiliation(s)
- Orsolya Gereben
- Research Institute for Solid State Physics and Optics, Hungarian Academy of Sciences , P.O. Box 49, H-1525 Budapest, Hungary
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16
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Homsi Brandeburgo W, van der Post ST, Meijer EJ, Ensing B. On the slowdown mechanism of water dynamics around small amphiphiles. Phys Chem Chem Phys 2015; 17:24968-77. [DOI: 10.1039/c5cp03486h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Partitioning the water molecules depending on their location with respect to the solute makes it possible to probe the cause of the orientational slowdown in aqueous tetramethylurea.
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Affiliation(s)
- Wagner Homsi Brandeburgo
- Van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- Amsterdam Center for Multiscale Modeling
| | | | - Evert Jan Meijer
- Van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- Amsterdam Center for Multiscale Modeling
| | - Bernd Ensing
- Van't Hoff Institute for Molecular Sciences
- Universiteit van Amsterdam
- 1098 XH Amsterdam
- The Netherlands
- Amsterdam Center for Multiscale Modeling
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17
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Sappidi P, Natarajan U. Influence of hydrogen bonding on the structural transition of poly(methacrylic acid) chain in water–ethanol solution by molecular dynamics simulations. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.992018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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18
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Löytynoja T, Niskanen J, Jänkälä K, Vahtras O, Rinkevicius Z, Ågren H. Quantum Mechanics/Molecular Mechanics Modeling of Photoelectron Spectra: The Carbon 1s Core–Electron Binding Energies of Ethanol–Water Solutions. J Phys Chem B 2014; 118:13217-25. [DOI: 10.1021/jp506410w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- T. Löytynoja
- Department
of Physics, University of Oulu, P.O. Box 3000, FI-90014 University of Oulu, Finland
- Division of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - J. Niskanen
- Department
of Physics, University of Helsinki, P.O. Box 64, FI-00014 University of Helsinki, Finland
| | - K. Jänkälä
- Department
of Physics, University of Oulu, P.O. Box 3000, FI-90014 University of Oulu, Finland
| | - O. Vahtras
- Division of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Z. Rinkevicius
- Division of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
- Swedish
e-Science Research Centre (SeRC), KTH Royal Institute of Technology, S-100 44 Stockholm, Sweden
| | - H. Ågren
- Division of Theoretical Chemistry & Biology, School of Biotechnology, Royal Institute of Technology, S-106 91 Stockholm, Sweden
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19
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Ballal D, Chapman WG. Hydrophobic and hydrophilic interactions in aqueous mixtures of alcohols at a hydrophobic surface. J Chem Phys 2013; 139:114706. [DOI: 10.1063/1.4821604] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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20
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Heger M, Scharge T, Suhm MA. From hydrogen bond donor to acceptor: the effect of ethanol fluorination on the first solvating water molecule. Phys Chem Chem Phys 2013; 15:16065-73. [DOI: 10.1039/c3cp53115e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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21
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Matvejev V, Zizi M, Stiens J. Hydration Shell Parameters of Aqueous Alcohols: THz Excess Absorption and Packing Density. J Phys Chem B 2012; 116:14071-7. [DOI: 10.1021/jp305356d] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- V. Matvejev
- Laboratory of Micro- and Photonelectronics
LAMI-ETRO, Vrije Universiteit Brussel,
Pleinlaan 2, B-1050 Brussels, Belgium
| | - M. Zizi
- Department of Physiology FYSP, Vrije Universiteit Brussel, Laarbeeklaan 101B, B-1090
Brussels, Belgium
| | - J. Stiens
- Laboratory of Micro- and Photonelectronics
LAMI-ETRO, Vrije Universiteit Brussel,
Pleinlaan 2, B-1050 Brussels, Belgium
- Unit SSET,
Department HIM, Group
RFCDM, IMEC, Kapeldreef 75, B-3001 Leuven,
Belgium
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22
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Rossato L, Rossetto F, Silvestrelli PL. Aqueous solvation of methane from first principles. J Phys Chem B 2012; 116:4552-60. [PMID: 22443455 DOI: 10.1021/jp300774z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methane molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical molecular dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces (by a less than 2 factor) the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to methane, similarly to what was obtained by previous first-principles simulations of soluted methanol. Moreover, the rotational slowing down is compatible with the one predicted on the basis of the excluded volume fraction, which leads to a slower hydrogen bond exchange rate. The analysis of simulations performed at different temperatures suggests that the target temperature of the soluted system must be carefully chosen, in order to avoid artificial slowing-down effects. By generating maximally localized Wannier functions, a detailed description of the polarization effects in both solute and solvent molecules is obtained, which better characterizes the solvation process.
