51
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Tainter CJ, Shi L, Skinner JL. Reparametrized E3B (Explicit Three-Body) Water Model Using the TIP4P/2005 Model as a Reference. J Chem Theory Comput 2015; 11:2268-77. [DOI: 10.1021/acs.jctc.5b00117] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Craig J. Tainter
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Liang Shi
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - James L. Skinner
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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52
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Conte R, Qu C, Bowman JM. Permutationally Invariant Fitting of Many-Body, Non-covalent Interactions with Application to Three-Body Methane–Water–Water. J Chem Theory Comput 2015; 11:1631-8. [DOI: 10.1021/acs.jctc.5b00091] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Riccardo Conte
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M. Bowman
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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53
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Hernández-Rojas J, Wales DJ. The effect of dispersion damping functions on the structure of water clusters. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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54
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Pérez C, Zaleski DP, Seifert NA, Temelso B, Shields GC, Kisiel Z, Pate BH. Hydrogen Bond Cooperativity and the Three-Dimensional Structures of Water Nonamers and Decamers. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407447] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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55
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Pérez C, Zaleski DP, Seifert NA, Temelso B, Shields GC, Kisiel Z, Pate BH. Hydrogen Bond Cooperativity and the Three-Dimensional Structures of Water Nonamers and Decamers. Angew Chem Int Ed Engl 2014; 53:14368-72. [DOI: 10.1002/anie.201407447] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 09/11/2014] [Indexed: 11/10/2022]
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56
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Gadre SR, Yeole SD, Sahu N. Quantum chemical investigations on molecular clusters. Chem Rev 2014; 114:12132-73. [PMID: 25341561 DOI: 10.1021/cr4006632] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur , Kanpur 208 016, India
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57
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Liu H, Wang Y, Bowman JM. Local-monomer calculations of the intramolecular IR spectra of the cage and prism isomers of HOD(D2O)5 and HOD and D2O ice Ih. J Phys Chem B 2014; 118:14124-31. [PMID: 25010120 DOI: 10.1021/jp5061182] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Dilute mixtures of HOD in pure H2O and D2O ices and liquid have been used by experimentalists to focus on the spectrum and vibrational dynamics of the local OH and OD stretches and bend of HOD in these complex and highly heterogeneous environments. The hexamer version of the mixture is HOD(D2O)5. The cage isomer of this cluster was recently studied and analyzed theoretically using local-mode calculations of the IR spectrum by Skinner and co-workers. This and the further possibility of experimental investigation of this cluster have stimulated us to study HOD(D2O)5 using the three-mode, local-monomer model, with the ab initio WHBB dipole moment and potential energy surfaces. Both the cage and prism isomers of this cluster are considered. In addition to providing additional insight into the HOD portion of the spectrum, the spectral signatures of each D2O are also presented in the range of 1000-4000 cm(-1). The OH stretch bands of both the prism and cage isotopomers exhibit rich structures in the range of 3100-3700 cm(-1) that are indicative of the position of the HOD in these hexamers. A preliminary investigation of the site preference of the HOD is also reported for both cage and prism HOD(D2O)5 using an harmonic zero-point energy analysis of the entire cluster. This indicates that the energies of free-OH sites are lower than the ones of H-bonded OH sites. Finally, following our earlier work on the IR spectra of H2O ice models, we present IR spectra of pure D2O and HOD.
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Affiliation(s)
- Hanchao Liu
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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58
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Gruenbaum SM, Skinner JL. Vibrational spectroscopy of water in hydrated lipid multi-bilayers. III. Water clustering and vibrational energy transfer. J Chem Phys 2014; 139:175103. [PMID: 24206336 DOI: 10.1063/1.4827018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Water clustering and connectivity around lipid bilayers strongly influences the properties of membranes and is important for functions such as proton and ion transport. Vibrational anisotropic pump-probe spectroscopy is a powerful tool for understanding such clustering, as the measured anisotropy depends upon the time-scale and degree of intra- and intermolecular vibrational energy transfer. In this article, we use molecular dynamics simulations and theoretical vibrational spectroscopy to help interpret recent experimental measurements of the anisotropy of water in lipid multi-bilayers as a function of both lipid hydration level and isotopic substitution. Our calculations are in satisfactory agreement with the experiments of Piatkowski, Heij, and Bakker, and from our simulations we can directly probe water clustering and connectivity. We find that at low hydration levels, many water molecules are in fact isolated, although up to 70% of hydration water forms small water clusters or chains. At intermediate hydration levels, water forms a wide range of cluster sizes, while at higher hydration levels, the majority of water molecules are part of a large, percolating water cluster. Therefore, the size, number, and nature of water clusters are strongly dependent on lipid hydration level, and the measured anisotropy reflects this through its dependence on intermolecular energy transfer.