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Affiliation(s)
- Lorenzo Rossato
- Dipartimento di Fisica e Astronomia G. Galilei, Università di Padova, Padova, Italy
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23
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Juurinen I, Nakahara K, Ando N, Nishiumi T, Seta H, Yoshida N, Morinaga T, Itou M, Ninomiya T, Sakurai Y, Salonen E, Nordlund K, Hämäläinen K, Hakala M. Measurement of two solvation regimes in water-ethanol mixtures using x-ray compton scattering. PHYSICAL REVIEW LETTERS 2011; 107:197401. [PMID: 22181642 DOI: 10.1103/physrevlett.107.197401] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2010] [Revised: 06/17/2011] [Indexed: 05/31/2023]
Abstract
Water-ethanol mixtures exhibit interesting anomalies in their macroscopic properties. Despite a lot of research, the origin of the anomalies and the microscopic structure itself is still far from completely known. We have utilized the synchrotron x-ray Compton scattering technique to elucidate the structure of aqueous ethanol from a new experimental perspective. The technique is uniquely sensitive to the local molecular geometries at the angstrom and subangstrom scales. The experiments reveal two distinct mixing regimes in terms of geometry: the dilute 5 mol % and the concentrated >15 mol % regimes. By comparing with pure liquids, the former regime is characterized by an intramolecular and the latter by an intermolecular change. The findings bring new light to evaluating the hypothesis of formation of clathratelike structures at the dilute concentrations.
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Affiliation(s)
- I Juurinen
- Department of Physics, PO Box 64, FI-00014 University of Helsinki, Finland
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24
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di Dio PJ, Brehm M, Kirchner B. Singular Value Decomposition for Analyzing Temperature- and Pressure-Dependent Radial Distribution Functions: Decomposition into Grund RDFs (GRDFs). J Chem Theory Comput 2011; 7:3035-9. [PMID: 26598145 DOI: 10.1021/ct2003385] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Singular value decomposition paves the way for systematic investigations of temperature- and pressure-dependent radial distribution functions. The decomposition into (weighted) Grund radial distribution functions (GRDF) shows that the temperature-dependent water structure can easily be understood by only three contributions: a major temperature-independent contribution from the first GRDF, a major temperature-dependent contribution from the second GRDF, and a minor temperature-dependent fine structure contribution from the third GRDF.
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Affiliation(s)
- Philipp J di Dio
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstr. 2, D-04103 Leipzig, Germany
| | - Martin Brehm
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstr. 2, D-04103 Leipzig, Germany
| | - Barbara Kirchner
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig , Linnéstr. 2, D-04103 Leipzig, Germany
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25
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Guevara-Carrion G, Vrabec J, Hasse H. Prediction of self-diffusion coefficient and shear viscosity of water and its binary mixtures with methanol and ethanol by molecular simulation. J Chem Phys 2011; 134:074508. [DOI: 10.1063/1.3515262] [Citation(s) in RCA: 163] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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26
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Mejía SM, Mills MJL, Shaik MS, Mondragon F, Popelier PLA. The dynamic behavior of a liquid ethanol–water mixture: a perspective from quantum chemical topology. Phys Chem Chem Phys 2011; 13:7821-33. [DOI: 10.1039/c0cp02869j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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27
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Kirchner B, di Dio PJ, Hutter J. Real-world predictions from ab initio molecular dynamics simulations. Top Curr Chem (Cham) 2011; 307:109-53. [PMID: 21842358 DOI: 10.1007/128_2011_195] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.
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Affiliation(s)
- Barbara Kirchner
- Wilhelm-Ostwald Institute of Physical and Theoretical Chemistry, University of Leipzig, Linnéstr. 2, 04103 Leipzig, Germany.
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28
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Cooke DJ, Gray RJ, Sand KK, Stipp SLS, Elliott JA. Interaction of ethanol and water with the {1014} surface of calcite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:14520-14529. [PMID: 20795691 DOI: 10.1021/la100670k] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Molecular dynamics simulations have been used to model the interaction between ethanol, water, and the {1014} surface of calcite. Our results demonstrate that a single ethanol molecule is able to form two interactions with the mineral surface (both Ca-O and O-H), resulting in a highly ordered, stable adsorption layer. In contrast, a single water molecule can only form one or other of these interactions and is thus less well bound, resulting in a more unstable adsorption layer. Consequently, when competitive adsorption is considered, ethanol dominates the adsorption layer that forms even when the starting configuration consists of a complete monolayer of water at the surface. The computational results are in good agreement with the results from atomic force microscopy experiments where it is observed that a layer of ethanol remains attached to the calcite surface, decreasing its ability to interact with water and for growth at the {1014} surface to occur. This observation, and its corresponding molecular explanation, may give some insight into the ability to control crystal form using mixtures of different organic solvents.
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Affiliation(s)
- D J Cooke
- Department of Chemical and Biological Sciences, University of Huddersfield, United Kingdom.
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29
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Calzolari A, Monti S, Ruini A, Catellani A. Hydration of cyanin dyes. J Chem Phys 2010; 132:114304. [DOI: 10.1063/1.3352380] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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30
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Te JA, Tan ML, Ichiye T. Solvation of Biomolecules by the Soft Sticky Dipole-Quadrupole-Octupole Water Model. Chem Phys Lett 2010; 486:70-73. [PMID: 21031143 PMCID: PMC2963461 DOI: 10.1016/j.cplett.2009.12.089] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The soft sticky dipole-quadrupole-octupole (SSDQO) potential energy function represents a water molecule by a single site with a van der Waals sphere and point multipoles. Previously, SSDQO was shown to give good properties for liquid water and solvation of simple ions and is faster than three point models. Here, SSDQO is assessed for solvating biologically relevant molecules having a multi-site, partial charge description. Monte Carlo simulations of ethanol, benzene, and N-methylacetamide in SSDQO with SPC/E moments showed the water structure was as good as in SPC/E. Thus, SSDQO is potentially useful for simulations of biological macromolecules in aqueous solution.
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Affiliation(s)
- Jerez A. Te
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, DC, 20057
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, DC, 20057
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31
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Mandal A, Prakash M, Kumar RM, Parthasarathi R, Subramanian V. Ab Initio and DFT Studies on Methanol−Water Clusters. J Phys Chem A 2010; 114:2250-8. [DOI: 10.1021/jp909397z] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Abhishek Mandal
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600 020, India
| | - Muthuramalingam Prakash
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600 020, India
| | - Ravva Mahesh Kumar
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600 020, India
| | - Ramakrishnan Parthasarathi
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600 020, India
| | - Venkatesan Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai-600 020, India
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32
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Silvestrelli PL. Are there immobilized water molecules around hydrophobic groups? Aqueous solvation of methanol from first principles. J Phys Chem B 2009; 113:10728-31. [PMID: 19606832 DOI: 10.1021/jp9044447] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Structural, dynamical, bonding, and electronic properties of water molecules around a soluted methanol molecule are studied from first principles. The results are compatible with experiments and qualitatively support the conclusions of recent classical molecular dynamics simulations concerning the controversial issue on the presence of "immobilized" water molecules around hydrophobic groups: the hydrophobic solute slightly reduces the mobility of many surrounding water molecules rather than immobilizing just the few ones which are closest to the methyl group. By generating maximally localized Wannier functions, a detailed description of the polarization effects in both solute and solvent molecules is obtained, which better elucidates the solvation process.