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Affiliation(s)
- S M Gruenbaum
- Theoretical Chemistry Institute and Department of Chemistry, 1101 University Ave., University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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59
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Yang M. Effects of excluded volume and correlated molecular orientations on Förster resonance energy transfer in liquid water. J Chem Phys 2014; 140:144508. [PMID: 24735306 DOI: 10.1063/1.4870937] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Förster theory for the survival probability of excited chromophores is generalized to include the effects of excluded volume and orientation correlation in the molecular distribution. An analytical expression for survival probability was derived and written in terms of a few simple elementary functions. Because of the excluded volume, the survival probability exhibits exponential decay at early times and stretched exponential decay at later times. Experimental schemes to determine the size of the molecular excluded volume are suggested. With the present generalization of theory, we analyzed vibrational resonance energy transfer kinetics in neat water. Excluded volume effects prove to be important and slow down the kinetics at early times. The majority of intermolecular resonance energy transfer was found to occur with exponential kinetics, as opposed to the stretched exponential behavior predicted by Förster theory. Quantum yields of intra-molecular vibrational relaxation, intra-, and intermolecular energy transfer were calculated to be 0.413, 0.167, and 0.420, respectively.
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Affiliation(s)
- Mino Yang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 361-763, South Korea
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60
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Zischang J, Suhm MA. The OH stretching spectrum of warm water clusters. J Chem Phys 2014; 140:064312. [DOI: 10.1063/1.4865130] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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61
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Affiliation(s)
- F. Weinhold
- Theoretical Chemistry Institute
and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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62
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Otto KE, Xue Z, Zielke P, Suhm MA. The Raman spectrum of isolated water clusters. Phys Chem Chem Phys 2014; 16:9849-58. [DOI: 10.1039/c3cp54272f] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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63
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Buck U, Pradzynski CC, Zeuch T, Dieterich JM, Hartke B. A size resolved investigation of large water clusters. Phys Chem Chem Phys 2014; 16:6859-71. [DOI: 10.1039/c3cp55185g] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Bingham R, Ballone P. Energy, structure and vibrational modes of small water clusters by a simple many-body potential mimicking polarisation effects. Mol Phys 2013. [DOI: 10.1080/00268976.2013.831142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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65
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Kusaka R, Zhang D, Walsh PS, Gord JR, Fisher BF, Gellman SH, Zwier TS. Role of Ring-Constrained γ-Amino Acid Residues in α/γ-Peptide Folding: Single-Conformation UV and IR Spectroscopy. J Phys Chem A 2013; 117:10847-62. [PMID: 24070234 DOI: 10.1021/jp408258w] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Ryoji Kusaka
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
- Department
of Chemistry, Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan
| | - Di Zhang
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S. Walsh
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Joseph R. Gord
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Brian F. Fisher
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department
of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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66
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Albrecht L, Chowdhury S, Boyd RJ. Hydrogen Bond Cooperativity in Water Hexamers: Atomic Energy Perspective of Local Stabilities. J Phys Chem A 2013; 117:10790-9. [DOI: 10.1021/jp407371c] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laura Albrecht
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Saptarshi Chowdhury
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Russell J. Boyd
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
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67
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Miliordos E, Aprà E, Xantheas SS. Optimal geometries and harmonic vibrational frequencies of the global minima of water clusters (H2O)n, n = 2–6, and several hexamer local minima at the CCSD(T) level of theory. J Chem Phys 2013; 139:114302. [DOI: 10.1063/1.4820448] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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68
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Guevara-Vela JM, Chávez-Calvillo R, García-Revilla M, Hernández-Trujillo J, Christiansen O, Francisco E, Martín Pendás Á, Rocha-Rinza T. Hydrogen-Bond Cooperative Effects in Small Cyclic Water Clusters as Revealed by the Interacting Quantum Atoms Approach. Chemistry 2013; 19:14304-15. [DOI: 10.1002/chem.201300656] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 05/11/2013] [Indexed: 11/08/2022]
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69
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70
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Foley JJ, Mazziotti DA. Cage versus Prism: Electronic Energies of the Water Hexamer. J Phys Chem A 2013; 117:6712-6. [DOI: 10.1021/jp405739d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jonathan J. Foley
- Department of Chemistry and The James
Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60439, United
States
| | - David A. Mazziotti
- Department of Chemistry and The James
Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
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71
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Steele RP. Communication: Multiple-timestep ab initio molecular dynamics with electron correlation. J Chem Phys 2013; 139:011102. [DOI: 10.1063/1.4812568] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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72