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Affiliation(s)
- Pier Luigi Silvestrelli
- Dipartimento di Fisica G. Galilei, Universita di Padova, via Marzolo 8, I-35131 Padova, Italy
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33
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Zhong Y, Patel S. Electrostatic Polarization Effects and Hydrophobic Hydration in Ethanol−Water Solutions from Molecular Dynamics Simulations. J Phys Chem B 2008; 113:767-78. [DOI: 10.1021/jp807053p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Yang Zhong
- University of Delaware, Department of Chemistry and Biochemistry, 238 Brown Laboratory, Newark, Delaware 19716
| | - Sandeep Patel
- University of Delaware, Department of Chemistry and Biochemistry, 238 Brown Laboratory, Newark, Delaware 19716
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34
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A chemometrical study of intermolecular properties of hydrogen-bonded complexes formed by C2H4O⋅⋅⋅HX and C2H5N⋅⋅⋅HX with X = F, CN, NC, and CCH. J Mol Model 2008; 15:421-32. [DOI: 10.1007/s00894-008-0422-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Accepted: 11/13/2008] [Indexed: 10/21/2022]
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35
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Abstract
Most organic and organometallic catalysts have been discovered through serendipity or trial and error, rather than by rational design. Computational methods, however, are rapidly becoming a versatile tool for understanding and predicting the roles of such catalysts in asymmetric reactions. Such methods should now be regarded as a first line of attack in the design of catalysts.
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Affiliation(s)
- K N Houk
- University of California, Department of Chemistry and Biochemistry, 607 Charles E. Young Drive East, Los Angeles, California 90095, USA.
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36
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Zhong Y, Warren GL, Patel S. Thermodynamic and structural properties of methanol-water solutions using nonadditive interaction models. J Comput Chem 2008; 29:1142-52. [PMID: 18074339 DOI: 10.1002/jcc.20877] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be -5.6 +/- 0.2 kcal/mol, in respectable agreement with the experimental value of -5.1 kcal/mol. With respect to solution microstructure, the present cluster analysis suggests that the microscale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bipercolating network structure.
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Affiliation(s)
- Yang Zhong
- Department of Chemistry and Biochemistry, 238 Brown Laboratory, University of Delaware, Newark, Delaware 19716, USA
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37
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Bakó I, Megyes T, Bálint S, Grósz T, Chihaia V. Water–methanol mixtures: topology of hydrogen bonded network. Phys Chem Chem Phys 2008; 10:5004-11. [DOI: 10.1039/b808326f] [Citation(s) in RCA: 114] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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38
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Yan W, Zhang L, Xie D, Zeng J. Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions. J Phys Chem B 2007; 111:14055-63. [PMID: 18044868 DOI: 10.1021/jp0756202] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While green fluorescent proteins (GFPs) have been widely used as tools in biochemistry, cell biology, and molecular genetics, novel red fluorescent proteins (RFPs) with red fluorescence emission have also been identified, as complements to the existing GFP technology. The unusual spectrophotometric and fluorescence properties of GFPs and RFPs are controlled by the protonation states and possibly cis/trans isomerization within their chromophores. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the possible neutral and anionic protonated states and the cis/trans isomerization of a RFP chromophore model compound HBMPI in aqueous solutions. The calculations reproduced the experimental absorption solvatochromatic shifts of dilute HBMPI in water under neutral and anionic conditions. Unlike the GFP chromophore, the RFP chromophore model compound HBMPI in basic solution can only adopt a conformation where the C=C bond between the bridge group and the imidazolinone ring and the C-C bond between the imidazolinone and ethylene groups exist in cis and trans conformations, respectively. Moreover, the solvent-solute hydrogen-bonding interactions are found to contribute significantly to the total solvent shifts of pi-pi* excitations of aqueous HBMPI solutions, signifying the importance of protein environment in the determination of the conformation of the chromophores in red fluorescent proteins.
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Affiliation(s)
- Weizhong Yan
- Institute of Theoretical and Computational Chemistry, Laboratory of Mesoscopic Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
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39
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Tolosa Arroyo S, Corchado Martin-Romo JC, Hidalgo Garcia A, Sansón Martín JA. Molecular Simulation of the Hydration of Ethene to Ethanol Using Ab Initio Potentials and Free Energy Curves. J Phys Chem A 2007; 111:13515-20. [DOI: 10.1021/jp0757661] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- S. Tolosa Arroyo
- Departamento de Química Física, Universidad de Extremadura, 06071 Badajoz, Spain
| | | | - A. Hidalgo Garcia
- Departamento de Química Física, Universidad de Extremadura, 06071 Badajoz, Spain
| | - J. A. Sansón Martín
- Departamento de Química Física, Universidad de Extremadura, 06071 Badajoz, Spain
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40
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Carnevale V, Raugei S, Micheletti C, Carloni P. Large-Scale Motions and Electrostatic Properties of Furin and HIV-1 Protease. J Phys Chem A 2007; 111:12327-32. [DOI: 10.1021/jp0751716] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- V. Carnevale
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - S. Raugei
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - C. Micheletti
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
| | - P. Carloni
- International School for Advanced Studies and CNR-INFM Democritos, Via Beirut 2-4, I-34014 Trieste, Italy
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41
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Mejía SM, Espinal JF, Restrepo A, Mondragón F. Molecular Interaction of (Ethanol)2−Water Heterotrimers. J Phys Chem A 2007; 111:8250-6. [PMID: 17665885 DOI: 10.1021/jp073168g] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential energy surface of the (ethanol)2-water heterotrimers for the trans and gauche conformers of ethanol was studied using density functional theory. The same approximation was used for characterizing representative clusters of (ethanol)3, (methanol)3, and (methanol)2-water. Trimerization energies and enthalpies as well as the analysis of geometric parameters suggest that the structures with a cyclic pattern in the three hydrogen bonds of the type O-H---O (primary hydrogen bonds), where all molecules are proton donor-acceptor at the same time, are more stable than those with just two primary hydrogen bonds. Additionally, we propose the formation of "secondary hydrogen bonds" between hydrogen atoms of the methyl group of ethanol and the oxygen atom of water or other ethanol molecule (C-H---O), which were found to be weaker than the primary hydrogen bonds.
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Affiliation(s)
- Sol M Mejía
- Institute of Chemistry, University of Antioquia, A. A. 1226, Medellín, Colombia
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42
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Patel S, Brooks CL. Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. J Chem Phys 2007; 123:164502. [PMID: 16268707 DOI: 10.1063/1.2009730] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We present a molecular-dynamics simulation study of the bulk and liquid-vapor interfacial properties of ethanol using a polarizable force field based on the fluctuating charge (FQ) formalism, as well as the nonpolarizable CHARMM22 force field. Both models are competitive with respect to the prediction of ambient liquid properties such as liquid density, enthalpy of vaporization, dielectric constant, and self-diffusion constants. The polarizable model predicts an average condensed-phase dipole moment of 2.2 D associated with an induced liquid-phase dipole moment of 0.6 D; though qualitatively in agreement with earlier nonadditive models as well as recent Car-Parinello calculations, the current FQ model underestimates the condensed-phase dipole moment. In terms of liquid structure, both models are in agreement with recent neutron-diffraction results of liquid ethanol structure, although the polarizable model predicts the hydroxyl-hydrogen-hydroxyl-hydrogen structure factor in closer agreement with the experimental data. In terms of interfacial properties, both models predict ambient surface tension to within 4% of the experimental value of 22.8 dyncm, while overestimating the surface excess entropy by almost a factor of 2. Both models display the characteristic preferential orientation of interfacial molecules. The polarizable model allows for a monotonic variation of the average molecular dipole moment from the bulk value to that of the vapor phase. Consequently, there is a dramatic difference in the surface potential predicted by the polarizable and nonpolarizable models. The polarizable model estimates a surface potential of -209+/-3 mV, while the nonpolarizable model yields a value of -944+/-10 mV. Finally, based on the vapor-liquid equilibrium simulation data from several temperatures, we estimate the critical properties of both models. As observed with other FQ models for associating fluids (such as water and methanol), and counter to what one would anticipate by modeling more physically the electrostatic response to local environment, the current FQ model underestimates the critical temperature and overestimates the critical density of ethanol; moreover, the FQ model is, in this respect, equivalent to the underlying fixed-charge model. These results further suggest the need to revisit polarizable models in terms of quantitative vapor-liquid equilibrium prediction.