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Gruenbaum SM, Tainter CJ, Shi L, Ni Y, Skinner JL. Robustness of Frequency, Transition Dipole, and Coupling Maps for Water Vibrational Spectroscopy. J Chem Theory Comput 2013; 9:3109-17. [DOI: 10.1021/ct400292q] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- S. M. Gruenbaum
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - C. J. Tainter
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - L. Shi
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - Y. Ni
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
| | - J. L. Skinner
- Theoretical Chemistry Institute and
Department of Chemistry,
1101 University Ave., University of Wisconsin-Madison Madison, Wisconsin 53706, United States
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73
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Wang Y, Bowman JM. IR Spectra of the Water Hexamer: Theory, with Inclusion of the Monomer Bend Overtone, and Experiment Are in Agreement. J Phys Chem Lett 2013; 4:1104-1108. [PMID: 26282028 DOI: 10.1021/jz400414a] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Signature IR spectra of isomers of the water hexamer in the spectral range 3000-3800 cm(-1) have been reported by experimentalists, but crucial theoretical interpretation has still not been definitive. Using ab initio potential and dipole moment surfaces and a fully coupled quantum treatment of the intramolecular modes, the ring and book are assigned to spectra obtained in the He nanodroplet and Ar tagging experiments, respectively. The overtone of the intramolecular bend at ca. 3200 cm(-1) is a new calculated feature that completes an important missing piece in previous experimental and theoretical comparisons and leads to a consistent assignment of these two experimental spectra. Calculated IR spectra for the lowest energy forms of the water heptamer and octomer are also presented and compared to experiment. In all the calculated spectra, the bend overtone is demonstrated to be a noticeable feature, and this is one important conclusion from the work. Also, the danger in using scaled double-harmonic spectra to assign spectra is demonstrated.
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Affiliation(s)
- Yimin Wang
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
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74
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Brown SE, Georgescu I, Mandelshtam VA. Self-consistent phonons revisited. II. A general and efficient method for computing free energies and vibrational spectra of molecules and clusters. J Chem Phys 2013; 138:044317. [DOI: 10.1063/1.4788977] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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75
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Medders GR, Babin V, Paesani F. A Critical Assessment of Two-Body and Three-Body Interactions in Water. J Chem Theory Comput 2013; 9:1103-14. [PMID: 26588754 DOI: 10.1021/ct300913g] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The microscopic behavior of water under different conditions and in different environments remains the subject of intense debate. A great number of the controversies arise due to the contradictory predictions obtained within different theoretical models. Relative to conclusions derived from force fields or density functional theory, there is comparably less room to dispute highly correlated electronic structure calculations. Unfortunately, such ab initio calculations are severely limited by system size. In this study, a detailed analysis of the two- and three-body water interactions evaluated at the CCSD(T) level is carried out to quantitatively assess the accuracy of several force fields, DFT models, and ab initio based interaction potentials that are commonly used in molecular simulations. On the basis of this analysis, a new model, HBB2-pol, is introduced which is capable of accurately mapping CCSD(T) results for water dimers and trimers into an efficient analytical function. The accuracy of HBB2-pol is further established through comparison with the experimentally determined second and third virial coefficients.
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Affiliation(s)
- Gregory R Medders
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92103, United States
| | - Volodymyr Babin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92103, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92103, United States
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76
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Tainter CJ, Ni Y, Shi L, Skinner JL. Hydrogen Bonding and OH-Stretch Spectroscopy in Water: Hexamer (Cage), Liquid Surface, Liquid, and Ice. J Phys Chem Lett 2013; 4:12-17. [PMID: 26291204 DOI: 10.1021/jz301780k] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present a unified picture of how OH-stretch spectroscopy in water can be understood in terms of hydrogen bonding for the four systems listed in the title. To understand the strength, and hence OH-stretch frequency, of a hydrogen bond, it is crucial to consider the number of additional acceptor hydrogen bonds made by both the donor and acceptor molecules. This necessity for focusing on the hydrogen-bond environment of both donor and acceptor molecules follows from quantum chemical considerations and is related to the three-body interactions in water. Armed with this understanding we can make a detailed interpretation of the OH-stretch IR absorption spectrum of the cage conformer for HOD(D2O)5 and the imaginary part of the ssp OH-stretch sum-frequency spectrum of the surface of liquid D2O with dilute HOD.
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Affiliation(s)
- C J Tainter
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Y Ni
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - L Shi
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - J L Skinner
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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77
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Sánchez-Lozano M, Cabaleiro-Lago EM, Hermida-Ramón JM, Estévez CM. A computational study of the protonation of simple amines in water clusters. Phys Chem Chem Phys 2013; 15:18204-16. [DOI: 10.1039/c3cp51668g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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