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Affiliation(s)
- Sandeep Patel
- Department of Molecular Biology (TPC-6), The Scripps Research Institute, La Jolla, California 92037, USA
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43
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Anisimov VM, Vorobyov IV, Roux B, MacKerell AD. Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model. J Chem Theory Comput 2007; 3:1927-1946. [PMID: 18802495 PMCID: PMC2542883 DOI: 10.1021/ct700100a] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A polarizable empirical force field based on the classical Drude oscillator has been developed for the aliphatic alcohol series. The model is optimized with emphasis on condensed-phase properties and is validated against a variety of experimental data. Transferability of the developed parameters is emphasized by the use of a single electrostatic model for the hydroxyl group throughout the alcohol series. Aliphatic moiety parameters were transferred from the polarizable alkane parameter set, with only the Lennard-Jones parameters on the carbon in methanol optimized. The developed model yields good agreement with pure solvent properties with the exception of the heats of vaporization of 1-propanol and 1-butanol, which are underestimated by approximately 6%; special LJ parameters for the oxygen in these two molecules that correct for this limitation are presented. Accurate treatment of the free energies of aqueous solvation required the use of atom-type specific O(alcohol)-O(water) LJ interaction terms, with specific terms used for the primary and secondary alcohols. With respect to gas phase properties the polarizable model overestimates experimental dipole moments and quantum mechanical interaction energies with water by approximately 10 and 8 %, respectively, a significant improvement over 44 and 46 % overestimations of the corresponding properties in the CHARMM22 fixed-charge additive model. Comparison of structural properties of the polarizable and additive models for the pure solvents and in aqueous solution shows significant differences indicating atomic details of intermolecular interactions to be sensitive to the applied force field. The polarizable model predicts pure solvent and aqueous phase dipole moment distributions for ethanol centered at 2.4 and 2.7 D, respectively, a significant increase over the gas phase value of 1.8 D, whereas in a solvent of lower polarity, benzene, a value of 1.9 is obtained. The ability of the polarizable model to yield changes in dipole moment as well as the reproduction of a range of condensed phase properties indicates its utility in the study of the properties of alcohols in a variety of condensed phase environments as well as representing an important step in the development of a comprehensive force field for biological molecules.
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Affiliation(s)
- Victor M. Anisimov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
| | - Igor V. Vorobyov
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
| | - Benoît Roux
- Institute of Molecular Pediatric Sciences, Gordon Center for Integrative Science, University of Chicago 929 E. 57 St. Chicago, IL 60637
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, MD, 21201
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44
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Hydrogen bonds in alcohols:water complexes: A theoretical study about new intramolecular interactions via CHELPG and AIM calculations. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.06.018] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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45
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Beta IA, Sorensen CM. Quantitative Information about the Hydrogen Bond Strength in Dilute Aqueous Solutions of Methanol from the Temperature Dependence of the Raman Spectra of the Decoupled OD Stretch. J Phys Chem A 2005; 109:7850-3. [PMID: 16834164 DOI: 10.1021/jp050337t] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We have obtained quantitative information about the hydrogen bond strength in pure water and in dilute aqueous solutions of methanol by analyzing the temperature dependence of Raman spectra of the decoupled OD stretch from 21 to 160 degrees C with the hydrogen bond energy dispersion method. A minimum at 2440 cm(-1) assigned to strong icelike hydrogen bonds and a maximum at 2650 cm(-1) due to maximally (but not completely) broken hydrogen bonds result in all cases. The energy of the minimum decreases upon addition of methanol due to formation of stronger water-methanol hydrogen bonds, whereas the energy of the maximum increases because water hydrogen atoms in the vicinity of the methyl group might participate in "more broken" hydrogen bonds than in bulk water.
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Affiliation(s)
- Ilir A Beta
- Department of Physics, Kansas State University, Manhattan, Kansas 66506, USA
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46
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Emmeluth C, Dyczmons V, Kinzel T, Botschwina P, Suhm MA, Yáñez M. Combined jet relaxation and quantum chemical study of the pairing preferences of ethanol. Phys Chem Chem Phys 2005; 7:991-7. [DOI: 10.1039/b417870j] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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47
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Dougan L, Bates SP, Hargreaves R, Fox JP, Crain J, Finney JL, Reat V, Soper AK. Methanol-water solutions: A bi-percolating liquid mixture. J Chem Phys 2004; 121:6456-62. [PMID: 15446945 DOI: 10.1063/1.1789951] [Citation(s) in RCA: 223] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
An extensive series of neutron diffraction experiments and molecular dynamics simulations has shown that mixtures of methanol and water exhibit extended structures in solution despite the components being fully miscible in all proportions. Of particular interest is a concentration region (methanol mole fraction between 0.27 and 0.54) where both methanol and water appear to form separate, percolating networks. This is the concentration range where many transport properties and thermodynamic excess functions reach extremal values. The observed concentration dependence of several of these material properties of the solution may therefore have a structural origin.
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Affiliation(s)
- L Dougan
- School of Physics, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
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